From 978c5ba3d9955fd3e54ced121ef007d2b2c13f22 Mon Sep 17 00:00:00 2001 From: Christian Vedel Date: Tue, 26 May 2026 12:49:59 +0200 Subject: [PATCH 01/14] Copilot created docstrings --- docs/mkdocs.yml | 2 +- src/easyimaging/measurement/measurement.py | 397 ++++++++++++++++++-- src/easyimaging/measurement/regions.py | 414 +++++++++++++++++++-- 3 files changed, 751 insertions(+), 62 deletions(-) diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml index 5bf28fe..f08ec56 100644 --- a/docs/mkdocs.yml +++ b/docs/mkdocs.yml @@ -180,6 +180,6 @@ nav: - Tutorials: - Tutorials: tutorials/index.md - Getting Started: - - Dummy tutorial: tutorials/plotting.ipynb + - Dummy tutorial: tutorials/measurement.ipynb - API Reference: - API Reference: api-reference/index.md diff --git a/src/easyimaging/measurement/measurement.py b/src/easyimaging/measurement/measurement.py index c8dfc14..9389414 100644 --- a/src/easyimaging/measurement/measurement.py +++ b/src/easyimaging/measurement/measurement.py @@ -34,6 +34,32 @@ def __init__( unique_name: str | None = None, display_name: str | None = None, ): + """Initialize a Measurement instance. + + Parameters + ---------- + data_array : sc.DataArray + The measurement data array with dimensions ``('t', 'y', 'x')``. Must have a + ``'tof'`` coordinate for time-of-flight values and both ``'x'`` and ``'y'`` + dimensions. Optionally may include ``'x'`` and ``'y'`` coordinates for + physical pixel positions. + unique_name : str | None, optional + Unique identifier for the measurement. By default, None. + display_name : str | None, optional + Human-readable display name for the measurement. By default, None. + + Raises + ------ + TypeError + If ``data_array`` is not a :class:`scipp.DataArray`. + ValueError + If the data array is missing the ``'tof'`` coordinate, contains negative + time-of-flight values, or has inconsistent coordinate/dimension configuration. + DimensionError + If the data array does not have both ``'x'`` and ``'y'`` dimensions. + UnitError + If any coordinate has an incompatible unit. + """ if not isinstance(data_array, sc.DataArray): raise TypeError('data_array must be an instance of scipp.DataArray.') @@ -90,7 +116,6 @@ def from_scitiff( Parameters ---------- - cls : filename : str | Path Path to the SciTIFF file. unique_name : str | None, optional @@ -102,6 +127,13 @@ def from_scitiff( ------- Measurement An instance of the Measurement class containing the loaded data. + + Raises + ------ + TypeError + If ``filename`` is not a string or :class:`pathlib.Path` object. + RuntimeError + If the file cannot be loaded or is not a valid SciTIFF file. """ if not isinstance(filename, (str, Path)): raise TypeError('filename must be a string or Path object.') @@ -129,7 +161,6 @@ def from_tiff_stack( Parameters ---------- - cls : filename : str | Path Path to the TIFF stack file. time_of_flights : sc.Variable | np.ndarray @@ -150,6 +181,13 @@ def from_tiff_stack( ------- Measurement An instance of the Measurement class containing the loaded data. + + Raises + ------ + TypeError + If ``filename`` is not a string or :class:`pathlib.Path` object. + RuntimeError + If the file cannot be loaded or its dimensions cannot be renamed. """ if not isinstance(filename, (str, Path)): raise TypeError('filename must be a string or Path object.') @@ -210,6 +248,19 @@ def save_scitiff(self, filename: str | Path) -> None: ---------- filename : str | Path Path to the output SciTIFF file. + + Raises + ------ + TypeError + If ``filename`` is not a string or :class:`pathlib.Path` object. + RuntimeError + If the file cannot be written. + + Warns + ----- + UserWarning + If the data array is of type ``float64``, which will be downcast to ``float32`` + when saving, potentially causing loss of precision. """ if not isinstance(filename, (str, Path)): raise TypeError('filename must be a string or Path object.') @@ -230,15 +281,27 @@ def save_scitiff(self, filename: str | Path) -> None: @property def data_array_copy(self) -> sc.DataArray: - """Get the current data array of the measurement, either rebinned or the original full resolution. + """Get a full deep copy of the current data array. + + Returns the rebinned data array if rebinning has been applied, otherwise the + original full-resolution data array. Use with caution for large datasets. - Note that this will make a full copy of the data array, so it should be used with caution for large datasets. + Returns + ------- + sc.DataArray + A deep copy of the current data array. """ return self._data_array.copy(deep=True) @data_array_copy.setter def data_array_copy(self, value: sc.DataArray) -> None: - """Data array copy.""" + """Raise AttributeError — ``data_array_copy`` is a read-only property. + + Raises + ------ + AttributeError + Always. To use a different data array, create a new :class:`Measurement` instance. + """ raise AttributeError( 'Cannot set data_array, it is a read-only property. ' 'Please make a new Measurement instance if you want to use a different data array.' @@ -246,19 +309,39 @@ def data_array_copy(self, value: sc.DataArray) -> None: @property def _data_array(self) -> sc.DataArray: - """Get the current data array, either rebinned or the original full resolution.""" + """Get the current data array, either rebinned or the original full resolution. + + Returns + ------- + sc.DataArray + The rebinned data array if rebinning has been applied, otherwise the + original full-resolution data array. + """ if hasattr(self, '_rebinned_data_array'): return self._rebinned_data_array return self._full_data_array @_data_array.setter def _data_array(self, value: sc.DataArray) -> None: - """Data array.""" + """Raise AttributeError — ``_data_array`` is a read-only property. + + Raises + ------ + AttributeError + Always. + """ raise AttributeError('Cannot set _data_array, it is a read-only property.') @property def x_positions(self) -> sc.Variable | None: - """Get the x-coordinate positions of the pixels, if available.""" + """Get the x-coordinate positions of the pixels. + + Returns + ------- + sc.Variable or None + The x-coordinate positions as a :class:`scipp.Variable`, or ``None`` if + physical coordinates are not available. + """ if self._has_physical_coords: return self._data_array.coords['x'].copy() return None @@ -272,6 +355,16 @@ def x_positions(self, value: sc.Variable | np.ndarray) -> None: value : sc.Variable | np.ndarray The new x-coordinate positions to set. If a numpy array is provided, the unit is assumed to be meters. + + Raises + ------ + ValueError + If physical coordinate positions have not been initialised yet. Use + :meth:`set_physical_coord_positions` to set both axes simultaneously. + TypeError + If ``value`` is not a :class:`scipp.Variable` or :class:`numpy.ndarray`. + UnitError + If ``value`` does not carry a unit of length. """ if not self._has_physical_coords: raise ValueError( @@ -291,7 +384,14 @@ def x_positions(self, value: sc.Variable | np.ndarray) -> None: @property def y_positions(self) -> sc.Variable | None: - """Get the y-coordinate positions of the pixels, if available.""" + """Get the y-coordinate positions of the pixels. + + Returns + ------- + sc.Variable or None + The y-coordinate positions as a :class:`scipp.Variable`, or ``None`` if + physical coordinates are not available. + """ if self._has_physical_coords: return self._data_array.coords['y'].copy() return None @@ -305,6 +405,16 @@ def y_positions(self, value: sc.Variable | np.ndarray) -> None: value : sc.Variable | np.ndarray The new y-coordinate positions to set. If a numpy array is provided, the unit is assumed to be meters. + + Raises + ------ + ValueError + If physical coordinate positions have not been initialised yet. Use + :meth:`set_physical_coord_positions` to set both axes simultaneously. + TypeError + If ``value`` is not a :class:`scipp.Variable` or :class:`numpy.ndarray`. + UnitError + If ``value`` does not carry a unit of length. """ if not self._has_physical_coords: raise ValueError( @@ -359,7 +469,13 @@ def set_physical_coord_positions( self._has_physical_coords = True def delete_physical_coord_positions(self) -> None: - """Delete the physical coordinate positions for the measurement.""" + """Delete the physical coordinate positions for the measurement. + + Raises + ------ + ValueError + If physical coordinate positions are not currently set. + """ if self._has_physical_coords: del self._data_array.coords['x'] del self._data_array.coords['y'] @@ -369,7 +485,13 @@ def delete_physical_coord_positions(self) -> None: @property def time_of_flights(self) -> sc.Variable: - """Get the time-of-flight values of the measurement.""" + """Get the time-of-flight values of the measurement. + + Returns + ------- + sc.Variable + A copy of the time-of-flight coordinate array. + """ return self._data_array.coords['tof'].copy() @time_of_flights.setter @@ -381,6 +503,16 @@ def time_of_flights(self, value: sc.Variable | np.ndarray) -> None: value : sc.Variable | np.ndarray The new time-of-flight values to set. If a numpy array is provided, the unit is assumed to be seconds. + + Raises + ------ + TypeError + If ``value`` is not a :class:`scipp.Variable` or :class:`numpy.ndarray`. + ValueError + If the length of ``value`` does not match the number of frames, or if any + time-of-flight value is negative. + UnitError + If ``value`` does not carry a unit of time. """ value = self._validate_provided_coord( data_array=self._data_array, @@ -397,12 +529,25 @@ def time_of_flights(self, value: sc.Variable | np.ndarray) -> None: @property def regions_of_interest(self) -> EasyList[RectROI]: - """Get the list of regions of interest (ROIs) defined for this measurement.""" + """Get the list of regions of interest (ROIs) defined for this measurement. + + Returns + ------- + EasyList[RectROI] + The list of :class:`~easyimaging.measurement.regions.RectROI` objects + associated with this measurement. + """ return self._regions_of_interest @regions_of_interest.setter def regions_of_interest(self, value: EasyList[RectROI]) -> None: - """Regions of interest.""" + """Raise AttributeError — ``regions_of_interest`` is a read-only property. + + Raises + ------ + AttributeError + Always. Add or remove ROIs directly from the list instead. + """ raise AttributeError( 'Cannot set regions_of_interest, it is a read-only property. ' 'Please simply add or remove ROIs directly from the list.' @@ -418,7 +563,19 @@ def rebin(self, dimensions: dict[str, Numeric]) -> None: ---------- dimensions : dict[str, Numeric] A dictionary specifying the rebinning factors for each dimension. - For example, {'t': 2} will rebin the time dimension by a factor of 2. + For example, ``{'x': 2, 'y': 2}`` will halve the spatial resolution. + + Raises + ------ + TypeError + If ``dimensions`` is not a :class:`dict`, or a dimension key is not a string, + or a rebin factor is not a positive integer (or integer-valued float). + ValueError + If rebinning of the ``'t'`` dimension is requested (not yet supported), if a + rebin factor is less than 1, or if a dimension size is not evenly divisible by + the rebin factor. + KeyError + If a specified dimension name does not exist in the data array. """ if not isinstance(dimensions, dict): raise TypeError('dimensions must be a dictionary mapping dimension names to rebin factors.') @@ -450,7 +607,11 @@ def rebin(self, dimensions: dict[str, Numeric]) -> None: self._rebinned_data_array = temp_array def revert_rebin(self) -> None: - """Revert any rebinning applied to the measurement data, restoring it to its original resolution.""" + """Revert any rebinning applied to the measurement data, restoring it to its original resolution. + + If no rebinning has been applied, a :class:`UserWarning` is issued and no action + is taken. + """ if hasattr(self, '_rebinned_data_array'): del self._rebinned_data_array else: @@ -474,6 +635,19 @@ def plot(self, time_of_flight: int | sc.Variable | None = None, **kwargs) -> Non **kwargs : dict Additional keyword arguments to pass to the plotting function. See https://scipp.github.io/plopp/generated/plopp.plot.html for options. + + Returns + ------- + plopp.Figure or None + The plot object when running inside a Jupyter notebook, otherwise ``None`` + (the plot is displayed directly via :meth:`show`). + + Raises + ------ + TypeError + If ``time_of_flight`` is not an integer, :class:`scipp.Variable` scalar, or ``None``. + UnitError + If a :class:`scipp.Variable` ``time_of_flight`` does not carry a unit of time. """ if time_of_flight is None: title_suffix = ' (averaged over TOF)' @@ -516,6 +690,16 @@ def slicer_plot(self, **kwargs) -> None: **kwargs : dict Additional keyword arguments to pass to the slicer function. See https://scipp.github.io/plopp/generated/plopp.slicer.html for options. + + Returns + ------- + plopp.widgets.Slicer + The interactive slicer widget. + + Raises + ------ + RuntimeError + If called outside a Jupyter notebook environment. """ slicer_kwargs_defaults = self._plot_defaults() slicer_kwargs_defaults.update({ @@ -544,6 +728,16 @@ def spectrum_inspector(self, **kwargs) -> None: **kwargs : dict Additional keyword arguments to pass to the inspector function. See https://scipp.github.io/plopp/generated/plopp.inspector.html for options. + + Returns + ------- + list + A list of plopp figure objects comprising the inspector widget. + + Raises + ------ + RuntimeError + If called outside a Jupyter notebook environment. """ inspector_kwargs_defaults = self._plot_defaults() inspector_kwargs_defaults['ymax'] = inspector_kwargs_defaults['cmax'] @@ -580,6 +774,17 @@ def roi_creator(self, **kwargs) -> None: **kwargs : dict Additional keyword arguments to pass to the ROI creator function. See https://scipp.github.io/plopp/generated/plopp.inspector.html for options. + + Returns + ------- + list + A list of plopp figure objects comprising the ROI creator widget. + Changes made interactively are reflected in :attr:`regions_of_interest`. + + Raises + ------ + RuntimeError + If called outside a Jupyter notebook environment. """ if not _is_notebook(): @@ -639,7 +844,17 @@ def roi_creator(self, **kwargs) -> None: # The callback to be used by the Scipp RectangleTool when drawing a new rectangle. def create_rectangle_roi(rect, roi_list, data_array): - """Create rectangle roi.""" + """Create a new :class:`RectROI` from a drawn rectangle and append it to ``roi_list``. + + Parameters + ---------- + rect : + The rectangle object provided by the plopp RectangleTool. + roi_list : EasyList[RectROI] + The list of ROIs to append the new ROI to. + data_array : sc.DataArray + The data array used to derive pixel and physical coordinate ranges. + """ # Get the pixel and physical coordinate ranges from the rectangle vertices using the helper method. x_pixel_range, y_pixel_range, x_range, y_range = Measurement._ranges_from_rectangle(rect, data_array) new_roi = RectROI( @@ -653,7 +868,17 @@ def create_rectangle_roi(rect, roi_list, data_array): # The callback to be used by the Scipp RectangleTool when dragging the corners of an existing rectangle. def edit_rectangle_roi(rect, roi_list, data_array): - """Edit rectangle roi.""" + """Update the matching :class:`RectROI` in ``roi_list`` when a rectangle is resized. + + Parameters + ---------- + rect : + The rectangle object provided by the plopp RectangleTool. + roi_list : EasyList[RectROI] + The list of ROIs containing the ROI to update. + data_array : sc.DataArray + The data array used to derive updated coordinate ranges. + """ x_pixel_range, y_pixel_range, x_range, y_range = Measurement._ranges_from_rectangle(rect, data_array) # Find the ROI corresponding to the rectangle being edited based on the stored rectangle ID. for roi in roi_list: @@ -666,7 +891,15 @@ def edit_rectangle_roi(rect, roi_list, data_array): matching_roi.set_physical_coord_range(x_range, y_range) def delete_rectangle_roi(rect, roi_list): - """Delete rectangle roi.""" + """Remove the :class:`RectROI` corresponding to ``rect`` from ``roi_list``. + + Parameters + ---------- + rect : + The rectangle object provided by the plopp RectangleTool. + roi_list : EasyList[RectROI] + The list of ROIs from which the matching ROI will be removed. + """ for roi in roi_list: if hasattr(roi, '_rect_ids') and rect.id in roi._rect_ids: roi_list.remove(roi) @@ -709,7 +942,15 @@ def spectrum(self, roi: RectROI | str | None = None) -> sc.DataArray: Returns ------- sc.DataArray - A DataArray containing the spectrum data. + A 1-D DataArray containing the spatially averaged spectrum along the + time-of-flight axis. + + Raises + ------ + TypeError + If ``roi`` is not a :class:`RectROI`, string, or ``None``. + KeyError + If a string ``roi`` does not match any ROI in :attr:`regions_of_interest`. """ if roi is not None and not isinstance(roi, (RectROI, str)): raise TypeError('roi must be a string, None, or an instance of RectROI.') @@ -749,6 +990,19 @@ def spectrum_plot(self, roi: RectROI | str | None = None, **kwargs) -> None: **kwargs : dict Additional keyword arguments to pass to the plotting function. See https://scipp.github.io/plopp/generated/plopp.plot.html for options. + + Returns + ------- + plopp.Figure or None + The plot object when running inside a Jupyter notebook, otherwise ``None`` + (the plot is displayed directly via :meth:`show`). + + Raises + ------ + TypeError + If ``roi`` is not a :class:`RectROI`, string, or ``None``. + KeyError + If a string ``roi`` does not match any ROI in :attr:`regions_of_interest`. """ spectrum_data = self.spectrum(roi=roi) @@ -776,7 +1030,28 @@ def _validate_data_array_coordinate( expected_dim_string: str, expected_unit: str, ) -> None: - """Validate data array coordinate.""" + """Validate that a named coordinate of a data array has the expected dimension and unit. + + Parameters + ---------- + data_array : sc.DataArray + The data array whose coordinate is to be validated. + coord_name : str + Name of the coordinate to validate. + expected_dim : str + The single dimension name the coordinate must have (e.g. ``'t'``). + expected_dim_string : str + Human-readable name of the physical dimension (e.g. ``'time'``). + expected_unit : str + The SI unit string the coordinate must be convertible to (e.g. ``'s'``). + + Raises + ------ + DimensionError + If the coordinate does not have exactly the expected dimension. + UnitError + If the coordinate cannot be converted to ``expected_unit``. + """ if data_array.coords[coord_name].dims != (expected_dim,): raise DimensionError(f"'{coord_name}' coordinate must be of dimension '{expected_dim}'.") try: @@ -796,7 +1071,43 @@ def _validate_provided_coord( expected_dim_string: str, expected_unit: str, ) -> sc.Variable: - """Validate provided coord.""" + """Validate and normalise a coordinate array provided by the caller. + + Accepts either a :class:`scipp.Variable` or a :class:`numpy.ndarray` and + returns a validated :class:`scipp.Variable`. A numpy array is wrapped with + ``dim`` and ``expected_unit``. + + Parameters + ---------- + data_array : sc.DataArray + The data array the coordinate will be assigned to (used for length checks). + coord : sc.Variable | np.ndarray + The coordinate values to validate. + coord_name : str + Human-readable name of the coordinate (used in error messages). + dim : str + Dimension name along which the coordinate runs (e.g. ``'t'``). + length_context : str + Description of what the length should match (used in error messages). + expected_dim_string : str + Human-readable name of the physical dimension (e.g. ``'time'``). + expected_unit : str + The SI unit string the coordinate must be convertible to (e.g. ``'s'``). + + Returns + ------- + sc.Variable + The validated (and possibly converted) coordinate variable. + + Raises + ------ + TypeError + If ``coord`` is not a :class:`scipp.Variable` array or :class:`numpy.ndarray`. + ValueError + If the length of ``coord`` does not match the dimension size of ``data_array``. + UnitError + If ``coord`` cannot be converted to ``expected_unit``. + """ if not (isinstance(coord, sc.Variable) and coord.sizes) and not isinstance(coord, np.ndarray): raise TypeError(f'{coord_name} must be a scipp Variable or a numpy ndarray.') if len(coord) not in (data_array.sizes[dim], data_array.sizes[dim] + 1): @@ -813,7 +1124,31 @@ def _validate_provided_coord( def _ranges_from_rectangle( rect, data_array: sc.DataArray ) -> tuple[tuple[int, int], None] | tuple[tuple[int, int], tuple[sc.Variable, sc.Variable]]: # noqa: E501 - """Ranges from rectangle.""" + """Convert rectangle vertices from the plopp RectangleTool to pixel and physical coordinate ranges. + + Used internally by :meth:`roi_creator` when the user draws or edits a rectangle. + + Parameters + ---------- + rect : + Rectangle object from the plopp RectangleTool exposing a ``vertices`` attribute. + data_array : sc.DataArray + The current data array, used to determine whether physical coordinates are + available and to look up pixel indices. + + Returns + ------- + x_pixel_range : tuple[int, int] + ``(x_start, x_end)`` pixel indices. + y_pixel_range : tuple[int, int] + ``(y_start, y_end)`` pixel indices. + x_range : tuple[sc.Variable, sc.Variable] or None + ``(x_start, x_end)`` physical coordinates, or ``None`` if no physical + coordinates are present. + y_range : tuple[sc.Variable, sc.Variable] or None + ``(y_start, y_end)`` physical coordinates, or ``None`` if no physical + coordinates are present. + """ # To be used in the roi_selector method to convert the rectangle vertices to pixel and # physical coordinate ranges for the new ROI. x_vertex_list, y_vertex_list = rect.vertices @@ -845,7 +1180,14 @@ def _ranges_from_rectangle( return x_pixel_range, y_pixel_range, x_range, y_range def _plot_defaults(self): - """Plot defaults.""" + """Return the default keyword arguments shared across all plot methods. + + Returns + ------- + dict + A dictionary of default plopp keyword arguments including title, colour-bar + label and limits, mask colour, and the coordinate names to use for the axes. + """ return { 'title': self.display_name, 'clabel': 'Transmission', @@ -856,5 +1198,12 @@ def _plot_defaults(self): } def __repr__(self): - """Repr function.""" + """Return a string representation of the Measurement. + + Returns + ------- + str + A human-readable summary including the display name, data shape, and the + display names of all associated regions of interest. + """ return f'{self.display_name} with shape {self._data_array.shape} and regions of interest: {[roi.display_name for roi in self.regions_of_interest]}' # noqa: E501 diff --git a/src/easyimaging/measurement/regions.py b/src/easyimaging/measurement/regions.py index 2708958..9f9c3d9 100644 --- a/src/easyimaging/measurement/regions.py +++ b/src/easyimaging/measurement/regions.py @@ -32,13 +32,38 @@ def __init__( ) -> None: """Initialize a RectROI instance. - Parameters: - x_pixel_range (Sequence[int]): The pixel range for the x-coordinate. - y_pixel_range (Sequence[int]): The pixel range for the y-coordinate. - x_range (Sequence[sc.Variable], optional): The physical coordinate range for the x-axis. - y_range (Sequence[sc.Variable], optional): The physical coordinate range for the y-axis. - unique_name (str | None, optional): A unique identifier for the ROI. Defaults to RectROI appended by a unique integer. - display_name (str | None, optional): A pretty name for the ROI. Defaults to the unique_name if not provided. + Parameters + ---------- + x_pixel_range : Sequence[int] + A two-element sequence ``[x_start, x_end]`` giving the pixel range in the + x direction. + y_pixel_range : Sequence[int] + A two-element sequence ``[y_start, y_end]`` giving the pixel range in the + y direction. + x_range : Sequence[sc.Variable] | None, optional + A two-element sequence ``[x_start, x_end]`` of :class:`scipp.Variable` scalars + giving the physical coordinate range in the x direction. Must be provided + together with ``y_range``. By default, None. + y_range : Sequence[sc.Variable] | None, optional + A two-element sequence ``[y_start, y_end]`` of :class:`scipp.Variable` scalars + giving the physical coordinate range in the y direction. Must be provided + together with ``x_range``. By default, None. + unique_name : str | None, optional + A unique identifier for the ROI. Defaults to ``'RectROI'`` appended by a + unique integer. + display_name : str | None, optional + A human-readable name for the ROI. Defaults to ``unique_name`` if not provided. + + Raises + ------ + TypeError + If ``x_pixel_range`` or ``y_pixel_range`` is not a two-element sequence of + integers, or if physical ranges are not sequences of :class:`scipp.Variable`. + ValueError + If any pixel index is negative, if only one of ``x_range`` / ``y_range`` is + provided, or if physical coordinate scalars do not have a unit of length. + UnitError + If a physical coordinate scalar cannot be converted to metres. """ super().__init__(unique_name=unique_name, display_name=display_name) self.set_pixel_coord_range(x_pixel_range, y_pixel_range) @@ -53,9 +78,21 @@ def __init__( def set_pixel_coord_range(self, x_pixel_range: Sequence[int], y_pixel_range: Sequence[int]) -> None: """Set the pixel coordinate ranges for the ROI. - Parameters: - x_pixel_range (Sequence[int]): The start and end pixel coordinates in the x direction. - y_pixel_range (Sequence[int]): The start and end pixel coordinates in the y direction. + Parameters + ---------- + x_pixel_range : Sequence[int] + A two-element sequence ``[x_start, x_end]`` of non-negative integer pixel + coordinates in the x direction. + y_pixel_range : Sequence[int] + A two-element sequence ``[y_start, y_end]`` of non-negative integer pixel + coordinates in the y direction. + + Raises + ------ + TypeError + If either argument is not a two-element sequence of integers. + ValueError + If any pixel index is negative. """ self._check_input_sequence(x_pixel_range, 'x_pixel_range', 'integers', int) self._check_input_sequence(y_pixel_range, 'y_pixel_range', 'integers', int) @@ -68,9 +105,23 @@ def set_pixel_coord_range(self, x_pixel_range: Sequence[int], y_pixel_range: Seq def set_physical_coord_range(self, x_range: Sequence[sc.Variable], y_range: Sequence[sc.Variable]) -> None: """Set the physical coordinate ranges for the ROI. - Parameters: - x_range (Sequence[sc.Variable]): The start and end physical coordinates in the x direction. - y_range (Sequence[sc.Variable]): The start and end physical coordinates in the y direction. + Parameters + ---------- + x_range : Sequence[sc.Variable] + A two-element sequence ``[x_start, x_end]`` of :class:`scipp.Variable` scalars + with units of length representing the physical extent in the x direction. + y_range : Sequence[sc.Variable] + A two-element sequence ``[y_start, y_end]`` of :class:`scipp.Variable` scalars + with units of length representing the physical extent in the y direction. + + Raises + ------ + TypeError + If either argument is not a two-element sequence of :class:`scipp.Variable`. + ValueError + If any element is not a 0-dimensional (scalar) variable. + UnitError + If any scalar cannot be converted to metres. """ self._check_input_sequence(x_range, 'x_range', 'scipp scalars', sc.Variable) @@ -82,7 +133,13 @@ def set_physical_coord_range(self, x_range: Sequence[sc.Variable], y_range: Sequ self._has_physical_coords = True def delete_physical_coord_range(self) -> None: - """Delete the physical coordinate ranges for the ROI.""" + """Delete the physical coordinate ranges for the ROI. + + Raises + ------ + ValueError + If physical coordinate ranges are not currently set. + """ if self._has_physical_coords: del self._x_start del self._x_end @@ -117,51 +174,138 @@ def slice(self) -> Tuple[slice, slice]: @property def x_pixel_start(self) -> int: - """X pixel start.""" + """Start pixel index in the x direction. + + Returns + ------- + int + The start pixel index along the x axis. + """ return self._x_pixel_start.value @x_pixel_start.setter def x_pixel_start(self, value: int): - """X pixel start.""" + """Set the start pixel index in the x direction. + + Parameters + ---------- + value : int + A non-negative integer pixel index. + + Raises + ------ + TypeError + If ``value`` is not an integer. + ValueError + If ``value`` is negative. + """ self._check_index(value, 'x_pixel_start') self._x_pixel_start = sc.scalar(value) @property def x_pixel_end(self) -> int: - """X pixel end.""" + """End pixel index in the x direction. + + Returns + ------- + int + The end pixel index along the x axis. + """ return self._x_pixel_end.value @x_pixel_end.setter def x_pixel_end(self, value: int): - """X pixel end.""" + """Set the end pixel index in the x direction. + + Parameters + ---------- + value : int + A non-negative integer pixel index. + + Raises + ------ + TypeError + If ``value`` is not an integer. + ValueError + If ``value`` is negative. + """ self._check_index(value, 'x_pixel_end') self._x_pixel_end = sc.scalar(value) @property def y_pixel_start(self) -> int: - """Y pixel start.""" + """Start pixel index in the y direction. + + Returns + ------- + int + The start pixel index along the y axis. + """ return self._y_pixel_start.value @y_pixel_start.setter def y_pixel_start(self, value: int): - """Y pixel start.""" + """Set the start pixel index in the y direction. + + Parameters + ---------- + value : int + A non-negative integer pixel index. + + Raises + ------ + TypeError + If ``value`` is not an integer. + ValueError + If ``value`` is negative. + """ self._check_index(value, 'y_pixel_start') self._y_pixel_start = sc.scalar(value) @property def y_pixel_end(self) -> int: - """Y pixel end.""" + """End pixel index in the y direction. + + Returns + ------- + int + The end pixel index along the y axis. + """ return self._y_pixel_end.value @y_pixel_end.setter def y_pixel_end(self, value: int): - """Y pixel end.""" + """Set the end pixel index in the y direction. + + Parameters + ---------- + value : int + A non-negative integer pixel index. + + Raises + ------ + TypeError + If ``value`` is not an integer. + ValueError + If ``value`` is negative. + """ self._check_index(value, 'y_pixel_end') self._y_pixel_end = sc.scalar(value) @property def x_start(self) -> sc.Variable: - """X start.""" + """Start physical coordinate in the x direction. + + Returns + ------- + sc.Variable + A copy of the start coordinate scalar along the x axis. + + Raises + ------ + ValueError + If physical coordinate ranges are not set. + """ if self._has_physical_coords: return self._x_start.copy() else: @@ -169,14 +313,41 @@ def x_start(self) -> sc.Variable: @x_start.setter def x_start(self, value: sc.Variable): - """X start.""" + """Set the start physical coordinate in the x direction. + + Parameters + ---------- + value : sc.Variable + A 0-dimensional :class:`scipp.Variable` scalar with a unit of length. + + Raises + ------ + TypeError + If ``value`` is not a :class:`scipp.Variable`. + ValueError + If physical coordinate ranges are not yet set (use + :meth:`set_physical_coord_range` first), or if ``value`` is not a scalar. + UnitError + If ``value`` cannot be converted to metres. + """ self._single_coord_setter_check(value, 'x_start') self._check_scalar(value, 'x_start') self._x_start = value @property def x_end(self) -> sc.Variable: - """X end.""" + """End physical coordinate in the x direction. + + Returns + ------- + sc.Variable + A copy of the end coordinate scalar along the x axis. + + Raises + ------ + ValueError + If physical coordinate ranges are not set. + """ if self._has_physical_coords: return self._x_end.copy() else: @@ -184,14 +355,40 @@ def x_end(self) -> sc.Variable: @x_end.setter def x_end(self, value: sc.Variable): - """X end.""" + """Set the end physical coordinate in the x direction. + + Parameters + ---------- + value : sc.Variable + A 0-dimensional :class:`scipp.Variable` scalar with a unit of length. + + Raises + ------ + TypeError + If ``value`` is not a :class:`scipp.Variable`. + ValueError + If physical coordinate ranges are not yet set, or if ``value`` is not a scalar. + UnitError + If ``value`` cannot be converted to metres. + """ self._single_coord_setter_check(value, 'x_end') self._check_scalar(value, 'x_end') self._x_end = value @property def y_start(self) -> sc.Variable: - """Y start.""" + """Start physical coordinate in the y direction. + + Returns + ------- + sc.Variable + A copy of the start coordinate scalar along the y axis. + + Raises + ------ + ValueError + If physical coordinate ranges are not set. + """ if self._has_physical_coords: return self._y_start.copy() else: @@ -199,14 +396,40 @@ def y_start(self) -> sc.Variable: @y_start.setter def y_start(self, value: sc.Variable): - """Y start.""" + """Set the start physical coordinate in the y direction. + + Parameters + ---------- + value : sc.Variable + A 0-dimensional :class:`scipp.Variable` scalar with a unit of length. + + Raises + ------ + TypeError + If ``value`` is not a :class:`scipp.Variable`. + ValueError + If physical coordinate ranges are not yet set, or if ``value`` is not a scalar. + UnitError + If ``value`` cannot be converted to metres. + """ self._single_coord_setter_check(value, 'y_start') self._check_scalar(value, 'y_start') self._y_start = value @property def y_end(self) -> sc.Variable: - """Y end.""" + """End physical coordinate in the y direction. + + Returns + ------- + sc.Variable + A copy of the end coordinate scalar along the y axis. + + Raises + ------ + ValueError + If physical coordinate ranges are not set. + """ if self._has_physical_coords: return self._y_end.copy() else: @@ -214,13 +437,46 @@ def y_end(self) -> sc.Variable: @y_end.setter def y_end(self, value: sc.Variable): - """Y end.""" + """Set the end physical coordinate in the y direction. + + Parameters + ---------- + value : sc.Variable + A 0-dimensional :class:`scipp.Variable` scalar with a unit of length. + + Raises + ------ + TypeError + If ``value`` is not a :class:`scipp.Variable`. + ValueError + If physical coordinate ranges are not yet set, or if ``value`` is not a scalar. + UnitError + If ``value`` cannot be converted to metres. + """ self._single_coord_setter_check(value, 'y_end') self._check_scalar(value, 'y_end') self._y_end = value def _check_input_sequence(self, value: Sequence, name: str, typename: str, expected_type: any) -> None: - """Check if the input value is a sequence of the expected type and length.""" + """Validate that ``value`` is a two-element sequence of the expected type. + + Parameters + ---------- + value : Sequence + The value to validate. + name : str + Name of the parameter (used in error messages). + typename : str + Human-readable name of the expected element type (used in error messages). + expected_type : type + The type each element must be an instance of. + + Raises + ------ + TypeError + If ``value`` is not a two-element sequence or its elements are not of + ``expected_type``. + """ if not isinstance(value, Sequence) or len(value) != 2: raise TypeError(f'{name} must be a tuple or a list of two {typename}, got a {type(value).__name__}.') if not (isinstance(value[0], expected_type) and isinstance(value[1], expected_type)): @@ -230,14 +486,44 @@ def _check_input_sequence(self, value: Sequence, name: str, typename: str, expec ) def _check_index(self, value: int, name: str) -> None: - """Check if the input value is a valid index (non-negative integer).""" + """Validate that ``value`` is a non-negative integer suitable as a pixel index. + + Parameters + ---------- + value : int + The value to validate. + name : str + Name of the parameter (used in error messages). + + Raises + ------ + TypeError + If ``value`` is not an integer. + ValueError + If ``value`` is negative. + """ if not isinstance(value, int): raise TypeError(f'{name} index must be an integer.') if value < 0: raise ValueError(f'{name} index must be non-negative.') def _check_scalar(self, value: sc.Variable, name: str) -> None: - """Check if the input value is a scipp scalar with a unit of length.""" + """Validate that ``value`` is a 0-dimensional :class:`scipp.Variable` with a unit of length. + + Parameters + ---------- + value : sc.Variable + The value to validate. + name : str + Name of the parameter (used in error messages). + + Raises + ------ + ValueError + If ``value`` has dimensions (i.e. is not a scalar). + UnitError + If ``value`` cannot be converted to metres. + """ if value.dims: raise ValueError(f'{name} must be a scipp scalar (0-dimensional Variable).') try: @@ -247,7 +533,25 @@ def _check_scalar(self, value: sc.Variable, name: str) -> None: raise UnitError(f"{name} must be a scipp scalar with a unit of length (e.g., 'm').") from e def _single_coord_setter_check(self, value: sc.Variable, name: str) -> None: - """Check if the input value is a scipp scalar and if physical coordinates are set.""" + """Validate preconditions for setting a single physical coordinate scalar. + + Checks that ``value`` is a :class:`scipp.Variable` and that physical coordinate + ranges have already been initialised. + + Parameters + ---------- + value : sc.Variable + The candidate value to set. + name : str + Name of the coordinate being set (used in error messages). + + Raises + ------ + TypeError + If ``value`` is not a :class:`scipp.Variable`. + ValueError + If physical coordinate ranges have not been set yet. + """ if not isinstance(value, sc.Variable): raise TypeError(f'{name} must be a scipp scalar.') if not self._has_physical_coords: @@ -257,7 +561,22 @@ def _single_coord_setter_check(self, value: sc.Variable, name: str) -> None: ) def to_dict(self, skip: List[str] | None = None) -> Dict[str, Any]: - """Convert the RectROI instance to a dictionary representation.""" + """Convert the RectROI instance to a dictionary representation. + + Parameters + ---------- + skip : list[str] | None, optional + A list of attribute names to exclude from the output dictionary. + The ``'x_pixel_range'``, ``'y_pixel_range'``, ``'x_range'``, and + ``'y_range'`` keys are always handled explicitly and appended + regardless of this parameter. By default, None. + + Returns + ------- + dict + A dictionary containing the serialised ROI data, including pixel ranges + and, if available, physical coordinate ranges encoded as scipp scalar dicts. + """ if skip is None: skip = [] elif isinstance(skip, str): @@ -300,7 +619,21 @@ def to_dict(self, skip: List[str] | None = None) -> Dict[str, Any]: @classmethod def from_dict(cls, input_dict: Dict[str, Any]) -> RectROI: - """Create a RectROI instance from a dictionary representation.""" + """Create a RectROI instance from a dictionary representation. + + Parameters + ---------- + input_dict : dict + A dictionary as produced by :meth:`to_dict`, containing at minimum + ``'x_pixel_range'`` and ``'y_pixel_range'`` keys. If ``'x_range'`` and + ``'y_range'`` are present they are deserialised from their scipp scalar + dict format. + + Returns + ------- + RectROI + A new :class:`RectROI` instance initialised from the dictionary. + """ temp_dict = input_dict.copy() if 'x_range' in input_dict and 'y_range' in input_dict: temp_dict['x_range'] = [sc.from_dict(item['dict']) for item in input_dict['x_range']] @@ -308,7 +641,14 @@ def from_dict(cls, input_dict: Dict[str, Any]) -> RectROI: return super().from_dict(temp_dict) def __repr__(self) -> str: - """Repr function.""" + """Return a string representation of the RectROI. + + Returns + ------- + str + A human-readable summary including pixel ranges and, when available, + physical coordinate ranges. + """ repr_str = ( f'RectROI(x_pixel_range=({self._x_pixel_start}, {self._x_pixel_end}), ' f'y_pixel_range=({self._y_pixel_start}, {self._y_pixel_end})' From 3e1a9ef4bc8083ae13cbc26662d031e1c4c851d6 Mon Sep 17 00:00:00 2001 From: Christian Vedel Date: Wed, 27 May 2026 15:54:45 +0200 Subject: [PATCH 02/14] Updates to Measurement class to further pretify the Measurements tutorial notebook. Also added missing unit tests. --- docs/docs/tutorials/measurement.ipynb | 4029 +++++++++++++++++++- pixi.lock | 1454 +++---- src/easyimaging/datasets.py | 2 +- src/easyimaging/measurement/measurement.py | 79 +- tests/unit/measurement/test_measurement.py | 141 +- 5 files changed, 4905 insertions(+), 800 deletions(-) diff --git a/docs/docs/tutorials/measurement.ipynb b/docs/docs/tutorials/measurement.ipynb index 2a4d58d..0b3b201 100644 --- a/docs/docs/tutorials/measurement.ipynb +++ b/docs/docs/tutorials/measurement.ipynb @@ -11,7 +11,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "id": "bfb22357", "metadata": {}, "outputs": [], @@ -23,14 +23,15 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 2, "id": "49155b72", "metadata": {}, "outputs": [], "source": [ "from easyimaging.datasets import iron_alpha_scitiff\n", "\n", - "scitiff_path = iron_alpha_scitiff() # If you use your own file, simply specify the path like: 'some_path/some_file.tiff'" + "# If you use your own file, simply specify the path like: 'some_path/some_file.tiff'\n", + "scitiff_path = iron_alpha_scitiff()" ] }, { @@ -43,7 +44,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 3, "id": "c4e759bd", "metadata": {}, "outputs": [], @@ -63,7 +64,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 4, "id": "de262785", "metadata": {}, "outputs": [], @@ -75,13 +76,11 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 5, "id": "45d76213", "metadata": {}, "outputs": [], "source": [ - "from easyimaging.datasets import iron_alpha_tiff\n", - "\n", "measurement = Measurement.from_tiff_stack(\n", " filename=tiff_path,\n", " time_of_flights=sc.arange('t', 0, 1501, 1, unit='s'), # mandatory\n", @@ -100,7 +99,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 6, "id": "8081110a", "metadata": {}, "outputs": [], @@ -121,7 +120,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 7, "id": "decf64b7", "metadata": {}, "outputs": [], @@ -147,7 +146,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 8, "id": "531b3ea0", "metadata": {}, "outputs": [], @@ -165,7 +164,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 9, "id": "577cc5ad", "metadata": {}, "outputs": [], @@ -183,10 +182,108 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 10, "id": "5aa49556", "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "
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scipp.DataArray (36.84 KB)
    • t: 1500
    • Ltotal
      ()
      int64
      m
      61
      Values:
      array(61)
    • c
      ()
      string
      intensities
      Values:
      'intensities'
    • tof
      (t [bin-edge])
      float64
      s
      0.022, 0.022, ..., 0.092, 0.093
      Values:
      array([0.02158728, 0.02163456, 0.02168185, ..., 0.09242233, 0.09246961,\n",
+       "       0.0925169 ], shape=(1501,))
    • wavelength
      (t [bin-edge])
      float64
      Å
      1.4, 1.403, ..., 5.997, 6.0
      Values:
      array([1.4       , 1.40306667, 1.40613333, ..., 5.99386667, 5.99693333,\n",
+       "       6.        ], shape=(1501,))
    • (t)
      float32
      𝟙
      0.5531428, 0.56375575, ..., 0.63517606, 0.63194895
      σ = 0.002992472, 0.003154994, ..., 0.006249289, 0.006158047
      Values:
      array([0.5531428 , 0.56375575, 0.5592331 , ..., 0.6236488 , 0.63517606,\n",
+       "       0.63194895], shape=(1500,), dtype=float32)

      Variances (σ²):
      array([8.9548885e-06, 9.9539866e-06, 9.6888207e-06, ..., 3.6184254e-05,\n",
+       "       3.9053615e-05, 3.7921542e-05], shape=(1500,), dtype=float32)
" + ], + "text/plain": [ + "\n", + "Dimensions: Sizes[t:1500, ]\n", + "Coordinates:\n", + "* Ltotal int64 [m] () 61\n", + " c string () \"intensities\"\n", + "* tof float64 [s] (t [bin-edge]) [0.0215873, 0.0216346, ..., 0.0924696, 0.0925169]\n", + "* wavelength float64 [Å] (t [bin-edge]) [1.4, 1.40307, ..., 5.99693, 6]\n", + "Data:\n", + " float32 [dimensionless] (t) [0.553143, 0.563756, ..., 0.635176, 0.631949] [8.95489e-06, 9.95399e-06, ..., 3.90536e-05, 3.79215e-05]\n" + ] + }, + "execution_count": 18, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "measurement.spectrum()" ] @@ -350,10 +3862,26 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 19, "id": "3cf946ab", "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "f9efbd5255164e328e3e08f44c8066cd", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "InteractiveFigure(children=(HBar(), HBar(children=(VBar(children=(Toolbar(children=(ButtonTool(icon='home', la…" + ] + }, + "execution_count": 19, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "measurement.spectrum_plot()" ] @@ -370,10 +3898,26 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 20, "id": "e6da5628", "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "294103cf4efa422ca0ba2c4366401edc", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "Box(children=(InteractiveFigure(children=(HBar(), HBar(children=(VBar(children=(Toolbar(children=(ButtonTool(i…" + ] + }, + "execution_count": 20, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "measurement.spectrum_inspector()" ] @@ -390,7 +3934,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 21, "id": "4969d839", "metadata": {}, "outputs": [], @@ -408,7 +3952,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 22, "id": "6de05015", "metadata": {}, "outputs": [], @@ -416,8 +3960,8 @@ "roi = RectROI(\n", " x_pixel_range=(15, 35), # mandatory\n", " y_pixel_range=(15, 35), # mandatory\n", - " x_range=(sc.scalar(-0.05, unit='m'), sc.scalar(0.05, unit='m')), # optional\n", - " y_range=(sc.scalar(-0.05, unit='m'), sc.scalar(0.05, unit='m')), # optional\n", + " x_range=(sc.scalar(-2, unit='mm'), sc.scalar(2, unit='mm')), # optional\n", + " y_range=(sc.scalar(-2, unit='mm'), sc.scalar(2, unit='mm')), # optional\n", " unique_name='center_roi', # custom name for the ROI, optional, has to be unique in computer memory\n", ")" ] @@ -434,20 +3978,80 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 23, "id": "ed81cad4", "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "
\n", + "\n", + "\n", + "\n", + "\n", + "Show/Hide data repr\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "Show/Hide attributes\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "
scipp.DataArray (36.84 KB)
    • t: 1500
    • Ltotal
      ()
      int64
      m
      61
      Values:
      array(61)
    • c
      ()
      string
      intensities
      Values:
      'intensities'
    • tof
      (t [bin-edge])
      float64
      s
      0.022, 0.022, ..., 0.092, 0.093
      Values:
      array([0.02158728, 0.02163456, 0.02168185, ..., 0.09242233, 0.09246961,\n",
+       "       0.0925169 ], shape=(1501,))
    • wavelength
      (t [bin-edge])
      float64
      Å
      1.4, 1.403, ..., 5.997, 6.0
      Values:
      array([1.4       , 1.40306667, 1.40613333, ..., 5.99386667, 5.99693333,\n",
+       "       6.        ], shape=(1501,))
    • (t)
      float32
      𝟙
      0.36840674, 0.3425866, ..., 0.46642005, 0.45523798
      σ = 0.0058153444, 0.0056076236, ..., 0.013006445, 0.012870439
      Values:
      array([0.36840674, 0.3425866 , 0.35694158, ..., 0.43976402, 0.46642005,\n",
+       "       0.45523798], shape=(1500,), dtype=float32)

      Variances (σ²):
      array([3.3818233e-05, 3.1445445e-05, 3.3600576e-05, ..., 1.4671838e-04,\n",
+       "       1.6916762e-04, 1.6564821e-04], shape=(1500,), dtype=float32)
" + ], + "text/plain": [ + "\n", + "Dimensions: Sizes[t:1500, ]\n", + "Coordinates:\n", + "* Ltotal int64 [m] () 61\n", + " c string () \"intensities\"\n", + "* tof float64 [s] (t [bin-edge]) [0.0215873, 0.0216346, ..., 0.0924696, 0.0925169]\n", + "* wavelength float64 [Å] (t [bin-edge]) [1.4, 1.40307, ..., 5.99693, 6]\n", + "Data:\n", + " float32 [dimensionless] (t) [0.368407, 0.342587, ..., 0.46642, 0.455238] [3.38182e-05, 3.14454e-05, ..., 0.000169168, 0.000165648]\n" + ] + }, + "execution_count": 23, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "measurement.spectrum(roi=roi)" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 24, "id": "1e142cfe", "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "57b60acdcd8b4d8da74827bba55f7de7", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "InteractiveFigure(children=(HBar(), HBar(children=(VBar(children=(Toolbar(children=(ButtonTool(icon='home', la…" + ] + }, + "execution_count": 24, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "measurement.spectrum_plot(roi=roi)" ] @@ -462,7 +4066,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 25, "id": "123de71f", "metadata": {}, "outputs": [], @@ -480,10 +4084,26 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 26, "id": "01bb61d2", "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "19ffc42be05b4532a1ddb51f69e319eb", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "InteractiveFigure(children=(HBar(), HBar(children=(VBar(children=(Toolbar(children=(ButtonTool(icon='home', la…" + ] + }, + "execution_count": 26, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "measurement.spectrum_plot(roi='center_roi')" ] @@ -504,10 +4124,310 @@ }, { "cell_type": "code", - "execution_count": null, - "id": "7ff41a8e-7dd2-4a19-9d09-8a9221963459", + "execution_count": 27, + "id": "c24c19bf", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
\n", + "\n", + "\n", + "\n", + "\n", + "Show/Hide data repr\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "Show/Hide attributes\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "
scipp.DataArray (5.61 KB out of 3.32 MB)
    • y: 16
    • x: 16
    • Ltotal
      ()
      int64
      m
      61
      Values:
      array(61)
    • c
      ()
      string
      intensities
      Values:
      'intensities'
    • tof
      (t [bin-edge])
      float64
      s
      0.022, 0.022
      Values:
      array([0.02158728, 0.02163456])
    • wavelength
      (t [bin-edge])
      float64
      Å
      1.4, 1.403
      Values:
      array([1.4       , 1.40306667])
    • x
      (x [bin-edge])
      float32
      mm
      -7.0382814, -6.158496, ..., 6.158496, 7.0382814
      Values:
      array([-7.0382814 , -6.158496  , -5.2787113 , -4.398926  , -3.5191407 ,\n",
+       "       -2.6393557 , -1.7595701 , -0.87978506,  0.        ,  0.87978506,\n",
+       "        1.7595701 ,  2.6393552 ,  3.5191412 ,  4.3989263 ,  5.2787113 ,\n",
+       "        6.158496  ,  7.0382814 ], dtype=float32)
    • x_pixels
      (x [bin-edge])
      int64
      𝟙
      0, 1, ..., 15, 16
      Values:
      array([ 0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14, 15, 16])
    • y
      (y [bin-edge])
      float32
      mm
      -7.0382814, -6.158496, ..., 6.158496, 7.0382814
      Values:
      array([-7.0382814 , -6.158496  , -5.2787113 , -4.398926  , -3.5191407 ,\n",
+       "       -2.6393557 , -1.7595701 , -0.87978506,  0.        ,  0.87978506,\n",
+       "        1.7595701 ,  2.6393552 ,  3.5191412 ,  4.3989263 ,  5.2787113 ,\n",
+       "        6.158496  ,  7.0382814 ], dtype=float32)
    • y_pixels
      (y [bin-edge])
      int64
      𝟙
      0, 1, ..., 15, 16
      Values:
      array([ 0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14, 15, 16])
    • (y, x)
      float32
      𝟙
      0.8669202, 0.97052157, ..., 1.0874317, 1.0111607
      σ = 0.055470176, 0.06585275, ..., 0.07875291, 0.067374334
      Values:
      array([[0.8669202 , 0.97052157, 0.76623374, 0.9045226 , 0.6839827 ,\n",
+       "        0.84288746, 1.0544218 , 1.0201511 , 0.76152307, 0.7402135 ,\n",
+       "        0.93783784, 1.1       , 0.9243856 , 1.2880435 , 1.2926829 ,\n",
+       "        1.0715935 ],\n",
+       "       [1.0714285 , 0.6044776 , 0.25614035, 0.5826087 , 0.70212764,\n",
+       "        0.61290324, 0.4251627 , 0.6125908 , 0.7882353 , 0.47901234,\n",
+       "        0.5829146 , 0.5978552 , 0.5504808 , 0.45771143, 0.77707005,\n",
+       "        1.0022422 ],\n",
+       "       [0.9056225 , 0.48404256, 0.47335422, 0.36511627, 0.36105478,\n",
+       "        0.5513126 , 0.3264463 , 0.4327354 , 0.31105992, 0.2041237 ,\n",
+       "        0.2963671 , 0.22344323, 0.28146452, 0.57106596, 0.5125348 ,\n",
+       "        1.0085471 ],\n",
+       "       [1.1310542 , 0.5735736 , 0.40681362, 0.3378016 , 0.30649352,\n",
+       "        0.491358  , 0.3204047 , 0.35443038, 0.23546945, 0.38482386,\n",
+       "        0.54108214, 0.47989276, 0.15136476, 0.2802303 , 0.51827955,\n",
+       "        1.9727892 ],\n",
+       "       [0.8003992 , 0.54376656, 0.26541555, 0.24024025, 0.28      ,\n",
+       "        0.36491936, 0.2251407 , 0.5135135 , 0.33568075, 0.3       ,\n",
+       "        0.1879845 , 0.622549  , 0.5       , 0.28540304, 0.70509386,\n",
+       "        1.0292792 ],\n",
+       "       [1.0357853 , 0.6827411 , 0.3326316 , 0.42553192, 0.34971097,\n",
+       "        0.25142857, 0.20326678, 0.28271028, 0.50793654, 0.23818181,\n",
+       "        0.31719127, 0.5095368 , 0.3047859 , 0.17567568, 0.6363636 ,\n",
+       "        0.81152993],\n",
+       "       [1.0813187 , 0.5121413 , 0.49552238, 0.32518336, 0.14587738,\n",
+       "        0.5185185 , 0.39823008, 0.24031007, 0.4297694 , 0.3079848 ,\n",
+       "        0.27513227, 0.29597703, 0.2733485 , 0.3586207 , 0.7105263 ,\n",
+       "        0.765625  ],\n",
+       "       [0.6879271 , 0.55744684, 0.5542857 , 0.42      , 0.16404887,\n",
+       "        0.33033708, 0.33505154, 0.28475335, 0.33901918, 0.36192468,\n",
+       "        0.6246575 , 0.25482625, 0.39119804, 0.31106472, 0.6658228 ,\n",
+       "        0.9976415 ],\n",
+       "       [0.75598085, 0.7943662 , 0.3048433 , 0.2518116 , 0.39909297,\n",
+       "        0.3173913 , 0.17777778, 0.3483366 , 0.50389105, 0.3306233 ,\n",
+       "        0.4187643 , 0.4168798 , 0.4074844 , 0.3206522 , 0.49357328,\n",
+       "        1.0029498 ],\n",
+       "       [1.055794  , 0.70886075, 0.45024875, 0.4125    , 0.4079602 ,\n",
+       "        0.39658847, 0.4288939 , 0.37328094, 0.4       , 0.525641  ,\n",
+       "        0.42606518, 0.12519084, 0.34016395, 0.38730854, 0.6096939 ,\n",
+       "        0.6706349 ],\n",
+       "       [1.4224719 , 0.60779816, 0.4       , 0.29894736, 0.3478261 ,\n",
+       "        0.37529692, 0.5575916 , 0.35756385, 0.273743  , 0.40677965,\n",
+       "        0.39800996, 0.42948717, 0.20498085, 0.36381322, 1.0917722 ,\n",
+       "        0.95      ],\n",
+       "       [0.6345292 , 0.6382429 , 0.42032966, 0.4837963 , 0.5451264 ,\n",
+       "        0.29135802, 0.25402504, 0.49761903, 0.54252875, 0.18774703,\n",
+       "        0.29817444, 0.34177214, 0.2719101 , 0.3073593 , 0.47826087,\n",
+       "        0.85714287],\n",
+       "       [0.95683455, 0.7441176 , 0.38423645, 0.5       , 0.39479393,\n",
+       "        0.3970894 , 0.21593292, 0.28370222, 0.36563072, 0.38333333,\n",
+       "        0.28490567, 0.22718446, 0.24724062, 0.4353234 , 0.63054186,\n",
+       "        1.4868035 ],\n",
+       "       [0.73067915, 0.581741  , 0.43589744, 0.47845805, 0.4778481 ,\n",
+       "        0.32589287, 0.36461127, 0.26254827, 0.25      , 0.50716335,\n",
+       "        0.31135532, 0.3149742 , 0.32214764, 0.22689076, 0.677305  ,\n",
+       "        1.067757  ],\n",
+       "       [0.7494407 , 0.64803314, 0.48630136, 0.52880657, 0.48910892,\n",
+       "        0.67723346, 0.4728682 , 0.5751295 , 0.37009346, 0.7643312 ,\n",
+       "        0.65122616, 0.57608694, 0.33867735, 0.5268595 , 0.68201756,\n",
+       "        0.8290993 ],\n",
+       "       [0.9951691 , 0.80638725, 1.1409922 , 1.0398406 , 1.115869  ,\n",
+       "        1.1509846 , 1.020316  , 0.9919028 , 0.9140969 , 1.1386862 ,\n",
+       "        1.164271  , 1.2727273 , 0.8613678 , 0.9543269 , 1.0874317 ,\n",
+       "        1.0111607 ]], dtype=float32)

      Variances (σ²):
      array([[0.00307694, 0.00433658, 0.00292932, 0.00432835, 0.00249311,\n",
+       "        0.00329798, 0.00491208, 0.00519108, 0.00268826, 0.00229205,\n",
+       "        0.00491183, 0.005775  , 0.00336271, 0.00800842, 0.00803174,\n",
+       "        0.0051268 ],\n",
+       "       [0.00495399, 0.00241261, 0.00056447, 0.00200444, 0.00282532,\n",
+       "        0.00227777, 0.00131437, 0.00239191, 0.00414574, 0.0017493 ,\n",
+       "        0.00231835, 0.00256109, 0.00205171, 0.00165973, 0.0043978 ,\n",
+       "        0.0044994 ],\n",
+       "       [0.00346541, 0.00191048, 0.00218626, 0.00115913, 0.00099679,\n",
+       "        0.00204119, 0.00089466, 0.00139012, 0.00093967, 0.00050678,\n",
+       "        0.00073461, 0.00050068, 0.00082537, 0.00227711, 0.00215941,\n",
+       "        0.00577126],\n",
+       "       [0.00686706, 0.00271039, 0.00114692, 0.00121156, 0.00104008,\n",
+       "        0.00180936, 0.00071343, 0.00101277, 0.00043355, 0.00144421,\n",
+       "        0.00167105, 0.00190399, 0.00043245, 0.0006886 , 0.00169224,\n",
+       "        0.01994791],\n",
+       "       [0.00287632, 0.00222665, 0.00090043, 0.00044738, 0.00095573,\n",
+       "        0.0010042 , 0.0005175 , 0.00190961, 0.00105249, 0.0008125 ,\n",
+       "        0.0004328 , 0.00247578, 0.00179426, 0.00079925, 0.00322319,\n",
+       "        0.00470427],\n",
+       "       [0.00419212, 0.00291593, 0.00093321, 0.00143406, 0.00136419,\n",
+       "        0.00059932, 0.00044389, 0.00084728, 0.00202629, 0.0005362 ,\n",
+       "        0.00101163, 0.00209582, 0.00100171, 0.00039872, 0.00305373,\n",
+       "        0.00325967],\n",
+       "       [0.0049463 , 0.00170956, 0.00221213, 0.00105361, 0.0003534 ,\n",
+       "        0.00265111, 0.0012319 , 0.00057763, 0.0012882 , 0.00076585,\n",
+       "        0.00092812, 0.00110224, 0.00079287, 0.00112007, 0.00355372,\n",
+       "        0.0042244 ],\n",
+       "       [0.00264504, 0.00184722, 0.00246148, 0.001491  , 0.00033327,\n",
+       "        0.00098755, 0.00115286, 0.00082026, 0.00096792, 0.0010312 ,\n",
+       "        0.00278042, 0.0006173 , 0.00133065, 0.00085141, 0.00280796,\n",
+       "        0.00470031],\n",
+       "       [0.00317581, 0.00401517, 0.00113326, 0.00057105, 0.00126614,\n",
+       "        0.00090898, 0.00051699, 0.00091913, 0.00147431, 0.00119224,\n",
+       "        0.00135956, 0.00151066, 0.00119237, 0.00115073, 0.00189508,\n",
+       "        0.00592584],\n",
+       "       [0.00465771, 0.00306669, 0.00162431, 0.00145664, 0.00142884,\n",
+       "        0.00118096, 0.00138339, 0.00100711, 0.00127273, 0.00257032,\n",
+       "        0.0015228 , 0.00021506, 0.00093417, 0.00117575, 0.00250362,\n",
+       "        0.00222299],\n",
+       "       [0.00774359, 0.00224132, 0.0014359 , 0.00081751, 0.00101915,\n",
+       "        0.001226  , 0.00227356, 0.00095367, 0.00064931, 0.00138559,\n",
+       "        0.00138413, 0.00131185, 0.00047318, 0.00096532, 0.00722702,\n",
+       "        0.00402717],\n",
+       "       [0.00232546, 0.0027018 , 0.00164013, 0.0016617 , 0.00304075,\n",
+       "        0.00092901, 0.00056986, 0.00177439, 0.00192383, 0.0004407 ,\n",
+       "        0.00078516, 0.00082926, 0.00077718, 0.00086976, 0.00170772,\n",
+       "        0.00392078],\n",
+       "       [0.00449009, 0.00381714, 0.00131003, 0.00210674, 0.00119448,\n",
+       "        0.00115337, 0.00055044, 0.00073277, 0.00091283, 0.00126257,\n",
+       "        0.00069071, 0.00054135, 0.00068073, 0.0015543 , 0.00253233,\n",
+       "        0.01084278],\n",
+       "       [0.00296153, 0.00195364, 0.0013374 , 0.00160404, 0.00223477,\n",
+       "        0.00096451, 0.00133392, 0.00063992, 0.00057445, 0.00219019,\n",
+       "        0.0007478 , 0.00071288, 0.00095286, 0.00058481, 0.00402854,\n",
+       "        0.00515856],\n",
+       "       [0.00293311, 0.00221114, 0.00165021, 0.00166346, 0.00144225,\n",
+       "        0.00327343, 0.00179967, 0.0023469 , 0.00094778, 0.00429469,\n",
+       "        0.00293003, 0.00197383, 0.00090858, 0.00166207, 0.00251571,\n",
+       "        0.00350232],\n",
+       "       [0.00479597, 0.00290748, 0.00637821, 0.00422532, 0.00594719,\n",
+       "        0.0054174 , 0.00465318, 0.00399954, 0.0038539 , 0.00592529,\n",
+       "        0.00517412, 0.006574  , 0.00296363, 0.00448333, 0.00620202,\n",
+       "        0.0045393 ]], dtype=float32)
    • non_finite
      (y, x)
      bool
      False, False, ..., False, False
      Values:
      array([[False, False, False, False, False, False, False, False, False,\n",
+       "        False, False, False, False, False, False, False],\n",
+       "       [False, False, False, False, False, False, False, False, False,\n",
+       "        False, False, False, False, False, False, False],\n",
+       "       [False, False, False, False, False, False, False, False, False,\n",
+       "        False, False, False, False, False, False, False],\n",
+       "       [False, False, False, False, False, False, False, False, False,\n",
+       "        False, False, False, False, False, False, False],\n",
+       "       [False, False, False, False, False, False, False, False, False,\n",
+       "        False, False, False, False, False, False, False],\n",
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'iron_alpha_scitiff/iron_alpha_v1.tiff': 'sha256:efb923947e5f5c0f46788c0f18836a3fce916745a05ad5fb8483e5ff17e08a1a', + 'iron_alpha_scitiff/iron_alpha_v1.tiff': 'sha256:ada3d50a5324362add0b8787e11b87b5f33e1dd7e3862f92face03671a20a282', 'iron_alpha_tiff/iron_alpha_v1.tiff': 'sha256:a1e4a14bfff3d7c0e92cc42f65f7931536d01f763ba7df2a0e4c0aac851f3594', 'small_test_scitiff/small_test_scitiff_v1.tiff': ( 'sha256:2ce4088fad10437a1180855fba4ebfefad0c98b252be36d6fc046a1aa6ca922d' diff --git a/src/easyimaging/measurement/measurement.py b/src/easyimaging/measurement/measurement.py index 9389414..884fdd2 100644 --- a/src/easyimaging/measurement/measurement.py +++ b/src/easyimaging/measurement/measurement.py @@ -17,6 +17,7 @@ from scipp import UnitError from scitiff import load_scitiff from scitiff import save_scitiff +from scitiff.io import ImageJMetadataNotFoundWarning from ..utils import _is_notebook from ..utils import _to_edges @@ -191,10 +192,14 @@ def from_tiff_stack( """ if not isinstance(filename, (str, Path)): raise TypeError('filename must be a string or Path object.') - try: - data_array = load_scitiff(filename)['image'] - except Exception as e: - raise RuntimeError(f"Failed to load TIFF stack file '{filename}': {e}") from e + + # We know this is not a scitiff, so supress that warning + with warnings.catch_warnings(): + warnings.simplefilter('ignore', category=ImageJMetadataNotFoundWarning) + try: + data_array = load_scitiff(filename)['image'] + except Exception as e: + raise RuntimeError(f"Failed to load TIFF stack file '{filename}': {e}") from e try: data_array = data_array.rename_dims({'dim_0': 't', 'dim_1': 'y', 'dim_2': 'x'}) @@ -620,6 +625,10 @@ def revert_rebin(self) -> None: UserWarning, ) + # ------------------------------------------------------------------------------------------------------------------------- + # ----------------------------------------- Plotting methods -------------------------------------------------------------- + # ------------------------------------------------------------------------------------------------------------------------- + def plot(self, time_of_flight: int | sc.Variable | None = None, **kwargs) -> None: """Plot the measurement image at a specific time-of-flight. @@ -662,18 +671,20 @@ def plot(self, time_of_flight: int | sc.Variable | None = None, **kwargs) -> Non else: raise TypeError('time_of_flight must be an integer, scipp scalar, or None.') - plot_kwargs_defaults = self._plot_defaults() - plot_kwargs_defaults['title'] = self.display_name + title_suffix + if time_of_flight is None: + plot_array = self._data_array.mean('t') + elif isinstance(time_of_flight, int): + plot_array = self._data_array['t', time_of_flight] + elif isinstance(time_of_flight, sc.Variable): + plot_array = self._data_array['tof', time_of_flight] # Overwrite defaults with any user-provided kwargs + plot_kwargs_defaults = self._plot_defaults() + plot_kwargs_defaults['title'] = self.display_name + title_suffix + plot_kwargs_defaults['cmax'] = min(3.0, float(plot_array.max().value * 1.1)) plot_kwargs_defaults.update(kwargs) - if time_of_flight is None: - plot = self._data_array.mean('t').plot(**plot_kwargs_defaults) - elif isinstance(time_of_flight, int): - plot = self._data_array['t', time_of_flight].plot(**plot_kwargs_defaults) - elif isinstance(time_of_flight, sc.Variable): - plot = self._data_array['tof', time_of_flight].plot(**plot_kwargs_defaults) + plot = plot_array.plot(**plot_kwargs_defaults) if _is_notebook(): return plot else: @@ -744,7 +755,7 @@ def spectrum_inspector(self, **kwargs) -> None: inspector_kwargs_defaults.update({ 'title': self.display_name + ' - Spectrum Inspector', 'ymin': 0.0, - 'dim': 't', + 'dim': 'Time of flight', # Due to https://github.com/scipp/plopp/issues/566 'orientation': 'vertical', 'operation': 'mean', 'mode': 'point', @@ -752,8 +763,18 @@ def spectrum_inspector(self, **kwargs) -> None: # Overwrite defaults with any user-provided kwargs inspector_kwargs_defaults.update(kwargs) + # Hack to cirmunvent the bug in https://github.com/scipp/plopp/issues/566 + temp_array = self._data_array.drop_coords(self._data_array.coords) + if self._has_physical_coords: + temp_array.coords['x'] = self._data_array.coords['x'] + temp_array.coords['y'] = self._data_array.coords['y'] + temp_array.coords['x_pixels'] = self._data_array.coords['x_pixels'] + temp_array.coords['y_pixels'] = self._data_array.coords['y_pixels'] + temp_array.coords['Time of flight'] = self._data_array.coords['tof'] + temp_array = temp_array.rename_dims({'t': 'Time of flight'}) + if _is_notebook(): - return pp.inspector(self._data_array, **inspector_kwargs_defaults) + return pp.inspector(temp_array, **inspector_kwargs_defaults) else: raise RuntimeError('Interactive spectrum inspector is only supported in Jupyter notebooks.') @@ -795,15 +816,27 @@ def roi_creator(self, **kwargs) -> None: roi_selector_kwargs_defaults.update({ 'title': self.display_name + ' - ROI Creator', 'ymin': 0.0, - 'dim': 't', + 'dim': 'Time of flight', # Due to https://github.com/scipp/plopp/issues/566 'orientation': 'vertical', 'operation': 'mean', 'mode': 'rectangle', + # 'autoscale' : False, }) # Overwrite defaults with any user-provided kwargs roi_selector_kwargs_defaults.update(kwargs) - plots = pp.inspector(self._data_array, **roi_selector_kwargs_defaults) + # Hack to cirmunvent the bug in https://github.com/scipp/plopp/issues/566 + temp_array = self._data_array.drop_coords(self._data_array.coords) + if self._has_physical_coords: + temp_array.coords['x'] = self._data_array.coords['x'] + temp_array.coords['y'] = self._data_array.coords['y'] + temp_array.coords['x_pixels'] = self._data_array.coords['x_pixels'] + temp_array.coords['y_pixels'] = self._data_array.coords['y_pixels'] + temp_array.coords['Time of flight'] = self._data_array.coords['tof'] + temp_array = temp_array.rename_dims({'t': 'Time of flight'}) + + plots = pp.inspector(temp_array, **roi_selector_kwargs_defaults) + # plots = pp.inspector(self._data_array, **roi_selector_kwargs_defaults) # ------------------------------------------------------------------------------------------------- # -------------------------- Plot the existing ROIs on the plot ----------------------------------- @@ -1006,12 +1039,20 @@ def spectrum_plot(self, roi: RectROI | str | None = None, **kwargs) -> None: """ spectrum_data = self.spectrum(roi=roi) + if roi is None: + roi_name = 'entire image' + elif isinstance(roi, str): + roi_name = f"ROI '{roi}'" + else: + roi_name = f"ROI '{roi.unique_name}'" + plot_kwargs_defaults = { - 'title': self.display_name + ' - Spectrum', - 'xlabel': 'Time of Flight', + 'title': self.display_name + ' - Spectrum of ' + roi_name, + 'xlabel': f'Time of flight [{spectrum_data.coords["tof"].unit}]', 'ylabel': 'Transmission', 'ymin': 0.0, - 'ymax': 3.0, + 'ymax': min(3.0, float(spectrum_data.max().value * 1.1)), + 'coords': ['tof'], } # Overwrite defaults with any user-provided kwargs plot_kwargs_defaults.update(kwargs) diff --git a/tests/unit/measurement/test_measurement.py b/tests/unit/measurement/test_measurement.py index c5d2fe2..ffbe280 100644 --- a/tests/unit/measurement/test_measurement.py +++ b/tests/unit/measurement/test_measurement.py @@ -89,7 +89,7 @@ def valid_roi(self): y_pixel_range=y_pixel_range, x_range=x_range, y_range=y_range, - unique_name='test_roi', + # unique_name='test_roi', display_name='Test ROI', ) @@ -351,6 +351,14 @@ def test_from_tiff_stack_valid_paths(self, path): assert 'x' not in measurement._data_array.coords assert 'y' not in measurement._data_array.coords + @pytest.mark.filterwarnings('error') + def test_from_tiff_stack_no_ImageJ_warning(self): + # When Then Expect + Measurement.from_tiff_stack( + filename=small_test_tiff(), + time_of_flights=sc.arange('t', 0, 240, 1, unit='s'), + ) + @pytest.mark.parametrize( 'coord, expected', [ @@ -542,7 +550,7 @@ def test_save_scitiff_downcast(self, valid_data_array, tmp_path): UserWarning, match='The data array is of type float64, which is not directly supported by the SciTIFF format. ' 'It will be downcast to float32 when saving, which may result in loss of precision.', - ): # noqa: E501 + ): measurement.save_scitiff(tmp_path / 'test.tiff') assert 'non_finite' in measurement._data_array.masks @@ -1071,6 +1079,16 @@ def test_plot_coordinates(self, valid_data_array, time_of_flight, title, plot_se assert fig.view.colormapper.vmax == 1.1 assert fig.view.colormapper.vmin == 0.0 + def test_plot_automatic_cmax_at_index(self, valid_data_array, plot_setup): + # When + valid_data_array['t', 0].data *= 0.5 # Scale data at first TOF index to ensure max is below 1.0 + measurement = Measurement(data_array=valid_data_array) + # Then + fig = measurement.plot(time_of_flight=0) + # Expect + assert fig.view.colormapper.vmax == 0.55 + assert fig.view.colormapper.vmin == 0.0 + def test_plot_automatic_cmax(self, valid_data_array, plot_setup): # When valid_data_array.data *= 10.0 # Scale data to ensure max is above 1.0 @@ -1214,6 +1232,8 @@ def test_spectrum_inspector(self, valid_data_array, plot_setup): assert figs[0].view.colormapper.vmax == 1.1 assert figs[0].view.colormapper.vmin == 0.0 assert figs[1].canvas.ymax == 1.1 + assert figs[1].canvas.dims['x'] == 'Time of flight' + assert figs[1].canvas.units['x'] == 's' def test_spectrum_inspector_user_overwrite(self, valid_data_array, plot_setup): # When @@ -1292,6 +1312,9 @@ def test_roi_creator_create_roi_physical_coordinates(self, valid_data_array, plo figs[0].toolbar['inspect']._tool.stop() # Expect assert figs[1].canvas.ymax == 1.1 + # The next 2 can only be tested when something is drawn on the plot. + assert figs[1].canvas.dims['x'] == 'Time of flight' + assert figs[1].canvas.units['x'] == 's' assert len(measurement.regions_of_interest) == 1 roi = measurement.regions_of_interest[0] assert isinstance(roi, RectROI) @@ -1305,6 +1328,58 @@ def test_roi_creator_create_roi_physical_coordinates(self, valid_data_array, plo assert roi.y_end == sc.scalar(5, unit='m') assert roi._has_physical_coords + def test_roi_creator_with_existing_roi_both_physical_coords(self, valid_data_array, valid_roi, plot_setup): + # When + measurement = Measurement(data_array=valid_data_array) + measurement.regions_of_interest.append(valid_roi) + # Then + figs = measurement.roi_creator() + # Expect + assert figs[1].canvas.ymax == 1.1 + # The next 2 can only be tested when something is drawn on the plot, + # hence this tests that the existing ROI is properly loaded into the plot. + assert figs[1].canvas.dims['x'] == 'Time of flight' + assert figs[1].canvas.units['x'] == 's' + + def test_roi_creator_with_existing_roi_pixel_coordinates(self, valid_data_array, plot_setup): + # When + x_pixel_range = (1, 4) + y_pixel_range = (2, 5) + roi = RectROI( + x_pixel_range=x_pixel_range, + y_pixel_range=y_pixel_range, + ) + measurement = Measurement(data_array=valid_data_array) + measurement.regions_of_interest.append(roi) + # Then + figs = measurement.roi_creator() + # Expect + assert figs[1].canvas.ymax == 1.1 + # The next 2 can only be tested when something is drawn on the plot, + # hence this tests that the existing ROI is properly loaded into the plot. + assert figs[1].canvas.dims['x'] == 'Time of flight' + assert figs[1].canvas.units['x'] == 's' + + def test_roi_creator_existing_roi_both_pixel_coords(self, valid_data_array, valid_data_array_no_xy_coords, plot_setup): + # When + x_pixel_range = (1, 4) + y_pixel_range = (2, 5) + roi = RectROI( + x_pixel_range=x_pixel_range, + y_pixel_range=y_pixel_range, + ) + valid_data_array_no_xy_coords.data += 0.5 + measurement = Measurement(data_array=valid_data_array_no_xy_coords) + measurement.regions_of_interest.append(roi) + # Then + figs = measurement.roi_creator() + # Expect + assert figs[1].canvas.ymax == 0.55 + # The next 2 can only be tested when something is drawn on the plot, + # hence this tests that the existing ROI is properly loaded into the plot. + assert figs[1].canvas.dims['x'] == 'Time of flight' + assert figs[1].canvas.units['x'] == 's' + def test_roi_creator_create_roi_pixel_coordinates(self, valid_data_array, plot_setup): # When valid_data_array.coords.pop('x') @@ -1407,10 +1482,10 @@ def test_spectrum_valid_roi_by_name(self, valid_data_array): # When valid_data_array['x', 2:5]['y', 3:6]['t', 0:10] = sc.zeros(dims=['x', 'y', 't'], shape=[3, 3, 10]) measurement = Measurement(data_array=valid_data_array) - roi = RectROI(x_pixel_range=(2, 6), y_pixel_range=(2, 4), unique_name='test_roi') + roi = RectROI(x_pixel_range=(2, 6), y_pixel_range=(2, 4), unique_name='test_roi_3') # Then measurement.regions_of_interest.append(roi) - spectrum = measurement.spectrum(roi='test_roi') + spectrum = measurement.spectrum(roi='test_roi_3') # Expect assert isinstance(spectrum, sc.DataArray) assert sc.identical(spectrum.coords['tof'], measurement._data_array.coords['tof']) @@ -1483,3 +1558,61 @@ def test_spectrum_invalid_roi_name(self, valid_data_array): match="ROI with unique name 'non_existent_roi' not found in the measurement's list of ROIs.", ): # noqa: E501 measurement.spectrum(roi='non_existent_roi') + + @pytest.mark.parametrize( + 'roi, expected', + [ + (None, 'entire image'), + (RectROI(x_pixel_range=(2, 6), y_pixel_range=(2, 4), unique_name='test_roi_2'), "ROI 'test_roi_2'"), + ], + ids=['no_roi', 'rect_roi'], + ) + def test_spectrum_plot(self, valid_data_array, plot_setup, roi, expected, valid_roi): + # When + measurement = Measurement(data_array=valid_data_array) + measurement.regions_of_interest.append(valid_roi) + # Then + fig = measurement.spectrum_plot(roi=roi) + # Expect + assert fig.canvas.dims['x'] == 'tof' + assert fig.canvas.units['x'] == 's' + assert fig.canvas.title == measurement.display_name + ' - Spectrum of ' + expected + assert fig.canvas.xlabel == 'Time of flight [s]' + assert fig.canvas.ylabel == 'Transmission' + + def test_spectrum_plot_unique_name_roi(self, valid_data_array, plot_setup, valid_roi): + # When + measurement = Measurement(data_array=valid_data_array) + measurement.regions_of_interest.append(valid_roi) + roi = valid_roi.unique_name + # Then + fig = measurement.spectrum_plot(roi=roi) + # Expect + assert fig.canvas.dims['x'] == 'tof' + assert fig.canvas.units['x'] == 's' + assert fig.canvas.title == measurement.display_name + ' - Spectrum of ' + "ROI '" + roi + "'" + assert fig.canvas.xlabel == 'Time of flight [s]' + assert fig.canvas.ylabel == 'Transmission' + + def test_spectrum_plot_user_overwrite(self, valid_data_array, plot_setup): + # When + measurement = Measurement(data_array=valid_data_array) + # Then + fig = measurement.spectrum_plot(xlabel='Custom X label') + # Expect + assert fig.canvas.xlabel == 'Custom X label' + assert fig.canvas.ylabel == 'Transmission' + assert fig.canvas.title == measurement.display_name + ' - Spectrum of ' + 'entire image' + + def test_spectrum_plot_automatic_ymax(self, valid_data_array, plot_setup): + # When + valid_data_array.data *= 10.0 # Scale data to ensure max is above 1.0 + measurement = Measurement(data_array=valid_data_array) + # Then + fig = measurement.spectrum_plot() + # Expect + assert fig.canvas.dims['x'] == 'tof' + assert fig.canvas.title == measurement.display_name + ' - Spectrum of ' + 'entire image' + assert fig.canvas.xlabel == 'Time of flight [s]' + assert fig.canvas.ylabel == 'Transmission' + assert fig.canvas.ymax == 3.0 From 1d70a6e853e8d336071ba2ec4bbce71c65102ef0 Mon Sep 17 00:00:00 2001 From: Christian Vedel Date: Thu, 28 May 2026 15:41:11 +0200 Subject: [PATCH 03/14] Update package structure/names and add API reference to docs --- docs/docs/api-reference/index.md | 6 + .../api-reference/measurement/measurement.md | 5 + .../regions_of_interest/index.md | 11 + .../regions_of_interest/rectangle_roi.md | 1 + docs/docs/tutorials/measurement.ipynb | 500 ++++-------------- docs/mkdocs.yml | 6 +- pixi.lock | 214 ++++---- src/easyimaging/__init__.py | 2 +- src/easyimaging/measurement/measurement.py | 42 +- .../regions_of_interest/__init__.py | 6 + .../rectangle_roi.py} | 20 +- tests/unit/measurement/test_measurement.py | 30 +- .../test_rectangle_roi.py} | 26 +- 13 files changed, 309 insertions(+), 560 deletions(-) create mode 100644 docs/docs/api-reference/measurement/measurement.md create mode 100644 docs/docs/api-reference/regions_of_interest/index.md create mode 100644 docs/docs/api-reference/regions_of_interest/rectangle_roi.md create mode 100644 src/easyimaging/regions_of_interest/__init__.py rename src/easyimaging/{measurement/regions.py => regions_of_interest/rectangle_roi.py} (97%) rename tests/unit/{measurement/test_regions.py => regions_of_interest/test_rectangle_roi.py} (95%) diff --git a/docs/docs/api-reference/index.md b/docs/docs/api-reference/index.md index 62b1c78..65398bf 100644 --- a/docs/docs/api-reference/index.md +++ b/docs/docs/api-reference/index.md @@ -6,3 +6,9 @@ icon: material/code-braces-box This section contains the reference detailing the functions and modules available in EasyImaging. + +- [Measurement](measurement.md) - Loads and inspects measurement data. +- [regions_of_interest](regions_of_interest/index.md) - This module + contains all types of Regions Of Interests (ROIs) available: + - [RectangleROI](regions_of_interest/rectangle_roi.md) - A rectangular + ROI. The most basic and common type of ROI diff --git a/docs/docs/api-reference/measurement/measurement.md b/docs/docs/api-reference/measurement/measurement.md new file mode 100644 index 0000000..5ebe871 --- /dev/null +++ b/docs/docs/api-reference/measurement/measurement.md @@ -0,0 +1,5 @@ +--- +icon: fontawesome/solid/microscope +--- + +::: easyimaging.Measurement diff --git a/docs/docs/api-reference/regions_of_interest/index.md b/docs/docs/api-reference/regions_of_interest/index.md new file mode 100644 index 0000000..c1e959f --- /dev/null +++ b/docs/docs/api-reference/regions_of_interest/index.md @@ -0,0 +1,11 @@ +--- +icon: fontawesome/solid/crop-simple +--- + +# :fontawesome-solid-crop-simple: Regions Of Interest (ROIs) + +This module contains the different kinds of Regions Of Interest (ROIs) +available in EasyImaging. More will be added at a later date + +- [RectangleROI](rectangle_roi.md) - A rectangular ROI. The most basic + and common type of ROI diff --git a/docs/docs/api-reference/regions_of_interest/rectangle_roi.md b/docs/docs/api-reference/regions_of_interest/rectangle_roi.md new file mode 100644 index 0000000..005f44b --- /dev/null +++ b/docs/docs/api-reference/regions_of_interest/rectangle_roi.md @@ -0,0 +1 @@ +::: easyimaging.regions_of_interest.RectangleROI diff --git a/docs/docs/tutorials/measurement.ipynb b/docs/docs/tutorials/measurement.ipynb index 0b3b201..f57c81c 100644 --- a/docs/docs/tutorials/measurement.ipynb +++ b/docs/docs/tutorials/measurement.ipynb @@ -44,13 +44,11 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "id": "c4e759bd", "metadata": {}, "outputs": [], "source": [ - "from easyimaging.datasets import iron_alpha_scitiff\n", - "\n", "measurement = Measurement.from_scitiff(filename=scitiff_path)" ] }, @@ -207,7 +205,7 @@ "\n", "\n", "\n", - "
scipp.Variable (324 Bytes)
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      float32
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      Values:
      array([-7.0382814 , -6.158496  , -5.2787113 , -4.398926  , -3.5191407 ,\n",
+       "
      scipp.Variable (324 Bytes)
        • (x: 17)
          float32
          mm
          -7.0382814, -6.158496, ..., 6.158496, 7.0382814
          Values:
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scipp.Variable (324 Bytes)
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      Values:
      array([-7.0382814 , -6.158496  , -5.2787113 , -4.398926  , -3.5191407 ,\n",
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        • (y: 17)
          float32
          mm
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          Values:
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" \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1263,7 +1261,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1278,7 +1276,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1293,7 +1291,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1308,7 +1306,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1364,7 +1362,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1440,7 +1438,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1484,7 +1482,7 @@ " \n", " \n", " \n", - " 2026-05-27T13:30:31.282637\n", + " 2026-05-28T11:32:56.468032\n", " image/svg+xml\n", " \n", " \n", @@ -1515,20 +1513,20 @@ "z\n", "\" style=\"fill: #ffffff\"/>\n", " \n", - " \n", + " \n", " \n", + "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\" id=\"image511b9550eb\" transform=\"scale(1 -1) translate(0 -221.76)\" x=\"42.620313\" y=\"-22.318125\" width=\"307.44\" height=\"221.76\"/>\n", " \n", " \n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1581,7 +1579,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1616,7 +1614,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1656,7 +1654,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1692,7 +1690,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1705,7 +1703,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1718,7 +1716,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1814,12 +1812,12 @@ " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1833,7 +1831,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1847,7 +1845,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1861,7 +1859,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1874,7 +1872,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1887,7 +1885,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1900,7 +1898,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2314,18 +2312,18 @@ "\" style=\"fill: #ffffff\"/>\n", " \n", " \n", + "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\" id=\"image1b66e35227\" transform=\"scale(1 -1) translate(0 -221.76)\" x=\"365.04\" y=\"-22.32\" width=\"12.24\" height=\"221.76\"/>\n", " \n", " \n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2350,7 +2348,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2393,7 +2391,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2409,7 +2407,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2437,7 +2435,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2469,7 +2467,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2485,7 +2483,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2501,7 +2499,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2517,7 +2515,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2586,7 +2584,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2644,7 +2642,7 @@ " \n", " \n", " \n", - " 2026-05-27T13:30:32.553104\n", + " 2026-05-28T11:33:00.201759\n", " image/svg+xml\n", " \n", " \n", @@ -2675,20 +2673,20 @@ "z\n", "\" style=\"fill: #ffffff\"/>\n", " \n", - " \n", + " \n", " \n", + "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\" id=\"imagee77392ea86\" transform=\"scale(1 -1) translate(0 -221.76)\" x=\"42.620313\" y=\"-22.318125\" width=\"307.44\" height=\"221.76\"/>\n", " \n", " \n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2741,7 +2739,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2776,7 +2774,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2816,7 +2814,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2852,7 +2850,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2865,7 +2863,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2878,7 +2876,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2974,12 +2972,12 @@ " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2993,7 +2991,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3007,7 +3005,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3021,7 +3019,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3034,7 +3032,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3047,7 +3045,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3060,7 +3058,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3474,18 +3472,18 @@ "\" style=\"fill: #ffffff\"/>\n", " \n", " \n", + "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\" id=\"image3ba6b33391\" transform=\"scale(1 -1) translate(0 -221.76)\" x=\"365.04\" y=\"-22.32\" width=\"12.24\" height=\"221.76\"/>\n", " \n", " \n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3509,7 +3507,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3524,7 +3522,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3539,7 +3537,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3554,7 +3552,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3610,7 +3608,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3694,7 +3692,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3768,7 +3766,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "2cbb5e0f42f24cfe86e7870d1dd6dcfe", + "model_id": "5eec3ae0c0b04761a352bd7598d94e01", "version_major": 2, "version_minor": 0 }, @@ -3822,9 +3820,9 @@ "\n", "\n", "\n", - "
scipp.DataArray (36.84 KB)
    • t: 1500
    • Ltotal
      ()
      int64
      m
      61
      Values:
      array(61)
    • c
      ()
      string
      intensities
      Values:
      'intensities'
    • tof
      (t [bin-edge])
      float64
      s
      0.022, 0.022, ..., 0.092, 0.093
      Values:
      array([0.02158728, 0.02163456, 0.02168185, ..., 0.09242233, 0.09246961,\n",
-       "       0.0925169 ], shape=(1501,))
    • wavelength
      (t [bin-edge])
      float64
      Å
      1.4, 1.403, ..., 5.997, 6.0
      Values:
      array([1.4       , 1.40306667, 1.40613333, ..., 5.99386667, 5.99693333,\n",
-       "       6.        ], shape=(1501,))
    • (t)
      float32
      𝟙
      0.5531428, 0.56375575, ..., 0.63517606, 0.63194895
      σ = 0.002992472, 0.003154994, ..., 0.006249289, 0.006158047
      Values:
      array([0.5531428 , 0.56375575, 0.5592331 , ..., 0.6236488 , 0.63517606,\n",
+       "
      scipp.DataArray (36.84 KB)
        • t: 1500
        • Ltotal
          ()
          int64
          m
          61
          Values:
          array(61)
        • c
          ()
          string
          intensities
          Values:
          'intensities'
        • tof
          (t [bin-edge])
          float64
          s
          0.022, 0.022, ..., 0.092, 0.093
          Values:
          array([0.02158728, 0.02163456, 0.02168185, ..., 0.09242233, 0.09246961,\n",
+       "       0.0925169 ], shape=(1501,))
        • wavelength
          (t [bin-edge])
          float64
          Å
          1.4, 1.403, ..., 5.997, 6.0
          Values:
          array([1.4       , 1.40306667, 1.40613333, ..., 5.99386667, 5.99693333,\n",
+       "       6.        ], shape=(1501,))
        • (t)
          float32
          𝟙
          0.5531428, 0.56375575, ..., 0.63517606, 0.63194895
          σ = 0.002992472, 0.003154994, ..., 0.006249289, 0.006158047
          Values:
          array([0.5531428 , 0.56375575, 0.5592331 , ..., 0.6236488 , 0.63517606,\n",
        "       0.63194895], shape=(1500,), dtype=float32)

          Variances (σ²):
          array([8.9548885e-06, 9.9539866e-06, 9.6888207e-06, ..., 3.6184254e-05,\n",
        "       3.9053615e-05, 3.7921542e-05], shape=(1500,), dtype=float32)
    " ], @@ -3869,7 +3867,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "f9efbd5255164e328e3e08f44c8066cd", + "model_id": "9b93b6a25ff949e0b76b5255e2f9cb9d", "version_major": 2, "version_minor": 0 }, @@ -3905,7 +3903,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "294103cf4efa422ca0ba2c4366401edc", + "model_id": "ae0910a141ff4e58b503a5d2e62158a7", "version_major": 2, "version_minor": 0 }, @@ -3934,12 +3932,12 @@ }, { "cell_type": "code", - "execution_count": 21, + "execution_count": null, "id": "4969d839", "metadata": {}, "outputs": [], "source": [ - "from easyimaging.measurement.regions import RectROI" + "from easyimaging.regions_of_interest.rectangle_roi import RectROI" ] }, { @@ -4003,9 +4001,9 @@ "\n", "\n", "\n", - "
    scipp.DataArray (36.84 KB)
      • t: 1500
      • Ltotal
        ()
        int64
        m
        61
        Values:
        array(61)
      • c
        ()
        string
        intensities
        Values:
        'intensities'
      • tof
        (t [bin-edge])
        float64
        s
        0.022, 0.022, ..., 0.092, 0.093
        Values:
        array([0.02158728, 0.02163456, 0.02168185, ..., 0.09242233, 0.09246961,\n",
-       "       0.0925169 ], shape=(1501,))
      • wavelength
        (t [bin-edge])
        float64
        Å
        1.4, 1.403, ..., 5.997, 6.0
        Values:
        array([1.4       , 1.40306667, 1.40613333, ..., 5.99386667, 5.99693333,\n",
-       "       6.        ], shape=(1501,))
      • (t)
        float32
        𝟙
        0.36840674, 0.3425866, ..., 0.46642005, 0.45523798
        σ = 0.0058153444, 0.0056076236, ..., 0.013006445, 0.012870439
        Values:
        array([0.36840674, 0.3425866 , 0.35694158, ..., 0.43976402, 0.46642005,\n",
+       "
        scipp.DataArray (36.84 KB)
          • t: 1500
          • Ltotal
            ()
            int64
            m
            61
            Values:
            array(61)
          • c
            ()
            string
            intensities
            Values:
            'intensities'
          • tof
            (t [bin-edge])
            float64
            s
            0.022, 0.022, ..., 0.092, 0.093
            Values:
            array([0.02158728, 0.02163456, 0.02168185, ..., 0.09242233, 0.09246961,\n",
+       "       0.0925169 ], shape=(1501,))
          • wavelength
            (t [bin-edge])
            float64
            Å
            1.4, 1.403, ..., 5.997, 6.0
            Values:
            array([1.4       , 1.40306667, 1.40613333, ..., 5.99386667, 5.99693333,\n",
+       "       6.        ], shape=(1501,))
          • (t)
            float32
            𝟙
            0.36840674, 0.3425866, ..., 0.46642005, 0.45523798
            σ = 0.0058153444, 0.0056076236, ..., 0.013006445, 0.012870439
            Values:
            array([0.36840674, 0.3425866 , 0.35694158, ..., 0.43976402, 0.46642005,\n",
        "       0.45523798], shape=(1500,), dtype=float32)

            Variances (σ²):
            array([3.3818233e-05, 3.1445445e-05, 3.3600576e-05, ..., 1.4671838e-04,\n",
        "       1.6916762e-04, 1.6564821e-04], shape=(1500,), dtype=float32)
      " ], @@ -4039,7 +4037,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "57b60acdcd8b4d8da74827bba55f7de7", + "model_id": "93a2186d5f864d4c90f86fb3abc64188", "version_major": 2, "version_minor": 0 }, @@ -4091,7 +4089,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "19ffc42be05b4532a1ddb51f69e319eb", + "model_id": "ff5b600fc3be451eb7d02430062f0c97", "version_major": 2, "version_minor": 0 }, @@ -4125,297 +4123,13 @@ { "cell_type": "code", "execution_count": 27, - "id": "c24c19bf", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
      \n", - "\n", - "\n", - "\n", - "\n", - "Show/Hide data repr\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "Show/Hide attributes\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "
      scipp.DataArray (5.61 KB out of 3.32 MB)
        • y: 16
        • x: 16
        • Ltotal
          ()
          int64
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          Values:
          array(61)
        • c
          ()
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        • tof
          (t [bin-edge])
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          0.022, 0.022
          Values:
          array([0.02158728, 0.02163456])
        • wavelength
          (t [bin-edge])
          float64
          Å
          1.4, 1.403
          Values:
          array([1.4       , 1.40306667])
        • x
          (x [bin-edge])
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          mm
          -7.0382814, -6.158496, ..., 6.158496, 7.0382814
          Values:
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-       "       -2.6393557 , -1.7595701 , -0.87978506,  0.        ,  0.87978506,\n",
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        • x_pixels
          (x [bin-edge])
          int64
          𝟙
          0, 1, ..., 15, 16
          Values:
          array([ 0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14, 15, 16])
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          (y [bin-edge])
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          Values:
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          (y [bin-edge])
          int64
          𝟙
          0, 1, ..., 15, 16
          Values:
          array([ 0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14, 15, 16])
        • (y, x)
          float32
          𝟙
          0.8669202, 0.97052157, ..., 1.0874317, 1.0111607
          σ = 0.055470176, 0.06585275, ..., 0.07875291, 0.067374334
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-       "       [1.0357853 , 0.6827411 , 0.3326316 , 0.42553192, 0.34971097,\n",
-       "        0.25142857, 0.20326678, 0.28271028, 0.50793654, 0.23818181,\n",
-       "        0.31719127, 0.5095368 , 0.3047859 , 0.17567568, 0.6363636 ,\n",
-       "        0.81152993],\n",
-       "       [1.0813187 , 0.5121413 , 0.49552238, 0.32518336, 0.14587738,\n",
-       "        0.5185185 , 0.39823008, 0.24031007, 0.4297694 , 0.3079848 ,\n",
-       "        0.27513227, 0.29597703, 0.2733485 , 0.3586207 , 0.7105263 ,\n",
-       "        0.765625  ],\n",
-       "       [0.6879271 , 0.55744684, 0.5542857 , 0.42      , 0.16404887,\n",
-       "        0.33033708, 0.33505154, 0.28475335, 0.33901918, 0.36192468,\n",
-       "        0.6246575 , 0.25482625, 0.39119804, 0.31106472, 0.6658228 ,\n",
-       "        0.9976415 ],\n",
-       "       [0.75598085, 0.7943662 , 0.3048433 , 0.2518116 , 0.39909297,\n",
-       "        0.3173913 , 0.17777778, 0.3483366 , 0.50389105, 0.3306233 ,\n",
-       "        0.4187643 , 0.4168798 , 0.4074844 , 0.3206522 , 0.49357328,\n",
-       "        1.0029498 ],\n",
-       "       [1.055794  , 0.70886075, 0.45024875, 0.4125    , 0.4079602 ,\n",
-       "        0.39658847, 0.4288939 , 0.37328094, 0.4       , 0.525641  ,\n",
-       "        0.42606518, 0.12519084, 0.34016395, 0.38730854, 0.6096939 ,\n",
-       "        0.6706349 ],\n",
-       "       [1.4224719 , 0.60779816, 0.4       , 0.29894736, 0.3478261 ,\n",
-       "        0.37529692, 0.5575916 , 0.35756385, 0.273743  , 0.40677965,\n",
-       "        0.39800996, 0.42948717, 0.20498085, 0.36381322, 1.0917722 ,\n",
-       "        0.95      ],\n",
-       "       [0.6345292 , 0.6382429 , 0.42032966, 0.4837963 , 0.5451264 ,\n",
-       "        0.29135802, 0.25402504, 0.49761903, 0.54252875, 0.18774703,\n",
-       "        0.29817444, 0.34177214, 0.2719101 , 0.3073593 , 0.47826087,\n",
-       "        0.85714287],\n",
-       "       [0.95683455, 0.7441176 , 0.38423645, 0.5       , 0.39479393,\n",
-       "        0.3970894 , 0.21593292, 0.28370222, 0.36563072, 0.38333333,\n",
-       "        0.28490567, 0.22718446, 0.24724062, 0.4353234 , 0.63054186,\n",
-       "        1.4868035 ],\n",
-       "       [0.73067915, 0.581741  , 0.43589744, 0.47845805, 0.4778481 ,\n",
-       "        0.32589287, 0.36461127, 0.26254827, 0.25      , 0.50716335,\n",
-       "        0.31135532, 0.3149742 , 0.32214764, 0.22689076, 0.677305  ,\n",
-       "        1.067757  ],\n",
-       "       [0.7494407 , 0.64803314, 0.48630136, 0.52880657, 0.48910892,\n",
-       "        0.67723346, 0.4728682 , 0.5751295 , 0.37009346, 0.7643312 ,\n",
-       "        0.65122616, 0.57608694, 0.33867735, 0.5268595 , 0.68201756,\n",
-       "        0.8290993 ],\n",
-       "       [0.9951691 , 0.80638725, 1.1409922 , 1.0398406 , 1.115869  ,\n",
-       "        1.1509846 , 1.020316  , 0.9919028 , 0.9140969 , 1.1386862 ,\n",
-       "        1.164271  , 1.2727273 , 0.8613678 , 0.9543269 , 1.0874317 ,\n",
-       "        1.0111607 ]], dtype=float32)

          Variances (σ²):
          array([[0.00307694, 0.00433658, 0.00292932, 0.00432835, 0.00249311,\n",
-       "        0.00329798, 0.00491208, 0.00519108, 0.00268826, 0.00229205,\n",
-       "        0.00491183, 0.005775  , 0.00336271, 0.00800842, 0.00803174,\n",
-       "        0.0051268 ],\n",
-       "       [0.00495399, 0.00241261, 0.00056447, 0.00200444, 0.00282532,\n",
-       "        0.00227777, 0.00131437, 0.00239191, 0.00414574, 0.0017493 ,\n",
-       "        0.00231835, 0.00256109, 0.00205171, 0.00165973, 0.0043978 ,\n",
-       "        0.0044994 ],\n",
-       "       [0.00346541, 0.00191048, 0.00218626, 0.00115913, 0.00099679,\n",
-       "        0.00204119, 0.00089466, 0.00139012, 0.00093967, 0.00050678,\n",
-       "        0.00073461, 0.00050068, 0.00082537, 0.00227711, 0.00215941,\n",
-       "        0.00577126],\n",
-       "       [0.00686706, 0.00271039, 0.00114692, 0.00121156, 0.00104008,\n",
-       "        0.00180936, 0.00071343, 0.00101277, 0.00043355, 0.00144421,\n",
-       "        0.00167105, 0.00190399, 0.00043245, 0.0006886 , 0.00169224,\n",
-       "        0.01994791],\n",
-       "       [0.00287632, 0.00222665, 0.00090043, 0.00044738, 0.00095573,\n",
-       "        0.0010042 , 0.0005175 , 0.00190961, 0.00105249, 0.0008125 ,\n",
-       "        0.0004328 , 0.00247578, 0.00179426, 0.00079925, 0.00322319,\n",
-       "        0.00470427],\n",
-       "       [0.00419212, 0.00291593, 0.00093321, 0.00143406, 0.00136419,\n",
-       "        0.00059932, 0.00044389, 0.00084728, 0.00202629, 0.0005362 ,\n",
-       "        0.00101163, 0.00209582, 0.00100171, 0.00039872, 0.00305373,\n",
-       "        0.00325967],\n",
-       "       [0.0049463 , 0.00170956, 0.00221213, 0.00105361, 0.0003534 ,\n",
-       "        0.00265111, 0.0012319 , 0.00057763, 0.0012882 , 0.00076585,\n",
-       "        0.00092812, 0.00110224, 0.00079287, 0.00112007, 0.00355372,\n",
-       "        0.0042244 ],\n",
-       "       [0.00264504, 0.00184722, 0.00246148, 0.001491  , 0.00033327,\n",
-       "        0.00098755, 0.00115286, 0.00082026, 0.00096792, 0.0010312 ,\n",
-       "        0.00278042, 0.0006173 , 0.00133065, 0.00085141, 0.00280796,\n",
-       "        0.00470031],\n",
-       "       [0.00317581, 0.00401517, 0.00113326, 0.00057105, 0.00126614,\n",
-       "        0.00090898, 0.00051699, 0.00091913, 0.00147431, 0.00119224,\n",
-       "        0.00135956, 0.00151066, 0.00119237, 0.00115073, 0.00189508,\n",
-       "        0.00592584],\n",
-       "       [0.00465771, 0.00306669, 0.00162431, 0.00145664, 0.00142884,\n",
-       "        0.00118096, 0.00138339, 0.00100711, 0.00127273, 0.00257032,\n",
-       "        0.0015228 , 0.00021506, 0.00093417, 0.00117575, 0.00250362,\n",
-       "        0.00222299],\n",
-       "       [0.00774359, 0.00224132, 0.0014359 , 0.00081751, 0.00101915,\n",
-       "        0.001226  , 0.00227356, 0.00095367, 0.00064931, 0.00138559,\n",
-       "        0.00138413, 0.00131185, 0.00047318, 0.00096532, 0.00722702,\n",
-       "        0.00402717],\n",
-       "       [0.00232546, 0.0027018 , 0.00164013, 0.0016617 , 0.00304075,\n",
-       "        0.00092901, 0.00056986, 0.00177439, 0.00192383, 0.0004407 ,\n",
-       "        0.00078516, 0.00082926, 0.00077718, 0.00086976, 0.00170772,\n",
-       "        0.00392078],\n",
-       "       [0.00449009, 0.00381714, 0.00131003, 0.00210674, 0.00119448,\n",
-       "        0.00115337, 0.00055044, 0.00073277, 0.00091283, 0.00126257,\n",
-       "        0.00069071, 0.00054135, 0.00068073, 0.0015543 , 0.00253233,\n",
-       "        0.01084278],\n",
-       "       [0.00296153, 0.00195364, 0.0013374 , 0.00160404, 0.00223477,\n",
-       "        0.00096451, 0.00133392, 0.00063992, 0.00057445, 0.00219019,\n",
-       "        0.0007478 , 0.00071288, 0.00095286, 0.00058481, 0.00402854,\n",
-       "        0.00515856],\n",
-       "       [0.00293311, 0.00221114, 0.00165021, 0.00166346, 0.00144225,\n",
-       "        0.00327343, 0.00179967, 0.0023469 , 0.00094778, 0.00429469,\n",
-       "        0.00293003, 0.00197383, 0.00090858, 0.00166207, 0.00251571,\n",
-       "        0.00350232],\n",
-       "       [0.00479597, 0.00290748, 0.00637821, 0.00422532, 0.00594719,\n",
-       "        0.0054174 , 0.00465318, 0.00399954, 0.0038539 , 0.00592529,\n",
-       "        0.00517412, 0.006574  , 0.00296363, 0.00448333, 0.00620202,\n",
-       "        0.0045393 ]], dtype=float32)
        • non_finite
          (y, x)
          bool
          False, False, ..., False, False
          Values:
          array([[False, False, False, False, False, False, False, False, False,\n",
-       "        False, False, False, False, False, False, False],\n",
-       "       [False, False, False, False, False, False, False, False, False,\n",
-       "        False, False, False, False, False, False, False],\n",
-       "       [False, False, False, False, False, False, False, False, False,\n",
-       "        False, False, False, False, False, False, False],\n",
-       "       [False, False, False, False, False, False, False, False, False,\n",
-       "        False, False, False, False, False, False, False],\n",
-       "       [False, False, False, False, False, False, False, False, False,\n",
-       "        False, False, False, False, False, False, False],\n",
-       "       [False, False, False, False, False, False, False, False, False,\n",
-       "        False, False, False, False, False, False, False],\n",
-       "       [False, False, False, False, False, False, False, False, False,\n",
-       "        False, False, False, False, False, False, False],\n",
-       "       [False, False, False, False, False, False, False, False, False,\n",
-       "        False, False, False, False, False, False, False],\n",
-       "       [False, False, False, False, False, False, False, False, False,\n",
-       "        False, False, False, False, False, False, False],\n",
-       "       [False, False, False, False, False, False, False, False, False,\n",
-       "        False, False, False, False, False, False, False],\n",
-       "       [False, False, False, False, False, False, False, False, False,\n",
-       "        False, False, False, False, False, False, False],\n",
-       "       [False, False, False, False, False, False, False, False, False,\n",
-       "        False, False, False, False, False, False, False],\n",
-       "       [False, False, False, False, False, False, False, False, False,\n",
-       "        False, False, False, False, False, False, False],\n",
-       "       [False, False, False, False, False, False, False, False, False,\n",
-       "        False, False, False, False, False, False, False],\n",
-       "       [False, False, False, False, False, False, False, False, False,\n",
-       "        False, False, False, False, False, False, False],\n",
-       "       [False, False, False, False, False, False, False, False, False,\n",
-       "        False, False, False, False, False, False, False]])
      " - ], - "text/plain": [ - "\n", - "Dimensions: Sizes[y:16, x:16, ]\n", - "Coordinates:\n", - "* Ltotal int64 [m] () 61\n", - " c string () \"intensities\"\n", - " tof float64 [s] (t [bin-edge]) [0.0215873, 0.0216346]\n", - " wavelength float64 [Å] (t [bin-edge]) [1.4, 1.40307]\n", - "* x float32 [mm] (x [bin-edge]) [-7.03828, -6.1585, ..., 6.1585, 7.03828]\n", - "* x_pixels int64 [dimensionless] (x [bin-edge]) [0, 1, ..., 15, 16]\n", - "* y float32 [mm] (y [bin-edge]) [-7.03828, -6.1585, ..., 6.1585, 7.03828]\n", - "* y_pixels int64 [dimensionless] (y [bin-edge]) [0, 1, ..., 15, 16]\n", - "Data:\n", - " float32 [dimensionless] (y, x) [0.86692, 0.970522, ..., 1.08743, 1.01116] [0.00307694, 0.00433658, ..., 0.00620202, 0.0045393]\n", - "Masks:\n", - " non_finite bool (y, x) [False, False, ..., False, False]\n" - ] - }, - "execution_count": 27, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "measurement._data_array['t', 0]" - ] - }, - { - "cell_type": "code", - "execution_count": 28, - "id": "29721fac", - "metadata": {}, - "outputs": [], - "source": [ - "import plopp as pp\n", - "from plopp.data.examples import clusters3d\n", - "\n", - "da = clusters3d(nclusters=50, seed=12).hist(z=100, y=100, x=100)" - ] - }, - { - "cell_type": "code", - "execution_count": 29, - "id": "863da646", - "metadata": {}, - "outputs": [ - { - "data": { - "application/vnd.jupyter.widget-view+json": { - "model_id": "91168bedafff4f94bfe8183c1fcf0bd0", - "version_major": 2, - "version_minor": 0 - }, - "text/plain": [ - "Box(children=(InteractiveFigure(children=(HBar(), HBar(children=(VBar(children=(Toolbar(children=(ButtonTool(i…" - ] - }, - "execution_count": 29, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "pp.inspector(da, dim='z', orientation='vertical', logc=True)" - ] - }, - { - "cell_type": "code", - "execution_count": 32, - "id": "ae94067f", - "metadata": {}, - "outputs": [ - { - "data": { - "application/vnd.jupyter.widget-view+json": { - "model_id": "451afc1f4d694c95b5962950685825dd", - "version_major": 2, - "version_minor": 0 - }, - "text/plain": [ - "Box(children=(InteractiveFigure(children=(HBar(), HBar(children=(VBar(children=(Toolbar(children=(ButtonTool(i…" - ] - }, - "execution_count": 32, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "pp.inspector(da, dim='z', orientation='vertical', logc=True, mode='polygon', operation='mean')" - ] - }, - { - "cell_type": "code", - "execution_count": 31, "id": "7ff41a8e-7dd2-4a19-9d09-8a9221963459", "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "0e5afdbadd574840baf1050ddfbb3b6b", + "model_id": "b4c0732e2f3a40ab9ccc6144c677d890", "version_major": 2, "version_minor": 0 }, @@ -4423,7 +4137,7 @@ "Box(children=(InteractiveFigure(children=(HBar(), HBar(children=(VBar(children=(Toolbar(children=(ButtonTool(i…" ] }, - "execution_count": 31, + "execution_count": 27, "metadata": {}, "output_type": "execute_result" } @@ -4449,7 +4163,7 @@ { "data": { "text/plain": [ - "EasyList of length 1 of type(s) []" + "EasyList of length 2 of type(s) []" ] }, "execution_count": 28, diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml index f08ec56..2db93c0 100644 --- a/docs/mkdocs.yml +++ b/docs/mkdocs.yml @@ -180,6 +180,10 @@ nav: - Tutorials: - Tutorials: tutorials/index.md - Getting Started: - - Dummy tutorial: tutorials/measurement.ipynb + - The Measurement class: tutorials/measurement.ipynb - API Reference: - API Reference: api-reference/index.md + - Measurement: api-reference/measurement/measurement.md + - regions_of_interest: + - regions_of_interest: api-reference/regions_of_interest/index.md + - RectangleROI: api-reference/regions_of_interest/rectangle_roi.md diff --git a/pixi.lock b/pixi.lock index 831d826..5b1ebdb 100644 --- a/pixi.lock +++ b/pixi.lock @@ -148,7 +148,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/tinycss2-1.4.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h366c992_103.conda - 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- pypi: https://files.pythonhosted.org/packages/8a/06/2c1bd1ee9eee3e65b0b6395dcf960e71b11576995eae3b4ab9ec63d89bea/essreduce-26.4.1-py3-none-any.whl + - pypi: https://files.pythonhosted.org/packages/83/ec/fdc3b36fab1ee0ae3ef1036e10fda4143ad97af7a9f5027a3f09ae83a6fe/essreduce-26.5.0-py3-none-any.whl - pypi: https://files.pythonhosted.org/packages/ab/84/02fc1827e8cdded4aa65baef11296a9bbe595c474f0d6d758af082d849fd/execnet-2.1.2-py3-none-any.whl - pypi: https://files.pythonhosted.org/packages/81/47/dd9a212ef6e343a6857485ffe25bba537304f1913bdbed446a23f7f592e1/filelock-3.29.0-py3-none-any.whl - pypi: https://files.pythonhosted.org/packages/ce/36/0b805d8c485f872f65a509cbe3b58a5d0d17bee855333b54a150c79d3061/fonttools-4.63.0-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.whl @@ -263,7 +263,7 @@ environments: - pypi: https://files.pythonhosted.org/packages/f1/d9/7fb5aa316bc299258e68c73ba3bddbc499654a07f151cba08f6153988714/pathspec-1.1.1-py3-none-any.whl - pypi: https://files.pythonhosted.org/packages/67/ee/21d4e8536afd1a328f01b359b4d3997b291ffd35a237c877b331c1c3b71c/pillow-12.2.0-cp313-cp313-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl - 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distlib>=0.3.7,<1 - filelock>=3.24.2,<4 ; python_full_version >= '3.10' - filelock>=3.16.1,<=3.19.1 ; python_full_version < '3.10' - importlib-metadata>=6.6 ; python_full_version < '3.8' - platformdirs>=3.9.1,<5 - - python-discovery>=1.3.1 + - python-discovery>=1.4 - typing-extensions>=4.13.2 ; python_full_version < '3.11' requires_python: '>=3.8' - pypi: https://files.pythonhosted.org/packages/b5/e8/dbf020b4d98251a9860752a094d09a65e1b436ad181faf929983f697048f/watchdog-6.0.0-py3-none-manylinux2014_x86_64.whl diff --git a/src/easyimaging/__init__.py b/src/easyimaging/__init__.py index b5a0e5b..45044bb 100644 --- a/src/easyimaging/__init__.py +++ b/src/easyimaging/__init__.py @@ -9,4 +9,4 @@ __version__ = version(__package__) -__all__ = [Measurement, __version__] +__all__ = [__version__, Measurement] diff --git a/src/easyimaging/measurement/measurement.py b/src/easyimaging/measurement/measurement.py index 884fdd2..1090933 100644 --- a/src/easyimaging/measurement/measurement.py +++ b/src/easyimaging/measurement/measurement.py @@ -19,9 +19,9 @@ from scitiff import save_scitiff from scitiff.io import ImageJMetadataNotFoundWarning +from ..regions_of_interest import RectangleROI from ..utils import _is_notebook from ..utils import _to_edges -from .regions import RectROI Numeric = int | float @@ -104,7 +104,7 @@ def __init__( self._full_data_array.coords['x_pixels'] = sc.arange('x', 0, self._full_data_array.sizes['x'] + 1, 1) self._full_data_array.coords['y_pixels'] = sc.arange('y', 0, self._full_data_array.sizes['y'] + 1, 1) - self._regions_of_interest = EasyList(protected_types=(RectROI,)) + self._regions_of_interest = EasyList(protected_types=(RectangleROI,)) non_finite_mask = ~sc.isfinite(self._full_data_array.data) self._full_data_array.masks['non_finite'] = non_finite_mask @@ -533,19 +533,19 @@ def time_of_flights(self, value: sc.Variable | np.ndarray) -> None: self._data_array.coords['tof'] = value @property - def regions_of_interest(self) -> EasyList[RectROI]: + def regions_of_interest(self) -> EasyList[RectangleROI]: """Get the list of regions of interest (ROIs) defined for this measurement. Returns ------- - EasyList[RectROI] - The list of :class:`~easyimaging.measurement.regions.RectROI` objects + EasyList[RectangleROI] + The list of :class:`~easyimaging.measurement.regions.RectangleROI` objects associated with this measurement. """ return self._regions_of_interest @regions_of_interest.setter - def regions_of_interest(self, value: EasyList[RectROI]) -> None: + def regions_of_interest(self, value: EasyList[RectangleROI]) -> None: """Raise AttributeError — ``regions_of_interest`` is a read-only property. Raises @@ -877,20 +877,20 @@ def roi_creator(self, **kwargs) -> None: # The callback to be used by the Scipp RectangleTool when drawing a new rectangle. def create_rectangle_roi(rect, roi_list, data_array): - """Create a new :class:`RectROI` from a drawn rectangle and append it to ``roi_list``. + """Create a new :class:`RectangleROI` from a drawn rectangle and append it to ``roi_list``. Parameters ---------- rect : The rectangle object provided by the plopp RectangleTool. - roi_list : EasyList[RectROI] + roi_list : EasyList[RectangleROI] The list of ROIs to append the new ROI to. data_array : sc.DataArray The data array used to derive pixel and physical coordinate ranges. """ # Get the pixel and physical coordinate ranges from the rectangle vertices using the helper method. x_pixel_range, y_pixel_range, x_range, y_range = Measurement._ranges_from_rectangle(rect, data_array) - new_roi = RectROI( + new_roi = RectangleROI( x_pixel_range=x_pixel_range, y_pixel_range=y_pixel_range, x_range=x_range, @@ -901,13 +901,13 @@ def create_rectangle_roi(rect, roi_list, data_array): # The callback to be used by the Scipp RectangleTool when dragging the corners of an existing rectangle. def edit_rectangle_roi(rect, roi_list, data_array): - """Update the matching :class:`RectROI` in ``roi_list`` when a rectangle is resized. + """Update the matching :class:`RectangleROI` in ``roi_list`` when a rectangle is resized. Parameters ---------- rect : The rectangle object provided by the plopp RectangleTool. - roi_list : EasyList[RectROI] + roi_list : EasyList[RectangleROI] The list of ROIs containing the ROI to update. data_array : sc.DataArray The data array used to derive updated coordinate ranges. @@ -924,13 +924,13 @@ def edit_rectangle_roi(rect, roi_list, data_array): matching_roi.set_physical_coord_range(x_range, y_range) def delete_rectangle_roi(rect, roi_list): - """Remove the :class:`RectROI` corresponding to ``rect`` from ``roi_list``. + """Remove the :class:`RectangleROI` corresponding to ``rect`` from ``roi_list``. Parameters ---------- rect : The rectangle object provided by the plopp RectangleTool. - roi_list : EasyList[RectROI] + roi_list : EasyList[RectangleROI] The list of ROIs from which the matching ROI will be removed. """ for roi in roi_list: @@ -960,14 +960,14 @@ def delete_rectangle_roi(rect, roi_list): return plots - def spectrum(self, roi: RectROI | str | None = None) -> sc.DataArray: + def spectrum(self, roi: RectangleROI | str | None = None) -> sc.DataArray: """Extract the spectrum (intensity vs. time-of-flight) for a specified region of interest (ROI). If no ROI is provided, the spectrum is calculated over the entire image. Parameters ---------- - roi : RectROI | str | None, optional + roi : RectangleROI | str | None, optional The region of interest for which to extract the spectrum. If a string is provided, it should be the unique name of a predefined ROI in the measurement's list of ROIs. By default, None. @@ -981,12 +981,12 @@ def spectrum(self, roi: RectROI | str | None = None) -> sc.DataArray: Raises ------ TypeError - If ``roi`` is not a :class:`RectROI`, string, or ``None``. + If ``roi`` is not a :class:`RectangleROI`, string, or ``None``. KeyError If a string ``roi`` does not match any ROI in :attr:`regions_of_interest`. """ - if roi is not None and not isinstance(roi, (RectROI, str)): - raise TypeError('roi must be a string, None, or an instance of RectROI.') + if roi is not None and not isinstance(roi, (RectangleROI, str)): + raise TypeError('roi must be a string, None, or an instance of RectangleROI.') if isinstance(roi, str): if roi in self.regions_of_interest: @@ -1006,7 +1006,7 @@ def spectrum(self, roi: RectROI | str | None = None) -> sc.DataArray: spectrum_data = self._data_array['x_pixels', x_slice]['y_pixels', y_slice].mean(dim=['x', 'y']) return spectrum_data - def spectrum_plot(self, roi: RectROI | str | None = None, **kwargs) -> None: + def spectrum_plot(self, roi: RectangleROI | str | None = None, **kwargs) -> None: """Plot the spectrum (intensity vs. time-of-flight) for a specified region of interest (ROI). If no ROI is provided, the spectrum is calculated over the entire image. @@ -1016,7 +1016,7 @@ def spectrum_plot(self, roi: RectROI | str | None = None, **kwargs) -> None: Parameters ---------- - roi : RectROI | str | None, optional + roi : RectangleROI | str | None, optional The region of interest for which to plot the spectrum. If a string is provided, it should be the unique name of a predefined ROI in the measurement's list of ROIs. By default, None. @@ -1033,7 +1033,7 @@ def spectrum_plot(self, roi: RectROI | str | None = None, **kwargs) -> None: Raises ------ TypeError - If ``roi`` is not a :class:`RectROI`, string, or ``None``. + If ``roi`` is not a :class:`RectangleROI`, string, or ``None``. KeyError If a string ``roi`` does not match any ROI in :attr:`regions_of_interest`. """ diff --git a/src/easyimaging/regions_of_interest/__init__.py b/src/easyimaging/regions_of_interest/__init__.py new file mode 100644 index 0000000..e6674ed --- /dev/null +++ b/src/easyimaging/regions_of_interest/__init__.py @@ -0,0 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + +from .rectangle_roi import RectangleROI + +__all__ = [RectangleROI] diff --git a/src/easyimaging/measurement/regions.py b/src/easyimaging/regions_of_interest/rectangle_roi.py similarity index 97% rename from src/easyimaging/measurement/regions.py rename to src/easyimaging/regions_of_interest/rectangle_roi.py index 9f9c3d9..4e64c41 100644 --- a/src/easyimaging/measurement/regions.py +++ b/src/easyimaging/regions_of_interest/rectangle_roi.py @@ -14,7 +14,7 @@ from scipp import UnitError -class RectROI(NewBase): +class RectangleROI(NewBase): """Class representing a rectangular region of interest (ROI) in an image. Physical coordinate ranges are used by default if they are provided and are usable in the Measurement. @@ -30,7 +30,7 @@ def __init__( unique_name: str | None = None, display_name: str | None = None, ) -> None: - """Initialize a RectROI instance. + """Initialize a RectangleROI instance. Parameters ---------- @@ -49,7 +49,7 @@ def __init__( giving the physical coordinate range in the y direction. Must be provided together with ``x_range``. By default, None. unique_name : str | None, optional - A unique identifier for the ROI. Defaults to ``'RectROI'`` appended by a + A unique identifier for the ROI. Defaults to ``'RectangleROI'`` appended by a unique integer. display_name : str | None, optional A human-readable name for the ROI. Defaults to ``unique_name`` if not provided. @@ -561,7 +561,7 @@ def _single_coord_setter_check(self, value: sc.Variable, name: str) -> None: ) def to_dict(self, skip: List[str] | None = None) -> Dict[str, Any]: - """Convert the RectROI instance to a dictionary representation. + """Convert the RectangleROI instance to a dictionary representation. Parameters ---------- @@ -618,8 +618,8 @@ def to_dict(self, skip: List[str] | None = None) -> Dict[str, Any]: return out_dict @classmethod - def from_dict(cls, input_dict: Dict[str, Any]) -> RectROI: - """Create a RectROI instance from a dictionary representation. + def from_dict(cls, input_dict: Dict[str, Any]) -> RectangleROI: + """Create a RectangleROI instance from a dictionary representation. Parameters ---------- @@ -631,8 +631,8 @@ def from_dict(cls, input_dict: Dict[str, Any]) -> RectROI: Returns ------- - RectROI - A new :class:`RectROI` instance initialised from the dictionary. + RectangleROI + A new :class:`RectangleROI` instance initialised from the dictionary. """ temp_dict = input_dict.copy() if 'x_range' in input_dict and 'y_range' in input_dict: @@ -641,7 +641,7 @@ def from_dict(cls, input_dict: Dict[str, Any]) -> RectROI: return super().from_dict(temp_dict) def __repr__(self) -> str: - """Return a string representation of the RectROI. + """Return a string representation of the RectangleROI. Returns ------- @@ -650,7 +650,7 @@ def __repr__(self) -> str: physical coordinate ranges. """ repr_str = ( - f'RectROI(x_pixel_range=({self._x_pixel_start}, {self._x_pixel_end}), ' + f'RectangleROI(x_pixel_range=({self._x_pixel_start}, {self._x_pixel_end}), ' f'y_pixel_range=({self._y_pixel_start}, {self._y_pixel_end})' ) if self._has_physical_coords: diff --git a/tests/unit/measurement/test_measurement.py b/tests/unit/measurement/test_measurement.py index ffbe280..c42d29e 100644 --- a/tests/unit/measurement/test_measurement.py +++ b/tests/unit/measurement/test_measurement.py @@ -18,7 +18,7 @@ from easyimaging import Measurement from easyimaging.datasets import small_test_scitiff from easyimaging.datasets import small_test_tiff -from easyimaging.measurement.regions import RectROI +from easyimaging.regions_of_interest import RectangleROI class TestMeasurement: @@ -84,7 +84,7 @@ def valid_roi(self): y_pixel_range = (2, 5) x_range = (sc.scalar(1.0, unit='m'), sc.scalar(4.0, unit='m')) y_range = (sc.scalar(2.0, unit='m'), sc.scalar(5.0, unit='m')) - return RectROI( + return RectangleROI( x_pixel_range=x_pixel_range, y_pixel_range=y_pixel_range, x_range=x_range, @@ -1317,7 +1317,7 @@ def test_roi_creator_create_roi_physical_coordinates(self, valid_data_array, plo assert figs[1].canvas.units['x'] == 's' assert len(measurement.regions_of_interest) == 1 roi = measurement.regions_of_interest[0] - assert isinstance(roi, RectROI) + assert isinstance(roi, RectangleROI) assert roi.x_pixel_start == 2 assert roi.x_pixel_end == 5 assert roi.y_pixel_start == 2 @@ -1345,7 +1345,7 @@ def test_roi_creator_with_existing_roi_pixel_coordinates(self, valid_data_array, # When x_pixel_range = (1, 4) y_pixel_range = (2, 5) - roi = RectROI( + roi = RectangleROI( x_pixel_range=x_pixel_range, y_pixel_range=y_pixel_range, ) @@ -1364,7 +1364,7 @@ def test_roi_creator_existing_roi_both_pixel_coords(self, valid_data_array, vali # When x_pixel_range = (1, 4) y_pixel_range = (2, 5) - roi = RectROI( + roi = RectangleROI( x_pixel_range=x_pixel_range, y_pixel_range=y_pixel_range, ) @@ -1396,7 +1396,7 @@ def test_roi_creator_create_roi_pixel_coordinates(self, valid_data_array, plot_s assert figs[1].canvas.ymax == 1.1 assert len(measurement.regions_of_interest) == 1 roi = measurement.regions_of_interest[0] - assert isinstance(roi, RectROI) + assert isinstance(roi, RectangleROI) assert roi.x_pixel_start == 2 assert roi.x_pixel_end == 5 assert roi.y_pixel_start == 2 @@ -1411,7 +1411,7 @@ def test_roi_creator_create_roi_pixel_coordinates(self, valid_data_array, plot_s # def test_roi_creator_delete_roi_both_physical_coords(self, valid_data_array, plot_setup): # # When # measurement = Measurement(data_array=valid_data_array) - # roi = RectROI( + # roi = RectangleROI( # x_pixel_range=(2, 5), # y_pixel_range=(2, 5), # x_range=(sc.scalar(2.5, unit='m'), sc.scalar(5, unit='m')), @@ -1443,7 +1443,7 @@ def test_spectrum_valid_with_pixel_roi(self, valid_data_array): # When valid_data_array['x', 2:5]['y', 3:6]['t', 0:10] = sc.zeros(dims=['x', 'y', 't'], shape=[3, 3, 10]) measurement = Measurement(data_array=valid_data_array) - roi = RectROI(x_pixel_range=(2, 6), y_pixel_range=(2, 4)) + roi = RectangleROI(x_pixel_range=(2, 6), y_pixel_range=(2, 4)) # Then spectrum = measurement.spectrum(roi=roi) # Expect @@ -1462,7 +1462,7 @@ def test_spectrum_valid_with_physical_roi(self, valid_data_array): x_positions=sc.arange('x', 0, 21, 3, unit='m'), y_positions=sc.arange('y', 0, 14, 2, unit='m'), ) - roi = RectROI( + roi = RectangleROI( x_pixel_range=(1, 6), y_pixel_range=(1, 6), x_range=(sc.scalar(6, unit='m'), sc.scalar(18, unit='m')), @@ -1482,7 +1482,7 @@ def test_spectrum_valid_roi_by_name(self, valid_data_array): # When valid_data_array['x', 2:5]['y', 3:6]['t', 0:10] = sc.zeros(dims=['x', 'y', 't'], shape=[3, 3, 10]) measurement = Measurement(data_array=valid_data_array) - roi = RectROI(x_pixel_range=(2, 6), y_pixel_range=(2, 4), unique_name='test_roi_3') + roi = RectangleROI(x_pixel_range=(2, 6), y_pixel_range=(2, 4), unique_name='test_roi_3') # Then measurement.regions_of_interest.append(roi) spectrum = measurement.spectrum(roi='test_roi_3') @@ -1497,7 +1497,7 @@ def test_spectrum_identical_after_rebin(self, valid_data_array): # then the spectrum should be identical before and after rebinning valid_data_array['x', 2:5]['y', 3:6]['t', 0:10] = sc.zeros(dims=['x', 'y', 't'], shape=[3, 3, 10]) measurement = Measurement(data_array=valid_data_array) - roi = RectROI(x_pixel_range=(2, 6), y_pixel_range=(2, 4)) + roi = RectangleROI(x_pixel_range=(2, 6), y_pixel_range=(2, 4)) spectrum_before_rebin = measurement.spectrum(roi=roi) # Then measurement.rebin(dimensions={'x': 2, 'y': 2}) @@ -1510,7 +1510,7 @@ def test_spectrum_not_identical_after_rebin(self, valid_data_array): # then the spectrum should not be identical before and after rebinning valid_data_array['x', 2:5]['y', 3:6]['t', 0:10] = sc.zeros(dims=['x', 'y', 't'], shape=[3, 3, 10]) measurement = Measurement(data_array=valid_data_array) - roi = RectROI(x_pixel_range=(2, 6), y_pixel_range=(2, 5)) + roi = RectangleROI(x_pixel_range=(2, 6), y_pixel_range=(2, 5)) spectrum_before_rebin = measurement.spectrum(roi=roi) # Then measurement.rebin(dimensions={'x': 2, 'y': 2}) @@ -1532,7 +1532,7 @@ def test_spectrum_roi_with_masked_data(self, valid_data_array, value): valid_data_array['x', 2:5]['y', 3:6]['t', 0:10] = sc.zeros(dims=['x', 'y', 't'], shape=[3, 3, 10]) valid_data_array['x', 3]['y', 3] = sc.full(value=value, dims=['t'], shape=[10]) measurement = Measurement(data_array=valid_data_array) - roi = RectROI(x_pixel_range=(2, 6), y_pixel_range=(2, 4)) + roi = RectangleROI(x_pixel_range=(2, 6), y_pixel_range=(2, 4)) # Then spectrum = measurement.spectrum(roi=roi) # Expect @@ -1546,7 +1546,7 @@ def test_spectrum_invalid_roi_type(self, valid_data_array): # When measurement = Measurement(data_array=valid_data_array) # Then Expect - with pytest.raises(TypeError, match='roi must be a string, None, or an instance of RectROI.'): + with pytest.raises(TypeError, match='roi must be a string, None, or an instance of RectangleROI.'): measurement.spectrum(roi=3.4) def test_spectrum_invalid_roi_name(self, valid_data_array): @@ -1563,7 +1563,7 @@ def test_spectrum_invalid_roi_name(self, valid_data_array): 'roi, expected', [ (None, 'entire image'), - (RectROI(x_pixel_range=(2, 6), y_pixel_range=(2, 4), unique_name='test_roi_2'), "ROI 'test_roi_2'"), + (RectangleROI(x_pixel_range=(2, 6), y_pixel_range=(2, 4), unique_name='test_roi_2'), "ROI 'test_roi_2'"), ], ids=['no_roi', 'rect_roi'], ) diff --git a/tests/unit/measurement/test_regions.py b/tests/unit/regions_of_interest/test_rectangle_roi.py similarity index 95% rename from tests/unit/measurement/test_regions.py rename to tests/unit/regions_of_interest/test_rectangle_roi.py index 48d8fdd..0cce228 100644 --- a/tests/unit/measurement/test_regions.py +++ b/tests/unit/regions_of_interest/test_rectangle_roi.py @@ -5,13 +5,13 @@ import scipp as sc from scipp import UnitError -from easyimaging.measurement.regions import RectROI +from easyimaging.regions_of_interest import RectangleROI -class TestRectROI: +class TestRectangleROI: @pytest.fixture def roi_basic(self): - return RectROI((10, 50), [20, 80]) + return RectangleROI((10, 50), [20, 80]) @pytest.fixture def roi_with_physical_coords(self): @@ -19,7 +19,7 @@ def roi_with_physical_coords(self): x_end = sc.scalar(10.0, unit='m') y_start = sc.scalar(0.0, unit='m') y_end = sc.scalar(5.0, unit='m') - return RectROI( + return RectangleROI( (10, 50), (20, 80), (x_start, x_end), @@ -48,8 +48,8 @@ def test_init_valid_pixel_only(self, roi_basic): # When Then roi = roi_basic # Expect - assert roi.unique_name.startswith('RectROI_') - assert roi.display_name.startswith('RectROI_') + assert roi.unique_name.startswith('RectangleROI_') + assert roi.display_name.startswith('RectangleROI_') assert roi.x_pixel_start == 10 assert roi.x_pixel_end == 50 assert roi.y_pixel_start == 20 @@ -62,12 +62,12 @@ def test_init_invalid_single_physical_coords(self): x_end = sc.scalar(10.0, unit='m') # Then Expect with pytest.raises(ValueError, match='Both x_range and y_range must be provided together or not at all.'): - RectROI((10, 50), (20, 80), (x_start, x_end)) + RectangleROI((10, 50), (20, 80), (x_start, x_end)) def test_init_invalid_negative_pixel_indices(self): # When Then Expect with pytest.raises(ValueError, match='Pixel indices must be non-negative integers.'): - RectROI((-10, 50), (20, 80)) + RectangleROI((-10, 50), (20, 80)) @pytest.mark.parametrize( 'x_pixel_range', @@ -82,7 +82,7 @@ def test_init_invalid_negative_pixel_indices(self): def test_init_invalid_x_pixel_range_arguments(self, x_pixel_range): # When Then Expect with pytest.raises(TypeError, match='x_pixel_range must be a tuple or a list of two integers'): - RectROI(x_pixel_range, (20, 80)) + RectangleROI(x_pixel_range, (20, 80)) @pytest.mark.parametrize( 'x_range, error, message', @@ -130,7 +130,7 @@ def test_init_invalid_x_pixel_range_arguments(self, x_pixel_range): def test_init_invalid_x_range_arguments(self, x_range, error, message): # When Then Expect with pytest.raises(error, match=message): - RectROI((10, 50), (20, 80), x_range, (sc.scalar(0.0, unit='m'), sc.scalar(1.0, unit='m'))) + RectangleROI((10, 50), (20, 80), x_range, (sc.scalar(0.0, unit='m'), sc.scalar(1.0, unit='m'))) def test_set_physical_coord_range(self, roi_basic): # When @@ -364,12 +364,12 @@ def test_from_dict_only_pixel_ranges(self): # Given input_dict = { '@module': 'easyimaging.measurement.regions', - '@class': 'RectROI', + '@class': 'RectangleROI', 'x_pixel_range': [10, 50], 'y_pixel_range': [20, 80], } # When Then - roi = RectROI.from_dict(input_dict) + roi = RectangleROI.from_dict(input_dict) # Expect assert roi.x_pixel_start == 10 assert roi.x_pixel_end == 50 @@ -382,7 +382,7 @@ def test_from_dict_with_physical_coords(self, roi_with_physical_coords): roi = roi_with_physical_coords input_dict = roi.to_dict(skip='unique_name') # Skip unique_name to allow auto-generation in from_dict # When Then - roi_from_dict = RectROI.from_dict(input_dict) + roi_from_dict = RectangleROI.from_dict(input_dict) # Expect assert roi_from_dict.x_pixel_start == roi.x_pixel_start assert roi_from_dict.x_pixel_end == roi.x_pixel_end From 67007745093f194597648e61a4e3afd1e8786540 Mon Sep 17 00:00:00 2001 From: Christian Vedel Date: Mon, 1 Jun 2026 16:08:11 +0200 Subject: [PATCH 04/14] Remove source code in docs and make docs width adjust better to new font-sizes / resolutions. --- docs/docs/api-reference/index.md | 3 ++- docs/docs/assets/stylesheets/extra.css | 2 +- docs/mkdocs.yml | 2 +- src/easyimaging/__init__.py | 2 -- src/easyimaging/measurement/__init__.py | 2 -- src/easyimaging/regions_of_interest/__init__.py | 2 -- 6 files changed, 4 insertions(+), 9 deletions(-) diff --git a/docs/docs/api-reference/index.md b/docs/docs/api-reference/index.md index 65398bf..c4a12ab 100644 --- a/docs/docs/api-reference/index.md +++ b/docs/docs/api-reference/index.md @@ -7,7 +7,8 @@ icon: material/code-braces-box This section contains the reference detailing the functions and modules available in EasyImaging. -- [Measurement](measurement.md) - Loads and inspects measurement data. +- [Measurement](measurement/measurement.md) - Loads and inspects + measurement data. - [regions_of_interest](regions_of_interest/index.md) - This module contains all types of Regions Of Interests (ROIs) available: - [RectangleROI](regions_of_interest/rectangle_roi.md) - A rectangular diff --git a/docs/docs/assets/stylesheets/extra.css b/docs/docs/assets/stylesheets/extra.css index a625be8..bc99907 100644 --- a/docs/docs/assets/stylesheets/extra.css +++ b/docs/docs/assets/stylesheets/extra.css @@ -200,7 +200,7 @@ label.md-nav__title[for="__drawer"] { /* Change the overall width of the page */ .md-grid { - max-width: 1280px; + max-width: 135em; } /* Needed for mkdocs-jupyter to show download and other buttons on top of the notebook */ diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml index 2db93c0..f02835c 100644 --- a/docs/mkdocs.yml +++ b/docs/mkdocs.yml @@ -156,7 +156,7 @@ plugins: show_root_heading: true show_root_full_path: false show_submodules: true - show_source: true + show_source: false - search # Determines additional directories to watch when running mkdocs serve diff --git a/src/easyimaging/__init__.py b/src/easyimaging/__init__.py index 45044bb..5ebe66d 100644 --- a/src/easyimaging/__init__.py +++ b/src/easyimaging/__init__.py @@ -8,5 +8,3 @@ from .measurement import Measurement __version__ = version(__package__) - -__all__ = [__version__, Measurement] diff --git a/src/easyimaging/measurement/__init__.py b/src/easyimaging/measurement/__init__.py index eb1f0c1..5dc8def 100644 --- a/src/easyimaging/measurement/__init__.py +++ b/src/easyimaging/measurement/__init__.py @@ -2,5 +2,3 @@ # SPDX-License-Identifier: BSD-3-Clause from .measurement import Measurement - -__all__ = [Measurement] diff --git a/src/easyimaging/regions_of_interest/__init__.py b/src/easyimaging/regions_of_interest/__init__.py index e6674ed..3ca52e4 100644 --- a/src/easyimaging/regions_of_interest/__init__.py +++ b/src/easyimaging/regions_of_interest/__init__.py @@ -2,5 +2,3 @@ # SPDX-License-Identifier: BSD-3-Clause from .rectangle_roi import RectangleROI - -__all__ = [RectangleROI] From 4845371340d6439f1e5c85c2ae3b623cb580767a Mon Sep 17 00:00:00 2001 From: Christian Vedel Date: Tue, 2 Jun 2026 15:34:39 +0200 Subject: [PATCH 05/14] Better mkdocstrings options --- docs/mkdocs.yml | 9 + pixi.lock | 19319 +++++++++++++++++++++++----------------------- 2 files changed, 9665 insertions(+), 9663 deletions(-) diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml index f02835c..e76cc0a 100644 --- a/docs/mkdocs.yml +++ b/docs/mkdocs.yml @@ -157,6 +157,15 @@ plugins: show_root_full_path: false show_submodules: true show_source: false + show_bases: false + preload_modules: + - easyscience + inherited_members: true + show_category_heading: true + merge_init_into_class: true + docstring_options: + ignore_init_summary: true + summary: true - search # Determines additional directories to watch when running mkdocs serve diff --git a/pixi.lock b/pixi.lock index 5b1ebdb..72ca995 100644 --- a/pixi.lock +++ b/pixi.lock @@ -1,4 +1,8 @@ -version: 6 +version: 7 +platforms: +- name: linux-64 +- name: osx-arm64 +- name: win-64 environments: default: channels: @@ -6,36 +10,74 @@ environments: - 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md5: ab136e4c34e97f34fb621d2592a393d8 - depends: - - __osx >=11.0 - - libzlib >=1.3.1,<2.0a0 - license: BSD-3-Clause - license_family: BSD - purls: [] - size: 433413 - timestamp: 1764777166076 -- conda: https://conda.anaconda.org/conda-forge/win-64/zstd-1.5.7-h534d264_6.conda - sha256: 368d8628424966fd8f9c8018326a9c779e06913dd39e646cf331226acc90e5b2 - md5: 053b84beec00b71ea8ff7a4f84b55207 - depends: - - vc >=14.3,<15 - - vc14_runtime >=14.44.35208 - - ucrt >=10.0.20348.0 - - libzlib >=1.3.1,<2.0a0 - license: BSD-3-Clause - license_family: BSD - purls: [] - size: 388453 - timestamp: 1764777142545 From e168fd8f10c04c26d9ea91f29c7e7ad52a1a5937 Mon Sep 17 00:00:00 2001 From: Christian Vedel Date: Thu, 4 Jun 2026 12:00:14 +0200 Subject: [PATCH 06/14] Update all docstrings in RectangleROI --- .../regions_of_interest/rectangle_roi.md | 2 + docs/docs/assets/stylesheets/extra.css | 9 +- docs/mkdocs.yml | 1 + .../regions_of_interest/rectangle_roi.py | 204 ++++++++++-------- 4 files changed, 128 insertions(+), 88 deletions(-) diff --git a/docs/docs/api-reference/regions_of_interest/rectangle_roi.md b/docs/docs/api-reference/regions_of_interest/rectangle_roi.md index 005f44b..e464b0c 100644 --- a/docs/docs/api-reference/regions_of_interest/rectangle_roi.md +++ b/docs/docs/api-reference/regions_of_interest/rectangle_roi.md @@ -1 +1,3 @@ ::: easyimaging.regions_of_interest.RectangleROI + options: + filters: ["!^_[^_]", "!__repr__", "!__dir__"] \ No newline at end of file diff --git a/docs/docs/assets/stylesheets/extra.css b/docs/docs/assets/stylesheets/extra.css index bc99907..5bc1db1 100644 --- a/docs/docs/assets/stylesheets/extra.css +++ b/docs/docs/assets/stylesheets/extra.css @@ -200,7 +200,14 @@ label.md-nav__title[for="__drawer"] { /* Change the overall width of the page */ .md-grid { - max-width: 135em; + max-width: 116em; +} + +/* Keep prose line length stable when sidebars are hidden at narrower widths */ +.md-main .md-content > .md-content__inner { + width: min(100%, 40.5em); + margin-left: auto !important; + margin-right: auto !important; } /* Needed for mkdocs-jupyter to show download and other buttons on top of the notebook */ diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml index e76cc0a..7c51420 100644 --- a/docs/mkdocs.yml +++ b/docs/mkdocs.yml @@ -166,6 +166,7 @@ plugins: docstring_options: ignore_init_summary: true summary: true + relative_crossrefs: true - search # Determines additional directories to watch when running mkdocs serve diff --git a/src/easyimaging/regions_of_interest/rectangle_roi.py b/src/easyimaging/regions_of_interest/rectangle_roi.py index 4e64c41..e607237 100644 --- a/src/easyimaging/regions_of_interest/rectangle_roi.py +++ b/src/easyimaging/regions_of_interest/rectangle_roi.py @@ -17,8 +17,27 @@ class RectangleROI(NewBase): """Class representing a rectangular region of interest (ROI) in an image. - Physical coordinate ranges are used by default if they are provided and are usable in the Measurement. - Otherwise, the obligatory pixel coordinate ranges are used as fallback. + This class is most simply instantiated by the [`roi_creator`][...Measurement.roi_creator] method in the + [Measurement][...Measurement] class. Alternatively it can be created manually as shown in the example below. + + Physical coordinate ranges are used by default, if they are provided **and** can be used in the + associated [Measurement][...Measurement] class. + Otherwise, the obligatory pixel coordinate ranges are used as a fallback. + + Example + ------- + ```python + import scipp as sc + from easyimaging.regions_of_interest import RectangleROI + + roi = RectangleROI( + x_pixel_range = (10, 50), + y_pixel_range = (20, 80), + x_range = (sc.scalar(0.0, unit='m'), sc.scalar(10.0, unit='m')), + y_range = (sc.scalar(0.0, unit='m'), sc.scalar(5.0, unit='m')), + unique_name = 'my_rectangle_roi', + ) + ``` """ def __init__( @@ -35,35 +54,38 @@ def __init__( Parameters ---------- x_pixel_range : Sequence[int] - A two-element sequence ``[x_start, x_end]`` giving the pixel range in the - x direction. + A two-element integer sequence ``[x_start, x_end]`` indicating the pixel range in the + x-direction. y_pixel_range : Sequence[int] - A two-element sequence ``[y_start, y_end]`` giving the pixel range in the - y direction. - x_range : Sequence[sc.Variable] | None, optional - A two-element sequence ``[x_start, x_end]`` of :class:`scipp.Variable` scalars - giving the physical coordinate range in the x direction. Must be provided - together with ``y_range``. By default, None. - y_range : Sequence[sc.Variable] | None, optional - A two-element sequence ``[y_start, y_end]`` of :class:`scipp.Variable` scalars - giving the physical coordinate range in the y direction. Must be provided - together with ``x_range``. By default, None. - unique_name : str | None, optional + A two-element integer sequence ``[y_start, y_end]`` indicating the pixel range in the + y-direction. + x_range : Sequence[sc.Variable] | None + A two-element sequence ``[x_start, x_end]`` of [`sc.Variable`](https://scipp.github.io/generated/functions/scipp.scalar.html) + scalars with units of length, indicating the spatial coordinate range in the x-direction.
      + Must be provided together with ``y_range``. + y_range : Sequence[sc.Variable] | None + A two-element sequence ``[y_start, y_end]`` of [`sc.Variable`](https://scipp.github.io/generated/functions/scipp.scalar.html) + scalars with units of length, indicating the spatial coordinate range in the y-direction.
      + Must be provided together with ``x_range``. + unique_name : str | None A unique identifier for the ROI. Defaults to ``'RectangleROI'`` appended by a unique integer. - display_name : str | None, optional - A human-readable name for the ROI. Defaults to ``unique_name`` if not provided. + display_name : str | None + A human-readable name for the ROI. Defaults to [`unique_name`][..unique_name] if not provided. Raises ------ TypeError - If ``x_pixel_range`` or ``y_pixel_range`` is not a two-element sequence of - integers, or if physical ranges are not sequences of :class:`scipp.Variable`. + If ``x_pixel_range`` or ``y_pixel_range`` is not a two-element sequence of integers.
      + If physical ranges are not two-element sequences of [`sc.Variable`](https://scipp.github.io/generated/functions/scipp.scalar.html). ValueError - If any pixel index is negative, if only one of ``x_range`` / ``y_range`` is - provided, or if physical coordinate scalars do not have a unit of length. + If any pixel index in ``x_pixel_range`` or ``y_pixel_range`` is negative.
      + If only one of ``x_range`` / ``y_range`` is provided.
      + If any [`sc.Variable`](https://scipp.github.io/generated/classes/scipp.Variable.html#scipp.Variable) in ``x_range`` + or ``y_range`` is not 0-dimensional (i.e., not a scalar).
      UnitError - If a physical coordinate scalar cannot be converted to metres. + If any [`sc.Variable`](https://scipp.github.io/generated/functions/scipp.scalar.html) scalar in ``x_range`` or + ``y_range`` does not have a unit of length. """ super().__init__(unique_name=unique_name, display_name=display_name) self.set_pixel_coord_range(x_pixel_range, y_pixel_range) @@ -76,16 +98,18 @@ def __init__( raise ValueError('Both x_range and y_range must be provided together or not at all.') def set_pixel_coord_range(self, x_pixel_range: Sequence[int], y_pixel_range: Sequence[int]) -> None: - """Set the pixel coordinate ranges for the ROI. + """Set the pixel coordinate ranges defining the ROI. Parameters ---------- x_pixel_range : Sequence[int] - A two-element sequence ``[x_start, x_end]`` of non-negative integer pixel - coordinates in the x direction. + The pixel coordinate range in the x-direction to set. + Must be a two-element sequence ``[x_start, x_end]`` of pixel + indices defining an x-axis range. y_pixel_range : Sequence[int] - A two-element sequence ``[y_start, y_end]`` of non-negative integer pixel - coordinates in the y direction. + The pixel coordinate range in the y-direction to set. + Must be a two-element sequence ``[y_start, y_end]`` of pixel + indices defining a y-axis range. Raises ------ @@ -98,30 +122,36 @@ def set_pixel_coord_range(self, x_pixel_range: Sequence[int], y_pixel_range: Seq self._check_input_sequence(y_pixel_range, 'y_pixel_range', 'integers', int) for index in tuple(x_pixel_range) + tuple(y_pixel_range): if index < 0: - raise ValueError('Pixel indices must be non-negative integers.') # Do I need this check? + raise ValueError('Pixel indices must be non-negative integers.') self._x_pixel_start, self._x_pixel_end = sc.array(values=x_pixel_range, dims='x') self._y_pixel_start, self._y_pixel_end = sc.array(values=y_pixel_range, dims='y') def set_physical_coord_range(self, x_range: Sequence[sc.Variable], y_range: Sequence[sc.Variable]) -> None: - """Set the physical coordinate ranges for the ROI. + """Set the physical coordinate ranges defining the ROI. Parameters ---------- x_range : Sequence[sc.Variable] - A two-element sequence ``[x_start, x_end]`` of :class:`scipp.Variable` scalars - with units of length representing the physical extent in the x direction. + The physical coordinate range in the x-direction to set. + Must be a two-element sequence ``[x_start, x_end]`` of + [`sc.Variable`](https://scipp.github.io/generated/classes/scipp.Variable.html#scipp.Variable) scalars + with units of length. y_range : Sequence[sc.Variable] - A two-element sequence ``[y_start, y_end]`` of :class:`scipp.Variable` scalars - with units of length representing the physical extent in the y direction. + The physical coordinate range in the y-direction to set. + Must be a two-element sequence ``[y_start, y_end]`` of + [`sc.Variable`](https://scipp.github.io/generated/classes/scipp.Variable.html#scipp.Variable) scalars + with units of length. Raises ------ TypeError - If either argument is not a two-element sequence of :class:`scipp.Variable`. + If either argument is not a two-element sequence of [`sc.Variable`](https://scipp.github.io/generated/functions/scipp.scalar.html). ValueError - If any element is not a 0-dimensional (scalar) variable. + If any [`sc.Variable`](https://scipp.github.io/generated/classes/scipp.Variable.html#scipp.Variable) in ``x_range`` + or ``y_range`` is not 0-dimensional (i.e., not a scalar). UnitError - If any scalar cannot be converted to metres. + If any [`sc.Variable`](https://scipp.github.io/generated/functions/scipp.scalar.html) scalar in ``x_range`` or + ``y_range`` does not have a unit of length. """ self._check_input_sequence(x_range, 'x_range', 'scipp scalars', sc.Variable) @@ -133,7 +163,7 @@ def set_physical_coord_range(self, x_range: Sequence[sc.Variable], y_range: Sequ self._has_physical_coords = True def delete_physical_coord_range(self) -> None: - """Delete the physical coordinate ranges for the ROI. + """Delete the physical coordinate ranges for the ROI, reverting the ROI to using pixel coordinates only. Raises ------ @@ -150,22 +180,23 @@ def delete_physical_coord_range(self) -> None: raise ValueError('Cannot delete physical coordinate ranges because they are not set.') def pixel_slice(self) -> Tuple[slice, slice]: - """Get the pixel slice corresponding to the ROI. + """Get the pixel index slice corresponding to the ROI. Returns ------- tuple - Two (x,y) slice objects representing the pixel range of the ROI. + Two (x,y) slice objects representing the pixel ranges of the ROI. """ return slice(self._x_pixel_start, self._x_pixel_end), slice(self._y_pixel_start, self._y_pixel_end) def slice(self) -> Tuple[slice, slice]: - """Get the slice corresponding to the ROI, using physical coordinates if available. + """Get the slice corresponding to the ROI, using physical coordinates if available, + but falling back to pixel coordinates if not. Returns ------- tuple - Two (x,y) slice objects representing the range of the ROI. + Two (x,y) slice objects representing the physical coordinate ranges of the ROI. """ if self._has_physical_coords: return slice(self._x_start, self._x_end), slice(self._y_start, self._y_end) @@ -174,18 +205,18 @@ def slice(self) -> Tuple[slice, slice]: @property def x_pixel_start(self) -> int: - """Start pixel index in the x direction. + """Pixel index defining the start of the ROI in the x-direction. Returns ------- int - The start pixel index along the x axis. + The x-axis pixel index defining the start of the ROI. """ return self._x_pixel_start.value @x_pixel_start.setter def x_pixel_start(self, value: int): - """Set the start pixel index in the x direction. + """Set the pixel index defining the start of the ROI in the x-direction. Parameters ---------- @@ -204,18 +235,18 @@ def x_pixel_start(self, value: int): @property def x_pixel_end(self) -> int: - """End pixel index in the x direction. + """Pixel index defining the end of the ROI in the x-direction. Returns ------- int - The end pixel index along the x axis. + The x-axis pixel index defining the end of the ROI. """ return self._x_pixel_end.value @x_pixel_end.setter def x_pixel_end(self, value: int): - """Set the end pixel index in the x direction. + """Set the pixel index defining the end of the ROI in the x-direction. Parameters ---------- @@ -234,18 +265,18 @@ def x_pixel_end(self, value: int): @property def y_pixel_start(self) -> int: - """Start pixel index in the y direction. + """Pixel index defining the start of the ROI in the y-direction. Returns ------- int - The start pixel index along the y axis. + The y-axis pixel index defining the start of the ROI. """ return self._y_pixel_start.value @y_pixel_start.setter def y_pixel_start(self, value: int): - """Set the start pixel index in the y direction. + """Set the pixel index defining the start of the ROI in the y-direction. Parameters ---------- @@ -264,18 +295,18 @@ def y_pixel_start(self, value: int): @property def y_pixel_end(self) -> int: - """End pixel index in the y direction. + """Pixel index defining the end of the ROI in the y-direction. Returns ------- int - The end pixel index along the y axis. + The y-axis pixel index defining the end of the ROI. """ return self._y_pixel_end.value @y_pixel_end.setter def y_pixel_end(self, value: int): - """Set the end pixel index in the y direction. + """Set the pixel index defining the end of the ROI in the y-direction. Parameters ---------- @@ -294,12 +325,12 @@ def y_pixel_end(self, value: int): @property def x_start(self) -> sc.Variable: - """Start physical coordinate in the x direction. + """Physical coordinate defining the start of the ROI in the x-direction. Returns ------- sc.Variable - A copy of the start coordinate scalar along the x axis. + A copy of the x-axis physical coordinate defining the start of the ROI. Raises ------ @@ -313,22 +344,23 @@ def x_start(self) -> sc.Variable: @x_start.setter def x_start(self, value: sc.Variable): - """Set the start physical coordinate in the x direction. + """Set the physical coordinate defining the start of the ROI in the x-direction. Parameters ---------- value : sc.Variable - A 0-dimensional :class:`scipp.Variable` scalar with a unit of length. + A 0-dimensional `sc.Variable` scalar with a unit of length. Raises ------ TypeError - If ``value`` is not a :class:`scipp.Variable`. + If ``value`` is not a `sc.Variable`. ValueError - If physical coordinate ranges are not yet set (use - :meth:`set_physical_coord_range` first), or if ``value`` is not a scalar. + If physical coordinate ranges are not set (use + [`set_physical_coord_range`][..set_physical_coord_range] first). + If ``value`` is not a 0-dimensional `sc.Variable` (i.e., a scalar). UnitError - If ``value`` cannot be converted to metres. + If ``value`` does not have a unit of length. """ self._single_coord_setter_check(value, 'x_start') self._check_scalar(value, 'x_start') @@ -336,12 +368,12 @@ def x_start(self, value: sc.Variable): @property def x_end(self) -> sc.Variable: - """End physical coordinate in the x direction. + """Physical coordinate defining the end of the ROI in the x-direction. Returns ------- sc.Variable - A copy of the end coordinate scalar along the x axis. + A copy of the x-axis physical coordinate defining the end of the ROI. Raises ------ @@ -355,21 +387,21 @@ def x_end(self) -> sc.Variable: @x_end.setter def x_end(self, value: sc.Variable): - """Set the end physical coordinate in the x direction. + """Set the physical coordinate defining the end of the ROI in the x-direction. Parameters ---------- value : sc.Variable - A 0-dimensional :class:`scipp.Variable` scalar with a unit of length. + A 0-dimensional `sc.Variable` scalar with a unit of length. Raises ------ TypeError - If ``value`` is not a :class:`scipp.Variable`. + If ``value`` is not a `sc.Variable`. ValueError - If physical coordinate ranges are not yet set, or if ``value`` is not a scalar. + If physical coordinate ranges are not set, or if ``value`` is not a 0-dimensional `sc.Variable` (i.e., a scalar). UnitError - If ``value`` cannot be converted to metres. + If ``value`` does not have a unit of length. """ self._single_coord_setter_check(value, 'x_end') self._check_scalar(value, 'x_end') @@ -377,12 +409,12 @@ def x_end(self, value: sc.Variable): @property def y_start(self) -> sc.Variable: - """Start physical coordinate in the y direction. + """Physical coordinate defining the start of the ROI in the y-direction. Returns ------- sc.Variable - A copy of the start coordinate scalar along the y axis. + A copy of the y-axis physical coordinate defining the start of the ROI. Raises ------ @@ -396,7 +428,7 @@ def y_start(self) -> sc.Variable: @y_start.setter def y_start(self, value: sc.Variable): - """Set the start physical coordinate in the y direction. + """Set the physical coordinate defining the start of the ROI in the y-direction. Parameters ---------- @@ -408,9 +440,9 @@ def y_start(self, value: sc.Variable): TypeError If ``value`` is not a :class:`scipp.Variable`. ValueError - If physical coordinate ranges are not yet set, or if ``value`` is not a scalar. + If physical coordinate ranges are not set, or if ``value`` is not a 0-dimensional `sc.Variable` (i.e., a scalar). UnitError - If ``value`` cannot be converted to metres. + If ``value`` does not have a unit of length. """ self._single_coord_setter_check(value, 'y_start') self._check_scalar(value, 'y_start') @@ -418,12 +450,12 @@ def y_start(self, value: sc.Variable): @property def y_end(self) -> sc.Variable: - """End physical coordinate in the y direction. + """Physical coordinate defining the end of the ROI in the y-direction. Returns ------- sc.Variable - A copy of the end coordinate scalar along the y axis. + A copy of the y-axis physical coordinate defining the end of the ROI. Raises ------ @@ -437,7 +469,7 @@ def y_end(self) -> sc.Variable: @y_end.setter def y_end(self, value: sc.Variable): - """Set the end physical coordinate in the y direction. + """Set the physical coordinate defining the end of the ROI in the y-direction. Parameters ---------- @@ -449,9 +481,9 @@ def y_end(self, value: sc.Variable): TypeError If ``value`` is not a :class:`scipp.Variable`. ValueError - If physical coordinate ranges are not yet set, or if ``value`` is not a scalar. + If physical coordinate ranges are not set, or if ``value`` is not a 0-dimensional `sc.Variable` (i.e., a scalar). UnitError - If ``value`` cannot be converted to metres. + If ``value`` does not have a unit of length. """ self._single_coord_setter_check(value, 'y_end') self._check_scalar(value, 'y_end') @@ -561,15 +593,15 @@ def _single_coord_setter_check(self, value: sc.Variable, name: str) -> None: ) def to_dict(self, skip: List[str] | None = None) -> Dict[str, Any]: - """Convert the RectangleROI instance to a dictionary representation. + """Convert the ROI instance to a dictionary representation. Used for saving the ROI to file. Parameters ---------- - skip : list[str] | None, optional - A list of attribute names to exclude from the output dictionary. + skip : list[str] | None + A list of attribute names to exclude from the output dictionary.
      The ``'x_pixel_range'``, ``'y_pixel_range'``, ``'x_range'``, and ``'y_range'`` keys are always handled explicitly and appended - regardless of this parameter. By default, None. + regardless of this parameter. Returns ------- @@ -624,15 +656,13 @@ def from_dict(cls, input_dict: Dict[str, Any]) -> RectangleROI: Parameters ---------- input_dict : dict - A dictionary as produced by :meth:`to_dict`, containing at minimum - ``'x_pixel_range'`` and ``'y_pixel_range'`` keys. If ``'x_range'`` and - ``'y_range'`` are present they are deserialised from their scipp scalar - dict format. + A dictionary in a format as produced by [`to_dict`][..to_dict], containing at minimum + ``'x_pixel_range'`` and ``'y_pixel_range'`` keys. Returns ------- RectangleROI - A new :class:`RectangleROI` instance initialised from the dictionary. + A new [`RectangleROI`][..] instance initialised with the data from the dictionary. """ temp_dict = input_dict.copy() if 'x_range' in input_dict and 'y_range' in input_dict: From c17189bf7ad827106d8079b948d0650a65a17ec8 Mon Sep 17 00:00:00 2001 From: Christian Vedel Date: Thu, 4 Jun 2026 16:29:50 +0200 Subject: [PATCH 07/14] Start of updating Measurement docstring --- .../regions_of_interest/rectangle_roi.md | 2 - docs/mkdocs.yml | 1 + src/easyimaging/measurement/measurement.py | 43 +++++++++++++++---- .../regions_of_interest/rectangle_roi.py | 7 +-- 4 files changed, 39 insertions(+), 14 deletions(-) diff --git a/docs/docs/api-reference/regions_of_interest/rectangle_roi.md b/docs/docs/api-reference/regions_of_interest/rectangle_roi.md index e464b0c..005f44b 100644 --- a/docs/docs/api-reference/regions_of_interest/rectangle_roi.md +++ b/docs/docs/api-reference/regions_of_interest/rectangle_roi.md @@ -1,3 +1 @@ ::: easyimaging.regions_of_interest.RectangleROI - options: - filters: ["!^_[^_]", "!__repr__", "!__dir__"] \ No newline at end of file diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml index 7c51420..8bb5267 100644 --- a/docs/mkdocs.yml +++ b/docs/mkdocs.yml @@ -167,6 +167,7 @@ plugins: ignore_init_summary: true summary: true relative_crossrefs: true + filters: ["!^_[^_]", "!__repr__", "!__dir__"] - search # Determines additional directories to watch when running mkdocs serve diff --git a/src/easyimaging/measurement/measurement.py b/src/easyimaging/measurement/measurement.py index 1090933..69e9554 100644 --- a/src/easyimaging/measurement/measurement.py +++ b/src/easyimaging/measurement/measurement.py @@ -27,7 +27,29 @@ class Measurement(NewBase): - """Class responsible for managing the measurement data of a time-of-flight neutron imaging experiment.""" + """Object responsible for managing and inspecting the measurement data of a time-of-flight neutron imaging experiment. + This object can be created in 3 ways: + + - by loading the data from a [SciTiff](https://scipp.github.io/scitiff/) file with the [from_scitiff][.from_scitiff] + method.
      + This is the recommended approach, as the [SciTiff](https://scipp.github.io/scitiff/) format natively contains all the + necessary metadata for the analysis of the measurement data. + - by directly providing a properly formatted + [`sc.DataArray`](https://scipp.github.io/generated/classes/scipp.DataArray.html#scipp.DataArray).
      + This is mostly useful for when working directly in a reduction notebook. + - by loading from a regular .tiff stack file with the [from_tiff_stack][.from_tiff_stack] method.
      + This method is provided to support older datasets that are not in the SciTiff format. + + Examples of all 3 methods are supplied below. + + When the [Measurement][.] object is created, a mask is automatically applied to filter out non-finite values in the data. + + Examples + -------- + Creating a Measurement instance by loading from a SciTiff file: + + ```python + """ def __init__( self, @@ -40,14 +62,17 @@ def __init__( Parameters ---------- data_array : sc.DataArray - The measurement data array with dimensions ``('t', 'y', 'x')``. Must have a - ``'tof'`` coordinate for time-of-flight values and both ``'x'`` and ``'y'`` - dimensions. Optionally may include ``'x'`` and ``'y'`` coordinates for - physical pixel positions. - unique_name : str | None, optional - Unique identifier for the measurement. By default, None. - display_name : str | None, optional - Human-readable display name for the measurement. By default, None. + The measurement data in a + [`sc.DataArray`](https://scipp.github.io/generated/classes/scipp.DataArray.html#scipp.DataArray) with dimensions + ``('x', 'y', 't')``.
      + Must have a ``'tof'`` coordinate for time-of-flight values in the dimension ``t``.
      + Optionally may include ``'x'`` and ``'y'`` coordinates for spatial pixel positions.
      + Other coordinates in the + [`sc.DataArray`](https://scipp.github.io/generated/classes/scipp.DataArray.html#scipp.DataArray) are ignored. + unique_name : str | None + A unique identifier for the ``Measurement``. Defaults to ``'Measurement'`` appended by a unique integer. + display_name : str | None + A prettily formatted name for the ``Measurement``. Defaults to [`unique_name`][..unique_name] if not provided. Raises ------ diff --git a/src/easyimaging/regions_of_interest/rectangle_roi.py b/src/easyimaging/regions_of_interest/rectangle_roi.py index e607237..30c77b1 100644 --- a/src/easyimaging/regions_of_interest/rectangle_roi.py +++ b/src/easyimaging/regions_of_interest/rectangle_roi.py @@ -15,9 +15,9 @@ class RectangleROI(NewBase): - """Class representing a rectangular region of interest (ROI) in an image. + """Object representing a rectangular region of interest (ROI) in an image. - This class is most simply instantiated by the [`roi_creator`][...Measurement.roi_creator] method in the + This object is most simply created by the [`roi_creator`][...Measurement.roi_creator] method in the [Measurement][...Measurement] class. Alternatively it can be created manually as shown in the example below. Physical coordinate ranges are used by default, if they are provided **and** can be used in the @@ -26,6 +26,7 @@ class RectangleROI(NewBase): Example ------- + Creating a [RectangleROI][.] instance manually: ```python import scipp as sc from easyimaging.regions_of_interest import RectangleROI @@ -71,7 +72,7 @@ def __init__( A unique identifier for the ROI. Defaults to ``'RectangleROI'`` appended by a unique integer. display_name : str | None - A human-readable name for the ROI. Defaults to [`unique_name`][..unique_name] if not provided. + A prettily formatted name for the ROI. Defaults to [`unique_name`][..unique_name] if not provided. Raises ------ From 2c7f8ca8d6abaf3d6fbcc7fe638a70d6d9811130 Mon Sep 17 00:00:00 2001 From: Christian Vedel Date: Thu, 11 Jun 2026 16:26:05 +0200 Subject: [PATCH 08/14] Many updates to mkdocs.yml and docstrings. --- docs/mkdocs.yml | 7 +- src/easyimaging/measurement/measurement.py | 280 +++++++++++------- .../regions_of_interest/rectangle_roi.py | 260 +++++++--------- tests/unit/measurement/test_measurement.py | 7 +- 4 files changed, 293 insertions(+), 261 deletions(-) diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml index 8bb5267..97fcdf7 100644 --- a/docs/mkdocs.yml +++ b/docs/mkdocs.yml @@ -167,7 +167,12 @@ plugins: ignore_init_summary: true summary: true relative_crossrefs: true - filters: ["!^_[^_]", "!__repr__", "!__dir__"] + scoped_crossrefs: true + filters: ['!^_[^_]', '!__repr__', '!__dir__'] + inventories: + - url: https://scipp.github.io/objects.inv + - url: https://numpy.org/doc/stable/objects.inv + - url: https://easyscience.github.io/core/2.3.1/objects.inv - search # Determines additional directories to watch when running mkdocs serve diff --git a/src/easyimaging/measurement/measurement.py b/src/easyimaging/measurement/measurement.py index 69e9554..da3bb52 100644 --- a/src/easyimaging/measurement/measurement.py +++ b/src/easyimaging/measurement/measurement.py @@ -27,15 +27,14 @@ class Measurement(NewBase): - """Object responsible for managing and inspecting the measurement data of a time-of-flight neutron imaging experiment. - This object can be created in 3 ways: + """Object responsible for managing and inspecting the **normalized** measurement data of a time-of-flight neutron imaging + experiment. This object can be created in 3 ways: - - by loading the data from a [SciTiff](https://scipp.github.io/scitiff/) file with the [from_scitiff][.from_scitiff] - method.
      + - by loading the data from a [SciTiff](https://scipp.github.io/scitiff/) file with the + [from_scitiff][.from_scitiff] method.
      This is the recommended approach, as the [SciTiff](https://scipp.github.io/scitiff/) format natively contains all the necessary metadata for the analysis of the measurement data. - - by directly providing a properly formatted - [`sc.DataArray`](https://scipp.github.io/generated/classes/scipp.DataArray.html#scipp.DataArray).
      + - by directly providing a properly formatted [`sc.DataArray`][scipp.DataArray] to the constructor.
      This is mostly useful for when working directly in a reduction notebook. - by loading from a regular .tiff stack file with the [from_tiff_stack][.from_tiff_stack] method.
      This method is provided to support older datasets that are not in the SciTiff format. @@ -44,11 +43,58 @@ class Measurement(NewBase): When the [Measurement][.] object is created, a mask is automatically applied to filter out non-finite values in the data. - Examples - -------- - Creating a Measurement instance by loading from a SciTiff file: + Example + ------- + **Creating a [Measurement][.] instance by loading from a [SciTiff](https://scipp.github.io/scitiff/) file** + Using the example data provided by the library: ```python + from easyimaging.datasets import iron_alpha_scitiff + from easyimaging import Measurement + + scitiff_path = iron_alpha_scitiff() + + measurement = Measurement.from_scitiff(filename=scitiff_path) + ``` + + **Creating a [Measurement][.] instance by directly providing a [`sc.DataArray`][scipp.DataArray]** + + Note that the dimension names must be exactly `'x'`, `'y'`, and `'t'`, and that the coordinate names must be exactly + `'x'`, `'y'`, and `'tof'` to be recognised by the constructor, and that the `'tof'` coordinate must be provided, whereas + `'x'` and `'y'` are optional: + ```python + import scipp as sc + from easyimaging import Measurement + + tof = sc.arange('t', 0, 10, 1, unit='s') + x = sc.arange('x', 0, 7, 1, unit='m') # Optional + y = sc.arange('y', 0, 7, 1, unit='m') # Optional + coords = {'tof': tof, 'x': x, 'y': y} + data = sc.ones(dims=['t', 'y', 'x'], shape=[10, 6, 6]) + + data_array = sc.DataArray(data=data, coords=coords) + + measurement = Measurement(data_array=data_array) + ``` + + **Creating a [Measurement][.] instance by loading from a regular .tiff stack file** + + Using the example data provided by the library, note that the time_of_flights must be provided, whereas the x_positions + and y_positions are optional: + ```python + from easyimaging.datasets import iron_alpha_tiff + from easyimaging import Measurement + import scipp as sc + + tiff_path = iron_alpha_tiff() + + measurement = Measurement.from_tiff_stack( + filename=tiff_path, + time_of_flights=sc.arange('t', 0, 1501, 1, unit='s'), # mandatory + # x_positions=sc.arange('x', 0, 50, 1, unit='mm'), # optional + # y_positions=sc.arange('y', 0, 50, 1, unit='mm'), # optional + ) + ``` """ def __init__( @@ -62,13 +108,10 @@ def __init__( Parameters ---------- data_array : sc.DataArray - The measurement data in a - [`sc.DataArray`](https://scipp.github.io/generated/classes/scipp.DataArray.html#scipp.DataArray) with dimensions - ``('x', 'y', 't')``.
      - Must have a ``'tof'`` coordinate for time-of-flight values in the dimension ``t``.
      - Optionally may include ``'x'`` and ``'y'`` coordinates for spatial pixel positions.
      - Other coordinates in the - [`sc.DataArray`](https://scipp.github.io/generated/classes/scipp.DataArray.html#scipp.DataArray) are ignored. + The measurement data in a [`sc.DataArray`][scipp.DataArray] with dimensions ``('x', 'y', 't')``.
      + Must have a ``'tof'`` coordinate for time-of-flight values in the dimension ``'t'``.
      + Optionally may include ``'x'`` and ``'y'`` coordinates for physical pixel positions.
      + Other coordinates in the [`sc.DataArray`][scipp.DataArray] are ignored. unique_name : str | None A unique identifier for the ``Measurement``. Defaults to ``'Measurement'`` appended by a unique integer. display_name : str | None @@ -77,14 +120,19 @@ def __init__( Raises ------ TypeError - If ``data_array`` is not a :class:`scipp.DataArray`. + If ``data_array`` is not a [`sc.DataArray`][scipp.DataArray]. ValueError - If the data array is missing the ``'tof'`` coordinate, contains negative - time-of-flight values, or has inconsistent coordinate/dimension configuration. + If the ``data_array`` is missing the ``'tof'`` coordinate.
      + If the ``'tof'`` coordinate contains negative time-of-flight values.
      + If the ``data_array`` has only one of the ``'x'`` or ``'y'`` coordinates, but not both.
      DimensionError - If the data array does not have both ``'x'`` and ``'y'`` dimensions. + If the ``'tof'`` coordinate does not have the dimension ``'t'``.
      + If the ``'x'`` and ``'y'`` coordinates do not have the dimensions ``'x'`` and ``'y'``, respectively, when + provided.
      + If the ``data_array`` does not have both ``'x'`` and ``'y'`` dimensions. UnitError - If any coordinate has an incompatible unit. + If the ``'tof'`` coordinate does not have a unit of time.
      + If the ``'x'`` and ``'y'`` coordinates do not have a unit of length, when provided. """ if not isinstance(data_array, sc.DataArray): raise TypeError('data_array must be an instance of scipp.DataArray.') @@ -311,10 +359,10 @@ def save_scitiff(self, filename: str | Path) -> None: @property def data_array_copy(self) -> sc.DataArray: - """Get a full deep copy of the current data array. + """Get a full deep copy of the current data array. This attribute is **read-only**. Returns the rebinned data array if rebinning has been applied, otherwise the - original full-resolution data array. Use with caution for large datasets. + original full-resolution data array. Use with caution for large datasets to avoid memory issues. Returns ------- @@ -323,19 +371,20 @@ def data_array_copy(self) -> sc.DataArray: """ return self._data_array.copy(deep=True) - @data_array_copy.setter - def data_array_copy(self, value: sc.DataArray) -> None: - """Raise AttributeError — ``data_array_copy`` is a read-only property. - - Raises - ------ - AttributeError - Always. To use a different data array, create a new :class:`Measurement` instance. - """ - raise AttributeError( - 'Cannot set data_array, it is a read-only property. ' - 'Please make a new Measurement instance if you want to use a different data array.' - ) + # Can't have setters due to MkDocstrings then showing the property as writable. + # @data_array_copy.setter + # def data_array_copy(self, value: sc.DataArray) -> None: + # """Raise AttributeError — ``data_array_copy`` is a read-only property. + + # Raises + # ------ + # AttributeError + # Always. To use a different data array, create a new :class:`Measurement` instance. + # """ + # raise AttributeError( + # 'Cannot set data_array, it is a read-only property. ' + # 'Please make a new Measurement instance if you want to use a different data array.' + # ) @property def _data_array(self) -> sc.DataArray: @@ -363,39 +412,39 @@ def _data_array(self, value: sc.DataArray) -> None: raise AttributeError('Cannot set _data_array, it is a read-only property.') @property - def x_positions(self) -> sc.Variable | None: - """Get the x-coordinate positions of the pixels. - - Returns - ------- - sc.Variable or None - The x-coordinate positions as a :class:`scipp.Variable`, or ``None`` if - physical coordinates are not available. - """ - if self._has_physical_coords: - return self._data_array.coords['x'].copy() - return None - - @x_positions.setter - def x_positions(self, value: sc.Variable | np.ndarray) -> None: - """Set the x-coordinate positions of the pixels. + def x_positions(self) -> sc.Variable: + """The x-coordinate physical positions of the pixels. Parameters ---------- value : sc.Variable | np.ndarray - The new x-coordinate positions to set. + The new x-coordinate positions to set.
      If a numpy array is provided, the unit is assumed to be meters. + Returns + ------- + sc.Variable + A copy of the physical x-coordinate positions as a [`sc.Variable`][scipp.Variable]. + Raises ------ ValueError - If physical coordinate positions have not been initialised yet. Use - :meth:`set_physical_coord_positions` to set both axes simultaneously. + If physical coordinate positions are not set (use + [`set_physical_coord_positions`][..set_physical_coord_positions] to set)
      + If ``value`` is not 1-dimensional with the same length as the number of pixels (or pixel-edges) in the x-dimension. TypeError - If ``value`` is not a :class:`scipp.Variable` or :class:`numpy.ndarray`. + If ``value`` is not a [`sc.Variable`][scipp.Variable] or [`np.ndarray`][numpy.ndarray]. UnitError - If ``value`` does not carry a unit of length. + If ``value`` is a [`sc.Variable`][scipp.Variable] and does not have a unit of length. """ + if self._has_physical_coords: + return self._data_array.coords['x'].copy() + else: + raise ValueError('Physical coordinate positions are not set for this Measurement.') + + @x_positions.setter + def x_positions(self, value: sc.Variable | np.ndarray) -> None: + # Setters have no docstrings. They should be written in the getter docstring instead. if not self._has_physical_coords: raise ValueError( 'Cannot set x_positions before setting all physical coordinate positions. ' @@ -413,39 +462,39 @@ def x_positions(self, value: sc.Variable | np.ndarray) -> None: self._data_array.coords['x'] = value @property - def y_positions(self) -> sc.Variable | None: - """Get the y-coordinate positions of the pixels. - - Returns - ------- - sc.Variable or None - The y-coordinate positions as a :class:`scipp.Variable`, or ``None`` if - physical coordinates are not available. - """ - if self._has_physical_coords: - return self._data_array.coords['y'].copy() - return None - - @y_positions.setter - def y_positions(self, value: sc.Variable | np.ndarray) -> None: - """Set the y-coordinate positions of the pixels. + def y_positions(self) -> sc.Variable: + """The y-coordinate physical positions of the pixels. Parameters ---------- value : sc.Variable | np.ndarray - The new y-coordinate positions to set. + The new y-coordinate positions to set.
      If a numpy array is provided, the unit is assumed to be meters. + Returns + ------- + sc.Variable + A copy of the physical y-coordinate positions as a [`sc.Variable`][scipp.Variable]. + Raises ------ ValueError - If physical coordinate positions have not been initialised yet. Use - :meth:`set_physical_coord_positions` to set both axes simultaneously. + If physical coordinate positions are not set (use + [`set_physical_coord_positions`][..set_physical_coord_positions] to set)
      + If ``value`` is not 1-dimensional with the same length as the number of pixels (or pixel-edges) in the y-dimension. TypeError - If ``value`` is not a :class:`scipp.Variable` or :class:`numpy.ndarray`. + If ``value`` is not a [`sc.Variable`][scipp.Variable] or [`np.ndarray`][numpy.ndarray]. UnitError - If ``value`` does not carry a unit of length. + If ``value`` is a [`sc.Variable`][scipp.Variable] and does not have a unit of length. """ + if self._has_physical_coords: + return self._data_array.coords['y'].copy() + else: + raise ValueError('Physical coordinate positions are not set for this Measurement.') + + @y_positions.setter + def y_positions(self, value: sc.Variable | np.ndarray) -> None: + # Setters have no docstrings. They should be written in the getter docstring instead. if not self._has_physical_coords: raise ValueError( 'Cannot set y_positions before setting all physical coordinate positions. ' @@ -515,35 +564,34 @@ def delete_physical_coord_positions(self) -> None: @property def time_of_flights(self) -> sc.Variable: - """Get the time-of-flight values of the measurement. - - Returns - ------- - sc.Variable - A copy of the time-of-flight coordinate array. - """ - return self._data_array.coords['tof'].copy() - - @time_of_flights.setter - def time_of_flights(self, value: sc.Variable | np.ndarray) -> None: - """Set the time-of-flight values of the measurement. + """The time-of-flight values of the measurement. Parameters ---------- value : sc.Variable | np.ndarray - The new time-of-flight values to set. + The new time-of-flight values to set.
      If a numpy array is provided, the unit is assumed to be seconds. + Returns + ------- + sc.Variable + A copy of the time-of-flight values as a [`sc.Variable`][scipp.Variable]. + Raises ------ - TypeError - If ``value`` is not a :class:`scipp.Variable` or :class:`numpy.ndarray`. ValueError - If the length of ``value`` does not match the number of frames, or if any - time-of-flight value is negative. + If ``value`` is not 1-dimensional with the same length as the number of frames.
      + If any element in ``value`` is negative. + TypeError + If ``value`` is not a [`sc.Variable`][scipp.Variable] or [`np.ndarray`][numpy.ndarray]. UnitError - If ``value`` does not carry a unit of time. + If ``value`` is a [`sc.Variable`][scipp.Variable] and does not have a unit of time. """ + return self._data_array.coords['tof'].copy() + + @time_of_flights.setter + def time_of_flights(self, value: sc.Variable | np.ndarray) -> None: + # Setters have no docstrings. They should be written in the getter docstring instead. value = self._validate_provided_coord( data_array=self._data_array, coord=value, @@ -559,29 +607,37 @@ def time_of_flights(self, value: sc.Variable | np.ndarray) -> None: @property def regions_of_interest(self) -> EasyList[RectangleROI]: - """Get the list of regions of interest (ROIs) defined for this measurement. + """Get the list of regions of interest (ROIs) defined for this measurement.
      + This attribute is **read-only**, to modify or set new ROIs, interact directly with the list. + + Example + ------- + ```python + measurement.regions_of_interest.append(new_roi) # Add a new ROI to the measurement + measurement.regions_of_interest.remove(existing_roi) # Remove an existing ROI + ``` Returns ------- EasyList[RectangleROI] - The list of :class:`~easyimaging.measurement.regions.RectangleROI` objects - associated with this measurement. + A list of the regions of interest (ROIs) attached to this measurement.[`ROIs`][...regions_of_interest.RectangleROI] """ return self._regions_of_interest - @regions_of_interest.setter - def regions_of_interest(self, value: EasyList[RectangleROI]) -> None: - """Raise AttributeError — ``regions_of_interest`` is a read-only property. - - Raises - ------ - AttributeError - Always. Add or remove ROIs directly from the list instead. - """ - raise AttributeError( - 'Cannot set regions_of_interest, it is a read-only property. ' - 'Please simply add or remove ROIs directly from the list.' - ) + # Can't have setters due to MkDocstrings then showing the property as writable. + # @regions_of_interest.setter + # def regions_of_interest(self, value: EasyList[RectangleROI]) -> None: + # """Raise AttributeError — ``regions_of_interest`` is a read-only property. + + # Raises + # ------ + # AttributeError + # Always. Add or remove ROIs directly from the list instead. + # """ + # raise AttributeError( + # 'Cannot set regions_of_interest, it is a read-only property. ' + # 'Please simply add or remove ROIs directly from the list.' + # ) def rebin(self, dimensions: dict[str, Numeric]) -> None: """Rebin the measurement image stack. diff --git a/src/easyimaging/regions_of_interest/rectangle_roi.py b/src/easyimaging/regions_of_interest/rectangle_roi.py index 30c77b1..1f0eb2b 100644 --- a/src/easyimaging/regions_of_interest/rectangle_roi.py +++ b/src/easyimaging/regions_of_interest/rectangle_roi.py @@ -32,11 +32,11 @@ class RectangleROI(NewBase): from easyimaging.regions_of_interest import RectangleROI roi = RectangleROI( - x_pixel_range = (10, 50), - y_pixel_range = (20, 80), - x_range = (sc.scalar(0.0, unit='m'), sc.scalar(10.0, unit='m')), - y_range = (sc.scalar(0.0, unit='m'), sc.scalar(5.0, unit='m')), - unique_name = 'my_rectangle_roi', + x_pixel_range=(10, 50), + y_pixel_range=(20, 80), + x_range=(sc.scalar(0.0, unit='m'), sc.scalar(10.0, unit='m')), + y_range=(sc.scalar(0.0, unit='m'), sc.scalar(5.0, unit='m')), + unique_name='my_rectangle_roi', ) ``` """ @@ -61,16 +61,15 @@ def __init__( A two-element integer sequence ``[y_start, y_end]`` indicating the pixel range in the y-direction. x_range : Sequence[sc.Variable] | None - A two-element sequence ``[x_start, x_end]`` of [`sc.Variable`](https://scipp.github.io/generated/functions/scipp.scalar.html) - scalars with units of length, indicating the spatial coordinate range in the x-direction.
      + A two-element sequence ``[x_start, x_end]`` of [`sc.Variable`][scipp.Variable] scalars with units of length, + indicating the spatial coordinate range in the x-direction.
      Must be provided together with ``y_range``. y_range : Sequence[sc.Variable] | None - A two-element sequence ``[y_start, y_end]`` of [`sc.Variable`](https://scipp.github.io/generated/functions/scipp.scalar.html) - scalars with units of length, indicating the spatial coordinate range in the y-direction.
      + A two-element sequence ``[y_start, y_end]`` of [`sc.Variable`][scipp.Variable] scalars with units of length, + indicating the spatial coordinate range in the y-direction.
      Must be provided together with ``x_range``. unique_name : str | None - A unique identifier for the ROI. Defaults to ``'RectangleROI'`` appended by a - unique integer. + A unique identifier for the ROI. Defaults to ``'RectangleROI'`` appended by a unique integer. display_name : str | None A prettily formatted name for the ROI. Defaults to [`unique_name`][..unique_name] if not provided. @@ -78,15 +77,13 @@ def __init__( ------ TypeError If ``x_pixel_range`` or ``y_pixel_range`` is not a two-element sequence of integers.
      - If physical ranges are not two-element sequences of [`sc.Variable`](https://scipp.github.io/generated/functions/scipp.scalar.html). + If physical ranges are not two-element sequences of [`sc.Variable`][scipp.Variable]. ValueError If any pixel index in ``x_pixel_range`` or ``y_pixel_range`` is negative.
      If only one of ``x_range`` / ``y_range`` is provided.
      - If any [`sc.Variable`](https://scipp.github.io/generated/classes/scipp.Variable.html#scipp.Variable) in ``x_range`` - or ``y_range`` is not 0-dimensional (i.e., not a scalar).
      + If any [`sc.Variable`][scipp.Variable] in ``x_range`` or ``y_range`` is not 0-dimensional (i.e., not a scalar).
      UnitError - If any [`sc.Variable`](https://scipp.github.io/generated/functions/scipp.scalar.html) scalar in ``x_range`` or - ``y_range`` does not have a unit of length. + If any [`sc.Variable`][scipp.Variable] scalar in ``x_range`` or ``y_range`` does not have a unit of length. """ super().__init__(unique_name=unique_name, display_name=display_name) self.set_pixel_coord_range(x_pixel_range, y_pixel_range) @@ -105,12 +102,10 @@ def set_pixel_coord_range(self, x_pixel_range: Sequence[int], y_pixel_range: Seq ---------- x_pixel_range : Sequence[int] The pixel coordinate range in the x-direction to set. - Must be a two-element sequence ``[x_start, x_end]`` of pixel - indices defining an x-axis range. + Must be a two-element sequence ``[x_start, x_end]`` of pixel indices defining an x-axis range. y_pixel_range : Sequence[int] The pixel coordinate range in the y-direction to set. - Must be a two-element sequence ``[y_start, y_end]`` of pixel - indices defining a y-axis range. + Must be a two-element sequence ``[y_start, y_end]`` of pixel indices defining a y-axis range. Raises ------ @@ -134,25 +129,19 @@ def set_physical_coord_range(self, x_range: Sequence[sc.Variable], y_range: Sequ ---------- x_range : Sequence[sc.Variable] The physical coordinate range in the x-direction to set. - Must be a two-element sequence ``[x_start, x_end]`` of - [`sc.Variable`](https://scipp.github.io/generated/classes/scipp.Variable.html#scipp.Variable) scalars - with units of length. + Must be a two-element sequence ``[x_start, x_end]`` of [`sc.Variable`][scipp.Variable] scalars with units of length y_range : Sequence[sc.Variable] The physical coordinate range in the y-direction to set. - Must be a two-element sequence ``[y_start, y_end]`` of - [`sc.Variable`](https://scipp.github.io/generated/classes/scipp.Variable.html#scipp.Variable) scalars - with units of length. + Must be a two-element sequence ``[y_start, y_end]`` of [`sc.Variable`][scipp.Variable] scalars with units of length Raises ------ TypeError - If either argument is not a two-element sequence of [`sc.Variable`](https://scipp.github.io/generated/functions/scipp.scalar.html). + If either argument is not a two-element sequence of [`sc.Variable`][scipp.Variable]. ValueError - If any [`sc.Variable`](https://scipp.github.io/generated/classes/scipp.Variable.html#scipp.Variable) in ``x_range`` - or ``y_range`` is not 0-dimensional (i.e., not a scalar). + If any [`sc.Variable`][scipp.Variable] in ``x_range`` or ``y_range`` is not 0-dimensional (i.e., not a scalar). UnitError - If any [`sc.Variable`](https://scipp.github.io/generated/functions/scipp.scalar.html) scalar in ``x_range`` or - ``y_range`` does not have a unit of length. + If any [`sc.Variable`][scipp.Variable] scalar in ``x_range`` or ``y_range`` does not have a unit of length. """ self._check_input_sequence(x_range, 'x_range', 'scipp scalars', sc.Variable) @@ -208,22 +197,16 @@ def slice(self) -> Tuple[slice, slice]: def x_pixel_start(self) -> int: """Pixel index defining the start of the ROI in the x-direction. - Returns - ------- - int - The x-axis pixel index defining the start of the ROI. - """ - return self._x_pixel_start.value - - @x_pixel_start.setter - def x_pixel_start(self, value: int): - """Set the pixel index defining the start of the ROI in the x-direction. - Parameters ---------- value : int A non-negative integer pixel index. + Returns + ------- + int + The x-axis pixel index defining the start of the ROI. + Raises ------ TypeError @@ -231,6 +214,11 @@ def x_pixel_start(self, value: int): ValueError If ``value`` is negative. """ + return self._x_pixel_start.value + + @x_pixel_start.setter + def x_pixel_start(self, value: int): + # Setters have no docstrings. They should be written in the getter docstring instead. self._check_index(value, 'x_pixel_start') self._x_pixel_start = sc.scalar(value) @@ -238,22 +226,16 @@ def x_pixel_start(self, value: int): def x_pixel_end(self) -> int: """Pixel index defining the end of the ROI in the x-direction. - Returns - ------- - int - The x-axis pixel index defining the end of the ROI. - """ - return self._x_pixel_end.value - - @x_pixel_end.setter - def x_pixel_end(self, value: int): - """Set the pixel index defining the end of the ROI in the x-direction. - Parameters ---------- value : int A non-negative integer pixel index. + Returns + ------- + int + The x-axis pixel index defining the end of the ROI. + Raises ------ TypeError @@ -261,6 +243,11 @@ def x_pixel_end(self, value: int): ValueError If ``value`` is negative. """ + return self._x_pixel_end.value + + @x_pixel_end.setter + def x_pixel_end(self, value: int): + # Setters have no docstrings. They should be written in the getter docstring instead. self._check_index(value, 'x_pixel_end') self._x_pixel_end = sc.scalar(value) @@ -268,22 +255,16 @@ def x_pixel_end(self, value: int): def y_pixel_start(self) -> int: """Pixel index defining the start of the ROI in the y-direction. - Returns - ------- - int - The y-axis pixel index defining the start of the ROI. - """ - return self._y_pixel_start.value - - @y_pixel_start.setter - def y_pixel_start(self, value: int): - """Set the pixel index defining the start of the ROI in the y-direction. - Parameters ---------- value : int A non-negative integer pixel index. + Returns + ------- + int + The y-axis pixel index defining the start of the ROI. + Raises ------ TypeError @@ -291,6 +272,11 @@ def y_pixel_start(self, value: int): ValueError If ``value`` is negative. """ + return self._y_pixel_start.value + + @y_pixel_start.setter + def y_pixel_start(self, value: int): + # Setters have no docstrings. They should be written in the getter docstring instead. self._check_index(value, 'y_pixel_start') self._y_pixel_start = sc.scalar(value) @@ -298,22 +284,16 @@ def y_pixel_start(self, value: int): def y_pixel_end(self) -> int: """Pixel index defining the end of the ROI in the y-direction. - Returns - ------- - int - The y-axis pixel index defining the end of the ROI. - """ - return self._y_pixel_end.value - - @y_pixel_end.setter - def y_pixel_end(self, value: int): - """Set the pixel index defining the end of the ROI in the y-direction. - Parameters ---------- value : int A non-negative integer pixel index. + Returns + ------- + int + The y-axis pixel index defining the end of the ROI. + Raises ------ TypeError @@ -321,6 +301,11 @@ def y_pixel_end(self, value: int): ValueError If ``value`` is negative. """ + return self._y_pixel_end.value + + @y_pixel_end.setter + def y_pixel_end(self, value: int): + # Setters have no docstrings. They should be written in the getter docstring instead. self._check_index(value, 'y_pixel_end') self._y_pixel_end = sc.scalar(value) @@ -328,6 +313,12 @@ def y_pixel_end(self, value: int): def x_start(self) -> sc.Variable: """Physical coordinate defining the start of the ROI in the x-direction. + Parameters + ---------- + value : sc.Variable + A 0-dimensional [`sc.Variable`][scipp.Variable] scalar with a unit + of length. + Returns ------- sc.Variable @@ -335,8 +326,14 @@ def x_start(self) -> sc.Variable: Raises ------ + TypeError + If ``value`` is not a [`sc.Variable`][scipp.Variable]. ValueError - If physical coordinate ranges are not set. + If physical coordinate ranges are not set (use + [`set_physical_coord_range`][..set_physical_coord_range] to set).
      + If ``value`` is not a 0-dimensional [`sc.Variable`][scipp.Variable] (i.e., a scalar). + UnitError + If ``value`` does not have a unit of length. """ if self._has_physical_coords: return self._x_start.copy() @@ -345,24 +342,7 @@ def x_start(self) -> sc.Variable: @x_start.setter def x_start(self, value: sc.Variable): - """Set the physical coordinate defining the start of the ROI in the x-direction. - - Parameters - ---------- - value : sc.Variable - A 0-dimensional `sc.Variable` scalar with a unit of length. - - Raises - ------ - TypeError - If ``value`` is not a `sc.Variable`. - ValueError - If physical coordinate ranges are not set (use - [`set_physical_coord_range`][..set_physical_coord_range] first). - If ``value`` is not a 0-dimensional `sc.Variable` (i.e., a scalar). - UnitError - If ``value`` does not have a unit of length. - """ + # Setters have no docstrings. They should be written in the getter docstring instead. self._single_coord_setter_check(value, 'x_start') self._check_scalar(value, 'x_start') self._x_start = value @@ -371,6 +351,11 @@ def x_start(self, value: sc.Variable): def x_end(self) -> sc.Variable: """Physical coordinate defining the end of the ROI in the x-direction. + Parameters + ---------- + value : sc.Variable + A 0-dimensional [`sc.Variable`][scipp.Variable] scalar with a unit of length. + Returns ------- sc.Variable @@ -378,8 +363,14 @@ def x_end(self) -> sc.Variable: Raises ------ + TypeError + If ``value`` is not a [`sc.Variable`][scipp.Variable]. ValueError - If physical coordinate ranges are not set. + If physical coordinate ranges are not set (use + [`set_physical_coord_range`][..set_physical_coord_range] to set).
      + If ``value`` is not a 0-dimensional [`sc.Variable`][scipp.Variable] (i.e., a scalar). + UnitError + If ``value`` does not have a unit of length. """ if self._has_physical_coords: return self._x_end.copy() @@ -388,22 +379,7 @@ def x_end(self) -> sc.Variable: @x_end.setter def x_end(self, value: sc.Variable): - """Set the physical coordinate defining the end of the ROI in the x-direction. - - Parameters - ---------- - value : sc.Variable - A 0-dimensional `sc.Variable` scalar with a unit of length. - - Raises - ------ - TypeError - If ``value`` is not a `sc.Variable`. - ValueError - If physical coordinate ranges are not set, or if ``value`` is not a 0-dimensional `sc.Variable` (i.e., a scalar). - UnitError - If ``value`` does not have a unit of length. - """ + # Setters have no docstrings. They should be written in the getter docstring instead. self._single_coord_setter_check(value, 'x_end') self._check_scalar(value, 'x_end') self._x_end = value @@ -412,6 +388,12 @@ def x_end(self, value: sc.Variable): def y_start(self) -> sc.Variable: """Physical coordinate defining the start of the ROI in the y-direction. + Parameters + ---------- + value : sc.Variable + A 0-dimensional [`sc.Variable`][scipp.Variable] scalar with a unit + of length. + Returns ------- sc.Variable @@ -419,8 +401,14 @@ def y_start(self) -> sc.Variable: Raises ------ + TypeError + If ``value`` is not a [`sc.Variable`][scipp.Variable]. ValueError - If physical coordinate ranges are not set. + If physical coordinate ranges are not set (use + [`set_physical_coord_range`][..set_physical_coord_range] to set).
      + If ``value`` is not a 0-dimensional [`sc.Variable`][scipp.Variable] (i.e., a scalar). + UnitError + If ``value`` does not have a unit of length. """ if self._has_physical_coords: return self._y_start.copy() @@ -429,22 +417,7 @@ def y_start(self) -> sc.Variable: @y_start.setter def y_start(self, value: sc.Variable): - """Set the physical coordinate defining the start of the ROI in the y-direction. - - Parameters - ---------- - value : sc.Variable - A 0-dimensional :class:`scipp.Variable` scalar with a unit of length. - - Raises - ------ - TypeError - If ``value`` is not a :class:`scipp.Variable`. - ValueError - If physical coordinate ranges are not set, or if ``value`` is not a 0-dimensional `sc.Variable` (i.e., a scalar). - UnitError - If ``value`` does not have a unit of length. - """ + # Setters have no docstrings. They should be written in the getter docstring instead. self._single_coord_setter_check(value, 'y_start') self._check_scalar(value, 'y_start') self._y_start = value @@ -453,6 +426,12 @@ def y_start(self, value: sc.Variable): def y_end(self) -> sc.Variable: """Physical coordinate defining the end of the ROI in the y-direction. + Parameters + ---------- + value : sc.Variable + A 0-dimensional [`sc.Variable`][scipp.Variable] scalar with a unit + of length. + Returns ------- sc.Variable @@ -460,8 +439,14 @@ def y_end(self) -> sc.Variable: Raises ------ + TypeError + If ``value`` is not a [`sc.Variable`][scipp.Variable]. ValueError - If physical coordinate ranges are not set. + If physical coordinate ranges are not set (use + [`set_physical_coord_range`][..set_physical_coord_range] to set).
      + If ``value`` is not a 0-dimensional [`sc.Variable`][scipp.Variable] (i.e., a scalar). + UnitError + If ``value`` does not have a unit of length. """ if self._has_physical_coords: return self._y_end.copy() @@ -470,22 +455,7 @@ def y_end(self) -> sc.Variable: @y_end.setter def y_end(self, value: sc.Variable): - """Set the physical coordinate defining the end of the ROI in the y-direction. - - Parameters - ---------- - value : sc.Variable - A 0-dimensional :class:`scipp.Variable` scalar with a unit of length. - - Raises - ------ - TypeError - If ``value`` is not a :class:`scipp.Variable`. - ValueError - If physical coordinate ranges are not set, or if ``value`` is not a 0-dimensional `sc.Variable` (i.e., a scalar). - UnitError - If ``value`` does not have a unit of length. - """ + # Setters have no docstrings. They should be written in the getter docstring instead. self._single_coord_setter_check(value, 'y_end') self._check_scalar(value, 'y_end') self._y_end = value diff --git a/tests/unit/measurement/test_measurement.py b/tests/unit/measurement/test_measurement.py index c42d29e..2b0abcb 100644 --- a/tests/unit/measurement/test_measurement.py +++ b/tests/unit/measurement/test_measurement.py @@ -621,7 +621,7 @@ def test_data_array_copy_write(self, valid_data_array): # Then Expect with pytest.raises( AttributeError, - match='Cannot set data_array, it is a read-only property. Please make a new Measurement instance if you want to use a different data array.', # noqa: E501 + match="property 'data_array_copy' of 'Measurement' object has no setter", ): measurement.data_array_copy = copy(measurement._data_array) @@ -640,7 +640,8 @@ def test_positions_no_coord(self, valid_data_array_no_xy_coords, coordinate): # When measurement = Measurement(data_array=valid_data_array_no_xy_coords) # Then Expect - assert getattr(measurement, coordinate) is None + with pytest.raises(ValueError, match='Physical coordinate positions are not set for this Measurement.'): + getattr(measurement, coordinate) @pytest.mark.parametrize('coordinate', ['x_positions', 'y_positions'], ids=['x_coordinate', 'y_coordinate']) def test_positions_setter_valid(self, valid_data_array, coordinate): @@ -846,7 +847,7 @@ def test_regions_of_interest_setter(self, valid_data_array, valid_roi): # Then Expect with pytest.raises( AttributeError, - match='Cannot set regions_of_interest, it is a read-only property. Please simply add or remove ROIs directly from the list.', # noqa: E501 + match="property 'regions_of_interest' of 'Measurement' object has no setter", ): # noqa: E501 measurement.regions_of_interest = EasyList([valid_roi]) From 93ee05d92261ae1ea57d2c15f6a145f50966c5d5 Mon Sep 17 00:00:00 2001 From: Christian Dam Vedel Date: Tue, 16 Jun 2026 22:54:00 +0200 Subject: [PATCH 09/14] More docstring changes --- docs/mkdocs.yml | 1 + src/easyimaging/measurement/measurement.py | 144 ++++++++++++++------- 2 files changed, 97 insertions(+), 48 deletions(-) diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml index 97fcdf7..119a73f 100644 --- a/docs/mkdocs.yml +++ b/docs/mkdocs.yml @@ -173,6 +173,7 @@ plugins: - url: https://scipp.github.io/objects.inv - url: https://numpy.org/doc/stable/objects.inv - url: https://easyscience.github.io/core/2.3.1/objects.inv + - url: https://scipp.github.io/scitiff/objects.inv - search # Determines additional directories to watch when running mkdocs serve diff --git a/src/easyimaging/measurement/measurement.py b/src/easyimaging/measurement/measurement.py index da3bb52..ccdbefa 100644 --- a/src/easyimaging/measurement/measurement.py +++ b/src/easyimaging/measurement/measurement.py @@ -113,9 +113,9 @@ def __init__( Optionally may include ``'x'`` and ``'y'`` coordinates for physical pixel positions.
      Other coordinates in the [`sc.DataArray`][scipp.DataArray] are ignored. unique_name : str | None - A unique identifier for the ``Measurement``. Defaults to ``'Measurement'`` appended by a unique integer. + A unique identifier for the [`Measurement`][..]. Defaults to ``'Measurement'`` appended by a unique integer. display_name : str | None - A prettily formatted name for the ``Measurement``. Defaults to [`unique_name`][..unique_name] if not provided. + A prettily formatted name for the [`Measurement`][..]. Defaults to [`unique_name`][..unique_name] if not provided. Raises ------ @@ -186,28 +186,39 @@ def __init__( def from_scitiff( cls, filename: str | Path, unique_name: str | None = None, display_name: str | None = None ) -> Measurement: # noqa: E501 - """Create a Measurement instance by loading data from a SciTIFF file. + """Create a [`Measurement`][..] object by loading normalized image data from a + [SciTiff](https://scipp.github.io/scitiff/) file. + + Time-of-flight values and other relevant metadata, such as the flight-path, are automatically extracted from the file, + if present. + + Uses the [SciTiff](https://scipp.github.io/scitiff/) library's + [`load_scitiff`][scitiff.load_scitiff] method internally to load the data. + + Example + ---------- + An example of how to use this method is given in the [Measurement][..] class description. Parameters ---------- filename : str | Path - Path to the SciTIFF file. - unique_name : str | None, optional - Unique identifier for the measurement. By default, None. - display_name : str | None, optional - Display name for the measurement. By default, None. + The path to the [SciTiff](https://scipp.github.io/scitiff/) file. + unique_name : str | None + A unique identifier for the [`Measurement`][..]. Defaults to ``'Measurement'`` appended by a unique integer. + display_name : str | None + A prettily formatted name for the [`Measurement`][..]. Defaults to [`unique_name`][..unique_name] if not provided. Returns ------- Measurement - An instance of the Measurement class containing the loaded data. + An instance of the [`Measurement`][..] class containing the loaded data. Raises ------ TypeError - If ``filename`` is not a string or :class:`pathlib.Path` object. + If ``filename`` is not a string or a [`Path`](https://docs.python.org/3/library/pathlib.html) object. RuntimeError - If the file cannot be loaded or is not a valid SciTIFF file. + If the ``filename`` cannot be loaded or is not a valid [SciTiff](https://scipp.github.io/scitiff/) file. """ if not isinstance(filename, (str, Path)): raise TypeError('filename must be a string or Path object.') @@ -231,37 +242,59 @@ def from_tiff_stack( unique_name: str | None = None, display_name: str | None = None, ) -> Measurement: - """Create a Measurement instance by loading data from a TIFF stack file. + """Create a [`Measurement`][..] object by loading data from a regular TIFF stack file. + + Since a regular TIFF file does not contain the necessary metadata for Bragg-edge imaging, + such as **time-of-flight** values for each frame in the image stack, they have to be provided manually. + + The optional metadata can also be set after the object has already been created. + + Example + ---------- + An example of how to use this method is given in the [Measurement][..] class description. Parameters ---------- filename : str | Path - Path to the TIFF stack file. + The path to the TIFF stack file. time_of_flights : sc.Variable | np.ndarray - Array of time-of-flight values corresponding to the frames in the TIFF stack. - If a numpy array is provided, the unit is assumed to be seconds. - x_positions : sc.Variable | np.ndarray | None, optional - Array of x-coordinate positions for the pixels. - If a numpy array is provided, the unit is assumed to be meters. By default, None. - y_positions : sc.Variable | np.ndarray | None, optional - Array of y-coordinate positions for the pixels. - If a numpy array is provided, the unit is assumed to be meters. By default, None. - unique_name : str | None, optional - Unique identifier for the measurement. By default, None. - display_name : str | None, optional - Display name for the measurement. By default, None. + A 1-dimensional array of time-of-flight values corresponding to the frames in the TIFF stack.
      + If a [numpy array][numpy.ndarray] is provided, it is assumed to be in units of seconds. + x_positions : sc.Variable | np.ndarray | None + A 1-dimensional array of physical x-axis positions for the TIFF stack pixels.
      + If a [numpy array][numpy.ndarray] is provided, it is assumed to be in units of meters. + y_positions : sc.Variable | np.ndarray | None + A 1-dimensional array of physical y-axis positions for the TIFF stack pixels.
      + If a [numpy array][numpy.ndarray] is provided, it is assumed to be in units of meters. + unique_name : str | None + A unique identifier for the [`Measurement`][..].
      + Defaults to ``'Measurement'`` appended by a unique integer. + display_name : str | None + A prettily formatted name for the [`Measurement`][..]. Defaults to [`unique_name`][..unique_name] if not provided. Returns ------- Measurement - An instance of the Measurement class containing the loaded data. + An instance of the [`Measurement`][..] class containing the loaded and provided data. Raises ------ TypeError - If ``filename`` is not a string or :class:`pathlib.Path` object. + If ``filename`` is not a string or a [`Path`](https://docs.python.org/3/library/pathlib.html) object.
      + If ``time_of_flights``, ``x_positions``, or ``y_positions`` are not a [`sc.Variable`][scipp.Variable] or a + [numpy.ndarray][numpy.ndarray].
      + ValueError + If ``time_of_flights`` is not 1-dimensional with the same length as the number of frames in the TIFF stack.
      + If either ``x_positions`` or ``y_positions`` are not 1-dimensional with the same length as the number of pixels in + the corresponding dimension of the TIFF stack.
      + If the ``'time_of_flights'`` contain negative values.
      + UnitError + If ``time_of_flights`` is a [`sc.Variable`][scipp.Variable] that does not have a unit of time.
      + If either ``x_positions`` or ``y_positions`` are a [`sc.Variable`][scipp.Variable] without a unit of + length. RuntimeError - If the file cannot be loaded or its dimensions cannot be renamed. + If the ``filename`` cannot be loaded.
      + If the file is a [SciTiff](https://scipp.github.io/scitiff/) file: Use [from_scitiff][..from_scitiff] instead. """ if not isinstance(filename, (str, Path)): raise TypeError('filename must be a string or Path object.') @@ -318,27 +351,29 @@ def from_tiff_stack( return instance def save_scitiff(self, filename: str | Path) -> None: - """Save the measurement data to a SciTIFF file with its time-of-flight and physical coordinate information. + """Save the [Measurement][..] data to a [SciTIFF](https://scipp.github.io/scitiff/) file with the time-of-flight values + and other provided metadata. - Note that it is the rebinned data array that is saved if rebinning has been applied. + Note that [SciTIFF](https://scipp.github.io/scitiff/) does not support ``float64`` precision numbers, so if the + [Measurement][..] contains data of type ``float64``, it will be downcast to ``float32`` when saving, causing a small + loss of precision. Parameters ---------- filename : str | Path - Path to the output SciTIFF file. + Path to the output [SciTIFF](https://scipp.github.io/scitiff/) file. Raises ------ TypeError - If ``filename`` is not a string or :class:`pathlib.Path` object. + If ``filename`` is not a string or a [`Path`](https://docs.python.org/3/library/pathlib.html) object. RuntimeError - If the file cannot be written. + If the file cannot be written to the specified ``filename`` path. Warns ----- UserWarning - If the data array is of type ``float64``, which will be downcast to ``float32`` - when saving, potentially causing loss of precision. + If the [Measurement][..] object's data is of type ``float64``; It will be downcast to ``float32``. """ if not isinstance(filename, (str, Path)): raise TypeError('filename must be a string or Path object.') @@ -514,16 +549,28 @@ def y_positions(self, value: sc.Variable | np.ndarray) -> None: def set_physical_coord_positions( self, x_positions: sc.Variable | np.ndarray, y_positions: sc.Variable | np.ndarray ) -> None: - """Set the physical coordinate positions for the measurement corresponding to the pixel indices. + """Set the physical xy-coordinate positions for the pixels of the [Measurement][..] image stack. Parameters ---------- x_positions : sc.Variable | np.ndarray - The x-coordinate positions to set. - If a numpy array is provided, the unit is assumed to be meters. + A 1-dimensional array of physical x-axis positions for the image stack pixels.
      + If a [numpy array][numpy.ndarray] is provided, it is assumed to be in units of meters. y_positions : sc.Variable | np.ndarray - The y-coordinate positions to set. - If a numpy array is provided, the unit is assumed to be meters. + A 1-dimensional array of physical y-axis positions for the image stack pixels.
      + If a [numpy array][numpy.ndarray] is provided, it is assumed to be in units of meters. + + Raises + ------ + TypeError + If either of ``x_positions`` or ``y_positions`` are not a [`sc.Variable`][scipp.Variable] or a + [numpy.ndarray][numpy.ndarray]. + ValueError + If either ``x_positions`` or ``y_positions`` are not 1-dimensional with the same length as the number of pixels in + the corresponding dimension of the image stack. + UnitError + If either ``x_positions`` or ``y_positions`` are a [`sc.Variable`][scipp.Variable] without a unit of + length. """ x_positions = self._validate_provided_coord( data_array=self._data_array, @@ -548,12 +595,12 @@ def set_physical_coord_positions( self._has_physical_coords = True def delete_physical_coord_positions(self) -> None: - """Delete the physical coordinate positions for the measurement. + """Delete the physical coordinate positions for the pixels of the [Measurement][..] image stack. Raises ------ ValueError - If physical coordinate positions are not currently set. + If the [Measurement][..] does not currently have physical coordinate positions set. """ if self._has_physical_coords: del self._data_array.coords['x'] @@ -607,20 +654,21 @@ def time_of_flights(self, value: sc.Variable | np.ndarray) -> None: @property def regions_of_interest(self) -> EasyList[RectangleROI]: - """Get the list of regions of interest (ROIs) defined for this measurement.
      - This attribute is **read-only**, to modify or set new ROIs, interact directly with the list. + """Get the [list][easyscience.base_classes.EasyList] of [regions of interest][...regions_of_interest.RectangleROI] + (ROIs) defined for this measurement.
      + This attribute is **read-only**, to modify or set new ROIs, interact with the returned list. Example ------- ```python measurement.regions_of_interest.append(new_roi) # Add a new ROI to the measurement - measurement.regions_of_interest.remove(existing_roi) # Remove an existing ROI + measurement.regions_of_interest.remove("existing_roi") # Remove an existing ROI ``` Returns ------- EasyList[RectangleROI] - A list of the regions of interest (ROIs) attached to this measurement.[`ROIs`][...regions_of_interest.RectangleROI] + A list of the regions of interest (ROIs) attached to this measurement. """ return self._regions_of_interest @@ -640,9 +688,9 @@ def regions_of_interest(self) -> EasyList[RectangleROI]: # ) def rebin(self, dimensions: dict[str, Numeric]) -> None: - """Rebin the measurement image stack. + """Rebin the [Measurement][..] image stack. - This operation reduces the resolution of the data by combining adjacent pixels or time bins. + This operation reduces the resolution of the data by combining adjacent pixels. The rebinned dimensions must be evenly divisible by their specific rebin factor. Parameters From 71f1e3ff619e8f6dde4fc16cd0aa18543a0b2650 Mon Sep 17 00:00:00 2001 From: Christian Vedel Date: Wed, 17 Jun 2026 15:37:59 +0200 Subject: [PATCH 10/14] Update pixi lock and fix docstring summaries --- pixi.lock | 3879 +++++++++-------- src/easyimaging/measurement/measurement.py | 92 +- .../regions_of_interest/rectangle_roi.py | 20 +- tests/unit/measurement/test_measurement.py | 10 +- 4 files changed, 2245 insertions(+), 1756 deletions(-) diff --git a/pixi.lock b/pixi.lock index 72ca995..88becc8 100644 --- a/pixi.lock +++ b/pixi.lock @@ -14,12 +14,12 @@ environments: linux-64: - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/argon2-cffi-bindings-25.1.0-py313h07c4f96_2.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/backports.zstd-1.5.0-py313h18e8e13_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/backports.zstd-1.6.0-py313h18e8e13_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.2.0-py313hf159716_1.conda - 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build ; extra == 'dev' + - twine ; extra == 'dev' + - sphinx ; extra == 'doc' + - pytest ; extra == 'test' + - pytest-cov ; extra == 'test' + - coverage ; extra == 'test' + - asteval[dev,doc,test] ; extra == 'all' + requires_python: '>=3.10' diff --git a/src/easyimaging/measurement/measurement.py b/src/easyimaging/measurement/measurement.py index ccdbefa..871429d 100644 --- a/src/easyimaging/measurement/measurement.py +++ b/src/easyimaging/measurement/measurement.py @@ -186,8 +186,7 @@ def __init__( def from_scitiff( cls, filename: str | Path, unique_name: str | None = None, display_name: str | None = None ) -> Measurement: # noqa: E501 - """Create a [`Measurement`][..] object by loading normalized image data from a - [SciTiff](https://scipp.github.io/scitiff/) file. + """Create a `Measurement` object by loading normalized image data from a **SciTiff** file. Time-of-flight values and other relevant metadata, such as the flight-path, are automatically extracted from the file, if present. @@ -242,7 +241,7 @@ def from_tiff_stack( unique_name: str | None = None, display_name: str | None = None, ) -> Measurement: - """Create a [`Measurement`][..] object by loading data from a regular TIFF stack file. + """Create a `Measurement` object by loading normalized image data from a regular **TIFF** stack file. Since a regular TIFF file does not contain the necessary metadata for Bragg-edge imaging, such as **time-of-flight** values for each frame in the image stack, they have to be provided manually. @@ -351,17 +350,16 @@ def from_tiff_stack( return instance def save_scitiff(self, filename: str | Path) -> None: - """Save the [Measurement][..] data to a [SciTIFF](https://scipp.github.io/scitiff/) file with the time-of-flight values - and other provided metadata. + """Save the `Measurement` data to a **SciTiff** file with the time-of-flight values and other provided metadata. - Note that [SciTIFF](https://scipp.github.io/scitiff/) does not support ``float64`` precision numbers, so if the - [Measurement][..] contains data of type ``float64``, it will be downcast to ``float32`` when saving, causing a small + Note that [SciTiff](https://scipp.github.io/scitiff/) does not support ``float64`` precision numbers, so if the + [`Measurement`][..] contains data of type ``float64``, it will be downcast to ``float32`` when saving, causing a small loss of precision. Parameters ---------- filename : str | Path - Path to the output [SciTIFF](https://scipp.github.io/scitiff/) file. + Path to the output [SciTiff](https://scipp.github.io/scitiff/) file. Raises ------ @@ -448,7 +446,7 @@ def _data_array(self, value: sc.DataArray) -> None: @property def x_positions(self) -> sc.Variable: - """The x-coordinate physical positions of the pixels. + """The x-coordinates of the physical positions of the pixels. Parameters ---------- @@ -498,7 +496,7 @@ def x_positions(self, value: sc.Variable | np.ndarray) -> None: @property def y_positions(self) -> sc.Variable: - """The y-coordinate physical positions of the pixels. + """The y-coordinates of the physical positions of the pixels. Parameters ---------- @@ -549,7 +547,7 @@ def y_positions(self, value: sc.Variable | np.ndarray) -> None: def set_physical_coord_positions( self, x_positions: sc.Variable | np.ndarray, y_positions: sc.Variable | np.ndarray ) -> None: - """Set the physical xy-coordinate positions for the pixels of the [Measurement][..] image stack. + """Set the physical xy-coordinate positions for the pixels of the measurement image stack. Parameters ---------- @@ -595,7 +593,7 @@ def set_physical_coord_positions( self._has_physical_coords = True def delete_physical_coord_positions(self) -> None: - """Delete the physical coordinate positions for the pixels of the [Measurement][..] image stack. + """Delete the physical coordinate positions for the pixels of the measurement image stack. Raises ------ @@ -654,9 +652,11 @@ def time_of_flights(self, value: sc.Variable | np.ndarray) -> None: @property def regions_of_interest(self) -> EasyList[RectangleROI]: - """Get the [list][easyscience.base_classes.EasyList] of [regions of interest][...regions_of_interest.RectangleROI] - (ROIs) defined for this measurement.
      - This attribute is **read-only**, to modify or set new ROIs, interact with the returned list. + """The list of regions of interest (ROIs) defined for this measurement.
      This attribute is **read-only**. + + The returned list is an [EasyList][easyscience.base_classes.EasyList] of + [regions of interest][...regions_of_interest.RectangleROI] objects. + To modify the list or set new ROIs, interact directly with the returned list. Example ------- @@ -688,28 +688,58 @@ def regions_of_interest(self) -> EasyList[RectangleROI]: # ) def rebin(self, dimensions: dict[str, Numeric]) -> None: - """Rebin the [Measurement][..] image stack. + """Rebin the measurement image stack. + + This operation increases the signal-to-noise ratio of the [Measurement][..] data, at the cost of a reduced resolution, + by averaging adjacent pixels.
      + The rebinned dimensions must be evenly divisible by their specific rebin factors, as the operation is otherwise + ill-defined. + + Example + ------- + Setting up a [Measurement][..]: + ```python + import scipp as sc + from easyimaging import Measurement + + tof = sc.arange('t', 0, 10, 1, unit='s') + coords = {'tof': tof} + data = sc.ones(dims=['t', 'y', 'x'], shape=[10, 6, 6]) + + data_array = sc.DataArray(data=data, coords=coords) - This operation reduces the resolution of the data by combining adjacent pixels. - The rebinned dimensions must be evenly divisible by their specific rebin factor. + measurement = Measurement(data_array=data_array) + ``` + Halve the spatial resolution by rebinning by a factor of 2 in both dimensions: + ```python + measurement.rebin({'x': 2, 'y': 2}) + ``` + You can also rebin by different factors in the different dimensions, + if the `Measurement` data dimensions are evenly divisible by those factors: + ```python + measurement.rebin({'x': 3, 'y': 2}) + ``` + You can also rebin only one dimension, leaving the other unchanged: + ```python + measurement.rebin({'x': 2}) + ``` Parameters ---------- - dimensions : dict[str, Numeric] - A dictionary specifying the rebinning factors for each dimension. - For example, ``{'x': 2, 'y': 2}`` will halve the spatial resolution. + dimensions : dict[str, int | float] + A dictionary of dimension-rebin factor pairs, specifying the rebinning factors for each dimension. Raises ------ TypeError - If ``dimensions`` is not a :class:`dict`, or a dimension key is not a string, - or a rebin factor is not a positive integer (or integer-valued float). + If ``dimensions`` is not a `dict`.
      + If any keys in ``dimensions`` are not strings.
      + If a rebin factor is not a positive integer (or integer-valued float). ValueError - If rebinning of the ``'t'`` dimension is requested (not yet supported), if a - rebin factor is less than 1, or if a dimension size is not evenly divisible by - the rebin factor. + If a dimension size is not evenly divisible by the requested rebin factor. KeyError - If a specified dimension name does not exist in the data array. + If rebinning of the ``'t'`` dimension is requested (not yet supported).
      + If rebinning is attempted on a non-existing dimension. """ if not isinstance(dimensions, dict): raise TypeError('dimensions must be a dictionary mapping dimension names to rebin factors.') @@ -718,7 +748,7 @@ def rebin(self, dimensions: dict[str, Numeric]) -> None: return sizes = dimensions.copy() if 't' in dimensions: - raise ValueError("Rebinning of the time-of-flight ('t') dimension is not yet supported.") + raise KeyError("Rebinning of the time-of-flight ('t') dimension is not yet supported.") for dim, value in dimensions.items(): if not isinstance(dim, str): raise TypeError(f'Dimension keys must be strings. Got {type(dim)} for {dim} instead.') @@ -729,11 +759,11 @@ def rebin(self, dimensions: dict[str, Numeric]) -> None: if isinstance(value, float) and value.is_integer(): # I allow eg. 2.0 as well as 2 value = int(value) if not isinstance(value, int) or value < 1: - raise ValueError(f"Rebin size for dimension '{dim}' must be a positive integer of at least 1.") + raise TypeError(f"Rebin size for dimension '{dim}' must be a positive integer of at least 1.") if self._full_data_array.sizes[dim] % value != 0: raise ValueError( - f"Dimension '{dim}' with size {self._full_data_array.sizes[dim]} is not evenly divisible by rebin size {value}." # noqa: E501 - ) # noqa: E501 + f"Dimension '{dim}' with size {self._full_data_array.sizes[dim]} is not evenly divisible by the requested rebin factor {value}." + ) sizes[dim] = int(self._data_array.sizes[dim] // value) # Convert to target size temp_array = essimaging.tools.analysis.resize(self._data_array, sizes=sizes, method='mean') non_finite_mask = ~sc.isfinite(temp_array.data) diff --git a/src/easyimaging/regions_of_interest/rectangle_roi.py b/src/easyimaging/regions_of_interest/rectangle_roi.py index 1f0eb2b..2f95d0e 100644 --- a/src/easyimaging/regions_of_interest/rectangle_roi.py +++ b/src/easyimaging/regions_of_interest/rectangle_roi.py @@ -153,7 +153,9 @@ def set_physical_coord_range(self, x_range: Sequence[sc.Variable], y_range: Sequ self._has_physical_coords = True def delete_physical_coord_range(self) -> None: - """Delete the physical coordinate ranges for the ROI, reverting the ROI to using pixel coordinates only. + """Delete the physical coordinate ranges for the ROI. + + This enforces the ROI to use pixel coordinates only. Raises ------ @@ -170,7 +172,7 @@ def delete_physical_coord_range(self) -> None: raise ValueError('Cannot delete physical coordinate ranges because they are not set.') def pixel_slice(self) -> Tuple[slice, slice]: - """Get the pixel index slice corresponding to the ROI. + """Get a pixel index slice object corresponding to the ROI. Returns ------- @@ -180,13 +182,17 @@ def pixel_slice(self) -> Tuple[slice, slice]: return slice(self._x_pixel_start, self._x_pixel_end), slice(self._y_pixel_start, self._y_pixel_end) def slice(self) -> Tuple[slice, slice]: - """Get the slice corresponding to the ROI, using physical coordinates if available, - but falling back to pixel coordinates if not. + """Get a physical coordinate slice object corresponding to the ROI. Returns ------- tuple Two (x,y) slice objects representing the physical coordinate ranges of the ROI. + + Raises + ------ + ValueError + If physical coordinate ranges are not set for this ROI. """ if self._has_physical_coords: return slice(self._x_start, self._x_end), slice(self._y_start, self._y_end) @@ -564,7 +570,9 @@ def _single_coord_setter_check(self, value: sc.Variable, name: str) -> None: ) def to_dict(self, skip: List[str] | None = None) -> Dict[str, Any]: - """Convert the ROI instance to a dictionary representation. Used for saving the ROI to file. + """Convert the ROI instance to a dictionary representation. + + Used for saving the ROI to file. Parameters ---------- @@ -622,7 +630,7 @@ def to_dict(self, skip: List[str] | None = None) -> Dict[str, Any]: @classmethod def from_dict(cls, input_dict: Dict[str, Any]) -> RectangleROI: - """Create a RectangleROI instance from a dictionary representation. + """Create a [`RectangleROI`][..] instance from a dictionary representation. Parameters ---------- diff --git a/tests/unit/measurement/test_measurement.py b/tests/unit/measurement/test_measurement.py index 2b0abcb..1d21cdf 100644 --- a/tests/unit/measurement/test_measurement.py +++ b/tests/unit/measurement/test_measurement.py @@ -976,7 +976,7 @@ def test_rebin_time_dimension(self, valid_data_array): # When measurement = Measurement(data_array=valid_data_array) # Then Expect - with pytest.raises(ValueError, match='Rebinning of the time-of-flight'): + with pytest.raises(KeyError, match='Rebinning of the time-of-flight'): measurement.rebin(dimensions={'t': 2, 'x': 2}) def test_rebin_invalid_dimensions_key_type(self, valid_data_array): @@ -998,7 +998,7 @@ def test_rebin_invalid_dimensions_value_type(self, valid_data_array): measurement = Measurement(data_array=valid_data_array) # Then Expect with pytest.raises( - ValueError, + TypeError, match="Rebin size for dimension 'x' must be a positive integer of at least 1.", ): measurement.rebin(dimensions={'x': 'not_an_integer'}) @@ -1008,7 +1008,7 @@ def test_rebin_invalid_dimensions_value_zero(self, valid_data_array): measurement = Measurement(data_array=valid_data_array) # Then Expect with pytest.raises( - ValueError, + TypeError, match="Rebin size for dimension 'x' must be a positive integer of at least 1.", ): measurement.rebin(dimensions={'x': 0}) @@ -1018,7 +1018,7 @@ def test_rebin_invalid_dimensions_value_negative(self, valid_data_array): measurement = Measurement(data_array=valid_data_array) # Then Expect with pytest.raises( - ValueError, + TypeError, match="Rebin size for dimension 'x' must be a positive integer of at least 1.", ): measurement.rebin(dimensions={'x': -2}) @@ -1027,7 +1027,7 @@ def test_rebin_invalid_dimensions_value_non_divisable(self, valid_data_array): # When measurement = Measurement(data_array=valid_data_array) # Then Expect - with pytest.raises(ValueError, match="Dimension 'x' with size 6 is not evenly divisible by rebin size 4."): + with pytest.raises(ValueError, match="Dimension 'x' with size 6 is not evenly divisible by the requested rebin factor 4."): measurement.rebin(dimensions={'x': 4}) def test_revert_rebin(self, valid_data_array): From 3ed0611ea021ee91b0fb8830660c2e773874a86a Mon Sep 17 00:00:00 2001 From: Christian Vedel Date: Thu, 18 Jun 2026 13:37:26 +0200 Subject: [PATCH 11/14] More docstring changes, upload icons to use on docs. --- docs/docs/assets/images/crosshairs.png | Bin 0 -> 646 bytes docs/docs/assets/images/vector-square.png | Bin 0 -> 758 bytes docs/mkdocs.yml | 1 + src/easyimaging/measurement/measurement.py | 119 +++++++++++------- .../regions_of_interest/rectangle_roi.py | 2 +- tests/unit/measurement/test_measurement.py | 4 +- 6 files changed, 77 insertions(+), 49 deletions(-) create mode 100644 docs/docs/assets/images/crosshairs.png create mode 100644 docs/docs/assets/images/vector-square.png diff --git a/docs/docs/assets/images/crosshairs.png b/docs/docs/assets/images/crosshairs.png new file mode 100644 index 0000000000000000000000000000000000000000..c91fec5be69e736855d0c5beab6cca170d43e43a GIT binary patch literal 646 zcmeAS@N?(olHy`uVBq!ia0vp^3LwnE0wix1Z>k4UEa{HEjtmSN`?>!lvVtU&J%W50 z7^>757#dm_7=8hT8eT9klo~KFyh>nTu$sZZAYL$MSD+10f+@+{-G$+Qd;gjJKpuOE zr>`sfOExBMVW#LLp?M4pjD4Oijv*e$_fEa<#pEb*tp29!H=SiGT3K}OPF?qMHHTBa zpcB7h*!IqSP7xmAY)|Kw&AzKOI8= zbWmL!v{60N=4SPhn~p(OUT$`f%y#Ub^|-iAL^2|zcyG}xm;KMwr>zUn$=vl~yVwuq zq~!ry9_^QN2-|Y9X^(RspLS*cmqjY)>I*e9d3YG6%=A<^p7_hod0~1Ix2Ce%yu*?! zyFZJc^Zs^p^{Uzn*I$(-&3bRLDO-zwY0jojwog))&lA?#TtD@Ft(K|Bs`R)iJFiVI zJE|W1=fcvq4S`?9PKdN7C6zos=JheXu=Rm)s*|eZYtOU!%E`TU#_jGCj>RbL6`1Pw zBC}Ne;(@(xcDG*5no@MrbG_G>x{98?FPdjAp4s=~+KPkEDy$PV)wCwQjS>AdDQQZz zZ}NhY6VYs3HWDYZkGS60RAke4LsP_jop+X(LZS24iFeldZ~UUT^lhC^=&m!mujaVd zl)aj>MP$dJ&8y$duUp5Ef6Umej&a+{6y;Tu4}StimTHM>L`h0wNvc(HQ7VvPFfuSQ z)ip5FH82V>G_*3bv@$T#HZZUj;*|<2h_me>FVdQ&MBb@ E0Kqy1R{#J2 literal 0 HcmV?d00001 diff --git a/docs/docs/assets/images/vector-square.png b/docs/docs/assets/images/vector-square.png new file mode 100644 index 0000000000000000000000000000000000000000..4dbcfbd9a5ca1acea4b389fbdb19b9a0f930e22e GIT binary patch literal 758 zcmeAS@N?(olHy`uVBq!ia0vp^3LwnE1|*BCs=ffJQ<=`r0nVkxCHc7w3=&h56B6#6 zV_@;&LflrzF189feup? 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      + This operation can be undone by using the [revert_rebin][..revert_rebin] method, + which restores the original full-resolution data. + Example ------- Setting up a [Measurement][..]: @@ -762,7 +766,8 @@ def rebin(self, dimensions: dict[str, Numeric]) -> None: raise TypeError(f"Rebin size for dimension '{dim}' must be a positive integer of at least 1.") if self._full_data_array.sizes[dim] % value != 0: raise ValueError( - f"Dimension '{dim}' with size {self._full_data_array.sizes[dim]} is not evenly divisible by the requested rebin factor {value}." + f"Dimension '{dim}' with size {self._full_data_array.sizes[dim]} is not" + f' evenly divisible by the requested rebin factor {value}.' ) sizes[dim] = int(self._data_array.sizes[dim] // value) # Convert to target size temp_array = essimaging.tools.analysis.resize(self._data_array, sizes=sizes, method='mean') @@ -773,8 +778,12 @@ def rebin(self, dimensions: dict[str, Numeric]) -> None: def revert_rebin(self) -> None: """Revert any rebinning applied to the measurement data, restoring it to its original resolution. - If no rebinning has been applied, a :class:`UserWarning` is issued and no action - is taken. + This method undos the rebinning performed by the [rebin][..rebin] method, if it has been applied. + + Warns + ------ + UserWarning + If no rebinning has been applied and the measurement data is already in its original state. """ if hasattr(self, '_rebinned_data_array'): del self._rebinned_data_array @@ -789,33 +798,32 @@ def revert_rebin(self) -> None: # ------------------------------------------------------------------------------------------------------------------------- def plot(self, time_of_flight: int | sc.Variable | None = None, **kwargs) -> None: - """Plot the measurement image at a specific time-of-flight. + """Plot the 2d spatial measurement image data. - If no time-of-flight is provided, the plot will average over all time-of-flight values. + If no `time-of-flight` is provided, the plot will average over all time-of-flight values.
      + If `time-of-flight` is provided as a [Scipp](https://scipp.github.io/) variable scalar, the nearest time-of-flight + frame in time will be plotted. - This method uses the plopp library for plotting: - https://scipp.github.io/plopp/plotting/image-plot.html + This method uses the [plopp](https://scipp.github.io/plopp/plotting/image-plot.html) library for plotting. + + To customize the plot appearance, additional keyword arguments can be passed to the underlying plopp plotting function. + See [plopp.plot][] for which keyword arguments are available and how to use them. Parameters ---------- - time_of_flight : int | sc.Variable | None, optional - The time-of-flight value to plot. If None, the time-of-flight axis is averaged. By default, None. + time_of_flight : int | sc.Variable | None + The time-of-flight value to plot, as an index (int) or a value (sc.Variable).
      + If None, the time-of-flight axis is averaged. **kwargs : dict - Additional keyword arguments to pass to the plotting function. - See https://scipp.github.io/plopp/generated/plopp.plot.html for options. - - Returns - ------- - plopp.Figure or None - The plot object when running inside a Jupyter notebook, otherwise ``None`` - (the plot is displayed directly via :meth:`show`). + Additional keyword arguments to pass to the plotting function.
      + See [plopp.plot][] for options. Raises ------ TypeError - If ``time_of_flight`` is not an integer, :class:`scipp.Variable` scalar, or ``None``. + If ``time_of_flight`` is not an integer, a `sc.Variable` scalar, or ``None``. UnitError - If a :class:`scipp.Variable` ``time_of_flight`` does not carry a unit of time. + If a `sc.Variable` ``time_of_flight`` is provided without a unit of time. """ if time_of_flight is None: title_suffix = ' (averaged over TOF)' @@ -850,21 +858,18 @@ def plot(self, time_of_flight: int | sc.Variable | None = None, **kwargs) -> Non plot.show() def slicer_plot(self, **kwargs) -> None: - """Launch an interactive slicer plot for exploring the measurement data. + """Launch an interactive slicer plot for exploring the 2d spatial measurement image data. + + This method uses the [plopp](https://scipp.github.io/plopp/plotting/slicer-plot.html) library for interactive slicing. - This method uses the plopp library for interactive slicing: - https://scipp.github.io/plopp/plotting/slicer-plot.html + To customize the plot appearance, additional keyword arguments can be passed to the underlying plopp plotting function. + See [plopp.slicer][] for which keyword arguments are available and how to use them. Parameters ---------- **kwargs : dict - Additional keyword arguments to pass to the slicer function. - See https://scipp.github.io/plopp/generated/plopp.slicer.html for options. - - Returns - ------- - plopp.widgets.Slicer - The interactive slicer widget. + Additional keyword arguments to pass to the slicer function.
      + See [plopp.slicer][] for options. Raises ------ @@ -888,21 +893,28 @@ def slicer_plot(self, **kwargs) -> None: raise RuntimeError('Interactive slicer is only supported in Jupyter notebooks.') def spectrum_inspector(self, **kwargs) -> None: - """Launch an interactive spectrum inspector plot for exploring the measurement data. + """Launch an interactive spectrum inspector plot for exploring the measurements time-of-flight spectrums. + + This method uses the [plopp](https://scipp.github.io/plopp/plotting/inspector-plot.html) library for interactive + inspection. - This method uses the plopp library for interactive inspection: - https://scipp.github.io/plopp/plotting/inspector-plot.html + To customize the plot appearance, additional keyword arguments can be passed to the underlying plopp plotting function. + See [plopp.inspector][] for which keyword arguments are available and how to use them. + + Interactive controls + -------- + Click the ![](../../assets/images/crosshairs.png){width=15px} button in the toolbar on the left to activate/deactivate + the spectrum investigator tool. When active, the following controls are available: + + - Left-click on a pixel to make a new point and view the spectrum for that pixel + - Left-click and drag existing points to adjust which pixel's spectrum is being viewed + - Middle-click on a point to delete it and remove its spectrum Parameters ---------- **kwargs : dict - Additional keyword arguments to pass to the inspector function. - See https://scipp.github.io/plopp/generated/plopp.inspector.html for options. - - Returns - ------- - list - A list of plopp figure objects comprising the inspector widget. + Additional keyword arguments to pass to the inspector function.
      + See [plopp.inspector][] for options. Raises ------ @@ -940,14 +952,27 @@ def spectrum_inspector(self, **kwargs) -> None: def roi_creator(self, **kwargs) -> None: """Launch an interactive ROI creator for defining regions of interest on the measurement data. - This method uses the plopp library for interactive ROI creation: - https://scipp.github.io/plopp/plotting/roi-selector.html + This method uses the [plopp](https://scipp.github.io/plopp/plotting/roi-selector.html) library for interactive ROI + creation. + + To customize the plot appearance, additional keyword arguments can be passed to the underlying plopp plotting function. + See [plopp.inspector][] for which keyword arguments are available and how to use them. - Controls: - - Left-click to make new rectangles - - Left-click and hold on rectangle vertices to resize rectangle - - Right-click and hold to drag/move the entire rectangle - - Middle-click to delete rectangle + + Interactive controls + -------- + Click the ![](../../assets/images/vector-square.png){width=15px} button in the toolbar on the left to + activate/deactivate the ROI creator tool. When active, the following controls are available: + + - Left-click to start drawing a new rectangular ROI, and left-click again to finish drawing the rectangle and create + the ROI + - Left-click and hold on ROI corners to resize the ROI + - Right-click and hold to drag/move the entire ROI + - Middle-click in the ROI to delete it + + Example + --------- + An example on how to use this method is shown in the tutorial notebook Parameters ---------- diff --git a/src/easyimaging/regions_of_interest/rectangle_roi.py b/src/easyimaging/regions_of_interest/rectangle_roi.py index 2f95d0e..06f81c3 100644 --- a/src/easyimaging/regions_of_interest/rectangle_roi.py +++ b/src/easyimaging/regions_of_interest/rectangle_roi.py @@ -570,7 +570,7 @@ def _single_coord_setter_check(self, value: sc.Variable, name: str) -> None: ) def to_dict(self, skip: List[str] | None = None) -> Dict[str, Any]: - """Convert the ROI instance to a dictionary representation. + """Convert the ROI instance to a dictionary representation. Used for saving the ROI to file. diff --git a/tests/unit/measurement/test_measurement.py b/tests/unit/measurement/test_measurement.py index 1d21cdf..86dd608 100644 --- a/tests/unit/measurement/test_measurement.py +++ b/tests/unit/measurement/test_measurement.py @@ -1027,7 +1027,9 @@ def test_rebin_invalid_dimensions_value_non_divisable(self, valid_data_array): # When measurement = Measurement(data_array=valid_data_array) # Then Expect - with pytest.raises(ValueError, match="Dimension 'x' with size 6 is not evenly divisible by the requested rebin factor 4."): + with pytest.raises( + ValueError, match="Dimension 'x' with size 6 is not evenly divisible by the requested rebin factor 4." + ): measurement.rebin(dimensions={'x': 4}) def test_revert_rebin(self, valid_data_array): From 765e43882dddf67bd9d0cfa7241520556479c6b2 Mon Sep 17 00:00:00 2001 From: Christian Vedel Date: Thu, 18 Jun 2026 15:18:30 +0200 Subject: [PATCH 12/14] Final fixes to docstrings and light-mode version of icons. --- docs/docs/assets/images/crosshairs_dark.png | Bin 0 -> 996 bytes .../{crosshairs.png => crosshairs_light.png} | Bin .../docs/assets/images/vector-square_dark.png | Bin 0 -> 692 bytes ...tor-square.png => vector-square_light.png} | Bin docs/docs/tutorials/index.md | 2 +- src/easyimaging/measurement/measurement.py | 82 +++++++++--------- 6 files changed, 40 insertions(+), 44 deletions(-) create mode 100644 docs/docs/assets/images/crosshairs_dark.png rename docs/docs/assets/images/{crosshairs.png => crosshairs_light.png} (100%) create mode 100644 docs/docs/assets/images/vector-square_dark.png rename docs/docs/assets/images/{vector-square.png => vector-square_light.png} (100%) diff --git a/docs/docs/assets/images/crosshairs_dark.png b/docs/docs/assets/images/crosshairs_dark.png new file mode 100644 index 0000000000000000000000000000000000000000..8bc7eae4dd8fa778825a88ccc4ae372c612d66f5 GIT binary patch literal 996 zcmV6vk&U@lmO@k4h-Spr{z5Xk&~hVyXD3O{j>d(SO09Xl&F!K+skN6m1M78sE`C zA$Cw}=+H#g-*?%$oSD75dv^=T`SzUo&STDcL)IY3ikXFvC5u}{ z&=9q5p))0`xFbPN-XCQY89xMVg+ieP9Y~4W2{{53i%MmHnwcw6)&PN8?i*?9vhfqu z#UvNNH|$Ko_Z6JOslDP6qD_35Z~ zH(6H9eTr@Zo52GROIA);caZpcT04$0e;M#(1h>pr2YLI#l@D!DHA_ zU?*qj2B`f>hDERf-a+7P>>*%9U&mR9&rD+Pb||N(7N-eLCq(#hlbUx!YI&5|fLtV8 zMh^fj9V!reth^(OQ*J-C;uZBdu3`gs!V ztw8ZbFl9N};(%5_!`!I50aMw&?W}D=oU1kX2LJ&7|0J%Nv;Y7A21!IgR09BCM?mZe S91e*90000|~vLbeou%uxbtcXt_B1#m2G`wWaDY-4X<*~X)h_69)UFCY* zE_WlkShQ_>+P3XA*d)eIKUDreR>Zr2_Z%F7O=4^X;j#vht$?+tNilYA1Ba90vD4(g zxN2YxC9`s91I-|%#eVFdjTvIj5~~K*P!b~7B(DubM)!C^e+S>d3wSG$OHR36qvy>V zFkrIKPVft!d8vUll=LE}82R%CK9c?)+<`ri#KJGUlpcY()=&~6mz;8c3Qza2fni6U z+deU&joHg{(=;z7pu(L(^&*#?LOTUo8~B~xX7sHK&%{TeF86lioPN2nfnUU~!Eh(E z{R(01jCieBW33!Q&cvZ@>})}|7kE#=14!ced5%ls$H1HvE7I10W0L*7kxNcqLtN{G z_=P*5$BxuP#F-Br+t@7P!tOv`9&4rs^5DC@?;6Li@~sUZd%K zE8TH;3+DB)W=zFIF2QGz#D%@T*AQHRZKvWZ2-iR^IWa?A>r!5Kz^V8L?&t`uXxp_g z=7g)i2G&?BhmbSXYa3hHK*>~mK)1s$NJNvm%RQJ3j-5v~U^mI_4du-xw3A=GCvgc# z&YP7>PN7XoNMi$Gbq^=juh{whE#WQSF)UPJD!KrN8W%w3v<7_@>}4f_&lHh0000 None: Interactive controls -------- - Click the ![](../../assets/images/crosshairs.png){width=15px} button in the toolbar on the left to activate/deactivate - the spectrum investigator tool. When active, the following controls are available: + Click the ![](../../assets/images/crosshairs_dark.png#gh-dark-mode-only){width=15px} + ![](../../assets/images/crosshairs_light.png#gh-light-mode-only){width=15px} button in the toolbar on the left to + activate/deactivate the spectrum investigator tool. When active, the following controls are available: - Left-click on a pixel to make a new point and view the spectrum for that pixel - Left-click and drag existing points to adjust which pixel's spectrum is being viewed @@ -950,18 +951,19 @@ def spectrum_inspector(self, **kwargs) -> None: raise RuntimeError('Interactive spectrum inspector is only supported in Jupyter notebooks.') def roi_creator(self, **kwargs) -> None: - """Launch an interactive ROI creator for defining regions of interest on the measurement data. + """Launch an interactive Region Of Interest (ROI) creator for defining regions of interest on the measurement data. This method uses the [plopp](https://scipp.github.io/plopp/plotting/roi-selector.html) library for interactive ROI - creation. + creation. ROI's created with this method are automatically added to the [Measurement][..] object's + [list of ROIs][..regions_of_interest]. To customize the plot appearance, additional keyword arguments can be passed to the underlying plopp plotting function. See [plopp.inspector][] for which keyword arguments are available and how to use them. - Interactive controls -------- - Click the ![](../../assets/images/vector-square.png){width=15px} button in the toolbar on the left to + Click the ![](../../assets/images/vector-square_dark.png#gh-dark-mode-only){width=15px} + ![](../../assets/images/vector-square_light.png#gh-light-mode-only){width=15px} button in the toolbar on the left to activate/deactivate the ROI creator tool. When active, the following controls are available: - Left-click to start drawing a new rectangular ROI, and left-click again to finish drawing the rectangle and create @@ -972,19 +974,14 @@ def roi_creator(self, **kwargs) -> None: Example --------- - An example on how to use this method is shown in the tutorial notebook + An example on how to use this method is shown in the tutorial: + [The **Measurement** class](../../tutorials/measurement.ipynb). Parameters ---------- **kwargs : dict - Additional keyword arguments to pass to the ROI creator function. - See https://scipp.github.io/plopp/generated/plopp.inspector.html for options. - - Returns - ------- - list - A list of plopp figure objects comprising the ROI creator widget. - Changes made interactively are reflected in :attr:`regions_of_interest`. + Additional keyword arguments to pass to the inspector function.
      + See [plopp.inspector][] for options. Raises ------ @@ -1145,29 +1142,30 @@ def delete_rectangle_roi(rect, roi_list): return plots def spectrum(self, roi: RectangleROI | str | None = None) -> sc.DataArray: - """Extract the spectrum (intensity vs. time-of-flight) for a specified region of interest (ROI). + """Extract the measured time-of-flight spectrum in a specified Region Of Interest (ROI). - If no ROI is provided, the spectrum is calculated over the entire image. + The ROI can either be passed directly as an object, or by its ``unique_name`` as a string, if it has been added to + the measurement's [regions of interest list][..regions_of_interest]. + + If no ROI is provided, the spectrum is calculated over the entire measurement image stack. Parameters ---------- - roi : RectangleROI | str | None, optional - The region of interest for which to extract the spectrum. - If a string is provided, it should be the unique name of a predefined ROI in the measurement's list of ROIs. - By default, None. + roi : RectangleROI | str | None + The ROI for which to extract the spectrum.
      + If a string, it should be the ``unique_name`` of a ROI in the [regions_of_interest][] list.
      Returns ------- sc.DataArray - A 1-D DataArray containing the spatially averaged spectrum along the - time-of-flight axis. + A 1-D [sc.DataArray][scipp.DataArray] containing the spatially averaged time-of-flight spectrum. Raises ------ TypeError - If ``roi`` is not a :class:`RectangleROI`, string, or ``None``. + If ``roi`` is not a [`RectangleROI`][RectangleROI], string, or ``None``. KeyError - If a string ``roi`` does not match any ROI in :attr:`regions_of_interest`. + If a string ``roi`` does not match the `unique_name` of any ROI in [`regions_of_interest`][regions_of_interest]. """ if roi is not None and not isinstance(roi, (RectangleROI, str)): raise TypeError('roi must be a string, None, or an instance of RectangleROI.') @@ -1191,35 +1189,33 @@ def spectrum(self, roi: RectangleROI | str | None = None) -> sc.DataArray: return spectrum_data def spectrum_plot(self, roi: RectangleROI | str | None = None, **kwargs) -> None: - """Plot the spectrum (intensity vs. time-of-flight) for a specified region of interest (ROI). + """Plot the measured time-of-flight spectrum in a specified Region Of Interest (ROI). + + The ROI can either be passed directly as an object, or by its ``unique_name`` as a string, if it has been added to + the measurement's [regions of interest list][..regions_of_interest]. - If no ROI is provided, the spectrum is calculated over the entire image. + If no ROI is provided, the spectrum is calculated over the entire measurement image stack. - This method uses the plopp library for plotting: - https://scipp.github.io/plopp/plotting/line-plot.html + This method uses the [plopp](https://scipp.github.io/plopp/plotting/line-plot.html) library for plotting. + + To customize the plot appearance, additional keyword arguments can be passed to the underlying plopp plotting function. + See [plopp.plot][] for which keyword arguments are available and how to use them. Parameters ---------- - roi : RectangleROI | str | None, optional - The region of interest for which to plot the spectrum. - If a string is provided, it should be the unique name of a predefined ROI in the measurement's list of ROIs. - By default, None. + roi : RectangleROI | str | None + The ROI for which to extract the spectrum.
      + If a string, it should be the ``unique_name`` of a ROI in the [regions_of_interest][] list.
      **kwargs : dict - Additional keyword arguments to pass to the plotting function. - See https://scipp.github.io/plopp/generated/plopp.plot.html for options. - - Returns - ------- - plopp.Figure or None - The plot object when running inside a Jupyter notebook, otherwise ``None`` - (the plot is displayed directly via :meth:`show`). + Additional keyword arguments to pass to the plotting function.
      + See [plopp.plot][] for options. Raises ------ TypeError - If ``roi`` is not a :class:`RectangleROI`, string, or ``None``. + If ``roi`` is not a [`RectangleROI`][RectangleROI], string, or ``None``. KeyError - If a string ``roi`` does not match any ROI in :attr:`regions_of_interest`. + If a string ``roi`` does not match the `unique_name` of any ROI in [`regions_of_interest`][regions_of_interest]. """ spectrum_data = self.spectrum(roi=roi) From 4704d6b1ce31fb24c5deb6ffee490b18bb453b29 Mon Sep 17 00:00:00 2001 From: Christian Vedel Date: Thu, 18 Jun 2026 15:43:57 +0200 Subject: [PATCH 13/14] Fix linting --- docs/docs/tutorials/index.md | 2 +- docs/docs/tutorials/measurement.ipynb | 1338 ++++++++++++------------- 2 files changed, 670 insertions(+), 670 deletions(-) diff --git a/docs/docs/tutorials/index.md b/docs/docs/tutorials/index.md index bd0fd57..6152008 100644 --- a/docs/docs/tutorials/index.md +++ b/docs/docs/tutorials/index.md @@ -17,6 +17,6 @@ The tutorials are organized into the following categories: ## Getting Started -- [The **Measurement** class](measurement.ipynb){ #measurement_tutorial} – A tutorial which +- [The **Measurement** class](measurement.ipynb) – A tutorial which explores the purpose and functions of the core-component: The **Measurement** class. diff --git a/docs/docs/tutorials/measurement.ipynb b/docs/docs/tutorials/measurement.ipynb index f57c81c..1414f61 100644 --- a/docs/docs/tutorials/measurement.ipynb +++ b/docs/docs/tutorials/measurement.ipynb @@ -44,7 +44,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 3, "id": "c4e759bd", "metadata": {}, "outputs": [], @@ -205,7 +205,7 @@ "\n", "\n", "\n", - "
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        • (x: 17)
          float32
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          Values:
          array([-7.0382814 , -6.158496  , -5.2787113 , -4.398926  , -3.5191407 ,\n",
+       "
          scipp.Variable (324 Bytes)
            • (x: 17)
              float32
              mm
              -7.0382814, -6.158496, ..., 6.158496, 7.0382814
              Values:
              array([-7.0382814 , -6.158496  , -5.2787113 , -4.398926  , -3.5191407 ,\n",
        "       -2.6393557 , -1.7595701 , -0.87978506,  0.        ,  0.87978506,\n",
        "        1.7595701 ,  2.6393552 ,  3.5191412 ,  4.3989263 ,  5.2787113 ,\n",
        "        6.158496  ,  7.0382814 ], dtype=float32)
      " @@ -238,7 +238,7 @@ "\n", "\n", "\n", - "
      scipp.Variable (324 Bytes)
        • (y: 17)
          float32
          mm
          -7.0382814, -6.158496, ..., 6.158496, 7.0382814
          Values:
          array([-7.0382814 , -6.158496  , -5.2787113 , -4.398926  , -3.5191407 ,\n",
+       "
          scipp.Variable (324 Bytes)
            • (y: 17)
              float32
              mm
              -7.0382814, -6.158496, ..., 6.158496, 7.0382814
              Values:
              array([-7.0382814 , -6.158496  , -5.2787113 , -4.398926  , -3.5191407 ,\n",
        "       -2.6393557 , -1.7595701 , -0.87978506,  0.        ,  0.87978506,\n",
        "        1.7595701 ,  2.6393552 ,  3.5191412 ,  4.3989263 ,  5.2787113 ,\n",
        "        6.158496  ,  7.0382814 ], dtype=float32)
      " @@ -271,7 +271,7 @@ "\n", "\n", "\n", - "
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          Values:
          array([0.02158728, 0.02163456, 0.02168185, ..., 0.09242233, 0.09246961,\n",
+       "
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" \n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", "\n" @@ -1477,16 +1477,16 @@ "\n", "\n", - "\n", + "\n", " \n", " \n", " \n", " \n", - " 2026-05-28T11:32:56.468032\n", + " 2026-06-18T15:35:44.192436\n", " image/svg+xml\n", " \n", " \n", - " Matplotlib v3.10.9, https://matplotlib.org/\n", + " Matplotlib v3.11.0, https://matplotlib.org/\n", " \n", " \n", " \n", @@ -1497,50 +1497,50 @@ " \n", " \n", " \n", - " \n", " \n", " \n", " \n", - " \n", " \n", - " \n", + " \n", " \n", + "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\" id=\"imageeb985161ed\" transform=\"scale(1 -1) translate(0 -221.76)\" x=\"43.2\" y=\"-22.358906\" width=\"306.72\" height=\"221.76\"/>\n", " \n", " \n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", - " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", - " \n", - " \n", + " \n", - " \n", - " \n", " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", @@ -1812,99 +1812,99 @@ " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", " \n", @@ -1912,7 +1912,7 @@ " \n", " \n", " \n", - " \n", " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", " \n", " \n", + "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\" id=\"image866ec390e7\" transform=\"scale(1 -1) translate(0 -221.76)\" x=\"365.76\" y=\"-22.32\" width=\"12.24\" height=\"221.76\"/>\n", " \n", " \n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", "\n" @@ -2637,16 +2637,16 @@ "\n", "\n", - "\n", + "\n", " \n", " \n", " \n", " \n", - " 2026-05-28T11:33:00.201759\n", + " 2026-06-18T15:35:46.311081\n", " image/svg+xml\n", " \n", " \n", - " Matplotlib v3.10.9, https://matplotlib.org/\n", + " Matplotlib v3.11.0, https://matplotlib.org/\n", " \n", " \n", " \n", @@ -2657,50 +2657,50 @@ " \n", " \n", " \n", - " \n", " \n", " \n", " \n", - " \n", " \n", - " \n", + " \n", " \n", + "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\" id=\"image5b424a7a11\" transform=\"scale(1 -1) translate(0 -221.76)\" x=\"43.2\" y=\"-22.358906\" width=\"306.72\" height=\"221.76\"/>\n", " \n", " \n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", - " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", - " \n", - " \n", + " \n", - " \n", - " \n", " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", @@ -2972,99 +2972,99 @@ " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", " \n", @@ -3072,7 +3072,7 @@ " \n", " \n", " \n", - " \n", " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", " \n", " \n", + "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\" id=\"image57381f6699\" transform=\"scale(1 -1) translate(0 -221.76)\" x=\"365.76\" y=\"-22.32\" width=\"12.24\" height=\"221.76\"/>\n", " \n", " \n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", "\n" @@ -3766,7 +3766,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "5eec3ae0c0b04761a352bd7598d94e01", + "model_id": "108be8cf344645dba4c41c0116e093e5", "version_major": 2, "version_minor": 0 }, @@ -3820,9 +3820,9 @@ "\n", "\n", "\n", - "
      scipp.DataArray (36.84 KB)
        • t: 1500
        • Ltotal
          ()
          int64
          m
          61
          Values:
          array(61)
        • c
          ()
          string
          intensities
          Values:
          'intensities'
        • tof
          (t [bin-edge])
          float64
          s
          0.022, 0.022, ..., 0.092, 0.093
          Values:
          array([0.02158728, 0.02163456, 0.02168185, ..., 0.09242233, 0.09246961,\n",
-       "       0.0925169 ], shape=(1501,))
        • wavelength
          (t [bin-edge])
          float64
          Å
          1.4, 1.403, ..., 5.997, 6.0
          Values:
          array([1.4       , 1.40306667, 1.40613333, ..., 5.99386667, 5.99693333,\n",
-       "       6.        ], shape=(1501,))
        • (t)
          float32
          𝟙
          0.5531428, 0.56375575, ..., 0.63517606, 0.63194895
          σ = 0.002992472, 0.003154994, ..., 0.006249289, 0.006158047
          Values:
          array([0.5531428 , 0.56375575, 0.5592331 , ..., 0.6236488 , 0.63517606,\n",
+       "
          scipp.DataArray (36.84 KB)
            • t: 1500
            • Ltotal
              ()
              int64
              m
              61
              Values:
              array(61)
            • c
              ()
              string
              intensities
              Values:
              'intensities'
            • tof
              (t [bin-edge])
              float64
              s
              0.022, 0.022, ..., 0.092, 0.093
              Values:
              array([0.02158728, 0.02163456, 0.02168185, ..., 0.09242233, 0.09246961,\n",
+       "       0.0925169 ], shape=(1501,))
            • wavelength
              (t [bin-edge])
              float64
              Å
              1.4, 1.403, ..., 5.997, 6.0
              Values:
              array([1.4       , 1.40306667, 1.40613333, ..., 5.99386667, 5.99693333,\n",
+       "       6.        ], shape=(1501,))
            • (t)
              float32
              𝟙
              0.5531428, 0.56375575, ..., 0.63517606, 0.63194895
              σ = 0.002992472, 0.003154994, ..., 0.006249289, 0.006158047
              Values:
              array([0.5531428 , 0.56375575, 0.5592331 , ..., 0.6236488 , 0.63517606,\n",
        "       0.63194895], shape=(1500,), dtype=float32)

              Variances (σ²):
              array([8.9548885e-06, 9.9539866e-06, 9.6888207e-06, ..., 3.6184254e-05,\n",
        "       3.9053615e-05, 3.7921542e-05], shape=(1500,), dtype=float32)
        " ], @@ -3867,7 +3867,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "9b93b6a25ff949e0b76b5255e2f9cb9d", + "model_id": "90742002e2bb4e9aab50053089e2cd50", "version_major": 2, "version_minor": 0 }, @@ -3903,7 +3903,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "ae0910a141ff4e58b503a5d2e62158a7", + "model_id": "fd1de66dd5324bf8856a8e7043a5c102", "version_major": 2, "version_minor": 0 }, @@ -3932,12 +3932,12 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 22, "id": "4969d839", "metadata": {}, "outputs": [], "source": [ - "from easyimaging.regions_of_interest.rectangle_roi import RectROI" + "from easyimaging.regions_of_interest.rectangle_roi import RectangleROI" ] }, { @@ -3950,12 +3950,12 @@ }, { "cell_type": "code", - "execution_count": 22, + "execution_count": 23, "id": "6de05015", "metadata": {}, "outputs": [], "source": [ - "roi = RectROI(\n", + "roi = RectangleROI(\n", " x_pixel_range=(15, 35), # mandatory\n", " y_pixel_range=(15, 35), # mandatory\n", " x_range=(sc.scalar(-2, unit='mm'), sc.scalar(2, unit='mm')), # optional\n", @@ -3976,7 +3976,7 @@ }, { "cell_type": "code", - "execution_count": 23, + "execution_count": 24, "id": "ed81cad4", "metadata": {}, "outputs": [ @@ -4001,9 +4001,9 @@ "\n", "\n", "\n", - "
        scipp.DataArray (36.84 KB)
          • t: 1500
          • Ltotal
            ()
            int64
            m
            61
            Values:
            array(61)
          • c
            ()
            string
            intensities
            Values:
            'intensities'
          • tof
            (t [bin-edge])
            float64
            s
            0.022, 0.022, ..., 0.092, 0.093
            Values:
            array([0.02158728, 0.02163456, 0.02168185, ..., 0.09242233, 0.09246961,\n",
-       "       0.0925169 ], shape=(1501,))
          • wavelength
            (t [bin-edge])
            float64
            Å
            1.4, 1.403, ..., 5.997, 6.0
            Values:
            array([1.4       , 1.40306667, 1.40613333, ..., 5.99386667, 5.99693333,\n",
-       "       6.        ], shape=(1501,))
          • (t)
            float32
            𝟙
            0.36840674, 0.3425866, ..., 0.46642005, 0.45523798
            σ = 0.0058153444, 0.0056076236, ..., 0.013006445, 0.012870439
            Values:
            array([0.36840674, 0.3425866 , 0.35694158, ..., 0.43976402, 0.46642005,\n",
+       "
            scipp.DataArray (36.84 KB)
              • t: 1500
              • Ltotal
                ()
                int64
                m
                61
                Values:
                array(61)
              • c
                ()
                string
                intensities
                Values:
                'intensities'
              • tof
                (t [bin-edge])
                float64
                s
                0.022, 0.022, ..., 0.092, 0.093
                Values:
                array([0.02158728, 0.02163456, 0.02168185, ..., 0.09242233, 0.09246961,\n",
+       "       0.0925169 ], shape=(1501,))
              • wavelength
                (t [bin-edge])
                float64
                Å
                1.4, 1.403, ..., 5.997, 6.0
                Values:
                array([1.4       , 1.40306667, 1.40613333, ..., 5.99386667, 5.99693333,\n",
+       "       6.        ], shape=(1501,))
              • (t)
                float32
                𝟙
                0.36840674, 0.3425866, ..., 0.46642005, 0.45523798
                σ = 0.0058153444, 0.0056076236, ..., 0.013006445, 0.012870439
                Values:
                array([0.36840674, 0.3425866 , 0.35694158, ..., 0.43976402, 0.46642005,\n",
        "       0.45523798], shape=(1500,), dtype=float32)

                Variances (σ²):
                array([3.3818233e-05, 3.1445445e-05, 3.3600576e-05, ..., 1.4671838e-04,\n",
        "       1.6916762e-04, 1.6564821e-04], shape=(1500,), dtype=float32)
          " ], @@ -4019,7 +4019,7 @@ " float32 [dimensionless] (t) [0.368407, 0.342587, ..., 0.46642, 0.455238] [3.38182e-05, 3.14454e-05, ..., 0.000169168, 0.000165648]\n" ] }, - "execution_count": 23, + "execution_count": 24, "metadata": {}, "output_type": "execute_result" } @@ -4030,14 +4030,14 @@ }, { "cell_type": "code", - "execution_count": 24, + "execution_count": 25, "id": "1e142cfe", "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "93a2186d5f864d4c90f86fb3abc64188", + "model_id": "013a16a07ed147cbbfd3f8ed4e2180e4", "version_major": 2, "version_minor": 0 }, @@ -4045,7 +4045,7 @@ "InteractiveFigure(children=(HBar(), HBar(children=(VBar(children=(Toolbar(children=(ButtonTool(icon='home', la…" ] }, - "execution_count": 24, + "execution_count": 25, "metadata": {}, "output_type": "execute_result" } @@ -4064,7 +4064,7 @@ }, { "cell_type": "code", - "execution_count": 25, + "execution_count": 26, "id": "123de71f", "metadata": {}, "outputs": [], @@ -4082,14 +4082,14 @@ }, { "cell_type": "code", - "execution_count": 26, + "execution_count": 27, "id": "01bb61d2", "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "ff5b600fc3be451eb7d02430062f0c97", + "model_id": "4b8de46e94f24f72adabec77e114abf8", "version_major": 2, "version_minor": 0 }, @@ -4097,7 +4097,7 @@ "InteractiveFigure(children=(HBar(), HBar(children=(VBar(children=(Toolbar(children=(ButtonTool(icon='home', la…" ] }, - "execution_count": 26, + "execution_count": 27, "metadata": {}, "output_type": "execute_result" } @@ -4122,14 +4122,14 @@ }, { "cell_type": "code", - "execution_count": 27, + "execution_count": 28, "id": "7ff41a8e-7dd2-4a19-9d09-8a9221963459", "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "b4c0732e2f3a40ab9ccc6144c677d890", + "model_id": "40221aacaf994af1a7462168f20bdfae", "version_major": 2, "version_minor": 0 }, @@ -4137,7 +4137,7 @@ "Box(children=(InteractiveFigure(children=(HBar(), HBar(children=(VBar(children=(Toolbar(children=(ButtonTool(i…" ] }, - "execution_count": 27, + "execution_count": 28, "metadata": {}, "output_type": "execute_result" } @@ -4156,17 +4156,17 @@ }, { "cell_type": "code", - "execution_count": 28, + "execution_count": 29, "id": "5ef8713d-4844-4afa-ac26-309ed2154613", "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "EasyList of length 2 of type(s) []" + "EasyList of length 1 of type(s) []" ] }, - "execution_count": 28, + "execution_count": 29, "metadata": {}, "output_type": "execute_result" } @@ -4185,7 +4185,7 @@ }, { "cell_type": "code", - "execution_count": 29, + "execution_count": 30, "id": "41a4cd39", "metadata": { "tags": [ @@ -4204,7 +4204,7 @@ }, { "cell_type": "code", - "execution_count": 30, + "execution_count": 31, "id": "f02fe391", "metadata": {}, "outputs": [], @@ -4229,7 +4229,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.13.13" + "version": "3.13.14" } }, "nbformat": 4, From f433093ed9866a04bcf21fcaef066711ff456421 Mon Sep 17 00:00:00 2001 From: Christian Vedel Date: Fri, 19 Jun 2026 15:28:32 +0200 Subject: [PATCH 14/14] Fix scipp repr issue in docs by adding their stylesheet --- docs/docs/assets/stylesheets/scipp_style.css | 495 ++++++++++++ docs/docs/tutorials/measurement.ipynb | 18 +- docs/mkdocs.yml | 1 + pixi.lock | 765 ++++++++++--------- 4 files changed, 930 insertions(+), 349 deletions(-) create mode 100644 docs/docs/assets/stylesheets/scipp_style.css diff --git a/docs/docs/assets/stylesheets/scipp_style.css b/docs/docs/assets/stylesheets/scipp_style.css new file mode 100644 index 0000000..2727d42 --- /dev/null +++ b/docs/docs/assets/stylesheets/scipp_style.css @@ -0,0 +1,495 @@ +/* CSS stylesheet for displaying scipp objects in jupyterlab. +* Original source from +* https://github.com/jsignell/xarray/blob/1d960933ab252e0f79f7e050e6c9261d55568057/xarray/static/css/style.css +*/ + +.sc-root { + --sc-background-color0: var(--jp-layout-color0, #fff) !important; + --sc-background-color1: var(--jp-layout-color1, #fcfcfc) !important; + --sc-background-color2: var(--jp-layout-color2, #efefef) !important; + --sc-inverse-background-color0: var(--jp-inverse-layout-color4, #111) !important; + --sc-font-color0: var(--jp-content-font-color0, #000) !important; + --sc-font-color1: var(--jp-content-font-color1, #555) !important; + --sc-font-color2: var(--jp-content-font-color2, #888) !important; + --sc-font-color3: var(--jp-content-font-color3, #ccc) !important; +} + +body.vscode-dark .sc-root { + --sc-font-color0: rgba(255, 255, 255, 1) !important; + --sc-font-color1: rgba(255, 255, 255, 0.70) !important; + --sc-font-color2: rgba(255, 255, 255, 0.54) !important; + --sc-font-color3: rgba(255, 255, 255, 0.38) !important; + --sc-border-color: #1F1F1F !important; + --sc-disabled-color: #515151 !important; + --sc-background-color0: #111111 !important; + --sc-background-color1: #111111 !important; + --sc-background-color2: #313131 !important; +} + +.sc-wrap { + font-size: 14px !important; + min-width: 300px !important; + max-width: 800px !important; +} + +/* The CSS styling for the inline attributes table */ +.sc-var-attrs .sc-wrap{ + padding-left: 3em !important; +} + +.sc-header { + padding-top: 6px !important; + padding-bottom: 6px !important; + margin-bottom: 4px !important; + border-bottom: solid 1px #ddd !important; +} + +.sc-header > div, +.sc-header > ul { + display: inline !important; + margin-top: 0 !important; + margin-bottom: 0 !important; +} + +.sc-obj-type, +.sc-array-name { + margin-left: 2px !important; + margin-right: 10px !important; +} + +.sc-obj-type { + color: var(--sc-font-color1) !important; +} + +.sc-underlying-size { + color: var(--sc-font-color2) !important; +} + +/* Also override settings of reveal.js as introduced when + generating slides using the rise package. + There are selectors for `.reveal ul` and `.reveal ul ul` + which take precedence over ours and mess up the formatting.*/ +.sc-sections, .reveal .sc-sections { + padding-left: 0 !important; + display: grid !important; + grid-template-columns: 150px auto auto auto 1fr 20px 20px !important; +} + +.sc-section-item { + display: contents !important; +} + +.sc-section-item input { + display: none !important; +} + +.sc-section-item input:enabled + label { + cursor: pointer !important; + color: var(--sc-font-color1) !important; +} + +.sc-section-item input:enabled + label:hover { + color: var(--sc-font-color0) !important; +} + +.sc-section-summary { + grid-column: 1 !important; + font-weight: 500 !important; +} + +.sc-section-summary > span { + display: inline-block !important; + padding-left: 0.5em !important; +} + +.sc-section-summary-in:disabled + label { + color: var(--sc-font-color1) !important; +} + +.sc-section-summary-in + label:before { + display: inline-block !important; + content: '►' !important; + font-size: 11px !important; + width: 15px !important; + text-align: center !important; +} + +.sc-section-summary-in:disabled + label:before { + display: none !important; +} + +.sc-section-summary-in:checked + label:before { + content: '▼' !important; +} + +.sc-section-summary-in:checked + label > span { + display: none !important; +} + +.sc-section-summary, +.sc-section-inline-details { + padding-top: 4px !important; + padding-bottom: 4px !important; +} + +.sc-section-inline-details { + grid-column: 2 / 6 !important; +} + +.sc-section-details { + display: none !important; + grid-column: 1 / -1 !important; + margin-bottom: 5px !important; +} + +.sc-section-summary-in:checked ~ .sc-section-details { + display: contents !important; +} + +.sc-array-wrap { + grid-column: 1 / -1 !important; + display: grid !important; + grid-template-columns: 20px auto !important; +} + +.sc-array-wrap > label { + grid-column: 1 !important; + vertical-align: top !important; +} + +.sc-preview { + color: var(--sc-font-color2) !important; +} + +.sc-array-preview, +.sc-array-data { + padding: 0 5px !important; + grid-column: 2 !important; +} + +.sc-array-data, +.sc-array-in:checked ~ .sc-array-preview { + display: none !important; +} + +.sc-array-in:checked ~ .sc-array-data, +.sc-array-preview { + display: inline-block !important; +} + +.sc-dim-list { + display: inline-block !important; + list-style: none !important; + padding: 0 !important; + margin: 0 !important; +} + +.sc-dim-list li { + display: inline-block !important; + padding: 0 !important; + margin: 0 !important; +} + +.sc-dim-list:before { + content: '(' !important; +} + +.sc-dim-list:after { + content: ')' !important; +} + +.sc-dim-list li:not(:last-child):after { + content: ',' !important; + padding-right: 5px !important; +} + +/* +This selector is for avoiding unexpected extra padding +caused by tag wrapping around the dollar-sign in the Jpyter notebook. +*/ +.sc-dim-list li span, +.sc-standalone-var-name > span span, +.sc-var-name > span span { + padding: 0 !important; +} + +.sc-aligned { + font-weight: bold !important; +} + +.sc-var-list, +.sc-var-item, +.reveal .sc-var-list, +.reveal .sc-var-item { + display: contents !important; +} + +.sc-var-item > div, +.sc-var-item label, +.sc-var-item > .sc-var-name span { + background-color: var(--sc-background-color1) !important; + margin-bottom: 0 !important; +} + +.sc-var-item > .sc-var-name:hover span { + padding-right: 5px !important; +} + +.sc-var-list > li:nth-child(odd) > div, +.sc-var-list > li:nth-child(odd) > label, +.sc-var-list > li:nth-child(odd) > .sc-var-name span { + background-color: var(--sc-background-color2) !important; +} + +.sc-var-name { + grid-column: 1 !important; +} + +.sc-var-dims { + grid-column: 2 !important; +} + +.sc-var-dtype { + grid-column: 3 !important; + text-align: right !important; + color: var(--sc-font-color2) !important; +} +.sc-var-unit{ + grid-column: 4 !important; + text-align: left !important; + color: var(--sc-font-color1) !important; + max-width: 50pt !important; + text-overflow: ellipsis !important; +} +.sc-value-preview { + grid-column: 5 !important; +} +.sc-var-preview-variances{ + text-align:right !important; +} + +.sc-sections .sc-section-item .sc-section-summary, +.sc-sections .sc-section-item .sc-section-inline-details, +.sc-section-item .sc-var-list .sc-var-item > div, +.sc-section-item .sc-var-list .sc-var-item > label, +.sc-section-details .sc-var-list .sc-var-item > div, +.sc-section-details .sc-var-list .sc-var-item > label { + margin-top: 0 !important; + margin-bottom: 0 !important; +} + +.sc-var-name, +.sc-var-dims, +.sc-var-dtype, +.sc-var-unit, +.sc-preview, +.sc-attrs dt { + white-space: nowrap !important; + overflow: hidden !important; + text-overflow: ellipsis !important; + padding-right: 10px !important; +} + +.sc-var-name:hover, +.sc-var-dims:hover, +.sc-var-dtype:hover, +.sc-var-unit:hover, +.sc-attrs dt:hover { + overflow: visible !important; + width: auto !important; + z-index: 1 !important; +} + +.sc-var-attrs { + display: block !important; +} +.sc-var-data, .reveal .sc-var-data { + display: none !important; +} +.sc-var-attrs, +.sc-var-data { + background-color: var(--sc-background-color0) !important; + padding-bottom: 5px !important; +} + +.sc-var-attrs-in:checked ~ .sc-var-attrs { + display: none !important; +} +.sc-var-data-in:checked ~ .sc-var-data { + display: block !important; +} + +.sc-var-data > table { + float: right !important; +} + +.sc-var-name span, +.sc-var-data { + padding-left: 25px !important; +} + +.sc-var-attrs, +.sc-var-data { + grid-column: 1 / -1 !important; +} + +dl.sc-attrs { + padding: 0 !important; + margin: 0 !important; + display: grid !important; + grid-template-columns: 125px auto !important; +} + +.sc-attrs dt, dd { + padding: 0 !important; + margin: 0 !important; + float: left !important; + padding-right: 10px !important; + width: auto !important; +} + +.sc-attrs dt { + font-weight: normal !important; + grid-column: 1 !important; +} + +.sc-attrs dt:hover span { + display: inline-block !important; + padding-right: 10px !important; +} + +.sc-attrs dd { + grid-column: 2 !important; + white-space: pre-wrap !important; + word-break: break-all !important; +} + +.sc-icon-database, +.sc-icon-file-text2 { + display: inline-block !important; + vertical-align: middle !important; + width: 1em !important; + height: 1.5em !important; + stroke-width: 0 !important; + stroke: currentColor !important; + fill: currentColor !important; +} + +label.sc-hide-icon svg{ + opacity: 0; +} + +.sc-standalone-var-name{ + grid-column: 1/3 !important; +} + +.sc-standalone-var-name span{ + padding-left: 25px !important; + padding-right:10px !important; +} + +.sc-title { + font-weight:bold !important; + font-size:1.5em !important; +} + +.sc-subtitle { + font-weight:normal !important; + font-style:italic !important; + text-align:left !important; + font-size:1.2em !important; + padding: 1px !important; +} + +.sc-label { + fill: var(--sc-font-color0, #444444) !important; + text-anchor: middle !important; +} + +.sc-name { + fill: var(--sc-font-color0, #111111) !important; +} + +.sc-inset-line { + stroke: var(--sc-font-color1) !important; + stroke-width: 0.05 !important; + stroke-dasharray: 0.2, 0.2 !important; +} + +.sc-log-wrap { + height: 25ex; + resize: vertical; + overflow-y: scroll; + display: flex; + flex-direction: column-reverse; + border: 1px solid !important; + border-color: var(--jp-border-color2) !important; + background-color: var(--sc-background-color1) !important; +} + +div.sc-log { + line-height: 2.5ex !important; +} + +table.sc-log { + table-layout: auto !important; + border-collapse: collapse !important; +} + +tr.sc-log:nth-child(even) { + background-color: var(--sc-background-color0) !important; +} + +tr.sc-log > td { + vertical-align: top !important; + padding-bottom: 0.5ex !important; +} + +.sc-log-time-stamp { + min-width: 22ch !important; + font-family: var(--jp-code-font-family) !important; + color: var(--sc-font-color2) !important; +} + +.sc-log-level { + min-width: 10ch !important; +} + +tr.sc-log-debug td.sc-log-level { + color: var(--jp-accent-color1) !important; +} + +tr.sc-log-info td.sc-log-level { + color: var(--jp-info-color1) !important; +} + +tr.sc-log-warning td.sc-log-level { + color: var(--jp-warn-color1) !important; +} + +tr.sc-log-error td.sc-log-level { + font-weight: bold !important; + color: var(--jp-error-color2) !important; +} + +tr.sc-log-critical td.sc-log-level { + font-weight: bold !important; + color: var(--sc-background-color0) !important; + background-color: var(--jp-error-color1) !important; +} + +.sc-log-message { + white-space: pre-wrap !important; + width: 100% !important; +} + +.sc-log-html-payload { + white-space: normal !important; +} + +.sc-log-name { + padding-right: 0.5em !important; + text-align: right !important; + white-space: pre-wrap !important; + color: var(--sc-font-color3) !important; +} diff --git a/docs/docs/tutorials/measurement.ipynb b/docs/docs/tutorials/measurement.ipynb index 1414f61..05c8873 100644 --- a/docs/docs/tutorials/measurement.ipynb +++ b/docs/docs/tutorials/measurement.ipynb @@ -11,7 +11,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "id": "bfb22357", "metadata": {}, "outputs": [], @@ -180,7 +180,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 42, "id": "5aa49556", "metadata": {}, "outputs": [ @@ -205,7 +205,7 @@ "\n", "\n", "\n", - "
          scipp.Variable (324 Bytes)
            • (x: 17)
              float32
              mm
              -7.0382814, -6.158496, ..., 6.158496, 7.0382814
              Values:
              array([-7.0382814 , -6.158496  , -5.2787113 , -4.398926  , -3.5191407 ,\n",
+       "
              scipp.Variable (324 Bytes)
                • (x: 17)
                  float32
                  mm
                  -7.0382814, -6.158496, ..., 6.158496, 7.0382814
                  Values:
                  array([-7.0382814 , -6.158496  , -5.2787113 , -4.398926  , -3.5191407 ,\n",
        "       -2.6393557 , -1.7595701 , -0.87978506,  0.        ,  0.87978506,\n",
        "        1.7595701 ,  2.6393552 ,  3.5191412 ,  4.3989263 ,  5.2787113 ,\n",
        "        6.158496  ,  7.0382814 ], dtype=float32)
          " @@ -238,7 +238,7 @@ "\n", "\n", "\n", - "
          scipp.Variable (324 Bytes)
            • (y: 17)
              float32
              mm
              -7.0382814, -6.158496, ..., 6.158496, 7.0382814
              Values:
              array([-7.0382814 , -6.158496  , -5.2787113 , -4.398926  , -3.5191407 ,\n",
+       "
              scipp.Variable (324 Bytes)
                • (y: 17)
                  float32
                  mm
                  -7.0382814, -6.158496, ..., 6.158496, 7.0382814
                  Values:
                  array([-7.0382814 , -6.158496  , -5.2787113 , -4.398926  , -3.5191407 ,\n",
        "       -2.6393557 , -1.7595701 , -0.87978506,  0.        ,  0.87978506,\n",
        "        1.7595701 ,  2.6393552 ,  3.5191412 ,  4.3989263 ,  5.2787113 ,\n",
        "        6.158496  ,  7.0382814 ], dtype=float32)
          " @@ -271,7 +271,7 @@ "\n", "\n", "\n", - "
          scipp.Variable (11.98 KB)
            • (t: 1501)
              float64
              s
              0.022, 0.022, ..., 0.092, 0.093
              Values:
              array([0.02158728, 0.02163456, 0.02168185, ..., 0.09242233, 0.09246961,\n",
+       "
              scipp.Variable (11.98 KB)
                • (t: 1501)
                  float64
                  s
                  0.022, 0.022, ..., 0.092, 0.093
                  Values:
                  array([0.02158728, 0.02163456, 0.02168185, ..., 0.09242233, 0.09246961,\n",
        "       0.0925169 ], shape=(1501,))
          " ], "text/plain": [ @@ -3741,7 +3741,7 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": 36, "id": "75774206", "metadata": {}, "outputs": [], @@ -3759,14 +3759,14 @@ }, { "cell_type": "code", - "execution_count": 17, + "execution_count": 38, "id": "9d5de1be", "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "108be8cf344645dba4c41c0116e093e5", + "model_id": "c5697e2266e54c818c26947db4dfc29d", "version_major": 2, "version_minor": 0 }, @@ -3774,7 +3774,7 @@ "InteractiveFigure(children=(HBar(), HBar(children=(VBar(children=(Toolbar(children=(ButtonTool(icon='home', la…" ] }, - "execution_count": 17, + "execution_count": 38, "metadata": {}, "output_type": "execute_result" } diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml index 010434a..6e5a42c 100644 --- a/docs/mkdocs.yml +++ b/docs/mkdocs.yml @@ -84,6 +84,7 @@ extra: # Customization to be included by the theme extra_css: - assets/stylesheets/extra.css + - assets/stylesheets/scipp_style.css # Scipp's style.css got overwritten by the Material theme. extra_javascript: - assets/javascripts/extra.js diff --git a/pixi.lock b/pixi.lock index 88becc8..5bfeb2f 100644 --- a/pixi.lock +++ b/pixi.lock @@ -22,7 +22,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/debugpy-1.8.21-py313h5d5ffb9_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/icu-78.3-h33c6efd_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.3-hb9d3cd8_0.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/krb5-1.22.2-ha1258a1_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/krb5-1.22.2-hbde042b_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45.1-default_hbd61a6d_102.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/libabseil-20260107.1-cxx17_h7b12aa8_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/libbrotlicommon-1.2.0-hb03c661_1.conda @@ -47,7 +47,7 @@ environments: - 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