diff --git a/docs/docs/api-reference/index.md b/docs/docs/api-reference/index.md index 62b1c78..c4a12ab 100644 --- a/docs/docs/api-reference/index.md +++ b/docs/docs/api-reference/index.md @@ -6,3 +6,10 @@ icon: material/code-braces-box This section contains the reference detailing the functions and modules available in EasyImaging. + +- [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 + 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/assets/images/crosshairs_dark.png b/docs/docs/assets/images/crosshairs_dark.png new file mode 100644 index 0000000..8bc7eae Binary files /dev/null and b/docs/docs/assets/images/crosshairs_dark.png differ diff --git a/docs/docs/assets/images/crosshairs_light.png b/docs/docs/assets/images/crosshairs_light.png new file mode 100644 index 0000000..c91fec5 Binary files /dev/null and b/docs/docs/assets/images/crosshairs_light.png differ diff --git a/docs/docs/assets/images/vector-square_dark.png b/docs/docs/assets/images/vector-square_dark.png new file mode 100644 index 0000000..38ba6ad Binary files /dev/null and b/docs/docs/assets/images/vector-square_dark.png differ diff --git a/docs/docs/assets/images/vector-square_light.png b/docs/docs/assets/images/vector-square_light.png new file mode 100644 index 0000000..4dbcfbd Binary files /dev/null and b/docs/docs/assets/images/vector-square_light.png differ diff --git a/docs/docs/assets/stylesheets/extra.css b/docs/docs/assets/stylesheets/extra.css index a625be8..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: 1280px; + 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/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; 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scipp.DataArray (36.84 KB)
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      (t [bin-edge])
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      Variances (σ²):
      array([8.9548885e-06, 9.9539866e-06, 9.6888207e-06, ..., 3.6184254e-05,\n",
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scipp.DataArray (36.84 KB)
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+       "       0.0925169 ], shape=(1501,))
    • wavelength
      (t [bin-edge])
      float64
      Å
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      Values:
      array([1.4       , 1.40306667, 1.40613333, ..., 5.99386667, 5.99693333,\n",
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      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)
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"execution_count": null, + "execution_count": 26, "id": "123de71f", "metadata": {}, "outputs": [], @@ -480,10 +4082,26 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 27, "id": "01bb61d2", "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "4b8de46e94f24f72adabec77e114abf8", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "InteractiveFigure(children=(HBar(), HBar(children=(VBar(children=(Toolbar(children=(ButtonTool(icon='home', la…" + ] + }, + "execution_count": 27, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "measurement.spectrum_plot(roi='center_roi')" ] @@ -504,10 +4122,26 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 28, "id": "7ff41a8e-7dd2-4a19-9d09-8a9221963459", "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "40221aacaf994af1a7462168f20bdfae", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "Box(children=(InteractiveFigure(children=(HBar(), HBar(children=(VBar(children=(Toolbar(children=(ButtonTool(i…" + ] + }, + "execution_count": 28, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "measurement.roi_creator()" ] @@ -522,10 +4156,21 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 29, "id": "5ef8713d-4844-4afa-ac26-309ed2154613", "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "EasyList of length 1 of type(s) []" + ] + }, + "execution_count": 29, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "measurement.regions_of_interest" ] @@ -540,11 +4185,11 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 30, "id": "41a4cd39", "metadata": { "tags": [ - "remove-cell" + "hide-in-docs" ] }, "outputs": [], @@ -559,7 +4204,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 31, "id": "f02fe391", "metadata": {}, "outputs": [], @@ -584,7 +4229,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.13.13" + "version": "3.13.14" } }, "nbformat": 4, diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml index 5bf28fe..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 @@ -156,7 +157,25 @@ plugins: show_root_heading: true show_root_full_path: false show_submodules: true - show_source: 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 + relative_crossrefs: true + 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 + - url: https://scipp.github.io/scitiff/objects.inv + - url: https://scipp.github.io/plopp/objects.inv - search # Determines additional directories to watch when running mkdocs serve @@ -180,6 +199,10 @@ nav: - Tutorials: - Tutorials: tutorials/index.md - Getting Started: - - Dummy tutorial: tutorials/plotting.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 3713a70..5bfeb2f 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: @@ -9,68 +13,16 @@ environments: packages: 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/noarch/_python_abi3_support-1.0-hd8ed1ab_2.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/anyio-4.13.0-pyhcf101f3_0.conda - 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-__all__ = [Measurement] diff --git a/src/easyimaging/measurement/measurement.py b/src/easyimaging/measurement/measurement.py index c8dfc14..8ee91a3 100644 --- a/src/easyimaging/measurement/measurement.py +++ b/src/easyimaging/measurement/measurement.py @@ -17,16 +17,85 @@ from scipp import UnitError from scitiff import load_scitiff 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 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 **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.
+ 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`][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. + + 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. + + 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__( self, @@ -34,6 +103,37 @@ def __init__( unique_name: str | None = None, display_name: str | None = None, ): + """Initialize a Measurement instance. + + Parameters + ---------- + data_array : sc.DataArray + 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 + A prettily formatted name for the [`Measurement`][..]. Defaults to [`unique_name`][..unique_name] if not provided. + + Raises + ------ + TypeError + If ``data_array`` is not a [`sc.DataArray`][scipp.DataArray]. + ValueError + 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 ``'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 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.') @@ -77,7 +177,7 @@ 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 @@ -86,22 +186,38 @@ 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** 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 ---------- - cls : 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 a [`Path`](https://docs.python.org/3/library/pathlib.html) object. + RuntimeError + 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.') @@ -125,38 +241,70 @@ 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 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. + + 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 ---------- - cls : 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 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 ``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.') - 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'}) @@ -202,14 +350,28 @@ 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** 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 a [`Path`](https://docs.python.org/3/library/pathlib.html) object. + RuntimeError + If the file cannot be written to the specified ``filename`` path. + + Warns + ----- + UserWarning + 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.') @@ -230,49 +392,92 @@ 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. This attribute is **read-only**. - Note that this will make a full copy of the data array, so it should be used with caution for large datasets. + Returns the rebinned data array if rebinning has been applied, otherwise the + original full-resolution data array. Use with caution for large datasets to avoid memory issues. + + 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( - '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: - """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.""" - 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-coordinates of the 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 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 [`sc.Variable`][scipp.Variable] or [`np.ndarray`][numpy.ndarray]. + UnitError + 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. ' @@ -290,22 +495,39 @@ 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, if 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-coordinates of the 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 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 [`sc.Variable`][scipp.Variable] or [`np.ndarray`][numpy.ndarray]. + UnitError + 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. ' @@ -325,16 +547,28 @@ 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, @@ -359,7 +593,13 @@ 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 pixels of the measurement image stack. + + Raises + ------ + ValueError + If the [Measurement][..] does not currently have physical coordinate positions set. + """ if self._has_physical_coords: del self._data_array.coords['x'] del self._data_array.coords['y'] @@ -369,19 +609,34 @@ def delete_physical_coord_positions(self) -> None: @property def time_of_flights(self) -> sc.Variable: - """Get the time-of-flight values of the measurement.""" - 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 + ------ + ValueError + 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`` 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, @@ -396,29 +651,99 @@ 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]: - """Get the list of regions of interest (ROIs) defined for this measurement.""" + def regions_of_interest(self) -> EasyList[RectangleROI]: + """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 + ------- + ```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] + A list of the regions of interest (ROIs) attached to 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( - '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. - This operation reduces the resolution of the data by combining adjacent pixels or time bins. - The rebinned dimensions must be evenly divisible by their specific rebin factor. + 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. + + Repeating this operation will rebin the already rebinned data, not the original data.
+ 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][..]: + ```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) + + 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, {'t': 2} will rebin the time dimension by a factor of 2. + 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 `dict`.
+ If any keys in ``dimensions`` are not strings.
+ If a rebin factor is not a positive integer (or integer-valued float). + ValueError + If a dimension size is not evenly divisible by the requested rebin factor. + KeyError + 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.') @@ -427,7 +752,7 @@ 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.') @@ -438,11 +763,12 @@ 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" + 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') non_finite_mask = ~sc.isfinite(temp_array.data) @@ -450,7 +776,15 @@ 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. + + 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 else: @@ -459,21 +793,37 @@ 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. + """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 `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. - If no time-of-flight is provided, the plot will average over all time-of-flight values. + This method uses the [plopp](https://scipp.github.io/plopp/plotting/image-plot.html) library for plotting. - This method uses the plopp library for plotting: - https://scipp.github.io/plopp/plotting/image-plot.html + 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. + Additional keyword arguments to pass to the plotting function.
+ See [plopp.plot][] for options. + + Raises + ------ + TypeError + If ``time_of_flight`` is not an integer, a `sc.Variable` scalar, or ``None``. + UnitError + 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)' @@ -488,34 +838,43 @@ 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: 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 library for interactive slicing: - https://scipp.github.io/plopp/plotting/slicer-plot.html + This method uses the [plopp](https://scipp.github.io/plopp/plotting/slicer-plot.html) library for interactive slicing. + + 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. + Additional keyword arguments to pass to the slicer function.
+ See [plopp.slicer][] for options. + + Raises + ------ + RuntimeError + If called outside a Jupyter notebook environment. """ slicer_kwargs_defaults = self._plot_defaults() slicer_kwargs_defaults.update({ @@ -534,23 +893,41 @@ 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 library for interactive inspection: - https://scipp.github.io/plopp/plotting/inspector-plot.html + This method uses the [plopp](https://scipp.github.io/plopp/plotting/inspector-plot.html) library for interactive + inspection. + + 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_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 + - 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. + Additional keyword arguments to pass to the inspector function.
+ See [plopp.inspector][] for options. + + Raises + ------ + RuntimeError + If called outside a Jupyter notebook environment. """ inspector_kwargs_defaults = self._plot_defaults() inspector_kwargs_defaults['ymax'] = inspector_kwargs_defaults['cmax'] 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', @@ -558,28 +935,58 @@ 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.') 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. 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. - This method uses the plopp library for interactive ROI creation: - https://scipp.github.io/plopp/plotting/roi-selector.html + Interactive controls + -------- + 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: - 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 + - 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: + [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. + Additional keyword arguments to pass to the inspector function.
+ See [plopp.inspector][] for options. + + Raises + ------ + RuntimeError + If called outside a Jupyter notebook environment. """ if not _is_notebook(): @@ -590,15 +997,27 @@ 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 ----------------------------------- @@ -639,10 +1058,20 @@ 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 rectangle roi.""" + """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[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, @@ -653,7 +1082,17 @@ 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:`RectangleROI` in ``roi_list`` when a rectangle is resized. + + Parameters + ---------- + rect : + The rectangle object provided by the plopp RectangleTool. + 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. + """ 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 +1105,15 @@ 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:`RectangleROI` corresponding to ``rect`` from ``roi_list``. + + Parameters + ---------- + rect : + The rectangle object provided by the plopp RectangleTool. + roi_list : EasyList[RectangleROI] + 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) @@ -694,25 +1141,34 @@ def delete_rectangle_roi(rect, roi_list): return plots - def spectrum(self, roi: RectROI | str | None = None) -> sc.DataArray: - """Extract the spectrum (intensity vs. time-of-flight) for a specified region of interest (ROI). + def spectrum(self, roi: RectangleROI | str | None = None) -> sc.DataArray: + """Extract 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. Parameters ---------- - roi : RectROI | 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 DataArray containing the spectrum data. + A 1-D [sc.DataArray][scipp.DataArray] containing the spatially averaged time-of-flight spectrum. + + Raises + ------ + TypeError + If ``roi`` is not a [`RectangleROI`][RectangleROI], string, or ``None``. + KeyError + 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, (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: @@ -732,32 +1188,51 @@ 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: - """Plot the spectrum (intensity vs. time-of-flight) for a specified region of interest (ROI). + def spectrum_plot(self, roi: RectangleROI | str | None = None, **kwargs) -> None: + """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 : RectROI | 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. + Additional keyword arguments to pass to the plotting function.
+ See [plopp.plot][] for options. + + Raises + ------ + TypeError + If ``roi`` is not a [`RectangleROI`][RectangleROI], string, or ``None``. + KeyError + 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) + 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) @@ -776,7 +1251,28 @@ 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 +1292,43 @@ 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 +1345,31 @@ 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 +1401,14 @@ 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 +1419,12 @@ 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 deleted file mode 100644 index 2708958..0000000 --- a/src/easyimaging/measurement/regions.py +++ /dev/null @@ -1,319 +0,0 @@ -# SPDX-FileCopyrightText: 2026 EasyScience contributors -# SPDX-License-Identifier: BSD-3-Clause - -from __future__ import annotations - -from typing import Any -from typing import Dict -from typing import List -from typing import Sequence -from typing import Tuple - -import scipp as sc -from easyscience.base_classes import NewBase -from scipp import UnitError - - -class RectROI(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. - """ - - def __init__( - self, - x_pixel_range: Sequence[int], - y_pixel_range: Sequence[int], - x_range: Sequence[sc.Variable] | None = None, - y_range: Sequence[sc.Variable] | None = None, - unique_name: str | None = None, - display_name: str | None = None, - ) -> 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. - """ - super().__init__(unique_name=unique_name, display_name=display_name) - self.set_pixel_coord_range(x_pixel_range, y_pixel_range) - - if x_range is not None and y_range is not None: - self.set_physical_coord_range(x_range, y_range) - elif x_range is None and y_range is None: - self._has_physical_coords = False - else: - 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. - - 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. - """ - self._check_input_sequence(x_pixel_range, 'x_pixel_range', 'integers', int) - 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? - 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. - - 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. - """ - - self._check_input_sequence(x_range, 'x_range', 'scipp scalars', sc.Variable) - self._check_input_sequence(y_range, 'y_range', 'scipp scalars', sc.Variable) - for scalar in tuple(x_range) + tuple(y_range): - self._check_scalar(scalar, 'Physical coordinates') - self._x_start, self._x_end = x_range - self._y_start, self._y_end = y_range - self._has_physical_coords = True - - def delete_physical_coord_range(self) -> None: - """Delete the physical coordinate ranges for the ROI.""" - if self._has_physical_coords: - del self._x_start - del self._x_end - del self._y_start - del self._y_end - self._has_physical_coords = False - else: - 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. - - Returns - ------- - tuple - Two (x,y) slice objects representing the pixel range 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. - - Returns - ------- - tuple - Two (x,y) slice objects representing the range of the ROI. - """ - if self._has_physical_coords: - return slice(self._x_start, self._x_end), slice(self._y_start, self._y_end) - else: - raise ValueError('Physical coordinate ranges are not set for this ROI.') - - @property - def x_pixel_start(self) -> int: - """X pixel start.""" - return self._x_pixel_start.value - - @x_pixel_start.setter - def x_pixel_start(self, value: int): - """X pixel start.""" - self._check_index(value, 'x_pixel_start') - self._x_pixel_start = sc.scalar(value) - - @property - def x_pixel_end(self) -> int: - """X pixel end.""" - return self._x_pixel_end.value - - @x_pixel_end.setter - def x_pixel_end(self, value: int): - """X pixel end.""" - self._check_index(value, 'x_pixel_end') - self._x_pixel_end = sc.scalar(value) - - @property - def y_pixel_start(self) -> int: - """Y pixel start.""" - return self._y_pixel_start.value - - @y_pixel_start.setter - def y_pixel_start(self, value: int): - """Y pixel start.""" - self._check_index(value, 'y_pixel_start') - self._y_pixel_start = sc.scalar(value) - - @property - def y_pixel_end(self) -> int: - """Y pixel end.""" - return self._y_pixel_end.value - - @y_pixel_end.setter - def y_pixel_end(self, value: int): - """Y pixel end.""" - self._check_index(value, 'y_pixel_end') - self._y_pixel_end = sc.scalar(value) - - @property - def x_start(self) -> sc.Variable: - """X start.""" - if self._has_physical_coords: - return self._x_start.copy() - else: - raise ValueError('Physical coordinate ranges are not set for this ROI.') - - @x_start.setter - def x_start(self, value: sc.Variable): - """X start.""" - 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.""" - if self._has_physical_coords: - return self._x_end.copy() - else: - raise ValueError('Physical coordinate ranges are not set for this ROI.') - - @x_end.setter - def x_end(self, value: sc.Variable): - """X end.""" - 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.""" - if self._has_physical_coords: - return self._y_start.copy() - else: - raise ValueError('Physical coordinate ranges are not set for this ROI.') - - @y_start.setter - def y_start(self, value: sc.Variable): - """Y start.""" - 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.""" - if self._has_physical_coords: - return self._y_end.copy() - else: - raise ValueError('Physical coordinate ranges are not set for this ROI.') - - @y_end.setter - def y_end(self, value: sc.Variable): - """Y end.""" - 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.""" - 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)): - raise TypeError( - f'{name} must be a tuple or a list of two {typename}, ' - f'got {type(value[0]).__name__} and {type(value[1]).__name__}.' - ) - - def _check_index(self, value: int, name: str) -> None: - """Check if the input value is a valid index (non-negative integer).""" - 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.""" - if value.dims: - raise ValueError(f'{name} must be a scipp scalar (0-dimensional Variable).') - try: - test_value = value.copy() - test_value.to(unit='m') - except Exception as e: - 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.""" - if not isinstance(value, sc.Variable): - raise TypeError(f'{name} must be a scipp scalar.') - if not self._has_physical_coords: - raise ValueError( - f'Cannot set {name} before setting all physical coordinate ranges. ' - 'Please use the set_physical_coord_range method.' - ) - - def to_dict(self, skip: List[str] | None = None) -> Dict[str, Any]: - """Convert the RectROI instance to a dictionary representation.""" - if skip is None: - skip = [] - elif isinstance(skip, str): - skip = [skip] - skip = list(skip) # Create a copy of the skip list to avoid modifying the original - skip.extend(['x_pixel_range', 'y_pixel_range', 'x_range', 'y_range']) - out_dict = super().to_dict(skip=skip) - out_dict['x_pixel_range'] = [int(self.x_pixel_start), int(self.x_pixel_end)] - out_dict['y_pixel_range'] = [int(self.y_pixel_start), int(self.y_pixel_end)] - if self._has_physical_coords: - out_dict['x_range'] = [ - { - '@module': 'scipp', - '@version': sc.__version__, - '@class': 'scalar', - 'dict': sc.to_dict(self.x_start), - }, - { - '@module': 'scipp', - '@version': sc.__version__, - '@class': 'scalar', - 'dict': sc.to_dict(self.x_end), - }, - ] - out_dict['y_range'] = [ - { - '@module': 'scipp', - '@version': sc.__version__, - '@class': 'scalar', - 'dict': sc.to_dict(self.y_start), - }, - { - '@module': 'scipp', - '@version': sc.__version__, - '@class': 'scalar', - 'dict': sc.to_dict(self.y_end), - }, - ] - return out_dict - - @classmethod - def from_dict(cls, input_dict: Dict[str, Any]) -> RectROI: - """Create a RectROI instance from a dictionary representation.""" - 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']] - temp_dict['y_range'] = [sc.from_dict(item['dict']) for item in input_dict['y_range']] - return super().from_dict(temp_dict) - - def __repr__(self) -> str: - """Repr function.""" - 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})' - ) - if self._has_physical_coords: - repr_str += f', x_range=({self._x_start}, {self._x_end}), y_range=({self._y_start}, {self._y_end})' - repr_str += ')' - return repr_str diff --git a/src/easyimaging/regions_of_interest/__init__.py b/src/easyimaging/regions_of_interest/__init__.py new file mode 100644 index 0000000..3ca52e4 --- /dev/null +++ b/src/easyimaging/regions_of_interest/__init__.py @@ -0,0 +1,4 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + +from .rectangle_roi import RectangleROI diff --git a/src/easyimaging/regions_of_interest/rectangle_roi.py b/src/easyimaging/regions_of_interest/rectangle_roi.py new file mode 100644 index 0000000..06f81c3 --- /dev/null +++ b/src/easyimaging/regions_of_interest/rectangle_roi.py @@ -0,0 +1,668 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + +from __future__ import annotations + +from typing import Any +from typing import Dict +from typing import List +from typing import Sequence +from typing import Tuple + +import scipp as sc +from easyscience.base_classes import NewBase +from scipp import UnitError + + +class RectangleROI(NewBase): + """Object representing a rectangular region of interest (ROI) in an image. + + 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 + associated [Measurement][...Measurement] class. + Otherwise, the obligatory pixel coordinate ranges are used as a fallback. + + Example + ------- + Creating a [RectangleROI][.] instance manually: + ```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__( + self, + x_pixel_range: Sequence[int], + y_pixel_range: Sequence[int], + x_range: Sequence[sc.Variable] | None = None, + y_range: Sequence[sc.Variable] | None = None, + unique_name: str | None = None, + display_name: str | None = None, + ) -> None: + """Initialize a RectangleROI instance. + + Parameters + ---------- + x_pixel_range : Sequence[int] + 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 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`][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`][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. + display_name : str | None + A prettily formatted 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.
+ 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`][scipp.Variable] in ``x_range`` or ``y_range`` is not 0-dimensional (i.e., not a scalar).
+ UnitError + 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) + + if x_range is not None and y_range is not None: + self.set_physical_coord_range(x_range, y_range) + elif x_range is None and y_range is None: + self._has_physical_coords = False + else: + 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 defining the ROI. + + Parameters + ---------- + 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. + 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. + + 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) + for index in tuple(x_pixel_range) + tuple(y_pixel_range): + if index < 0: + 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 defining the ROI. + + Parameters + ---------- + 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`][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`][scipp.Variable] scalars with units of length + + Raises + ------ + TypeError + If either argument is not a two-element sequence of [`sc.Variable`][scipp.Variable]. + ValueError + 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`][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) + self._check_input_sequence(y_range, 'y_range', 'scipp scalars', sc.Variable) + for scalar in tuple(x_range) + tuple(y_range): + self._check_scalar(scalar, 'Physical coordinates') + self._x_start, self._x_end = x_range + self._y_start, self._y_end = y_range + self._has_physical_coords = True + + def delete_physical_coord_range(self) -> None: + """Delete the physical coordinate ranges for the ROI. + + This enforces the ROI to use pixel coordinates only. + + Raises + ------ + ValueError + If physical coordinate ranges are not currently set. + """ + if self._has_physical_coords: + del self._x_start + del self._x_end + del self._y_start + del self._y_end + self._has_physical_coords = False + else: + raise ValueError('Cannot delete physical coordinate ranges because they are not set.') + + def pixel_slice(self) -> Tuple[slice, slice]: + """Get a pixel index slice object corresponding to the ROI. + + Returns + ------- + tuple + 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 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) + else: + raise ValueError('Physical coordinate ranges are not set for this ROI.') + + @property + def x_pixel_start(self) -> int: + """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 + If ``value`` is not an integer. + 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) + + @property + def x_pixel_end(self) -> int: + """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 + If ``value`` is not an integer. + 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) + + @property + def y_pixel_start(self) -> int: + """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 + If ``value`` is not an integer. + 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) + + @property + def y_pixel_end(self) -> int: + """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 + If ``value`` is not an integer. + 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) + + @property + 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 + A copy of the x-axis physical coordinate defining the start of the ROI. + + Raises + ------ + TypeError + If ``value`` is not a [`sc.Variable`][scipp.Variable]. + ValueError + 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() + else: + raise ValueError('Physical coordinate ranges are not set for this ROI.') + + @x_start.setter + def x_start(self, value: sc.Variable): + # 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 + + @property + 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 + A copy of the x-axis physical coordinate defining the end of the ROI. + + Raises + ------ + TypeError + If ``value`` is not a [`sc.Variable`][scipp.Variable]. + ValueError + 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() + else: + raise ValueError('Physical coordinate ranges are not set for this ROI.') + + @x_end.setter + def x_end(self, value: sc.Variable): + # 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 + + @property + 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 + A copy of the y-axis physical coordinate defining the start of the ROI. + + Raises + ------ + TypeError + If ``value`` is not a [`sc.Variable`][scipp.Variable]. + ValueError + 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() + else: + raise ValueError('Physical coordinate ranges are not set for this ROI.') + + @y_start.setter + def y_start(self, value: sc.Variable): + # 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 + + @property + 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 + A copy of the y-axis physical coordinate defining the end of the ROI. + + Raises + ------ + TypeError + If ``value`` is not a [`sc.Variable`][scipp.Variable]. + ValueError + 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() + else: + raise ValueError('Physical coordinate ranges are not set for this ROI.') + + @y_end.setter + def y_end(self, value: sc.Variable): + # 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 + + def _check_input_sequence(self, value: Sequence, name: str, typename: str, expected_type: any) -> None: + """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)): + raise TypeError( + f'{name} must be a tuple or a list of two {typename}, ' + f'got {type(value[0]).__name__} and {type(value[1]).__name__}.' + ) + + def _check_index(self, value: int, name: str) -> None: + """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: + """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: + test_value = value.copy() + test_value.to(unit='m') + except Exception as e: + 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: + """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: + raise ValueError( + f'Cannot set {name} before setting all physical coordinate ranges. ' + 'Please use the set_physical_coord_range method.' + ) + + 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. + + Parameters + ---------- + 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. + + 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): + skip = [skip] + skip = list(skip) # Create a copy of the skip list to avoid modifying the original + skip.extend(['x_pixel_range', 'y_pixel_range', 'x_range', 'y_range']) + out_dict = super().to_dict(skip=skip) + out_dict['x_pixel_range'] = [int(self.x_pixel_start), int(self.x_pixel_end)] + out_dict['y_pixel_range'] = [int(self.y_pixel_start), int(self.y_pixel_end)] + if self._has_physical_coords: + out_dict['x_range'] = [ + { + '@module': 'scipp', + '@version': sc.__version__, + '@class': 'scalar', + 'dict': sc.to_dict(self.x_start), + }, + { + '@module': 'scipp', + '@version': sc.__version__, + '@class': 'scalar', + 'dict': sc.to_dict(self.x_end), + }, + ] + out_dict['y_range'] = [ + { + '@module': 'scipp', + '@version': sc.__version__, + '@class': 'scalar', + 'dict': sc.to_dict(self.y_start), + }, + { + '@module': 'scipp', + '@version': sc.__version__, + '@class': 'scalar', + 'dict': sc.to_dict(self.y_end), + }, + ] + return out_dict + + @classmethod + def from_dict(cls, input_dict: Dict[str, Any]) -> RectangleROI: + """Create a [`RectangleROI`][..] instance from a dictionary representation. + + Parameters + ---------- + input_dict : dict + 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 [`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: + temp_dict['x_range'] = [sc.from_dict(item['dict']) for item in input_dict['x_range']] + temp_dict['y_range'] = [sc.from_dict(item['dict']) for item in input_dict['y_range']] + return super().from_dict(temp_dict) + + def __repr__(self) -> str: + """Return a string representation of the RectangleROI. + + Returns + ------- + str + A human-readable summary including pixel ranges and, when available, + physical coordinate ranges. + """ + repr_str = ( + 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: + repr_str += f', x_range=({self._x_start}, {self._x_end}), y_range=({self._y_start}, {self._y_end})' + repr_str += ')' + return repr_str diff --git a/tests/unit/measurement/test_measurement.py b/tests/unit/measurement/test_measurement.py index c5d2fe2..86dd608 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: @@ -84,12 +84,12 @@ 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, 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 @@ -613,7 +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) @@ -632,7 +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): @@ -838,7 +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]) @@ -967,7 +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): @@ -989,7 +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'}) @@ -999,7 +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}) @@ -1009,7 +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}) @@ -1018,7 +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 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): @@ -1071,6 +1082,16 @@ 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 +1235,8 @@ 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 @@ -1292,9 +1315,12 @@ 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) + assert isinstance(roi, RectangleROI) assert roi.x_pixel_start == 2 assert roi.x_pixel_end == 5 assert roi.y_pixel_start == 2 @@ -1305,6 +1331,58 @@ 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 = RectangleROI( + 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 = RectangleROI( + 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') @@ -1321,7 +1399,7 @@ 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 @@ -1336,7 +1414,7 @@ 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')), @@ -1368,7 +1446,7 @@ 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 @@ -1387,7 +1465,7 @@ 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')), @@ -1407,10 +1485,10 @@ 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 = 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') + spectrum = measurement.spectrum(roi='test_roi_3') # Expect assert isinstance(spectrum, sc.DataArray) assert sc.identical(spectrum.coords['tof'], measurement._data_array.coords['tof']) @@ -1422,7 +1500,7 @@ 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}) @@ -1435,7 +1513,7 @@ 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}) @@ -1457,7 +1535,7 @@ 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 @@ -1471,7 +1549,7 @@ 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): @@ -1483,3 +1561,61 @@ 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'), + (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'], + ) + 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 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