Fluorescence-Tools · benmwebb · Nov 13, 2024 · Nov 13, 2024 · Nov 13, 2024 · Nov 13, 2024
diff --git a/.gitignore b/.gitignore
@@ -7,7 +7,7 @@
 *.gcno
 .vscode
 *.gcda
-*/Files.cmake
+Files.cmake
 db/
 *_run*
 *out
@@ -25,7 +25,7 @@ doc/auto_examples
 examples/CMakeLists.txt
 .history
 doc/IMP.bff.docset
-
+CMakeModules/
 test/CMakeLists.txt
 src/CMakeLists.txt
 pyext/CMakeLists.txt

diff --git a/.gitmodules b/.gitmodules
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -36,7 +36,7 @@ if(CMAKE_SOURCE_DIR STREQUAL CMAKE_CURRENT_SOURCE_DIR)
     SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread")
     SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -pthread")
 
-    # compatability with older systems
+    # compatibility with older systems
     SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -mmacosx-version-min=10.13")
     SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mmacosx-version-min=10.13")
     SET(CMAKE_LFLAGS "${CMAKE_LFLAGS} -mmacosx-version-min=10.13")
@@ -75,5 +75,3 @@ if(CMAKE_SOURCE_DIR STREQUAL CMAKE_CURRENT_SOURCE_DIR)
 else()
   INCLUDE(ModuleBuild.cmake)
 endif()
-
-INCLUDE(Setup.cmake)
diff --git a/bin/imp_bff b/bin/imp_bff
@@ -229,7 +229,7 @@ def rmsd(
         -r ~/science/Papers/00_in_preparation/Bayesian_Fluorescence_Toolkit/Test_case_candiates/01_Antibody/targets/nodes1_045.pdb \
         -k structure
 
-    With provided column for RMSD reference calcualtion
+    With provided column for RMSD reference calculation
 
     structure rmsd \
         -f /home/tpeulen/science/Papers/00_in_preparation/Bayesian_Fluorescence_Toolkit/Test_case_candiates/01_Antibody/targets/experiments/eTCSPC/ucfret/02_structure_search/local_scaling/species_sampling.sort.ol4 \
@@ -343,7 +343,7 @@ def auto_model(input_file, output_path=None, settings=None, fret_efficiency=None
         output_path = pathlib.Path(input_file).parent.absolute()
     input_file = pathlib.Path(input_file).absolute()
 
-    print("OUPTUT DIRECTORIES")
+    print("OUTPUT DIRECTORIES")
     print("===============================")
     OUT_PREANALYSIS = output_path / 'init'
     OUT_PREANALYSIS.mkdir(exist_ok=True)

diff --git a/dependencies.py b/dependencies.py
@@ -1,3 +1,3 @@
 required_modules = 'container:core:em:atom'
-required_dependencies = 'IMP.em'
-optional_dependencies = ''
+required_dependencies = 'NumPy'
+optional_dependencies = 'AVX'
diff --git a/Setup.cmake → dependency/AVX.cmake b/Setup.cmake → dependency/AVX.cmake
@@ -4,12 +4,12 @@
 option(WITH_AVX "Enable AVX support" OFF)
 
 if (WITH_AVX AND NOT APPLE AND CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "x86_64")
-    set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_CURRENT_SOURCE_DIR}/dependency)
+    set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_CURRENT_SOURCE_DIR})
     include(simd)
 
     if (${AVX_FOUND})
         message("BUILD WITH SIMD")
-        add_definitions(-DWITH_AVX)
+        file(WRITE "${CMAKE_BINARY_DIR}/build_info/AVX" "ok=True")
 
         if (MSVC)
             # https://devblogs.microsoft.com/cppblog/simd-extension-to-c-openmp-in-visual-studio/
@@ -19,10 +19,10 @@ if (WITH_AVX AND NOT APPLE AND CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "x86_64")
             set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mavx -mfma")
         endif (MSVC)
     else (${AVX_FOUND})
-        unset(WITH_AVX)
+        file(WRITE "${CMAKE_BINARY_DIR}/build_info/AVX" "ok=False")
     endif (${AVX_FOUND})
 else ()
     # AVX only on x86_64 and not on Apple
     message("BUILD WITHOUT SIMD")
-    unset(WITH_AVX)
-endif()
+    file(WRITE "${CMAKE_BINARY_DIR}/build_info/AVX" "ok=False")
+endif()
diff --git a/dependency/AVX.description b/dependency/AVX.description
@@ -0,0 +1 @@
+#
diff --git a/doc/README.md b/doc/README.md
diff --git a/doc/conf.py b/doc/conf.py
@@ -1,7 +1,6 @@
 # -*- coding: utf-8 -*-
 #
 import os
-import subprocess
 import sys
 import warnings
 import re
@@ -14,7 +13,7 @@
 # absolute, like shown here.
 sys.path.insert(0, os.path.abspath('sphinxext'))
 
-import sphinx_gallery
+import sphinx_gallery  # noqa: E402
 
 # -- General configuration ---------------------------------------------------
 root_doc = 'contents'
@@ -76,7 +75,7 @@
 copyright = (
     f'2021 - {datetime.now().year}, IMP developers'
 )
-import IMP.bff
+import IMP.bff  # noqa: E402
 version = IMP.bff.__version__
 
 # List of patterns, relative to source directory, that match files and
@@ -108,18 +107,18 @@
         html_theme_path = sphinx_rtd_theme.get_html_theme_path()
     html_theme = 'sphinx_rtd_theme'
 else:
-    # Add any paths that contain custom themes here, relative to this directory.
+    # Add any paths that contain custom themes here, relative to this directory
     html_theme_path = ['themes']
     html_theme = 'scikit-learn-modern'
-    # Theme options are theme-specific and customize the look and feel of a theme
-    # further.  For a list of options available for each theme, see the
-    # documentation.
+    # Theme options are theme-specific and customize the look and feel
+    # of a theme further.  For a list of options available for each theme,
+    # see the documentation.
     html_theme_options = {'google_analytics': True,
                           'mathjax_path': mathjax_path}
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-#html_title = None
+# html_title = None
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
 html_short_title = 'IMP.bff'
@@ -164,9 +163,10 @@
 # Finds the highlight with the latest version number
 latest_highlights = sorted(release_highlights_dir.glob("*.py"))[-1]
 latest_highlights = latest_highlights.with_suffix('').name
-html_context["release_highlights"] = f"auto_examples/release_highlights/{latest_highlights}"
+html_context["release_highlights"] = \
+    f"auto_examples/release_highlights/{latest_highlights}"
 
-# get version from higlight name assuming highlights have the form
+# get version from highlight name assuming highlights have the form
 # plot_release_highlights_0_22_0
 highlight_version = ".".join(latest_highlights.split("_")[-3:-1])
 html_context["release_highlights_version"] = highlight_version
@@ -192,7 +192,8 @@
 
 # intersphinx configuration
 intersphinx_mapping = {
-    'python': ('https://docs.python.org/{.major}'.format(sys.version_info), None),
+    'python': ('https://docs.python.org/{.major}'.format(sys.version_info),
+               None),
     'numpy': ('https://numpy.org/doc/stable', None),
     'scipy': ('https://docs.scipy.org/doc/scipy/reference', None),
     'matplotlib': ('https://matplotlib.org/', None),
@@ -324,5 +325,3 @@ def setup(app):
 warnings.filterwarnings("ignore", category=UserWarning,
                         message='Matplotlib is currently using agg, which is a'
                                 ' non-GUI backend, so cannot show the figure.')
-
-
diff --git a/doc/install.ipynb b/doc/install.ipynb
@@ -6,7 +6,7 @@
    "metadata": {},
    "source": [
     "# Installation\n",
-    "`IMP.bff` is installed from prebuilt binaries using the [Conda](https://docs.conda.io) package manager. Conda is included as part of the Anaconda Python distribution, which you can download from https://docs.continuum.io/anaconda/install. Anaconda is a Python distribution specifically designed for scientific applications, with many of the most popular mathematical and scientific packages preinstalled. Alternatively, `IMP.bff` can be installed in a Miniconda distribuition (available from https://docs.conda.io/en/latest/miniconda.html). Miniconda includes only Python itself, plus the Conda package manager. Miniconda offers a much smaller initial download, with the ability to then install only the packages you want."
+    "`IMP.bff` is installed from prebuilt binaries using the [Conda](https://docs.conda.io) package manager. Conda is included as part of the Anaconda Python distribution, which you can download from https://docs.continuum.io/anaconda/install. Anaconda is a Python distribution specifically designed for scientific applications, with many of the most popular mathematical and scientific packages preinstalled. Alternatively, `IMP.bff` can be installed in a Miniconda distribution (available from https://docs.conda.io/en/latest/miniconda.html). Miniconda includes only Python itself, plus the Conda package manager. Miniconda offers a much smaller initial download, with the ability to then install only the packages you want."
    ]
   },
   {

diff --git a/doc/manual/decays/decay_forward_model.ipynb b/doc/manual/decays/decay_forward_model.ipynb
@@ -210,7 +210,7 @@
     ")\n",
     "lifetime_settings = {\n",
     "    'lifetime_spectrum': lifetime_spectrum.flatten(),\n",
-    "    'abs_lifetime_spectrum': False,   # True -> take abs of liftime spectrum\n",
+    "    'abs_lifetime_spectrum': False,   # True -> take abs of lifetime spectrum\n",
     "    'use_amplitude_threshold': False, # True -> discriminate lifetimes below threshold\n",
     "    'amplitude_threshold': 0.0\n",
     "}\n",

diff --git a/doc/manual/decays/decay_objective_function.ipynb b/doc/manual/decays/decay_objective_function.ipynb
@@ -154,7 +154,7 @@
     "    },\n",
     "    \"lifetime_settings\": {\n",
     "        'lifetime_spectrum': [0.8, 4.0, 0.2, 2.0],\n",
-    "        'abs_lifetime_spectrum': False,   # True -> take abs of liftime spectrum\n",
+    "        'abs_lifetime_spectrum': False,   # True -> take abs of lifetime spectrum\n",
     "        'use_amplitude_threshold': False, # True -> discriminate lifetimes below threshold\n",
     "        'amplitude_threshold': 0.0\n",
     "    },\n",

diff --git a/doc/manual/imaging/flim_intro.rst b/doc/manual/imaging/flim_intro.rst
@@ -204,7 +204,7 @@ time resolution by a factor of 2.
 Pixel averaged decays
 ---------------------
 Using selection masks the signal to noise of the fluorescence decays can be greatly
-improved to allow for a detailed analyis. Here it is briefly outlined, how pixels
+improved to allow for a detailed analysis. Here it is briefly outlined, how pixels
 are selected and fluorescence decays of these pixel sub-populations can be created.
 
 #.. plot:: ../examples/imaging/imaging_pixel_masks.py
@@ -400,7 +400,6 @@ object with a ``TTTR`` object that contains the photon stream a set of ``CLSMFra
 
 .. code-block:: python
 
-    from __future__ import print_function
     import tttrlib
     import numpy as np
     import pylab as p

diff --git a/doc/manual/input_output/tttr_operations.rst b/doc/manual/input_output/tttr_operations.rst
@@ -51,7 +51,7 @@ data that are offset by the last macro time record in the first set in addition
 the value specified by ``macro_time_offset``. The parameter ``macro_time_offset``
 is set to zero by default.
 
-By appending TTTR objects to each other data that is splitted into multiple files
+By appending TTTR objects to each other data that is split into multiple files
 can be joined into a single TTTR object as follows
 
 
@@ -77,7 +77,7 @@ can be joined into a single TTTR object as follows
 Selections
 ==========
 A defining feature of TTTR data is that subsets can be selected and defined for
-more detailed analysis. This is for instance exploited in single-molecule experimetns
+more detailed analysis. This is for instance exploited in single-molecule experiments
 There are different methods to access subsets of a TTTR object that are described
 in this section.
 
@@ -130,7 +130,7 @@ fluorescence were (0, 8) and (1, 9) for the red detection window.
 The method 'get_selection_by_channel' provides an array that contains the indices
 of the events when a the channel equals the channel number of the provided
 arguments. To obtain the indices where the channel number. In the example below
-the indices of the green (channel = 0 or channel = 8) and the indeces of the red
+the indices of the green (channel = 0 or channel = 8) and the indices of the red
 (channel = 1 or channel = 9) are saved in the variables ``green_indices``  and
 ``red_indices``, respectively.
 
@@ -185,4 +185,4 @@ experiments or to generate filters for advanced FCS analysis :cite:`laurence2004
 TTTR ranges
 ===========
 
-STOP
+STOP
diff --git a/doc/manual/input_output/tttr_write.rst b/doc/manual/input_output/tttr_write.rst
@@ -3,7 +3,7 @@
 
 Writing TTTR-files
 ==================
-TTTR objects can be writen to files using the method ``write`` of TTTR objects.
+TTTR objects can be written to files using the method ``write`` of TTTR objects.
 
 .. code-block:: python
 
@@ -74,9 +74,9 @@ writing to a file.
     data_ptu = tttrlib.TTTR(ptu_file)
 
 
-When a TTTR file is writen to another format certain meta data need to be provided.
+When a TTTR file is written to another format certain meta data need to be provided.
 The combination of tttr_container_type and tttr_record_type determines of the header
-determines the ouput format of the TTTR writer method.
+determines the output format of the TTTR writer method.
 
 For PTU files at least the instrument and the measurement mode (T2, T3) need to be
 provided.

diff --git a/doc/manual/intensity/intensity_pda.ipynb b/doc/manual/intensity/intensity_pda.ipynb
@@ -188,7 +188,7 @@
     "        c_{12} \\frac{1}{\\sqrt{2\\pi \\sigma_{12}^2}} \\exp{\\left(-\\frac{(E-E_{12})^2}{2\\sigma_{12}^2}\\right)}\n",
     "$$\n",
     "\n",
-    "here, :math:`E_1` and :math:`E_2` corresond to the FRET efficiencies of the states :math:`S_1` and :math:`S_2`,\n",
+    "here, :math:`E_1` and :math:`E_2` correspond to the FRET efficiencies of the states :math:`S_1` and :math:`S_2`,\n",
     "respectively. The pre-factors are given by:\n",
     "\n",
     "$$\n",

diff --git a/doc/manual/programming/programming_imp_decorator.ipynb b/doc/manual/programming/programming_imp_decorator.ipynb
@@ -15,7 +15,7 @@
    "source": [
     "# IMP Decorator\n",
     "\n",
-    "IMP particles can be decorated to add functionality. Here it is outlined how a the paramters of a fluorescence decay can be decorated to a particle. "
+    "IMP particles can be decorated to add functionality. Here it is outlined how a the parameters of a fluorescence decay can be decorated to a particle. "
    ]
   },
   {
@@ -132,7 +132,7 @@
     "p = IMP.Particle(m)\n",
     "lifetime_settings = {\n",
     "    'lifetime_spectrum': [0.8, 4.0, 0.2, 2.0],\n",
-    "    'abs_lifetime_spectrum': False,   # True -> take abs of liftime spectrum\n",
+    "    'abs_lifetime_spectrum': False,   # True -> take abs of lifetime spectrum\n",
     "    'use_amplitude_threshold': False, # True -> discriminate lifetimes below threshold\n",
     "    'amplitude_threshold': 0.0\n",
     "}\n",

diff --git a/doc/manual/single-molecule/decay.rst b/doc/manual/single-molecule/decay.rst
@@ -54,7 +54,7 @@ are accessible via a simplified object-based interface that reduces the number o
 lines of code that need to be written for analyzing fluorescence decay histograms.
 The code blocks that are used below to illustrate the tttrlib functionality are
 extracts from the tests located in the test folder of the tttrlib repository. The
-test can be used as a more detailed refernce on how to use tttrlib.
+test can be used as a more detailed reference on how to use tttrlib.
 
 Model functions can be computed using for instance the ``DecayFit23.modelf``
 function of the ``tttrlib`` module. Here, the ``23`` represents a particular model
@@ -117,7 +117,7 @@ interface handles the creation of auxiliary data structures such as ``tttrlib.MP
 In the example shown above, first a fit object of the type ``fit2x.DecayFit23`` is
 created. All necessary data except for the experimental data for a fit is passed
 to the fit object when it is created. To perform a fit on experimental data for
-a set for a set of initial values, the fit object is called using the inital values
+a set for a set of initial values, the fit object is called using the initial values
 and the data as parameters.
 
 
diff --git a/doc/manual/single-molecule/single_molecule_experiment_simulation.ipynb b/doc/manual/single-molecule/single_molecule_experiment_simulation.ipynb
@@ -61,7 +61,7 @@
     "\n",
     "---\n",
     "\n",
-    "`QuEst` simulates the diffusion and interaction of dyes tethered to a protein to simulate dynmaic quenching by PET, [[ET]](https://pubs.acs.org/doi/full/10.1021/acs.jpcb.7b03441)). `QuEst` is available at https://github.com/fluorescence-tools/QuEst. The output of a `QuEst` simulation is a fluorescence decay curve of a dye along with the corresponding fluorescence quantum yield that can serve as an input for donor fluorescence properties in FRET experiment simulations. \n",
+    "`QuEst` simulates the diffusion and interaction of dyes tethered to a protein to simulate dynamic quenching by PET, [[ET]](https://pubs.acs.org/doi/full/10.1021/acs.jpcb.7b03441)). `QuEst` is available at https://github.com/fluorescence-tools/QuEst. The output of a `QuEst` simulation is a fluorescence decay curve of a dye along with the corresponding fluorescence quantum yield that can serve as an input for donor fluorescence properties in FRET experiment simulations. \n",
     "\n",
     "![Quest_gui](https://github.com/Fluorescence-Tools/quest/raw/master/doc/img/readme_screenshot_0.png?raw=true)\n",
     "\n",
@@ -115,7 +115,7 @@
     "\n",
     "---\n",
     "\n",
-    "The simulation software for confocal single molecule (FRET) experiment (`Burbulator`) was developed for Windows and that can be used on other platforms such as Linux and macOS using [Wine](https://www.winehq.org/). To obtain Burbulator download the data accompanying [[CO]](https://www.sciencedirect.com/science/article/pii/S0959440X1630197X) either with curl or using a webbrowser with the following [link](https://www.modelarchive.org/doi/10.5452/ma-a2hbq). Unfortunatelly, the `modelarchive` website will provide you with a file named wrongly as a `.cif`. Thus, you need to rename the file to correct file type `.tar.gz`. "
+    "The simulation software for confocal single molecule (FRET) experiment (`Burbulator`) was developed for Windows and that can be used on other platforms such as Linux and macOS using [Wine](https://www.winehq.org/). To obtain Burbulator download the data accompanying [[CO]](https://www.sciencedirect.com/science/article/pii/S0959440X1630197X) either with curl or using a webbrowser with the following [link](https://www.modelarchive.org/doi/10.5452/ma-a2hbq). Unfortunately, the `modelarchive` website will provide you with a file named wrongly as a `.cif`. Thus, you need to rename the file to correct file type `.tar.gz`. "
    ]
   },
   {

diff --git a/doc/related_projects.rst b/doc/related_projects.rst
@@ -27,7 +27,7 @@ enhance the functionality of tttrlib estimators.
 **Fluorescence lifetime imaging**
 
 - `clsmview <https://gitlab.peulen.xyz/tpeulen/clsmview/>`_ A python program with
-  graphical user interface to vizualize and process confocal laser scanning data
+  graphical user interface to visualize and process confocal laser scanning data
   with tttrlib.
 
 **Model definition/optimization/sampling**

diff --git a/examples/labels/plot_AVDecorator.py b/examples/labels/plot_AVDecorator.py
@@ -70,7 +70,7 @@
 # Access AV features
 # ------------------
 # AV decorated particles use PathMaps to sample the accessible volume.
-# Thus, features of the AV are accesses trough PathMap. The features can
+# Thus, features of the AV are accessed through PathMap. The features can
 # be written to density maps (see: PathMapTile). PathMaps derive from
 # IMP EM density maps and sampled obstacles can be written to density files
 # using standard IMP methods.
@@ -82,7 +82,7 @@
 # %%
 # Features of a IMP.bff.PathMap are identified by the following constants
 pm_features = [
-    IMP.bff.PM_TILE_PENALTY,             # Penality of visiting a tile
+    IMP.bff.PM_TILE_PENALTY,             # Penalty of visiting a tile
     IMP.bff.PM_TILE_COST,                # Cost of a path to the tile
     IMP.bff.PM_TILE_DENSITY,             # Density of tile
     IMP.bff.PM_TILE_COST_DENSITY,        # Cost * Density of tile
@@ -176,4 +176,6 @@
 rda = np.linspace(rda_start, rda_stop, n_bins)
 p_rda = IMP.bff.av_distance_distribution(av1, av2, rda, n_samples=n_samples)
 plt.plot(rda, p_rda)
-plt.show()
+print("See plot.png for the distance distribution between two AVs")
+plt.savefig('plot.png')
+#plt.show()
diff --git a/examples/labels/plot_AVNetworkRestraint.py b/examples/labels/plot_AVNetworkRestraint.py
@@ -19,7 +19,6 @@
 import numpy as np
 import pylab as plt
 
-import RMF
 import IMP
 import IMP.rmf
 import IMP.atom
@@ -76,4 +75,6 @@
 plt.plot(x, x, "-")
 plt.xlabel("Model distance [Ang.]")
 plt.ylabel("Experimental distance [Ang.]")
-plt.show()
+print("See plot.png for experiment against model distance")
+plt.savefig('plot.png')
+#plt.show()