bactoscoop.features =================== .. py:module:: bactoscoop.features Per-cell feature implementations called by Image and ImageCollection. See :doc:`../reference/feature-dictionary`. Classes and public operations ----------------------------- Features ~~~~~~~~ .. py:class:: Features(image_obj) Calculate per-cell geometry and signal feature families for an image. Collection and Image methods coordinate the required loading, filtering, feature error recording, and table construction. :param image_obj: Image instance supplying calibration, geometry, and channel data. :returns: None (no explicit return statement). **Assigned state:** ``self.image_obj``. `View current source, line 14 <../source-code/features.html#features-14>`_. Features.discard_large_meshes ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:method:: Features.discard_large_meshes(cell, max_mesh_size=600) Discard cells with meshes that are too small or large. :param cell: Cell instance containing geometry and measurements. :param max_mesh_size: Maximum accepted mesh row count; cells above this limit are removed from the image cell population. :returns: None (no explicit return statement). **Assigned state:** ``cell.discard``. `View current source, line 20 <../source-code/features.html#features-20>`_. .. raw:: html
Original docstring (legacy wording may differ from the current signature) .. code-block:: text Discard cells with meshes that are too small or large. This method checks the size of a cell's mesh and flags it for discard if the mesh size does not fall within the acceptable range. Parameters ---------- cell : Cell The Cell object representing the cell to be checked. Returns ------- None .. raw:: html
Features.discard_bad_meshes ~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:method:: Features.discard_bad_meshes(cell) Discard bad meshes. :param cell: Cell instance containing geometry and measurements. :returns: None (no explicit return statement). **Assigned state:** ``cell.discard``. `View current source, line 42 <../source-code/features.html#features-42>`_. Features.contour_selection ~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:method:: Features.contour_selection(cell, use_shifted_contours) Contour selection. :param cell: Cell instance containing geometry and measurements. :param use_shifted_contours: Select stored shifted contour, midline, and mesh geometry; the correction must already exist. **Return expressions in source:** .. code-block:: python (cell.shifted_contour, cell.shifted_midline, cell.shifted_mesh) (cell.contour, cell.midline, cell.mesh) `View current source, line 57 <../source-code/features.html#features-57>`_. Features.morphological ~~~~~~~~~~~~~~~~~~~~~~ .. py:method:: Features.morphological(cell, channel, all_data, *args) Calculate morphological features for a cell. :param cell: Cell instance containing geometry and measurements. :param channel: Channel identifier for the selected signal, or None for phase/morphology where supported. :param all_data: Feature-method-specific option; objects includes detailed per-object arrays when true. :returns: None (no explicit return statement). **Assigned state:** ``cell.morphological_features``, ``cell.profiling_data``, ``cell.profile_mesh``, ``cell.discard``. `View current source, line 63 <../source-code/features.html#features-63>`_. .. raw:: html
Original docstring (legacy wording may differ from the current signature) .. code-block:: text Calculate morphological features for a cell. .. raw:: html
Features.profiling ~~~~~~~~~~~~~~~~~~ .. py:method:: Features.profiling(cell, channel, all_data, use_shifted_contours, shift_signal, *args) Calculate profiling features for a cell. :param cell: Cell instance containing geometry and measurements. :param channel: Channel identifier for the selected signal, or None for phase/morphology where supported. :param all_data: Feature-method-specific option; objects includes detailed per-object arrays when true. :param use_shifted_contours: Select stored shifted contour, midline, and mesh geometry; the correction must already exist. :param shift_signal: Enable the method-specific optional signal cropping/shift path; this is not a universal object-coordinate shift. **Return expressions in source:** .. code-block:: python None **Assigned state:** ``cell.profiling_features``, ``cell.discard``. **Explicitly raised exceptions:** ``AttributeError``. Errors from called functions can also propagate or be recorded. `View current source, line 241 <../source-code/features.html#features-241>`_. .. raw:: html
Original docstring (legacy wording may differ from the current signature) .. code-block:: text Calculate profiling features for a cell. .. raw:: html
Features.svm ~~~~~~~~~~~~ .. py:method:: Features.svm(cell, channel, all_data, *args) Calculate features of a cell to be used in training the Support Vector Machine (SVM) or curate a dataset using a trained SVM model. :param cell: Cell instance containing geometry and measurements. :param channel: Channel identifier for the selected signal, or None for phase/morphology where supported. :param all_data: Feature-method-specific option; objects includes detailed per-object arrays when true. :returns: None (no explicit return statement). **Assigned state:** ``cell.svm_features``, ``cell.profiling_data``. `View current source, line 375 <../source-code/features.html#features-375>`_. .. raw:: html
Original docstring (legacy wording may differ from the current signature) .. code-block:: text Calculate features of a cell to be used in training the Support Vector Machine (SVM) or curate a dataset using a trained SVM model. .. raw:: html
Features.objects ~~~~~~~~~~~~~~~~ .. py:method:: Features.objects(cell, channel, all_data, use_shifted_contours, *args, retain_contour_on_object_mesh_failure=False) Calculates features related to the identified objects within a cell. :param cell: Cell instance containing geometry and measurements. :param channel: Channel identifier for the selected signal, or None for phase/morphology where supported. :param all_data: Feature-method-specific option; objects includes detailed per-object arrays when true. :param use_shifted_contours: Select stored shifted contour, midline, and mesh geometry; the correction must already exist. :param retain_contour_on_object_mesh_failure: Per-cell objects option used by the collection retention-channel setting. **Return expressions in source:** .. code-block:: python None **Assigned state:** ``cell.objects_features``, ``cell.discard``. **Explicitly raised exceptions:** ``AttributeError``, ``ValueError``. Errors from called functions can also propagate or be recorded. `View current source, line 501 <../source-code/features.html#features-501>`_. .. raw:: html
Original docstring (legacy wording may differ from the current signature) .. code-block:: text Calculates features related to the identified objects within a cell. .. raw:: html
Features.membrane ~~~~~~~~~~~~~~~~~ .. py:method:: Features.membrane(cell, channel, all_data, use_shifted_contours, shift_signal) Membrane. :param cell: Cell instance containing geometry and measurements. :param channel: Channel identifier for the selected signal, or None for phase/morphology where supported. :param all_data: Feature-method-specific option; objects includes detailed per-object arrays when true. :param use_shifted_contours: Select stored shifted contour, midline, and mesh geometry; the correction must already exist. :param shift_signal: Enable the method-specific optional signal cropping/shift path; this is not a universal object-coordinate shift. **Return expressions in source:** .. code-block:: python None **Assigned state:** ``cell.membrane_features``, ``cell.discard``. **Explicitly raised exceptions:** ``AttributeError``, ``ValueError``. Errors from called functions can also propagate or be recorded. `View current source, line 836 <../source-code/features.html#features-836>`_. Features.colocalization ~~~~~~~~~~~~~~~~~~~~~~~ .. py:method:: Features.colocalization(cell, signal1, signal2, shift_signal1, shift_signal2, all_data, use_shifted_contours) Incomplete preliminary colocalization implementation. Prepares channel crops but does not complete a measurement; do not use as an analysis feature family. :param cell: Cell instance containing geometry and measurements. :param signal1: Input ``signal1`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. :param signal2: Input ``signal2`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. :param shift_signal1: Input ``shift_signal1`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. :param shift_signal2: Input ``shift_signal2`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. :param all_data: Feature-method-specific option; objects includes detailed per-object arrays when true. :param use_shifted_contours: Select stored shifted contour, midline, and mesh geometry; the correction must already exist. :returns: None (no explicit return statement). **Assigned state:** ``cell.signal_correlation_features``. **Explicitly raised exceptions:** ``AttributeError``. Errors from called functions can also propagate or be recorded. `View current source, line 937 <../source-code/features.html#features-937>`_.