bactoscoop.utilities ==================== .. py:module:: bactoscoop.utilities Low-level numerical and image helpers. Prefer the collection workflow for routine analysis; inspect geometry conventions before calling these directly. Classes and public operations ----------------------------- smallest_path ~~~~~~~~~~~~~ .. py:function:: smallest_path(x_coords, y_coords, start_x, start_y) Smallest path. :param x_coords: Input ``x_coords`` 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 y_coords: Input ``y_coords`` 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 start_x: Input ``start_x`` 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 start_y: Input ``start_y`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python ([x_coords[i] for i in sorted_points], [y_coords[i] for i in sorted_points]) `View current source, line 41 <../source-code/utilities.html#utilities-41>`_. skeleton_endpoints ~~~~~~~~~~~~~~~~~~ .. py:function:: skeleton_endpoints(skel) Skeleton endpoints. :param skel: Input ``skel`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python out `View current source, line 65 <../source-code/utilities.html#utilities-65>`_. get_ordered_list ~~~~~~~~~~~~~~~~ .. py:function:: get_ordered_list(points, x, y) Get ordered list. :param points: Input ``points`` 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 x: Input ``x`` 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 y: Input ``y`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python args `View current source, line 81 <../source-code/utilities.html#utilities-81>`_. line_intersect ~~~~~~~~~~~~~~ .. py:function:: line_intersect(x1, y1, x2, y2, x3, y3, x4, y4) Line intersect. :param x1: Input ``x1`` 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 y1: Input ``y1`` 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 x2: Input ``x2`` 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 y2: Input ``y2`` 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 x3: Input ``x3`` 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 y3: Input ``y3`` 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 x4: Input ``x4`` 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 y4: Input ``y4`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (intersect_x, intersect_y) `View current source, line 89 <../source-code/utilities.html#utilities-89>`_. line_contour_intersection ~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: line_contour_intersection(p1, p2, contour) Line contour intersection. :param p1: Input ``p1`` 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 p2: Input ``p2`` 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 contour: Boundary points in (row, column) pixel coordinates. **Return expressions in source:** .. code-block:: python intersection_points `View current source, line 102 <../source-code/utilities.html#utilities-102>`_. unit_perpendicular_vector ~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: unit_perpendicular_vector(data, closed=True) Unit perpendicular vector. :param data: Input ``data`` 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 closed: Input ``closed`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python unit_dxy `View current source, line 123 <../source-code/utilities.html#utilities-123>`_. get_major_axis_line_coordinates ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_major_axis_line_coordinates(masks) Get major axis line coordinates. :param masks: Input ``masks`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python line_coordinates `View current source, line 138 <../source-code/utilities.html#utilities-138>`_. extract_skeleton ~~~~~~~~~~~~~~~~ .. py:function:: extract_skeleton(masks) Extract skeleton. :param masks: Input ``masks`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python smoothed_skel get_major_axis_line_coordinates(masks) `View current source, line 174 <../source-code/utilities.html#utilities-174>`_. find_poles ~~~~~~~~~~ .. py:function:: find_poles(smoothed_skeleton, smoothed_contour, find_pole1=True, find_pole2=True) Find poles. :param smoothed_skeleton: Input ``smoothed_skeleton`` 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 smoothed_contour: Input ``smoothed_contour`` 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 find_pole1: Input ``find_pole1`` 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 find_pole2: Input ``find_pole2`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (extended_pole1, extended_pole2, trimmed_midline) `View current source, line 215 <../source-code/utilities.html#utilities-215>`_. extend_skeleton ~~~~~~~~~~~~~~~ .. py:function:: extend_skeleton(smoothed_skeleton, smoothed_contour, find_pole1=True, find_pole2=True) Extend skeleton. :param smoothed_skeleton: Input ``smoothed_skeleton`` 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 smoothed_contour: Input ``smoothed_contour`` 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 find_pole1: Input ``find_pole1`` 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 find_pole2: Input ``find_pole2`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (extended_skeleton, new_pole1, new_pole2) `View current source, line 266 <../source-code/utilities.html#utilities-266>`_. straighten_by_orthogonal_lines ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: straighten_by_orthogonal_lines(contour, midline, length, width, unit_micron=0.5) Straighten by orthogonal lines. :param contour: Boundary points in (row, column) pixel coordinates. :param midline: Central-axis points in (row, column) pixel coordinates. :param length: Input ``length`` 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 width: Input ``width`` 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 unit_micron: Input ``unit_micron`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (l1, l2, profile_mesh, midline) `View current source, line 285 <../source-code/utilities.html#utilities-285>`_. radial_intensities ~~~~~~~~~~~~~~~~~~ .. py:function:: radial_intensities(cropped_signal_interp2d, contour, width, min_val, max_val, num_erosions, erosion_scale=None) Radial intensities. :param cropped_signal_interp2d: Input ``cropped_signal_interp2d`` 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 contour: Boundary points in (row, column) pixel coordinates. :param width: Input ``width`` 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 min_val: Input ``min_val`` 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 max_val: Input ``max_val`` 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 num_erosions: Input ``num_erosions`` 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 erosion_scale: Input ``erosion_scale`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python intensities_per_mesh `View current source, line 314 <../source-code/utilities.html#utilities-314>`_. spline_approximation ~~~~~~~~~~~~~~~~~~~~ .. py:function:: spline_approximation(init_contour, n=200, smooth_factor=1, closed=True) Spline approximation. :param init_contour: Input ``init_contour`` 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 n: Selected image positions; wrapper accepts None for all. Indices must be nonempty, unique valid integers. :param smooth_factor: Input ``smooth_factor`` 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 closed: Input ``closed`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python np.array([x_new, y_new]).T `View current source, line 348 <../source-code/utilities.html#utilities-348>`_. divide_contour_by_midline ~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: divide_contour_by_midline(midline, contour) Divide contour by midline. :param midline: Central-axis points in (row, column) pixel coordinates. :param contour: Boundary points in (row, column) pixel coordinates. **Return expressions in source:** .. code-block:: python (half_contour_1, half_contour_2) **Explicitly raised exceptions:** ``ValueError``. Errors from called functions can also propagate or be recorded. `View current source, line 359 <../source-code/utilities.html#utilities-359>`_. distance_matrix ~~~~~~~~~~~~~~~ .. py:function:: distance_matrix(data1, data2) Distance matrix. :param data1: Input ``data1`` 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 data2: Input ``data2`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python dxy `View current source, line 396 <../source-code/utilities.html#utilities-396>`_. orthogonal_intersection_point ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: orthogonal_intersection_point(midline, outerline, precomputed_orthogonal_vector=None, min_dist=1e-100) Orthogonal intersection point. :param midline: Central-axis points in (row, column) pixel coordinates. :param outerline: Input ``outerline`` 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 precomputed_orthogonal_vector: Input ``precomputed_orthogonal_vector`` 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 min_dist: Input ``min_dist`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python pos_list `View current source, line 406 <../source-code/utilities.html#utilities-406>`_. intersect_matrix ~~~~~~~~~~~~~~~~ .. py:function:: intersect_matrix(line, contour, orthogonal_vectors=None) Intersect matrix. :param line: Input ``line`` 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 contour: Boundary points in (row, column) pixel coordinates. :param orthogonal_vectors: Input ``orthogonal_vectors`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (intersect_x, intersect_y) `View current source, line 446 <../source-code/utilities.html#utilities-446>`_. add_poles ~~~~~~~~~ .. py:function:: add_poles(coords1, coords2, pole1, pole2) Add poles. :param coords1: Input ``coords1`` 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 coords2: Input ``coords2`` 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 pole1: Input ``pole1`` 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 pole2: Input ``pole2`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (result, coords1, coords2) `View current source, line 476 <../source-code/utilities.html#utilities-476>`_. line_length ~~~~~~~~~~~ .. py:function:: line_length(line) Line length. :param line: Input ``line`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python np.sum(np.sqrt(np.sum(d ** 2, axis=1))) `View current source, line 486 <../source-code/utilities.html#utilities-486>`_. direct_intersect_distance ~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: direct_intersect_distance(skeleton, contour) Direct intersect distance. :param skeleton: Input ``skeleton`` 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 contour: Boundary points in (row, column) pixel coordinates. **Return expressions in source:** .. code-block:: python np.concatenate([[0], dists, [0]]) `View current source, line 494 <../source-code/utilities.html#utilities-494>`_. contour2mesh ~~~~~~~~~~~~ .. py:function:: contour2mesh(contour, cropped_mask) Contour2mesh. :param contour: Boundary points in (row, column) pixel coordinates. :param cropped_mask: Input ``cropped_mask`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python ([], [], []) (contour, result, midline) `View current source, line 522 <../source-code/utilities.html#utilities-522>`_. draw_mask ~~~~~~~~~ .. py:function:: draw_mask(contour, image) Draw mask. :param contour: Boundary points in (row, column) pixel coordinates. :param image: Input ``image`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python mask_dilated `View current source, line 548 <../source-code/utilities.html#utilities-548>`_. crop_image ~~~~~~~~~~ .. py:function:: crop_image(image=None, contour=None, mask_to_crop=None, phase_img=None, pad=10) Crop image. :param image: Input ``image`` 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 contour: Boundary points in (row, column) pixel coordinates. :param mask_to_crop: Input ``mask_to_crop`` 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 phase_img: Input ``phase_img`` 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 pad: Input ``pad`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (cropped_img, cropped_mask, cropped_contour, x, y) `View current source, line 554 <../source-code/utilities.html#utilities-554>`_. crop ~~~~ .. py:function:: crop(to_be_cropped, pad, image, xy_coordinates=False) Crop. :param to_be_cropped: Input ``to_be_cropped`` 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 pad: Input ``pad`` 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 image: Input ``image`` 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 xy_coordinates: Input ``xy_coordinates`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (x, y, w, h) `View current source, line 585 <../source-code/utilities.html#utilities-585>`_. get_object_contours ~~~~~~~~~~~~~~~~~~~ .. py:function:: get_object_contours(mask, smoothing=0.1) Get object contours. :param mask: Input ``mask`` 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 smoothing: Smoothing passed to the contour/mesh fitting path. **Return expressions in source:** .. code-block:: python interpolated_contours `View current source, line 606 <../source-code/utilities.html#utilities-606>`_. maybe_reverse_orientation ~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: maybe_reverse_orientation(contour, result, midline) Maybe reverse orientation. :param contour: Boundary points in (row, column) pixel coordinates. :param result: Input ``result`` 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 midline: Central-axis points in (row, column) pixel coordinates. **Return expressions in source:** .. code-block:: python (contour, result, midline) `View current source, line 627 <../source-code/utilities.html#utilities-627>`_. get_label_neighbor_counts ~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_label_neighbor_counts(labels, connectivity=1) Get label neighbor counts. :param labels: 2D integer label mask with zero background. :param connectivity: Touching-label neighborhood: 1/4 for edges, 2/8 including diagonals. **Return expressions in source:** .. code-block:: python {label: len(neighbors) for label, neighbors in neighbor_map.items()} **Explicitly raised exceptions:** ``ValueError``. Errors from called functions can also propagate or be recorded. `View current source, line 650 <../source-code/utilities.html#utilities-650>`_. filter_labels_by_neighbor_count ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: filter_labels_by_neighbor_count(labels, max_neighbors, connectivity=1) Filter labels by neighbor count. :param labels: 2D integer label mask with zero background. :param max_neighbors: Remove labels whose distinct touching-label count is greater than this limit. :param connectivity: Touching-label neighborhood: 1/4 for edges, 2/8 including diagonals. **Return expressions in source:** .. code-block:: python (relabeled, stats) **Explicitly raised exceptions:** ``ValueError``. Errors from called functions can also propagate or be recorded. `View current source, line 687 <../source-code/utilities.html#utilities-687>`_. get_cellular_mesh ~~~~~~~~~~~~~~~~~ .. py:function:: get_cellular_mesh(masks, smoothing) Get cellular mesh. :param masks: Input ``masks`` 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 smoothing: Smoothing passed to the contour/mesh fitting path. **Return expressions in source:** .. code-block:: python meshdataframe `View current source, line 730 <../source-code/utilities.html#utilities-730>`_. distance ~~~~~~~~ .. py:function:: distance(v1, v2) Distance. :param v1: Input ``v1`` 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 v2: Input ``v2`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python np.sqrt(np.sum((np.array(v1) - np.array(v2)) ** 2)) `View current source, line 764 <../source-code/utilities.html#utilities-764>`_. measure_width ~~~~~~~~~~~~~ .. py:function:: measure_width(extended_skeleton, smoothed_contour) Measure width. :param extended_skeleton: Input ``extended_skeleton`` 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 smoothed_contour: Input ``smoothed_contour`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (np.array([0] + width_list + [0]), length) **Explicitly raised exceptions:** ``ValueError``. Errors from called functions can also propagate or be recorded. `View current source, line 770 <../source-code/utilities.html#utilities-770>`_. get_cell_pairs ~~~~~~~~~~~~~~ .. py:function:: get_cell_pairs(pole_1, pole_2, cell_ID, maxdist=None) Get cell pairs. :param pole_1: Input ``pole_1`` 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 pole_2: Input ``pole_2`` 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 cell_ID: Input ``cell_ID`` 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 maxdist: Input ``maxdist`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python unique_nc2 `View current source, line 788 <../source-code/utilities.html#utilities-788>`_. mesh2contour ~~~~~~~~~~~~ .. py:function:: mesh2contour(x1, y1, x2, y2) Mesh2contour. :param x1: Input ``x1`` 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 y1: Input ``y1`` 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 x2: Input ``x2`` 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 y2: Input ``y2`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python np.array([outx, outy]).T `View current source, line 891 <../source-code/utilities.html#utilities-891>`_. split_point ~~~~~~~~~~~ .. py:function:: split_point(x1, y1, x2, y2, ctpos) Split point. :param x1: Input ``x1`` 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 y1: Input ``y1`` 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 x2: Input ``x2`` 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 y2: Input ``y2`` 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 ctpos: Input ``ctpos`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (newpole_x, newpole_y, np.array([[xt13, yt13, xt23, yt23]]), np.array([[xs13, ys13, xs23, ys23]])) `View current source, line 905 <../source-code/utilities.html#utilities-905>`_. constr_degree_single_cell_min ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: constr_degree_single_cell_min(intensity, new_step_length, upper_limit=0.75, lower_limit=0.25, interp_factor=10) Compute constriction degree and return both coarse and fine minima positions. :param intensity: 1D intensity profile. :param new_step_length: Currently unused here, kept for API compatibility. :param upper_limit: Upper bound of region to search, as fraction of profile length. :param lower_limit: Lower bound of region to search, as fraction of profile length. :param interp_factor: Upsampling factor for fine-scale interpolation. **Return expressions in source:** .. code-block:: python (minsize, ctposr, minsizeabs, ctpos_coarse, ctpos_fine) `View current source, line 953 <../source-code/utilities.html#utilities-953>`_. .. raw:: html
Original docstring (legacy wording may differ from the current signature) .. code-block:: text Compute constriction degree and return both coarse and fine minima positions. Parameters ---------- intensity : array-like 1D intensity profile. new_step_length : array-like Currently unused here, kept for API compatibility. upper_limit : float, optional Upper bound of region to search, as fraction of profile length. lower_limit : float, optional Lower bound of region to search, as fraction of profile length. interp_factor : int, optional Upsampling factor for fine-scale interpolation. Returns ------- minsize : float Relative constriction degree. ctposr : float Relative position of the constriction in [0, 1]. minsizeabs : float Absolute constriction depth. ctpos_coarse : int or list Constriction position in original intensity index space. ctpos_fine : int or list Constriction position in interpolated fine index space. .. raw:: html
interp2d ~~~~~~~~ .. py:function:: interp2d(image) Interp2d. :param image: Input ``image`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python ff `View current source, line 1059 <../source-code/utilities.html#utilities-1059>`_. get_image_for_frame ~~~~~~~~~~~~~~~~~~~ .. py:function:: get_image_for_frame(df_nr, images) Get image for frame. :param df_nr: Input ``df_nr`` 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 images: Input ``images`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python images[df_nr] `View current source, line 1066 <../source-code/utilities.html#utilities-1066>`_. get_cell_mask ~~~~~~~~~~~~~ .. py:function:: get_cell_mask(contour, midline, image) Get cell mask. :param contour: Boundary points in (row, column) pixel coordinates. :param midline: Central-axis points in (row, column) pixel coordinates. :param image: Input ``image`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (mask, cropped_img, cropped_contour, cropped_midline, x, y) `View current source, line 1070 <../source-code/utilities.html#utilities-1070>`_. keep_significant_masks ~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: keep_significant_masks(nucleoid_mask, cropped_mask, min_overlap_ratio=0.01, max_external_ratio=0.1) Keep significant masks. :param nucleoid_mask: Input ``nucleoid_mask`` 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 cropped_mask: Input ``cropped_mask`` 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 min_overlap_ratio: Minimum accepted overlap ratio under the utility implementation; inspect its denominator in source. :param max_external_ratio: Maximum accepted outside-cell ratio under the utility implementation. **Return expressions in source:** .. code-block:: python significant_mask `View current source, line 1081 <../source-code/utilities.html#utilities-1081>`_. get_object_masks ~~~~~~~~~~~~~~~~ .. py:function:: get_object_masks(contour, object_contours, object_midlines, object_meshes, signal) Get object masks. :param contour: Boundary points in (row, column) pixel coordinates. :param object_contours: Input ``object_contours`` 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 object_midlines: Input ``object_midlines`` 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 object_meshes: Input ``object_meshes`` 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 signal: Input ``signal`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (masks, cropped_img, cropped_object_contours, cropped_object_midlines, cropped_object_meshes, x, y) `View current source, line 1116 <../source-code/utilities.html#utilities-1116>`_. get_subcellular_objects ~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_subcellular_objects(contour, signal, image, cell_id, smoothing, log_sigma, kernel_width, min_overlap_ratio=0.01, max_external_ratio=0.1) Get subcellular objects. :param contour: Boundary points in (row, column) pixel coordinates. :param signal: Input ``signal`` 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 image: Input ``image`` 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 cell_id: Cell identifier local to the selected image; check that it remains after curation/filtering. :param smoothing: Smoothing passed to the contour/mesh fitting path. :param log_sigma: Laplacian-of-Gaussian sigma for signal-object detection. :param kernel_width: Width of the square dilation kernel used for candidate object masks. :param min_overlap_ratio: Minimum accepted overlap ratio under the utility implementation; inspect its denominator in source. :param max_external_ratio: Maximum accepted outside-cell ratio under the utility implementation. **Return expressions in source:** .. code-block:: python (object_contours, cropped_img, object_mask, x_offset, y_offset) `View current source, line 1141 <../source-code/utilities.html#utilities-1141>`_. get_object_mesh ~~~~~~~~~~~~~~~ .. py:function:: get_object_mesh(contour, signal, image, cell_id, smoothing, log_sigma, kernel_width, min_overlap_ratio, max_external_ratio) Get object mesh. :param contour: Boundary points in (row, column) pixel coordinates. :param signal: Input ``signal`` 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 image: Input ``image`` 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 cell_id: Cell identifier local to the selected image; check that it remains after curation/filtering. :param smoothing: Smoothing passed to the contour/mesh fitting path. :param log_sigma: Laplacian-of-Gaussian sigma for signal-object detection. :param kernel_width: Width of the square dilation kernel used for candidate object masks. :param min_overlap_ratio: Minimum accepted overlap ratio under the utility implementation; inspect its denominator in source. :param max_external_ratio: Maximum accepted outside-cell ratio under the utility implementation. **Return expressions in source:** .. code-block:: python meshdata `View current source, line 1188 <../source-code/utilities.html#utilities-1188>`_. image_field_key ~~~~~~~~~~~~~~~ .. py:function:: image_field_key(filename, suffix='', is_mask=False) Return a normalized acquisition/field key from a TIFF filename. :param filename: Input ``filename`` 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 suffix: Input ``suffix`` 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 is_mask: Input ``is_mask`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python stem.strip().casefold() `View current source, line 1255 <../source-code/utilities.html#utilities-1255>`_. .. raw:: html
Original docstring (legacy wording may differ from the current signature) .. code-block:: text Return a normalized acquisition/field key from a TIFF filename. Channel suffixes such as ``C1``/``C2`` and mask suffixes such as ``cp_masks`` are removed so corresponding files can be matched by field. .. raw:: html
read_channels ~~~~~~~~~~~~~ .. py:function:: read_channels(folder_path, images_dict, channel_list=None) Read channels. :param folder_path: Input ``folder_path`` 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 images_dict: Input ``images_dict`` 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 channel_list: Sequence of channel suffixes to load or attach. **Return expressions in source:** .. code-block:: python images_dict **Explicitly raised exceptions:** ``ValueError``. Errors from called functions can also propagate or be recorded. `View current source, line 1280 <../source-code/utilities.html#utilities-1280>`_. read_tiff_folder ~~~~~~~~~~~~~~~~ .. py:function:: read_tiff_folder(folder_path, suffix='', include_paths=False) Read tiff folder. :param folder_path: Input ``folder_path`` 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 suffix: Input ``suffix`` 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 include_paths: Input ``include_paths`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (images, file_names, paths) (images, file_names) **Explicitly raised exceptions:** ``ValueError``. Errors from called functions can also propagate or be recorded. `View current source, line 1312 <../source-code/utilities.html#utilities-1312>`_. separate_meshdata ~~~~~~~~~~~~~~~~~ .. py:function:: separate_meshdata(df_nr, cell_nr, data) Separate meshdata. :param df_nr: Input ``df_nr`` 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 cell_nr: Input ``cell_nr`` 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 data: Input ``data`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (x1, y1, x2, y2, contour) `View current source, line 1353 <../source-code/utilities.html#utilities-1353>`_. separate_singleframe_meshdata ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: separate_singleframe_meshdata(cell_id, data) Separate singleframe meshdata. :param cell_id: Cell identifier local to the selected image; check that it remains after curation/filtering. :param data: Input ``data`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (x1, y1, x2, y2, contour, midline) `View current source, line 1362 <../source-code/utilities.html#utilities-1362>`_. get_cropped_object_data ~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_cropped_object_data(cnts, mdls, mshs, x, y) Get cropped object data. :param cnts: Input ``cnts`` 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 mdls: Input ``mdls`` 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 mshs: Input ``mshs`` 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 x: Input ``x`` 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 y: Input ``y`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (cropped_cnts, cropped_mdls, cropped_mshs) `View current source, line 1373 <../source-code/utilities.html#utilities-1373>`_. get_cropped_cell_data ~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_cropped_cell_data(cnt, mdl, msh, x, y) Get cropped cell data. :param cnt: Input ``cnt`` 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 mdl: Input ``mdl`` 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 msh: Input ``msh`` 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 x: Input ``x`` 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 y: Input ``y`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (cropped_cn, cropped_ml, cropped_msh) `View current source, line 1396 <../source-code/utilities.html#utilities-1396>`_. get_uncropped_cell_data ~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_uncropped_cell_data(cnt, mdl, msh, x, y) Get uncropped cell data. :param cnt: Input ``cnt`` 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 mdl: Input ``mdl`` 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 msh: Input ``msh`` 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 x: Input ``x`` 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 y: Input ``y`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (uncropped_cn, uncropped_ml, uncropped_msh) `View current source, line 1408 <../source-code/utilities.html#utilities-1408>`_. mesh2midline ~~~~~~~~~~~~ .. py:function:: mesh2midline(x1, y1, x2, y2) Mesh2midline. :param x1: Input ``x1`` 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 y1: Input ``y1`` 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 x2: Input ``x2`` 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 y2: Input ``y2`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python line `View current source, line 1420 <../source-code/utilities.html#utilities-1420>`_. get_weighted_intprofile ~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_weighted_intprofile(intensity, width) Get weighted intprofile. :param intensity: Input ``intensity`` 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 width: Input ``width`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python intensity * width [] `View current source, line 1428 <../source-code/utilities.html#utilities-1428>`_. get_width ~~~~~~~~~ .. py:function:: get_width(x1, y1, x2, y2) Get width. :param x1: Input ``x1`` 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 y1: Input ``y1`` 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 x2: Input ``x2`` 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 y2: Input ``y2`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python width_not_ordered `View current source, line 1437 <../source-code/utilities.html#utilities-1437>`_. split_mesh2mesh ~~~~~~~~~~~~~~~ .. py:function:: split_mesh2mesh(x1, y1, x2, y2, max_daughter_cell_mesh_rows=800) Rebuild a daughter, rejecting oversized resampling before allocation. :param x1: Input ``x1`` 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 y1: Input ``y1`` 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 x2: Input ``x2`` 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 y2: Input ``y2`` 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 max_daughter_cell_mesh_rows: Maximum rebuilt mesh rows per daughter during cell splitting (default 800; integer >= 4). Rejects oversized predicted counts before reconstruction; both final daughters must have 4..limit rows. Does not limit unsplit parents and is separate from feature extraction max_mesh_size. **Return expressions in source:** .. code-block:: python (result, contour, midline) (np.empty((0, 4)), np.empty((0, 2)), np.empty((0, 2))) `View current source, line 1452 <../source-code/utilities.html#utilities-1452>`_. .. raw:: html
Original docstring (legacy wording may differ from the current signature) .. code-block:: text Rebuild a daughter, rejecting oversized resampling before allocation. The limit applies to straightened rows here and to final daughter rows in Image.split_cells. Pole extension can add rows, so the minimum stays there. .. raw:: html
get_profile_mesh ~~~~~~~~~~~~~~~~ .. py:function:: get_profile_mesh(mesh, width, micron_unit=1) Get profile mesh. :param mesh: Paired-boundary geometry with four columns in pixel coordinates. :param width: Input ``width`` 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 micron_unit: Input ``micron_unit`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python profile_mesh `View current source, line 1493 <../source-code/utilities.html#utilities-1493>`_. expand_contour ~~~~~~~~~~~~~~ .. py:function:: expand_contour(contour, scale=1) enlarges contour :param contour: :param scale: :return: :param contour: Boundary points in (row, column) pixel coordinates. :param scale: Input ``scale`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python contour - scale * dxy `View current source, line 1510 <../source-code/utilities.html#utilities-1510>`_. .. raw:: html
Original docstring (legacy wording may differ from the current signature) .. code-block:: text enlarges contour :param contour: :param scale: :return: .. raw:: html
erode_contour ~~~~~~~~~~~~~ .. py:function:: erode_contour(contour, scale=1) shrinks contour :param contour: :param scale: :return: :param contour: Boundary points in (row, column) pixel coordinates. :param scale: Input ``scale`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python contour + scale * dxy `View current source, line 1529 <../source-code/utilities.html#utilities-1529>`_. .. raw:: html
Original docstring (legacy wording may differ from the current signature) .. code-block:: text shrinks contour :param contour: :param scale: :return: .. raw:: html
mean_background ~~~~~~~~~~~~~~~ .. py:function:: mean_background(image, cell_mask) Mean background. :param image: Input ``image`` 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 cell_mask: Input ``cell_mask`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python bgr `View current source, line 1552 <../source-code/utilities.html#utilities-1552>`_. median_background ~~~~~~~~~~~~~~~~~ .. py:function:: median_background(image, cell_mask) Median background. :param image: Input ``image`` 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 cell_mask: Input ``cell_mask`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python bgr `View current source, line 1563 <../source-code/utilities.html#utilities-1563>`_. poly_func ~~~~~~~~~ .. py:function:: poly_func(coords, a, b, c, d, e, f) Poly func. :param coords: Input ``coords`` 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 a: Input ``a`` 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 b: Input ``b`` 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 c: Input ``c`` 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 d: Input ``d`` 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 e: Input ``e`` 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 f: Input ``f`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python a + b * x + c * y + d * x ** 2 + e * x * y + f * y ** 2 `View current source, line 1574 <../source-code/utilities.html#utilities-1574>`_. construct_bg_function ~~~~~~~~~~~~~~~~~~~~~ .. py:function:: construct_bg_function(image, seg_mat, sampling_interval=None, plotF=False) Reconstructs the background of an image using 2D polynomial fitting. :param image: seg\_mat (ndarray): Binary segmentation mask (non-zero = foreground). sampling\_interval (int): Interval between samples. Default: height // 64. plotF (bool): Whether to plot the background fit. :param seg_mat: sampling\_interval (int): Interval between samples. Default: height // 64. plotF (bool): Whether to plot the background fit. :param sampling_interval: plotF (bool): Whether to plot the background fit. :param plotF: Whether to plot the background fit. **Return expressions in source:** .. code-block:: python (bg_function, bg_matrix) `View current source, line 1579 <../source-code/utilities.html#utilities-1579>`_. .. raw:: html
Original docstring (legacy wording may differ from the current signature) .. code-block:: text Reconstructs the background of an image using 2D polynomial fitting. Parameters: image (ndarray): Input grayscale image. seg_mat (ndarray): Binary segmentation mask (non-zero = foreground). sampling_interval (int): Interval between samples. Default: height // 64. plotF (bool): Whether to plot the background fit. Returns: bg_function (function): Background function F(x, y). bg_matrix (ndarray): Estimated background image. .. raw:: html
get_step_length ~~~~~~~~~~~~~~~ .. py:function:: get_step_length(x1, y1, x2, y2, px) Get step length. :param x1: Input ``x1`` 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 y1: Input ``y1`` 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 x2: Input ``x2`` 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 y2: Input ``y2`` 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 px: Micrometres per pixel. Geometry arrays remain in pixel coordinates. **Return expressions in source:** .. code-block:: python np.sqrt(dx ** 2 + dy ** 2) / 2 * px `View current source, line 1638 <../source-code/utilities.html#utilities-1638>`_. get_step_length_no_px ~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_step_length_no_px(x1, y1, x2, y2) Get step length no px. :param x1: Input ``x1`` 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 y1: Input ``y1`` 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 x2: Input ``x2`` 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 y2: Input ``y2`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python np.sqrt(dx ** 2 + dy ** 2) / 2 `View current source, line 1644 <../source-code/utilities.html#utilities-1644>`_. get_length ~~~~~~~~~~ .. py:function:: get_length(step_length) Get length. :param step_length: Input ``step_length`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python np.sum(step_length) `View current source, line 1650 <../source-code/utilities.html#utilities-1650>`_. get_avg_width ~~~~~~~~~~~~~ .. py:function:: get_avg_width(x1, y1, x2, y2, px) Get avg width. :param x1: Input ``x1`` 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 y1: Input ``y1`` 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 x2: Input ``x2`` 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 y2: Input ``y2`` 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 px: Micrometres per pixel. Geometry arrays remain in pixel coordinates. **Return expressions in source:** .. code-block:: python (width * px, width_not_ordered * px) `View current source, line 1654 <../source-code/utilities.html#utilities-1654>`_. get_avg_width_no_px ~~~~~~~~~~~~~~~~~~~ .. py:function:: get_avg_width_no_px(x1, y1, x2, y2) Get avg width no px. :param x1: Input ``x1`` 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 y1: Input ``y1`` 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 x2: Input ``x2`` 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 y2: Input ``y2`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (width, width_not_ordered) `View current source, line 1663 <../source-code/utilities.html#utilities-1663>`_. get_area ~~~~~~~~ .. py:function:: get_area(contour, px) Get area. :param contour: Boundary points in (row, column) pixel coordinates. :param px: Micrometres per pixel. Geometry arrays remain in pixel coordinates. **Return expressions in source:** .. code-block:: python area * px * px `View current source, line 1672 <../source-code/utilities.html#utilities-1672>`_. get_volume ~~~~~~~~~~ .. py:function:: get_volume(x1, y1, x2, y2, step_length, px) Get volume. :param x1: Input ``x1`` 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 y1: Input ``y1`` 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 x2: Input ``x2`` 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 y2: Input ``y2`` 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 step_length: Input ``step_length`` 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 px: Micrometres per pixel. Geometry arrays remain in pixel coordinates. **Return expressions in source:** .. code-block:: python volume * px * px `View current source, line 1678 <../source-code/utilities.html#utilities-1678>`_. get_surface_area ~~~~~~~~~~~~~~~~ .. py:function:: get_surface_area(width_no, step_length) Get surface area. :param width_no: Input ``width_no`` 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 step_length: Input ``step_length`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python total_surface_area `View current source, line 1684 <../source-code/utilities.html#utilities-1684>`_. get_surface_area_over_volume ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_surface_area_over_volume(sa, vol) Get surface area over volume. :param sa: Input ``sa`` 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 vol: Input ``vol`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python sa / vol `View current source, line 1691 <../source-code/utilities.html#utilities-1691>`_. get_cell_perimeter_measurements ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_cell_perimeter_measurements(contour, area, px) Get cell perimeter measurements. :param contour: Boundary points in (row, column) pixel coordinates. :param area: Input ``area`` 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 px: Micrometres per pixel. Geometry arrays remain in pixel coordinates. **Return expressions in source:** .. code-block:: python (perimeter, circularity, compactness, sphericity) `View current source, line 1695 <../source-code/utilities.html#utilities-1695>`_. get_cell_width_variability ~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_cell_width_variability(width_no) Get cell width variability. :param width_no: Input ``width_no`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python width_var `View current source, line 1707 <../source-code/utilities.html#utilities-1707>`_. get_curvature_characteristics ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_curvature_characteristics(contour, px) Get curvature characteristics. :param contour: Boundary points in (row, column) pixel coordinates. :param px: Micrometres per pixel. Geometry arrays remain in pixel coordinates. **Return expressions in source:** .. code-block:: python (curvature, max_c, min_c, mean_c, std_c) `View current source, line 1715 <../source-code/utilities.html#utilities-1715>`_. get_total_phaco_intensity ~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_total_phaco_intensity(contour, shape, interp2d) Get total phaco intensity. :param contour: Boundary points in (row, column) pixel coordinates. :param shape: Input ``shape`` 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 interp2d: Input ``interp2d`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (np.sum(values), np.max(values), np.mean(values)) `View current source, line 1728 <../source-code/utilities.html#utilities-1728>`_. get_contour_intensity ~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_contour_intensity(contour, interp2d) Get contour intensity. :param contour: Boundary points in (row, column) pixel coordinates. :param interp2d: Input ``interp2d`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python data `View current source, line 1737 <../source-code/utilities.html#utilities-1737>`_. find_signal_peaks ~~~~~~~~~~~~~~~~~ .. py:function:: find_signal_peaks(signal, maximum) Find signal peaks. :param signal: Input ``signal`` 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 maximum: Input ``maximum`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python len(peaks) `View current source, line 1742 <../source-code/utilities.html#utilities-1742>`_. measure_contour_variability ~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: measure_contour_variability(signal) Measure contour variability. :param signal: Input ``signal`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python contour_intensities_variability `View current source, line 1747 <../source-code/utilities.html#utilities-1747>`_. get_kurtosis ~~~~~~~~~~~~ .. py:function:: get_kurtosis(signal) Get kurtosis. :param signal: Input ``signal`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python kurtosis(signal) `View current source, line 1758 <../source-code/utilities.html#utilities-1758>`_. get_skew ~~~~~~~~ .. py:function:: get_skew(signal) Get skew. :param signal: Input ``signal`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python skew(signal) `View current source, line 1762 <../source-code/utilities.html#utilities-1762>`_. sinuosity ~~~~~~~~~ .. py:function:: sinuosity(midline) Sinuosity. :param midline: Central-axis points in (row, column) pixel coordinates. **Return expressions in source:** .. code-block:: python sinuosity **Explicitly raised exceptions:** ``ValueError``. Errors from called functions can also propagate or be recorded. `View current source, line 1766 <../source-code/utilities.html#utilities-1766>`_. get_area_asymmetry ~~~~~~~~~~~~~~~~~~ .. py:function:: get_area_asymmetry(step_length, width_no) Get area asymmetry. :param step_length: Input ``step_length`` 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 width_no: Input ``width_no`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python asymmetry_ratio 1.0 `View current source, line 1780 <../source-code/utilities.html#utilities-1780>`_. get_object_params ~~~~~~~~~~~~~~~~~ .. py:function:: get_object_params(object_contours, px) Get object params. :param object_contours: Input ``object_contours`` 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 px: Micrometres per pixel. Geometry arrays remain in pixel coordinates. **Return expressions in source:** .. code-block:: python (total_length, average_width) `View current source, line 1801 <../source-code/utilities.html#utilities-1801>`_. get_object_width_variability ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_object_width_variability(widths_no) Get object width variability. :param widths_no: Input ``widths_no`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (width_var_list, avg_width_var) `View current source, line 1820 <../source-code/utilities.html#utilities-1820>`_. get_mesh_coordinates ~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_mesh_coordinates(mesh) Get mesh coordinates. :param mesh: Paired-boundary geometry with four columns in pixel coordinates. **Return expressions in source:** .. code-block:: python (x1, y1, x2, y2) `View current source, line 1833 <../source-code/utilities.html#utilities-1833>`_. get_object_rect_length ~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_object_rect_length(nucleoid_contours, px) Get object rect length. :param nucleoid_contours: Input ``nucleoid_contours`` 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 px: Micrometres per pixel. Geometry arrays remain in pixel coordinates. **Return expressions in source:** .. code-block:: python (rect_length_list, rect_width_list, total_rect_length, average_rect_width) `View current source, line 1841 <../source-code/utilities.html#utilities-1841>`_. get_additional_regionprops_features ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_additional_regionprops_features(mask, px) Get additional regionprops features. :param mask: Input ``mask`` 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 px: Micrometres per pixel. Geometry arrays remain in pixel coordinates. **Return expressions in source:** .. code-block:: python features `View current source, line 1891 <../source-code/utilities.html#utilities-1891>`_. get_object_avg_width ~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_object_avg_width(nucleoid_masks, px) Get object avg width. :param nucleoid_masks: Input ``nucleoid_masks`` 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 px: Micrometres per pixel. Geometry arrays remain in pixel coordinates. **Return expressions in source:** .. code-block:: python (np.mean(nucleoid_avg_width_list), width_not_ordered_list) `View current source, line 1944 <../source-code/utilities.html#utilities-1944>`_. get_object_aspect_ratio ~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_object_aspect_ratio(rect_length_lists, rect_width_lists) Get object aspect ratio. :param rect_length_lists: Input ``rect_length_lists`` 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 rect_width_lists: Input ``rect_width_lists`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (aspect_ratio_list, avg_aspect_ratio) `View current source, line 1967 <../source-code/utilities.html#utilities-1967>`_. get_object_area ~~~~~~~~~~~~~~~ .. py:function:: get_object_area(contours, px) Get object area. :param contours: Input ``contours`` 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 px: Micrometres per pixel. Geometry arrays remain in pixel coordinates. **Return expressions in source:** .. code-block:: python (area_list, total_area) `View current source, line 1979 <../source-code/utilities.html#utilities-1979>`_. get_object_curvature_characteristics ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_object_curvature_characteristics(contours, px) Get object curvature characteristics. :param contours: Input ``contours`` 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 px: Micrometres per pixel. Geometry arrays remain in pixel coordinates. **Return expressions in source:** .. code-block:: python (curvatures, max_c_list, min_c_list, mean_c_list, std_c_list, avg_mean_c, avg_std_c) `View current source, line 1992 <../source-code/utilities.html#utilities-1992>`_. get_object_perimeter_measurements ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_object_perimeter_measurements(contours, areas, px) Get object perimeter measurements. :param contours: Input ``contours`` 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 areas: Input ``areas`` 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 px: Micrometres per pixel. Geometry arrays remain in pixel coordinates. **Return expressions in source:** .. code-block:: python (perimeter_list, circularity_list, compactness_list, sphericity_list, avg_perimeter, avg_circularity, avg_compactness, avg_sphericity) `View current source, line 2024 <../source-code/utilities.html#utilities-2024>`_. get_cell_convexity ~~~~~~~~~~~~~~~~~~ .. py:function:: get_cell_convexity(mask) Get cell convexity. :param mask: Input ``mask`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (image_eccentricity, image_solidity, convexity) `View current source, line 2057 <../source-code/utilities.html#utilities-2057>`_. get_object_convexity ~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_object_convexity(cropped_masks) Get object convexity. :param cropped_masks: Input ``cropped_masks`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (convexity_list, eccentricity_list, solidity_list, avg_convexity, avg_eccentricity, avg_solidity) `View current source, line 2072 <../source-code/utilities.html#utilities-2072>`_. get_approx_nucleoid_volume ~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_approx_nucleoid_volume(cell_volume, nucleoid_areas, cell_area) Get approx nucleoid volume. :param cell_volume: Input ``cell_volume`` 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 nucleoid_areas: Input ``nucleoid_areas`` 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 cell_area: Input ``cell_area`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (nucleoid_volume_list, total_volume) `View current source, line 2102 <../source-code/utilities.html#utilities-2102>`_. get_nucleoid_width_variability ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_nucleoid_width_variability(widths) Get nucleoid width variability. :param widths: Input ``widths`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (width_var_list, avg_width_var) `View current source, line 2116 <../source-code/utilities.html#utilities-2116>`_. get_obj_mesh_coords ~~~~~~~~~~~~~~~~~~~ .. py:function:: get_obj_mesh_coords(nucleoid_meshes) Get obj mesh coords. :param nucleoid_meshes: Input ``nucleoid_meshes`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (x1_list, y1_list, x2_list, y2_list) `View current source, line 2133 <../source-code/utilities.html#utilities-2133>`_. measure_along_objects_midline_interp2d ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: measure_along_objects_midline_interp2d(midlines, im_interp2d, width=7, subpixel=0.5) Measure along objects midline interp2d. :param midlines: Input ``midlines`` 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 im_interp2d: Input ``im_interp2d`` 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 width: Input ``width`` 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 subpixel: Input ``subpixel`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python prf_list `View current source, line 2156 <../source-code/utilities.html#utilities-2156>`_. constr_degree ~~~~~~~~~~~~~ .. py:function:: constr_degree(intensities, new_step_lengths, width_not_ordered) Constr degree. :param intensities: Input ``intensities`` 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 new_step_lengths: Input ``new_step_lengths`` 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 width_not_ordered: Input ``width_not_ordered`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (constrDegree_list, relPos_list, constrDegree_abs_list, ctpos_list, avg_consDegree, avg_abs_consDegree) `View current source, line 2208 <../source-code/utilities.html#utilities-2208>`_. fill_nan_values ~~~~~~~~~~~~~~~ .. py:function:: fill_nan_values(constrDegree_list, constrDegree_abs_list, ctpos_list, relPos_list) Fill nan values. :param constrDegree_list: Input ``constrDegree_list`` 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 constrDegree_abs_list: Input ``constrDegree_abs_list`` 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 ctpos_list: Input ``ctpos_list`` 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 relPos_list: Input ``relPos_list`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. :returns: None (no explicit return statement). `View current source, line 2259 <../source-code/utilities.html#utilities-2259>`_. get_minima ~~~~~~~~~~ .. py:function:: get_minima(weighted_intensity) Get minima. :param weighted_intensity: Input ``weighted_intensity`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python np.concatenate(([False], (weighted_intensity.T[1:-1] < weighted_intensity.T[:-2]) & (weighted_intensity.T[1:-1] < weighted_intensity.T[2:]), [False])) `View current source, line 2266 <../source-code/utilities.html#utilities-2266>`_. identify_minima ~~~~~~~~~~~~~~~ .. py:function:: identify_minima(intensity, minima) Identify minima. :param intensity: Input ``intensity`` 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 minima: Input ``minima`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (index, dh, dhi, hgt) `View current source, line 2277 <../source-code/utilities.html#utilities-2277>`_. assign_values ~~~~~~~~~~~~~ .. py:function:: assign_values(constrDegree_list, constrDegree_abs_list, ctpos_list, relPos_list, minsize, minsizeabs, ctpos, ctposr) Assign values. :param constrDegree_list: Input ``constrDegree_list`` 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 constrDegree_abs_list: Input ``constrDegree_abs_list`` 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 ctpos_list: Input ``ctpos_list`` 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 relPos_list: Input ``relPos_list`` 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 minsize: Minimum accepted segmentation-mask size in pixels. :param minsizeabs: Input ``minsizeabs`` 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 ctpos: Input ``ctpos`` 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 ctposr: Input ``ctposr`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. :returns: None (no explicit return statement). `View current source, line 2294 <../source-code/utilities.html#utilities-2294>`_. get_obj_avg_width ~~~~~~~~~~~~~~~~~ .. py:function:: get_obj_avg_width(x1s, y1s, x2s, y2s, px) Get obj avg width. :param x1s: Input ``x1s`` 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 y1s: Input ``y1s`` 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 x2s: Input ``x2s`` 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 y2s: Input ``y2s`` 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 px: Micrometres per pixel. Geometry arrays remain in pixel coordinates. **Return expressions in source:** .. code-block:: python (width_list, width_not_ordered_list, average_width) `View current source, line 2311 <../source-code/utilities.html#utilities-2311>`_. get_nucleoid_volume ~~~~~~~~~~~~~~~~~~~ .. py:function:: get_nucleoid_volume(x1s, y1s, x2s, y2s, step_lengths, px) Get nucleoid volume. :param x1s: Input ``x1s`` 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 y1s: Input ``y1s`` 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 x2s: Input ``x2s`` 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 y2s: Input ``y2s`` 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 step_lengths: Input ``step_lengths`` 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 px: Micrometres per pixel. Geometry arrays remain in pixel coordinates. **Return expressions in source:** .. code-block:: python (nucleoid_volume_list, total_volume) `View current source, line 2335 <../source-code/utilities.html#utilities-2335>`_. get_object_step_length ~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_object_step_length(x1s, y1s, x2s, y2s, px) Get object step length. :param x1s: Input ``x1s`` 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 y1s: Input ``y1s`` 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 x2s: Input ``x2s`` 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 y2s: Input ``y2s`` 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 px: Micrometres per pixel. Geometry arrays remain in pixel coordinates. **Return expressions in source:** .. code-block:: python (nuc_step_length_list, nuc_length_list) `View current source, line 2349 <../source-code/utilities.html#utilities-2349>`_. get_object_surface_area ~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_object_surface_area(width_nos, step_lengths) Get object surface area. :param width_nos: Input ``width_nos`` 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 step_lengths: Input ``step_lengths`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (sum_surface_area_list, total_surface_area) `View current source, line 2372 <../source-code/utilities.html#utilities-2372>`_. get_object_surface_area_over_volume ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_object_surface_area_over_volume(surface_areas, volumes) Get object surface area over volume. :param surface_areas: Input ``surface_areas`` 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 volumes: Input ``volumes`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (ratio_list, avg_ratio) `View current source, line 2396 <../source-code/utilities.html#utilities-2396>`_. object_bending_energy ~~~~~~~~~~~~~~~~~~~~~ .. py:function:: object_bending_energy(data, px) Simplification of the formula from https://doi.org/10.1016/j.comgeo.2013.09.001 :param data: Input ``data`` 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 px: Micrometres per pixel. Geometry arrays remain in pixel coordinates. **Return expressions in source:** .. code-block:: python (bending_energy_list, avg_bending_energy) `View current source, line 2410 <../source-code/utilities.html#utilities-2410>`_. .. raw:: html
Original docstring (legacy wording may differ from the current signature) .. code-block:: text Simplification of the formula from https://doi.org/10.1016/j.comgeo.2013.09.001 .. raw:: html
bending_energy ~~~~~~~~~~~~~~ .. py:function:: bending_energy(line, curvature, px) Bending energy. :param line: Input ``line`` 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 curvature: Input ``curvature`` 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 px: Micrometres per pixel. Geometry arrays remain in pixel coordinates. **Return expressions in source:** .. code-block:: python np.round(bending_energy, 5) `View current source, line 2426 <../source-code/utilities.html#utilities-2426>`_. midline_midpoint ~~~~~~~~~~~~~~~~ .. py:function:: midline_midpoint(midline) Midline midpoint. :param midline: Central-axis points in (row, column) pixel coordinates. **Return expressions in source:** .. code-block:: python middle_point `View current source, line 2433 <../source-code/utilities.html#utilities-2433>`_. get_object_midpoint ~~~~~~~~~~~~~~~~~~~ .. py:function:: get_object_midpoint(midlines) Get object midpoint. :param midlines: Input ``midlines`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python centroid_coordinates `View current source, line 2439 <../source-code/utilities.html#utilities-2439>`_. get_centroid ~~~~~~~~~~~~ .. py:function:: get_centroid(cropped_masks) Get centroid. :param cropped_masks: Input ``cropped_masks`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python [centroids[0][0], centroids[1][0]] `View current source, line 2447 <../source-code/utilities.html#utilities-2447>`_. get_object_centroid ~~~~~~~~~~~~~~~~~~~ .. py:function:: get_object_centroid(cropped_masks) Get object centroid. :param cropped_masks: Input ``cropped_masks`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python centroid_list `View current source, line 2456 <../source-code/utilities.html#utilities-2456>`_. get_interobject_distance ~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_interobject_distance(centroid_coordinates, px) Get interobject distance. :param centroid_coordinates: Input ``centroid_coordinates`` 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 px: Micrometres per pixel. Geometry arrays remain in pixel coordinates. **Return expressions in source:** .. code-block:: python (average_distance, distances) (np.nan, np.nan) `View current source, line 2467 <../source-code/utilities.html#utilities-2467>`_. get_object_sinuosity ~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_object_sinuosity(midlines) Get object sinuosity. :param midlines: Input ``midlines`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (sinuosity_list, avg_sinuosity) `View current source, line 2480 <../source-code/utilities.html#utilities-2480>`_. get_mesh_area ~~~~~~~~~~~~~ .. py:function:: get_mesh_area(width_no, step_length) Get mesh area. :param width_no: Input ``width_no`` 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 step_length: Input ``step_length`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python mesh_area `View current source, line 2492 <../source-code/utilities.html#utilities-2492>`_. ratio_mesh_over_total_area ~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: ratio_mesh_over_total_area(step_length, width_no, areas) Ratio mesh over total area. :param step_length: Input ``step_length`` 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 width_no: Input ``width_no`` 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 areas: Input ``areas`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python ratio_list `View current source, line 2498 <../source-code/utilities.html#utilities-2498>`_. get_shortest_pole_object_distances ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_shortest_pole_object_distances(pole_coordinates, centroid_coordinates, px) Get shortest pole object distances. :param pole_coordinates: Input ``pole_coordinates`` 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 centroid_coordinates: Input ``centroid_coordinates`` 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 px: Micrometres per pixel. Geometry arrays remain in pixel coordinates. **Return expressions in source:** .. code-block:: python (average_distance, distances) (np.nan, np.nan) `View current source, line 2507 <../source-code/utilities.html#utilities-2507>`_. get_pole_coordinates ~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_pole_coordinates(mesh) Get pole coordinates. :param mesh: Paired-boundary geometry with four columns in pixel coordinates. **Return expressions in source:** .. code-block:: python (pole1, pole2) `View current source, line 2519 <../source-code/utilities.html#utilities-2519>`_. get_pole_object_distances ~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_pole_object_distances(mesh, centroid_coordinates, px) Get pole object distances. :param mesh: Paired-boundary geometry with four columns in pixel coordinates. :param centroid_coordinates: Input ``centroid_coordinates`` 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 px: Micrometres per pixel. Geometry arrays remain in pixel coordinates. **Return expressions in source:** .. code-block:: python (avg_distance, min_2_distances, distances) (np.nan, np.nan) `View current source, line 2525 <../source-code/utilities.html#utilities-2525>`_. angle_between_vector ~~~~~~~~~~~~~~~~~~~~ .. py:function:: angle_between_vector(v1, v2) Angle between vector. :param v1: Input ``v1`` 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 v2: Input ``v2`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python np.arccos(np.dot(v1, v2) / (d1 * d2)) `View current source, line 2540 <../source-code/utilities.html#utilities-2540>`_. projection_on_midline ~~~~~~~~~~~~~~~~~~~~~ .. py:function:: projection_on_midline(centroids, midline, width, px) Projection on midline. :param centroids: Input ``centroids`` 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 midline: Central-axis points in (row, column) pixel coordinates. :param width: Input ``width`` 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 px: Micrometres per pixel. Geometry arrays remain in pixel coordinates. **Return expressions in source:** .. code-block:: python (l_list, dl_list, norm_l_list, norm_dl_list) `View current source, line 2546 <../source-code/utilities.html#utilities-2546>`_. get_avg_distance_from_center ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_avg_distance_from_center(l_norm_list) Subtract 0.5 from the mean normalized longitudinal object position. Returns a signed mean position offset, not the mean absolute distance from the center. :param l_norm_list: Input ``l_norm_list`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python avg_dist `View current source, line 2605 <../source-code/utilities.html#utilities-2605>`_. get_object_intensities ~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_object_intensities(object_masks, cropped_signal) Get object intensities. :param object_masks: Input ``object_masks`` 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 cropped_signal: Input ``cropped_signal`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (combined_intensity_values, individual_intensity_values) `View current source, line 2611 <../source-code/utilities.html#utilities-2611>`_. get_objects_mean ~~~~~~~~~~~~~~~~ .. py:function:: get_objects_mean(intensity_values_list) Get objects mean. :param intensity_values_list: Input ``intensity_values_list`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python means `View current source, line 2625 <../source-code/utilities.html#utilities-2625>`_. get_objects_std ~~~~~~~~~~~~~~~ .. py:function:: get_objects_std(intensity_values_list) Get objects std. :param intensity_values_list: Input ``intensity_values_list`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python stds `View current source, line 2630 <../source-code/utilities.html#utilities-2630>`_. get_objects_kurtosis ~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_objects_kurtosis(intensity_values_list) Get objects kurtosis. :param intensity_values_list: Input ``intensity_values_list`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python kurtoses `View current source, line 2635 <../source-code/utilities.html#utilities-2635>`_. get_objects_skewness ~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_objects_skewness(intensity_values_list) Get objects skewness. :param intensity_values_list: Input ``intensity_values_list`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python skewnesses `View current source, line 2642 <../source-code/utilities.html#utilities-2642>`_. get_variance ~~~~~~~~~~~~ .. py:function:: get_variance(data) Get variance. :param data: Input ``data`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python np.var(data) `View current source, line 2647 <../source-code/utilities.html#utilities-2647>`_. measure_smoothened_intensity ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: measure_smoothened_intensity(midline, im_interp2d, width=7, subpixel=0.5) Measure smoothened intensity. :param midline: Central-axis points in (row, column) pixel coordinates. :param im_interp2d: Input ``im_interp2d`` 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 width: Input ``width`` 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 subpixel: Input ``subpixel`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python prf `View current source, line 2652 <../source-code/utilities.html#utilities-2652>`_. gaussian_smoothing ~~~~~~~~~~~~~~~~~~ .. py:function:: gaussian_smoothing(data) Gaussian smoothing. :param data: Input ``data`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python prf.flatten() `View current source, line 2661 <../source-code/utilities.html#utilities-2661>`_. measure_intensity_interp2d ~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: measure_intensity_interp2d(midline, im_interp2d, width=7, subpixel=0.5) Measure intensity interp2d. :param midline: Central-axis points in (row, column) pixel coordinates. :param im_interp2d: Input ``im_interp2d`` 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 width: Input ``width`` 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 subpixel: Input ``subpixel`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python data `View current source, line 2668 <../source-code/utilities.html#utilities-2668>`_. normalize_per_cell ~~~~~~~~~~~~~~~~~~ .. py:function:: normalize_per_cell(profile) Min–max normalize a profile within one cell. Returns an array scaled to [0, 1]; a constant profile returns zeros. :param profile: A 1D array-like object representing the profile. **Return expressions in source:** .. code-block:: python normalized_profile np.zeros_like(profile) `View current source, line 2684 <../source-code/utilities.html#utilities-2684>`_. .. raw:: html
Original docstring (legacy wording may differ from the current signature) .. code-block:: text Normalize the values in a 1D profile using Min-Max scaling. Parameters: profile (array-like): A 1D array-like object representing the profile. Returns: normalized_profile (ndarray): Normalized profile. .. raw:: html
get_cumulative_step_length_midline ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_cumulative_step_length_midline(midline, px) Calculate cumulative step lengths for each segment in the midline. :param midline: Central-axis points in (row, column) pixel coordinates. :param px: Micrometres per pixel. Geometry arrays remain in pixel coordinates. **Return expressions in source:** .. code-block:: python cumulative_step_lengths `View current source, line 2713 <../source-code/utilities.html#utilities-2713>`_. .. raw:: html
Original docstring (legacy wording may differ from the current signature) .. code-block:: text Calculate cumulative step lengths for each segment in the midline. Parameters: midline (ndarray): An array containing X and Y coordinates of the midline. px (float): The pixel size. Returns: cumulative_step_lengths (ndarray): Array containing cumulative step lengths for each segment in the midline. .. raw:: html
linear_interpolation ~~~~~~~~~~~~~~~~~~~~ .. py:function:: linear_interpolation(array, num_values) Linear interpolation. :param array: Input ``array`` 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 num_values: Input ``num_values`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python interpolated_values `View current source, line 2740 <../source-code/utilities.html#utilities-2740>`_. get_phase_mask ~~~~~~~~~~~~~~ .. py:function:: get_phase_mask(phase_cropped_img, phase_log_sigma=0.5) Get phase mask. :param phase_cropped_img: Input ``phase_cropped_img`` 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 phase_log_sigma: Input ``phase_log_sigma`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python cropped_phase_mask `View current source, line 2751 <../source-code/utilities.html#utilities-2751>`_. closing_mask ~~~~~~~~~~~~ .. py:function:: closing_mask(cropped_phase_mask, closing_level=2) Closing mask. :param cropped_phase_mask: Input ``cropped_phase_mask`` 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 closing_level: Input ``closing_level`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python mask_closed `View current source, line 2765 <../source-code/utilities.html#utilities-2765>`_. find_centroid_in_largest_mask ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: find_centroid_in_largest_mask(phase_mask_closed, phase_cropped_contour) Find centroid in largest mask. :param phase_mask_closed: Input ``phase_mask_closed`` 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 phase_cropped_contour: Input ``phase_cropped_contour`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python [] [phase_centroid] `View current source, line 2774 <../source-code/utilities.html#utilities-2774>`_. align ~~~~~ .. py:function:: align(signal_centroid, phase_centroid, cropped_contour) Align. :param signal_centroid: Input ``signal_centroid`` 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 phase_centroid: Input ``phase_centroid`` 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 cropped_contour: Input ``cropped_contour`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python aligned_contour `View current source, line 2796 <../source-code/utilities.html#utilities-2796>`_. align_objects ~~~~~~~~~~~~~ .. py:function:: align_objects(signal_centroid, phase_centroid, cropped_mesh, cropped_contour, cropped_midline) Align objects. :param signal_centroid: Input ``signal_centroid`` 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 phase_centroid: Input ``phase_centroid`` 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 cropped_mesh: Input ``cropped_mesh`` 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 cropped_contour: Input ``cropped_contour`` 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 cropped_midline: Input ``cropped_midline`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (aligned_contour, aligned_midline, aligned_mesh) `View current source, line 2820 <../source-code/utilities.html#utilities-2820>`_. get_signal_mask ~~~~~~~~~~~~~~~ .. py:function:: get_signal_mask(signal, contour, log_sigma, min_overlap_ratio, max_external_ratio) Get signal mask. :param signal: Input ``signal`` 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 contour: Boundary points in (row, column) pixel coordinates. :param log_sigma: Laplacian-of-Gaussian sigma for signal-object detection. :param min_overlap_ratio: Minimum accepted overlap ratio under the utility implementation; inspect its denominator in source. :param max_external_ratio: Maximum accepted outside-cell ratio under the utility implementation. **Return expressions in source:** .. code-block:: python (object_mask, cropped_img, x_offset, y_offset) `View current source, line 2833 <../source-code/utilities.html#utilities-2833>`_. shift_contour ~~~~~~~~~~~~~ .. py:function:: shift_contour(phase_image, signal_image, contour, mesh, midline, log_sigma=1.5, kernel_width=3, min_overlap_ratio=0.3, max_external_ratio=0.8, phase_log_sigma=0.5, phase_closing_level=2, signal_closing_level=12, max_shift_correction=10) Aligns the contour, mesh, and midline based on the centroids of the phase and signal masks. :param phase_image: Input ``phase_image`` 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 signal_image: Input ``signal_image`` 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 contour: Boundary points in (row, column) pixel coordinates. :param mesh: Paired-boundary geometry with four columns in pixel coordinates. :param midline: Central-axis points in (row, column) pixel coordinates. :param log_sigma: Laplacian-of-Gaussian sigma for signal-object detection. :param kernel_width: Width of the square dilation kernel used for candidate object masks. :param min_overlap_ratio: Minimum accepted overlap ratio under the utility implementation; inspect its denominator in source. :param max_external_ratio: Maximum accepted outside-cell ratio under the utility implementation. :param phase_log_sigma: Input ``phase_log_sigma`` 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 phase_closing_level: Input ``phase_closing_level`` 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 signal_closing_level: Input ``signal_closing_level`` 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 max_shift_correction: Input ``max_shift_correction`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (aligned_contour, aligned_mesh, aligned_midline) (None, None, None) `View current source, line 2855 <../source-code/utilities.html#utilities-2855>`_. .. raw:: html
Original docstring (legacy wording may differ from the current signature) .. code-block:: text Aligns the contour, mesh, and midline based on the centroids of the phase and signal masks. Parameters: - phase_image (array): The phase image. - signal_image (array): The signal image. - contour (array): The contour data. - mesh (array): The mesh data. - midline (array): The midline data. - log_sigma (float): Sigma for the log filter for the signal mask. - kernel_width (int): Width of the dilation kernel. - min_overlap_ratio (float): Minimum overlap ratio for the signal mask. - max_external_ratio (float): Maximum external ratio for the signal mask. - phase_log_sigma (float): Sigma for the log filter for the phase mask. - phase_closing_level (int): Closing level for the phase mask. - signal_closing_level (int): Closing level for the signal mask. - max_shift_correction (float): Maximum allowable distance between centroids for correction. Returns: - aligned_contour (array): The aligned contour data. - aligned_mesh (array): The aligned mesh data. - aligned_midline (array): The aligned midline data. .. raw:: html
crop_signal_with_optional_shift ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: crop_signal_with_optional_shift(image_obj, channel, contour, shift_signal) Crop signal with optional shift. :param image_obj: Image instance supplying calibration, geometry, and channel data. :param channel: Channel identifier for the selected signal, or None for phase/morphology where supported. :param contour: Boundary points in (row, column) pixel coordinates. :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 (cropped_signal, cropped_mask, cropped_contour, x_offset, y_offset) `View current source, line 2956 <../source-code/utilities.html#utilities-2956>`_. change_contour_array_length ~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: change_contour_array_length(cell_perimeter, contour, scale=0.02, smooth=1) Change contour array length. :param cell_perimeter: Input ``cell_perimeter`` 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 contour: Boundary points in (row, column) pixel coordinates. :param scale: Input ``scale`` 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 smooth: Input ``smooth`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python adjust_eroded_contour `View current source, line 2967 <../source-code/utilities.html#utilities-2967>`_. normalized_intensity_by_image ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: normalized_intensity_by_image(profile, cropped_image) Normalized intensity by image. :param profile: Input ``profile`` 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 cropped_image: Input ``cropped_image`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python normalized_profile np.zeros_like(prof) `View current source, line 2974 <../source-code/utilities.html#utilities-2974>`_. get_homogeneity ~~~~~~~~~~~~~~~ .. py:function:: get_homogeneity(normalized_intensity) Get homogeneity. :param normalized_intensity: Input ``normalized_intensity`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python homogeneity `View current source, line 3000 <../source-code/utilities.html#utilities-3000>`_. set_bg_zero ~~~~~~~~~~~ .. py:function:: set_bg_zero(contour, cropped_img) Set bg zero. :param contour: Boundary points in (row, column) pixel coordinates. :param cropped_img: Input ``cropped_img`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python bg_zero_img `View current source, line 3007 <../source-code/utilities.html#utilities-3007>`_. rescale_image_255 ~~~~~~~~~~~~~~~~~ .. py:function:: rescale_image_255(cropped_image, max_value=255) Rescale image 255. :param cropped_image: Input ``cropped_image`` 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 max_value: Input ``max_value`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python scaled_image `View current source, line 3013 <../source-code/utilities.html#utilities-3013>`_. create_co_occurrence_matrix ~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: create_co_occurrence_matrix(cropped_img, distances=[1], angles=[0, np.pi / 4, np.pi / 2, 3 * np.pi / 4], levels=256, symmetric=True, normed=True) Create a co-occurrence matrix from a cropped image. :param cropped_img: Input ``cropped_img`` 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 distances: Input ``distances`` 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 angles: Input ``angles`` 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 levels: Input ``levels`` 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 symmetric: Input ``symmetric`` 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 normed: Input ``normed`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python co_occurrence_matrix `View current source, line 3030 <../source-code/utilities.html#utilities-3030>`_. .. raw:: html
Original docstring (legacy wording may differ from the current signature) .. code-block:: text Create a co-occurrence matrix from a cropped image. Parameters: - cropped_image: The cropped grayscale image. - distances: List of pixel pair distances. - angles: List of angles in radians for pixel pairs. - levels: Number of gray levels (typically 256 for 8-bit images). - symmetric: If True, the output matrix P[:, :, d, theta] is symmetric. This is accomplished by ignoring the order of value pairs, so both (i, j) and (j, i) are accumulated when (i, j) is encountered for a given offset. - normed: If True, normalize each matrix P[:, :, d, theta] by dividing by the total number of accumulated co-occurrences for the given offset. Returns: - co_occurrence_matrix: The co-occurrence matrix. .. raw:: html
get_glcm_feature_means ~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_glcm_feature_means(glcm) Compute the mean Haralick properties for a GLCM in one pass. :param glcm: Input ``glcm`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (dissimilarity, correlation.mean(), homogeneity, energy, contrast, entropy) **Explicitly raised exceptions:** ``ValueError``. Errors from called functions can also propagate or be recorded. `View current source, line 3072 <../source-code/utilities.html#utilities-3072>`_. .. raw:: html
Original docstring (legacy wording may differ from the current signature) .. code-block:: text Compute the mean Haralick properties for a GLCM in one pass. The formulas mirror skimage.feature.graycoprops so callers keep the same numerical behavior while avoiding repeated scans of the same matrix. .. raw:: html
calculate_haralick_features ~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: calculate_haralick_features(contour, cropped_img, distances=[2], angles=[0, np.pi / 4, np.pi / 2, 3 * np.pi / 4], levels=256) Calculate haralick features. :param contour: Boundary points in (row, column) pixel coordinates. :param cropped_img: Input ``cropped_img`` 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 distances: Input ``distances`` 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 angles: Input ``angles`` 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 levels: Input ``levels`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python get_glcm_feature_means(glcm) `View current source, line 3128 <../source-code/utilities.html#utilities-3128>`_. align_contour_start ~~~~~~~~~~~~~~~~~~~ .. py:function:: align_contour_start(eroded_contour, first_point) Rotates the eroded_contour so that its point closest to the first point of p2p_contour comes first. :param eroded_contour: Array of shape (N, 2), representing the contour after erosion. :param first_point: Input ``first_point`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python aligned_contour `View current source, line 3147 <../source-code/utilities.html#utilities-3147>`_. .. raw:: html
Original docstring (legacy wording may differ from the current signature) .. code-block:: text Rotates the eroded_contour so that its point closest to the first point of p2p_contour comes first. Parameters ---------- eroded_contour : np.ndarray Array of shape (N, 2), representing the contour after erosion. p2p_contour : np.ndarray Original contour array of shape (N, 2) before erosion. Returns ------- np.ndarray Rotated eroded_contour starting from the closest point to the original start. .. raw:: html
calculate_object_haralick_features ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: calculate_object_haralick_features(object_masks, cropped_img, distances=[2], angles=[0, np.pi / 4, np.pi / 2, 3 * np.pi / 4], levels=256) Calculate object haralick features. :param object_masks: Input ``object_masks`` 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 cropped_img: Input ``cropped_img`` 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 distances: Input ``distances`` 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 angles: Input ``angles`` 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 levels: Input ``levels`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python get_glcm_feature_means(glcm) `View current source, line 3172 <../source-code/utilities.html#utilities-3172>`_. calculate_contour_haralick_features ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: calculate_contour_haralick_features(contour_intensities, distances=[2], angles=[0, np.pi / 4, np.pi / 2, 3 * np.pi / 4], levels=256) Calculate contour haralick features. :param contour_intensities: Input ``contour_intensities`` 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 distances: Input ``distances`` 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 angles: Input ``angles`` 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 levels: Input ``levels`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python get_glcm_feature_means(glcm) `View current source, line 3193 <../source-code/utilities.html#utilities-3193>`_. split_array ~~~~~~~~~~~ .. py:function:: split_array(row) Split array. :param row: Input ``row`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python (first_half, second_half) `View current source, line 3212 <../source-code/utilities.html#utilities-3212>`_. get_complemented_contour_intensity ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: get_complemented_contour_intensity(row) Get complemented contour intensity. :param row: Input ``row`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python complemented_contour_intensity_profile `View current source, line 3219 <../source-code/utilities.html#utilities-3219>`_. shift_image ~~~~~~~~~~~ .. py:function:: shift_image(img, shift) Correct XY drift between phase contrast image and fluorescent image(s). :param img: Input image :param shift: Subpixel XY drift :return: Drift corrected image :param img: Input ``img`` 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: Input ``shift`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python offset_image.astype(np.uint16) `View current source, line 3235 <../source-code/utilities.html#utilities-3235>`_. .. raw:: html
Original docstring (legacy wording may differ from the current signature) .. code-block:: text Correct XY drift between phase contrast image and fluorescent image(s). :param img: Input image :param shift: Subpixel XY drift :return: Drift corrected image .. raw:: html
Internal helpers ---------------- _collect_touching_label_pairs ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: _collect_touching_label_pairs(label_slice_a, label_slice_b) collect touching label pairs. :param label_slice_a: Input ``label_slice_a`` 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 label_slice_b: Input ``label_slice_b`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python np.unique(pairs, axis=0) np.empty((0, 2), dtype=np.int64) `View current source, line 636 <../source-code/utilities.html#utilities-636>`_. _validate_max_daughter_cell_mesh_rows ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: _validate_max_daughter_cell_mesh_rows(value) validate max daughter cell mesh rows. :param value: Input ``value`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python int(value) **Explicitly raised exceptions:** ``ValueError``. Errors from called functions can also propagate or be recorded. `View current source, line 1442 <../source-code/utilities.html#utilities-1442>`_. _max_feret_diameter_px ~~~~~~~~~~~~~~~~~~~~~~ .. py:function:: _max_feret_diameter_px(coords) Exact point-set diameter with bounded pairwise-distance memory. :param coords: Input ``coords`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring. **Return expressions in source:** .. code-block:: python maximum 0.0 `View current source, line 1862 <../source-code/utilities.html#utilities-1862>`_. .. raw:: html
Original docstring (legacy wording may differ from the current signature) .. code-block:: text Exact point-set diameter with bounded pairwise-distance memory. .. raw:: html