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Functions1,666 in github.com/CellProfiler/CellProfiler-plugins

⨍ Functions 1,666◇ Types & classes 129
↓ 77 callersMethodadd_measurement
(self, base, removable=True)
active_plugins/callbarcodes.py:283
↓ 47 callersMethodrun
(self, workspace)
unmaintained_plugins/CellProfiler3/DoGNet.py:90
↓ 28 callersMethodadd_objects
(self, can_delete=True)
unmaintained_plugins/CellProfiler3/exporttocellh5.py:183
↓ 28 callersFunctionbytes_to_str
(b)
active_plugins/runvista2d.py:65
↓ 26 callersFunctiondraw_disc
(img, center, radius, value)
unmaintained_tests/test_identifyyeastcells.py:721
↓ 26 callersMethodget
(self, x, y)
unmaintained_plugins/CellProfiler3/cellstar/core/seeder.py:304
↓ 20 callersFunctiondraw_brightfield_cell
(img, x, y, radius, content_dark=True)
unmaintained_tests/test_identifyyeastcells.py:695
↓ 20 callersMethodinfo
Invoke /info/ request over MONAILabel Server :return: json response
active_plugins/runvista2d.py:154
↓ 17 callersMethodget_value
(self, reraise=False)
active_plugins/cpij/server.py:110
↓ 16 callersMethodassertRange
(self, range_start, range_end, value)
unmaintained_tests/test_identifyyeastcells.py:50
↓ 16 callersMethodupdate
(steps)
unmaintained_plugins/CellProfiler3/identifyyeastcells.py:906
↓ 16 callersMethodurllib_quote_plus
(s)
active_plugins/runvista2d.py:693
↓ 15 callersMethodrun
(self, workspace)
unmaintained_plugins/CellProfiler3/identifyyeastcells.py:624
↓ 13 callersMethodhttp_method
(method, server_url, selector, body=None, headers=None, content_type=None)
active_plugins/runvista2d.py:531
↓ 11 callersMethodupdate
(steps)
unmaintained_plugins/CellProfiler4_autoconverted/identifyyeastcells.py:909
↓ 10 callersMethodapply_threshold
(self, image, threshold, smoothing)
unmaintained_plugins/CellProfiler3/thresh_all.py:590
↓ 10 callersMethodapply_threshold
(self, image, threshold, smoothing)
unmaintained_plugins/CellProfiler4_autoconverted/testallthresholds.py:600
↓ 10 callersFunctionimage_save
Displays image with title using matplotlib.pyplot @param image: @param title:
unmaintained_plugins/CellProfiler3/cellstar/utils/debug_util.py:101
↓ 9 callersMethodencode_auto_params_from_all_params
(parameters)
unmaintained_plugins/CellProfiler3/cellstar/segmentation.py:137
↓ 9 callersMethodget_threshold
(self, image, workspace, method)
unmaintained_plugins/CellProfiler3/thresh_all.py:517
↓ 9 callersMethodget_threshold
(self, image, workspace, method)
unmaintained_plugins/CellProfiler4_autoconverted/testallthresholds.py:527
↓ 9 callersFunctionget_two_cell_mask
()
unmaintained_tests/test_identifyyeastcells.py:675
↓ 8 callersMethodadd_objects
(self, can_delete=True)
unmaintained_plugins/CellProfiler4_autoconverted/exporttocellh5.py:183
↓ 8 callersMethodrecord_measurement
Record the result of a measurement in the workspace's measurements
unmaintained_plugins/CellProfiler2/enhancedmeasuretexture.py:967
↓ 8 callersMethodrecord_measurement
Record the result of a measurement in the workspace's measurements
unmaintained_plugins/CellProfiler3/enhancedmeasuretexture.py:966
↓ 8 callersMethodrecord_measurement
Record the result of a measurement in the workspace's measurements
active_plugins/enhancedmeasuretexture.py:1152
↓ 7 callersMethod_update_client_id
(self, params)
active_plugins/runvista2d.py:86
↓ 7 callersFunctionto_int
(num)
unmaintained_plugins/CellProfiler3/cellstar/utils/calc_util.py:230
↓ 7 callersMethodwants_distance_to_edge
(self)
unmaintained_plugins/CellProfiler3/measure_population_context.py:105
↓ 7 callersMethodwants_distance_to_edge
(self)
unmaintained_plugins/CellProfiler4_autoconverted/measurepopulationcontext.py:108
↓ 7 callersMethodwants_population_density
(self)
unmaintained_plugins/CellProfiler3/measure_population_context.py:102
↓ 7 callersMethodwants_population_density
(self)
unmaintained_plugins/CellProfiler4_autoconverted/measurepopulationcontext.py:105
↓ 6 callersFunctiondefault_parameters
(segmentation_precision=-1, avg_cell_diameter=-1)
unmaintained_plugins/CellProfiler3/cellstar/utils/params_util.py:13
↓ 6 callersMethodimshow
(x, y, image, *args, **kwargs)
active_plugins/addnoise.py:270
↓ 6 callersFunctionmymax
(a, b)
unmaintained_plugins/CellProfiler3/activecontourmodel.py:637
↓ 6 callersFunctionmymax
(a, b)
unmaintained_plugins/CellProfiler4_autoconverted/activecontourmodel.py:639
↓ 6 callersMethodrand_seeds
Generate (len(seeds) * times) random seeds within (min_random_radius:max_random_radius). @type seeds: list[Seed]
unmaintained_plugins/CellProfiler3/cellstar/core/seeder.py:85
↓ 6 callersMethodrun
Run the module workspace - The workspace contains pipeline - instance of cpp for this run image_set - the i
active_plugins/addnoise.py:197
↓ 5 callersFunctioncleanup
(self)
active_plugins/runcellpose.py:110
↓ 5 callersMethodevaluate
Analyse contour and calculate all it properties and ranking. @type polar_transform: cellstar.core.vectorized.polar_transform.PolarTra
unmaintained_plugins/CellProfiler3/cellstar/core/snake.py:256
↓ 5 callersFunctionexplorer_expected
()
unmaintained_plugins/CellProfiler3/cellstar/utils/debug_util.py:141
↓ 5 callersFunctionget_circle_kernel
Creates radius x radius bool image of the circle. @param radius: radius of the circle
unmaintained_plugins/CellProfiler3/cellstar/utils/image_util.py:68
↓ 5 callersFunctionimage_normalize
Performs image normalization (vide: matlab mat2gray) @param image: image to be normalized (assumed as numpy.array of values from 0 to 1)
unmaintained_plugins/CellProfiler3/cellstar/utils/image_util.py:280
↓ 5 callersFunctionis_segmentation_correct
(ground_truth, segmentation)
unmaintained_tests/test_identifyyeastcells.py:713
↓ 5 callersMethodon_setting_changed
(self, setting, pipeline)
unmaintained_plugins/CellProfiler3/runimagej.py:113
↓ 5 callersFunctionprepare_debug_folder
()
unmaintained_plugins/CellProfiler3/cellstar/utils/debug_util.py:63
↓ 5 callersMethodrecord_image_measurement
Record the result of a measurement in the workspace's measurements
unmaintained_plugins/CellProfiler2/enhancedmeasuretexture.py:998
↓ 5 callersMethodrecord_image_measurement
Record the result of a measurement in the workspace's measurements
unmaintained_plugins/CellProfiler3/enhancedmeasuretexture.py:997
↓ 5 callersMethodrecord_image_measurement
Record the result of a measurement in the workspace's measurements
active_plugins/enhancedmeasuretexture.py:1198
↓ 5 callersMethodstart
(self)
unmaintained_plugins/CellProfiler3/identifyyeastcells.py:1131
↓ 4 callersMethodcompute_TrAM
Compute the TrAM statistic for a single trajectory :param tram_feature_names: Names of the features to use (in order of the
unmaintained_plugins/CellProfiler3/measuretrackquality.py:377
↓ 4 callersFunctionconvert_to_brightfield
(img, content_dark)
unmaintained_tests/test_identifyyeastcells.py:682
↓ 4 callersMethodcreate_mutation
(self, dilation, random_poly=False)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_rank_snake.py:36
↓ 4 callersMethodencode_auto_params
(self)
unmaintained_plugins/CellProfiler3/cellstar/segmentation.py:152
↓ 4 callersMethodfind_seeds_from_border_or_content
Finds seeds from given image. @param image: image (border or content) from which seeds are being extracted @type image: np.nd
unmaintained_plugins/CellProfiler3/cellstar/core/seeder.py:107
↓ 4 callersMethodget_blurred
(self, image, blur_param, cache_result=False)
unmaintained_plugins/CellProfiler3/cellstar/core/image_repo.py:310
↓ 4 callersFunctionget_custom_model_vars
(self)
active_plugins/runcellpose.py:104
↓ 4 callersMethodget_feature_name
(self, name)
unmaintained_plugins/CellProfiler3/measureimagefocus.py:84
↓ 4 callersMethodget_feature_name
(self, name)
unmaintained_plugins/CellProfiler4_autoconverted/measureimagefocus.py:88
↓ 4 callersFunctionget_gt_snake_seeds
Create random seeds inside gt snake. @type gt_snake: GTSnake
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_process.py:118
↓ 4 callersMethodget_site_path
Get the plate / well / site tuple that identifies a field of view workspace - workspace for the analysis containing the metadata
unmaintained_plugins/CellProfiler3/exporttocellh5.py:263
↓ 4 callersMethodget_site_path
Get the plate / well / site tuple that identifies a field of view workspace - workspace for the analysis containing the metadata
unmaintained_plugins/CellProfiler4_autoconverted/exporttocellh5.py:263
↓ 4 callersFunctionimage_smooth
Performs image blur with circular kernel. @param image: image to be blurred (assumed as numpy.array of values from 0 to 1) @param radius:
unmaintained_plugins/CellProfiler3/cellstar/utils/image_util.py:258
↓ 4 callersMethodinstance
(cls, avg_cell_diameter, points, step, max_size)
unmaintained_plugins/CellProfiler3/cellstar/core/polar_transform.py:77
↓ 4 callersMethodload_image_grayscale
(path)
unmaintained_plugins/CellProfiler3/identifyyeastcells.py:951
↓ 4 callersMethodload_image_grayscale
(path)
unmaintained_plugins/CellProfiler4_autoconverted/identifyyeastcells.py:954
↓ 4 callersMethodpreprocess_images
(self, input_image, background_image, ignore_mask)
unmaintained_plugins/CellProfiler3/identifyyeastcells.py:787
↓ 3 callersFunction_manager
Helper method to return a QueueManager connected to the ImageJ server
active_plugins/cpij/bridge.py:99
↓ 3 callersMethodadd_image
Add an image to the image_groups collection can_delete - set this to False to keep from showing the "remove" button for
unmaintained_plugins/CellProfiler3/compensatecolors.py:224
↓ 3 callersMethodadd_image
Add an image to the image_groups collection can_delete - set this to False to keep from showing the "remove" button for
active_plugins/compensatecolors.py:220
↓ 3 callersMethodapply_mask
@param ignore_mask: binary mask of places which are to be ignored @type ignore_mask: np.ndarray
unmaintained_plugins/CellProfiler3/cellstar/core/image_repo.py:114
↓ 3 callersMethodcalculate_cell_border_content_mask
Splits foreground pixels into cell content and cell borders.
unmaintained_plugins/CellProfiler3/cellstar/core/image_repo.py:283
↓ 3 callersMethodcalculate_forebackground_masks
Determines foreground which is the part of the image different substantialy from provided background. Holes in initial foreground are
unmaintained_plugins/CellProfiler3/cellstar/core/image_repo.py:221
↓ 3 callersMethodcreate_from_seed
(cls, parameters, seed, points_num, images)
unmaintained_plugins/CellProfiler3/cellstar/core/snake.py:50
↓ 3 callersFunctioncreate_size_weights
(size_weight_average, length)
unmaintained_plugins/CellProfiler3/cellstar/utils/params_util.py:24
↓ 3 callersFunctionexplore_cellstar
(cellstar=None, seeds=[], snakes=[], images=None, image=None, params=None)
unmaintained_plugins/CellProfiler3/cellstar/utils/debug_util.py:149
↓ 3 callersMethodfit_parameters
:param wait_callback: function that wait and potentially updates UI :param update_callback: function that take number of steps compl
unmaintained_plugins/CellProfiler3/identifyyeastcells.py:838
↓ 3 callersMethodget_categories
(self, pipeline, object_name)
unmaintained_plugins/CellProfiler3/measure_population_context.py:283
↓ 3 callersMethodget_categories
(self, pipeline, object_name)
unmaintained_plugins/CellProfiler4_autoconverted/measurepopulationcontext.py:286
↓ 3 callersMethodget_features
Return the feature names for this pipeline's configuration
unmaintained_plugins/CellProfiler2/enhancedmeasuretexture.py:397
↓ 3 callersMethodget_features
Return a measurement feature name
unmaintained_plugins/CellProfiler2/calculatehistogram.py:286
↓ 3 callersMethodget_features
Return a measurement feature name
unmaintained_plugins/CellProfiler2/calculatemoments.py:303
↓ 3 callersMethodget_features
Return the feature names for this pipeline's configuration
unmaintained_plugins/CellProfiler3/enhancedmeasuretexture.py:396
↓ 3 callersMethodget_features
Return a measurement feature name
unmaintained_plugins/CellProfiler3/calculatehistogram.py:286
↓ 3 callersMethodget_features
Return a measurement feature name
unmaintained_plugins/CellProfiler3/calculatemoments.py:303
↓ 3 callersMethodget_features
Return a measurement feature name
unmaintained_plugins/CellProfiler4_autoconverted/calculatehistogram.py:287
↓ 3 callersMethodget_features
Return a measurement feature name
unmaintained_plugins/CellProfiler4_autoconverted/calculatemoments.py:308
↓ 3 callersMethodget_features
Return the feature names for this pipeline's configuration
active_plugins/enhancedmeasuretexture.py:448
↓ 3 callersMethodget_features
Return a measurement feature name
active_plugins/calculatemoments.py:347
↓ 3 callersMethodget_ws_dictionary
(self, workspace)
unmaintained_plugins/CellProfiler3/identifyyeastcells.py:516
↓ 3 callersMethodget_ws_dictionary
(self, workspace)
unmaintained_plugins/CellProfiler4_autoconverted/identifyyeastcells.py:519
↓ 3 callersFunctionhaar_transform
(image, scales, mask=None)
unmaintained_plugins/CellProfiler3/transformfilters.py:268
↓ 3 callersMethodhttp_multipart
(method, server_url, selector, fields, files, headers={})
active_plugins/runvista2d.py:577
↓ 3 callersMethodinit_pyimagej
(self)
active_plugins/runimagejscript.py:347
↓ 3 callersFunctioninverse_haar_transform
(image, scale, mask=None)
unmaintained_plugins/CellProfiler3/transformfilters.py:317
↓ 3 callersFunctionmake_workspace
Return a workspace with the given image and the runimagejscript module
tests/test_runimagejscript.py:26
↓ 3 callersMethodmerge_rank_parameters
(initial_parameters, new_params)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_rank_snake.py:44
↓ 3 callersMethodnormalize
(self, im)
unmaintained_plugins/CellProfiler3/DoGNet.py:159
↓ 3 callersMethodnormalize
(self, im)
unmaintained_plugins/CellProfiler4_autoconverted/DoGNet.py:160
↓ 3 callersMethodopen_csv
Open the csv file or URL, returning a file descriptor
unmaintained_plugins/CellProfiler3/callbarcodes.py:325
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