CellProfiler-nightly 5.0.0.dev496__tar.gz → 5.0.0.dev509__tar.gz

{cellprofiler_nightly-5.0.0.dev496 → cellprofiler_nightly-5.0.0.dev509}/CellProfiler_nightly.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: CellProfiler-nightly
-Version: 5.0.0.dev496
+Version: 5.0.0.dev509
 Summary: CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.
 Author: Anne Carpenter, Thouis (Ray) Jones, Lee Kamentsky, Vebjorn Ljosa, David Logan, Mark Bray, Madison Swain-Bowden, Allen Goodman, Claire McQuinn, Alice Lucas, Callum Tromans-Coia
 Author-email: Beth Cimini <bcimini@broadinstitute.org>, David Stirling <dstirling@glencoesoftware.com>, Nodar Gogoberidze <ngogober@broadinstitute.org>

{cellprofiler_nightly-5.0.0.dev496 → cellprofiler_nightly-5.0.0.dev509}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: CellProfiler-nightly
-Version: 5.0.0.dev496
+Version: 5.0.0.dev509
 Summary: CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.
 Author: Anne Carpenter, Thouis (Ray) Jones, Lee Kamentsky, Vebjorn Ljosa, David Logan, Mark Bray, Madison Swain-Bowden, Allen Goodman, Claire McQuinn, Alice Lucas, Callum Tromans-Coia
 Author-email: Beth Cimini <bcimini@broadinstitute.org>, David Stirling <dstirling@glencoesoftware.com>, Nodar Gogoberidze <ngogober@broadinstitute.org>

{cellprofiler_nightly-5.0.0.dev496 → cellprofiler_nightly-5.0.0.dev509}/cellprofiler/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '5.0.0.dev496'
-__version_tuple__ = version_tuple = (5, 0, 0, 'dev496')
+__version__ = version = '5.0.0.dev509'
+__version_tuple__ = version_tuple = (5, 0, 0, 'dev509')
 
-__commit_id__ = commit_id = 'g8d098d2ce'
+__commit_id__ = commit_id = 'gc5c07ce88'

{cellprofiler_nightly-5.0.0.dev496 → cellprofiler_nightly-5.0.0.dev509}/cellprofiler/modules/measurecolocalization.py

@@ -98,6 +98,7 @@ from cellprofiler_library.functions.image_processing import apply_threshold_to_o
 import cellprofiler_library.opts.threshold as Threshold
 from cellprofiler_library.opts.measurecolocalization import MeasurementType, TemplateMeasurementFormat, Target, CostesMethod
 from cellprofiler_library.modules._measurecolocalization import run_image_pair_images, run_image_pair_objects, crop_image_pair_similarly, crop_image_pair_and_object_similarly
+from cellprofiler_library.measurement_model import LibraryMeasurements
 
 # The number of settings per threshold
 THRESHOLD_SETTING_COUNT = 2
@@ -614,6 +615,10 @@ You can set a different threshold for each image selected in the module.
         col_labels = ["First image", "Second image", "Objects", "Measurement", "Value"]
         statistics = []
         image_dims = None
+        
+        # Accumulate all measurements here and unpack once at the end
+        all_measurements = LibraryMeasurements()
+        
         if len(self.images_list.value) < 2:
             raise ValueError("At least 2 images must be selected for analysis.")
         for im1_name, im2_name in self.get_image_pairs():
@@ -651,8 +656,7 @@ You can set a different threshold for each image selected in the module.
                     costes_method = costes_method
                 )
                 statistics += measurements_summary
-                for measurement_name, measurement_value in colocalization_measurements.items():
-                    workspace.measurements.add_image_measurement(measurement_name, measurement_value)
+                all_measurements = all_measurements.merge(colocalization_measurements)
 
             if self.wants_objects():
                 for object_name in self.objects_list.value:
@@ -704,8 +708,15 @@ You can set a different threshold for each image selected in the module.
 
                     )
                     statistics += measurements_summary
-                    for measurement_name, measurement_value in colocalization_measurements.items():
-                        workspace.measurements.add_measurement(object_name, measurement_name, measurement_value)
+                    all_measurements = all_measurements.merge(colocalization_measurements)
+
+        # Unpack all measurements to workspace
+        for measurement_name, measurement_value in all_measurements.image.items():
+            workspace.measurements.add_image_measurement(measurement_name, measurement_value)
+            
+        for object_name, features in all_measurements.objects.items():
+            for measurement_name, measurement_value in features.items():
+                workspace.measurements.add_measurement(object_name, measurement_name, measurement_value)
 
         if self.wants_masks_saved.value:
             self.save_requested_masks(workspace)

{cellprofiler_nightly-5.0.0.dev496 → cellprofiler_nightly-5.0.0.dev509}/cellprofiler/modules/measuregranularity.py

@@ -1,9 +1,5 @@
 import logging
-
-import cellprofiler_core.workspace
 import numpy
-import scipy.ndimage
-import skimage.morphology
 from cellprofiler_core.constants.measurement import COLTYPE_FLOAT
 from cellprofiler_core.module import Module
 from cellprofiler_core.setting import Divider, Binary, ValidationError
@@ -12,9 +8,10 @@ from cellprofiler_core.setting.subscriber import (
     LabelListSubscriber,
 )
 from cellprofiler_core.setting.text import Float, Integer
-from centrosome.cpmorphology import fixup_scipy_ndimage_result as fix
 
 from cellprofiler.gui.help.content import image_resource
+from cellprofiler_library.modules._measuregranularity import measure_granularity, ObjectRecord
+from cellprofiler_library.opts.measuregranularity import TemplateMeasurementFormat
 
 LOGGER = logging.getLogger(__name__)
 
@@ -88,9 +85,6 @@ References
 )
 
 
-"Granularity category"
-C_GRANULARITY = "Granularity_%s_%s"
-
 IMAGE_SETTING_COUNT_V2 = 5
 IMAGE_SETTING_COUNT_V3 = 6
 IMAGE_SETTING_COUNT = IMAGE_SETTING_COUNT_V3
@@ -268,210 +262,52 @@ class MeasureGranularity(Module):
             title="If individual objects were measured, use an Export module to view their results",
         )
 
-    def run_on_image_setting(self, workspace, image_name):
-        assert isinstance(workspace, cellprofiler_core.workspace.Workspace)
-        image_set = workspace.image_set
-        measurements = workspace.measurements
-        im = image_set.get_image(image_name, must_be_grayscale=True)
-        #
-        # Downsample the image and mask
-        #
-        new_shape = numpy.array(im.pixel_data.shape)
-        if self.subsample_size.value < 1:
-            new_shape = new_shape * self.subsample_size.value
-            if im.dimensions == 2:
-                i, j = (
-                    numpy.mgrid[0 : new_shape[0], 0 : new_shape[1]].astype(float)
-                    / self.subsample_size.value
-                )
-                pixels = scipy.ndimage.map_coordinates(im.pixel_data, (i, j), order=1)
-                mask = (
-                    scipy.ndimage.map_coordinates(im.mask.astype(float), (i, j)) > 0.9
-                )
-            else:
-                k, i, j = (
-                    numpy.mgrid[
-                        0 : new_shape[0], 0 : new_shape[1], 0 : new_shape[2]
-                    ].astype(float)
-                    / self.subsample_size.value
-                )
-                pixels = scipy.ndimage.map_coordinates(
-                    im.pixel_data, (k, i, j), order=1
-                )
-                mask = (
-                    scipy.ndimage.map_coordinates(im.mask.astype(float), (k, i, j))
-                    > 0.9
-                )
-        else:
-            pixels = im.pixel_data.copy()
-            mask = im.mask.copy()
-        #
-        # Remove background pixels using a greyscale tophat filter
-        #
-        if self.image_sample_size.value < 1:
-            back_shape = new_shape * self.image_sample_size.value
-            if im.dimensions == 2:
-                i, j = (
-                    numpy.mgrid[0 : back_shape[0], 0 : back_shape[1]].astype(float)
-                    / self.image_sample_size.value
-                )
-                back_pixels = scipy.ndimage.map_coordinates(pixels, (i, j), order=1)
-                back_mask = (
-                    scipy.ndimage.map_coordinates(mask.astype(float), (i, j)) > 0.9
-                )
-            else:
-                k, i, j = (
-                    numpy.mgrid[
-                        0 : new_shape[0], 0 : new_shape[1], 0 : new_shape[2]
-                    ].astype(float)
-                    / self.subsample_size.value
-                )
-                back_pixels = scipy.ndimage.map_coordinates(pixels, (k, i, j), order=1)
-                back_mask = (
-                    scipy.ndimage.map_coordinates(mask.astype(float), (k, i, j)) > 0.9
-                )
-        else:
-            back_pixels = pixels
-            back_mask = mask
-            back_shape = new_shape
-        radius = self.element_size.value
-        if im.dimensions == 2:
-            footprint = skimage.morphology.disk(radius, dtype=bool)
-        else:
-            footprint = skimage.morphology.ball(radius, dtype=bool)
-        back_pixels_mask = numpy.zeros_like(back_pixels)
-        back_pixels_mask[back_mask == True] = back_pixels[back_mask == True]
-        back_pixels = skimage.morphology.erosion(back_pixels_mask, footprint=footprint)
-        back_pixels_mask = numpy.zeros_like(back_pixels)
-        back_pixels_mask[back_mask == True] = back_pixels[back_mask == True]
-        back_pixels = skimage.morphology.dilation(back_pixels_mask, footprint=footprint)
-        if self.image_sample_size.value < 1:
-            if im.dimensions == 2:
-                i, j = numpy.mgrid[0 : new_shape[0], 0 : new_shape[1]].astype(float)
-                #
-                # Make sure the mapping only references the index range of
-                # back_pixels.
-                #
-                i *= float(back_shape[0] - 1) / float(new_shape[0] - 1)
-                j *= float(back_shape[1] - 1) / float(new_shape[1] - 1)
-                back_pixels = scipy.ndimage.map_coordinates(
-                    back_pixels, (i, j), order=1
-                )
-            else:
-                k, i, j = numpy.mgrid[
-                    0 : new_shape[0], 0 : new_shape[1], 0 : new_shape[2]
-                ].astype(float)
-                k *= float(back_shape[0] - 1) / float(new_shape[0] - 1)
-                i *= float(back_shape[1] - 1) / float(new_shape[1] - 1)
-                j *= float(back_shape[2] - 1) / float(new_shape[2] - 1)
-                back_pixels = scipy.ndimage.map_coordinates(
-                    back_pixels, (k, i, j), order=1
-                )
-        pixels -= back_pixels
-        pixels[pixels < 0] = 0
-
-        #
-        # For each object, build a little record
-        #
-        class ObjectRecord(object):
-            def __init__(self, name):
-                self.name = name
-                self.labels = workspace.object_set.get_objects(name).segmented
-                self.nobjects = numpy.max(self.labels)
-                if self.nobjects != 0:
-                    self.range = numpy.arange(1, numpy.max(self.labels) + 1)
-                    self.labels = self.labels.copy()
-                    self.labels[~im.mask] = 0
-                    self.current_mean = fix(
-                        scipy.ndimage.mean(im.pixel_data, self.labels, self.range)
-                    )
-                    self.start_mean = numpy.maximum(
-                        self.current_mean, numpy.finfo(float).eps
-                    )
+    def add_names_to_measurements(self, measurements_arr, image_measurements_arr, statistics, image_name, granular_spectrum_length):
+        _statistics = [image_name] + statistics
+        _measurements_arr = []
+        _image_measurements_arr = []
+        ng = granular_spectrum_length
+        for i in range(1, ng+1):
+            feature = TemplateMeasurementFormat.GRANULARITY % (i, image_name)
+            _image_measurements_arr += [(feature, image_measurements_arr[i-1])]
+            if i < len(measurements_arr):
+                if measurements_arr[i-1]:
+                    for (obj_name, obj_gss) in measurements_arr[i-1]:
+                        _measurements_arr += [(obj_name, feature, obj_gss)]
+                        # _measurements_arr += [(measurements_arr[i-1][j][0], feature, measurements_arr[i-1][j][1])]
+        return _measurements_arr, _image_measurements_arr, _statistics
 
+    def run_on_image_setting(self, workspace, image_name):
+        im = workspace.image_set.get_image(image_name, must_be_grayscale=True)
+        im_pixel_data = im.pixel_data
+        im_mask = im.mask
+        subsample_size = self.subsample_size.value
+        image_sample_size = self.image_sample_size.value
+        element_size = self.element_size.value
         object_records = [
-            ObjectRecord(objects_name) for objects_name in self.objects_list.value
+            ObjectRecord(objects_name, workspace.object_set.get_objects(objects_name).segmented, im_mask, im_pixel_data) for objects_name in self.objects_list.value
         ]
-        #
-        # Transcribed from the Matlab module: granspectr function
-        #
-        # CALCULATES GRANULAR SPECTRUM, ALSO KNOWN AS SIZE DISTRIBUTION,
-        # GRANULOMETRY, AND PATTERN SPECTRUM, SEE REF.:
-        # J.Serra, Image Analysis and Mathematical Morphology, Vol. 1. Academic Press, London, 1989
-        # Maragos,P. "Pattern spectrum and multiscale shape representation", IEEE Transactions on Pattern Analysis and Machine Intelligence, 11, N 7, pp. 701-716, 1989
-        # L.Vincent "Granulometries and Opening Trees", Fundamenta Informaticae, 41, No. 1-2, pp. 57-90, IOS Press, 2000.
-        # L.Vincent "Morphological Area Opening and Closing for Grayscale Images", Proc. NATO Shape in Picture Workshop, Driebergen, The Netherlands, pp. 197-208, 1992.
-        # I.Ravkin, V.Temov "Bit representation techniques and image processing", Applied Informatics, v.14, pp. 41-90, Finances and Statistics, Moskow, 1988 (in Russian)
-        # THIS IMPLEMENTATION INSTEAD OF OPENING USES EROSION FOLLOWED BY RECONSTRUCTION
-        #
-        ng = self.granular_spectrum_length.value
-        startmean = numpy.mean(pixels[mask])
-        ero = pixels.copy()
-        # Mask the test image so that masked pixels will have no effect
-        # during reconstruction
-        #
-        ero[~mask] = 0
-        currentmean = startmean
-        startmean = max(startmean, numpy.finfo(float).eps)
-
-        if im.dimensions == 2:
-            footprint = skimage.morphology.disk(1, dtype=bool)
-        else:
-            footprint = skimage.morphology.ball(1, dtype=bool)
-        statistics = [image_name]
-        for i in range(1, ng + 1):
-            prevmean = currentmean
-            ero_mask = numpy.zeros_like(ero)
-            ero_mask[mask == True] = ero[mask == True]
-            ero = skimage.morphology.erosion(ero_mask, footprint=footprint)
-            rec = skimage.morphology.reconstruction(ero, pixels, footprint=footprint)
-            currentmean = numpy.mean(rec[mask])
-            gs = (prevmean - currentmean) * 100 / startmean
-            statistics += ["%.2f" % gs]
-            feature = self.granularity_feature(i, image_name)
-            measurements.add_image_measurement(feature, gs)
-            #
-            # Restore the reconstructed image to the shape of the
-            # original image so we can match against object labels
-            #
-            orig_shape = im.pixel_data.shape
-            if im.dimensions == 2:
-                i, j = numpy.mgrid[0 : orig_shape[0], 0 : orig_shape[1]].astype(float)
-                #
-                # Make sure the mapping only references the index range of
-                # back_pixels.
-                #
-                i *= float(new_shape[0] - 1) / float(orig_shape[0] - 1)
-                j *= float(new_shape[1] - 1) / float(orig_shape[1] - 1)
-                rec = scipy.ndimage.map_coordinates(rec, (i, j), order=1)
-            else:
-                k, i, j = numpy.mgrid[
-                    0 : orig_shape[0], 0 : orig_shape[1], 0 : orig_shape[2]
-                ].astype(float)
-                k *= float(new_shape[0] - 1) / float(orig_shape[0] - 1)
-                i *= float(new_shape[1] - 1) / float(orig_shape[1] - 1)
-                j *= float(new_shape[2] - 1) / float(orig_shape[2] - 1)
-                rec = scipy.ndimage.map_coordinates(rec, (k, i, j), order=1)
-            #
-            # Calculate the means for the objects
-            #
-            for object_record in object_records:
-                assert isinstance(object_record, ObjectRecord)
-                if object_record.nobjects > 0:
-                    new_mean = fix(
-                        scipy.ndimage.mean(
-                            rec, object_record.labels, object_record.range
-                        )
-                    )
-                    gss = (
-                        (object_record.current_mean - new_mean)
-                        * 100
-                        / object_record.start_mean
-                    )
-                    object_record.current_mean = new_mean
-                else:
-                    gss = numpy.zeros((0,))
-                measurements.add_measurement(object_record.name, feature, gss)
+        granular_spectrum_length = self.granular_spectrum_length.value
+        image_name = image_name
+        dimensions = im.dimensions
+
+        measurements_arr, image_measurements_arr, statistics = measure_granularity(
+            im_pixel_data, 
+            im_mask, 
+            subsample_size, 
+            image_sample_size, 
+            element_size, 
+            object_records, 
+            granular_spectrum_length, 
+            dimensions
+        )
+        measurements_arr, image_measurements_arr, statistics = self.add_names_to_measurements(measurements_arr, image_measurements_arr, statistics, image_name, granular_spectrum_length)
+
+        for packed_measurements in measurements_arr:
+            workspace.measurements.add_measurement(*packed_measurements)
+        for packed_measurements in image_measurements_arr:
+            workspace.measurements.add_image_measurement(*packed_measurements)
+
         return statistics
 
     def get_measurement_columns(self, pipeline, return_sources=False):
@@ -544,7 +380,7 @@ class MeasureGranularity(Module):
         return result
 
     def granularity_feature(self, length, image_name):
-        return C_GRANULARITY % (length, image_name)
+        return TemplateMeasurementFormat.GRANULARITY % (length, image_name)
 
     def upgrade_settings(self, setting_values, variable_revision_number, module_name):
         if variable_revision_number == 1: