CellProfiler-nightly 5.0.0.dev562__tar.gz → 5.0.0.dev572__tar.gz

{cellprofiler_nightly-5.0.0.dev562 → cellprofiler_nightly-5.0.0.dev572}/CellProfiler_nightly.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: CellProfiler-nightly
-Version: 5.0.0.dev562
+Version: 5.0.0.dev572
 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.dev562 → cellprofiler_nightly-5.0.0.dev572}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: CellProfiler-nightly
-Version: 5.0.0.dev562
+Version: 5.0.0.dev572
 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.dev562 → cellprofiler_nightly-5.0.0.dev572}/cellprofiler/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '5.0.0.dev562'
-__version_tuple__ = version_tuple = (5, 0, 0, 'dev562')
+__version__ = version = '5.0.0.dev572'
+__version_tuple__ = version_tuple = (5, 0, 0, 'dev572')
 
-__commit_id__ = commit_id = 'g9d892da07'
+__commit_id__ = commit_id = 'g4d69e6b29'

{cellprofiler_nightly-5.0.0.dev562 → cellprofiler_nightly-5.0.0.dev572}/cellprofiler/modules/measureimageintensity.py

@@ -238,10 +238,10 @@ class MeasureImageIntensity(Module):
                 self._add_library_measurements_to_core(lib_measurements, workspace)
                 statistics += lib_display.statistics
 
-        # TODO: library_cleanup - wrap in self.show_window
-        col_labels = ["Image", "Masking object", "Feature", "Value"]
-        workspace.display_data.statistics = statistics
-        workspace.display_data.col_labels = col_labels
+        if self.show_window:
+            col_labels = ["Image", "Masking object", "Feature", "Value"]
+            workspace.display_data.statistics = statistics
+            workspace.display_data.col_labels = col_labels
 
     def display(self, workspace, figure):
         figure.set_subplots((1, 1))

{cellprofiler_nightly-5.0.0.dev562 → cellprofiler_nightly-5.0.0.dev572}/cellprofiler/modules/measureobjectintensity.py

@@ -237,7 +237,7 @@ class MeasureObjectIntensity(Module):
                 objects = workspace.object_set.get_objects(object_name)
                 nobjects = objects.count
                 
-                lib_measurements, lib_stats = measure_object_intensity(
+                lib_measurements, lib_display = measure_object_intensity(
                     img=img,
                     image_name=image_name,
                     object_name=object_name,
@@ -245,8 +245,8 @@ class MeasureObjectIntensity(Module):
                     object_labels=objects.get_labels(),
                     nobjects=nobjects,
                     image_dimensions=image.dimensions,
+                    return_visualization_data=True,
                 )
-
                 m = workspace.measurements
 
                 # Feature Name -> Template String
@@ -255,7 +255,11 @@ class MeasureObjectIntensity(Module):
                     for val in (getattr(TemplateMeasurementFormat, x.name) for x in IntensityFeature)
                 }
 
-                for stat in lib_stats:
+                if self.show_window:
+                    workspace.display_data.statistics += lib_display.statistics
+
+                # TODO: library cleanup - should just iterate on measurements not stats
+                for stat in lib_display.statistics:
                     image_name = stat[0]
                     object_name = stat[1]
                     feature_name = stat[2]
@@ -265,8 +269,6 @@ class MeasureObjectIntensity(Module):
                     if lib_measurements.has_feature(object_name, measurement_name):
                         measurement = lib_measurements.get_measurement(object_name, measurement_name)
                         m.add_measurement(object_name, measurement_name, measurement)
-                        if self.show_window and len(measurement) > 0:
-                            workspace.display_data.statistics.append(stat)
 
     def display(self, workspace, figure):
         figure.set_subplots((1, 1))

{cellprofiler_nightly-5.0.0.dev562 → cellprofiler_nightly-5.0.0.dev572}/cellprofiler/modules/measureobjectsizeshape.py

@@ -1,19 +1,12 @@
-import centrosome.cpmorphology
-import centrosome.zernike
-import numpy
-import scipy.ndimage
-import skimage.measure
 from cellprofiler_core.constants.measurement import COLTYPE_FLOAT
 from cellprofiler_core.module import Module
-from cellprofiler_core.object import Objects
 from cellprofiler_core.setting import Divider, Binary, ValidationError
 from cellprofiler_core.setting.subscriber import LabelListSubscriber
 
 import cellprofiler.gui.help.content
-import cellprofiler.icons
 
 from cellprofiler_library.modules import measureobjectsizeshape
-from cellprofiler_library.opts.objectsizeshapefeatures import ObjectSizeShapeFeatures
+from cellprofiler_library.opts.objectsizeshapefeatures import get_zernike_indexes, ObjectSizeShapeFeatures, F_STD_2D, F_STD_3D, F_ADV_2D, F_ADV_3D, F_STANDARD
 
 __doc__ = """\
 MeasureObjectSizeShape
@@ -281,15 +274,6 @@ module.""".format(
         else:
             return []
 
-    def get_zernike_numbers(self):
-        """The Zernike numbers measured by this module"""
-        if self.calculate_zernikes.value:
-            return centrosome.zernike.get_zernike_indexes(
-                ObjectSizeShapeFeatures.ZERNIKE_N.value + 1
-            )
-        else:
-            return []
-
     def get_zernike_name(self, zernike_index):
         """Return the name of a Zernike feature, given a (N,M) 2-tuple
 
@@ -299,20 +283,20 @@ module.""".format(
 
     def get_feature_names(self, pipeline):
         """Return the names of the features measured"""
-        feature_names = list(ObjectSizeShapeFeatures.F_STANDARD.value)
+        feature_names = [i.value for i in F_STANDARD]
 
         if pipeline.volumetric():
-            feature_names += list(ObjectSizeShapeFeatures.F_STD_3D.value)
+            feature_names += [i.value for i in F_STD_3D]
             if self.calculate_advanced.value:
-                feature_names += list(ObjectSizeShapeFeatures.F_ADV_3D.value)
+                feature_names += [i.value for i in F_ADV_3D]
         else:
-            feature_names += list(ObjectSizeShapeFeatures.F_STD_2D.value)
+            feature_names += [i.value for i in F_STD_2D]
             if self.calculate_zernikes.value:
                 feature_names += [
-                    self.get_zernike_name(index) for index in self.get_zernike_numbers()
+                    self.get_zernike_name(index) for index in get_zernike_indexes()
                 ]
             if self.calculate_advanced.value:
-                feature_names += list(get_feature_names.F_ADV_2D.values)
+                feature_names += [i.value for i in F_ADV_2D]
 
         return feature_names
 
@@ -333,32 +317,44 @@ module.""".format(
     def run(self, workspace):
         """Run, computing the area measurements for the objects"""
 
-        if self.show_window:
-            workspace.display_data.col_labels = (
-                "Object",
-                "Feature",
-                "Mean",
-                "Median",
-                "STD",
-            )
-
-            workspace.display_data.statistics = []
         for object_name in self.objects_list.value:
 
             objects = workspace.get_objects(object_name)
 
-            features_to_record = measureobjectsizeshape(
+            res = measureobjectsizeshape(
                 objects=objects.dense,
+                object_name=object_name,
                 calculate_advanced=self.calculate_advanced.value,
                 calculate_zernikes=self.calculate_zernikes.value,
                 volumetric=workspace.pipeline.volumetric(),
                 spacing=objects.parent_image.spacing
                 if objects.has_parent_image
                 else (1.0,) * objects.dimensions,  # TODO: Check this change is OK
+                return_visualization_data=self.show_window,
             )
+            if self.show_window:
+                lib_measurements, lib_display = res
+
+                workspace.display_data.col_labels = (
+                    "Object",
+                    "Feature",
+                    "Mean",
+                    "Median",
+                    "STD",
+                )
+
+                workspace.display_data.statistics = lib_display.statistics
+            else:
+                lib_measurements = res
 
-            for f, m in features_to_record.items():
-                self.record_measurement(workspace, object_name, f, m)
+            # Unpack LibraryMeasurements into workspace
+            for obj_name, features in lib_measurements.objects.items():
+                for feature_name, values in features.items():
+                    if not feature_name.startswith(ObjectSizeShapeFeatures.AREA_SHAPE.value):
+                        f = "%s_%s" % (ObjectSizeShapeFeatures.AREA_SHAPE.value, feature_name),
+                    else:
+                        f = feature_name
+                    workspace.add_measurement(object_name, f, values)
 
     def display(self, workspace, figure):
         figure.set_subplots((1, 1))
@@ -370,26 +366,6 @@ module.""".format(
             title="default",
         )
 
-    def record_measurement(self, workspace, object_name, feature_name, result):
-        """Record the result of a measurement in the workspace's measurements"""
-        data = centrosome.cpmorphology.fixup_scipy_ndimage_result(result)
-        workspace.add_measurement(
-            object_name,
-            "%s_%s" % (ObjectSizeShapeFeatures.AREA_SHAPE.value, feature_name),
-            data,
-        )
-        if self.show_window and numpy.any(numpy.isfinite(data)) > 0:
-            data = data[numpy.isfinite(data)]
-            workspace.display_data.statistics.append(
-                (
-                    object_name,
-                    feature_name,
-                    "%.2f" % numpy.mean(data),
-                    "%.2f" % numpy.median(data),
-                    "%.2f" % numpy.std(data),
-                )
-            )
-
     def get_measurement_columns(self, pipeline):
         """Return measurement column definitions.
         All cols returned as float even though "Area" will only ever be int"""