cellprofiler-core-nightly 5.0.0.dev562__tar.gz → 5.0.0.dev592__tar.gz

{cellprofiler_core_nightly-5.0.0.dev562 → cellprofiler_core_nightly-5.0.0.dev592}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-core-nightly
-Version: 5.0.0.dev562
+Version: 5.0.0.dev592
 Summary: cellprofiler-core implements the bulk of CellProfiler's non-gui functionality
 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_core_nightly-5.0.0.dev562 → cellprofiler_core_nightly-5.0.0.dev592}/cellprofiler_core/_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.dev592'
+__version_tuple__ = version_tuple = (5, 0, 0, 'dev592')
 
-__commit_id__ = commit_id = 'g9d892da07'
+__commit_id__ = commit_id = 'g9880bd09c'

{cellprofiler_core_nightly-5.0.0.dev562 → cellprofiler_core_nightly-5.0.0.dev592}/cellprofiler_core/measurement/_measurements.py

@@ -60,7 +60,7 @@ from ..utilities.hdf5_dict import HDF5Dict, NullLock
 from ..utilities.measurement import agg_ignore_feature
 from ..utilities.measurement import get_agg_measurement_name
 from ..utilities.measurement import make_temporary_file
-
+from cellprofiler_library.measurement_model import LibraryMeasurements, Relationship
 
 LOGGER = logging.getLogger(__name__)
 
@@ -532,7 +532,7 @@ class Measurements:
                         second objects in these image numbers.
 
         returns a recarray with the following fields:
-        R_FIRST_IMAGE_NUMBER, R_SECOND_IMAGE_NUMBER, R_FIRST_OBJECT_NUMBER,
+        R_FIRST_IMAGE_NUMBER, R_FIRST_OBJECT_NUMBER, R_SECOND_IMAGE_NUMBER, 
         R_SECOND_OBJECT_NUMBER
         """
         features = (
@@ -1764,3 +1764,56 @@ class Measurements:
             return []
 
         return json.loads(self.get_experiment_measurement(M_GROUPING_TAGS))
+
+    def to_library_measurements(self, image_numbers=None):
+        """Convert a Measurements instance to a LibraryMeasurements instance
+        
+        Args:
+            measurements: A Measurements instance
+            
+        Returns:
+            A LibraryMeasurements instance
+        """        
+        image = {}
+        objects = {}
+        experiment = {}
+        relationships = []
+        
+        for object_name in self.get_object_names():
+            objects[object_name] = {}
+            for feature in self.get_feature_names(object_name):
+                objects[object_name][feature] = self.get_measurement(object_name, feature)
+        
+        for feature in self.get_feature_names("Image"):
+            image[feature] = self.get_measurement("Image", feature)
+        try:
+            for feature in self.get_feature_names("Experiment"):
+                experiment[feature] = self.get_measurement("Experiment", feature)
+        except KeyError:
+            pass
+        
+        for relationship in self.get_relationship_groups():
+            relationship_measurements = self.get_relationships(
+                relationship.module_number,
+                relationship.relationship,
+                relationship.object_name1,
+                relationship.object_name2,
+                image_numbers=image_numbers
+            )
+            
+            relationships.append(Relationship(
+                relationship.relationship,
+                relationship.object_name1,
+                relationship.object_name2,
+                relationship_measurements[R_FIRST_OBJECT_NUMBER],
+                relationship_measurements[R_SECOND_OBJECT_NUMBER],
+            ))
+        
+        return LibraryMeasurements(
+            image=image,
+            objects=objects,
+            experiment=experiment,
+            relationships=relationships
+        )
+
+        

{cellprofiler_core_nightly-5.0.0.dev562 → cellprofiler_core_nightly-5.0.0.dev592}/cellprofiler_core/object/_objects.py

@@ -8,9 +8,11 @@ from cellprofiler_library.functions.segmentation import areas_from_ijv
 from cellprofiler_library.functions.segmentation import convert_labels_to_dense
 from cellprofiler_library.functions.segmentation import convert_ijv_to_sparse
 from cellprofiler_library.functions.segmentation import make_rgb_outlines
-from cellprofiler_library.functions.segmentation import find_label_overlaps
 from cellprofiler_library.functions.segmentation import find_ijv_overlaps
 from cellprofiler_library.functions.segmentation import center_of_labels_mass
+from cellprofiler_library.functions.segmentation import histogram_from_labels as _histogram_from_labels
+from cellprofiler_library.functions.segmentation import relate_histogram as _relate_histogram
+from cellprofiler_library.functions.segmentation import relate_labels as _relate_labels
 
 from ._segmentation import Segmentation
 
@@ -300,8 +302,7 @@ class Objects:
         each parent. The second gives the mapping of each child to its parent's
         object number.
         """
-        histogram = self.histogram_from_labels(parent_labels, child_labels)
-        return self.relate_histogram(histogram)
+        return _relate_labels(parent_labels, child_labels)
 
     @staticmethod
     def relate_histogram(histogram):
@@ -309,21 +310,7 @@ class Objects:
 
         histogram - histogram from histogram_from_ijv or histogram_from_labels
         """
-        parent_count = histogram.shape[0] - 1
-
-        parents_of_children = np.asarray(histogram.argmax(axis=0))
-        if len(parents_of_children.shape) == 2:
-            parents_of_children = np.squeeze(parents_of_children, axis=0)
-        #
-        # Create a histogram of # of children per parent
-        children_per_parent = np.histogram(
-            parents_of_children[1:], np.arange(parent_count + 2)
-        )[0][1:]
-
-        #
-        # Make sure to remove the background elements at index 0
-        #
-        return children_per_parent, parents_of_children[1:]
+        return _relate_histogram(histogram)
 
     @staticmethod
     def histogram_from_labels(parent_labels, child_labels):
@@ -336,7 +323,7 @@ class Objects:
         Note that the first row and column are empty, as these
         correspond to parent and child labels of 0.
         """
-        return find_label_overlaps(parent_labels, child_labels, validate=True)
+        return _histogram_from_labels(parent_labels, child_labels)
 
     @staticmethod
     def histogram_from_ijv(parent_ijv, child_ijv):

{cellprofiler_core_nightly-5.0.0.dev562 → cellprofiler_core_nightly-5.0.0.dev592}/cellprofiler_core_nightly.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-core-nightly
-Version: 5.0.0.dev562
+Version: 5.0.0.dev592
 Summary: cellprofiler-core implements the bulk of CellProfiler's non-gui functionality
 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>