How to use the identify.FF_PARENT function in identify

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github CellProfiler / CellProfiler / pyCellProfiler / cellprofiler / modules / identifysecondaryobjects.py View on Github external
np.max(new_objects.segmented))
            cpmi.add_object_location_measurements(measurements,
                                                  self.new_primary_objects_name.value,
                                                  new_objects.segmented)
            for parent_objects, parent_name, child_objects, child_name in (
                (objects, self.primary_objects.value,
                 new_objects, self.new_primary_objects_name.value),
                (new_objects, self.new_primary_objects_name.value,
                 objects_out, objname)):
                children_per_parent, parents_of_children = \
                    parent_objects.relate_children(child_objects)
                measurements.add_measurement(parent_name,
                                             cpmi.FF_CHILDREN_COUNT%child_name,
                                             children_per_parent)
                measurements.add_measurement(child_name,
                                             cpmi.FF_PARENT%parent_name,
                                             parents_of_children)
github CellProfiler / CellProfiler / pyCellProfiler / cellprofiler / modules / editobjectsmanually.py View on Github external
def get_measurement_columns(self, pipeline):
        '''Return information to use when creating database columns'''
        orig_image_name = self.object_name.value
        filtered_image_name = self.filtered_objects.value
        columns = I.get_object_measurement_columns(filtered_image_name)
        columns += [(orig_image_name,
                     I.FF_CHILDREN_COUNT % filtered_image_name,
                     cpmeas.COLTYPE_INTEGER),
                    (filtered_image_name,
                     I.FF_PARENT %  orig_image_name,
                     cpmeas.COLTYPE_INTEGER)]
        return columns
github CellProfiler / CellProfiler / pyCellProfiler / cellprofiler / modules / identifytertiaryobjects.py View on Github external
# Write out the objects
        #
        workspace.object_set.add_objects(tertiary_objects,
                                         self.subregion_objects_name.value)
        #
        # Write out the measurements
        #
        m = workspace.measurements
        #
        # The parent/child associations
        #
        for parent_objects_name, parents_of, child_count\
         in ((self.primary_objects_name, primary_parents,child_count_of_primary),
             (self.secondary_objects_name, secondary_parents, child_count_of_secondary)):
            m.add_measurement(self.subregion_objects_name.value,
                              cpmi.FF_PARENT%(parent_objects_name.value),
                              parents_of)
            m.add_measurement(parent_objects_name.value,
                              cpmi.FF_CHILDREN_COUNT%(self.subregion_objects_name.value),
                              child_count)
        object_count = np.max(tertiary_labels)
        #
        # The object count
        #
        cpmi.add_object_count_measurements(workspace.measurements,
                                           self.subregion_objects_name.value,
                                           object_count)
        #
        # The object locations
        #
        cpmi.add_object_location_measurements(workspace.measurements,
                                              self.subregion_objects_name.value,
github CellProfiler / CellProfiler / pyCellProfiler / cellprofiler / modules / maskobjects.py View on Github external
else:
            parent_objects = np.arange(1, nobjects+1)
        #
        # Add the objects
        #
        remaining_objects = cpo.Objects()
        remaining_objects.segmented = labels
        remaining_objects.unedited_segmented = original_objects.unedited_segmented
        workspace.object_set.add_objects(remaining_objects, 
                                         remaining_object_name)
        #
        # Add measurements
        #
        m = workspace.measurements
        m.add_measurement(remaining_object_name,
                          I.FF_PARENT % object_name,
                          parent_objects)
        if np.max(original_objects.segmented) == 0:
            child_count = np.array([],int)
        else:
            child_count = fix(scind.sum(labels, original_objects.segmented,
                                        np.arange(1, nobjects+1)))
            child_count = (child_count > 0).astype(int)
        m.add_measurement(object_name,
                          I.FF_CHILDREN_COUNT % remaining_object_name,
                          child_count)
        if self.retain_or_renumber == R_RETAIN:
            remaining_object_count = nobjects
        else:
            remaining_object_count = len(unique_labels)
        I.add_object_count_measurements(m, remaining_object_name,
                                        remaining_object_count)