cellprofiler-library-nightly 5.0.0.dev243__tar.gz → 5.0.0.dev259__tar.gz

{cellprofiler_library_nightly-5.0.0.dev243 → cellprofiler_library_nightly-5.0.0.dev259}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-library-nightly
-Version: 5.0.0.dev243
+Version: 5.0.0.dev259
 Summary: cellprofiler-library implements CellProfiler's image processing and mathematical code, and is usable as a standalone library
 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_library_nightly-5.0.0.dev243 → cellprofiler_library_nightly-5.0.0.dev259}/cellprofiler_library/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '5.0.0.dev243'
-__version_tuple__ = version_tuple = (5, 0, 0, 'dev243')
+__version__ = version = '5.0.0.dev259'
+__version_tuple__ = version_tuple = (5, 0, 0, 'dev259')

{cellprofiler_library_nightly-5.0.0.dev243 → cellprofiler_library_nightly-5.0.0.dev259}/cellprofiler_library/functions/measurement.py

@@ -6,6 +6,9 @@ import centrosome.filter
 import centrosome.propagate
 import centrosome.fastemd
 from sklearn.cluster import KMeans
+from typing import Tuple
+import numpy
+import skimage
 
 from cellprofiler_library.opts import measureimageoverlap as mio
 from cellprofiler_library.functions.segmentation import convert_labels_to_ijv
@@ -14,6 +17,8 @@ from cellprofiler_library.functions.segmentation import count_from_ijv
 from cellprofiler_library.functions.segmentation import areas_from_ijv
 from cellprofiler_library.functions.segmentation import cast_labels_to_label_set
 
+from cellprofiler_library.opts.objectsizeshapefeatures import ObjectSizeShapeFeatures
+
 
 def measure_image_overlap_statistics(
     ground_truth_image,
@@ -456,3 +461,219 @@ def get_weights(i, j, labels_mask):
     bc = np.bincount(total_skel[ii, jj])[1:]
     result[: len(bc)] = bc
     return result
+
+
+def measure_object_size_shape(
+    labels,
+    desired_properties,
+    calculate_zernikes: bool = True,
+    calculate_advanced: bool = True,
+    spacing: Tuple = None
+):
+    label_indices = numpy.unique(labels[labels != 0])
+    nobjects = len(label_indices)
+    
+    if spacing is None:
+        spacing = (1.0,) * labels.ndim
+
+    if len(labels.shape) == 2:
+        # 2D
+        props = skimage.measure.regionprops_table(labels, properties=desired_properties)
+
+        formfactor = 4.0 * numpy.pi * props["area"] / props["perimeter"] ** 2
+        denom = [max(x, 1) for x in 4.0 * numpy.pi * props["area"]]
+        compactness = props["perimeter"] ** 2 / denom
+
+        max_radius = numpy.zeros(nobjects)
+        median_radius = numpy.zeros(nobjects)
+        mean_radius = numpy.zeros(nobjects)
+        min_feret_diameter = numpy.zeros(nobjects)
+        max_feret_diameter = numpy.zeros(nobjects)
+        zernike_numbers = centrosome.zernike.get_zernike_indexes(ObjectSizeShapeFeatures.ZERNIKE_N.value + 1)
+
+        zf = {}
+        for n, m in zernike_numbers:
+            zf[(n, m)] = numpy.zeros(nobjects)
+
+        for index, mini_image in enumerate(props["image"]):
+            # Pad image to assist distance tranform
+            mini_image = numpy.pad(mini_image, 1)
+            distances = scipy.ndimage.distance_transform_edt(mini_image)
+            max_radius[index] = centrosome.cpmorphology.fixup_scipy_ndimage_result(
+                scipy.ndimage.maximum(distances, mini_image)
+            )
+            mean_radius[index] = centrosome.cpmorphology.fixup_scipy_ndimage_result(
+                scipy.ndimage.mean(distances, mini_image)
+            )
+            median_radius[index] = centrosome.cpmorphology.median_of_labels(
+                distances, mini_image.astype("int"), [1]
+            )
+
+        #
+        # Zernike features
+        #
+        if calculate_zernikes:
+            zf_l = centrosome.zernike.zernike(zernike_numbers, labels, label_indices)
+            for (n, m), z in zip(zernike_numbers, zf_l.transpose()):
+                zf[(n, m)] = z
+
+        if nobjects > 0:
+            chulls, chull_counts = centrosome.cpmorphology.convex_hull(
+                labels, label_indices
+            )
+            #
+            # Feret diameter
+            #
+            (
+                min_feret_diameter,
+                max_feret_diameter,
+            ) = centrosome.cpmorphology.feret_diameter(
+                chulls, chull_counts, label_indices
+            )
+
+            features_to_record = {
+                ObjectSizeShapeFeatures.F_AREA.value: props["area"],
+                ObjectSizeShapeFeatures.F_PERIMETER.value: props["perimeter"],
+                ObjectSizeShapeFeatures.F_MAJOR_AXIS_LENGTH.value: props["major_axis_length"],
+                ObjectSizeShapeFeatures.F_MINOR_AXIS_LENGTH.value: props["minor_axis_length"],
+                ObjectSizeShapeFeatures.F_ECCENTRICITY.value: props["eccentricity"],
+                ObjectSizeShapeFeatures.F_ORIENTATION.value: props["orientation"] * (180 / numpy.pi),
+                ObjectSizeShapeFeatures.F_CENTER_X.value: props["centroid-1"],
+                ObjectSizeShapeFeatures.F_CENTER_Y.value: props["centroid-0"],
+                ObjectSizeShapeFeatures.F_BBOX_AREA.value: props["bbox_area"],
+                ObjectSizeShapeFeatures.F_MIN_X.value: props["bbox-1"],
+                ObjectSizeShapeFeatures.F_MAX_X.value: props["bbox-3"],
+                ObjectSizeShapeFeatures.F_MIN_Y.value: props["bbox-0"],
+                ObjectSizeShapeFeatures.F_MAX_Y.value: props["bbox-2"],
+                ObjectSizeShapeFeatures.F_FORM_FACTOR.value: formfactor,
+                ObjectSizeShapeFeatures.F_EXTENT.value: props["extent"],
+                ObjectSizeShapeFeatures.F_SOLIDITY.value: props["solidity"],
+                ObjectSizeShapeFeatures.F_COMPACTNESS.value: compactness,
+                ObjectSizeShapeFeatures.F_EULER_NUMBER.value: props["euler_number"],
+                ObjectSizeShapeFeatures.F_MAXIMUM_RADIUS.value: max_radius,
+                ObjectSizeShapeFeatures.F_MEAN_RADIUS.value: mean_radius,
+                ObjectSizeShapeFeatures.F_MEDIAN_RADIUS.value: median_radius,
+                ObjectSizeShapeFeatures.F_CONVEX_AREA.value: props["convex_area"],
+                ObjectSizeShapeFeatures.F_MIN_FERET_DIAMETER.value: min_feret_diameter,
+                ObjectSizeShapeFeatures.F_MAX_FERET_DIAMETER.value: max_feret_diameter,
+                ObjectSizeShapeFeatures.F_EQUIVALENT_DIAMETER.value: props["equivalent_diameter"],
+            }
+            if calculate_advanced:
+                features_to_record.update(
+                    {
+                        ObjectSizeShapeFeatures.F_SPATIAL_MOMENT_0_0.value: props["moments-0-0"],
+                        ObjectSizeShapeFeatures.F_SPATIAL_MOMENT_0_1.value: props["moments-0-1"],
+                        ObjectSizeShapeFeatures.F_SPATIAL_MOMENT_0_2.value: props["moments-0-2"],
+                        ObjectSizeShapeFeatures.F_SPATIAL_MOMENT_0_3.value: props["moments-0-3"],
+                        ObjectSizeShapeFeatures.F_SPATIAL_MOMENT_1_0.value: props["moments-1-0"],
+                        ObjectSizeShapeFeatures.F_SPATIAL_MOMENT_1_1.value: props["moments-1-1"],
+                        ObjectSizeShapeFeatures.F_SPATIAL_MOMENT_1_2.value: props["moments-1-2"],
+                        ObjectSizeShapeFeatures.F_SPATIAL_MOMENT_1_3.value: props["moments-1-3"],
+                        ObjectSizeShapeFeatures.F_SPATIAL_MOMENT_2_0.value: props["moments-2-0"],
+                        ObjectSizeShapeFeatures.F_SPATIAL_MOMENT_2_1.value: props["moments-2-1"],
+                        ObjectSizeShapeFeatures.F_SPATIAL_MOMENT_2_2.value: props["moments-2-2"],
+                        ObjectSizeShapeFeatures.F_SPATIAL_MOMENT_2_3.value: props["moments-2-3"],
+                        ObjectSizeShapeFeatures.F_CENTRAL_MOMENT_0_0.value: props["moments_central-0-0"],
+                        ObjectSizeShapeFeatures.F_CENTRAL_MOMENT_0_1.value: props["moments_central-0-1"],
+                        ObjectSizeShapeFeatures.F_CENTRAL_MOMENT_0_2.value: props["moments_central-0-2"],
+                        ObjectSizeShapeFeatures.F_CENTRAL_MOMENT_0_3.value: props["moments_central-0-3"],
+                        ObjectSizeShapeFeatures.F_CENTRAL_MOMENT_1_0.value: props["moments_central-1-0"],
+                        ObjectSizeShapeFeatures.F_CENTRAL_MOMENT_1_1.value: props["moments_central-1-1"],
+                        ObjectSizeShapeFeatures.F_CENTRAL_MOMENT_1_2.value: props["moments_central-1-2"],
+                        ObjectSizeShapeFeatures.F_CENTRAL_MOMENT_1_3.value: props["moments_central-1-3"],
+                        ObjectSizeShapeFeatures.F_CENTRAL_MOMENT_2_0.value: props["moments_central-2-0"],
+                        ObjectSizeShapeFeatures.F_CENTRAL_MOMENT_2_1.value: props["moments_central-2-1"],
+                        ObjectSizeShapeFeatures.F_CENTRAL_MOMENT_2_2.value: props["moments_central-2-2"],
+                        ObjectSizeShapeFeatures.F_CENTRAL_MOMENT_2_3.value: props["moments_central-2-3"],
+                        ObjectSizeShapeFeatures.F_NORMALIZED_MOMENT_0_0.value: props["moments_normalized-0-0"],
+                        ObjectSizeShapeFeatures.F_NORMALIZED_MOMENT_0_1.value: props["moments_normalized-0-1"],
+                        ObjectSizeShapeFeatures.F_NORMALIZED_MOMENT_0_2.value: props["moments_normalized-0-2"],
+                        ObjectSizeShapeFeatures.F_NORMALIZED_MOMENT_0_3.value: props["moments_normalized-0-3"],
+                        ObjectSizeShapeFeatures.F_NORMALIZED_MOMENT_1_0.value: props["moments_normalized-1-0"],
+                        ObjectSizeShapeFeatures.F_NORMALIZED_MOMENT_1_1.value: props["moments_normalized-1-1"],
+                        ObjectSizeShapeFeatures.F_NORMALIZED_MOMENT_1_2.value: props["moments_normalized-1-2"],
+                        ObjectSizeShapeFeatures.F_NORMALIZED_MOMENT_1_3.value: props["moments_normalized-1-3"],
+                        ObjectSizeShapeFeatures.F_NORMALIZED_MOMENT_2_0.value: props["moments_normalized-2-0"],
+                        ObjectSizeShapeFeatures.F_NORMALIZED_MOMENT_2_1.value: props["moments_normalized-2-1"],
+                        ObjectSizeShapeFeatures.F_NORMALIZED_MOMENT_2_2.value: props["moments_normalized-2-2"],
+                        ObjectSizeShapeFeatures.F_NORMALIZED_MOMENT_2_3.value: props["moments_normalized-2-3"],
+                        ObjectSizeShapeFeatures.F_NORMALIZED_MOMENT_3_0.value: props["moments_normalized-3-0"],
+                        ObjectSizeShapeFeatures.F_NORMALIZED_MOMENT_3_1.value: props["moments_normalized-3-1"],
+                        ObjectSizeShapeFeatures.F_NORMALIZED_MOMENT_3_2.value: props["moments_normalized-3-2"],
+                        ObjectSizeShapeFeatures.F_NORMALIZED_MOMENT_3_3.value: props["moments_normalized-3-3"],
+                        ObjectSizeShapeFeatures.F_HU_MOMENT_0.value: props["moments_hu-0"],
+                        ObjectSizeShapeFeatures.F_HU_MOMENT_1.value: props["moments_hu-1"],
+                        ObjectSizeShapeFeatures.F_HU_MOMENT_2.value: props["moments_hu-2"],
+                        ObjectSizeShapeFeatures.F_HU_MOMENT_3.value: props["moments_hu-3"],
+                        ObjectSizeShapeFeatures.F_HU_MOMENT_4.value: props["moments_hu-4"],
+                        ObjectSizeShapeFeatures.F_HU_MOMENT_5.value: props["moments_hu-5"],
+                        ObjectSizeShapeFeatures.F_HU_MOMENT_6.value: props["moments_hu-6"],
+                        ObjectSizeShapeFeatures.F_INERTIA_TENSOR_0_0.value: props["inertia_tensor-0-0"],
+                        ObjectSizeShapeFeatures.F_INERTIA_TENSOR_0_1.value: props["inertia_tensor-0-1"],
+                        ObjectSizeShapeFeatures.F_INERTIA_TENSOR_1_0.value: props["inertia_tensor-1-0"],
+                        ObjectSizeShapeFeatures.F_INERTIA_TENSOR_1_1.value: props["inertia_tensor-1-1"],
+                        ObjectSizeShapeFeatures.F_INERTIA_TENSOR_EIGENVALUES_0.value: props[
+                            "inertia_tensor_eigvals-0"
+                        ],
+                        ObjectSizeShapeFeatures.F_INERTIA_TENSOR_EIGENVALUES_1.value: props[
+                            "inertia_tensor_eigvals-1"
+                        ],
+                    }
+                )
+
+            if calculate_zernikes:
+                features_to_record.update(
+                    {f"Zernike_{n}_{m}": zf[(n, m)] for n, m in zernike_numbers}
+                )
+
+    else:
+        # 3D
+        props = skimage.measure.regionprops_table(labels, properties=desired_properties)
+        # SurfaceArea
+        surface_areas = numpy.zeros(len(props["label"]))
+        for index, label in enumerate(props["label"]):
+            # this seems less elegant than you might wish, given that regionprops returns a slice,
+            # but we need to expand the slice out by one voxel in each direction, or surface area freaks out
+            volume = labels[
+                max(props["bbox-0"][index] - 1, 0) : min(
+                    props["bbox-3"][index] + 1, labels.shape[0]
+                ),
+                max(props["bbox-1"][index] - 1, 0) : min(
+                    props["bbox-4"][index] + 1, labels.shape[1]
+                ),
+                max(props["bbox-2"][index] - 1, 0) : min(
+                    props["bbox-5"][index] + 1, labels.shape[2]
+                ),
+            ]
+            volume = volume == label
+            verts, faces, _normals, _values = skimage.measure.marching_cubes(
+                volume,
+                method="lewiner",
+                spacing=spacing,
+                level=0,
+            )
+            surface_areas[index] = skimage.measure.mesh_surface_area(verts, faces)
+
+        features_to_record = {
+            ObjectSizeShapeFeatures.F_VOLUME.value: props["area"],
+            ObjectSizeShapeFeatures.F_SURFACE_AREA.value: surface_areas,
+            ObjectSizeShapeFeatures.F_MAJOR_AXIS_LENGTH.value: props["major_axis_length"],
+            ObjectSizeShapeFeatures.F_MINOR_AXIS_LENGTH.value: props["minor_axis_length"],
+            ObjectSizeShapeFeatures.F_CENTER_X.value: props["centroid-2"],
+            ObjectSizeShapeFeatures.F_CENTER_Y.value: props["centroid-1"],
+            ObjectSizeShapeFeatures.F_CENTER_Z.value: props["centroid-0"],
+            ObjectSizeShapeFeatures.F_BBOX_VOLUME.value: props["bbox_area"],
+            ObjectSizeShapeFeatures.F_MIN_X.value: props["bbox-2"],
+            ObjectSizeShapeFeatures.F_MAX_X.value: props["bbox-5"],
+            ObjectSizeShapeFeatures.F_MIN_Y.value: props["bbox-1"],
+            ObjectSizeShapeFeatures.F_MAX_Y.value: props["bbox-4"],
+            ObjectSizeShapeFeatures.F_MIN_Z.value: props["bbox-0"],
+            ObjectSizeShapeFeatures.F_MAX_Z.value: props["bbox-3"],
+            ObjectSizeShapeFeatures.F_EXTENT.value: props["extent"],
+            ObjectSizeShapeFeatures.F_EULER_NUMBER.value: props["euler_number"],
+            ObjectSizeShapeFeatures.F_EQUIVALENT_DIAMETER.value: props["equivalent_diameter"],
+        }
+        if calculate_advanced:
+            features_to_record[ObjectSizeShapeFeatures.F_SOLIDITY.value] = props["solidity"]
+    return features_to_record, props["label"], nobjects
+

{cellprofiler_library_nightly-5.0.0.dev243 → cellprofiler_library_nightly-5.0.0.dev259}/cellprofiler_library/modules/__init__.py

@@ -15,3 +15,4 @@ from ._reducenoise import reducenoise
 from ._watershed import watershed
 from ._measureimageoverlap import measureimageoverlap
 from ._gaussianfilter import gaussianfilter
+from ._measureobjectsizeshape import measureobjectsizeshape

cellprofiler_library_nightly-5.0.0.dev259/cellprofiler_library/modules/_measureobjectsizeshape.py

@@ -0,0 +1,160 @@
+from typing import Tuple
+import numpy
+import skimage
+import scipy
+
+import centrosome
+import centrosome.zernike
+
+from cellprofiler_library.functions.measurement import measure_object_size_shape
+from cellprofiler_library.opts.objectsizeshapefeatures import ObjectSizeShapeFeatures
+from cellprofiler_library.functions.segmentation import (
+    _validate_dense,
+    convert_dense_to_label_set,
+)
+
+DEFAULT_INVALID_VALUE_DTYPE = {
+    numpy.float64: numpy.nan,
+    numpy.float32: numpy.nan,
+    numpy.float16: numpy.nan,
+    numpy.uint8: 0,
+    numpy.uint16: 0,
+    numpy.uint32: 0,
+    numpy.uint64: 0,
+    numpy.int8: 0,
+    numpy.int16: 0,
+    numpy.int32: 0,
+    numpy.int64: 0,
+    numpy.bool_: False,
+    numpy.object_: None,
+    numpy.str_: "",
+}
+
+def measureobjectsizeshape(
+    objects,
+    calculate_advanced: bool = True,
+    calculate_zernikes: bool = True,
+    volumetric: bool = False,
+    spacing: Tuple = None,
+):
+    """
+    Objects: dense, sparse, ijv, or label objects?
+    For now, we will assume dense
+    """
+    # _validate_dense(objects)
+
+    # Define the feature names
+    feature_names = list(ObjectSizeShapeFeatures.F_STANDARD.value)
+    if volumetric:
+        feature_names += list(ObjectSizeShapeFeatures.F_STD_3D.value)
+        if calculate_advanced:
+            feature_names += list(ObjectSizeShapeFeatures.F_ADV_3D.value)
+    else:
+        feature_names += list(ObjectSizeShapeFeatures.F_STD_2D.value)
+        if calculate_zernikes:
+            feature_names += [
+                f"Zernike_{index[0]}_{index[1]}"
+                for index in centrosome.zernike.get_zernike_indexes(
+                    ObjectSizeShapeFeatures.ZERNIKE_N.value + 1
+                )
+            ]
+        if calculate_advanced:
+            feature_names += list(ObjectSizeShapeFeatures.F_ADV_2D.value)
+
+    if len(objects[objects != 0]) == 0:
+        data = dict(zip(feature_names, [None] * len(feature_names)))
+        for ft in feature_names:
+            data[ft] = numpy.zeros((0,))
+        return data
+
+    if not volumetric:
+        desired_properties = [
+            "label",
+            "image",
+            "area",
+            "perimeter",
+            "bbox",
+            "bbox_area",
+            "major_axis_length",
+            "minor_axis_length",
+            "orientation",
+            "centroid",
+            "equivalent_diameter",
+            "extent",
+            "eccentricity",
+            "convex_area",
+            "solidity",
+            "euler_number",
+        ]
+        if calculate_advanced:
+            desired_properties += [
+                "inertia_tensor",
+                "inertia_tensor_eigvals",
+                "moments",
+                "moments_central",
+                "moments_hu",
+                "moments_normalized",
+            ]
+    else:
+        desired_properties = [
+            "label",
+            "image",
+            "area",
+            "centroid",
+            "bbox",
+            "bbox_area",
+            "major_axis_length",
+            "minor_axis_length",
+            "extent",
+            "equivalent_diameter",
+            "euler_number",
+        ]
+        if calculate_advanced:
+            desired_properties += [
+                "solidity",
+            ]
+
+    labels = convert_dense_to_label_set(objects, validate=False)
+    labels = [i[0] for i in labels]  # Just need the labelmaps, not indices
+
+    if len(labels) > 1:
+        # Overlapping labels
+        features_to_record = {}
+        for labelmap in labels:
+            buffer, measured_labels, nobjects = measure_object_size_shape(
+                labels=labelmap,
+                desired_properties=desired_properties,
+                calculate_zernikes=calculate_zernikes,
+                calculate_advanced=calculate_advanced,
+                spacing=spacing,
+            )
+            for f, m in buffer.items():
+                if f in features_to_record:
+                    features_to_record[f] = numpy.concatenate(
+                        (features_to_record[f], m)
+                    )
+                else:
+                    features_to_record[f] = m
+    else:
+        features_to_record, measured_labels, nobjects = measure_object_size_shape(
+            labels=labels[0],
+            desired_properties=desired_properties,
+            calculate_zernikes=calculate_zernikes,
+            calculate_advanced=calculate_advanced,
+            spacing=spacing,
+        )
+
+    # ensure that all objects (objects.indices) are represented in the
+    # output, even if they are not present in the label matrix. Fill with nan if missing
+    if len(measured_labels) < nobjects:
+        for i in objects.indices:
+            if i not in measured_labels:
+                for f in features_to_record:
+                    features_to_record[f] = numpy.insert(
+                        features_to_record[f], i-1, DEFAULT_INVALID_VALUE_DTYPE.get(
+                            features_to_record[f].dtype.type, numpy.nan
+                        )
+                    )
+
+
+    return features_to_record

cellprofiler_library_nightly-5.0.0.dev259/cellprofiler_library/opts/objectsizeshapefeatures.py

@@ -0,0 +1,191 @@
+from enum import Enum
+
+
+class ObjectSizeShapeFeatures(Enum):
+    """The category of the per-object measurements made by the MeasureObjectSizeShape module"""
+
+    AREA_SHAPE = "AreaShape"
+
+    ZERNIKE_N = 9
+
+    F_AREA = "Area"
+    F_PERIMETER = "Perimeter"
+    F_VOLUME = "Volume"
+    F_SURFACE_AREA = "SurfaceArea"
+    F_ECCENTRICITY = "Eccentricity"
+    F_SOLIDITY = "Solidity"
+    F_CONVEX_AREA = "ConvexArea"
+    F_EXTENT = "Extent"
+    F_CENTER_X = "Center_X"
+    F_CENTER_Y = "Center_Y"
+    F_CENTER_Z = "Center_Z"
+    F_BBOX_AREA = "BoundingBoxArea"
+    F_BBOX_VOLUME = "BoundingBoxVolume"
+    F_MIN_X = "BoundingBoxMinimum_X"
+    F_MAX_X = "BoundingBoxMaximum_X"
+    F_MIN_Y = "BoundingBoxMinimum_Y"
+    F_MAX_Y = "BoundingBoxMaximum_Y"
+    F_MIN_Z = "BoundingBoxMinimum_Z"
+    F_MAX_Z = "BoundingBoxMaximum_Z"
+    F_EULER_NUMBER = "EulerNumber"
+    F_FORM_FACTOR = "FormFactor"
+    F_MAJOR_AXIS_LENGTH = "MajorAxisLength"
+    F_MINOR_AXIS_LENGTH = "MinorAxisLength"
+    F_ORIENTATION = "Orientation"
+    F_COMPACTNESS = "Compactness"
+    F_INERTIA = "InertiaTensor"
+    F_MAXIMUM_RADIUS = "MaximumRadius"
+    F_MEDIAN_RADIUS = "MedianRadius"
+    F_MEAN_RADIUS = "MeanRadius"
+    F_MIN_FERET_DIAMETER = "MinFeretDiameter"
+    F_MAX_FERET_DIAMETER = "MaxFeretDiameter"
+
+    F_CENTRAL_MOMENT_0_0 = "CentralMoment_0_0"
+    F_CENTRAL_MOMENT_0_1 = "CentralMoment_0_1"
+    F_CENTRAL_MOMENT_0_2 = "CentralMoment_0_2"
+    F_CENTRAL_MOMENT_0_3 = "CentralMoment_0_3"
+    F_CENTRAL_MOMENT_1_0 = "CentralMoment_1_0"
+    F_CENTRAL_MOMENT_1_1 = "CentralMoment_1_1"
+    F_CENTRAL_MOMENT_1_2 = "CentralMoment_1_2"
+    F_CENTRAL_MOMENT_1_3 = "CentralMoment_1_3"
+    F_CENTRAL_MOMENT_2_0 = "CentralMoment_2_0"
+    F_CENTRAL_MOMENT_2_1 = "CentralMoment_2_1"
+    F_CENTRAL_MOMENT_2_2 = "CentralMoment_2_2"
+    F_CENTRAL_MOMENT_2_3 = "CentralMoment_2_3"
+    F_EQUIVALENT_DIAMETER = "EquivalentDiameter"
+    F_HU_MOMENT_0 = "HuMoment_0"
+    F_HU_MOMENT_1 = "HuMoment_1"
+    F_HU_MOMENT_2 = "HuMoment_2"
+    F_HU_MOMENT_3 = "HuMoment_3"
+    F_HU_MOMENT_4 = "HuMoment_4"
+    F_HU_MOMENT_5 = "HuMoment_5"
+    F_HU_MOMENT_6 = "HuMoment_6"
+    F_INERTIA_TENSOR_0_0 = "InertiaTensor_0_0"
+    F_INERTIA_TENSOR_0_1 = "InertiaTensor_0_1"
+    F_INERTIA_TENSOR_1_0 = "InertiaTensor_1_0"
+    F_INERTIA_TENSOR_1_1 = "InertiaTensor_1_1"
+    F_INERTIA_TENSOR_EIGENVALUES_0 = "InertiaTensorEigenvalues_0"
+    F_INERTIA_TENSOR_EIGENVALUES_1 = "InertiaTensorEigenvalues_1"
+    F_NORMALIZED_MOMENT_0_0 = "NormalizedMoment_0_0"
+    F_NORMALIZED_MOMENT_0_1 = "NormalizedMoment_0_1"
+    F_NORMALIZED_MOMENT_0_2 = "NormalizedMoment_0_2"
+    F_NORMALIZED_MOMENT_0_3 = "NormalizedMoment_0_3"
+    F_NORMALIZED_MOMENT_1_0 = "NormalizedMoment_1_0"
+    F_NORMALIZED_MOMENT_1_1 = "NormalizedMoment_1_1"
+    F_NORMALIZED_MOMENT_1_2 = "NormalizedMoment_1_2"
+    F_NORMALIZED_MOMENT_1_3 = "NormalizedMoment_1_3"
+    F_NORMALIZED_MOMENT_2_0 = "NormalizedMoment_2_0"
+    F_NORMALIZED_MOMENT_2_1 = "NormalizedMoment_2_1"
+    F_NORMALIZED_MOMENT_2_2 = "NormalizedMoment_2_2"
+    F_NORMALIZED_MOMENT_2_3 = "NormalizedMoment_2_3"
+    F_NORMALIZED_MOMENT_3_0 = "NormalizedMoment_3_0"
+    F_NORMALIZED_MOMENT_3_1 = "NormalizedMoment_3_1"
+    F_NORMALIZED_MOMENT_3_2 = "NormalizedMoment_3_2"
+    F_NORMALIZED_MOMENT_3_3 = "NormalizedMoment_3_3"
+    F_SPATIAL_MOMENT_0_0 = "SpatialMoment_0_0"
+    F_SPATIAL_MOMENT_0_1 = "SpatialMoment_0_1"
+    F_SPATIAL_MOMENT_0_2 = "SpatialMoment_0_2"
+    F_SPATIAL_MOMENT_0_3 = "SpatialMoment_0_3"
+    F_SPATIAL_MOMENT_1_0 = "SpatialMoment_1_0"
+    F_SPATIAL_MOMENT_1_1 = "SpatialMoment_1_1"
+    F_SPATIAL_MOMENT_1_2 = "SpatialMoment_1_2"
+    F_SPATIAL_MOMENT_1_3 = "SpatialMoment_1_3"
+    F_SPATIAL_MOMENT_2_0 = "SpatialMoment_2_0"
+    F_SPATIAL_MOMENT_2_1 = "SpatialMoment_2_1"
+    F_SPATIAL_MOMENT_2_2 = "SpatialMoment_2_2"
+    F_SPATIAL_MOMENT_2_3 = "SpatialMoment_2_3"
+
+    """The non-Zernike features"""
+    F_STD_2D = [
+        F_AREA,
+        F_PERIMETER,
+        F_MAXIMUM_RADIUS,
+        F_MEAN_RADIUS,
+        F_MEDIAN_RADIUS,
+        F_MIN_FERET_DIAMETER,
+        F_MAX_FERET_DIAMETER,
+        F_ORIENTATION,
+        F_ECCENTRICITY,
+        F_FORM_FACTOR,
+        F_SOLIDITY,
+        F_CONVEX_AREA,
+        F_COMPACTNESS,
+        F_BBOX_AREA,
+    ]
+    F_STD_3D = [
+        F_VOLUME,
+        F_SURFACE_AREA,
+        F_CENTER_Z,
+        F_BBOX_VOLUME,
+        F_MIN_Z,
+        F_MAX_Z,
+    ]
+    F_ADV_2D = [
+        F_SPATIAL_MOMENT_0_0,
+        F_SPATIAL_MOMENT_0_1,
+        F_SPATIAL_MOMENT_0_2,
+        F_SPATIAL_MOMENT_0_3,
+        F_SPATIAL_MOMENT_1_0,
+        F_SPATIAL_MOMENT_1_1,
+        F_SPATIAL_MOMENT_1_2,
+        F_SPATIAL_MOMENT_1_3,
+        F_SPATIAL_MOMENT_2_0,
+        F_SPATIAL_MOMENT_2_1,
+        F_SPATIAL_MOMENT_2_2,
+        F_SPATIAL_MOMENT_2_3,
+        F_CENTRAL_MOMENT_0_0,
+        F_CENTRAL_MOMENT_0_1,
+        F_CENTRAL_MOMENT_0_2,
+        F_CENTRAL_MOMENT_0_3,
+        F_CENTRAL_MOMENT_1_0,
+        F_CENTRAL_MOMENT_1_1,
+        F_CENTRAL_MOMENT_1_2,
+        F_CENTRAL_MOMENT_1_3,
+        F_CENTRAL_MOMENT_2_0,
+        F_CENTRAL_MOMENT_2_1,
+        F_CENTRAL_MOMENT_2_2,
+        F_CENTRAL_MOMENT_2_3,
+        F_NORMALIZED_MOMENT_0_0,
+        F_NORMALIZED_MOMENT_0_1,
+        F_NORMALIZED_MOMENT_0_2,
+        F_NORMALIZED_MOMENT_0_3,
+        F_NORMALIZED_MOMENT_1_0,
+        F_NORMALIZED_MOMENT_1_1,
+        F_NORMALIZED_MOMENT_1_2,
+        F_NORMALIZED_MOMENT_1_3,
+        F_NORMALIZED_MOMENT_2_0,
+        F_NORMALIZED_MOMENT_2_1,
+        F_NORMALIZED_MOMENT_2_2,
+        F_NORMALIZED_MOMENT_2_3,
+        F_NORMALIZED_MOMENT_3_0,
+        F_NORMALIZED_MOMENT_3_1,
+        F_NORMALIZED_MOMENT_3_2,
+        F_NORMALIZED_MOMENT_3_3,
+        F_HU_MOMENT_0,
+        F_HU_MOMENT_1,
+        F_HU_MOMENT_2,
+        F_HU_MOMENT_3,
+        F_HU_MOMENT_4,
+        F_HU_MOMENT_5,
+        F_HU_MOMENT_6,
+        F_INERTIA_TENSOR_0_0,
+        F_INERTIA_TENSOR_0_1,
+        F_INERTIA_TENSOR_1_0,
+        F_INERTIA_TENSOR_1_1,
+        F_INERTIA_TENSOR_EIGENVALUES_0,
+        F_INERTIA_TENSOR_EIGENVALUES_1,
+    ]
+    F_ADV_3D = [F_SOLIDITY]
+    F_STANDARD = [
+        F_EXTENT,
+        F_EULER_NUMBER,
+        F_EQUIVALENT_DIAMETER,
+        F_MAJOR_AXIS_LENGTH,
+        F_MINOR_AXIS_LENGTH,
+        F_CENTER_X,
+        F_CENTER_Y,
+        F_MIN_X,
+        F_MIN_Y,
+        F_MAX_X,
+        F_MAX_Y,
+    ]

{cellprofiler_library_nightly-5.0.0.dev243 → cellprofiler_library_nightly-5.0.0.dev259}/cellprofiler_library_nightly.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-library-nightly
-Version: 5.0.0.dev243
+Version: 5.0.0.dev259
 Summary: cellprofiler-library implements CellProfiler's image processing and mathematical code, and is usable as a standalone library
 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_library_nightly-5.0.0.dev243 → cellprofiler_library_nightly-5.0.0.dev259}/cellprofiler_library_nightly.egg-info/SOURCES.txt

@@ -19,6 +19,7 @@ cellprofiler_library/modules/_expandorshrinkobjects.py
 cellprofiler_library/modules/_fillobjects.py
 cellprofiler_library/modules/_gaussianfilter.py
 cellprofiler_library/modules/_measureimageoverlap.py
+cellprofiler_library/modules/_measureobjectsizeshape.py
 cellprofiler_library/modules/_medialaxis.py
 cellprofiler_library/modules/_medianfilter.py
 cellprofiler_library/modules/_morphologicalskeleton.py
@@ -30,6 +31,7 @@ cellprofiler_library/modules/_threshold.py
 cellprofiler_library/modules/_watershed.py
 cellprofiler_library/opts/__init__.py
 cellprofiler_library/opts/measureimageoverlap.py
+cellprofiler_library/opts/objectsizeshapefeatures.py
 cellprofiler_library_nightly.egg-info/PKG-INFO
 cellprofiler_library_nightly.egg-info/SOURCES.txt
 cellprofiler_library_nightly.egg-info/dependency_links.txt