cellprofiler-library-nightly 5.0.0.dev509__tar.gz → 5.0.0.dev512__tar.gz

{cellprofiler_library_nightly-5.0.0.dev509 → cellprofiler_library_nightly-5.0.0.dev512}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-library-nightly
-Version: 5.0.0.dev509
+Version: 5.0.0.dev512
 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.dev509 → cellprofiler_library_nightly-5.0.0.dev512}/cellprofiler_library/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '5.0.0.dev509'
-__version_tuple__ = version_tuple = (5, 0, 0, 'dev509')
+__version__ = version = '5.0.0.dev512'
+__version_tuple__ = version_tuple = (5, 0, 0, 'dev512')
 
-__commit_id__ = commit_id = 'gc5c07ce88'
+__commit_id__ = commit_id = 'g36bc7931b'

{cellprofiler_library_nightly-5.0.0.dev509 → cellprofiler_library_nightly-5.0.0.dev512}/cellprofiler_library/functions/measurement.py

@@ -11,7 +11,7 @@ import centrosome.fastemd
 
 from centrosome.cpmorphology import fixup_scipy_ndimage_result as fix
 from sklearn.cluster import KMeans
-from typing import Tuple, Optional, Dict, Callable, List
+from typing import Tuple, Optional, Dict, Callable, List, Union
 from scipy.linalg import lstsq
 from numpy.typing import NDArray
 
@@ -1419,8 +1419,7 @@ def get_granularity_measurements(
         granular_spectrum_length: int,
         dimensions: int,
         object_records: List[ObjectRecord]
-        ):
-    # TODO: PR #5034 update the return types of this funciton
+        ) -> Tuple[List[List[List[Union[str, NDArray[numpy.float64]]]]], List[float]]:
     # Transcribed from the Matlab module: granspectr function
     #
     # CALCULATES GRANULAR SPECTRUM, ALSO KNOWN AS SIZE DISTRIBUTION,
@@ -1445,14 +1444,12 @@ def get_granularity_measurements(
     measurements_arr = []
     image_measurements_arr = []
 
-    statistics = []
     for i in range(1, ng + 1):
         prevmean = currentmean
         ero = masked_erode(ero, mask, footprint)
         rec = skimage.morphology.reconstruction(ero, pixels, footprint=footprint)
         currentmean = np.mean(rec[mask])
         gs = (prevmean - currentmean) * 100 / startmean
-        statistics += ["%.2f" % gs]
         image_measurements_arr += [gs]
         # measurements.add_image_measurement(feature, gs)
         #
@@ -1484,5 +1481,6 @@ def get_granularity_measurements(
                 gss = np.zeros((0,))
             obj_measurements += [[object_record.name, gss]]
         measurements_arr += [obj_measurements]
-    return measurements_arr, image_measurements_arr, statistics
+    return measurements_arr, image_measurements_arr
 
+            

cellprofiler_library_nightly-5.0.0.dev512/cellprofiler_library/modules/_measuregranularity.py

@@ -0,0 +1,80 @@
+from pydantic import validate_call, ConfigDict, Field
+from typing import Annotated, List, Dict, Any, Tuple
+from enum import Enum
+import numpy as np
+
+from cellprofiler_library.measurement_model import LibraryMeasurements
+from cellprofiler_library.functions.measurement import get_granularity_measurements, ObjectRecord
+from cellprofiler_library.functions.image_processing import apply_grayscale_tophat_filter, downsample_image_and_mask
+from cellprofiler_library.types import ImageGrayscale, ImageGrayscaleMask
+
+class GranularityMeasurementFormat(str, Enum):
+    GRANULARITY = "Granularity_%d_%s"
+
+@validate_call(config=ConfigDict(arbitrary_types_allowed=True))
+def measure_granularity(
+        image_name:                 Annotated[str, Field(description="Name of the image")],
+        im_pixel_data:              Annotated[ImageGrayscale, Field(description="Pixel values of the image")],
+        im_mask:                    Annotated[ImageGrayscaleMask, Field(description="Boolean mask of where the measurements should be made")],
+        subsample_size:             Annotated[float, Field(description="Subsampling factor for granularity measurements")],
+        image_sample_size:          Annotated[float, Field(description="Subsampling factor for background reduction")],
+        element_size:               Annotated[int, Field(description="Radius of structuring element")],
+        object_records:             Annotated[List[ObjectRecord], Field(description="Object records")],
+        granular_spectrum_length:   Annotated[int, Field(description="Range of the granular spectrum")],
+        dimensions:                 Annotated[int, Field(description="Dimensionality of the image")] = 2,
+        ) -> Tuple[LibraryMeasurements, List[str]]:
+    #
+    # Downsample the image and mask
+    #
+    pixels, mask, new_shape = downsample_image_and_mask(im_pixel_data, im_mask, dimensions, subsample_size)
+    
+    #
+    # Remove background pixels using a greyscale tophat filter
+    #
+    pixels = apply_grayscale_tophat_filter(pixels, mask, dimensions, image_sample_size, element_size, new_shape)
+    
+    #
+    # Compute measurements
+    #
+    measurements_arr, image_measurements_arr = get_granularity_measurements(
+        im_pixel_data,
+        pixels, 
+        mask, 
+        new_shape,
+        granular_spectrum_length,
+        dimensions,
+        object_records
+    )
+
+    measurements = LibraryMeasurements()
+    stats_strings = []
+
+    # Process Image Measurements
+    for i, gs_value in enumerate(image_measurements_arr):
+        spectrum_index = i + 1
+        feature_name = GranularityMeasurementFormat.GRANULARITY % (spectrum_index, image_name)
+        measurements.add_image_measurement(feature_name, gs_value)
+        stats_strings.append("%.2f" % gs_value)
+
+    # Process Object Measurements
+    # measurements_arr is list of lists. Outer list index i corresponds to spectrum_index i+1.
+    for i, obj_measurements_list in enumerate(measurements_arr):
+        spectrum_index = i + 1
+        feature_name = GranularityMeasurementFormat.GRANULARITY % (spectrum_index, image_name)
+        
+        for obj_name, obj_gss in obj_measurements_list:
+            measurements.add_measurement(obj_name, feature_name, obj_gss)
+            
+            # Calculate stats for this object measurement and add to Image measurements
+            stat_name_base = f"{feature_name}_{obj_name}"
+            
+            measurements.add_image_measurement(f"Mean_{stat_name_base}", np.mean(obj_gss) if len(obj_gss) > 0 else 0.0)
+            measurements.add_image_measurement(f"Median_{stat_name_base}", np.median(obj_gss) if len(obj_gss) > 0 else 0.0)
+            measurements.add_image_measurement(f"Max_{stat_name_base}", np.max(obj_gss) if len(obj_gss) > 0 else 0.0)
+            measurements.add_image_measurement(f"Min_{stat_name_base}", np.min(obj_gss) if len(obj_gss) > 0 else 0.0)
+            measurements.add_image_measurement(f"StDev_{stat_name_base}", np.std(obj_gss) if len(obj_gss) > 0 else 0.0)
+
+    # Summary for UI display
+    summary = [image_name] + stats_strings
+    
+    return measurements, summary

{cellprofiler_library_nightly-5.0.0.dev509 → cellprofiler_library_nightly-5.0.0.dev512}/cellprofiler_library_nightly.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-library-nightly
-Version: 5.0.0.dev509
+Version: 5.0.0.dev512
 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.dev509/cellprofiler_library/modules/_measuregranularity.py

@@ -1,42 +0,0 @@
-from pydantic import validate_call, ConfigDict, Field
-from typing import Annotated, List
-from cellprofiler_library.functions.measurement import get_granularity_measurements, ObjectRecord
-from cellprofiler_library.functions.image_processing import apply_grayscale_tophat_filter, downsample_image_and_mask
-from cellprofiler_library.types import ImageGrayscale, ImageGrayscaleMask
-
-@validate_call(config=ConfigDict(arbitrary_types_allowed=True))
-def measure_granularity(
-        im_pixel_data:              Annotated[ImageGrayscale, Field(description="Pixel values of the image")],
-        im_mask:                    Annotated[ImageGrayscaleMask, Field(description="Boolean mask of where the measurements should be made")],
-        subsample_size:             Annotated[float, Field(description="Subsampling factor for granularity measurements")],
-        image_sample_size:          Annotated[float, Field(description="Subsampling factor for background reduction")],
-        element_size:               Annotated[int, Field(description="Radius of structuring element")],
-        object_records:             Annotated[List[ObjectRecord], Field(description="Object records")],
-        granular_spectrum_length:   Annotated[int, Field(description="Range of the granular spectrum")],
-        dimensions:                 Annotated[int, Field(description="Dimensionality of the image")] = 2,
-        ):
-    # TODO: PR #5034 update the return types of this funciton
-    #
-    # Downsample the image and mask
-    #
-    pixels, mask, new_shape = downsample_image_and_mask(im_pixel_data, im_mask, dimensions, subsample_size)
-    
-    #
-    # Remove background pixels using a greyscale tophat filter
-    #
-    pixels = apply_grayscale_tophat_filter(pixels, mask, dimensions, image_sample_size, element_size, new_shape)
-    
-    #
-    # Compute measurements
-    #
-    _measurements_arr, _image_measurements_arr, _statistics = get_granularity_measurements(
-        im_pixel_data,
-        pixels, 
-        mask, 
-        new_shape,
-        granular_spectrum_length,
-        dimensions,
-        object_records
-    )
-
-    return _measurements_arr, _image_measurements_arr, _statistics