cellprofiler-library-nightly 5.0.0.dev496__tar.gz → 5.0.0.dev501__tar.gz

{cellprofiler_library_nightly-5.0.0.dev496 → cellprofiler_library_nightly-5.0.0.dev501}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-library-nightly
-Version: 5.0.0.dev496
+Version: 5.0.0.dev501
 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.dev501/cellprofiler_library/__init__.py

@@ -0,0 +1 @@
+from .measurement_model import LibraryMeasurements

{cellprofiler_library_nightly-5.0.0.dev496 → cellprofiler_library_nightly-5.0.0.dev501}/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.dev496'
-__version_tuple__ = version_tuple = (5, 0, 0, 'dev496')
+__version__ = version = '5.0.0.dev501'
+__version_tuple__ = version_tuple = (5, 0, 0, 'dev501')
 
-__commit_id__ = commit_id = 'g8d098d2ce'
+__commit_id__ = commit_id = 'gb8fc0acf1'

cellprofiler_library_nightly-5.0.0.dev501/cellprofiler_library/measurement_model.py

@@ -0,0 +1,154 @@
+from typing import Any, Dict, List
+from pydantic import BaseModel, Field, ConfigDict
+
+class LibraryMeasurements(BaseModel):
+    """
+    A Pydantic implementation mirroring CellProfiler's Measurements class functionality.
+    
+    This class represents measurements for a single image set context, designed to be
+    constructed from and serializable to the "Primitive Dictionary" contract.
+    """
+    model_config = ConfigDict(
+        arbitrary_types_allowed=True, 
+        populate_by_name=True
+    )
+
+    # Primary data structures matching the MDC contract
+    image: Dict[str, Any] = Field(default_factory=dict)
+    objects: Dict[str, Dict[str, Any]] = Field(default_factory=dict)
+    
+    # Additional storage for full Measurements compatibility (e.g. Experiment metadata)
+    experiment: Dict[str, Any] = Field(default_factory=dict)
+    
+    # Placeholder for relationships if needed in the future
+    relationships: List[Dict[str, Any]] = Field(default_factory=list)
+
+    def add_measurement(self, object_name: str, feature_name: str, data: Any):
+        """
+        Add a measurement. Mirrors Measurements.add_measurement.
+        
+        Args:
+            object_name: Name of the object (e.g., 'Image', 'Nuclei').
+            feature_name: Name of the feature (e.g., 'AreaShape_Area').
+            data: The value to store (float, string, or numpy array).
+        """
+        if object_name == "Experiment":
+            self.experiment[feature_name] = data
+        elif object_name == "Image":
+            self.image[feature_name] = data
+        else:
+            if object_name not in self.objects:
+                self.objects[object_name] = {}
+            self.objects[object_name][feature_name] = data
+
+    def get_measurement(self, object_name: str, feature_name: str) -> Any:
+        """
+        Get a measurement. Mirrors Measurements.get_measurement.
+        """
+        if object_name == "Experiment":
+            return self.experiment.get(feature_name)
+        elif object_name == "Image":
+            return self.image.get(feature_name)
+        else:
+            return self.objects.get(object_name, {}).get(feature_name)
+
+    def add_image_measurement(self, feature_name: str, data: Any):
+        """Helper to add an image measurement."""
+        self.add_measurement("Image", feature_name, data)
+
+    def add_experiment_measurement(self, feature_name: str, data: Any):
+        """Helper to add an experiment measurement."""
+        self.add_measurement("Experiment", feature_name, data)
+
+    def get_experiment_measurement(self, feature_name: str) -> Any:
+        """Helper to get an experiment measurement."""
+        return self.get_measurement("Experiment", feature_name)
+    
+    def get_object_names(self) -> List[str]:
+        """Return a list of all object names (including Image and Experiment if present)."""
+        names = list(self.objects.keys())
+        if self.image:
+            names = ["Image"] + names
+        if self.experiment:
+            names = ["Experiment"] + names
+        return names
+
+    def get_feature_names(self, object_name: str) -> List[str]:
+        """Return feature names for a specific object."""
+        if object_name == "Experiment":
+            return list(self.experiment.keys())
+        elif object_name == "Image":
+            return list(self.image.keys())
+        else:
+            return list(self.objects.get(object_name, {}).keys())
+            
+    def has_feature(self, object_name: str, feature_name: str) -> bool:
+        """Check if a feature exists."""
+        if object_name == "Experiment":
+            return feature_name in self.experiment
+        elif object_name == "Image":
+            return feature_name in self.image
+        else:
+            return feature_name in self.objects.get(object_name, {})
+
+    def __getitem__(self, key):
+        """Support dict-style access: m['Image', 'Count_Cells']"""
+        if isinstance(key, tuple):
+             assert len(key) == 2
+             return self.get_measurement(*key)
+        raise KeyError("Invalid key format. Expected (Object, Feature)")
+        
+    def __setitem__(self, key, value):
+        """Support dict-style assignment: m['Image', 'Count_Cells'] = 5"""
+        if isinstance(key, tuple):
+             assert len(key) == 2
+             self.add_measurement(*key, value)
+        else:
+             raise KeyError("Invalid key format. Expected (Object, Feature)")
+
+    def to_dict(self) -> Dict[str, Any]:
+        """
+        Serialize to the primitive dictionary format required by the refactoring contract.
+        """
+        return self.model_dump(exclude_none=True)
+
+    def merge(self, other: 'LibraryMeasurements') -> 'LibraryMeasurements':
+        """
+        Merge this LibraryMeasurements object with another one, returning a new instance.
+        
+        Collision resolution:
+        - Image measurements: 'other' overwrites 'self'
+        - Experiment measurements: 'other' overwrites 'self'
+        - Object measurements: Merged by object name. Within an object, 'other' features overwrite 'self'.
+        - Relationships: Concatenated
+        
+        Args:
+            other: Another LibraryMeasurements instance
+            
+        Returns:
+            A new LibraryMeasurements instance containing merged data
+        """
+        # Create deep copies of dictionaries to avoid side effects
+        new_image = self.image.copy()
+        new_image.update(other.image)
+        
+        new_experiment = self.experiment.copy()
+        new_experiment.update(other.experiment)
+        
+        new_objects = {}
+        # Merge objects
+        all_objects = set(self.objects.keys()) | set(other.objects.keys())
+        for obj_name in all_objects:
+            obj_measurements = self.objects.get(obj_name, {}).copy()
+            obj_measurements.update(other.objects.get(obj_name, {}))
+            new_objects[obj_name] = obj_measurements
+            
+        # Concatenate relationships
+        new_relationships = self.relationships + other.relationships
+        
+        return LibraryMeasurements(
+            image=new_image,
+            objects=new_objects,
+            experiment=new_experiment,
+            relationships=new_relationships
+        )

{cellprofiler_library_nightly-5.0.0.dev496 → cellprofiler_library_nightly-5.0.0.dev501}/cellprofiler_library/modules/_measurecolocalization.py

@@ -1,11 +1,12 @@
 import numpy as np
 from numpy.typing import NDArray
-from typing import List, Tuple, Annotated, Optional, Dict, Union
+from typing import List, Tuple, Annotated, Optional, Union
 from pydantic import validate_call, ConfigDict, BeforeValidator, Field
 from cellprofiler_library.functions.measurement import measure_correlation_and_slope_from_objects, measure_manders_coefficient_from_objects, measure_rwc_coefficient_from_objects, measure_overlap_coefficient_from_objects, measure_costes_coefficient_from_objects, get_thresholded_images_and_counts, measure_correlation_and_slope, measure_manders_coefficient, measure_rwc_coefficient, measure_overlap_coefficient, measure_costes_coefficient
 from cellprofiler_library.opts.measurecolocalization import TemplateMeasurementFormat, MeasurementType
 from cellprofiler_library.types import ImageGrayscale, ImageGrayscaleMask, Pixel, ObjectLabel, ObjectSegmentation, ImageAny, ImageAnyMask
 from cellprofiler_library.opts.measurecolocalization import CostesMethod
+from cellprofiler_library.measurement_model import LibraryMeasurements
 from cellprofiler_library.functions.image_processing import crop_image_similarly
 from cellprofiler_library.functions.object_processing import size_similarly, object_crop_image_similarly
 
@@ -121,14 +122,14 @@ def run_image_pair_images(
     costes_method:      Annotated[Optional[CostesMethod], Field(description="")] = CostesMethod.FAST,
     ) -> Annotated[
         Tuple[
-            Dict[str, np.float64],
+            LibraryMeasurements,
             List[Tuple[str, str, str, str, str]]
         ], Field(description="List of measurement results and a dictionary of measurements with precise values")]:
     """Calculate the correlation between the pixels of two images"""
 
 
     summary: List[Tuple[str, str, str, str, str]] = []
-    measurements: Dict[str, np.float64] = {}
+    measurements = LibraryMeasurements()
     corr =      np.float64(np.NaN)
     slope =     np.float64(np.NaN)
     C1 =        np.float64(np.NaN)
@@ -210,22 +211,22 @@ def run_image_pair_images(
     costes_measurement_2 = TemplateMeasurementFormat.COSTES_FORMAT % (im2_name, im1_name)
     
     if MeasurementType.CORRELATION in measurement_types:
-        measurements[corr_measurement] = corr
-        measurements[slope_measurement] = slope
+        measurements.add_image_measurement(corr_measurement, corr)
+        measurements.add_image_measurement(slope_measurement, slope)
     if MeasurementType.OVERLAP in measurement_types:        
-        measurements[overlap_measurement] = overlap
-        measurements[k_measurement_1] = K1
-        measurements[k_measurement_2] = K2
+        measurements.add_image_measurement(overlap_measurement, overlap)
+        measurements.add_image_measurement(k_measurement_1, K1)
+        measurements.add_image_measurement(k_measurement_2, K2)
 
     if MeasurementType.MANDERS in measurement_types:
-        measurements[manders_measurement_1] = M1
-        measurements[manders_measurement_2] = M2
+        measurements.add_image_measurement(manders_measurement_1, M1)
+        measurements.add_image_measurement(manders_measurement_2, M2)
     if MeasurementType.RWC in measurement_types:
-        measurements[rwc_measurement_1] = RWC1
-        measurements[rwc_measurement_2] = RWC2
+        measurements.add_image_measurement(rwc_measurement_1, RWC1)
+        measurements.add_image_measurement(rwc_measurement_2, RWC2)
     if MeasurementType.COSTES in measurement_types:
-        measurements[costes_measurement_1] = C1
-        measurements[costes_measurement_2] = C2
+        measurements.add_image_measurement(costes_measurement_1, C1)
+        measurements.add_image_measurement(costes_measurement_2, C2)
 
     return measurements, summary
 
@@ -259,7 +260,7 @@ def run_image_pair_objects(
     im2_scale:          Annotated[Optional[Union[float, int]], Field(description="Second image scale for costes thresholding")]=None,
     costes_method:      Annotated[Optional[CostesMethod], Field(description="Costes method for costes thresholding")]=CostesMethod.FAST
     ) -> Tuple[
-        Dict[str, NDArray[np.float64]],
+        LibraryMeasurements,
         List[Tuple[str, str, str, str, str]]
         ]:
     if MeasurementType.COSTES in measurement_types:
@@ -346,41 +347,40 @@ def run_image_pair_objects(
             summary += __get_object_result_array((im2_name, im1_name, object_name), "Manders coeff (Costes)", C2)
 
 
-    measurements: Dict[str, NDArray[np.float64]] = {}
+    measurements = LibraryMeasurements()
+    
     if MeasurementType.CORRELATION in measurement_types:
         measurement = TemplateMeasurementFormat.CORRELATION_FORMAT % (im1_name, im2_name)
-        measurements[measurement] = corr
+        measurements.add_measurement(object_name, measurement, corr)
     if MeasurementType.MANDERS in measurement_types:
         manders_measurement_1 = TemplateMeasurementFormat.MANDERS_FORMAT % (im1_name, im2_name)
         manders_measurement_2 = TemplateMeasurementFormat.MANDERS_FORMAT % (im2_name, im1_name)
         
-        measurements[manders_measurement_1] = M1
-        measurements[manders_measurement_2] = M2
+        measurements.add_measurement(object_name, manders_measurement_1, M1)
+        measurements.add_measurement(object_name, manders_measurement_2, M2)
     
     if MeasurementType.RWC in measurement_types:
         rwc_measurement_1 = TemplateMeasurementFormat.RWC_FORMAT % (im1_name, im2_name)
         rwc_measurement_2 = TemplateMeasurementFormat.RWC_FORMAT % (im2_name, im1_name)
 
-        measurements[rwc_measurement_1] = RWC1
-        measurements[rwc_measurement_2] = RWC2
+        measurements.add_measurement(object_name, rwc_measurement_1, RWC1)
+        measurements.add_measurement(object_name, rwc_measurement_2, RWC2)
     
     if MeasurementType.OVERLAP in measurement_types:
         overlap_measurement = TemplateMeasurementFormat.OVERLAP_FORMAT % (im1_name, im2_name)
         k_measurement_1 = TemplateMeasurementFormat.K_FORMAT % (im1_name, im2_name)
         k_measurement_2 = TemplateMeasurementFormat.K_FORMAT % (im2_name, im1_name)
         
-        measurements[overlap_measurement] = overlap
-        measurements[k_measurement_1] = K1
-        measurements[k_measurement_2] = K2
+        measurements.add_measurement(object_name, overlap_measurement, overlap)
+        measurements.add_measurement(object_name, k_measurement_1, K1)
+        measurements.add_measurement(object_name, k_measurement_2, K2)
     
     if MeasurementType.COSTES in measurement_types:
         costes_measurement_1 = TemplateMeasurementFormat.COSTES_FORMAT % (im1_name, im2_name)
         costes_measurement_2 = TemplateMeasurementFormat.COSTES_FORMAT % (im2_name, im1_name)
         
-        measurements[costes_measurement_1] = C1
-        measurements[costes_measurement_2] = C2
-
-    if n_objects == 0:
+        measurements.add_measurement(object_name, costes_measurement_1, C1)
+        measurements.add_measurement(object_name, costes_measurement_2, C2)
         col_order_1 = (im1_name, im2_name, object_name)
         summary +=  [
             (*col_order_1, "Mean correlation", "-"),

{cellprofiler_library_nightly-5.0.0.dev496 → cellprofiler_library_nightly-5.0.0.dev501}/cellprofiler_library_nightly.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-library-nightly
-Version: 5.0.0.dev496
+Version: 5.0.0.dev501
 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.dev496 → cellprofiler_library_nightly-5.0.0.dev501}/cellprofiler_library_nightly.egg-info/SOURCES.txt

@@ -4,6 +4,7 @@ environment.yml
 pyproject.toml
 cellprofiler_library/__init__.py
 cellprofiler_library/_version.py
+cellprofiler_library/measurement_model.py
 cellprofiler_library/py.typed
 cellprofiler_library/types.py
 cellprofiler_library/functions/__init__.py