cellprofiler-core-nightly 5.0.0.dev475__tar.gz → 5.0.0.dev501__tar.gz

{cellprofiler_core_nightly-5.0.0.dev475 → cellprofiler_core_nightly-5.0.0.dev501}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-core-nightly
-Version: 5.0.0.dev475
+Version: 5.0.0.dev501
 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.dev475 → cellprofiler_core_nightly-5.0.0.dev501}/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.dev475'
-__version_tuple__ = version_tuple = (5, 0, 0, 'dev475')
+__version__ = version = '5.0.0.dev501'
+__version_tuple__ = version_tuple = (5, 0, 0, 'dev501')
 
-__commit_id__ = commit_id = 'gc4686c345'
+__commit_id__ = commit_id = 'gb8fc0acf1'

{cellprofiler_core_nightly-5.0.0.dev475 → cellprofiler_core_nightly-5.0.0.dev501}/cellprofiler_core/image/_image.py

@@ -1,7 +1,7 @@
 import math
 import numpy
 
-from cellprofiler_library.functions.image_processing import crop_image
+from cellprofiler_library.functions.image_processing import crop_image_similarly
 
 class Image:
     """
@@ -287,31 +287,7 @@ class Image:
 
         image - a np.ndarray to be cropped (of any type)
         """
-        if image.shape[:2] == self.pixel_data.shape[:2]:
-            # Same size - no cropping needed
-            return image
-        if any(
-            [
-                my_size > other_size
-                for my_size, other_size in zip(self.pixel_data.shape, image.shape)
-            ]
-        ):
-            raise ValueError(
-                "Image to be cropped is smaller: %s vs %s"
-                % (repr(image.shape), repr(self.pixel_data.shape))
-            )
-        if not self.has_crop_mask:
-            raise RuntimeError(
-                "Images are of different size and no crop mask available.\n"
-                "Use the Crop and Align modules to match images of different sizes."
-            )
-        cropped_image = crop_image(image, self.crop_mask)
-        if cropped_image.shape[0:2] != self.pixel_data.shape[0:2]:
-            raise ValueError(
-                "Cropped image is not the same size as the reference image: %s vs %s"
-                % (repr(cropped_image.shape), repr(self.pixel_data.shape))
-            )
-        return cropped_image
+        return crop_image_similarly(self.pixel_data, image, self.crop_mask)
 
     @property
     def file_name(self):

{cellprofiler_core_nightly-5.0.0.dev475 → cellprofiler_core_nightly-5.0.0.dev501}/cellprofiler_core/utilities/core/object.py

@@ -3,7 +3,7 @@ import numpy
 import skimage.color
 
 from ...preferences import get_default_colormap
-
+from cellprofiler_library.functions.object_processing import size_similarly as _size_similarly
 
 def crop_labels_and_image(labels, image):
     """Crop a labels matrix and an image to the lowest common size
@@ -48,35 +48,7 @@ def size_similarly(labels, secondary):
     Either the mask is all ones or the result is a copy, so you can
     modify the output within the unmasked region w/o destroying the original.
     """
-    if labels.shape[:2] == secondary.shape[:2]:
-        return secondary, numpy.ones(secondary.shape, bool)
-    if labels.shape[0] <= secondary.shape[0] and labels.shape[1] <= secondary.shape[1]:
-        if secondary.ndim == 2:
-            return (
-                secondary[: labels.shape[0], : labels.shape[1]],
-                numpy.ones(labels.shape, bool),
-            )
-        else:
-            return (
-                secondary[: labels.shape[0], : labels.shape[1], :],
-                numpy.ones(labels.shape, bool),
-            )
-
-    #
-    # Some portion of the secondary matrix does not cover the labels
-    #
-    result = numpy.zeros(
-        list(labels.shape) + list(secondary.shape[2:]), secondary.dtype
-    )
-    i_max = min(secondary.shape[0], labels.shape[0])
-    j_max = min(secondary.shape[1], labels.shape[1])
-    if secondary.ndim == 2:
-        result[:i_max, :j_max] = secondary[:i_max, :j_max]
-    else:
-        result[:i_max, :j_max, :] = secondary[:i_max, :j_max, :]
-    mask = numpy.zeros(labels.shape, bool)
-    mask[:i_max, :j_max] = 1
-    return result, mask
+    return _size_similarly(labels, secondary)
 
 
 def overlay_labels(pixel_data, labels, opacity=0.7, max_label=None, seed=None):

{cellprofiler_core_nightly-5.0.0.dev475 → cellprofiler_core_nightly-5.0.0.dev501}/cellprofiler_core_nightly.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-core-nightly
-Version: 5.0.0.dev475
+Version: 5.0.0.dev501
 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>