PyPI - dcnum - Versions diffs - 0.20.4__tar.gz → 0.21.1__tar.gz - Mend

@@ -19,7 +19,7 @@ class Segmenter(abc.ABC):
     #: Whether to enable mask post-processing. If disabled, you should
     #: make sure that your mask is properly defined and cleaned or you
     #: have to call `process_mask` in your `segment_approach` implementation.
-    mask_postprocessing = False
+    mask_postprocessing = True
     #: Default keyword arguments for mask post-processing. See `process_mask`
     #: for available options.
     mask_default_kwargs = {}
@@ -184,8 +184,8 @@ class Segmenter(abc.ABC):
         Parameters
         ----------
-        labels: 2d integer ndarray
-            Labeled input (contains blobs with same number)
+        labels: 2d integer or boolean ndarray
+            Labeled input (contains blobs consisting of unique numbers)
         clear_border: bool
             clear the image boarder using
             :func:`skimage.segmentation.clear_border`
@@ -196,6 +196,12 @@ class Segmenter(abc.ABC):
             if > 0, perform a binary closing with a disk
             of that radius in pixels
         """
+        if labels.dtype == np.bool_:
+            # Convert mask image to labels
+            labels, _ = ndi.label(
+                input=labels,
+                structure=ndi.generate_binary_structure(2, 2))
         if clear_border:
             #
             # from skimage import segmentation

@@ -1,3 +1,9 @@
+0.21.1
+ - enh: support boolean images in mask postprocessing
+0.21.0
+ - fix: GPUSegmenter did not perform mask postprocessing
+ - ref: enable mask postprocessing by default for all segmenters
+ - ref: increment DCNUM_PPID_GENERATION to 9
 0.20.4
  - fix: slot_chunks were not performed in increasing order, making it
    impossible for writer to continue writing and consequent OOM

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcnum
-Version: 0.20.4
+Version: 0.21.1
 Summary: numerics toolbox for imaging deformability cytometry
 Author: Maximilian Schlögel, Paul Müller
 Maintainer-email: Paul Müller <dev@craban.de>

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
-__version__ = version = '0.20.4'
-__version_tuple__ = version_tuple = (0, 20, 4)
+__version__ = version = '0.21.1'
+__version_tuple__ = version_tuple = (0, 21, 1)

@@ -10,7 +10,7 @@ import warnings
 #: Increment this string if there are breaking changes that make
 #: previous pipelines unreproducible.
-DCNUM_PPID_GENERATION = "8"
+DCNUM_PPID_GENERATION = "9"
 class ClassWithPPIDCapabilities(Protocol):

@@ -10,7 +10,6 @@ from .segmenter import Segmenter
 class GPUSegmenter(Segmenter, abc.ABC):
     hardware_processor = "gpu"
-    mask_postprocessing = False
     def __init__(self,
                  *,

dcnum 0.20.4tar.gz → 0.21.1tar.gz

@@ -37,6 +37,12 @@ class MockImageData:
         return chunk
+def test_segmenter_properties():
+    assert segm.CPUSegmenter.mask_postprocessing  # sanity check
+    assert segm.GPUSegmenter.mask_postprocessing  # fixed in 0.21.0
+    assert segm.Segmenter.mask_postprocessing  # new default in 0.21.0
 def test_segmenter_labeled_mask():
     mask = np.array([
         [0, 0, 0, 0, 0, 0, 0, 0],