dcnum 0.11.0__tar.gz → 0.11.1__tar.gz

{dcnum-0.11.0 → dcnum-0.11.1}/CHANGELOG

@@ -1,3 +1,5 @@
+0.11.1
+ - fix: fix GPUSegmenter labeling
 0.11.0
  - feat: introduce GPUSegmenter base class
  - fix: handle bytes-values in HDF5 attributes

{dcnum-0.11.0 → dcnum-0.11.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcnum
-Version: 0.11.0
+Version: 0.11.1
 Summary: numerics toolbox for imaging deformability cytometry
 Author: Paul Müller
 Maintainer-email: Paul Müller <dev@craban.de>

{dcnum-0.11.0 → dcnum-0.11.1}/dcnum/_version.py

@@ -1,4 +1,4 @@
 # file generated by setuptools_scm
 # don't change, don't track in version control
-__version__ = version = '0.11.0'
-__version_tuple__ = version_tuple = (0, 11, 0)
+__version__ = version = '0.11.1'
+__version_tuple__ = version_tuple = (0, 11, 1)

{dcnum-0.11.0 → dcnum-0.11.1}/dcnum/segm/segmenter.py

@@ -173,7 +173,9 @@ class Segmenter(abc.ABC):
             labels_uint8 = np.array(labels, dtype=np.uint8)
             labels_dilated = cv2.dilate(labels_uint8, element)
             labels_eroded = cv2.erode(labels_dilated, element)
-            labels, _ = ndi.label(labels_eroded > 0)
+            labels, _ = ndi.label(
+                input=labels_eroded > 0,
+                structure=ndi.generate_binary_structure(2, 2))
 
         if fill_holes:
             # Floodfill only works with uint8 (too small) or int32
@@ -206,7 +208,7 @@ class Segmenter(abc.ABC):
         mol = segm_wrap(image)
         if mol.dtype == bool:
             # convert mask to label
-            labels, num_labels = ndi.label(
+            labels, _ = ndi.label(
                 input=mol,
                 structure=ndi.generate_binary_structure(2, 2))
         else:

{dcnum-0.11.0 → dcnum-0.11.1}/dcnum/segm/segmenter_gpu.py

@@ -2,6 +2,7 @@ import abc
 import pathlib
 
 import numpy as np
+import scipy.ndimage as ndi
 
 
 from .segmenter import Segmenter
@@ -10,7 +11,7 @@ from .segmenter import Segmenter
 class GPUSegmenter(Segmenter, abc.ABC):
     mask_postprocessing = False
 
-    def __init__(self, model_file, *args, **kwargs):
+    def __init__(self, model_file=None, *args, **kwargs):
         super(GPUSegmenter, self).__init__(*args, **kwargs)
         self.model_path = self._get_model_path(model_file)
 
@@ -28,6 +29,18 @@ class GPUSegmenter(Segmenter, abc.ABC):
             stop = len(image_data)
 
         image_slice = image_data[start:stop]
-        segm = self.segment_frame_wrapper(self.model_path)
+        segm = self.segment_frame_wrapper()
 
-        return segm(image_slice)
+        labels = segm(image_slice)
+
+        # Make sure we have integer labels
+        if labels.dtype == bool:
+            new_labels = np.zeros_like(labels, dtype=np.uint16)
+            for ii in range(len(labels)):
+                ndi.label(
+                    input=labels[ii],
+                    output=new_labels[ii],
+                    structure=ndi.generate_binary_structure(2, 2))
+            labels = new_labels
+
+        return labels

{dcnum-0.11.0 → dcnum-0.11.1}/dcnum.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcnum
-Version: 0.11.0
+Version: 0.11.1
 Summary: numerics toolbox for imaging deformability cytometry
 Author: Paul Müller
 Maintainer-email: Paul Müller <dev@craban.de>