dcnum 0.11.0__py3-none-any.whl → 0.11.1__py3-none-any.whl

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/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/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.dist-info → dcnum-0.11.1.dist-info}/METADATA

@@ -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.dist-info → dcnum-0.11.1.dist-info}/RECORD

@@ -1,5 +1,5 @@
 dcnum/__init__.py,sha256=hcawIKS7utYiOyVhOAX9t7K3xYzP1b9862VV0b6qSrQ,74
-dcnum/_version.py,sha256=Zl7Bo-WQiiNZwnp-zeuyFKzcZ9ykPaawnk_0wuzNx2I,162
+dcnum/_version.py,sha256=faVe-ZqiCxNFY2N3XG4067QpoPpTt1Bvjudys2n4bGY,162
 dcnum/feat/__init__.py,sha256=0oX765AyfL1BcVt-FI6R_i6x5LgYYLeyO5lkxSauI0Y,299
 dcnum/feat/event_extractor_manager_thread.py,sha256=lu0Xw64JiSRYMPRnW7GJQwuX56mfELZaZ7DOqUYIrcQ,5458
 dcnum/feat/gate.py,sha256=UEHbj3hkMWNm4tlY8Tz8sOsruhByjJxgO1s-ztQ7WTw,6235
@@ -25,9 +25,9 @@ dcnum/read/const.py,sha256=SVlvEJiRIHyTyUlWG24_ogcnT5nTxCi0CRslNuNP56I,282
 dcnum/read/hdf5_data.py,sha256=vTft5pCaI4dr8kqclWDdA5vA7XFHnQ7GQcAGn7hx9KQ,11702
 dcnum/segm/__init__.py,sha256=BNFn7VvWsRmOzxCtvr4AXi3mmWsJSsQlEmGlq7umCac,510
 dcnum/segm/segm_thresh.py,sha256=fim5HRNWq0DUhVRwLf6nmu4gOHAFtydGDRS1Ww_XzFo,1134
-dcnum/segm/segmenter.py,sha256=dvCHFkxk-Xe5UupgJ609NK2iDB9BkyXBc6OVYBRghIg,8929
+dcnum/segm/segmenter.py,sha256=5YAwkFOA8UcdEDEXQ-DP1YvDTnlSKFwg-XQRNwJc140,9006
 dcnum/segm/segmenter_cpu.py,sha256=O9t9SYenZz8Cbu9FIAxv8uU8cebQVUp1Abe4Rf53tKE,9626
-dcnum/segm/segmenter_gpu.py,sha256=LoFCjIW3-XQ79O0HJspJkDpIXc7qf3jTQz5jkFnkK24,879
+dcnum/segm/segmenter_gpu.py,sha256=F-6H425eQc9B2-k5PURJziU5uQubdF96GTkoysD2JDM,1312
 dcnum/segm/segmenter_manager_thread.py,sha256=-GsNJrljPOvDLRJLe0OB6AObQVIRo1xj5nnR_j-nOnA,4951
 dcnum/write/__init__.py,sha256=Oy-ORTyzUUswsaJvd0C6LyXtOgAY0iTIRqFNU9d7M8Y,160
 dcnum/write/deque_writer_thread.py,sha256=UUn5OYxDvckvhLw3llLYu7y8MI7RfsOhdJhMonKKB3k,1625
@@ -54,8 +54,8 @@ tests/test_write_deque_writer_thread.py,sha256=EAnqKayr4_jskv_599QYD3gdBZhtyVM7-
 tests/test_write_writer.py,sha256=SzNTLsHz4RZceRwqflc4Wfn02vYc4Hb4WQVk1X8dmiw,1107
 tests/data/fmt-hdf5_cytoshot_full-features_2023.zip,sha256=LfkFxAXTIkcqxrJYYNMC364Q1x5HT5X9cTHuNz5eeuk,650653
 tests/data/fmt-hdf5_cytoshot_full-features_legacy_allev_2023.zip,sha256=z2Bk6u3wjr-bJa7sOxBcNKOQ0Zoi3Xmf_cMi6d-3CMk,154010
-dcnum-0.11.0.dist-info/LICENSE,sha256=YRChA1C8A2E-amJbudwMcbTCZy_HzmeY0hMIvduh1MM,1089
-dcnum-0.11.0.dist-info/METADATA,sha256=B2F6UhQaUvCBD_WQUNCoEj2YcptDKkaHhsey9cdJUhc,2180
-dcnum-0.11.0.dist-info/WHEEL,sha256=pkctZYzUS4AYVn6dJ-7367OJZivF2e8RA9b_ZBjif18,92
-dcnum-0.11.0.dist-info/top_level.txt,sha256=Utc_P-_-7hbtniTp00IsHTry4h3rY5KFmwHfYM9g44k,22
-dcnum-0.11.0.dist-info/RECORD,,
+dcnum-0.11.1.dist-info/LICENSE,sha256=YRChA1C8A2E-amJbudwMcbTCZy_HzmeY0hMIvduh1MM,1089
+dcnum-0.11.1.dist-info/METADATA,sha256=4z1DpHSXes9Ka1AVn9PyaD_-46x9pykbL47oovbhylg,2180
+dcnum-0.11.1.dist-info/WHEEL,sha256=pkctZYzUS4AYVn6dJ-7367OJZivF2e8RA9b_ZBjif18,92
+dcnum-0.11.1.dist-info/top_level.txt,sha256=Utc_P-_-7hbtniTp00IsHTry4h3rY5KFmwHfYM9g44k,22
+dcnum-0.11.1.dist-info/RECORD,,