dcnum 0.10.0__tar.gz → 0.11.1__tar.gz

{dcnum-0.10.0 → dcnum-0.11.1}/.github/workflows/deploy_pypi.yml

@@ -6,21 +6,16 @@ on:
       - '*'
 
 jobs:
-  build_wheels:
-    name: Build wheels on ${{ matrix.os }}
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        python-version: ['3.10', '3.11']
-        os: [ubuntu-20.04, windows-2019, macos-11]
-
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
 
-      - name: Build wheels
-        uses: pypa/cibuildwheel@v2.12.1
+      - name: Build sdist
+        run: pipx run build --sdist
 
       - name: publish
         env:
@@ -28,9 +23,9 @@ jobs:
           TWINE_PASSWORD: ${{ secrets.PYPI_PWD }}
         run: |
           pipx install twine
-          twine upload --skip-existing wheelhouse/*
+          twine upload --skip-existing dist/*
 
-  build_sdist:
+  build_wheels:
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
@@ -39,7 +34,7 @@ jobs:
           fetch-depth: 0
 
       - name: Build sdist
-        run: pipx run build --sdist
+        run: pipx run build --wheel
 
       - name: publish
         env:

{dcnum-0.10.0 → dcnum-0.11.1}/CHANGELOG

@@ -1,4 +1,11 @@
-0.0.10
+0.11.1
+ - fix: fix GPUSegmenter labeling
+0.11.0
+ - feat: introduce GPUSegmenter base class
+ - fix: handle bytes-values in HDF5 attributes
+ - ref: correctly introduce `requires_background_correction` for segmenters
+ - setup: don't requrie cibuildwheel
+0.10.0
  - enh: some minor improvements in efficiency
  - ref: increment DCNUM_PPID_GENERATION for the sake of clarity
  - ref: unify dealing with num_workers and debugging

{dcnum-0.10.0 → dcnum-0.11.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcnum
-Version: 0.10.0
+Version: 0.11.1
 Summary: numerics toolbox for imaging deformability cytometry
 Author: Paul Müller
 Maintainer-email: Paul Müller <dev@craban.de>

{dcnum-0.10.0 → 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 = '0.10.0'
-__version_tuple__ = version_tuple = (0, 10, 0)
+__version__ = version = '0.11.1'
+__version_tuple__ = version_tuple = (0, 11, 1)

{dcnum-0.10.0 → dcnum-0.11.1}/dcnum/read/hdf5_data.py

@@ -91,6 +91,9 @@ class HDF5Data:
                            locking=False,
                            ) as h5:
                 self.meta = dict(h5.attrs)
+                for key in self.meta:
+                    if isinstance(self.meta[key], bytes):
+                        self.meta[key] = self.meta[key].decode("utf-8")
                 for key in h5.get("logs", []):
                     alog = list(h5["logs"][key])
                     if isinstance(alog[0], bytes):

{dcnum-0.10.0 → dcnum-0.11.1}/dcnum/segm/__init__.py

@@ -3,6 +3,7 @@ import functools
 
 from .segmenter import Segmenter
 from .segmenter_cpu import CPUSegmenter
+from .segmenter_gpu import GPUSegmenter
 from .segmenter_manager_thread import SegmenterManagerThread
 from . import segm_thresh
 

{dcnum-0.10.0 → dcnum-0.11.1}/dcnum/segm/segmenter.py

@@ -19,8 +19,8 @@ class Segmenter(abc.ABC):
     #: Default keyword arguments for mask post-processing. See `process_mask`
     #: for available options.
     mask_default_kwargs = {}
-    #: If the segmenter requires a background image, set this to True
-    requires_background = False
+    #: If the segmenter requires a background-corrected image, set this to True
+    requires_background_correction = False
 
     def __init__(self, kwargs_mask=None, debug=False, **kwargs):
         """Base segemnter
@@ -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:
@@ -232,7 +234,7 @@ class Segmenter(abc.ABC):
     def segment_approach(image):
         """Perform segmentation and return integer label or binary mask image
 
-        This is the approach the subclasses implements.
+        This is the approach the subclasses implement.
         """
 
     @abc.abstractmethod

dcnum-0.11.1/dcnum/segm/segmenter_gpu.py

@@ -0,0 +1,46 @@
+import abc
+import pathlib
+
+import numpy as np
+import scipy.ndimage as ndi
+
+
+from .segmenter import Segmenter
+
+
+class GPUSegmenter(Segmenter, abc.ABC):
+    mask_postprocessing = False
+
+    def __init__(self, model_file=None, *args, **kwargs):
+        super(GPUSegmenter, self).__init__(*args, **kwargs)
+        self.model_path = self._get_model_path(model_file)
+
+    @staticmethod
+    def _get_model_path(model_file):
+        """Custom hook that may be defined by subclasses"""
+        return pathlib.Path(model_file)
+
+    def segment_batch(self,
+                      image_data: np.ndarray,
+                      start: int = None,
+                      stop: int = None):
+        if stop is None or start is None:
+            start = 0
+            stop = len(image_data)
+
+        image_slice = image_data[start:stop]
+        segm = self.segment_frame_wrapper()
+
+        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-0.10.0 → dcnum-0.11.1}/dcnum.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcnum
-Version: 0.10.0
+Version: 0.11.1
 Summary: numerics toolbox for imaging deformability cytometry
 Author: Paul Müller
 Maintainer-email: Paul Müller <dev@craban.de>

{dcnum-0.10.0 → dcnum-0.11.1}/dcnum.egg-info/SOURCES.txt

@@ -40,6 +40,7 @@ dcnum/segm/__init__.py
 dcnum/segm/segm_thresh.py
 dcnum/segm/segmenter.py
 dcnum/segm/segmenter_cpu.py
+dcnum/segm/segmenter_gpu.py
 dcnum/segm/segmenter_manager_thread.py
 dcnum/write/__init__.py
 dcnum/write/deque_writer_thread.py

{dcnum-0.10.0 → dcnum-0.11.1}/pyproject.toml

@@ -1,12 +1,5 @@
 [build-system]
-# Defined by PEP 518:
-# use oldest-supported-numpy (https://github.com/pypa/pip/issues/9542#issuecomment-771200755)
-requires = [
-    # for building Cython extensions
-    "cython", "oldest-supported-numpy", "setuptools", "wheel",
-    # for version management
-    "setuptools>=45", "setuptools_scm[toml]>=6.2"
-]
+requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2"]
 build-backend = "setuptools.build_meta"
 
 [project]