dcnum 0.17.0__tar.gz → 0.17.2__tar.gz

{dcnum-0.17.0 → dcnum-0.17.2}/CHANGELOG

@@ -1,3 +1,10 @@
+0.17.2
+ - fix: make sure unsupported features are not propagated in
+   `concatenated_hdf5_data` (#27)
+0.17.1
+ - ref: remove "bg_med" and "index_online" from protected scalar features,
+   because "bg_med" may change due to a different background computation
+   method and "index_online" enumerates events from online segmentation
 0.17.0
  - feat: allow to register topical search paths
  - ref: remove deprecated `get_ppid_from_kwargs` methods

{dcnum-0.17.0 → dcnum-0.17.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcnum
-Version: 0.17.0
+Version: 0.17.2
 Summary: numerics toolbox for imaging deformability cytometry
 Author: Maximilian Schlögel, Paul Müller
 Maintainer-email: Paul Müller <dev@craban.de>

{dcnum-0.17.0 → dcnum-0.17.2}/src/dcnum/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.17.0'
-__version_tuple__ = version_tuple = (0, 17, 0)
+__version__ = version = '0.17.2'
+__version_tuple__ = version_tuple = (0, 17, 2)

{dcnum-0.17.0 → dcnum-0.17.2}/src/dcnum/read/const.py

@@ -1,10 +1,9 @@
-#: Scalar features that apply to all events in a frame
+#: Scalar features that apply to all events in a frame and which are
+#: not computed from image or image_bg data.
 PROTECTED_FEATURES = [
-    "bg_med",
     "flow_rate",
     "frame",
     "g_force",
-    "index_online",
     "pressure",
     "temp",
     "temp_amb",

{dcnum-0.17.0 → dcnum-0.17.2}/src/dcnum/read/hdf5_data.py

@@ -432,6 +432,7 @@ def concatenated_hdf5_data(paths: List[pathlib.Path],
                     if not isinstance(h5["events"][feat], h5py.Dataset):
                         warnings.warn(
                             f"Ignoring {feat}; not implemented yet!")
+                        continue
                     if feat in ["frame", "time"]:
                         continue
                     shapes.setdefault(feat, []).append(

{dcnum-0.17.0 → dcnum-0.17.2}/src/dcnum.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcnum
-Version: 0.17.0
+Version: 0.17.2
 Summary: numerics toolbox for imaging deformability cytometry
 Author: Maximilian Schlögel, Paul Müller
 Maintainer-email: Paul Müller <dev@craban.de>

{dcnum-0.17.0 → dcnum-0.17.2}/tests/test_read_concat_hdf5.py

@@ -54,6 +54,27 @@ def test_concat_basic_to_file(tmp_path):
     assert path_out.exists()
 
 
+def test_concat_ignore_contour(tmp_path):
+    # get file wtih contour information
+    path = retrieve_data(data_path /
+                         "fmt-hdf5_cytoshot_full-features_2023.zip")
+    cdata = np.array([[2, 2], [2, 3], [2, 5], [4, 5], [4, 2]])
+    with h5py.File(path, mode="a") as h5:
+        contour = h5["events"].create_group("contour")
+
+        for ii in range(40):
+            contour.create_dataset(name=f"{ii}", data=cdata, dtype=np.uint64)
+
+    path_out = tmp_path / "test.rtdc"
+    with pytest.warns(UserWarning,
+                      match="Ignoring contour; not implemented yet!"):
+        data = read.concatenated_hdf5_data([path, path, path],
+                                           path_out=path_out)
+
+    assert "deform" in data
+    assert "conotur" not in data
+
+
 def test_concat_invalid_input_feature_number():
     path = retrieve_data(data_path /
                          "fmt-hdf5_cytoshot_full-features_2023.zip")

{dcnum-0.17.0 → dcnum-0.17.2}/tests/test_read_hdf5.py

@@ -201,7 +201,10 @@ def test_open_real_data():
 
         # scalar features
         fsc = h5dat.features_scalar_frame
-        exp = ['bg_med', 'frame', 'time']
+        # Changed in version 0.17.1: bg_med is not returned anymore,
+        # because it is computed from the background image which
+        # depends on the background method employed.
+        exp = ['frame', 'time']
         assert set(fsc) == set(exp)
 
         # feature names