dcnum 0.25.3__tar.gz → 0.25.5__tar.gz

{dcnum-0.25.3 → dcnum-0.25.5}/CHANGELOG

@@ -1,3 +1,8 @@
+0.25.5
+ - enh: support unnamed table data in `HDF5Data`
+ - setup: pin scipy<1.15 due to https://github.com/scipy/scipy/issues/22333
+0.25.4
+ - enh: support passing a single file to `concatenated_hdf5_data`
 0.25.3
  - enh: request single threaded operations when going into mp.Process (#17)
  - enh: new module `dcnum.single_thread_osenv`

{dcnum-0.25.3 → dcnum-0.25.5}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: dcnum
-Version: 0.25.3
+Version: 0.25.5
 Summary: numerics toolbox for imaging deformability cytometry
 Author: Maximilian Schlögel, Paul Müller, Raghava Alajangi
 Maintainer-email: Paul Müller <dev@craban.de>
@@ -24,7 +24,7 @@ Requires-Dist: numba<1,>=0.60
 Requires-Dist: numpy<3,>=1.21
 Requires-Dist: opencv-python-headless<5,>=4
 Requires-Dist: scikit-image<1,>=0.24
-Requires-Dist: scipy<2,>=1.8.0
+Requires-Dist: scipy<1.15.0,>=1.8.0
 Provides-Extra: torch
 Requires-Dist: torch>=2.2; extra == "torch"
 

{dcnum-0.25.3 → dcnum-0.25.5}/pyproject.toml

@@ -32,7 +32,8 @@ dependencies = [
     "numpy>=1.21, <3",  # BSD
     "opencv-python-headless>=4, <5",  # Apache 2.0
     "scikit-image>=0.24, <1",  # BSD
-    "scipy>=1.8.0, <2",  # BSD
+    # https://github.com/scipy/scipy/issues/22333
+    "scipy>=1.8.0, <1.15.0",  # BSD
 ]
 dynamic = ["version"]
 

{dcnum-0.25.3 → dcnum-0.25.5}/src/dcnum/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.25.3'
-__version_tuple__ = version_tuple = (0, 25, 3)
+__version__ = version = '0.25.5'
+__version_tuple__ = version_tuple = (0, 25, 5)

{dcnum-0.25.3 → dcnum-0.25.5}/src/dcnum/read/hdf5_data.py

@@ -198,11 +198,17 @@ class HDF5Data:
                         self.logs[key] = alog
                 # tables
                 for tab in sorted(h5.get("tables", {}).keys()):
-                    tabdict = {}
-                    for tkey in h5["tables"][tab].dtype.fields.keys():
-                        tabdict[tkey] = \
-                            np.array(h5["tables"][tab][tkey]).reshape(-1)
-                    self.tables[tab] = tabdict
+                    fields = h5["tables"][tab].dtype.fields
+                    if fields is None:
+                        # No individual curves, but an image array
+                        self.tables[tab] = h5["tables"][tab][:]
+                    else:
+                        # List of curves with predefined dtypes
+                        tabdict = {}
+                        for tkey in fields.keys():
+                            tabdict[tkey] = \
+                                np.array(h5["tables"][tab][tkey]).reshape(-1)
+                        self.tables[tab] = tabdict
                 # basins
                 basins = self.extract_basin_dicts(h5)
                 self.basins = sorted(basins, key=lambda x: x["name"])
@@ -593,8 +599,11 @@ def concatenated_hdf5_data(paths: List[pathlib.Path],
         raise ValueError(
             f"Invalid type for `path_out`: {type(path_out)} ({path_out}")
 
-    if len(paths) <= 1:
-        raise ValueError("Please specify at least two files in `paths`!")
+    if len(paths) == 0:
+        raise ValueError("Please specify at least one file in `paths`!")
+    elif len(paths) == 1:
+        warnings.warn("Only one file passed to `concatenated_hdf5_data`; this "
+                      "is equivalent to using `HDF5Data`, but slower.")
 
     frames = []
 

{dcnum-0.25.3 → dcnum-0.25.5}/src/dcnum.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: dcnum
-Version: 0.25.3
+Version: 0.25.5
 Summary: numerics toolbox for imaging deformability cytometry
 Author: Maximilian Schlögel, Paul Müller, Raghava Alajangi
 Maintainer-email: Paul Müller <dev@craban.de>
@@ -24,7 +24,7 @@ Requires-Dist: numba<1,>=0.60
 Requires-Dist: numpy<3,>=1.21
 Requires-Dist: opencv-python-headless<5,>=4
 Requires-Dist: scikit-image<1,>=0.24
-Requires-Dist: scipy<2,>=1.8.0
+Requires-Dist: scipy<1.15.0,>=1.8.0
 Provides-Extra: torch
 Requires-Dist: torch>=2.2; extra == "torch"
 

{dcnum-0.25.3 → dcnum-0.25.5}/src/dcnum.egg-info/requires.txt

@@ -5,7 +5,7 @@ numba<1,>=0.60
 numpy<3,>=1.21
 opencv-python-headless<5,>=4
 scikit-image<1,>=0.24
-scipy<2,>=1.8.0
+scipy<1.15.0,>=1.8.0
 
 [torch]
 torch>=2.2

{dcnum-0.25.3 → dcnum-0.25.5}/tests/test_read_concat_hdf5.py

@@ -89,9 +89,15 @@ def test_concat_invalid_input_path():
 
 
 def test_concat_invalid_input_path_number():
+    with pytest.raises(ValueError, match="Please specify at least one"):
+        read.concatenated_hdf5_data([])
+
+
+def test_concat_invalid_input_path_number_warn():
     path = retrieve_data("fmt-hdf5_cytoshot_full-features_2023.zip")
-    with pytest.raises(ValueError, match="Please specify at least two"):
-        read.concatenated_hdf5_data([path])
+    with pytest.warns(UserWarning, match="is equivalent to using"):
+        hd = read.concatenated_hdf5_data([path])
+        assert len(hd) == 40
 
 
 def test_concat_specify_input_feature_number():

{dcnum-0.25.3 → dcnum-0.25.5}/tests/test_read_hdf5.py

@@ -306,6 +306,30 @@ def test_pickling_state_tables():
                            h5d2.tables["sample_table"][lk])
 
 
+def test_pickling_state_tables_unnamed():
+    path = retrieve_data(
+        "fmt-hdf5_cytoshot_full-features_legacy_allev_2023.zip")
+    # The original file does not contain any tables, so we write
+    # generate a table
+    tab_data = np.random.random((400,200))
+
+    # add table to source file
+    with h5py.File(path, "a") as h5:
+        h5tab = h5.require_group("tables")
+        h5tab.create_dataset(name="unnamed_table",
+                             data=tab_data)
+
+    h5d1 = read.HDF5Data(path)
+    h5d1.pixel_size = 0.124
+    pstate = pickle.dumps(h5d1)
+    h5d2 = pickle.loads(pstate)
+    assert h5d1.tables
+    table = h5d1.tables["unnamed_table"]
+    table2 = h5d2.tables["unnamed_table"]
+    assert np.all(table[:] == tab_data)
+    assert np.all(table2[:] == tab_data)
+
+
 def test_read_empty_logs():
     path = retrieve_data(
         "fmt-hdf5_cytoshot_full-features_legacy_allev_2023.zip")