dcnum 0.19.0__tar.gz → 0.19.1__tar.gz

{dcnum-0.19.0 → dcnum-0.19.1}/CHANGELOG

@@ -1,3 +1,5 @@
+0.19.1
+ - enh: support steps when specifying data slices in `index_mapping`
 0.19.0
  - enh: elevate `HDF5Data`s `index_mapping` to pipeline identifier status
    (this changes the pipeline identifier)

{dcnum-0.19.0/src/dcnum.egg-info → dcnum-0.19.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcnum
-Version: 0.19.0
+Version: 0.19.1
 Summary: numerics toolbox for imaging deformability cytometry
 Author: Maximilian Schlögel, Paul Müller
 Maintainer-email: Paul Müller <dev@craban.de>

{dcnum-0.19.0 → dcnum-0.19.1}/src/dcnum/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.19.0'
-__version_tuple__ = version_tuple = (0, 19, 0)
+__version__ = version = '0.19.1'
+__version_tuple__ = version_tuple = (0, 19, 1)

{dcnum-0.19.0 → dcnum-0.19.1}/src/dcnum/read/hdf5_data.py

@@ -355,8 +355,12 @@ class HDF5Data:
                 elif val == "0":
                     kwargs["index_mapping"] = None
                 elif val.count("-"):
-                    start, stop = [int(v) for v in val.split("-")]
-                    kwargs["index_mapping"] = slice(start, stop)
+                    start, stop, step = val.split("-")
+                    kwargs["index_mapping"] = slice(
+                        None if start == "n" else int(start),
+                        None if stop == "n" else int(stop),
+                        None if step == "n" else int(step)
+                    )
                 else:
                     kwargs["index_mapping"] = int(val)
             else:

{dcnum-0.19.0 → dcnum-0.19.1}/src/dcnum/read/mapped.py

@@ -54,12 +54,10 @@ def _get_mapping_indices_cached(
         return np.arange(index_mapping)
     elif isinstance(index_mapping, tuple):
         im_slice = slice(*index_mapping)
-        if im_slice.step is not None:
-            raise NotImplementedError("Slices with step not implemented yet")
         if im_slice.stop is None or im_slice.start is None:
             raise NotImplementedError(
                 "Slices must have start and stop defined")
-        return np.arange(im_slice.start, im_slice.stop)
+        return np.arange(im_slice.start, im_slice.stop, im_slice.step)
     elif isinstance(index_mapping, list):
         return np.array(index_mapping, dtype=np.uint32)
     else:

{dcnum-0.19.0 → dcnum-0.19.1/src/dcnum.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcnum
-Version: 0.19.0
+Version: 0.19.1
 Summary: numerics toolbox for imaging deformability cytometry
 Author: Maximilian Schlögel, Paul Müller
 Maintainer-email: Paul Müller <dev@craban.de>

{dcnum-0.19.0 → dcnum-0.19.1}/tests/test_meta_ppid_data.py

@@ -12,7 +12,9 @@ def test_ppid_decoding_dat_check_kwargs():
 @pytest.mark.parametrize("imppid,value", [
     ["0", None],
     ["10", 10],
-    ["10-20", slice(10, 20)]
+    ["10-20-n", slice(10, 20)],
+    ["10-20-2", slice(10, 20, 2)],
+    ["n-n-2", slice(None, None, 2)],
 ])
 def test_ppid_decoding_dat_check_kwargs_index_mapping(imppid, value):
     dat_ppid = f"hdf:p=0.2658^i={imppid}"

{dcnum-0.19.0 → dcnum-0.19.1}/tests/test_read_hdf5.py

@@ -158,6 +158,25 @@ def test_image_cache_iter_chunks(size, chunks, tmp_path):
         assert list(hic.iter_chunks()) == list(range(chunks))
 
 
+@pytest.mark.parametrize("index_mapping,result_data", [
+    [2, [0, 1]],
+    [slice(1, 10, 2), [1, 3, 5, 7, 9]],
+    [slice(1, 11, 3), [1, 4, 7, 10]],
+    [slice(10, 11), [10]],
+    [slice(1, 3, None), [1, 2]],
+])
+def test_index_mapping(index_mapping, result_data):
+    path = retrieve_data(
+        "fmt-hdf5_cytoshot_full-features_legacy_allev_2023.zip")
+    with h5py.File(path, "a") as h5:
+        size = len(h5["events/image"])
+        assert size == 11
+        h5["events/temp"] = np.arange(size, dtype=np.float64)
+
+    with read.HDF5Data(path, index_mapping=index_mapping) as hd:
+        assert np.allclose(hd["temp"], result_data)
+
+
 def test_keyerror_when_image_is_none(tmp_path):
     path = tmp_path / "test.hdf5"
     with h5py.File(path, "w") as hw: