dclab 0.62.10__tar.gz → 0.62.12__tar.gz

{dclab-0.62.10 → dclab-0.62.12}/.readthedocs.yml

@@ -8,6 +8,8 @@ build:
   jobs:
     post_checkout:
       - git fetch --unshallow || true
+sphinx:
+  configuration: docs/conf.py
 python:
   install:
     - requirements: docs/requirements.txt

{dclab-0.62.10 → dclab-0.62.12}/CHANGELOG

@@ -1,3 +1,7 @@
+0.62.12
+ - fix: viscosity computation for MP-PBS at zero flow rate should be NaN
+0.62.11
+ - enh: support plain `numpy.array` tables
 0.62.10
  - fix: `basin_definition_copy` failed when more than one basins defined
    due to redundant loop

{dclab-0.62.10 → dclab-0.62.12}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: dclab
-Version: 0.62.10
+Version: 0.62.12
 Summary: Library for real-time deformability cytometry (RT-DC)
 Author: Benedikt Hartmann, Eoghan O'Connell, Maik Herbig, Maximilian Schlögel, Nadia Sbaa, Paul Müller, Philipp Rosendahl, Raghava Alajangi
 Maintainer-email: Paul Müller <dev@craban.de>

{dclab-0.62.10 → dclab-0.62.12}/dclab/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.62.10'
-__version_tuple__ = version_tuple = (0, 62, 10)
+__version__ = version = '0.62.12'
+__version_tuple__ = version_tuple = (0, 62, 12)

{dclab-0.62.10 → dclab-0.62.12}/dclab/features/emodulus/viscosity.py

@@ -120,6 +120,10 @@ def get_viscosity(medium: str = "0.49% MC-PBS",
     if medium == "water":
         # We ignore the `model`, because it's user convenient.
         eta = get_viscosity_water_kestin_1978(temperature=temperature)
+    elif not flow_rate:
+        # When flow rate is zero, we cannot compute the viscosity for
+        # anything other than water above.
+        eta = np.nan
     elif medium in ["0.49% MC-PBS", "0.59% MC-PBS", "0.83% MC-PBS"]:
         kwargs = {"medium": medium,
                   "temperature": temperature,

{dclab-0.62.10 → dclab-0.62.12}/dclab/rtdc_dataset/fmt_dcor/tables.py

@@ -30,11 +30,13 @@ class DCORTables:
             tables = {}
             for key in table_data:
                 columns, data = table_data[key]
-                ds_dt = np.dtype({'names': columns,
-                                  'formats': [np.float64] * len(columns)})
                 tab_data = np.asarray(data)
-                rec_arr = np.rec.array(tab_data, dtype=ds_dt)
-                tables[key] = rec_arr
+                if columns is not None:
+                    # We have a rec-array (named columns)
+                    ds_dt = np.dtype({'names': columns,
+                                      'formats': [np.float64] * len(columns)})
+                    tab_data = np.rec.array(tab_data, dtype=ds_dt)
+                tables[key] = tab_data
 
             self._tables_cache = tables
         return self._tables_cache

{dclab-0.62.10 → dclab-0.62.12}/dclab/rtdc_dataset/writer.py

@@ -616,7 +616,7 @@ class RTDCWriter:
                     convfunc = dfn.get_config_value_func(sec, ck)
                     self.h5file.attrs[idk] = convfunc(value)
 
-    def store_table(self, name, cmp_array):
+    def store_table(self, name, cmp_array, h5_attrs=None):
         """Store a compound array table
 
         Tables are semi-metadata. They may contain information collected
@@ -629,16 +629,33 @@ class RTDCWriter:
         ----------
         name: str
             Name of the table
-        cmp_array: np.recarray, h5py.Dataset, or dict
+        cmp_array: np.recarray, h5py.Dataset, np.ndarray, or dict
             If a np.recarray or h5py.Dataset are provided, then they
             are written as-is to the file. If a dictionary is provided,
             then the dictionary is converted into a numpy recarray.
+            If a numpy array is provided, then the array is written
+            as a raw table (no column names) to the file.
+        h5_attrs: dict, optional
+            Attributes to store alongside the corresponding HDF5 dataset
         """
-        if isinstance(cmp_array, (np.recarray, h5py.Dataset)):
+        if h5_attrs is None:
+            h5_attrs = {}
+
+        if isinstance(cmp_array, np.recarray):
             # A table is a compound array (np.recarray). If we are here,
-            # this means that the user passed an instance of np.recarray
-            # or an instance h5py.Dataset (which we trust to be a proper
+            # this means that the user passed an instance of np.recarray.
+            pass
+        elif isinstance(cmp_array, h5py.Dataset):
+            # An instance of h5py.Dataset (which we trust to be a proper
             # compound dataset at this point). No additional steps needed.
+            h5_attrs.update(cmp_array.attrs)
+            pass
+        elif isinstance(cmp_array, np.ndarray):
+            # A numpy array was passed. This usually means we have something
+            # that we can look at, so we add image tags.
+            h5_attrs['CLASS'] = np.bytes_('IMAGE')
+            h5_attrs['IMAGE_VERSION'] = np.bytes_('1.2')
+            h5_attrs['IMAGE_SUBCLASS'] = np.bytes_('IMAGE_GRAYSCALE')
             pass
         elif isinstance(cmp_array, dict):
             # The user passed a dict which we now have to convert to a
@@ -659,16 +676,18 @@ class RTDCWriter:
         else:
             raise NotImplementedError(
                 f"Cannot convert {type(cmp_array)} to table!")
+
+        # data
         group = self.h5file.require_group("tables")
         tab = group.create_dataset(
             name,
             data=cmp_array,
             fletcher32=True,
             **self.compression_kwargs)
-        # Also store metadata
-        if hasattr(cmp_array, "attrs"):
-            for key in cmp_array.attrs:
-                tab.attrs[key] = cmp_array.attrs[key]
+
+        # metadata
+        if h5_attrs:
+            tab.attrs.update(h5_attrs)
 
     def version_brand(self, old_version=None, write_attribute=True):
         """Perform version branding

{dclab-0.62.10 → dclab-0.62.12}/dclab.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: dclab
-Version: 0.62.10
+Version: 0.62.12
 Summary: Library for real-time deformability cytometry (RT-DC)
 Author: Benedikt Hartmann, Eoghan O'Connell, Maik Herbig, Maximilian Schlögel, Nadia Sbaa, Paul Müller, Philipp Rosendahl, Raghava Alajangi
 Maintainer-email: Paul Müller <dev@craban.de>

{dclab-0.62.10 → dclab-0.62.12}/tests/test_feat_emodulus_viscosity.py

@@ -62,6 +62,15 @@ def test_buyukurganci_cell_carrier():
         assert np.allclose(eta, b)
 
 
+def test_buyukurganci_cell_carrier_zero_flow_rate():
+    eta = emodulus.viscosity.get_viscosity(medium="0.59% MC-PBS",
+                                           channel_width=20,
+                                           flow_rate=0,
+                                           temperature=21.5,
+                                           model='buyukurganci-2022')
+    assert np.isnan(eta)
+
+
 @pytest.mark.parametrize("medium", ["0.49% MC-PBS", "0.59% MC-PBS"])
 def test_buyukurganci_mcpbs_range(medium):
     # test values
@@ -166,6 +175,14 @@ def test_kestin_water():
                                            temperature=ref[:, 0])
     assert np.allclose(res, ref[:, 1], rtol=8e-5, atol=0)
 
+    # Since water viscosity is not dependent on flow rate, setting
+    # flow rate to zero should still work.
+    res2 = emodulus.viscosity.get_viscosity(medium="water",
+                                            temperature=ref[:, 0],
+                                            flow_rate=0,
+                                            )
+    assert np.allclose(res2, ref[:, 1], rtol=8e-5, atol=0)
+
 
 def test_kestin_water_range():
     # test values

{dclab-0.62.10 → dclab-0.62.12}/tests/test_rtdc_copier.py

@@ -457,6 +457,31 @@ def test_copy_tables():
             np.pi, 2 * np.pi, 10))
 
 
+def test_copy_tables_array_only():
+    path = retrieve_data("fmt-hdf5_image-bg_2020.zip")
+    path_copy = path.with_name("test_copy.rtdc")
+
+    # generate a table that consists of an array, not a dict-like object
+    tab_data = np.random.random((1000, 300))
+
+    # add table to source file
+    with h5py.File(path, "a") as h5:
+        h5tab = h5.require_group("tables")
+        h5tab.create_dataset(name="random_data",
+                             data=tab_data)
+        assert not is_properly_compressed(h5["tables/random_data"])
+
+    # copy
+    with h5py.File(path) as h5, h5py.File(path_copy, "w") as hc:
+        rtdc_copy(src_h5file=h5,
+                  dst_h5file=hc)
+
+    # Make sure this worked
+    with h5py.File(path_copy) as hc:
+        assert is_properly_compressed(hc["tables/random_data"])
+        assert np.all(tab_data == hc["tables/random_data"])
+
+
 def test_copy_tables_hdf5_issue_3214():
     """Checks for a bug in HDF5
 

{dclab-0.62.10 → dclab-0.62.12}/tests/test_rtdc_export_hdf5.py

@@ -609,6 +609,27 @@ def test_hdf5_tables(tables):
             assert "src_iratrax" not in h5.get("tables", {})
 
 
+def test_hdf5_tables_array_only():
+    keys = ["area_um", "deform", "time", "frame", "index_online"]
+    ddict = example_data_dict(size=10, keys=keys)
+    ds1 = dclab.new_dataset(ddict)
+    ds1.config["experiment"]["sample"] = "test"
+    ds1.config["experiment"]["run index"] = 1
+    ds1.config["imaging"]["frame rate"] = 2000
+
+    # generate a table that consists of an array, not a dict-like object
+    tab_data = np.random.random((1000, 300))
+    ds1.tables["iratrax"] = tab_data
+
+    edest = pathlib.Path(tempfile.mkdtemp())
+    f1 = edest / "dclab_test_export_hdf5_1.rtdc"
+    ds1.export.hdf5(f1, keys, tables=True)
+    with h5py.File(f1, "r") as h5:
+        assert "src_iratrax" in h5.get("tables", {})
+        assert np.all(h5["tables"]["src_iratrax"] == tab_data)
+        assert h5["tables"]["src_iratrax"].attrs["CLASS"] == np.bytes_("IMAGE")
+
+
 def test_hdf5_trace_from_tdms():
     pytest.importorskip("nptdms")
     ds = new_dataset(retrieve_data("fmt-tdms_2fl-no-image_2017.zip"))

{dclab-0.62.10 → dclab-0.62.12}/tests/test_rtdc_fmt_tdms.py

@@ -263,7 +263,11 @@ def test_image_basic():
     # Transition image
     assert np.allclose(ds["image"][0], 0)
     # Real image
-    assert np.allclose(np.average(ds["image"][1]), 45.1490478515625)
+    # 2025-01-23: paulmueller added the atol value, because CI was failing
+    #             on macOS. Possible reason is underlying ffmpeg build
+    #             for M1 etc. arm processors :zany_face:
+    assert np.allclose(np.average(ds["image"][1]), 45.1490478515625,
+                       atol=0.5)
 
 
 @pytest.mark.filterwarnings(