dclab 0.62.11__tar.gz → 0.62.13__tar.gz

{dclab-0.62.11 → dclab-0.62.13}/.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-0.62.11 → dclab-0.62.13}/CHANGELOG

@@ -1,3 +1,7 @@
+0.62.13
+ - ref: add custom table class for `hdf5` and `dcor` formats
+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

{dclab-0.62.11 → dclab-0.62.13}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: dclab
-Version: 0.62.11
+Version: 0.62.13
 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-0.62.11 → dclab-0.62.13}/dclab/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.62.11'
-__version_tuple__ = version_tuple = (0, 62, 11)
+__version__ = version = '0.62.13'
+__version_tuple__ = version_tuple = (0, 62, 13)

{dclab-0.62.11 → dclab-0.62.13}/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-0.62.13/dclab/rtdc_dataset/fmt_dcor/tables.py

@@ -0,0 +1,64 @@
+import numpy as np
+
+
+class DCORTables:
+    def __init__(self, api):
+        self.api = api
+        self._tables_cache = None
+
+    def __contains__(self, key):
+        return key in self.keys()
+
+    def __getitem__(self, key):
+        return self._tables[key]
+
+    def __iter__(self):
+        for key in self.keys():
+            yield key
+
+    def __len__(self):
+        return len(self._tables)
+
+    def keys(self):
+        return self._tables.keys()
+
+    @property
+    def _tables(self):
+        if self._tables_cache is None:
+            table_data = self.api.get(query="tables")
+            # assemble the tables
+            tables = {}
+            for key in table_data:
+                tables[key] = DCORTable(table_data[key])
+
+            self._tables_cache = tables
+        return self._tables_cache
+
+
+class DCORTable:
+    def __init__(self, table_content):
+        self._columns, data = table_content
+        self._tab_data = np.asarray(data)
+        if self._columns is not None:
+            # We have a rec-array (named columns)
+
+            ds_dt = np.dtype({'names': self._columns,
+                              'formats': [np.float64] * len(self._columns)})
+            self._tab_data = np.rec.array(self._tab_data, dtype=ds_dt)
+
+    def __array__(self, *args, **kwargs):
+        return self._tab_data.__array__(*args, **kwargs)
+
+    @property
+    def meta(self):
+        # TODO: Implement metadata sending from DCOR.
+        return {}
+
+    def has_graphs(self):
+        return self._columns is not None
+
+    def keys(self):
+        return self._columns
+
+    def __getitem__(self, key):
+        return self._tab_data[key]

{dclab-0.62.11 → dclab-0.62.13}/dclab/rtdc_dataset/fmt_hdf5/tables.py

@@ -5,7 +5,7 @@ class H5Tables:
 
     def __getitem__(self, key):
         if key in self.keys():
-            tab = self.h5file["tables"][key]
+            tab = H5Table(self.h5file["tables"][key])
         else:
             raise KeyError(f"Table '{key}' not found or empty "
                            f"in {self.h5file.file.filename}!")
@@ -28,3 +28,30 @@ class H5Tables:
                         names.append(key)
             self._cache_keys = names
         return self._cache_keys
+
+
+class H5Table:
+    def __init__(self, h5_ds):
+        self._h5_ds = h5_ds
+        self._keys = None
+        self._meta = None
+
+    def __array__(self, *args, **kwargs):
+        return self._h5_ds.__array__(*args, **kwargs)
+
+    @property
+    def meta(self):
+        if self._meta is None:
+            self._meta = dict(self._h5_ds.attrs)
+        return self._meta
+
+    def has_graphs(self):
+        return self.keys() is not None
+
+    def keys(self):
+        if self._keys is None:
+            self._keys = self._h5_ds.dtype.names
+        return self._keys
+
+    def __getitem__(self, key):
+        return self._h5_ds[key]

{dclab-0.62.11 → dclab-0.62.13}/dclab.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: dclab
-Version: 0.62.11
+Version: 0.62.13
 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-0.62.11 → dclab-0.62.13}/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-0.62.11 → dclab-0.62.13}/tests/test_rtdc_export_hdf5.py

@@ -582,7 +582,7 @@ def test_hdf5_override():
 def test_hdf5_tables(tables):
     keys = ["area_um", "deform", "time", "frame", "index_online"]
     ddict = example_data_dict(size=10, keys=keys)
-    ds1 = dclab.new_dataset(ddict)
+    ds1 = new_dataset(ddict)
     ds1.config["experiment"]["sample"] = "test"
     ds1.config["experiment"]["run index"] = 1
     ds1.config["imaging"]["frame rate"] = 2000
@@ -608,11 +608,18 @@ def test_hdf5_tables(tables):
         else:
             assert "src_iratrax" not in h5.get("tables", {})
 
+    if tables:
+        # reading the file with dclab
+        with new_dataset(f1) as ds:
+            assert "src_iratrax" in ds.tables
+            assert ds.tables["src_iratrax"].has_graphs()
+            assert np.all(ds.tables["src_iratrax"] == rec_arr)
+
 
 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 = new_dataset(ddict)
     ds1.config["experiment"]["sample"] = "test"
     ds1.config["experiment"]["run index"] = 1
     ds1.config["imaging"]["frame rate"] = 2000
@@ -629,6 +636,13 @@ def test_hdf5_tables_array_only():
         assert np.all(h5["tables"]["src_iratrax"] == tab_data)
         assert h5["tables"]["src_iratrax"].attrs["CLASS"] == np.bytes_("IMAGE")
 
+    # reading the file with dclab
+    with new_dataset(f1) as ds:
+        assert "src_iratrax" in ds.tables
+        assert not ds.tables["src_iratrax"].has_graphs()
+        assert np.all(ds.tables["src_iratrax"] == tab_data)
+        assert ds.tables["src_iratrax"].meta["CLASS"] == np.bytes_("IMAGE")
+
 
 def test_hdf5_trace_from_tdms():
     pytest.importorskip("nptdms")

{dclab-0.62.11 → dclab-0.62.13}/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(

dclab-0.62.11/dclab/rtdc_dataset/fmt_dcor/tables.py

@@ -1,42 +0,0 @@
-import numpy as np
-
-
-class DCORTables:
-    def __init__(self, api):
-        self.api = api
-        self._tables_cache = None
-
-    def __contains__(self, key):
-        return key in self.keys()
-
-    def __getitem__(self, key):
-        return self._tables[key]
-
-    def __iter__(self):
-        for key in self.keys():
-            yield key
-
-    def __len__(self):
-        return len(self._tables)
-
-    def keys(self):
-        return self._tables.keys()
-
-    @property
-    def _tables(self):
-        if self._tables_cache is None:
-            table_data = self.api.get(query="tables")
-            # assemble the tables
-            tables = {}
-            for key in table_data:
-                columns, data = table_data[key]
-                tab_data = np.asarray(data)
-                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