dclab 0.62.12__tar.gz → 0.62.13__tar.gz

{dclab-0.62.12 → dclab-0.62.13}/CHANGELOG

@@ -1,3 +1,5 @@
+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

{dclab-0.62.12 → dclab-0.62.13}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: dclab
-Version: 0.62.12
+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-0.62.12 → dclab-0.62.13}/dclab/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.62.12'
-__version_tuple__ = version_tuple = (0, 62, 12)
+__version__ = version = '0.62.13'
+__version_tuple__ = version_tuple = (0, 62, 13)

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-0.62.12 → 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-0.62.12 → dclab-0.62.13}/dclab.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: dclab
-Version: 0.62.12
+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-0.62.12 → 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-0.62.12/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