dclab 0.62.13__tar.gz → 0.62.15__tar.gz

{dclab-0.62.13 → dclab-0.62.15}/CHANGELOG

@@ -1,3 +1,8 @@
+0.62.15
+ - fix: support opening files on non-mounted network shares on Windows
+0.62.14
+ - fix: exporting table data broken
+ - ref: introduce base class for tables `TableMeta`
 0.62.13
  - ref: add custom table class for `hdf5` and `dcor` formats
 0.62.12

{dclab-0.62.13 → dclab-0.62.15}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: dclab
-Version: 0.62.13
+Version: 0.62.15
 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-0.62.13 → dclab-0.62.15}/dclab/_version.py

@@ -1,8 +1,13 @@
-# file generated by setuptools_scm
+# file generated by setuptools-scm
 # don't change, don't track in version control
+
+__all__ = ["__version__", "__version_tuple__", "version", "version_tuple"]
+
 TYPE_CHECKING = False
 if TYPE_CHECKING:
-    from typing import Tuple, Union
+    from typing import Tuple
+    from typing import Union
+
     VERSION_TUPLE = Tuple[Union[int, str], ...]
 else:
     VERSION_TUPLE = object
@@ -12,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.62.13'
-__version_tuple__ = version_tuple = (0, 62, 13)
+__version__ = version = '0.62.15'
+__version_tuple__ = version_tuple = (0, 62, 15)

{dclab-0.62.13 → dclab-0.62.15}/dclab/rtdc_dataset/fmt_dcor/tables.py

@@ -1,5 +1,7 @@
 import numpy as np
 
+from ..meta_table import MetaTable
+
 
 class DCORTables:
     def __init__(self, api):
@@ -35,7 +37,7 @@ class DCORTables:
         return self._tables_cache
 
 
-class DCORTable:
+class DCORTable(MetaTable):
     def __init__(self, table_content):
         self._columns, data = table_content
         self._tab_data = np.asarray(data)

{dclab-0.62.13 → dclab-0.62.15}/dclab/rtdc_dataset/fmt_hdf5/tables.py

@@ -1,3 +1,6 @@
+from ..meta_table import MetaTable
+
+
 class H5Tables:
     def __init__(self, h5):
         self.h5file = h5
@@ -30,7 +33,7 @@ class H5Tables:
         return self._cache_keys
 
 
-class H5Table:
+class H5Table(MetaTable):
     def __init__(self, h5_ds):
         self._h5_ds = h5_ds
         self._keys = None

{dclab-0.62.13 → dclab-0.62.15}/dclab/rtdc_dataset/load.py

@@ -61,6 +61,11 @@ def new_dataset(data, identifier=None, **kwargs):
         return fmt_hierarchy.RTDC_Hierarchy(data, identifier=identifier,
                                             **kwargs)
     elif isinstance(data, (pathlib.Path, str)):
+        # If we are given a `file:` specifier, remove it. We might be
+        # looking at a network share (not mounted as a drive) on Windows
+        # (e.g. "file:\\127.0.0.1\shared\data.rtdc").
+        if isinstance(data, str) and data.startswith("file:"):
+            data = data[5:]
         path = pathlib.Path(data).resolve()
         if not path.exists():
             raise FileNotFoundError(

dclab-0.62.15/dclab/rtdc_dataset/meta_table.py

@@ -0,0 +1,25 @@
+import abc
+
+
+class MetaTable(abc.ABC):
+    @abc.abstractmethod
+    def __array__(self, *args, **kwargs):
+        """Return array representation of the table"""
+
+    @property
+    @abc.abstractmethod
+    def meta(self):
+        """Return metadata of the table (e.g. graph colors)"""
+
+    @abc.abstractmethod
+    def has_graphs(self):
+        """Return True when the table has key-based graphs"""
+
+    @abc.abstractmethod
+    def keys(self):
+        """Return keys of the graphs, None if `not self.has_graphs()`"""
+
+    @abc.abstractmethod
+    def __getitem__(self, key):
+        """Return a graph or otherwise part of the data array"""
+        pass

{dclab-0.62.13 → dclab-0.62.15}/dclab/rtdc_dataset/writer.py

@@ -17,6 +17,7 @@ from ..util import hashobj
 from .._version import version
 
 from .feat_anc_plugin import PlugInFeature
+from .meta_table import MetaTable
 
 #: DEPRECATED (use `CHUNK_SIZE_BYTES` instead)
 CHUNK_SIZE = 100
@@ -641,6 +642,12 @@ class RTDCWriter:
         if h5_attrs is None:
             h5_attrs = {}
 
+        # Convert MetaTable to numpy data
+        if isinstance(cmp_array, MetaTable):
+            h5_attrs.update(cmp_array.meta)
+            cmp_array = cmp_array.__array__()
+
+        # Handle individual cases
         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.

{dclab-0.62.13 → dclab-0.62.15}/dclab.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: dclab
-Version: 0.62.13
+Version: 0.62.15
 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-0.62.13 → dclab-0.62.15}/dclab.egg-info/SOURCES.txt

@@ -102,6 +102,7 @@ dclab/rtdc_dataset/fmt_dict.py
 dclab/rtdc_dataset/fmt_http.py
 dclab/rtdc_dataset/fmt_s3.py
 dclab/rtdc_dataset/load.py
+dclab/rtdc_dataset/meta_table.py
 dclab/rtdc_dataset/writer.py
 dclab/rtdc_dataset/feat_anc_core/__init__.py
 dclab/rtdc_dataset/feat_anc_core/af_basic.py

{dclab-0.62.13 → dclab-0.62.15}/tests/test_rtdc_export_hdf5.py

@@ -644,6 +644,56 @@ def test_hdf5_tables_array_only():
         assert ds.tables["src_iratrax"].meta["CLASS"] == np.bytes_("IMAGE")
 
 
+def test_hdf5_table_from_file(tmp_path):
+    ds = new_dataset(retrieve_data("fmt-hdf5_raw-cytoshot-exported.zip"))
+
+    f1 = join(tmp_path, "test.rtdc")
+    ds.export.hdf5(f1, ["temp"], tables=True)
+
+    ds2 = new_dataset(f1)
+    tab = ds2.tables["src_so2exp_cytoshot_monitor"]
+
+    assert np.allclose(
+        tab["focus"][0],
+        6.241900073522602,
+        atol=1e-7, rtol=0)
+
+    assert tab.meta["COLOR_focus"] == "#a03000"
+
+
+def test_hdf5_table_from_file_with_unnamed_table(tmp_path):
+    path = retrieve_data("fmt-hdf5_raw-cytoshot-exported.zip")
+    with RTDCWriter(path) as hw:
+        hw.store_table("just_an_array", np.ones((30, 50)),
+                       h5_attrs={"heinz": "kunz"})
+
+    # Make sure that worked with tables
+    with new_dataset(path) as ds:
+        tab = ds.tables["just_an_array"]
+        assert not tab.has_graphs()
+        assert np.array(tab).shape == (30, 50)
+        assert tab.meta["heinz"] == "kunz"
+
+    with new_dataset(path) as ds:
+        f1 = join(tmp_path, "test.rtdc")
+        ds.export.hdf5(f1, ["temp"], tables=True)
+
+    with new_dataset(f1) as ds2:
+        tab = ds2.tables["src_so2exp_cytoshot_monitor"]
+        assert tab.has_graphs()
+        assert np.allclose(
+            tab["focus"][0],
+            6.241900073522602,
+            atol=1e-7, rtol=0)
+
+        assert tab.meta["COLOR_focus"] == "#a03000"
+
+        tab2 = ds2.tables["src_just_an_array"]
+        assert not tab2.has_graphs()
+        assert np.array(tab2).shape == (30, 50)
+        assert tab2.meta["heinz"] == "kunz"
+
+
 def test_hdf5_trace_from_tdms():
     pytest.importorskip("nptdms")
     ds = new_dataset(retrieve_data("fmt-tdms_2fl-no-image_2017.zip"))