dclab 0.66.0__tar.gz → 0.67.0__tar.gz

{dclab-0.66.0 → dclab-0.67.0}/CHANGELOG

@@ -1,3 +1,11 @@
+0.67.0
+ - BREAKING CHANGE: make it difficult to export the "contour" feature
+ - fix: `BasinProxyFeature` returned incorrect `shape` and `size`
+ - enh: implement `size` for `H5MaskEvent` and `H5ScalarEvent`
+ - enh: implement `BasinProxyContour`
+ - enh: improve hashing of `H5ContourEvent`
+ - docs: acknowledge Shape-Out is being continued as DCscope
+ - tests: correct DCOR IP address
 0.66.0
  - feat: introduce optional identifiers for basins
  - ref: rename `measurement_identifier` to `referrer_identifier`
@@ -1495,7 +1503,7 @@
    - Contour accuracy for Defo overridden by that of Circ
 0.1.5
  - Fix regressions with filtering.
-   https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut/issues/43 
+   https://github.com/DC-analysis/DCscope/issues/43
  - Ignore empty columns in .tdms files (#1)
  - Moved RTDC_DataSet and PolygonFilter classes to separate files
  - Introduce more transparent caching - improves speed in some cases
@@ -1504,10 +1512,10 @@
 0.1.3
  - Fixed minor polygon filter problems.
  - Fix a couple of Shape-Out-related issues:
-   - https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut/issues/17 
-   - https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut/issues/20
-   - https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut/issues/37
-   - https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut/issues/38
+   - https://github.com/DC-analysis/DCscope/issues/17
+   - https://github.com/DC-analysis/DCscope/issues/20
+   - https://github.com/DC-analysis/DCscope/issues/37
+   - https://github.com/DC-analysis/DCscope/issues/38
 0.1.2
  - Add support for limiting amount of data points analyzed
    with the configuration keyword "Limit Events"

{dclab-0.66.0 → dclab-0.67.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dclab
-Version: 0.66.0
+Version: 0.67.0
 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>
@@ -46,7 +46,13 @@ Dynamic: license-file
 
 This is a Python library for the post-measurement analysis of
 real-time deformability cytometry (RT-DC) datasets; an essential part of
-`Shape-Out <https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut2>`__.
+the DC Cosmos (
+`DCscope <https://github.com/DC-analysis/DCscope>`__,
+`DCOR <https://github.com/DCOR-dev/dcor_control>`__,
+`DCOR-Aid <https://github.com/DCOR-dev/DCOR-Aid>`__,
+`DCTag <https://github.com/DC-analysis/DCTag>`__,
+`DCKit <https://github.com/DC-analysis/DCKit>`__,
+).
 
 Documentation
 -------------

{dclab-0.66.0 → dclab-0.67.0}/README.rst

@@ -6,7 +6,13 @@
 
 This is a Python library for the post-measurement analysis of
 real-time deformability cytometry (RT-DC) datasets; an essential part of
-`Shape-Out <https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut2>`__.
+the DC Cosmos (
+`DCscope <https://github.com/DC-analysis/DCscope>`__,
+`DCOR <https://github.com/DCOR-dev/dcor_control>`__,
+`DCOR-Aid <https://github.com/DCOR-dev/DCOR-Aid>`__,
+`DCTag <https://github.com/DC-analysis/DCTag>`__,
+`DCKit <https://github.com/DC-analysis/DCKit>`__,
+).
 
 Documentation
 -------------

{dclab-0.66.0 → dclab-0.67.0}/dclab/_version.py

@@ -1,7 +1,14 @@
 # file generated by setuptools-scm
 # don't change, don't track in version control
 
-__all__ = ["__version__", "__version_tuple__", "version", "version_tuple"]
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
 
 TYPE_CHECKING = False
 if TYPE_CHECKING:
@@ -9,13 +16,19 @@ if TYPE_CHECKING:
     from typing import Union
 
     VERSION_TUPLE = Tuple[Union[int, str], ...]
+    COMMIT_ID = Union[str, None]
 else:
     VERSION_TUPLE = object
+    COMMIT_ID = object
 
 version: str
 __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
+commit_id: COMMIT_ID
+__commit_id__: COMMIT_ID
 
-__version__ = version = '0.66.0'
-__version_tuple__ = version_tuple = (0, 66, 0)
+__version__ = version = '0.67.0'
+__version_tuple__ = version_tuple = (0, 67, 0)
+
+__commit_id__ = commit_id = 'g52c420117'

{dclab-0.66.0 → dclab-0.67.0}/dclab/cli/task_tdms2rtdc.py

@@ -158,7 +158,7 @@ def tdms2rtdc_parser():
                         help='Compute features, such as volume or emodulus, '
                              + 'that are otherwise computed on-the-fly. '
                              + 'Use this if you want to minimize analysis '
-                             + 'time in e.g. Shape-Out. CAUTION: ancillary '
+                             + 'time in e.g. DCscope. CAUTION: ancillary '
                              + 'feature recipes might be subject to change '
                              + '(e.g. if an error is found in the recipe). '
                              + 'Disabling this option maximizes '

{dclab-0.66.0 → dclab-0.67.0}/dclab/definitions/__init__.py

@@ -6,7 +6,7 @@ from .feat_const import (
     # these should not be used
     feature_names, feature_labels, feature_name2label,
     # this one should also not be used, but we wait with deprecation,
-    # because Shape-Out heavily relies on it (it shouldn't)
+    # because DCscope heavily relies on it (it shouldn't)
     scalar_feature_names
     )
 from .feat_logic import (

{dclab-0.66.0 → dclab-0.67.0}/dclab/definitions/feat_const.py

@@ -149,7 +149,7 @@ for _i in range(10):
 #: consist of the integer array `[1, 3, 5, 7, ...]` (indexing starts at zero).
 #: The `basinmap1` feature must then be referenced in the corresponding basin
 #: definition. These features should not be presented explicitly to the
-#: normal user (e.g. in Shape-Out) to avoid ambiguities, and they should
+#: normal user (e.g. in DCscope) to avoid ambiguities, and they should
 #: always be exported alongside basins that refer to them.
 for _j in range(10):
     FEATURES_SCALAR.append([f"basinmap{_j}", f"Basin mapping {_j}"])

{dclab-0.66.0 → dclab-0.67.0}/dclab/rtdc_dataset/config.py

@@ -437,7 +437,7 @@ def load_from_file(cfg_file):
                 convfunc = dfn.get_config_value_func(sec, var)
                 val = convfunc(val)
             else:
-                # unknown parameter (e.g. plotting in Shape-Out), guess type
+                # unknown parameter (e.g. plotting in DCscope), guess type
                 var, val = keyval_str2typ(var, val)
             if len(var) != 0 and len(str(val)) != 0:
                 cfg[sec][var] = val

{dclab-0.66.0 → dclab-0.67.0}/dclab/rtdc_dataset/export.py

@@ -39,6 +39,10 @@ class LimitingExportSizeWarning(UserWarning):
     pass
 
 
+class ContourNotExportedWarning(UserWarning):
+    pass
+
+
 class Export(object):
     def __init__(self, rtdc_ds):
         """Export functionalities for RT-DC datasets"""
@@ -228,6 +232,7 @@ class Export(object):
              logs: bool = False,
              tables: bool = False,
              basins: bool = False,
+             allow_contour: bool = False,
              meta_prefix: str = "src_",
              override: bool = False,
              compression_kwargs: Dict = None,
@@ -260,6 +265,14 @@ class Export(object):
             Whether to export basins. If filtering is disabled, basins
             are copied directly to the output file. If filtering is enabled,
             then mapped basins are exported.
+        allow_contour: bool
+            Whether to allow exporting the "contour" feature. Writing this
+            feature to an HDF5 file is extremely inefficient, because it
+            cannot be represented by an ND array and thus must be stored
+            in a group, each contour stored in a separate dataset. The
+            contour can easily be computed via the mask, so actually storing
+            the contour should be avoided. If "contour" is in `features`,
+            it will only be written to the output file if `allow_contour=True`.
         meta_prefix: str
             Prefix for log and table names in the exported file
         override: bool
@@ -318,8 +331,25 @@ class Export(object):
         # for convenience
         ds = self.rtdc_ds
 
+        # remove contour information from user-specified features
+        if "contour" in (features or []) and not allow_contour:
+            features = list(features)
+            features.remove("contour")
+            warnings.warn(
+                "Feature 'contour' not exported to output file, because "
+                "`allow_contour` is `False`. If you really need the "
+                "'contour' feature in the output file (unlikely, unless you "
+                "are venturing outside the DC Cosmos), you must set "
+                "`allow_contour=True`. Otherwise, you can safely ignore "
+                "this warning or silence it by not providing 'contour' in "
+                "`features`.",
+                ContourNotExportedWarning)
+
         if features is None:
             features = ds.features_innate
+            # silently remove contour information
+            if "contour" in features and not allow_contour:
+                features.remove("contour")
 
         # decide which metadata to export
         meta = {}

{dclab-0.66.0 → dclab-0.67.0}/dclab/rtdc_dataset/feat_basin.py

@@ -567,8 +567,8 @@ class BasinProxy:
     def __getitem__(self, feat):
         if feat not in self._features:
             if feat == "contour":
-                raise NotImplementedError("Feature 'contour' cannot be "
-                                          "handled by BasinProxy.")
+                feat_obj = BasinProxyContour(feat_obj=self.ds[feat],
+                                             basinmap=self.basinmap)
             else:
                 feat_obj = BasinProxyFeature(feat_obj=self.ds[feat],
                                              basinmap=self.basinmap)
@@ -579,14 +579,61 @@ class BasinProxy:
         return len(self.basinmap)
 
 
+class BasinProxyContour:
+    def __init__(self, feat_obj, basinmap):
+        """Wrap around a contour, mapping it upon data access, no caching"""
+        self.feat_obj = feat_obj
+        self.basinmap = basinmap
+        self.is_scalar = False
+        self.shape = (len(self.basinmap), np.nan, 2)
+        self.identifier = feat_obj.identifier
+
+    def __getattr__(self, item):
+        if item in [
+            "dtype",
+        ]:
+            return getattr(self.feat_obj, item)
+        else:
+            raise AttributeError(
+                f"BasinProxyContour does not implement {item}")
+
+    def __getitem__(self, index):
+        if isinstance(index, numbers.Integral):
+            # single index, cheap operation
+            return self.feat_obj[self.basinmap[index]]
+        else:
+            raise NotImplementedError(
+                "Cannot index contours without anything else than integers.")
+
+    def __len__(self):
+        return self.shape[0]
+
+
 class BasinProxyFeature(np.lib.mixins.NDArrayOperatorsMixin):
     def __init__(self, feat_obj, basinmap):
         """Wrap around a feature object, mapping it upon data access"""
         self.feat_obj = feat_obj
         self.basinmap = basinmap
         self._cache = None
+        self._shape = None
+        self._size = None
         self.is_scalar = bool(len(self.feat_obj.shape) == 1)
 
+    @property
+    def shape(self):
+        if self._shape is None:
+            if self.is_scalar:
+                self._shape = self.basinmap.shape
+            else:
+                self._shape = (self.basinmap.size,) + self.feat_obj.shape[1:]
+        return self._shape
+
+    @property
+    def size(self):
+        if self._size is None:
+            self._size = np.prod(self.shape)
+        return self._size
+
     def __array__(self, dtype=None, copy=copy_if_needed, *args, **kwargs):
         if self._cache is None and self.is_scalar:
             self._cache = self.feat_obj[:][self.basinmap]
@@ -603,8 +650,6 @@ class BasinProxyFeature(np.lib.mixins.NDArrayOperatorsMixin):
     def __getattr__(self, item):
         if item in [
             "dtype",
-            "shape",
-            "size",
         ]:
             return getattr(self.feat_obj, item)
         else:

{dclab-0.66.0 → dclab-0.67.0}/dclab/rtdc_dataset/fmt_hdf5/events.py

@@ -1,6 +1,7 @@
 """RT-DC hdf5 format"""
 from __future__ import annotations
 
+import pathlib
 import warnings
 
 import numbers
@@ -17,7 +18,17 @@ class H5ContourEvent:
         self._length = length
         self.h5group = h5group
         # for hashing in util.obj2bytes
-        self.identifier = (h5group.file.filename, h5group["0"].name)
+        # path within the HDF5 file
+        o_name = h5group["0"].name,
+        # filename
+        o_filename = h5group.file.filename
+        _data = [o_name, o_filename]
+        if pathlib.Path(o_filename).exists():
+            # when the file was changed
+            _data.append(pathlib.Path(h5group.file.filename).stat().st_mtime)
+            # size of the file
+            _data.append(pathlib.Path(h5group.file.filename).stat().st_size)
+        self.identifier = _data
 
     def __getitem__(self, key):
         if not isinstance(key, numbers.Integral):
@@ -168,6 +179,10 @@ class H5MaskEvent:
     def shape(self):
         return self.h5dataset.shape
 
+    @property
+    def size(self):
+        return np.prod(self.shape)
+
 
 class H5ScalarEvent(np.lib.mixins.NDArrayOperatorsMixin):
     def __init__(self, h5ds):
@@ -224,6 +239,10 @@ class H5ScalarEvent(np.lib.mixins.NDArrayOperatorsMixin):
     def shape(self):
         return self.h5ds.shape
 
+    @property
+    def size(self):
+        return len(self)
+
 
 class H5TraceEvent:
     def __init__(self, h5group):

{dclab-0.66.0 → dclab-0.67.0}/dclab/rtdc_dataset/fmt_hierarchy/base.py

@@ -29,7 +29,7 @@ class RTDC_Hierarchy(RTDCBase):
         Children in hierarchies always update their data according to
         the filtered event data from their parent when `apply_filter`
         is called. This makes it easier to save and load hierarchy
-        children with e.g. Shape-Out and it makes the handling of
+        children with e.g. DCscope and it makes the handling of
         hierarchies more intuitive (when the parent changes,
         the child changes as well).
 

{dclab-0.66.0 → dclab-0.67.0}/dclab/rtdc_dataset/fmt_tdms/event_trace.py

@@ -17,7 +17,7 @@ class TraceColumn(object):
 
         The trace data is loaded when __getitem__, __len__, or __iter__
         are called. This saves time and memory when the trace data is
-        not needed at all, e.g. for batch processing with Shape-Out.
+        not needed at all, e.g. for batch processing with DCscope.
         """
         self._trace = None
         self.mname = rtdc_dataset.path

{dclab-0.66.0 → dclab-0.67.0}/dclab/rtdc_dataset/fmt_tdms/naming.py

@@ -49,7 +49,7 @@ for kk in dclab2tdms:
     tdms2dclab[dclab2tdms[kk]] = kk
 
 # Add capitalized userdef features as well.
-# see https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut/issues/212
+# see https://github.com/DC-analysis/DCscope/issues/212
 for _i in range(10):
     tdms2dclab["UserDef{}".format(_i)] = "userdef{}".format(_i)
 

{dclab-0.66.0 → dclab-0.67.0}/dclab/warn.py

@@ -9,7 +9,7 @@ class PipelineWarning(UserWarning):
     computation) in his analysis pipeline. All of these
     warnings should be subclassed from PipelineWarning
     to allow identifying them in higher-level software
-    such as Shape-Out and to present them correctly to the
+    such as DCscope and to present them correctly to the
     user.
     """
     pass

{dclab-0.66.0 → dclab-0.67.0}/dclab.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dclab
-Version: 0.66.0
+Version: 0.67.0
 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>
@@ -46,7 +46,13 @@ Dynamic: license-file
 
 This is a Python library for the post-measurement analysis of
 real-time deformability cytometry (RT-DC) datasets; an essential part of
-`Shape-Out <https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut2>`__.
+the DC Cosmos (
+`DCscope <https://github.com/DC-analysis/DCscope>`__,
+`DCOR <https://github.com/DCOR-dev/dcor_control>`__,
+`DCOR-Aid <https://github.com/DCOR-dev/DCOR-Aid>`__,
+`DCTag <https://github.com/DC-analysis/DCTag>`__,
+`DCKit <https://github.com/DC-analysis/DCKit>`__,
+).
 
 Documentation
 -------------

{dclab-0.66.0 → dclab-0.67.0}/docs/conf.py

@@ -206,5 +206,5 @@ intersphinx_mapping = {
     "numpy": ('https://numpy.org/doc/stable/', None),
     "skimage": ('https://scikit-image.org/docs/stable/', None),
     "scipy": ('https://docs.scipy.org/doc/scipy/', None),
-    "shapeout2": ('https://shapeout2.readthedocs.io/en/stable/', None),
+    "dcscope": ('https://dcscope.readthedocs.io/en/stable/', None),
     }

{dclab-0.66.0 → dclab-0.67.0}/docs/data/example.poly

@@ -1,7 +1,7 @@
 [Polygon 00000000]
 X Axis = area_um
 Y Axis = deform
-Name = Example polygon filter created with Shape-Out
+Name = Example polygon filter created with DCscope
 Inverted = False
 point00000000 = 4.806285699729710e+01 3.159643080378363e-02
 point00000001 = 4.707025517531432e+01 2.200807132494297e-02

{dclab-0.66.0 → dclab-0.67.0}/docs/sec_av_basins/index.rst

@@ -14,7 +14,7 @@ file to the input file. Feature data "flows" from the basins to the
 files downstream.
 
 Due to the fact that basins are implemented in dclab, all software that relies
-on dclab for opening data files (e.g. Shape-Out or CytoPlot) automatically
+on dclab for opening data files (e.g. DCscope or CytoPlot) automatically
 supports basins as well.
 
 
@@ -46,7 +46,7 @@ B. You have an automated data analysis pipeline that relies entirely on DCOR.
    connection.
 
 C. Let's say your pipeline is designed to compute a new feature ``userdef1``
-   and you would like to open the output file in Shape-Out, visualizing
+   and you would like to open the output file in DCscope, visualizing
    this feature in combination with other features defined in the input file
    (e.g. ``deform``). What you *could* do is write the ``userdef1`` feature
    directly to the input file or create a copy of your input file and write

{dclab-0.66.0 → dclab-0.67.0}/docs/sec_av_emodulus/figures_emodulus/plot_emodulus_lut.py

@@ -3,7 +3,7 @@
 The Young's modulus is corrected for pixelation (pixel size 0.34 µm).
 The temperature is set to 23°C.
 The 20µm plot is used in the dclab documentation. The others
-are used in the Shape-Out documentation.
+are used in the DCscope documentation.
 """
 from dclab.features import emodulus
 import numpy as np

{dclab-0.66.0 → dclab-0.67.0}/docs/sec_av_feat_temp.rst

@@ -14,7 +14,7 @@ in your dataset without modifying any files on disk.
 
 .. note::
 
-    Temporary features are not supported by Shape-Out, DCKit, or DCOR/DCOR-Aid.
+    Temporary features are not supported by DCscope, DCKit, or DCOR/DCOR-Aid.
     They are only really helpful if you quickly need to test things. If possible,
     it is recommended to work with :ref:`plugin features <sec_av_feat_plugin>`.
 

{dclab-0.66.0 → dclab-0.67.0}/docs/sec_av_notation.rst

@@ -199,7 +199,7 @@ a dataset is exported as an .rtdc (HDF5) file.
 .. note::
     It is recommended to use the following data types for the value of
     each key: ``str``, ``bool``, ``float`` and ``int``. Other data types may
-    not render nicely in ShapeOut2 or DCOR.
+    not render nicely in DCscope or DCOR.
 
 To edit the "user" section in dclab, simply modify the `config`
 property of a loaded dataset. The changes made are *not* written

{dclab-0.66.0 → dclab-0.67.0}/docs/sec_av_scatter.rst

@@ -191,12 +191,12 @@ using :func:`~dclab.kde.KernelDensityEstimator.get_contour_lines`.
 
 
 
-Polygon filters / Shape-Out
----------------------------
+Polygon filters / DCscope
+-------------------------
 Keep in mind that you can combine your dclab analysis pipeline with
-:ref:`Shape-Out <shapeout2:index>`. For instance, you can create and export
+:ref:`DCscope <dcscope:index>`. For instance, you can create and export
 :ref:`polygon filters <sec_ref_polygon_filter>`
-in Shape-Out and then import them in dclab.
+in DCscope and then import them in dclab.
 
 
 .. plot::

{dclab-0.66.0 → dclab-0.67.0}/docs/sec_code_reference.rst

@@ -17,7 +17,7 @@ Module-level methods
 
 Global definitions
 ==================
-These definitionas are used throughout the dclab/Shape-In/Shape-Out ecosystem.
+These definitionas are used throughout the dclab/Shape-In/DCscope ecosystem.
 
 Metadata
 --------

{dclab-0.66.0 → dclab-0.67.0}/docs/sec_getting_started.rst

@@ -43,11 +43,11 @@ Use cases
 =========
 If you are a frequent user of RT-DC, you might run into problems that
 cannot (yet) be addressed with the graphical user interface
-`Shape-Out <https://github.com/ZellMechanik-Dresden/ShapeOut2>`_.
+`DCscope <https://github.com/DC-analysis/DCscope>`_.
 Here is a list of use cases that would motivate an installation of dclab.
 
 - You would like to convert old .tdms-based datasets to the new .rtdc
-  file format, because of enhanced speed in Shape-Out and reduced
+  file format, because of enhanced speed in DCscope and reduced
   disk usage. What you are looking for is the command line program
   :ref:`sec_tdms2rtdc` that comes with dclab. It allows to batch-convert
   multiple measurements at a time. Note that you should keep the original
@@ -60,18 +60,18 @@ Here is a list of use cases that would motivate an installation of dclab.
   :class:`.RTDCWriter` class that allows you to convert your tabular data
   to *.rtdc* files.
 - You would like to apply a simple set of filters (e.g. polygon filters that you
-  exported from within Shape-Out) to every new measurement you take and
+  exported from within DCscope) to every new measurement you take and
   apply a custom data analysis pipeline to the filtered data. This is a
   straight-forward Python coding problem with dclab. After reading the
   basic usage section below, please have a look at the
   :ref:`polygon filter reference <sec_ref_polygon_filter>`.
 - You would like to do advanced statistics or combine your RT-DC
   analysis with other fancy approaches such as machine-learning.
-  It would be too laborious to do the analysis in Shape-Out, export the
+  It would be too laborious to do the analysis in DCscope, export the
   data as text files, and then open them in your custom Python script.
-  If your initial analysis step with Shape-Out only involves tasks
+  If your initial analysis step with DCscope only involves tasks
   that can be automated, why not use dclab from the beginning? 
-- You simulated RT-DC data and plan to import them in Shape-Out
+- You simulated RT-DC data and plan to import them in DCscope
   for testing. Once you have loaded your data as a numpy array, you
   can instantiate an :class:`RTDC_Dict <dclab.rtdc_dataset.RTDC_Dict>`
   class and then use the :class:`Export <dclab.rtdc_dataset.export.Export>`

{dclab-0.66.0 → dclab-0.67.0}/tests/helper_methods.py

@@ -14,7 +14,7 @@ from dclab.rtdc_dataset.fmt_s3 import BOTO3_AVAILABLE  # noqa: F401
 with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
     try:
         # dcor.mpl.mpg.de
-        s.connect(("130.183.206.45", 443))
+        s.connect(("130.183.217.150", 443))
     except (socket.gaierror, OSError):
         DCOR_AVAILABLE = False
     else:

{dclab-0.66.0 → dclab-0.67.0}/tests/test_cli_argparse.py

@@ -207,8 +207,19 @@ def test_split():
                                 "time",  # issue #204
                                 ]:
                         continue
-                    assert np.all(
-                        ds[feat][ecount:ecount+len(di)] == di[feat]), feat
+                    elif feat in ["volume"]:
+                        # Contour data is required for computing volume.
+                        # But contour data is not exported. Instead,
+                        # contour data must be computed from mask data.
+                        assert np.allclose(
+                            ds[feat][ecount:ecount + len(di)],
+                            di[feat],
+                            rtol=0,
+                            atol=1e-5,
+                        )
+                    else:
+                        assert np.all(
+                            ds[feat][ecount:ecount+len(di)] == di[feat]), feat
                 ecount += len(di)
 
 

{dclab-0.66.0 → dclab-0.67.0}/tests/test_cli_split.py

@@ -22,8 +22,20 @@ def test_split():
                                 "time",  # issue 204
                                 ]:
                         continue
-                    assert np.all(
-                        ds[feat][ecount:ecount + len(di)] == di[feat]), feat
+                    elif feat in ["volume"]:
+                        # Contour data is required for computing volume.
+                        # But contour data is not  exported. Instead,
+                        # contour data must be computed from mask data.
+                        assert np.allclose(
+                            ds[feat][ecount:ecount + len(di)],
+                            di[feat],
+                            rtol=0,
+                            atol=1e-5,
+                        )
+                    else:
+                        assert np.all(
+                            ds[feat][ecount:ecount + len(di)]
+                            == di[feat]), feat
                 ecount += len(di)
 
 

{dclab-0.66.0 → dclab-0.67.0}/tests/test_isoelastics.py

@@ -113,7 +113,7 @@ def test_convert():
                          viscosity_in=15,
                          viscosity_out=15)
     # These values were taken from previous isoelasticity files
-    # used in Shape-Out.
+    # used in DCscope.
     assert np.allclose(isoel15[0][:, 2], 7.11111111e-01)
     assert np.allclose(isoel15[1][:, 2], 9.48148148e-01)
     # area_um

{dclab-0.66.0 → dclab-0.67.0}/tests/test_rtdc_config.py

@@ -445,7 +445,7 @@ def test_user_section_set_save_reload_fmt_tdms():
     with new_dataset(h5path) as ds:
         ds.config.update({"user": metadata})
         expath = h5path.with_name("exported.rtdc")
-        ds.export.hdf5(expath, features=ds.features_innate)
+        ds.export.hdf5(expath)
     # make sure that worked
     with h5py.File(expath, "r") as h5:
         assert h5.attrs["user:channel area"] == 100.5