dcscope 2.25.2__tar.gz → 2.25.4__tar.gz

{dcscope-2.25.2 → dcscope-2.25.4}/CHANGELOG

@@ -1,3 +1,9 @@
+2.25.4
+ - setup: bump dclab to 0.68.0 (open SWMR files in read mode)
+2.25.3
+ - fix: `Pipeline.deduce_reduced_sample_names` failed for duplicate DCOR data
+ - fix: handle datasets without any events in the plot window (#223)
+ - setup: bump dclab to 0.67.5 (handle NaN-valued tables on DCOR)
 2.25.2
  - fix: check directory existence when loading files (#227)
 2.25.1

{dcscope-2.25.2/dcscope.egg-info → dcscope-2.25.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dcscope
-Version: 2.25.2
+Version: 2.25.4
 Summary: User interface for deformability cytometry (DC)
 Author: Benedikt Hartmann, Eoghan O'Connell, Maximilian Schlögel, Paul Müller, Raghava Alajangi
 Maintainer-email: Paul Müller <dev@craban.de>
@@ -16,7 +16,7 @@ Classifier: Intended Audience :: Science/Research
 Requires-Python: <4,>=3.9
 Description-Content-Type: text/x-rst
 License-File: LICENSE
-Requires-Dist: dclab[dcor,export,http,s3]>=0.67.4
+Requires-Dist: dclab[dcor,export,http,s3]>=0.68.0
 Requires-Dist: h5py>=2.8.0
 Requires-Dist: numpy>=1.21
 Requires-Dist: pygments

{dcscope-2.25.2 → dcscope-2.25.4}/dcscope/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '2.25.2'
-__version_tuple__ = version_tuple = (2, 25, 2)
+__version__ = version = '2.25.4'
+__version_tuple__ = version_tuple = (2, 25, 4)
 
-__commit_id__ = commit_id = 'g7db9e4d5b'
+__commit_id__ = commit_id = 'g568f827e5'

{dcscope-2.25.2 → dcscope-2.25.4}/dcscope/pipeline/core.py

@@ -1,4 +1,5 @@
 import copy
+import pathlib
 import threading
 import warnings
 
@@ -22,6 +23,10 @@ class MissingFeatureWarning(UserWarning):
     pass
 
 
+class ContourSpacingWarning(UserWarning):
+    pass
+
+
 class Pipeline(object):
     def __init__(self, state=None):
         self._plot_counter = 0
@@ -294,13 +299,16 @@ class Pipeline(object):
                     slot_id = slot_state["identifier"]
                     slot = self.get_slot(slot_id)
                     sp_min, sp_max = slot.get_sane_spacing_range(feat=feat)
+                    # Note that sp_min and sp_max may be `np.nan`
                     if spacing < sp_min:
                         warnings.warn(f"Setting contour spacing for {slot_id} "
-                                      f"to minimum ({spacing}<{sp_min})")
+                                      f"to minimum ({spacing}<{sp_min})",
+                                      ContourSpacingWarning)
                         spacing = sp_min
                     elif spacing > sp_max:
                         warnings.warn(f"Setting contour spacing for {slot_id} "
-                                      f"to maximum ({spacing}>{sp_max})")
+                                      f"to maximum ({spacing}>{sp_max})",
+                                      ContourSpacingWarning)
                         spacing = sp_max
                     plot_state["contour"][f"spacing {ax}"] = spacing
         if old_plot_state != plot_state:
@@ -363,7 +371,11 @@ class Pipeline(object):
                     slot = self.slots[ii]
                     if names[ii] == nn:
                         idx.append(ii)
-                        same_names.append(nn + slot.path.name)
+                        if isinstance(slot.path, pathlib.Path):
+                            slot_path_name = slot.path.name
+                        else:
+                            slot_path_name = str(slot.path).split("/")[-1]
+                        same_names.append(nn + slot_path_name)
                 new_names = strip_common_prefix_suffix(same_names)
                 for jj, ii in enumerate(idx):
                     names[ii] = new_names[jj]

{dcscope-2.25.2 → dcscope-2.25.4}/dcscope/pipeline/dataslot.py

@@ -212,7 +212,9 @@ def get_sane_contour_spacing_range(feat, data):
         feature data
     """
     # TODO: caching?
-    if feat in SLOPING_FEATURES:
+    if len(data) == 0:
+        frange = np.nan
+    elif feat in SLOPING_FEATURES:
         frange = np.abs(data[-1] - data[0])
         if np.isnan(frange) or np.isinf(frange):
             invalid = np.logical_or(np.isinf(data), np.isnan(data))

{dcscope-2.25.2 → dcscope-2.25.4/dcscope.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dcscope
-Version: 2.25.2
+Version: 2.25.4
 Summary: User interface for deformability cytometry (DC)
 Author: Benedikt Hartmann, Eoghan O'Connell, Maximilian Schlögel, Paul Müller, Raghava Alajangi
 Maintainer-email: Paul Müller <dev@craban.de>
@@ -16,7 +16,7 @@ Classifier: Intended Audience :: Science/Research
 Requires-Python: <4,>=3.9
 Description-Content-Type: text/x-rst
 License-File: LICENSE
-Requires-Dist: dclab[dcor,export,http,s3]>=0.67.4
+Requires-Dist: dclab[dcor,export,http,s3]>=0.68.0
 Requires-Dist: h5py>=2.8.0
 Requires-Dist: numpy>=1.21
 Requires-Dist: pygments

{dcscope-2.25.2 → dcscope-2.25.4}/dcscope.egg-info/SOURCES.txt

@@ -429,6 +429,7 @@ tests/data/blood_rbc_leukocytes.rtdc
 tests/data/blood_rbc_qpi_data.rtdc
 tests/data/calibration_beads_47.rtdc
 tests/data/cytoshot_blood.rtdc
+tests/data/empty_recording.rtdc
 tests/data/ext_feat_anc_plugin_ca.py
 tests/data/extreme_shear.rtdc
 tests/data/naiad-capture_blood_pipeline.rtdc

{dcscope-2.25.2 → dcscope-2.25.4}/dcscope.egg-info/requires.txt

@@ -1,4 +1,4 @@
-dclab[dcor,export,http,s3]>=0.67.4
+dclab[dcor,export,http,s3]>=0.68.0
 h5py>=2.8.0
 numpy>=1.21
 pygments

{dcscope-2.25.2 → dcscope-2.25.4}/pyproject.toml

@@ -30,7 +30,7 @@ classifiers = [
 ]
 license = "GPL-3.0-or-later"
 dependencies = [
-    "dclab[dcor,export,http,s3]>=0.67.4",
+    "dclab[dcor,export,http,s3]>=0.68.0",
     "h5py>=2.8.0",
     "numpy>=1.21",  # CVE-2021-33430
     "pygments",

{dcscope-2.25.2 → dcscope-2.25.4}/tests/test_gui_plotting.py

@@ -5,7 +5,7 @@ import tempfile
 import dclab
 import h5py
 import numpy as np
-from PyQt6 import QtCore
+from PyQt6 import QtCore, QtWidgets
 import pytest
 from dcscope.gui.main import DCscope
 from dcscope import pipeline, session
@@ -170,6 +170,50 @@ def test_handle_empty_plots_issue_27(qtbot):
         # activate (raises #27)
         qtbot.mouseClick(pe, QtCore.Qt.MouseButton.LeftButton)
 
+        QtWidgets.QApplication.processEvents(
+            QtCore.QEventLoop.ProcessEventsFlag.AllEvents, 500)
+
+
+@pytest.mark.filterwarnings('ignore::dclab.kde.base.ContourSpacingTooLarge')
+@pytest.mark.filterwarnings(
+    'ignore::dclab.kde.methods.KernelDensityEstimationForEmtpyArrayWarning')
+@pytest.mark.filterwarnings(
+    'ignore::dcscope.pipeline.core.ContourSpacingWarning')
+def test_handle_empty_plots_issue_223(qtbot):
+    """Correctly handle plots with empty datasets (before filtering)
+
+    https://github.com/DC-analysis/DCscope/issues/223
+    """
+    mw = DCscope()
+    qtbot.addWidget(mw)
+
+    # add a dataslot without any events
+    path = datapath / "empty_recording.rtdc"
+    mw.add_dataslot(paths=[path])
+
+    assert len(mw.pipeline.slot_ids) == 1, "we added those"
+    assert len(mw.pipeline.filter_ids) == 1, "automatically added"
+
+    # Check whether we really don't have any events
+    ds = mw.pipeline.get_dataset(slot_index=0, filt_index=0,
+                                 apply_filter=True)
+    assert len(ds) == 0
+    assert np.sum(ds.filter.all) == 0
+
+    # now create a plot window
+    plot_id = mw.add_plot()
+    pe = mw.block_matrix.get_widget(mw.pipeline.slot_ids[0], plot_id)
+
+    with pytest.warns(pipeline.core.EmptyDatasetWarning):
+        qtbot.mouseClick(pe, QtCore.Qt.MouseButton.LeftButton)
+
+        # this now only throws a warning
+        # activate (raises #223)
+        qtbot.mouseClick(pe, QtCore.Qt.MouseButton.LeftButton)
+
+        QtWidgets.QApplication.processEvents(
+            QtCore.QEventLoop.ProcessEventsFlag.AllEvents, 500)
+
 
 @pytest.mark.filterwarnings(
     'ignore::dclab.features.emodulus.YoungsModulusLookupTableExceededWarning')

{dcscope-2.25.2 → dcscope-2.25.4}/tests/test_pipeline_core.py

@@ -1,10 +1,21 @@
 import copy
 import pathlib
-import tempfile
+import socket
 
 import dclab
 import numpy as np
-from dcscope import pipeline
+from dcscope import pipeline, session
+import pytest
+
+
+data_path = pathlib.Path(__file__).parent / "data"
+with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
+    try:
+        s.connect(("www.python.org", 80))
+        NET_AVAILABLE = True
+    except socket.gaierror:
+        # no internet
+        NET_AVAILABLE = False
 
 
 def test_apply_filter_ray():
@@ -42,13 +53,38 @@ def test_apply_filter_ray():
     assert np.all(ds_ref.filter.all == ds_ext.filter.all)
 
 
-def test_get_min_max_inf():
+@pytest.mark.skipif(not NET_AVAILABLE, reason="No network connection!")
+@pytest.mark.filterwarnings(
+    'ignore::dclab.rtdc_dataset.config.WrongConfigurationTypeWarning')
+def test_session_dcor():
+    pipeline = session.open_session(data_path / "version_2_5_0_dcor_lme4.so2")
+    assert pipeline.deduce_reduced_sample_names() == [
+        'SSC 16uls rep1',
+        'SSC 16uls rep2',
+        'MG63 pure 16uls rep1',
+        'MG63 pure 16uls rep2',
+        'MG63 pure 16uls rep3',
+        ]
+    # Add the last slot again
+    dcor_id = pipeline.slots[-1].path
+    pipeline.add_slot(path=dcor_id)
+    assert pipeline.deduce_reduced_sample_names() == [
+        'SSC 16uls rep1',
+        'SSC 16uls rep2',
+        'MG63 pure 16uls rep1',
+        'MG63 pure 16uls rep2',
+        'MG63 pure 16uls rep3',
+        'MG63 pure 16uls rep3',
+        ]
+
+
+def test_get_min_max_inf(tmp_path):
     # generate fake dataset
     path = pathlib.Path(__file__).parent / "data" / "calibration_beads_47.rtdc"
     with dclab.new_dataset(path) as ds:
         config = copy.deepcopy(ds.config)
 
-    tmp = tempfile.mktemp(".rtdc", prefix="example_filter_inf_")
+    tmp = tmp_path / "example_filter_inf.rtdc"
     ddict = {"deform": np.linspace(0, .01, 100),
              "area_um": np.linspace(20, 200, 100),
              "area_ratio": np.linspace(1, 1.1, 100)