def test_export_single_plot(qtbot, monkeypatch):
"""Export of single plots not possible up until version 2.1.4"""
spath = datapath / "version_2_1_0_basic.so2"
mw = ShapeOut2()
qtbot.addWidget(mw)
mw.on_action_open(spath)
# perform the export
tmpd = tempfile.mkdtemp(suffix="", prefix="shapeout2_test_plot_export_")
tmpf = os.path.join(tmpd, "no_suffix")
assert not pathlib.Path(tmpf).exists()
monkeypatch.setattr(QtWidgets.QFileDialog, "getSaveFileName", lambda *args:
(tmpf, ""))
# create export dialog manually
dlg = export.ExportPlot(mw, pipeline=mw.pipeline)
# select a single plot to export
plot_id = mw.pipeline.plot_ids[0]
assert isinstance(plot_id, str)
plot_index = dlg.comboBox_plot.findData(plot_id)
assert plot_index > 0
dlg.comboBox_plot.setCurrentIndex(plot_index)
assert dlg.comboBox_plot.currentData() == plot_id
dlg.export_plots()
assert pathlib.Path(tmpf).with_suffix(".png").exists()
# cleanup
shutil.rmtree(tmpd, ignore_errors=True)
def test_matrix_slots_duplicate_issue_96(qtbot):
mw = ShapeOut2()
qtbot.addWidget(mw)
# add a dataslot
path = pathlib.Path(__file__).parent / "data" / "calibration_beads_47.rtdc"
mw.add_dataslot(paths=[path])
assert len(mw.pipeline.slot_ids) == 1, "we added that"
assert len(mw.pipeline.filter_ids) == 1, "automatically added"
# change the name of the dataset
# go to analysis view
qtbot.mouseClick(mw.toolButton_ana_view, QtCore.Qt.LeftButton)
# go to the dataset tab
av = mw.widget_ana_view
qtbot.mouseClick(av.tab_slot, QtCore.Qt.LeftButton)
# enter a name
ws = av.widget_slot
ws.lineEdit_name.setText("A Unique Name")
qtbot.mouseClick(ws.pushButton_apply, QtCore.Qt.LeftButton)
# See if that worked
assert mw.pipeline.slots[0].name == "A Unique Name"
# Now duplicate the dataset
swid = mw.block_matrix.get_widget(slot_id=mw.pipeline.slots[0].identifier)
swid.action_duplicate()
assert len(mw.pipeline.slot_ids) == 2, "initial + duplicate"
assert len(mw.pipeline.filter_ids) == 1, "automatically added"
# make sure that slot name is the same
assert mw.pipeline.slots[0].name == "A Unique Name"
assert mw.pipeline.slots[1].name == "A Unique Name"
def test_wrong_medium_viscosity(qtbot):
"""Deliberately set wrong visosity"""
mw = ShapeOut2()
qtbot.addWidget(mw)
# add a dataslot
path = datapath / "calibration_beads_47.rtdc"
mw.add_dataslot(paths=[path])
mw.add_dataslot(paths=[path])
# create bulk action dialog manually
dlg = bulk.BulkActionEmodulus(mw, pipeline=mw.pipeline)
dlg.comboBox_medium.setCurrentIndex(dlg.comboBox_medium.findData("other"))
dlg.doubleSpinBox_visc.setValue(1.0) # random number
dlg.on_ok()
for slot in mw.pipeline.slots:
ds = slot.get_dataset()
assert "emodulus" not in ds, "because medium is fixed"
assert ds.config["setup"]["medium"] == "CellCarrierB"
assert ds.config["calculation"]["emodulus lut"] == "LE-2D-FEM-19"
assert ds.config["calculation"]["emodulus medium"] == "CellCarrierB"
assert "emodulus temperature" not in ds.config["calculation"]
assert "emodulus viscosity" not in ds.config["calculation"]
def test_allow_to_set_manual_temperature_for_known_medium(qtbot):
"""Fixes regression introduced in 2.4.0"""
mw = ShapeOut2()
qtbot.addWidget(mw)
# add fake measurement
path1 = make_dataset(medium=None, temp=23.5)
mw.add_dataslot(paths=[path1])
wsl = mw.widget_ana_view.widget_slot
# 1. test whether we can actually select things in comboBox_temp
ccidx = wsl.comboBox_medium.findData("CellCarrier")
wsl.comboBox_medium.setCurrentIndex(ccidx)
assert wsl.comboBox_temp.isEnabled()
# 2. test whether we can select manual
manidx = wsl.comboBox_temp.findData("manual")
wsl.comboBox_temp.setCurrentIndex(manidx)
assert wsl.doubleSpinBox_temp.isEnabled()
assert not wsl.doubleSpinBox_temp.isReadOnly()
# 3. test whether we can select config and the the temperature
# should be 23.5
conidx = wsl.comboBox_temp.findData("config")
wsl.comboBox_temp.setCurrentIndex(conidx)
assert wsl.doubleSpinBox_temp.isEnabled()
assert wsl.doubleSpinBox_temp.isReadOnly()
assert wsl.doubleSpinBox_temp.value() == 23.5
def test_matrix_slots(qtbot):
mw = ShapeOut2()
qtbot.addWidget(mw)
# add a dataslot
path = pathlib.Path(__file__).parent / "data" / "calibration_beads_47.rtdc"
mw.add_dataslot(paths=[path])
# add another one
mw.add_dataslot(paths=[path])
assert len(mw.pipeline.slot_ids) == 2, "we added those"
assert len(mw.pipeline.filter_ids) == 1, "automatically added"
# activate a dataslot
slot_id = mw.pipeline.slot_ids[0]
filt_id = mw.pipeline.filter_ids[0]
em = mw.block_matrix.get_widget(slot_id, filt_id)
qtbot.mouseClick(em, QtCore.Qt.LeftButton)
# did that work?
assert mw.pipeline.is_element_active(slot_id, filt_id)
slot_id2 = mw.pipeline.slot_ids[1]
assert not mw.pipeline.is_element_active(slot_id2, filt_id)
# remove a dataslot
wd = mw.block_matrix.get_widget(slot_id=slot_id)
wd.action_remove()
assert not mw.pipeline.is_element_active(slot_id2, filt_id)
def test_manual_basic(qtbot):
"""Most simple test"""
mw = ShapeOut2()
qtbot.addWidget(mw)
# add a dataslot
path = datapath / "calibration_beads_47.rtdc"
mw.add_dataslot(paths=[path])
mw.add_dataslot(paths=[path])
# sanity check (no emodulus should be available)
for slot in mw.pipeline.slots:
ds = slot.get_dataset()
assert "emodulus" not in ds
assert ds.config["setup"]["medium"] == "CellCarrierB"
# create bulk action dialog manually
dlg = bulk.BulkActionEmodulus(mw, pipeline=mw.pipeline)
dlg.comboBox_temp.setCurrentIndex(dlg.comboBox_temp.findData("manual"))
dlg.doubleSpinBox_temp.setValue(29.5)
dlg.on_ok()
for slot in mw.pipeline.slots:
ds = slot.get_dataset()
assert "emodulus" in ds
assert ds.config["setup"]["medium"] == "CellCarrierB"
assert ds.config["calculation"]["emodulus lut"] == "LE-2D-FEM-19"
assert ds.config["calculation"]["emodulus medium"] == "CellCarrierB"
assert ds.config["calculation"]["emodulus temperature"] == 29.5
assert "emodulus viscosity" not in ds.config["calculation"]
def test_remove_plots_issue_36(qtbot):
"""Correctly handle empty plots
https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut2/issues/36
Traceback (most recent call last):
File "/home/paul/repos/ShapeOut2/shapeout2/gui/main.py",
line 193, in adopt_pipeline
lay = pipeline_state["plots"][plot_index]["layout"]
IndexError: list index out of range
"""
mw = ShapeOut2()
qtbot.addWidget(mw)
# add a dataslots
path = datapath / "calibration_beads_47.rtdc"
mw.add_dataslot(paths=[path, path, path])
assert len(mw.pipeline.slot_ids) == 3, "we added those"
assert len(mw.pipeline.filter_ids) == 1, "automatically added"
# now create a plot window
plot_id = mw.add_plot()
# and another one
mw.add_plot()
# remove a plot
pw = mw.block_matrix.get_widget(filt_plot_id=plot_id)
pw.action_remove()
def test_empty_plot_with_one_plot_per_dataset_issue_41(qtbot):
"""
Setting "one plot per dataset" for an empty plot resulted in
zero-division error when determining col/row numbers
"""
mw = ShapeOut2()
qtbot.addWidget(mw)
# add a dataslot
path = datapath / "calibration_beads_47.rtdc"
mw.add_dataslot(paths=[path])
# add a plot
plot_id = mw.add_plot()
# activate analysis view
pe = mw.block_matrix.get_widget(filt_plot_id=plot_id)
qtbot.mouseClick(pe.toolButton_modify, QtCore.Qt.LeftButton)
pv = mw.widget_ana_view.widget_plot
# Change to "each" and apply
idx = pv.comboBox_division.findData("each")
pv.comboBox_division.setCurrentIndex(idx)
# Lead to zero-division error in "get_plot_col_row_count"
qtbot.mouseClick(pv.pushButton_apply, QtCore.Qt.LeftButton)
def test_simple(qtbot):
mw = ShapeOut2()
qtbot.addWidget(mw)
# add fake measurement
path = make_dataset(medium="CellCarrier", temp=22.5, temp_range=[22, 23])
with dclab.new_dataset(path) as ds:
# Youngs modulus can readily be computed
# https://dclab.readthedocs.io/en/latest/sec_av_emodulus.html
ds.config["calculation"]["emodulus medium"] = \
ds.config["setup"]["medium"]
ds.config["calculation"]["emodulus lut"] = "LE-2D-FEM-19"
emodA = np.array(ds["emodulus"], copy=True)
ds.config["calculation"]["emodulus temperature"] = \
ds.config["setup"]["temperature"]
emodC = np.array(ds["emodulus"], copy=True)
assert not np.allclose(
emodA, emodC, atol=0, rtol=1e-12, equal_nan=True), "sanity check"
mw.add_dataslot(paths=[path])
wsl = mw.widget_ana_view.widget_slot
# default values
assert wsl.comboBox_medium.currentData() == "CellCarrier"
assert wsl.comboBox_temp.currentData() == "feature"
# scenario A (this is already set by default)
ds1 = mw.pipeline.slots[0].get_dataset()
assert np.allclose(ds1["emodulus"],
emodA,
atol=0,
rtol=1e-12,
equal_nan=True)
# scenario C (switch to config)
wsl.comboBox_temp.setCurrentIndex(wsl.comboBox_temp.findData("config"))
qtbot.mouseClick(wsl.pushButton_apply, QtCore.Qt.LeftButton)
ds2 = mw.pipeline.slots[0].get_dataset()
assert np.allclose(ds2["emodulus"],
emodC,
atol=0,
rtol=1e-12,
equal_nan=True)
# scenario C (switch to manual)
wsl.comboBox_temp.setCurrentIndex(wsl.comboBox_temp.findData("manual"))
wsl.doubleSpinBox_temp.setValue(22.5)
qtbot.mouseClick(wsl.pushButton_apply, QtCore.Qt.LeftButton)
ds3 = mw.pipeline.slots[0].get_dataset()
assert np.allclose(ds3["emodulus"],
emodC,
atol=0,
rtol=1e-12,
equal_nan=True)
try:
path.unlink()
except BaseException:
pass
def test_manual_wrong_medium(qtbot):
"""Deliberately set wrong medium"""
mw = ShapeOut2()
qtbot.addWidget(mw)
# add a dataslot
path = datapath / "calibration_beads_47.rtdc"
mw.add_dataslot(paths=[path])
mw.add_dataslot(paths=[path])
# create bulk action dialog manually
dlg = bulk.BulkActionEmodulus(mw, pipeline=mw.pipeline)
dlg.comboBox_temp.setCurrentIndex(dlg.comboBox_temp.findData("manual"))
dlg.doubleSpinBox_temp.setValue(29.5)
# Set medium to "water". This should not change the emodulus medium.
dlg.comboBox_medium.setCurrentIndex(dlg.comboBox_medium.findData("water"))
dlg.on_ok()
for slot in mw.pipeline.slots:
ds = slot.get_dataset()
assert "emodulus" in ds
assert ds.config["setup"]["medium"] == "CellCarrierB"
assert ds.config["calculation"]["emodulus lut"] == "LE-2D-FEM-19"
assert ds.config["calculation"]["emodulus medium"] == "CellCarrierB"
assert ds.config["calculation"]["emodulus temperature"] == 29.5
assert "emodulus viscosity" not in ds.config["calculation"]
def test_filter_min_max_inf(qtbot):
path = make_fake_dataset()
mw = ShapeOut2()
qtbot.addWidget(mw)
# add the file
mw.add_dataslot(paths=[path])
assert len(mw.pipeline.slot_ids) == 1, "we added that"
assert len(mw.pipeline.filter_ids) == 1, "automatically added"
# open the filter edit in the Analysis View
fe = mw.block_matrix.get_widget(filt_plot_id=mw.pipeline.filter_ids[0])
qtbot.mouseClick(fe.toolButton_modify, QtCore.Qt.LeftButton)
# box filtering
wf = mw.widget_ana_view.widget_filter
# enable selection
qtbot.mouseClick(wf.toolButton_moreless, QtCore.Qt.LeftButton)
# find the porosity item and click the checkbox
rc = wf._box_range_controls["area_ratio"]
qtbot.mouseClick(rc.checkBox, QtCore.Qt.LeftButton)
# disable selection
qtbot.mouseClick(wf.toolButton_moreless, QtCore.Qt.LeftButton)
# check that the range control does not have all-zero values
rcstate = rc.__getstate__()
assert rcstate["start"] != 0
assert rcstate["end"] != 0
# only approximate (b/c they were converted on the range scale)
ds = dclab.new_dataset(path)
assert np.allclose(rcstate["start"], ds["area_ratio"][2], rtol=1e-4)
assert np.allclose(rcstate["end"], 1.1, rtol=1e-4)
def test_no_events_disable(qtbot):
"""When all events are removed, a message should be displayed"""
mw = ShapeOut2()
qtbot.addWidget(mw)
# This session also contains a plot, so this is essentially
# also a test for empty plots.
spath = datapath / "version_2_1_6_no_events.so2"
mw.on_action_open(spath)
# Matrix widgets
slot_id1 = mw.pipeline.slot_ids[0]
slot_id2 = mw.pipeline.slot_ids[1]
filt_id = mw.pipeline.filter_ids[0]
em1 = mw.block_matrix.get_widget(slot_id1, filt_id)
em2 = mw.block_matrix.get_widget(slot_id2, filt_id)
# Now activate Quick View
qtbot.mouseClick(em1, QtCore.Qt.LeftButton, QtCore.Qt.ShiftModifier)
# Get Quick View instance
qv = mw.widget_quick_view
# This will display the "Hoppla!" message
assert qv.label_noevents.isVisible()
# Check the reverse
qtbot.mouseClick(em2, QtCore.Qt.LeftButton, QtCore.Qt.ShiftModifier)
assert not qv.label_noevents.isVisible()
def test_filter_min_max_inf(qtbot):
mw = ShapeOut2()
qtbot.addWidget(mw)
# add 3 dataslots
path = datapath / "calibration_beads_47.rtdc"
mw.add_dataslot(paths=[path, path, path])
# change the slot names
for ii, slot in enumerate(mw.pipeline.slots):
slot.name = "slot numero {}".format(ii)
mw.adopt_slot(slot.__getstate__())
# sanity checks
assert mw.pipeline.slots[0].name == "slot numero 0"
assert mw.pipeline.slots[1].name == "slot numero 1"
assert mw.pipeline.slots[2].name == "slot numero 2"
# create reorder dialog manually
dlg = DlgSlotReorder(mw.pipeline, mw)
dlg.pipeline_changed.connect(mw.adopt_pipeline)
# reorder plots
dlg.listWidget.setCurrentRow(0)
dlg.toolButton_down.clicked.emit()
dlg.on_ok()
# now check that reordering happened
assert mw.pipeline.slots[0].name == "slot numero 1"
assert mw.pipeline.slots[1].name == "slot numero 0"
assert mw.pipeline.slots[2].name == "slot numero 2"
def test_polygon_filter_basic(qtbot):
path = data_path / "calibration_beads_47.rtdc"
with dclab.new_dataset(path) as ds:
pf1 = dclab.PolygonFilter(
axes=("deform", "area_um"),
points=[
[ds["deform"].min(), ds["area_um"].min()],
[ds["deform"].min(), ds["area_um"].mean()],
[ds["deform"].mean(), ds["area_um"].mean()],
],
name="Triangle of Death",
)
mw = ShapeOut2()
qtbot.addWidget(mw)
# add the file
mw.add_dataslot(paths=[path])
# enable the filter
slot_id = mw.pipeline.slot_ids[0]
filt_id = mw.pipeline.filter_ids[0]
em = mw.block_matrix.get_widget(slot_id, filt_id)
qtbot.mouseClick(em, QtCore.Qt.LeftButton)
# did that work?
assert mw.pipeline.is_element_active(slot_id, filt_id)
assert len(mw.pipeline.slot_ids) == 1, "we added that"
assert len(mw.pipeline.filter_ids) == 1, "automatically added"
# open the filter edit in the Analysis View
fe = mw.block_matrix.get_widget(filt_plot_id=mw.pipeline.filter_ids[0])
qtbot.mouseClick(fe.toolButton_modify, QtCore.Qt.LeftButton)
# enable the polygon filter
wf = mw.widget_ana_view.widget_filter
filter_ids = list(wf._polygon_checkboxes.keys())
# sanity check
assert filter_ids == [pf1.unique_id]
wf._polygon_checkboxes[pf1.unique_id].setChecked(True)
assert wf._polygon_checkboxes[pf1.unique_id].isChecked()
# click apply
qtbot.mouseClick(wf.pushButton_apply, QtCore.Qt.LeftButton)
# check the filter
assert pf1.unique_id in mw.pipeline.filters[0].polylist
# get the dataset
assert len(mw.pipeline.slots) == 1
assert len(mw.pipeline.filters) == 1
ds_slot = mw.pipeline.slots[0].get_dataset()
ds = mw.pipeline.get_dataset(0)
assert ds_slot is not ds
assert np.sum(ds.filter.all) == 5
assert len(ds) == 47
def test_on_action_about(qtbot):
with mock.patch("PyQt5.QtWidgets.QMessageBox.about") as mock_about:
mw = ShapeOut2()
mw.on_action_about()
mw.close()
assert mock_about.call_args.args[1] == \
f"Shape-Out {shapeout2.__version__}"
assert "Shape-Out 2" in mock_about.call_args.args[2]
def test_handle_nan_valued_feature_color(qtbot):
"""User wants to color scatter data points with feature containing nans"""
spath = datapath / "version_2_1_2_plot_color_emodulus.so2"
mw = ShapeOut2()
qtbot.addWidget(mw)
# lead to:
# OverflowError: argument 4 overflowed: value must be in the range
# -2147483648 to 2147483647
mw.on_action_open(spath)
def test_init_print_version(qtbot):
mock_stdout = io.StringIO()
mock_exit = mock.Mock()
with mock.patch("sys.exit", mock_exit):
with mock.patch('sys.stdout', mock_stdout):
mw = ShapeOut2("--version")
mw.close()
assert mock_exit.call_args.args[0] == 0
assert mock_stdout.getvalue().strip() == shapeout2.__version__
def test_other_medium_viscosity_editable_issue_49(qtbot):
mw = ShapeOut2()
qtbot.addWidget(mw)
# add fake measurement
path1 = make_dataset(medium=None)
mw.add_dataslot(paths=[path1])
wsl = mw.widget_ana_view.widget_slot
ds = mw.pipeline.slots[0].get_dataset()
assert "medium" not in ds.config["setup"], "sanity check (medium removed)"
oidx = wsl.comboBox_medium.findData("other")
wsl.comboBox_medium.setCurrentIndex(oidx)
assert not wsl.doubleSpinBox_visc.isReadOnly(), "Should be editable"
assert wsl.doubleSpinBox_visc.isEnabled(), "Should be editable"
def test_no_events_issue_37(qtbot):
"""https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut2/issues/37
"ValueError: zero-size array to reduction operation minimum
which has no identity" when all events are filtered out.
"""
mw = ShapeOut2()
qtbot.addWidget(mw)
# add a dataslot
path = datapath / "calibration_beads_47.rtdc"
mw.add_dataslot(paths=[path, path])
assert len(mw.pipeline.slot_ids) == 2, "we added those"
assert len(mw.pipeline.filter_ids) == 1, "automatically added"
# activate a dataslot
slot_id = mw.pipeline.slot_ids[0]
filt_id = mw.pipeline.filter_ids[0]
em = mw.block_matrix.get_widget(slot_id, filt_id)
qtbot.mouseClick(em, QtCore.Qt.LeftButton) # activate
# did that work?
assert mw.pipeline.is_element_active(slot_id, filt_id)
# filter away all events
fe = mw.block_matrix.get_widget(filt_plot_id=filt_id)
qtbot.mouseClick(fe.toolButton_modify, QtCore.Qt.LeftButton)
fv = mw.widget_ana_view.widget_filter
qtbot.mouseClick(fv.toolButton_moreless, QtCore.Qt.LeftButton)
rc = fv._box_range_controls["area_um"]
qtbot.mouseClick(rc.checkBox, QtCore.Qt.LeftButton)
# did that work?
assert rc.checkBox.isChecked()
qtbot.mouseClick(fv.toolButton_moreless, QtCore.Qt.LeftButton)
# set range
rc.doubleSpinBox_min.setValue(0)
rc.doubleSpinBox_max.setValue(1)
qtbot.mouseClick(fv.pushButton_apply, QtCore.Qt.LeftButton)
# did that work?
ds = mw.pipeline.get_dataset(slot_index=0, filt_index=0, apply_filter=True)
assert np.sum(ds.filter.all) == 0
# open QuickView
slot_id = mw.pipeline.slot_ids[0]
filt_id = mw.pipeline.filter_ids[0]
em = mw.block_matrix.get_widget(slot_id, filt_id)
# this raised the error
qtbot.mouseClick(em, QtCore.Qt.LeftButton, QtCore.Qt.ShiftModifier)
mw.close()
def test_handle_empty_plots_issue_27(qtbot):
"""Correctly handle empty plots
https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut2/issues/27
"""
mw = ShapeOut2()
qtbot.addWidget(mw)
# add a dataslot
path = datapath / "calibration_beads_47.rtdc"
mw.add_dataslot(paths=[path])
# add another one
mw.add_dataslot(paths=[path])
assert len(mw.pipeline.slot_ids) == 2, "we added those"
assert len(mw.pipeline.filter_ids) == 1, "automatically added"
# activate a dataslot
slot_id = mw.pipeline.slot_ids[0]
filt_id = mw.pipeline.filter_ids[0]
em = mw.block_matrix.get_widget(slot_id, filt_id)
qtbot.mouseClick(em, QtCore.Qt.LeftButton) # activate
# did that work?
assert mw.pipeline.is_element_active(slot_id, filt_id)
# filter away all events
fe = mw.block_matrix.get_widget(filt_plot_id=filt_id)
qtbot.mouseClick(fe.toolButton_modify, QtCore.Qt.LeftButton)
fv = mw.widget_ana_view.widget_filter
qtbot.mouseClick(fv.toolButton_moreless, QtCore.Qt.LeftButton)
rc = fv._box_range_controls["area_um"]
qtbot.mouseClick(rc.checkBox, QtCore.Qt.LeftButton)
# did that work?
assert rc.checkBox.isChecked()
qtbot.mouseClick(fv.toolButton_moreless, QtCore.Qt.LeftButton)
# set range
rc.doubleSpinBox_min.setValue(0)
rc.doubleSpinBox_max.setValue(1)
qtbot.mouseClick(fv.pushButton_apply, QtCore.Qt.LeftButton)
# did that work?
ds = mw.pipeline.get_dataset(slot_index=0, filt_index=0, apply_filter=True)
assert np.sum(ds.filter.all) == 0
# now create a plot window
plot_id = mw.add_plot()
pe = mw.block_matrix.get_widget(slot_id, plot_id)
with pytest.warns(pipeline.core.EmptyDatasetWarning):
# this now only throws a warning
qtbot.mouseClick(pe, QtCore.Qt.LeftButton) # activate (raises #27)
def test_remove_dataset_h5py_error(qtbot):
"""Removing an activated dataset and activating Quick View fails
Unhandled exception in Shape-Out version 2.0.1.post2:
Traceback (most recent call last):
File "/home/paul/repos/ShapeOut2/shapeout2/gui/main.py", line 235,
in adopt_pipeline
self.widget_quick_view.update_feature_choices()
File "/home/paul/repos/ShapeOut2/shapeout2/gui/quick_view/qv_main.py",
line 635, in update_feature_choices
ds_feats = [f for f in self.rtdc_ds.features if f in feats_scalar]
[...]
File "/home/paul/repos/dclab/dclab/rtdc_dataset/fmt_hdf5.py", line 101,
in _is_defective_feature
if attr in self._h5.attrs:
[...]
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "h5py/h5o.pyx", line 190, in h5py.h5o.open
ValueError: Not a location (invalid object ID)
"""
mw = ShapeOut2()
qtbot.addWidget(mw)
# add a dataslot
path = datapath / "calibration_beads_47.rtdc"
mw.add_dataslot(paths=[path, path])
assert len(mw.pipeline.slot_ids) == 2, "we added those"
assert len(mw.pipeline.filter_ids) == 1, "automatically added"
# activate a dataslot
slot_id = mw.pipeline.slot_ids[0]
filt_id = mw.pipeline.filter_ids[0]
em = mw.block_matrix.get_widget(slot_id, filt_id)
qtbot.mouseClick(em, QtCore.Qt.LeftButton) # activate
qtbot.mouseClick(em, QtCore.Qt.LeftButton, QtCore.Qt.ShiftModifier)
# did that work?
assert mw.pipeline.is_element_active(slot_id, filt_id)
# close Quick View
qtbot.mouseClick(mw.toolButton_quick_view, QtCore.Qt.LeftButton)
# now remove the dataset
pw = mw.block_matrix.get_widget(slot_id=slot_id)
pw.action_remove()
# open Quick View
qtbot.mouseClick(mw.toolButton_quick_view, QtCore.Qt.LeftButton)
mw.close()
def test_empty_medium_string_should_offer_user_edit(qtbot):
mw = ShapeOut2()
qtbot.addWidget(mw)
# add fake measurement
path1 = make_dataset(medium=" ")
mw.add_dataslot(paths=[path1])
wsl = mw.widget_ana_view.widget_slot
ds = mw.pipeline.slots[0].get_dataset()
assert ds.config["setup"]["medium"] == " "
assert wsl.comboBox_medium.currentData() == "other"
assert not wsl.doubleSpinBox_visc.isReadOnly(), "Should be editable"
assert wsl.doubleSpinBox_visc.isEnabled(), "Should be editable"
assert np.isnan(wsl.__getstate__()["emodulus"]["emodulus temperature"])
assert wsl.__getstate__()["emodulus"]["emodulus medium"] == "other"
assert wsl.__getstate__()["emodulus"]["emodulus scenario"] is None
def test_box_filter_selection_no_preselection_issue_67(qtbot):
"""
The user creates a filter and selects a few features for box
filtering. Then the user creates a new filter and tries to add
new box filters. There should not be any preselected filters.
"""
path = make_fake_dataset()
mw = ShapeOut2()
qtbot.addWidget(mw)
# add the file
mw.add_dataslot(paths=[path])
# edit the initial filter in the Analysis View
fe = mw.block_matrix.get_widget(filt_plot_id=mw.pipeline.filter_ids[0])
qtbot.mouseClick(fe.toolButton_modify, QtCore.Qt.LeftButton)
# box filtering
wf = mw.widget_ana_view.widget_filter
# enable selection
qtbot.mouseClick(wf.toolButton_moreless, QtCore.Qt.LeftButton)
# find the porosity item and click the checkbox
rc = wf._box_range_controls["area_ratio"]
qtbot.mouseClick(rc.checkBox, QtCore.Qt.LeftButton)
# disable selection
qtbot.mouseClick(wf.toolButton_moreless, QtCore.Qt.LeftButton)
# now add second filter
mw.add_filter()
# edit the second filter in the Analysis View
fe = mw.block_matrix.get_widget(filt_plot_id=mw.pipeline.filter_ids[1])
qtbot.mouseClick(fe.toolButton_modify, QtCore.Qt.LeftButton)
# make sure that "area_ratio" is not preselected
wf = mw.widget_ana_view.widget_filter
# enable selection
qtbot.mouseClick(wf.toolButton_moreless, QtCore.Qt.LeftButton)
# find the porosity item and click the checkbox
rc = wf._box_range_controls["area_ratio"]
assert not rc.checkBox.isChecked()
# and a sanity check
rc2 = wf._box_range_controls["deform"]
assert not rc2.checkBox.isChecked()
# cleanup: disable selection
qtbot.mouseClick(wf.toolButton_moreless, QtCore.Qt.LeftButton)
def test_lme4_with_dcor_session_differential(qtbot):
"""
Perform differential deformation test
"""
mw = ShapeOut2()
qtbot.addWidget(mw)
mw.on_action_open(data_path / "version_2_5_0_dcor_lme4_diff.so2")
# create dialog manually
dlg = ComputeSignificance(mw, pipeline=mw.pipeline)
# set the variables
# treatment rep 1
dlg.datasets[0].comboBox_group.setCurrentIndex(1)
# treatment rep 2
dlg.datasets[1].comboBox_group.setCurrentIndex(1)
dlg.datasets[1].spinBox_repeat.setValue(2)
# res treatment rep 1
dlg.datasets[2].comboBox_group.setCurrentIndex(1)
# res treatment rep 2
dlg.datasets[3].comboBox_group.setCurrentIndex(1)
dlg.datasets[3].spinBox_repeat.setValue(2)
# control rep 1
pass
# control rep 2
dlg.datasets[5].spinBox_repeat.setValue(2)
# control rep 3
dlg.datasets[6].spinBox_repeat.setValue(3)
# res control rep 1
pass
# res control rep 2
dlg.datasets[8].spinBox_repeat.setValue(2)
# res control rep 3
dlg.datasets[9].spinBox_repeat.setValue(3)
# set the feature
feat_id = dlg.comboBox_feat.findData("deform")
dlg.comboBox_feat.setCurrentIndex(feat_id)
dlgr = dlg.on_lme4(ret_dlg=True)
assert dlgr.label_model.text() == "lmer"
assert dlgr.label_feature.text() == "Deformation"
assert dlgr.label_differential.text() == "Yes"
assert dlgr.lineEdit_pvalue.text() == "0.0000035055"
assert dlgr.lineEdit_intercept.text() == "0.020509"
assert dlgr.lineEdit_treatment.text() == "-0.0052991"
def test_switch_and_update_chip_region(qtbot):
mw = ShapeOut2()
qtbot.addWidget(mw)
# add fake measurement
path1 = make_dataset(medium="CellCarrier",
temp=22.5,
temp_range=[22, 23],
chip_region="channel")
path2 = make_dataset(medium="CellCarrier",
temp=22.5,
temp_range=[22, 23],
chip_region="reservoir")
slot_id1, slot_id2 = mw.add_dataslot(paths=[path1, path2])
wsl = mw.widget_ana_view.widget_slot
# select the first slot
em1 = mw.block_matrix.get_widget(slot_id=slot_id1)
em2 = mw.block_matrix.get_widget(slot_id=slot_id2)
qtbot.mouseClick(em1.toolButton_modify, QtCore.Qt.LeftButton)
# set temperature manually
idm = wsl.comboBox_temp.findData("manual")
wsl.comboBox_temp.setCurrentIndex(idm)
assert wsl.comboBox_temp.currentData() == "manual"
wsl.doubleSpinBox_temp.setValue(20.0)
assert wsl.doubleSpinBox_temp.value() == 20
qtbot.mouseClick(wsl.pushButton_apply, QtCore.Qt.LeftButton)
QtWidgets.QApplication.processEvents(QtCore.QEventLoop.AllEvents, 300)
# check whether that worked
assert wsl.get_dataset(
).config["calculation"]["emodulus temperature"] == 20
# switch to the second (reservoir) measurement
qtbot.mouseClick(em2.toolButton_modify, QtCore.Qt.LeftButton)
assert not wsl.groupBox_emod.isVisible()
# now switch back
qtbot.mouseClick(em1.toolButton_modify, QtCore.Qt.LeftButton)
# This is the actual test
assert wsl.doubleSpinBox_temp.value() == 20
try:
path1.unlink()
path2.unlink()
except BaseException:
pass
def test_user_defined_medium_should_work(qtbot):
mw = ShapeOut2()
qtbot.addWidget(mw)
# add fake measurement
path1 = make_dataset(medium="MyMedium")
mw.add_dataslot(paths=[path1])
wsl = mw.widget_ana_view.widget_slot
ds = mw.pipeline.slots[0].get_dataset()
assert ds.config["setup"]["medium"] == "MyMedium", "sanity check"
assert wsl.comboBox_medium.currentData() == "MyMedium"
assert not wsl.doubleSpinBox_visc.isReadOnly(), "Should be editable"
assert wsl.doubleSpinBox_visc.isEnabled(), "Should be editable"
wsl.doubleSpinBox_visc.setValue(12.1)
assert wsl.__getstate__()["emodulus"]["emodulus viscosity"] == 12.1
assert np.isnan(wsl.__getstate__()["emodulus"]["emodulus temperature"])
assert wsl.__getstate__()["emodulus"]["emodulus medium"] == "MyMedium"
assert wsl.__getstate__()["emodulus"]["emodulus scenario"] is None
def test_export_datasets_rtdc_emodulus_only_in_one_issue_80(qtbot):
mw = ShapeOut2()
qtbot.addWidget(mw)
# add 3 dataslots
path = data_path / "calibration_beads_47.rtdc"
mw.add_dataslot(paths=[path, path, path])
# set metadata for Young's modulus only in one slot
wsl = mw.widget_ana_view.widget_slot
wsl.doubleSpinBox_temp.setValue(23)
qtbot.mouseClick(wsl.pushButton_apply, QtCore.Qt.LeftButton)
# make sure that worked
ds0 = mw.pipeline.slots[0].get_dataset()
assert "emodulus" in ds0
# perform the export
tmpd = tempfile.mkdtemp(prefix="shapeout2_test_data_export_")
with mock.patch.object(QtWidgets.QFileDialog,
"getExistingDirectory",
return_value=tmpd):
with mock.patch.object(QtWidgets.QMessageBox, "warning") as mwarn:
# create export dialog manually (asks user for directory)
dlg = export.ExportData(mw, pipeline=mw.pipeline)
# Everything is set-up already
# (.rtdc export, all features selected).
# Click OK.
buttons = dlg.buttonBox.buttons()
qtbot.mouseClick(buttons[0], QtCore.Qt.LeftButton)
# make sure that we got two warning messages
assert mwarn.call_count == 2
# make sure we have three .rtdc files
exported = sorted(list(pathlib.Path(tmpd).glob("*.rtdc")))
assert len(exported) == 3
# the first exported file should have Young's modulus
with dclab.new_dataset(exported[0]) as ds:
assert "emodulus" in ds
with dclab.new_dataset(exported[1]) as ds:
assert "emodulus" not in ds
with dclab.new_dataset(exported[2]) as ds:
assert "emodulus" not in ds
def test_feature_bright_avg_not_present_issue_62(qtbot):
"""Plot a dataset that does not contain the "bright_avg" feature
...or any means of computing it (i.e. via "image")
"""
# create fake dataset without bright_avg
tmp = tempfile.mktemp(".rtdc", prefix="example_hue_")
with dclab.new_dataset(datapath / "calibration_beads_47.rtdc") as ds:
ds.export.hdf5(tmp, features=["area_um", "pos_x", "pos_y", "deform"])
mw = ShapeOut2()
qtbot.addWidget(mw)
# add dataset
slot_id = mw.add_dataslot([tmp])[0]
# add plot
plot_id = mw.add_plot()
# and activate it
pw = mw.block_matrix.get_widget(filt_plot_id=plot_id, slot_id=slot_id)
# this raised "ValueError: 'bright_avg' is not in list" (issue #62)
qtbot.mouseClick(pw, QtCore.Qt.LeftButton)
def test_temperature_feature(qtbot):
mw = ShapeOut2()
qtbot.addWidget(mw)
# add custom dataslot
path = make_dataset(medium="CellCarrier", temp=22.5, temp_range=[22, 23])
mw.add_dataslot(paths=[path])
mw.add_dataslot(paths=[path])
# create bulk action dialog manually
dlg = bulk.BulkActionEmodulus(mw, pipeline=mw.pipeline)
dlg.comboBox_temp.setCurrentIndex(dlg.comboBox_temp.findData("feature"))
dlg.on_ok()
for slot in mw.pipeline.slots:
ds = slot.get_dataset()
assert "emodulus" in ds
assert ds.config["setup"]["medium"] == "CellCarrier"
assert ds.config["calculation"]["emodulus lut"] == "LE-2D-FEM-19"
assert ds.config["calculation"]["emodulus medium"] == "CellCarrier"
assert "emodulus temperature" not in ds.config["calculation"]
assert "emodulus viscosity" not in ds.config["calculation"]
def test_clear_session_issue_25(qtbot):
"""https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut2/issues/25"""
mw = ShapeOut2()
qtbot.addWidget(mw)
# add a dataslot
path = datapath / "calibration_beads_47.rtdc"
mw.add_dataslot(paths=[path])
assert len(mw.pipeline.slot_ids) == 1, "we added that"
assert len(mw.pipeline.filter_ids) == 1, "automatically added"
# activate a dataslot
slot_id = mw.pipeline.slot_ids[0]
filt_id = mw.pipeline.filter_ids[0]
em = mw.block_matrix.get_widget(slot_id, filt_id)
qtbot.mouseClick(em, QtCore.Qt.LeftButton, QtCore.Qt.ShiftModifier)
# did that work?
assert mw.toolButton_quick_view.isChecked()
# now clear the session (this raised the errror in #25)
mw.on_action_clear(assume_yes=True)