def test_task_compress_and_repack_strip_issue19(qtbot, monkeypatch):
"""Same test as above, only tests whether repack and strip logs works"""
path = retrieve_data("rtdc_data_hdf5_rtfdc.zip")
path_out = path.with_name("compressed")
path_out.mkdir()
# Monkeypatch
monkeypatch.setattr(QDialog, "exec_", lambda *args: QMessageBox.Ok)
monkeypatch.setattr(QMessageBox, "exec_", lambda *args: QMessageBox.Ok)
monkeypatch.setattr(QFileDialog, "getExistingDirectory",
lambda *args: str(path_out))
mw = DCKit(check_update=False)
qtbot.addWidget(mw)
mw.append_paths([path])
mw.checkBox_repack.setChecked(True)
pouts, invalid = mw.on_task_compress()
assert len(pouts) == 1
assert len(invalid) == 0
with dclab.new_dataset(pouts[0]) as ds, dclab.new_dataset(path) as ds0:
assert len(ds) == len(ds0)
assert len(ds.logs) == 0
scf = list(set(ds.features_scalar + ds0.features_scalar))
for feat in scf:
assert feat in ds0
assert feat in ds
assert np.all(ds[feat] == ds0[feat])
def test_task_tdms2rtdc_bad_online_contour_no_absdiff(qtbot, monkeypatch):
"""This tests for a regression
The [online_contour]: "no absdiff" keyword was somehow set to
"please select" instead of ignoring it if the user did not choose
anything.
ValueError: could not convert string to float: 'please select'
"""
path = retrieve_data("rtdc_data_traces_video.zip")
# modify the data to not have the [online_contour]: "no absdiff" keyword
p_para = path.parent / "M1_para.ini"
ptext = p_para.read_text().split("\n")
# remove [online_contour]: "no absdiff"
for ii in range(len(ptext)):
if ptext[ii].strip() == "Diff_Method = 1":
ptext.pop(ii)
break
p_para.write_text("\n".join(ptext))
path_out = path.with_name("converted")
path_out.mkdir()
# Monkeypatch message box to always return OK
monkeypatch.setattr(QMessageBox, "exec_", lambda *args: QMessageBox.Ok)
monkeypatch.setattr(QFileDialog, "getExistingDirectory",
lambda *args: str(path_out))
mw = DCKit(check_update=False)
qtbot.addWidget(mw)
mw.append_paths([path])
assert mw.tableWidget.rowCount() == 1
paths_converted, invalid, errors = mw.on_task_tdms2rtdc()
assert len(errors) == 0
assert len(invalid) == 0
assert len(paths_converted) == 1
with dclab.new_dataset(paths_converted[0]) as ds:
assert ds.config["setup"]["module composition"] == "Cell_Flow_2, Fluor"
def test_list_entries(qtbot):
mw = DCKit(check_update=False)
qtbot.addWidget(mw)
path = retrieve_data("rtdc_data_hdf5_rtfdc.zip")
mw.append_paths([path])
meta = mw.get_metadata(0)
assert meta["experiment"]["sample"] == "calibration_beads"
def test_task_split_trace(qtbot, monkeypatch):
path = retrieve_data("rtdc_data_hdf5_rtfdc.zip")
path_out = path.parent / "split"
path_out.mkdir()
# Monkeypatch
monkeypatch.setattr(QDialog, "exec_", lambda *args: QMessageBox.Ok)
monkeypatch.setattr(QMessageBox, "exec_", lambda *args: QMessageBox.Ok)
monkeypatch.setattr(QFileDialog, "getExistingDirectory",
lambda *args: str(path_out))
monkeypatch.setattr(QInputDialog, "getInt",
lambda *args: [3, QMessageBox.Ok])
# Initialize
mw = DCKit(check_update=False)
qtbot.addWidget(mw)
mw.append_paths([path])
paths_split, errors = mw.on_task_split()
assert not errors
assert len(paths_split) == 1
paths_out = sorted(path_out.glob("*.rtdc"))
assert len(paths_out) == 3
for pp, size in zip(paths_out, [3, 3, 1]):
with h5py.File(pp, mode="r") as h5:
assert len(h5["events"]["trace"]["fl1_raw"]) == size, pp
def test_integrity_with_medium_remove(qtbot, monkeypatch):
"""Same test as above but also test removal"""
path = retrieve_data("rtdc_data_traces_video.zip")
path_out = pathlib.Path(path).parent
# Monkeypatch message box to always return OK
monkeypatch.setattr(QMessageBox, "exec_", lambda *args: QMessageBox.Ok)
monkeypatch.setattr(QFileDialog, "getExistingDirectory",
lambda *args: str(path_out))
mw = DCKit(check_update=False)
qtbot.addWidget(mw)
mw.append_paths([path])
# set medium to CellCarrier
dlg = IntegrityCheckDialog(mw, path)
wid = dlg.user_widgets["setup"]["medium"]
wid.setCurrentText("CellCarrier")
dlg.done(True)
# reset the medium to nothing
dlg2 = IntegrityCheckDialog(mw, path)
wid2 = dlg2.user_widgets["setup"]["medium"]
wid2.setCurrentText("")
dlg2.done(True)
# 1. Get metadata from dict
dlg3 = IntegrityCheckDialog(mw, path)
wid3 = dlg3.user_widgets["setup"]["medium"]
assert dlg3.get_metadata_value("setup", "medium") is None
# 2. Make sure the combobox is set correctly
assert wid3.currentText() == ""
def test_task_metadata_sample(qtbot, monkeypatch):
# Monkeypatch message box to always return OK
monkeypatch.setattr(QMessageBox, "exec_", lambda *args: QMessageBox.Ok)
mw = DCKit(check_update=False)
qtbot.addWidget(mw)
path = retrieve_data("rtdc_data_hdf5_rtfdc.zip")
mw.append_paths([path])
mw.tableWidget.item(0, 3).setText("Peter Pan")
mw.on_task_metadata()
with dclab.new_dataset(path) as ds:
assert ds.config["experiment"]["sample"] == "Peter Pan"
def test_integrity_shapein_issue3(qtbot, monkeypatch):
"""Shape-In did not store the medium correctly
https://github.com/ZELLMECHANIK-DRESDEN/ShapeIn_Issues/issues/3
We don't do anything in this test. We just make sure that
CellCarrierB is set automatically.
"""
h5path = retrieve_data("rtdc_data_hdf5_rtfdc.zip")
with h5py.File(h5path, "a") as h5:
h5.attrs["setup:software version"] = "2.2.2.0"
h5.attrs["setup:medium"] = "CellCarrierB"
h5path_m = h5path.with_name("M001_data.rtdc")
h5path.rename(h5path_m)
# Create SoftwareSettings.ini
sinipath = h5path_m.with_name("M001_SoftwareSettings.ini")
sinipath.write_text("Buffer_Medium_ID=0\nBuffer_Medium=CellCarrierB")
# Proceed with loading
path_out = pathlib.Path(h5path_m).parent
# Monkeypatch message box to always return OK
monkeypatch.setattr(QMessageBox, "exec_", lambda *args: QMessageBox.Ok)
monkeypatch.setattr(QFileDialog, "getExistingDirectory",
lambda *args: str(path_out))
mw = DCKit(check_update=False)
qtbot.addWidget(mw)
mw.append_paths([h5path_m])
assert mw.tableWidget.rowCount() == 1, "sanity check"
# Now edit the medium (create dialog manually)
with pytest.warns(MetadataEditedWarning):
dlg = IntegrityCheckDialog(mw, h5path_m)
assert dlg.get_metadata_value("setup", "medium") == "CellCarrier"
assert "setup" in dlg.user_widgets, "setup section must be there"
assert "medium" in dlg.user_widgets["setup"], "medium must be there"
# finish the dialog
dlg.done(True)
# 1. Get metadata from dict (just to be sure)
dlg2 = IntegrityCheckDialog(mw, h5path_m)
assert dlg2.get_metadata_value("setup", "medium") == "CellCarrier"
# 2. Make sure the combobox is set correctly (just to be sure)
wid2 = dlg2.user_widgets["setup"]["medium"]
assert wid2.currentText() == "CellCarrier"
# 3. Compress and check (just to be sure)
paths_compressed, invalid = mw.on_task_compress()
assert len(invalid) == 0
assert len(paths_compressed) == 1
with dclab.new_dataset(paths_compressed[0]) as ds:
assert ds.config["setup"]["medium"] == "CellCarrier"
def test_task_join(qtbot, monkeypatch):
path = retrieve_data("rtdc_data_hdf5_rtfdc.zip")
path_out = path.with_name("out.rtdc")
# Monkeypatch
monkeypatch.setattr(QDialog, "exec_", lambda *args: QDialog.Accepted)
monkeypatch.setattr(QMessageBox, "exec_", lambda *args: QMessageBox.Ok)
monkeypatch.setattr(QFileDialog, "getSaveFileName", lambda *args:
(str(path_out), None))
mw = DCKit(check_update=False)
qtbot.addWidget(mw)
mw.append_paths([path, path])
mw.on_task_join()
with dclab.new_dataset(path_out) as ds, dclab.new_dataset(path) as ds0:
assert len(ds) == 2 * len(ds0)
def test_online_contour_no_absdiff(qtbot, monkeypatch):
"""Test booleanness of the metadata combo box"""
path = retrieve_data("rtdc_data_traces_video.zip")
# modify the data to not have the [online_contour]: "no absdiff" keyword
p_para = path.parent / "M1_para.ini"
ptext = p_para.read_text().split("\n")
# remove [online_contour]: "no absdiff"
for ii in range(len(ptext)):
if ptext[ii].strip() == "Diff_Method = 1":
ptext.pop(ii)
break
p_para.write_text("\n".join(ptext))
path_out = path.with_name("converted")
path_out.mkdir()
# Monkeypatch message box to always return OK
monkeypatch.setattr(QMessageBox, "exec_", lambda *args: QMessageBox.Ok)
monkeypatch.setattr(QFileDialog, "getExistingDirectory",
lambda *args: str(path_out))
mw = DCKit(check_update=False)
qtbot.addWidget(mw)
mw.append_paths([path])
# set value to True
dlg = IntegrityCheckDialog(mw, path)
wid = dlg.user_widgets["online_contour"]["no absdiff"]
assert wid.currentIndex() == 0
assert wid.currentData() == "no selection"
idx = wid.findData("true")
wid.setCurrentIndex(idx)
assert wid.currentData() == "true"
dlg.done(True)
# 1. Get metadata from dict
dlg2 = IntegrityCheckDialog(mw, path)
assert dlg2.get_metadata_value("online_contour", "no absdiff")
# 2. Make sure the combobox is set correctly
wid2 = dlg2.user_widgets["online_contour"]["no absdiff"]
assert wid2.currentData()
# 3. Convert and check
paths_converted, invalid, errors = mw.on_task_tdms2rtdc()
assert len(errors) == 0
assert len(invalid) == 0
assert len(paths_converted) == 1
with dclab.new_dataset(paths_converted[0]) as ds:
assert ds.config["online_contour"]["no absdiff"]
def test_task_tdms2rtdc(qtbot, monkeypatch):
path = retrieve_data("rtdc_data_traces_video.zip")
path_out = path.with_name("converted")
path_out.mkdir()
# Monkeypatch message box to always return OK
monkeypatch.setattr(QMessageBox, "exec_", lambda *args: QMessageBox.Ok)
monkeypatch.setattr(QFileDialog, "getExistingDirectory",
lambda *args: str(path_out))
mw = DCKit(check_update=False)
qtbot.addWidget(mw)
mw.append_paths([path])
assert mw.tableWidget.rowCount() == 1
paths_converted, invalid, errors = mw.on_task_tdms2rtdc()
assert len(errors) == 0
assert len(invalid) == 0
assert len(paths_converted) == 1
with dclab.new_dataset(paths_converted[0]) as ds:
assert ds.config["setup"]["module composition"] == "Cell_Flow_2, Fluor"
def test_integrity_shapein_issue3_control(qtbot, monkeypatch):
"""Shape-In did not store the medium correctly
https://github.com/ZELLMECHANIK-DRESDEN/ShapeIn_Issues/issues/3
With a functional Shape-In version, DCKit should not attempt anything.
"""
h5path = retrieve_data("rtdc_data_hdf5_rtfdc.zip")
with h5py.File(h5path, "a") as h5:
h5.attrs["setup:software version"] = "2.2.3.0" # [sic]
h5.attrs["setup:medium"] = "CellCarrierB"
h5path_m = h5path.with_name("M001_data.rtdc")
# Create SoftwareSettings.ini (should not have any effect, because
# the Shape-In version is expected to be safe.
sinipath = h5path_m.with_name("M001_SoftwareSettings.ini")
sinipath.write_text("Buffer_Medium_ID=0\nBuffer_Medium=CellCarrierB")
h5path.rename(h5path_m)
# Proceed with loading
path_out = pathlib.Path(h5path_m).parent
# Monkeypatch message box to always return OK
monkeypatch.setattr(QMessageBox, "exec_", lambda *args: QMessageBox.Ok)
monkeypatch.setattr(QFileDialog, "getExistingDirectory",
lambda *args: str(path_out))
mw = DCKit(check_update=False)
qtbot.addWidget(mw)
mw.append_paths([h5path_m])
assert mw.tableWidget.rowCount() == 1, "sanity check"
# Now edit the medium (create dialog manually)
dlg = IntegrityCheckDialog(mw, h5path_m)
assert dlg.get_metadata_value("setup", "medium") == "CellCarrierB"
assert "setup" not in dlg.user_widgets, "setup section must not be there"
# finish the dialog
dlg.done(True)
# 1. Get metadata from dict (just to be sure)
dlg2 = IntegrityCheckDialog(mw, h5path_m)
assert dlg2.get_metadata_value("setup", "medium") == "CellCarrierB"
# 2. Compress and check (just to be sure)
paths_compressed, invalid = mw.on_task_compress()
assert len(invalid) == 0
assert len(paths_compressed) == 1
with dclab.new_dataset(paths_compressed[0]) as ds:
assert ds.config["setup"]["medium"] == "CellCarrierB"
def test_integrity_with_medium(qtbot, monkeypatch):
"""This tests for a regression
It must be possible to edit the medium and the medium has to be
stored in the user-defined metadata.
"""
path = retrieve_data("rtdc_data_traces_video.zip")
path_out = pathlib.Path(path).parent
# Monkeypatch message box to always return OK
monkeypatch.setattr(QMessageBox, "exec_", lambda *args: QMessageBox.Ok)
monkeypatch.setattr(QFileDialog, "getExistingDirectory",
lambda *args: str(path_out))
mw = DCKit(check_update=False)
qtbot.addWidget(mw)
mw.append_paths([path])
assert mw.tableWidget.rowCount() == 1, "sanity check"
# Now edit the medium (create dialog manually)
dlg = IntegrityCheckDialog(mw, path)
assert dlg.get_metadata_value("setup", "medium") is None
assert "setup" in dlg.user_widgets, "setup section must be there"
assert "medium" in dlg.user_widgets["setup"], "medium must be there"
# set medium to CellCarrier
wid = dlg.user_widgets["setup"]["medium"]
assert wid.currentData() is None
wid.setCurrentText("CellCarrier")
# finish the dialog
dlg.done(True)
# 1. Get metadata from dict
dlg2 = IntegrityCheckDialog(mw, path)
assert dlg2.get_metadata_value("setup", "medium") == "CellCarrier"
# 2. Make sure the combobox is set correctly
wid2 = dlg2.user_widgets["setup"]["medium"]
assert wid2.currentText() == "CellCarrier"
# 3. Convert and check
paths_converted, invalid, errors = mw.on_task_tdms2rtdc()
assert len(errors) == 0
assert len(invalid) == 0
assert len(paths_converted) == 1
with dclab.new_dataset(paths_converted[0]) as ds:
assert ds.config["setup"]["medium"] == "CellCarrier"