def test_laser_widget(qtbot: QtBot):
x = rand_data(["A1", "B2"])
y = x["A1"].copy()
viewspace = LaserViewSpace()
qtbot.addWidget(viewspace)
viewspace.show()
view = viewspace.activeView()
view.addLaser(Laser(x))
widget = view.activeWidget()
widget.applyConfig(Config(1.0, 1.0, 1.0))
assert widget.laser.config.spotsize == 1.0
widget.applyCalibration({"B2": Calibration(2.0, 2.0)})
assert widget.laser.calibration["B2"].intercept == 2.0
widget.updateNames({"A1": "A1", "B2": "2B"})
assert np.all(viewspace.uniqueElements() == ["2B", "A1"])
widget.transform(flip="horizontal")
assert np.all(widget.laser.get("A1") == np.flip(y, axis=1))
widget.transform(flip="horizontal")
widget.transform(flip="vertical")
assert np.all(widget.laser.get("A1") == np.flip(y, axis=0))
widget.transform(flip="vertical")
assert np.all(widget.laser.get("A1") == y)
widget.transform(rotate="right")
assert np.all(widget.laser.get("A1") == np.rot90(y, k=1, axes=(1, 0)))
widget.transform(rotate="left")
assert np.all(widget.laser.get("A1") == y)
def __init__(
self,
orientaion: QtCore.Qt.Orientation = QtCore.Qt.Horizontal,
parent: QtWidgets.QWidget = None,
):
super().__init__(orientaion, parent)
self.config = Config()
self.options = GraphicsOptions()
def test_import_thread(qtbot: QtBot):
path = Path(__file__).parent.joinpath("data", "io")
paths = [
path.joinpath("agilent", "test_ms.b"),
path.joinpath("csv", "generic"),
path.joinpath("npz", "test.npz"),
path.joinpath("perkinelmer", "perkinelmer"),
path.joinpath("textimage", "csv.csv"),
path.joinpath("textimage", "text.text"),
path.joinpath("thermo", "icap_columns.csv"),
]
thread = ImportThread(paths, Config())
signals = [(thread.importFinished, path.name) for path in paths]
signals.extend([(thread.progressChanged, path.name) for path in paths])
with qtbot.waitSignals(signals):
thread.run()
# Failing import
paths = [path.joinpath("fake", "data.npz")]
thread = ImportThread(paths, Config())
with qtbot.waitSignal(thread.importFailed):
thread.run()
def keyPressEvent(self, event: QtGui.QKeyEvent) -> None:
if event.matches(QtGui.QKeySequence.Cancel):
self.graphics.endSelection()
self.graphics.endWidget()
elif event.matches(QtGui.QKeySequence.Paste):
mime = QtWidgets.QApplication.clipboard().mimeData()
if mime.hasFormat("arplication/x-pew2config"):
with BytesIO(mime.data("application/x-pew2config")) as fp:
array = np.load(fp)
if self.is_srr:
config = SRRConfig.from_array(array)
else:
config = Config.from_array(array)
self.applyConfig(config)
elif mime.hasFormat("application/x-pew2calibration"):
with BytesIO(mime.data("application/x-pew2calibration")) as fp:
npy = np.load(fp)
calibrations = {k: Calibration.from_array(npy[k]) for k in npy}
self.applyCalibration(calibrations)
super().keyPressEvent(event)
def test_wizard_srr_config(qtbot: QtBot):
path = Path(__file__).parent.joinpath("data", "io")
wiz = SRRImportWizard(
[
path.joinpath("textimage", "csv.csv"),
path.joinpath("textimage", "csv.csv"),
],
config=Config(10.0, 40.0, 0.25),
)
qtbot.addWidget(wiz)
wiz.show()
qtbot.waitExposed(wiz)
# Format
page = wiz.currentPage()
page.radio_text.setChecked(True)
wiz.next()
assert wiz.currentId() == wiz.page_text
# Path and Options
wiz.next()
# Config
page = wiz.currentPage()
assert page.getNames() == ("_Element_", )
assert not page.isComplete()
page.lineedit_warmup.setText("0")
assert page.isComplete()
page.lineedit_warmup.setText("-1")
assert not page.isComplete()
page.lineedit_speed.setText("0")
assert not page.isComplete()
dlg = page.buttonNamesPressed()
dlg.close()
page.updateNames({"_Element_": "Pew"})
assert page.getNames() == ("Pew", )
def accept(self) -> None:
if self.field("agilent"):
paths = [Path(p) for p in self.field("agilent.paths")]
elif self.field("csv"):
paths = [Path(p) for p in self.field("csv.paths")]
elif self.field("perkinelmer"):
paths = [Path(p) for p in self.field("perkinelmer.paths")]
elif self.field("text"):
paths = [Path(p) for p in self.field("text.paths")]
elif self.field("thermo"):
paths = [Path(p) for p in self.field("thermo.paths")]
else: # pragma: no cover
raise ValueError("Invalid filetype selection.")
datas = self.field("laserdata")
infos = self.field("laserinfo")
for path, data, info in zip(paths, datas, infos):
config = Config(
spotsize=float(self.field("spotsize")),
scantime=float(self.field("scantime")),
speed=float(self.field("speed")),
)
info.update({
"Name":
path.stem,
"File Path":
str(path.resolve()),
"Import Date":
time.strftime("%Y-%m-%dT%H:%M:%S%z",
time.localtime(time.time())),
"Import Path":
str(path.resolve()),
"Import Version pewlib":
pewlib_version,
"Import Version pew2":
pewpew_version,
})
self.laserImported.emit(Laser(data, config=config, info=info))
super().accept()
def test_config_dialog(qtbot: QtBot):
config = Config()
dialog = dialogs.ConfigDialog(config)
qtbot.addWidget(dialog)
dialog.open()
assert not hasattr(dialog, "lineedit_warmup")
assert not hasattr(dialog, "spinbox_offsets")
# Check the texts are correct
assert dialog.lineedit_spotsize.text() == str(config.spotsize)
assert dialog.lineedit_speed.text() == str(config.speed)
assert dialog.lineedit_scantime.text() == str(config.scantime)
dialog.lineedit_spotsize.setText("1")
dialog.lineedit_speed.setText("2.")
dialog.lineedit_scantime.setText("3.0000")
dialog.updateConfig()
# Check it updated
assert dialog.config.spotsize == 1.0
assert dialog.config.speed == 2.0
assert dialog.config.scantime == 3.0
assert dialog.isComplete()
dialog.lineedit_scantime.setText("-1")
assert not dialog.isComplete()
dialog.lineedit_speed.setText("-1")
assert not dialog.isComplete()
dialog.lineedit_spotsize.setText("-1")
assert not dialog.isComplete()
# Just run code as can't test clipboard
dialog.copyToClipboard()
dialog.apply()
dialog.check_all.setChecked(True)
dialog.apply()
def test_laser_view_space(qtbot: QtBot):
viewspace = LaserViewSpace()
qtbot.addWidget(viewspace)
viewspace.show()
viewspace.toggleCalibrate(False)
viewspace.toggleColorbar(False)
viewspace.toggleLabel(False)
viewspace.toggleScalebar(False)
viewspace.toggleSmooth(False)
assert not viewspace.options.calibrate
assert not viewspace.options.items["colorbar"]
assert not viewspace.options.items["label"]
assert not viewspace.options.items["scalebar"]
assert not viewspace.options.smoothing
viewspace.splitActiveHorizontal()
assert viewspace.currentElement() is None
viewspace.views[0].addLaser(Laser(rand_data(["A1", "B2"])))
viewspace.views[0].addLaser(Laser(rand_data(["A1", "C3"])))
viewspace.views[1].addLaser(Laser(rand_data(["A1", "C3"])))
viewspace.views[1].addLaser(Laser(rand_data(["B2", "D4"])))
assert viewspace.uniqueElements() == ["A1", "B2", "C3", "D4"]
assert viewspace.currentElement() == "A1"
# Apply config
viewspace.applyConfig(Config(10, 10, 10))
for view in viewspace.views:
for widget in view.widgets():
assert widget.laser.config.spotsize == 10
assert widget.laser.config.speed == 10
assert widget.laser.config.scantime == 10
# Try to apply calibraiton
viewspace.applyCalibration({
"A1": Calibration(1.0, 1.0),
"B2": Calibration(2.0, 2.0)
})
qtbot.waitExposed(viewspace)
for view in viewspace.views:
for widget in view.widgets():
if "A1" in widget.laser.elements:
assert widget.laser.calibration["A1"].intercept == 1.0
assert widget.laser.calibration["A1"].gradient == 1.0
if "B2" in widget.laser.elements:
assert widget.laser.calibration["B2"].intercept == 2.0
assert widget.laser.calibration["B2"].gradient == 2.0
if "C3" in widget.laser.elements:
assert widget.laser.calibration["C3"].intercept == 0.0
assert widget.laser.calibration["C3"].gradient == 1.0
# Check element changed if avilable
assert viewspace.views[0].activeWidget().combo_element.currentText(
) == "A1"
assert viewspace.views[1].activeWidget().combo_element.currentText(
) == "A1"
viewspace.setCurrentElement("B2")
assert viewspace.views[0].activeWidget().combo_element.currentText(
) == "B2"
assert viewspace.views[1].activeWidget().combo_element.currentText(
) == "A1"
# Close all
for view in viewspace.views:
for widget in view.widgets():
widget.close()
def __init__(
self,
path: Union[str, Path] = "",
config: Config = None,
parent: QtWidgets.QWidget = None,
):
super().__init__(parent)
self.setWindowTitle("Import Wizard")
if isinstance(path, str): # pragma: no cover
path = Path(path)
config = config or Config()
overview = (
"This wizard will guide you through importing LA-ICP-MS data "
"and provides a higher level to control than the standard import. "
"To begin select the format of the file being imported.")
format_page = FormatPage(
overview,
page_id_dict={
"agilent": self.page_agilent,
"csv": self.page_csv,
"numpy": -1,
"perkinelmer": self.page_perkinelmer,
"text": self.page_text,
"thermo": self.page_thermo,
},
parent=self,
)
format_page.radio_numpy.setEnabled(False)
format_page.radio_numpy.setVisible(False)
self.setPage(self.page_format, format_page)
self.setPage(
self.page_agilent,
PathAndOptionsPage([path],
"agilent",
nextid=self.page_config,
parent=self),
)
self.setPage(
self.page_csv,
PathAndOptionsPage([path],
"csv",
nextid=self.page_config,
parent=self),
)
self.setPage(
self.page_perkinelmer,
PathAndOptionsPage([path],
"perkinelmer",
nextid=self.page_config,
parent=self),
)
self.setPage(
self.page_text,
PathAndOptionsPage([path],
"text",
nextid=self.page_config,
parent=self),
)
self.setPage(
self.page_thermo,
PathAndOptionsPage([path],
"thermo",
nextid=self.page_config,
parent=self),
)
self.setPage(self.page_config, ConfigPage(config, parent=self))