def test_tool_filter(qtbot: QtBot):
viewspace = LaserViewSpace()
qtbot.addWidget(viewspace)
viewspace.show()
view = viewspace.activeView()
widget = view.addLaser(Laser(linear_data(["a", "b", "c"])))
tool = DriftTool(view.activeWidget())
view.addTab("Tool", tool)
qtbot.waitExposed(tool)
tool.combo_element.setCurrentText("a")
tool.combo_element.activated.emit(0)
tool.spinbox_degree.setValue(1)
tool.apply()
assert np.all(np.isclose(widget.laser.data["a"], widget.laser.data["a"][0][0]))
tool.combo_element.setCurrentText("b")
tool.combo_element.activated.emit(0)
assert not np.all(np.isclose(widget.laser.data["b"], widget.laser.data["c"][0][0]))
tool.check_apply_all.setChecked(True)
tool.apply()
assert np.all(np.isclose(widget.laser.data["b"], widget.laser.data["c"][0][0]))
def test_export_dialog_names(qtbot: QtBot):
viewspace = LaserViewSpace()
qtbot.addWidget(viewspace)
view = viewspace.activeView()
widget = view.addLaser(
Laser(
rand_data(["A", "\\B", "C>_<"]),
info={
"Name": "inv@|d",
"File Path": "/invalid.npz"
},
))
dlg = ExportDialog(widget)
dlg.lineedit_directory.setText(str(Path(".")))
assert dlg.isComplete()
dlg.lineedit_filename.setText("invalid.csv")
assert dlg.isComplete()
dlg.check_export_all.setChecked(True)
paths = dlg.generatePaths(widget.laser)
assert paths[0][0].name == "invalid_A.csv"
assert paths[1][0].name == "invalid__B.csv"
assert paths[2][0].name == "invalid_C___.csv"
def test_standards_tool(qtbot: QtBot):
viewspace = LaserViewSpace()
qtbot.addWidget(viewspace)
viewspace.show()
view = viewspace.activeView()
data = linear_data(["A1", "B2"])
data["B2"][6] = 1.0
view.addLaser(Laser(data))
tool = StandardsTool(view.activeWidget())
view.addTab("Tool", tool)
qtbot.waitExposed(tool)
# Units
tool.lineedit_units.setText("unit")
tool.lineedit_units.editingFinished.emit()
tool.combo_weighting.setCurrentIndex(2)
# Table
tool.spinbox_levels.setValue(5)
assert not tool.isComplete()
assert not tool.button_plot.isEnabled()
for i in range(0, tool.table.model().rowCount()):
index = tool.table.model().index(i, 0)
tool.table.model().setData(index, i)
# Change element, check weighting
tool.combo_element.setCurrentIndex(1)
assert not tool.table.isComplete()
for i in range(0, tool.table.model().rowCount()):
index = tool.table.model().index(i, 0)
tool.table.model().setData(index, i)
assert tool.isComplete()
assert tool.button_plot.isEnabled()
assert tool.combo_weighting.currentIndex() == 0
assert tool.lineedit_units.text() == ""
tool.lineedit_units.setText("none")
assert tool.calibration["B2"].gradient == 1.75
# Check weighting updates results
tool.combo_weighting.setCurrentText("y")
assert tool.calibration["B2"].weighting == "y"
assert np.isclose(tool.calibration["B2"].gradient, 1.954022988)
# Change element back, check weighting, unit, table restored
tool.combo_element.setCurrentIndex(0)
assert tool.isComplete()
assert tool.lineedit_units.text() == "unit"
assert tool.combo_weighting.currentIndex() == 2
# Test SD weighting
tool.combo_weighting.setCurrentIndex(1)
assert np.all(tool.calibration["A1"].weights == 4.0)
tool.combo_element.setCurrentIndex(1)
dlg = tool.showCurve()
qtbot.waitExposed(dlg)
dlg.close()
def test_tool_calculator(qtbot: QtBot):
viewspace = LaserViewSpace()
qtbot.addWidget(viewspace)
viewspace.show()
view = viewspace.activeView()
widget = view.addLaser(Laser(rand_data(["a", "b"])))
tool = CalculatorTool(view.activeWidget())
view.addTab("Tool", tool)
qtbot.waitExposed(tool)
assert tool.lineedit_name.text() == "calc0"
tool.apply()
assert "calc0" in widget.laser.elements
assert tool.lineedit_name.text() == "calc1"
# overwrite
tool.lineedit_name.setText("a")
tool.apply()
assert len(widget.laser.elements) == 3
# Inserters
assert tool.formula.toPlainText() == "a"
tool.insertFunction(1)
assert tool.formula.toPlainText() == "abs(a"
tool.insertVariable(2)
assert tool.formula.toPlainText() == "abs(ba"
# Test output of previewData and output lineedit
x = np.array(np.random.random((10, 10)), dtype=[("a", float)])
tool.formula.setPlainText("mean(a)")
assert tool.previewData(x) is None
assert tool.output.text() == f"{np.mean(x['a']):.10g}"
# Array access in output
tool.formula.setPlainText("a[0]")
assert tool.previewData(x) is None
assert tool.output.text() == f"{list(map('{:.4g}'.format, x['a'][0]))}"
# Simple op
tool.formula.setPlainText("a + 1.0")
assert np.all(tool.previewData(x) == x["a"] + 1.0)
assert tool.isComplete()
# Invalid input
tool.formula.setPlainText("fail")
assert tool.previewData(x) is None
assert not tool.isComplete()
def test_laser_widget_cursor(qtbot: QtBot):
main = QtWidgets.QMainWindow()
qtbot.addWidget(main)
main.statusBar() # Create bar
viewspace = LaserViewSpace()
main.setCentralWidget(viewspace)
view = viewspace.activeView()
view.addLaser(Laser(rand_data(["a"])))
widget = view.activeWidget()
# Cursor
widget.updateCursorStatus(2.0, 2.0, 1.0)
assert main.statusBar().currentMessage() == "2,2 [1]"
widget.updateCursorStatus(1.0, 3.0, np.nan)
assert main.statusBar().currentMessage() == "1,3 [nan]"
def test_laser_widget_actions(qtbot: QtBot):
viewspace = LaserViewSpace()
qtbot.addWidget(viewspace)
viewspace.show()
view = viewspace.activeView()
view.addLaser(
Laser(rand_data(["a", "b"]),
info={"File Path": "/home/pewpew/real.npz"}))
widget = view.activeWidget()
dlg = widget.actionCalibration()
dlg.close()
dlg = widget.actionConfig()
dlg.close()
widget.actionDuplicate()
widget.actionCopyImage()
dlg = widget.actionExport()
dlg.close()
dlg = widget.actionSave()
dlg.close()
dlg = widget.actionStatistics()
dlg.close()
dlg = widget.actionSelectDialog()
dlg.close()
dlg = widget.actionColocal()
dlg.close()
widget.contextMenuEvent(
QtGui.QContextMenuEvent(QtGui.QContextMenuEvent.Mouse,
QtCore.QPoint(0, 0)))
# Test contextmenu
widget.graphics.mask = np.ones((10, 10), dtype=bool)
widget.contextMenuEvent(
QtGui.QContextMenuEvent(
QtGui.QContextMenuEvent.Mouse,
widget.graphics.mapFromScene(QtCore.QPointF(0, 0)),
))
widget.actionCopySelectionText()
widget.actionCropSelection()
dlg = widget.actionStatisticsSelection()
dlg.close()
dlg = widget.actionColocalSelection()
dlg.close()
def test_merge_tool(qtbot: QtBot):
viewspace = LaserViewSpace()
qtbot.addWidget(viewspace)
viewspace.show()
view = viewspace.activeView()
data = rand_data(["A", "B"])
view.addLaser(Laser(data, info={"Name": "Laser 1", "File Path": "/test/laser1"}))
data = rand_data(["B", "C"])
view.addLaser(Laser(data, info={"Name": "Laser 2", "File Path": "/test/laser1"}))
tool = MergeTool(view.activeWidget())
view.addTab("Tool", tool)
qtbot.waitExposed(tool)
assert tool.list.count() == 1
# Test load via dialog
dlg = tool.addLaserDialog()
assert dlg.comboBoxItems() == ["Laser 2"]
dlg.accept()
assert tool.list.count() == 2
assert [row.offset() == (0, 0) for row in tool.list.rows]
assert tool.list.rows[0].combo_element.currentText() == "A"
assert tool.list.rows[1].combo_element.currentText() == "B"
tool.action_align_horz.trigger()
assert tool.list.rows[0].offset() == (0, 0)
assert tool.list.rows[1].offset() == (0, 10)
tool.action_align_vert.trigger()
assert tool.list.rows[0].offset() == (0, 0)
assert tool.list.rows[1].offset() == (10, 0)
tool.action_align_auto.trigger()
assert tool.list.rows[0].offset() == (0, 0)
# Second image position unknown
tool.apply()
def test_laser_view(qtbot: QtBot):
viewspace = LaserViewSpace()
qtbot.addWidget(viewspace)
viewspace.show()
view = viewspace.activeView()
laser = view.addLaser(Laser(rand_data(["A1", "B2", "C3"])))
qtbot.waitExposed(laser)
view.tabs.setTabText(0, "newname")
assert view.stack.widget(0).laserName() == "newname"
view.contextMenuEvent(
QtGui.QContextMenuEvent(QtGui.QContextMenuEvent.Mouse,
QtCore.QPoint(0, 0)))
# Drop event
drag_mime = QtCore.QMimeData()
path = Path(__file__).parent.joinpath("data", "io", "npz", "test.npz")
drag_mime.setUrls([QtCore.QUrl.fromLocalFile(str(path.resolve()))])
drag_event = QtGui.QDragEnterEvent(
QtCore.QPoint(0, 0),
QtCore.Qt.CopyAction,
drag_mime,
QtCore.Qt.LeftButton,
QtCore.Qt.NoModifier,
)
view.dragEnterEvent(drag_event)
assert drag_event.isAccepted()
drop_event = QtGui.QDropEvent(
QtCore.QPoint(0, 0),
QtCore.Qt.CopyAction,
drag_mime,
QtCore.Qt.LeftButton,
QtCore.Qt.NoModifier,
)
with qtbot.waitSignal(view.numTabsChanged):
view.dropEvent(drop_event)
assert drop_event.isAccepted()
assert len(view.widgets()) == 2
dlg = view.actionOpen()
dlg.show()
dlg.close()
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 test_tool_filter(qtbot: QtBot):
viewspace = LaserViewSpace()
qtbot.addWidget(viewspace)
viewspace.show()
view = viewspace.activeView()
view.addLaser(Laser(rand_data(["a"])))
tool = FilteringTool(view.activeWidget())
view.addTab("Tool", tool)
qtbot.waitExposed(tool)
tool.combo_filter.setCurrentText("Mean")
tool.combo_filter.activated.emit(0)
tool.lineedit_fparams[0].setText("3.0")
tool.lineedit_fparams[1].setText("3.0")
tool.lineedit_fparams[0].editingFinished.emit()
assert np.all(tool.fparams == [3.0, 3.0])
assert tool.isComplete()
tool.lineedit_fparams[0].setText("5.0")
tool.lineedit_fparams[0].editingFinished.emit()
assert np.all(tool.fparams == [5.0, 3.0])
assert tool.isComplete()
tool.combo_filter.setCurrentText("Median")
tool.combo_filter.activated.emit(0)
assert np.all(tool.fparams == [5.0, 3.0])
assert tool.isComplete()
tool.lineedit_fparams[0].setText("4.0")
tool.lineedit_fparams[0].editingFinished.emit()
assert not tool.isComplete()
tool.combo_filter.setCurrentText("Mean")
tool.combo_filter.activated.emit(0)
assert np.all(tool.fparams == [5.0, 3.0])
assert tool.isComplete()
tool.apply()
def test_laser_view_space_apply_dialogs(qtbot: QtBot):
viewspace = LaserViewSpace()
qtbot.addWidget(viewspace)
viewspace.show()
qtbot.addWidget(viewspace)
viewspace.views[0].addLaser(Laser(rand_data("A1")))
viewspace.refresh()
dlg = viewspace.configDialog()
dlg.applyPressed.emit(dlg)
dlg.close()
dlg = viewspace.colortableRangeDialog()
dlg.applyPressed.emit(dlg)
dlg.close()
dlg = viewspace.fontsizeDialog()
dlg.intValueSelected.emit(5)
dlg.close()
assert viewspace.options.font.pointSize() == 5
def __init__(self, parent: QtWidgets.QWidget = None):
super().__init__(parent)
self.resize(1280, 800)
self.log = LoggingDialog()
self.help = HelpDialog()
self.viewspace = LaserViewSpace()
self.viewspace.numTabsChanged.connect(self.updateActionAvailablity)
self.viewspace.activeViewChanged.connect(self.updateActionAvailablity)
self.setCentralWidget(self.viewspace)
self.createActions()
self.createMenus()
self.statusBar().showMessage(f"Welcome to pew² version {__version__}.")
self.button_status_um = QtWidgets.QRadioButton("μ")
self.button_status_index = QtWidgets.QRadioButton("i")
self.button_status_um.setChecked(True)
self.button_status_um.toggled.connect(self.buttonStatusUnit)
self.button_status_index.toggled.connect(self.buttonStatusUnit)
self.statusBar().addPermanentWidget(self.button_status_um)
self.statusBar().addPermanentWidget(self.button_status_index)
self.updateActionAvailablity()
def test_tool_widget(qtbot: QtBot):
viewspace = LaserViewSpace()
qtbot.addWidget(viewspace)
viewspace.show()
view = viewspace.activeView()
widget = view.addLaser(Laser(rand_data("A1"), info={"Name": "Widget"}))
tool = ToolWidget(widget, apply_all=True)
index = widget.index
widget.view.removeTab(index)
widget.view.insertTab(index, "Tool", tool)
qtbot.waitExposed(tool)
tool.requestClose()
view.tabs.tabText(index) == "Widget"
with qtbot.wait_signal(tool.applyPressed):
button = tool.button_box.button(QtWidgets.QDialogButtonBox.Apply)
button.click()
with qtbot.wait_signal(tool.applyPressed):
button = tool.button_box.button(QtWidgets.QDialogButtonBox.Ok)
button.click()
def test_overlay_tool(qtbot: QtBot):
data = np.zeros((10, 10), dtype=[("r", float), ("g", float), ("b", float)])
data["r"][:, :] = 1.0
data["g"][:10, :] = 1.0
data["b"][:, :10] = 1.0
viewspace = LaserViewSpace()
qtbot.addWidget(viewspace)
viewspace.show()
view = viewspace.activeView()
view.addLaser(
Laser(data,
info={
"Name": "real",
"File Path": "/home/pewpew/real.npz"
}))
tool = OverlayTool(view.activeWidget())
view.addTab("Tool", tool)
qtbot.waitExposed(tool)
# Test rgb mode
assert tool.rows.color_model == "rgb"
tool.comboAdd(1) # r
assert np.all(tool.graphics.data[0, 0] == (255 << 24) + (255 << 16))
tool.comboAdd(2) # g
assert np.all(tool.graphics.data[:10] == (255 << 24) + (255 << 16) +
(255 << 8))
assert np.all(tool.graphics.data[10:] == (255 << 24) + (255 << 16))
tool.comboAdd(3) # g
assert np.all(tool.graphics.data[:10, :10] == (255 << 24) + (255 << 16) +
(255 << 8) + 255)
assert np.all(tool.graphics.data[10:, :10] == (255 << 24) + (255 << 16))
assert np.all(tool.graphics.data[10:, 10:] == (255 << 24) + (255 << 16) +
(255 << 8))
assert np.all(tool.graphics.data[10:, 10:] == (255 << 24) + (255 << 16))
# Test cmyk mode
tool.radio_cmyk.toggle()
assert tool.rows.color_model == "cmyk"
assert np.all(tool.graphics.data[:10, :10] == (255 << 24))
assert np.all(tool.graphics.data[10:, :10] == (255 << 24) + (255 << 8))
assert np.all(tool.graphics.data[10:, 10:] == (255 << 25) + 255)
assert np.all(tool.graphics.data[10:,
10:] == (255 << 24) + (255 << 8) + 255)
# Check that the rows are limited to 3
assert tool.rows.max_rows == 3
assert not tool.combo_add.isEnabled()
assert tool.rows.rowCount() == 3
with qtbot.assert_not_emitted(tool.rows.rowsChanged):
tool.addRow("r")
assert tool.rows.rowCount() == 3
# Check color buttons are not enabled
for row in tool.rows.rows:
assert not row.button_color.isEnabled()
# Test any mode
tool.radio_custom.toggle()
assert tool.rows.color_model == "any"
assert tool.combo_add.isEnabled()
assert tool.check_normalise.isEnabled()
for row in tool.rows.rows:
assert row.button_color.isEnabled()
tool.addRow("g")
tool.rows[3].setColor(QtGui.QColor.fromRgbF(0.0, 1.0, 1.0))
assert tool.rows.rowCount() == 4
# Test normalise
assert np.amin(tool.graphics.data) > (255 << 24)
tool.check_normalise.setChecked(True)
tool.refresh()
assert tool.graphics.data.min() == (255 << 24) + (255 << 8) + 255 # No red
tool.check_normalise.setChecked(False)
# Test export
dlg = tool.openExportDialog()
dlg2 = dlg.selectDirectory()
dlg2.close()
with tempfile.NamedTemporaryFile() as tf:
dlg.export(Path(tf.name))
assert Path(tf.name).exists()
with tempfile.TemporaryDirectory() as td:
dlg.lineedit_directory.setText(td)
dlg.lineedit_filename.setText("test.png")
dlg.check_individual.setChecked(True)
dlg.accept()
qtbot.wait(300)
assert Path(td).joinpath("test_1.png").exists()
assert Path(td).joinpath("test_2.png").exists()
assert Path(td).joinpath("test_3.png").exists()
# Test close
with qtbot.wait_signal(tool.rows.rowsChanged):
tool.rows.rows[-1].close()
assert tool.rows.rowCount() == 3
# Test hide
tool.radio_rgb.toggle()
with qtbot.wait_signal(tool.rows.rows[0].itemChanged):
tool.rows.rows[0].button_hide.click()
assert np.all(tool.graphics.data <= ((255 << 24) + (255 << 8) + 255))
dlg = tool.rows[0].selectColor()
dlg.close()
def test_export_all_dialog(qtbot: QtBot):
viewspace = LaserViewSpace()
qtbot.addWidget(viewspace)
view = viewspace.activeView()
lasers = [
Laser(
rand_data("A1"),
info={
"Name": "laser1",
"File Path": "/fake/directory/laser1.npz"
},
),
Laser(
rand_data("B2"),
info={
"Name": "laser2",
"File Path": "/fake/directory/laser2.npz"
},
),
Laser(
rand_data("C3"),
info={
"Name": "laser3",
"File Path": "/fake/directory/laser3.npz"
},
),
Laser(
rand_data(["B2", "C3"]),
info={
"Name": "laser4",
"File Path": "/fake/directory/laser4.npz"
},
),
]
widgets = [view.addLaser(laser) for laser in lasers]
dlg = ExportAllDialog(widgets)
dlg.open()
assert dlg.lineedit_directory.text() == "/fake/directory"
assert dlg.lineedit_filename.text() == "<name>.npz"
assert dlg.lineedit_preview.text() == "<name>.npz"
assert not dlg.isComplete()
dlg.lineedit_prefix.setText("01")
assert dlg.lineedit_preview.text() == "01_<name>.npz"
assert not dlg.check_export_all.isEnabled()
assert not dlg.check_calibrate.isEnabled()
assert not dlg.combo_element.isEnabled()
dlg.options.setCurrentIndex(dlg.options.indexForExt(".csv"))
assert dlg.lineedit_preview.text() == "01_<name>.csv"
assert dlg.check_export_all.isEnabled()
assert dlg.check_calibrate.isEnabled()
assert dlg.combo_element.isEnabled()
dlg.check_export_all.click()
assert dlg.lineedit_preview.text() == "01_<name>_<element>.csv"
assert not dlg.combo_element.isEnabled()
with tempfile.TemporaryDirectory() as tempdir:
dlg.lineedit_directory.setText(tempdir)
assert dlg.isComplete()
dlg.accept()
assert Path(tempdir, "01_laser1_A1.csv").exists()
assert Path(tempdir, "01_laser2_B2.csv").exists()
assert Path(tempdir, "01_laser3_C3.csv").exists()
assert Path(tempdir, "01_laser4_B2.csv").exists()
assert Path(tempdir, "01_laser4_C3.csv").exists()
class MainWindow(QtWidgets.QMainWindow):
"""Pewpew mainwindow, holding a LaserViewSpace.
Actions for the menu and status bars are created and stored here.
"""
def __init__(self, parent: QtWidgets.QWidget = None):
super().__init__(parent)
self.resize(1280, 800)
self.log = LoggingDialog()
self.help = HelpDialog()
self.viewspace = LaserViewSpace()
self.viewspace.numTabsChanged.connect(self.updateActionAvailablity)
self.viewspace.activeViewChanged.connect(self.updateActionAvailablity)
self.setCentralWidget(self.viewspace)
self.createActions()
self.createMenus()
self.statusBar().showMessage(f"Welcome to pew² version {__version__}.")
self.button_status_um = QtWidgets.QRadioButton("μ")
self.button_status_index = QtWidgets.QRadioButton("i")
self.button_status_um.setChecked(True)
self.button_status_um.toggled.connect(self.buttonStatusUnit)
self.button_status_index.toggled.connect(self.buttonStatusUnit)
self.statusBar().addPermanentWidget(self.button_status_um)
self.statusBar().addPermanentWidget(self.button_status_index)
self.updateActionAvailablity()
def createActions(self) -> None:
self.action_about = qAction("help-about", "&About", "About pew².",
self.actionAbout)
self.action_help = qAction("help-contents", "&Help",
"Show the help contents.", self.actionHelp)
self.action_colortable_range = qAction(
"",
"Set &Range",
"Set the range of the colortable.",
self.viewspace.colortableRangeDialog,
)
self.action_colortable_range.setShortcut("Ctrl+R")
self.action_config = qAction(
"document-edit",
"Default Config",
"Edit the default config.",
self.viewspace.configDialog,
)
self.action_config.setShortcut("Ctrl+K")
self.action_exit = qAction("application-exit", "Quit",
"Exit the program.", self.close)
self.action_exit.setShortcut("Ctrl+Shift+Q")
self.action_export_all = qAction(
"document-save-all",
"E&xport All",
"Export all open documents.",
self.actionExportAll,
)
self.action_export_all.setShortcut("Ctrl+Shift+X")
self.action_fontsize = qAction(
"insert-text",
"Fontsize",
"Set the font size in points.",
self.viewspace.fontsizeDialog,
)
self.action_group_colortable = qActionGroup(
self,
list(self.viewspace.options.colortables.keys()),
self.actionGroupColortable,
checked=self.viewspace.options.colortable,
statuses=list(self.viewspace.options.colortables.values()),
)
self.action_smooth = qAction(
"smooth",
"&Smooth",
"Smooth images with bilinear interpolation.",
self.viewspace.toggleSmooth,
)
self.action_smooth.setCheckable(True)
self.action_smooth.setChecked(self.viewspace.options.smoothing)
self.action_wizard_import = qAction(
"",
"Import Wizard",
"Start the line-wise import wizard. .",
self.actionWizardImport,
)
self.action_wizard_spot = qAction(
"",
"Spotwise Wizard",
"Start the import wizard for data collected spot-wise.",
self.actionWizardSpot,
)
self.action_wizard_srr = qAction(
"",
"Kriss Kross Wizard",
"Start the Super-Resolution-Reconstruction import wizard.",
self.actionWizardSRR,
)
self.action_log = qAction("clock", "&Show Log",
"Show the pew² event and error log.",
self.actionLog)
self.action_open = qAction("document-open", "&Open",
"Open new document(s).", self.actionOpen)
self.action_open.setShortcut("Ctrl+O")
self.action_toggle_calibrate = qAction(
"go-top",
"Ca&librate",
"Toggle calibration.",
self.viewspace.toggleCalibrate,
)
self.action_toggle_calibrate.setShortcut("Ctrl+L")
self.action_toggle_calibrate.setCheckable(True)
self.action_toggle_calibrate.setChecked(
self.viewspace.options.calibrate)
self.action_toggle_colorbar = qAction(
"", "Show Colorbar", "Toggle colorbars.",
self.viewspace.setColorbarVisible)
self.action_toggle_colorbar.setCheckable(True)
self.action_toggle_colorbar.setChecked(
self.viewspace.options.items["colorbar"])
self.action_toggle_label = qAction("", "Show Labels",
"Toggle element labels.",
self.viewspace.setLabelVisible)
self.action_toggle_label.setCheckable(True)
self.action_toggle_label.setChecked(
self.viewspace.options.items["label"])
self.action_toggle_scalebar = qAction(
"", "Show Scalebar", "Toggle scalebar.",
self.viewspace.setScalebarVisible)
self.action_toggle_scalebar.setCheckable(True)
self.action_toggle_scalebar.setChecked(
self.viewspace.options.items["scalebar"])
self.action_tool_calculator = qAction(
"document-properties",
"Calculator",
"Open the calculator.",
self.actionToolCalculator,
)
self.action_tool_drift = qAction(
"document-properties",
"Drift Compensation",
"Open the drift compensation tool.",
self.actionToolDrift,
)
self.action_tool_filter = qAction(
"document-properties",
"Filtering",
"Open the filtering tool.",
self.actionToolFilter,
)
self.action_tool_merge = qAction(
"align-vertical-top",
"Merge Tool",
"Open tool for merging multiple images.",
self.actionToolMerge,
)
self.action_tool_standards = qAction(
"document-properties",
"Calibration Standards",
"Open the standards calibration tool.",
self.actionToolStandards,
)
self.action_tool_overlay = qAction(
"document-properties",
"Image Overlay",
"Open the overlay tool.",
self.actionToolOverlay,
)
self.action_transform_flip_horizontal = qAction(
"object-flip-horizontal",
"Flip Horizontal",
"Flip the image about vertical axis.",
self.actionTransformFlipHorz,
)
self.action_transform_flip_vertical = qAction(
"object-flip-vertical",
"Flip Vertical",
"Flip the image about horizontal axis.",
self.actionTransformFlipVert,
)
self.action_transform_rotate_left = qAction(
"object-rotate-left",
"Rotate Left",
"Rotate the image 90° counter clockwise.",
self.actionTransformRotateLeft,
)
self.action_transform_rotate_right = qAction(
"object-rotate-right",
"Rotate Right",
"Rotate the image 90° clockwise.",
self.actionTransformRotateRight,
)
self.action_refresh = qAction("view-refresh", "Refresh",
"Redraw documents.",
self.viewspace.refresh)
self.action_refresh.setShortcut("F5")
def actionAbout(self) -> QtWidgets.QDialog:
dlg = QtWidgets.QMessageBox(
QtWidgets.QMessageBox.Information,
"About pew²",
("Import, process and export of LA-ICP-MS data.\n"
f"Version {__version__}\n"
"Developed by the Atomic Medicine Initiative.\n"
"https://github.com/djdt/pewpew"),
parent=self,
)
if self.windowIcon() is not None:
dlg.setIconPixmap(self.windowIcon().pixmap(64, 64))
dlg.open()
return dlg
def actionExportAll(self) -> QtWidgets.QDialog:
widgets = [
w for v in self.viewspace.views for w in v.widgets()
if isinstance(w, LaserWidget)
]
dlg = ExportAllDialog(widgets, self)
dlg.open()
return dlg
def actionGroupColortable(self, action: QtWidgets.QAction) -> None:
text = action.text().replace("&", "")
self.viewspace.options.colortable = text
self.viewspace.refresh()
def actionHelp(self) -> None:
self.help.show()
def actionLog(self) -> None:
self.log.show()
def actionOpen(self) -> QtWidgets.QDialog:
view = self.viewspace.activeView()
return view.actionOpen()
def openTool(self, tool: ToolWidget, name: str) -> None:
widget = self.viewspace.activeWidget()
if widget is None:
return
index = widget.index
if isinstance(widget, ToolWidget):
widget = widget.widget
tool = tool(widget)
name = f"{name}: {widget.laserName()}"
widget.view.removeTab(index)
widget.view.insertTab(index, name, tool)
tool.activate()
def actionToolCalculator(self) -> None:
self.openTool(CalculatorTool, "Calculator")
def actionToolDrift(self) -> None:
self.openTool(DriftTool, "Drift")
def actionToolFilter(self) -> None:
self.openTool(FilteringTool, "Filter")
def actionToolMerge(self) -> None:
self.openTool(MergeTool, "Merge")
def actionToolStandards(self) -> None:
self.openTool(StandardsTool, "Standards")
def actionToolOverlay(self) -> None:
self.openTool(OverlayTool, "Overlay")
def actionTransformFlipHorz(self) -> None:
widget = self.viewspace.activeWidget()
if widget is None:
return
widget.transform(flip="horizontal")
def actionTransformFlipVert(self) -> None:
widget = self.viewspace.activeWidget()
if widget is None:
return
widget.transform(flip="vertical")
def actionTransformRotateLeft(self) -> None:
widget = self.viewspace.activeWidget()
if widget is None:
return
widget.transform(rotate="left")
def actionTransformRotateRight(self) -> None:
widget = self.viewspace.activeWidget()
if widget is None:
return
widget.transform(rotate="right")
def actionWizardImport(self) -> QtWidgets.QWizard:
wiz = ImportWizard(config=self.viewspace.config, parent=self)
wiz.laserImported.connect(self.viewspace.activeView().addLaser)
wiz.open()
return wiz
def actionWizardSpot(self) -> QtWidgets.QWizard:
config = SpotConfig(self.viewspace.config.spotsize,
self.viewspace.config.spotsize)
wiz = SpotImportWizard(config=config,
options=self.viewspace.options,
parent=self)
wiz.laserImported.connect(self.viewspace.activeView().addLaser)
wiz.open()
return wiz
def actionWizardSRR(self) -> QtWidgets.QWizard:
wiz = SRRImportWizard(config=self.viewspace.config, parent=self)
wiz.laserImported.connect(self.viewspace.activeView().addLaser)
wiz.open()
return wiz
def createMenus(self) -> None:
# File
menu_file = self.menuBar().addMenu("&File")
menu_file.addAction(self.action_open)
# File -> Import
menu_import = menu_file.addMenu("&Import")
menu_import.addAction(self.action_wizard_import)
menu_import.addAction(self.action_wizard_spot)
menu_import.addAction(self.action_wizard_srr)
menu_file.addSeparator()
menu_file.addAction(self.action_export_all)
menu_file.addSeparator()
menu_file.addAction(self.action_exit)
# Edit
menu_edit = self.menuBar().addMenu("&Edit")
menu_edit.addAction(self.action_config)
menu_edit.addAction(self.action_toggle_calibrate)
menu_edit.addSeparator()
menu_edit.addAction(self.action_transform_flip_horizontal)
menu_edit.addAction(self.action_transform_flip_vertical)
menu_edit.addAction(self.action_transform_rotate_left)
menu_edit.addAction(self.action_transform_rotate_right)
menu_tools = self.menuBar().addMenu("&Tools")
menu_tools.addAction(self.action_tool_calculator)
menu_tools.addAction(self.action_tool_drift)
menu_tools.addAction(self.action_tool_filter)
menu_tools.addAction(self.action_tool_merge)
menu_tools.addAction(self.action_tool_standards)
menu_tools.addAction(self.action_tool_overlay)
# View
menu_view = self.menuBar().addMenu("&View")
menu_cmap = menu_view.addMenu("&Colortable")
menu_cmap.setIcon(QtGui.QIcon.fromTheme("color-management"))
menu_cmap.setStatusTip("Colortable of displayed images.")
menu_cmap.addActions(self.action_group_colortable.actions())
menu_cmap.addAction(self.action_colortable_range)
# View - interpolation
menu_view.addAction(self.action_smooth)
menu_view.addAction(self.action_fontsize)
menu_view.addSeparator()
menu_view.addAction(self.action_toggle_colorbar)
menu_view.addAction(self.action_toggle_label)
menu_view.addAction(self.action_toggle_scalebar)
menu_view.addSeparator()
menu_view.addAction(self.action_refresh)
# Help
menu_help = self.menuBar().addMenu("&Help")
menu_help.addAction(self.action_log)
menu_help.addAction(self.action_help)
menu_help.addAction(self.action_about)
def buttonStatusUnit(self, toggled: bool) -> None:
"""Callback for 'button_status_um'."""
if self.button_status_um.isChecked():
self.viewspace.options.units = "μm"
elif self.button_status_index.isChecked():
self.viewspace.options.units = "index"
def updateActionAvailablity(self) -> None:
"""Enables tools if at least one view is present."""
enabled = self.viewspace.countViewTabs() > 0
self.action_export_all.setEnabled(enabled)
# Tools require an active view
enabled = enabled and self.viewspace.activeView().tabs.count() > 0
self.action_tool_calculator.setEnabled(enabled)
self.action_tool_drift.setEnabled(enabled)
self.action_tool_filter.setEnabled(enabled)
self.action_tool_standards.setEnabled(enabled)
self.action_tool_overlay.setEnabled(enabled)
def exceptHook(self, etype: type, value: BaseException,
tb: TracebackType) -> None: # pragma: no cover
"""Redirect errors to the log."""
if etype == KeyboardInterrupt:
logger.info("Keyboard interrupt, exiting.")
sys.exit(1)
logger.exception("Uncaught exception", exc_info=(etype, value, tb))
QtWidgets.QMessageBox.critical(self, "Uncaught Exception", str(value))
def test_export_dialog(qtbot: QtBot):
viewspace = LaserViewSpace()
qtbot.addWidget(viewspace)
view = viewspace.activeView()
widget = view.addLaser(
Laser(rand_data("A1"),
info={
"Name": "laser",
"File Path": "/home/user/laser.npz"
}))
dlg = ExportDialog(widget)
dlg.open()
assert dlg.lineedit_directory.text() == "/home/user"
assert dlg.lineedit_filename.text() == "laser.npz"
assert dlg.lineedit_preview.text() == "laser.npz"
assert dlg.options.currentExt() == ".npz"
assert not dlg.check_export_all.isEnabled()
assert not dlg.check_calibrate.isEnabled()
dlg.lineedit_filename.setText("laser.png")
assert dlg.lineedit_preview.text() == "laser.png"
assert dlg.options.currentExt() == ".png"
dlg.lineedit_filename.setText("laser")
assert dlg.lineedit_preview.text() == "laser.png"
assert dlg.options.currentExt() == ".png"
dlg.check_export_all.click()
assert dlg.lineedit_preview.text() == "laser_<element>.png"
dlg.lineedit_filename.setText("laser.npz")
assert dlg.options.currentExt() == ".npz"
assert not dlg.check_export_all.isEnabled()
assert dlg.lineedit_preview.text() == "laser.npz"
dlg.lineedit_filename.setText("laser.abc")
assert not dlg.isComplete()
dlg.lineedit_filename.setText("laser.npz")
dir_dlg = dlg.selectDirectory()
dir_dlg.close()
dlg.lineedit_filename.setText("/fake/directory")
assert not dlg.isComplete()
with tempfile.TemporaryDirectory() as tempdir:
# Test export
dlg.lineedit_directory.setText(tempdir)
dlg.lineedit_filename.setText("temp.npz")
paths = dlg.generatePaths(dlg.widget)
assert paths == [(Path(tempdir, "temp.npz"), "A1", None)]
dlg.export(paths[0][0], paths[0][1], None, dlg.widget)
assert Path(tempdir, "temp.npz").exists()
# Test export all elements and png
with tempfile.TemporaryDirectory() as tempdir:
dlg.lineedit_directory.setText(tempdir)
dlg.lineedit_filename.setText("temp.png")
dlg.accept()
assert Path(tempdir, "temp_A1.png").exists()
with tempfile.TemporaryDirectory() as tempdir:
dlg.lineedit_directory.setText(tempdir)
dlg.lineedit_filename.setText("temp.vti")
dlg.accept()
assert Path(tempdir, "temp.vti").exists()
dlg.close()
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()