def test_explorer(explorer_one_channel: ExplorerTuple, qtbot: QtBot):
main_win, explorer = explorer_one_channel
mmc = main_win._mmc
mmc.setXYPosition(0.0, 0.0)
mmc.setPosition(0.0)
mmc.setConfig(
"Objective",
"10X") # this it is also setting mmc.setPixelSizeConfig('Res10x')
assert not main_win.viewer.layers
# grab these in callback so we get the real meta that is
# created once we start the scan
sequence = None
meta = None
@mmc.mda.events.sequenceStarted.connect
def get_seq(seq: MDASequence):
nonlocal sequence, meta
sequence = seq
meta = _mda.SEQUENCE_META[seq]
with qtbot.waitSignals(
[mmc.mda.events.sequenceStarted, mmc.mda.events.sequenceFinished]):
explorer.start_scan_Button.click()
# wait to finish returning to start pos
mmc.waitForSystem()
assert main_win.explorer.set_grid() == [
[-256.0, 256.0, 0.0],
[256.0, 256.0, 0.0],
[256.0, -256.0, 0.0],
[-256.0, -256.0, 0.0],
]
assert mmc.getPixelSizeUm() == 1
assert mmc.getROI(mmc.getCameraDevice())[-1] == 512
assert mmc.getROI(mmc.getCameraDevice())[-2] == 512
assert meta.mode == "explorer"
assert main_win.viewer.layers[-1].data.shape == (512, 512)
assert len(main_win.viewer.layers) == 4
_layer = main_win.viewer.layers[-1]
assert _layer.metadata["ch_name"] == "Cy5"
assert _layer.metadata["ch_id"] == 0
assert _layer.metadata["uid"] == sequence.uid
# checking the linking of the layers
assert len(main_win.viewer.layers) == 4
layer_0 = main_win.viewer.layers[0]
layer_0.visible = False
# check that also the last layer is not visible
layer_1 = main_win.viewer.layers[1]
assert not layer_1.visible
def test_saving_explorer(qtbot: QtBot, explorer_two_channel: ExplorerTuple):
main_win, explorer = explorer_two_channel
mmc = main_win._mmc
# grab these in callback so we get the real meta that is
# created once we start the scan
sequence = None
meta = None
@mmc.mda.events.sequenceStarted.connect
def get_seq(seq: MDASequence):
nonlocal sequence, meta
sequence = seq
meta = _mda.SEQUENCE_META[seq]
with tempfile.TemporaryDirectory() as td:
tmp_path = Path(td)
explorer.dir_explorer_lineEdit.setText(str(tmp_path))
explorer.save_explorer_groupBox.setChecked(True)
with qtbot.waitSignals(
[mmc.mda.events.sequenceStarted, mmc.mda.events.sequenceFinished]):
explorer.start_scan_Button.click()
layer_list = list(main_win.viewer.layers)
assert len(layer_list) == 8
save_sequence(sequence, layer_list, meta)
folder = tmp_path / "scan_Experiment_000" # after _imsave()
file_list = sorted(pth.name for pth in folder.iterdir())
assert file_list == ["Cy5.tif", "FITC.tif"]
saved_file = tifffile.imread(folder / "Cy5.tif")
assert saved_file.shape == (4, 512, 512)
saved_file = tifffile.imread(folder / "FITC.tif")
assert saved_file.shape == (4, 512, 512)
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()
