def test_state_device_widget(qtbot, global_mmcore: CMMCorePlus):
for label in global_mmcore.getLoadedDevicesOfType(DeviceType.StateDevice):
wdg: StateDeviceWidget = DeviceWidget.for_device(label)
qtbot.addWidget(wdg)
wdg.show()
assert wdg.deviceLabel() == label
# assert wdg.deviceName() == "DObjective"
assert global_mmcore.getStateLabel(label) == wdg._combo.currentText()
assert global_mmcore.getState(label) == wdg._combo.currentIndex()
start_state = wdg.state()
next_state = (wdg.state() + 1) % len(wdg.stateLabels())
with qtbot.waitSignal(global_mmcore.events.propertyChanged):
global_mmcore.setState(label, next_state)
assert wdg.state() != start_state
assert wdg.state() == global_mmcore.getState(
label) == wdg._combo.currentIndex()
assert (wdg.stateLabel() == global_mmcore.getStateLabel(label) ==
wdg._combo.currentText())
wdg._disconnect()
# once disconnected, core changes shouldn't call out to the widget
global_mmcore.setState(label, start_state)
assert global_mmcore.getStateLabel(label) != wdg._combo.currentText()
def test_search_paths(core: CMMCorePlus):
"""Make sure search paths get added to path"""
core.setDeviceAdapterSearchPaths(["test_path"])
assert "test_path" in os.getenv("PATH")
with pytest.raises(TypeError):
core.setDeviceAdapterSearchPaths("test_path")
def test_metadata(core: CMMCorePlus):
core.startContinuousSequenceAcquisition(10)
core.stopSequenceAcquisition()
image, md = core.getLastImageMD()
assert isinstance(md, Metadata)
assert md["Height"] == "512"
assert "ImageNumber" in md.keys()
assert ("Binning", "1") in md.items()
assert "GRAY16" in md.values()
assert "Camera" in md
md["Camera"] = "new"
assert md["Camera"] == "new" == md.get("Camera")
cpy = md.copy()
assert cpy == md
del md["Camera"]
assert "Camera" not in md
assert "Camera" in cpy
assert md.get("", 1) == 1 # default
md.clear()
assert not md
assert isinstance(md.json(), str)
def test_prop_browser(qtbot):
from pymmcore_plus import CMMCorePlus
mmcore = CMMCorePlus()
cfg = Path(__file__).parent / "test_config.cfg"
mmcore.loadSystemConfiguration(str(cfg))
pb = PropBrowser(mmcore)
qtbot.addWidget(pb)
pb.show()
def _creat_prop_widget(core: CMMCorePlus, dev: str,
prop: str) -> PPropValueWidget:
"""The type -> widget selection part used in the above function."""
if core.isPropertyReadOnly(dev, prop):
return ReadOnlyWidget()
ptype = core.getPropertyType(dev, prop)
if allowed := core.getAllowedPropertyValues(dev, prop):
if ptype is PropertyType.Integer and set(allowed) == {"0", "1"}:
return IntBoolWidget()
return ChoiceWidget(core, dev, prop)
def test_mda(core: CMMCorePlus, qtbot: "QtBot"):
"""Test signal emission during MDA"""
mda = MDASequence(
time_plan={
"interval": 0.1,
"loops": 2
},
stage_positions=[(1, 1, 1)],
z_plan={
"range": 3,
"step": 1
},
channels=[{
"config": "DAPI",
"exposure": 1
}],
)
fr_mock = MagicMock()
ss_mock = MagicMock()
sf_mock = MagicMock()
xystage_mock = MagicMock()
stage_mock = MagicMock()
exp_mock = MagicMock()
core.mda._events.frameReady.connect(fr_mock)
core.mda._events.sequenceStarted.connect(ss_mock)
core.mda._events.sequenceFinished.connect(sf_mock)
core.events.XYStagePositionChanged.connect(xystage_mock)
core.events.stagePositionChanged.connect(stage_mock)
core.events.exposureChanged.connect(exp_mock)
with qtbot.waitSignal(core.mda._events.sequenceFinished):
core.run_mda(mda)
assert fr_mock.call_count == len(list(mda))
for event, _call in zip(mda, fr_mock.call_args_list):
assert isinstance(_call.args[0], np.ndarray)
assert _call.args[1] == event
ss_mock.assert_called_once_with(mda)
sf_mock.assert_called_once_with(mda)
xystage_mock.assert_called_with("XY", 1.0, 1.0)
exp_mock.assert_called_with("Camera", 1.0)
stage_mock.assert_has_calls([
call("Z", -0.5),
call("Z", 0.5),
call("Z", 1.5),
call("Z", 2.5),
call("Z", -0.5),
call("Z", 0.5),
call("Z", 1.5),
call("Z", 2.5),
])
def test_lock_and_callbacks(core: CMMCorePlus, qtbot):
if not isinstance(core.events, QObject):
pytest.skip(
reason="Skip lock tests on psygnal until we can remove qtbot.")
# when a function with a lock triggers a callback
# that callback should be able to call locked functions
# without hanging.
# do some threading silliness here so we don't accidentally hang our
# test if things go wrong have to use *got_lock* to check because we
# can't assert in the function as theads don't throw their exceptions
# back into the calling thread.
got_lock = False
def cb(*args, **kwargs):
nonlocal got_lock
got_lock = core.lock.acquire(timeout=0.1)
if got_lock:
core.lock.release()
core.events.XYStagePositionChanged.connect(cb)
def trigger_cb():
core.setXYPosition(4, 5)
th = Thread(target=trigger_cb)
with qtbot.waitSignal(core.events.XYStagePositionChanged):
th.start()
assert got_lock
got_lock = False
core.mda._events.frameReady.connect(cb)
mda = MDASequence(
time_plan={
"interval": 0.1,
"loops": 2
},
stage_positions=[(1, 1, 1)],
z_plan={
"range": 3,
"step": 1
},
channels=[{
"config": "DAPI",
"exposure": 1
}],
)
with qtbot.waitSignal(core.mda._events.sequenceFinished):
core.run_mda(mda)
assert got_lock
def test_guess_channel_group(core: CMMCorePlus):
chan_group = core.getChannelGroup()
assert chan_group == "Channel"
assert core.getOrGuessChannelGroup() == ["Channel"]
with patch.object(core, "getChannelGroup", return_value=""):
assert core.getOrGuessChannelGroup() == ["Channel"]
with pytest.raises(TypeError):
core.channelGroup_pattern = 4
# assign a new regex that won't match Channel using a str
# this will return all the mm groups, but that's because this a bad regex
# to use
core.channelGroup_pattern = "^((?!(Channel)).)*$"
assert core.getOrGuessChannelGroup() == [
"Camera",
"LightPath",
"Objective",
"System",
]
# assign new using a pre-compile pattern
core.channelGroup_pattern = re.compile("Channel")
chan_group = core.getOrGuessChannelGroup()
assert chan_group == ["Channel"]
def test_mda_pause_cancel(core: CMMCorePlus, qtbot: "QtBot"):
"""Test signal emission during MDA with cancelation"""
mda = MDASequence(
time_plan={
"interval": 0.25,
"loops": 10
},
stage_positions=[(1, 1, 1)],
z_plan={
"range": 3,
"step": 1
},
channels=[{
"config": "DAPI",
"exposure": 1
}],
)
pause_mock = MagicMock()
cancel_mock = MagicMock()
sf_mock = MagicMock()
ss_mock = MagicMock()
core.mda._events.sequenceStarted.connect(ss_mock)
core.mda._events.sequencePauseToggled.connect(pause_mock)
core.mda._events.sequenceCanceled.connect(cancel_mock)
core.mda._events.sequenceFinished.connect(sf_mock)
_fcount = 0
@core.mda._events.frameReady.connect
def _onframe(frame, event):
nonlocal _fcount
_fcount += 1
if _fcount == 1:
core.mda.toggle_pause()
pause_mock.assert_called_with(True)
core.mda.toggle_pause()
pause_mock.assert_called_with(False)
elif _fcount == 2:
core.mda.cancel()
with qtbot.waitSignal(core.mda._events.sequenceFinished):
core.run_mda(mda)
ss_mock.assert_called_once_with(mda)
cancel_mock.assert_called_once_with(mda)
assert _fcount < len(list(mda))
sf_mock.assert_called_once_with(mda)
def test_core(core: CMMCorePlus):
assert isinstance(core, CMMCorePlus)
assert isinstance(core, CMMCore)
# because the fixture tries to find micromanager, this should be populated
assert core.getDeviceAdapterSearchPaths()
assert isinstance(core.events.propertyChanged,
(psygnal.SignalInstance, QSignalInstance))
assert isinstance(core.mda.events.frameReady,
(psygnal.SignalInstance, QSignalInstance))
assert not core.mda._canceled
assert not core.mda._paused
# because the fixture loadsSystemConfig 'demo'
assert len(core.getLoadedDevices()) == 12
assert "CMMCorePlus" in repr(core)
def test_device_type_overrides(core: CMMCorePlus):
dt = core.getDeviceType("Camera")
assert isinstance(dt, DeviceType)
assert str(dt) == "Camera"
assert int(dt) == 2
assert dt == DeviceType["Camera"]
assert dt == DeviceType["CameraDevice"]
assert dt == DeviceType(2)
def test_mmproperty(core: CMMCorePlus):
for prop in core.iterProperties(as_object=True):
assert prop.isValid()
assert prop.dict()
if prop.isReadOnly():
with pytest.warns(UserWarning):
prop.value = "asdf"
def test_load_system_config(core: CMMCorePlus):
with pytest.raises(FileNotFoundError):
core.loadSystemConfiguration("nonexistent")
config_path = Path(__file__).parent / "local_config.cfg"
core.loadSystemConfiguration(str(config_path))
assert core.getLoadedDevices() == (
"DHub",
"Camera",
"Dichroic",
"Emission",
"Excitation",
"Objective",
"Z",
"Path",
"XY",
"Shutter",
"Autofocus",
"Core",
)
def test_setContext(core: CMMCorePlus):
# should work with either leading capitalization
with core.setContext(shutterOpen=False):
assert not core.getShutterOpen()
with core.setContext(ShutterOpen=False):
assert not core.getShutterOpen()
# if we set an invalid value make sure initial state is still restored
with pytest.raises(TypeError):
with core.setContext(autoShutter=False, shutterOpen="sadfsd"):
assert not core.getAutoShutter()
assert core.getAutoShutter()
with pytest.raises(ValueError):
with core.setContext(autoShutter=False):
raise ValueError
assert core.getAutoShutter()
def test_configuration(core: CMMCorePlus):
state = core.getSystemState()
assert isinstance(state, Configuration)
assert not isinstance(core.getSystemState(native=True), Configuration)
assert str(state)
tup = tuple(state)
assert isinstance(tup, tuple)
assert all(isinstance(x, tuple) and len(x) == 3 for x in tup)
with pytest.raises(TypeError):
assert state["Camera"] == 1
with pytest.raises(TypeError):
assert "Camera" in state
assert state["Camera", "Binning"] == "1"
assert PropertySetting("Camera", "Binning", "1") in state
assert state in state
assert ("Camera", "Binning") in state
def global_mmcore(request):
_core._SESSION_CORE = CMMCorePlus() # refresh singleton
if request.param == "remote":
from pymmcore_plus import server
server.try_kill_server()
mmc = _core.get_core_singleton(remote=request.param == "remote")
if len(mmc.getLoadedDevices()) < 2:
mmc.loadSystemConfiguration(
str(Path(__file__).parent / "test_config.cfg"))
return mmc
def test_prop_browser_core_reset(global_mmcore: CMMCorePlus, qtbot):
"""test that loading and resetting doesn't cause errors."""
global_mmcore.unloadAllDevices()
pb = PropertyBrowser(mmcore=global_mmcore)
qtbot.addWidget(pb)
global_mmcore.loadSystemConfiguration()
global_mmcore.reset()
def test_objective_widget_changes_objective(global_mmcore: CMMCorePlus, qtbot):
obj_wdg = MMObjectivesWidget()
qtbot.addWidget(obj_wdg)
start_z = 100.0
global_mmcore.setPosition("Z", start_z)
stage_mock = Mock()
obj_wdg._mmc.events.stagePositionChanged.connect(stage_mock)
assert obj_wdg._combo.currentText() == "Nikon 10X S Fluor"
with pytest.raises(ValueError):
obj_wdg._combo.setCurrentText("10asdfdsX")
assert global_mmcore.getCurrentPixelSizeConfig() == "Res10x"
new_val = "Nikon 40X Plan Fluor ELWD"
with qtbot.waitSignal(global_mmcore.events.propertyChanged):
obj_wdg._combo.setCurrentText(new_val)
stage_mock.assert_has_calls([call("Z", 0), call("Z", start_z)])
assert obj_wdg._combo.currentText() == new_val
assert global_mmcore.getStateLabel(obj_wdg._objective_device) == new_val
assert global_mmcore.getCurrentPixelSizeConfig() == "Res40x"
assert global_mmcore.getPosition("Z") == start_z
def test_register_mda_engine(core: CMMCorePlus, qtbot: "QtBot"):
orig_engine = core.mda
registered_mock = MagicMock()
core.events.mdaEngineRegistered.connect(registered_mock)
# fake that mda is running
# with an actual mda the threading and timing is
# such that this ends up being a flaky test if we
# use `core.run_mda`
core.mda._running = True
new_engine = MDAEngine(core)
with pytest.raises(ValueError):
core.register_mda_engine(new_engine)
core.mda._running = False
with qtbot.waitSignal(core.events.mdaEngineRegistered):
core.register_mda_engine(new_engine)
assert core._mda_engine is new_engine
# invalid engine
class nonconforming_engine:
pass
with pytest.raises(TypeError):
core.register_mda_engine(nonconforming_engine())
registered_mock.assert_called_once_with(new_engine, orig_engine)
def test_device_callbacks(core: CMMCorePlus):
dev = Device("Camera", core)
mock = Mock()
mock2 = Mock()
# regular connection
dev.propertyChanged.connect(mock)
dev.propertyChanged("Gain").connect(mock2)
core.setProperty("Camera", "Gain", "6")
mock.assert_called_once_with("Gain", "6")
mock2.assert_called_once_with("6")
mock.reset_mock()
mock2.reset_mock()
core.setProperty("Camera", "Binning", "2")
mock.assert_called_once_with("Binning", "2")
mock2.assert_not_called()
# regular disconnection
mock.reset_mock()
mock2.reset_mock()
dev.propertyChanged.disconnect(mock)
dev.propertyChanged("Gain").disconnect(mock2)
core.setProperty("Camera", "Gain", "4")
mock.assert_not_called()
mock2.assert_not_called()
def test_md_overrides(core: CMMCorePlus):
core.startContinuousSequenceAcquisition(10)
core.stopSequenceAcquisition()
image, md = core.getNBeforeLastImageMD(0)
assert isinstance(md, Metadata)
image, md = core.popNextImageMD()
assert isinstance(md, Metadata)
def get_core_singleton(remote=False) -> CMMCorePlus:
"""Retrieve the MMCore singleton for this session.
The first call to this function determines whether we're running remote or not.
perhaps a temporary function for now...
"""
global _SESSION_CORE
if _SESSION_CORE is None:
if remote:
from pymmcore_plus import RemoteMMCore
_SESSION_CORE = RemoteMMCore() # type: ignore # it has the same interface.
else:
_SESSION_CORE = CMMCorePlus.instance()
return _SESSION_CORE
def test_new_position_methods(core: CMMCorePlus):
x1, y1 = core.getXYPosition()
z1 = core.getZPosition()
core.setRelativeXYZPosition(1, 1, 1)
x2, y2 = core.getXYPosition()
z2 = core.getZPosition()
assert round(x2, 2) == x1 + 1
assert round(y2, 2) == y1 + 1
assert round(z2, 2) == z1 + 1
def test_device_object(core: CMMCorePlus):
for device in core.iterDevices(as_object=True):
device.wait()
assert not device.isBusy()
assert device.schema()
assert device.description()
lib = device.library()
assert lib if device.type() is not DeviceType.Core else not lib
assert device.name()
assert repr(device)
assert device.core is core
assert device.isLoaded()
if device.supportsDetection():
assert device.detect() is not DeviceDetectionStatus.Unimplemented
else:
assert device.detect() is DeviceDetectionStatus.Unimplemented
if device.type() is not DeviceType.Core:
device.unload()
assert not device.isLoaded()
assert "NOT LOADED" in repr(device)
def test_get_objectives(core: CMMCorePlus):
devices = core.guessObjectiveDevices()
assert len(devices) == 1
assert devices[0] == "Objective"
with pytest.raises(TypeError):
core.objective_device_pattern = 4
# assign a new regex that won't match Objective using a str
core.objective_device_pattern = "^((?!Objective).)*$"
assert "Objective" not in core.guessObjectiveDevices()
# assign new using a pre-compile pattern
core.objective_device_pattern = re.compile("Objective")
devices = core.guessObjectiveDevices()
assert len(devices) == 1
assert devices[0] == "Objective"
from pymmcore_plus import CMMCorePlus
# see https://github.com/tlambert03/useq-schema
sequence = MDASequence(
channels=["DAPI", {
"config": "FITC",
"exposure": 50
}],
time_plan={
"interval": 2,
"loops": 5
},
z_plan={
"range": 4,
"step": 0.5
},
axis_order="tpcz",
)
mmc = CMMCorePlus.instance()
mmc.loadSystemConfiguration()
@mmc.mda.events.frameReady.connect
def new_frame(img, event):
print(img.shape)
mda_thread = mmc.run_mda(sequence)
import pytest
from pymmcore_plus import CMMCorePlus, PropertyType
from micromanager_gui._core_widgets import PropertyWidget
# not sure how else to parametrize the test without instantiating here at import ...
CORE = CMMCorePlus()
CORE.loadSystemConfiguration()
dev_props = [(dev, prop) for dev in CORE.getLoadedDevices()
for prop in CORE.getDevicePropertyNames(dev)]
def _assert_equal(a, b):
try:
assert float(a) == float(b)
except ValueError:
assert str(a) == str(b)
@pytest.mark.parametrize("dev, prop", dev_props)
def test_property_widget(dev, prop, qtbot):
wdg = PropertyWidget(dev, prop, core=CORE)
qtbot.addWidget(wdg)
if CORE.isPropertyReadOnly(dev, prop) or prop in (
"SimulateCrash",
"Trigger",
"AsyncPropertyLeader",
):
return
start_val = CORE.getProperty(dev, prop)
Whether to force a change away from tracking the default camera.
"""
if not force:
raise RuntimeError(
"Setting the camera on a DefaultCameraExposureWidget "
"may cause it to malfunction. Either use *force=True* "
" or create an ExposureWidget"
)
return super().setCamera(camera)
def _camera_updated(self, value: str):
# This will not always fire
# see https://github.com/micro-manager/mmCoreAndDevices/issues/181
self._camera = value
# this will result in a double call of _on_load if this callback
# was triggered by a configuration load. But I don't see an easy way around that
# fortunately _on_load should be low cost
self._on_load()
if __name__ == "__main__": # pragma: no cover
import sys
from pymmcore_plus import CMMCorePlus # noqa
CMMCorePlus.instance().loadSystemConfiguration()
app = QtW.QApplication(sys.argv)
win = DefaultCameraExposureWidget()
win.show()
sys.exit(app.exec_())
def iter_dev_props(mmc: CMMCorePlus) -> Iterator[Tuple[str, str]]:
for dev in mmc.getLoadedDevices():
for prop in mmc.getDevicePropertyNames(dev):
yield dev, prop
from __future__ import annotations
from pathlib import Path
from typing import TYPE_CHECKING
import pytest
from pymmcore_plus import CMMCorePlus
from micromanager_gui._core_widgets import DefaultCameraExposureWidget
if TYPE_CHECKING:
from pytestqt.qtbot import QtBot
# not sure how else to parametrize the test without instantiating here at import ...
CORE = CMMCorePlus()
CORE.loadSystemConfiguration(Path(__file__).parent.parent / "test_config.cfg")
def test_exposure_widget(qtbot: QtBot):
CORE.setExposure(15)
wdg = DefaultCameraExposureWidget(core=CORE)
qtbot.addWidget(wdg)
# check that it get's whatever core is set to.
assert wdg.spinBox.value() == 15
with qtbot.waitSignal(CORE.events.exposureChanged):
CORE.setExposure(30)
assert wdg.spinBox.value() == 30
with qtbot.wait_signal(CORE.events.exposureChanged):
wdg.spinBox.setValue(45)