def _test_applyCommandLine(panel, overlayList, displayCtx):
displayCtx = panel.displayCtx
panel.sceneOpts.layout = 'horizontal'
with tempdir():
img = fslimage.Image(np.random.randint(1, 255, (20, 20, 20)))
img.save('image.nii.gz')
applycommandline.applyCommandLineArgs(
overlayList,
panel.displayCtx,
['-lo', 'vertical',
'image.nii.gz', '-b', '75', '-c', '25', '-g', '-0.5'],
panel=panel,
blocking=True)
# scene args are applied asynchronously
waitUntilIdle()
assert len(overlayList) == 1
assert np.all(overlayList[0][:] == img[:])
img = overlayList[0]
assert displayCtx.getDisplay(img).brightness == 75
assert displayCtx.getDisplay(img).contrast == 25
assert displayCtx.getOpts( img).gamma == -0.5
assert panel.sceneOpts.layout == 'vertical'
def _test_complex_image(panel, overlayList, displayCtx):
with tempdir.tempdir():
data = np.random.randint(1, 255, (10, 10, 10)) + \
1j * np.random.randint(1, 255, (10, 10, 10))
data = np.array(data, dtype=np.complex64)
img = fslimage.Image(data, xform=np.eye(4))
img.save('complex.nii')
args = ['complex.nii', '-cmr', '25', '-g', '0.5']
applycommandline.applyCommandLineArgs(
overlayList,
displayCtx,
args)
realYield(50)
assert len(overlayList) == 2
real, imag = overlayList
# make sure CLI args were applied to both overlays
assert displayCtx.getOpts(real).cmapResolution == 25
assert displayCtx.getOpts(imag).cmapResolution == 25
assert displayCtx.getOpts(real).gamma == 0.5
assert displayCtx.getOpts(imag).gamma == 0.5
assert np.all(real[:] == np.real(img[:]))
assert np.all(imag[:] == np.imag(img[:]))
def _test_applyCommandLine_baseDir(panel, overlayList, displayCtx):
displayCtx = panel.displayCtx
with tempdir():
basedir = op.join(*'sub/dir/to/test/base/dir/'.split('/'))
os.makedirs(basedir)
img = fslimage.Image(np.random.randint(1, 255, (20, 20, 20)))
img.save(op.join(basedir, 'image.nii.gz'))
applycommandline.applyCommandLineArgs(
overlayList,
panel.displayCtx, [
'-lo', 'vertical', 'image.nii.gz', '-b', '75', '-c', '25',
'-g', '-0.5'
],
baseDir=basedir,
panel=panel,
blocking=True)
# scene args are applied asynchronously
waitUntilIdle()
assert len(overlayList) == 1
assert np.all(overlayList[0][:] == img[:])
img = overlayList[0]
assert displayCtx.getDisplay(img).brightness == 75
assert displayCtx.getDisplay(img).contrast == 25
assert displayCtx.getOpts(img).gamma == -0.5
assert panel.sceneOpts.layout == 'vertical'
def callback(line):
# first arg is the directory that
# the client was executed from,
# which is used by applyCLIArgs
# in case overlays were specified
# with relative paths
args = shlex.split(line)
baseDir = args[0]
args = args[1:]
applycli.applyCommandLineArgs(overlayList,
displayCtx,
args,
baseDir=baseDir)
def MacOpenURL(self, url):
"""On OSX, support opening files via a ``fsleyes://`` url. """
if self.__overlayList is None:
return
import fsleyes_widgets.utils.status as status
import fsleyes.strings as strings
import fsleyes.parseargs as parseargs
import fsleyes.actions.applycommandline as applycommandline
errTitle = strings.titles[self, 'openURLError']
errMsg = strings.messages[self, 'openURLError']
with status.reportIfError(errTitle, errMsg):
applycommandline.applyCommandLineArgs(
self.__overlayList, self.__displayCtx,
parseargs.fsleyesUrlToArgs(url))
def setState(frame, state):
"""Set the state of FSLeyes from the given ``state`` string.
.. warning:: This function will remove all view panels, and remove all
overlays, before loading the new state.
:arg frame: The :class:`.FSLeyesFrame`
:arg state: A FSLeyes state string, generated by :func:`getState`.
"""
displayCtx = frame.displayCtx
overlayList = frame.overlayList
bits = state.split(SEP)
layout = bits[0]
cli = bits[1:]
cli = [c.split(CLISEP) for c in cli]
# First clear the current state
frame.removeAllViewPanels()
overlayList.clear()
# Then load all new overlays
applycommandline.applyCommandLineArgs(overlayList,
displayCtx,
cli[0],
blocking=True)
# After overlays have been loaded,
# apply the new layout, and apply
# view-specific overlay arguments.
layouts.applyLayout(frame, 'state', layout)
panels = [
p for p in frame.viewPanels if isinstance(p, canvaspanel.CanvasPanel)
]
for i, panel in enumerate(panels, 1):
applycommandline.applyCommandLineArgs(overlayList,
panel.displayCtx,
cli[i],
panel,
loadOverlays=False)
def _test_applyCommandLine_sceneOnly(panel, overlayList, displayCtx):
panel.sceneOpts.layout = 'horizontal'
with tempdir():
img = fslimage.Image(np.random.randint(1, 255, (20, 20, 20)))
img.save('image.nii.gz')
applycommandline.applyCommandLineArgs(
overlayList,
panel.displayCtx,
['-lo', 'vertical',
'image.nii.gz', '-b', '75', '-c', '25', '-g', '-0.5'],
panel=panel,
applyOverlayArgs=False)
# scene args are applied asynchronously
waitUntilIdle()
assert len(overlayList) == 0
assert panel.sceneOpts.layout == 'vertical'
def _test_melodic_IC(frame, overlayList, displayCtx):
loaded = [False]
def onLoad(*_):
loaded[0] = True
with tempdir():
mdir = op.abspath(create_melodic_dir())
mean = op.join(mdir, 'mean.nii.gz')
mic = op.join(mdir, 'melodic_IC.nii.gz')
applyCommandLineArgs(overlayList,
displayCtx, ['-ad', mdir],
onLoad=onLoad)
while not loaded[0]:
realYield()
assert len(overlayList) == 2
assert overlayList[0].dataSource == mean
assert overlayList[1].dataSource == mic
assert displayCtx.getSelectedOverlay() is overlayList[1]
