def fsleyes_embed(parent=None, make_fsleyesframe=True, **kwargs):
"""Initialise FSLeyes and create a :class:`.FSLeyesFrame`, when
running within another application.
.. note:: If a ``wx.App`` does not exist, one is created.
:arg parent: ``wx`` parent object
:arg make_fsleyesframe: bool, default is True to make a new :class:`.FSLeyesFrame`
:returns: A tuple containing:
- The :class:`.OverlayList`
- The master :class:`.DisplayContext`
- The :class:`.FSLeyesFrame` or None if make_fsleyesframe=False
All other arguments are passed to :meth:`.FSLeyesFrame.__init__`.
"""
import fsleyes_props as props
import fsleyes.gl as fslgl
import fsleyes.frame as fslframe
import fsleyes.overlay as fsloverlay
import fsleyes.displaycontext as fsldc
app = wx.GetApp()
ownapp = app is None
if ownapp:
app = FSLeyesApp()
fsleyes.initialise()
colourmaps.init()
props.initGUI()
called = [False]
ret = [None]
def until():
return called[0]
def ready():
frame = None
fslgl.bootstrap()
overlayList = fsloverlay.OverlayList()
displayCtx = fsldc.DisplayContext(overlayList)
if make_fsleyesframe:
frame = fslframe.FSLeyesFrame(parent, overlayList, displayCtx,
**kwargs)
if ownapp:
app.SetOverlayListAndDisplayContext(overlayList, displayCtx)
# Keep a ref to prevent the app from being GC'd
if make_fsleyesframe:
frame._embed_app = app
called[0] = True
ret[0] = (overlayList, displayCtx, frame)
fslgl.getGLContext(ready=ready, raiseErrors=True)
idle.block(10, until=until)
if ret[0] is None:
raise RuntimeError('Failed to start FSLeyes')
return ret[0]
def _test_block_until():
ev = threading.Event()
def task():
time.sleep(1)
ev.set()
threading.Thread(target=task).start()
start = time.time()
idle.block(3, until=ev.is_set)
end = time.time()
assert end - start < 3
def _test_block():
called = [False]
if fslplatform.haveGui:
import wx
def idlefunc():
called[0] = True
wx.CallLater(1000, idlefunc)
start = time.time()
idle.block(2)
end = time.time()
# Be relaxed about precision - timing
# can sometimes be pretty sloppy when
# running in a docker container.
assert abs((end - start) - 2) < 0.05
if fslplatform.haveGui:
assert called[0]
def _test_editable(ortho, overlayList, displayCtx):
# must be an image
# must have one value per voxel (e.g. no RGB)
# must be displayed as volume, mask, or label
img = Image(op.join(datadir, '3d'))
surf = VTKMesh(op.join(datadir, 'mesh_l_thal.vtk'))
dti = Image(op.join(datadir, 'dti', 'dti_V1'))
rgb = Bitmap(op.join(datadir, 'test_screenshot_3d.png')).asImage()
editable = [(img, 'volume'), (img, 'mask'), (img, 'label')]
notEditable = [(img, 'mip'), (surf, 'mesh'), (dti, 'rgbvector'),
(rgb, 'volume')]
def setprof(profile):
ortho.profile = profile
savedprof = [None]
def saveprof():
savedprof[0] = ortho.profile
for ovl, ot in editable:
idle.idle(setprof, 'edit')
idle.idle(overlayList.append, ovl, overlayType=ot)
idle.idle(displayCtx.selectOverlay, ovl)
idle.block(3)
idle.idle(saveprof)
idle.idle(overlayList.clear)
idle.block(3)
assert savedprof[0] == 'edit'
for ovl, ot in notEditable:
idle.idle(setprof, 'edit')
idle.idle(overlayList.append, ovl, overlayType=ot)
idle.idle(displayCtx.selectOverlay, ovl)
idle.block(3)
idle.idle(saveprof)
idle.idle(overlayList.clear)
idle.block(3)
assert savedprof[0] == 'view'
def _test_SelectionActions(ortho, overlayList, displayCtx):
img1 = Image(np.random.randint(1, 65536, (20, 20, 20)))
img2 = Image(np.random.randint(1, 65536, (20, 20, 20)))
overlayList[:] = [img1, img2]
displayCtx.selectOverlay(img1)
idle.block(2)
ortho.profile = 'edit'
idle.block(2)
profile = ortho.getCurrentProfile()
profile.mode = 'sel'
profile.drawMode = False
idle.block(2)
ed = profile.editor(img1)
# clear
ed.getSelection().addToSelection(np.ones((4, 4, 4)), offset=(8, 8, 8))
idle.block(2)
profile.clearSelection()
assert np.all(ed.getSelection().getSelection() == 0)
# fill
ed.getSelection().addToSelection(np.ones((4, 4, 4)), offset=(8, 8, 8))
idle.block(2)
profile.fillValue = 999
profile.fillSelection()
exp = np.copy(img1[:])
exp[8:12, 8:12, 8:12] = 999
assert np.all(img1[:] == exp)
# erase
profile.clearSelection()
ed.getSelection().addToSelection(np.ones((4, 4, 4)), offset=(3, 3, 3))
idle.block(2)
profile.eraseValue = -999
profile.eraseSelection()
exp = np.copy(img1[:])
exp[3:7, 3:7, 3:7] = -999
assert np.all(img1[:] == exp)
# invert
ed.getSelection().addToSelection(np.ones((4, 4, 4)), offset=(8, 8, 8))
idle.block(2)
profile.invertSelection()
exp = np.ones(img1.shape)
exp[8:12, 8:12, 8:12] = 0
assert np.all(ed.getSelection().getSelection() == exp)
# copy+paste
profile.clearSelection()
ed.getSelection().addToSelection(np.ones((4, 4, 4)), offset=(8, 8, 8))
displayCtx.selectOverlay(img2)
profile.copySelection()
displayCtx.selectOverlay(img1)
idle.block(2)
profile.pasteSelection()
idle.block(2)
exp = np.copy(img1[:])
exp[8:12, 8:12, 8:12] = img2[8:12, 8:12, 8:12]
assert np.all(img1[:] == exp)
def _test_newMask(ortho, overlayList, displayCtx):
img = Image(np.random.randint(1, 65536, (20, 20, 20)))
overlayList[:] = [img]
idle.block(2.5)
ortho.profile = 'edit'
idle.block(2.5)
profile = ortho.getCurrentProfile()
profile.createMask()
idle.block(2.5)
assert len(overlayList) == 2
mask = overlayList[1]
assert mask.sameSpace(img)
assert np.all(mask[:] == 0)
overlayList.remove(mask)
idle.block(2.5)
profile.mode = 'sel'
idle.block(2.5)
ed = profile.editor(img)
ed.getSelection().addToSelection(np.ones((4, 4, 4)), offset=(8, 8, 8))
idle.block(2.5)
profile.createMask()
idle.block(2.5)
assert len(overlayList) == 2
mask = overlayList[1]
assert mask.sameSpace(img)
exp = np.zeros(mask.shape)
exp[8:12, 8:12, 8:12] = 1
assert np.all(mask[:] == exp)
overlayList[:] = []
idle.block(2.5)
def embed(mkFrame=True, **kwargs):
"""Initialise FSLeyes and create a :class:`.FSLeyesFrame`, when
running within another application.
.. note:: In most cases, this function must be called from the
``wx.MainLoop``.
:arg mkFrame: Defaults to ``True``. If ``False``, FSLeyes is
initialised, but a :class:`.FSLeyesFrame` is not created.
If you set this to ``False``, you must ensure that a
``wx.App`` object exists before calling this function.
:returns: A tuple containing:
- The :class:`.OverlayList`
- The master :class:`.DisplayContext`
- The :class:`.FSLeyesFrame` (or ``None``, if
``makeFrame is False``).
All other arguments are passed to :meth:`.FSLeyesFrame.__init__`.
"""
import fsleyes_props as props
import fsleyes.gl as fslgl
import fsleyes.frame as fslframe
import fsleyes.overlay as fsloverlay
import fsleyes.displaycontext as fsldc
# initialise must be called before
# a FSLeyesApp gets created, as it
# tries to access app_icon.png
fsleyes.initialise()
app = wx.GetApp()
ownapp = app is None
if ownapp and (mkFrame is False):
raise RuntimeError('If mkFrame is False, you '
'must create a wx.App before '
'calling fsleyes.main.embed')
if ownapp:
app = FSLeyesApp()
colourmaps.init()
props.initGUI()
called = [False]
ret = [None]
def until():
return called[0]
def ready():
fslgl.bootstrap()
overlayList = fsloverlay.OverlayList()
displayCtx = fsldc.DisplayContext(overlayList)
if mkFrame:
frame = fslframe.FSLeyesFrame(None, overlayList, displayCtx,
**kwargs)
else:
frame = None
if ownapp:
app.SetOverlayListAndDisplayContext(overlayList, displayCtx)
# Keep a ref to prevent the app from being GC'd
frame._embed_app = app
called[0] = True
ret[0] = (overlayList, displayCtx, frame)
fslgl.getGLContext(ready=ready, raiseErrors=True)
idle.block(10, until=until)
if ret[0] is None:
raise RuntimeError('Failed to start FSLeyes')
return ret[0]