def __onCrop(self, ev):
"""Crops the selected image. This is done via a call to
:func:`.copyoverlay.copyImage`. Also calls :meth:`__onCancel`,
to finish cropping.
"""
overlayList = self.overlayList
displayCtx = self.displayCtx
overlay = displayCtx.getSelectedOverlay()
display = displayCtx.getDisplay(overlay)
name = '{}_roi'.format(display.name)
cropBox = self.__profile.cropBox
roi = [cropBox.x,
cropBox.y,
cropBox.z]
if overlay.ndim >= 4:
roi.append(self.__volumeWidget.GetRange())
copyoverlay.copyImage(
overlayList,
displayCtx,
overlay,
createMask=False,
copy4D=True,
copyDisplay=True,
name=name,
roi=roi)
self.__onCancel()
def _test_copyImage_3d(panel, overlayList, displayCtx):
img3d = fslimage.Image(np.random.randint(1, 255, (20, 20, 20)),
name='img3d')
overlayList.append(img3d)
# standard copy. Make sure
# display settings are copied
displayCtx.getDisplay(img3d).alpha = 75
displayCtx.getOpts(img3d).gamma = 0.5
copyoverlay.copyImage(overlayList, displayCtx, img3d, name='my cool copy')
assert len(overlayList) == 2
# the copy should be inserted directly
# after the original in the list
copy = overlayList[1]
assert np.all(img3d[:] == copy[:])
assert displayCtx.getDisplay(copy).alpha == 75
assert displayCtx.getDisplay(copy).name == 'my cool copy'
assert displayCtx.getOpts(copy).gamma == 0.5
overlayList.remove(copy)
# without copying display settings
copyoverlay.copyImage(overlayList, displayCtx, img3d, copyDisplay=False)
assert len(overlayList) == 2
copy = overlayList[1]
assert np.all(img3d[:] == copy[:])
assert displayCtx.getDisplay(copy).alpha == 100
assert displayCtx.getOpts(copy).gamma == 0
overlayList.remove(copy)
# empty mask
copyoverlay.copyImage(overlayList, displayCtx, img3d, createMask=True)
assert len(overlayList) == 2
copy = overlayList[1]
assert np.all(copy.shape == img3d.shape)
assert np.all(copy[:] == 0)
overlayList.remove(copy)
# new data (createMask should be ignored)
data = np.random.randint(1, 100, img3d.shape)
copyoverlay.copyImage(overlayList,
displayCtx,
img3d,
createMask=True,
data=data)
assert len(overlayList) == 2
copy = overlayList[1]
assert np.all(copy.shape == img3d.shape)
assert np.all(copy[:] == data)
overlayList.remove(copy)
# roi
copyoverlay.copyImage(overlayList,
displayCtx,
img3d,
roi=((5, 10), (5, 10), (5, 10)))
assert len(overlayList) == 2
copy = overlayList[1]
assert tuple(copy.shape) == (5, 5, 5)
assert np.all(copy[:] == img3d[5:10, 5:10, 5:10])
overlayList.remove(copy)
# roi, expanding FOV
copyoverlay.copyImage(overlayList,
displayCtx,
img3d,
roi=((-5, 25), (-5, 25), (-5, 25)))
assert len(overlayList) == 2
copy = overlayList[1]
assert tuple(copy.shape) == (30, 30, 30)
assert np.all(copy[5:25, 5:25, 5:25] == img3d[:, :, :])
overlayList.remove(copy)
def _test_copyImage_4d(panel, overlayList, displayCtx):
img4d = fslimage.Image(np.random.randint(1, 255, (20, 20, 20, 20)),
name='img4d')
overlayList.append(img4d)
# 4D
copyoverlay.copyImage(overlayList, displayCtx, img4d)
assert len(overlayList) == 2
copy = overlayList[1]
assert np.all(copy[:] == img4d[:])
overlayList.remove(copy)
# 4D mask
copyoverlay.copyImage(overlayList, displayCtx, img4d, createMask=True)
assert len(overlayList) == 2
copy = overlayList[1]
assert np.all(copy.shape == img4d.shape)
assert np.all(copy[:] == 0)
overlayList.remove(copy)
# 4D current volume
displayCtx.getOpts(img4d).volume = 6
copyoverlay.copyImage(overlayList, displayCtx, img4d, copy4D=False)
assert len(overlayList) == 2
copy = overlayList[1]
assert np.all(copy[:] == img4d[..., 6])
overlayList.remove(copy)
# roi 4D, unspecified 4th dim bounds
copyoverlay.copyImage(overlayList,
displayCtx,
img4d,
roi=((5, 10), (5, 10), (5, 10)))
assert len(overlayList) == 2
copy = overlayList[1]
assert tuple(copy.shape) == (5, 5, 5, 20)
assert np.all(copy[:] == img4d[5:10, 5:10, 5:10, :])
overlayList.remove(copy)
# roi 4D, specified 4th dim bounds
copyoverlay.copyImage(overlayList,
displayCtx,
img4d,
roi=((5, 10), (5, 10), (5, 10), (5, 10)))
assert len(overlayList) == 2
copy = overlayList[1]
assert tuple(copy.shape) == (5, 5, 5, 5)
assert np.all(copy[:] == img4d[5:10, 5:10, 5:10, 5:10])
overlayList.remove(copy)
# roi 4D, current volume
displayCtx.getOpts(img4d).volume = 10
copyoverlay.copyImage(overlayList,
displayCtx,
img4d,
copy4D=False,
roi=((5, 10), (5, 10), (5, 10)))
assert len(overlayList) == 2
copy = overlayList[1]
assert tuple(copy.shape) == (5, 5, 5)
assert np.all(copy[:] == img4d[5:10, 5:10, 5:10, 10])
overlayList.remove(copy)
# roi, 4D, expanding FOV
copyoverlay.copyImage(overlayList,
displayCtx,
img4d,
roi=((-5, 25), (-5, 25), (-5, 25)))
assert len(overlayList) == 2
copy = overlayList[1]
assert tuple(copy.shape) == (30, 30, 30, 20)
assert np.all(copy[5:25, 5:25, 5:25, :] == img4d[:, :, :, :])
overlayList.remove(copy)
# roi, 4D, current vol
copyoverlay.copyImage(overlayList,
displayCtx,
img4d,
copy4D=False,
roi=((-5, 25), (-5, 25), (-5, 25)))
assert len(overlayList) == 2
copy = overlayList[1]
assert tuple(copy.shape) == (30, 30, 30)
assert np.all(copy[5:25, 5:25, 5:25] == img4d[:, :, :, 10])
overlayList.remove(copy)
def _test_copyImage_multiValued(panel, overlayList, displayCtx):
complex = make_complex()
rgb = make_rgb()
overlayList.extend((complex, rgb))
# normal copy - complex
copyoverlay.copyImage(overlayList, displayCtx, complex)
assert len(overlayList) == 3
copy = overlayList[1]
assert complex.dtype == copy.dtype
assert np.all(copy[:] == complex[:])
overlayList.remove(copy)
# normal copy - rgb
copyoverlay.copyImage(overlayList, displayCtx, rgb)
assert len(overlayList) == 3
copy = overlayList[2]
assert rgb.dtype == copy.dtype
assert np.all(rgb[:] == copy[:])
overlayList.remove(copy)
# copy real component
copyoverlay.copyImage(overlayList, displayCtx, complex, channel='real')
assert len(overlayList) == 3
copy = overlayList[1]
assert np.all(copy[:] == complex[:].real)
overlayList.remove(copy)
# copy imag component
copyoverlay.copyImage(overlayList, displayCtx, complex, channel='imag')
assert len(overlayList) == 3
copy = overlayList[1]
assert np.all(copy[:] == complex[:].imag)
overlayList.remove(copy)
# copy r component
copyoverlay.copyImage(overlayList, displayCtx, rgb, channel='R')
assert len(overlayList) == 3
copy = overlayList[2]
assert np.all(copy[:] == rgb[:]['R'])
overlayList.remove(copy)
# copy g component
copyoverlay.copyImage(overlayList, displayCtx, rgb, channel='G')
assert len(overlayList) == 3
copy = overlayList[2]
assert np.all(copy[:] == rgb[:]['G'])
overlayList.remove(copy)
# copy b component
copyoverlay.copyImage(overlayList, displayCtx, rgb, channel='B')
assert len(overlayList) == 3
copy = overlayList[2]
assert np.all(copy[:] == rgb[:]['B'])
overlayList.remove(copy)
def _test_copyImage(panel, overlayList, displayCtx):
img3d = fslimage.Image(np.random.randint(1, 255, (20, 20, 20)))
img4d = fslimage.Image(np.random.randint(1, 255, (20, 20, 20, 20)))
overlayList.extend((img3d, img4d))
# standard copy. Make sure
# display settings are copied
displayCtx.getDisplay(img3d).alpha = 75
displayCtx.getOpts(img3d).gamma = 0.5
copyoverlay.copyImage(overlayList, displayCtx, img3d, name='my cool copy')
assert len(overlayList) == 3
# the copy should be inserted directly
# after the original in the list
copy = overlayList[1]
assert np.all(img3d[:] == copy[:])
assert displayCtx.getDisplay(copy).alpha == 75
assert displayCtx.getDisplay(copy).name == 'my cool copy'
assert displayCtx.getOpts(copy).gamma == 0.5
overlayList.remove(copy)
# without copying display settings
copyoverlay.copyImage(overlayList, displayCtx, img3d, copyDisplay=False)
assert len(overlayList) == 3
copy = overlayList[1]
assert np.all(img3d[:] == copy[:])
assert displayCtx.getDisplay(copy).alpha == 100
assert displayCtx.getOpts(copy).gamma == 0
overlayList.remove(copy)
# empty mask
copyoverlay.copyImage(overlayList, displayCtx, img3d, createMask=True)
assert len(overlayList) == 3
copy = overlayList[1]
assert np.all(copy.shape == img3d.shape)
assert np.all(copy[:] == 0)
overlayList.remove(copy)
# 4D
copyoverlay.copyImage(overlayList, displayCtx, img4d)
assert len(overlayList) == 3
copy = overlayList[2]
assert np.all(copy[:] == img4d[:])
overlayList.remove(copy)
# 4D mask
copyoverlay.copyImage(overlayList, displayCtx, img4d, createMask=True)
assert len(overlayList) == 3
copy = overlayList[2]
assert np.all(copy.shape == img4d.shape)
assert np.all(copy[:] == 0)
overlayList.remove(copy)
# 4D current volume
displayCtx.getOpts(img4d).volume = 6
copyoverlay.copyImage(overlayList, displayCtx, img4d, copy4D=False)
assert len(overlayList) == 3
copy = overlayList[2]
assert np.all(copy[:] == img4d[..., 6])
overlayList.remove(copy)
# roi
copyoverlay.copyImage(overlayList,
displayCtx,
img3d,
roi=((5, 10), (5, 10), (5, 10)))
assert len(overlayList) == 3
copy = overlayList[1]
assert tuple(copy.shape) == (5, 5, 5)
assert np.all(copy[:] == img3d[5:10, 5:10, 5:10])
overlayList.remove(copy)
# roi 4D, unspecified 4th dim bounds
copyoverlay.copyImage(overlayList,
displayCtx,
img4d,
roi=((5, 10), (5, 10), (5, 10)))
assert len(overlayList) == 3
copy = overlayList[2]
assert tuple(copy.shape) == (5, 5, 5, 20)
assert np.all(copy[:] == img4d[5:10, 5:10, 5:10, :])
overlayList.remove(copy)
# roi 4D, specified 4th dim bounds
copyoverlay.copyImage(overlayList,
displayCtx,
img4d,
roi=((5, 10), (5, 10), (5, 10), (5, 10)))
assert len(overlayList) == 3
copy = overlayList[2]
assert tuple(copy.shape) == (5, 5, 5, 5)
assert np.all(copy[:] == img4d[5:10, 5:10, 5:10, 5:10])
overlayList.remove(copy)
# roi 4D, current volume
displayCtx.getOpts(img4d).volume = 10
copyoverlay.copyImage(overlayList,
displayCtx,
img4d,
copy4D=False,
roi=((5, 10), (5, 10), (5, 10)))
assert len(overlayList) == 3
copy = overlayList[2]
assert tuple(copy.shape) == (5, 5, 5)
assert np.all(copy[:] == img4d[5:10, 5:10, 5:10, 10])
overlayList.remove(copy)