def __getCurrentXform(self):
"""Returns the current transformation matrix defined by the scale,
offset, and rotation widgets.
"""
scales, offsets, rotations = self.__getCurrentXformComponents()
rotations = [r * np.pi / 180 for r in rotations]
# We need to figure out the centre
# of the image in world coordinates
# to define the origin of rotation.
shape = self.__overlay.shape
lo, hi = transform.axisBounds(shape, self.__overlay.voxToWorldMat)
origin = [l + (h - l) / 2.0 for h, l in zip(hi, lo)]
return transform.compose(scales, offsets, rotations, origin)
def __drawLegend(self):
"""Draws a legend in the bottom left corner of the screen, showing
anatomical orientation.
"""
copts = self.opts
b = self.__displayCtx.bounds
w, h = self.GetSize()
xlen, ylen = glroutines.adjust(b.xlen, b.ylen, w, h)
# A line for each axis
vertices = np.zeros((6, 3), dtype=np.float32)
vertices[0, :] = [-1, 0, 0]
vertices[1, :] = [1, 0, 0]
vertices[2, :] = [0, -1, 0]
vertices[3, :] = [0, 1, 0]
vertices[4, :] = [0, 0, -1]
vertices[5, :] = [0, 0, 1]
# Each axis line is scaled to
# 60 pixels, and the legend is
# offset from the bottom-left
# corner by twice this amount.
scale = [xlen * 30.0 / w] * 3
offset = [
-0.5 * xlen + 2.0 * scale[0], -0.5 * ylen + 2.0 * scale[1], 0
]
# Apply the current camera
# angle and rotation settings
# to the legend vertices. Offset
# anatomical labels off each
# axis line by a small amount.
rotation = transform.decompose(self.__viewMat)[2]
xform = transform.compose(scale, offset, rotation)
labelPoses = transform.transform(vertices * 1.2, xform)
vertices = transform.transform(vertices, xform)
# Draw the legend lines
gl.glDisable(gl.GL_DEPTH_TEST)
gl.glColor3f(*copts.cursorColour[:3])
gl.glLineWidth(2)
gl.glBegin(gl.GL_LINES)
gl.glVertex3f(*vertices[0])
gl.glVertex3f(*vertices[1])
gl.glVertex3f(*vertices[2])
gl.glVertex3f(*vertices[3])
gl.glVertex3f(*vertices[4])
gl.glVertex3f(*vertices[5])
gl.glEnd()
# Figure out the anatomical
# labels for each axis.
overlay = self.__displayCtx.getSelectedOverlay()
dopts = self.__displayCtx.getOpts(overlay)
labels = dopts.getLabels()[0]
# getLabels returns (xlo, ylo, zlo, xhi, yhi, zhi) -
# - rearrange them to (xlo, xhi, ylo, yhi, zlo, zhi)
labels = [
labels[0], labels[3], labels[1], labels[4], labels[2], labels[5]
]
canvas = np.array([w, h])
view = np.array([xlen, ylen])
# Draw each label
for i in range(6):
# Calculate pixel x/y
# location for this label
xx, xy = canvas * (labelPoses[i, :2] + 0.5 * view) / view
# Calculate the size of the label
# in pixels, so we can centre the
# label
tw, th = glroutines.text2D(labels[i], (xx, xy),
10, (w, h),
calcSize=True)
# Draw the text
xx -= 0.5 * tw
xy -= 0.5 * th
gl.glColor3f(*copts.legendColour[:3])
glroutines.text2D(labels[i], (xx, xy), 10, (w, h))
def _test_Image_init_xform(imgtype):
with tempdir() as td:
sform = transform.compose(np.random.random(3), np.random.random(3),
np.random.random(3))
qform = transform.compose(np.random.random(3), np.random.random(3),
np.random.random(3))
sform_code = 3
qform_code = 4
# Create a base nifti image
img = make_image('file.nii')
img.set_sform(sform, code=sform_code)
img.set_qform(qform, code=qform_code)
nib.save(img, 'file.nii')
img = nib.load('file.nii')
# an image created off a
# header should have
# identical sform/qform
fimg = fslimage.Image(img.get_data(), header=img.header)
fsform, fsform_code = fimg.header.get_sform(True)
fqform, fqform_code = fimg.header.get_qform(True)
xform = fimg.voxToWorldMat
assert np.all(np.isclose(fsform, sform))
assert np.all(np.isclose(fqform, qform))
assert np.all(np.isclose(xform, sform))
assert fsform_code == sform_code
assert fqform_code == qform_code
# an image created off
# an xform only should
# get its sform set
# set to that xform,
# qform to None, and
# and codes set to (s2, q0)
fimg = fslimage.Image(img.get_data(), xform=sform)
fsform, fsform_code = fimg.header.get_sform(True)
fqform, fqform_code = fimg.header.get_qform(True)
xform = fimg.voxToWorldMat
assert np.all(np.isclose(fsform, sform))
assert np.all(np.isclose(xform, sform))
assert fqform is None
assert fsform_code == 2
assert fqform_code == 0
# an image created with a
# header and an xform should
# have its s/q forms set
# to the xform. and its
# s/q form codes the same
# as what is in the header
rxform = transform.compose(np.random.random(3), np.random.random(3),
np.random.random(3))
fimg = fslimage.Image(img.get_data(), header=img.header, xform=rxform)
fsform, fsform_code = fimg.header.get_sform(True)
fqform, fqform_code = fimg.header.get_qform(True)
xform = fimg.voxToWorldMat
assert np.all(np.isclose(fsform, rxform))
assert np.all(np.isclose(fqform, rxform))
assert np.all(np.isclose(xform, rxform))
assert fsform_code == sform_code
assert fqform_code == qform_code