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improve visualization utilities
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@talonchandler
talonchandler committed Feb 21, 2024
1 parent c324a98 commit af3c94a
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Showing 2 changed files with 33 additions and 19 deletions.
2 changes: 1 addition & 1 deletion polaris/data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -125,7 +125,7 @@ def visualize(self, filename, **kwargs):
# Calculate arrow positions
X = np.float(self.g.shape[0])
Y = np.float(self.g.shape[1])
Z = np.float(self.g.shape[2]) - kwargs['z_shift']
Z = np.float(self.g.shape[2])# - kwargs['z_shift']
max_dim = np.max([X,Y,Z])

tips = np.array([[(X-max_dim)/2,Y/2,Z/2],
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50 changes: 32 additions & 18 deletions polaris/spang.py
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Original file line number Diff line number Diff line change
Expand Up @@ -261,7 +261,7 @@ def visualize(self, out_path='out/', outer_box=True, axes=True,
arrows=None, arrow_color=np.array([0,0,0]), linewidth=0.1,
mark_slices=None, shift=[0,0,0], profiles=[], markers=[],
marker_colors=[], marker_scale=1, normalize_glyphs=True,
gamma=1, density_max=1, z_shift=None):
gamma=1, density_max=1, xyz_shift=(0,0,0), odf_scale=1.0, view_parallel=False):
log.info('Preparing to render ' + out_path)

# Handle scalemap
Expand Down Expand Up @@ -354,7 +354,7 @@ def visualize(self, out_path='out/', outer_box=True, axes=True,
renWin.SetMultiSamples(4)
log.info('Rendering '+str(np.sum(my_mask)) + ' ODFs')
fodf_spheres = viz.odf_sparse(data, self.Binv, sphere=self.sphere,
scale=skip_n*scale*0.5, norm=False,
scale=skip_n*odf_scale*scale*0.35, norm=False,
colormap=colormap, mask=my_mask,
global_cm=global_cm, scalemap=scalemap,
odf_sphere=False, flat=flat, normalize=normalize_glyphs)
Expand Down Expand Up @@ -455,20 +455,30 @@ def visualize(self, out_path='out/', outer_box=True, axes=True,
# Draw marked slices
if mark_slices is not None:
for slicen in mark_slices:
md = np.max((X, Z))
frac = slicen/data.shape[1]
rr = 0.83*md
t1 = 0
t2 = np.pi/2
t3 = np.pi
t4 = 3*np.pi/2
points = [np.array([[X/2+rr*np.cos(t1),frac*Y,Z/2+rr*np.sin(t1)],
[X/2+rr*np.cos(t2),frac*Y,Z/2+rr*np.sin(t2)],
[X/2+rr*np.cos(t3),frac*Y,Z/2+rr*np.sin(t3)],
[X/2+rr*np.cos(t4),frac*Y,Z/2+rr*np.sin(t4)],
[X/2+rr*np.cos(t1),frac*Y,Z/2+rr*np.sin(t1)],
[X/2+rr*np.cos(t2),frac*Y,Z/2+rr*np.sin(t2)]])]
viz.draw_unlit_line(ren, points, 6*[line_color+0.6], lw=0.3, scale=1.0)
if isinstance(slicen, int):
md = np.max((X, Z))
frac = slicen/data.shape[1]
rr = 0.83*md
t1 = 0
t2 = np.pi/2
t3 = np.pi
t4 = 3*np.pi/2
points = [np.array([[X/2+rr*np.cos(t1),frac*Y,Z/2+rr*np.sin(t1)],
[X/2+rr*np.cos(t2),frac*Y,Z/2+rr*np.sin(t2)],
[X/2+rr*np.cos(t3),frac*Y,Z/2+rr*np.sin(t3)],
[X/2+rr*np.cos(t4),frac*Y,Z/2+rr*np.sin(t4)],
[X/2+rr*np.cos(t1),frac*Y,Z/2+rr*np.sin(t1)],
[X/2+rr*np.cos(t2),frac*Y,Z/2+rr*np.sin(t2)]])]
viz.draw_unlit_line(ren, points, 6*[line_color+0.6], lw=0.3, scale=1.0)
elif isinstance(slicen, tuple):
slicey, a, b, c, d = slicen
points = [np.array([[X/2+((a+b)/np.sqrt(2)), slicey, Z/2+((-a+b)/np.sqrt(2))],
[X/2+((b-c)/np.sqrt(2)), slicey, Z/2+((b+c)/np.sqrt(2))],
[X/2+((-c-d)/np.sqrt(2)), slicey, Z/2+((c-d)/np.sqrt(2))],
[X/2+((a-d)/np.sqrt(2)), slicey, Z/2+((-a-d)/np.sqrt(2))],
[X/2+((a+b)/np.sqrt(2)), slicey, Z/2+((-a+b)/np.sqrt(2))]])]

viz.draw_unlit_line(ren, points, 5*[line_color+0.6], lw=0.3, scale=1.0)

# Draw markers
for i, marker in enumerate(markers):
Expand Down Expand Up @@ -542,7 +552,7 @@ def visualize(self, out_path='out/', outer_box=True, axes=True,
else:
cam.SetPosition(((X-1)/2 + Rcam, (Y-1)/2, (Z-1)/2))
cam.SetViewUp((0, 0, 1))
cam.SetFocalPoint(((X-1)/2, (Y-1)/2, (Z-1)/2))
cam.SetFocalPoint(((X-1)/2 - xyz_shift[0], (Y-1)/2 - xyz_shift[1], (Z-1)/2 - xyz_shift[2]))
#ren.reset_camera()
else:
ren.set_camera(*my_cam)
Expand Down Expand Up @@ -599,6 +609,10 @@ def visualize(self, out_path='out/', outer_box=True, axes=True,
ren.zoom(1 + ((zoom_end[j] - zoom_start[j])/n_frames))
ren.azimuth(az)
ren.reset_clipping_range()
if view_parallel: # For viewing slices
ren.projection(proj_type="parallel")
ren.reset_camera()
ren.zoom(zoom_start[j])

renderLarge = vtk.vtkRenderLargeImage()
renderLarge.SetMagnification(1)
Expand Down Expand Up @@ -684,7 +698,7 @@ def vis_profiles(self, filename, profilesi, colors=None, dx=0.13, prof_type='den
maxx = np.max(np.concatenate(xpos_out))

f, ax = plt.subplots(1, 1, figsize=(1.5,1.5))
ax.set_xlabel('Pos. on prof. ($\mu$m)')
ax.set_xlabel('Profile position ($\mu$m)')
ax.set_ylabel(ylabel)
if xlim is None:
ax.set_xlim([-0.05*maxx,maxx])
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