def load_unit(self, unit_id):
"""Loads the image data for display."""
image1_path, image2_path = self.path_getter_inputs(unit_id)
self.image_one = read_image(image1_path, error_msg='first image')
self.image_two = read_image(image2_path, error_msg='second image')
skip_subject = False
if np.count_nonzero(self.image_one) == 0:
skip_subject = True
print('image {} of {} is empty!'.format(self.image1_name,
self.current_unit_id))
if np.count_nonzero(self.image_two) == 0:
skip_subject = True
print('image {} of {} is empty!'.format(self.image2_name,
self.current_unit_id))
if not skip_subject:
# crop and rescale
self.image_one, self.image_two = crop_to_seg_extents(
self.image_one, self.image_two, self.padding)
self.image_one = scale_0to1(self.image_one)
self.image_two = scale_0to1(self.image_two)
self.slices = pick_slices(self.image_one, self.views,
self.num_slices_per_view)
# flag to keep track of whether data has been changed.
self._histogram_updated = False
# # where to save the visualization to
# out_vis_path = pjoin(self.out_dir, 'visual_qc_{}_{}'.format(self.vis_type, unit_id))
return skip_subject
def load_unit(self, unit_id):
"""Loads the image data for display."""
t1_mri_path = get_freesurfer_mri_path(self.in_dir, unit_id,
self.mri_name)
fs_seg_path = get_freesurfer_mri_path(self.in_dir, unit_id,
self.seg_name)
temp_t1_mri = read_image(t1_mri_path, error_msg='T1 mri')
temp_fs_seg = read_image(fs_seg_path, error_msg='segmentation')
if temp_t1_mri.shape != temp_fs_seg.shape:
raise ValueError('size mismatch! MRI: {} Seg: {}\n'
'Size must match in all dimensions.'.format(
self.current_t1_mri.shape, temp_fs_seg.shape))
skip_subject = False
if self.vis_type in ('cortical_volumetric', 'cortical_contour'):
temp_seg_uncropped, roi_set_is_empty = void_subcortical_symmetrize_cortical(
temp_fs_seg)
elif self.vis_type in ('labels_volumetric', 'labels_contour'):
if self.label_set is not None:
# TODO same colors for same labels is not guaranteed
# if one subject fewer labels than others
# due to remapping of labels for each subject
temp_seg_uncropped, roi_set_is_empty = get_label_set(
temp_fs_seg, self.label_set)
else:
raise ValueError(
'--label_set must be specified for visualization types: '
' labels_volumetric and labels_contour')
else:
raise NotImplementedError(
'Invalid visualization type - '
'choose from: {}'.format(
cfg.visualization_combination_choices))
if roi_set_is_empty:
skip_subject = True
print('segmentation image for {} '
'does not contain requested label set!'.format(unit_id))
return skip_subject
# T1 mri must be rescaled - to avoid strange distributions skewing plots
rescaled_t1_mri = scale_0to1(temp_t1_mri, cfg.max_cmap_range_t1_mri)
self.current_t1_mri, self.current_seg = crop_to_seg_extents(
rescaled_t1_mri, temp_seg_uncropped, self.padding)
out_vis_path = pjoin(
self.out_dir, 'visual_qc_{}_{}_{}'.format(self.vis_type,
self.suffix, unit_id))
return skip_subject
def overlay_images(qcw, mri, seg,
subject_id=None,
annot=None,
figsize=None,
padding=default_padding,
output_path=None):
"""Backend engine for overlaying a given seg on MRI with freesurfer label."""
num_rows_per_view, num_slices_per_view, padding = check_params(qcw.num_rows, qcw.num_slices, padding)
mri, seg = crop_to_seg_extents(mri, seg, padding)
surf_vis = dict() # empty - no vis to include
# TODO broaden this to include subcortical structures as well
if 'cortical' in qcw.vis_type:
if qcw.in_dir is not None and subject_id is not None and qcw.out_dir is not None:
surf_vis = make_vis_pial_surface(qcw.in_dir, subject_id, qcw.out_dir)
num_surf_vis = len(surf_vis)
# TODO calculation below is redundant, if surf vis does not fail
# i.e. if num_surf_vis is fixed, no need to recompute for every subject
num_views = len(qcw.views)
num_rows = num_rows_per_view * num_views
slices = pick_slices(seg, qcw.views, num_slices_per_view)
num_volumetric_slices = len(slices)
total_num_panels = num_volumetric_slices + num_surf_vis
num_rows_for_surf_vis = 1 if num_surf_vis > 0 else 0
num_rows = num_rows + num_rows_for_surf_vis
num_cols = check_layout(total_num_panels, num_views, num_rows_per_view, num_rows_for_surf_vis)
plt.style.use('dark_background')
if figsize is None:
# figsize = [min(15,4*num_rows), min(12,4*num_cols)] # max (15,12)
figsize = [4 * num_rows, 2* num_cols]
fig, ax = plt.subplots(num_rows, num_cols, figsize=figsize)
display_params_mri = dict(interpolation='none', aspect='equal', origin='lower',
alpha=qcw.alpha_mri)
display_params_seg = dict(interpolation='none', aspect='equal', origin='lower',
alpha=qcw.alpha_seg)
normalize_labels = colors.Normalize(vmin=seg.min(), vmax=seg.max(), clip=True)
fs_cmap = get_freesurfer_cmap(qcw.vis_type)
seg_mapper = cm.ScalarMappable(norm=normalize_labels, cmap=fs_cmap)
normalize_mri = colors.Normalize(vmin=mri.min(), vmax=mri.max(), clip=True)
mri_mapper = cm.ScalarMappable(norm=normalize_mri, cmap='gray')
# deciding colors for the whole image
unique_labels = np.unique(seg)
# removing background - 0 stays 0
unique_labels = np.delete(unique_labels, 0)
if len(unique_labels) == 1:
color4label = [qcw.contour_color]
else:
color4label = seg_mapper.to_rgba(unique_labels)
handles_seg = list()
handles_mri = list()
ax = ax.flatten()
# display surfaces
for sf_counter, ((hemi, view), spath) in enumerate(surf_vis.items()):
plt.sca(ax[sf_counter])
img = mpimg.imread(spath)
# img = crop_image(img)
plt.imshow(img)
ax[sf_counter].text(0, 0, '{} {}'.format(hemi, view))
plt.axis('off')
# display slices
for ax_counter, (dim_index, slice_num) in enumerate(slices):
plt.sca(ax[ax_counter + num_surf_vis])
slice_mri = get_axis(mri, dim_index, slice_num)
slice_seg = get_axis(seg, dim_index, slice_num)
# display MRI
mri_rgb = mri_mapper.to_rgba(slice_mri)
h_mri = plt.imshow(mri_rgb, **display_params_mri)
if 'volumetric' in qcw.vis_type:
seg_rgb = seg_mapper.to_rgba(slice_seg)
h_seg = plt.imshow(seg_rgb, **display_params_seg)
elif 'contour' in qcw.vis_type:
h_seg = plot_contours_in_slice(slice_seg, unique_labels, color4label)
plt.axis('off')
# # encoding the souce of the object (image/line) being displayed
# handle_seg.set_label('seg {} {}'.format(dim_index, slice_num))
# handle_mri.set_label('mri {} {}'.format(dim_index, slice_num))
handles_mri.append(h_mri)
if len(h_seg) >= 1:
handles_seg.extend(h_seg)
else:
handles_seg.append(h_seg)
# hiding unused axes
for ua in range(total_num_panels, len(ax)):
ax[ua].set_visible(False)
if annot is not None:
h_annot = fig.suptitle(annot, **cfg.annot_text_props)
h_annot.set_position(cfg.position_annot_text)
fig.set_size_inches(figsize)
if output_path is not None:
# no space left unused
plt.subplots_adjust(**cfg.no_blank_area)
output_path = output_path.replace(' ', '_')
layout_str = 'v{}_ns{}_{}x{}'.format(''.join([ str(v) for v in qcw.views]),num_slices_per_view,num_rows,num_cols)
fig.savefig(output_path + '_{}.png'.format(layout_str), bbox_inches='tight')
# leaving some space on the right for review elements
plt.subplots_adjust(**cfg.review_area)
return fig, handles_mri, handles_seg, figsize
def aseg_on_mri(mri_spec,
aseg_spec,
alpha_mri=1.0,
alpha_seg=1.0,
num_rows=2,
num_cols=6,
rescale_method='global',
aseg_cmap='freesurfer',
sub_cortical=False,
annot=None,
padding=5,
bkground_thresh=0.05,
output_path=None,
figsize=None,
**kwargs):
"Produces a collage of various slices from different orientations in the given 3D image"
num_rows, num_cols, padding = check_params(num_rows, num_cols, padding)
mri = read_image(mri_spec, bkground_thresh=bkground_thresh)
seg = read_image(aseg_spec, bkground_thresh=0)
mri, seg = crop_to_seg_extents(mri, seg, padding)
num_slices_per_view = num_rows * num_cols
slices = pick_slices(seg, num_slices_per_view)
plt.style.use('dark_background')
num_axes = 3
if figsize is None:
figsize = [5 * num_axes * num_rows, 5 * num_cols]
fig, ax = plt.subplots(num_axes * num_rows, num_cols, figsize=figsize)
# displaying some annotation text if provided
if annot is not None:
fig.suptitle(annot, backgroundcolor='black', color='g')
display_params_mri = dict(interpolation='none',
aspect='equal',
origin='lower',
cmap='gray',
alpha=alpha_mri,
vmin=mri.min(),
vmax=mri.max())
display_params_seg = dict(interpolation='none',
aspect='equal',
origin='lower',
alpha=alpha_seg)
normalize_labels = colors.Normalize(vmin=seg.min(),
vmax=seg.max(),
clip=True)
fs_cmap = get_freesurfer_cmap(sub_cortical)
label_mapper = cm.ScalarMappable(norm=normalize_labels, cmap=fs_cmap)
ax = ax.flatten()
ax_counter = 0
for dim_index in range(3):
for slice_num in slices[dim_index]:
plt.sca(ax[ax_counter])
ax_counter = ax_counter + 1
slice_mri = get_axis(mri, dim_index, slice_num)
slice_seg = get_axis(seg, dim_index, slice_num)
# # masking data to set no-value pixels to transparent
# seg_background = np.isclose(slice_seg, 0.0)
# slice_seg = np.ma.masked_where(seg_background, slice_seg)
# slice_mri = np.ma.masked_where(np.logical_not(seg_background), slice_mri)
seg_rgb = label_mapper.to_rgba(slice_seg)
plt.imshow(seg_rgb, **display_params_seg)
plt.imshow(slice_mri, **display_params_mri)
plt.axis('off')
# plt.subplots_adjust(wspace=0.0, hspace=0.0)
plt.subplots_adjust(left=0.01,
right=0.99,
bottom=0.01,
top=0.99,
wspace=0.05,
hspace=0.02)
# fig.tight_layout()
if output_path is not None:
output_path = output_path.replace(' ', '_')
fig.savefig(output_path + '.png', bbox_inches='tight')
# plt.close()
return fig