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def init_layout(self, views, num_rows_per_view,
num_slices_per_view, padding=cfg.default_padding):
self.views = views
self.num_slices_per_view = num_slices_per_view
self.num_rows_per_view = num_rows_per_view
self.num_rows = len(self.views) * self.num_rows_per_view
self.num_cols = int((len(self.views) * self.num_slices_per_view) / self.num_rows)
self.padding = padding
def init_layout(self, views, num_rows_per_view,
num_slices_per_view, padding=cfg.default_padding):
self.views = views
self.num_slices_per_view = num_slices_per_view
self.num_rows_per_view = num_rows_per_view
self.num_rows = len(self.views) * self.num_rows_per_view
self.num_cols = int((len(self.views) * self.num_slices_per_view) / self.num_rows)
self.padding = padding
def init_layout(self, views, num_rows_per_view,
num_slices_per_view, padding=cfg.default_padding):
self.views = views
self.num_slices_per_view = num_slices_per_view
self.num_rows_per_view = num_rows_per_view
self.num_rows = len(self.views) * self.num_rows_per_view
self.num_cols = int((len(self.views) * self.num_slices_per_view) / self.num_rows)
self.padding = padding
def init_layout(self, views, num_rows_per_view,
num_slices_per_view, padding=cfg.default_padding):
self.padding = padding
self.views = views
self.num_slices_per_view = num_slices_per_view
self.num_rows_per_view = num_rows_per_view
num_cols_volumetric = num_slices_per_view / num_rows_per_view
num_rows_volumetric = len(self.views) * self.num_rows_per_view
total_num_panels_vol = int(num_cols_volumetric * num_rows_volumetric)
# surf vis generation happens at the beginning - no option to defer for user
if not self.no_surface_vis and 'cortical' in self.vis_type:
extra_panels_surface_vis = cfg.num_cortical_surface_vis
extra_rows_surface_vis = 1
self.volumetric_start_index = extra_panels_surface_vis
else:
extra_panels_surface_vis = 0
def init_layout(self, views, num_rows_per_view,
num_slices_per_view, padding=cfg.default_padding):
plt.style.use('dark_background')
# vmin/vmax are controlled, because we rescale all to [0, 1]
self.display_params = dict(interpolation='none', aspect='equal',
origin='lower', cmap='gray', vmin=0.0, vmax=1.0)
self.figsize = cfg.default_review_figsize
self.collage = Collage(view_set=views,
num_slices=num_slices_per_view, num_rows=num_rows_per_view,
display_params=self.display_params,
bounding_rect=cfg.bounding_box_review,
figsize=self.figsize)
self.fig = self.collage.fig
self.fig.canvas.set_window_title('VisualQC T1 MRI : {} {} '
''.format(self.in_dir, self.mri_name))
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)
def init_layout(self,
view_set=cfg.defacing_view_set,
num_rows_per_view=cfg.defacing_num_rows_per_view,
num_slices_per_view=cfg.defacing_num_slices_per_view,
padding=cfg.default_padding):
"""initializes the layout"""
plt.style.use('dark_background')
# vmin/vmax are controlled, because we rescale all to [0, 1]
self.display_params = dict(interpolation='none', aspect='equal',
origin='lower', cmap='gray',
vmin=0.0, vmax=1.0)
self.figsize = cfg.default_review_figsize
self.collage = Collage(view_set=view_set,
num_slices=num_slices_per_view,
num_rows=num_rows_per_view,
display_params=self.display_params,
bounding_rect=cfg.bbox_defacing_MRI_review,
figsize=self.figsize)
def init_layout(self, views, num_rows_per_view,
num_slices_per_view, padding=cfg.default_padding):
self.views = views
self.num_slices_per_view = num_slices_per_view
self.num_rows_per_view = num_rows_per_view
self.num_rows = len(self.views) * self.num_rows_per_view
self.num_cols = int(
(len(self.views) * self.num_slices_per_view) / self.num_rows)
self.padding = padding