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def open_figure(self):
"""Creates the master figure to show everything in."""
self.figsize = cfg.default_review_figsize
plt.style.use('dark_background')
self.fig, self.axes = plt.subplots(self.num_rows, self.num_cols,
figsize=self.figsize)
self.axes = self.axes.flatten()
self.fig.canvas.set_window_title('VisualQC Alignment : {} {} {} '
''.format(self.in_dir, self.image1_name, self.image2_name))
# vmin/vmax are controlled, because we rescale all to [0, 1]
self.display_params = dict(interpolation='none', aspect='equal', origin='lower',
cmap=self.current_cmap, vmin=0.0, vmax=1.0)
# turning off axes, creating image objects
self.h_images = [None] * len(self.axes)
empty_image = np.full((10, 10, 3), 0.0)
for ix, ax in enumerate(self.axes):
def open_figure(self):
"""Creates the master figure to show everything in."""
# number of stats to be overlaid on top of carpet plot
self.num_stats = 3
self.figsize = cfg.default_review_figsize
# empty/dummy data for placeholding
empty_image = np.full((200, 200), 0.0)
empty_vec = np.full((200, 1), 0.0)
time_points = list(range(200))
# overlay order -- larger appears on top of smaller
self.layer_order_carpet = 1
self.layer_order_stats = 2
self.layer_order_zoomedin = 3
self.layer_order_to_hide = -1
self.total_num_layers = 3
plt.style.use('dark_background')
# 1. main carpet, in the background
def open_figure(self):
"""Creates the master figure to show everything in."""
# number of stats to be overlaid on top of carpet plot
self.num_stats = 3
self.figsize = cfg.default_review_figsize
# empty/dummy data for placeholding
empty_image = np.full((200, 200), 0.0)
label_x, label_y = (5, 5) # x, y in image data space
empty_vec = np.full((200, 1), 0.0)
gradients = list(range(200))
# overlay order -- larger appears on top of smaller
self.layer_order_carpet = 1
self.layer_order_stats = 2
self.layer_order_zoomedin = 3
self.layer_order_to_hide = -1
self.total_num_layers = 3
plt.style.use('dark_background')
def open_figure(self):
"""Creates the master figure to show everything in."""
self.figsize = cfg.default_review_figsize
plt.style.use('dark_background')
self.fig, self.axes = plt.subplots(self.num_rows, self.num_cols,
figsize=self.figsize)
self.axes = self.axes.flatten()
self.fig.canvas.set_window_title('VisualQC Quantitative MR : {} '
''.format(self.in_dir))
# vmin/vmax are controlled, because we rescale all to [0, 1]
self.display_params = dict(interpolation='none', aspect='equal',
origin='lower', cmap=self.current_cmap,
vmin=0.0, vmax=1.0)
# turning off axes, creating image objects
self.h_images = [None] * len(self.axes)
self.h_slice_numbers = [None] * len(self.axes)
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))
self.padding = padding
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)
self.fig = self.collage.fig
self.fig.canvas.set_window_title('VisualQC defacing : {} {} '
''.format(self.in_dir,
self.defaced_name))
self.padding = padding
def open_figure(self):
"""Creates the master figure to show everything in."""
self.figsize = cfg.default_review_figsize
plt.style.use('dark_background')
self.fig, self.axes = plt.subplots(self.num_rows_total, self.num_cols_final,
figsize=self.figsize)
self.axes = self.axes.flatten()
self.fig.canvas.set_window_title('VisualQC {} {} : {}'
' '.format(self.vis_type, self.seg_name, self.in_dir))
self.display_params_mri = dict(interpolation='none', aspect='equal',
origin='lower',
alpha=self.alpha_mri)
self.display_params_seg = dict(interpolation='none', aspect='equal',
origin='lower',
alpha=self.alpha_seg)
normalize_mri = colors.Normalize(vmin=cfg.min_cmap_range_t1_mri,
vmax=cfg.max_cmap_range_t1_mri, clip=True)