def run(self, args, extra_args):
if args.items:
items = []
for path in args.items:
items.append(os.path.realpath(path))
data = SimpleDataInfo.from_paths(items)
else:
data = SimpleDataInfo.from_paths([os.getcwd()])
to_file = None
if args.to_file:
to_file = os.path.realpath(args.to_file)
config = None
if args.config:
filename = os.path.realpath(args.config)
if os.path.exists(filename):
with open(filename, 'r') as f:
config = f.read()
figure_options = {}
if to_file:
if args.width:
figure_options.update({'width': args.width})
if args.height:
figure_options.update({'height': args.height})
if args.dpi:
figure_options.update({'dpi': args.dpi})
view_maps(data,
config,
figure_options=figure_options,
save_filename=to_file)
else:
view_maps(data, config, show_maximized=args.maximize)
def check_registration():
map_configs = ''
maps = {}
particularly_bad_subjects = [
'mgh_1002', 'mgh_1004', 'mgh_1008', 'mgh_1009', 'mgh_1012', 'mgh_1013',
'mgh_1015', 'mgh_1017', 'mgh_1021', 'mgh_1022', 'mgh_1032'
]
for subject in os.listdir(output_pjoin()):
# for subject in particularly_bad_subjects:
point_map = mdt.load_nifti(
output_pjoin(subject,
'warped_BinghamNODDI_r1_w_in0.w')).get_data()
std_map = mdt.load_nifti(
output_pjoin(subject,
'warped_BinghamNODDI_r1_w_in0.w.std')).get_data()
maps[subject + '.std'] = std_map
maps[subject] = point_map
map_configs += '''
{0}:
scale: {{use_max: true, use_min: true, vmax: 0.8, vmin: 0.0}}
{0}.std:
scale: {{use_max: true, use_min: true, vmax: 0.1, vmin: 0.0}}
'''.format(subject)
config = '''
colorbar_settings:
location: right
nmr_ticks: 4
power_limits: [-3, 4]
round_precision: 3
visible: false
grid_layout:
- Rectangular
- cols: null
rows: 4
spacings: {bottom: 0.03, hspace: 0.15, left: 0.1, right: 0.86, top: 0.97, wspace: 0.4}
slice_index: 90
zoom:
p0: {x: 16, y: 14}
p1: {x: 161, y: 200}
colormap_masked_color: 'k'
'''
if map_configs:
config += '''
map_plot_options:
''' + map_configs + '''
'''
config += '''
maps_to_show: [''' + ', '.join(sorted(maps)) + ''']
'''
mdt.view_maps(maps, config=config)
def run(self, args):
if args.dir:
data = DataInfo.from_dir(os.path.realpath(args.dir))
else:
data = DataInfo.from_dir(os.getcwd())
to_file = None
if args.to_file:
to_file = os.path.realpath(args.to_file)
config = None
if args.config:
filename = os.path.realpath(args.config)
if os.path.exists(filename):
with open(filename, 'r') as f:
config = f.read()
view_maps(data, config, show_maximized=args.maximize, to_file=to_file)
def check_registration():
map_configs = ''
maps = {}
for subject in os.listdir(output_pjoin()):
fa_map = mdt.load_nifti(output_pjoin(subject, 'warped_Tensor_Tensor.FA')).get_data()
maps[subject] = fa_map
map_configs += '''
{}:
scale: {{use_max: true, use_min: true, vmax: 0.5, vmin: 0.0}}
'''.format(subject)
config = '''
colorbar_settings:
location: right
nmr_ticks: 4
power_limits: [-3, 4]
round_precision: 3
visible: false
grid_layout:
- Rectangular
- cols: null
rows: 4
spacings: {bottom: 0.03, hspace: 0.15, left: 0.1, right: 0.86, top: 0.97, wspace: 0.4}
slice_index: 90
zoom:
p0: {x: 16, y: 14}
p1: {x: 161, y: 200}
colormap_masked_color: 'k'
'''
config += '''
map_plot_options:
''' + map_configs + '''
maps_to_show: [''' + ', '.join(sorted(maps)) + ''']
'''
mdt.view_maps(maps, config=config)
def plot_maps(dataset_name, model_name, voxel_volume_ind, maps, out_name):
scales = {'point_vmin': 0,
'point_vmax': 1,
'std_vmin': 0,
'std_vmax': 0.04}
if model_name == 'Tensor':
scales['std_vmax'] = 0.15
maps['diff'] = np.abs(maps['mcmc'] - maps['mle'])
plot_config = dedent('''
font: {{family: sans-serif, size: 20}}
maps_to_show: [mle, mle_std, mcmc, mcmc_std]
map_plot_options:
mle:
title: FR (MLE)
scale: {{use_max: true, use_min: true, vmax: {point_vmax}, vmin: {point_vmin}}}
colorbar_settings: {{round_precision: 2}}
mle_std:
title: FR std. (MLE)
scale: {{use_max: true, use_min: true, vmax: {std_vmax}, vmin: {std_vmin}}}
colorbar_settings: {{round_precision: 3}}
mcmc:
title: FR (MCMC)
scale: {{use_max: true, use_min: true, vmax: {point_vmax}, vmin: {point_vmin}}}
colorbar_settings: {{round_precision: 2}}
mcmc_std:
title: FR std. (MCMC)
scale: {{use_max: true, use_min: true, vmax: {std_vmax}, vmin: {std_vmin}}}
colorbar_settings: {{round_precision: 3}}
'''.format(map_title=map_titles[model_name], **scales))
if dataset_name == 'mgh':
plot_config += '''
rotate: 270
zoom:
p0: {x: 19, y: 17}
p1: {x: 117, y: 128}
'''
else:
plot_config += dedent('''
annotations:
- arrow_width: 0.6
font_size: 14
marker_size: 3.0
text_distance: 0.05
text_location: top left
text_template: '{value:.3f}'
voxel_index: [''' + ', '.join(map(str, voxel_volume_ind)) + ''']
colorbar_settings:
location: right
nmr_ticks: 4
power_limits: [-3, 4]
round_precision: 2
visible: true
grid_layout:
- Rectangular
- cols: null
rows: null
spacings: {bottom: 0.03, hspace: 0.0, left: 0.1, right: 0.86, top: 0.97, wspace: 0.5}
zoom:
p0: {x: 19, y: 6}
p1: {x: 87, y: 97}
title_spacing: 0.03
''')
mdt.view_maps(
maps,
save_filename=out_name,
figure_options={'width': 520, 'dpi': 80},
config=plot_config)
mdt.view_maps(maps,
config='''
colorbar_settings:
location: right
nmr_ticks: 4
power_limits: [-3, 4]
round_precision: 3
visible: false
colormap_masked_color: k
font: {family: sans-serif, size: 21}
grid_layout:
- Rectangular
- cols: 2
rows: null
spacings: {bottom: 0.03, hspace: 0.1, left: 0.1, right: 0.86, top: 0.97, wspace: 0.1}
map_plot_options:
mgh_1005:
colorbar_settings: {location: bottom, nmr_ticks: 3, power_limits: null, round_precision: null,
visible: true}
scale: {use_max: true, use_min: true, vmax: 0.9, vmin: 0.1}
title: ' '
mgh_1005.std:
colorbar_settings: {location: bottom, nmr_ticks: 3, power_limits: null, round_precision: null,
visible: true}
clipping: {use_max: true, use_min: true, vmax: 0.045, vmin: 0.0}
scale: {use_max: true, use_min: true, vmax: 0.05, vmin: 0.0}
title: ' '
mgh_1016:
colorbar_settings: {location: bottom, nmr_ticks: 3, power_limits: null, round_precision: null,
visible: false}
scale: {use_max: true, use_min: true, vmax: 0.9, vmin: 0.1}
title: ' '
mgh_1016.std:
clipping: {use_max: true, use_min: true, vmax: 0.04, vmin: 0.0}
colorbar_settings: {location: bottom, nmr_ticks: 3, power_limits: null, round_precision: null,
visible: false}
scale: {use_max: true, use_min: true, vmax: 0.05, vmin: 0.0}
title: ' '
mgh_1017:
scale: {use_max: true, use_min: true, vmax: 0.9, vmin: 0.1}
title: Mean
mgh_1017.std:
clipping: {use_max: true, use_min: true, vmax: 0.045, vmin: 0.0}
scale: {use_max: true, use_min: true, vmax: 0.05, vmin: 0.0}
title: std.
maps_to_show: [mgh_1017, mgh_1017.std, mgh_1016, mgh_1016.std, mgh_1005, mgh_1005.std]
slice_index: 90
zoom:
p0: {x: 23, y: 25}
p1: {x: 155, y: 191}
''')
mdt.view_maps(
all_maps,
# save_filename='/tmp/uncertainty_paper/bingham_noddi.png',
config='''
annotations:
- arrow_width: 1.0
font_size: null
marker_size: 3.0
text_distance: 0.08
text_location: upper left
text_template: '{value:.2g}'
voxel_index: [60, 149, 90]
colorbar_settings:
location: right
nmr_ticks: 4
power_limits: [-3, 4]
round_precision: 3
visible: true
colormap: hot
colormap_masked_color: k
dimension: 2
flipud: false
font: {family: sans-serif, size: 21}
grid_layout:
- Rectangular
- cols: null
rows: 3
spacings: {bottom: 0.03, hspace: 0.23, left: 0.1, right: 0.86, top: 0.97, wspace: 0}
interpolation: bilinear
map_plot_options:
point_diff_BinghamNODDI_r1:
clipping: {use_max: false, use_min: false, vmax: 0.0, vmin: 0.0}
colorbar_label: null
colorbar_settings: {location: bottom, nmr_ticks: 3, power_limits: null, round_precision: null,
visible: null}
colormap: BrBG_r
colormap_masked_color: null
colormap_order: null
colormap_weight_map: null
interpret_as_colormap: false
mask_name: null
scale: {use_max: true, use_min: true, vmax: 10.0, vmin: -10.0}
show_title: null
title: '% difference mean'
title_spacing: null
regular_BinghamNODDI_r1_w_in0.w:
clipping: {use_max: false, use_min: false, vmax: 0.0, vmin: 0.0}
colorbar_label: null
colorbar_settings: {location: null, nmr_ticks: null, power_limits: null, round_precision: null,
visible: false}
colormap: null
colormap_masked_color: null
colormap_order: null
colormap_weight_map: null
interpret_as_colormap: false
mask_name: null
scale: {use_max: true, use_min: true, vmax: 0.8, vmin: 0.2}
show_title: null
title: Regular mean
title_spacing: null
regular_BinghamNODDI_r1_w_in0.w.std:
clipping: {use_max: false, use_min: false, vmax: 0.0, vmin: 0.0}
colorbar_label: null
colorbar_settings: {location: null, nmr_ticks: null, power_limits: null, round_precision: null,
visible: false}
colormap: null
colormap_masked_color: null
colormap_order: null
colormap_weight_map: null
interpret_as_colormap: false
mask_name: null
scale: {use_max: true, use_min: true, vmax: 0.15, vmin: 0.0}
show_title: null
title: Regular std.
title_spacing: null
std_diff_BinghamNODDI_r1:
clipping: {use_max: false, use_min: false, vmax: 0.0, vmin: 0.0}
colorbar_label: null
colorbar_settings: {location: bottom, nmr_ticks: 3, power_limits: null, round_precision: null,
visible: null}
colormap: BrBG_r
colormap_masked_color: null
colormap_order: null
colormap_weight_map: null
interpret_as_colormap: false
mask_name: null
scale: {use_max: true, use_min: true, vmax: 20.0, vmin: -20.0}
show_title: null
title: '% difference std.'
title_spacing: null
weighted_BinghamNODDI_r1_w_in0.w:
clipping: {use_max: false, use_min: false, vmax: 0.0, vmin: 0.0}
colorbar_label: null
colorbar_settings: {location: bottom, nmr_ticks: 3, power_limits: null, round_precision: null,
visible: null}
colormap: null
colormap_masked_color: null
colormap_order: null
colormap_weight_map: null
interpret_as_colormap: false
mask_name: null
scale: {use_max: true, use_min: true, vmax: 0.8, vmin: 0.2}
show_title: null
title: Weighted mean
title_spacing: null
weighted_BinghamNODDI_r1_w_in0.w.std:
clipping: {use_max: false, use_min: false, vmax: 0.0, vmin: 0.0}
colorbar_label: null
colorbar_settings: {location: bottom, nmr_ticks: 3, power_limits: null, round_precision: null,
visible: null}
colormap: null
colormap_masked_color: null
colormap_order: null
colormap_weight_map: null
interpret_as_colormap: false
mask_name: null
scale: {use_max: true, use_min: true, vmax: 0.15, vmin: 0.0}
show_title: null
title: Weighted std.
title_spacing: null
maps_to_show: [regular_BinghamNODDI_r1_w_in0.w, regular_BinghamNODDI_r1_w_in0.w.std,
weighted_BinghamNODDI_r1_w_in0.w, weighted_BinghamNODDI_r1_w_in0.w.std, point_diff_BinghamNODDI_r1,
std_diff_BinghamNODDI_r1]
mask_name: null
rotate: 90
show_axis: false
show_titles: true
slice_index: 90
title: null
title_spacing: null
volume_index: 0
zoom:
p0: {x: 22, y: 24}
p1: {x: 156, y: 192}
''')
mdt.view_maps(results['mgh'],
config='''
annotations: []
colorbar_settings: {location: null, nmr_ticks: 3, power_limits: null, round_precision: null,
visible: null}
colormap: hot
colormap_masked_color: null
dimension: 2
flipud: false
font: {family: sans-serif, size: 20}
grid_layout:
- Rectangular
- cols: null
rows: 2
spacings: {bottom: 0.03, hspace: 0.2, left: 0.01, right: 0.92, top: 0.94, wspace: 0.5}
interpolation: bilinear
map_plot_options:
BallStick_r1:
clipping: {use_max: false, use_min: false, vmax: 0.0, vmin: 0.0}
colorbar_label: null
colorbar_settings: {location: null, nmr_ticks: null, power_limits: null, round_precision: null,
visible: false}
colormap: null
colormap_masked_color: null
colormap_order: null
colormap_weight_map: null
interpret_as_colormap: false
mask_name: null
scale: {use_max: true, use_min: true, vmax: 0.03, vmin: 0.0}
show_title: null
title: 'BallStick_in1 -
Stick0.w (std.)'
title_spacing: null
BallStick_r2:
clipping: {use_max: false, use_min: false, vmax: 0.0, vmin: 0.0}
colorbar_label: null
colorbar_settings: {location: null, nmr_ticks: null, power_limits: null, round_precision: null,
visible: false}
colormap: null
colormap_masked_color: null
colormap_order: null
colormap_weight_map: null
interpret_as_colormap: false
mask_name: null
scale: {use_max: true, use_min: true, vmax: 0.03, vmin: 0.0}
show_title: null
title: 'BallStick_in2 -
Stick0.w (std.)'
title_spacing: null
BallStick_r3:
clipping: {use_max: true, use_min: true, vmax: 0.028, vmin: 0.0}
colorbar_label: null
colorbar_settings:
location: null
nmr_ticks: null
power_limits: [-2, 5]
round_precision: null
visible: null
colormap: null
colormap_masked_color: null
colormap_order: null
colormap_weight_map: null
interpret_as_colormap: false
mask_name: null
scale: {use_max: true, use_min: true, vmax: 0.03, vmin: 0.0}
show_title: null
title: 'BallStick_in3 -
Stick0.w (std.)'
title_spacing: null
BinghamNODDI_r1:
clipping: {use_max: false, use_min: false, vmax: 0.0, vmin: 0.0}
colorbar_label: null
colorbar_settings:
location: null
nmr_ticks: null
power_limits: [-2, 5]
round_precision: null
visible: null
colormap: null
colormap_masked_color: null
colormap_order: null
colormap_weight_map: null
interpret_as_colormap: false
mask_name: null
scale: {use_max: true, use_min: true, vmax: 0.04, vmin: 0.0}
show_title: null
title: 'Bingham-NODDI -
FR (std.)'
title_spacing: null
CHARMED_r1:
clipping: {use_max: false, use_min: false, vmax: 0.0, vmin: 0.0}
colorbar_label: null
colorbar_settings:
location: null
nmr_ticks: null
power_limits: [-2, 5]
round_precision: null
visible: null
colormap: null
colormap_masked_color: null
colormap_order: null
colormap_weight_map: null
interpret_as_colormap: false
mask_name: null
scale: {use_max: true, use_min: true, vmax: 0.04, vmin: 0.0}
show_title: null
title: 'CHARMED_in1 -
FR (std.)'
title_spacing: null
NODDI:
clipping: {use_max: false, use_min: false, vmax: 0.0, vmin: 0.0}
colorbar_label: null
colorbar_settings: {location: null, nmr_ticks: null, power_limits: null, round_precision: null,
visible: false}
colormap: null
colormap_masked_color: null
colormap_order: null
colormap_weight_map: null
interpret_as_colormap: false
mask_name: null
scale: {use_max: true, use_min: true, vmax: 0.04, vmin: 0.0}
show_title: null
title: 'NODDI
(FR)'
title_spacing: null
Tensor:
clipping: {use_max: false, use_min: false, vmax: 0.0, vmin: 0.0}
colorbar_label: null
colorbar_settings: {location: null, nmr_ticks: null, power_limits: null, round_precision: null,
visible: null}
colormap: null
colormap_masked_color: null
colormap_order: null
colormap_weight_map: null
interpret_as_colormap: false
mask_name: null
scale: {use_max: true, use_min: true, vmax: 0.12, vmin: 0.0}
show_title: null
title: 'Tensor -
FA (std.)'
title_spacing: null
inverse_snr:
clipping: {use_max: false, use_min: false, vmax: 0.0, vmin: 0.0}
colorbar_label: null
colorbar_settings: {location: null, nmr_ticks: null, power_limits: null, round_precision: null,
visible: null}
colormap: null
colormap_masked_color: null
colormap_order: null
colormap_weight_map: null
interpret_as_colormap: false
mask_name: null
scale: {use_max: true, use_min: true, vmax: 0.15, vmin: 0.0}
show_title: null
title: 1 / SNR
title_spacing: null
snr:
clipping: {use_max: false, use_min: false, vmax: 0.0, vmin: 0.0}
colorbar_label: null
colorbar_settings: {location: null, nmr_ticks: null, power_limits: null, round_precision: null,
visible: null}
colormap: null
colormap_masked_color: null
colormap_order: null
colormap_weight_map: null
interpret_as_colormap: false
mask_name: null
scale: {use_max: true, use_min: true, vmax: 30.0, vmin: 0.0}
show_title: null
title: SNR
title_spacing: null
maps_to_show: [snr, BallStick_r1, BallStick_r2, BallStick_r3, inverse_snr, BinghamNODDI_r1,
CHARMED_r1, Tensor]
mask_name: null
rotate: 270
show_axis: false
show_titles: true
slice_index: 0
title: null
title_spacing: 0.03
volume_index: 0
zoom:
p0: {x: 19, y: 17}
p1: {x: 117, y: 128}
''')