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[WIP] Add overlays to tissues masks #63

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[WIP] Add overlays to tissues masks #63

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a1e02b3
Add blending possibility to mask screenshotting (tissues + tracking m…
AlexVCaron Sep 13, 2023
064ce73
Add arg
AlexVCaron Sep 14, 2023
11e1d80
add gif to from_screenshots
AlexVCaron Oct 24, 2023
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2 changes: 1 addition & 1 deletion scripts/dmriqc_from_screenshot.py
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Original file line number Diff line number Diff line change
Expand Up @@ -63,7 +63,7 @@ def main():
screenshot_files = []
stats_files = []

for ext in ["png","jpeg","jpg"]:
for ext in ["png","jpeg","jpg","gif"]:
screenshot_files = screenshot_files + sorted(glob.glob(folder + '/*' + ext))
if args.stats:
stats_files = sorted(glob.glob(folder + '/*.csv'))
Expand Down
47 changes: 35 additions & 12 deletions scripts/dmriqc_tissues.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,8 @@
assert_inputs_exist, assert_outputs_exist,
list_files_from_paths)
from dmriqcpy.viz.graph import graph_mask_volume
from dmriqcpy.viz.screenshot import screenshot_mosaic_wrapper
from dmriqcpy.viz.screenshot import (screenshot_mosaic_wrapper,
screenshot_mosaic_blend)
from dmriqcpy.viz.utils import analyse_qa, dataframe_to_html


Expand All @@ -41,6 +42,9 @@ def _build_arg_parser():
p.add_argument('--csf', nargs='+', required=True,
help='CSF mask in Nifti format')

p.add_argument('--background', nargs='+',
help='Background image in Nifti format.')

p.add_argument('--skip', default=2, type=int,
help='Number of images skipped to build the '
'mosaic. [%(default)s]')
Expand All @@ -57,13 +61,23 @@ def _build_arg_parser():
return p


def _subj_parralel(subj_metric, summary, name, skip, nb_columns):
def _subj_parralel(subj_metric, summary, name, skip, nb_columns, bg=None):
subjects_dict = {}
curr_key = os.path.basename(subj_metric).split('.')[0]
screenshot_path = screenshot_mosaic_wrapper(subj_metric,
output_prefix=name,
directory="data", skip=skip,
nb_columns=nb_columns)

if bg is None:
screenshot_path = screenshot_mosaic_wrapper(subj_metric,
output_prefix=name,
directory="data", skip=skip,
nb_columns=nb_columns)
else:
screenshot_path = screenshot_mosaic_blend(bg, subj_metric,
output_prefix=name,
directory="data",
blend_val=0.3,
skip=skip,
nb_columns=nb_columns,
is_mask=True)

summary_html = dataframe_to_html(summary.loc[curr_key].to_frame())
subjects_dict[curr_key] = {}
Expand All @@ -84,6 +98,14 @@ def main():
parser.error("Not the same number of images in input.")

all_images = np.concatenate([wm, gm, csf])

background = []
if args.background is not None and len(args.background) > 0:
background = list_files_from_paths(args.background)
if not len(wm) == len(background):
parser.error("Not the same number of images in input.")
all_images = np.concatenate([all_images, background])

assert_inputs_exist(parser, all_images)
assert_outputs_exist(parser, args, [args.output_report, "data", "libs"])

Expand All @@ -94,14 +116,14 @@ def main():
if os.path.exists("libs"):
shutil.rmtree("libs")

metrics_names = [[wm, 'WM mask'],
[gm, 'GM mask'],
[csf, 'CSF mask']]
metrics_names = [[background, wm, 'WM mask'],
[background, gm, 'GM mask'],
[background, csf, 'CSF mask']]
metrics_dict = {}
summary_dict = {}
graphs = []
warning_dict = {}
for metrics, name in metrics_names:
for bg, metrics, name in metrics_names:
columns = ["{} volume".format(name)]
summary, stats = stats_mask_volume(columns, metrics)

Expand All @@ -119,11 +141,12 @@ def main():
subjects_dict = {}
pool = Pool(args.nb_threads)
subjects_dict_pool = pool.starmap(_subj_parralel,
zip(metrics,
itertools.zip_longest(metrics,
itertools.repeat(summary),
itertools.repeat(name),
itertools.repeat(args.skip),
itertools.repeat(args.nb_columns)))
itertools.repeat(args.nb_columns),
bg))
pool.close()
pool.join()

Expand Down
51 changes: 37 additions & 14 deletions scripts/dmriqc_tracking_maps.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,8 @@
assert_inputs_exist, assert_outputs_exist,
list_files_from_paths)
from dmriqcpy.viz.graph import graph_mask_volume
from dmriqcpy.viz.screenshot import screenshot_mosaic_wrapper
from dmriqcpy.viz.screenshot import (screenshot_mosaic_wrapper,
screenshot_mosaic_blend)
from dmriqcpy.viz.utils import analyse_qa, dataframe_to_html


Expand Down Expand Up @@ -47,6 +48,9 @@ def _build_arg_parser():
p.add_argument('--map_exclude', nargs='+',
help='Folder or list of map exlude in Nifti format')

p.add_argument('--background', nargs='+',
help='Folder or list of background images in Nifti format')

p.add_argument('--skip', default=2, type=int,
help='Number of images skipped to build the '
'mosaic. [%(default)s]')
Expand All @@ -63,13 +67,23 @@ def _build_arg_parser():
return p


def _subj_parralel(subj_metric, summary, name, skip, nb_columns):
def _subj_parralel(subj_metric, summary, name, skip, nb_columns, bg=None):
subjects_dict = {}
curr_key = os.path.basename(subj_metric).split('.')[0]
screenshot_path = screenshot_mosaic_wrapper(subj_metric,
output_prefix=name,
directory="data", skip=skip,
nb_columns=nb_columns)

if bg is None:
screenshot_path = screenshot_mosaic_wrapper(subj_metric,
output_prefix=name,
directory="data", skip=skip,
nb_columns=nb_columns)
else:
screenshot_path = screenshot_mosaic_blend(bg, subj_metric,
output_prefix=name,
directory="data",
blend_val=0.3,
skip=skip,
nb_columns=nb_columns,
is_mask=True)

summary_html = dataframe_to_html(summary.loc[curr_key].to_frame())
subjects_dict[curr_key] = {}
Expand Down Expand Up @@ -98,6 +112,13 @@ def main():
all_images = np.concatenate([seeding_mask, map_include,
map_exclude])

background = []
if args.background is not None and len(args.background) > 0:
background = list_files_from_paths(args.background)
if not len(seeding_mask) == len(background):
parser.error("Not the same number of images in input.")
all_images = np.concatenate([all_images, background])

assert_inputs_exist(parser, all_images)
assert_outputs_exist(parser, args, [args.output_report, "data", "libs"])

Expand All @@ -109,17 +130,17 @@ def main():
shutil.rmtree("libs")

if args.tracking_type == "local":
metrics_names = [[seeding_mask, 'Seeding mask'],
[tracking_mask, 'Tracking mask']]
metrics_names = [[background, seeding_mask, 'Seeding mask'],
[background, tracking_mask, 'Tracking mask']]
else:
metrics_names = [[seeding_mask, 'Seeding mask'],
[map_include, 'Map include'],
[map_exclude, 'Maps exclude']]
metrics_names = [[background, seeding_mask, 'Seeding mask'],
[background, map_include, 'Map include'],
[background, map_exclude, 'Maps exclude']]
metrics_dict = {}
summary_dict = {}
graphs = []
warning_dict = {}
for metrics, name in metrics_names:
for bg, metrics, name in metrics_names:
columns = ["{} volume".format(name)]
summary, stats = stats_mask_volume(columns, metrics)

Expand All @@ -137,11 +158,13 @@ def main():
subjects_dict = {}
pool = Pool(args.nb_threads)
subjects_dict_pool = pool.starmap(_subj_parralel,
zip(metrics,
itertools.zip_longest(
metrics,
itertools.repeat(summary),
itertools.repeat(name),
itertools.repeat(args.skip),
itertools.repeat(args.nb_columns)))
itertools.repeat(args.nb_columns),
bg))
pool.close()
pool.join()

Expand Down