def cases_scans_lesions(mode, samplelist, thresholds=None):
"""Iterate (case_id, scan_id, lesions)."""
mode = ImageMode(mode)
path = dwi.paths.samplelist_path(mode, samplelist)
patients = dwi.files.read_patients_file(path)
dwi.patient.label_lesions(patients, thresholds=thresholds)
return ((p.num, s, p.lesions) for p in patients for s in p.scans)
def main():
mode = ImageMode('DWI-Mono-ADCm')
paths = dwi.paths.Paths(mode)
cases = read_cases()
cases = cases[:5]
it = product(cases, [1, 2], 'ab')
it = ((c, '{}{}'.format(r, s)) for c, r, s in it)
# for case, _scan1, _scan2 in it:
# scan = '{}{}'.format(_scan1, _scan2)
# get_image_stats(paths, case, scan)
it = (get_image_stats(paths, c, s) for c, s in it)
it = filter(None, it)
d = dict(headers='keys', tablefmt='tsv', floatfmt='1.5f', missingval='-')
s = tabulate(it, **d)
s = s.replace('\t', ', ')
print(s)
def main():
modes = ['DWI-Mono-ADCm', 'DWI-Kurt-ADCk', 'DWI-Kurt-K']
modes = [ImageMode(x) for x in modes]
samplelist = 'bothscansonly'
logging.basicConfig(level=LOGLEVEL)
process_all(modes, samplelist)
],
help='imaging modes')
p.add('-s', '--samplelist', default='all',
help='samplelist identifier')
p.add('-c', '--cases', nargs='+', type=int,
help='cases to include, if not all')
return p.parse_args()
def read_case(mode, case, scan, lesions):
"""Read case. Return raw DWI, pmap, pmask, lmasks, initial prostate slice
index.
"""
img = dwi.dataset.read_tmap(mode, case, scan)[:, :, :, 0]
img = dwi.util.normalize(img, mode)
rawmode = ImageMode('DWI-b2000')
raw = dwi.dataset.read_tmap(rawmode[0], case, scan,
params=[-1])[:, :, :, 0]
raw = dwi.util.normalize(raw, rawmode)
pmask = dwi.dataset.read_prostate_mask(mode, case, scan)
lmasks = [dwi.dataset.read_lesion_mask(mode, case, scan, x) for x in
lesions]
mbb = img.mbb()
img = img[mbb]
raw = raw[mbb]
pmask = pmask[mbb]
lmasks = [x[mbb] for x in lmasks]
prostate_slices = pmask.mbb(pad=(0, np.inf, np.inf))
img = img[prostate_slices]
# centroids = [int(round(dwi.util.centroid(x)[0])) for x in masks]
# centroid = int(round(dwi.util.centroid(mask)[0]))
logging.debug('Lesion centroids (total): %s (%s)', centroids, centroid)
logging.info('Mask shape: %s, centroid: %i, slice: %s', mask.shape,
centroid, slice_index)
if slice_index is None:
slice_index = centroid
mask = mask[slice_index]
return mask, slice_index
def read_lmask(mode, case, scan):
mode = ImageMode(mode)
paths = []
try:
for i in range(1, 4):
path = Path(
dwi.paths.mask_path(mode, 'lesion', case, scan, lesion=i))
if path.exists():
paths.append(path)
except IOError:
pass
masks = [dwi.files.read_mask(x) for x in paths]
# # Manually override slice index.
# slice_indices = {
# (64, '1a', 'T2w-std'): 7,
# (64, '1a', 'T2-fitted'): 5,
# centroids = [int(round(dwi.util.centroid(x)[0])) for x in masks]
# centroid = int(round(dwi.util.centroid(mask)[0]))
logging.debug('Lesion centroids (total): %s (%s)', centroids, centroid)
logging.info('Mask shape: %s, centroid: %i, slice: %s', mask.shape,
centroid, slice_index)
if slice_index is None:
slice_index = centroid
mask = mask[slice_index]
return mask, slice_index
def read_lmask(mode, case, scan):
mode = ImageMode(mode)
paths = []
try:
for i in range(1, 4):
paths.append(dwi.paths.mask_path(mode, 'lesion', case, scan, i))
except IOError:
pass
masks = [dwi.files.read_mask(x) for x in paths]
# Manually override slice index.
slice_indices = {
(64, '1a', 'T2w-std'): 7,
(64, '1a', 'T2-fitted'): 5,
}
slice_index = slice_indices.get((case, scan, str(mode)))