def read_hdf5(filename, ondisk=False, dsetname=DEFAULT_DSETNAME):
"""Read an array with attributes from an HDF5 file.
With parameter "ondisk" True it will not be read into memory."""
try:
f = h5py.File(filename, 'r')
# On missing file, h5py raises OSError without errno (or filename).
except OSError as e:
if not Path(filename).exists():
raise FileNotFoundError(2, 'No such file or directory', filename)
e.filename = e.filename or filename
raise
except IOError as e:
e.filename = e.filename or filename
raise
if dsetname not in f:
# No dataset of given name, try the one there is.
try:
dsetname, = f.keys()
except ValueError:
raise ValueError('Ambiguous content: {}'.format(filename))
dset = f[dsetname]
if ondisk:
array = dset
else:
array = np.array(dset)
attrs = read_attrs(dset)
if not ondisk:
f.close()
return array, attrs
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,
# }
# slice_index = slice_indices.get((case, scan, str(mode)))
slice_index = None
lmask, img_slice = get_lesion_mask(masks, slice_index=slice_index)
return lmask, img_slice, [x[img_slice] for x in masks]
def main():
"""Main."""
args = parse_args()
logging.basicConfig()
# logging.basicConfig(level=logging.INFO)
# thresholds = None
# thresholds = ('3+3', '3+4')
thresholds = ('3+3', )
blacklist = [] # + [21, 22, 27, 42, 74, 79]
# whitelist = [] # + [23, 24, 26, 29, 64]
whitelist = [26, 42, 64]
for i, line in enumerate(dwi.files.valid_lines(args.featlist)):
words = line.split()
mode = words[0]
texture_spec = TextureSpec(*words[1:])
it = cases_scans_lesions(mode, args.samplelist, thresholds=thresholds)
for c, s, l in it:
if blacklist and c in blacklist:
continue
if whitelist and c not in whitelist:
continue
# if 0 not in (x.label for x in l):
# continue # Exclude if there's no first score group present.
print(i, mode, texture_spec, c, s, l)
try:
images, _ = read(mode, c, s, texture_spec)
except IOError as e:
logging.error(e)
continue
labelnames = ['low', 'high']
lesions = ', '.join(
'{} {} {}'.format(x.score, x.location, labelnames[x.label])
for x in l)
d = dict(m=mode,
c=c,
s=s,
l=lesions,
tw=texture_spec.winsize,
tm=texture_spec.method,
tf=texture_spec.feature,
suffix='png')
title = '{c}-{s} ({l})\n{m} {tm}({tf})-{tw}'.format(**d)
path = '{c:03}-{s}_{m}_{tm}({tf})-{tw}.{suffix}'.format(**d)
plot(images, title, Path(args.outdir, path))
import argparse
# import logging
import dwi.autoroi
import dwi.dataset
import dwi.mask
import dwi.patient
import dwi.util
from dwi.types import AlgParams, Path
# import matplotlib
import matplotlib.pyplot as plt
import numpy as np
DEFAULT_OUT_IMAGE_DIR = Path('find_roi_images')
DEFAULT_OUT_MASK_DIR = Path('masks_auto')
def parse_args():
"""Parse command-line arguments."""
p = argparse.ArgumentParser(description=__doc__)
p.add_argument('-v', '--verbose', action='count',
help='increase verbosity')
p.add_argument('--patients', type=Path,
help='patients file')
p.add_argument('--pmapdir', type=Path,
help='input parametric map directory')
p.add_argument('--subregiondir', type=Path,
help='subregion bounding box directory')
p.add_argument('--prostatemaskdir', type=Path,
#!/usr/bin/python3
"""List lesion statistics."""
from collections import OrderedDict
from itertools import product
import dwi.dataset
import dwi.image
from dwi.types import ImageMode, Path
import numpy as np
from tabulate import tabulate
BASE = Path('/mri')
LIST = 'misc/list/all.txt'
def read_cases():
return sorted(int(x) for x in (BASE / LIST).read_text().split())
def read_lmasks(paths, case, scan):
for les in [1, 2, 3]:
try:
yield dwi.image.Image.read_mask(
paths.mask('lesion', case, scan, les))
except OSError:
yield None
def get_image_stats(paths, case, scan):
try:
# logging.info(masks[-1][1])
# logging.info(len(parse_mask(masks[-1][1])))
for i, m in enumerate(masks, 1):
number, mask = m
logging.info('Mask: %i, $i', number, len(mask))
mask = parse_mask(mask)
try:
mask.shape = shape + (1,)
except ValueError as e:
logging.error('%s: %s', e, path)
continue
assert mask.ndim == 4, mask.shape
outname = '{p}.{i:02d}-{n}.{f}'.format(p=path.name, i=i, n=number,
f=fmt)
outpath = outdir / outname
attrs = {}
print('Writing mask shape {}: {}'.format(mask.shape, outpath))
dwi.files.ensure_dir(outpath)
dwi.files.write_pmap(outpath, mask, attrs)
if __name__ == '__main__':
# Arguments: input file; output directory; shape (eg 20,224,224).
logging.basicConfig(level=logging.INFO)
path, outdir, shape = sys.argv[1:]
logging.info(path, outdir, shape, sys.argv[1:])
path = Path(path)
shape = tuple(int(x) for x in shape.split(','))
outdir = Path(outdir)
main(path, shape, outdir)