/usr/bin/nib-dicomfs is in python-nibabel 1.2.2-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 | #!/usr/bin/python
# emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
#
# See COPYING file distributed along with the NiBabel package for the
# copyright and license terms.
#
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
# Copyright (C) 2011 Christian Haselgrove
import sys
import os
import stat
import errno
import time
import locale
import logging
import fuse
import nibabel as nib
import nibabel.dft as dft
from optparse import OptionParser, Option
uid = os.getuid()
gid = os.getgid()
encoding = locale.getdefaultlocale()[1]
fuse.fuse_python_api = (0, 2)
logger = logging.getLogger('nibabel.dft')
class FileHandle:
def __init__(self, fno):
self.fno = fno
self.keep_cache = False
self.direct_io = False
return
def __str__(self):
return 'FileHandle(%d)' % self.fno
class DICOMFS(fuse.Fuse):
def __init__(self, *args, **kwargs):
self.followlinks = kwargs.pop('followlinks', False)
fuse.Fuse.__init__(self, *args, **kwargs)
self.fhs = {}
return
def get_paths(self):
paths = {}
for study in dft.get_studies(self.dicom_path, self.followlinks):
pd = paths.setdefault(study.patient_name_or_uid(), {})
patient_info = 'patient information\n'
patient_info = 'name: %s\n' % study.patient_name
patient_info += 'ID: %s\n' % study.patient_id
patient_info += 'birth date: %s\n' % study.patient_birth_date
patient_info += 'sex: %s\n' % study.patient_sex
pd['INFO'] = patient_info.encode('ascii', 'replace')
study_datetime = '%s_%s' % (study.date, study.time)
study_info = 'study info\n'
study_info += 'UID: %s\n' % study.uid
study_info += 'date: %s\n' % study.date
study_info += 'time: %s\n' % study.time
study_info += 'comments: %s\n' % study.comments
d = {'INFO': study_info.encode('ascii', 'replace')}
for series in study.series:
series_info = 'series info\n'
series_info += 'UID: %s\n' % series.uid
series_info += 'number: %s\n' % series.number
series_info += 'description: %s\n' % series.description
series_info += 'rows: %d\n' % series.rows
series_info += 'columns: %d\n' % series.columns
series_info += 'bits allocated: %d\n' % series.bits_allocated
series_info += 'bits stored: %d\n' % series.bits_stored
series_info += 'storage instances: %d\n' % len(series.storage_instances)
d[series.number] = {'INFO': series_info.encode('ascii', 'replace'),
'%s.nii' % series.number: (series.nifti_size, series.as_nifti),
'%s.png' % series.number: (series.png_size, series.as_png)}
pd[study_datetime] = d
return paths
def match_path(self, path):
wd = self.get_paths()
if path == '/':
logger.debug('return root')
return wd
for part in path.lstrip('/').split('/'):
logger.debug("path:%s part:%s" % (path, part))
if part not in wd:
return None
wd = wd[part]
logger.debug('return')
return wd
def readdir(self, path, fh):
logger.info('readdir %s' % (path,))
matched_path = self.match_path(path)
if matched_path is None:
return -errno.ENOENT
logger.debug('matched %s' % (matched_path,))
fnames = [ k.encode('ascii', 'replace') for k in matched_path.keys() ]
fnames.append('.')
fnames.append('..')
return [ fuse.Direntry(f) for f in fnames ]
def getattr(self, path):
logger.debug('getattr %s' % path)
matched_path = self.match_path(path)
logger.debug('matched: %s' % (matched_path,))
now = time.time()
st = fuse.Stat()
if isinstance(matched_path, dict):
st.st_mode = stat.S_IFDIR | 0755
st.st_ctime = now
st.st_mtime = now
st.st_atime = now
st.st_uid = uid
st.st_gid = gid
st.st_nlink = len(matched_path)
return st
if isinstance(matched_path, str):
st.st_mode = stat.S_IFREG | 0644
st.st_ctime = now
st.st_mtime = now
st.st_atime = now
st.st_uid = uid
st.st_gid = gid
st.st_size = len(matched_path)
st.st_nlink = 1
return st
if isinstance(matched_path, tuple):
st.st_mode = stat.S_IFREG | 0644
st.st_ctime = now
st.st_mtime = now
st.st_atime = now
st.st_uid = uid
st.st_gid = gid
st.st_size = matched_path[0]()
st.st_nlink = 1
return st
return -errno.ENOENT
def open(self, path, flags):
logger.debug('open %s' % (path,))
matched_path = self.match_path(path)
if matched_path is None:
return -errno.ENOENT
for i in xrange(1, 10):
if i not in self.fhs:
if isinstance(matched_path, str):
self.fhs[i] = matched_path
elif isinstance(matched_path, tuple):
self.fhs[i] = matched_path[1]()
else:
raise -errno.EFTYPE
return FileHandle(i)
raise -errno.ENFILE
# not done
def read(self, path, size, offset, fh):
logger.debug('read')
logger.debug(path)
logger.debug(size)
logger.debug(offset)
logger.debug(fh)
return self.fhs[fh.fno][offset:offset+size]
def release(self, path, flags, fh):
logger.debug('release')
logger.debug(path)
logger.debug(fh)
del self.fhs[fh.fno]
return
def get_opt_parser():
# use module docstring for help output
p = OptionParser(
usage="%s [OPTIONS] <DIRECTORY CONTAINING DICOMSs> <mount point>"
% os.path.basename(sys.argv[0]),
version="%prog " + nib.__version__)
p.add_options([
Option("-v", "--verbose", action="count",
dest="verbose", default=0,
help="make noise. Could be specified multiple times"),
])
p.add_options([
Option("-L", "--follow-links", action="store_true",
dest="followlinks", default=False,
help="Follow symbolic links in DICOM directory"),
])
return p
if __name__ == '__main__':
parser = get_opt_parser()
(opts, files) = parser.parse_args()
if opts.verbose:
logger.addHandler(logging.StreamHandler(sys.stdout))
logger.setLevel(opts.verbose > 1 and logging.DEBUG or logging.INFO)
if len(files) != 2:
sys.stderr.write("Please provide two arguments:\n%s\n" % parser.usage)
sys.exit(1)
fs = DICOMFS(dash_s_do='setsingle', followlinks=opts.followlinks)
fs.parse(['-f', '-s', files[1]])
fs.dicom_path = files[0].decode(encoding)
try:
fs.main()
except fuse.FuseError:
# fuse prints the error message
sys.exit(1)
sys.exit(0)
# eof
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