Merge pull request #615 from chrispycheng/master

RF: moving more cmdline things to the cmdline folder

Author: effigies

.gitignore

@@ -16,6 +16,7 @@
 .project
 .pydevproject
 *.py.orig
+.DS_Store
 
 # Not sure what the next one is for
 *.kpf

bin/nib-dicomfs

@@ -9,213 +9,7 @@
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 # 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 range(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
+from nibabel.cmdline.dicomfs import main
 
 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
+    main()

bin/nib-nifti-dx

@@ -8,32 +8,8 @@
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 ''' Print nifti diagnostics for header files '''
-from __future__ import division, print_function, absolute_import
-
-import sys
-
-from optparse import OptionParser
-
-import nibabel as nib
-
-
-def main():
-    """ Go go team """
-    parser = OptionParser(
-        usage="%s [FILE ...]\n\n" % sys.argv[0] + __doc__,
-        version="%prog " + nib.__version__)
-    (opts, files) = parser.parse_args()
-
-    for fname in files:
-        with nib.openers.ImageOpener(fname) as fobj:
-            hdr = fobj.read(nib.nifti1.header_dtype.itemsize)
-        result = nib.Nifti1Header.diagnose_binaryblock(hdr)
-        if len(result):
-            print('Picky header check output for "%s"\n' % fname)
-            print(result + '\n')
-        else:
-            print('Header for "%s" is clean' % fname)
 
+from nibabel.cmdline.nifti_dx import main
 
 if __name__ == '__main__':
     main()

bin/parrec2nii

@@ -2,7 +2,7 @@
 """PAR/REC to NIfTI converter
 """
 
-from nibabel.parrec2nii_cmd import main
+from nibabel.cmdline.parrec2nii import main
 
 
 if __name__ == '__main__':