Merge pull request #129 from matthew-brett/optional-dicomfs-followlinks

RF: followlinks optional for dicom file system

followlinks keyword argument to os.walk was causing an error in python
2.5. Maybe it should be optional anyway.

Author: matthew-brett

bin/nib-dicomfs

@@ -44,13 +44,14 @@ class FileHandle:
 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):
+        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
@@ -187,6 +188,11 @@ def get_opt_parser():
                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__':
@@ -201,7 +207,7 @@ if __name__ == '__main__':
         sys.stderr.write("Please provide two arguments:\n%s\n"  % parser.usage)
         sys.exit(1)
 
-    fs = DICOMFS(dash_s_do='setsingle')
+    fs = DICOMFS(dash_s_do='setsingle', followlinks=opts.followlinks)
     fs.parse(['-f', '-s', files[1]])
     fs.dicom_path = files[0].decode(encoding)
     try:

nibabel/dft.py

@@ -259,9 +259,11 @@ def __exit__(self, type, value, traceback):
             DB.rollback()
         return
 
-def _get_subdirs(base_dir, files_dict=None):
+def _get_subdirs(base_dir, files_dict=None, followlinks=False):
     dirs = []
-    for (dirpath, dirnames, filenames) in os.walk(base_dir, followlinks=True):
+    # followlinks keyword not available for python 2.5.
+    kwargs = {} if not followlinks else {'followlinks': True}
+    for (dirpath, dirnames, filenames) in os.walk(base_dir, **kwargs):
         abs_dir = os.path.realpath(dirpath)
         if abs_dir in dirs:
             raise CachingError, 'link cycle detected under %s' % base_dir
@@ -270,10 +272,10 @@ def _get_subdirs(base_dir, files_dict=None):
             files_dict[abs_dir] = filenames
     return dirs
 
-def update_cache(base_dir):
+def update_cache(base_dir, followlinks=False):
     mtimes = {}
     files_by_dir = {}
-    dirs = _get_subdirs(base_dir, files_by_dir)
+    dirs = _get_subdirs(base_dir, files_by_dir, followlinks)
     for d in dirs:
         os.stat(d)
         mtimes[d] = os.stat(d).st_mtime
@@ -300,9 +302,9 @@ def update_cache(base_dir):
                 c.execute(query, (dir, mtimes[dir]))
     return
 
-def get_studies(base_dir=None):
+def get_studies(base_dir=None, followlinks=False):
     if base_dir is not None:
-        update_cache(base_dir)
+        update_cache(base_dir, followlinks)
     if base_dir is None:
         with _db_nochange() as c:
             c.execute("SELECT * FROM study")
@@ -321,7 +323,7 @@ def get_studies(base_dir=None):
                                               WHERE directory = ?))"""
     with _db_nochange() as c:
         study_uids = {}
-        for dir in _get_subdirs(base_dir):
+        for dir in _get_subdirs(base_dir, followlinks=followlinks):
             c.execute(query, (dir, ))
             for row in c:
                 study_uids[row[0]] = None

tools/dicomfs.wsgi

@@ -10,17 +10,29 @@
 
 import sys
 import traceback
+from functools import partial
 import urllib
 import cgi
+
 import jinja2
+
 from nibabel import dft
 
+# this is the directory containing the DICOM data, or None for all cached data
+BASE_DIR = '/path/to/DICOM'
+BASE_DIR = None
+
+# default setting for whether to follow symlinks in BASE_DIR. Python 2.5 only
+# accepts False for this setting, Python >= 2.6 accepts True or False
+FOLLOWLINKS=False
+
+# Define routine to get studies
+studies_getter = partial(dft.get_studies, followlinks=FOLLOWLINKS)
+
+
 def html_unicode(u):
     return cgi.escape(u.encode('utf-8'))
 
-# this is the directory containing the DICOM data, or None for all cached data
-base_dir = '/path/to/DICOM'
-base_dir = None
 
 template_env = jinja2.Environment(autoescape=True)
 template_env.filters['urlquote'] = urllib.quote
@@ -161,13 +173,13 @@ def study_cmp(a, b):
 
 def index(environ):
     patients = {}
-    for s in dft.get_studies(base_dir):
+    for s in studies_getter(BASE_DIR):
         patients.setdefault(s.patient_name_or_uid(), []).append(s)
     template = template_env.from_string(index_template)
     return template.render(patients=patients).encode('utf-8')
 
 def patient(patient):
-    studies = [ s for s in dft.get_studies() if s.patient_name_or_uid() == patient ]
+    studies = [ s for s in studies_getter() if s.patient_name_or_uid() == patient ]
     if len(studies) == 0:
         raise HandlerError('404 Not Found', 'patient %s not found\n' % patient)
     studies.sort(study_cmp)
@@ -176,7 +188,7 @@ def patient(patient):
 
 def patient_date_time(patient, date_time):
     study = None
-    for s in dft.get_studies():
+    for s in studies_getter():
         if s.patient_name_or_uid() != patient:
             continue
         if date_time != '%s_%s' % (s.date, s.time):
@@ -190,7 +202,7 @@ def patient_date_time(patient, date_time):
 
 def nifti(patient, date_time, scan):
     study = None
-    for s in dft.get_studies():
+    for s in studies_getter():
         if s.patient_name_or_uid() != patient:
             continue
         if date_time != '%s_%s' % (s.date, s.time):
@@ -211,7 +223,7 @@ def nifti(patient, date_time, scan):
 
 def png(patient, date_time, scan):
     study = None
-    for s in dft.get_studies():
+    for s in studies_getter():
         if s.patient_name_or_uid() != patient:
             continue
         if date_time != '%s_%s' % (s.date, s.time):