Merge pull request #119 from yarikoptic/_enh/dft_use_logging

dicomfs: control its verbosity from cmdline (silent by default) + use python's logging

otherwise it bombards user with lots of information he doesn't need (ideally it also should fall into background unless -f (not yet present) or any -v provided)

Author: matthew-brett

bin/dicomfs

@@ -15,15 +15,21 @@ 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):
@@ -78,33 +84,31 @@ class DICOMFS(fuse.Fuse):
     def match_path(self, path):
         wd = self.get_paths()
         if path == '/':
-            print 'return root'
+            logger.debug('return root')
             return wd
         for part in path.lstrip('/').split('/'):
-            print path, part
+            logger.debug("path:%s part:%s" % (path, part))
             if part not in wd:
                 return None
             wd = wd[part]
-        print 'return'
+        logger.debug('return')
         return wd
 
     def readdir(self, path, fh):
-        print 'readdir'
-        print path
+        logger.info('readdir %s' % (path,))
         matched_path = self.match_path(path)
         if matched_path is None:
             return -errno.ENOENT
-        print 'match', matched_path
+        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):
-        print 'getattr'
-        print 'path:', path
+        logger.debug('getattr %s' % path)
         matched_path = self.match_path(path)
-        print matched_path
+        logger.debug('matched: %s' % (matched_path,))
         now = time.time()
         st = fuse.Stat()
         if isinstance(matched_path, dict):
@@ -137,10 +141,9 @@ class DICOMFS(fuse.Fuse):
             st.st_nlink = 1
             return st
         return -errno.ENOENT
-    
+
     def open(self, path, flags):
-        print 'open'
-        print path
+        logger.debug('open %s' % (path,))
         matched_path = self.match_path(path)
         if matched_path is None:
             return -errno.ENOENT
@@ -157,34 +160,56 @@ class DICOMFS(fuse.Fuse):
 
     # not done
     def read(self, path, size, offset, fh):
-        print 'read'
-        print path
-        print size
-        print offset
-        print 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):
-        print 'release'
-        print path
-        print fh
+        logger.debug('release')
+        logger.debug(path)
+        logger.debug(fh)
         del self.fhs[fh.fno]
         return
-    
-progname = os.path.basename(sys.argv[0])
-if len(sys.argv) != 3:
-    sys.stderr.write('usage: %s <directory containing DICOMs> <mount point>\n' % progname)
-    sys.exit(1)
-
-fs = DICOMFS(dash_s_do='setsingle')
-fs.parse(['-f', '-s', sys.argv[2]])
-fs.dicom_path = sys.argv[1].decode(encoding)
-try:
-    fs.main()
-except fuse.FuseError:
-    # fuse prints the error message
-    sys.exit(1)
-
-sys.exit(0)
+
+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"),
+        ])
+
+    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')
+    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

nibabel/dft.py

@@ -14,6 +14,7 @@
 from os.path import join as pjoin
 import tempfile
 import getpass
+import logging
 import warnings
 import sqlite3
 
@@ -27,6 +28,7 @@
 from .optpkg import optional_package
 dicom, have_dicom, _ = optional_package('dicom')
 
+logger = logging.getLogger('nibabel.dft')
 
 class DFTError(Exception):
     "base class for DFT exceptions"
@@ -153,7 +155,7 @@ def as_nifti(self):
         for (i, si) in enumerate(self.storage_instances):
             if i + 1 != si.instance_number:
                 raise InstanceStackError(self, i, si)
-            print 'reading %d/%d' % (i+1, len(self.storage_instances))
+            logger.info('reading %d/%d' % (i+1, len(self.storage_instances)))
             d = self.storage_instances[i].dicom()
             data[i, :, :] = d.pixel_array
 
@@ -288,7 +290,7 @@ def update_cache(base_dir):
         for dir in sorted(mtimes.keys()):
             if dir in db_mtimes and mtimes[dir] <= db_mtimes[dir]:
                 continue
-            print 'updating %s' % dir
+            logger.debug('updating %s' % dir)
             _update_dir(c, dir, files_by_dir[dir], studies, series, storage_instances)
             if dir in db_mtimes:
                 query = "UPDATE directory SET mtime = ? WHERE path = ?"
@@ -332,20 +334,20 @@ def get_studies(base_dir=None):
     return studies
 
 def _update_dir(c, dir, files, studies, series, storage_instances):
-    print dir
+    logger.debug('Updating directory %s' % dir)
     c.execute("SELECT name, mtime FROM file WHERE directory = ?", (dir, ))
     db_mtimes = dict(c)
     for fname in db_mtimes:
         if fname not in files:
-            print '    remove %s' % fname
+            logger.debug('    remove %s' % fname)
             c.execute("DELETE FROM file WHERE directory = ? AND name = ?", 
                       (dir, fname))
     for fname in files:
         mtime = os.lstat('%s/%s' % (dir, fname)).st_mtime
         if fname in db_mtimes and mtime <= db_mtimes[fname]:
-            print '    okay %s' % fname
+            logger.debug('    okay %s' % fname)
         else:
-            print '    update %s' % fname
+            logger.debug('    update %s' % fname)
             si_uid = _update_file(c, dir, fname, studies, series, storage_instances)
             if fname not in db_mtimes:
                 query = """INSERT INTO file (directory, 
@@ -365,14 +367,14 @@ def _update_file(c, path, fname, studies, series, storage_instances):
     try:
         do = dicom.read_file('%s/%s' % (path, fname))
     except dicom.filereader.InvalidDicomError:
-        print '        not a DICOM file'
+        logger.debug('        not a DICOM file')
         return None
     try:
         study_comments = do.StudyComments
     except AttributeError:
         study_comments = ''
     try:
-        print '        storage instance %s' % str(do.SOPInstanceUID)
+        logger.debug('        storage instance %s' % str(do.SOPInstanceUID))
         if str(do.StudyInstanceUID) not in studies:
             query = """INSERT INTO study (uid, 
                                           date, 
@@ -420,7 +422,7 @@ def _update_file(c, path, fname, studies, series, storage_instances):
             c.execute(query, params)
             storage_instances.append(str(do.SOPInstanceUID))
     except AttributeError, data:
-        print '        %s' % str(data)
+        logger.debug('        %s' % str(data))
         return None
     return str(do.SOPInstanceUID)
 
@@ -468,13 +470,13 @@ def clear_cache():
 def _init_db(verbose=True):
     """ Initialize database """
     if verbose:
-        print 'db filename: ' + DB_FNAME
+        logger.info('db filename: ' + DB_FNAME)
     global DB
     DB = sqlite3.connect(DB_FNAME, check_same_thread=False)
     with _db_change() as c:
         c.execute("SELECT COUNT(*) FROM sqlite_master WHERE type = 'table'")
         if c.fetchone()[0] == 0:
-            print 'create'
+            logger.debug('create')
             for q in CREATE_QUERIES:
                 c.execute(q)