Merge branch 'dft'

Author: mih

COPYING

@@ -22,6 +22,7 @@ documentation is covered by the MIT license.
   Copyright (c) 2009-2011 Matthew Brett <[email protected]>
   Copyright (c) 2010-2011 Stephan Gerhard <[email protected]>
   Copyright (c) 2006-2010 Michael Hanke <[email protected]>
+  Copyright (c) 2011 Christian Haselgrove <[email protected]>
   Copyright (c) 2010-2011 Jarrod Millman <[email protected]>
 
   Permission is hereby granted, free of charge, to any person obtaining a copy

bin/dicomfs

@@ -0,0 +1,190 @@
+#!/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 fuse
+import nibabel.dft as dft
+
+uid = os.getuid()
+gid = os.getgid()
+encoding = locale.getdefaultlocale()[1]
+
+fuse.fuse_python_api = (0, 2)
+
+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):
+        fuse.Fuse.__init__(self, *args, **kwargs)
+        self.fhs = {}
+        return
+
+    def get_paths(self):
+        paths = {}
+        for study in dft.get_studies(self.dicom_path):
+            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 == '/':
+            print 'return root'
+            return wd
+        for part in path.lstrip('/').split('/'):
+            print path, part
+            if part not in wd:
+                return None
+            wd = wd[part]
+        print 'return'
+        return wd
+
+    def readdir(self, path, fh):
+        print 'readdir'
+        print path
+        matched_path = self.match_path(path)
+        if matched_path is None:
+            return -errno.ENOENT
+        print 'match', 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
+        matched_path = self.match_path(path)
+        print 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):
+        print 'open'
+        print 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):
+        print 'read'
+        print path
+        print size
+        print offset
+        print fh
+        return self.fhs[fh.fno][offset:offset+size]
+
+    def release(self, path, flags, fh):
+        print 'release'
+        print path
+        print 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)
+
+# eof

doc/source/installation.rst

@@ -74,6 +74,7 @@ Requirements
 *  NumPy_ 1.2 or greater
 *  SciPy_ (for full SPM-ANALYZE support)
 *  PyDICOM_ 0.9.5 or greater (for DICOM support)
+*  `Python Imaging Library`_ (for PNG conversion in DICOMFS)
 *  nose_ 0.11 or greater (to run the tests)
 *  sphinx_ (to build the documentation)
 

doc/source/links_names.txt

@@ -92,6 +92,7 @@
 .. _setuptools: http://pypi.python.org/pypi/setuptools
 .. _distribute: http://packages.python.org/distribute
 .. _datapkg: http://okfn.org/projects/datapkg
+.. _python imaging library: http://www.pythonware.com
 
 .. Python imaging projects
 .. _PyMVPA: http://www.pymvpa.org