Merge branch 'main-master' into maint/1.2.x

* main-master:
  BF: use smaller float type for rounding error test
  RF: followlinks optional for dicom file system
  RF+TST: make big_bad_ulp less likely to / 0 error
  RF: rename orientation_affine to inv_ornt_aff
  RF+DOC: remove unused _ornt_affine function
  BF: fix nasty bug for orientations and 0 columns
  BF: add missing scripts to setup.py
  RF: refactor, rename nifti diagnostic script
  RF: use map instead of list comprehensions
  DOC: point to nipy organization's nibabel instead of the original Michael's for issues and changes
  BF: make compatible with pydicom 0.9.7
  RF: add informative message when check-files is OK
  DOC: add/expand docstrings, move code for testers
  RF: refactor installation checks to check scripts
  RF: move dicomfs script to nib- naming convention
  TEST: make travis test with latest pydicom
  ENH: use logging in dicomfs + optparse to provide control over logging etc
  ENH: use Python's logging (nibabel.dft level) instead of print statements
  DOC: add pypirc note for uploading release
  MISC: start next development series 1.3.x

Conflicts:
	nibabel/info.py

Author: matthew-brett

.travis.yml

@@ -17,9 +17,18 @@ before_install:
     - popd
 # command to install dependencies, e.g. pip install -r requirements.txt --use-mirrors
 install:
+    # This has to be on a single "virtual line" because of how Travis
+    # munges each line before executing it to print out the exit status.
+    # It's okay for it to be on multiple physical lines, so long as you remember:
+    # - There can't be any leading "-"s
+    # - All newlines will be removed, so use ";"s
+    - if [ "${TRAVIS_PYTHON_VERSION:0:1}" \< "3" ]; then
+        easy_install -U pydicom;
+        fi
     - python setup.py install
 # command to run tests, e.g. python setup.py test
 script:
     # Change into an innocuous directory and find tests from installation
-    - cd doc
+    - mkdir for_testing
+    - cd for_testing
     - nosetests `python -c "import os; import nibabel; print(os.path.dirname(nibabel.__file__))"`

Changelog

@@ -11,11 +11,11 @@ releases for both packages.
 
 'Close gh-' statements refer to GitHub issues that are available at::
 
-  http://github.com/hanke/nibabel/issues
+  http://github.com/nipy/nibabel/issues
 
 The full VCS changelog is available here:
 
-  http://github.com/hanke/nibabel/commits/master
+  http://github.com/nipy/nibabel/commits/master
 
 Releases
 ~~~~~~~~

Makefile

@@ -229,6 +229,9 @@ bdist_rpm:
 bdist_mpkg:
 	$(PYTHON) tools/mpkg_wrapper.py setup.py install
 
+# Check for files not installed
+check-files:
+	$(PYTHON) -c 'from nisext.testers import check_files; check_files("nibabel")'
 
 # Print out info for possible install methods
 check-version-info:

bin/dicomfs renamed to bin/nib-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):
@@ -38,13 +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
@@ -78,33 +85,31 @@ 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 +142,9 @@ 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 +161,61 @@ 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"),
+        ])
+
+    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

bin/nib-nifti-dx

@@ -0,0 +1,39 @@
+#!/usr/bin/env 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.
+#
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+''' Print nifti diagnostics for header files '''
+
+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:
+        fobj = nib.volumeutils.allopen(fname)
+        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
+            print
+        else:
+            print 'Header for "%s" is clean' % fname
+
+
+if __name__ == '__main__':
+    main()

bin/nifti1_diagnose.py

@@ -96,11 +96,20 @@ Release checklist
     {'sys_version': '2.6.6 (r266:84374, Aug 31 2010, 11:00:51) \n[GCC 4.0.1 (Apple Inc. build 5493)]', 'commit_source': 'archive substitution', 'np_version': '1.5.0', 'commit_hash': '25b4125', 'pkg_path': '/var/folders/jg/jgfZ12ZXHwGSFKD85xLpLk+++TI/-Tmp-/tmpGPiD3E/pylib/nibabel', 'sys_executable': '/Library/Frameworks/Python.framework/Versions/2.6/Resources/Python.app/Contents/MacOS/Python', 'sys_platform': 'darwin'}
     /var/folders/jg/jgfZ12ZXHwGSFKD85xLpLk+++TI/-Tmp-/tmpGPiD3E/pylib/nibabel/__init__.pyc
     {'sys_version': '2.6.6 (r266:84374, Aug 31 2010, 11:00:51) \n[GCC 4.0.1 (Apple Inc. build 5493)]', 'commit_source': 'installation', 'np_version': '1.5.0', 'commit_hash': '25b4125', 'pkg_path': '/var/folders/jg/jgfZ12ZXHwGSFKD85xLpLk+++TI/-Tmp-/tmpGPiD3E/pylib/nibabel', 'sys_executable': '/Library/Frameworks/Python.framework/Versions/2.6/Resources/Python.app/Contents/MacOS/Python', 'sys_platform': 'darwin'}
-    Files not taken across by the installation:
-    []
     /Users/mb312/dev_trees/nibabel/nibabel/__init__.pyc
     {'sys_version': '2.6.6 (r266:84374, Aug 31 2010, 11:00:51) \n[GCC 4.0.1 (Apple Inc. build 5493)]', 'commit_source': 'repository', 'np_version': '1.5.0', 'commit_hash': '25b4125', 'pkg_path': '/Users/mb312/dev_trees/nibabel/nibabel', 'sys_executable': '/Library/Frameworks/Python.framework/Versions/2.6/Resources/Python.app/Contents/MacOS/Python', 'sys_platform': 'darwin'}
 
+* Check the ``setup.py`` file is picking up all the library code and scripts,
+  with::
+
+    make check-files
+
+  Look for output at the end about missed files, such as::
+
+    Missed script files:  /Users/mb312/dev_trees/nibabel/bin/nib-dicomfs, /Users/mb312/dev_trees/nibabel/bin/nifti1_diagnose.py
+
+  Fix ``setup.py`` to carry across any files that should be in the distribution.
+
 * You probably have virtualenvs for different python versions.  Check the tests
   pass for different configurations.  If you have pytox_ and a network
   connnection, and lots of pythons installed, you might be able to do::
@@ -163,8 +172,23 @@ Release checklist
 
     make source-release
 
-* Once everything looks good, upload the source release to PyPi.  See
-  `setuptools intro`_::
+* Once everything looks good, you are ready to upload the source release to
+  PyPi.  See `setuptools intro`_.  Make sure you have a file ``\$HOME/.pypirc``,
+  of form::
+
+    [distutils]
+    index-servers =
+        pypi
+
+    [pypi]
+    username:your.pypi.username
+    password:your-password
+
+    [server-login]
+    username:your.pypi.username
+    password:your-password
+
+* When ready::
 
     python setup.py register
     python setup.py sdist --formats=gztar,zip upload