Merge branch 'mnt/fsl_ents' into 'master'

Mnt/fsl ents

See merge request fsl/fslpy!73

.ci/setup_ssh.sh

@@ -31,9 +31,7 @@ if [[ -f /.dockerenv ]]; then
  echo "$SSH_PRIVATE_KEY_FSL_DOWNLOAD" > $HOME/.ssh/id_fsl_download;
 
  if [[ "$CI_PROJECT_PATH" == "$UPSTREAM_PROJECT" ]]; then
-   echo "$SSH_PRIVATE_KEY_DOC_DEPLOY"   > $HOME/.ssh/id_doc_deploy;
-   echo "$SSH_PRIVATE_KEY_CONDA_DEPLOY" > $HOME/.ssh/id_conda_deploy;
-   echo "$SSH_PRIVATE_KEY_CONDA_INDEX"  > $HOME/.ssh/id_conda_index;
+   echo "$SSH_PRIVATE_KEY_DOC_DEPLOY"  > $HOME/.ssh/id_doc_deploy;
  fi;
 
  chmod go-rwx $HOME/.ssh/id_*;
@@ -43,10 +41,11 @@ if [[ -f /.dockerenv ]]; then
 
  if [[ "$CI_PROJECT_PATH" == "$UPSTREAM_PROJECT" ]]; then
    ssh-add $HOME/.ssh/id_doc_deploy;
-   ssh-add $HOME/.ssh/id_conda_deploy;
  fi
 
- echo "$SSH_SERVER_HOSTKEYS" > $HOME/.ssh/known_hosts;
+ ssh-keyscan ${UPSTREAM_URL##*@} >> $HOME/.ssh/known_hosts;
+ ssh-keyscan ${DOC_HOST##*@}     >> $HOME/.ssh/known_hosts;
+ ssh-keyscan ${FSL_HOST##*@}     >> $HOME/.ssh/known_hosts;
 
  touch $HOME/.ssh/config;
 
@@ -59,16 +58,6 @@ if [[ -f /.dockerenv ]]; then
  echo "    User ${DOC_HOST%@*}"                     >> $HOME/.ssh/config;
  echo "    IdentityFile $HOME/.ssh/id_doc_deploy"   >> $HOME/.ssh/config;
 
- echo "Host condadeploy"                            >> $HOME/.ssh/config;
- echo "    HostName ${CONDA_HOST##*@}"              >> $HOME/.ssh/config;
- echo "    User ${CONDA_HOST%@*}"                   >> $HOME/.ssh/config;
- echo "    IdentityFile $HOME/.ssh/id_conda_deploy" >> $HOME/.ssh/config;
-
- echo "Host condaindex"                             >> $HOME/.ssh/config;
- echo "    HostName ${CONDA_HOST##*@}"              >> $HOME/.ssh/config;
- echo "    User ${CONDA_HOST%@*}"                   >> $HOME/.ssh/config;
- echo "    IdentityFile $HOME/.ssh/id_conda_index"  >> $HOME/.ssh/config;
-
  echo "Host fsldownload"                            >> $HOME/.ssh/config;
  echo "    HostName ${FSL_HOST##*@}"                >> $HOME/.ssh/config;
  echo "    User ${FSL_HOST%@*}"                     >> $HOME/.ssh/config;

CHANGELOG.rst

@@ -2,6 +2,26 @@ This document contains the ``fslpy`` release history in reverse chronological
 order.
 
 
+1.12.0 (Under development)
+--------------------------
+
+
+Changed
+^^^^^^^
+
+
+* The ``extract_noise`` script has been renamed to :mod:`.fsl_ents`.
+* Increased the minimum required version of ``dcm2niix`` in the
+  :mod:`fsl.data.dicom` module.
+
+
+Deprecated
+^^^^^^^^^^
+
+
+* The ``extract_noise`` script.
+
+
 1.11.1 (Friday September 14th 2018
 ----------------------------------
 

doc/fsl.scripts.fsl_ents.rst

+``fsl.scripts.fsl_ents``
+========================
+
+.. automodule:: fsl.scripts.fsl_ents
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.scripts.rst

@@ -5,6 +5,7 @@
    :hidden:
 
    fsl.scripts.atlasq
+   fsl.scripts.fsl_ents
    fsl.scripts.imcp
    fsl.scripts.imglob
    fsl.scripts.immv

fsl/data/dicom.py

@@ -44,6 +44,10 @@ import fsl.data.image    as fslimage
 log = logging.getLogger(__name__)
 
 
+MIN_DCM2NIIX_VERSION = (1, 0, 2017, 12, 15)
+"""Minimum version of dcm2niix that is required for this module to work. """
+
+
 class DicomImage(fslimage.Image):
     """The ``DicomImage`` is a volumetric :class:`.Image` with some associated
     DICOM metadata.
@@ -115,13 +119,12 @@ def enabled():
     """
 
     cmd            = 'dcm2niix -h'
-    minimumVersion = (1, 0, 2016, 9, 30)
-    versionPattern = re.compile('v'
-                                '(?P<major>[0-9]+)\.'
-                                '(?P<minor>[0-9]+)\.'
-                                '(?P<year>[0-9]{4})'
-                                '(?P<month>[0-9]{2})'
-                                '(?P<day>[0-9]{2})')
+    versionPattern = re.compile(r'v'
+                                r'(?P<major>[0-9]+)\.'
+                                r'(?P<minor>[0-9]+)\.'
+                                r'(?P<year>[0-9]{4})'
+                                r'(?P<month>[0-9]{2})'
+                                r'(?P<day>[0-9]{2})')
 
     try:
         output = sp.check_output(cmd.split()).decode()
@@ -145,7 +148,7 @@ def enabled():
             # make sure installed version
             # is equal to or newer than
             # minimum required version
-            for iv, mv in zip(installedVersion, minimumVersion):
+            for iv, mv in zip(installedVersion, MIN_DCM2NIIX_VERSION):
                 if   iv > mv: return True
                 elif iv < mv: return False
 
@@ -225,7 +228,7 @@ def loadSeries(series):
     dcmdir = series['DicomDir']
     snum   = series['SeriesNumber']
     desc   = series['SeriesDescription']
-    cmd    = 'dcm2niix -b n -f %s -z n -o . {}'.format(dcmdir)
+    cmd    = 'dcm2niix -b n -f %s -z n -o . -n {} {}'.format(snum, dcmdir)
 
     with tempdir.tempdir() as td:
 

fsl/data/dtifit.py

@@ -50,7 +50,7 @@ def getDTIFitDataPrefix(path):
     # Gather all of the existing file
     # prefixes into a dictionary of
     # prefix : [file list] mappings.
-    pattern  = '^(.*)_(?:V1|V2|V3|L1|L2|L3).*$'
+    pattern  = r'^(.*)_(?:V1|V2|V3|L1|L2|L3).*$'
     prefixes = {}
 
     for f in [f for flist in files for f in flist]:

fsl/scripts/extract_noise.py

+#!/usr/bin/env python
+#
+# extract_noise.py - Deprecated - replaced by fsl_ents.py
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+"""This module is deprecated - it has been replaced by :mod:`.fsl_ents`. """
+
+
+import sys
+
+
+if __name__ == '__main__':
+    print('extract_noise is deprecated and will be removed in fslpy 2.0. '
+          'Use fsl_ents instead.')
+    from fsl.scripts.fsl_ents import main
+    sys.exit(main())

fsl/version.py

@@ -130,7 +130,7 @@ def patchVersion(filename, newversion):
     with open(filename, 'rt') as f:
         lines = f.readlines()
 
-    pattern = re.compile('^__version__ *= *\'.*\' *$')
+    pattern = re.compile(r'^__version__ *= *\'.*\' *$')
 
     for i, line in enumerate(lines):
         if pattern.match(line):

tests/test_dicom.py

@@ -47,9 +47,13 @@ def test_enabled():
                         side_effect=Exception()):
             assert not fsldcm.enabled()
 
+
         # test presence of different versions
         tests = [(b'version v2.1.20191212', True),
-                 (b'version v1.0.20160930', True),
+                 (b'version v1.0.20171216', True),
+                 (b'version v1.0.20171215', True),
+                 (b'version v1.0.20171214', False),
+                 (b'version v1.0.20160930', False),
                  (b'version v1.0.20160929', False),
                  (b'version v0.0.00000000', False),
                  (b'version blurgh',        False)]
@@ -76,7 +80,7 @@ def test_scanDir():
             f.extractall()
 
         series = fsldcm.scanDir(td)
-        assert len(series) == 2
+        assert len(series) == 3
 
         for s in series:
             assert (s['PatientName'] == 'MCCARTHY_PAUL' or
@@ -104,13 +108,13 @@ def test_loadSeries():
 
             for img in imgs:
 
-                assert img.dicomDir           == td
-                assert img.shape              == expShape
-                assert img[:].shape           == expShape
-                assert img.get('PatientName') == 'MCCARTHY_PAUL' or \
-                       img.get('PatientName') == 'MCCARTHY_PAUL_2'
-                assert 'PatientName'                      in img.keys()
-                assert 'MCCARTHY_PAUL'                    in img.values() or \
-                       'MCCARTHY_PAUL_2'                  in img.values()
-                assert ('PatientName', 'MCCARTHY_PAUL')   in img.items() or \
-                       ('PatientName', 'MCCARTHY_PAUL_2') in img.items()
+                assert img.dicomDir               == td
+                assert img.shape                  == expShape
+                assert img[:].shape               == expShape
+                assert img.getMeta('PatientName') == 'MCCARTHY_PAUL' or \
+                       img.getMeta('PatientName') == 'MCCARTHY_PAUL_2'
+                assert 'PatientName'                      in img.metaKeys()
+                assert 'MCCARTHY_PAUL'                    in img.metaValues() or \
+                       'MCCARTHY_PAUL_2'                  in img.metaValues()
+                assert ('PatientName', 'MCCARTHY_PAUL')   in img.metaItems() or \
+                       ('PatientName', 'MCCARTHY_PAUL_2') in img.metaItems()