diff --git a/.ci/setup_ssh.sh b/.ci/setup_ssh.sh
index e42264cd3032439b52363e2448937c5e928240c4..40c0c5c1ef96d9633aac885f0ba0bba4c1168ca3 100644
--- a/.ci/setup_ssh.sh
+++ b/.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;
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 2dc4299e7cc1a14d6cdc9072eb88e6006e87ddf6..40b0b8b68c63059f829d6cced064835b21180f85 100644
--- a/CHANGELOG.rst
+++ b/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
----------------------------------
diff --git a/doc/fsl.scripts.fsl_ents.rst b/doc/fsl.scripts.fsl_ents.rst
new file mode 100644
index 0000000000000000000000000000000000000000..373fc83b1ba94e0a6a34a318a7fefc199ef9bb29
--- /dev/null
+++ b/doc/fsl.scripts.fsl_ents.rst
@@ -0,0 +1,7 @@
+``fsl.scripts.fsl_ents``
+========================
+
+.. automodule:: fsl.scripts.fsl_ents
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/fsl.scripts.rst b/doc/fsl.scripts.rst
index 91dff4d9f3a0fca1ccd848b1255e2c8e50fb608e..2d18375d7aba2f04189ed4347cdac76c94c5358d 100644
--- a/doc/fsl.scripts.rst
+++ b/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
diff --git a/fsl/data/dicom.py b/fsl/data/dicom.py
index 57e0a227da55527e36f3166a81379ee57fd9b72e..53b7edefe067583d0ea94aaddcc4024b5faa663e 100644
--- a/fsl/data/dicom.py
+++ b/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:
diff --git a/fsl/data/dtifit.py b/fsl/data/dtifit.py
index a2c36fb332661f4f030b8f0c907b6b08fdf8bf04..34948669865a86209fffb1d8851ba867f99f7d46 100644
--- a/fsl/data/dtifit.py
+++ b/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).*$'
prefixes = {}
for f in [f for flist in files for f in flist]:
diff --git a/fsl/scripts/extract_noise.py b/fsl/scripts/extract_noise.py
new file mode 100644
index 0000000000000000000000000000000000000000..68c10c605c2531f3630c6554c2e876e46ef15fd9
--- /dev/null
+++ b/fsl/scripts/extract_noise.py
@@ -0,0 +1,17 @@
+#!/usr/bin/env python
+#
+# extract_noise.py - Deprecated - replaced by fsl_ents.py
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+"""This module is deprecated - it has been replaced by :mod:`.fsl_ents`. """
+
+
+import sys
+
+
+if __name__ == '__main__':
+ print('extract_noise is deprecated and will be removed in fslpy 2.0. '
+ 'Use fsl_ents instead.')
+ from fsl.scripts.fsl_ents import main
+ sys.exit(main())
diff --git a/fsl/version.py b/fsl/version.py
index 095ab8c41912ec89d5527c4977ea7375a400c895..d9f53ecd2bb4ef133db868b24045842403ea1464 100644
--- a/fsl/version.py
+++ b/fsl/version.py
@@ -130,7 +130,7 @@ def patchVersion(filename, newversion):
with open(filename, 'rt') as f:
lines = f.readlines()
- pattern = re.compile('^__version__ *= *\'.*\' *$')
+ pattern = re.compile(r'^__version__ *= *\'.*\' *$')
for i, line in enumerate(lines):
if pattern.match(line):
diff --git a/tests/test_dicom.py b/tests/test_dicom.py
index 325a15b4a8cc94b172998e8712a4d87318a8b100..70b5117bc20019249f15cb6298b2ab45c95c222c 100644
--- a/tests/test_dicom.py
+++ b/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()