Commit 4f7f208c authored by Paul McCarthy's avatar Paul McCarthy 🚵
Browse files

RF: Modifications to dicom module to allow version-dependent behaviour. Not tested

parent e9c81ad6
......@@ -29,9 +29,12 @@ import os
import os.path as op
import subprocess as sp
import re
import sys
import glob
import json
import shlex
import logging
import binascii
import nibabel as nib
......@@ -44,7 +47,16 @@ log = logging.getLogger(__name__)
MIN_DCM2NIIX_VERSION = (1, 0, 2017, 12, 15)
"""Minimum version of dcm2niix that is required for this module to work. """
"""Minimum version of ``dcm2niix`` that is required for this module to work.
CRC_DCM2NIIX_VERSION = (1, 0, 2019, 09, 02)
"""For versions of ``dcm2niix`` orf this version or newer, the ``-n`` flag,
used to convert a single DICOM series, requires that a CRC checksum
identifying the series be passed (see the :func:`seriesCRC`
function). Versions prior to this require the series number to be passed.
class DicomImage(fslimage.Image):
......@@ -80,9 +92,16 @@ class DicomImage(fslimage.Image):
def enabled():
"""Returns ``True`` if ``dcm2niix`` is present, and recent enough,
``False`` otherwise.
def installedVersion(version):
"""Return a tuple describing the version of ``dcm2niix`` that is installed,
or ``None`` if dcm2niix cannot be found, or its version not parsed.
The returned tuple contains the following fields, all integers:
- Major version number
- Minor version number
- Year
- Month
- Day
cmd = 'dcm2niix -h'
......@@ -112,70 +131,115 @@ def enabled():
# make sure installed version
# is equal to or newer than
# minimum required version
for iv, mv in zip(installedVersion, MIN_DCM2NIIX_VERSION):
if iv > mv: return True
elif iv < mv: return False
# if we get here, versions are equal
return True
return installedVersion
except Exception as e:
log.debug('Error parsing dcm2niix version string: {}'.format(e))
return None
def compareVersions(v1, v2):
"""Compares two ``dcm2niix`` versions ``v1`` and ``v2``. The versions are
assumed to be in the format returned by :func:`installedVersion`.
return False
:returns: - 1 if ``v1`` is newer than ``v2``
- -1 if ``v1`` is older than ``v2``
- 0 if ``v1`` the same as ``v2``.
for iv1, iv2 in zip(v1, v2):
if iv1 > iv2: return 1
elif iv1 < iv2: return -1
return 0
def enabled():
"""Returns ``True`` if ``dcm2niix`` is present, and recent enough,
``False`` otherwise.
installed = installedVersion()
return installed is None or compareVersions(installed, required) < 0
def scanDir(dcmdir):
"""Uses ``dcm2niix`` to scans the given DICOM directory, and returns a
list of dictionaries, one for each data series that was identified.
Each dictionary is populated with some basic metadata about the series.
"""Uses the ``dcm2niix -b o`` option to generate a BIDS sidecar JSON
file for each series in the given DICOM directory. Reads them all in,
and returns them as a sequence of dicts.
:arg dcmdir: Directory containing DICOM files.
Some additional metadata is added to each dictionary:
- ``DicomDir``: The absolute path to ``dcmdir``
:returns: A list of dictionaries, each containing metadata about
one DICOM data series.
:arg dcmdir: Directory containing DICOM series
:returns: A list of dicts, each containing the BIDS sidecar JSON
metadata for one DICOM series.
if not enabled():
raise RuntimeError('dcm2niix is not available or is too old')
dcmdir = op.abspath(dcmdir)
cmd = 'dcm2niix -b o -ba n -f %s -o . {}'.format(dcmdir)
snumPattern = re.compile('^[0-9]+')
dcmdir = op.abspath(dcmdir)
cmd = 'dcm2niix -b o -ba n -f %s -o . "{}"'.format(dcmdir)
series = []
with tempdir.tempdir() as td:
with open(os.devnull, 'wb') as devnull:, stdout=devnull, stderr=devnull), stdout=devnull, stderr=devnull)
files = glob.glob(op.join(td, '*.json'))
if len(files) == 0:
return []
# sort numerically by series number if possible
def sortkey(f):
match = re.match(snumPattern, f)
snum = int(
return snum
files = sorted(files, key=sortkey)
except Exception:
files = sorted(files)
series = []
for fn in files:
with open(fn, 'rt') as f:
meta = json.load(f)
meta = json.load(f)
meta['DicomDir'] = dcmdir
return series
# sort by series number
def key(s):
return s.get('SeriesNumber', sys.maxsize)
series = list(sorted(series, key=key))
return series
def seriesCRC(series):
"""Calculate a checksum string of the given DICOM series.
The returned string is of the form::
Where ``SeriesCRC`` is an unsigned integer which is the CRC32
checksum of the ``SeriesInstanceUID``, and ``echonumber`` is
the ``EchoNumber`` of the series - this is only present for
multi-echo data, where the series is from the second or subsequent
:arg series: Dict containing BIDS metadata about a DICOM series,
as returned by :func:`scanDir`.
:returns: String containing a CRC32 checksum for the series.
uid = series.get('SeriesInstanceUID', None)
echo = series.get('EchoNumber', None)
if uid is None:
return None
crc32 = str(binascii.crc32(uid.encode()))
if echo is not None and echo > 1:
crc32 = '{}.{}'.format(crc32, echo)
return crc32
def loadSeries(series):
......@@ -195,12 +259,12 @@ def loadSeries(series):
dcmdir = series['DicomDir']
snum = series['SeriesNumber']
desc = series['SeriesDescription']
cmd = 'dcm2niix -b n -f %s -z n -o . -n {} {}'.format(snum, dcmdir)
cmd = 'dcm2niix -b n -f %s -z n -o . -n "{}" "{}"'.format(snum, dcmdir)
with tempdir.tempdir() as td:
with open(os.devnull, 'wb') as devnull:, stdout=devnull, stderr=devnull), stdout=devnull, stderr=devnull)
files = glob.glob(op.join(td, '{}*.nii'.format(snum)))
images = [nib.load(f, mmap=False) for f in files]
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