From 4f7f208cf8bd75ee15660f28ef1a91add9a9dd31 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Wed, 4 Sep 2019 20:03:31 +0100
Subject: [PATCH] RF: Modifications to dicom module to allow version-dependent
behaviour. Not tested
---
fsl/data/dicom.py | 146 +++++++++++++++++++++++++++++++++-------------
1 file changed, 105 insertions(+), 41 deletions(-)
diff --git a/fsl/data/dicom.py b/fsl/data/dicom.py
index f7c9a97c7..0d85a4e99 100644
--- a/fsl/data/dicom.py
+++ b/fsl/data/dicom.py
@@ -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):
@memoize.memoize
-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():
int(match.group('month')),
int(match.group('day')))
- # 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
+
+
+@memoize.memoize
+def enabled():
+ """Returns ``True`` if ``dcm2niix`` is present, and recent enough,
+ ``False`` otherwise.
+ """
+ installed = installedVersion()
+ required = MIN_DCM2NIIX_VERSION
+ 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:
- sp.call(cmd.split(), stdout=devnull, stderr=devnull)
+ sp.call(shlex.split(cmd), stdout=devnull, stderr=devnull)
files = glob.glob(op.join(td, '*.json'))
if len(files) == 0:
return []
- # sort numerically by series number if possible
- try:
- def sortkey(f):
- match = re.match(snumPattern, f)
- snum = int(match.group(0))
- 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
series.append(meta)
- 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::
+
+ SeriesCRC[.echonumber]
+
+ 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
+ echos.
+
+ :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:
- sp.call(cmd.split(), stdout=devnull, stderr=devnull)
+ sp.call(shlex.split(cmd), 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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