From 2777a1905ae7c472f5c6b14f3d4b228c8f320a6d Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Thu, 14 Dec 2017 11:16:59 +1030
Subject: [PATCH] Bugfix - dicom json file sorting was not taking into account
file names with non-numeric characters in prefix.
---
fsl/data/dicom.py | 19 +++++++++++++------
1 file changed, 13 insertions(+), 6 deletions(-)
diff --git a/fsl/data/dicom.py b/fsl/data/dicom.py
index 88d4f6023..9abee46b9 100644
--- a/fsl/data/dicom.py
+++ b/fsl/data/dicom.py
@@ -152,8 +152,9 @@ def scanDir(dcmdir):
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)
+ dcmdir = op.abspath(dcmdir)
+ cmd = 'dcm2niix -b o -ba n -f %s -o . {}'.format(dcmdir)
+ snumPattern = re.compile('^[0-9]+')
with tempdir.tempdir() as td:
@@ -165,11 +166,17 @@ def scanDir(dcmdir):
if len(files) == 0:
return []
- # sort numerically by series number
- def sortkey(f):
- return int(op.splitext(op.basename(f))[0])
+ # 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)
+ files = sorted(files, key=sortkey)
+
+ except Exception:
+ files = sorted(files)
series = []
for fn in files:
--
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