From 18bb892c7de8776d82ddc7fb99b227ac675e2e96 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Sun, 10 Dec 2017 13:20:42 +1030
Subject: [PATCH] Little adjustments
---
fsl/data/dicom.py | 23 ++++++++++++++---------
1 file changed, 14 insertions(+), 9 deletions(-)
diff --git a/fsl/data/dicom.py b/fsl/data/dicom.py
index fe3795fe8..8f9e6d742 100644
--- a/fsl/data/dicom.py
+++ b/fsl/data/dicom.py
@@ -15,7 +15,7 @@ wrappers around functionality provided by Chris Rorden's ``dcm2niix`` program:
:nosignatures:
scanDir
- loadNifti
+ loadSeries
.. note:: These functions will not work if an executable called ``dcm2niix``
cannot be found.
@@ -29,6 +29,8 @@ import subprocess as sp
import glob
import json
+import nibabel as nib
+
import fsl.utils.tempdir as tempdir
import fsl.data.image as fslimage
@@ -41,13 +43,13 @@ class DicomImage(fslimage.Image):
transformation. Additional DICOM metadata may be accessed via TODO
"""
- def __init__(self, image, meta):
+ def __init__(self, image, meta, *args, **kwargs):
"""Create a ``DicomImage``.
:arg image: Passed through to :meth:`.Image.__init__`.
:arg meta: Dictionary containing DICOM meta-data.
"""
- fslimage.Image.__init__(self, image)
+ fslimage.Image.__init__(self, image, *args, **kwargs)
self.__meta = meta
@@ -94,7 +96,7 @@ def scanDir(dcmdir):
with tempdir.tempdir() as td:
- sp.call(cmd.split())
+ sp.call(cmd.split(), stdout=sp.DEVNULL, stderr=sp.DEVNULL)
files = glob.glob(op.join(td, '*.json'))
@@ -117,7 +119,7 @@ def scanDir(dcmdir):
return series
-def loadNifti(series):
+def loadSeries(series):
"""Takes a DICOM series meta data dictionary, as returned by
:func:`scanDir`, and loads the associated data as one or more NIFTI
images.
@@ -130,11 +132,14 @@ def loadNifti(series):
dcmdir = series['DicomDir']
snum = series['SeriesNumber']
- cmd = 'dcm2niix -b n -f %s -z n -o n {}'.format(dcmdir)
+ desc = series['SeriesDescription']
+ cmd = 'dcm2niix -b n -f %s -z n -o . {}'.format(dcmdir)
with tempdir.tempdir() as td:
- sp.call(cmd.split())
- files = glob.glob(op.join(td, '{}.nii'.format(snum)))
+ sp.call(cmd.split(), stdout=sp.DEVNULL, stderr=sp.DEVNULL)
+
+ files = glob.glob(op.join(td, '{}.nii'.format(snum)))
+ images = [nib.load(f, mmap=False) for f in files]
- return [DicomImage(f, series) for f in files]
+ return [DicomImage(i, series, name=desc) for i in images]
--
GitLab