From d74b3d88c593f3ce29aeade3f529dfda6a11ec24 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 8 Dec 2017 16:45:09 +1030
Subject: [PATCH] Fleshed out wrappers around pydicom/dcmstack. But I think
I've just decided to use dcm2niix instead as it is orders of magnitude
faster.
---
fsl/data/dicom.py | 146 +++++++++++++++++++++++++++++++++++++++++++++-
1 file changed, 145 insertions(+), 1 deletion(-)
diff --git a/fsl/data/dicom.py b/fsl/data/dicom.py
index 8fe27c4f9..8fb388e6e 100644
--- a/fsl/data/dicom.py
+++ b/fsl/data/dicom.py
@@ -4,5 +4,149 @@
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
+"""This module provides the :class:`.DicomImage` class, which represents a
+volumetric DICOM data series. The ``DicomImage`` is simply an :class:`.`Image`
+which provides accessors for additional DICOM meta data.
-# TODO make dcmstack do all the work
+The following other functions are provided in this module, which are thin
+wrappers around functionality provided by ``pydicom`` and ``dcmstack``:
+
+.. autosummary::
+ :nosignatures:
+
+ scanDir
+ stack
+"""
+
+
+import os
+import fnmatch
+
+import pydicom as dicom
+
+from . import dcmstack
+
+from . import image as fslimage
+
+
+class DicomImage(fslimage.Image):
+ """The ``DicomImage`` is a volumetric :class:`.Image` with associated
+ DICOM metadata.
+
+ The ``Image`` class is used to manage the data and the voxel-to-world
+ transformation. Additional DICOM metadata may be accessed via TODO
+ """
+
+ def __init__(self, image, meta):
+ """Create a ``DicomImage``.
+ """
+ fslimage.Image.__init__(self, image)
+
+
+def scanDir(dcmdir, filePattern='*.dcm', callback=None):
+ """Recursively scans the given DICOM directory, and returns a dictionary
+ which contains all of the data series that were found.
+
+ :arg dcmdir: Directory containing DICOM files.
+
+ :arg filePattern: Glob-like pattern with which to identify DICOM files.
+ Defaults to ``'*.dcm'``.
+
+ :arg callback: Function which will get called every time a file is
+ loaded, and can be used for e.g. updating progress.
+ Must accept three positional parameters:
+ - ``path``: Path
+ - ``n``: Index of current path
+ - ``ttl``: Total number of paths
+
+ After all files have been loaded, this function is called
+ once more before the files are grouped into data series.
+ For this final call, ``path is None``, and ``n == ttl``.
+
+ :returns: A list containing one element for each identified data
+ series. Each element itself is a list with one element
+ for each file, where each element is a tuple containing
+ the ``pydicom.dataset.FileDataset``, and a ``dict``
+ containing some basic metadata extracted from the file.
+
+ .. see:: ``dcmstack.parse_and_group`` and ``pydicom.dicomio.dcmread``.
+ """
+
+ def default_callback(path, n, ttl):
+ pass
+
+ if callback is None:
+ callback = default_callback
+
+ # Find all the DICOM files in the directory.
+ # If/when we drop python < 3.5, we can use:
+ #
+ # glob.glob(op.join(dcmdir, '**', filePattern), recursive=True)
+ dcmfiles = []
+ for root, dirnames, filenames in os.walk(dcmdir):
+ for filename in fnmatch.filter(filenames, filePattern):
+ dcmfiles.append(os.path.join(root, filename))
+
+ # No files found
+ if len(dcmfiles) == 0:
+ return {}
+
+ # Tell pydicom to only load the tags that
+ # are necessary to group files into series,
+ # and to give us basic metadata.
+ tags = [
+ 'SeriesInstanceUID',
+ 'SeriesNumber',
+ 'SeriesDescription',
+ 'ProtocolName',
+ 'ImageOrientationPatient',
+ 'Rows',
+ 'Columns',
+ 'PixelSpacing']
+
+ # Load the files one by one
+ dcms = []
+ for i, path in enumerate(dcmfiles):
+ callback(path, i, len(dcmfiles))
+ dcms.append(dicom.dcmread(path, defer_size=64, specific_tags=tags))
+
+ callback(None, len(dcmfiles), len(dcmfiles))
+
+ # Group the files into data series
+ series = dcmstack.parse_and_group(dcms)
+
+ # parse_and_group returns a dict, with
+ # one entry for each data series, where
+ # each entry is a list containing
+ # (pydicom file, metadata, filepath)
+ #
+ # We don't care about the dict keys,
+ series = list(series.values())
+
+ return series
+
+
+def stack(series, callback=None):
+ """Takes a DICOM data series, as returned by :func:`scanDir`, and converts
+ it to a ``dcmstack.DicomStack``.
+
+ :arg series:
+
+ :arg callback:
+
+ :returns:
+ """
+
+ def default_callback(path, n, ttl):
+ pass
+
+ if callback is None:
+ callback = default_callback
+
+ ds = dcmstack.DicomStack()
+
+ for i, (_, meta, filename) in enumerate(series):
+ callback(filename, i, len(series))
+ ds.add_dcm(dicom.dcmread(filename), meta)
+
+ return ds
--
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