diff --git a/fsl/data/dicom.py b/fsl/data/dicom.py
index 8c8b8a7e73cd5f9e1375409edd04835f21b69a95..f09383dcc8f4e0bb203fb748b9ebf15811ce4021 100644
--- a/fsl/data/dicom.py
+++ b/fsl/data/dicom.py
@@ -32,6 +32,7 @@ import re
import glob
import json
import logging
+import deprecation
import nibabel as nib
@@ -48,44 +49,63 @@ class DicomImage(fslimage.Image):
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
+ transformation. Additional DICOM metadata may be accessed via the
+ :class:`.Image` metadata access methods.
"""
- def __init__(self, image, meta, *args, **kwargs):
+
+ def __init__(self, image, metadata, dicomDir, *args, **kwargs):
"""Create a ``DicomImage``.
- :arg image: Passed through to :meth:`.Image.__init__`.
- :arg meta: Dictionary containing DICOM meta-data.
+ :arg image: Passed through to :meth:`.Image.__init__`.
+ :arg metadata: Dictionary containing DICOM meta-data.
+ :arg dicomDir: Directory that the dicom image was loaded from.
"""
fslimage.Image.__init__(self, image, *args, **kwargs)
- self.__meta = meta
+
+ self.__dicomDir = dicomDir
+
+ if metadata is not None:
+ for k, v in metadata.items():
+ self.addMeta(k, v)
+
+
+ @property
+ def dicomDir(self):
+ """Returns the directory that the DICOM image data was loaded from. """
+ return self.__dicomDir
+ @deprecation.deprecated(deprecated_in='1.6.0',
+ removed_in='2.0.0',
+ details='Use metaKeys instead')
def keys(self):
- """Returns the keys contained in the DICOM metadata dictionary
- (``dict.keys``).
- """
- return self.__meta.keys()
+ """Deprecated - use :meth:`.Image.metaKeys`. """
+ return self.metaKeys()
+ @deprecation.deprecated(deprecated_in='1.6.0',
+ removed_in='2.0.0',
+ details='Use metaValues instead')
def values(self):
- """Returns the values contained in the DICOM metadata dictionary
- (``dict.values``).
- """
- return self.__meta.values()
+ """Deprecated - use :meth:`.Image.metaValues`. """
+ return self.metaValues()
+ @deprecation.deprecated(deprecated_in='1.6.0',
+ removed_in='2.0.0',
+ details='Use metaItems instead')
def items(self):
- """Returns the items contained in the DICOM metadata dictionary
- (``dict.items``).
- """
- return self.__meta.items()
+ """Deprecated - use :meth:`.Image.metaItems`. """
+ return self.metaItems()
+ @deprecation.deprecated(deprecated_in='1.6.0',
+ removed_in='2.0.0',
+ details='Use getMeta instead')
def get(self, *args, **kwargs):
- """Returns the metadata value with the specified key (``dict.get``).
- """
- return self.__meta.get(*args, **kwargs)
+ """Deprecated - use :meth:`.Image.getMeta`. """
+ return self.getMeta(*args, **kwargs)
@memoize.memoize
@@ -218,4 +238,4 @@ def loadSeries(series):
# Force-load images into memory
[i.get_data() for i in images]
- return [DicomImage(i, series, name=desc) for i in images]
+ return [DicomImage(i, series, dcmdir, name=desc) for i in images]
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 0afc47c7473690970554cea7aab95ec385bcfd45..32da2f14b06eca040593381bd1660d73c52746a5 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -36,6 +36,7 @@ import os
import os.path as op
import string
import logging
+import collections
import six
import deprecation
@@ -158,6 +159,23 @@ class Nifti(notifier.Notifier):
:attr:`.constants.NIFTI_XFORM_ANALYZE`.
+ **Metadata**
+
+
+ The ``Image`` class has a handful of methods allowing you to add and access
+ additional metadata associated with the image. These methods are used by
+ the :class:`.DicomImage` and :class:`.MGHImage` to store additional
+ meta-data that cannot be stored in the NIFTI header:
+
+ .. autosummary::
+ :nosignatures:
+
+ metaKeys
+ metaValues
+ metaItems
+ getMeta
+
+
**Notification**
@@ -193,6 +211,7 @@ class Nifti(notifier.Notifier):
worldToVoxMat = transform.invert(voxToWorldMat)
self.header = header
+ self.__meta = collections.OrderedDict()
self.__shape = shape
self.__intent = header.get('intent_code',
constants.NIFTI_INTENT_NONE)
@@ -667,6 +686,33 @@ class Nifti(notifier.Notifier):
return code
+ def metaKeys(self):
+ """Returns the keys contained in the image metadata dictionary
+ (``dict.keys``).
+ """
+ return self.__meta.keys()
+
+
+ def metaValues(self):
+ """Returns the values contained in the image metadata dictionary
+ (``dict.values``).
+ """
+ return self.__meta.values()
+
+
+ def metaItems(self):
+ """Returns the items contained in the image metadata dictionary
+ (``dict.items``).
+ """
+ return self.__meta.items()
+
+
+ def getMeta(self, *args, **kwargs):
+ """Returns the metadata value with the specified key (``dict.get``).
+ """
+ return self.__meta.get(*args, **kwargs)
+
+
class Image(Nifti):
"""Class which represents a NIFTI image. Internally, the image is
loaded/stored using a :mod:`nibabel.nifti1.Nifti1Image` or
@@ -831,7 +877,7 @@ class Image(Nifti):
# Otherwise we let nibabel
# manage the file reference(s)
else:
- nibImage = nib.load(image, **kwargs)
+ nibImage = nib.load(image, **kwargs)
dataSource = image
@@ -1311,7 +1357,7 @@ Made available in this module for convenience.
def looksLikeImage(filename, allowedExts=None):
- """Returns ``True`` if the given file looks like an image, ``False``
+ """Returns ``True`` if the given file looks like a NIFTI image, ``False``
otherwise.
.. note:: The ``filename`` cannot just be a file prefix - it must