From c24eaeca5ac3115f8702274346f4f590bbd83f94 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 19 Jan 2018 15:29:02 +0000
Subject: [PATCH] Nifti.meta* methods are now in a base-class. Also used by
TriangleMesh.
---
fsl/data/image.py | 52 +++-----------------------------------
fsl/data/mesh.py | 3 ++-
fsl/utils/meta.py | 64 +++++++++++++++++++++++++++++++++++++++++++++++
3 files changed, 70 insertions(+), 49 deletions(-)
create mode 100644 fsl/utils/meta.py
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 9a9869d34..4c22ad402 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -46,6 +46,7 @@ import scipy.ndimage as ndimage
import nibabel as nib
import nibabel.fileslice as fileslice
+import fsl.utils.meta as meta
import fsl.utils.transform as transform
import fsl.utils.notifier as notifier
import fsl.utils.memoize as memoize
@@ -57,7 +58,7 @@ import fsl.data.imagewrapper as imagewrapper
log = logging.getLogger(__name__)
-class Nifti(notifier.Notifier):
+class Nifti(notifier.Notifier, meta.Meta):
"""The ``Nifti`` class is intended to be used as a base class for
things which either are, or are associated with, a NIFTI image.
The ``Nifti`` class is intended to represent information stored in
@@ -162,19 +163,8 @@ class Nifti(notifier.Notifier):
**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
- setMeta
+ The ``Image`` class inherits from the :class:`.Meta` class - its methods
+ can be used to store and query any meta-data associated with the image.
**Notification**
@@ -212,7 +202,6 @@ 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)
@@ -687,39 +676,6 @@ 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)
-
-
- def setMeta(self, *args, **kwargs):
- """Add some metadata with the specified key (``dict.__setitem__``).
- """
- self.__meta.__setitem__(*args, **kwargs)
-
-
class Image(Nifti):
"""Class which represents a NIFTI image. Internally, the image is
loaded/stored using a :mod:`nibabel.nifti1.Nifti1Image` or
diff --git a/fsl/data/mesh.py b/fsl/data/mesh.py
index 1ad40139e..a979c01cc 100644
--- a/fsl/data/mesh.py
+++ b/fsl/data/mesh.py
@@ -27,6 +27,7 @@ import numpy as np
import six
+import fsl.utils.meta as meta
import fsl.utils.memoize as memoize
import fsl.utils.transform as transform
@@ -36,7 +37,7 @@ from . import image as fslimage
log = logging.getLogger(__name__)
-class TriangleMesh(object):
+class TriangleMesh(meta.Meta):
"""The ``TriangleMesh`` class represents a 3D model. A mesh is defined by a
collection of ``N`` vertices, and ``M`` triangles. The triangles are
defined by ``(M, 3)`` indices into the list of vertices.
diff --git a/fsl/utils/meta.py b/fsl/utils/meta.py
new file mode 100644
index 000000000..f380fdbf1
--- /dev/null
+++ b/fsl/utils/meta.py
@@ -0,0 +1,64 @@
+#!/usr/bin/env python
+#
+# meta.py - The Meta class/mixin.
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+"""This module provides the :class:`Meta` class. """
+
+
+import collections
+
+
+class Meta(object):
+ """The ``Meta`` class is intended to be used as a mixin for other classes. It
+ is simply a wrapper for a dictionary of key-value pairs.
+
+ It has a handful of methods allowing you to add and access additional
+ metadata associated with an object.
+
+ .. autosummary::
+ :nosignatures:
+
+ metaKeys
+ metaValues
+ metaItems
+ getMeta
+ setMeta
+ """
+
+ def __init__(self):
+ self.__meta = collections.OrderedDict()
+
+
+ def metaKeys(self):
+ """Returns the keys contained in the metadata dictionary
+ (``dict.keys``).
+ """
+ return self.__meta.keys()
+
+
+ def metaValues(self):
+ """Returns the values contained in the metadata dictionary
+ (``dict.values``).
+ """
+ return self.__meta.values()
+
+
+ def metaItems(self):
+ """Returns the items contained in the 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)
+
+
+ def setMeta(self, *args, **kwargs):
+ """Add some metadata with the specified key (``dict.__setitem__``).
+ """
+ self.__meta.__setitem__(*args, **kwargs)
--
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