From a98bf65ccfdfc6b15a454767cb3d27c508b4d685 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Sun, 21 Jan 2018 13:34:34 +0000
Subject: [PATCH] Re-added loadVertexData method, and a new vertexKeys method.
---
fsl/data/mesh.py | 54 +++++++++++++++++++++++++++++++++++++++++++-----
1 file changed, 49 insertions(+), 5 deletions(-)
diff --git a/fsl/data/mesh.py b/fsl/data/mesh.py
index ee0681a21..dcf4054e4 100644
--- a/fsl/data/mesh.py
+++ b/fsl/data/mesh.py
@@ -15,8 +15,8 @@ See also the following modules:
fsl.data.gifti
fsl.data.freesurfer
-A handful of standalone functions are provided in this module, for doing various
-things with meshes:
+A handful of standalone functions are provided in this module, for doing
+various things with meshes:
.. autosummary::
:nosignatures:
@@ -40,7 +40,6 @@ import fsl.utils.meta as meta
import fsl.utils.notifier as notifier
import fsl.utils.memoize as memoize
import fsl.utils.transform as transform
-import fsl.data.image as fslimage
log = logging.getLogger(__name__)
@@ -86,7 +85,15 @@ class Mesh(notifier.Notifier, meta.Meta):
:meth:`addVertices` method. Each vertex set must be associated with a
unique key - you can then select the current vertex set via the
:meth:`vertices` property. Most ``Mesh`` methods will raise a ``KeyError``
- if you have not added any vertex sets, or selected a vertex set.
+ if you have not added any vertex sets, or selected a vertex set. The
+ following methods are available for managing vertex sets:
+
+ .. autosummary::
+ :nosignatures:
+
+ addVertices
+ selectedVertices
+ vertexKeys
**Vertex data**
@@ -98,6 +105,7 @@ class Mesh(notifier.Notifier, meta.Meta):
.. autosummary::
:nosignatures:
+ loadVertexData
addVertexData
getVertexData
clearVertexData
@@ -358,17 +366,53 @@ class Mesh(notifier.Notifier, meta.Meta):
self.__faceNormals[k] = fn * -1
+ def vertexKeys(self):
+ """Returns a list containing the keys of all vertex sets. """
+ return list(self.__vertices.keys())
+
def selectedVertices(self):
"""Returns the key of the currently selected vertex set. """
return self.__selected
+ def loadVertexData(self, infile, key=None):
+ """Loads vertex-wise data from the given ``infile``, and adds it with
+ the given ``key``. This implementation supports loading data from
+ whitespace-delimited text files via ``numpy.loadtxt``, but sub-classes
+ may override this method to support additional file types.
+
+ :arg infile: File to load data from.
+
+ :arg key: Key to pass to :meth:`addVertexData`. If not provided,
+ set to ``infile`` (converted to an absolute path)
+ """
+
+ infile = op.abspath(infile)
+
+ if key is None:
+ key = infile
+
+ nvertices = self.vertices.shape[0]
+ vertexData = np.loadtxt(infile)
+ vertexData = vertexData.reshape(nvertices, -1)
+
+ self.addVertexData(key, vertexData)
+
+ return vertexData
+
+
def addVertexData(self, key, vdata):
"""Adds a vertex-wise data set to the ``Mesh``. It can be retrieved
by passing the specified ``key`` to the :meth:`getVertexData` method.
"""
- self.__vertexData[key] = vdata.reshape(vdata.shape[0], -1)
+
+ nvertices = self.vertices.shape[0]
+
+ if vdata.shape[0] != nvertices:
+ raise ValueError('Incompatible vertex data size: {}'.format(key))
+
+ self.__vertexData[key] = vdata.reshape(nvertices, -1)
def getVertexData(self, key):
--
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