From 0467986e2c2047a48cf65613b39da8e91d6186a7 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Tue, 23 Jan 2018 08:44:48 +0000
Subject: [PATCH] New Mesh.loadVertices method. Mesh.vertices only raises a
notification if the vertex set changes.
---
fsl/data/freesurfer.py | 26 ++++++++++++++++++++++++++
fsl/data/gifti.py | 32 +++++++++++++++++++++++++++++---
fsl/data/mesh.py | 42 ++++++++++++++++++++++++++++++++++++++++--
3 files changed, 95 insertions(+), 5 deletions(-)
diff --git a/fsl/data/freesurfer.py b/fsl/data/freesurfer.py
index 029274eab..23622047b 100644
--- a/fsl/data/freesurfer.py
+++ b/fsl/data/freesurfer.py
@@ -104,6 +104,32 @@ class FreesurferMesh(fslmesh.Mesh):
self.addVertices(verts, f, select=False)
+ def loadVertices(self, infile, key=None, **kwargs):
+ """Overrides :meth:`.Mesh.loadVertices`. If the given ``infile``
+ looks like a Freesurfer file, it is loaded via
+ ``nibabel.freesurfer.load_geometry``. Otherwise, it is passed to
+ :meth:`.Mesh.loadVertices`.
+ """
+ if not fslpath.hasExt(infile, GEOMETRY_EXTENSIONS):
+ return fslmesh.Mesh.loadVertices(
+ self, infile, key, **kwargs)
+
+ infile = op.abspath(infile)
+ if key is None:
+ key = infile
+
+ # TODO merge metadata
+ vertices, indices, meta, comment = nibfs.read_geometry(
+ infile,
+ read_metadata=True,
+ read_stamp=True)
+
+ vertices = vertices.reshape(self.vertices.shape)
+ self.addVertices(vertices, key, **kwargs)
+
+ return vertices
+
+
def loadVertexData(self, infile, key=None):
"""Overrides :meth:`.Mesh.loadVertexData`. If the given ``infile``
looks like a Freesurfer file, it is loaded via the
diff --git a/fsl/data/gifti.py b/fsl/data/gifti.py
index c8ddd0685..d83d9b430 100644
--- a/fsl/data/gifti.py
+++ b/fsl/data/gifti.py
@@ -104,12 +104,38 @@ class GiftiMesh(fslmesh.Mesh):
self.setMeta( sfile, surfimg)
+ def loadVertices(self, infile, key=None, *args, **kwargs):
+ """Overrides the :meth:`.Mesh.loadVertices` method.
+
+ Attempts to load vertices for this ``GiftiMesh`` from the given
+ ``infile``, which may be a GIFTI file or a plain text file containing
+ vertices.
+ """
+
+ if not infile.endswith('.gii'):
+ return fslmesh.Mesh.loadVertices(
+ self, infile, key, *args, **kwargs)
+
+ infile = op.abspath(infile)
+
+ if key is None:
+ key = infile
+
+ surfimg, vertices, _ = loadGiftiMesh(infile)
+ vertices = vertices.reshape(self.vertices.shape[0], 3)
+
+ self.addVertices(vertices, key, *args, **kwargs)
+ self.setMeta( infile, surfimg)
+
+ return vertices
+
+
def loadVertexData(self, infile, key=None):
- """Overrides the :meth:`.TriangleMesh.loadVertexData` method.
+ """Overrides the :meth:`.Mesh.loadVertexData` method.
Attempts to load data associated with each vertex of this
- ``GiftiMesh`` from the given ``dataSource``, which may be
- a GIFTI file or a plain text file which contains vertex data.
+ ``GiftiMesh`` from the given ``infile``, which may be a GIFTI file or
+ a plain text file which contains vertex data.
"""
infile = op.abspath(infile)
diff --git a/fsl/data/mesh.py b/fsl/data/mesh.py
index 3abf6f695..01b6cf40d 100644
--- a/fsl/data/mesh.py
+++ b/fsl/data/mesh.py
@@ -91,6 +91,7 @@ class Mesh(notifier.Notifier, meta.Meta):
.. autosummary::
:nosignatures:
+ loadVertices
addVertices
selectedVertices
vertexSets
@@ -253,14 +254,19 @@ class Mesh(notifier.Notifier, meta.Meta):
def vertices(self, key):
"""Select the current vertex set - a ``KeyError`` is raised
if no vertex set with the specified ``key`` has been added.
+
+ When the current vertex set is changed, a notification is emitted
+ through the :class:`.Notifier` interface, with the topic
+ ``'vertices'``.
"""
# Force a key error if
# the key is invalid
self.__vertices[key]
- self.__selected = key
- self.notify(topic='vertices')
+ if self.__selected != key:
+ self.__selected = key
+ self.notify(topic='vertices')
@property
@@ -320,6 +326,36 @@ class Mesh(notifier.Notifier, meta.Meta):
return lo, hi
+ def loadVertices(self, infile, key=None, **kwargs):
+ """Loads vertex data from the given ``infile``, and adds it as a vertex
+ set with the given ``key``. This implementation supports loading vertex
+ data from white-space 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:`addVertices`. If not provided,
+ set to ``infile`` (converted to an absolute path)
+
+ All of the other arguments are passed through to :meth:`addVertices`.
+
+ :returns: The loaded vertices.
+ """
+
+ infile = op.abspath(infile)
+
+ if key is None:
+ key = infile
+
+ vertices = np.loadtxt(infile)
+ vertices = vertices.reshape(self.vertices.shape)
+
+ self.addVertices(vertices, key, **kwargs)
+
+ return vertices
+
+
def addVertices(self, vertices, key=None, select=True, fixWinding=False):
"""Adds a set of vertices to this ``Mesh``.
@@ -387,6 +423,8 @@ class Mesh(notifier.Notifier, meta.Meta):
:arg key: Key to pass to :meth:`addVertexData`. If not provided,
set to ``infile`` (converted to an absolute path)
+
+ :returns: The loaded vertex data.
"""
infile = op.abspath(infile)
--
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