def updateVertices(self, *a):
"""Called by :meth:`__init__`, and when certain display properties
change. (Re-)generates the mesh vertices, indices and normals (if
being displayed in 3D). They are stored as attributes called
``vertices``, ``indices``, and ``normals`` respectively.
"""
overlay = self.overlay
vertices = overlay.vertices
indices = overlay.indices
normals = self.overlay.vnormals
xform = self.opts.getTransform('mesh', 'display')
if not np.all(np.isclose(xform, np.eye(4))):
vertices = affine.transform(vertices, xform)
if self.threedee:
nmat = affine.invert(xform).T
normals = affine.transform(normals, nmat, vector=True)
self.vertices = np.asarray(vertices, dtype=np.float32)
self.indices = np.asarray(indices.flatten(), dtype=np.uint32)
self.vertices = dutils.makeWriteable(self.vertices)
self.indices = dutils.makeWriteable(self.indices)
if self.threedee:
self.normals = np.array(normals, dtype=np.float32)
def updateVertices(self, *a):
"""Called by :meth:`__init__`, and when certain display properties
change. (Re-)generates the mesh vertices, indices and normals (if
being displayed in 3D). They are stored as attributes called
``vertices``, ``indices``, and ``normals`` respectively.
"""
overlay = self.overlay
opts = self.opts
threedee = self.threedee
vertices = overlay.vertices
indices = overlay.indices
normals = self.overlay.vnormals
vdata = opts.getVertexData('vertex')
xform = opts.getTransform('mesh', 'display')
if not np.all(np.isclose(xform, np.eye(4))):
vertices = affine.transform(vertices, xform)
if self.threedee:
nmat = affine.invert(xform).T
normals = affine.transform(normals, nmat, vector=True)
self.origIndices = indices
indices = np.asarray(indices.flatten(), dtype=np.uint32)
# If flatShading is active, we cannot share
# vertices between triangles, so we generate
# a set of unique vertices for each triangle,
# and then re-generate the triangle indices.
# The original indices are saved above, as
# they will be used by the getVertexData
# method to duplicate the vertex data.
if threedee and (vdata is not None) and opts.flatShading:
self.vertices = vertices[indices].astype(np.float32)
self.indices = np.arange(0, len(self.vertices), dtype=np.uint32)
normals = normals[indices, :]
else:
self.vertices = np.asarray(vertices, dtype=np.float32)
self.indices = indices
self.vertices = dutils.makeWriteable(self.vertices)
self.indices = dutils.makeWriteable(self.indices)
if self.threedee:
self.normals = np.array(normals, dtype=np.float32)
def test_makeWriteable():
robuf = bytes(b'\01\02\03\04')
wbuf = bytearray(b'\01\02\03\04')
roarr = np.ndarray((4, ), dtype=np.uint8, buffer=robuf)
warr = np.ndarray((4, ), dtype=np.uint8, buffer=wbuf)
warr.flags['WRITEABLE'] = False
rocopy = dutils.makeWriteable(roarr)
wcopy = dutils.makeWriteable(warr)
assert rocopy.base is not roarr.base
assert wcopy.base is warr.base
rocopy[1] = 100
wcopy[1] = 100
def doRefresh(self):
"""Overrides :meth:`.Texture.doRefresh`.
(Re-)configures the OpenGL texture.
"""
data = self.preparedData
if data is None:
return
log.debug('Configuring 3D texture (id %s) for %s (data shape: %s)',
self.name, self.handle, self.shape)
# First dimension for multi-
# valued textures
if self.nvals > 1: shape = data.shape[1:]
else: shape = data.shape
# The image data is flattened, with
# fortran dimension ordering, so the
# data, as stored on the GPU, has its
# first dimension as the fastest
# changing.
data = np.array(data.ravel(order='F'), copy=False)
# PyOpenGL needs the data array
# to be writeable, as it uses
# PyArray_ISCARRAY to check
# for contiguousness. but if the
# data has come from a nibabel
# ArrayProxy, the writeable flag
# will be set to False for some
# reason.
data = dutils.makeWriteable(data)
interp = self.interp
intFmt = self.internalFormat
baseFmt = self.baseFormat
ttype = self.textureType
if interp is None:
interp = gl.GL_NEAREST
with self.bound():
# Enable storage of tightly packed data of any size (i.e.
# our texture shape does not have to be divisible by 4).
gl.glPixelStorei(gl.GL_PACK_ALIGNMENT, 1)
gl.glPixelStorei(gl.GL_UNPACK_ALIGNMENT, 1)
gl.glTexParameteri(gl.GL_TEXTURE_3D, gl.GL_TEXTURE_MAG_FILTER,
interp)
gl.glTexParameteri(gl.GL_TEXTURE_3D, gl.GL_TEXTURE_MIN_FILTER,
interp)
# Clamp texture borders to
# the specified border value(s)
if self.border is not None:
gl.glTexParameteri(gl.GL_TEXTURE_3D, gl.GL_TEXTURE_WRAP_S,
gl.GL_CLAMP_TO_BORDER)
gl.glTexParameteri(gl.GL_TEXTURE_3D, gl.GL_TEXTURE_WRAP_T,
gl.GL_CLAMP_TO_BORDER)
gl.glTexParameteri(gl.GL_TEXTURE_3D, gl.GL_TEXTURE_WRAP_R,
gl.GL_CLAMP_TO_BORDER)
gl.glTexParameterfv(gl.GL_TEXTURE_3D,
gl.GL_TEXTURE_BORDER_COLOR,
np.asarray(self.border, dtype=np.float32))
# Clamp texture borders to the edge
# values - it is the responsibility
# of the rendering logic to not draw
# anything outside of the image space
else:
gl.glTexParameteri(gl.GL_TEXTURE_3D, gl.GL_TEXTURE_WRAP_S,
gl.GL_CLAMP_TO_EDGE)
gl.glTexParameteri(gl.GL_TEXTURE_3D, gl.GL_TEXTURE_WRAP_T,
gl.GL_CLAMP_TO_EDGE)
gl.glTexParameteri(gl.GL_TEXTURE_3D, gl.GL_TEXTURE_WRAP_R,
gl.GL_CLAMP_TO_EDGE)
# The macOS GL driver sometimes corrupts
# the texture data if we don't generate
# mipmaps
gl.glTexParameteri(gl.GL_TEXTURE_3D, gl.GL_GENERATE_MIPMAP,
gl.GL_TRUE)
# create the texture according to
# the format determined by the
# determineTextureType method.
#
# note: The ancient Chromium driver (still
# in use by VirtualBox) will improperly
# create 3D textures without two calls
# (to glTexImage3D and glTexSubImage3D).
# If I specify the texture size and set
# the data in a single call, it seems to
# expect that the data or texture
# dimensions always have even size - odd
# sized images will be displayed
# incorrectly.
gl.glTexImage3D(gl.GL_TEXTURE_3D, 0, intFmt, shape[0], shape[1],
shape[2], 0, baseFmt, ttype, None)
gl.glTexSubImage3D(gl.GL_TEXTURE_3D, 0, 0, 0, 0, shape[0],
shape[1], shape[2], baseFmt, ttype, data)
def doRefresh(self):
"""Overrides :meth:`.Texture.doRefresh`. Configures this ``Texture2D``.
This includes setting up interpolation, and setting the texture size
and data.
"""
data = self.preparedData
if data is None: width, height = self.shape
elif self.nvals == 1: width, height = data.shape
else: width, height = data.shape[1:]
if data is not None:
data = np.array(data.ravel('F'), copy=False)
data = dutils.makeWriteable(data)
interp = self.interp
if interp is None:
interp = gl.GL_NEAREST
with self.bound():
gl.glPixelStorei(gl.GL_PACK_ALIGNMENT, 1)
gl.glPixelStorei(gl.GL_UNPACK_ALIGNMENT, 1)
gl.glTexParameteri(gl.GL_TEXTURE_2D,
gl.GL_TEXTURE_MAG_FILTER,
interp)
gl.glTexParameteri(gl.GL_TEXTURE_2D,
gl.GL_TEXTURE_MIN_FILTER,
interp)
if self.border is not None:
gl.glTexParameteri(gl.GL_TEXTURE_2D,
gl.GL_TEXTURE_WRAP_S,
gl.GL_CLAMP_TO_BORDER)
gl.glTexParameteri(gl.GL_TEXTURE_2D,
gl.GL_TEXTURE_WRAP_T,
gl.GL_CLAMP_TO_BORDER)
gl.glTexParameterfv(gl.GL_TEXTURE_2D,
gl.GL_TEXTURE_BORDER_COLOR,
self.border)
else:
gl.glTexParameteri(gl.GL_TEXTURE_2D,
gl.GL_TEXTURE_WRAP_S,
gl.GL_CLAMP_TO_EDGE)
gl.glTexParameteri(gl.GL_TEXTURE_2D,
gl.GL_TEXTURE_WRAP_T,
gl.GL_CLAMP_TO_EDGE)
# If the width and height have not
# changed, then we don't need to
# re-define the texture. But we can
# use glTexSubImage2D if we have
# data to upload
if width == self.__width and \
height == self.__height and \
data is not None:
gl.glTexSubImage2D(gl.GL_TEXTURE_2D,
0,
0,
0,
width,
height,
self.baseFormat,
self.textureType,
data)
# If the width and/or height have
# changed, we need to re-define
# the texture properties
else:
self.__width = width
self.__height = height
gl.glTexImage2D(gl.GL_TEXTURE_2D,
0,
self.internalFormat,
width,
height,
0,
self.baseFormat,
self.textureType,
data)
def __vdataChanged(self, value, valid, ctx, name):
"""Called when the :attr:`vertexData` or :attr:`modulateData`
properties changes. Attempts to load the data if possible. The data may
subsequently be retrieved via the :meth:`getVertexData` method.
"""
vdata = None
vdataRange = None
overlay = self.overlay
vdfile = value
if name == 'vertexData': key = 'vertex'
elif name == 'modulateData': key = 'modulate'
else: raise RuntimeError()
try:
if vdfile is not None:
if vdfile not in overlay.vertexDataSets():
log.debug('Loading vertex data: {}'.format(vdfile))
vdata = overlay.loadVertexData(vdfile)
else:
vdata = overlay.getVertexData(vdfile)
vdataRange = np.nanmin(vdata), np.nanmax(vdata)
if len(vdata.shape) == 1:
vdata = vdata.reshape(-1, 1)
vdata = dutils.makeWriteable(vdata)
except Exception as e:
# TODO show a warning
log.warning('Unable to load vertex data from {}: {}'.format(
vdfile, e, exc_info=True))
vdata = None
vdataRange = None
self.__vdata[key] = vdata
self.__vdataRange[key] = vdataRange
if key == 'vertex':
if vdata is not None: npoints = vdata.shape[1]
else: npoints = 1
self.vertexDataIndex = 0
self.setAttribute('vertexDataIndex', 'maxval', npoints - 1)
# if modulate data has changed,
# don't update display/clipping
# ranges (unless modulateData is
# None, meaning that it is using
# vertexData)
if key == 'vertex':
drange = True
mrange = self.modulateData is None
# and vice versa
else:
drange = False
mrange = True
self.updateDataRange(drange, drange, mrange)