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test_gl_item.py
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test_gl_item.py
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import logging
import string
import weakref
import numpy
from silx.gui.plot import items
from silx.gui.plot.backends.BackendOpenGL import BackendOpenGL
from silx.gui.plot.backends.glutils import GLPlotItem
from silx.gui import _glutils
from silx.gui._glutils import gl, Texture
from silx.gui.plot3d import items as plot3d_items
from silx.gui.plot3d.scene import (
function,
mixins,
transform,
primitives,
utils,
viewport,
window,
)
from silx.gui.plot3d.scene.cutplane import ColormapMesh3D
logging.basicConfig(level=logging.DEBUG)
_logger = logging.getLogger(__name__)
# Base class for plot3d.scene integration in PlotWidget OpenGL backend
class GLPlotItemPlot3DWrapper(GLPlotItem):
"""Allow to use silx.gui.plot3d.scene within :class:`PlotWidget`
:param ~silx.gui.plot3d.scene.Base primitive: 3D rendering primitive
"""
_CONTEXTS = {} # To map system GL context id to Context objects
def __init__(self, primitive):
super().__init__()
self._backendRef = None
self._viewport = viewport.Viewport()
self._viewport.camera.intrinsic = transform.Orthographic(
near=1000.0, far=-1000.0, keepaspect=False
)
self._viewport.camera.extrinsic.position = 0.0, 0.0, 0.0
self._viewport.scene.children = [primitive]
def setGLBackend(self, backend):
"""Set the :class:`PlotWidget` OpenGL backend to use.
:param BackendOpenGL backend:
"""
self._backendRef = None if backend is None else weakref.ref(backend)
def getGLBackend(self):
"""Returns the :class:`PlotWidget` OpenGL backend in use.
:rtype: Union[BackendOpenGL,None]
"""
return None if self._backendRef is None else self._backendRef()
def getScenePrimitive(self):
"""Returns the scene primitive doing the rendering
:rtype: ~silx.gui.plot3d.scene.Base
"""
return self._viewport.scene.children[0]
def _syncViewport(self):
"""Synchronize viewport with current state of the backend"""
backend = self.getGLBackend()
if backend is None:
_logger.error("Cannot synchronize viewport, no backend")
return
ox, oy, width, height = backend.getPlotBoundsInPixels()
# Change from top to bottom reference
oy = backend.getDevicePixelRatio() * backend.height() - height - oy
self._viewport.origin = ox, oy
self._viewport.size = width, height
plotFrame = backend._plotFrame
trBounds = plotFrame.transformedDataRanges
left, right = trBounds[0]
if plotFrame.isYAxisInverted:
top, bottom = trBounds[1]
else:
bottom, top = trBounds[1]
self._viewport.camera.intrinsic.size = self._viewport.size
self._viewport.camera.intrinsic.setClipping(left, right, bottom, top)
def _getContext(self):
"""Returns context to use for rendering.
:rtype: Union[~silx.gui.plot3d.scene.window.ContextGL2,None]
"""
backend = self.getGLBackend()
if backend is None:
return None
glcontext = backend.context()
if glcontext not in self._CONTEXTS:
self._CONTEXTS[glcontext] = window.ContextGL2(glcontext) # New context
context = self._CONTEXTS[glcontext]
context.devicePixelRatio = backend.getDevicePixelRatio()
return context
# GLPlotItem methods
def render(self, matrix, isXLog, isYLog):
if isXLog or isYLog: # Log axes are not supported
return
context = self._getContext()
if context is None:
_logger.error("Cannot render, no backend")
return
with context as ctx:
context.cleanGLGarbage() # Get a chance to run deferred delete
self._syncViewport()
ctx = viewport.RenderContext(self._viewport, context)
self._viewport.scene.render(ctx)
self._viewport.scene.postRender(ctx)
def discard(self): # TODO here or not needed?
self._viewport.scene.children = []
# TODO call self.getGLBackend().context().cleanGLGarbage()
# TODO make it neat
def pick(self, x, y):
"""Override in subclass"""
pass
class PlotItemPlot3DWrapperMixIn:
"""Ease usage of GLPlotItemPlot3DWrapper in PlotWidget Items.
This class MUST come before Item in the method resolution order.
:param GLPlotItemPlot3DWrapper renderer:
"""
def __init__(self, renderer):
assert isinstance(renderer, GLPlotItemPlot3DWrapper)
self._backendRenderer = renderer
def getScenePrimitive(self):
"""Returns associated renderer.
:rtype: GLPlotItemPlot3DWrapper
"""
return self._backendRenderer.getScenePrimitive()
def _setPlot(self, plot):
"""Overrides to keep a reference to the backend in use."""
assert plot is None or isinstance(plot._backend, BackendOpenGL)
self._backendRenderer.setGLBackend(plot._backend)
super()._setPlot(plot)
def _update(self, backend):
"""Overrides update strategy"""
if backend != self._backendRenderer.getGLBackend():
self._backendRenderer.setGLBackend(backend)
self._dirty = False # Reset dirty flag
def _addBackendRenderer(self, backend):
"""Overrides backend renderer creation"""
_logger.error("This should never be called!")
return self._backendRenderer
def _removeBackendRenderer(self, backend):
"""Overrides backend render removal"""
if self._backendRenderer.getGLBackend() is backend:
# TODO check if OK
backend.remove(self._backendRenderer)
self._backendRenderer.setGLBackend(None)
def _getBounds(self):
"""Overrides bounds computation to use that of plot3d.
Log scale axes are not supported.
"""
plot = self.getPlot()
if plot is not None and (
plot.getXAxis().getScale() != items.Axis.LINEAR
or plot.getYAxis().getScale() != items.Axis.LINEAR
):
return None # No display with log scale for now
image = self.getScenePrimitive()
bounds = image.bounds(transformed=True, dataBounds=True)
if bounds is None:
return None
else:
return bounds[0, 0], bounds[1, 0], bounds[0, 1], bounds[1, 1]
# plot3d-based Image PlotWidget item replacement
class GLImageBackendItem(GLPlotItemPlot3DWrapper):
"""PlotWidget OpenGL backend data image primitive using plot3d.scene."""
def __init__(self, image):
image.transforms = [transform.Translate(), transform.Scale()] + image.transforms
super().__init__(image)
def pick(self, x, y):
image = self.getScenePrimitive()
origin = image.transforms[0].translation[:2]
scale = image.transforms[1].scale[:2]
shape = image.getData(copy=False).shape
# print('shape', shape)
# TODO convert shape to 2D for stack
# Get image extent
xmin, ymin = origin
xmax = xmin + scale[0] * shape[1]
if xmin > xmax:
xmin, xmax = xmax, xmin
ymax = ymin + scale[1] * shape[0]
if ymin > ymax:
ymin, ymax = ymax, ymin
# Get indices
if xmin <= x <= xmax and ymin <= y <= ymax:
col = int((x - origin[0]) / scale[0])
row = int((y - origin[1]) / scale[1])
return (row,), (col,)
else:
return None
class GLImage(
PlotItemPlot3DWrapperMixIn,
items.ImageBase,
plot3d_items.ColormapMixIn,
plot3d_items.InterpolationMixIn,
):
"""Data image PlotWidget item based on plot3d.scene"""
def __init__(self):
items.ImageBase.__init__(self)
plot3d_items.ColormapMixIn.__init__(self)
plot3d_items.InterpolationMixIn.__init__(self)
image = self._initPrimitive()
PlotItemPlot3DWrapperMixIn.__init__(self, GLImageBackendItem(image))
# Connect scene primitive to mix-in class
plot3d_items.InterpolationMixIn._setPrimitive(self, image)
plot3d_items.ColormapMixIn._setSceneColormap(self, image.colormap)
self._glsync()
def _initPrimitive(self):
return primitives.ImageData(data=numpy.zeros((0, 0), dtype=numpy.float32))
def _glsync(self):
"""Perform synchronisation that is not performed by mixin"""
image = self.getScenePrimitive()
image.alpha = self.getAlpha()
translate, scale = image.transforms
translate.tx, translate.ty = self.getOrigin()
scale.sx, scale.sy = self.getScale()
def _updated(self, event=None, checkVisibility: bool = True):
if event in (
items.ItemChangedType.ALPHA,
items.ItemChangedType.POSITION,
items.ItemChangedType.SCALE,
):
self._glsync()
return super()._updated(event=event, checkVisibility=checkVisibility)
def getRgbaImageData(self, copy: bool = True): # TODO remove?
"""Get the displayed RGB(A) image
:returns: Array of uint8 of shape (height, width, 4)
:rtype: numpy.ndarray
"""
return self.getColormap().applyToData(self)
def getData(self, copy: bool = True):
"""Returns the image data
:param bool copy: True (Default) to get a copy,
False to use internal representation (do not modify!)
"""
return self.getScenePrimitive().getData(copy=copy)
def setData(self, data, copy: bool = True):
""" "Set the image data
:param numpy.ndarray data: Data array with 2 dimensions (h, w)
:param bool copy: True (Default) to make a copy,
False to use as is (do not modify!)
"""
data = numpy.array(data, copy=copy)
assert data.ndim == 2
if data.dtype.kind == "b":
_logger.warning("Converting boolean image to int8 to plot it.")
data = numpy.array(data, copy=False, dtype=numpy.int8)
elif numpy.iscomplexobj(data):
_logger.warning("Converting complex image to absolute value to plot it.")
data = numpy.absolute(data)
# TODO cast to valid type (u)int8|16 or float32
self.getScenePrimitive().setData(data, copy=False)
self._setColormappedData(self.getData(copy=False), copy=False)
# TODO hackish data range implementation
if self.isVisible():
plot = self.getPlot()
if plot is not None:
plot._invalidateDataRange()
self._updated(items.ItemChangedType.DATA)
class ColormapTexturedMesh3D(primitives.Geometry, mixins.DataTextureMixIn):
"""A 3D mesh with color from a 3D texture, no lighting."""
_shaders = (
"""
attribute vec3 position;
attribute vec3 texcoord;
uniform mat4 matrix;
uniform mat4 transformMat;
varying vec4 vCameraPosition;
varying vec3 vTexCoord;
void main(void)
{
vCameraPosition = transformMat * vec4(position, 1.0);
vTexCoord = texcoord;
gl_Position = matrix * vec4(position, 1.0);
}
""",
string.Template(
"""
varying vec4 vCameraPosition;
varying vec3 vTexCoord;
uniform sampler3D data;
uniform float alpha;
$colormapDecl
$sceneDecl
void main(void)
{
$scenePreCall(vCameraPosition);
float value = texture3D(data, vTexCoord).r;
gl_FragColor = $colormapCall(value);
gl_FragColor.a *= alpha;
$scenePostCall(vCameraPosition);
}
"""
),
)
def __init__(
self,
position,
texcoord,
data,
copy=True,
mode="triangles",
indices=None,
colormap=None,
):
assert mode in self._TRIANGLE_MODES
self._alpha = 1.0
self._colormap = colormap or function.Colormap() # Default colormap
self._colormap.addListener(self._cmapChanged)
mixins.DataTextureMixIn.__init__(self, ndim=3, data=data, copy=copy)
primitives.Geometry.__init__(
self, mode, indices, position=position, texcoord=texcoord
)
def setData(self, data, copy=True):
super().setData(data, copy)
@property
def alpha(self):
"""Transparency of the plane, float in [0, 1]"""
return self._alpha
@alpha.setter
def alpha(self, alpha):
self._alpha = float(alpha)
self.notify()
@property
def colormap(self):
"""The colormap used by this primitive"""
return self._colormap
def _cmapChanged(self, source, *args, **kwargs):
"""Broadcast colormap changes"""
self.notify(*args, **kwargs)
def prepareGL2(self, ctx):
mixins.DataTextureMixIn.prepareGL2(self, ctx)
primitives.Geometry.prepareGL2(self, ctx)
def renderGL2(self, ctx):
fragment = self._shaders[1].substitute(
sceneDecl=ctx.fragDecl,
scenePreCall=ctx.fragCallPre,
scenePostCall=ctx.fragCallPost,
colormapDecl=self.colormap.decl,
colormapCall=self.colormap.call,
)
program = ctx.glCtx.prog(self._shaders[0], fragment)
program.use()
self.colormap.setupProgram(ctx, program)
program.setUniformMatrix("matrix", ctx.objectToNDC.matrix)
program.setUniformMatrix("transformMat", ctx.objectToCamera.matrix, safe=True)
gl.glUniform1f(program.uniforms["alpha"], self._alpha)
gl.glUniform1i(program.uniforms["data"], self.texture.texUnit)
ctx.setupProgram(program)
with self.texture:
self._draw(program)
class GLImageStack(GLImage):
"""Data image PlotWidget item based on plot3d.scene"""
# TODO origin and scale taking 3 values
def __init__(self):
GLImage.__init__(self)
self.__index = 0
self.__axis = 0
def _initPrimitive(self):
return ColormapTexturedMesh3D(
position=numpy.zeros((4, 3), dtype=numpy.float32),
texcoord=numpy.zeros((4, 3), dtype=numpy.float32),
data=numpy.zeros((0, 0, 0), dtype=numpy.float32),
copy=False,
mode="triangle_strip",
)
def __updatePrimitive(self):
"""Update the vertices and tex coords"""
mesh = self.getScenePrimitive()
shape = mesh.getData(copy=False).shape
axis = self.getSliceAxis()
unitsquare = numpy.array(
[(0.0, 0.0, 0.0), (0.0, 1.0, 0.0), (1.0, 0.0, 0.0), (1.0, 1.0, 0.0)],
dtype=numpy.float32,
)
size = list(reversed(shape))
size.pop(2 - axis)
vertices = unitsquare[:, :2] * size
mesh.setAttribute("position", vertices, copy=False)
texcoord = numpy.array(unitsquare, copy=True)
texcoord[:, -1] = (self.getSliceIndex() + 0.5) / shape[axis]
texcoord = numpy.roll(texcoord, axis=1, shift=-axis)
mesh.setAttribute("texcoord", texcoord, copy=False)
def _updated(self, event=None, checkVisibility: bool = True):
if event == items.ItemChangedType.DATA:
self.__updatePrimitive()
self._setColormappedData(self.getData(copy=False), copy=False)
return super()._updated(event=event, checkVisibility=checkVisibility)
def _invalidateDataRange(self):
"""Invalidate PlotWidget data range if needed"""
# TODO hackish data range implementation
if self.isVisible():
plot = self.getPlot()
if plot is not None:
plot._invalidateDataRange()
def getRgbaImageData(self, copy: bool = True):
"""Get the displayed RGB(A) image
:returns: Array of uint8 of shape (height, width, 4)
:rtype: numpy.ndarray
"""
return self.getColormap().applyToData(self)
def getData(self, copy: bool = True):
"""Returns the image data
:param bool copy: True (Default) to get a copy,
False to use internal representation (do not modify!)
"""
slicing = [slice(None)] * 3
slicing[self.getSliceAxis()] = self.getSliceIndex()
return numpy.array(self.getStackData(copy=False)[tuple(slicing)], copy=copy)
def setData(self, data, copy: bool = True):
data = numpy.array(data, copy=False)
if data.ndim == 2: # Make it a 3D stack
data.shape = (1,) + data.shape
self.setStackData(data, copy)
def getStackData(self, copy: bool = True):
"""Returns the image stack data
:param bool copy: True (Default) to get a copy,
False to use internal representation (do not modify!)
"""
return self.getScenePrimitive().getData(copy=copy)
def setStackData(self, data, copy: bool = True):
""" "Set the image stack data
:param numpy.ndarray data:
Data array with 3 dimensions (depth, height, width)
:param bool copy: True (Default) to make a copy,
False to use as is (do not modify!)
"""
data = numpy.array(data, copy=copy)
assert data.ndim == 3
if data.dtype.kind == "b":
_logger.warning("Converting boolean image to int8 to plot it.")
data = numpy.array(data, copy=False, dtype=numpy.int8)
elif numpy.iscomplexobj(data):
_logger.warning("Converting complex image to absolute value to plot it.")
data = numpy.absolute(data)
# TODO cast to valid type (u)int8|16 or float32
previousShape = self.getStackData(copy=False).shape
self.getScenePrimitive().setData(data, copy=False)
if previousShape != data.shape:
self._invalidateDataRange()
self._updated(items.ItemChangedType.DATA)
def __validSliceIndex(self, index: int, axis: int) -> int:
"""Returns a valid slice index for given axis and current data."""
length = self.getStackData(copy=False).shape[axis]
if index < 0: # Handle negative index
index += length
index = numpy.clip(index, 0, length - 1)
return index
def setSlice(self, index: int, axis: int) -> None:
"""Set both the slice index and dimension index at once.
:param int index: Slice index
:param int axis: Dimension index to slice
"""
assert 0 <= axis <= 2
index = self.__validSliceIndex(index, axis)
if index != self.__index or axis != self.__axis:
self.__index = index
if axis != self.__axis:
self.__axis = axis
self._invalidateDataRange()
self._updated(items.ItemChangedType.DATA)
def getSliceIndex(self) -> int:
"""Returns slice index.
:rtype: int
"""
return self.__index
def setSliceIndex(self, index: int) -> None:
"""Set the slice index.
Negative index are converted to positive ones.
Index is clipped to the stack shape.
:param int index: The index of the slice.
"""
index = self.__validSliceIndex(index, self.getSliceAxis())
if index != self.__index:
self.__index = index
self._updated(items.ItemChangedType.DATA)
def getSliceAxis(self) -> int:
"""Returns slice dimension index in [0, 2].
:rtype: int
"""
return self.__axis
def setSliceAxis(self, axis: int) -> None:
"""Set the slice dimension index in [0, 2].
:param int index: The index of the slice.
"""
assert 0 <= axis <= 2
if axis != self.__axis:
self.__axis = axis
self._invalidateDataRange()
self._updated(items.ItemChangedType.DATA)
class DataTexture(Texture):
"""Texture keeping a CPU memory copy of the data"""
def __init__(
self,
internalFormat,
data,
format_=None,
texUnit=0,
minFilter=None,
magFilter=None,
wrap=None,
):
self.__data = numpy.array(data, copy=False)
super().__init__(
internalFormat,
self.__data,
format_,
None,
texUnit,
minFilter,
magFilter,
wrap,
)
def getData(self, copy=True):
"""Returns the image data
:param bool copy: True (Default) to get a copy,
False to use internal representation (do not modify!)
"""
return numpy.array(self.__data, copy=copy)
def update(self, format_, data, offset=(0, 0, 0), copy=True):
data = numpy.array(data, copy=False)
oz, oy, oz = offset
depth, height, width = data.shape
self.__data[oz : oz + depth, oy : oy + height, ox : ox + width] = data
super().update(format_, data, offset, copy)
class ColormapTexturedMesh3D(primitives.Geometry):
"""A 3D mesh with color from a 3D texture, no lighting."""
_shaders = (
"""
attribute vec3 position;
attribute vec3 texcoord;
uniform mat4 matrix;
uniform mat4 transformMat;
varying vec4 vCameraPosition;
varying vec3 vTexCoord;
void main(void)
{
vCameraPosition = transformMat * vec4(position, 1.0);
vTexCoord = texcoord;
gl_Position = matrix * vec4(position, 1.0);
}
""",
string.Template(
"""
varying vec4 vCameraPosition;
varying vec3 vTexCoord;
uniform sampler3D data;
uniform float alpha;
$colormapDecl
$sceneDecl
void main(void)
{
$scenePreCall(vCameraPosition);
float value = texture3D(data, vTexCoord).r;
gl_FragColor = $colormapCall(value);
gl_FragColor.a *= alpha;
$scenePostCall(vCameraPosition);
}
"""
),
)
def __init__(
self, position, texcoord, texture, mode="triangles", indices=None, colormap=None
):
assert mode in self._TRIANGLE_MODES
assert texture is None or isinstance(texture, Texture)
self._alpha = 1.0
self._colormap = colormap or function.Colormap() # Default colormap
self._colormap.addListener(self._cmapChanged)
self._texturesToDiscard = []
self._texture = texture
super().__init__(mode, indices, position=position, texcoord=texcoord)
@property
def texture(self):
"""Texture storing the data"""
return self._texture
@texture.setter
def texture(self, texture):
if self._texture is not None:
self._texturesToDiscard.append(self._texture)
self._texture = texture
@property
def alpha(self):
"""Transparency of the plane, float in [0, 1]"""
return self._alpha
@alpha.setter
def alpha(self, alpha):
self._alpha = float(alpha)
self.notify()
@property
def colormap(self):
"""The colormap used by this primitive"""
return self._colormap
def _cmapChanged(self, source, *args, **kwargs):
"""Broadcast colormap changes"""
self.notify(*args, **kwargs)
def getData(self, copy: bool = True):
"""Returns the image data
:param bool copy: True (Default) to get a copy,
False to use internal representation (do not modify!)
"""
return self.texture.getData(copy=copy)
def prepareGL2(self, ctx):
while self._texturesToDiscard:
self._texturesToDiscard.pop(0).discard()
if self.texture is not None:
self.texture.prepare()
super().prepareGL2(ctx)
def renderGL2(self, ctx):
if self.texture is None:
return
fragment = self._shaders[1].substitute(
sceneDecl=ctx.fragDecl,
scenePreCall=ctx.fragCallPre,
scenePostCall=ctx.fragCallPost,
colormapDecl=self.colormap.decl,
colormapCall=self.colormap.call,
)
program = ctx.glCtx.prog(self._shaders[0], fragment)
program.use()
self.colormap.setupProgram(ctx, program)
program.setUniformMatrix("matrix", ctx.objectToNDC.matrix)
program.setUniformMatrix("transformMat", ctx.objectToCamera.matrix, safe=True)
gl.glUniform1f(program.uniforms["alpha"], self._alpha)
gl.glUniform1i(program.uniforms["data"], self.texture.texUnit)
ctx.setupProgram(program)
with self.texture:
self._draw(program)
class ImageStackSlice(ColormapTexturedMesh3D):
"""Display an image corresponding to a slice of a stack"""
def __init__(self):
self.__axis = 0
self.__index = 0
super().__init__(
position=numpy.zeros((4, 3), dtype=numpy.float32),
texcoord=numpy.zeros((4, 3), dtype=numpy.float32),
texture=None,
mode="triangle_strip",
)
def __updatePrimitive(self):
"""Update the vertices and tex coords"""
if self.texture is None:
return
shape = self.getStackData(copy=False).shape
axis = self.getSliceAxis()
unitsquare = numpy.array(
[(0.0, 0.0, 0.0), (0.0, 1.0, 0.0), (1.0, 0.0, 0.0), (1.0, 1.0, 0.0)],
dtype=numpy.float32,
)
size = list(reversed(shape))
size.pop(2 - axis)
vertices = unitsquare[:, :2] * size
self.setAttribute("position", vertices, copy=False)
texcoord = numpy.array(unitsquare, copy=True)
texcoord[:, -1] = (self.getSliceIndex() + 0.5) / shape[axis]
texcoord = numpy.roll(texcoord, axis=1, shift=-axis)
self.setAttribute("texcoord", texcoord, copy=False)
def getStackData(self, copy: bool = True):
"""Returns the stack data
:param bool copy: True (Default) to get a copy,
False to use internal representation (do not modify!)
"""
return super().getData(copy=copy)
def getData(self, copy: bool = True):
"""Returns the image data
:param bool copy: True (Default) to get a copy,
False to use internal representation (do not modify!)
"""
slicing = [slice(None)] * 3
slicing[self.getSliceAxis()] = self.getSliceIndex()
return numpy.array(self.getStackData(copy=False)[tuple(slicing)], copy=copy)
def getSliceIndex(self) -> int:
"""Returns slice index.
:rtype: int
"""
return self.__index
def __validSliceIndex(self, index: int, axis: int) -> int:
"""Returns a valid slice index for given axis and current data."""
length = self.getData(copy=False).shape[axis]
if index < 0: # Handle negative index
index += length
return numpy.clip(index, 0, length - 1)
def setSliceIndex(self, index: int) -> None:
"""Set the slice index.
Negative index are converted to positive ones.
Index is clipped to the stack shape.
:param int index: The index of the slice.
"""
index = self.__validSliceIndex(index, self.getSliceAxis())
if index != self.__index:
self.__index = index
self.__updatePrimitive()
def getSliceAxis(self) -> int:
"""Returns slice dimension index in [0, 2].
:rtype: int
"""
return self.__axis
def setSliceAxis(self, axis: int) -> None:
"""Set the slice dimension index in [0, 2].
:param int index: The index of the slice.
"""
assert 0 <= axis <= 2
if axis != self.__axis:
self.__axis = axis
self.__updatePrimitive()
class GLImageStack(GLImage):
"""Data image PlotWidget item based on plot3d.scene"""
# TODO origin and scale taking 3 values
def __init__(self):
GLImage.__init__(self)
self.__index = 0
self.__axis = 0
self.__texture = None
def _initPrimitive(self):
return ColormapTexturedMesh3D(
position=numpy.zeros((4, 3), dtype=numpy.float32),
texcoord=numpy.zeros((4, 3), dtype=numpy.float32),
texture=None,
mode="triangle_strip",
)
def __updatePrimitive(self):
"""Update the vertices and tex coords"""
if self.__texture is None:
return
shape = self.__texture.getData(copy=False).shape
axis = self.getSliceAxis()
mesh = self.getScenePrimitive()
unitsquare = numpy.array(
[(0.0, 0.0, 0.0), (0.0, 1.0, 0.0), (1.0, 0.0, 0.0), (1.0, 1.0, 0.0)],
dtype=numpy.float32,
)
size = list(reversed(shape))
size.pop(2 - axis)
vertices = unitsquare[:, :2] * size
mesh.setAttribute("position", vertices, copy=False)
texcoord = numpy.array(unitsquare, copy=True)
texcoord[:, -1] = (self.getSliceIndex() + 0.5) / shape[axis]
texcoord = numpy.roll(texcoord, axis=1, shift=-axis)
mesh.setAttribute("texcoord", texcoord, copy=False)
def _updated(self, event=None, checkVisibility: bool = True):
if event == items.ItemChangedType.DATA:
self.__updatePrimitive()
self._setColormappedData(self.getData(copy=False), copy=False)
return super()._updated(event=event, checkVisibility=checkVisibility)
def _invalidateDataRange(self):
"""Invalidate PlotWidget data range if needed"""
# TODO hackish data range implementation
if self.isVisible():
plot = self.getPlot()
if plot is not None:
plot._invalidateDataRange()
def getRgbaImageData(self, copy: bool = True):
"""Get the displayed RGB(A) image
:returns: Array of uint8 of shape (height, width, 4)
:rtype: numpy.ndarray
"""
return self.getColormap().applyToData(self)
def getData(self, copy: bool = True):
"""Returns the image data
:param bool copy: True (Default) to get a copy,
False to use internal representation (do not modify!)
"""
slicing = [slice(None)] * 3
slicing[self.getSliceAxis()] = self.getSliceIndex()
return numpy.array(self.getStackData(copy=False)[tuple(slicing)], copy=copy)
def setData(self, data, copy: bool = True):
data = numpy.array(data, copy=False)
if data.ndim == 2: # Make it a 3D stack
data.shape = (1,) + data.shape
self.setStackData(data, copy)
def getStackData(self, copy: bool = True):
"""Returns the image stack data
:param bool copy: True (Default) to get a copy,
False to use internal representation (do not modify!)
"""
if self.__texture is None:
return numpy.zeros((0, 0, 0), dtype=numpy.float32)
else:
return self.__texture.getData(copy=copy)
def setStackData(self, data, copy: bool = True):
""" "Set the image stack data
:param numpy.ndarray data:
Data array with 3 dimensions (depth, height, width)
:param bool copy: True (Default) to make a copy,
False to use as is (do not modify!)
"""
data = numpy.array(data, copy=copy)
assert data.ndim == 3
if data.dtype.kind == "b":
_logger.warning("Converting boolean image to int8 to plot it.")
data = numpy.array(data, copy=False, dtype=numpy.int8)
elif numpy.iscomplexobj(data):
_logger.warning("Converting complex image to absolute value to plot it.")
data = numpy.absolute(data)
# TODO cast to valid type (u)int8|16 or float32