#
# annotations.py - 2D annotations on a SliceCanvas.
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
"""This module provides the :class:`Annotations` class, which implements
functionality to draw 2D OpenGL annotations on a :class:`.SliceCanvas`.
The :class:`Annotations` class is used by the :class:`.SliceCanvas` and
:class:`.LightBoxCanvas` classes, and users of those class, to annotate the
canvas.
All annotations derive from the :class:`AnnotationObject` base class. The
following annotation types are defined:
.. autosummary::
:nosignatures:
Line
Rect
VoxelGrid
VoxelSelection
"""
import logging
import time
import numpy as np
import OpenGL.GL as gl
import fsleyes.gl.globject as globject
import fsleyes.gl.routines as glroutines
import fsleyes.gl.resources as glresources
import fsleyes.gl.textures as textures
import fsleyes.gl.textures.data as texdata
import fsl.transform.affine as affine
log = logging.getLogger(__name__)
[docs]class Annotations(object):
"""An :class:`Annotations` object provides functionality to draw 2D
annotations on a :class:`.SliceCanvas`. Annotations may be enqueued via
any of the :meth:`line`, :meth:`rect`, :meth:`grid`, :meth:`selection` or
:meth:`obj`, methods.
A call to :meth:`draw` will then draw each of the queued annotations on
the canvas, and clear the queue.
If an annotation is to be persisted, it can be enqueued, as above, but
passing ``hold=True`` to the queueing method. The annotation will then
remain in the queue until it is removed via :meth:`dequeue`, or the
entire annotations queue is cleared via :meth:`clear`.
Annotations can be queued by one of the helper methods on the
:class:`Annotations` object (e.g. :meth:`line` or :meth:`rect`), or by
manually creating an :class:`AnnotationObject` and passing it to the
:meth:`obj` method.
"""
[docs] def __init__(self, canvas, xax, yax):
"""Creates an :class:`Annotations` object.
:arg canvas: The :class:`.SliceCanvas` that owns this
``Annotations`` object.
:arg xax: Index of the display coordinate system axis that
corresponds to the horizontal screen axis.
:arg yax: Index of the display coordinate system axis that
corresponds to the vertical screen axis.
"""
self.__q = []
self.__holdq = []
self.__xax = xax
self.__yax = yax
self.__zax = 3 - xax - yax
self.__canvas = canvas
@property
def canvas(self):
"""Returns a ref to the canvas that owns this ``Annotations`` instance.
"""
return self.__canvas
[docs] def setAxes(self, xax, yax):
"""This method must be called if the display orientation changes. See
:meth:`__init__`.
"""
self.__xax = xax
self.__yax = yax
self.__zax = 3 - xax - yax
[docs] def getDisplayBounds(self):
"""Returns a tuple containing the ``(xmin, xmax, ymin, ymax)`` display
bounds of the ``SliceCanvas`` that owns this ``Annotations`` object.
"""
return self.__canvas.opts.displayBounds
[docs] def line(self, *args, **kwargs):
"""Queues a line for drawing - see the :class:`Line` class. """
hold = kwargs.pop('hold', False)
obj = Line(self, *args, **kwargs)
return self.obj(obj, hold)
[docs] def rect(self, *args, **kwargs):
"""Queues a rectangle for drawing - see the :class:`Rectangle` class.
"""
hold = kwargs.pop('hold', False)
obj = Rect(self, *args, **kwargs)
return self.obj(obj, hold)
[docs] def grid(self, *args, **kwargs):
"""Queues a voxel grid for drawing - see the :class:`VoxelGrid` class.
"""
hold = kwargs.pop('hold', False)
obj = VoxelGrid(self, *args, **kwargs)
return self.obj(obj, hold)
[docs] def selection(self, *args, **kwargs):
"""Queues a selection for drawing - see the :class:`VoxelSelection`
class.
"""
hold = kwargs.pop('hold', False)
obj = VoxelSelection(self, *args, **kwargs)
return self.obj(obj, hold)
[docs] def text(self, *args, **kwargs):
"""Queues a text annotation for drawing - see the :class:`Text`
class.
"""
hold = kwargs.pop('hold', False)
obj = Text(self, *args, **kwargs)
return self.obj(obj, hold)
[docs] def obj(self, obj, hold=False):
"""Queues the given :class:`AnnotationObject` for drawing.
:arg hold: If ``True``, the given ``AnnotationObject`` will be kept in
the queue until it is explicitly removed. Otherwise (the
default), the object will be removed from the queue after
it has been drawn.
"""
if hold: self.__holdq.append(obj)
else: self.__q .append(obj)
return obj
[docs] def dequeue(self, obj, hold=False):
"""Removes the given :class:`AnnotationObject` from the queue, but
does not call its :meth:`.GLObject.destroy` method - this is the
responsibility of the caller.
"""
if hold:
try: self.__holdq.remove(obj)
except ValueError: pass
else:
try: self.__q.remove(obj)
except ValueError: pass
[docs] def clear(self):
"""Clears both the normal queue and the persistent (a.k.a. ``hold``)
queue, and calls the :meth:`.GLObject.destroy` method on every object
in the queue.
"""
for obj in self.__q: obj.destroy()
for obj in self.__holdq: obj.destroy()
self.__q = []
self.__holdq = []
[docs] def draw(self, zpos, xform=None, skipHold=False):
"""Draws all enqueued annotations.
:arg zpos: Position along the Z axis, above which all annotations
should be drawn.
:arg xform: Transformation matrix which should be applied to all
objects.
:arg skipHold: Do not draw items on the hold queue - only draw one-off
items.
"""
if not skipHold: objs = self.__holdq + self.__q
else: objs = self.__q
if xform is not None:
gl.glMatrixMode(gl.GL_MODELVIEW)
gl.glPushMatrix()
gl.glMultMatrixf(xform.ravel('F'))
drawTime = time.time()
axes = (self.__xax, self.__yax, self.__zax)
for obj in objs:
if obj.expired(drawTime): continue
if not obj.enabled: continue
if obj.zmin is not None and zpos < obj.zmin: continue
if obj.zmax is not None and zpos > obj.zmax: continue
if obj.xform is not None:
gl.glMatrixMode(gl.GL_MODELVIEW)
gl.glPushMatrix()
gl.glMultMatrixf(obj.xform.ravel('F'))
if obj.colour is not None:
if len(obj.colour) == 3: colour = list(obj.colour) + [1.0]
else: colour = list(obj.colour)
gl.glColor4f(*colour)
if obj.width is not None:
gl.glLineWidth(obj.width)
try:
obj.preDraw()
obj.draw2D(zpos, axes)
obj.postDraw()
except Exception as e:
log.warn('{}'.format(e), exc_info=True)
if obj.xform is not None:
gl.glPopMatrix()
if xform is not None:
gl.glMatrixMode(gl.GL_MODELVIEW)
gl.glPopMatrix()
# Clear the regular queue after each draw
self.__q = []
[docs]class AnnotationObject(globject.GLSimpleObject):
"""Base class for all annotation objects. An ``AnnotationObject`` is drawn
by an :class:`Annotations` instance. The ``AnnotationObject`` contains some
attributes which are common to all annotation types:
============ =============================================================
``colour`` Annotation colour
``width`` Annotation line width (if the annotation is made up of lines)
``xform`` Custom transformation matrix to apply to annotation vertices.
``expiry`` Time (in seconds) after which the annotation will expire and
not be drawn.
``zmin`` Minimum z value below which this annotation will not be
drawn.
``zmax`` Maximum z value above which this annotation will not be
drawn.
``creation`` Time of creation.
============ =============================================================
All of these attributes can be modified directly, after which you should
trigger a draw on the owning ``SliceCanvas`` to refresh the annotation.
You shouldn't touch the ``expiry`` or ``creation`` attributes though.
Subclasses must, at the very least, override the
:meth:`globject.GLObject.draw2D` method.
"""
[docs] def __init__(self,
annot,
xform=None,
colour=None,
width=None,
enabled=True,
expiry=None,
zmin=None,
zmax=None):
"""Create an ``AnnotationObject``.
:arg annot: The :class:`Annotations` object that created this
``AnnotationObject``.
:arg xform: Transformation matrix which will be applied to all
vertex coordinates.
:arg colour: RGB/RGBA tuple specifying the annotation colour.
:arg width: Line width to use for the annotation.
:arg enabled: Initially enabled or disabled.
:arg expiry: Time (in seconds) after which this annotation should be
expired and not drawn.
:arg zmin: Minimum z value below which this annotation should not
be drawn.
:arg zmax: Maximum z value above which this annotation should not
be drawn.
"""
globject.GLSimpleObject.__init__(self, False)
self.annot = annot
self.colour = colour
self.enabled = enabled
self.width = width
self.xform = xform
self.expiry = expiry
self.zmin = zmin
self.zmax = zmax
self.creation = time.time()
if self.xform is not None:
self.xform = np.array(self.xform, dtype=np.float32)
[docs] def resetExpiry(self):
"""Resets the expiry for this ``AnnotationObject`` so that it is
valid from the current time.
"""
self.creation = time.time()
[docs] def expired(self, now):
"""Returns ``True`` if this ``Annotation`` has expired, ``False``
otherwise.
:arg now: The current time
"""
if self.expiry is None:
return False
return (self.creation + self.expiry) < now
[docs] def preDraw(self, *args, **kwargs):
gl.glEnableClientState(gl.GL_VERTEX_ARRAY)
[docs] def postDraw(self, *args, **kwargs):
gl.glDisableClientState(gl.GL_VERTEX_ARRAY)
[docs]class Line(AnnotationObject):
"""The ``Line`` class is an :class:`AnnotationObject` which represents a
2D line.
"""
[docs] def __init__(self, annot, xy1, xy2, *args, **kwargs):
"""Create a ``Line`` annotation.
The ``xy1`` and ``xy2`` coordinate tuples should be in relation to the
axes which map to the horizontal/vertical screen axes on the target
canvas.
:arg annot: The :class:`Annotations` object that owns this ``Line``.
:arg xy1: Tuple containing the (x, y) coordinates of one endpoint.
:arg xy2: Tuple containing the (x, y) coordinates of the second
endpoint.
All other arguments are passed through to
:meth:`AnnotationObject.__init__`.
"""
AnnotationObject.__init__(self, annot, *args, **kwargs)
self.xy1 = xy1
self.xy2 = xy2
[docs] def draw2D(self, zpos, axes):
"""Draws this ``Line`` annotation. """
xax, yax, zax = axes
idxs = np.arange(2, dtype=np.uint32)
verts = np.zeros((2, 3), dtype=np.float32)
verts[0, [xax, yax]] = self.xy1
verts[1, [xax, yax]] = self.xy2
verts[:, zax] = zpos
verts = verts.ravel('C')
gl.glVertexPointer(3, gl.GL_FLOAT, 0, verts)
gl.glDrawElements(gl.GL_LINES, len(idxs), gl.GL_UNSIGNED_INT, idxs)
[docs]class Rect(AnnotationObject):
"""The ``Rect`` class is an :class:`AnnotationObject` which represents a
2D rectangle.
"""
[docs] def __init__(self,
annot,
xy,
w,
h,
filled=False,
fillColour=None,
*args,
**kwargs):
"""Create a :class:`Rect` annotation.
:arg annot: The :class:`Annotations` object that owns this
``Rect``.
:arg xy: Tuple specifying bottom left of the rectangle, in
the display coordinate system.
:arg w: Rectangle width.
:arg h: Rectangle height.
:arg filled: If ``True``, the rectangle is filled with the
``fillColour``.
:arg fillColour: If ``filled=True``, the colour to fill the rectangle
with. Defaults to a transparent version of the
``colour``.
All other arguments are passed through to
:meth:`AnnotationObject.__init__`.
"""
AnnotationObject.__init__(self, annot, *args, **kwargs)
self.xy = xy
self.w = w
self.h = h
self.filled = filled
self.fillColour = fillColour
[docs] def draw2D(self, zpos, axes):
"""Draws this ``Rectangle`` annotation. """
if self.w == 0 or self.h == 0:
return
xax, yax, zax = axes
xy = self.xy
w = self.w
h = self.h
bl = [xy[0], xy[1]]
br = [xy[0] + w, xy[1]]
tl = [xy[0], xy[1] + h]
tr = [xy[0] + w, xy[1] + h]
self.__drawRect(zpos, xax, yax, zax, bl, br, tl, tr)
if self.filled:
self.__drawFill(zpos, xax, yax, zax, bl, br, tl, tr)
def __drawFill(self, zpos, xax, yax, zax, bl, br, tl, tr):
"""Draw a filled version of the rectangle. """
fillColour = self.fillColour
if fillColour is None:
if self.colour is not None:
fillColour = list(self.colour[:3])
else:
fillColour = [1, 1, 1]
if len(fillColour) == 3:
fillColour = list(fillColour) + [0.2]
idxs = np.array([0, 1, 2, 2, 1, 3], dtype=np.uint32)
verts = np.zeros((4, 3), dtype=np.float32)
verts[0, [xax, yax]] = bl
verts[1, [xax, yax]] = br
verts[2, [xax, yax]] = tl
verts[3, [xax, yax]] = tr
verts[:, zax] = zpos
verts = verts.ravel('C')
# I'm assuming that glPolygonMode
# is already set to GL_FILL
gl.glColor4f(*fillColour)
gl.glVertexPointer(3, gl.GL_FLOAT, 0, verts)
gl.glDrawElements(gl.GL_TRIANGLES, len(idxs), gl.GL_UNSIGNED_INT, idxs)
def __drawRect(self, zpos, xax, yax, zax, bl, br, tl, tr):
"""Draw the rectangle outline. """
idxs = np.array([0, 1, 2, 3, 0, 2, 1, 3], dtype=np.uint32)
verts = np.zeros((4, 3), dtype=np.float32)
verts[0, [xax, yax]] = bl
verts[1, [xax, yax]] = br
verts[2, [xax, yax]] = tl
verts[3, [xax, yax]] = tr
verts[:, zax] = zpos
verts = verts.ravel('C')
gl.glVertexPointer(3, gl.GL_FLOAT, 0, verts)
gl.glDrawElements(gl.GL_LINES, len(idxs), gl.GL_UNSIGNED_INT, idxs)
[docs]class VoxelGrid(AnnotationObject):
"""The ``VoxelGrid`` is an :class:`AnnotationObject` which represents a
collection of selected voxels. See also the :class:`VoxelSelection`
annotation.
Each selected voxel is highlighted with a rectangle around its border.
"""
[docs] def __init__(self,
annot,
selectMask,
displayToVoxMat,
voxToDisplayMat,
offsets=None,
*args,
**kwargs):
"""Create a ``VoxelGrid`` annotation.
:arg annot: The :class:`Annotations` object that owns this
``VoxelGrid``.
:arg selectMask: A 3D numpy array, the same shape as the image
being annotated (or a sub-space of the image -
see the ``offsets`` argument), which is
interpreted as a mask array - values which are
``True`` denote selected voxels.
:arg displayToVoxMat: A transformation matrix which transforms from
display space coordinates into voxel space
coordinates.
:arg voxToDisplayMat: A transformation matrix which transforms from
voxel coordinates into display space
coordinates.
:arg offsets: If ``None`` (the default), the ``selectMask``
must have the same shape as the image data
being annotated. Alternately, you may set
``offsets`` to a sequence of three values,
which are used as offsets for the xyz voxel
values. This is to allow for a sub-space of
the full image space to be annotated.
"""
kwargs['xform'] = voxToDisplayMat
AnnotationObject.__init__(self, annot, *args, **kwargs)
if offsets is None:
offsets = [0, 0, 0]
self.displayToVoxMat = displayToVoxMat
self.selectMask = selectMask
self.offsets = offsets
[docs] def draw2D(self, zpos, axes):
"""Draws this ``VoxelGrid`` annotation. """
xax, yax, zax = axes
dispLoc = [0] * 3
dispLoc[zax] = zpos
voxLoc = affine.transform([dispLoc], self.displayToVoxMat)[0]
vox = int(round(voxLoc[zax]))
restrictions = [slice(None)] * 3
restrictions[zax] = slice(vox - self.offsets[zax],
vox - self.offsets[zax] + 1)
xs, ys, zs = np.where(self.selectMask[restrictions])
voxels = np.vstack((xs, ys, zs)).T
for ax in range(3):
off = restrictions[ax].start
if off is None:
off = 0
voxels[:, ax] += off + self.offsets[ax]
verts, idxs = glroutines.voxelGrid(voxels, xax, yax, 1, 1)
verts = verts.ravel('C')
gl.glVertexPointer(3, gl.GL_FLOAT, 0, verts)
gl.glDrawElements(gl.GL_LINES, len(idxs), gl.GL_UNSIGNED_INT, idxs)
[docs]class VoxelSelection(AnnotationObject):
"""A ``VoxelSelection`` is an :class:`AnnotationObject` which draws
selected voxels from a :class:`.selection.Selection` instance. A
:class:`.SelectionTexture` is used to draw the selected voxels.
"""
[docs] def __init__(self,
annot,
selection,
opts,
offsets=None,
*args,
**kwargs):
"""Create a ``VoxelSelection`` annotation.
:arg annot: The :class:`Annotations` object that owns this
``VoxelSelection``.
:arg selection: A :class:`.selection.Selection` instance which defines
the voxels to be highlighted.
:arg opts: A :class:`.NiftiOpts` instance which is used
for its voxel-to-display transformation matrices.
:arg offsets: If ``None`` (the default), the ``selection`` must have
the same shape as the image data being
annotated. Alternately, you may set ``offsets`` to a
sequence of three values, which are used as offsets
for the xyz voxel values. This is to allow for a
sub-space of the full image space to be annotated.
All other arguments are passed through to the
:meth:`AnnotationObject.__init__` method.
"""
AnnotationObject.__init__(self, annot, *args, **kwargs)
if offsets is None:
offsets = [0, 0, 0]
self.__selection = selection
self.__opts = opts
self.__offsets = offsets
texName = '{}_{}'.format(type(self).__name__, id(selection))
ndims = texdata.numTextureDims(selection.shape)
if ndims == 2: ttype = textures.SelectionTexture2D
else: ttype = textures.SelectionTexture3D
self.__texture = glresources.get(
texName,
ttype,
texName,
selection)
[docs] def destroy(self):
"""Must be called when this ``VoxelSelection`` is no longer needed.
Destroys the :class:`.SelectionTexture`.
"""
glresources.delete(self.__texture.name)
self.__texture = None
self.__opts = None
@property
def texture(self):
"""Return the :class:`.SelectionTexture` used by this
``VoxelSelection``.
"""
return self.__texture
[docs] def draw2D(self, zpos, axes):
"""Draws this ``VoxelSelection``."""
xax, yax = axes[:2]
opts = self.__opts
texture = self.__texture
shape = self.__selection.getSelection().shape
displayToVox = opts.getTransform('display', 'voxel')
voxToDisplay = opts.getTransform('voxel', 'display')
voxToTex = opts.getTransform('voxel', 'texture')
voxToTex = affine.concat(texture.texCoordXform(shape), voxToTex)
verts, voxs = glroutines.slice2D(shape,
xax,
yax,
zpos,
voxToDisplay,
displayToVox)
texs = affine.transform(voxs, voxToTex)[:, :texture.ndim]
verts = np.array(verts, dtype=np.float32).ravel('C')
texs = np.array(texs, dtype=np.float32).ravel('C')
texture.bindTexture(gl.GL_TEXTURE0)
gl.glClientActiveTexture(gl.GL_TEXTURE0)
gl.glTexEnvf(gl.GL_TEXTURE_ENV, gl.GL_TEXTURE_ENV_MODE, gl.GL_MODULATE)
with glroutines.enabled((texture.target,
gl.GL_TEXTURE_COORD_ARRAY,
gl.GL_VERTEX_ARRAY)):
gl.glVertexPointer( 3, gl.GL_FLOAT, 0, verts)
gl.glTexCoordPointer(texture.ndim, gl.GL_FLOAT, 0, texs)
gl.glDrawArrays( gl.GL_TRIANGLES, 0, 6)
texture.unbindTexture()
[docs]class Text(AnnotationObject):
"""A ``Text`` is an :class:`AnnotationObject` which draws a string of
text on the display.
"""
[docs] def __init__(self,
annot,
text,
xpos,
ypos,
fontSize=10,
xoff=None,
yoff=None,
halign=None,
valign=None,
bgColour=None,
angle=None,
*args,
**kwargs):
"""Create a ``Text`` annotation.
:arg annot: The :class:`Annotations` object that owns this
``Text``.
:arg text: The text to draw.
:arg xpos: Position along the horizontal axis as a proportion
between 0 (left) and 1 (right).
:arg xpos: Position along the vertial axis as a proportion
between 0 (bottom) and 1 (top).
:arg xoff: Fixed horizontal offset in pixels
:arg yoff: Fixed vertical offset in pixels
:arg fontSize: Font size.
:arg halign: Horizontal alignemnt - ``'left'``, ``'centre'``, or
``right``.
:arg valign: Vertical alignemnt - ``'bottom'``, ``'centre'``, or
``top``.
:arg bcColour: If not ``None``, a border will be drawn around the
text.
:arg angle: Angle, in degrees, by which to rotate the text.
NOT IMPLEMENTED YET
"""
AnnotationObject.__init__(self, annot, *args, **kwargs)
# We need to know the text size in pixels
# in order to correctly align/offset the
# text on the display. But we don't want
# to have to calculate the size on every
# draw. Therefore, updates to the text and
# font size attributes are protected,
# because they affect the final pixel text
# size. When they are changed, we clear the
# __textSize attribute to indicate that the
# text size needs to be re-calculated.
self.__text = text
self.__fontSize = fontSize
self.__textSize = None
self.xpos = xpos
self.ypos = ypos
self.xoff = xoff
self.yoff = yoff
self.bgColour = bgColour
self.halign = halign
self.valign = valign
self.angle = angle
@property
def text(self):
"""Returns the current text value."""
return self.__text
@text.setter
def text(self, value):
"""Update the text."""
self.__text = value
self.__textSize = None
@property
def fontSize(self):
"""Returns the current font size."""
return self.__fontSize
@fontSize.setter
def fontSize(self, value):
"""Update the font size."""
self.__fontSize = value
self.__textSize = None
[docs] def draw2D(self, zpos, axes):
"""Draws this ``Text`` annotation. """
canvasSize = self.annot.canvas.GetSize()
pos = [self.xpos * canvasSize[0], self.ypos * canvasSize[1]]
if self.__textSize is None:
self.__textSize = glroutines.text2D(self.text,
pos,
self.fontSize,
canvasSize,
calcSize=True)
textSize = self.__textSize
if self.halign == 'centre': pos[0] -= textSize[0] / 2.0
elif self.halign == 'right': pos[0] -= textSize[0]
if self.valign == 'centre': pos[1] -= textSize[1] / 2.0
elif self.valign == 'top': pos[1] -= textSize[1]
if self.xoff is not None: pos[0] += self.xoff
if self.yoff is not None: pos[1] += self.yoff
glroutines.text2D(self.text, pos, self.fontSize, canvasSize)