def test_surface():
N = 128
x = np.linspace(-1,1,N)
Z,Y,X = np.meshgrid(x,x,x,indexing="ij")
R = np.sqrt(X**2+Y**2+Z**2)
data = 900.*np.exp(-10*R)
#data = 200*(1+Z)
rend = VolumeRenderer((400,400))
rend.set_modelView(mat4_translate(0,0,-5.))
rend.render(data=data.astype(np.uint16), maxVal = 20., method="iso_surface")
#rend.render(data=data.astype(np.float32), maxVal = 100., method="max_project")
# drawing
plt.ion()
plt.figure(1)
plt.clf()
plt.imshow(rend.output)
plt.axis("off")
plt.show()
plt.pause(1.)
plt.close()
return rend
def test_speed_multipass():
import time
from gputools import get_device
N = 256
x = np.linspace(-1, 1, N)
Z, Y, X = np.meshgrid(x, x, x, indexing="ij")
R = np.sqrt(X ** 2 + Y ** 2 + Z ** 2)
d = 200 * np.exp(-10 * R ** 2)
rend = VolumeRenderer((800,) * 2)
rend.set_modelView(mat4_translate(0, 0, -10.))
rend.set_data(d.astype(np.float32))
get_device().queue.finish()
for niter in range(1, 10):
get_device().queue.finish()
t = time.time()
rend.render(method="max_project", maxVal=200.,
currentPart=0, numParts=niter)
get_device().queue.finish()
print("time to render with %s substeps:\t %.2f ms" % (niter, 1000 * (time.time() - t)))
return rend
def test_surface():
N = 128
x = np.linspace(-1, 1, N)
Z, Y, X = np.meshgrid(x, x, x, indexing="ij")
R = np.sqrt(X**2 + Y**2 + Z**2)
data = 900. * np.exp(-10 * R)
#data = 200*(1+Z)
rend = VolumeRenderer((400, 400))
rend.set_modelView(mat4_translate(0, 0, -5.))
rend.render(data=data.astype(np.uint16), maxVal=20., method="iso_surface")
#rend.render(data=data.astype(np.float32), maxVal = 100., method="max_project")
# drawing
#plt.ioff()
plt.figure(1)
plt.clf()
plt.imshow(rend.output)
plt.axis("off")
plt.close()
plt.show()
plt.pause(.1)
plt.close()
return rend
def test_speed_multipass():
import time
from gputools import get_device
N = 256
x = np.linspace(-1, 1, N)
Z, Y, X = np.meshgrid(x, x, x, indexing="ij")
R = np.sqrt(X**2 + Y**2 + Z**2)
d = 200 * np.exp(-10 * R**2)
rend = VolumeRenderer((800, ) * 2)
rend.set_modelView(mat4_translate(0, 0, -10.))
rend.set_data(d.astype(np.float32))
get_device().queue.finish()
for niter in range(1, 10):
get_device().queue.finish()
t = time.time()
rend.render(method="max_project",
maxVal=200.,
currentPart=0,
numParts=niter)
get_device().queue.finish()
print("time to render with %s substeps:\t %.2f ms" %
(niter, 1000 * (time.time() - t)))
return rend
def render_iso(data, t = -.8):
from gputools.utils.utils import remove_cache_dir, get_cache_dir
remove_cache_dir()
rend = VolumeRenderer((400,400))
# rend.set_occ_strength(0)
# rend.set_occ_radius(21)
# rend.set_occ_n_points(30)
rend.set_modelView(mat4_translate(0, 0, t))
rend.render(data, maxVal = 130., method="iso_surface")
return rend
def render_iso(data, is_ao=True):
from gputools.utils.utils import remove_cache_dir, get_cache_dir
remove_cache_dir()
rend = VolumeRenderer((400, 400))
if is_ao:
rend.set_occ_strength(1)
rend.set_occ_radius(101)
rend.set_occ_n_points(1000)
else:
rend.set_occ_strength(0)
rend.set_occ_radius(21)
rend.set_occ_n_points(30)
rend.set_modelView(mat4_translate(0, 0, -1.))
rend.render(data, maxVal=70., method="iso_surface")
return rend
def test_opacity():
N = 128
x = np.linspace(-1, 1, N)
Z, Y, X = np.meshgrid(x, x, x, indexing="ij")
R = np.sqrt(X**2 + Y**2 + Z**2)
d = 200 * np.exp(-10 * R**2)
rend = VolumeRenderer((600, ) * 2)
rend.set_modelView(mat4_translate(0, 0, -10.))
rend.set_alpha_pow(.6)
rend.set_data(d.astype(np.float32))
rend.render(method="max_project", maxVal=200.)
out = rend.output
plt.imshow(out, cmap="magma")
plt.axis("off")
plt.show()
return rend
def test_time_to_render():
import time
from gputools import get_device
get_device().print_info()
N = 256
x = np.linspace(-1, 1, N)
Z, Y, X = np.meshgrid(x, x, x, indexing="ij")
R = np.sqrt(X**2+Y**2+Z**2)
d = 10000*np.exp(-10*R**2)
rend = VolumeRenderer((600, 600))
rend.set_modelView(mat4_translate(0, 0, -10.))
# rend.set_box_boundaries(.3*np.array([-1,1,-1,1,-1,1]))
t1 = time.time()
get_device().queue.finish()
rend.set_data(d, autoConvert=True)
get_device().queue.finish()
t2 = time.time()
get_device().queue.finish()
rend.render(maxVal=10000.)
out = rend.output
get_device().queue.finish()
print("time to set data %s^3:\t %.2f ms"%(N, 1000*(t2-t1)))
print("time to render %s^3:\t %.2f ms"%(N, 1000*(time.time()-t2)))
return d, rend, out
def test_opacity():
N = 128
x = np.linspace(-1, 1, N)
Z, Y, X = np.meshgrid(x, x, x, indexing="ij")
R = np.sqrt(X ** 2 + Y ** 2 + Z ** 2)
d = 200 * np.exp(-10 * R ** 2)
rend = VolumeRenderer((600,) * 2)
rend.set_modelView(mat4_translate(0, 0, -10.))
rend.set_alpha_pow(.6)
rend.set_data(d.astype(np.float32))
rend.render(method="max_project", maxVal=200.)
out = rend.output
plt.imshow(out, cmap="magma")
plt.axis("off")
plt.show()
return rend
def test_time_to_render():
import time
from gputools import get_device
get_device().print_info()
N = 256
x = np.linspace(-1, 1, N)
Z, Y, X = np.meshgrid(x, x, x, indexing="ij")
R = np.sqrt(X**2 + Y**2 + Z**2)
d = 10000 * np.exp(-10 * R**2)
rend = VolumeRenderer((600, 600))
rend.set_modelView(mat4_translate(0, 0, -10.))
# rend.set_box_boundaries(.3*np.array([-1,1,-1,1,-1,1]))
t1 = time.time()
get_device().queue.finish()
rend.set_data(d, autoConvert=True)
get_device().queue.finish()
t2 = time.time()
get_device().queue.finish()
rend.render(maxVal=10000.)
out = rend.output
get_device().queue.finish()
print("time to set data %s^3:\t %.2f ms" % (N, 1000 * (t2 - t1)))
print("time to render %s^3:\t %.2f ms" % (N, 1000 * (time.time() - t2)))
return d, rend, out
class GLWidget(QtOpenGL.QGLWidget):
_dataModelChanged = QtCore.pyqtSignal()
_BACKGROUND_BLACK = (0., 0., 0., 0.)
_BACKGROUND_WHITE = (1., 1., 1., 0.)
def __init__(self,
parent=None,
N_PREFETCH=0,
interpolation="linear",
**kwargs):
logger.debug("init")
#
# fmt = QtOpenGL.QGLFormat(QtOpenGL.QGL.AlphaChannel)
#
# super(GLWidget, self).__init__(fmt,parent, **kwargs)
super(GLWidget, self).__init__(parent, **kwargs)
self.parent = parent
self.texture_LUT = None
self.setAcceptDrops(True)
self.renderer = VolumeRenderer(
(spimagine.config.__DEFAULT_TEXTURE_WIDTH__,
spimagine.config.__DEFAULT_TEXTURE_WIDTH__),
interpolation=interpolation)
self.renderer.set_projection(mat4_perspective(60, 1., .1, 100))
# self.renderer.set_projection(projMatOrtho(-2,2,-2,2,-10,10))
self.output = np.zeros([self.renderer.height, self.renderer.width],
dtype=np.float32)
self.output_alpha = np.zeros(
[self.renderer.height, self.renderer.width], dtype=np.float32)
self.sliceOutput = np.zeros((100, 100), dtype=np.float32)
self.setTransform(TransformModel())
self.renderTimer = QtCore.QTimer(self)
self.renderTimer.setInterval(10)
self.renderTimer.timeout.connect(self.onRenderTimer)
self.renderTimer.start()
self.renderedSteps = 0
self.N_PREFETCH = N_PREFETCH
self.NSubrenderSteps = 1
self.dataModel = None
self.meshes = []
# self.setMouseTracking(True)
self._dataModelChanged.connect(self.dataModelChanged)
self.refresh()
# self.installEventFilter(self)
def set_background_mode_black(self, mode_back=True):
self._background_mode_black = mode_back
self.refresh()
def setModel(self, dataModel):
logger.debug("setModel to %s" % dataModel)
if self.dataModel is None or (self.dataModel != dataModel):
self.dataModel = dataModel
self.transform.setModel(dataModel)
self.dataModel._dataSourceChanged.connect(self.dataSourceChanged)
self.dataModel._dataPosChanged.connect(self.dataPosChanged)
self._dataModelChanged.emit()
def dragEnterEvent(self, event):
if event.mimeData().hasUrls():
event.accept()
else:
event.ignore()
def dropEvent(self, event):
for url in event.mimeData().urls():
# path = url.toLocalFile().toLocal8Bit().data()
path = url.toLocalFile()
if spimagine.config.__SYSTEM_DARWIN__:
path = spimagine.config._parseFileNameFix(path)
self.setCursor(QtCore.Qt.BusyCursor)
if self.dataModel:
self.dataModel.loadFromPath(path, prefetchSize=self.N_PREFETCH)
else:
self.setModel(
DataModel.fromPath(path, prefetchSize=self.N_PREFETCH))
self.setCursor(QtCore.Qt.ArrowCursor)
def set_colormap(self, name):
"""name should be either jet, hot, gray, coolwarm"""
try:
arr = spimagine.config.__COLORMAPDICT__[name]
self._set_colormap_array(arr)
except KeyError:
print("could not load colormap '%s'" % name)
print("valid names: %s" %
list(spimagine.config.__COLORMAPDICT__.keys()))
def set_colormap_rgb(self, color=[1., 1., 1.]):
self._set_colormap_array(
np.outer(np.linspace(0, 1., 255), np.array(color)))
def _set_colormap_array(self, arr):
"""arr should be of shape (N,3) and gives the rgb components of the colormap"""
self.makeCurrent()
self.texture_LUT = fillTexture2d(arr.reshape((1, ) + arr.shape),
self.texture_LUT)
self.refresh()
def _shader_from_file(self, fname_vert, fname_frag):
shader = QOpenGLShaderProgram()
shader.addShaderFromSourceFile(QOpenGLShader.Vertex, fname_vert)
shader.addShaderFromSourceFile(QOpenGLShader.Fragment, fname_frag)
shader.link()
shader.bind()
logger.debug("GLSL program log:%s", shader.log())
return shader
def initializeGL(self):
self.resized = True
logger.debug("initializeGL")
self.programTex = self._shader_from_file(
absPath("shaders/texture.vert"), absPath("shaders/texture.frag"))
self.programCube = self._shader_from_file(absPath("shaders/box.vert"),
absPath("shaders/box.frag"))
self.programSlice = self._shader_from_file(
absPath("shaders/slice.vert"), absPath("shaders/slice.frag"))
self.programMesh = self._shader_from_file(absPath("shaders/mesh.vert"),
absPath("shaders/mesh.frag"))
self.programMeshLight = self._shader_from_file(
absPath("shaders/mesh_light.vert"),
absPath("shaders/mesh_light.frag"))
self.texture = None
self.textureAlpha = None
self.textureSlice = None
self.quadCoord = np.array([[-1., -1., 0.], [1., -1., 0.], [1., 1., 0.],
[1., 1., 0.], [-1., 1., 0.], [-1., -1.,
0.]])
self.quadCoordTex = np.array([[0, 0], [1., 0.], [1., 1.], [1., 1.],
[0, 1.], [0, 0]])
# self.cubeCoords = create_cube_coords([-1,1,-1,1,-1,1])
self.set_colormap(spimagine.config.__DEFAULTCOLORMAP__)
glEnable(GL_BLEND)
# glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA)
# self.set_interpolation(spimagine.config.__DEFAULT_INTERP__ != "nearest")
# glLineWidth(1.0);
glBlendFunc(GL_ONE, GL_ONE)
glEnable(GL_LINE_SMOOTH)
glDisable(GL_DEPTH_TEST)
glLineWidth(spimagine.config.__DEFAULT_BOX_LINEWIDTH__)
# self.set_background_color(0,0,0,.0)
self.set_background_mode_black(True)
self.clear_canvas()
# self.set_background_color(1,1,1,.6)
def clear_canvas(self):
if self._background_mode_black:
glClearColor(*self._BACKGROUND_BLACK)
else:
glClearColor(*self._BACKGROUND_WHITE)
if glCheckFramebufferStatus(GL_FRAMEBUFFER) == GL_FRAMEBUFFER_COMPLETE:
glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT)
def set_interpolation(self, interpolate=True):
interp = "linear" if interpolate else "nearest"
self.renderer.rebuild_program(interpolation=interp)
self.refresh()
def setTransform(self, transform):
self.transform = transform
self.transform._transformChanged.connect(self.refresh)
self.transform._stackUnitsChanged.connect(self.setStackUnits)
self.transform._boundsChanged.connect(self.setBounds)
def dataModelChanged(self):
logger.debug("+++++++++ data model changed")
if self.dataModel:
logger.debug("dataModelchanged")
self.renderer.set_data(self.dataModel[0], autoConvert=True)
mi, ma = self._get_min_max()
self.transform.reset(minVal=mi,
maxVal=ma,
stackUnits=self.dataModel.stackUnits())
self.meshes = []
self.refresh()
def _get_min_max(self):
# as amax is too slow for bug arrays, do it on the gpu
if self.dataModel:
try:
im = self.renderer.dataImg
tmp_buf = OCLArray.empty(im.shape, im.dtype)
tmp_buf.copy_image(im)
mi = float(cl_array.min(tmp_buf).get())
ma = float(cl_array.max(tmp_buf).get())
except Exception as e:
print(e)
mi = np.amin(self.dataModel[0])
ma = np.amax(self.dataModel[0])
return mi, ma
def set_background_color(self, r, g, b, a=1.):
self._background_color = (r, g, b, a)
glClearColor(r, g, b, a)
def dataSourceChanged(self):
logger.debug("dataSourcechanged")
self.renderer.set_data(self.dataModel[0], autoConvert=True)
mi, ma = self._get_min_max()
self.transform.reset(minVal=mi,
maxVal=ma,
stackUnits=self.dataModel.stackUnits())
self.refresh()
def setBounds(self, x1, x2, y1, y2, z1, z2):
self.cubeCoords = create_cube_coords([x1, x2, y1, y2, z1, z2])
self.renderer.set_box_boundaries([x1, x2, y1, y2, z1, z2])
def setStackUnits(self, px, py, pz):
logger.debug("setStackUnits to %s" % [px, py, pz])
self.renderer.set_units([px, py, pz])
def dataPosChanged(self, pos):
self.renderer.update_data(self.dataModel[pos])
self.refresh()
def refresh(self):
# if self.parentWidget() and self.dataModel:
# self.parentWidget().setWindowTitle("SpImagine %s"%self.dataModel.name())
self.renderUpdate = True
self.renderedSteps = 0
def resizeGL(self, width, height):
# somehow in qt5 the OpenGLWidget width/height parameters above are double the value of self.width/height
self._viewport_width, self._viewport_height = width, height
def add_mesh(self, mesh=SphericalMesh()):
"""
adds a mesh with vertices and facecolor/edgecolor to be drawn
mesh is an instance of spimagine.gui.Mesh, e.g.
mesh = Mesh(vertices = [[0,1,0],[0,1,0],...],
normals = [[0,1,0],[0,1,0],...],
facecolor = (1.,.4,.4,.2),
edgecolor = None,...)
there are some predefined meshes like
SphericalMesh, EllipsoidMesh ...
"""
self.meshes.append([
mesh,
glvbo.VBO(mesh.vertices.astype(np.float32, copy=False)),
glvbo.VBO(np.array(mesh.normals).astype(np.float32, copy=False)),
glvbo.VBO(np.array(mesh.indices).astype(np.uint32, copy=False),
target=GL_ELEMENT_ARRAY_BUFFER)
])
self.refresh()
# sort according to opacity as the opaque objects should be drawn first
# self.meshes.sort(key=lambda x: x[0].alpha, reverse=True)
def _paintGL_render(self):
# Draw the render texture
self.programTex.bind()
self.texture = fillTexture2d(self.output, self.texture)
# self.textureAlpha = fillTexture2d(self.output_alpha, self.textureAlpha)
glEnable(GL_BLEND)
glEnable(GL_TEXTURE_2D)
glDisable(GL_DEPTH_TEST)
self.programTex.enableAttributeArray("position")
self.programTex.enableAttributeArray("texcoord")
self.programTex.setAttributeArray("position", self.quadCoord)
self.programTex.setAttributeArray("texcoord", self.quadCoordTex)
self.programTex.setUniformValue("is_mode_black",
self._background_mode_black)
glActiveTexture(GL_TEXTURE0)
glBindTexture(GL_TEXTURE_2D, self.texture)
self.programTex.setUniformValue("texture", 0)
glActiveTexture(GL_TEXTURE1)
glBindTexture(GL_TEXTURE_2D, self.textureAlpha)
self.programTex.setUniformValue("texture_alpha", 1)
glActiveTexture(GL_TEXTURE2)
glBindTexture(GL_TEXTURE_2D, self.texture_LUT)
self.programTex.setUniformValue("texture_LUT", 2)
glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA)
glDrawArrays(GL_TRIANGLES, 0, len(self.quadCoord))
def _paintGL_slice(self):
# draw the slice
self.programSlice.bind()
self.programSlice.setUniformValue(
"mvpMatrix",
QtGui.QMatrix4x4(*self._mat_modelviewproject.flatten()))
self.programSlice.setUniformValue("is_mode_black",
self._background_mode_black)
self.programSlice.enableAttributeArray("position")
pos, dim = self.transform.slicePos, self.transform.sliceDim
coords = slice_coords(1. * pos / self.dataModel.size()[2 - dim + 1],
dim)
texcoords = [[0., 0.], [1, 0.], [1., 1.], [1., 1.], [0., 1.], [0., 0.]]
self.programSlice.setAttributeArray("position", coords)
self.programSlice.setAttributeArray("texcoord", texcoords)
self.textureSlice = fillTexture2d(self.sliceOutput, self.textureSlice)
glActiveTexture(GL_TEXTURE0)
glBindTexture(GL_TEXTURE_2D, self.textureSlice)
self.programSlice.setUniformValue("texture", 0)
glActiveTexture(GL_TEXTURE1)
glBindTexture(GL_TEXTURE_2D, self.texture_LUT)
self.programSlice.setUniformValue("texture_LUT", 1)
glDrawArrays(GL_TRIANGLES, 0, len(coords))
def _paintGL_box(self):
glEnable(GL_BLEND)
# Draw the cube
self.programCube.bind()
self.programCube.setUniformValue(
"mvpMatrix",
QtGui.QMatrix4x4(*self._mat_modelviewproject.flatten()))
self.programCube.enableAttributeArray("position")
if self._background_mode_black:
self.programCube.setUniformValue("color",
QtGui.QVector4D(1, 1, 1, 0.6))
else:
self.programCube.setUniformValue("color",
QtGui.QVector4D(0, 0, 0, 0.6))
self.programCube.setAttributeArray("position", self.cubeCoords)
glActiveTexture(GL_TEXTURE0)
glBindTexture(GL_TEXTURE_2D, self.textureAlpha)
self.programCube.setUniformValue("texture_alpha", 0)
glEnable(GL_DEPTH_TEST)
# glBlendFunc(GL_ONE_MINUS_SRC_ALPHA, GL_SRC_ALPHA)
glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA)
glDrawArrays(GL_LINES, 0, len(self.cubeCoords))
glDisable(GL_DEPTH_TEST)
def _paintGL_mesh(self, mesh, vbo_vertices, vbo_normals, vbo_indices):
"""
paint a mesh (which has all the coordinates and colors in it
"""
glEnable(GL_DEPTH_TEST)
glDisable(GL_BLEND)
prog = self.programMeshLight
prog.bind()
prog.setUniformValue(
"mvpMatrix",
QtGui.QMatrix4x4(*self._mat_modelviewproject.flatten()))
prog.setUniformValue("mvMatrix",
QtGui.QMatrix4x4(*self._mat_modelview.flatten()))
prog.setUniformValue("normMatrix",
QtGui.QMatrix4x4(*self._mat_normal.flatten()))
if mesh.light:
prog.setUniformValue("light", QtGui.QVector3D(*mesh.light))
prog.setUniformValue("light_components",
QtGui.QVector3D(.2, .5, .3))
else:
prog.setUniformValue("light", QtGui.QVector3D(0, 0, 0))
prog.setUniformValue("light_components", QtGui.QVector3D(1., 0, 0))
if not mesh.facecolor is None:
r, g, b = mesh.facecolor[:3]
a = mesh.alpha
prog.setUniformValue("color", QtGui.QVector4D(r, g, b, a))
prog.enableAttributeArray("position")
vbo_vertices.bind()
glVertexAttribPointer(prog.attributeLocation("position"), 3,
GL_FLOAT, GL_FALSE, 0, vbo_vertices)
prog.enableAttributeArray("normal")
vbo_normals.bind()
glVertexAttribPointer(prog.attributeLocation("normal"), 3,
GL_FLOAT, GL_FALSE, 0, vbo_normals)
vbo_indices.bind()
glDrawElements(GL_TRIANGLES, len(vbo_indices.data),
GL_UNSIGNED_INT, None)
vbo_indices.unbind()
vbo_vertices.unbind()
glDisable(GL_DEPTH_TEST)
prog.disableAttributeArray("position")
prog.disableAttributeArray("normal")
#
# if not mesh.edgecolor is None:
# r, g, b = mesh.edgecolor
# a = mesh.alpha
#
# prog.enableAttributeArray("position")
# vbo_vertices.bind()
# glVertexAttribPointer(prog.attributeLocation("position"), 2, GL_FLOAT, GL_FALSE, 0, vbo_edges)
#
# prog.setUniformValue("color",
# QtGui.QVector4D(r, g, b, a))
#
# glDrawArrays(GL_LINES, 0, len(mesh.edges))
def paintGL(self):
self.makeCurrent()
if not glCheckFramebufferStatus(
GL_FRAMEBUFFER) == GL_FRAMEBUFFER_COMPLETE:
return
w = max(self._viewport_width, self._viewport_height)
# force viewport to always be a square
glViewport((self._viewport_width - w) // 2,
(self._viewport_height - w) // 2, w, w)
self.clear_canvas()
self._mat_modelview = self.transform.getModelView()
self._mat_proj = self.transform.getProjection()
self._mat_normal = np.linalg.inv(self._mat_modelview).T
self._mat_modelviewproject = np.dot(self._mat_proj,
self._mat_modelview)
if self.dataModel:
self.textureAlpha = fillTexture2d(self.output_alpha,
self.textureAlpha)
if self.transform.isBox:
self._paintGL_box()
if self.transform.isSlice and self.sliceOutput is not None:
self._paintGL_slice()
self._paintGL_render()
for (m, vbo_verts, vbo_normals, vbo_indices) in self.meshes:
self._paintGL_mesh(m, vbo_verts, vbo_normals, vbo_indices)
def render(self):
logger.debug("render")
if self.dataModel:
self.renderer.set_modelView(self.transform.getUnscaledModelView())
self.renderer.set_projection(self.transform.getProjection())
self.renderer.set_min_val(self.transform.minVal)
self.renderer.set_max_val(self.transform.maxVal)
self.renderer.set_gamma(self.transform.gamma)
self.renderer.set_alpha_pow(self.transform.alphaPow)
self.renderer.set_occ_strength(self.transform.occ_strength)
self.renderer.set_occ_radius(self.transform.occ_radius)
self.renderer.set_occ_n_points(self.transform.occ_n_points)
if self.transform.isIso:
renderMethod = "iso_surface"
else:
renderMethod = "max_project"
self.renderer.render(
method=renderMethod,
return_alpha=True,
numParts=self.NSubrenderSteps,
currentPart=(self.renderedSteps *
_next_golden(self.NSubrenderSteps)) %
self.NSubrenderSteps)
self.output, self.output_alpha = self.renderer.output, self.renderer.output_alpha
if self.transform.isSlice:
if self.transform.sliceDim == 0:
out = self.dataModel[
self.transform.dataPos][:, :, self.transform.slicePos]
elif self.transform.sliceDim == 1:
out = self.dataModel[
self.transform.dataPos][:, self.transform.slicePos, :]
elif self.transform.sliceDim == 2:
out = self.dataModel[self.transform.dataPos][
self.transform.slicePos, :, :]
min_out, max_out = np.amin(out), np.amax(out)
if max_out > min_out:
self.sliceOutput = (1. * (out - min_out) /
(max_out - min_out))
else:
self.sliceOutput = np.zeros_like(out)
# def getFrame(self):
# self.render()
# self.paintGL()
# glFlush()
# im = self.grabFrameBuffer()
# im = im.convertToFormat(QtGui.QImage.Format_RGB32)
#
# width = im.width()
# height = im.height()
#
# ptr = im.bits()
# ptr.setsize(im.byteCount())
# arr = np.array(ptr).reshape(height, width, 4) # Copies the data
# return arr[..., [2, 1, 0, 3]].copy()
def saveFrame(self, fName, with_alpha=False):
"""FIXME: scaling behaviour still hast to be implemented (e.g. after setGamma)"""
logger.info("saving frame as %s", fName)
# has to be png
name, ext = os.path.splitext(fName)
if ext != ".png":
fName = name + ".png"
self.render()
self.paintGL()
glFlush()
im = self.grabFrameBuffer(withAlpha=with_alpha)
im.save(fName)
def onRenderTimer(self):
# if self.renderUpdate:
# self.render()
# self.renderUpdate = False
# self.updateGL()
if self.renderedSteps < self.NSubrenderSteps:
# print ((self.renderedSteps*7)%self.NSubrenderSteps)
s = time.time()
self.render()
logger.debug("time to render: %.2f" % (1000. * (time.time() - s)))
self.renderedSteps += 1
self.updateGL()
def wheelEvent(self, event):
""" self.transform.zoom should be within [1,2]"""
newZoom = self.transform.zoom * 1.2**(event.angleDelta().y() / 1000.)
newZoom = np.clip(newZoom, .4, 3)
self.transform.setZoom(newZoom)
logger.debug("newZoom: %s", newZoom)
# self.refresh()
def posToVec3(self, x, y, r0=.8, isRot=True):
x, y = 2. * x / self.width() - 1., 1. - 2. * y / self.width()
r = np.sqrt(x * x + y * y)
if r > r0 - 1.e-7:
x, y = 1. * x * r0 / r, 1. * y * r0 / r
z = np.sqrt(max(0, r0**2 - x * x - y * y))
if isRot:
M = np.linalg.inv(self.transform.quatRot.toRotation3())
x, y, z = np.dot(M, [x, y, z])
return x, y, z
def posToVec2(self, x, y):
x, y = 2. * x / self.width() - 1., 1. - 2. * y / self.width()
return x, y
def mousePressEvent(self, event):
super(GLWidget, self).mousePressEvent(event)
if event.buttons() == QtCore.Qt.LeftButton:
self._x0, self._y0, self._z0 = self.posToVec3(event.x(), event.y())
if event.buttons() == QtCore.Qt.RightButton:
(self._x0, self._y0), self._invRotM = self.posToVec2(
event.x(),
event.y()), linalg.inv(self.transform.quatRot.toRotation3())
# self.setCursor(QtCore.Qt.ClosedHandCursor)
def mouseReleaseEvent(self, event):
super(GLWidget, self).mouseReleaseEvent(event)
# self.setCursor(QtCore.Qt.ArrowCursor)
def mouseMoveEvent(self, event):
# c = append(self.cubeCoords,ones(24)[:,newaxis],axis=1)
# cUser = dot(c,self.finalMat)
# cUser = cUser[:,:3]/cUser[:,-1,newaxis]
# print self.finalMat
# print c[0], cUser[0]
# Rotation
if event.buttons() == QtCore.Qt.LeftButton:
x1, y1, z1 = self.posToVec3(event.x(), event.y())
logger.debug("mouse position: %s %s %s " % (x1, y1, z1))
n = np.cross(np.array([self._x0, self._y0, self._z0]),
np.array([x1, y1, z1]))
nnorm = linalg.norm(n)
if np.abs(nnorm) >= 1.:
nnorm *= 1. / np.abs(nnorm)
w = np.arcsin(nnorm)
n *= 1. / (nnorm + 1.e-10)
q = Quaternion(np.cos(.5 * w), *(np.sin(.5 * w) * n))
self.transform.setQuaternion(self.transform.quatRot * q)
# Translation
if event.buttons() == QtCore.Qt.RightButton:
x, y = self.posToVec2(event.x(), event.y())
dx, dy, foo = np.dot(self._invRotM,
[x - self._x0, y - self._y0, 0])
self.transform.addTranslate(dx, dy, foo)
self._x0, self._y0 = x, y
self.refresh()
def resizeEvent(self, event):
# enforce each dimension to be divisable by 4 (and so the saved frames)
super(GLWidget, self).resizeEvent(event)
size = event.size()
w, h = size.width(), size.height()
if not ((w % 4 == 0) and (h % 4 == 0)):
self.resize(QtCore.QSize((w // 4) * 4, (h // 4) * 4))
def _enforce_resize(self):
""" this is to enforce the resizeGL event """
self.resize(self.width() + 1, self.height())
self.resize(self.width() - 1, self.height())
def onScreenNumberChange(self, evt):
self._enforce_resize()
def _get_screen_number(self):
return QtGui.QGuiApplication.instance().desktop().screenNumber(
QtGui.QCursor.pos())
def moveEvent(self, evt):
current_screen = self._get_screen_number()
if hasattr(
self,
"_current_screen") and self._current_screen != current_screen:
self.onScreenNumberChange(evt)
self._current_screen = current_screen
class GLWidget(QtOpenGL.QGLWidget):
_dataModelChanged = QtCore.pyqtSignal()
_BACKGROUND_BLACK = (0., 0., 0., 0.)
_BACKGROUND_WHITE = (1., 1., 1., 0.)
def __init__(self, parent=None, N_PREFETCH=0, interpolation="linear", **kwargs):
logger.debug("init")
#
# fmt = QtOpenGL.QGLFormat(QtOpenGL.QGL.AlphaChannel)
#
# super(GLWidget, self).__init__(fmt,parent, **kwargs)
super(GLWidget, self).__init__(parent, **kwargs)
self.parent = parent
self.texture_LUT = None
self.setAcceptDrops(True)
self.renderer = VolumeRenderer((spimagine.config.__DEFAULT_TEXTURE_WIDTH__,
spimagine.config.__DEFAULT_TEXTURE_WIDTH__),
interpolation=interpolation)
self.renderer.set_projection(mat4_perspective(60, 1., .1, 100))
# self.renderer.set_projection(projMatOrtho(-2,2,-2,2,-10,10))
self.output = np.zeros([self.renderer.height, self.renderer.width], dtype=np.float32)
self.output_alpha = np.zeros([self.renderer.height, self.renderer.width], dtype=np.float32)
self.sliceOutput = np.zeros((100, 100), dtype=np.float32)
self.setTransform(TransformModel())
self.renderTimer = QtCore.QTimer(self)
self.renderTimer.setInterval(10)
self.renderTimer.timeout.connect(self.onRenderTimer)
self.renderTimer.start()
self.renderedSteps = 0
self.N_PREFETCH = N_PREFETCH
self.NSubrenderSteps = 1
self.dataModel = None
self.meshes = []
# self.setMouseTracking(True)
self._dataModelChanged.connect(self.dataModelChanged)
self.refresh()
# self.installEventFilter(self)
def set_background_mode_black(self, mode_back=True):
self._background_mode_black = mode_back
self.refresh()
def setModel(self, dataModel):
logger.debug("setModel to %s" % dataModel)
if self.dataModel is None or (self.dataModel != dataModel):
self.dataModel = dataModel
self.transform.setModel(dataModel)
self.dataModel._dataSourceChanged.connect(self.dataSourceChanged)
self.dataModel._dataPosChanged.connect(self.dataPosChanged)
self._dataModelChanged.emit()
def dragEnterEvent(self, event):
if event.mimeData().hasUrls():
event.accept()
else:
event.ignore()
def dropEvent(self, event):
def _url_to_path(url):
path = url.toLocalFile()
if spimagine.config.__SYSTEM_DARWIN__:
path = spimagine.config._parseFileNameFix(path)
return path
self.setCursor(QtCore.Qt.BusyCursor)
urls = event.mimeData().urls()
if len(urls) == 0:
return
elif len(urls) == 1:
path = _url_to_path(urls[0])
elif len(urls) > 1:
path = tuple(_url_to_path(url) for url in urls)
try:
if self.dataModel:
self.dataModel.loadFromPath(path, prefetchSize=self.N_PREFETCH)
else:
self.setModel(DataModel.fromPath(path, prefetchSize=self.N_PREFETCH))
self.setCursor(QtCore.Qt.ArrowCursor)
except Exception as e:
QtWidgets.QMessageBox.warning(self, "", "Error loading Data:\n %s" % str(e))
def set_colormap(self, name):
"""name should be either jet, hot, gray, coolwarm"""
try:
arr = spimagine.config.__COLORMAPDICT__[name]
self._set_colormap_array(arr)
except KeyError:
print("could not load colormap '%s'" % name)
print("valid names: %s" % list(spimagine.config.__COLORMAPDICT__.keys()))
def set_colormap_rgb(self, color=[1., 1., 1.]):
self._set_colormap_array(np.outer(np.linspace(0, 1., 255), np.array(color)))
def _set_colormap_array(self, arr):
"""arr should be of shape (N,3) and gives the rgb components of the colormap"""
if not arr.ndim == 2 and arr.shape[-1] == 3:
raise ValueError("wrong shape of color array: should be (N,3) but is %s")
self.makeCurrent()
self.texture_LUT = fillTexture2d(arr.reshape((1,) + arr.shape), self.texture_LUT)
self.refresh()
def _shader_from_file(self, fname_vert, fname_frag):
shader = QOpenGLShaderProgram()
shader.addShaderFromSourceFile(QOpenGLShader.Vertex, fname_vert)
shader.addShaderFromSourceFile(QOpenGLShader.Fragment, fname_frag)
shader.link()
shader.bind()
logger.debug("GLSL program log:%s", shader.log())
return shader
def initializeGL(self):
self.resized = True
logger.debug("initializeGL")
self.programTex = self._shader_from_file(absPath("shaders/texture.vert"),
absPath("shaders/texture.frag"))
self.programCube = self._shader_from_file(absPath("shaders/box.vert"),
absPath("shaders/box.frag"))
self.programSlice = self._shader_from_file(absPath("shaders/slice.vert"),
absPath("shaders/slice.frag"))
self.programMesh = self._shader_from_file(absPath("shaders/mesh.vert"),
absPath("shaders/mesh.frag"))
self.programMeshLight = self._shader_from_file(
absPath("shaders/mesh_light.vert"),
absPath("shaders/mesh_light.frag"))
self.texture = None
self.textureAlpha = None
self.textureSlice = None
self.quadCoord = np.array([[-1., -1., 0.],
[1., -1., 0.],
[1., 1., 0.],
[1., 1., 0.],
[-1., 1., 0.],
[-1., -1., 0.]])
self.quadCoordTex = np.array([[0, 0],
[1., 0.],
[1., 1.],
[1., 1.],
[0, 1.],
[0, 0]])
# self.cubeCoords = create_cube_coords([-1,1,-1,1,-1,1])
self.set_colormap(spimagine.config.__DEFAULTCOLORMAP__)
glEnable(GL_BLEND)
# glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA)
# self.set_interpolation(spimagine.config.__DEFAULT_INTERP__ != "nearest")
# glLineWidth(1.0);
glBlendFunc(GL_ONE, GL_ONE)
glEnable(GL_LINE_SMOOTH);
glDisable(GL_DEPTH_TEST)
glLineWidth(spimagine.config.__DEFAULT_BOX_LINEWIDTH__)
# self.set_background_color(0,0,0,.0)
self.set_background_mode_black(True)
self.clear_canvas()
# self.set_background_color(1,1,1,.6)
def clear_canvas(self):
if self._background_mode_black:
glClearColor(*self._BACKGROUND_BLACK)
else:
glClearColor(*self._BACKGROUND_WHITE)
if glCheckFramebufferStatus(GL_FRAMEBUFFER) == GL_FRAMEBUFFER_COMPLETE:
glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT)
def set_interpolation(self, interpolate=True):
interp = "linear" if interpolate else "nearest"
self.renderer.rebuild_program(interpolation=interp)
self.refresh()
def setTransform(self, transform):
self.transform = transform
self.transform._transformChanged.connect(self.refresh)
self.transform._stackUnitsChanged.connect(self.setStackUnits)
self.transform._boundsChanged.connect(self.setBounds)
def dataModelChanged(self):
logger.debug("+++++++++ data model changed")
if self.dataModel:
logger.debug("dataModelchanged")
self.renderer.set_data(self.dataModel[0], autoConvert=True)
mi, ma = self._get_min_max()
self.transform.reset(minVal=mi,
maxVal=ma,
stackUnits=self.dataModel.stackUnits())
self.meshes = []
self.refresh()
def _get_min_max(self):
# as amax is too slow for bug arrays, do it on the gpu
if self.dataModel:
try:
im = self.renderer.dataImg
tmp_buf = OCLArray.empty(im.shape, im.dtype)
tmp_buf.copy_image(im)
mi = float(cl_array.min(tmp_buf).get())
ma = float(cl_array.max(tmp_buf).get())
except Exception as e:
print(e)
mi = np.amin(self.dataModel[0])
ma = np.amax(self.dataModel[0])
return mi, ma
def set_background_color(self, r, g, b, a=1.):
self._background_color = (r, g, b, a)
glClearColor(r, g, b, a)
def dataSourceChanged(self):
logger.debug("dataSourcechanged")
self.renderer.set_data(self.dataModel[0], autoConvert=True)
mi, ma = self._get_min_max()
self.transform.reset(minVal=mi,
maxVal=ma,
stackUnits=self.dataModel.stackUnits())
self.refresh()
def setBounds(self, x1, x2, y1, y2, z1, z2):
self.cubeCoords = create_cube_coords([x1, x2, y1, y2, z1, z2])
self.renderer.set_box_boundaries([x1, x2, y1, y2, z1, z2])
def setStackUnits(self, px, py, pz):
logger.debug("setStackUnits to %s" % [px, py, pz])
self.renderer.set_units([px, py, pz])
def dataPosChanged(self, pos):
self.renderer.update_data(self.dataModel[pos])
self.refresh()
def refresh(self):
# if self.parentWidget() and self.dataModel:
# self.parentWidget().setWindowTitle("SpImagine %s"%self.dataModel.name())
self.renderUpdate = True
self.renderedSteps = 0
def resizeGL(self, width, height):
# somehow in qt5 the OpenGLWidget width/height parameters above are double the value of self.width/height
self._viewport_width, self._viewport_height = width, height
def add_mesh(self, mesh=SphericalMesh()):
"""
adds a mesh with vertices and facecolor/edgecolor to be drawn
mesh is an instance of spimagine.gui.Mesh, e.g.
mesh = Mesh(vertices = [[0,1,0],[0,1,0],...],
normals = [[0,1,0],[0,1,0],...],
facecolor = (1.,.4,.4,.2),
edgecolor = None,...)
there are some predefined meshes like
SphericalMesh, EllipsoidMesh ...
"""
self.meshes.append([mesh,
glvbo.VBO(mesh.vertices.astype(np.float32, copy=False)),
glvbo.VBO(np.array(mesh.normals).astype(np.float32, copy=False)),
glvbo.VBO(np.array(mesh.indices).astype(np.uint32, copy=False),
target=GL_ELEMENT_ARRAY_BUFFER)])
self.refresh()
# sort according to opacity as the opaque objects should be drawn first
# self.meshes.sort(key=lambda x: x[0].alpha, reverse=True)
def _paintGL_render(self):
# Draw the render texture
self.programTex.bind()
self.texture = fillTexture2d(self.output, self.texture)
# self.textureAlpha = fillTexture2d(self.output_alpha, self.textureAlpha)
glEnable(GL_BLEND)
glEnable(GL_TEXTURE_2D)
glDisable(GL_DEPTH_TEST)
self.programTex.enableAttributeArray("position")
self.programTex.enableAttributeArray("texcoord")
self.programTex.setAttributeArray("position", self.quadCoord)
self.programTex.setAttributeArray("texcoord", self.quadCoordTex)
self.programTex.setUniformValue("is_mode_black", self._background_mode_black)
glActiveTexture(GL_TEXTURE0)
glBindTexture(GL_TEXTURE_2D, self.texture)
self.programTex.setUniformValue("texture", 0)
glActiveTexture(GL_TEXTURE1)
glBindTexture(GL_TEXTURE_2D, self.textureAlpha)
self.programTex.setUniformValue("texture_alpha", 1)
glActiveTexture(GL_TEXTURE2)
glBindTexture(GL_TEXTURE_2D, self.texture_LUT)
self.programTex.setUniformValue("texture_LUT", 2)
glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA)
glDrawArrays(GL_TRIANGLES, 0, len(self.quadCoord))
def _paintGL_slice(self):
# draw the slice
self.programSlice.bind()
self.programSlice.setUniformValue("mvpMatrix", QtGui.QMatrix4x4(*self._mat_modelviewproject.flatten()))
self.programSlice.setUniformValue("is_mode_black", self._background_mode_black)
self.programSlice.enableAttributeArray("position")
pos, dim = self.transform.slicePos, self.transform.sliceDim
coords = slice_coords(1. * pos / self.dataModel.size()[2 - dim + 1], dim)
texcoords = [[0., 0.], [1, 0.], [1., 1.],
[1., 1.], [0., 1.], [0., 0.]]
self.programSlice.setAttributeArray("position", coords)
self.programSlice.setAttributeArray("texcoord", texcoords)
self.textureSlice = fillTexture2d(self.sliceOutput, self.textureSlice)
glActiveTexture(GL_TEXTURE0)
glBindTexture(GL_TEXTURE_2D, self.textureSlice)
self.programSlice.setUniformValue("texture", 0)
glActiveTexture(GL_TEXTURE1)
glBindTexture(GL_TEXTURE_2D, self.texture_LUT)
self.programSlice.setUniformValue("texture_LUT", 1)
glDrawArrays(GL_TRIANGLES, 0, len(coords))
def _paintGL_box(self):
glEnable(GL_BLEND)
# Draw the cube
self.programCube.bind()
self.programCube.setUniformValue("mvpMatrix", QtGui.QMatrix4x4(*self._mat_modelviewproject.flatten()))
self.programCube.enableAttributeArray("position")
if self._background_mode_black:
self.programCube.setUniformValue("color",
QtGui.QVector4D(1, 1, 1, 0.6))
else:
self.programCube.setUniformValue("color",
QtGui.QVector4D(0, 0, 0, 0.6))
self.programCube.setAttributeArray("position", self.cubeCoords)
glActiveTexture(GL_TEXTURE0)
glBindTexture(GL_TEXTURE_2D, self.textureAlpha)
self.programCube.setUniformValue("texture_alpha", 0)
glEnable(GL_DEPTH_TEST)
# glBlendFunc(GL_ONE_MINUS_SRC_ALPHA, GL_SRC_ALPHA)
glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA)
glDrawArrays(GL_LINES, 0, len(self.cubeCoords))
glDisable(GL_DEPTH_TEST)
def _paintGL_mesh(self, mesh, vbo_vertices, vbo_normals, vbo_indices):
"""
paint a mesh (which has all the coordinates and colors in it
"""
glEnable(GL_DEPTH_TEST)
glDisable(GL_BLEND)
prog = self.programMeshLight
prog.bind()
prog.setUniformValue("mvpMatrix",
QtGui.QMatrix4x4(*self._mat_modelviewproject.flatten()))
prog.setUniformValue("mvMatrix",
QtGui.QMatrix4x4(*self._mat_modelview.flatten()))
prog.setUniformValue("normMatrix",
QtGui.QMatrix4x4(*self._mat_normal.flatten()))
if mesh.light:
prog.setUniformValue("light",
QtGui.QVector3D(*mesh.light))
prog.setUniformValue("light_components",
QtGui.QVector3D(.2, .5, .3))
else:
prog.setUniformValue("light",
QtGui.QVector3D(0, 0, 0))
prog.setUniformValue("light_components",
QtGui.QVector3D(1., 0, 0))
if not mesh.facecolor is None:
r, g, b = mesh.facecolor[:3]
a = mesh.alpha
prog.setUniformValue("color",
QtGui.QVector4D(r, g, b, a))
prog.enableAttributeArray("position")
vbo_vertices.bind()
glVertexAttribPointer(prog.attributeLocation("position"), 3, GL_FLOAT, GL_FALSE, 0, vbo_vertices)
prog.enableAttributeArray("normal")
vbo_normals.bind()
glVertexAttribPointer(prog.attributeLocation("normal"), 3, GL_FLOAT, GL_FALSE, 0, vbo_normals)
vbo_indices.bind()
glDrawElements(GL_TRIANGLES, len(vbo_indices.data), GL_UNSIGNED_INT, None)
vbo_indices.unbind()
vbo_vertices.unbind()
glDisable(GL_DEPTH_TEST)
prog.disableAttributeArray("position")
prog.disableAttributeArray("normal")
#
# if not mesh.edgecolor is None:
# r, g, b = mesh.edgecolor
# a = mesh.alpha
#
# prog.enableAttributeArray("position")
# vbo_vertices.bind()
# glVertexAttribPointer(prog.attributeLocation("position"), 2, GL_FLOAT, GL_FALSE, 0, vbo_edges)
#
# prog.setUniformValue("color",
# QtGui.QVector4D(r, g, b, a))
#
# glDrawArrays(GL_LINES, 0, len(mesh.edges))
def paintGL(self):
self.makeCurrent()
if not glCheckFramebufferStatus(GL_FRAMEBUFFER) == GL_FRAMEBUFFER_COMPLETE:
return
w = max(self._viewport_width, self._viewport_height)
# force viewport to always be a square
glViewport((self._viewport_width - w) // 2, (self._viewport_height - w) // 2, w, w)
self.clear_canvas()
self._mat_modelview = self.transform.getModelView()
self._mat_proj = self.transform.getProjection()
self._mat_normal = np.linalg.inv(self._mat_modelview).T
self._mat_modelviewproject = np.dot(self._mat_proj, self._mat_modelview)
if self.dataModel:
self.textureAlpha = fillTexture2d(self.output_alpha, self.textureAlpha)
if self.transform.isBox:
self._paintGL_box()
if self.transform.isSlice and self.sliceOutput is not None:
self._paintGL_slice()
self._paintGL_render()
for (m, vbo_verts, vbo_normals, vbo_indices) in self.meshes:
self._paintGL_mesh(m, vbo_verts, vbo_normals, vbo_indices)
def render(self):
logger.debug("render")
if self.dataModel:
self.renderer.set_modelView(self.transform.getUnscaledModelView())
self.renderer.set_projection(self.transform.getProjection())
self.renderer.set_min_val(self.transform.minVal)
self.renderer.set_max_val(self.transform.maxVal)
self.renderer.set_gamma(self.transform.gamma)
self.renderer.set_alpha_pow(self.transform.alphaPow)
self.renderer.set_occ_strength(self.transform.occ_strength)
self.renderer.set_occ_radius(self.transform.occ_radius)
self.renderer.set_occ_n_points(self.transform.occ_n_points)
if self.transform.isIso:
renderMethod = "iso_surface"
else:
renderMethod = "max_project"
self.renderer.render(method=renderMethod, return_alpha=True, numParts=self.NSubrenderSteps, currentPart=(
self.renderedSteps * _next_golden(
self.NSubrenderSteps)) % self.NSubrenderSteps)
self.output, self.output_alpha = self.renderer.output, self.renderer.output_alpha
if self.transform.isSlice:
if self.transform.sliceDim == 0:
out = self.dataModel[self.transform.dataPos][:, :, self.transform.slicePos]
elif self.transform.sliceDim == 1:
out = self.dataModel[self.transform.dataPos][:, self.transform.slicePos, :]
elif self.transform.sliceDim == 2:
out = self.dataModel[self.transform.dataPos][self.transform.slicePos, :, :]
min_out, max_out = np.amin(out), np.amax(out)
if max_out > min_out:
self.sliceOutput = (1. * (out - min_out) / (max_out - min_out))
else:
self.sliceOutput = np.zeros_like(out)
# def getFrame(self):
# self.render()
# self.paintGL()
# glFlush()
# im = self.grabFrameBuffer()
# im = im.convertToFormat(QtGui.QImage.Format_RGB32)
#
# width = im.width()
# height = im.height()
#
# ptr = im.bits()
# ptr.setsize(im.byteCount())
# arr = np.array(ptr).reshape(height, width, 4) # Copies the data
# return arr[..., [2, 1, 0, 3]].copy()
def saveFrame(self, fName, with_alpha=False):
"""FIXME: scaling behaviour still hast to be implemented (e.g. after setGamma)"""
logger.info("saving frame as %s", fName)
# has to be png
name, ext = os.path.splitext(fName)
if ext != ".png":
fName = name + ".png"
self.render()
self.paintGL()
glFlush()
im = self.grabFrameBuffer(withAlpha=with_alpha)
im.save(fName)
def onRenderTimer(self):
# if self.renderUpdate:
# self.render()
# self.renderUpdate = False
# self.updateGL()
if self.renderedSteps < self.NSubrenderSteps:
# print ((self.renderedSteps*7)%self.NSubrenderSteps)
s = time.time()
self.render()
logger.debug("time to render: %.2f" % (1000. * (time.time() - s)))
self.renderedSteps += 1
self.updateGL()
def wheelEvent(self, event):
""" self.transform.zoom should be within [1,2]"""
newZoom = self.transform.zoom * 1.2 ** (event.angleDelta().y() / 1000.)
newZoom = np.clip(newZoom, .4, 3)
self.transform.setZoom(newZoom)
logger.debug("newZoom: %s", newZoom)
# self.refresh()
def posToVec3(self, x, y, r0=.8, isRot=True):
x, y = 2. * x / self.width() - 1., 1. - 2. * y / self.width()
r = np.sqrt(x * x + y * y)
if r > r0 - 1.e-7:
x, y = 1. * x * r0 / r, 1. * y * r0 / r
z = np.sqrt(max(0, r0 ** 2 - x * x - y * y))
if isRot:
M = np.linalg.inv(self.transform.quatRot.toRotation3())
x, y, z = np.dot(M, [x, y, z])
return x, y, z
def posToVec2(self, x, y):
x, y = 2. * x / self.width() - 1., 1. - 2. * y / self.width()
return x, y
def mousePressEvent(self, event):
super(GLWidget, self).mousePressEvent(event)
if event.buttons() == QtCore.Qt.LeftButton:
self._x0, self._y0, self._z0 = self.posToVec3(event.x(), event.y())
if event.buttons() == QtCore.Qt.RightButton:
(self._x0, self._y0), self._invRotM = self.posToVec2(event.x(), event.y()), linalg.inv(
self.transform.quatRot.toRotation3())
# self.setCursor(QtCore.Qt.ClosedHandCursor)
def mouseReleaseEvent(self, event):
super(GLWidget, self).mouseReleaseEvent(event)
# self.setCursor(QtCore.Qt.ArrowCursor)
def mouseMoveEvent(self, event):
# c = append(self.cubeCoords,ones(24)[:,newaxis],axis=1)
# cUser = dot(c,self.finalMat)
# cUser = cUser[:,:3]/cUser[:,-1,newaxis]
# print self.finalMat
# print c[0], cUser[0]
# Rotation
if event.buttons() == QtCore.Qt.LeftButton:
x1, y1, z1 = self.posToVec3(event.x(), event.y())
logger.debug("mouse position: %s %s %s " % (x1, y1, z1))
n = np.cross(np.array([self._x0, self._y0, self._z0]), np.array([x1, y1, z1]))
nnorm = linalg.norm(n)
if np.abs(nnorm) >= 1.:
nnorm *= 1. / np.abs(nnorm)
w = np.arcsin(nnorm)
n *= 1. / (nnorm + 1.e-10)
q = Quaternion(np.cos(.5 * w), *(np.sin(.5 * w) * n))
self.transform.setQuaternion(self.transform.quatRot * q)
# Translation
if event.buttons() == QtCore.Qt.RightButton:
x, y = self.posToVec2(event.x(), event.y())
dx, dy, foo = np.dot(self._invRotM, [x - self._x0, y - self._y0, 0])
self.transform.addTranslate(dx, dy, foo)
self._x0, self._y0 = x, y
self.refresh()
def resizeEvent(self, event):
# enforce each dimension to be divisable by 4 (and so the saved frames)
super(GLWidget, self).resizeEvent(event)
size = event.size()
w, h = size.width(), size.height()
if not ((w % 4 == 0) and (h % 4 == 0)):
self.resize(QtCore.QSize((w // 4) * 4, (h // 4) * 4))
def _enforce_resize(self):
""" this is to enforce the resizeGL event """
self.resize(self.width() + 1, self.height())
self.resize(self.width() - 1, self.height())
def onScreenNumberChange(self, evt):
self._enforce_resize()
def _get_screen_number(self):
return QtGui.QGuiApplication.instance().desktop().screenNumber(QtGui.QCursor.pos())
def moveEvent(self, evt):
current_screen = self._get_screen_number()
if hasattr(self, "_current_screen") and self._current_screen != current_screen:
self.onScreenNumberChange(evt)
self._current_screen = current_screen
def main():
parser = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter,
description="""renders max projectios of 3d data
example usage:
Tif data: \t \tspim_render -i mydata.tif -o myoutput.png -t 0 0 -4 -u 1 1 4
Bscope data: \tspim_render -f bscope -i mydataFolder -o myoutput.png -t 0 0 -4 -u 1 1 4
""")
parser.add_argument("-f","--format",dest="format",metavar="format",
help = """format currently supported:
tif (default)
bscope """,
type=str,default = "tif", required = False)
parser.add_argument("-i","--input",dest="input",metavar="infile",
help = "name of the input file to render, currently only 3d Tiff is supported",
type=str,default = None, required = True)
parser.add_argument("-o","--output",dest="output",metavar="outfile",
help = "name of the output file, png extension is recommended",
type=str,default = "out.png")
parser.add_argument("-p","--pos",dest="pos",metavar="timepoint position",
help = "timepoint to render if format=='bscope' ",
type=int,default = 0)
parser.add_argument("-w","--width",dest="width",metavar="width",
help = "pixelwidth of the rendered output ",
type=int,default = 400)
parser.add_argument("-s","--scale",dest="scale",metavar="scale",
type=float,nargs=1 ,default = [1.])
parser.add_argument("-u","--units",dest="units",metavar="units",
type=float,nargs= 3 ,default = [1.,1.,5.])
parser.add_argument("-t","--translate",dest="translate",
type = float, nargs=3,default = [0,0,-4],
metavar=("x","y","z"))
parser.add_argument("-r","--rotation",dest="rotation", type =
float, nargs=4,default = [0,1,0,0],
metavar=("w","x","y","z"))
parser.add_argument("-R","--range",dest="range", type =
float, nargs=2,default = None,
help = "if --16bit is set, the range of the data values to consider, defaults to [min,max]",
metavar=("min","max"))
parser.add_argument("-O","--Orthoview",help="use parallel projection (default: perspective)",
dest="ortho",action="store_true")
parser.add_argument("--16bit",help="render into 16 bit png",
dest="is16Bit",action="store_true")
if len(sys.argv)==1:
parser.print_help()
return
args = parser.parse_args()
for k,v in six.iteritems(vars(args)):
print(k,v)
rend = VolumeRenderer((args.width,args.width))
if args.format=="tif":
data = read3dTiff(args.input)
elif args.format=="bscope":
data = fromSpimFolder(args.input,pos=args.pos,count=1)[0,...]
else:
raise ValueError("format %s not supported (should be tif/bscope)" %args.format)
rend.set_data(data)
rend.set_units(args.units)
M = mat4_scale(*(args.scale*3))
M = np.dot(mat4_rotation(*args.rotation),M)
M = np.dot(mat4_translate(*args.translate),M)
rend.set_modelView(M)
if args.ortho:
rend.set_projection(mat4_ortho(-1,1,-1,1,-1,1))
else:
rend.set_projection(mat4_perspective(60,1.,1,10))
out = rend.render()
# image is saved by scipy.misc.toimage(out,low,high,cmin,cmax)
# p' = p * high/cmax
if not args.is16Bit:
imsave(args.output,out)
# if not args.range:
# imsave(args.output,out)
# else:
# img = toimage(out, low = args.range[0], high = args.range[1])
# img.save(args.output)
else:
if not args.range:
print("min/max: ", np.amin(out), np.amax(out))
img = toimage(out, low = np.amin(out), high = np.amax(out),mode = "I")
else:
img = toimage(out, low = args.range[0], high = args.range[1], mode = "I")
img.save(args.output)