def correlate2(data, h, dev=None):
"""computes normalized cross correlation of 2d <data> with template <h> on the GPU Device <dev>
boundary conditions are clamping to edge.
h is converted to float32
if dev == None a new one is created
"""
if not dev:
dev = OCLDevice(useDevice=imgtools.__OPENCLDEVICE__)
# normalize data and template
#data
dtype = data.dtype.type
dtypes_kernels = {
np.float32: "mean_var_2d_float",
np.uint16: "mean_var_2d_short"
}
if not dtype in dtypes_kernels.keys():
raise TypeError(
"data type %s not supported yet, please convert to:" % dtype,
dtypes_kernels.keys())
proc = OCLProcessor(dev, absPath("kernels/correlate_kernels.cl"))
Ny, Nx = h.shape
inImg = dev.createImage_like(data)
meanBuf = dev.createBuffer(data.size,
dtype=dtype,
mem_flags=cl.mem_flags.READ_WRITE)
varBuf = dev.createBuffer(data.size,
dtype=dtype,
mem_flags=cl.mem_flags.READ_WRITE)
dev.writeImage(inImg, data)
proc.runKernel(dtypes_kernels[dtype], inImg.shape, None, inImg,
np.int32(data.shape[1]), np.int32(Nx), np.int32(Ny),
meanBuf, varBuf)
dataMean, dataVar = dev.readBuffer(meanBuf, dtype).reshape(
data.shape), dev.readBuffer(varBuf, dtype).reshape(data.shape)
#template
hMean = 1. * np.mean(h.flatten())
hVar = 1. * np.var(h.flatten())
res = convolve2(dev, data - dataMean, h - hMean)
print hMean, hVar
# # res = convolve2(dev,data-dataMean,h)
# return res
# return dataVar
return res / np.maximum(1.e-6, np.sqrt(dataVar * hVar))
def correlate2(data,h, dev = None):
"""computes normalized cross correlation of 2d <data> with template <h> on the GPU Device <dev>
boundary conditions are clamping to edge.
h is converted to float32
if dev == None a new one is created
"""
if not dev:
dev = OCLDevice(useDevice = imgtools.__OPENCLDEVICE__)
# normalize data and template
#data
dtype = data.dtype.type
dtypes_kernels = {np.float32:"mean_var_2d_float",
np.uint16:"mean_var_2d_short"}
if not dtype in dtypes_kernels.keys():
raise TypeError("data type %s not supported yet, please convert to:"%dtype,dtypes_kernels.keys())
proc = OCLProcessor(dev,absPath("kernels/correlate_kernels.cl"))
Ny,Nx = h.shape
inImg = dev.createImage_like(data)
meanBuf = dev.createBuffer(data.size,dtype=dtype,mem_flags= cl.mem_flags.READ_WRITE)
varBuf = dev.createBuffer(data.size,dtype=dtype,mem_flags= cl.mem_flags.READ_WRITE)
dev.writeImage(inImg,data)
proc.runKernel(dtypes_kernels[dtype],inImg.shape,None,inImg,np.int32(data.shape[1]),np.int32(Nx),np.int32(Ny),meanBuf,varBuf)
dataMean, dataVar = dev.readBuffer(meanBuf,dtype).reshape(data.shape),dev.readBuffer(varBuf,dtype).reshape(data.shape)
#template
hMean = 1.*np.mean(h.flatten())
hVar = 1.*np.var(h.flatten())
res = convolve2(dev,data-dataMean,h - hMean)
print hMean, hVar
# # res = convolve2(dev,data-dataMean,h)
# return res
# return dataVar
return res/np.maximum(1.e-6,np.sqrt(dataVar*hVar))
def _correlate2(data, h, dev=None):
"""computes normalized cross correlation of 2d <data> with template <h> on the GPU Device <dev>
boundary conditions are clamping to edge.
h is converted to float32
if dev == None a new one is created
"""
if not dev:
dev = OCLDevice(useDevice=imgtools.__OPENCLDEVICE__)
dtype = data.dtype.type
dtypes_kernels = {
np.float32: "correlate2d_float",
np.uint16: "correlate2d_short"
}
if not dtype in dtypes_kernels.keys():
raise TypeError(
"data type %s not supported yet, please convert to:" % dtype,
dtypes_kernels.keys())
proc = OCLProcessor(dev, absPath("kernels/correlate_kernels.cl"))
Ny, Nx = h.shape
hbuf = dev.createBuffer(Nx * Ny,
dtype=np.float32,
mem_flags=cl.mem_flags.READ_ONLY)
inImg = dev.createImage_like(data)
outImg = dev.createImage_like(data, mem_flags="READ_WRITE")
dev.writeImage(inImg, data)
dev.writeBuffer(hbuf, h.astype(np.float32).flatten())
proc.runKernel(dtypes_kernels[dtype], inImg.shape, None, inImg, hbuf,
np.int32(Nx), np.int32(Ny), outImg)
return dev.readImage(outImg)
def _correlate2(data,h, dev = None):
"""computes normalized cross correlation of 2d <data> with template <h> on the GPU Device <dev>
boundary conditions are clamping to edge.
h is converted to float32
if dev == None a new one is created
"""
if not dev:
dev = OCLDevice(useDevice = imgtools.__OPENCLDEVICE__)
dtype = data.dtype.type
dtypes_kernels = {np.float32:"correlate2d_float",
np.uint16:"correlate2d_short"}
if not dtype in dtypes_kernels.keys():
raise TypeError("data type %s not supported yet, please convert to:"%dtype,dtypes_kernels.keys())
proc = OCLProcessor(dev,absPath("kernels/correlate_kernels.cl"))
Ny,Nx = h.shape
hbuf = dev.createBuffer(Nx*Ny,dtype=np.float32,mem_flags= cl.mem_flags.READ_ONLY)
inImg = dev.createImage_like(data)
outImg = dev.createImage_like(data,mem_flags="READ_WRITE")
dev.writeImage(inImg,data)
dev.writeBuffer(hbuf,h.astype(np.float32).flatten())
proc.runKernel(dtypes_kernels[dtype],inImg.shape,None,inImg,hbuf,np.int32(Nx),np.int32(Ny),outImg)
return dev.readImage(outImg)
def __init__(self, size = None):
""" e.g. size = (300,300)"""
try:
# simulate GPU fail...
# raise Exception()
self.dev = OCLDevice(useGPU = True,
useDevice = spimagine.__OPENCLDEVICE__)
self.isGPU = True
self.dtypes = [np.float32,np.uint16]
except Exception as e:
print e
print "could not find GPU OpenCL device - trying CPU..."
try:
self.dev = OCLDevice(useGPU = False)
self.isGPU = False
self.dtypes = [np.float32]
except Exception as e:
print e
print "could not find any OpenCL device ... sorry"
self.memMax = .4*self.dev.device.get_info(getattr(
cl.device_info,"MAX_MEM_ALLOC_SIZE"))
self.memMax = 2.*self.dev.device.get_info(getattr(
cl.device_info,"MAX_MEM_ALLOC_SIZE"))
self.proc = OCLProcessor(self.dev,absPath("kernels/volume_render.cl"),
"-cl-fast-relaxed-math -cl-unsafe-math-optimizations -cl-mad-enable")
# self.proc = OCLProcessor(self.dev,absPath("kernels/volume_render.cl"),options="-cl-fast-relaxed-math")
self.invMBuf = self.dev.createBuffer(16,dtype=np.float32,
mem_flags = cl.mem_flags.READ_ONLY)
self.invPBuf = self.dev.createBuffer(16,dtype=np.float32,
mem_flags = cl.mem_flags.READ_ONLY)
self.projection = np.zeros((4,4))
self.modelView = np.zeros((4,4))
if size:
self.resize(size)
else:
self.resize((200,200))
self.set_dtype()
self.set_gamma()
self.set_max_val()
self.set_min_val()
self.set_alpha_pow()
self.set_box_boundaries()
self.set_units()
self.set_modelView()
self.set_projection()
class VolumeRenderer:
""" renders a data volume by ray casting/max projection
usage:
rend = VolumeRenderer((400,400))
rend.set_data(d)
rend.set_units(1.,1.,2.)
rend.set_modelView(rotMatX(.7))
"""
def __init__(self, size = None):
""" e.g. size = (300,300)"""
try:
# simulate GPU fail...
# raise Exception()
self.dev = OCLDevice(useGPU = True,
useDevice = spimagine.__OPENCLDEVICE__)
self.isGPU = True
self.dtypes = [np.float32,np.uint16]
except Exception as e:
print e
print "could not find GPU OpenCL device - trying CPU..."
try:
self.dev = OCLDevice(useGPU = False)
self.isGPU = False
self.dtypes = [np.float32]
except Exception as e:
print e
print "could not find any OpenCL device ... sorry"
self.memMax = .4*self.dev.device.get_info(getattr(
cl.device_info,"MAX_MEM_ALLOC_SIZE"))
self.memMax = 2.*self.dev.device.get_info(getattr(
cl.device_info,"MAX_MEM_ALLOC_SIZE"))
self.proc = OCLProcessor(self.dev,absPath("kernels/volume_render.cl"),
"-cl-fast-relaxed-math -cl-unsafe-math-optimizations -cl-mad-enable")
# self.proc = OCLProcessor(self.dev,absPath("kernels/volume_render.cl"),options="-cl-fast-relaxed-math")
self.invMBuf = self.dev.createBuffer(16,dtype=np.float32,
mem_flags = cl.mem_flags.READ_ONLY)
self.invPBuf = self.dev.createBuffer(16,dtype=np.float32,
mem_flags = cl.mem_flags.READ_ONLY)
self.projection = np.zeros((4,4))
self.modelView = np.zeros((4,4))
if size:
self.resize(size)
else:
self.resize((200,200))
self.set_dtype()
self.set_gamma()
self.set_max_val()
self.set_min_val()
self.set_alpha_pow()
self.set_box_boundaries()
self.set_units()
self.set_modelView()
self.set_projection()
def set_dtype(self,dtype = None):
if hasattr(self,"dtype") and dtype is self.dtype:
return
if dtype is None:
dtype = self.dtypes[0]
if dtype in self.dtypes:
self.dtype = dtype
else:
raise NotImplementedError("data type should be either %s not %s"%(self.dtypes,dtype))
self.reset_buffer()
def resize(self,size):
self.width, self.height = size
self.reset_buffer()
def reset_buffer(self):
self.buf = self.dev.createBuffer(self.height*self.width,dtype=np.float32)
self.bufAlpha = self.dev.createBuffer(self.height*self.width,dtype=np.float32)
self.bufDepth = self.dev.createBuffer(self.height*self.width,dtype=np.float32)
self.bufNormals = self.dev.createBuffer(3*self.height*self.width,dtype=np.float32)
self.bufNormalsScratch = self.dev.createBuffer(3*self.height*self.width,dtype=np.float32)
def _get_downsampled_data_slices(self,data):
"""in case data is bigger then gpu texture memory, we should downsample it
if so returns the slice of data to be rendered
else returns None (no downsampling)
"""
# Nstep = int(np.ceil(np.sqrt(1.*data.nbytes/self.memMax)))
Nstep = int(np.ceil((1.*data.nbytes/self.memMax)**(1./3)))
slices = [slice(0,d,Nstep) for d in data.shape]
if Nstep>1:
logger.info("downsample image by factor of %s"%Nstep)
return slices
else:
return None
def set_max_val(self,maxVal = 0.):
self.maxVal = maxVal
def set_min_val(self,minVal = 0.):
self.minVal = minVal
def set_gamma(self,gamma = 1.):
self.gamma = gamma
def set_alpha_pow(self,alphaPow = 10.):
self.alphaPow = alphaPow
def set_data(self,data, autoConvert = True, copyData = False):
if not autoConvert and not data.dtype in self.dtypes:
raise NotImplementedError("data type should be either %s not %s"%(self.dtypes,data.dtype))
if data.dtype.type in self.dtypes:
self.set_dtype(data.dtype.type)
_data = data
else:
print "converting type from %s to %s"%(data.dtype.type,self.dtype)
_data = data.astype(self.dtype)
self.dataSlices = self._get_downsampled_data_slices(_data)
if self.dataSlices is not None:
self.set_shape(_data[self.dataSlices].shape[::-1])
else:
self.set_shape(_data.shape[::-1])
self.update_data(_data, copyData = copyData)
self.update_matrices()
def set_shape(self,dataShape):
if self.isGPU:
self.dataImg = self.dev.createImage(dataShape,
mem_flags = cl.mem_flags.READ_ONLY,
channel_type = cl_datatype_dict[self.dtype])
else:
self.dataImg = self.dev.createImage(dataShape,
mem_flags = cl.mem_flags.READ_ONLY,
channel_order = cl.channel_order.INTENSITY,
channel_type = cl_datatype_dict[self.dtype])
def update_data(self,data, copyData = False):
#do we really want to copy here?
if self.dataSlices is not None:
self._data = data[self.dataSlices].copy()
else:
if copyData:
self._data = data.copy()
else:
self._data = data
if self._data.dtype != self.dtype:
self._data = self._data.astype(self.dtype)
self.dev.writeImage(self.dataImg,self._data)
def set_box_boundaries(self,boxBounds = [-1,1,-1,1,-1,1]):
self.boxBounds = np.array(boxBounds)
def set_units(self,stackUnits = np.ones(3)):
self.stackUnits = np.array(stackUnits)
def set_projection(self,projection = mat4_identity()):
self.projection = projection
self.update_matrices()
def set_modelView(self, modelView = mat4_identity()):
self.modelView = 1.*modelView
self.update_matrices()
def update_matrices(self):
if hasattr(self,"dataImg"):
mScale = self._stack_scale_mat()
invM = inv(np.dot(self.modelView,mScale))
self.dev.writeBuffer(self.invMBuf,invM.flatten().astype(np.float32))
invP = inv(self.projection)
self.dev.writeBuffer(self.invPBuf,invP.flatten().astype(np.float32))
# def _get_user_coords(self,x,y,z):
# p = array([x,y,z,1])
# worldp = dot(self.modelView,p)[:-2]
# userp = (worldp+[1.,1.])*.5*array([self.width,self.height])
# return userp[0],userp[1]
def _stack_scale_mat(self):
# scaling the data according to size and units
Nx,Ny,Nz = self.dataImg.shape
dx,dy,dz = self.stackUnits
# mScale = scaleMat(1.,1.*dx*Nx/dy/Ny,1.*dx*Nx/dz/Nz)
maxDim = max(d*N for d,N in zip([dx,dy,dz],[Nx,Ny,Nz]))
return mat4_scale(1.*dx*Nx/maxDim,1.*dy*Ny/maxDim,1.*dz*Nz/maxDim)
def render(self,data = None, stackUnits = None,
minVal = None, maxVal = None, gamma = None,
modelView = None, projection = None,
boxBounds = None, return_alpha = False, method="max_project",
numParts = 1, currentPart = 0):
if data is not None:
self.set_data(data)
if maxVal is not None:
self.set_max_val(maxVal)
if minVal is not None:
self.set_min_val(minVal)
if gamma is not None:
self.set_gamma(gamma)
if stackUnits is not None:
self.set_units(stackUnits)
if modelView is not None:
self.set_modelView(modelView)
if projection is not None:
self.set_projection(projection)
if not hasattr(self,'dataImg'):
print "no data provided, set_data(data) before"
if return_alpha:
return self.dev.readBuffer(self.buf,dtype = np.float32).reshape(self.width,self.height), self.dev.readBuffer(self.bufAlpha,dtype = np.float32).reshape(self.width,self.height)
else:
return self.dev.readBuffer(self.buf,dtype = np.float32).reshape(self.width,self.height)
if not modelView and not hasattr(self,'modelView'):
print "no modelView provided and set_modelView() not called before!"
if return_alpha:
return self.dev.readBuffer(self.buf,dtype = np.float32).reshape(self.width,self.height), self.dev.readBuffer(self.bufAlpha,dtype = np.float32).reshape(self.width,self.height)
else:
return self.dev.readBuffer(self.buf,dtype = np.float32).reshape(self.width,self.height)
# mScale = self._stack_scale_mat()
# invM = inv(np.dot(self.modelView,mScale))
# self.dev.writeBuffer(self.invMBuf,invM.flatten().astype(np.float32))
# invP = inv(self.projection)
# self.dev.writeBuffer(self.invPBuf,invP.flatten().astype(np.float32))
if method=="max_project":
if self.dtype == np.uint16:
method = "max_project_short"
else:
method = "max_project_float"
self.proc.runKernel(method,
(self.width,self.height),
None,
self.buf,self.bufAlpha,
np.int32(self.width),np.int32(self.height),
np.float32(self.boxBounds[0]),
np.float32(self.boxBounds[1]),
np.float32(self.boxBounds[2]),
np.float32(self.boxBounds[3]),
np.float32(self.boxBounds[4]),
np.float32(self.boxBounds[5]),
np.float32(self.minVal),
np.float32(self.maxVal),
np.float32(self.gamma),
np.float32(self.alphaPow),
self.invPBuf,
self.invMBuf,
self.dataImg)
if method=="max_project_part":
if self.dtype == np.uint16:
method = "max_project_part_short"
else:
method = "max_project_part_float"
self.proc.runKernel(method,
(self.width,self.height),
None,
self.buf,self.bufAlpha,
np.int32(self.width),np.int32(self.height),
np.float32(self.boxBounds[0]),
np.float32(self.boxBounds[1]),
np.float32(self.boxBounds[2]),
np.float32(self.boxBounds[3]),
np.float32(self.boxBounds[4]),
np.float32(self.boxBounds[5]),
np.float32(self.minVal),
np.float32(self.maxVal),
np.float32(self.gamma),
np.float32(self.alphaPow),
np.int32(numParts),
np.int32(currentPart),
self.invPBuf,
self.invMBuf,
self.dataImg)
if method=="iso_surface":
self.proc.runKernel("iso_surface",
(self.width,self.height),
None,
self.buf,self.bufAlpha,
np.int32(self.width),np.int32(self.height),
np.float32(self.boxBounds[0]),
np.float32(self.boxBounds[1]),
np.float32(self.boxBounds[2]),
np.float32(self.boxBounds[3]),
np.float32(self.boxBounds[4]),
np.float32(self.boxBounds[5]),
np.float32(self.maxVal/2),
np.float32(self.gamma),
self.invPBuf,
self.invMBuf,
self.dataImg,
np.int32(self.dtype == np.uint16)
)
if method=="iso_surface_new":
self.proc.runKernel("iso_surface_new",
(self.width,self.height),
None,
self.bufNormals,
self.bufAlpha,
np.int32(self.width),np.int32(self.height),
np.float32(self.boxBounds[0]),
np.float32(self.boxBounds[1]),
np.float32(self.boxBounds[2]),
np.float32(self.boxBounds[3]),
np.float32(self.boxBounds[4]),
np.float32(self.boxBounds[5]),
np.float32(self.maxVal/2),
np.float32(self.gamma),
self.invPBuf,
self.invMBuf,
self.dataImg,
np.int32(self.dtype == np.uint16)
)
self.proc.runKernel("blur_normals_x",
(self.width,self.height),
None,
self.bufNormals,
self.bufNormalsScratch,
np.int32(3))
self.proc.runKernel("blur_normals_y",
(self.width,self.height),
None,
self.bufNormalsScratch,
self.bufNormals,
np.int32(3))
self.proc.runKernel("iso_shading",
(self.width,self.height),
None,
self.bufNormals,
self.bufAlpha,
self.invMBuf,
self.invPBuf,
self.buf)
# return self.dev.readBuffer(self.bufNormals,dtype = np.float32).reshape(self.width,self.height,3)
if return_alpha:
return self.dev.readBuffer(self.buf,dtype = np.float32).reshape(self.width,self.height), self.dev.readBuffer(self.bufAlpha,dtype = np.float32).reshape(self.width,self.height)
else:
return self.dev.readBuffer(self.buf,dtype = np.float32).reshape(self.width,self.height)