def process(self):
"""
The PythonScriptProcessor will call this process function whenever the processor process
function is called. The argument 'self' represents the PythonScriptProcessor.
"""
# create a small float volume filled with random noise
numpy.random.seed(546465)
dim = self.properties.dim.value
volume = Volume(
numpy.random.rand(dim[0], dim[1], dim[2]).astype(numpy.float32))
volume.dataMap.dataRange = dvec2(0.0, 1.0)
volume.dataMap.valueRange = dvec2(0.0, 1.0)
self.outports.outport.setData(volume)
pass
def dataLoaded(self, data, extents):
buffer = numpy.concatenate(data, axis=3)
volume = ivw.data.Volume(buffer)
if self.overwriteDataRange.value:
volume.dataMap.dataRange = self.dataRange.value
else:
minVal = numpy.amin(buffer)
maxVal = numpy.amax(buffer)
volume.dataMap.dataRange = dvec2(minVal, maxVal)
volume.dataMap.valueRange = volume.dataMap.dataRange
if self.overwriteModel:
volume.modelMatrix = self.modelMatrix.value
else:
volume.modelMatrix = mat4(vec4(extents[2], 0, 0, 0),
vec4(0, extents[1], 0, 0),
vec4(0, 0, extents[0], 0),
vec4(0, 0, 0, 1))
volume.interpolation = ivw.data.InterpolationType(
self.interpolation.value)
volume.wrapping = [
ivw.data.Wrapping(self.wrappingX.value),
ivw.data.Wrapping(self.wrappingY.value),
ivw.data.Wrapping(self.wrappingZ.value)
]
self.volumeOutport.setData(volume)
def process(self):
"""
The PythonScriptProcessor will call this process function whenever the processor process
function is called. The argument 'self' represents the PythonScriptProcessor.
"""
if self.properties.use_nifti.value == True:
print("Loading nii data at " + self.properties.location.value)
img = nib.load(self.properties.location.value)
print(img.header)
print(img.get_data_dtype())
data = img.get_fdata()
else:
print("Loading numpy data at " + self.properties.location.value)
data = np.load(self.properties.location.value)
dim = data.shape
max_desired_val = self.properties.max.value
max_val = min(data.max(), max_desired_val)
print("Max data value is {}, cut down to {}".format(data.max(), max_val))
data = np.where(data > max_desired_val, np.zeros_like(data), data)
# data = np.where(data < (max_val / 10), np.zeros_like(data), data)
volume = Volume(data.astype(np.uint16))
volume.dataMap.dataRange = dvec2(0.0, max_val)
volume.dataMap.valueRange = dvec2(0.0, max_desired_val)
self.outports.outport.setData(volume)
# shifting the model by a set translation along all axes
if self.properties.use_scan_basis.value == False:
basis_vals = self.properties.basis.value
volume.modelMatrix = mat4(basis_vals.x, 0, 0, 0, 0, basis_vals.y, 0, 0,
0, 0, basis_vals.z, 0, -(basis_vals.x / 2),
-(basis_vals.y / 2), -(basis_vals.z / 2), 1)
else:
affine_trans = img.affine.transpose()
volume.modelMatrix = mat4(*affine_trans.reshape(16))
volume.worldMatrix = mat4(1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1)
def dataLoaded(self, data, extents):
volumeSequence = []
for timeStep in range(data[0].shape[3]):
subData = []
for comp in data:
# A bit brute force, but delivers correct data.
numElems = comp.shape[0] * comp.shape[1] * comp.shape[2]
subBuffer = comp.flat[(numElems * timeStep):(numElems *
(timeStep + 1))]
subBuffer.shape = (comp.shape[0], comp.shape[1], comp.shape[2],
1)
subData.append(subBuffer)
buffer = numpy.concatenate(subData, axis=3)
volume = ivw.data.Volume(buffer)
if self.overwriteDataRange.value:
volume.dataMap.dataRange = self.dataRange.value
else:
minVal = numpy.amin(buffer)
maxVal = numpy.amax(buffer)
volume.dataMap.dataRange = dvec2(minVal, maxVal)
volume.dataMap.valueRange = volume.dataMap.dataRange
if self.overwriteModel:
volume.modelMatrix = self.modelMatrix.value
else:
volume.modelMatrix = mat4(vec4(extents[2], 0, 0, 0),
vec4(0, extents[1], 0, 0),
vec4(0, 0, extents[0], 0),
vec4(0, 0, 0, 1))
volume.interpolation = ivw.data.InterpolationType(
self.interpolation.value)
volume.wrapping = [
ivw.data.Wrapping(self.wrappingX.value),
ivw.data.Wrapping(self.wrappingY.value),
ivw.data.Wrapping(self.wrappingZ.value)
]
volumeSequence.append(volume)
sequence = ivw.data.VolumeSequence(volumeSequence)
self.volumeOutport.setData(sequence)