def main(self, surf_coord, surf_topo, faces_csv, vertices_csv,
vertexlimits_csv):
F = LoadFaces.fromParent(self).setInput(surf_topo).run().getOutput(
'faces')
F = numpy.array(F, int)
with open(faces_csv, 'w') as fp:
for line in F:
fp.write(','.join([str(v) for v in line]) + '\n')
V = LoadVertices.fromParent(self).setInput(surf_coord).run().getOutput(
'vertices')
V = numpy.array(V, float)
with open(vertices_csv, 'w') as fp:
for line in V:
fp.write(','.join([str(v) for v in line]) + '\n')
minmax = [
','.join([str(v) for v in V.min(axis=0)]),
','.join([str(v) for v in V.max(axis=0)])
]
with open(vertexlimits_csv, 'w') as fp:
fp.write('\n'.join(minmax))
return FancyDict(faces_csv=faces_csv,
vertices_csv=vertices_csv,
vertexlimits_csv=vertexlimits_csv)
def main(self,surf_coord,surf_topo,faces_csv,vertices_csv,vertexlimits_csv):
F = LoadFaces.fromParent(self).setInput(surf_topo).run().getOutput('faces')
F = numpy.array(F,int)
with open(faces_csv,'w') as fp:
for line in F:
fp.write(','.join([str(v) for v in line])+'\n')
V = LoadVertices.fromParent(self).setInput(surf_coord).run().getOutput('vertices')
V = numpy.array(V,float)
with open(vertices_csv,'w') as fp:
for line in V:
fp.write(','.join([str(v) for v in line])+'\n')
minmax = [
','.join([str(v) for v in V.min(axis=0)]),
','.join([str(v) for v in V.max(axis=0)])
]
with open(vertexlimits_csv,'w') as fp:
fp.write('\n'.join(minmax))
return FancyDict(
faces_csv = faces_csv,
vertices_csv = vertices_csv,
vertexlimits_csv = vertexlimits_csv
)
def main(self,gm_vertices_csv,wm_vertices_csv,mid_vertices_csv,mid_vertexlimits_csv,wm_pct):
V_gm = LoadVertices.fromParent(self).setInput(gm_vertices_csv).run().getOutput('vertices')
V_gm = numpy.array(V_gm,float)
V_wm = LoadVertices.fromParent(self).setInput(wm_vertices_csv).run().getOutput('vertices')
V_wm = numpy.array(V_wm,float)
V = V_gm*(1-0.01*wm_pct)+V_wm*0.01*wm_pct
with open(mid_vertices_csv,'w') as fp:
for line in V:
fp.write(','.join([str(v) for v in line])+'\n')
minmax = [
','.join([str(v) for v in V.min(axis=0)]),
','.join([str(v) for v in V.max(axis=0)])
]
with open(mid_vertexlimits_csv,'w') as fp:
fp.write('\n'.join(minmax))
return FancyDict(
mid_vertices_csv = mid_vertices_csv,
mid_vertexlimits_csv = mid_vertexlimits_csv
)
def main(self,vertices_csv,faces_csv,datavolume_nii,paintmode):
V = LoadVertices.fromParent(self).setInput(vertices_csv).run().getOutput('vertices')
if paintmode=='F':
F = LoadFaces.fromParent(self).setInput(faces_csv).requestOutput('faces')
X = FaceCenters.fromParent(self).setInput(F,V).requestOutput('centers')
elif paintmode=='V':
X = V
elif paintmode=='FV':
F = LoadFaces.fromParent(self).setInput(faces_csv).run().getOutput('faces')
X = FaceVertexCenters.fromParent(self).setInput(F,V).requestOutput('centers')
else:
raise RuntimeError('Invalid paintmode "{}".'.format(paintmode))
nii = nibabel.load(datavolume_nii)
affine = nii.get_header().get_sform()
dataVolume = nii.get_data()
indexedPoints = IndexedPoints.fromParent(self).setInput(
X,affine
)
labelsFromVolume = LabelsFromVolume.fromParent(self).setInput(
labelVolume = dataVolume,
points = indexedPoints.requestOutput('points'),
bgIndex = 0
)
meshdata = labelsFromVolume.run().getOutput('labels').tolist()
meshdata = [str(v) for v in meshdata]
if paintmode == 'FV':
offset = numpy.cumsum([0]+[len(line) for line in F])
meshdata = [','.join(labels[offset[i]:offset[i+1]]) for i in range(0,len(F))]
meshdata_csv = self.tempfile('meshdata.csv')
with open(meshdata_csv,'w') as fp:
fp.write('\n'.join(meshdata))
minmax = numpy.array(V,float)
minmax = [
','.join([str(v) for v in minmax.min(axis=0)]),
','.join([str(v) for v in minmax.max(axis=0)])
]
vertexlimits_csv = self.tempfile('vertexlimits.csv')
with open(vertexlimits_csv,'w') as fp:
fp.write('\n'.join(minmax))
return FancyDict(
vertexlimits_csv = vertexlimits_csv,
meshdata_csv = meshdata_csv
)
def main(self,space,mesh,deformation,labelvolume,labelnames,name2value,colormap,colorlimits,spacesroot,jsonrpc2):
spacesFolder = '{}/{}'.format(spacesroot,space)
with open( '{}/config.json'.format(spacesFolder) ) as fp:
spaceConfig = json.load(fp)
meshConfig = spaceConfig['meshes'][mesh]['deformations']['fiducial']
facesFile = None
verticesFile = None
faceLabels = None
label2value = None
label2rgb = None
if labelvolume:
nii = nibabel.load(labelvolume)
hdr = nii.get_header()
img = nii.get_data()
sform = hdr.get_sform()
bgIndex = 0
facesFile = '{}/meshes/{}'.format(spacesFolder,meshConfig['faces'])
verticesFile = '{}/meshes/{}'.format(spacesFolder,meshConfig['vertices'])
F = LoadFaces.fromParent(self).setInput(facesFile).requestOutput('faces')
V = LoadVertices.fromParent(self).setInput(verticesFile).requestOutput('vertices')
X = FaceCenters.fromParent(self).setInput(F,V).requestOutput('centers')
faceCenters = IndexedPoints.fromParent(self).setInput(X,sform).requestOutput('points')
faceLabels = LabelsFromVolume.fromParent(self).setInput(
labelVolume = img,
points = faceCenters,
bgIndex = bgIndex
).run().requestOutput('labels')
with open(self.tempfile('facelabels.csv'),'w') as fp:
fp.write('\n'.join([str(v) for v in faceLabels]))
getLabelValues = GetLabelValues.fromParent(self).setInput(faceLabels,labelnames,name2value,colormap,colorlimits)
label2value = getLabelValues.requestOutput('label2value')
label2rgb = getLabelValues.requestOutput('label2rgb')
colormap = getLabelValues.requestOutput('colormap')
meshConfig = spaceConfig['meshes'][mesh]['deformations'][deformation]
deformedVerticesFile = '{}/meshes/{}'.format(spacesFolder,meshConfig['vertices'])
deformedFacesFile = '{}/meshes/{}'.format(spacesFolder,meshConfig['faces'])
if deformedVerticesFile != verticesFile:
V = LoadVertices.fromParent(self).setInput(deformedVerticesFile).requestOutput('vertices')
if deformedFacesFile != facesFile:
F = LoadFaces.fromParent(self).setInput(deformedFacesFile).requestOutput('faces')
if labelnames:
with open(labelnames) as fp:
labelnames = json.load(fp)
generateX3D = GenerateX3D.fromParent(self).setInput(
vertices = V,
faces = F,
facelabels = faceLabels,
label2rgb = label2rgb,
label2name = labelnames,
label2value = label2value,
colormap = colormap
)
return FancyDict(
x3dfile = generateX3D.requestOutput('x3dfile'),
x3dviewer = generateX3D.requestOutput('x3dviewer'),
x3d_files = generateX3D.requestOutput('x3dviewer_files')
)
def main(self, space, mesh, deformation, labelvolume, labelnames,
name2value, colormap, colorlimits, spacesroot, jsonrpc2):
spacesFolder = '{}/{}'.format(spacesroot, space)
with open('{}/config.json'.format(spacesFolder)) as fp:
spaceConfig = json.load(fp)
meshConfig = spaceConfig['meshes'][mesh]['deformations']['fiducial']
facesFile = None
verticesFile = None
faceLabels = None
label2value = None
label2rgb = None
if labelvolume:
nii = nibabel.load(labelvolume)
hdr = nii.get_header()
img = nii.get_data()
sform = hdr.get_sform()
bgIndex = 0
facesFile = '{}/meshes/{}'.format(spacesFolder,
meshConfig['faces'])
verticesFile = '{}/meshes/{}'.format(spacesFolder,
meshConfig['vertices'])
F = LoadFaces.fromParent(self).setInput(facesFile).requestOutput(
'faces')
V = LoadVertices.fromParent(self).setInput(
verticesFile).requestOutput('vertices')
X = FaceCenters.fromParent(self).setInput(
F, V).requestOutput('centers')
faceCenters = IndexedPoints.fromParent(self).setInput(
X, sform).requestOutput('points')
faceLabels = LabelsFromVolume.fromParent(self).setInput(
labelVolume=img, points=faceCenters,
bgIndex=bgIndex).run().requestOutput('labels')
with open(self.tempfile('facelabels.csv'), 'w') as fp:
fp.write('\n'.join([str(v) for v in faceLabels]))
getLabelValues = GetLabelValues.fromParent(self).setInput(
faceLabels, labelnames, name2value, colormap, colorlimits)
label2value = getLabelValues.requestOutput('label2value')
label2rgb = getLabelValues.requestOutput('label2rgb')
colormap = getLabelValues.requestOutput('colormap')
meshConfig = spaceConfig['meshes'][mesh]['deformations'][deformation]
deformedVerticesFile = '{}/meshes/{}'.format(spacesFolder,
meshConfig['vertices'])
deformedFacesFile = '{}/meshes/{}'.format(spacesFolder,
meshConfig['faces'])
if deformedVerticesFile != verticesFile:
V = LoadVertices.fromParent(self).setInput(
deformedVerticesFile).requestOutput('vertices')
if deformedFacesFile != facesFile:
F = LoadFaces.fromParent(self).setInput(
deformedFacesFile).requestOutput('faces')
if labelnames:
with open(labelnames) as fp:
labelnames = json.load(fp)
generateX3D = GenerateX3D.fromParent(self).setInput(
vertices=V,
faces=F,
facelabels=faceLabels,
label2rgb=label2rgb,
label2name=labelnames,
label2value=label2value,
colormap=colormap)
return FancyDict(
x3dfile=generateX3D.requestOutput('x3dfile'),
x3dviewer=generateX3D.requestOutput('x3dviewer'),
x3d_files=generateX3D.requestOutput('x3dviewer_files'))