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, surface_x3d, faces_csv, vertices_csv, vertexlimits_csv):
# custom parser needed to parse files larger than approx. 10 MB.
tree = etree.parse(surface_x3d,
parser=etree.ETCompatXMLParser(huge_tree=True))
rootNode = tree.getroot()
faceNode = rootNode.find('.//IndexedFaceSet')
faces = re.sub('[\s,]+', ',', faceNode.attrib['coordIndex'].strip())
faces = re.sub(',-1,', '\n', faces)
faces = re.sub(',-1$', '', faces)
with open(faces_csv, 'w') as fp:
fp.write(faces)
# experimental: save binary data (works well, but gz is more useful)
"""
faces = json.loads('[['+re.sub('\n','],[',faces)+']]')
faces = numpy.array(faces,numpy.dtype('<u4'))
faces_dat = re.sub('\.csv$','',faces_csv)+'.dat';
with open(faces_dat,'w') as fp:
fp.write(faces.tostring())
"""
vertexNode = faceNode.find('Coordinate')
with open(vertices_csv, 'w') as fp:
vertices = re.sub('[\s,]+', ' ',
vertexNode.attrib['point'].strip())
vertices = vertices.split(' ')
vertices = [
','.join(vertices[i:i + 3])
for i in range(0, len(vertices), 3)
]
fp.write('\n'.join(vertices))
V = LoadVertices().setInput(vertices_csv).getOutput('vertices')
V = numpy.array(V, float)
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,surface_x3d,faces_csv,vertices_csv,vertexlimits_csv):
# custom parser needed to parse files larger than approx. 10 MB.
tree = etree.parse(surface_x3d,parser=etree.ETCompatXMLParser(huge_tree=True))
rootNode = tree.getroot()
faceNode = rootNode.find('.//IndexedFaceSet')
faces = re.sub('[\s,]+',',',faceNode.attrib['coordIndex'].strip())
faces = re.sub(',-1,','\n',faces)
faces = re.sub(',-1$','',faces)
with open(faces_csv,'w') as fp:
fp.write(faces)
# experimental: save binary data (works well, but gz is more useful)
"""
faces = json.loads('[['+re.sub('\n','],[',faces)+']]')
faces = numpy.array(faces,numpy.dtype('<u4'))
faces_dat = re.sub('\.csv$','',faces_csv)+'.dat';
with open(faces_dat,'w') as fp:
fp.write(faces.tostring())
"""
vertexNode = faceNode.find('Coordinate')
with open(vertices_csv,'w') as fp:
vertices = re.sub('[\s,]+',' ',vertexNode.attrib['point'].strip())
vertices = vertices.split(' ')
vertices = [','.join(vertices[i:i+3]) for i in range(0,len(vertices),3)]
fp.write('\n'.join(vertices))
V = LoadVertices().setInput(vertices_csv).getOutput('vertices')
V = numpy.array(V,float)
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,faces_csv,vertices_csv,labels_nii,volume_nii):
V = LoadVertices().setInput(vertices_csv).getOutput('vertices')
F = LoadFaces().setInput(faces_csv).getOutput('faces')
X = FaceCenters().setInput(F,V).getOutput('centers')
nii = nibabel.load(labels_nii)
affine = nii.get_header().get_best_affine()
points = IndexedPoints().setInput(X,affine).getOutput('points')
if volume_nii is None: volume_nii = self.tempfile('volume.nii.gz')
output_nii = VolumeFromLabels().setInput(
points = points,
labels = numpy.zeros((len(points),),numpy.uint8)+255,
reference = labels_nii,
output = volume_nii
).getOutput('output')
return FancyDict(
volume_nii = output_nii
)
def main(self,
faces_csv,
vertices_csv,
vertexlimits_csv,
output_x3d,
x3d_width=800,
x3d_height=800):
if isinstance(vertices_csv, list): V = vertices_csv
else: V = LoadVertices().setInput(vertices_csv).getOutput('vertices')
if isinstance(faces_csv, list): F = faces_csv
else: F = LoadFaces().setInput(faces_csv).getOutput('faces')
with open(vertexlimits_csv, 'r') as fp:
limits = fp.readlines()
mn = [float(v) for v in limits[0].split(',')]
mx = [float(v) for v in limits[1].split(',')]
centerX = 0.5 * (mx[0] + mn[0])
centerY = 0.5 * (mx[1] + mn[1])
centerZ = 0.5 * (mx[2] + mn[2])
distanceW = 32 * max(mx[0] - mn[0],
mx[1] - mn[1]) * x3d_height / x3d_width
distanceH = 32 * max(mx[0] - mn[0],
mx[2] - mn[2]) * x3d_width / x3d_height
distance = max(distanceW, distanceH)
position = '{},{},{}'.format(centerX - distance, centerY, centerZ)
centerOfRotation = '{},{},{}'.format(centerX, centerY, centerZ)
faces = ' -1 '.join([' '.join([str(v) for v in line]) for line in F])
vertices = ' '.join([','.join([str(v) for v in line]) for line in V])
with open(output_x3d, 'w') as fp:
fp.write(
'<X3D id="X3D_ROOT" width="{}px" height="{}px" profile="Interchange" version="3.2" xmlns:xsd="http://www.w3.org/2001/XMLSchema-instance" xsd:noNamespaceSchemaLocation="http://www.web3d.org/specifications/x3d-3.2.xsd">\n'
.format(x3d_width, x3d_height))
fp.write('<Scene id="X3D_SCENE">\n')
fp.write('<Background id="X3D_BACKGROUND" skyColor="0 0 0"/>\n')
fp.write(
'<Viewpoint id="X3D_VIEW" fieldOfView="0.032725" position="{}" description="Left" orientation="-0.57735 0.57735 0.57735 -2.0944" centerOfRotation="{}"/>\n'
.format(position, centerOfRotation))
fp.write(
'<NavigationInfo type=""EXAMINE" "FLY" "ANY"" speed="4" headlight="true"/>\n'
)
fp.write(
'<DirectionalLight ambientIntensity="1" intensity="0" color="1 1 1"/>\n'
)
fp.write('<Transform DEF="ROOT" translation="0 0 0">\n')
fp.write('<Shape>\n')
fp.write('<Appearance>\n')
fp.write(
'<Material ambientIntensity="0" emissiveColor="0 0 0" diffuseColor="1 1 1" specularColor="0 0 0" shininess="0.0078125" transparency="0"/>\n'
)
fp.write('</Appearance>\n')
fp.write(
'<IndexedFaceSet id="X3D_SURF" creaseAngle="0.785" solid="false" colorPerVertex="false" normalPerVertex="false" coordIndex="{}">\n'
.format(faces))
fp.write('<Coordinate point="{}"/>\n'.format(vertices))
fp.write('</IndexedFaceSet>\n')
fp.write('</Shape>\n')
fp.write('</Transform>\n')
fp.write('</Scene>\n')
fp.write('</X3D>\n')
return FancyDict(output_x3d=output_x3d)
def main(self, faces_csv, vertices_csv, labels_nii, multilabelfilter,
colormap_json, labels_csv, labelmode, label2rgb_csv,
mesh2labels_nii):
last = lastUpdate(faces_csv, vertices_csv, labels_nii)
first = firstUpdate(labels_csv, label2rgb_csv)
fancyLog(dict(last=last, first=first), 'debug')
if last < first:
return FancyDict(labels_csv=labels_csv,
label2rgb_csv=label2rgb_csv)
V = LoadVertices().setInput(vertices_csv).getOutput('vertices')
if labelmode == 'F':
F = LoadFaces().setInput(faces_csv).requestOutput('faces')
X = FaceCenters().setInput(F, V).requestOutput('centers')
elif labelmode == 'V':
X = V
elif labelmode == 'FV':
F = LoadFaces().setInput(faces_csv).getOutput('faces')
X = FaceVertexCenters().setInput(F, V).requestOutput('centers')
else:
raise RuntimeError('Invalid labelmode "{}".'.format(labelmode))
if multilabelfilter:
labels_nii = MultiLabelSmooth().setInput(
raw_nii=labels_nii, filter=multilabelfilter,
ignore=[0]).getOutput('smoothed_nii')
nii = nibabel.load(labels_nii)
affine = nii.get_header().get_best_affine()
labelVolume = nii.get_data()
indexedPoints = IndexedPoints().setInput(X, affine)
labelsFromVolume = LabelsFromVolume().setInput(
labelVolume=labelVolume,
points=indexedPoints.requestOutput('points'),
bgIndex=0)
labels = labelsFromVolume.getOutput('labels').tolist()
labels = [str(v) for v in labels]
if labelmode == 'FV':
offset = numpy.cumsum([0] + [len(line) for line in F])
labels = [
','.join(labels[offset[i]:offset[i + 1]])
for i in range(0, len(F))
]
with open(labels_csv, 'w') as fp:
fp.write('\n'.join(labels))
if mesh2labels_nii:
VolumeFromLabels().setInput(
points=indexedPoints.requestOutput('points'),
labels=labelsFromVolume.requestOutput('labels'),
reference=labels_nii,
output=mesh2labels_nii).getOutput()
with open(colormap_json, 'r') as fp:
colormap = json.load(fp)
if isinstance(colormap, dict):
mx = 0
for k in colormap.keys():
if int(k) > mx:
mx = int(k)
baseColor = 'AAAAAA'
colormap = [
colormap[str(i)] if str(i) in colormap else baseColor
for i in range(0, mx + 1)
]
colormap = [
','.join([
'{0:.3f}'.format(int(v[i:i + 2], 16) / 255.0)
for i in range(0, 6, 2)
]) for v in colormap
]
with open(label2rgb_csv, 'w') as fp:
fp.write('\n'.join(colormap))
return FancyDict(labels_csv=labels_csv, label2rgb_csv=label2rgb_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'))