def getImageTransform(filename, scaleFactor=1):
""" Returns dim, voxelsize and rigid position of an image given an .mhd header image file
a scaleFactor can be given to normalize image length units (usually in mm)
"""
scale=[0,0,0]
tr=[0,0,0]
dim=[0,0,0]
with open(filename,'r') as f:
for line in f:
splitted = line.split()
if len(splitted)!=0:
if 'ElementSpacing'==splitted[0] or 'spacing'==splitted[0] or 'scale3d'==splitted[0] or 'voxelSize'==splitted[0]:
scale = map(float,splitted[2:5])
if 'Position'==splitted[0] or 'Offset'==splitted[0] or 'translation'==splitted[0] or 'origin'==splitted[0]:
tr = map(float,splitted[2:5])
if 'Orientation'==splitted[0] or 'Rotation'==splitted[0] or 'TransformMatrix'==splitted[0] :
R = numpy.array([map(float,splitted[2:5]),map(float,splitted[5:8]),map(float,splitted[8:11])])
if 'DimSize'==splitted[0] or 'dimensions'==splitted[0] or 'dim'==splitted[0]:
dim = map(int,splitted[2:5])
q = quat.from_matrix(R)
if scaleFactor!=1:
scale = [s*scaleFactor for s in scale]
tr = [t*scaleFactor for t in tr]
offset=[tr[0],tr[1],tr[2],q[0],q[1],q[2],q[3]]
return (dim,scale,offset)
def getImageTransform(filename, scaleFactor=1):
""" Returns dim, voxelsize and rigid position of an image given an .mhd header image file
a scaleFactor can be given to normalize image length units (usually in mm)
"""
scale=[0,0,0]
tr=[0,0,0]
dim=[0,0,0]
with open(filename,'r') as f:
for line in f:
splitted = line.split()
if len(splitted)!=0:
if 'ElementSpacing'==splitted[0] or 'spacing'==splitted[0] or 'scale3d'==splitted[0] or 'voxelSize'==splitted[0]:
scale = map(float,splitted[2:5])
if 'Position'==splitted[0] or 'Offset'==splitted[0] or 'translation'==splitted[0] or 'origin'==splitted[0]:
tr = map(float,splitted[2:5])
if 'Orientation'==splitted[0] or 'Rotation'==splitted[0] or 'TransformMatrix'==splitted[0] :
R = numpy.array([map(float,splitted[2:5]),map(float,splitted[5:8]),map(float,splitted[8:11])])
if 'DimSize'==splitted[0] or 'dimensions'==splitted[0] or 'dim'==splitted[0]:
dim = map(int,splitted[2:5])
q = quat.from_matrix(R)
if scaleFactor!=1:
scale = [s*scaleFactor for s in scale]
tr = [t*scaleFactor for t in tr]
offset=[tr[0],tr[1],tr[2],q[0],q[1],q[2],q[3]]
return (dim,scale,offset)
def decomposeInertia(inertia):
""" Decompose an inertia matrix into
- a diagonal inertia
- the rotation (quaternion) to get to the frame in wich the inertia is diagonal
"""
U, diagonal_inertia, V = numpy.linalg.svd(inertia)
# det should be 1->rotation or -1->reflexion
if numpy.linalg.det(U) < 0: # reflexion
# made it a rotation by negating a column
U[:, 0] = -U[:, 0]
inertia_rotation = Quaternion.from_matrix(U)
return diagonal_inertia, inertia_rotation
def decomposeInertia(inertia):
""" Decompose an inertia matrix into
- a diagonal inertia
- the rotation (quaternion) to get to the frame in wich the inertia is diagonal
"""
U, diagonal_inertia, V = numpy.linalg.svd(inertia)
# det should be 1->rotation or -1->reflexion
if numpy.linalg.det(U) < 0 : # reflexion
# made it a rotation by negating a column
U[:,0] = -U[:,0]
inertia_rotation = Quaternion.from_matrix( U )
return diagonal_inertia, inertia_rotation
def read_rigid(rigidFileName):
rigidFile = open(rigidFileName, "r")
line = list(rigidFile)
rigidFile.close()
# for i in xrange(len(line)):
# print str(i) + str(line[i])
start = 1
res = MassInfo()
res.mass = float(line[start].split(' ')[1])
#volm = float( line[start + 1].split(' ')[1])
res.com = map(float, line[start + 3].split(' ')[1:])
inertia = map(
float, line[start + 2].split(' ')[1:]) # pick inertia matrix from file
res.inertia = array([res.mass * x for x in inertia
]).reshape(3, 3) # convert it in numpy 3x3 matrix
# extracting principal axes basis and corresponding rotation and diagonal inertia
if inertia[1] > 1e-5 or inertia[2] > 1e-5 or inertia[
5] > 1e-5: # if !diagonal (1e-5 seems big but the precision from a mesh is poor)
# print res.inertia
U, res.diagonal_inertia, V = linalg.svd(res.inertia)
# det should be 1->rotation or -1->reflexion
if linalg.det(U) < 0: # reflexion
# made it a rotation by negating a column
# print "REFLEXION"
U[:, 0] = -U[:, 0]
res.inertia_rotation = quat.from_matrix(U)
# print "generate_rigid not diagonal U" +str(U)
# print "generate_rigid not diagonal V" +str(V)
# print "generate_rigid not diagonal d" +str(res.diagonal_inertia)
else:
res.diagonal_inertia = res.inertia.diagonal()
res.inertia_rotation = [0, 0, 0, 1]
# print "generate_rigid " + str(res.mass) + " " + str( res.inertia ) + " " + str( res.diagonal_inertia )
return res
def read_rigid(rigidFileName):
rigidFile = open( rigidFileName, "r" )
line = list( rigidFile )
rigidFile.close()
# for i in xrange(len(line)):
# print str(i) + str(line[i])
start = 1
res = MassInfo()
res.mass = float( line[start].split(' ')[1] )
#volm = float( line[start + 1].split(' ')[1])
res.com = map(float, line[start + 3].split(' ')[1:] )
inertia = map(float, line[start + 2].split(' ')[1:] ) # pick inertia matrix from file
res.inertia = array( [res.mass * x for x in inertia] ).reshape( 3, 3 ) # convert it in numpy 3x3 matrix
# extracting principal axes basis and corresponding rotation and diagonal inertia
if inertia[1]>1e-5 or inertia[2]>1e-5 or inertia[5]>1e-5 : # if !diagonal (1e-5 seems big but the precision from a mesh is poor)
# print res.inertia
U, res.diagonal_inertia, V = linalg.svd(res.inertia)
# det should be 1->rotation or -1->reflexion
if linalg.det(U) < 0 : # reflexion
# made it a rotation by negating a column
# print "REFLEXION"
U[:,0] = -U[:,0]
res.inertia_rotation = quat.from_matrix( U )
# print "generate_rigid not diagonal U" +str(U)
# print "generate_rigid not diagonal V" +str(V)
# print "generate_rigid not diagonal d" +str(res.diagonal_inertia)
else :
res.diagonal_inertia = res.inertia.diagonal()
res.inertia_rotation = [0,0,0,1]
# print "generate_rigid " + str(res.mass) + " " + str( res.inertia ) + " " + str( res.diagonal_inertia )
return res
def generate_rigid(filename, density = 1000.0, scale=[1,1,1], rotation=[0,0,0]):
# TODO bind GenerateRigid
# - faster than writing in a file
# - more robust (if several processes try to work in the same file)
tmpfilename = Tools.path( __file__ ) +"/tmp.rigid"
cmd = [ Sofa.build_dir() + '/bin/GenerateRigid', filename, tmpfilename, str(density), str(scale[0]), str(scale[1]), str(scale[2]), str(rotation[0]), str(rotation[1]), str(rotation[2]) ]
# print cmd
try:
output = Popen(cmd, stdout=PIPE)
except OSError:
# try the debug version
cmd[0] += 'd'
try:
output = Popen(cmd, stdout=PIPE)
except OSError:
print 'error when calling GenerateRigid, do you have GenerateRigid built in SOFA?'
raise
output.communicate() # wait until Popen command is finished!!!
# GenerateRigid output is stored in the file tmpfilename
rigidFile = open( tmpfilename, "r" )
line = list( rigidFile )
rigidFile.close()
# for i in xrange(len(line)):
# print str(i) + str(line[i])
start = 1
res = MassInfo()
res.mass = float( line[start].split(' ')[1] )
#volm = float( line[start + 1].split(' ')[1] )
res.com = map(float, line[start + 3].split(' ')[1:] )
inertia = map(float, line[start + 2].split(' ')[1:] ) # pick inertia matrix from file
res.inertia = array( [res.mass * x for x in inertia] ).reshape( 3, 3 ) # convert it in numpy 3x3 matrix
# extracting principal axes basis and corresponding rotation and diagonal inertia
if inertia[1]>1e-5 or inertia[2]>1e-5 or inertia[5]>1e-5 : # if !diagonal (1e-5 seems big but the precision from a mesh is poor)
# print res.inertia
U, res.diagonal_inertia, V = linalg.svd(res.inertia)
# det should be 1->rotation or -1->reflexion
if linalg.det(U) < 0 : # reflexion
# made it a rotation by negating a column
# print "REFLEXION"
U[:,0] = -U[:,0]
res.inertia_rotation = quat.from_matrix( U )
# print "generate_rigid not diagonal U" +str(U)
# print "generate_rigid not diagonal V" +str(V)
# print "generate_rigid not diagonal d" +str(res.diagonal_inertia)
else :
res.diagonal_inertia = res.inertia.diagonal()
res.inertia_rotation = [0,0,0,1]
# print "generate_rigid " + str(res.mass) + " " + str( res.inertia ) + " " + str( res.diagonal_inertia )
return res
