def is_9DOF(self):
tra, scale, rot, rot_axis = self.to_translation_scale_rotation()
if tra is None:
return False
tra_mat = tr.translation_matrix(tra)
scale_mat = numpy.diag([scale[0],scale[1],scale[2],1.0])
rot_mat = tr.rotation_matrix(rot,rot_axis)
mat = numpy.dot(tra_mat, numpy.dot(scale_mat, rot_mat ) )
return tr.is_same_transform(mat,self.data)
def is_9DOF(self):
tra, scale, rot, rot_axis = self.to_translation_scale_rotation()
if tra is None:
return False
tra_mat = tr.translation_matrix(tra)
scale_mat = numpy.diag([scale[0],scale[1],scale[2],1.0])
rot_mat = tr.rotation_matrix(rot,rot_axis)
mat = numpy.dot(tra_mat, numpy.dot(scale_mat, rot_mat ) )
return tr.is_same_transform(mat,self.data)
def load_from_file(self, filename, channels=['B']):
f = open(filename)
self._reset()
while 1:
l = f.readline()
if l == '':
break
d = l.split()
channel = d[0][1]
do_process = False
if channels is None:
do_process = True
elif channels == []:
do_process = True
elif channels == '':
do_process = True
else:
if channel in channels:
do_process = True
else:
do_process = False
if do_process:
data = d[1]
x = float32(d[2])
y = float32(d[3])
z = float32(d[4])
q0 = float32(d[5])
q1 = float32(d[6])
q2 = float32(d[7])
q3 = float32(d[8])
q = [q0, q1, q2, q3]
#q = tr.quaternion_conjugate(q)
status = int32(d[11])
uncertainty = float32(d[12])
self._n_time_points += 1
tra_mat = tr.translation_matrix([x, y, z])
rot_mat = tr.quaternion_matrix(q)
self._motion.append(numpy.dot(tra_mat, rot_mat))
rotation = quaternion_to_rotation(q)
self._tx.append(x)
self._ty.append(y)
self._tz.append(z)
self._rx.append(rotation[0])
self._ry.append(rotation[1])
self._rz.append(rotation[2])
self._q0.append(q[0])
self._q1.append(q[1])
self._q2.append(q[2])
self._q3.append(q[3])
def load_from_file(self,filename, channels=['B']):
f = open(filename)
self._reset()
while 1:
l = f.readline()
if l=='':
break
d = l.split()
channel = d[0][1]
do_process = False
if channels is None:
do_process = True
elif channels == []:
do_process = True
elif channels == '':
do_process = True
else:
if channel in channels:
do_process = True
else:
do_process = False
if do_process:
data = d[1]
x = float32(d[2])
y = float32(d[3])
z = float32(d[4])
q0 = float32(d[5])
q1 = float32(d[6])
q2 = float32(d[7])
q3 = float32(d[8])
q = [q0,q1,q2,q3]
#q = tr.quaternion_conjugate(q)
status = int32(d[11])
uncertainty = float32(d[12])
self._n_time_points += 1
tra_mat = tr.translation_matrix([x,y,z])
rot_mat = tr.quaternion_matrix(q)
self._motion.append( numpy.dot(tra_mat,rot_mat) )
rotation = quaternion_to_rotation(q)
self._tx.append(x)
self._ty.append(y)
self._tz.append(z)
self._rx.append(rotation[0])
self._ry.append(rotation[1])
self._rz.append(rotation[2])
self._q0.append(q[0])
self._q1.append(q[1])
self._q2.append(q[2])
self._q3.append(q[3])
def to_translation_scale_rotation(self):
# FIXME
mat = self.data.copy()
tra = tr.translation_from_matrix(mat)
tra_mat = tr.translation_matrix(tra)
mat = numpy.dot(numpy.linalg.inv(tra_mat), mat)
factor, origin, direction = tr.scale_from_matrix(mat)
scale_mat = tr.scale_matrix(factor, origin, direction)
scale = numpy.diag(scale_mat)
mat = numpy.dot(numpy.linalg.inv(scale_mat), mat)
try:
rot,rot_axis,point = tr.rotation_from_matrix(mat)
except ValueError:
#print "Not a rotation matrix. "
return None, None, None, None
#print "Rotation axis: ",rot_axis
return tra, scale, rot, rot_axis
def to_translation_scale_rotation(self):
# FIXME
mat = self.data.copy()
tra = tr.translation_from_matrix(mat)
tra_mat = tr.translation_matrix(tra)
mat = numpy.dot(numpy.linalg.inv(tra_mat), mat)
factor, origin, direction = tr.scale_from_matrix(mat)
scale_mat = tr.scale_matrix(factor, origin, direction)
scale = numpy.diag(scale_mat)
mat = numpy.dot(numpy.linalg.inv(scale_mat), mat)
try:
rot,rot_axis,point = tr.rotation_from_matrix(mat)
except ValueError:
#print "Not a rotation matrix. "
return None, None, None, None
#print "Rotation axis: ",rot_axis
return tra, scale, rot, rot_axis
def load_data_files(self, path, from_dicom_comments=True, files_start_with=None, files_end_with=".dcm", exclude_files_end_with=['.dat','.txt','.py','.pyc','.nii','.gz','.png','.jpg','.jpeg','.eps','.hdr','.l'] ):
"""Load vNAV dicom files from given path and extract motion information.
If from_dicom_comments==True, use the information stored in the dicom comments.
If from_dicom_comments==False, use the information stored in the dicom MOCO field.
As of April 2014, these two express motion in different coordinate systems.
The dicom comments report absolute motion in scanner coordinates (origin is the magnetic iso-center of the scanner).
The dicom MOCO field is currently for proprietary use (??). """
self._n_time_points = 0
self._duration = []
self._motion = []
self._paths = []
self._tx = []; self._ty = []; self._tz = [];
self._rx = []; self._ry = []; self._rz = [];
self._tx_comm = []; self._ty_comm = []; self._tz_comm = [];
self._rx_comm = []; self._ry_comm = []; self._rz_comm = [];
self._q0_comm = []; self._q1_comm = []; self._q2_comm = []; self._q3_comm = [];
self._a0_comm = []; self._a1_comm = []; self._a2_comm = []; self._a3_comm = [];
N=0
# pick the first dicom file found in path
files = os.listdir(path)
files.sort()
# CASE 1: there exist files named with .dcm extension
for file_name in files:
file_valid = True
if files_start_with is not None:
if not file_name.startswith(files_start_with):
file_valid = False
if files_end_with is not None:
if not file_name.endswith(files_end_with):
file_valid = False
for s in exclude_files_end_with:
if file_name.endswith(s):
file_valid = False
if file_valid:
full_path = path+os.sep+file_name
# read moco information from files
self._paths.append(full_path)
try:
f = dicom.read_file(full_path)
except:
print "Could not read file ",full_path
return
t = f.get(0x00191025).value
r = f.get(0x00191026).value
self._tx.append(t[0]); self._ty.append(t[1]); self._tz.append(t[2]);
self._rx.append(r[0]); self._ry.append(r[1]); self._rz.append(r[2]);
motion_dicom_moco = []
# extract moco information stored in the dicom comment field
if from_dicom_comments:
s = f.get(0x00204000).value
if N:
a = numpy.float32(s.split(' ')[1:5])
t = numpy.float32(s.split(' ')[6:9])
freq = numpy.float32(s.split(' ')[10])
r = angle_axis_to_rotation(a[0],a[1:4])
else:
t = numpy.float32([0,0,0])
r = numpy.float32([0,0,0])
a = numpy.float32([0,1,0,0]) #FIXME: is this right?
q = angle_axis_to_quaternion(a.copy()[0],a.copy()[1:4])
self._a0_comm.append(a[0]); self._a1_comm.append(a[1]); self._a2_comm.append(a[2]); self._a3_comm.append(a[3]);
self._tx_comm.append(t[0]); self._ty_comm.append(t[1]); self._tz_comm.append(t[2])
self._q0_comm.append(q[0]); self._q1_comm.append(q[1]); self._q2_comm.append(q[2]); self._q3_comm.append(q[3]);
self._rx_comm.append(r[0]); self._ry_comm.append(r[1]); self._rz_comm.append(r[2]);
tra_mat = tr.translation_matrix(t)
rot_mat = tr.quaternion_matrix(q)
motion_dicom_comments = numpy.dot(tra_mat,rot_mat)
#xaxis, yaxis, zaxis = [1, 0, 0], [0, 1, 0], [0, 0, 1]
#Rx = tr.rotation_matrix(r[0], xaxis)
#Ry = tr.rotation_matrix(r[1], yaxis)
#Rz = tr.rotation_matrix(r[2], zaxis)
#rot_mat = tr.concatenate_matrices(Rx, Ry, Rz)
#rot_mat = Ry.copy()
#motion_dicom_comments = numpy.dot(tra_mat,rot_mat)
#motion_dicom_comments = rot_mat.copy()
N += 1
if from_dicom_comments:
self._motion.append(motion_dicom_comments)
else:
self._motion.append(motion_dicom_moco)
acquisition_number = f.get(0x00200012).value
creation_time = f.get(0x00080013).value
# print "Acquisition number: ", acquisition_number
# print "Creation time: ",creation_time
self._n_time_points = N
def load_data_files(self,
path,
from_dicom_comments=True,
files_start_with=None,
files_end_with=None,
exclude_files_end_with=[
'.dat', '.txt', '.py', '.pyc', '.nii', '.gz'
]):
"""Load vNAV dicom files from given path and extract motion information.
If from_dicom_comments==True, use the information stored in the dicom comments.
If from_dicom_comments==False, use the information stored in the dicom MOCO field.
As of April 2014, these two express motion in different coordinate systems.
The dicom comments report absolute motion in scanner coordinates (origin is the magnetic iso-center of the scanner).
The dicom MOCO field is currently for Siemens use (??). """
self._n_time_points = 0
self._duration = []
self._motion = []
self._paths = []
self._tx = []
self._ty = []
self._tz = []
self._rx = []
self._ry = []
self._rz = []
self._tx_comm = []
self._ty_comm = []
self._tz_comm = []
self._rx_comm = []
self._ry_comm = []
self._rz_comm = []
self._q0_comm = []
self._q1_comm = []
self._q2_comm = []
self._q3_comm = []
self._a0_comm = []
self._a1_comm = []
self._a2_comm = []
self._a3_comm = []
N = 0
# pick the first dicom file found in path
files = os.listdir(path)
# CASE 1: there exist files named with .dcm extension
for file_name in files:
file_valid = True
if files_start_with is not None:
if not file_name.startswith(files_start_with):
file_valid = False
if files_end_with is not None:
if not file_name.endswith(files_end_with):
file_valid = False
for s in exclude_files_end_with:
if file_name.endswith(s):
file_valid = False
if file_valid:
full_path = path + os.sep + file_name
# read moco information from files
self._paths.append(full_path)
f = dicom.read_file(full_path)
t = f.get(0x00191025).value
r = f.get(0x00191026).value
self._tx.append(t[0])
self._ty.append(t[1])
self._tz.append(t[2])
self._rx.append(r[0])
self._ry.append(r[1])
self._rz.append(r[2])
motion_dicom_moco = []
# extract moco information stored in the dicom comment field
s = f.get(0x00204000).value
if N:
a = numpy.float32(s.split(' ')[1:5])
t = numpy.float32(s.split(' ')[6:9])
freq = numpy.float32(s.split(' ')[10])
r = angle_axis_to_rotation(a[0], a[1:4])
else:
t = numpy.float32([0, 0, 0])
r = numpy.float32([0, 0, 0])
a = numpy.float32([0, 1, 0, 0]) #FIXME: is this right?
q = angle_axis_to_quaternion(a.copy()[0], a.copy()[1:4])
self._a0_comm.append(a[0])
self._a1_comm.append(a[1])
self._a2_comm.append(a[2])
self._a3_comm.append(a[3])
self._tx_comm.append(t[0])
self._ty_comm.append(t[1])
self._tz_comm.append(t[2])
self._q0_comm.append(q[0])
self._q1_comm.append(q[1])
self._q2_comm.append(q[2])
self._q3_comm.append(q[3])
self._rx_comm.append(r[0])
self._ry_comm.append(r[1])
self._rz_comm.append(r[2])
tra_mat = tr.translation_matrix(t)
rot_mat = tr.quaternion_matrix(q)
motion_dicom_comments = numpy.dot(tra_mat, rot_mat)
#xaxis, yaxis, zaxis = [1, 0, 0], [0, 1, 0], [0, 0, 1]
#Rx = tr.rotation_matrix(r[0], xaxis)
#Ry = tr.rotation_matrix(r[1], yaxis)
#Rz = tr.rotation_matrix(r[2], zaxis)
#rot_mat = tr.concatenate_matrices(Rx, Ry, Rz)
#rot_mat = Ry.copy()
#motion_dicom_comments = numpy.dot(tra_mat,rot_mat)
#motion_dicom_comments = rot_mat.copy()
N += 1
if from_dicom_comments:
self._motion.append(motion_dicom_comments)
else:
self._motion.append(motion_dicom_moco)
acquisition_number = f.get(0x00200012).value
creation_time = f.get(0x00080013).value
# print "Acquisition number: ", acquisition_number
# print "Creation time: ",creation_time
self._n_time_points = N
def __init__(self, translation, rotation_angle, rotation_direction, rotation_point=None, map_from="",map_to=""):
rot = tr.rotation_matrix(rotation_angle, rotation_direction, rotation_point)
tra = tr.translation_matrix(translation)
mat = numpy.dot(tra,rot)
Transform_Affine.__init__(self, mat,map_from,map_to)
def __init__(self, direction, map_from="",map_to=""):
mat = tr.translation_matrix(direction)
Transform_Affine.__init__(self, mat,map_from,map_to)
def from_translation_rotation(self, tra, rot, axis=[0,0,1]):
return numpy.dot(tr.translation_matrix(tra), tr.rotation_matrix(rot,axis) )
def __init__(self, translation, rotation_angle, rotation_direction, rotation_point=None, map_from="",map_to=""):
rot = tr.rotation_matrix(rotation_angle, rotation_direction, rotation_point)
tra = tr.translation_matrix(translation)
mat = numpy.dot(tra,rot)
Transform_Affine.__init__(self, mat,map_from,map_to)
def __init__(self, direction, map_from="",map_to=""):
mat = tr.translation_matrix(direction)
Transform_Affine.__init__(self, mat,map_from,map_to)
def from_translation_rotation(self, tra, rot, axis=[0,0,1]):
return numpy.dot(tr.translation_matrix(tra), tr.rotation_matrix(rot,axis) )