def __calculate_calibration(self,file_name):
calibration_samples = read_and_transform.extract_calibration_samples(self.normalized_points)
self.calibration_points = {}
point_function = read_and_transform.get_pointer_transform_function(self.mid_date)
for label, index in read_and_transform.CALIBRATION_LABELS.iteritems():
raw_point = calibration_samples[index]
tip = point_function(raw_point)
self.calibration_points[label] = tip
#Get file name
temp = file_name.split('/')
lastone = len(temp)
newfile = temp[lastone-1]
datalist=[]
#Create order list of calibration points
calibration_names = ['right', 'vertex', 'nasion', 'left']
for key in calibration_names:
temp_points = self.calibration_points[key]
datalist.append([temp_points[0], temp_points[1], temp_points[2]])
#Write csv file with calibration points
with open("calib_data/calib_pills/tms/"+newfile, 'wb') as f:
writer = csv.writer(f, delimiter=',')
writer.writerows(datalist)
#Matlab method, rigid transformation
# Input new_data/calib_pills/tms/subject.csv (429.csv)
# Output new_data/calib_pills/tms/new_pos/subject.csv (TMS-429.csv)
#
#
#
#
#Get result of matlab method new pills position
textlist = []
with open('calib_data/calib_pills/tms/new_pos/'+newfile, 'rb') as csvfile:
textlist = csv.reader(csvfile, delimiter=',', lineterminator='\n')
my_list=list(textlist)
#Parsing float the list items
my_list = [[float(i) for i in tt] for tt in my_list]
#Gen new calibration points
for newvalue in range(0,self.calibration_points.__len__()):
if newvalue == 0 :
self.calibration_points['right'][0] = my_list[newvalue][0]
self.calibration_points['right'][1] = my_list[newvalue][1]
self.calibration_points['right'][2] = my_list[newvalue][2]
if newvalue == 1 :
self.calibration_points['vertex'][0] = my_list[newvalue][0]
self.calibration_points['vertex'][1] = my_list[newvalue][1]
self.calibration_points['vertex'][2] = my_list[newvalue][2]
if newvalue == 2 :
self.calibration_points['nasion'][0] = my_list[newvalue][0]
self.calibration_points['nasion'][1] = my_list[newvalue][1]
self.calibration_points['nasion'][2] = my_list[newvalue][2]
if newvalue == 3 :
self.calibration_points['left'][0] = my_list[newvalue][0]
self.calibration_points['left'][1] = my_list[newvalue][1]
self.calibration_points['left'][2] = my_list[newvalue][2]
print 'Nuevos puntos calibracion'
print self.calibration_points
if self.hacks is not None:
skip = set(self.hacks.get("skip_calib",set()))
pts = [v for k,v in self.calibration_points.iteritems() if k not in skip]
r, ctr = tms_geom.adjust_sphere(pts)
else:
r, ctr = tms_geom.adjust_sphere(self.calibration_points.itervalues())
self.sphere_radius, self.sphere_center = r, ctr
def __test_one():
import os
import vtk
from itertools import izip
test_dir = os.path.join(os.path.dirname(__file__), "data")
test_file = os.path.join(test_dir, "TMS-441.csv")
test_file = os.path.join(test_dir, "TMS-758.csv")
#test_file = os.path.join(test_dir, "TMS-310.csv")
points = tms_rt.read_csv_file(test_file)
calibs = tms_rt.extract_calibration_samples(points)
assert set(calibs.keys()) == {1, 2, 3, 4}
ref = calibs[3]
calibs_norm = dict(((k, tms_rt.normalize_point_to_ref(v, ref) ) for k, v in calibs.iteritems() ))
ren_win = vtk.vtkRenderWindow()
iren = vtk.vtkRenderWindowInteractor()
iren.SetInteractorStyle(vtk.vtkInteractorStyleTrackballCamera())
iren.SetRenderWindow(ren_win)
ren = vtk.vtkRenderer()
ren_win.AddRenderer(ren)
date = ref.date
pointer_fun = tms_rt.get_pointer_transform_function(date)
calib_points = [pointer_fun(p) for p in calibs_norm.itervalues()]
r,ctr = tms_geom.adjust_sphere(calib_points)
for p in calib_points:
__add_sphere_to_ren(p,r/20,ren)
ac = __add_sphere_to_ren(ctr,r,ren)
ac.GetProperty().SetColor(1,0,0)
#fit sphere to calibration
coil_samples = tms_rt.extract_coil_samples(points)[:50]
coil_samples_norm = tms_rt.normalize_to_ref(coil_samples, ref)
coil_function = tms_rt.get_coil_transform_function(date)
coil_pairs = [coil_function(p) for p in coil_samples_norm]
cc = (0, 1, 0)
cc2 = (0.2,0.7,0.2)
for (c, t),p in izip(coil_pairs,coil_samples_norm):
ac = __add_sphere_to_ren(c, 0.002, ren)
ac.GetProperty().SetColor(cc)
ac = __add_line_to_ren(c, np.subtract(t, c), ren)
ac.GetProperty().SetColor(cc)
#draw intersection with sphere
intersects = [tms_geom.intersect_point_with_sphere(c,np.subtract(t,c),r,ctr) for c,t in coil_pairs]
for p in intersects:
ac = __add_sphere_to_ren(p, 0.001, ren)
ac.GetProperty().SetColor(cc2)
ac.GetProperty().SetOpacity(0.5)
#find plane
vec, circle_radius = tms_geom.circle_from_points_in_sphere(intersects,r,ctr)
__add_plane_to_ren(ctr+vec,vec,r,ren)
iren.Initialize()
iren.Start()
