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Commit af3ad6f5f9c784393dbf58dc76f264462fc26146

Authored by Thiago Franco de Moraes
2 parents 5be3e861 b59df909
Exists in master

Merge remote-tracking branch 'upstream/master'

Showing 7 changed files with 614 additions and 142 deletions   Show diff stats
invesalius/data/bases.py
  Diff comments   View file @af3ad6f
1 import numpy as np 1 import numpy as np
2 import invesalius.data.coordinates as dco 2 import invesalius.data.coordinates as dco
3 import invesalius.data.transformations as tr 3 import invesalius.data.transformations as tr
4 - 4 +import invesalius.data.coregistration as dcr
5 5
6 def angle_calculation(ap_axis, coil_axis): 6 def angle_calculation(ap_axis, coil_axis):
7 """ 7 """
@@ -100,78 +100,31 @@ def base_creation(fiducials): @@ -100,78 +100,31 @@ def base_creation(fiducials):
100 return m, q 100 return m, q
101 101
102 102
103 -# def calculate_fre(fiducials, minv, n, q, o):  
104 -# """  
105 -# Calculate the Fiducial Registration Error for neuronavigation.  
106 -#  
107 -# :param fiducials: array of 6 rows (image and tracker fiducials) and 3 columns (x, y, z) with coordinates  
108 -# :param minv: inverse matrix given by base creation  
109 -# :param n: base change matrix given by base creation  
110 -# :param q: origin of first base  
111 -# :param o: origin of second base  
112 -# :return: float number of fiducial registration error  
113 -# """  
114 -#  
115 -# img = np.zeros([3, 3])  
116 -# dist = np.zeros([3, 1])  
117 -#  
118 -# q1 = np.mat(q).reshape(3, 1)  
119 -# q2 = np.mat(o).reshape(3, 1)  
120 -#  
121 -# p1 = np.mat(fiducials[3, :]).reshape(3, 1)  
122 -# p2 = np.mat(fiducials[4, :]).reshape(3, 1)  
123 -# p3 = np.mat(fiducials[5, :]).reshape(3, 1)  
124 -#  
125 -# img[0, :] = np.asarray((q1 + (minv * n) * (p1 - q2)).reshape(1, 3))  
126 -# img[1, :] = np.asarray((q1 + (minv * n) * (p2 - q2)).reshape(1, 3))  
127 -# img[2, :] = np.asarray((q1 + (minv * n) * (p3 - q2)).reshape(1, 3))  
128 -#  
129 -# dist[0] = np.sqrt(np.sum(np.power((img[0, :] - fiducials[0, :]), 2)))  
130 -# dist[1] = np.sqrt(np.sum(np.power((img[1, :] - fiducials[1, :]), 2)))  
131 -# dist[2] = np.sqrt(np.sum(np.power((img[2, :] - fiducials[2, :]), 2)))  
132 -#  
133 -# return float(np.sqrt(np.sum(dist ** 2) / 3))  
134 -  
135 -  
136 -def calculate_fre_m(fiducials): 103 +def calculate_fre(fiducials_raw, fiducials, ref_mode_id, m_change, m_icp=None):
137 """ 104 """
138 Calculate the Fiducial Registration Error for neuronavigation. 105 Calculate the Fiducial Registration Error for neuronavigation.
139 106
  107 + :param fiducials_raw: array of 6 rows (tracker probe and reference) and 3 columns (x, y, z) with coordinates
  108 + :type fiducials_raw: numpy.ndarray
140 :param fiducials: array of 6 rows (image and tracker fiducials) and 3 columns (x, y, z) with coordinates 109 :param fiducials: array of 6 rows (image and tracker fiducials) and 3 columns (x, y, z) with coordinates
141 - :param minv: inverse matrix given by base creation  
142 - :param n: base change matrix given by base creation  
143 - :param q: origin of first base  
144 - :param o: origin of second base 110 + :type fiducials: numpy.ndarray
  111 + :param ref_mode_id: Reference mode ID
  112 + :type ref_mode_id: int
  113 + :param m_change: 3x3 array representing change of basis from head in tracking system to vtk head system
  114 + :type m_change: numpy.ndarray
  115 + :param m_icp: list with icp flag and 3x3 affine array
  116 + :type m_icp: list[int, numpy.ndarray]
145 :return: float number of fiducial registration error 117 :return: float number of fiducial registration error
146 """ 118 """
  119 + if m_icp is not None:
  120 + icp = [True, m_icp]
  121 + else:
  122 + icp = [False, None]
147 123
148 - m, q1, minv = base_creation_old(fiducials[:3, :])  
149 - n, q2, ninv = base_creation_old(fiducials[3:, :])  
150 -  
151 - # TODO: replace the old by the new base creation  
152 - # the values differ greatly if FRE is computed using the old or new base_creation  
153 - # check the reason for the difference, because they should be the same  
154 - # m, q1 = base_creation(fiducials[:3, :])  
155 - # n, q2 = base_creation(fiducials[3:, :])  
156 - # minv = np.linalg.inv(m)  
157 -  
158 - img = np.zeros([3, 3])  
159 dist = np.zeros([3, 1]) 124 dist = np.zeros([3, 1])
160 -  
161 - q1 = q1.reshape(3, 1)  
162 - q2 = q2.reshape(3, 1)  
163 -  
164 - p1 = fiducials[3, :].reshape(3, 1)  
165 - p2 = fiducials[4, :].reshape(3, 1)  
166 - p3 = fiducials[5, :].reshape(3, 1)  
167 -  
168 - img[0, :] = (q1 + (minv @ n) * (p1 - q2)).reshape(1, 3)  
169 - img[1, :] = (q1 + (minv @ n) * (p2 - q2)).reshape(1, 3)  
170 - img[2, :] = (q1 + (minv @ n) * (p3 - q2)).reshape(1, 3)  
171 -  
172 - dist[0] = np.sqrt(np.sum(np.power((img[0, :] - fiducials[0, :]), 2)))  
173 - dist[1] = np.sqrt(np.sum(np.power((img[1, :] - fiducials[1, :]), 2)))  
174 - dist[2] = np.sqrt(np.sum(np.power((img[2, :] - fiducials[2, :]), 2))) 125 + for i in range(0, 6, 2):
  126 + p_m, _ = dcr.corregistrate_dynamic((m_change, 0), fiducials_raw[i:i+2], ref_mode_id, icp)
  127 + dist[int(i/2)] = np.sqrt(np.sum(np.power((p_m[:3] - fiducials[int(i/2), :]), 2)))
175 128
176 return float(np.sqrt(np.sum(dist ** 2) / 3)) 129 return float(np.sqrt(np.sum(dist ** 2) / 3))
177 130
@@ -203,6 +156,13 @@ def calculate_fre_m(fiducials): @@ -203,6 +156,13 @@ def calculate_fre_m(fiducials):
203 # 156 #
204 # return point_rot 157 # return point_rot
205 158
  159 +def transform_icp(m_img, m_icp):
  160 + coord_img = [m_img[0, -1], -m_img[1, -1], m_img[2, -1], 1]
  161 + m_img[0, -1], m_img[1, -1], m_img[2, -1], _ = m_icp @ coord_img
  162 + m_img[0, -1], m_img[1, -1], m_img[2, -1] = m_img[0, -1], -m_img[1, -1], m_img[2, -1]
  163 +
  164 + return m_img
  165 +
206 166
207 def object_registration(fiducials, orients, coord_raw, m_change): 167 def object_registration(fiducials, orients, coord_raw, m_change):
208 """ 168 """
invesalius/data/coordinates.py
  Diff comments   View file @af3ad6f
@@ -259,7 +259,7 @@ def DebugCoord(trk_init, trck_id, ref_mode): @@ -259,7 +259,7 @@ def DebugCoord(trk_init, trck_id, ref_mode):
259 coord4 = np.array([uniform(*dx), uniform(*dx), uniform(*dx), 259 coord4 = np.array([uniform(*dx), uniform(*dx), uniform(*dx),
260 uniform(*dt), uniform(*dt), uniform(*dt)]) 260 uniform(*dt), uniform(*dt), uniform(*dt)])
261 261
262 - sleep(0.05) 262 + sleep(0.15)
263 263
264 # coord1 = np.array([uniform(1, 200), uniform(1, 200), uniform(1, 200), 264 # coord1 = np.array([uniform(1, 200), uniform(1, 200), uniform(1, 200),
265 # uniform(-180.0, 180.0), uniform(-180.0, 180.0), uniform(-180.0, 180.0)]) 265 # uniform(-180.0, 180.0), uniform(-180.0, 180.0), uniform(-180.0, 180.0)])
invesalius/data/coregistration.py
  Diff comments   View file @af3ad6f
@@ -24,6 +24,7 @@ from time import sleep @@ -24,6 +24,7 @@ from time import sleep
24 24
25 import invesalius.data.coordinates as dco 25 import invesalius.data.coordinates as dco
26 import invesalius.data.transformations as tr 26 import invesalius.data.transformations as tr
  27 +import invesalius.data.bases as bases
27 28
28 29
29 # TODO: Replace the use of degrees by radians in every part of the navigation pipeline 30 # TODO: Replace the use of degrees by radians in every part of the navigation pipeline
@@ -101,7 +102,7 @@ def tracker_to_image(m_change, m_probe_ref, r_obj_img, m_obj_raw, s0_dyn): @@ -101,7 +102,7 @@ def tracker_to_image(m_change, m_probe_ref, r_obj_img, m_obj_raw, s0_dyn):
101 return m_img 102 return m_img
102 103
103 104
104 -def corregistrate_object_dynamic(inp, coord_raw, ref_mode_id): 105 +def corregistrate_object_dynamic(inp, coord_raw, ref_mode_id, icp):
105 106
106 m_change, obj_ref_mode, t_obj_raw, s0_raw, r_s0_raw, s0_dyn, m_obj_raw, r_obj_img = inp 107 m_change, obj_ref_mode, t_obj_raw, s0_raw, r_s0_raw, s0_dyn, m_obj_raw, r_obj_img = inp
107 108
@@ -116,6 +117,8 @@ def corregistrate_object_dynamic(inp, coord_raw, ref_mode_id): @@ -116,6 +117,8 @@ def corregistrate_object_dynamic(inp, coord_raw, ref_mode_id):
116 m_probe_ref[2, -1] = -m_probe_ref[2, -1] 117 m_probe_ref[2, -1] = -m_probe_ref[2, -1]
117 # corregistrate from tracker to image space 118 # corregistrate from tracker to image space
118 m_img = tracker_to_image(m_change, m_probe_ref, r_obj_img, m_obj_raw, s0_dyn) 119 m_img = tracker_to_image(m_change, m_probe_ref, r_obj_img, m_obj_raw, s0_dyn)
  120 + if icp[0]:
  121 + m_img = bases.transform_icp(m_img, icp[1])
119 # compute rotation angles 122 # compute rotation angles
120 _, _, angles, _, _ = tr.decompose_matrix(m_img) 123 _, _, angles, _, _ = tr.decompose_matrix(m_img)
121 # create output coordiante list 124 # create output coordiante list
@@ -124,6 +127,9 @@ def corregistrate_object_dynamic(inp, coord_raw, ref_mode_id): @@ -124,6 +127,9 @@ def corregistrate_object_dynamic(inp, coord_raw, ref_mode_id):
124 127
125 return coord, m_img 128 return coord, m_img
126 129
  130 +def UpdateICP(self, m_icp, flag):
  131 + self.m_icp = m_icp
  132 + self.icp = flag
127 133
128 def compute_marker_transformation(coord_raw, obj_ref_mode): 134 def compute_marker_transformation(coord_raw, obj_ref_mode):
129 psi, theta, phi = np.radians(coord_raw[obj_ref_mode, 3:]) 135 psi, theta, phi = np.radians(coord_raw[obj_ref_mode, 3:])
@@ -133,7 +139,7 @@ def compute_marker_transformation(coord_raw, obj_ref_mode): @@ -133,7 +139,7 @@ def compute_marker_transformation(coord_raw, obj_ref_mode):
133 return m_probe 139 return m_probe
134 140
135 141
136 -def corregistrate_dynamic(inp, coord_raw, ref_mode_id): 142 +def corregistrate_dynamic(inp, coord_raw, ref_mode_id, icp):
137 143
138 m_change, obj_ref_mode = inp 144 m_change, obj_ref_mode = inp
139 145
@@ -150,6 +156,10 @@ def corregistrate_dynamic(inp, coord_raw, ref_mode_id): @@ -150,6 +156,10 @@ def corregistrate_dynamic(inp, coord_raw, ref_mode_id):
150 m_probe_ref[2, -1] = -m_probe_ref[2, -1] 156 m_probe_ref[2, -1] = -m_probe_ref[2, -1]
151 # corregistrate from tracker to image space 157 # corregistrate from tracker to image space
152 m_img = m_change @ m_probe_ref 158 m_img = m_change @ m_probe_ref
  159 +
  160 + if icp[0]:
  161 + m_img = bases.transform_icp(m_img, icp[1])
  162 +
153 # compute rotation angles 163 # compute rotation angles
154 _, _, angles, _, _ = tr.decompose_matrix(m_img) 164 _, _, angles, _, _ = tr.decompose_matrix(m_img)
155 # create output coordiante list 165 # create output coordiante list
@@ -160,16 +170,19 @@ def corregistrate_dynamic(inp, coord_raw, ref_mode_id): @@ -160,16 +170,19 @@ def corregistrate_dynamic(inp, coord_raw, ref_mode_id):
160 170
161 171
162 class CoordinateCorregistrate(threading.Thread): 172 class CoordinateCorregistrate(threading.Thread):
163 - def __init__(self, ref_mode_id, trck_info, coreg_data, coord_queue, view_tracts, coord_tracts_queue, event, sle): 173 + def __init__(self, ref_mode_id, trck_info, coreg_data, view_tracts, queues, event, sle):
164 threading.Thread.__init__(self, name='CoordCoregObject') 174 threading.Thread.__init__(self, name='CoordCoregObject')
165 self.ref_mode_id = ref_mode_id 175 self.ref_mode_id = ref_mode_id
166 self.trck_info = trck_info 176 self.trck_info = trck_info
167 self.coreg_data = coreg_data 177 self.coreg_data = coreg_data
168 - self.coord_queue = coord_queue 178 + self.coord_queue = queues[0]
169 self.view_tracts = view_tracts 179 self.view_tracts = view_tracts
170 - self.coord_tracts_queue = coord_tracts_queue 180 + self.coord_tracts_queue = queues[1]
171 self.event = event 181 self.event = event
172 self.sle = sle 182 self.sle = sle
  183 + self.icp_queue = queues[2]
  184 + self.icp = None
  185 + self.m_icp = None
173 186
174 def run(self): 187 def run(self):
175 trck_info = self.trck_info 188 trck_info = self.trck_info
@@ -180,19 +193,20 @@ class CoordinateCorregistrate(threading.Thread): @@ -180,19 +193,20 @@ class CoordinateCorregistrate(threading.Thread):
180 # print('CoordCoreg: event {}'.format(self.event.is_set())) 193 # print('CoordCoreg: event {}'.format(self.event.is_set()))
181 while not self.event.is_set(): 194 while not self.event.is_set():
182 try: 195 try:
  196 + if self.icp_queue.empty():
  197 + None
  198 + else:
  199 + self.icp, self.m_icp = self.icp_queue.get_nowait()
183 # print(f"Set the coordinate") 200 # print(f"Set the coordinate")
184 coord_raw = dco.GetCoordinates(trck_init, trck_id, trck_mode) 201 coord_raw = dco.GetCoordinates(trck_init, trck_id, trck_mode)
185 - coord, m_img = corregistrate_object_dynamic(coreg_data, coord_raw, self.ref_mode_id)  
186 - # m_img = np.array([[0.38, -0.8, -0.45, 40.17],  
187 - # [0.82, 0.52, -0.24, 152.28],  
188 - # [0.43, -0.28, 0.86, 235.78],  
189 - # [0., 0., 0., 1.]])  
190 - # angles = [-0.318, -0.441, 1.134]  
191 - # coord = m_img[0, -1], m_img[1, -1], m_img[2, -1], \  
192 - # np.degrees(angles[0]), np.degrees(angles[1]), np.degrees(angles[2]) 202 + coord, m_img = corregistrate_object_dynamic(coreg_data, coord_raw, self.ref_mode_id, [self.icp, self.m_icp])
193 m_img_flip = m_img.copy() 203 m_img_flip = m_img.copy()
194 m_img_flip[1, -1] = -m_img_flip[1, -1] 204 m_img_flip[1, -1] = -m_img_flip[1, -1]
195 # self.pipeline.set_message(m_img_flip) 205 # self.pipeline.set_message(m_img_flip)
  206 +
  207 + if self.icp:
  208 + m_img = bases.transform_icp(m_img, self.m_icp)
  209 +
196 self.coord_queue.put_nowait([coord, m_img, view_obj]) 210 self.coord_queue.put_nowait([coord, m_img, view_obj])
197 # print('CoordCoreg: put {}'.format(count)) 211 # print('CoordCoreg: put {}'.format(count))
198 # count += 1 212 # count += 1
@@ -200,6 +214,9 @@ class CoordinateCorregistrate(threading.Thread): @@ -200,6 +214,9 @@ class CoordinateCorregistrate(threading.Thread):
200 if self.view_tracts: 214 if self.view_tracts:
201 self.coord_tracts_queue.put_nowait(m_img_flip) 215 self.coord_tracts_queue.put_nowait(m_img_flip)
202 216
  217 + if not self.icp_queue.empty():
  218 + self.icp_queue.task_done()
  219 +
203 # The sleep has to be in both threads 220 # The sleep has to be in both threads
204 sleep(self.sle) 221 sleep(self.sle)
205 except queue.Full: 222 except queue.Full:
@@ -207,16 +224,19 @@ class CoordinateCorregistrate(threading.Thread): @@ -207,16 +224,19 @@ class CoordinateCorregistrate(threading.Thread):
207 224
208 225
209 class CoordinateCorregistrateNoObject(threading.Thread): 226 class CoordinateCorregistrateNoObject(threading.Thread):
210 - def __init__(self, ref_mode_id, trck_info, coreg_data, coord_queue, view_tracts, coord_tracts_queue, event, sle): 227 + def __init__(self, ref_mode_id, trck_info, coreg_data, view_tracts, queues, event, sle):
211 threading.Thread.__init__(self, name='CoordCoregNoObject') 228 threading.Thread.__init__(self, name='CoordCoregNoObject')
212 self.ref_mode_id = ref_mode_id 229 self.ref_mode_id = ref_mode_id
213 self.trck_info = trck_info 230 self.trck_info = trck_info
214 self.coreg_data = coreg_data 231 self.coreg_data = coreg_data
215 - self.coord_queue = coord_queue 232 + self.coord_queue = queues[0]
216 self.view_tracts = view_tracts 233 self.view_tracts = view_tracts
217 - self.coord_tracts_queue = coord_tracts_queue 234 + self.coord_tracts_queue = queues[1]
218 self.event = event 235 self.event = event
219 self.sle = sle 236 self.sle = sle
  237 + self.icp_queue = queues[2]
  238 + self.icp = None
  239 + self.m_icp = None
220 240
221 def run(self): 241 def run(self):
222 trck_info = self.trck_info 242 trck_info = self.trck_info
@@ -227,17 +247,28 @@ class CoordinateCorregistrateNoObject(threading.Thread): @@ -227,17 +247,28 @@ class CoordinateCorregistrateNoObject(threading.Thread):
227 # print('CoordCoreg: event {}'.format(self.event.is_set())) 247 # print('CoordCoreg: event {}'.format(self.event.is_set()))
228 while not self.event.is_set(): 248 while not self.event.is_set():
229 try: 249 try:
  250 + if self.icp_queue.empty():
  251 + None
  252 + else:
  253 + self.icp, self.m_icp = self.icp_queue.get_nowait()
230 # print(f"Set the coordinate") 254 # print(f"Set the coordinate")
  255 + #print(self.icp, self.m_icp)
231 coord_raw = dco.GetCoordinates(trck_init, trck_id, trck_mode) 256 coord_raw = dco.GetCoordinates(trck_init, trck_id, trck_mode)
232 - coord, m_img = corregistrate_dynamic(coreg_data, coord_raw, self.ref_mode_id) 257 + coord, m_img = corregistrate_dynamic(coreg_data, coord_raw, self.ref_mode_id, [self.icp, self.m_icp])
233 # print("Coord: ", coord) 258 # print("Coord: ", coord)
234 m_img_flip = m_img.copy() 259 m_img_flip = m_img.copy()
235 m_img_flip[1, -1] = -m_img_flip[1, -1] 260 m_img_flip[1, -1] = -m_img_flip[1, -1]
  261 +
  262 + if self.icp:
  263 + m_img = bases.transform_icp(m_img, self.m_icp)
  264 +
236 self.coord_queue.put_nowait([coord, m_img, view_obj]) 265 self.coord_queue.put_nowait([coord, m_img, view_obj])
237 266
238 if self.view_tracts: 267 if self.view_tracts:
239 self.coord_tracts_queue.put_nowait(m_img_flip) 268 self.coord_tracts_queue.put_nowait(m_img_flip)
240 269
  270 + if not self.icp_queue.empty():
  271 + self.icp_queue.task_done()
241 # The sleep has to be in both threads 272 # The sleep has to be in both threads
242 sleep(self.sle) 273 sleep(self.sle)
243 except queue.Full: 274 except queue.Full:
invesalius/data/tractography.py
  Diff comments   View file @af3ad6f
@@ -230,7 +230,7 @@ def tracts_computation_branch(trk_list, alpha=255): @@ -230,7 +230,7 @@ def tracts_computation_branch(trk_list, alpha=255):
230 230
231 class ComputeTractsThread(threading.Thread): 231 class ComputeTractsThread(threading.Thread):
232 232
233 - def __init__(self, inp, coord_tracts_queue, tracts_queue, event, sle): 233 + def __init__(self, inp, queues, event, sle):
234 """Class (threading) to compute real time tractography data for visualization. 234 """Class (threading) to compute real time tractography data for visualization.
235 235
236 Tracts are computed using the Trekker library by Baran Aydogan (https://dmritrekker.github.io/) 236 Tracts are computed using the Trekker library by Baran Aydogan (https://dmritrekker.github.io/)
@@ -243,10 +243,9 @@ class ComputeTractsThread(threading.Thread): @@ -243,10 +243,9 @@ class ComputeTractsThread(threading.Thread):
243 243
244 :param inp: List of inputs: trekker instance, affine numpy array, seed_offset, seed_radius, n_threads 244 :param inp: List of inputs: trekker instance, affine numpy array, seed_offset, seed_radius, n_threads
245 :type inp: list 245 :type inp: list
246 - :param coord_tracts_queue: Queue instance that manage co-registered coordinates  
247 - :type coord_tracts_queue: queue.Queue  
248 - :param tracts_queue: Queue instance that manage the tracts to be visualized  
249 - :type tracts_queue: queue.Queue 246 + :param queues: Queue list with coord_tracts_queue (Queue instance that manage co-registered coordinates) and
  247 + tracts_queue (Queue instance that manage the tracts to be visualized)
  248 + :type queues: list[queue.Queue, queue.Queue]
250 :param event: Threading event to coordinate when tasks as done and allow UI release 249 :param event: Threading event to coordinate when tasks as done and allow UI release
251 :type event: threading.Event 250 :type event: threading.Event
252 :param sle: Sleep pause in seconds 251 :param sle: Sleep pause in seconds
@@ -256,8 +255,8 @@ class ComputeTractsThread(threading.Thread): @@ -256,8 +255,8 @@ class ComputeTractsThread(threading.Thread):
256 threading.Thread.__init__(self, name='ComputeTractsThread') 255 threading.Thread.__init__(self, name='ComputeTractsThread')
257 self.inp = inp 256 self.inp = inp
258 # self.coord_queue = coord_queue 257 # self.coord_queue = coord_queue
259 - self.coord_tracts_queue = coord_tracts_queue  
260 - self.tracts_queue = tracts_queue 258 + self.coord_tracts_queue = queues[0]
  259 + self.tracts_queue = queues[1]
261 # self.visualization_queue = visualization_queue 260 # self.visualization_queue = visualization_queue
262 self.event = event 261 self.event = event
263 self.sle = sle 262 self.sle = sle
@@ -362,7 +361,7 @@ class ComputeTractsThread(threading.Thread): @@ -362,7 +361,7 @@ class ComputeTractsThread(threading.Thread):
362 361
363 class ComputeTractsACTThread(threading.Thread): 362 class ComputeTractsACTThread(threading.Thread):
364 363
365 - def __init__(self, inp, coord_tracts_queue, tracts_queue, event, sle): 364 + def __init__(self, inp, queues, event, sle):
366 """Class (threading) to compute real time tractography data for visualization. 365 """Class (threading) to compute real time tractography data for visualization.
367 366
368 Tracts are computed using the Trekker library by Baran Aydogan (https://dmritrekker.github.io/) 367 Tracts are computed using the Trekker library by Baran Aydogan (https://dmritrekker.github.io/)
@@ -375,10 +374,9 @@ class ComputeTractsACTThread(threading.Thread): @@ -375,10 +374,9 @@ class ComputeTractsACTThread(threading.Thread):
375 374
376 :param inp: List of inputs: trekker instance, affine numpy array, seed_offset, seed_radius, n_threads 375 :param inp: List of inputs: trekker instance, affine numpy array, seed_offset, seed_radius, n_threads
377 :type inp: list 376 :type inp: list
378 - :param coord_tracts_queue: Queue instance that manage co-registered coordinates  
379 - :type coord_tracts_queue: queue.Queue  
380 - :param tracts_queue: Queue instance that manage the tracts to be visualized  
381 - :type tracts_queue: queue.Queue 377 + :param queues: Queue list with coord_tracts_queue (Queue instance that manage co-registered coordinates) and
  378 + tracts_queue (Queue instance that manage the tracts to be visualized)
  379 + :type queues: list[queue.Queue, queue.Queue]
382 :param event: Threading event to coordinate when tasks as done and allow UI release 380 :param event: Threading event to coordinate when tasks as done and allow UI release
383 :type event: threading.Event 381 :type event: threading.Event
384 :param sle: Sleep pause in seconds 382 :param sle: Sleep pause in seconds
@@ -388,8 +386,8 @@ class ComputeTractsACTThread(threading.Thread): @@ -388,8 +386,8 @@ class ComputeTractsACTThread(threading.Thread):
388 threading.Thread.__init__(self, name='ComputeTractsThreadACT') 386 threading.Thread.__init__(self, name='ComputeTractsThreadACT')
389 self.inp = inp 387 self.inp = inp
390 # self.coord_queue = coord_queue 388 # self.coord_queue = coord_queue
391 - self.coord_tracts_queue = coord_tracts_queue  
392 - self.tracts_queue = tracts_queue 389 + self.coord_tracts_queue = queues[0]
  390 + self.tracts_queue = queues[1]
393 # on first pilots (january 12, 2021) used (-4, 4) 391 # on first pilots (january 12, 2021) used (-4, 4)
394 self.coord_list_w = img_utils.create_grid((-2, 2), (0, 20), inp[2]-5, 1) 392 self.coord_list_w = img_utils.create_grid((-2, 2), (0, 20), inp[2]-5, 1)
395 # self.coord_list_sph = img_utils.create_spherical_grid(10, 1) 393 # self.coord_list_sph = img_utils.create_spherical_grid(10, 1)
invesalius/data/viewer_slice.py
  Diff comments   View file @af3ad6f
@@ -837,8 +837,7 @@ class Viewer(wx.Panel): @@ -837,8 +837,7 @@ class Viewer(wx.Panel):
837 # Publisher.subscribe(self.__update_cross_position, 837 # Publisher.subscribe(self.__update_cross_position,
838 # 'Update cross position %s' % self.orientation) 838 # 'Update cross position %s' % self.orientation)
839 Publisher.subscribe(self.SetCrossFocalPoint, 'Set cross focal point') 839 Publisher.subscribe(self.SetCrossFocalPoint, 'Set cross focal point')
840 - # Publisher.subscribe(self.UpdateSlicesPosition,  
841 - # 'Co-registered points') 840 + Publisher.subscribe(self.UpdateSlicesPosition, 'Update slices position')
842 ### 841 ###
843 # Publisher.subscribe(self.ChangeBrushColour, 842 # Publisher.subscribe(self.ChangeBrushColour,
844 # 'Add mask') 843 # 'Add mask')
@@ -849,9 +848,9 @@ class Viewer(wx.Panel): @@ -849,9 +848,9 @@ class Viewer(wx.Panel):
849 Publisher.subscribe(self.UpdateWindowLevelText, 848 Publisher.subscribe(self.UpdateWindowLevelText,
850 'Update window level text') 849 'Update window level text')
851 850
852 - #Publisher.subscribe(self._set_cross_visibility,\  
853 - # 'Set cross visibility')  
854 - ### 851 + Publisher.subscribe(self._set_cross_visibility,
  852 + 'Set cross visibility')
  853 +
855 Publisher.subscribe(self.__set_layout, 854 Publisher.subscribe(self.__set_layout,
856 'Set slice viewer layout') 855 'Set slice viewer layout')
857 856
invesalius/gui/dialogs.py
  Diff comments   View file @af3ad6f
@@ -23,6 +23,7 @@ import os @@ -23,6 +23,7 @@ import os
23 import random 23 import random
24 import sys 24 import sys
25 import time 25 import time
  26 +from functools import partial
26 27
27 from concurrent import futures 28 from concurrent import futures
28 29
@@ -58,10 +59,12 @@ import invesalius.data.coordinates as dco @@ -58,10 +59,12 @@ import invesalius.data.coordinates as dco
58 import invesalius.gui.widgets.gradient as grad 59 import invesalius.gui.widgets.gradient as grad
59 import invesalius.session as ses 60 import invesalius.session as ses
60 import invesalius.utils as utils 61 import invesalius.utils as utils
  62 +import invesalius.data.bases as bases
61 from invesalius.gui.widgets.inv_spinctrl import InvSpinCtrl, InvFloatSpinCtrl 63 from invesalius.gui.widgets.inv_spinctrl import InvSpinCtrl, InvFloatSpinCtrl
62 from invesalius.gui.widgets import clut_imagedata 64 from invesalius.gui.widgets import clut_imagedata
63 from invesalius.gui.widgets.clut_imagedata import CLUTImageDataWidget, EVT_CLUT_NODE_CHANGED 65 from invesalius.gui.widgets.clut_imagedata import CLUTImageDataWidget, EVT_CLUT_NODE_CHANGED
64 import numpy as np 66 import numpy as np
  67 +from numpy.core.umath_tests import inner1d
65 68
66 from invesalius import inv_paths 69 from invesalius import inv_paths
67 70
@@ -887,6 +890,35 @@ def ShowNavigationTrackerWarning(trck_id, lib_mode): @@ -887,6 +890,35 @@ def ShowNavigationTrackerWarning(trck_id, lib_mode):
887 dlg.ShowModal() 890 dlg.ShowModal()
888 dlg.Destroy() 891 dlg.Destroy()
889 892
  893 +def ICPcorregistration(fre):
  894 + msg = _("The fiducial registration error is: ") + str(round(fre, 2)) + '\n\n' + \
  895 + _("Would you like to improve accuracy?")
  896 + if sys.platform == 'darwin':
  897 + dlg = wx.MessageDialog(None, "", msg,
  898 + wx.YES_NO)
  899 + else:
  900 + dlg = wx.MessageDialog(None, msg, "InVesalius 3",
  901 + wx.YES_NO)
  902 +
  903 + if dlg.ShowModal() == wx.ID_YES:
  904 + flag = True
  905 + else:
  906 + flag = False
  907 +
  908 + dlg.Destroy()
  909 + return flag
  910 +
  911 +def ReportICPerror(prev_error, final_error):
  912 + msg = _("Error after refine: ") + str(round(final_error, 2)) + ' mm' + '\n\n' + \
  913 + _("Previous error: ") + str(round(prev_error, 2)) + ' mm'
  914 + if sys.platform == 'darwin':
  915 + dlg = wx.MessageDialog(None, "", msg,
  916 + wx.OK)
  917 + else:
  918 + dlg = wx.MessageDialog(None, msg, "InVesalius 3",
  919 + wx.OK)
  920 + dlg.ShowModal()
  921 + dlg.Destroy()
890 922
891 def ShowEnterMarkerID(default): 923 def ShowEnterMarkerID(default):
892 msg = _("Edit marker ID") 924 msg = _("Edit marker ID")
@@ -1155,7 +1187,7 @@ def ShowAboutDialog(parent): @@ -1155,7 +1187,7 @@ def ShowAboutDialog(parent):
1155 1187
1156 info.SetWebSite("https://www.cti.gov.br/invesalius") 1188 info.SetWebSite("https://www.cti.gov.br/invesalius")
1157 info.SetIcon(icon) 1189 info.SetIcon(icon)
1158 - 1190 +
1159 info.License = _("GNU GPL (General Public License) version 2") 1191 info.License = _("GNU GPL (General Public License) version 2")
1160 1192
1161 info.Developers = [u"Paulo Henrique Junqueira Amorim", 1193 info.Developers = [u"Paulo Henrique Junqueira Amorim",
@@ -1343,7 +1375,7 @@ class NewSurfaceDialog(wx.Dialog): @@ -1343,7 +1375,7 @@ class NewSurfaceDialog(wx.Dialog):
1343 def ExportPicture(type_=""): 1375 def ExportPicture(type_=""):
1344 import invesalius.constants as const 1376 import invesalius.constants as const
1345 import invesalius.project as proj 1377 import invesalius.project as proj
1346 - 1378 +
1347 INDEX_TO_EXTENSION = {0: "bmp", 1: "jpg", 2: "png", 3: "ps", 4:"povray", 5:"tiff"} 1379 INDEX_TO_EXTENSION = {0: "bmp", 1: "jpg", 2: "png", 3: "ps", 4:"povray", 5:"tiff"}
1348 WILDCARD_SAVE_PICTURE = _("BMP image")+" (*.bmp)|*.bmp|"+\ 1380 WILDCARD_SAVE_PICTURE = _("BMP image")+" (*.bmp)|*.bmp|"+\
1349 _("JPG image")+" (*.jpg)|*.jpg|"+\ 1381 _("JPG image")+" (*.jpg)|*.jpg|"+\
@@ -1513,7 +1545,7 @@ class SurfaceCreationOptionsPanel(wx.Panel): @@ -1513,7 +1545,7 @@ class SurfaceCreationOptionsPanel(wx.Panel):
1513 project = prj.Project() 1545 project = prj.Project()
1514 index_list = project.mask_dict.keys() 1546 index_list = project.mask_dict.keys()
1515 self.mask_list = [project.mask_dict[index].name for index in sorted(index_list)] 1547 self.mask_list = [project.mask_dict[index].name for index in sorted(index_list)]
1516 - 1548 +
1517 active_mask = slc.Slice().current_mask.index 1549 active_mask = slc.Slice().current_mask.index
1518 #active_mask = len(self.mask_list)-1 1550 #active_mask = len(self.mask_list)-1
1519 1551
@@ -2093,17 +2125,17 @@ class ImportBitmapParameters(wx.Dialog): @@ -2093,17 +2125,17 @@ class ImportBitmapParameters(wx.Dialog):
2093 2125
2094 2126
2095 def _init_gui(self): 2127 def _init_gui(self):
2096 - 2128 +
2097 import invesalius.project as prj 2129 import invesalius.project as prj
2098 - 2130 +
2099 p = wx.Panel(self, -1, style = wx.TAB_TRAVERSAL 2131 p = wx.Panel(self, -1, style = wx.TAB_TRAVERSAL
2100 | wx.CLIP_CHILDREN 2132 | wx.CLIP_CHILDREN
2101 | wx.FULL_REPAINT_ON_RESIZE) 2133 | wx.FULL_REPAINT_ON_RESIZE)
2102 - 2134 +
2103 gbs_principal = self.gbs = wx.GridBagSizer(4,1) 2135 gbs_principal = self.gbs = wx.GridBagSizer(4,1)
2104 2136
2105 gbs = self.gbs = wx.GridBagSizer(5, 2) 2137 gbs = self.gbs = wx.GridBagSizer(5, 2)
2106 - 2138 +
2107 flag_labels = wx.ALIGN_RIGHT | wx.ALIGN_CENTER_VERTICAL 2139 flag_labels = wx.ALIGN_RIGHT | wx.ALIGN_CENTER_VERTICAL
2108 2140
2109 stx_name = wx.StaticText(p, -1, _(u"Project name:")) 2141 stx_name = wx.StaticText(p, -1, _(u"Project name:"))
@@ -2134,7 +2166,7 @@ class ImportBitmapParameters(wx.Dialog): @@ -2134,7 +2166,7 @@ class ImportBitmapParameters(wx.Dialog):
2134 2166
2135 #--- spacing -------------- 2167 #--- spacing --------------
2136 gbs_spacing = wx.GridBagSizer(2, 6) 2168 gbs_spacing = wx.GridBagSizer(2, 6)
2137 - 2169 +
2138 stx_spacing_x = stx_spacing_x = wx.StaticText(p, -1, _(u"X:")) 2170 stx_spacing_x = stx_spacing_x = wx.StaticText(p, -1, _(u"X:"))
2139 fsp_spacing_x = self.fsp_spacing_x = InvFloatSpinCtrl(p, -1, min_value=0, max_value=1000000000, 2171 fsp_spacing_x = self.fsp_spacing_x = InvFloatSpinCtrl(p, -1, min_value=0, max_value=1000000000,
2140 increment=0.25, value=1.0, digits=8) 2172 increment=0.25, value=1.0, digits=8)
@@ -2151,7 +2183,7 @@ class ImportBitmapParameters(wx.Dialog): @@ -2151,7 +2183,7 @@ class ImportBitmapParameters(wx.Dialog):
2151 2183
2152 try: 2184 try:
2153 proj = prj.Project() 2185 proj = prj.Project()
2154 - 2186 +
2155 sx = proj.spacing[0] 2187 sx = proj.spacing[0]
2156 sy = proj.spacing[1] 2188 sy = proj.spacing[1]
2157 sz = proj.spacing[2] 2189 sz = proj.spacing[2]
@@ -2174,7 +2206,7 @@ class ImportBitmapParameters(wx.Dialog): @@ -2174,7 +2206,7 @@ class ImportBitmapParameters(wx.Dialog):
2174 2206
2175 #----- buttons ------------------------ 2207 #----- buttons ------------------------
2176 gbs_button = wx.GridBagSizer(2, 4) 2208 gbs_button = wx.GridBagSizer(2, 4)
2177 - 2209 +
2178 btn_ok = self.btn_ok= wx.Button(p, wx.ID_OK) 2210 btn_ok = self.btn_ok= wx.Button(p, wx.ID_OK)
2179 btn_ok.SetDefault() 2211 btn_ok.SetDefault()
2180 2212
@@ -2197,14 +2229,14 @@ class ImportBitmapParameters(wx.Dialog): @@ -2197,14 +2229,14 @@ class ImportBitmapParameters(wx.Dialog):
2197 2229
2198 box = wx.BoxSizer() 2230 box = wx.BoxSizer()
2199 box.Add(gbs_principal, 1, wx.ALL|wx.EXPAND, 10) 2231 box.Add(gbs_principal, 1, wx.ALL|wx.EXPAND, 10)
2200 - 2232 +
2201 p.SetSizer(box) 2233 p.SetSizer(box)
2202 box.Fit(self) 2234 box.Fit(self)
2203 self.Layout() 2235 self.Layout()
2204 2236
2205 def bind_evts(self): 2237 def bind_evts(self):
2206 self.btn_ok.Bind(wx.EVT_BUTTON, self.OnOk) 2238 self.btn_ok.Bind(wx.EVT_BUTTON, self.OnOk)
2207 - 2239 +
2208 def SetInterval(self, v): 2240 def SetInterval(self, v):
2209 self.interval = v 2241 self.interval = v
2210 2242
@@ -2228,10 +2260,10 @@ class ImportBitmapParameters(wx.Dialog): @@ -2228,10 +2260,10 @@ class ImportBitmapParameters(wx.Dialog):
2228 2260
2229 2261
2230 def BitmapNotSameSize(): 2262 def BitmapNotSameSize():
2231 - 2263 +
2232 dlg = wx.MessageDialog(None,_("All bitmaps files must be the same \n width and height size."), 'Error',\ 2264 dlg = wx.MessageDialog(None,_("All bitmaps files must be the same \n width and height size."), 'Error',\
2233 wx.OK | wx.ICON_ERROR) 2265 wx.OK | wx.ICON_ERROR)
2234 - 2266 +
2235 dlg.ShowModal() 2267 dlg.ShowModal()
2236 dlg.Destroy() 2268 dlg.Destroy()
2237 2269
@@ -2908,7 +2940,7 @@ class FFillSegmentationOptionsDialog(wx.Dialog): @@ -2908,7 +2940,7 @@ class FFillSegmentationOptionsDialog(wx.Dialog):
2908 2940
2909 2941
2910 class CropOptionsDialog(wx.Dialog): 2942 class CropOptionsDialog(wx.Dialog):
2911 - 2943 +
2912 def __init__(self, config, ID=-1, title=_(u"Crop mask"), style=wx.DEFAULT_DIALOG_STYLE|wx.FRAME_FLOAT_ON_PARENT|wx.STAY_ON_TOP): 2944 def __init__(self, config, ID=-1, title=_(u"Crop mask"), style=wx.DEFAULT_DIALOG_STYLE|wx.FRAME_FLOAT_ON_PARENT|wx.STAY_ON_TOP):
2913 self.config = config 2945 self.config = config
2914 wx.Dialog.__init__(self, wx.GetApp().GetTopWindow(), ID, title=title, style=style) 2946 wx.Dialog.__init__(self, wx.GetApp().GetTopWindow(), ID, title=title, style=style)
@@ -3316,7 +3348,7 @@ class ObjectCalibrationDialog(wx.Dialog): @@ -3316,7 +3348,7 @@ class ObjectCalibrationDialog(wx.Dialog):
3316 main_sizer = wx.BoxSizer(wx.VERTICAL) 3348 main_sizer = wx.BoxSizer(wx.VERTICAL)
3317 main_sizer.Add(self.interactor, 0, wx.EXPAND) 3349 main_sizer.Add(self.interactor, 0, wx.EXPAND)
3318 main_sizer.Add(group_sizer, 0, 3350 main_sizer.Add(group_sizer, 0,
3319 - wx.EXPAND|wx.GROW|wx.LEFT|wx.TOP|wx.RIGHT|wx.BOTTOM|wx.ALIGN_CENTER_HORIZONTAL, 10) 3351 + wx.EXPAND|wx.GROW|wx.LEFT|wx.TOP|wx.RIGHT|wx.BOTTOM, 10)
3320 3352
3321 self.SetSizer(main_sizer) 3353 self.SetSizer(main_sizer)
3322 main_sizer.Fit(self) 3354 main_sizer.Fit(self)
@@ -3493,6 +3525,363 @@ class ObjectCalibrationDialog(wx.Dialog): @@ -3493,6 +3525,363 @@ class ObjectCalibrationDialog(wx.Dialog):
3493 def GetValue(self): 3525 def GetValue(self):
3494 return self.obj_fiducials, self.obj_orients, self.obj_ref_id, self.obj_name, self.polydata 3526 return self.obj_fiducials, self.obj_orients, self.obj_ref_id, self.obj_name, self.polydata
3495 3527
  3528 +class ICPCorregistrationDialog(wx.Dialog):
  3529 +
  3530 + def __init__(self, nav_prop):
  3531 + import invesalius.project as prj
  3532 +
  3533 + self.__bind_events()
  3534 +
  3535 + self.tracker_id = nav_prop[0]
  3536 + self.trk_init = nav_prop[1]
  3537 + self.obj_ref_id = 2
  3538 + self.obj_name = None
  3539 + self.obj_actor = None
  3540 + self.polydata = None
  3541 + self.m_icp = None
  3542 + self.initial_focus = None
  3543 + self.prev_error = None
  3544 + self.final_error = None
  3545 + self.icp_mode = 0
  3546 + self.staticballs = []
  3547 + self.point_coord = []
  3548 + self.transformed_points = []
  3549 +
  3550 + self.obj_fiducials = np.full([5, 3], np.nan)
  3551 + self.obj_orients = np.full([5, 3], np.nan)
  3552 +
  3553 + wx.Dialog.__init__(self, wx.GetApp().GetTopWindow(), -1, _(u"Refine Corregistration"), size=(380, 440),
  3554 + style=wx.DEFAULT_DIALOG_STYLE | wx.FRAME_FLOAT_ON_PARENT|wx.STAY_ON_TOP)
  3555 +
  3556 + self.proj = prj.Project()
  3557 +
  3558 + self._init_gui()
  3559 +
  3560 + def __bind_events(self):
  3561 + Publisher.subscribe(self.UpdateCurrentCoord, 'Set cross focal point')
  3562 +
  3563 + def UpdateCurrentCoord(self, position):
  3564 + self.current_coord = position[:]
  3565 +
  3566 + def _init_gui(self):
  3567 + self.interactor = wxVTKRenderWindowInteractor(self, -1, size=self.GetSize())
  3568 + self.interactor.Enable(1)
  3569 + self.ren = vtk.vtkRenderer()
  3570 + self.interactor.GetRenderWindow().AddRenderer(self.ren)
  3571 +
  3572 + self.timer = wx.Timer(self)
  3573 + self.Bind(wx.EVT_TIMER, self.OnUpdate, self.timer)
  3574 +
  3575 + txt_surface = wx.StaticText(self, -1, _('Select the surface:'))
  3576 + txt_mode = wx.StaticText(self, -1, _('Registration mode:'))
  3577 +
  3578 + combo_surface_name = wx.ComboBox(self, -1, size=(210, 23),
  3579 + style=wx.CB_DROPDOWN | wx.CB_READONLY)
  3580 + # combo_surface_name.SetSelection(0)
  3581 + if sys.platform != 'win32':
  3582 + combo_surface_name.SetWindowVariant(wx.WINDOW_VARIANT_SMALL)
  3583 + combo_surface_name.Bind(wx.EVT_COMBOBOX, self.OnComboName)
  3584 + for n in range(len(self.proj.surface_dict)):
  3585 + combo_surface_name.Insert(str(self.proj.surface_dict[n].name), n)
  3586 +
  3587 + self.combo_surface_name = combo_surface_name
  3588 +
  3589 + init_surface = 0
  3590 + combo_surface_name.SetSelection(init_surface)
  3591 + self.surface = self.proj.surface_dict[init_surface].polydata
  3592 + self.LoadActor()
  3593 +
  3594 + tooltip = wx.ToolTip(_("Choose the registration mode:"))
  3595 + choice_icp_method = wx.ComboBox(self, -1, "", size=(100, 23),
  3596 + choices=([_("Affine"), _("Similarity"), _("RigidBody")]),
  3597 + style=wx.CB_DROPDOWN|wx.CB_READONLY)
  3598 + choice_icp_method.SetSelection(0)
  3599 + choice_icp_method.SetToolTip(tooltip)
  3600 + choice_icp_method.Bind(wx.EVT_COMBOBOX, self.OnChoiceICPMethod)
  3601 +
  3602 + # Buttons to acquire and remove points
  3603 + create_point = wx.Button(self, -1, label=_('Create point'))
  3604 + create_point.Bind(wx.EVT_BUTTON, self.OnCreatePoint)
  3605 +
  3606 + cont_point = wx.ToggleButton(self, -1, label=_('Continuous acquisition'))
  3607 + cont_point.Bind(wx.EVT_TOGGLEBUTTON, partial(self.OnContinuousAcquisition, btn=cont_point))
  3608 + self.cont_point = cont_point
  3609 +
  3610 + btn_reset = wx.Button(self, -1, label=_('Remove points'))
  3611 + btn_reset.Bind(wx.EVT_BUTTON, self.OnReset)
  3612 +
  3613 + btn_apply_icp = wx.Button(self, -1, label=_('Apply registration'))
  3614 + btn_apply_icp.Bind(wx.EVT_BUTTON, self.OnICP)
  3615 +
  3616 + # Buttons to finish or cancel object registration
  3617 + tooltip = wx.ToolTip(_(u"Refine done"))
  3618 + btn_ok = wx.Button(self, wx.ID_OK, _(u"Done"))
  3619 + btn_ok.SetToolTip(tooltip)
  3620 +
  3621 + btn_cancel = wx.Button(self, wx.ID_CANCEL)
  3622 + btn_cancel.SetHelpText("")
  3623 +
  3624 + top_sizer = wx.FlexGridSizer(rows=2, cols=2, hgap=50, vgap=5)
  3625 + top_sizer.AddMany([txt_surface, txt_mode,
  3626 + combo_surface_name, choice_icp_method])
  3627 +
  3628 + btn_acqui_sizer = wx.FlexGridSizer(rows=1, cols=3, hgap=15, vgap=15)
  3629 + btn_acqui_sizer.AddMany([create_point, cont_point, btn_reset])
  3630 +
  3631 + btn_ok_sizer = wx.FlexGridSizer(rows=1, cols=3, hgap=20, vgap=20)
  3632 + btn_ok_sizer.AddMany([btn_apply_icp, btn_ok, btn_cancel])
  3633 +
  3634 + btn_sizer = wx.FlexGridSizer(rows=2, cols=1, hgap=50, vgap=20)
  3635 + btn_sizer.AddMany([(btn_acqui_sizer, 1, wx.ALIGN_CENTER_HORIZONTAL),
  3636 + (btn_ok_sizer, 1, wx.ALIGN_RIGHT)])
  3637 +
  3638 + self.progress = wx.Gauge(self, -1)
  3639 +
  3640 + main_sizer = wx.BoxSizer(wx.VERTICAL)
  3641 + main_sizer.Add(top_sizer, 0, wx.LEFT|wx.TOP|wx.BOTTOM, 10)
  3642 + main_sizer.Add(self.interactor, 0, wx.EXPAND)
  3643 + main_sizer.Add(btn_sizer, 0,
  3644 + wx.EXPAND|wx.GROW|wx.LEFT|wx.TOP|wx.BOTTOM, 10)
  3645 + main_sizer.Add(self.progress, 0, wx.EXPAND | wx.ALL, 5)
  3646 +
  3647 + self.SetSizer(main_sizer)
  3648 + main_sizer.Fit(self)
  3649 +
  3650 + def LoadActor(self):
  3651 + '''
  3652 + Load the selected actor from the project (self.surface) into the scene
  3653 + :return:
  3654 + '''
  3655 + mapper = vtk.vtkPolyDataMapper()
  3656 + mapper.SetInputData(self.surface)
  3657 + mapper.ScalarVisibilityOff()
  3658 + #mapper.ImmediateModeRenderingOn()
  3659 +
  3660 + obj_actor = vtk.vtkActor()
  3661 + obj_actor.SetMapper(mapper)
  3662 + self.obj_actor = obj_actor
  3663 +
  3664 + self.ren.AddActor(obj_actor)
  3665 + self.ren.ResetCamera()
  3666 + self.interactor.Render()
  3667 +
  3668 + def RemoveActor(self):
  3669 + #self.ren.RemoveActor(self.obj_actor)
  3670 + self.ren.RemoveAllViewProps()
  3671 + self.point_coord = []
  3672 + self.transformed_points = []
  3673 + self.m_icp = None
  3674 + self.SetProgress(0)
  3675 + self.ren.ResetCamera()
  3676 + self.interactor.Render()
  3677 +
  3678 + def AddMarker(self, size, colour, coord):
  3679 + """
  3680 + Points are rendered into the scene. These points give visual information about the registration.
  3681 + :param size: value of the marker size
  3682 + :type size: int
  3683 + :param colour: RGB Color Code for the marker
  3684 + :type colour: tuple (int(R),int(G),int(B))
  3685 + :param coord: x, y, z of the marker
  3686 + :type coord: np.ndarray
  3687 + """
  3688 +
  3689 + x, y, z = coord[0], -coord[1], coord[2]
  3690 +
  3691 + ball_ref = vtk.vtkSphereSource()
  3692 + ball_ref.SetRadius(size)
  3693 + ball_ref.SetCenter(x, y, z)
  3694 +
  3695 + mapper = vtk.vtkPolyDataMapper()
  3696 + mapper.SetInputConnection(ball_ref.GetOutputPort())
  3697 +
  3698 + prop = vtk.vtkProperty()
  3699 + prop.SetColor(colour[0:3])
  3700 +
  3701 + #adding a new actor for the present ball
  3702 + sphere_actor = vtk.vtkActor()
  3703 +
  3704 + sphere_actor.SetMapper(mapper)
  3705 + sphere_actor.SetProperty(prop)
  3706 +
  3707 + self.ren.AddActor(sphere_actor)
  3708 + self.point_coord.append([x, y, z])
  3709 +
  3710 + self.Refresh()
  3711 +
  3712 + def SetProgress(self, progress):
  3713 + self.progress.SetValue(progress * 100)
  3714 + self.Refresh()
  3715 +
  3716 + def vtkmatrix_to_numpy(self, matrix):
  3717 + """
  3718 + Copies the elements of a vtkMatrix4x4 into a numpy array.
  3719 +
  3720 + :param matrix: The matrix to be copied into an array.
  3721 + :type matrix: vtk.vtkMatrix4x4
  3722 + :rtype: numpy.ndarray
  3723 + """
  3724 + m = np.ones((4, 4))
  3725 + for i in range(4):
  3726 + for j in range(4):
  3727 + m[i, j] = matrix.GetElement(i, j)
  3728 + return m
  3729 +
  3730 + def SetCameraVolume(self, position):
  3731 + """
  3732 + Positioning of the camera based on the acquired point
  3733 + :param position: x, y, z of the last acquired point
  3734 + :return:
  3735 + """
  3736 + cam_focus = np.array([position[0], -position[1], position[2]])
  3737 + cam = self.ren.GetActiveCamera()
  3738 +
  3739 + if self.initial_focus is None:
  3740 + self.initial_focus = np.array(cam.GetFocalPoint())
  3741 +
  3742 + cam_pos0 = np.array(cam.GetPosition())
  3743 + cam_focus0 = np.array(cam.GetFocalPoint())
  3744 + v0 = cam_pos0 - cam_focus0
  3745 + v0n = np.sqrt(inner1d(v0, v0))
  3746 +
  3747 + v1 = (cam_focus - self.initial_focus)
  3748 +
  3749 + v1n = np.sqrt(inner1d(v1, v1))
  3750 + if not v1n:
  3751 + v1n = 1.0
  3752 + cam_pos = (v1/v1n)*v0n + cam_focus
  3753 +
  3754 + cam.SetFocalPoint(cam_focus)
  3755 + cam.SetPosition(cam_pos)
  3756 + self.Refresh()
  3757 +
  3758 + def ErrorEstimation(self, surface, points):
  3759 + """
  3760 + Estimation of the average squared distance between the cloud of points to the closest mesh
  3761 + :param surface: Surface polydata of the scene
  3762 + :type surface: vtk.polydata
  3763 + :param points: Cloud of points
  3764 + :type points: np.ndarray
  3765 + :return: mean distance
  3766 + """
  3767 + cell_locator = vtk.vtkCellLocator()
  3768 + cell_locator.SetDataSet(surface)
  3769 + cell_locator.BuildLocator()
  3770 +
  3771 + cellId = vtk.mutable(0)
  3772 + c = [0.0, 0.0, 0.0]
  3773 + subId = vtk.mutable(0)
  3774 + d = vtk.mutable(0.0)
  3775 + error = []
  3776 + for i in range(len(points)):
  3777 + cell_locator.FindClosestPoint(points[i], c, cellId, subId, d)
  3778 + error.append(np.sqrt(float(d)))
  3779 +
  3780 + return np.mean(error)
  3781 +
  3782 + def OnComboName(self, evt):
  3783 + surface_name = evt.GetString()
  3784 + surface_index = evt.GetSelection()
  3785 + self.surface = self.proj.surface_dict[surface_index].polydata
  3786 + if self.obj_actor:
  3787 + self.RemoveActor()
  3788 + self.LoadActor()
  3789 +
  3790 + def OnChoiceICPMethod(self, evt):
  3791 + self.icp_mode = evt.GetSelection()
  3792 +
  3793 + def OnContinuousAcquisition(self, evt=None, btn=None):
  3794 + value = btn.GetValue()
  3795 + if value:
  3796 + self.timer.Start(500)
  3797 + else:
  3798 + self.timer.Stop()
  3799 +
  3800 + def OnUpdate(self, evt):
  3801 + self.AddMarker(3, (1, 0, 0), self.current_coord[:3])
  3802 + self.SetCameraVolume(self.current_coord[:3])
  3803 +
  3804 + def OnCreatePoint(self, evt):
  3805 + self.AddMarker(3,(1,0,0),self.current_coord[:3])
  3806 + self.SetCameraVolume(self.current_coord[:3])
  3807 +
  3808 + def OnReset(self, evt):
  3809 + self.RemoveActor()
  3810 + self.LoadActor()
  3811 +
  3812 + def OnICP(self, evt):
  3813 + self.SetProgress(0.3)
  3814 + if self.cont_point:
  3815 + self.cont_point.SetValue(False)
  3816 + self.OnContinuousAcquisition(evt=None, btn=self.cont_point)
  3817 + sourcePoints = np.array(self.point_coord)
  3818 + sourcePoints_vtk = vtk.vtkPoints()
  3819 +
  3820 + for i in range(len(sourcePoints)):
  3821 + id0 = sourcePoints_vtk.InsertNextPoint(sourcePoints[i])
  3822 +
  3823 + source = vtk.vtkPolyData()
  3824 + source.SetPoints(sourcePoints_vtk)
  3825 +
  3826 + icp = vtk.vtkIterativeClosestPointTransform()
  3827 + icp.SetSource(source)
  3828 + icp.SetTarget(self.surface)
  3829 +
  3830 + if self.icp_mode == 0:
  3831 + print("Affine mode")
  3832 + icp.GetLandmarkTransform().SetModeToAffine()
  3833 + elif self.icp_mode == 1:
  3834 + print("Similarity mode")
  3835 + icp.GetLandmarkTransform().SetModeToSimilarity()
  3836 + elif self.icp_mode == 2:
  3837 + print("Rigid mode")
  3838 + icp.GetLandmarkTransform().SetModeToRigidBody()
  3839 +
  3840 + #icp.DebugOn()
  3841 + icp.SetMaximumNumberOfIterations(1000)
  3842 +
  3843 + icp.Modified()
  3844 +
  3845 + icp.Update()
  3846 +
  3847 + self.m_icp = self.vtkmatrix_to_numpy(icp.GetMatrix())
  3848 +
  3849 + icpTransformFilter = vtk.vtkTransformPolyDataFilter()
  3850 + icpTransformFilter.SetInputData(source)
  3851 +
  3852 + icpTransformFilter.SetTransform(icp)
  3853 + icpTransformFilter.Update()
  3854 +
  3855 + transformedSource = icpTransformFilter.GetOutput()
  3856 +
  3857 + self.SetProgress(1)
  3858 +
  3859 + for i in range(transformedSource.GetNumberOfPoints()):
  3860 + p = [0, 0, 0]
  3861 + transformedSource.GetPoint(i, p)
  3862 + self.transformed_points.append(p)
  3863 + point = vtk.vtkSphereSource()
  3864 + point.SetCenter(p)
  3865 + point.SetRadius(3)
  3866 + point.SetPhiResolution(3)
  3867 + point.SetThetaResolution(3)
  3868 +
  3869 + mapper = vtk.vtkPolyDataMapper()
  3870 + mapper.SetInputConnection(point.GetOutputPort())
  3871 +
  3872 + actor = vtk.vtkActor()
  3873 + actor.SetMapper(mapper)
  3874 + actor.GetProperty().SetColor((0,1,0))
  3875 +
  3876 + self.ren.AddActor(actor)
  3877 +
  3878 + self.prev_error = self.ErrorEstimation(self.surface, sourcePoints)
  3879 + self.final_error = self.ErrorEstimation(self.surface, self.transformed_points)
  3880 +
  3881 + self.Refresh()
  3882 +
  3883 + def GetValue(self):
  3884 + return self.m_icp, self.point_coord, self.transformed_points, self.prev_error, self.final_error
3496 3885
3497 class SurfaceProgressWindow(object): 3886 class SurfaceProgressWindow(object):
3498 def __init__(self): 3887 def __init__(self):
@@ -3752,20 +4141,20 @@ class SetNDIconfigs(wx.Dialog): @@ -3752,20 +4141,20 @@ class SetNDIconfigs(wx.Dialog):
3752 wildcard="Rom files (*.rom)|*.rom", message="Select probe's rom file") 4141 wildcard="Rom files (*.rom)|*.rom", message="Select probe's rom file")
3753 row_probe = wx.BoxSizer(wx.VERTICAL) 4142 row_probe = wx.BoxSizer(wx.VERTICAL)
3754 row_probe.Add(wx.StaticText(self, wx.ID_ANY, "Set probe's rom file"), 0, wx.TOP|wx.RIGHT, 5) 4143 row_probe.Add(wx.StaticText(self, wx.ID_ANY, "Set probe's rom file"), 0, wx.TOP|wx.RIGHT, 5)
3755 - row_probe.Add(self.dir_probe, 0, wx.EXPAND|wx.ALIGN_CENTER) 4144 + row_probe.Add(self.dir_probe, 0, wx.ALIGN_CENTER)
3756 4145
3757 self.dir_ref = wx.FilePickerCtrl(self, path=last_ndi_ref_marker, style=wx.FLP_USE_TEXTCTRL|wx.FLP_SMALL, 4146 self.dir_ref = wx.FilePickerCtrl(self, path=last_ndi_ref_marker, style=wx.FLP_USE_TEXTCTRL|wx.FLP_SMALL,
3758 wildcard="Rom files (*.rom)|*.rom", message="Select reference's rom file") 4147 wildcard="Rom files (*.rom)|*.rom", message="Select reference's rom file")
3759 row_ref = wx.BoxSizer(wx.VERTICAL) 4148 row_ref = wx.BoxSizer(wx.VERTICAL)
3760 row_ref.Add(wx.StaticText(self, wx.ID_ANY, "Set reference's rom file"), 0, wx.TOP | wx.RIGHT, 5) 4149 row_ref.Add(wx.StaticText(self, wx.ID_ANY, "Set reference's rom file"), 0, wx.TOP | wx.RIGHT, 5)
3761 - row_ref.Add(self.dir_ref, 0, wx.EXPAND|wx.ALIGN_CENTER) 4150 + row_ref.Add(self.dir_ref, 0, wx.ALIGN_CENTER)
3762 4151
3763 self.dir_obj = wx.FilePickerCtrl(self, path=last_ndi_obj_marker, style=wx.FLP_USE_TEXTCTRL|wx.FLP_SMALL, 4152 self.dir_obj = wx.FilePickerCtrl(self, path=last_ndi_obj_marker, style=wx.FLP_USE_TEXTCTRL|wx.FLP_SMALL,
3764 wildcard="Rom files (*.rom)|*.rom", message="Select object's rom file") 4153 wildcard="Rom files (*.rom)|*.rom", message="Select object's rom file")
3765 #self.dir_probe.Bind(wx.EVT_FILEPICKER_CHANGED, self.Selected) 4154 #self.dir_probe.Bind(wx.EVT_FILEPICKER_CHANGED, self.Selected)
3766 row_obj = wx.BoxSizer(wx.VERTICAL) 4155 row_obj = wx.BoxSizer(wx.VERTICAL)
3767 row_obj.Add(wx.StaticText(self, wx.ID_ANY, "Set object's rom file"), 0, wx.TOP|wx.RIGHT, 5) 4156 row_obj.Add(wx.StaticText(self, wx.ID_ANY, "Set object's rom file"), 0, wx.TOP|wx.RIGHT, 5)
3768 - row_obj.Add(self.dir_obj, 0, wx.EXPAND|wx.ALIGN_CENTER) 4157 + row_obj.Add(self.dir_obj, 0, wx.ALIGN_CENTER)
3769 4158
3770 btn_ok = wx.Button(self, wx.ID_OK) 4159 btn_ok = wx.Button(self, wx.ID_OK)
3771 btn_ok.SetHelpText("") 4160 btn_ok.SetHelpText("")
invesalius/gui/task_navigator.py
  Diff comments   View file @af3ad6f
@@ -309,17 +309,24 @@ class NeuronavigationPanel(wx.Panel): @@ -309,17 +309,24 @@ class NeuronavigationPanel(wx.Panel):
309 309
310 # Initialize global variables 310 # Initialize global variables
311 self.fiducials = np.full([6, 3], np.nan) 311 self.fiducials = np.full([6, 3], np.nan)
  312 + self.fiducials_raw = np.zeros((6, 6))
312 self.correg = None 313 self.correg = None
313 self.current_coord = 0, 0, 0 314 self.current_coord = 0, 0, 0
314 self.trk_init = None 315 self.trk_init = None
  316 + self.nav_status = False
315 self.trigger = None 317 self.trigger = None
316 self.trigger_state = False 318 self.trigger_state = False
317 self.obj_reg = None 319 self.obj_reg = None
318 self.obj_reg_status = False 320 self.obj_reg_status = False
319 self.track_obj = False 321 self.track_obj = False
  322 + self.m_icp = None
  323 + self.fre = None
  324 + self.icp_fre = None
  325 + self.icp = False
320 self.event = threading.Event() 326 self.event = threading.Event()
321 327
322 self.coord_queue = QueueCustom(maxsize=1) 328 self.coord_queue = QueueCustom(maxsize=1)
  329 + self.icp_queue = QueueCustom(maxsize=1)
323 # self.visualization_queue = QueueCustom(maxsize=1) 330 # self.visualization_queue = QueueCustom(maxsize=1)
324 self.trigger_queue = QueueCustom(maxsize=1) 331 self.trigger_queue = QueueCustom(maxsize=1)
325 self.coord_tracts_queue = QueueCustom(maxsize=1) 332 self.coord_tracts_queue = QueueCustom(maxsize=1)
@@ -385,6 +392,7 @@ class NeuronavigationPanel(wx.Panel): @@ -385,6 +392,7 @@ class NeuronavigationPanel(wx.Panel):
385 392
386 # TODO: Find a better allignment between FRE, text and navigate button 393 # TODO: Find a better allignment between FRE, text and navigate button
387 txt_fre = wx.StaticText(self, -1, _('FRE:')) 394 txt_fre = wx.StaticText(self, -1, _('FRE:'))
  395 + txt_icp = wx.StaticText(self, -1, _('Refine:'))
388 396
389 # Fiducial registration error text box 397 # Fiducial registration error text box
390 tooltip = wx.ToolTip(_("Fiducial registration error")) 398 tooltip = wx.ToolTip(_("Fiducial registration error"))
@@ -401,6 +409,14 @@ class NeuronavigationPanel(wx.Panel): @@ -401,6 +409,14 @@ class NeuronavigationPanel(wx.Panel):
401 btn_nav.SetToolTip(tooltip) 409 btn_nav.SetToolTip(tooltip)
402 btn_nav.Bind(wx.EVT_TOGGLEBUTTON, partial(self.OnNavigate, btn=(btn_nav, choice_trck, choice_ref))) 410 btn_nav.Bind(wx.EVT_TOGGLEBUTTON, partial(self.OnNavigate, btn=(btn_nav, choice_trck, choice_ref)))
403 411
  412 + tooltip = wx.ToolTip(_(u"Refine the coregistration"))
  413 + checkicp = wx.CheckBox(self, -1, _(' '))
  414 + checkicp.SetValue(False)
  415 + checkicp.Enable(False)
  416 + checkicp.Bind(wx.EVT_CHECKBOX, partial(self.Oncheckicp, ctrl=checkicp))
  417 + checkicp.SetToolTip(tooltip)
  418 + self.checkicp = checkicp
  419 +
404 # Image and tracker coordinates number controls 420 # Image and tracker coordinates number controls
405 for m in range(len(self.btns_coord)): 421 for m in range(len(self.btns_coord)):
406 for n in range(3): 422 for n in range(3):
@@ -421,10 +437,12 @@ class NeuronavigationPanel(wx.Panel): @@ -421,10 +437,12 @@ class NeuronavigationPanel(wx.Panel):
421 if m in range(1, 6): 437 if m in range(1, 6):
422 self.numctrls_coord[m][n].SetEditable(False) 438 self.numctrls_coord[m][n].SetEditable(False)
423 439
424 - nav_sizer = wx.FlexGridSizer(rows=1, cols=3, hgap=5, vgap=5) 440 + nav_sizer = wx.FlexGridSizer(rows=1, cols=5, hgap=5, vgap=5)
425 nav_sizer.AddMany([(txt_fre, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL), 441 nav_sizer.AddMany([(txt_fre, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL),
426 (txtctrl_fre, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL), 442 (txtctrl_fre, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL),
427 - (btn_nav, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL)]) 443 + (btn_nav, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL),
  444 + (txt_icp, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL),
  445 + (checkicp, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL)])
428 446
429 group_sizer = wx.FlexGridSizer(rows=9, cols=1, hgap=5, vgap=5) 447 group_sizer = wx.FlexGridSizer(rows=9, cols=1, hgap=5, vgap=5)
430 group_sizer.AddGrowableCol(0, 1) 448 group_sizer.AddGrowableCol(0, 1)
@@ -459,6 +477,7 @@ class NeuronavigationPanel(wx.Panel): @@ -459,6 +477,7 @@ class NeuronavigationPanel(wx.Panel):
459 Publisher.subscribe(self.UpdateTractsVisualization, 'Update tracts visualization') 477 Publisher.subscribe(self.UpdateTractsVisualization, 'Update tracts visualization')
460 Publisher.subscribe(self.EnableACT, 'Enable ACT') 478 Publisher.subscribe(self.EnableACT, 'Enable ACT')
461 Publisher.subscribe(self.UpdateACTData, 'Update ACT data') 479 Publisher.subscribe(self.UpdateACTData, 'Update ACT data')
  480 + Publisher.subscribe(self.UpdateNavigationStatus, 'Navigation status')
462 481
463 def LoadImageFiducials(self, marker_id, coord): 482 def LoadImageFiducials(self, marker_id, coord):
464 for n in const.BTNS_IMG_MKS: 483 for n in const.BTNS_IMG_MKS:
@@ -470,6 +489,14 @@ class NeuronavigationPanel(wx.Panel): @@ -470,6 +489,14 @@ class NeuronavigationPanel(wx.Panel):
470 for m in [0, 1, 2]: 489 for m in [0, 1, 2]:
471 self.numctrls_coord[btn_id][m].SetValue(coord[m]) 490 self.numctrls_coord[btn_id][m].SetValue(coord[m])
472 491
  492 + def UpdateNavigationStatus(self, nav_status, vis_status):
  493 + self.nav_status = nav_status
  494 + if nav_status and (self.m_icp is not None):
  495 + self.checkicp.Enable(True)
  496 + else:
  497 + self.checkicp.Enable(False)
  498 + #self.checkicp.SetValue(False)
  499 +
473 def UpdateFRE(self, fre): 500 def UpdateFRE(self, fre):
474 # TODO: Exhibit FRE in a warning dialog and only starts navigation after user clicks ok 501 # TODO: Exhibit FRE in a warning dialog and only starts navigation after user clicks ok
475 self.txtctrl_fre.SetValue(str(round(fre, 2))) 502 self.txtctrl_fre.SetValue(str(round(fre, 2)))
@@ -661,9 +688,57 @@ class NeuronavigationPanel(wx.Panel): @@ -661,9 +688,57 @@ class NeuronavigationPanel(wx.Panel):
661 # Update number controls with tracker coordinates 688 # Update number controls with tracker coordinates
662 if coord is not None: 689 if coord is not None:
663 self.fiducials[btn_id, :] = coord[0:3] 690 self.fiducials[btn_id, :] = coord[0:3]
  691 + if btn_id == 3:
  692 + self.fiducials_raw[0, :] = coord_raw[0, :]
  693 + self.fiducials_raw[1, :] = coord_raw[1, :]
  694 + elif btn_id == 4:
  695 + self.fiducials_raw[2, :] = coord_raw[0, :]
  696 + self.fiducials_raw[3, :] = coord_raw[1, :]
  697 + else:
  698 + self.fiducials_raw[4, :] = coord_raw[0, :]
  699 + self.fiducials_raw[5, :] = coord_raw[1, :]
  700 +
664 for n in [0, 1, 2]: 701 for n in [0, 1, 2]:
665 self.numctrls_coord[btn_id][n].SetValue(float(coord[n])) 702 self.numctrls_coord[btn_id][n].SetValue(float(coord[n]))
666 703
  704 + def OnICP(self):
  705 + dialog = dlg.ICPCorregistrationDialog(nav_prop=(self.tracker_id, self.trk_init, self.ref_mode_id))
  706 + if dialog.ShowModal() == wx.ID_OK:
  707 + self.m_icp, point_coord, transformed_points, prev_error, final_error = dialog.GetValue()
  708 + #TODO: checkbox in the dialog to transfer the icp points to 3D viewer
  709 + #create markers
  710 + # for i in range(len(point_coord)):
  711 + # img_coord = point_coord[i][0],-point_coord[i][1],point_coord[i][2], 0, 0, 0
  712 + # transf_coord = transformed_points[i][0],-transformed_points[i][1],transformed_points[i][2], 0, 0, 0
  713 + # Publisher.sendMessage('Create marker', coord=img_coord, marker_id=None, colour=(1,0,0))
  714 + # Publisher.sendMessage('Create marker', coord=transf_coord, marker_id=None, colour=(0,0,1))
  715 + if self.m_icp is not None:
  716 + dlg.ReportICPerror(prev_error, final_error)
  717 + self.checkicp.Enable(True)
  718 + self.checkicp.SetValue(True)
  719 + self.icp = True
  720 + else:
  721 + self.checkicp.Enable(False)
  722 + self.checkicp.SetValue(False)
  723 + self.icp = False
  724 +
  725 + return self.m_icp
  726 +
  727 + def Oncheckicp(self, evt, ctrl):
  728 + if ctrl.GetValue() and evt and (self.m_icp is not None):
  729 + self.icp = True
  730 + else:
  731 + self.icp = False
  732 + self.ctrl_icp()
  733 +
  734 + def ctrl_icp(self):
  735 + if self.icp:
  736 + self.UpdateFRE(self.icp_fre)
  737 + else:
  738 + self.UpdateFRE(self.fre)
  739 + self.icp_queue.put_nowait([self.icp, self.m_icp])
  740 + #print(self.icp, self.m_icp)
  741 +
667 def OnNavigate(self, evt, btn): 742 def OnNavigate(self, evt, btn):
668 btn_nav = btn[0] 743 btn_nav = btn[0]
669 choice_trck = btn[1] 744 choice_trck = btn[1]
@@ -673,7 +748,7 @@ class NeuronavigationPanel(wx.Panel): @@ -673,7 +748,7 @@ class NeuronavigationPanel(wx.Panel):
673 # initialize jobs list 748 # initialize jobs list
674 jobs_list = [] 749 jobs_list = []
675 vis_components = [self.trigger_state, self.view_tracts] 750 vis_components = [self.trigger_state, self.view_tracts]
676 - vis_queues = [self.coord_queue, self.trigger_queue, self.tracts_queue] 751 + vis_queues = [self.coord_queue, self.trigger_queue, self.tracts_queue, self.icp_queue]
677 752
678 nav_id = btn_nav.GetValue() 753 nav_id = btn_nav.GetValue()
679 if not nav_id: 754 if not nav_id:
@@ -752,10 +827,9 @@ class NeuronavigationPanel(wx.Panel): @@ -752,10 +827,9 @@ class NeuronavigationPanel(wx.Panel):
752 tracker_mode = self.trk_init, self.tracker_id, self.ref_mode_id 827 tracker_mode = self.trk_init, self.tracker_id, self.ref_mode_id
753 828
754 # compute fiducial registration error (FRE) 829 # compute fiducial registration error (FRE)
755 - # this is the old way to compute the fre, left here to recheck if new works fine.  
756 - # fre = db.calculate_fre(self.fiducials, minv, n, q1, q2)  
757 - fre = db.calculate_fre_m(self.fiducials)  
758 - self.UpdateFRE(fre) 830 + if not self.icp_fre:
  831 + self.fre = db.calculate_fre(self.fiducials_raw, self.fiducials, self.ref_mode_id, m_change)
  832 + self.UpdateFRE(self.fre)
759 833
760 if self.track_obj: 834 if self.track_obj:
761 # if object tracking is selected 835 # if object tracking is selected
@@ -778,15 +852,15 @@ class NeuronavigationPanel(wx.Panel): @@ -778,15 +852,15 @@ class NeuronavigationPanel(wx.Panel):
778 obj_data = db.object_registration(obj_fiducials, obj_orients, coord_raw, m_change) 852 obj_data = db.object_registration(obj_fiducials, obj_orients, coord_raw, m_change)
779 coreg_data.extend(obj_data) 853 coreg_data.extend(obj_data)
780 854
781 - jobs_list.append(dcr.CoordinateCorregistrate(self.ref_mode_id, tracker_mode, coreg_data, self.coord_queue,  
782 - self.view_tracts, self.coord_tracts_queue, 855 + queues = [self.coord_queue, self.coord_tracts_queue, self.icp_queue]
  856 + jobs_list.append(dcr.CoordinateCorregistrate(self.ref_mode_id, tracker_mode, coreg_data,
  857 + self.view_tracts, queues,
783 self.event, self.sleep_nav)) 858 self.event, self.sleep_nav))
784 -  
785 else: 859 else:
786 coreg_data = (m_change, 0) 860 coreg_data = (m_change, 0)
  861 + queues = [self.coord_queue, self.coord_tracts_queue, self.icp_queue]
787 jobs_list.append(dcr.CoordinateCorregistrateNoObject(self.ref_mode_id, tracker_mode, coreg_data, 862 jobs_list.append(dcr.CoordinateCorregistrateNoObject(self.ref_mode_id, tracker_mode, coreg_data,
788 - self.coord_queue,  
789 - self.view_tracts, self.coord_tracts_queue, 863 + self.view_tracts, queues,
790 self.event, self.sleep_nav)) 864 self.event, self.sleep_nav))
791 865
792 if not errors: 866 if not errors:
@@ -807,12 +881,11 @@ class NeuronavigationPanel(wx.Panel): @@ -807,12 +881,11 @@ class NeuronavigationPanel(wx.Panel):
807 self.trk_inp = self.trekker, affine, self.seed_offset, self.n_tracts, self.seed_radius,\ 881 self.trk_inp = self.trekker, affine, self.seed_offset, self.n_tracts, self.seed_radius,\
808 self.n_threads, self.act_data, affine_vtk, matrix_shape[1] 882 self.n_threads, self.act_data, affine_vtk, matrix_shape[1]
809 # print("Appending the tract computation thread!") 883 # print("Appending the tract computation thread!")
  884 + queues = [self.coord_tracts_queue, self.tracts_queue]
810 if self.enable_act: 885 if self.enable_act:
811 - jobs_list.append(dti.ComputeTractsACTThread(self.trk_inp, self.coord_tracts_queue,  
812 - self.tracts_queue, self.event, self.sleep_nav)) 886 + jobs_list.append(dti.ComputeTractsACTThread(self.trk_inp, queues, self.event, self.sleep_nav))
813 else: 887 else:
814 - jobs_list.append(dti.ComputeTractsThread(self.trk_inp, self.coord_tracts_queue,  
815 - self.tracts_queue, self.event, self.sleep_nav)) 888 + jobs_list.append(dti.ComputeTractsThread(self.trk_inp, queues, self.event, self.sleep_nav))
816 889
817 jobs_list.append(UpdateNavigationScene(vis_queues, vis_components, 890 jobs_list.append(UpdateNavigationScene(vis_queues, vis_components,
818 self.event, self.sleep_nav)) 891 self.event, self.sleep_nav))
@@ -822,6 +895,13 @@ class NeuronavigationPanel(wx.Panel): @@ -822,6 +895,13 @@ class NeuronavigationPanel(wx.Panel):
822 jobs.start() 895 jobs.start()
823 # del jobs 896 # del jobs
824 897
  898 + if not self.checkicp.GetValue():
  899 + if dlg.ICPcorregistration(self.fre):
  900 + m_icp = self.OnICP()
  901 + self.icp_fre = db.calculate_fre(self.fiducials_raw, self.fiducials, self.ref_mode_id,
  902 + m_change, m_icp)
  903 + self.ctrl_icp()
  904 +
825 def ResetImageFiducials(self): 905 def ResetImageFiducials(self):
826 for m in range(0, 3): 906 for m in range(0, 3):
827 self.btns_coord[m].SetValue(False) 907 self.btns_coord[m].SetValue(False)
@@ -838,15 +918,25 @@ class NeuronavigationPanel(wx.Panel): @@ -838,15 +918,25 @@ class NeuronavigationPanel(wx.Panel):
838 self.txtctrl_fre.SetValue('') 918 self.txtctrl_fre.SetValue('')
839 self.txtctrl_fre.SetBackgroundColour('WHITE') 919 self.txtctrl_fre.SetBackgroundColour('WHITE')
840 920
  921 + def ResetIcp(self):
  922 + self.m_icp = None
  923 + self.fre = None
  924 + self.icp_fre = None
  925 + self.icp = False
  926 + self.checkicp.Enable(False)
  927 + self.checkicp.SetValue(False)
  928 +
841 def OnCloseProject(self): 929 def OnCloseProject(self):
842 self.ResetTrackerFiducials() 930 self.ResetTrackerFiducials()
843 self.ResetImageFiducials() 931 self.ResetImageFiducials()
  932 + self.ResetIcp()
844 self.OnChoiceTracker(False, self.choice_trck) 933 self.OnChoiceTracker(False, self.choice_trck)
845 Publisher.sendMessage('Update object registration') 934 Publisher.sendMessage('Update object registration')
846 Publisher.sendMessage('Update track object state', flag=False, obj_name=False) 935 Publisher.sendMessage('Update track object state', flag=False, obj_name=False)
847 Publisher.sendMessage('Delete all markers') 936 Publisher.sendMessage('Delete all markers')
848 Publisher.sendMessage("Update marker offset state", create=False) 937 Publisher.sendMessage("Update marker offset state", create=False)
849 Publisher.sendMessage("Remove tracts") 938 Publisher.sendMessage("Remove tracts")
  939 + Publisher.sendMessage("Set cross visibility", visibility=0)
850 # TODO: Reset camera initial focus 940 # TODO: Reset camera initial focus
851 Publisher.sendMessage('Reset cam clipping range') 941 Publisher.sendMessage('Reset cam clipping range')
852 942
@@ -1373,18 +1463,23 @@ class MarkersPanel(wx.Panel): @@ -1373,18 +1463,23 @@ class MarkersPanel(wx.Panel):
1373 self.marker_ind -= 1 1463 self.marker_ind -= 1
1374 Publisher.sendMessage('Remove marker', index=index) 1464 Publisher.sendMessage('Remove marker', index=index)
1375 1465
1376 - def OnCreateMarker(self, evt=None, coord=None, marker_id=None): 1466 + def OnCreateMarker(self, evt=None, coord=None, marker_id=None, colour=None):
1377 # OnCreateMarker is used for both pubsub and button click events 1467 # OnCreateMarker is used for both pubsub and button click events
1378 # Pubsub is used for markers created with fiducial buttons, trigger and create marker button 1468 # Pubsub is used for markers created with fiducial buttons, trigger and create marker button
  1469 + if not colour:
  1470 + colour = self.marker_colour
  1471 + if not coord:
  1472 + coord = self.current_coord
  1473 +
1379 if evt is None: 1474 if evt is None:
1380 if coord: 1475 if coord:
1381 self.CreateMarker(coord=coord, colour=(0.0, 1.0, 0.0), size=self.marker_size, 1476 self.CreateMarker(coord=coord, colour=(0.0, 1.0, 0.0), size=self.marker_size,
1382 marker_id=marker_id, seed=self.current_seed) 1477 marker_id=marker_id, seed=self.current_seed)
1383 else: 1478 else:
1384 - self.CreateMarker(coord=self.current_coord, colour=self.marker_colour, size=self.marker_size, 1479 + self.CreateMarker(coord=self.current_coord, colour=colour, size=self.marker_size,
1385 seed=self.current_seed) 1480 seed=self.current_seed)
1386 else: 1481 else:
1387 - self.CreateMarker(coord=self.current_coord, colour=self.marker_colour, size=self.marker_size, 1482 + self.CreateMarker(coord=self.current_coord, colour=colour, size=self.marker_size,
1388 seed=self.current_seed) 1483 seed=self.current_seed)
1389 1484
1390 def OnLoadMarkers(self, evt): 1485 def OnLoadMarkers(self, evt):
@@ -1807,7 +1902,6 @@ class TractographyPanel(wx.Panel): @@ -1807,7 +1902,6 @@ class TractographyPanel(wx.Panel):
1807 self.nav_status = nav_status 1902 self.nav_status = nav_status
1808 1903
1809 def OnLinkBrain(self, event=None): 1904 def OnLinkBrain(self, event=None):
1810 -  
1811 Publisher.sendMessage('Update status text in GUI', label=_("Busy")) 1905 Publisher.sendMessage('Update status text in GUI', label=_("Busy"))
1812 Publisher.sendMessage('Begin busy cursor') 1906 Publisher.sendMessage('Begin busy cursor')
1813 mask_path = dlg.ShowImportOtherFilesDialog(const.ID_NIFTI_IMPORT, _("Import brain mask")) 1907 mask_path = dlg.ShowImportOtherFilesDialog(const.ID_NIFTI_IMPORT, _("Import brain mask"))
@@ -2023,7 +2117,7 @@ class UpdateNavigationScene(threading.Thread): @@ -2023,7 +2117,7 @@ class UpdateNavigationScene(threading.Thread):
2023 2117
2024 threading.Thread.__init__(self, name='UpdateScene') 2118 threading.Thread.__init__(self, name='UpdateScene')
2025 self.trigger_state, self.view_tracts = vis_components 2119 self.trigger_state, self.view_tracts = vis_components
2026 - self.coord_queue, self.trigger_queue, self.tracts_queue = vis_queues 2120 + self.coord_queue, self.trigger_queue, self.tracts_queue, self.icp_queue = vis_queues
2027 self.sle = sle 2121 self.sle = sle
2028 self.event = event 2122 self.event = event
2029 2123
@@ -2055,6 +2149,7 @@ class UpdateNavigationScene(threading.Thread): @@ -2055,6 +2149,7 @@ class UpdateNavigationScene(threading.Thread):
2055 2149
2056 #TODO: If using the view_tracts substitute the raw coord from the offset coordinate, so the user 2150 #TODO: If using the view_tracts substitute the raw coord from the offset coordinate, so the user
2057 # see the red cross in the position of the offset marker 2151 # see the red cross in the position of the offset marker
  2152 + wx.CallAfter(Publisher.sendMessage, 'Update slices position', position=coord[:3])
2058 wx.CallAfter(Publisher.sendMessage, 'Set cross focal point', position=coord) 2153 wx.CallAfter(Publisher.sendMessage, 'Set cross focal point', position=coord)
2059 wx.CallAfter(Publisher.sendMessage, 'Update slice viewer') 2154 wx.CallAfter(Publisher.sendMessage, 'Update slice viewer')
2060 2155