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Commit d19662c85f107838c17e5a9920a2ff2fc6d8c641

Authored by tfmoraes
1 parent f55f4241
Exists in master and in 68 other branches 3d_inter_style, MIPs, beta3, beta4, brush_pix, canvas_reeng, canvas_text, casmoothing_cython, clean, command-line, cython_threshold, debian_cython, editor_improvements, encoding, ff_mask, ff_mask_improv, ffill_gui, ffill_segmentation, fill_holes_auto, fixes_pre_beta5, floodfill, get_pixel, import_mesh, interactor_style, inv3.0.1, invesalius-libift, mactoolbar, mactoolbar_bkp, manual_v3.1, mask_boolean_op, mask_boolean_op_bkp, mask_copy, mask_greatest_component, measure, measure_canvas, measure_improvements, measure_placement_test, measure_spacing, orientation, phoenix, region_growing_confidence, remote, remove_local_wxpython, rmatsuda-fix_ref_MTC, rmatsuda-fix_remove_marker_bug, rmatsuda-trigger_bug_fix, rotvol, segmentation_menu, select_part, smoothing_bin, smoothing_bin_pll, surface_area, threshold_history, user_guide_en, usp-navegador, vti, vtk6, watershed, watershed_improvements, watershed_improvements_bkp, watershed_merge, workdir, wwwlgui, wx2.9_mac, wxgtk3, wxgtk3_b5, wxgtk3_bkp, xmartlabs-command-line

It'was missing two files, data/co_registration.py and data/bases.py

Showing 3 changed files with 170 additions and 0 deletions   Show diff stats
.gitattributes
  Diff comments   View file @d19662c
... ... @@ -151,6 +151,8 @@ icons/volume_raycasting.png -text
151 151 icons/volume_raycasting_original.png -text
152 152 icons/zh_TW.bmp -text
153 153 invesalius/.svnignore -text
  154 +invesalius/data/bases.py -text
  155 +invesalius/data/co_registration.py -text
154 156 locale/de/LC_MESSAGES/invesalius.mo -text
155 157 locale/el/LC_MESSAGES/invesalius.mo -text
156 158 locale/en/LC_MESSAGES/invesalius.mo -text
... ...
invesalius/data/bases.py 0 → 100644
  Diff comments   View file @d19662c
... ... @@ -0,0 +1,85 @@
  1 +from numpy import *
  2 +from math import sqrt
  3 +
  4 +class Bases:
  5 +
  6 + def __init__(self, p1, p2, p3):
  7 +
  8 + self.p1 = array([p1[0], p1[1], p1[2]])
  9 + self.p2 = array([p2[0], p2[1], p2[2]])
  10 + self.p3 = array([p3[0], p3[1], p3[2]])
  11 +
  12 + print "p1: ", self.p1
  13 + print "p2: ", self.p2
  14 + print "p3: ", self.p3
  15 +
  16 + self.sub1 = self.p2 - self.p1
  17 + self.sub2 = self.p3 - self.p1
  18 +
  19 + def Basecreation(self):
  20 + #g1
  21 + g1 = self.sub1
  22 +
  23 + #g2
  24 + lamb1 = g1[0]*self.sub2[0] + g1[1]*self.sub2[1] + g1[2]*self.sub2[2]
  25 + lamb2 = dot(g1, g1)
  26 + lamb = lamb1/lamb2
  27 +
  28 + #Ponto q
  29 + q = self.p1 + lamb*self.sub1
  30 +
  31 + #g1 e g2 com origem em q
  32 + g1 = self.p1 - q
  33 + g2 = self.p3 - q
  34 +
  35 + #testa se o g1 nao eh um vetor nulo
  36 + if g1.any() == False:
  37 + g1 = self.p2 - q
  38 +
  39 + #g3 - Produto vetorial NumPy
  40 + g3 = cross(g2, g1)
  41 +
  42 + #normalizacao dos vetores
  43 + g1 = g1/sqrt(lamb2)
  44 + g2 = g2/sqrt(dot(g2, g2))
  45 + g3 = g3/sqrt(dot(g3, g3))
  46 +
  47 + M = matrix([[g1[0],g1[1],g1[2]], [g2[0],g2[1],g2[2]], [g3[0],g3[1],g3[2]]])
  48 + q.shape = (3, 1)
  49 + q = matrix(q.copy())
  50 + print"M: ", M
  51 + print
  52 + print"q: ", q
  53 + print
  54 + Minv = M.I
  55 +
  56 + return M, q, Minv
  57 +
  58 +def FlipX(point):
  59 +
  60 + point = matrix(point + (0,))
  61 +
  62 + #inverter o eixo z
  63 + ## possivel explicacaoo -- origem do eixo do imagedata esta no canto
  64 + ## superior esquerdo e origem da superfice eh no canto inferior esquerdo
  65 + ## ou a ordem de empilhamento das fatias
  66 +
  67 + point[0, 2] = -point[0, 2]
  68 +
  69 + #Flip em y
  70 + Mrot = matrix([[1.0, 0.0, 0.0, 0.0],
  71 + [0.0, -1.0, 0.0, 0.0],
  72 + [0.0, 0.0, -1.0, 0.0],
  73 + [0.0, 0.0, 0.0, 1.0]])
  74 + Mtrans = matrix([[1.0, 0, 0, -point[0, 0]],
  75 + [0.0, 1.0, 0, -point[0, 1]],
  76 + [0.0, 0.0, 1.0, -point[0, 2]],
  77 + [0.0, 0.0, 0.0, 1.0]])
  78 + Mtrans_return = matrix([[1.0, 0, 0, point[0, 0]],
  79 + [0.0, 1.0, 0, point[0, 1]],
  80 + [0.0, 0.0, 1.0, point[0, 2]],
  81 + [0.0, 0.0, 0.0, 1.0]])
  82 +
  83 + point_rot = point*Mtrans*Mrot*Mtrans_return
  84 + x, y, z = point_rot.tolist()[0][:3]
  85 + return x, y, z
... ...
invesalius/data/co_registration.py 0 → 100644
  Diff comments   View file @d19662c
... ... @@ -0,0 +1,83 @@
  1 +import threading
  2 +import serial
  3 +import wx.lib.pubsub as ps
  4 +from numpy import *
  5 +from math import sqrt
  6 +from time import sleep
  7 +import project
  8 +
  9 +class Corregister(threading.Thread):
  10 +
  11 + def __init__(self, bases, flag):
  12 +
  13 + threading.Thread.__init__(self)
  14 + self.M = bases[0]
  15 + self.Minv = bases[1]
  16 + self.N = bases[2]
  17 + self.Ninv = bases[3]
  18 + self.q1 = bases[4]
  19 + self.q2 = bases[5]
  20 + self.flag = flag
  21 + self._pause_ = 0
  22 + self.start()
  23 +
  24 + def stop(self):
  25 + # Stop neuronavigation
  26 + self._pause_ = 1
  27 +
  28 + def Coordinates(self):
  29 + #Get Polhemus points for neuronavigation
  30 + ser = serial.Serial(0)
  31 + ser.write("Y")
  32 + ser.write("P")
  33 + str = ser.readline()
  34 + ser.write("Y")
  35 + str = str.replace("\r\n","")
  36 + str = str.replace("-"," -")
  37 + aostr = [s for s in str.split()]
  38 + #aoflt -> 0:letter 1:x 2:y 3:z
  39 + aoflt = [float(aostr[1]), float(aostr[2]), float(aostr[3]),
  40 + float(aostr[4]), float(aostr[5]), float(aostr[6])]
  41 + ser.close()
  42 +
  43 + #Unit change: inches to millimeters
  44 + x = 25.4
  45 + y = 25.4
  46 + z = -25.4
  47 +
  48 + coord = (aoflt[0]*x, aoflt[1]*y, aoflt[2]*z)
  49 + return coord
  50 +
  51 + def run(self):
  52 + #Image limits to use in simulation
  53 + #bounds = array(project.Project().imagedata.GetBounds())
  54 + #im_simu = bounds
  55 + #im_simu[0] = bounds[0] - 10.0
  56 + #im_simu[2] = bounds[2] - 10.0
  57 + #im_simu[4] = bounds[4] - 10.0
  58 +
  59 + while self.flag == True:
  60 + #Neuronavigation with Polhemus
  61 + trck = self.Coordinates()
  62 + tracker = matrix([[trck[0]], [trck[1]], [trck[2]]])
  63 + img = self.q1 + (self.Minv*self.N)*(tracker - self.q2)
  64 + coord = [float(img[0]), float(img[1]), float(img[2])]
  65 + ps.Publisher().sendMessage('Co-registered Points', coord)
  66 +
  67 + if self._pause_:
  68 + return
  69 +
  70 + #Loop for simulate Polhemus movement and Neuronavigation
  71 + #for i in range(0, 5, 2):
  72 + # while im_simu[i] < (bounds[i+1]+10.0):
  73 + # im_init = matrix([[im_simu[0]], [im_simu[2]], [im_simu[4]]])
  74 + # #mudanca coordenada img2plh
  75 + # tr_simu = self.q2 + (self.Ninv*self.M)*(im_init - self.q1)
  76 + # #mudanca coordenada plh2img
  77 + # img_final = self.q1 + (self.Minv*self.N)*(tr_simu - self.q2)
  78 + # #publica as alteracoes que devem ser feitas nas fatias
  79 + # coord = [float(img_final[0]), float(img_final[1]), float(img_final[2])]
  80 + # ps.Publisher().sendMessage('Co-registered Points', coord)
  81 + # im_simu[i] = im_simu[i] + 4.0
  82 + # if self._pause_:
  83 + # return
... ...