From 94588307cb8d4b058c837fbb253e2388d03aecb5 Mon Sep 17 00:00:00 2001
From: Joshua Steer <Joshua.Steer@soton.ac.uk>
Date: Sat, 11 Aug 2018 11:49:27 +0100
Subject: [PATCH] Made registration into a class
---
AmpScan/registration.py | 142 +++++++++++++++-------------------------
GUIs/AmpScanGUI.py | 2 +-
2 files changed, 54 insertions(+), 90 deletions(-)
diff --git a/AmpScan/registration.py b/AmpScan/registration.py
index 895f397..62f0d28 100644
--- a/AmpScan/registration.py
+++ b/AmpScan/registration.py
@@ -5,113 +5,77 @@ Created on Wed Sep 13 16:07:10 2017
@author: js22g12
"""
import numpy as np
-import pandas as pd
-import copy
from scipy import spatial
from .core import AmpObject
-#"""
-#import os
-#path = ('J:\\Shared Resources\\AmpScan IfLS Team\\'
-# '100 PYTHON\\STLReader')
-#filename = '01_PhantomShell_ICEM_3mm.stl'
-#filename2 = '01_PhantomShell_ICEM_3mm_write.stl'
-#baseline = 'B_PTB.stl'
-#target = 'B_NormalLiner.stl'
-#os.chdir(path)
-#ampObj = AmpObject(filename)
-#regObj = regObject(ampObj)
-#ampObj.vert.loc[0,:]
-#regObj.vert.loc[0,:]
-#ampObj.icp()
-#regObj.icp()
-#regObj.registration()
-#ampObj.registration()
-
-#Data = AmpObject(target)
-#Data.getBaseline(baseline)
-#Reg = regObject(Data)
-#Reg.reg_fast()
-#
-#
-#Use mesh object as parent class with standard function
-#and then inherit for all other classes ie socket, residuum, registered
-#Either create from filename, object or fv
-#
-#Standard functions:
-# Rotation
-# Translation
-# Read
-# Write
-# Normals
-# Slice analyse
-#Child classes:
-# Residuum
-# Socket
-# Registration (Target)
-# Soft tissue mesh (Bones, Liner)
-# FE mesh
-#"""
-
-def registration(baseline, target, method='default', steps=5, direct=True):
- """
- Function to register the regObject to the baseline mesh
-
- Parameters
- ----------
- Steps: int, default 1
- Number of iterations
- """
- bV = baseline.vert
- # Calc FaceCentroids
- fC = target.vert[target.faces].mean(axis=1)
- # Construct knn tree
- tTree = spatial.cKDTree(fC)
- for step in np.arange(steps, 0, -1):
- # Index of 10 centroids nearest to each baseline vertex
- ind = tTree.query(bV, 10)[1]
- D = np.zeros(bV.shape)
- # Define normals for faces of nearest faces
- norms = target.norm[ind]
- # Get a point on each face
- fPoints = target.vert[target.faces[ind, 0]]
- # Calculate dot product between point on face and normals
- d = np.einsum('ijk, ijk->ij', norms, fPoints)
- t = d - np.einsum('ijk, ik->ij', norms, bV)
- # Calculate new points
- G = np.einsum('ijk, ij->ijk', norms, t)
- GMag = np.sqrt(np.einsum('ijk, ijk->ij', G, G)).argmin(axis=1)
- # Define vector from baseline point to intersect point
- D = G[np.arange(len(G)), GMag, :]
- bV = bV + D/step
- bData = dict(zip(['vert', 'faces', 'values'], [bV, baseline.faces, baseline.values]))
- regObj = AmpObject(bData, stype='reg')
- regObj.lp_smooth(5)
+class registration(object):
- def calcError(baseline, regObj, direct=True):
+ def __init__(self, baseline, target, method='point2plane', steps=5):
+ self.b = baseline
+ self.t = target
+ self.steps = steps
+ if method is not None:
+ getattr(self, method)()
+
+
+ def point2plane(self):
+ """
+ Function to register the regObject to the baseline mesh
+
+ Parameters
+ ----------
+ Steps: int, default 1
+ Number of iterations
+ """
+ # Calc FaceCentroids
+ fC = self.t.vert[self.t.faces].mean(axis=1)
+ # Construct knn tree
+ tTree = spatial.cKDTree(fC)
+ bData = dict(zip(['vert', 'faces', 'values'],
+ [self.b.vert, self.b.faces, self.b.values]))
+ self.reg = AmpObject(bData, stype='reg')
+ for step in np.arange(self.steps, 0, -1):
+ # Index of 10 centroids nearest to each baseline vertex
+ ind = tTree.query(self.reg.vert, 10)[1]
+ D = np.zeros(self.reg.vert.shape)
+ # Define normals for faces of nearest faces
+ norms = self.t.norm[ind]
+ # Get a point on each face
+ fPoints = self.t.vert[self.t.faces[ind, 0]]
+ # Calculate dot product between point on face and normals
+ d = np.einsum('ijk, ijk->ij', norms, fPoints)
+ t = d - np.einsum('ijk, ik->ij', norms, self.reg.vert)
+ # Calculate new points
+ G = np.einsum('ijk, ij->ijk', norms, t)
+ GMag = np.sqrt(np.einsum('ijk, ijk->ij', G, G)).argmin(axis=1)
+ # Define vector from baseline point to intersect point
+ D = G[np.arange(len(G)), GMag, :]
+ self.reg.vert += D/step
+ self.reg.lp_smooth(1)
+
+ self.reg.calcStruct()
+ self.reg.values[:] = self.calcError(False)
+
+ def calcError(self, direct):
"""
A function within a function will not be documented
"""
if direct is True:
- values = np.linalg.norm(regObj.vert - baseline.vert, axis=1)
+ values = np.linalg.norm(self.reg.vert - self.b.vert, axis=1)
# Calculate the unit vector normal between corresponding vertices
# baseline and target
- vector = (regObj.vert - baseline.vert)/values[:, None]
+ vector = (self.reg.vert - self.b.vert)/values[:, None]
# Calculate angle between the two unit vectors using normal of cross
# product between vNorm and vector and dot
- normcrossP = np.linalg.norm(np.cross(vector, target.vNorm), axis=1)
- dotP = np.einsum('ij,ij->i', vector, target.vNorm)
+ normcrossP = np.linalg.norm(np.cross(vector, self.t.vNorm), axis=1)
+ dotP = np.einsum('ij,ij->i', vector, self.t.vNorm)
angle = np.arctan2(normcrossP, dotP)
polarity = np.ones(angle.shape)
polarity[angle < np.pi/2] =-1.0
values = values * polarity
return values
else:
- values = np.linalg.norm(regObj.vert - baseline.vert, axis=1)
+ values = np.linalg.norm(self.reg.vert - self.b.vert, axis=1)
return values
- regObj.values[:] = calcError(baseline, regObj, False)
- return regObj
-
-
diff --git a/GUIs/AmpScanGUI.py b/GUIs/AmpScanGUI.py
index 96ab7b7..01c9dcc 100644
--- a/GUIs/AmpScanGUI.py
+++ b/GUIs/AmpScanGUI.py
@@ -138,7 +138,7 @@ class AmpScanGUI(QMainWindow):
target = str(self.regCont.target.currentText())
self.fileManager.setTable(baseline, [1,0,0], 0.5, 0)
self.fileManager.setTable(target, [0,0,1], 0.5, 0)
- reg = registration(self.files[baseline], self.files[target])
+ reg = registration(self.files[baseline], self.files[target], steps = 20).reg
reg.addActor(CMap = self.CMapN2P)
regName = target + '_reg'
self.files[regName] = reg
--
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