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Commit ca996b62 authored by Edward Andò's avatar Edward Andò
Browse files

adding the script...

parent d6b891ea
Pipeline #47962 passed with stages
in 12 minutes and 50 seconds
#!/usr/bin/env python
This python facilitates eye-alignment with a graphical QT interface
for Discrete Digital Image Correlation using SPAM functions
Copyright (C) 2020 SPAM Contributors
This program is free software: you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by the Free
Software Foundation, either version 3 of the License, or (at your option)
any later version.
This program is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
more details.
You should have received a copy of the GNU General Public License along with
this program. If not, see <http://www.gnu.org/licenses/>.
import os
import sys
import subprocess
import spam.helpers
import spam.label
import numpy
import tifffile
import spam.visual.visualClass as visual
import argparse
from PyQt5.QtWidgets import QApplication, QWidget, QFileDialog, QGridLayout, QPushButton
# Define argument parser object
parser = argparse.ArgumentParser(description="spam-ereg-discrete "+spam.helpers.optionsParser.GLPv3descriptionHeader +\
"This script facilitates eye-alignment for Discrete Digital Image Correlation two 3D greyscale images"+\
" (reference and deformed configurations) and requires the input of a labelled image for the reference configuration",
# Parse arguments with external helper function
args = spam.helpers.optionsParser.eregDiscreteParser(parser)
print("spam-ereg-discrete: Current Settings:")
argsDict = vars(args)
for key in sorted(argsDict):
print("\t{}: {}".format(key, argsDict[key]))
outFile = args.OUT_DIR+"/"+args.PREFIX+".tsv"
REFlab = tifffile.imread(args.lab1.name)
REFlabBB = spam.label.boundingBoxes(REFlab)
REFlabCOM = spam.label.centresOfMass(REFlab)
REFgrey = tifffile.imread(args.im1.name)
DEFgrey = tifffile.imread(args.im2.name)
# Some variable for nice filenames
REFstr = os.path.basename(args.im1.name)
DEFstr = os.path.basename(args.im2.name)
if args.PHIFILE is not None:
DDIC = spam.helpers.readCorrelationTSV(args.PHIFILE.name)
DDIC['error'] = numpy.genfromtxt(args.PHIFILE.name, delimiter='\t', names=True)['error']
DDIC['LabelDilate'] = numpy.genfromtxt(args.PHIFILE.name, delimiter='\t', names=True)['LabelDilate']
DDIC['PSCC'] = numpy.genfromtxt(args.PHIFILE.name, delimiter='\t', names=True)['PSCC']
labMax = REFlab.max()
DDIC = {}
DDIC['fieldCoords'] = REFlabCOM
DDIC['PhiField'] = numpy.zeros([labMax, 4, 4])
for label in range(labMax):
DDIC['PhiField'][label] = numpy.eye(4)
DDIC['returnStatus'] = numpy.zeros(labMax, dtype=int)
DDIC['deltaPhiNorm'] = numpy.zeros(labMax, dtype=int)
DDIC['iterations'] = numpy.zeros(labMax, dtype=int)
DDIC['error'] = numpy.zeros(labMax, dtype=int)
DDIC['LabelDilate'] = numpy.zeros(labMax, dtype=int)
DDIC['PSCC'] = numpy.zeros(labMax, dtype=int)
class MainWindow(QWidget):
def __init__(self):
self.Phi = numpy.eye(4)
self.mainWindowGrid = QGridLayout(self)
self.nonConvergedGrains = numpy.where(DDIC['returnStatus'] < args.RETURN_STAT_THRESHOLD)[0][1:]
self.N = 0 # Number of the current nonConvergedGrain that's being studied
print("Going to work on these labels:\n", self.nonConvergedGrains)
if len(self.nonConvergedGrains) > 0:
self.labAndPhi = []
print("No labels to work on")
def alignOneLabel(self):
nonConvergedGrain = self.nonConvergedGrains[self.N]
print("\tGrain {}".format(nonConvergedGrain))
Phi = DDIC['PhiField'][nonConvergedGrain]
displacement = Phi[0:3,-1]
displacementInt = displacement.astype(int)
self.diplacementInt = displacementInt
# Remove the int part of displacement
Phi[0:3,-1] -= displacementInt
print("\t\tSubtracted this displacement:", displacementInt)
#REFsubvol = REFgrey[REFlabBB[nonConvergedGrain,0]-args.margin : REFlabBB[nonConvergedGrain,1]+1+args.margin,
#REFlabBB[nonConvergedGrain,2]-args.margin : REFlabBB[nonConvergedGrain,3]+1+args.margin,
#REFlabBB[nonConvergedGrain,4]-args.margin : REFlabBB[nonConvergedGrain,5]+1+args.margin]
REFgl = spam.label.getLabel(REFlab, nonConvergedGrain,
boundingBoxes=REFlabBB, centresOfMass=REFlabCOM,
labelDilate=args.LABEL_DILATE, margin=args.margin,
REFsubvol = REFgrey[REFgl['slice']]
if args.MASK:
# If mask asked, also flatten greylevels
REFsubvol[REFgl['subvol'] == 0] = 0
DEFsubvol = DEFgrey[REFlabBB[nonConvergedGrain,0]+displacementInt[0]-args.margin : REFlabBB[nonConvergedGrain,1]+1+displacementInt[0]+args.margin,
REFlabBB[nonConvergedGrain,2]+displacementInt[1]-args.margin : REFlabBB[nonConvergedGrain,3]+1+displacementInt[1]+args.margin,
REFlabBB[nonConvergedGrain,4]+displacementInt[2]-args.margin : REFlabBB[nonConvergedGrain,5]+1+displacementInt[2]+args.margin]
self.eregWidget = visual.ereg( [REFsubvol, DEFsubvol],
Phi, 1,
["{} - label {}".format(REFstr, nonConvergedGrain), "{} - label {}".format(DEFstr, nonConvergedGrain)], 0)
self.mainWindowGrid.addWidget(self.eregWidget, 1, 1)
self.nextLabelButton = QPushButton("Accept and move on to next grain", self)
self.mainWindowGrid.addWidget(self.nextLabelButton, 2, 1)
def nextLabel(self):
#print("Phi:", self.eregWidget.output())
# Get Phi output from graphical
PhiTmp = self.eregWidget.output()
# Add back in int displacement
PhiTmp[0:3, -1] += self.diplacementInt
# nonConvergedGrain label number, eye-Phi
self.labAndPhi.append([self.nonConvergedGrains[self.N], PhiTmp])
# Move onto next grain, otherwise write and quit
self.N += 1
if self.N < len(self.nonConvergedGrains):
print("Updating output...")
for nonConvergedGrain, Phi in self.labAndPhi:
DDIC['PhiField'][nonConvergedGrain] = Phi
print("Writing output to {}...".format(outFile), end='')
outMatrix = numpy.array([numpy.array(range(DDIC['numberOfLabels'])),
DDIC['fieldCoords'][:, 0], DDIC['fieldCoords'][:, 1], DDIC['fieldCoords'][:, 2],
DDIC['PhiField'][:, 0, 3], DDIC['PhiField'][:, 1, 3], DDIC['PhiField'][:, 2, 3],
DDIC['PhiField'][:, 0, 0], DDIC['PhiField'][:, 0, 1], DDIC['PhiField'][:, 0, 2],
DDIC['PhiField'][:, 1, 0], DDIC['PhiField'][:, 1, 1], DDIC['PhiField'][:, 1, 2],
DDIC['PhiField'][:, 2, 0], DDIC['PhiField'][:, 2, 1], DDIC['PhiField'][:, 2, 2],
DDIC['error'], DDIC['iterations'],
DDIC['returnStatus'], DDIC['deltaPhiNorm'],
DDIC['LabelDilate'], DDIC['PSCC']]).T
header="Label\tZpos\tYpos\tXpos\t" +
"Zdisp\tYdisp\tXdisp\t" +
"Fzz\tFzy\tFzx\t" +
"Fyz\tFyy\tFyx\t" +
"Fxz\tFxy\tFxx\t" +
app = QApplication(["Label Registration"])
window = MainWindow()
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