regmaxs/regmaxsn/scripts/algorithms/alignAllTrans.py

import os
import numpy as np
from RegMaxSCore.iterativeRegistration import IterativeRegistration
import shutil


# ----------------------------------------------------------------------------------------------------------------------
# #
temp = os.path.split(__file__)[0]
temp1 = os.path.split(temp)[0]

dirPath = os.path.join(temp1, 'TestFiles')
expNames = [
                'HSN-fluoro01.CNG',
                'HSN-fluoro01.CNGRandTranslate',
              ]
refInd = 0
resDir = os.path.join(temp1, 'Results', 'translateRefined')
if not os.path.isdir(resDir):
    os.mkdir(resDir)
# ----------------------------------------------------------------------------------------------------------------------

gridSizes = [40.0, 20.0, 10.0]
transBounds = [[-30, 30], [-30, 30], [-30, 30]]
transMinRes = 1
nCPU = 6


refSWC = os.path.join(dirPath, expNames[refInd] + '.swc')
iterReg = IterativeRegistration(refSWC, gridSizes, None, transBounds,
                                transMinRes, None, None, nCPU)

ipParFile = os.path.join(resDir, 'tmp.json')
vals = ['trans']
tempOutFiles = {}
for val in vals:
    fle1 = os.path.join(resDir, val + '.swc')
    fle2 = os.path.join(resDir, val + 'bestSol.json')
    tempOutFiles[val] = [fle1, fle2]

for expInd, expName in enumerate(expNames):
    if refInd != expInd:
        print('Doing ' + expName + ' Scale')

        SWC2Align = os.path.join(dirPath, expName + '.swc')

        iterReg.transOnce(SWC2Align, tempOutFiles['trans'], ipParFile)

        shutil.copyfile(tempOutFiles['trans'][0], os.path.join(resDir, '{}.swc'.format(expName)))
        shutil.copyfile(tempOutFiles['trans'][1], os.path.join(resDir, '{}bestSol.json'.format(expName)))

        for g in vals:
            [os.remove(x) for x in tempOutFiles[g]]
        os.remove(ipParFile)