Preprocessing scripts for MICRESS

reindex_micress_vtk.py

import numpy as np
import re, sys
def reindex_micress_vtk(vtkfilename):
    pLUT = re.compile('\s*LOOKUP_TABLE\s+', flags=re.I)
    headers=[]
    with open(vtkfilename) as f:
        for l in f:
            headers.append(l.strip())
            if pLUT.match(l):
                break
    A= np.loadtxt(vtkfilename, skiprows=len(headers))
    a=set()
    for i in A.reshape([A.size,]):
        a.add(i)
    a=sorted(list(a))
    B = np.zeros(A.shape)
    for i in range(len(a)):
        B[A==a[i]]=i+1
    B = B.astype('int')
    assert np.all(B>0)
    return B, headers
  
if __name__ == "__main__":
    vtkfname = sys.argv[1]
    Tab, Hdrs = reindex_micress_vtk(vtkfname)
    np.savetxt('out_'+vtkfname, Tab, header='\n'.join(Hdrs) , fmt='%d', comments='')