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xfmspline.py
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xfmspline.py
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import pyminc.volumes.factory as pm
import numpy as np
import os
import time
from scipy import interpolate
import sys
import argparse
import bisect
def flcslist(s):
try:
sspl = map(float, s.split(','))
return sspl
except:
raise argparse.ArgumentTypeError("MUST BE A COMMA SEPERATED LIST OF NUMBERS")
def strcslist(s):
try:
sspl = s.split(',')
return sspl
except:
raise argparse.ArgumentTypeError("MUST BE A COMMA SEPERATED LIST OF FILES")
parser = argparse.ArgumentParser(description='Spline Interpolate xfm files')
parser.add_argument('timepoints',
help="corresponding timepoints of the xfmfiles (comma seperated list). The last timepoint is the reference timepoint.",
type=flcslist, nargs=1)
parser.add_argument('xfmfiles',
help="xfmfiles to be splined (comma seperated list)",
type=strcslist, nargs=1)
parser.add_argument('interp_time',
help="Timepoints for which to find interpolated xfm (comma seperated list)",
type=flcslist, nargs=1)
parser.add_argument('outdir',
help="Output Directory",
type=str, nargs=1)
args = parser.parse_args()
tknots=args.timepoints[0]
xfms=args.xfmfiles[0]
tinterp=args.interp_time[0]
outdir=args.outdir[0]
if len(xfms)!=(len(tknots)-1):
print "number of xfmfiles must be ONE LESS than number of timepoints"
print "THe Last Timepoint is the reference timepoint"
sys.exit()
comm="%"+time.strftime("%d/%m/%Y")+" "+time.strftime("%H:%M:%S")+">>> "+'python xfmspline.py "'+",".join(map(str,tknots))+'" "'+",".join(xfms)+'" "'+",".join(map(str,tinterp))+'" '+outdir
if not os.path.exists(outdir):
os.makedirs(outdir)
outdir=outdir+"/"
#for leading zeroes
def zpad(val, n):
bits = val.split('.')
return "%s.%s" % (bits[0].zfill(n), bits[1])
# Function that applies xfm-notation 3x4 matrix (Rotation | Translation) (arr) to 3-component vector a
def afftrans(a,arr):
return np.dot(arr[:,0:3],(a+arr[:,3]))
#Read the affine component of xfm
def read_affine_xfm(xfmfile):
with open(xfmfile) as f:
content = f.readlines()
startline=content.index("Linear_Transform =\n")+1 ; stopline=startline+3
content[startline-1]="EXTRACTED_Linear_Transform =\n"
content[stopline-1]=content[stopline-1].replace(';','')
xfmarr=np.genfromtxt(content[startline:stopline])
return xfmarr
#this function reads xfmfiles are outputs a vector field encoding the transformation
def xfm2vectorField(xfmfile):
with open(xfmfile) as f:
content = f.readlines()
#Extract All of Grid Transforms
search='Displacement_Volume = '
linestxt=filter(lambda x:search in x, content)
NUMtrans=len(linestxt) #Number of grid transforms
gridfilesbase=[linetxt.replace(search,"").replace(';\n',"") for linetxt in linestxt]
xfmgrids=gridfilesbase
if len(os.path.dirname(xfmfile))!=0:
xfmgrids=[os.path.dirname(xfmfile)+'/'+gridfilebase for gridfilebase in gridfilesbase]
xfmarrs = [None] * len(linestxt)
for i in range(NUMtrans):
startline=content.index("Linear_Transform =\n")+1 ; stopline=startline+3
content[startline-1]="EXTRACTED_Linear_Transform =\n"
content[stopline-1]=content[stopline-1].replace(';','')
xfmarr=np.genfromtxt(content[startline:stopline])
xfmarrs[i]=xfmarr
for i in range(NUMtrans):
print "concatenating transform "+str(i+1)+" of "+str(NUMtrans)
if i==0:
v=np.apply_along_axis(afftrans, 0, pm.volumeFromFile(xfmgrids[i]).data ,xfmarrs[i])
continue
v=v+np.apply_along_axis(afftrans, 0, pm.volumeFromFile(xfmgrids[i]).data ,xfmarrs[i])
return v
#this function reads xfmfile. Returns first nlin grid
def xfm2vfirstnlingrid(xfmfile):
with open(xfmfile) as f:
content = f.readlines()
search='Displacement_Volume = '
linetxt=filter(lambda x:search in x, content)[0]
linenum=content.index(linetxt)
gridfilebase=linetxt.replace(search,"").replace(';\n',"")
if len(os.path.dirname(xfmfile))==0:
xfmgrid=gridfilebase
else:
xfmgrid=os.path.dirname(xfmfile)+'/'+gridfilebase
return xfmgrid
#replace last number of occurances of string
def rreplace(s, old, new):
li = s.rsplit(old, 1)
return new.join(li)
def xfmwrite(xfmfile,likefile,outaffinearr,outnlingrid,comment):
outgridfile=rreplace(os.path.basename(xfmfile),'.xfm','_grid_0.mnc')
if len(os.path.dirname(xfmfile))!=0:
outgridfilefull=os.path.dirname(xfmfile)+"/"+outgridfile
else:
outgridfilefull=outgridfile
outgrid = pm.volumeLikeFile(likefile, outgridfilefull)
outgrid.data=outnlingrid
outgrid.writeFile()
outgrid.closeVolume()
outaffinearrlist=map(str,outaffinearr.tolist())
newcontent=['MNI Transform File']
newcontent.append("%"+comment)
newcontent.append("")
newcontent.append('Transform_Type = Grid_Transform;')
newcontent.append('Displacement_Volume = '+outgridfile+';')
newcontent.append('Transform_Type = Linear;')
newcontent.append('Linear_Transform =')
newcontent.append(outaffinearrlist[0].replace(",","").replace("[","").replace("]",""))
newcontent.append(outaffinearrlist[1].replace(",","").replace("[","").replace("]",""))
newcontent.append(outaffinearrlist[2].replace(",","").replace("[","").replace("]","")+";")
with open(xfmfile,'w') as f:
for item in newcontent:
f.write(item+"\n")
# Read all xfms
numKNOTS=len(xfms)
for i in range(numKNOTS):
print "reading "+xfms[i]
v=xfm2vectorField(xfms[i])
#Read first volume and initialize empty matrix (flattened and one for each vector component)
if i==0:
voldims=(np.prod(v.shape[1:4]),numKNOTS+1)
x_series=np.zeros(voldims)
y_series=np.zeros(voldims)
z_series=np.zeros(voldims)
#broadcast vector field into empty matrices
x_series[:,i]=np.ravel(v[0,:,:,:])
y_series[:,i]=np.ravel(v[1,:,:,:])
z_series[:,i]=np.ravel(v[2,:,:,:])
# The final timepoint is the reference timepoint
# Thus, its vector transformation is IDENTITY (AKA 0 everywhere)
print x_series.shape
def myInterpFunc(yknots):
return interpolate.interp1d(tknots, yknots,kind='cubic')(tinterp)
print "interpolating x components"
interp_x_series=np.apply_along_axis(myInterpFunc, 1, x_series)
print "interpolating y components"
interp_y_series=np.apply_along_axis(myInterpFunc, 1, y_series)
print "interpolating z components"
interp_z_series=np.apply_along_axis(myInterpFunc, 1, z_series)
likefile=xfm2vfirstnlingrid(xfms[-1])
voldims=tuple(list(pm.volumeFromFile(likefile).data.shape)[1:4])
def get_reference(x):
stk=sorted(tknots)
ntrv = bisect.bisect_right(stk,x)
if ntrv>(len(tknots)-1):
ntrv=len(tknots)-1
return stk[ntrv]
for i in range(len(tinterp)):
vectransgrid=np.empty(tuple([3]+list(voldims)))
vectransgrid[0,:,:,:]=np.reshape(interp_x_series[:,i],voldims)
vectransgrid[1,:,:,:]=np.reshape(interp_y_series[:,i],voldims)
vectransgrid[2,:,:,:]=np.reshape(interp_z_series[:,i],voldims)
outxfmname=outdir+'p'+zpad(str(float(get_reference(tinterp[i]))),2).replace(".","d")+"_to_"+'p'+zpad(str(float(tinterp[i])),2).replace(".","d")+".xfm"
xfmwrite(outxfmname,likefile,np.asarray([[1,0,0,0],[0,1,0,0],[0,0,1,0]]),vectransgrid,comm)