def write_tree_roi(interface_file, out_filename, tract_number, use_sample=False):
import os
import numpy as np
import nibabel as nb
from paux import image_dims
sampleSize = 500
interfaceFile = nb.load(interface_file)
data = np.array(interfaceFile.get_data())
voxelCoordList = []
for x, y, z in zip(*np.nonzero(data)):
voxelCoord = [x,y,z]
voxelCoordList.append(voxelCoord)
voxelCoordList.sort(key=lambda tup: tup[1])
voxelCoordList.sort(key=lambda tup: tup[2])
indexList = []
for coord in voxelCoordList:
index = int(data[coord[0],coord[1],coord[2]]) - 1
indexList.append(index)
finalIndexList = []
finalCoordList = []
if( use_sample ):
for i in xrange(len(indexList)):
if indexList[i] < sampleSize:
finalIndexList.append(indexList[i])
finalCoordList.append(voxelCoordList[i])
else:
finalIndexList = indexList
finalCoordList = voxelCoordList
dimensions = image_dims(interface_file)
with open(out_filename, 'w+') as roi_file:
roi_file.write("#imagesize\n")
roi_file.write(str(dimensions[0])+" "+str(dimensions[1])+" "+str(dimensions[2])+" nifti\n")
roi_file.write("#endimagesize\n\n")
roi_file.write("#streams\n")
roi_file.write(str(tract_number)+"\n")
roi_file.write("#endstreams\n\n")
roi_file.write("#trackindex\n")
for index in finalIndexList:
roi_file.write(str(index)+"\n")
roi_file.write("#endtrackindex\n\n")
roi_file.write("#roi\n")
for coord in finalCoordList:
roi_file.write(str(coord[0])+" "+str(coord[1])+" "+str(coord[2])+"\n")
roi_file.write("#endroi\n")
return os.path.abspath(out_filename)
def script_tracking(subject_ID, chunk_nr, output_dir, tract_number,tract_step, is_left, use_sample=False, postfix=''):
import numpy as np
from subprocess import call
import os.path as op
import time
from paux import write_sequence_file
from paux import fetch_sample
from paux import image_dims
if (is_left):
hemi_string = 'lh'
side_string = 'left'
else:
hemi_string = 'rh'
side_string = 'right'
seed_filename = output_dir+'/'+subject_ID+'/fa_masking/'+subject_ID+'_interface_'+side_string+'_mrtrix.txt'
voxel_filename = output_dir+'/'+subject_ID+'/fa_masking/'+subject_ID+'_interface_'+side_string+'_voxels.txt'
fa_filename = output_dir+'/'+subject_ID+'/fa_masking/'+subject_ID+'_fa_masked.nii'
script_dir = output_dir+'/'+subject_ID+'/track_scripts'+postfix+'/'
chunk_dir=script_dir+hemi_string+'_chunks'
seeds_dir=chunk_dir+"/seeds"
call("mkdir "+script_dir, shell=True)
call("mkdir "+chunk_dir, shell=True)
call("mkdir "+seeds_dir, shell=True)
if(is_left):
call("mkdir "+output_dir+"/"+subject_ID+"/raw_tracts"+postfix, shell=True)
call("mkdir "+output_dir+"/"+subject_ID+"/compact_tracts"+postfix, shell=True)
call("mkdir "+output_dir+"/"+subject_ID+"/raw_tracts"+postfix+"/"+hemi_string, shell=True)
chunk_file_prefix=seeds_dir+'/chunk_'
print("preparing for tracking of "+side_string+" hemisphere of subject "+subject_ID)
all_seed_coords = fetch_sample(seed_filename, use_sample)
out_sequence_filename=output_dir+"/"+subject_ID+"/compact_tracts"+postfix+"/"+subject_ID + "_" + side_string + ".txt"
write_sequence_file(all_seed_coords,out_sequence_filename)
if( use_sample ):
all_seed_voxels = fetch_sample(voxel_filename, use_sample)
dimensions = image_dims(fa_filename)
out_roi_filename = output_dir+"/"+subject_ID+"/compact_tracts"+postfix+"/"+subject_ID + "_treeroi_sample_" + side_string + ".txt"
temp_roi_filename = "/tmp/"+subject_ID + "_treeroi_" + side_string + ".txt"
np.savetxt(temp_roi_filename, np.array(all_seed_voxels), fmt='%d', delimiter=' ')
temp_trackid_filename = "/tmp/"+subject_ID + "_treetrackids_" + side_string + ".txt"
trackid_array = np.arange(len(all_seed_voxels))
np.savetxt(temp_trackid_filename, trackid_array, fmt='%d', delimiter='\n')
with open(out_roi_filename, 'w+') as roi_file:
roi_file.write("#imagesize\n")
roi_file.write(str(dimensions[0])+" "+str(dimensions[1])+" "+str(dimensions[2])+" nifti\n")
roi_file.write("#endimagesize\n\n")
roi_file.write("#streams\n")
roi_file.write(str(tract_number)+"\n")
roi_file.write("#endstreams\n\n")
roi_file.write("#trackindex\n")
with open(temp_roi_filename, "r")as index_file:
roi_file.write(index_file.read())
roi_file.write("#endtrackindex\n")
roi_file.write("#roi\n")
with open(temp_roi_filename, "r")as roi_file:
roi_file.write(roi_file.read())
roi_file.write("#endroi\n")
chunk_size = int(np.ceil(float(len(all_seed_coords))/chunk_nr))
for i in xrange(chunk_nr):
start_seed = i*chunk_size
if (i==chunk_nr-1):
end_seed = len(all_seed_coords)
else:
end_seed = (i+1)*chunk_size
this_chunk = all_seed_coords[start_seed:end_seed]
this_chunk_filename=chunk_file_prefix+str(i)+'.txt'
np.savetxt(this_chunk_filename, this_chunk, fmt='%f', delimiter=',')
print("created "+str(chunk_nr)+" tracking chunks with "+str(chunk_size)+" seeds each")
subject_line='SUBJECT="'+subject_ID+'"'
seedxfile_line="SEEDS_PER_FILE="+str(chunk_size)
hemi_line='HEMI="'+hemi_string+'"'
trackcount_line='TRACK_COUNT="'+str(tract_number)+'"'
trackcstep_line='STEP="'+str(tract_step)+'"'
chunksdir_line='CHUNKS_DIR="'+chunk_dir+'"'
outdir_line='OUTPUT_DIR="'+output_dir+'/'+subject_ID+'"'
postfix_line='POSTFIX="'+postfix+'"'
script_filename=chunk_dir+"/script_chunk"".sh"
with open(script_filename, 'w+') as script_file:
with open(output_dir+"/track_script_header.sh", "r") as header_file:
script_file.write(header_file.read())
script_file.write(subject_line+"\n")
script_file.write(seedxfile_line+"\n")
script_file.write(hemi_line+"\n")
script_file.write(trackcount_line+"\n")
script_file.write(trackcstep_line+"\n")
script_file.write(chunksdir_line+"\n")
script_file.write(outdir_line+"\n")
script_file.write(postfix_line+"\n")
with open(output_dir+"/track_script_body.sh", "r")as body_file:
script_file.write(body_file.read())
print("tracking script created in: "+ script_filename)
submit_filename = script_dir+subject_ID+"_"+hemi_string+"_tocondor.submit"
with open(submit_filename, "w") as submitter_file:
submitter_file.write('executable = '+script_filename+'\n')
submitter_file.write('getenv = True\nuniverse = vanilla\nrequest_memory = 500\nrequest_disk = 500000\nrequest_cpus = 1\nnotification = Error\n\n')
# submitter_file.write('requirements = Machine == "kalifornien.cbs.mpg.de"\n\n')
for i in xrange(chunk_nr):
submitter_file.write("arguments = "+str(i)+"\n")
submitter_file.write("output = "+chunk_dir+"/logs/op_chunk_"+str(i)+".out\n")
submitter_file.write("error = "+chunk_dir+"/logs/op_chunk_"+str(i)+".error\n")
submitter_file.write("log = "+chunk_dir+"/logs/op_chunk_"+str(i)+".log\n")
submitter_file.write("queue\n\n")
print("condor submitter file created in: "+ submit_filename)
call("chmod a+x "+script_filename, shell=True)
call("mkdir "+chunk_dir+"/logs", shell=True)
print("Submitting "+submit_filename+"...\n")