iplConcat.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-

#
# @author Daniel
# @date 10/07/2011

version = '1.0'

#
# Atlas registration
#

from iplGeneral import *
from ipl.minc_tools import mincTools,mincError


# Run preprocessing using patient info
# - Function to read info from the pipeline patient
# - pipeline_version is employed to select the correct version of the pipeline

def pipeline_concat(patient, tp):

    if os.path.exists(patient[tp].nl_xfm):
        print ' -- pipeline_concat already done!'
        
###
        with mincTools()  as minc:
            # create QC images
            atlas_outline = patient.modeldir + os.sep + patient.modelname + '_outline.mnc'
            
            if not os.path.exists(patient[tp].qc_jpg['nl_t1']):
                minc.resample_smooth(patient[tp].stx2_mnc['t1'],minc.tmp('nl_stx_t1.mnc'),transform=patient[tp].nl_xfm)
                minc.qc(
                    minc.tmp('nl_stx_t1.mnc'),
                    patient[tp].qc_jpg['nl_t1'],
                    title=patient[tp].qc_title,
                    image_range=[0, 120],
                    mask=atlas_outline,
                    big=True,
                    clamp=True,
                )

###
        return True
    
    concat_v10(patient, tp)  # beast by simon fristed


def concat_v10(patient, tp):
    
    with mincTools()  as minc:
        tmp_xfm = minc.tmp('tmp_concat.xfm')
        minc.xfmconcat([patient[tp].lng_xfm['t1'], patient.nl_xfm] , tmp_xfm)
        examplegrid = patient.nl_xfm[:-4] + '_grid_0.mnc'
        minc.xfm_normalize(tmp_xfm, examplegrid, patient[tp].nl_xfm, exact=True)
        
        
        # create QC images
        atlas_outline = patient.modeldir + os.sep + patient.modelname + '_outline.mnc'
        minc.resample_smooth(patient[tp].stx_mnc['t1'],minc.tmp('nl_stx_t1.mnc'),transform=patient[tp].nl_xfm)
        
        minc.qc(
            minc.tmp('nl_stx_t1.mnc'),
            patient[tp].qc_jpg['nl_t1'],
            title=patient[tp].qc_title,
            image_range=[0, 120],
            mask=atlas_outline,
            big=True,
            clamp=True,
            )
        
        
        


if __name__ == '__main__':
    # Concat not very useful in stand-alone i guess
    pass

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