<s> from __future__ import print_function <EOL> from pydpiper . application import AbstractApplication <EOL> import atoms_and_modules . registration_functions as rf <EOL> import atoms_and_modules . registration_file_handling as rfh <EOL> import atoms_and_modules . minc_modules as mm <EOL> import atoms_and_modules . minc_atoms as ma <EOL> import atoms_and_modules . LSQ6 as lsq6 <EOL> import atoms_and_modules . LSQ12 as lsq12 <EOL> import atoms_and_modules . NLIN as nlin <EOL> import atoms_and_modules . stats_tools as st <EOL> from os . path import abspath , isdir , isfile <EOL> import logging <EOL> import sys <EOL> from datetime import date <EOL> import csv <EOL> logger = logging . getLogger ( __name__ ) <EOL> def addRegChainArgumentGroup ( parser ) : <EOL> """<STR_LIT>""" <EOL> group = parser . add_argument_group ( "<STR_LIT>" , <EOL> "<STR_LIT>" ) <EOL> group . add_argument ( "<STR_LIT>" , dest = "<STR_LIT>" , <EOL> type = int , default = <NUM_LIT:1> , <EOL> help = "<STR_LIT>" <EOL> "<STR_LIT>" <EOL> "<STR_LIT>" ) <EOL> group . add_argument ( "<STR_LIT>" , dest = "<STR_LIT>" , <EOL> type = str , default = "<STR_LIT>" , <EOL> help = "<STR_LIT>" <EOL> "<STR_LIT>" <EOL> "<STR_LIT>" <EOL> "<STR_LIT>" ) <EOL> group . add_argument ( "<STR_LIT>" , dest = "<STR_LIT>" , <EOL> action = "<STR_LIT:store_true>" , <EOL> help = "<STR_LIT>" <EOL> "<STR_LIT>" ) <EOL> group . add_argument ( "<STR_LIT>" , dest = "<STR_LIT>" , <EOL> action = "<STR_LIT>" , <EOL> help = "<STR_LIT>" <EOL> "<STR_LIT>" <EOL> "<STR_LIT>" <EOL> "<STR_LIT>" <EOL> "<STR_LIT>" ) <EOL> group . add_argument ( "<STR_LIT>" , dest = "<STR_LIT>" , <EOL> type = str , default = None , <EOL> help = "<STR_LIT>" ) <EOL> group . add_argument ( "<STR_LIT>" , dest = "<STR_LIT>" , <EOL> type = str , default = None , <EOL> help = "<STR_LIT>" ) <EOL> parser . set_defaults ( run_groupwise = True ) <EOL> class RegistrationChain ( AbstractApplication ) : <EOL> def setup_options ( self ) : <EOL> """<STR_LIT>""" <EOL> addRegChainArgumentGroup ( self . parser ) <EOL> rf . addGenRegArgumentGroup ( self . parser ) <EOL> lsq6 . addLSQ6ArgumentGroup ( self . parser ) <EOL> lsq12 . addLSQ12ArgumentGroup ( self . parser ) <EOL> nlin . addNlinRegArgumentGroup ( self . parser ) <EOL> st . addStatsArguments ( self . parser ) <EOL> def setup_appName ( self ) : <EOL> appName = "<STR_LIT>" <EOL> return appName <EOL> def run ( self ) : <EOL> all_input_files = [ ] <EOL> fileList = open ( self . args [ <NUM_LIT:0> ] , '<STR_LIT:rb>' ) <EOL> subjectList = csv . reader ( fileList , delimiter = '<STR_LIT:U+002C>' , skipinitialspace = True ) <EOL> for subjLine in subjectList : <EOL> for subj in subjLine : <EOL> if subj != "<STR_LIT>" : <EOL> all_input_files . append ( subj ) <EOL> rf . checkInputFiles ( all_input_files ) <EOL> if not self . options . pipeline_name : <EOL> self . options . pipeline_name = str ( date . today ( ) ) + "<STR_LIT>" <EOL> dirs = rf . setupDirectories ( self . outputDir , self . options . pipeline_name , module = "<STR_LIT>" ) <EOL> if self . options . reg_method != "<STR_LIT>" and self . options . reg_method != "<STR_LIT>" : <EOL> logger . error ( "<STR_LIT>" + self . options . reg_method ) <EOL> sys . exit ( ) <EOL> if self . options . avg_time_point == - <NUM_LIT:1> : <EOL> avgTime = - <NUM_LIT:1> <EOL> else : <EOL> avgTime = self . options . avg_time_point - <NUM_LIT:1> <EOL> if avgTime == - <NUM_LIT:1> and self . options . run_groupwise : <EOL> print ( "<STR_LIT>" ) <EOL> subjects = rf . setupSubjectHash ( self . args [ <NUM_LIT:0> ] , dirs , self . options . mask_dir ) <EOL> resolutionForGroupWiseRegistration = None <EOL> if self . options . input_space == "<STR_LIT>" : <EOL> initModel , targetPipeFH = rf . setInitialTarget ( self . options . init_model , <EOL> self . options . lsq6_target , <EOL> dirs . lsq6Dir , <EOL> self . outputDir , <EOL> self . options . pipeline_name ) <EOL> inputFiles = [ ] <EOL> for subj in subjects : <EOL> for i in range ( len ( subjects [ subj ] ) ) : <EOL> inputFiles . append ( subjects [ subj ] [ i ] ) <EOL> montageBeforeRegistration = self . outputDir + "<STR_LIT:/>" + self . options . pipeline_name + "<STR_LIT>" <EOL> initialVerificationImages = mm . createQualityControlImages ( [ targetPipeFH ] + inputFiles , <EOL> montageOutPut = montageBeforeRegistration , <EOL> message = "<STR_LIT>" ) <EOL> self . pipeline . addPipeline ( initialVerificationImages . p ) <EOL> runLSQ6NucInorm = lsq6 . LSQ6NUCInorm ( inputFiles , <EOL> targetPipeFH , <EOL> initModel , <EOL> dirs . lsq6Dir , <EOL> self . options ) <EOL> for lsq6Stage in runLSQ6NucInorm . p . stages : <EOL> lsq6Stage . inputFiles . append ( montageBeforeRegistration ) <EOL> self . pipeline . addPipeline ( runLSQ6NucInorm . p ) <EOL> elif self . options . input_space == "<STR_LIT>" : <EOL> initModel = None <EOL> resolutionForGroupWiseRegistration = rf . getFinestResolution ( subjects [ <NUM_LIT:0> ] [ <NUM_LIT:0> ] ) <EOL> for subj in subjects : <EOL> for i in range ( len ( subjects [ subj ] ) ) : <EOL> if rf . getFinestResolution ( subjects [ subj ] [ i ] ) < resolutionForGroupWiseRegistration : <EOL> resolutionForGroupWiseRegistration = rf . getFinestResolution ( subjects [ subj ] [ i ] ) <EOL> else : <EOL> print ( """<STR_LIT>""" + str ( self . options . input_space ) ) <EOL> print ( "<STR_LIT>" ) <EOL> sys . exit ( ) <EOL> for subjKey in subjects : <EOL> s = subjects [ subjKey ] <EOL> count = len ( s ) <EOL> for i in range ( count ) : <EOL> s [ i ] . newGroup ( groupName = "<STR_LIT>" ) <EOL> for subjKey in subjects : <EOL> s = subjects [ subjKey ] <EOL> count = len ( s ) <EOL> for i in range ( count - <NUM_LIT:1> ) : <EOL> if self . options . reg_method == "<STR_LIT>" : <EOL> register = mm . LSQ12ANTSNlin ( s [ i ] , <EOL> s [ i + <NUM_LIT:1> ] , <EOL> lsq12_protocol = self . options . lsq12_protocol , <EOL> nlin_protocol = self . options . nlin_protocol ) <EOL> self . pipeline . addPipeline ( register . p ) <EOL> elif self . options . reg_method == "<STR_LIT>" : <EOL> hm = mm . HierarchicalMinctracc ( s [ i ] , <EOL> s [ i + <NUM_LIT:1> ] , <EOL> lsq12_protocol = self . options . lsq12_protocol , <EOL> nlin_protocol = self . options . nlin_protocol ) <EOL> self . pipeline . addPipeline ( hm . p ) <EOL> resample = ma . mincresample ( s [ i ] , s [ i + <NUM_LIT:1> ] , likeFile = s [ i + <NUM_LIT:1> ] , argArray = [ "<STR_LIT>" ] ) <EOL> self . pipeline . addStage ( resample ) <EOL> """<STR_LIT>""" <EOL> lastXfm = s [ i ] . getLastXfm ( s [ i + <NUM_LIT:1> ] ) <EOL> inverseXfm = s [ i + <NUM_LIT:1> ] . getLastXfm ( s [ i ] ) <EOL> if not inverseXfm : <EOL> "<STR_LIT>" <EOL> xi = ma . xfmInvert ( lastXfm , FH = s [ i ] ) <EOL> self . pipeline . addStage ( xi ) <EOL> s [ i + <NUM_LIT:1> ] . addAndSetXfmToUse ( s [ i ] , xi . outputFiles [ <NUM_LIT:0> ] ) <EOL> if self . options . run_groupwise : <EOL> inputs = [ ] <EOL> for s in subjects : <EOL> if avgTime >= <NUM_LIT:0> : <EOL> inputs . append ( subjects [ s ] [ avgTime ] ) <EOL> else : <EOL> lastTimePoint = len ( subjects [ s ] ) - <NUM_LIT:1> <EOL> inputs . append ( subjects [ s ] [ lastTimePoint ] ) <EOL> lsq12Nlin = mm . FullIterativeLSQ12Nlin ( inputs , <EOL> dirs , <EOL> self . options , <EOL> avgPrefix = self . options . common_name , <EOL> initModel = initModel , <EOL> fileResolution = resolutionForGroupWiseRegistration ) <EOL> self . pipeline . addPipeline ( lsq12Nlin . p ) <EOL> nlinFH = lsq12Nlin . nlinFH <EOL> else : <EOL> if self . options . mbm_dir and self . options . nlin_avg : <EOL> if ( not isdir ( self . options . mbm_dir ) ) or ( not isfile ( self . options . nlin_avg ) ) : <EOL> logger . error ( "<STR_LIT>" ) <EOL> logger . error ( "<STR_LIT>" + abspath ( self . options . mbm_dir ) ) <EOL> logger . error ( "<STR_LIT>" + abspath ( self . options . nlin_avg ) ) <EOL> sys . exit ( ) <EOL> nlinFH = rfh . RegistrationPipeFH ( abspath ( self . options . nlin_avg ) , basedir = dirs . processedDir ) <EOL> rf . getXfms ( nlinFH , subjects , "<STR_LIT>" , abspath ( self . options . mbm_dir ) , time = avgTime ) <EOL> else : <EOL> logger . info ( "<STR_LIT>" ) <EOL> logger . info ( "<STR_LIT>" ) <EOL> nlinFH = None <EOL> """<STR_LIT>""" <EOL> car = mm . LongitudinalStatsConcatAndResample ( subjects , <EOL> avgTime , <EOL> nlinFH , <EOL> self . options . stats_kernels , <EOL> self . options . common_name ) <EOL> self . pipeline . addPipeline ( car . p ) <EOL> if __name__ == "<STR_LIT:__main__>" : <EOL> application = RegistrationChain ( ) <EOL> application . start ( ) </s>
