Module ImportFrom alias ImportFrom alias Import alias identifier ImportFrom alias ImportFrom alias alias alias ImportFrom alias alias alias alias ImportFrom alias ImportFrom alias ImportFrom alias alias alias Import alias Import alias Import alias Import alias Assign NameStore Call AttributeLoad NameLoad attr NameLoad ClassDef bases NameLoad body FunctionDef arguments args NameParam defaults body Expr Call NameLoad AttributeLoad NameLoad attr Expr Call NameLoad AttributeLoad NameLoad attr Expr Call NameLoad AttributeLoad NameLoad attr Expr Call NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Str Return NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Call NameLoad AttributeLoad NameLoad attr If BoolOpAnd CompareNotEq AttributeLoad AttributeLoad NameLoad attr attr Str CompareNotEq AttributeLoad AttributeLoad NameLoad attr attr Str body Expr Call NameLoad Str AttributeLoad AttributeLoad NameLoad attr attr Expr Call AttributeLoad NameLoad attr If UnaryOpNot Call NameLoad AttributeLoad AttributeLoad NameLoad attr attr body Expr Call NameLoad Str AttributeLoad AttributeLoad NameLoad attr attr Expr Call NameLoad Str Expr Call AttributeLoad NameLoad attr If UnaryOpNot Call NameLoad AttributeLoad AttributeLoad NameLoad attr attr body Expr Call NameLoad Str AttributeLoad AttributeLoad NameLoad attr attr Expr Call NameLoad Str Expr Call AttributeLoad NameLoad attr If AttributeLoad AttributeLoad NameLoad attr attr body AugAssignAdd AttributeStore NameLoad attr BinOpAdd Str AttributeLoad AttributeLoad NameLoad attr attr Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Str Expr Str Assign NameStore ListLoad Assign NameStore ListLoad Assign NameStore ListLoad Assign NameStore ListLoad Assign NameStore Num For NameStore Call AttributeLoad NameLoad attr Call NameLoad AttributeLoad AttributeLoad NameLoad attr attr Str body If Call AttributeLoad NameLoad attr NameLoad Str body Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad orelse If Call AttributeLoad NameLoad attr NameLoad Str body Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad orelse Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad If BoolOpOr UnaryOpNot CompareEq Call NameLoad NameLoad Call NameLoad NameLoad UnaryOpNot CompareEq Call NameLoad NameLoad Call NameLoad NameLoad body Expr Call NameLoad Str Expr Call NameLoad Str Expr Call NameLoad Str Expr Call NameLoad BinOpAdd BinOpAdd Str Call NameLoad AttributeLoad AttributeLoad NameLoad attr attr Str Expr Call NameLoad Str Expr Call AttributeLoad NameLoad attr orelse Assign NameStore Call NameLoad NameLoad For NameStore NameLoad body Assign NameStore Call AttributeLoad NameLoad attr Str For NameStore NameLoad body Assign NameStore Call AttributeLoad NameLoad attr Str If Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num body For NameStore NameLoad body Assign NameStore Call AttributeLoad NameLoad attr Str If Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num body Assign NameStore Call NameLoad Call NameLoad NameLoad keyword Call NameLoad NameLoad keyword NameLoad Break Break Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad keyword NameLoad Expr Call AttributeLoad NameLoad attr NameLoad If CompareEq NameLoad Num body Expr Call NameLoad BinOpMod Str AttributeLoad AttributeLoad NameLoad attr attr Expr Call NameLoad Str Expr Call AttributeLoad NameLoad attr Expr Str Assign NameStore Call NameLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr keyword AttributeLoad AttributeLoad NameLoad attr attr Assign NameStore ListLoad Assign NameStore Call NameLoad AttributeLoad NameLoad attr Expr Str If BoolOpOr AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad AttributeLoad NameLoad attr attr body Assign NameStore Call NameLoad NameLoad NameLoad NameLoad AttributeLoad AttributeLoad NameLoad attr attr keyword AttributeLoad AttributeLoad NameLoad attr attr keyword AttributeLoad AttributeLoad NameLoad attr attr Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad If UnaryOpNot AttributeLoad AttributeLoad NameLoad attr attr body Assign NameStore NameLoad If CompareGt NameLoad AttributeLoad AttributeLoad NameLoad attr attr body Assign NameStore AttributeLoad AttributeLoad NameLoad attr attr For NameStore NameLoad body For NameStore Call NameLoad NameLoad body Assign NameStore Call NameLoad NameLoad SubscriptLoad NameLoad Index NameLoad AttributeLoad AttributeLoad NameLoad attr attr keyword Str keyword NameLoad keyword AttributeLoad AttributeLoad NameLoad attr attr keyword AttributeLoad AttributeLoad NameLoad attr attr Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call AttributeLoad NameLoad attr NameLoad If AttributeLoad AttributeLoad NameLoad attr attr body For NameStore NameLoad body Assign NameStore NameLoad For NameStore NameLoad body If CompareLt NameLoad AttributeLoad AttributeLoad NameLoad attr attr body If CompareNotEq Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr body Assign NameStore Call NameLoad NameLoad NameLoad AttributeLoad AttributeLoad NameLoad attr attr keyword Str keyword NameLoad keyword AttributeLoad AttributeLoad NameLoad attr attr keyword AttributeLoad AttributeLoad NameLoad attr attr Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad AugAssignAdd NameStore Num Assign NameStore Call NameLoad NameLoad AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad orelse If CompareGt NameLoad Num body For NameStore NameLoad body Assign NameStore Call NameLoad NameLoad AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call AttributeLoad NameLoad attr BinOpAdd Str Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr BinOpAdd Str Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr BinOpAdd Str Call NameLoad NameLoad decorator_list decorator_list If CompareEq NameLoad Str body Assign NameStore Call NameLoad Expr Call AttributeLoad NameLoad attr
N/A __future__ print_function pydpiper.application AbstractApplication N/A pydpiper.file_handling fh atoms_and_modules.registration_file_handling RegistrationPipeFH atoms_and_modules.registration_functions initializeInputFiles addGenRegArgumentGroup checkInputFiles atoms_and_modules.MAGeT_modules MAGeTMask MAGeTRegister voxelVote addMAGeTArgumentGroup atoms_and_modules.LSQ12 addLSQ12ArgumentGroup atoms_and_modules.NLIN addNlinRegArgumentGroup os.path abspath join exists N/A logging N/A glob N/A fnmatch N/A sys N/A logger N/A N/A logging getLogger __name__ MAGeTApplication N/A AbstractApplication N/A setup_options N/A N/A self N/A N/A N/A N/A addGenRegArgumentGroup N/A self parser N/A N/A addMAGeTArgumentGroup N/A self parser N/A N/A addLSQ12ArgumentGroup N/A self parser N/A N/A addNlinRegArgumentGroup N/A self parser N/A N/A N/A N/A self parser set_defaults reg_method minctracc N/A N/A N/A N/A self parser set_defaults nlin_protocol /projects/mice/share/arch/linux-3_2_0-36-generic-x86_64-eglibc-2_15/src/pydpiper/applications_testing/test_data/default_nlin_MAGeT_minctracc_prot.csv N/A N/A N/A N/A self parser set_defaults lsq12_protocol /projects/mice/share/arch/linux-3_2_0-36-generic-x86_64-eglibc-2_15/src/pydpiper/applications_testing/test_data/default_linear_MAGeT_prot.csv N/A setup_appName N/A N/A self N/A N/A N/A appName MAGeT N/A appName N/A run N/A N/A self N/A N/A N/A N/A checkInputFiles N/A self args N/A N/A N/A N/A N/A self options reg_method minctracc N/A N/A N/A self options reg_method mincANTS N/A N/A N/A print Incorrect registration method specified:  N/A N/A self options reg_method N/A N/A N/A sys exit N/A N/A N/A exists N/A N/A self options lsq12_protocol N/A N/A N/A print The lsq12 protocol does not exists:  N/A N/A self options lsq12_protocol N/A N/A print You can find the default MAGeT protocols in your pydpiper source directory, in: applications_testing/test_data/ N/A N/A N/A sys exit N/A N/A N/A exists N/A N/A self options nlin_protocol N/A N/A N/A print The nlin protocol does not exists:  N/A N/A self options nlin_protocol N/A N/A print You can find the default MAGeT protocols in your pydpiper source directory, in: applications_testing/test_data/ N/A N/A N/A sys exit N/A N/A N/A self options pipeline_name N/A N/A N/A self outputDir N/A / N/A N/A self options pipeline_name N/A N/A N/A fh makedirsIgnoreExisting N/A self outputDir N/A atlasDir N/A N/A fh createSubDir N/A self outputDir input_atlases N/A Read in atlases from directory specified in --atlas-library and 
            create fileHandling classes. Assumes atlas/label/mask groups have one 
            of the following naming schemes:
                name_average.mnc/name_labels.mnc/name_mask.mnc
                name.mnc/name_labels.mnc/name_mask.mnc
            Note that all three files are required even if masking is not used. N/A average N/A N/A labels N/A N/A masks N/A N/A atlases N/A N/A numLibraryAtlases 0 N/A inFile N/A N/A glob glob N/A join N/A N/A self options atlas_lib *.mnc N/A N/A N/A N/A fnmatch fnmatch inFile *labels.mnc N/A N/A N/A N/A labels append N/A abspath inFile N/A N/A N/A N/A fnmatch fnmatch inFile *mask.mnc N/A N/A N/A N/A masks append N/A abspath inFile N/A N/A N/A N/A average append N/A abspath inFile N/A N/A N/A N/A N/A len average N/A len labels N/A N/A N/A len average N/A len masks N/A N/A N/A print 
Error: not all atlases/labels/masks match. N/A N/A print The allowed naming conventions are:
{atlas}.mnc
{atlas}_labels.mnc
{atlas}_mask.mnc N/A N/A print 
and:
{atlas}_average.mnc
{atlas}_labels.mnc
{atlas}_mask.mnc
 N/A N/A print N/A N/A Check the atlas library directory:  N/A str N/A N/A self options atlas_lib  and try again. N/A N/A print Exiting... N/A N/A N/A sys exit N/A N/A numLibraryAtlases N/A len labels N/A iLabel labels N/A N/A atlasStart N/A N/A iLabel split _labels.mnc N/A iAvg average N/A N/A avgStart N/A N/A iAvg split _average.mnc N/A N/A N/A fnmatch fnmatch N/A atlasStart N/A 0 N/A avgStart N/A 0 N/A N/A iMask masks N/A N/A maskStart N/A N/A iMask split _mask.mnc N/A N/A N/A fnmatch fnmatch N/A atlasStart N/A 0 N/A maskStart N/A 0 N/A N/A atlasPipeFH N/A RegistrationPipeFH N/A abspath iAvg mask N/A abspath iMask basedir atlasDir N/A N/A N/A N/A N/A atlasPipeFH addLabels N/A abspath iLabel inputLabel True N/A N/A N/A atlases append atlasPipeFH N/A N/A numLibraryAtlases 0 N/A N/A N/A print N/A 
Error: no atlases were found in the specified directory: %s N/A N/A self options atlas_lib N/A N/A print Exiting... N/A N/A N/A sys exit N/A  Create fileHandling classes for images. If a directory of masks is specified, 
            they will be assigned to the appropriate input file handlers. N/A inputs N/A initializeInputFiles N/A self args N/A self outputDir maskDir N/A N/A self options mask_dir N/A templates N/A N/A numTemplates N/A len N/A self args N/A  If --mask is specified and we are masking brains, do it here. N/A N/A N/A N/A self options mask N/A N/A self options mask_only N/A N/A mp N/A MAGeTMask atlases inputs numLibraryAtlases N/A N/A self options mask_method lsq12_protocol N/A N/A self options lsq12_protocol nlin_protocol N/A N/A self options nlin_protocol N/A N/A N/A N/A self pipeline addPipeline mp N/A N/A N/A N/A self options mask_only N/A N/A numLibraryAtlasesUsed numLibraryAtlases N/A N/A numLibraryAtlases N/A N/A self options max_templates N/A N/A numLibraryAtlasesUsed N/A N/A self options max_templates N/A inputFH inputs N/A N/A afile N/A range numLibraryAtlasesUsed N/A N/A sp N/A MAGeTRegister inputFH N/A atlases N/A afile N/A N/A self options reg_method name initial createMask False lsq12_protocol N/A N/A self options lsq12_protocol nlin_protocol N/A N/A self options nlin_protocol N/A N/A N/A N/A self pipeline addPipeline sp N/A N/A N/A templates append inputFH N/A N/A N/A self options pairwise N/A N/A inputFH inputs N/A N/A num_currently_aligned_atlases numLibraryAtlasesUsed N/A tmplFH templates N/A N/A N/A num_currently_aligned_atlases N/A N/A self options max_templates N/A N/A N/A N/A N/A tmplFH getLastBasevol N/A N/A inputFH getLastBasevol N/A N/A sp N/A MAGeTRegister inputFH tmplFH N/A N/A self options reg_method name templates createMask False lsq12_protocol N/A N/A self options lsq12_protocol nlin_protocol N/A N/A self options nlin_protocol N/A N/A N/A N/A self pipeline addPipeline sp N/A num_currently_aligned_atlases 1 N/A voxel N/A voxelVote inputFH N/A N/A self options pairwise False N/A N/A N/A N/A self pipeline addStage voxel N/A N/A N/A numLibraryAtlases 1 N/A N/A inputFH inputs N/A N/A voxel N/A voxelVote inputFH N/A N/A self options pairwise False N/A N/A N/A N/A self pipeline addStage voxel N/A N/A N/A logger info N/A Number of input atlas/label pairs:  N/A str numLibraryAtlases N/A N/A N/A logger info N/A Number of templates created (all input files...):  N/A str numTemplates N/A N/A N/A logger info N/A Number of templates used for each inputfile:  N/A str numLibraryAtlasesUsed N/A N/A N/A N/A __name__ __main__ N/A N/A application N/A MAGeTApplication N/A N/A N/A application start