def mbm(imgs: List[MincAtom], options: MBMConf, prefix: str, output_dir: str = "", with_maget: bool = True): # TODO could also allow pluggable pipeline parts e.g. LSQ6 could be substituted out for the modified LSQ6 # for the kidney tips, etc... # TODO this is tedious and annoyingly similar to the registration chain ... lsq6_dir = os.path.join(output_dir, prefix + "_lsq6") lsq12_dir = os.path.join(output_dir, prefix + "_lsq12") nlin_dir = os.path.join(output_dir, prefix + "_nlin") s = Stages() if len(imgs) == 0: raise ValueError("Please, some files!") # FIXME: why do we have to call registration_targets *outside* of lsq6_nuc_inorm? is it just because of the extra # options required? Also, shouldn't options.registration be a required input (as it contains `input_space`) ...? targets = s.defer( registration_targets(lsq6_conf=options.mbm.lsq6, app_conf=options.application, reg_conf=options.registration, first_input_file=imgs[0].path)) # TODO this is quite tedious and duplicates stuff in the registration chain ... resolution = (options.registration.resolution or get_resolution_from_file( targets.registration_standard.path)) options.registration = options.registration.replace(resolution=resolution) # FIXME: this needs to go outside of the `mbm` function to avoid being run from within other pipelines (or # those other pipelines need to turn off this option) if with_maget: if options.mbm.segmentation.run_maget or options.mbm.maget.maget.mask: # temporary fix...? if options.mbm.maget.maget.mask and not options.mbm.segmentation.run_maget: # which means that --no-run-maget was specified if options.mbm.maget.maget.atlas_lib == None: # clearly you do not want to run MAGeT at any point in this pipeline err_msg_maget = "\nYou specified not to run MAGeT using the " \ "--no-run-maget flag. However, the code also " \ "wants to use MAGeT to generate masks for your " \ "input files after the 6 parameter alignment (lsq6). " \ "Because you did not specify a MAGeT atlas library " \ "this can not be done. \nTo run the pipeline without " \ "using MAGeT to mask your input files, please also " \ "specify: \n--maget-no-mask\n" raise ValueError(err_msg_maget) import copy maget_options = copy.deepcopy(options) #Namespace(maget=options) #maget_options #maget_options.maget = maget_options.mbm #maget_options.execution = options.execution #maget_options.application = options.application #maget_options.application.output_directory = os.path.join(options.application.output_directory, "segmentation") maget_options.maget = options.mbm.maget fixup_maget_options(maget_options=maget_options.maget, nlin_options=maget_options.mbm.nlin, lsq12_options=maget_options.mbm.lsq12) del maget_options.mbm #def with_new_output_dir(img : MincAtom): #img = copy.copy(img) #img.pipeline_sub_dir = img.pipeline_sub_dir + img.output_dir #img. #return img.newname_with_suffix(suffix="", subdir="segmentation") # FIXME it probably makes most sense if the lsq6 module itself (even within lsq6_nuc_inorm) handles the run_lsq6 # setting (via use of the identity transform) since then this doesn't have to be implemented for every pipeline if options.mbm.lsq6.run_lsq6: lsq6_result = s.defer( lsq6_nuc_inorm(imgs=imgs, resolution=resolution, registration_targets=targets, lsq6_dir=lsq6_dir, lsq6_options=options.mbm.lsq6)) else: # FIXME the code shouldn't branch here based on run_lsq6 (which should probably # be part of the lsq6 options rather than the MBM ones; see comments on #287. # TODO don't actually do this resampling if not required (i.e., if the imgs already have the same grids)?? # however, for now need to add the masks: identity_xfm = s.defer( param2xfm( out_xfm=FileAtom(name=os.path.join(lsq6_dir, 'tmp', "id.xfm"), pipeline_sub_dir=lsq6_dir, output_sub_dir='tmp'))) lsq6_result = [ XfmHandler(source=img, target=img, xfm=identity_xfm, resampled=s.defer( mincresample_new(img=img, like=targets.registration_standard, xfm=identity_xfm))) for img in imgs ] # what about running nuc/inorm without a linear registration step?? if with_maget and options.mbm.maget.maget.mask: masking_imgs = copy.deepcopy([xfm.resampled for xfm in lsq6_result]) masked_img = (s.defer( maget_mask(imgs=masking_imgs, resolution=resolution, maget_options=maget_options.maget, pipeline_sub_dir=os.path.join( options.application.output_directory, "%s_atlases" % prefix)))) masked_img.index = masked_img.apply(lambda x: x.path) # replace any masks of the resampled images with the newly created masks: for xfm in lsq6_result: xfm.resampled = masked_img.loc[xfm.resampled.path] elif with_maget: warnings.warn( "Not masking your images from atlas masks after LSQ6 alignment ... probably not what you want " "(this can have negative effects on your registration and statistics)" ) #full_hierarchy = get_nonlinear_configuration_from_options(nlin_protocol=options.mbm.nlin.nlin_protocol, # flag_nlin_protocol=next(iter(options.mbm.nlin.flags_.nlin_protocol)), # reg_method=options.mbm.nlin.reg_method, # file_resolution=resolution) #I = TypeVar("I") #X = TypeVar("X") #def wrap_minc(nlin_module: NLIN[I, X]) -> type[NLIN[MincAtom, XfmAtom]]: # class N(NLIN[MincAtom, XfmAtom]): pass # TODO now the user has to call get_nonlinear_component followed by parse_<...>; previously various things # like lsq12_nlin_pairwise all branched on the reg_method so one didn't have to call get_nonlinear_component; # they could still do this if it can be done safety (i.e., not breaking assumptions of various nonlinear units) nlin_module = get_nonlinear_component( reg_method=options.mbm.nlin.reg_method) nlin_build_model_component = get_model_building_procedure( options.mbm.nlin.reg_strategy, # was: model_building.reg_strategy reg_module=nlin_module) # does this belong here? # def model_building_with_initial_target_generation(prelim_model_building_component, # final_model_building_component): # class C(final_model_building_component): # @staticmethod # def build_model(imgs, # conf : BuildModelConf, # nlin_dir, # nlin_prefix, # initial_target, # output_name_wo_ext = None): pass # # return C #if options.mbm.model_building.prelim_reg_strategy is not None: # prelim_nlin_build_model_component = get_model_building_procedure(options.mbm.model_building.prelim_reg_strategy, # reg_module=nlin_module) # nlin_build_model_component = model_building_with_initial_target_generation( # final_model_building_component=nlin_build_model_component, # prelim_model_building_component=prelim_nlin_build_model_component) # TODO don't use name 'x_module' for something that's technically not a module ... perhaps unit/component? # TODO tedious: why can't parse_build_model_protocol handle the null protocol case? is this something we want? nlin_conf = (nlin_build_model_component.parse_build_model_protocol( options.mbm.nlin.nlin_protocol, resolution=resolution) if options.mbm.nlin.nlin_protocol is not None else nlin_build_model_component.get_default_build_model_conf( resolution=resolution)) lsq12_nlin_result = s.defer( lsq12_nlin_build_model( nlin_module=nlin_build_model_component, imgs=[xfm.resampled for xfm in lsq6_result], lsq12_dir=lsq12_dir, nlin_dir=nlin_dir, nlin_prefix=prefix, use_robust_averaging=options.mbm.nlin.use_robust_averaging, resolution=resolution, lsq12_conf=options.mbm.lsq12, nlin_conf=nlin_conf)) #options.mbm.nlin inverted_xfms = [ s.defer(invert_xfmhandler(xfm)) for xfm in lsq12_nlin_result.output ] if options.mbm.stats.stats_kernels: determinants = s.defer( determinants_at_fwhms(xfms=inverted_xfms, inv_xfms=lsq12_nlin_result.output, blur_fwhms=options.mbm.stats.stats_kernels)) else: determinants = None overall_xfms = [ s.defer(concat_xfmhandlers([rigid_xfm, lsq12_nlin_xfm])) for rigid_xfm, lsq12_nlin_xfm in zip(lsq6_result, lsq12_nlin_result.output) ] output_xfms = ( pd.DataFrame({ "rigid_xfm": lsq6_result, # maybe don't return this if LSQ6 not run?? "lsq12_nlin_xfm": lsq12_nlin_result.output, "overall_xfm": overall_xfms })) # we could `merge` the determinants with this table, but preserving information would cause lots of duplication # of the transforms (or storing determinants in more columns, but iterating over dynamically known columns # seems a bit odd ...) # TODO transpose these fields?}) #avg_img=lsq12_nlin_result.avg_img, # inconsistent w/ WithAvgImgs[...]-style outputs # "determinants" : determinants }) #output.avg_img = lsq12_nlin_result.avg_img #output.determinants = determinants # TODO temporary - remove once incorporated properly into `output` proper # TODO add more of lsq12_nlin_result? # FIXME moved above rest of registration for debugging ... shouldn't use and destructively modify lsq6_result!!! if with_maget and options.mbm.segmentation.run_maget: maget_options = copy.deepcopy(maget_options) maget_options.maget.maget.mask = maget_options.maget.maget.mask_only = False # already done above # use the original masks here otherwise the masking step will be re-run due to the previous masking run's # masks having been applied to the input images: maget_result = s.defer( maget( [xfm.resampled for xfm in lsq6_result], #[xfm.resampled for _ix, xfm in mbm_result.xfms.rigid_xfm.iteritems()], options=maget_options, prefix="%s_MAGeT" % prefix, output_dir=os.path.join(output_dir, prefix + "_processed"))) # FIXME add pipeline dir to path and uncomment! #maget.to_csv(path_or_buf="segmentations.csv", columns=['img', 'voted_labels']) # TODO return some MAGeT stuff from MBM function ?? # if options.mbm.mbm.run_maget: # import copy # maget_options = copy.deepcopy(options) #Namespace(maget=options) # #maget_options # #maget_options.maget = maget_options.mbm # #maget_options.execution = options.execution # #maget_options.application = options.application # maget_options.maget = options.mbm.maget # del maget_options.mbm # # s.defer(maget([xfm.resampled for xfm in lsq6_result], # options=maget_options, # prefix="%s_MAGeT" % prefix, # output_dir=os.path.join(output_dir, prefix + "_processed"))) # should also move outside `mbm` function ... #if options.mbm.thickness.run_thickness: # if not options.mbm.segmentation.run_maget: # warnings.warn("MAGeT files (atlases, protocols) are needed to run thickness calculation.") # # run MAGeT to segment the nlin average: # import copy # maget_options = copy.deepcopy(options) #Namespace(maget=options) # maget_options.maget = options.mbm.maget # del maget_options.mbm # segmented_avg = s.defer(maget(imgs=[lsq12_nlin_result.avg_img], # options=maget_options, # output_dir=os.path.join(options.application.output_directory, # prefix + "_processed"), # prefix="%s_thickness_MAGeT" % prefix)).ix[0].img # thickness = s.defer(cortical_thickness(xfms=pd.Series(inverted_xfms), atlas=segmented_avg, # label_mapping=FileAtom(options.mbm.thickness.label_mapping), # atlas_fwhm=0.56, thickness_fwhm=0.56)) # TODO magic fwhms # # TODO write CSV -- should `cortical_thickness` do this/return a table? output = Namespace(avg_img=lsq12_nlin_result.avg_img, xfms=output_xfms, determinants=determinants) if with_maget and options.mbm.segmentation.run_maget: output.maget_result = maget_result nlin_maget = ( s.defer( maget( [lsq12_nlin_result.avg_img], #[xfm.resampled for _ix, xfm in mbm_result.xfms.rigid_xfm.iteritems()], options=maget_options, prefix="%s_nlin_MAGeT" % prefix, output_dir=os.path.join( output_dir, prefix + "_processed")))).iloc[0] #.voted_labels #output.avg_img.mask = nlin_maget.mask # makes more sense, but might have weird effects elsewhere output.avg_img.labels = nlin_maget.labels return Result(stages=s, output=output)
def mbm(imgs : List[MincAtom], options : MBMConf, prefix : str, output_dir : str = ""): # TODO could also allow pluggable pipeline parts e.g. LSQ6 could be substituted out for the modified LSQ6 # for the kidney tips, etc... # TODO this is tedious and annoyingly similar to the registration chain ... lsq6_dir = os.path.join(output_dir, prefix + "_lsq6") lsq12_dir = os.path.join(output_dir, prefix + "_lsq12") nlin_dir = os.path.join(output_dir, prefix + "_nlin") s = Stages() if len(imgs) == 0: raise ValueError("Please, some files!") # FIXME: why do we have to call registration_targets *outside* of lsq6_nuc_inorm? is it just because of the extra # options required? Also, shouldn't options.registration be a required input (as it contains `input_space`) ...? targets = registration_targets(lsq6_conf=options.mbm.lsq6, app_conf=options.application, first_input_file=imgs[0].path) # TODO this is quite tedious and duplicates stuff in the registration chain ... resolution = (options.registration.resolution or get_resolution_from_file(targets.registration_standard.path)) options.registration = options.registration.replace(resolution=resolution) # FIXME it probably makes most sense if the lsq6 module itself (even within lsq6_nuc_inorm) handles the run_lsq6 # setting (via use of the identity transform) since then this doesn't have to be implemented for every pipeline if options.mbm.lsq6.run_lsq6: lsq6_result = s.defer(lsq6_nuc_inorm(imgs=imgs, resolution=resolution, registration_targets=targets, lsq6_dir=lsq6_dir, lsq6_options=options.mbm.lsq6)) else: # TODO don't actually do this resampling if not required (i.e., if the imgs already have the same grids) identity_xfm = s.defer(param2xfm(out_xfm=FileAtom(name="identity.xfm"))) lsq6_result = [XfmHandler(source=img, target=img, xfm=identity_xfm, resampled=s.defer(mincresample_new(img=img, like=targets.registration_standard, xfm=identity_xfm))) for img in imgs] # what about running nuc/inorm without a linear registration step?? full_hierarchy = get_nonlinear_configuration_from_options(nlin_protocol=options.mbm.nlin.nlin_protocol, reg_method=options.mbm.nlin.reg_method, file_resolution=resolution) lsq12_nlin_result = s.defer(lsq12_nlin_build_model(imgs=[xfm.resampled for xfm in lsq6_result], resolution=resolution, lsq12_dir=lsq12_dir, nlin_dir=nlin_dir, nlin_prefix=prefix, lsq12_conf=options.mbm.lsq12, nlin_conf=full_hierarchy)) inverted_xfms = [s.defer(invert_xfmhandler(xfm)) for xfm in lsq12_nlin_result.output] determinants = s.defer(determinants_at_fwhms( xfms=inverted_xfms, inv_xfms=lsq12_nlin_result.output, blur_fwhms=options.mbm.stats.stats_kernels)) overall_xfms = [s.defer(concat_xfmhandlers([rigid_xfm, lsq12_nlin_xfm])) for rigid_xfm, lsq12_nlin_xfm in zip(lsq6_result, lsq12_nlin_result.output)] output_xfms = (pd.DataFrame({ "rigid_xfm" : lsq6_result, # maybe don't return this if LSQ6 not run?? "lsq12_nlin_xfm" : lsq12_nlin_result.output, "overall_xfm" : overall_xfms })) # we could `merge` the determinants with this table, but preserving information would cause lots of duplication # of the transforms (or storing determinants in more columns, but iterating over dynamically known columns # seems a bit odd ...) # TODO transpose these fields?}) #avg_img=lsq12_nlin_result.avg_img, # inconsistent w/ WithAvgImgs[...]-style outputs # "determinants" : determinants }) #output.avg_img = lsq12_nlin_result.avg_img #output.determinants = determinants # TODO temporary - remove once incorporated properly into `output` proper # TODO add more of lsq12_nlin_result? # FIXME: this needs to go outside of the `mbm` function to avoid being run from within other pipelines (or # those other pipelines need to turn off this option) # TODO return some MAGeT stuff from MBM function ?? # if options.mbm.mbm.run_maget: # import copy # maget_options = copy.deepcopy(options) #Namespace(maget=options) # #maget_options # #maget_options.maget = maget_options.mbm # #maget_options.execution = options.execution # #maget_options.application = options.application # maget_options.maget = options.mbm.maget # del maget_options.mbm # # s.defer(maget([xfm.resampled for xfm in lsq6_result], # options=maget_options, # prefix="%s_MAGeT" % prefix, # output_dir=os.path.join(output_dir, prefix + "_processed"))) # should also move outside `mbm` function ... #if options.mbm.thickness.run_thickness: # if not options.mbm.segmentation.run_maget: # warnings.warn("MAGeT files (atlases, protocols) are needed to run thickness calculation.") # # run MAGeT to segment the nlin average: # import copy # maget_options = copy.deepcopy(options) #Namespace(maget=options) # maget_options.maget = options.mbm.maget # del maget_options.mbm # segmented_avg = s.defer(maget(imgs=[lsq12_nlin_result.avg_img], # options=maget_options, # output_dir=os.path.join(options.application.output_directory, # prefix + "_processed"), # prefix="%s_thickness_MAGeT" % prefix)).ix[0].img # thickness = s.defer(cortical_thickness(xfms=pd.Series(inverted_xfms), atlas=segmented_avg, # label_mapping=FileAtom(options.mbm.thickness.label_mapping), # atlas_fwhm=0.56, thickness_fwhm=0.56)) # TODO magic fwhms # # TODO write CSV -- should `cortical_thickness` do this/return a table? # FIXME: this needs to go outside of the `mbm` function to avoid being run from within other pipelines (or # those other pipelines need to turn off this option) if options.mbm.common_space.do_common_space_registration: warnings.warn("This feature is experimental ...") if not options.mbm.common_space.common_space_model: raise ValueError("No common space template provided!") # TODO allow lsq6 registration as well ... common_space_model = MincAtom(options.mbm.common_space.common_space_model, pipeline_sub_dir=os.path.join(options.application.output_directory, options.application.pipeline_name + "_processed")) # TODO allow different lsq12/nlin config params than the ones used in MBM ... # WEIRD ... see comment in lsq12_nlin code ... nlin_conf = full_hierarchy.confs[-1] if isinstance(full_hierarchy, MultilevelMincANTSConf) else full_hierarchy # also weird that we need to call get_linear_configuration_from_options here ... ? lsq12_conf = get_linear_configuration_from_options(conf=options.mbm.lsq12, transform_type=LinearTransType.lsq12, file_resolution=resolution) xfm_to_common = s.defer(lsq12_nlin(source=lsq12_nlin_result.avg_img, target=common_space_model, lsq12_conf=lsq12_conf, nlin_conf=nlin_conf, resample_source=True)) model_common = s.defer(mincresample_new(img=lsq12_nlin_result.avg_img, xfm=xfm_to_common.xfm, like=common_space_model, postfix="_common")) overall_xfms_common = [s.defer(concat_xfmhandlers([rigid_xfm, nlin_xfm, xfm_to_common])) for rigid_xfm, nlin_xfm in zip(lsq6_result, lsq12_nlin_result.output)] xfms_common = [s.defer(concat_xfmhandlers([nlin_xfm, xfm_to_common])) for nlin_xfm in lsq12_nlin_result.output] output_xfms = output_xfms.assign(xfm_common=xfms_common, overall_xfm_common=overall_xfms_common) log_nlin_det_common, log_full_det_common = [dets.map(lambda d: s.defer(mincresample_new( img=d, xfm=xfm_to_common.xfm, like=common_space_model, postfix="_common", extra_flags=("-keep_real_range",), interpolation=Interpolation.nearest_neighbour))) for dets in (determinants.log_nlin_det, determinants.log_full_det)] determinants = determinants.assign(log_nlin_det_common=log_nlin_det_common, log_full_det_common=log_full_det_common) output = Namespace(avg_img=lsq12_nlin_result.avg_img, xfms=output_xfms, determinants=determinants) if options.mbm.common_space.do_common_space_registration: output.model_common = model_common return Result(stages=s, output=output)
def chain(options): """Create a registration chain pipeline from the given options.""" # TODO: # one overall question for this entire piece of code is how # we are going to make sure that we can concatenate/add all # the transformations together. Many of the sub-registrations # that are performed (inter-subject registration, lsq6 using # multiple initial models) are applied to subsets of the entire # data, making it harder to keep the mapping simple/straightforward chain_opts = options.chain # type : ChainConf s = Stages() with open(options.chain.csv_file, 'r') as f: subject_info = parse_csv(rows=f, common_time_pt=options.chain.common_time_point) output_dir = options.application.output_directory pipeline_name = options.application.pipeline_name pipeline_processed_dir = os.path.join(output_dir, pipeline_name + "_processed") pipeline_lsq12_common_dir = os.path.join(output_dir, pipeline_name + "_lsq12_" + options.chain.common_time_point_name) pipeline_nlin_common_dir = os.path.join(output_dir, pipeline_name + "_nlin_" + options.chain.common_time_point_name) pipeline_montage_dir = os.path.join(output_dir, pipeline_name + "_montage") pipeline_subject_info = map_over_time_pt_dict_in_Subject( lambda subj_str: MincAtom(name=subj_str, pipeline_sub_dir=pipeline_processed_dir), subject_info) # type: Dict[str, Subject[MincAtom]] # verify that in input files are proper MINC files, and that there # are no duplicates in the filenames all_Minc_atoms = [] # type: List[MincAtom] for s_id, subj in pipeline_subject_info.items(): for subj_time_pt, subj_filename in subj.time_pt_dict.items(): all_Minc_atoms.append(subj_filename) # check_MINC_input_files takes strings, so pass along those instead of the actual MincAtoms check_MINC_input_files([minc_atom.path for minc_atom in all_Minc_atoms]) if options.registration.input_space == InputSpace.lsq6 or \ options.registration.input_space == InputSpace.lsq12: # the input files are not going through the lsq6 alignment. This is the place # where they will all be resampled using a single like file, and get the same # image dimensions/lengths/resolution. So in order for the subsequent stages to # finish (mincaverage stages for instance), all files need to have the same # image parameters: check_MINC_files_have_equal_dimensions_and_resolution([minc_atom.path for minc_atom in all_Minc_atoms], additional_msg="Given that the input images are " "already in " + str(options.registration.input_space) + " space, all input files need to have " "the same dimensions/starts/step sizes.") if options.registration.input_space not in InputSpace.__members__.values(): raise ValueError('unrecognized input space: %s; choices: %s' % (options.registration.input_space, ','.join(InputSpace.__members__))) if options.registration.input_space == InputSpace.native: if options.lsq6.target_type == TargetType.bootstrap: raise ValueError("\nA bootstrap model is ill-defined for the registration chain. " "(Which file is the 'first' input file?). Please use the --lsq6-target " "flag to specify a target for the lsq6 stage, or use an initial model.") if options.lsq6.target_type == TargetType.pride_of_models: pride_of_models_dict = get_pride_of_models_mapping(pride_csv=options.lsq6.target_file, output_dir=options.application.output_directory, pipeline_name=options.application.pipeline_name) subj_id_to_subj_with_lsq6_xfm_dict = map_with_index_over_time_pt_dict_in_Subject( lambda subj_atom, time_point: s.defer(lsq6_nuc_inorm([subj_atom], registration_targets=get_closest_model_from_pride_of_models( pride_of_models_dict, time_point), resolution=options.registration.resolution, lsq6_options=options.lsq6, lsq6_dir=None, # never used since no average # (could call this "average_dir" with None -> no avg ?) subject_matter=options.registration.subject_matter, create_qc_images=False, create_average=False))[0], pipeline_subject_info) # type: Dict[str, Subject[XfmHandler]] else: # if we are not dealing with a pride of models, we can retrieve a fixed # registration target for all input files: targets = registration_targets(lsq6_conf=options.lsq6, app_conf=options.application) # we want to store the xfm handlers in the same shape as pipeline_subject_info, # as such we will call lsq6_nuc_inorm for each file individually and simply extract # the first (and only) element from the resulting list via s.defer(...)[0]. subj_id_to_subj_with_lsq6_xfm_dict = map_over_time_pt_dict_in_Subject( lambda subj_atom: s.defer(lsq6_nuc_inorm([subj_atom], registration_targets=targets, resolution=options.registration.resolution, lsq6_options=options.lsq6, lsq6_dir=None, # no average will be create, is just one file... create_qc_images=False, create_average=False, subject_matter=options.registration.subject_matter) )[0], pipeline_subject_info) # type: Dict[str, Subject[XfmHandler]] # create verification images to show the 6 parameter alignment montageLSQ6 = pipeline_montage_dir + "/quality_control_montage_lsq6.png" # TODO, base scaling factor on resolution of initial model or target filesToCreateImagesFrom = [] for subj_id, subj in subj_id_to_subj_with_lsq6_xfm_dict.items(): for time_pt, subj_time_pt_xfm in subj.time_pt_dict.items(): filesToCreateImagesFrom.append(subj_time_pt_xfm.resampled) # TODO it's strange that create_quality_control_images gets the montage directory twice # TODO (in montages=output=montageLSQ6 and in montage_dir), suggesting a weirdness in create_q_c_images lsq6VerificationImages = s.defer(create_quality_control_images(filesToCreateImagesFrom, montage_output=montageLSQ6, montage_dir=pipeline_montage_dir, message=" the input images after the lsq6 alignment")) # NB currently LSQ6 expects an array of files, but we have a map. # possibilities: # - note that pairwise is enough (except for efficiency -- redundant blurring, etc.) # and just use the map fn above with an LSQ6 fn taking only a single source # - rewrite LSQ6 to use such a (nested) map # - write conversion which creates a tagged array from the map, performs LSQ6, # and converts back # - write 'over' which takes a registration, a data structure, and 'get/set' fns ...? # Intersubject registration: LSQ12/NLIN registration of common-timepoint images # The assumption here is that all these files are roughly aligned. Here is a toy # schematic of what happens. In this example, the common timepoint is set timepoint 2: # # ------------ # subject A A_time_1 -> | A_time_2 | -> A_time_3 # subject B B_time_1 -> | B_time_2 | -> B_time_3 # subject C C_time_1 -> | C_time_2 | -> C_time_3 # ------------ # | # group_wise registration on time point 2 # # dictionary that holds the transformations from the intersubject images # to the final common space average intersubj_img_to_xfm_to_common_avg_dict = {} # type: Dict[MincAtom, XfmHandler] if options.registration.input_space in (InputSpace.lsq6, InputSpace.lsq12): # no registrations have been performed yet, so we can point to the input files s_id_to_intersubj_img_dict = { s_id : subj.intersubject_registration_image for s_id, subj in pipeline_subject_info.items() } else: # lsq6 aligned images # When we ran the lsq6 alignment, we stored the XfmHandlers in the Subject dictionary. So when we call # xfmhandler.intersubject_registration_image, this returns an XfmHandler. From which # we want to extract the resampled file (in order to continue the registration with) s_id_to_intersubj_img_dict = { s_id : subj_with_xfmhandler.intersubject_registration_image.resampled for s_id, subj_with_xfmhandler in subj_id_to_subj_with_lsq6_xfm_dict.items() } if options.application.verbose: print("\nImages that are used for the inter-subject registration:") print("ID\timage") for subject in s_id_to_intersubj_img_dict: print(subject + '\t' + s_id_to_intersubj_img_dict[subject].path) # determine what configuration to use for the non linear registration nonlinear_configuration = get_nonlinear_configuration_from_options(options.nlin.nlin_protocol, options.nlin.reg_method, options.registration.resolution) if options.registration.input_space in [InputSpace.lsq6, InputSpace.native]: intersubj_xfms = s.defer(lsq12_nlin_build_model(imgs=list(s_id_to_intersubj_img_dict.values()), lsq12_conf=options.lsq12, nlin_conf=nonlinear_configuration, resolution=options.registration.resolution, lsq12_dir=pipeline_lsq12_common_dir, nlin_dir=pipeline_nlin_common_dir, nlin_prefix="common")) #, like={atlas_from_init_model_at_this_tp} elif options.registration.input_space == InputSpace.lsq12: #TODO: write reader that creates a mincANTS configuration out of an input protocol # if we're starting with files that are already aligned with an affine transformation # (overall scaling is also dealt with), then the target for the non linear registration # should be the averge of the current input files. first_nlin_target = s.defer(mincaverage(imgs=list(s_id_to_intersubj_img_dict.values()), name_wo_ext="avg_of_input_files", output_dir=pipeline_nlin_common_dir)) intersubj_xfms = s.defer(mincANTS_NLIN_build_model(imgs=list(s_id_to_intersubj_img_dict.values()), initial_target=first_nlin_target, nlin_dir=pipeline_nlin_common_dir, conf=nonlinear_configuration)) intersubj_img_to_xfm_to_common_avg_dict = { xfm.source : xfm for xfm in intersubj_xfms.output } # create one more convenience data structure: a mapping from subject_ID to the xfm_handler # that contains the transformation from the subject at the common time point to the # common time point average. subj_ID_to_xfm_handler_to_common_avg = {} for s_id, subj_at_common_tp in s_id_to_intersubj_img_dict.items(): subj_ID_to_xfm_handler_to_common_avg[s_id] = intersubj_img_to_xfm_to_common_avg_dict[subj_at_common_tp] # create verification images to show the inter-subject alignment montage_inter_subject = pipeline_montage_dir + "/quality_control_montage_inter_subject_registration.png" avg_and_inter_subject_images = [] avg_and_inter_subject_images.append(intersubj_xfms.avg_img) for xfmh in intersubj_xfms.output: avg_and_inter_subject_images.append(xfmh.resampled) inter_subject_verification_images = s.defer(create_quality_control_images( imgs=avg_and_inter_subject_images, montage_output=montage_inter_subject, montage_dir=pipeline_montage_dir, message=" the result of the inter-subject alignment")) if options.application.verbose: print("\nTransformations for intersubject images to final nlin common space:") print("MincAtom\ttransformation") for subj_atom, xfm_handler in intersubj_img_to_xfm_to_common_avg_dict.items(): print(subj_atom.path + '\t' + xfm_handler.xfm.path) ## within-subject registration # In the toy scenario below: # subject A A_time_1 -> A_time_2 -> A_time_3 # subject B B_time_1 -> B_time_2 -> B_time_3 # subject C C_time_1 -> C_time_2 -> C_time_3 # # The following registrations are run: # 1) A_time_1 -> A_time_2 # 2) A_time_2 -> A_time_3 # # 3) B_time_1 -> B_time_2 # 4) B_time_2 -> B_time_3 # # 5) C_time_1 -> C_time_2 # 6) C_time_2 -> C_time_3 subj_id_to_Subjec_for_within_dict = pipeline_subject_info if options.registration.input_space == InputSpace.native: # we started with input images that were not aligned whatsoever # in this case we should use the images that were rigidly # aligned files to continue the within-subject registration with # # type: Dict[str, Subject[XfmHandler]] subj_id_to_Subjec_for_within_dict = map_over_time_pt_dict_in_Subject(lambda x: x.resampled, subj_id_to_subj_with_lsq6_xfm_dict) if options.application.verbose: print("\n\nWithin subject registrations:") for s_id, subj in subj_id_to_Subjec_for_within_dict.items(): print("ID: ", s_id) for time_pt, subj_img in subj.time_pt_dict.items(): print(time_pt, " ", subj_img.path) print("\n") # dictionary that maps subject IDs to a list containing: # ( [(time_pt_n, time_pt_n+1, XfmHandler_from_n_to_n+1), ..., (,,,)], # index_of_common_time_pt) chain_xfms = { s_id : s.defer(intrasubject_registrations( subj=subj, linear_conf=default_lsq12_multilevel_minctracc, nlin_conf=mincANTS_default_conf.replace( file_resolution=options.registration.resolution, iterations="100x100x100x50"))) for s_id, subj in subj_id_to_Subjec_for_within_dict.items() } # create a montage image for each pair of time points for s_id, output_from_intra in chain_xfms.items(): for time_pt_n, time_pt_n_plus_1, transform in output_from_intra[0]: montage_chain = pipeline_montage_dir + "/quality_control_chain_ID_" + s_id + \ "_timepoint_" + str(time_pt_n) + "_to_" + str(time_pt_n_plus_1) + ".png" chain_images = [transform.resampled, transform.target] chain_verification_images = s.defer(create_quality_control_images(chain_images, montage_output=montage_chain, montage_dir=pipeline_montage_dir, message="the alignment between ID " + s_id + " time point " + str(time_pt_n) + " and " + str(time_pt_n_plus_1))) if options.application.verbose: print("\n\nTransformations gotten from the intrasubject registrations:") for s_id, output_from_intra in chain_xfms.items(): print("ID: ", s_id) for time_pt_n, time_pt_n_plus_1, transform in output_from_intra[0]: print("Time point: ", time_pt_n, " to ", time_pt_n_plus_1, " trans: ", transform.xfm.path) print("\n") ## stats # # The statistic files we want to create are the following: # 1) subject <----- subject_common_time_point (resampled to common average) # 2) subject <----- subject_common_time_point <- common_time_point_average (incorporates inter subject differences) # 3) subject_time_point_n <----- subject_time_point_n+1 (resampled to common average) # create transformation from each subject to the final common time point average, # and from each subject to the subject's common time point (non_rigid_xfms_to_common_avg, non_rigid_xfms_to_common_subj) = s.defer(get_chain_transforms_for_stats(subj_id_to_Subjec_for_within_dict, intersubj_img_to_xfm_to_common_avg_dict, chain_xfms)) # Ad 1) provide transformations from the subject's common time point to each subject # These are temporary, because they still need to be resampled into the # average common time point space determinants_from_subject_common_to_subject = map_over_time_pt_dict_in_Subject( lambda xfm: s.defer(determinants_at_fwhms(xfms=[s.defer(invert_xfmhandler(xfm))], inv_xfms=[xfm], # determinants_at_fwhms now vectorized-unhelpful here blur_fwhms=options.stats.stats_kernels)), non_rigid_xfms_to_common_subj) # the content of determinants_from_subject_common_to_subject is: # # {subject_ID : Subject(inter_subject_time_pt, time_pt_dict) # # where time_pt_dict contains: # # {time_point : Tuple(List[Tuple(float, Tuple(MincAtom, MincAtom))], # List[Tuple(float, Tuple(MincAtom, MincAtom))]) # # And to be a bit more verbose: # # {time_point : Tuple(relative_stat_files, # absolute_stat_files) # # where either the relative_stat_files or the absolute_stat_files look like: # # [blur_kernel_1, (determinant_file_1, log_of_determinant_file_1), # ..., # blur_kernel_n, (determinant_file_n, log_of_determinant_file_n)] # # Now the only thing we really want to do, is to resample the actual log # determinants that were generated into the space of the common average. # To make that a little easier, I'll create a mapping that will contain: # # {subject_ID: Subject(intersubject_timepoint, {time_pt_1: [stat_file_1, ..., stat_file_n], # ..., # time_pt_n: [stat_file_1, ..., stat_file_n]} # } for s_id, subject_with_determinants in determinants_from_subject_common_to_subject.items(): transform_from_common_subj_to_common_avg = subj_ID_to_xfm_handler_to_common_avg[s_id].xfm for time_pt, determinant_info in subject_with_determinants.time_pt_dict.items(): # here, each determinant_info is a DataFrame where each row contains # 'abs_det', 'nlin_det', 'log_nlin_det', 'log_abs_det', 'fwhm' fields # of the log-determinants, blurred at various fwhms (corresponding to different rows) for _ix, row in determinant_info.iterrows(): for log_det_file_to_resample in (row.log_full_det, row.log_nlin_det): # TODO the MincAtoms corresponding to the resampled files are never returned new_name_wo_ext = log_det_file_to_resample.filename_wo_ext + "_resampled_to_common" s.defer(mincresample(img=log_det_file_to_resample, xfm=transform_from_common_subj_to_common_avg, like=log_det_file_to_resample, new_name_wo_ext=new_name_wo_ext, subdir="stats-volumes")) # Ad 2) provide transformations from the common avg to each subject. That's the # inverse of what was provided by get_chain_transforms_for_stats() determinants_from_common_avg_to_subject = map_over_time_pt_dict_in_Subject( lambda xfm: s.defer(determinants_at_fwhms(xfms=[s.defer(invert_xfmhandler(xfm))], inv_xfms=[xfm], # determinants_at_fwhms now vectorized-unhelpful here blur_fwhms=options.stats.stats_kernels)), non_rigid_xfms_to_common_avg) # TODO don't just return an (unnamed-)tuple here return Result(stages=s, output=Namespace(non_rigid_xfms_to_common=non_rigid_xfms_to_common_avg, determinants_from_common_avg_to_subject=determinants_from_common_avg_to_subject, determinants_from_subject_common_to_subject=determinants_from_subject_common_to_subject))