def NLIN_pipeline(options):
# if options.application.files is None:
# raise ValueError("Please, some files! (or try '--help')") # TODO make a util procedure for this
output_dir = options.application.output_directory
pipeline_name = options.application.pipeline_name
# TODO this is tedious and annoyingly similar to the registration chain and MBM and LSQ6 ...
processed_dir = os.path.join(output_dir, pipeline_name + "_processed")
nlin_dir = os.path.join(output_dir, pipeline_name + "_nlin")
resolution = (options.registration.resolution # TODO does using the finest resolution here make sense?
or min([get_resolution_from_file(f) for f in options.application.files]))
imgs = get_imgs(options.application)
# imgs = [MincAtom(f, pipeline_sub_dir=processed_dir) for f in options.application.files]
# determine NLIN settings by overriding defaults with
# any settings present in protocol file, if it exists
# could add a hook to print a message announcing completion, output files,
# add more stages here to make a CSV
initial_target_mask = MincAtom(options.nlin.target_mask) if options.nlin.target_mask else None
initial_target = MincAtom(options.nlin.target, mask=initial_target_mask)
full_hierarchy = get_nonlinear_configuration_from_options(nlin_protocol=options.nlin.nlin_protocol,
reg_method=options.nlin.reg_method,
file_resolution=resolution)
s = Stages()
nlin_result = s.defer(nlin_build_model(imgs, initial_target=initial_target, conf=full_hierarchy, nlin_dir=nlin_dir))
# TODO return these?
inverted_xfms = [s.defer(invert_xfmhandler(xfm)) for xfm in nlin_result.output]
if options.stats.calc_stats:
# TODO: put the stats part behind a flag ...
determinants = [s.defer(determinants_at_fwhms(
xfm=inv_xfm,
inv_xfm=xfm,
blur_fwhms=options.stats.stats_kernels))
for xfm, inv_xfm in zip(nlin_result.output, inverted_xfms)]
return Result(stages=s,
output=Namespace(nlin_xfms=nlin_result,
avg_img=nlin_result.avg_img,
determinants=determinants))
else:
# there's no consistency in what gets returned, yikes ...
return Result(stages=s, output=Namespace(nlin_xfms=nlin_result, avg_img=nlin_result.avg_img))
def NLIN_pipeline(options):
if options.application.files is None:
raise ValueError("Please, some files! (or try '--help')") # TODO make a util procedure for this
output_dir = options.application.output_directory
pipeline_name = options.application.pipeline_name
# TODO this is tedious and annoyingly similar to the registration chain and MBM and LSQ6 ...
processed_dir = os.path.join(output_dir, pipeline_name + "_processed")
nlin_dir = os.path.join(output_dir, pipeline_name + "_nlin")
resolution = (options.registration.resolution # TODO does using the finest resolution here make sense?
or min([get_resolution_from_file(f) for f in options.application.files]))
imgs = [MincAtom(f, pipeline_sub_dir=processed_dir) for f in options.application.files]
# determine NLIN settings by overriding defaults with
# any settings present in protocol file, if it exists
# could add a hook to print a message announcing completion, output files,
# add more stages here to make a CSV
initial_target_mask = MincAtom(options.nlin.target_mask) if options.nlin.target_mask else None
initial_target = MincAtom(options.nlin.target, mask=initial_target_mask)
full_hierarchy = get_nonlinear_configuration_from_options(nlin_protocol=options.nlin.nlin_protocol,
flag_nlin_protocol=next(iter(options.nlin.flags_.nlin_protocol)),
reg_method=options.nlin.reg_method,
file_resolution=resolution)
s = Stages()
nlin_result = s.defer(nlin_build_model(imgs, initial_target=initial_target, conf=full_hierarchy, nlin_dir=nlin_dir))
# TODO return these?
inverted_xfms = [s.defer(invert_xfmhandler(xfm)) for xfm in nlin_result.output]
if options.stats.calc_stats:
# TODO: put the stats part behind a flag ...
determinants = [s.defer(determinants_at_fwhms(
xfm=inv_xfm,
inv_xfm=xfm,
blur_fwhms=options.stats.stats_kernels))
for xfm, inv_xfm in zip(nlin_result.output, inverted_xfms)]
return Result(stages=s,
output=Namespace(nlin_xfms=nlin_result,
avg_img=nlin_result.avg_img,
determinants=determinants))
else:
# there's no consistency in what gets returned, yikes ...
return Result(stages=s, output=Namespace(nlin_xfms=nlin_result, avg_img=nlin_result.avg_img))
def two_level(grouped_files_df, options: TwoLevelConf):
"""
grouped_files_df - must contain 'group':<any comparable, sortable type> and 'file':MincAtom columns
""" # TODO weird naming since the grouped_files_df isn't a GroupBy object? just files_df?
s = Stages()
if grouped_files_df.isnull().values.any():
raise ValueError("NaN values in input dataframe; can't go")
if options.mbm.lsq6.target_type == TargetType.bootstrap:
# won't work since the second level part tries to get the resolution of *its* "first input file", which
# hasn't been created. We could instead pass in a resolution to the `mbm` function,
# but instead disable for now:
raise ValueError(
"Bootstrap model building currently doesn't work with this pipeline; "
"just specify an initial target instead")
elif options.mbm.lsq6.target_type == TargetType.pride_of_models:
pride_of_models_mapping = get_pride_of_models_mapping(
pride_csv=options.mbm.lsq6.target_file,
output_dir=options.application.output_directory,
pipeline_name=options.application.pipeline_name)
# FIXME this is the same as in the 'tamarack' except for names of arguments/enclosing variables
def group_options(options, group):
options = copy.deepcopy(options)
if options.mbm.lsq6.target_type == TargetType.pride_of_models:
targets = get_closest_model_from_pride_of_models(
pride_of_models_dict=pride_of_models_mapping, time_point=group)
options.mbm.lsq6 = options.mbm.lsq6.replace(
target_type=TargetType.initial_model,
target_file=targets.registration_standard.path)
else:
# this will ensure that all groups have the same resolution -- is it necessary?
targets = s.defer(
registration_targets(
lsq6_conf=options.mbm.lsq6,
app_conf=options.application,
reg_conf=options.registration,
first_input_file=grouped_files_df.file.iloc[0]))
resolution = (options.registration.resolution
or get_resolution_from_file(
targets.registration_standard.path))
# This must happen after calling registration_targets otherwise it will resample to options.registration.resolution
options.registration = options.registration.replace(
resolution=resolution)
# no need to check common space settings here since they're turned off at the parser level
# (a bit strange)
return options
first_level_results = (
grouped_files_df.groupby(
'group', as_index=False
) # the usual annoying pattern to do a aggregate with access
.aggregate({'file': lambda files: list(files)
}) # to the groupby object's keys ... TODO: fix
.rename(columns={
'file': "files"
}).assign(build_model=lambda df: df.apply(
axis=1,
func=lambda row: s.defer(
mbm(imgs=row.files,
options=group_options(options, row.group),
prefix="%s" % row.group,
output_dir=os.path.join(
options.application.output_directory, options.
application.pipeline_name + "_first_level",
"%s_processed" % row.group))))))
# TODO replace .assign(...apply(...)...) with just an apply, producing a series right away?
# FIXME right now the same options set is being used for both levels -- use options.first/second_level
second_level_options = copy.deepcopy(options)
second_level_options.mbm.lsq6 = second_level_options.mbm.lsq6.replace(
run_lsq6=False)
second_level_options.mbm.segmentation.run_maget = False
second_level_options.mbm.maget.maget.mask_only = False
second_level_options.mbm.maget.maget.mask = False
# FIXME this is probably a hack -- instead add a --second-level-init-model option to specify which timepoint should be used
# as the initial model in the second level ??? (at this point it doesn't matter due to lack of lsq6 ...)
if second_level_options.mbm.lsq6.target_type == TargetType.pride_of_models:
second_level_options.mbm.lsq6 = second_level_options.mbm.lsq6.replace(
target_type=TargetType.
target, # target doesn't really matter as no lsq6 here, just used for resolution...
target_file=list(pride_of_models_mapping.values())
[0].registration_standard.path)
# NOTE: running lsq6_nuc_inorm here doesn't work in general (but possibly with rotational minctracc)
# since the native-space initial model is used, but our images are
# already in standard space (as we resampled there after the 1st-level lsq6).
# On the other hand, we might want to run it here (although of course NOT nuc/inorm!) in the future,
# for instance given a 'pride' of models (one for each group).
second_level_results = s.defer(
mbm(imgs=first_level_results.build_model.map(lambda m: m.avg_img),
options=second_level_options,
prefix=os.path.join(
options.application.output_directory,
options.application.pipeline_name + "_second_level")))
# FIXME sadly, `mbm` doesn't return a pd.Series of xfms, so we don't have convenient indexing ...
overall_xfms = [
s.defer(concat_xfmhandlers([xfm_1, xfm_2])) for xfms_1, xfm_2 in
zip([r.xfms.lsq12_nlin_xfm for r in first_level_results.build_model],
second_level_results.xfms.overall_xfm) for xfm_1 in xfms_1
]
resample = np.vectorize(mincresample_new, excluded={"extra_flags"})
defer = np.vectorize(s.defer)
# TODO using the avg_img here is a bit clunky -- maybe better to propagate group indices ...
# only necessary since `mbm` doesn't return DataFrames but namespaces ...
first_level_determinants = pd.concat(list(
first_level_results.build_model.apply(
lambda x: x.determinants.assign(first_level_avg=x.avg_img))),
ignore_index=True)
# first_level_xfms is only necessary because you otherwise have no access to the input file which is necessary
# for merging with the input csv. lsq12_nlin_xfm can be used to merge, and rigid_xfm contains the input file.
# If for some reason we want to output xfms in the future, just don't drop everything.
first_level_xfms = pd.concat(
list(
first_level_results.build_model.apply(
lambda x: x.xfms.assign(first_level_avg=x.avg_img))),
ignore_index=True)[["lsq12_nlin_xfm", "rigid_xfm"]]
if options.mbm.segmentation.run_maget:
maget_df = pd.DataFrame([
{
"label_file": x.labels.path,
"native_file": x.orig_path
} #, "_merge" : basename(x.orig_path)}
for x in pd.concat([
namespace.maget_result
for namespace in first_level_results.build_model
])
])
first_level_xfms = pd.merge(
left=first_level_xfms.assign(native_file=lambda df: df.rigid_xfm.
apply(lambda x: x.source.path)),
right=maget_df,
on="native_file")
first_level_determinants = (pd.merge(left=first_level_determinants,
right=first_level_xfms,
left_on="inv_xfm",
right_on="lsq12_nlin_xfm").drop(
["rigid_xfm", "lsq12_nlin_xfm"],
axis=1))
resampled_determinants = (pd.merge(
left=first_level_determinants,
right=pd.DataFrame({
'group_xfm': second_level_results.xfms.overall_xfm
}).assign(source=lambda df: df.group_xfm.apply(lambda r: r.source)),
left_on="first_level_avg",
right_on="source").assign(
resampled_log_full_det=lambda df: defer(
resample(img=df.log_full_det,
xfm=df.group_xfm.apply(lambda x: x.xfm),
like=second_level_results.avg_img)),
resampled_log_nlin_det=lambda df: defer(
resample(img=df.log_nlin_det,
xfm=df.group_xfm.apply(lambda x: x.xfm),
like=second_level_results.avg_img))))
# TODO only resamples the log determinants, but still a bit ugly ... abstract somehow?
# TODO shouldn't be called resampled_determinants since this is basically the whole (first_level) thing ...
inverted_overall_xfms = [
s.defer(invert_xfmhandler(xfm)) for xfm in overall_xfms
]
overall_determinants = (s.defer(
determinants_at_fwhms(
xfms=inverted_overall_xfms,
inv_xfms=overall_xfms,
blur_fwhms=options.mbm.stats.stats_kernels)).assign(
overall_log_full_det=lambda df: df.log_full_det,
overall_log_nlin_det=lambda df: df.log_nlin_det).drop(
['log_full_det', 'log_nlin_det'], axis=1))
# TODO return some MAGeT stuff from two_level function ??
# FIXME running MAGeT from within the `two_level` function has the same problem as running it from within `mbm`:
# it will now run when this pipeline is called from within another one (e.g., n-level), which will be
# redundant, create filename clashes, etc. -- this should be moved to `two_level_pipeline`.
# TODO do we need a `pride of atlases` for MAGeT in this pipeline ??
# TODO at the moment MAGeT is run within the MBM code, but it could be disabled there and run here
#if options.mbm.segmentation.run_maget:
# maget_options = copy.deepcopy(options)
# maget_options.maget = options.mbm.maget
# fixup_maget_options(maget_options=maget_options.maget,
# lsq12_options=maget_options.mbm.lsq12,
# nlin_options=maget_options.mbm.nlin)
# maget_options.maget.maget.mask = maget_options.maget.maget.mask_only = False # already done above
# del maget_options.mbm
# again using a weird combination of vectorized and loop constructs ...
# s.defer(maget([xfm.resampled for _ix, m in first_level_results.iterrows()
# for xfm in m.build_model.xfms.rigid_xfm],
# options=maget_options,
# prefix="%s_MAGeT" % options.application.pipeline_name,
# output_dir=os.path.join(options.application.output_directory,
# options.application.pipeline_name + "_processed")))
# TODO resampling to database model ...
# TODO there should be one table containing all determinants (first level, overall, resampled first level) for each file
# and another containing some groupwise information (averages and transforms to the common average)
return Result(stages=s,
output=Namespace(
first_level_results=first_level_results,
resampled_determinants=resampled_determinants,
overall_determinants=overall_determinants))
def two_level(grouped_files_df, options : TwoLevelConf):
"""
grouped_files_df - must contain 'group':<any comparable, sortable type> and 'file':MincAtom columns
""" # TODO weird naming since the grouped_files_df isn't a GroupBy object? just files_df?
s = Stages()
if grouped_files_df.isnull().values.any():
raise ValueError("NaN values in input dataframe; can't go")
if options.mbm.lsq6.target_type == TargetType.bootstrap:
# won't work since the second level part tries to get the resolution of *its* "first input file", which
# hasn't been created. We could instead pass in a resolution to the `mbm` function,
# but instead disable for now:
raise ValueError("Bootstrap model building currently doesn't work with this pipeline; "
"just specify an initial target instead")
elif options.mbm.lsq6.target_type == TargetType.pride_of_models:
pride_of_models_mapping = get_pride_of_models_mapping(pride_csv=options.mbm.lsq6.target_file,
output_dir=options.application.output_directory,
pipeline_name=options.application.pipeline_name)
# FIXME this is the same as in the 'tamarack' except for names of arguments/enclosing variables
def group_options(options, group):
options = copy.deepcopy(options)
if options.mbm.lsq6.target_type == TargetType.pride_of_models:
targets = get_closest_model_from_pride_of_models(pride_of_models_dict=pride_of_models_mapping,
time_point=group)
options.mbm.lsq6 = options.mbm.lsq6.replace(target_type=TargetType.initial_model,
target_file=targets.registration_standard.path)
else:
# this will ensure that all groups have the same resolution -- is it necessary?
targets = registration_targets(lsq6_conf=options.mbm.lsq6,
app_conf=options.application,
first_input_file=grouped_files_df.file.iloc[0])
resolution = (options.registration.resolution
or get_resolution_from_file(targets.registration_standard.path))
options.registration = options.registration.replace(resolution=resolution)
# no need to check common space settings here since they're turned off at the parser level
# (a bit strange)
return options
first_level_results = (
grouped_files_df
.groupby('group', as_index=False, sort=False) # the usual annoying pattern to do a aggregate with access
.aggregate({ 'file' : lambda files: list(files) }) # to the groupby object's keys ... TODO: fix
.rename(columns={ 'file' : "files" })
.assign(build_model=lambda df:
df.apply(axis=1,
func=lambda row:
s.defer(mbm(imgs=row.files,
options=group_options(options, row.group),
prefix="%s" % row.group,
output_dir=os.path.join(
options.application.output_directory,
options.application.pipeline_name + "_first_level",
"%s_processed" % row.group)))))
)
# TODO replace .assign(...apply(...)...) with just an apply, producing a series right away?
# FIXME right now the same options set is being used for both levels -- use options.first/second_level
second_level_options = copy.deepcopy(options)
second_level_options.mbm.lsq6 = second_level_options.mbm.lsq6.replace(run_lsq6=False)
second_level_options.mbm.segmentation.run_maget = False
second_level_options.mbm.maget.maget.mask_only = False
second_level_options.mbm.maget.maget.mask = False
# FIXME this is probably a hack -- instead add a --second-level-init-model option to specify which timepoint should be used
# as the initial model in the second level ??? (at this point it doesn't matter due to lack of lsq6 ...)
if second_level_options.mbm.lsq6.target_type == TargetType.pride_of_models:
second_level_options.mbm.lsq6 = second_level_options.mbm.lsq6.replace(
target_type=TargetType.target, # target doesn't really matter as no lsq6 here, just used for resolution...
target_file=list(pride_of_models_mapping.values())[0].registration_standard.path)
# NOTE: running lsq6_nuc_inorm here doesn't work in general (but possibly with rotational minctracc)
# since the native-space initial model is used, but our images are
# already in standard space (as we resampled there after the 1st-level lsq6).
# On the other hand, we might want to run it here (although of course NOT nuc/inorm!) in the future,
# for instance given a 'pride' of models (one for each group).
second_level_results = s.defer(mbm(imgs=first_level_results.build_model.map(lambda m: m.avg_img),
options=second_level_options,
prefix=os.path.join(options.application.output_directory,
options.application.pipeline_name + "_second_level")))
# FIXME sadly, `mbm` doesn't return a pd.Series of xfms, so we don't have convenient indexing ...
overall_xfms = [s.defer(concat_xfmhandlers([xfm_1, xfm_2]))
for xfms_1, xfm_2 in zip([r.xfms.lsq12_nlin_xfm for r in first_level_results.build_model],
second_level_results.xfms.overall_xfm)
for xfm_1 in xfms_1]
resample = np.vectorize(mincresample_new, excluded={"extra_flags"})
defer = np.vectorize(s.defer)
# TODO using the avg_img here is a bit clunky -- maybe better to propagate group indices ...
# only necessary since `mbm` doesn't return DataFrames but namespaces ...
first_level_determinants = pd.concat(list(first_level_results.build_model.apply(
lambda x: x.determinants.assign(first_level_avg=x.avg_img))),
ignore_index=True)
resampled_determinants = (pd.merge(
left=first_level_determinants,
right=pd.DataFrame({'group_xfm' : second_level_results.xfms.overall_xfm})
.assign(source=lambda df: df.group_xfm.apply(lambda r: r.source)),
left_on="first_level_avg",
right_on="source")
.assign(resampled_log_full_det=lambda df: defer(resample(img=df.log_full_det,
xfm=df.group_xfm.apply(lambda x: x.xfm),
like=second_level_results.avg_img)),
resampled_log_nlin_det=lambda df: defer(resample(img=df.log_nlin_det,
xfm=df.group_xfm.apply(lambda x: x.xfm),
like=second_level_results.avg_img))))
# TODO only resamples the log determinants, but still a bit ugly ... abstract somehow?
# TODO shouldn't be called resampled_determinants since this is basically the whole (first_level) thing ...
inverted_overall_xfms = [s.defer(invert_xfmhandler(xfm)) for xfm in overall_xfms]
overall_determinants = (s.defer(determinants_at_fwhms(
xfms=inverted_overall_xfms,
inv_xfms=overall_xfms,
blur_fwhms=options.mbm.stats.stats_kernels))
.assign(overall_log_full_det=lambda df: df.log_full_det,
overall_log_nlin_det=lambda df: df.log_nlin_det)
.drop(['log_full_det', 'log_nlin_det'], axis=1))
# TODO return some MAGeT stuff from two_level function ??
# FIXME running MAGeT from within the `two_level` function has the same problem as running it from within `mbm`:
# it will now run when this pipeline is called from within another one (e.g., n-level), which will be
# redundant, create filename clashes, etc. -- this should be moved to `two_level_pipeline`.
# TODO do we need a `pride of atlases` for MAGeT in this pipeline ??
# TODO at the moment MAGeT is run within the MBM code, but it could be disabled there and run here
#if options.mbm.segmentation.run_maget:
# maget_options = copy.deepcopy(options)
# maget_options.maget = options.mbm.maget
# fixup_maget_options(maget_options=maget_options.maget,
# lsq12_options=maget_options.mbm.lsq12,
# nlin_options=maget_options.mbm.nlin)
# maget_options.maget.maget.mask = maget_options.maget.maget.mask_only = False # already done above
# del maget_options.mbm
# again using a weird combination of vectorized and loop constructs ...
# s.defer(maget([xfm.resampled for _ix, m in first_level_results.iterrows()
# for xfm in m.build_model.xfms.rigid_xfm],
# options=maget_options,
# prefix="%s_MAGeT" % options.application.pipeline_name,
# output_dir=os.path.join(options.application.output_directory,
# options.application.pipeline_name + "_processed")))
# TODO resampling to database model ...
# TODO there should be one table containing all determinants (first level, overall, resampled first level) for each file
# and another containing some groupwise information (averages and transforms to the common average)
return Result(stages=s, output=Namespace(first_level_results=first_level_results,
resampled_determinants=resampled_determinants,
overall_determinants=overall_determinants))
def tamarack(imgs: pd.DataFrame, options):
# columns of the input df: `img` : MincAtom, `timept` : number, ...
# columns of the pride of models : 'timept' : number, 'model' : MincAtom
s = Stages()
# TODO some assertions that the pride_of_models, if provided, is correct, and that this is intended target type
def group_options(options, timepoint):
options = copy.deepcopy(options)
if options.mbm.lsq6.target_type == TargetType.pride_of_models:
options = copy.deepcopy(options)
targets = get_closest_model_from_pride_of_models(
pride_of_models_dict=get_pride_of_models_mapping(
pride_csv=options.mbm.lsq6.target_file,
output_dir=options.application.output_directory,
pipeline_name=options.application.pipeline_name),
time_point=timepoint)
options.mbm.lsq6 = options.mbm.lsq6.replace(
target_type=TargetType.initial_model,
target_file=targets.registration_standard.path)
# resolution = (options.registration.resolution
# or get_resolution_from_file(targets.registration_standard.path))
# options.registration = options.registration.replace(resolution=resolution)
# FIXME use of registration_standard here is quite wrong ...
# part of the trouble is that mbm calls registration_targets itself,
# so we can't send this RegistrationTargets to `mbm` directly ...
# one option: add yet another optional arg to `mbm` ...
else:
targets = s.defer(
registration_targets(lsq6_conf=options.mbm.lsq6,
app_conf=options.application,
reg_conf=options.registration,
first_input_file=imgs.filename.iloc[0]))
resolution = (options.registration.resolution
or get_resolution_from_file(
targets.registration_standard.path))
# This must happen after calling registration_targets otherwise it will resample to options.registration.resolution
options.registration = options.registration.replace(
resolution=resolution)
return options
# build all first-level models:
first_level_results = (
imgs # TODO 'group' => 'timept' ?
.groupby('group', as_index=False
) # the usual annoying pattern to do an aggregate with access
.aggregate({'file': lambda files: list(files)}
) # to the groupby object's keys ... TODO: fix
.rename(columns={
'file': "files"
}).assign(options=lambda df: df.apply(
axis=1, func=lambda row: group_options(options, row.group))
).assign(build_model=lambda df: df.apply(
axis=1,
func=lambda row: s.defer(
mbm(imgs=row.files,
options=row.options,
prefix="%s" % row.group,
output_dir=os.path.join(
options.application.output_directory, options
.application.pipeline_name + "_first_level",
"%s_processed" % row.group))))
).sort_values(by='group'))
if all(
first_level_results.options.map(
lambda opts: opts.registration.resolution) ==
first_level_results.options.iloc[0].registration.resolution):
options.registration = options.registration.replace(
resolution=first_level_results.options.iloc[0].registration.
resolution)
else:
raise ValueError(
"some first-level models are run at different resolutions, possibly not what you want ..."
)
# construction of the overall inter-average transforms will be done iteratively (for efficiency/aesthetics),
# which doesn't really fit the DataFrame mold ...
full_hierarchy = get_nonlinear_configuration_from_options(
nlin_protocol=options.mbm.nlin.nlin_protocol,
reg_method=options.mbm.nlin.reg_method,
file_resolution=options.registration.resolution)
# FIXME no good can come of this
nlin_protocol = full_hierarchy.confs[-1] if isinstance(
full_hierarchy, MultilevelANTSConf) else full_hierarchy
# first register consecutive averages together:
average_registrations = (
first_level_results[:-1].assign(
next_model=list(first_level_results[1:].build_model))
# TODO: we should be able to do lsq6 registration here as well!
.assign(xfm=lambda df: df.apply(
axis=1,
func=lambda row: s.defer(
lsq12_nlin(source=row.build_model.avg_img,
target=row.next_model.avg_img,
lsq12_conf=get_linear_configuration_from_options(
options.mbm.lsq12,
transform_type=LinearTransType.lsq12,
file_resolution=options.registration.resolution
),
nlin_conf=nlin_protocol)))))
# now compose the above transforms to produce transforms from each average to the common average:
common_time_pt = options.tamarack.common_time_pt
common_model = first_level_results[
first_level_results.group ==
common_time_pt].iloc[0].build_model.avg_img
#common = average_registrations[average_registrations.group == common_time_pt].iloc[0]
before = average_registrations[
average_registrations.group <
common_time_pt] # asymmetry in before/after since
after = average_registrations[
average_registrations.group >=
common_time_pt] # we used `next_`, not `previous_`
# compose 1st and 2nd level transforms and resample into the common average space:
def suffixes(xs):
if len(xs) == 0:
return [[]]
else:
ys = suffixes(xs[1:])
return [[xs[0]] + ys[0]] + ys
def prefixes(xs):
if len(xs) == 0:
return [[]]
else:
ys = prefixes(xs[1:])
return ys + [ys[-1] + [xs[0]]]
xfms_to_common = (first_level_results.assign(
uncomposed_xfms=suffixes(list(before.xfm))[:-1] + [None] +
prefixes(list(after.xfm))[1:]).assign(
xfm_to_common=lambda df: df.apply(
axis=1,
func=lambda row: ((lambda x: s.defer(invert_xfmhandler(
x)) if row.group >= common_time_pt else x)(s.defer(
concat_xfmhandlers(
row.uncomposed_xfms,
name=("%s_to_common" if row.group < common_time_pt
else "%s_from_common") % row.group))))
if row.uncomposed_xfms is not None else None)).drop(
'uncomposed_xfms', axis=1)) # TODO None => identity??
# TODO indexing here is not good ...
first_level_determinants = pd.concat(list(
first_level_results.build_model.apply(
lambda x: x.determinants.assign(first_level_avg=x.avg_img))),
ignore_index=True)
resampled_determinants = (pd.merge(
left=first_level_determinants,
right=xfms_to_common.assign(source=lambda df: df.xfm_to_common.apply(
lambda x: x.source if x is not None else None)),
left_on="first_level_avg",
right_on='source').assign(
resampled_log_full_det=lambda df: df.apply(
axis=1,
func=lambda row: s.defer(
mincresample_new(img=row.log_full_det,
xfm=row.xfm_to_common.xfm,
like=common_model))
if row.xfm_to_common is not None else row.img),
resampled_log_nlin_det=lambda df: df.apply(
axis=1,
func=lambda row: s.defer(
mincresample_new(img=row.log_nlin_det,
xfm=row.xfm_to_common.xfm,
like=common_model))
if row.xfm_to_common is not None else row.img)))
inverted_overall_xfms = pd.Series({
xfm: (s.defer(concat_xfmhandlers([xfm, row.xfm_to_common]))
if row.xfm_to_common is not None else xfm)
for _ix, row in xfms_to_common.iterrows()
for xfm in row.build_model.xfms.lsq12_nlin_xfm
})
overall_xfms = inverted_overall_xfms.apply(
lambda x: s.defer(invert_xfmhandler(x)))
overall_determinants = determinants_at_fwhms(
xfms=overall_xfms,
blur_fwhms=options.mbm.stats.stats_kernels,
inv_xfms=inverted_overall_xfms)
# TODO turn off bootstrap as with two-level code?
# TODO combine into one data frame
return Result(stages=s,
output=Namespace(
first_level_results=first_level_results,
overall_determinants=overall_determinants,
resampled_determinants=resampled_determinants.drop(
['options'], axis=1)))
def tamarack(imgs : pd.DataFrame, options):
# columns of the input df: `img` : MincAtom, `timept` : number, ...
# columns of the pride of models : 'timept' : number, 'model' : MincAtom
s = Stages()
# TODO some assertions that the pride_of_models, if provided, is correct, and that this is intended target type
def group_options(options, timepoint):
options = copy.deepcopy(options)
if options.mbm.lsq6.target_type == TargetType.pride_of_models:
options = copy.deepcopy(options)
targets = get_closest_model_from_pride_of_models(pride_of_models_dict=get_pride_of_models_mapping(
pride_csv=options.mbm.lsq6.target_file,
output_dir=options.application.output_directory,
pipeline_name=options.application.pipeline_name),
time_point=timepoint)
options.mbm.lsq6 = options.mbm.lsq6.replace(target_type=TargetType.initial_model,
target_file=targets.registration_standard.path)
# resolution = (options.registration.resolution
# or get_resolution_from_file(targets.registration_standard.path))
# options.registration = options.registration.replace(resolution=resolution)
# FIXME use of registration_standard here is quite wrong ...
# part of the trouble is that mbm calls registration_targets itself,
# so we can't send this RegistrationTargets to `mbm` directly ...
# one option: add yet another optional arg to `mbm` ...
else:
targets = s.defer(registration_targets(lsq6_conf=options.mbm.lsq6,
app_conf=options.application, reg_conf=options.registration,
first_input_file=imgs.filename.iloc[0]))
resolution = (options.registration.resolution or
get_resolution_from_file(targets.registration_standard.path))
# This must happen after calling registration_targets otherwise it will resample to options.registration.resolution
options.registration = options.registration.replace(resolution=resolution)
return options
# build all first-level models:
first_level_results = (
imgs # TODO 'group' => 'timept' ?
.groupby('group', as_index=False) # the usual annoying pattern to do an aggregate with access
.aggregate({ 'file' : lambda files: list(files) }) # to the groupby object's keys ... TODO: fix
.rename(columns={ 'file' : "files" })
.assign(options=lambda df: df.apply(axis=1, func=lambda row: group_options(options, row.group)))
.assign(build_model=lambda df:
df.apply(axis=1,
func=lambda row: s.defer(
mbm(imgs=row.files,
options=row.options,
prefix="%s" % row.group,
output_dir=os.path.join(
options.application.output_directory,
options.application.pipeline_name + "_first_level",
"%s_processed" % row.group)))))
.sort_values(by='group')
)
if all(first_level_results.options.map(lambda opts: opts.registration.resolution)
== first_level_results.options.iloc[0].registration.resolution):
options.registration = options.registration.replace(
resolution=first_level_results.options.iloc[0].registration.resolution)
else:
raise ValueError("some first-level models are run at different resolutions, possibly not what you want ...")
# construction of the overall inter-average transforms will be done iteratively (for efficiency/aesthetics),
# which doesn't really fit the DataFrame mold ...
full_hierarchy = get_nonlinear_configuration_from_options(
nlin_protocol=options.mbm.nlin.nlin_protocol,
reg_method=options.mbm.nlin.reg_method,
file_resolution=options.registration.resolution)
# FIXME no good can come of this
nlin_protocol = full_hierarchy.confs[-1] if isinstance(full_hierarchy, MultilevelANTSConf) else full_hierarchy
# first register consecutive averages together:
average_registrations = (
first_level_results[:-1]
.assign(next_model=list(first_level_results[1:].build_model))
# TODO: we should be able to do lsq6 registration here as well!
.assign(xfm=lambda df: df.apply(axis=1, func=lambda row: s.defer(
lsq12_nlin(source=row.build_model.avg_img,
target=row.next_model.avg_img,
lsq12_conf=get_linear_configuration_from_options(
options.mbm.lsq12,
transform_type=LinearTransType.lsq12,
file_resolution=options.registration.resolution),
nlin_conf=nlin_protocol)))))
# now compose the above transforms to produce transforms from each average to the common average:
common_time_pt = options.tamarack.common_time_pt
common_model = first_level_results[first_level_results.group == common_time_pt].iloc[0].build_model.avg_img
#common = average_registrations[average_registrations.group == common_time_pt].iloc[0]
before = average_registrations[average_registrations.group < common_time_pt] # asymmetry in before/after since
after = average_registrations[average_registrations.group >= common_time_pt] # we used `next_`, not `previous_`
# compose 1st and 2nd level transforms and resample into the common average space:
def suffixes(xs):
if len(xs) == 0:
return [[]]
else:
ys = suffixes(xs[1:])
return [[xs[0]] + ys[0]] + ys
def prefixes(xs):
if len(xs) == 0:
return [[]]
else:
ys = prefixes(xs[1:])
return ys + [ys[-1] + [xs[0]]]
xfms_to_common = (
first_level_results
.assign(uncomposed_xfms=suffixes(list(before.xfm))[:-1] + [None] + prefixes(list(after.xfm))[1:])
.assign(xfm_to_common=lambda df: df.apply(axis=1, func=lambda row:
((lambda x: s.defer(invert_xfmhandler(x)) if row.group >= common_time_pt else x)
(s.defer(concat_xfmhandlers(row.uncomposed_xfms,
name=("%s_to_common"
if row.group < common_time_pt
else "%s_from_common") % row.group))))
if row.uncomposed_xfms is not None else None))
.drop('uncomposed_xfms', axis=1)) # TODO None => identity??
# TODO indexing here is not good ...
first_level_determinants = pd.concat(list(first_level_results.build_model.apply(
lambda x: x.determinants.assign(first_level_avg=x.avg_img))),
ignore_index=True)
resampled_determinants = (
pd.merge(left=first_level_determinants,
right=xfms_to_common.assign(source=lambda df: df.xfm_to_common.apply(
lambda x:
x.source if x is not None else None)),
left_on="first_level_avg", right_on='source')
.assign(resampled_log_full_det=lambda df: df.apply(axis=1, func=lambda row:
s.defer(mincresample_new(img=row.log_full_det,
xfm=row.xfm_to_common.xfm,
like=common_model))
if row.xfm_to_common is not None else row.img),
resampled_log_nlin_det=lambda df: df.apply(axis=1, func=lambda row:
s.defer(mincresample_new(img=row.log_nlin_det,
xfm=row.xfm_to_common.xfm,
like=common_model))
if row.xfm_to_common is not None else row.img))
)
inverted_overall_xfms = pd.Series({ xfm : (s.defer(concat_xfmhandlers([xfm, row.xfm_to_common]))
if row.xfm_to_common is not None else xfm)
for _ix, row in xfms_to_common.iterrows()
for xfm in row.build_model.xfms.lsq12_nlin_xfm })
overall_xfms = inverted_overall_xfms.apply(lambda x: s.defer(invert_xfmhandler(x)))
overall_determinants = determinants_at_fwhms(xfms=overall_xfms,
blur_fwhms=options.mbm.stats.stats_kernels,
inv_xfms=inverted_overall_xfms)
# TODO turn off bootstrap as with two-level code?
# TODO combine into one data frame
return Result(stages=s, output=Namespace(first_level_results=first_level_results,
overall_determinants=overall_determinants,
resampled_determinants=resampled_determinants.drop(
['options'],
axis=1)))
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 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 common_space(mbm_result, options):
s = Stages()
# TODO: the interface of this function (basically a destructive 'id' function) is horrific
# TODO: instead, copy the mbm_result here ??
if not options.mbm.common_space.common_space_model:
raise ValueError("No common space template provided!")
if not options.mbm.common_space.common_space_mask:
warnings.warn(
"No common space mask provided ... might be OK if your consensus average mask is OK"
)
# TODO allow lsq6 registration as well ...
common_space_model = MincAtom(
options.mbm.common_space.common_space_model,
# TODO fix the subdirectories!
mask=MincAtom(options.mbm.common_space.common_space_mask,
pipeline_sub_dir=os.path.join(
options.application.output_directory,
options.application.pipeline_name + "_processed"))
if options.mbm.common_space.common_space_mask else None,
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 ...
# full_hierarchy = get_nonlinear_configuration_from_options(nlin_protocol=options.mbm.nlin.nlin_protocol,
# reg_method=options.mbm.nlin.reg_method,
# file_resolution=options.registration.resolution)
# WEIRD ... see comment in lsq12_nlin code ...
# nlin_conf = full_hierarchy.confs[-1] if isinstance(full_hierarchy, MultilevelANTSConf) else full_hierarchy
# also weird that we need to call get_linear_configuration_from_options here ... ?
# 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?
nlin_component = get_nonlinear_component(
reg_method=options.mbm.nlin.reg_method)
lsq12_conf = get_linear_configuration_from_options(
conf=options.mbm.lsq12,
transform_type=LinearTransType.lsq12,
file_resolution=options.registration.resolution)
# N.B.: options.registration.resolution has been *updated* correctly by mbm( ). sigh ...
model_to_common = s.defer(
lsq12_nlin(
source=mbm_result.avg_img,
target=common_space_model,
lsq12_conf=lsq12_conf,
nlin_module=nlin_component,
resolution=options.registration.resolution,
nlin_options=options.mbm.nlin.nlin_protocol, # =nlin_conf,
resample_source=True))
model_common = s.defer(
mincresample_new(img=mbm_result.avg_img,
xfm=model_to_common.xfm,
like=common_space_model,
postfix="_common"))
overall_xfms_to_common = [
s.defer(concat_xfmhandlers([rigid_xfm, nlin_xfm, model_to_common]))
for rigid_xfm, nlin_xfm in zip(mbm_result.xfms.rigid_xfm,
mbm_result.xfms.lsq12_nlin_xfm)
]
overall_xfms_to_common_inv = [
s.defer(invert_xfmhandler(xfmhandler)) for xfmhandler in [
s.defer(concat_xfmhandlers([rigid_xfm, nlin_xfm, model_to_common]))
for rigid_xfm, nlin_xfm in zip(mbm_result.xfms.rigid_xfm,
mbm_result.xfms.lsq12_nlin_xfm)
]
]
xfms_to_common = [
s.defer(concat_xfmhandlers([nlin_xfm, model_to_common]))
for nlin_xfm in mbm_result.xfms.lsq12_nlin_xfm
]
mbm_result.xfms = mbm_result.xfms.assign(
xfm_to_common=xfms_to_common,
overall_xfm_to_common=overall_xfms_to_common)
if options.mbm.stats.calc_stats:
log_nlin_det_common, log_full_det_common = ([
dets.map(lambda d: s.defer(
mincresample_new(img=d,
xfm=model_to_common.xfm,
like=common_space_model,
postfix="_common")))
for dets in (mbm_result.determinants.log_nlin_det,
mbm_result.determinants.log_full_det)
])
overall_determinants = s.defer(
determinants_at_fwhms(xfms=overall_xfms_to_common_inv,
blur_fwhms=options.mbm.stats.stats_kernels))
mbm_result.determinants = \
mbm_result.determinants.assign(log_nlin_det_common=log_nlin_det_common,
log_full_det_common=log_full_det_common,
log_nlin_overall_det_common=overall_determinants.log_nlin_det,
log_full_overall_det_common=overall_determinants.log_full_det
)
mbm_result.model_common = model_common
return Result(stages=s, output=mbm_result)
def NLIN_pipeline(options):
output_dir = options.application.output_directory
pipeline_name = options.application.pipeline_name
# TODO this is tedious and annoyingly similar to the registration chain and MBM and LSQ6 ...
processed_dir = os.path.join(output_dir, pipeline_name + "_processed")
nlin_dir = os.path.join(output_dir, pipeline_name + "_nlin")
resolution = (
options.registration.
resolution # TODO does using the finest resolution here make sense?
or min(
[get_resolution_from_file(f) for f in options.application.files]))
imgs = get_imgs(options.application)
initial_target_mask = MincAtom(
options.nlin.target_mask) if options.nlin.target_mask else None
initial_target = MincAtom(options.nlin.target, mask=initial_target_mask)
nlin_module = get_nonlinear_component(reg_method=options.nlin.reg_method)
nlin_build_model_component = get_model_building_procedure(
options.nlin.reg_strategy, reg_module=nlin_module)
nlin_conf = (nlin_build_model_component.parse_build_model_protocol(
options.nlin.nlin_protocol, resolution=resolution)
if options.nlin.nlin_protocol is not None else
nlin_build_model_component.get_default_build_model_conf(
resolution=resolution))
s = Stages()
nlin_result = s.defer(
nlin_build_model_component.build_model(
imgs=imgs,
initial_target=initial_target,
conf=nlin_conf,
nlin_dir=nlin_dir,
use_robust_averaging=options.nlin.use_robust_averaging,
nlin_prefix=""))
inverted_xfms = [
s.defer(invert_xfmhandler(xfm)) for xfm in nlin_result.output
]
if options.stats.calc_stats:
determinants = s.defer(
determinants_at_fwhms(xfms=inverted_xfms,
inv_xfms=nlin_result.output,
blur_fwhms=options.stats.stats_kernels))
return Result(stages=s,
output=Namespace(nlin_xfms=nlin_result,
avg_img=nlin_result.avg_img,
determinants=determinants))
else:
# there's no consistency in what gets returned, yikes ...
return Result(stages=s,
output=Namespace(nlin_xfms=nlin_result,
avg_img=nlin_result.avg_img))
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))
