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))
def get_chain_transforms_for_stats(pipeline_subject_info, intersubj_xfms_dict, chain_xfms_dict):
"""
pipeline_subject_info
intersubj_xfms_dict
chain_xfms_dict -- {subject_ID : ( [ (time_point_n, time_point_n+1, XfmHandler(time_point -> time_point + 1)),
..., (,,,) ],
index_of_common_time_point) }
This function takes a subject mapping (with timepoints to MincAtoms) and returns a
subject mapping of timepoints to `XfmHandler`s. Those transformations for
each subject will contain the non-rigid transformation to the common time point average
chain_xfms_dict maps subject_ids to a tuple containing a list of tuples
(time_point_n, time_point_n+1, transformation)
and the index to the common time point in that list
"""
s = Stages()
dict_transforms_to_common_avg = {}
dict_transforms_to_subject_common_tp = {}
dict_transforms_from_common_tp_to_common_avg = {}
for s_id, subj in pipeline_subject_info.items():
# dictionary: {time_pt : XfmHandler_time_pt_to_final_common_avg}
trans_to_final_common_avg_dict = {}
# dictionary: {time_pt : XfmHandler_time_pt_to_subject_common_time_pt}
trans_to_subject_common_time_pt = {}
##############################################################
# -------------
# time_1 ... | time_common | ... time_n
# -------------
#
# the transformation for the common time point is easy,
# intersubj_xfms_dict[subj.intersubject_registration_image]
# returns the XfmHandler from the subject common time point
# to the common time point average
trans_to_final_common_avg_dict[subj.intersubject_registration_time_pt] = \
intersubj_xfms_dict[subj.intersubject_registration_image]
# there is no transform from the common time point to the common time
# point. Technically it is the identity transformation, but there is
# no use in generating a stats file from the identity transformation,
# so we simply won't generate anything
chain_transforms, index_of_common_time_pt = chain_xfms_dict[s_id]
# will hold the XfmHandler from current to average of common time pt
current_xfm_to_common_avg = intersubj_xfms_dict[subj.intersubject_registration_image]
# and the XfmHandler from current to the subject common time point
# starts out as None (technically the identity transformation)
current_xfm_to_common_subject = None
# we start at the common time point and are going forward at this point
# so we will assign the concatenated transform to the target of each
# transform we are adding (which is why we take the inverse)
#
# - - - - - - - - >
# time_1 ... time_common ... time_n
#
#
for time_pt_n, time_pt_n_plus_1, transform in chain_transforms[index_of_common_time_pt:]:
current_xfm_to_common_avg = s.defer(concat_xfmhandlers([s.defer(invert_xfmhandler(transform)), current_xfm_to_common_avg],
name="id_%s_pt_%s_to_common_avg" % (s_id, time_pt_n_plus_1)))
# we are moving away from the common time point. That means that the transformation
# we are adding here is the inverse of n -> n+1, and should be added to time point n+1
trans_to_final_common_avg_dict[time_pt_n_plus_1] = current_xfm_to_common_avg
if current_xfm_to_common_subject == None:
current_xfm_to_common_subject = s.defer(invert_xfmhandler(transform))
else:
current_xfm_to_common_subject = s.defer(concat_xfmhandlers([s.defer(invert_xfmhandler(transform)), current_xfm_to_common_subject],
name="id_%s_pt_%s_to_common_subject" % (s_id, time_pt_n_plus_1)))
trans_to_subject_common_time_pt[time_pt_n_plus_1] = current_xfm_to_common_subject
# we need to do something similar moving backwards: make sure to reset
# the current_xfm_to_common_avg here!
#
# < - - - - - - - -
# time_1 ... time_common ... time_n
#
#
current_xfm_to_common_avg = intersubj_xfms_dict[subj.intersubject_registration_image]
current_xfm_to_common_subject = None
# we have to be careful here... if the index_of_common_time_pt is 0 (i.e. all images are
# registered towards the first file in the time line, the following command will call:
# .... chain_transforms[-1::-1] and that in turn will start at the end of the list
# because -1 wraps around. To prevent this case, we ensure that the index_of_common_time_pt
# is greater than 0
if index_of_common_time_pt > 0:
for time_pt_n, time_pt_n_plus_1, transform in chain_transforms[index_of_common_time_pt-1::-1]:
current_xfm_to_common_avg = s.defer(concat_xfmhandlers([transform, current_xfm_to_common_avg],
name="id_%s_pt_%s_to_common_avg" % (s_id, time_pt_n)))
trans_to_final_common_avg_dict[time_pt_n] = current_xfm_to_common_avg
if current_xfm_to_common_subject == None:
current_xfm_to_common_subject = transform
else:
current_xfm_to_common_subject = s.defer(concat_xfmhandlers([transform, current_xfm_to_common_subject],
name="id_%s_pt_%s_to_common_subject" % (s_id, time_pt_n)))
trans_to_subject_common_time_pt[time_pt_n] = current_xfm_to_common_subject
new_subj_to_common_avg = Subject(intersubject_registration_time_pt = subj.intersubject_registration_time_pt,
time_pt_dict = trans_to_final_common_avg_dict)
dict_transforms_to_common_avg[s_id] = new_subj_to_common_avg
new_subj_to_common_subj = Subject(intersubject_registration_time_pt = subj.intersubject_registration_time_pt,
time_pt_dict = trans_to_subject_common_time_pt)
dict_transforms_to_subject_common_tp[s_id] = new_subj_to_common_subj
return Result(stages=s, output=(dict_transforms_to_common_avg, dict_transforms_to_subject_common_tp))