deep_folding
README:
Deep folding
Prerequisites
Generates datasets of crops
Development
API documentation
deep_folding package
deep_folding
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Index
Index
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W
A
array_to_ana() (in module deep_folding.brainvisa.display_reconstructions)
AugDatasetTransformer (class in deep_folding.preprocessing.datasets)
B
Benchmark (class in deep_folding.brainvisa.benchmark_generation_distmap)
BenchmarkPipe (class in deep_folding.brainvisa.benchmark_pipeline)
BoundingBoxMax (class in deep_folding.brainvisa.compute_bounding_box)
box_ICBM2009c_to_aims_talairach() (in module deep_folding.brainvisa.compute_bounding_box)
build_bucket_filename() (in module deep_folding.brainvisa.utils.convert_volume_to_bucket)
build_distMap_filename() (in module deep_folding.brainvisa.utils.write_distance_map)
C
check() (in module deep_folding.brainvisa.mask_qc)
compare_array_aims_files() (in module deep_folding.brainvisa.utils.save_data)
compare_number_aims_files_with_expected() (in module deep_folding.brainvisa.utils.quality_checks)
compare_number_aims_files_with_number_in_source() (in module deep_folding.brainvisa.utils.quality_checks)
compare_one_array() (in module deep_folding.brainvisa.utils.save_data)
complete_sulci_name() (in module deep_folding.brainvisa.utils.sulcus)
compute() (deep_folding.brainvisa.compute_bounding_box.BoundingBoxMax method)
(deep_folding.brainvisa.compute_mask.MaskAroundSulcus method)
(deep_folding.brainvisa.generate_ICBM2009c_transforms.GraphGenerateTransform method)
(deep_folding.brainvisa.generate_crops.CropGenerator method)
(deep_folding.brainvisa.generate_distmaps.SkelConvert2DistMap method)
(deep_folding.brainvisa.generate_foldlabels.GraphConvert2FoldLabel method)
(deep_folding.brainvisa.generate_skeletons.GraphConvert2Skeleton method)
(deep_folding.brainvisa.remove_ventricle.RemoveVentricleFromSkeleton method)
(deep_folding.brainvisa.resample_files.FileResampler method)
compute_bbox_mask() (in module deep_folding.brainvisa.utils.mask)
compute_bounding_box() (in module deep_folding.brainvisa.compute_bounding_box)
compute_bounding_box_or_mask() (deep_folding.brainvisa.generate_crops.CropGenerator method)
compute_box_voxel() (in module deep_folding.brainvisa.compute_bounding_box)
compute_centered_mask() (in module deep_folding.brainvisa.utils.mask)
compute_intersection_mask() (in module deep_folding.brainvisa.utils.mask)
compute_mask() (in module deep_folding.brainvisa.compute_mask)
compute_max() (in module deep_folding.brainvisa.utils.bbox)
compute_max_box() (in module deep_folding.brainvisa.utils.bbox)
compute_simple_mask() (in module deep_folding.brainvisa.utils.mask)
convert_volume_to_bucket() (in module deep_folding.brainvisa.utils.remove_hull)
create_benchmark_test() (in module deep_folding.preprocessing.create_sets)
create_empty_volume_from_graph() (in module deep_folding.brainvisa.utils.graph)
create_file() (deep_folding.brainvisa.utils.logs.LogJson method)
create_folder() (in module deep_folding.brainvisa.utils.folder)
(in module deep_folding.utils.save_results)
create_hcp_benchmark() (in module deep_folding.preprocessing.create_sets)
create_hcp_sets() (in module deep_folding.preprocessing.create_sets)
create_left_handed_set() (in module deep_folding.preprocessing.create_sets)
create_loader_from_csv() (in module deep_folding.preprocessing.create_sets)
create_meshes() (deep_folding.brainvisa.utils.remove_hull.DatasetHullRemoved method)
create_one_mesh() (deep_folding.brainvisa.utils.remove_hull.DatasetHullRemoved method)
(in module deep_folding.brainvisa.utils.remove_hull)
crop_bbox() (in module deep_folding.brainvisa.generate_crops)
crop_files() (deep_folding.brainvisa.generate_crops.CropGenerator method)
crop_mask() (in module deep_folding.brainvisa.generate_crops)
crop_one_file() (deep_folding.brainvisa.benchmark_pipeline.BenchmarkPipe method)
(deep_folding.brainvisa.generate_crops.CropGenerator method)
CropGenerator (class in deep_folding.brainvisa.generate_crops)
D
DatasetHullRemoved (class in deep_folding.brainvisa.utils.remove_hull)
deep_folding (module)
deep_folding.brainvisa (module)
deep_folding.brainvisa.benchmark_generation_distmap (module)
deep_folding.brainvisa.benchmark_pipeline (module)
deep_folding.brainvisa.compute_bounding_box (module)
deep_folding.brainvisa.compute_mask (module)
deep_folding.brainvisa.display_reconstructions (module)
deep_folding.brainvisa.generate_crops (module)
deep_folding.brainvisa.generate_distmaps (module)
deep_folding.brainvisa.generate_foldlabels (module)
deep_folding.brainvisa.generate_ICBM2009c_transforms (module)
deep_folding.brainvisa.generate_skeletons (module)
deep_folding.brainvisa.mask_qc (module)
deep_folding.brainvisa.pipeline (module)
deep_folding.brainvisa.remove_ventricle (module)
deep_folding.brainvisa.resample_files (module)
deep_folding.brainvisa.utils (module)
deep_folding.brainvisa.utils.bbox (module)
deep_folding.brainvisa.utils.constants (module)
deep_folding.brainvisa.utils.convert_volume_to_bucket (module)
deep_folding.brainvisa.utils.dilate_mask (module)
deep_folding.brainvisa.utils.distmap (module)
deep_folding.brainvisa.utils.folder (module)
deep_folding.brainvisa.utils.foldlabel (module)
deep_folding.brainvisa.utils.graph (module)
deep_folding.brainvisa.utils.logs (module)
deep_folding.brainvisa.utils.mask (module)
deep_folding.brainvisa.utils.padding (module)
deep_folding.brainvisa.utils.parallel (module)
deep_folding.brainvisa.utils.quality_checks (module)
deep_folding.brainvisa.utils.referentials (module)
deep_folding.brainvisa.utils.remove_hull (module)
deep_folding.brainvisa.utils.resample (module)
deep_folding.brainvisa.utils.save_data (module)
deep_folding.brainvisa.utils.skeleton (module)
deep_folding.brainvisa.utils.subjects (module)
deep_folding.brainvisa.utils.sulcus (module)
deep_folding.brainvisa.utils.suppress_files_from_csv (module)
deep_folding.brainvisa.utils.write_distance_map (module)
deep_folding.info (module)
deep_folding.preprocessing (module)
deep_folding.preprocessing.create_sets (module)
deep_folding.preprocessing.datasets (module)
deep_folding.preprocessing.generate_numpy_array (module)
deep_folding.preprocessing.pynet_transforms (module)
deep_folding.utils (module)
deep_folding.utils.pytorchtools (module)
deep_folding.utils.save_results (module)
deep_folding.utils.split_train_test (module)
define_njobs() (in module deep_folding.brainvisa.benchmark_pipeline)
(in module deep_folding.brainvisa.utils.parallel)
(in module deep_folding.brainvisa.utils.remove_hull)
delete_ss() (deep_folding.brainvisa.benchmark_generation_distmap.Benchmark method)
dilate() (in module deep_folding.brainvisa.utils.dilate_mask)
DistMapCropGenerator (class in deep_folding.brainvisa.generate_crops)
DistMapResampler (class in deep_folding.brainvisa.resample_files)
Downsample (class in deep_folding.preprocessing.pynet_transforms)
DownsampleTensor (class in deep_folding.preprocessing.pynet_transforms)
E
EarlyStopping (class in deep_folding.utils.pytorchtools)
exception_handler() (in module deep_folding.brainvisa)
F
FileResampler (class in deep_folding.brainvisa.resample_files)
filter_mask() (in module deep_folding.brainvisa.generate_crops)
FoldLabelCropGenerator (class in deep_folding.brainvisa.generate_crops)
FoldLabelResampler (class in deep_folding.brainvisa.resample_files)
G
generate() (in module deep_folding.brainvisa.benchmark_generation_distmap)
generate_crops() (in module deep_folding.brainvisa.generate_crops)
generate_distmap_from_resampled_skeleton() (in module deep_folding.brainvisa.utils.distmap)
generate_distmap_from_skeleton_file() (in module deep_folding.brainvisa.utils.distmap)
generate_distmaps() (in module deep_folding.brainvisa.generate_distmaps)
generate_foldlabel() (deep_folding.brainvisa.benchmark_generation_distmap.Benchmark method)
generate_foldlabel_from_graph() (in module deep_folding.brainvisa.utils.foldlabel)
generate_foldlabel_from_graph_file() (in module deep_folding.brainvisa.utils.foldlabel)
generate_foldlabel_thin_junction() (in module deep_folding.brainvisa.utils.foldlabel)
generate_foldlabel_wide_junction() (in module deep_folding.brainvisa.utils.foldlabel)
generate_foldlabels() (in module deep_folding.brainvisa.generate_foldlabels)
generate_ICBM2009c_transforms() (in module deep_folding.brainvisa.generate_ICBM2009c_transforms)
generate_np_array() (in module deep_folding.preprocessing.generate_numpy_array)
generate_one_distmap() (deep_folding.brainvisa.generate_distmaps.SkelConvert2DistMap method)
generate_one_foldlabel() (deep_folding.brainvisa.generate_foldlabels.GraphConvert2FoldLabel method)
generate_one_skeleton() (deep_folding.brainvisa.generate_skeletons.GraphConvert2Skeleton method)
generate_one_transform() (deep_folding.brainvisa.generate_ICBM2009c_transforms.GraphGenerateTransform method)
generate_ref_volume_ICBM2009c() (in module deep_folding.brainvisa.utils.referentials)
generate_skeleton() (deep_folding.brainvisa.benchmark_generation_distmap.Benchmark method)
generate_skeleton_from_graph() (in module deep_folding.brainvisa.utils.skeleton)
generate_skeleton_from_graph_file() (in module deep_folding.brainvisa.utils.skeleton)
generate_skeleton_thin_junction() (in module deep_folding.brainvisa.utils.skeleton)
generate_skeleton_wide_junction() (in module deep_folding.brainvisa.utils.skeleton)
generate_skeletons() (in module deep_folding.brainvisa.generate_skeletons)
get_all_subjects_as_dictionary() (in module deep_folding.brainvisa.utils.subjects)
get_basename_without_extension() (in module deep_folding.brainvisa.utils.convert_volume_to_bucket)
(in module deep_folding.utils.split_train_test)
get_bounding_boxes() (in module deep_folding.brainvisa.compute_bounding_box)
get_foldlabel_filename() (deep_folding.brainvisa.generate_foldlabels.GraphConvert2FoldLabel method)
get_labelled_graph() (deep_folding.brainvisa.remove_ventricle.RemoveVentricleFromSkeleton method)
get_not_processed_cropped_files() (in module deep_folding.brainvisa.utils.quality_checks)
get_not_processed_files() (in module deep_folding.brainvisa.utils.quality_checks)
get_not_processed_subjects() (in module deep_folding.brainvisa.utils.quality_checks)
get_not_processed_subjects_dict() (in module deep_folding.brainvisa.utils.quality_checks)
get_not_processed_subjects_distmap() (in module deep_folding.brainvisa.utils.quality_checks)
get_not_processed_subjects_transform() (in module deep_folding.brainvisa.utils.quality_checks)
get_number_subjects() (in module deep_folding.brainvisa.utils.subjects)
get_one_bounding_box() (in module deep_folding.brainvisa.compute_bounding_box)
get_one_numpy_array() (in module deep_folding.brainvisa.utils.save_data)
get_simple_surfaces() (deep_folding.brainvisa.benchmark_generation_distmap.Benchmark method)
get_skeleton_filename() (deep_folding.brainvisa.generate_skeletons.GraphConvert2Skeleton method)
get_sub_list() (deep_folding.brainvisa.benchmark_pipeline.BenchmarkPipe method)
(in module deep_folding.brainvisa.benchmark_generation_distmap)
get_subject_name() (in module deep_folding.brainvisa.utils.write_distance_map)
get_sulci_list() (in module deep_folding.brainvisa.pipeline)
get_transform_filename() (deep_folding.brainvisa.generate_ICBM2009c_transforms.GraphGenerateTransform method)
GraphConvert2FoldLabel (class in deep_folding.brainvisa.generate_foldlabels)
GraphConvert2Skeleton (class in deep_folding.brainvisa.generate_skeletons)
GraphGenerateTransform (class in deep_folding.brainvisa.generate_ICBM2009c_transforms)
I
ICBM2009c_to_aims_talairach() (in module deep_folding.brainvisa.utils.referentials)
increment_mask() (in module deep_folding.brainvisa.compute_mask)
increment_one_mask() (in module deep_folding.brainvisa.compute_mask)
initialize_mask() (in module deep_folding.brainvisa.compute_mask)
intersect_binary() (in module deep_folding.brainvisa.utils.mask)
is_directory_empty() (in module deep_folding.brainvisa.pipeline)
is_file_nii() (in module deep_folding.brainvisa.utils.save_data)
is_it_a_subject() (in module deep_folding.brainvisa.utils.subjects)
is_skeleton() (in module deep_folding.brainvisa.utils.skeleton)
is_step_to_be_computed() (in module deep_folding.brainvisa.pipeline)
L
launch_pipe() (deep_folding.brainvisa.benchmark_pipeline.BenchmarkPipe method)
log_command_line() (in module deep_folding.brainvisa.utils.logs)
LogJson (class in deep_folding.brainvisa.utils.logs)
loop_over_directory() (in module deep_folding.brainvisa.utils.convert_volume_to_bucket)
(in module deep_folding.brainvisa.utils.write_distance_map)
M
main() (in module deep_folding.brainvisa.benchmark_pipeline)
(in module deep_folding.brainvisa.display_reconstructions)
(in module deep_folding.brainvisa.mask_qc)
(in module deep_folding.brainvisa.utils.convert_volume_to_bucket)
(in module deep_folding.brainvisa.utils.dilate_mask)
(in module deep_folding.brainvisa.utils.remove_hull)
(in module deep_folding.brainvisa.utils.suppress_files_from_csv)
(in module deep_folding.preprocessing.generate_numpy_array)
(in module deep_folding.utils.split_train_test)
MaskAroundSulcus (class in deep_folding.brainvisa.compute_mask)
N
NormalizeHisto (class in deep_folding.preprocessing.pynet_transforms)
NormalizeSkeleton (class in deep_folding.preprocessing.pynet_transforms)
P
padd() (in module deep_folding.brainvisa.utils.padding)
Padding (class in deep_folding.preprocessing.pynet_transforms)
PaddingTensor (class in deep_folding.preprocessing.pynet_transforms)
parse_args() (in module deep_folding.brainvisa.benchmark_pipeline)
(in module deep_folding.brainvisa.compute_bounding_box)
(in module deep_folding.brainvisa.compute_mask)
(in module deep_folding.brainvisa.generate_ICBM2009c_transforms)
(in module deep_folding.brainvisa.generate_crops)
(in module deep_folding.brainvisa.generate_distmaps)
(in module deep_folding.brainvisa.generate_foldlabels)
(in module deep_folding.brainvisa.generate_skeletons)
(in module deep_folding.brainvisa.mask_qc)
(in module deep_folding.brainvisa.pipeline)
(in module deep_folding.brainvisa.remove_ventricle)
(in module deep_folding.brainvisa.resample_files)
(in module deep_folding.brainvisa.utils.convert_volume_to_bucket)
(in module deep_folding.brainvisa.utils.remove_hull)
(in module deep_folding.brainvisa.utils.suppress_files_from_csv)
(in module deep_folding.brainvisa.utils.write_distance_map)
(in module deep_folding.utils.split_train_test)
print_info() (in module deep_folding.brainvisa.pipeline)
Q
quality_checks() (in module deep_folding.brainvisa.utils.save_data)
R
read_convert_write() (in module deep_folding.brainvisa.utils.convert_volume_to_bucket)
remove_hull() (in module deep_folding.brainvisa.utils.remove_hull)
remove_ventricle() (in module deep_folding.brainvisa.remove_ventricle)
remove_ventricle_from_one_skeleton() (in module deep_folding.brainvisa.remove_ventricle)
remove_ventricle_from_one_subject() (deep_folding.brainvisa.remove_ventricle.RemoveVentricleFromSkeleton method)
RemoveVentricleFromSkeleton (class in deep_folding.brainvisa.remove_ventricle)
resample() (in module deep_folding.brainvisa.utils.resample)
resample_files() (in module deep_folding.brainvisa.resample_files)
resample_one_distmap() (in module deep_folding.brainvisa.resample_files)
resample_one_foldlabel() (in module deep_folding.brainvisa.resample_files)
resample_one_skeleton() (in module deep_folding.brainvisa.resample_files)
resample_one_subject() (deep_folding.brainvisa.resample_files.DistMapResampler static method)
(deep_folding.brainvisa.resample_files.FileResampler static method)
(deep_folding.brainvisa.resample_files.FoldLabelResampler static method)
(deep_folding.brainvisa.resample_files.SkeletonResampler static method)
resample_one_subject_wrapper() (deep_folding.brainvisa.resample_files.FileResampler method)
S
save_checkpoint() (deep_folding.utils.pytorchtools.EarlyStopping method)
save_file() (deep_folding.brainvisa.benchmark_generation_distmap.Benchmark method)
save_list_to_csv() (in module deep_folding.brainvisa.utils.quality_checks)
save_lists() (deep_folding.brainvisa.benchmark_generation_distmap.Benchmark method)
save_logs() (in module deep_folding.utils.save_results)
save_to_dataframe_format_from_list() (in module deep_folding.brainvisa.utils.save_data)
save_to_numpy() (in module deep_folding.brainvisa.utils.save_data)
save_to_pickle() (in module deep_folding.brainvisa.utils.save_data)
select_good_qc() (in module deep_folding.brainvisa.utils.subjects)
select_subjects() (in module deep_folding.brainvisa.utils.subjects)
select_subjects_int() (in module deep_folding.brainvisa.utils.subjects)
setup_log() (in module deep_folding.brainvisa.utils.logs)
skel_2_distMap() (in module deep_folding.brainvisa.utils.write_distance_map)
SkelConvert2DistMap (class in deep_folding.brainvisa.generate_distmaps)
SkeletonCropGenerator (class in deep_folding.brainvisa.generate_crops)
SkeletonDataset (class in deep_folding.preprocessing.datasets)
SkeletonResampler (class in deep_folding.brainvisa.resample_files)
split_train_test() (in module deep_folding.utils.split_train_test)
suppress() (in module deep_folding.brainvisa.utils.suppress_files_from_csv)
T
TensorDataset (class in deep_folding.preprocessing.datasets)
threshold_and_binarize() (in module deep_folding.brainvisa.utils.remove_hull)
U
update() (deep_folding.brainvisa.utils.logs.LogJson method)
W
write_general_info() (deep_folding.brainvisa.utils.logs.LogJson method)
write_mask() (in module deep_folding.brainvisa.compute_mask)