Index

A

adjust_data_final() (in module cvasl.vendor.neurocombat.neurocombat) aprior() (in module cvasl.vendor.neurocombat.neurocombat)

AutoCombat (class in cvasl.vendor.comscan.neurocombat) avg_k_folds() (in module cvasl.seperated)

B

bin_dataset() (in module cvasl.seperated)

bprior() (in module cvasl.vendor.neurocombat.neurocombat)

C

check_exist_vars() (in module cvasl.vendor.comscan.utils) check_identical_columns() (in module cvasl.seperated) check_is_nii_exist() (in module cvasl.vendor.comscan.utils) check_sex_dimorph_expectations() (in module cvasl.seperated) column_var_dtype() (in module cvasl.vendor.comscan.utils) Combat (class in cvasl.vendor.comscan.neurocombat) common() (in module cvasl.cli) compare_harm_multi_site_violins() (in module cvasl.harmony) compare_harm_one_site_violins() (in module cvasl.harmony) concat_double_header() (in module cvasl.seperated) Config (class in cvasl.file_handler) config_override() (in module cvasl.cli) convert_zeroes() (in module cvasl.vendor.neurocombat.neurocombat) cvasl module cvasl.carve module cvasl.cli module cvasl.file_handler module cvasl.harmony module

cvasl.mold module cvasl.seperated module cvasl.vendor module cvasl.vendor.comscan module cvasl.vendor.comscan.clustering module cvasl.vendor.comscan.neurocombat module cvasl.vendor.comscan.nifti module cvasl.vendor.comscan.utils module cvasl.vendor.neurocombat module cvasl.vendor.neurocombat.neurocombat module cvasl.vendor.open_nested_combat module cvasl.vendor.open_nested_combat.nest module

D

date_fields (cvasl.carve.SimpleITKDicomReader attribute) debias_folder() (in module cvasl.mold) default_layout (cvasl.file_handler.Config attribute) default_locations (cvasl.file_handler.Config attribute) derived_function() (in module cvasl.seperated)

dicom_date_to_date() (cvasl.carve.SimpleITKDicomReader method) dicom_time_to_time() (cvasl.carve.SimpleITKDicomReader method) DirectorySource (class in cvasl.carve) draw() (cvasl.vendor.comscan.clustering.KElbowVisualizer method) drop_columns_folder() (in module cvasl.seperated) drop_y() (in module cvasl.seperated)

E

exclude_fields (cvasl.carve.SimpleITKDicomReader attribute)

extract_common_columns() (in module cvasl.file_handler)

F

feature_ad() (in module cvasl.vendor.open_nested_combat.nest) fetch_image() (cvasl.carve.MetadataHelper method) fetch_metadata() (cvasl.carve.MetadataHelper method) finalize() (cvasl.vendor.comscan.clustering.KElbowVisualizer method) find_non_eb_adjustments() (in module cvasl.vendor.neurocombat.neurocombat) find_non_parametric_adjustments() (in module cvasl.vendor.neurocombat.neurocombat) find_original_y_values() (in module cvasl.seperated) find_outliers_by_list() (in module cvasl.seperated) find_parametric_adjustments() (in module cvasl.vendor.neurocombat.neurocombat) find_where_column() (in module cvasl.file_handler)

fit() (cvasl.vendor.comscan.clustering.KElbowVisualizer method) (cvasl.vendor.comscan.clustering.KMeansConstrainedMissing method) (cvasl.vendor.comscan.neurocombat.AutoCombat method) (cvasl.vendor.comscan.neurocombat.Combat method) (cvasl.vendor.comscan.neurocombat.ImageCombat method) fit_LS_model_and_find_priors() (in module cvasl.vendor.neurocombat.neurocombat) fit_predict() (cvasl.vendor.comscan.clustering.KMeansConstrainedMissing method) fix_columns() (in module cvasl.vendor.comscan.utils) flatten_nifti_files() (in module cvasl.vendor.comscan.nifti) folder_chain_out_columns() (in module cvasl.seperated) from_file() (cvasl.file_handler.Config class method)

G

generate_transformation_matrix() (in module cvasl.seperated) get_column_index() (in module cvasl.vendor.comscan.utils) get_directory() (cvasl.file_handler.Config method) get_tag() (cvasl.carve.DirectorySource method) (cvasl.carve.GlobSource method) (cvasl.carve.MultiSource method)

GlobSource (class in cvasl.carve) GMMSplit() (in module cvasl.vendor.open_nested_combat.nest)

H

hash_folder() (in module cvasl.file_handler)

hash_rash() (in module cvasl.file_handler)

I

ImageCombat (class in cvasl.vendor.comscan.neurocombat) increment_keys() (in module cvasl.harmony) int_eprior() (in module cvasl.vendor.neurocombat.neurocombat) intersect_all() (in module cvasl.file_handler)

it_sol() (in module cvasl.vendor.neurocombat.neurocombat) items() (cvasl.carve.DirectorySource method) (cvasl.carve.GlobSource method) (cvasl.carve.MultiSource method)

K

KElbowVisualizer (class in cvasl.vendor.comscan.clustering)

KMeansConstrainedMissing (class in cvasl.vendor.comscan.clustering)

L

load() (cvasl.file_handler.Config method) load_fit() (cvasl.vendor.comscan.neurocombat.Combat method)

load_nifty_volume_as_array() (in module cvasl.vendor.comscan.utils) log_out_columns() (in module cvasl.harmony)

M

main() (in module cvasl.cli) make_columns() (in module cvasl.file_handler) make_design_matrix() (in module cvasl.vendor.neurocombat.neurocombat) make_log_file() (in module cvasl.seperated) make_log_folder() (in module cvasl.seperated) make_parser() (in module cvasl.cli) make_topper() (in module cvasl.harmony) mat_to_bytes() (in module cvasl.vendor.comscan.utils) MetadataHelper (class in cvasl.carve) module cvasl cvasl.carve cvasl.cli cvasl.file_handler cvasl.harmony cvasl.mold cvasl.seperated cvasl.vendor cvasl.vendor.comscan cvasl.vendor.comscan.clustering cvasl.vendor.comscan.neurocombat cvasl.vendor.comscan.nifti cvasl.vendor.comscan.utils cvasl.vendor.neurocombat cvasl.vendor.neurocombat.neurocombat cvasl.vendor.open_nested_combat cvasl.vendor.open_nested_combat.nest

MultiSource (class in cvasl.carve)

N

n4_debias_sitk() (in module cvasl.mold) negative_harm_outcomes() (in module cvasl.harmony) neuroCombat() (in module cvasl.vendor.neurocombat.neurocombat)

neuroCombatFromTraining() (in module cvasl.vendor.neurocombat.neurocombat) no_file() (cvasl.file_handler.Config class method) NormedSliceViewer (class in cvasl.mold)

O

one_hot_encoder() (in module cvasl.vendor.comscan.utils)

OPNestedComBat() (in module cvasl.vendor.open_nested_combat.nest) optimal_clustering() (in module cvasl.vendor.comscan.clustering)

P

parse() (cvasl.file_handler.Config method) parse_overrides() (cvasl.file_handler.Config method) plot_2on2_df() (in module cvasl.seperated) plot_slice() (cvasl.mold.NormedSliceViewer method) (cvasl.mold.SliceViewer method) polyfit_and_show() (in module cvasl.seperated) polyfit_second_degree_to_df() (in module cvasl.seperated)

postmean() (in module cvasl.vendor.neurocombat.neurocombat) postvar() (in module cvasl.vendor.neurocombat.neurocombat) pprint() (cvasl.file_handler.Config method) predict() (cvasl.vendor.comscan.clustering.KMeansConstrainedMissing method) prep_for_neurocombat() (in module cvasl.harmony) prep_for_neurocombat_5way() (in module cvasl.harmony) preprocess() (in module cvasl.seperated) pull_off_unnamed_column() (in module cvasl.seperated)

R

read() (cvasl.carve.SimpleITKDicomReader method) recode_sex() (in module cvasl.seperated) recode_sex_folder() (in module cvasl.seperated) recode_sex_to_numeric() (in module cvasl.seperated) relate_columns_graphs() (in module cvasl.seperated)

relate_columns_graphs_numeric() (in module cvasl.seperated) relate_columns_graphs_two_dfs() (in module cvasl.seperated) rename_file() (in module cvasl.carve) required_directories (cvasl.file_handler.Config attribute) rip_out_array_sitk() (in module cvasl.carve)

S

save_fit() (cvasl.vendor.comscan.neurocombat.Combat method) save_preprocessed() (in module cvasl.mold) save_to_nii() (in module cvasl.vendor.comscan.utils) scaler_encoder() (in module cvasl.vendor.comscan.utils) set_predict_request() (cvasl.vendor.comscan.clustering.KMeansConstrainedMissing method) show_diff_on_var() (in module cvasl.harmony) show_diff_on_var3() (in module cvasl.harmony) show_diff_on_var5() (in module cvasl.harmony)

SimpleITKDicomReader (class in cvasl.carve) SliceViewer (class in cvasl.mold) split_filename() (in module cvasl.vendor.comscan.utils) split_frame_half_balanced_by_column() (in module cvasl.harmony) standardize_across_features() (in module cvasl.vendor.neurocombat.neurocombat) static_bin_age() (in module cvasl.seperated) stratified_cat_and_cont_categories_shuffle_split() (in module cvasl.seperated) stratified_one_category_shuffle_split() (in module cvasl.seperated)

T

time_fields (cvasl.carve.SimpleITKDicomReader attribute) top_and_bottom_by_column() (in module cvasl.harmony) transform() (cvasl.vendor.comscan.neurocombat.AutoCombat method) (cvasl.vendor.comscan.neurocombat.Combat method) (cvasl.vendor.comscan.neurocombat.ImageCombat method)

transpose() (cvasl.mold.NormedSliceViewer method) (cvasl.mold.SliceViewer method) tsne() (in module cvasl.vendor.comscan.utils)

U

u_map() (in module cvasl.vendor.comscan.utils)

unduplicate_dfs() (in module cvasl.file_handler) usage() (cvasl.file_handler.Config method)

V

validate() (cvasl.file_handler.Config method)