Index

_

__call__() (MEDimage.learning.DataCleaner.DataCleaner method) __init__() (MEDimage.biomarkers.BatchExtractor.BatchExtractor method) (MEDimage.biomarkers.glcm.CooccurrenceMatrix method) (MEDimage.biomarkers.glrlm.RunLengthMatrix method) (MEDimage.biomarkers.ngldm.GreyLevelDependenceMatrix method) (MEDimage.filters.gabor.Gabor method) (MEDimage.filters.laws.Laws method) (MEDimage.filters.log.LaplacianOfGaussian method) (MEDimage.filters.mean.Mean method) (MEDimage.filters.wavelet.Wavelet method) (MEDimage.learning.DataCleaner.DataCleaner method) (MEDimage.learning.DesignExperiment.DesignExperiment method) (MEDimage.learning.FSR.FSR method) (MEDimage.learning.Normalization.Normalization method) (MEDimage.learning.RadiomicsLearner.RadiomicsLearner method) (MEDimage.learning.Results.Results method) (MEDimage.wrangling.DataManager.DataManager method) (MEDimage.wrangling.ProcessDICOM.ProcessDICOM method)

_copy() (MEDimage.biomarkers.glcm.CooccurrenceMatrix method) (MEDimage.biomarkers.glrlm.RunLengthMatrix method) _is_jsonable() (in module MEDimage.utils.json_utils) _pad_imgs() (MEDimage.filters.wavelet.Wavelet method) _parse_feature_names() (MEDimage.biomarkers.glrlm.RunLengthMatrix method) _parse_names() (MEDimage.biomarkers.glcm.CooccurrenceMatrix method) _parse_to_ndarray() (MEDimage.utils.imref.imref3d method) _set_empty() (MEDimage.biomarkers.glrlm.RunLengthMatrix method)

A

a_dens_aabb() (in module MEDimage.biomarkers.morph) a_dens_aee() (in module MEDimage.biomarkers.morph) a_dens_conv_hull() (in module MEDimage.biomarkers.morph) a_dens_mvee() (in module MEDimage.biomarkers.morph) a_dens_ombb() (in module MEDimage.biomarkers.morph) apply_combat() (MEDimage.learning.Normalization.Normalization method) apply_fda() (MEDimage.learning.FSR.FSR method) apply_fda_balanced() (MEDimage.learning.FSR.FSR method) apply_fda_one_space() (MEDimage.learning.FSR.FSR method) apply_filter() (in module MEDimage.filters.apply_filter) apply_fsr() (MEDimage.learning.FSR.FSR method) apply_gabor() (in module MEDimage.filters.gabor)

apply_laws() (in module MEDimage.filters.laws) apply_log() (in module MEDimage.filters.log) apply_mean() (in module MEDimage.filters.mean) apply_random_fsr() (MEDimage.learning.FSR.FSR method) apply_random_fsr_one_space() (MEDimage.learning.FSR.FSR method) apply_wavelet() (in module MEDimage.filters.wavelet) approx_vol() (in module MEDimage.biomarkers.morph) area() (in module MEDimage.biomarkers.morph) asphericity() (in module MEDimage.biomarkers.morph) auc() (in module MEDimage.biomarkers.int_vol_hist) auto_corr() (in module MEDimage.biomarkers.glcm) av() (in module MEDimage.biomarkers.morph) average_results() (MEDimage.learning.Results.Results method)

B

batch_patients() (in module MEDimage.utils.batch_patients)

BatchExtractor (class in MEDimage.biomarkers.BatchExtractor) busyness() (in module MEDimage.biomarkers.ngtdm)

C

calculate_cm_features() (MEDimage.biomarkers.glcm.CooccurrenceMatrix method) calculate_cm_matrix() (MEDimage.biomarkers.glcm.CooccurrenceMatrix method) calculate_feature() (MEDimage.biomarkers.glrlm.RunLengthMatrix method) calculate_ngldm_matrix() (MEDimage.biomarkers.ngldm.GreyLevelDependenceMatrix method) calculate_rlm_features() (MEDimage.biomarkers.glrlm.RunLengthMatrix method) calculate_rlm_matrix() (MEDimage.biomarkers.glrlm.RunLengthMatrix method) cell_frame_id (MEDimage.wrangling.DataManager.DataManager.DICOM attribute) cell_frame_rs (MEDimage.wrangling.DataManager.DataManager.DICOM attribute) cell_path_images (MEDimage.wrangling.DataManager.DataManager.DICOM attribute) cell_path_rs (MEDimage.wrangling.DataManager.DataManager.DICOM attribute) cell_series_id (MEDimage.wrangling.DataManager.DataManager.DICOM attribute) clust_prom() (in module MEDimage.biomarkers.glcm) clust_shade() (in module MEDimage.biomarkers.glcm) clust_tend() (in module MEDimage.biomarkers.glcm) coarseness() (in module MEDimage.biomarkers.ngtdm) com() (in module MEDimage.biomarkers.morph) combine_matrices() (in module MEDimage.biomarkers.glcm) combine_ngldm_matrices() (in module MEDimage.biomarkers.ngldm) combine_rlm_matrices() (in module MEDimage.biomarkers.glrlm) combine_slices() (MEDimage.wrangling.ProcessDICOM.ProcessDICOM method) comp_1() (in module MEDimage.biomarkers.morph) comp_2() (in module MEDimage.biomarkers.morph) complexity() (in module MEDimage.biomarkers.ngtdm) compute_bounding_box() (in module MEDimage.processing.segmentation) compute_box() (in module MEDimage.processing.segmentation) compute_ngldm_features() (MEDimage.biomarkers.ngldm.GreyLevelDependenceMatrix method) compute_radiomics() (MEDimage.biomarkers.BatchExtractor.BatchExtractor method) compute_roi() (in module MEDimage.processing.segmentation)

compute_suv_map() (in module MEDimage.processing.compute_suv_map) contains_point() (MEDimage.utils.imref.imref3d method) contrast() (in module MEDimage.biomarkers.glcm) (in module MEDimage.biomarkers.ngtdm) convolve() (in module MEDimage.filters.utils) (MEDimage.filters.gabor.Gabor method) (MEDimage.filters.laws.Laws method) (MEDimage.filters.log.LaplacianOfGaussian method) (MEDimage.filters.mean.Mean method) (MEDimage.filters.wavelet.Wavelet method) CooccurrenceMatrix (class in MEDimage.biomarkers.glcm) coord2index() (in module MEDimage.utils.textureTools) copy() (MEDimage.biomarkers.ngldm.GreyLevelDependenceMatrix method) corr() (in module MEDimage.biomarkers.glcm) cov() (in module MEDimage.biomarkers.intensity_histogram) (in module MEDimage.biomarkers.stats) create_experiment() (MEDimage.learning.DesignExperiment.DesignExperiment method) create_kernel() (MEDimage.filters.gabor.Gabor method) (MEDimage.filters.laws.Laws method) (MEDimage.filters.log.LaplacianOfGaussian method) (MEDimage.filters.mean.Mean method) (MEDimage.filters.wavelet.Wavelet method) create_radiomics_table() (in module MEDimage.utils.create_radiomics_table) crop_box() (in module MEDimage.processing.segmentation) crop_nifti_box() (in module MEDimage.processing.segmentation) cut_off_missing_per_feature() (MEDimage.learning.DataCleaner.DataCleaner method) cut_off_missing_per_sample() (MEDimage.learning.DataCleaner.DataCleaner method) cut_off_variation() (MEDimage.learning.DataCleaner.DataCleaner method)

D

data (MEDimage.utils.image_volume_obj.image_volume_obj attribute) DataCleaner (class in MEDimage.learning.DataCleaner) DataManager (class in MEDimage.wrangling.DataManager) DataManager.DICOM (class in MEDimage.wrangling.DataManager) DataManager.NIfTI (class in MEDimage.wrangling.DataManager) DataManager.Paths (class in MEDimage.wrangling.DataManager) dc_energy() (in module MEDimage.biomarkers.ngldm) dc_entr() (in module MEDimage.biomarkers.ngldm) dc_var() (in module MEDimage.biomarkers.ngldm) dcnu() (in module MEDimage.biomarkers.ngldm) dcnu_norm() (in module MEDimage.biomarkers.ngldm)

DesignExperiment (class in MEDimage.learning.DesignExperiment) diam() (in module MEDimage.biomarkers.morph) diff_avg() (in module MEDimage.biomarkers.glcm) diff_entr() (in module MEDimage.biomarkers.glcm) diff_var() (in module MEDimage.biomarkers.glcm) direction (MEDimage.biomarkers.glcm.CooccurrenceMatrix attribute) (MEDimage.biomarkers.glrlm.RunLengthMatrix attribute) direction_id (MEDimage.biomarkers.glcm.CooccurrenceMatrix attribute) (MEDimage.biomarkers.glrlm.RunLengthMatrix attribute) discretize() (in module MEDimage.processing.discretisation) dissimilarity() (in module MEDimage.biomarkers.glcm) distance (MEDimage.biomarkers.glcm.CooccurrenceMatrix attribute)

E

energy() (in module MEDimage.biomarkers.glcm) (in module MEDimage.biomarkers.stats) entropy() (in module MEDimage.biomarkers.intensity_histogram) equalization() (in module MEDimage.processing.discretisation) export_table() (in module MEDimage.utils.data_frame_export) extract_all() (in module MEDimage.biomarkers.diagnostics) (in module MEDimage.biomarkers.glcm) (in module MEDimage.biomarkers.gldzm) (in module MEDimage.biomarkers.glrlm) (in module MEDimage.biomarkers.glszm) (in module MEDimage.biomarkers.int_vol_hist) (in module MEDimage.biomarkers.intensity_histogram) (in module MEDimage.biomarkers.local_intensity) (in module MEDimage.biomarkers.morph) (in module MEDimage.biomarkers.ngldm) (in module MEDimage.biomarkers.ngtdm) (in module MEDimage.biomarkers.stats)

F

fill_learner_dict() (MEDimage.learning.DesignExperiment.DesignExperiment method) find_i_x() (in module MEDimage.biomarkers.utils)

find_spacing() (in module MEDimage.processing.segmentation) find_v_x() (in module MEDimage.biomarkers.utils) FSR (class in MEDimage.learning.FSR)

G

Gabor (class in MEDimage.filters.gabor) geary_c() (in module MEDimage.biomarkers.morph) generate_experiment() (MEDimage.learning.DesignExperiment.DesignExperiment method) generate_learner_dict() (MEDimage.learning.DesignExperiment.DesignExperiment method) get_area_dens_approx() (in module MEDimage.biomarkers.morph) (in module MEDimage.biomarkers.utils) get_axis_lengths() (in module MEDimage.biomarkers.morph) (in module MEDimage.biomarkers.utils) get_cm_data() (MEDimage.biomarkers.glcm.CooccurrenceMatrix method) get_cm_features() (in module MEDimage.biomarkers.glcm) get_com() (in module MEDimage.biomarkers.morph) (in module MEDimage.biomarkers.utils) get_dict() (in module MEDimage.biomarkers.ngldm) get_file_paths() (in module MEDimage.utils.get_file_paths) get_geary_c() (in module MEDimage.biomarkers.morph) get_glcm_cross_diag_prob() (in module MEDimage.biomarkers.utils) get_glcm_diag_prob() (in module MEDimage.biomarkers.utils) get_glcm_matrices() (in module MEDimage.biomarkers.glcm) get_glob_peak() (in module MEDimage.biomarkers.utils) get_hold_out_set_table() (MEDimage.learning.RadiomicsLearner.RadiomicsLearner method) get_institutions_from_ids() (in module MEDimage.utils.get_institutions_from_ids) get_loc_peak() (in module MEDimage.biomarkers.utils) get_matrix() (in module MEDimage.biomarkers.glcm) (in module MEDimage.biomarkers.gldzm) (in module MEDimage.biomarkers.glrlm) (in module MEDimage.biomarkers.glszm) (in module MEDimage.biomarkers.ngldm) (in module MEDimage.biomarkers.ngtdm) get_mesh() (in module MEDimage.biomarkers.morph) (in module MEDimage.biomarkers.utils) get_mesh_area() (in module MEDimage.biomarkers.morph) get_mesh_volume() (in module MEDimage.biomarkers.morph)

get_model_performance() (MEDimage.learning.Results.Results method) get_moran_i() (in module MEDimage.biomarkers.morph) get_neighbour_direction() (in module MEDimage.utils.textureTools) get_ngldm_features() (in module MEDimage.biomarkers.ngldm) get_optimal_level() (MEDimage.learning.Results.Results method) get_patient_id_from_scan_name() (in module MEDimage.utils.get_patient_id_from_scan_name) get_patient_names() (in module MEDimage.utils.get_patient_names) get_polygon_mask() (in module MEDimage.processing.segmentation) get_process_names() (in module MEDimage.utils.find_process_names) get_radiomic_names() (in module MEDimage.utils.get_radiomic_names) get_rlm_features() (in module MEDimage.biomarkers.glrlm) get_roi() (in module MEDimage.processing.segmentation) get_roi_from_indexes() (in module MEDimage.processing.segmentation) get_scan_name_from_rad_name() (in module MEDimage.utils.get_scan_name_from_rad_name) get_sep_roi_names() (in module MEDimage.processing.segmentation) get_single_matrix() (in module MEDimage.biomarkers.gldzm) (in module MEDimage.biomarkers.glszm) (in module MEDimage.biomarkers.ngtdm) get_value() (in module MEDimage.utils.textureTools) get_variables() (in module MEDimage.biomarkers.morph) gl_var() (in module MEDimage.biomarkers.gldzm) (in module MEDimage.biomarkers.glrlm) (in module MEDimage.biomarkers.glszm) (in module MEDimage.biomarkers.ngldm) glnu() (in module MEDimage.biomarkers.gldzm) (in module MEDimage.biomarkers.glrlm) (in module MEDimage.biomarkers.glszm) (in module MEDimage.biomarkers.ngldm) glnu_norm() (in module MEDimage.biomarkers.gldzm) (in module MEDimage.biomarkers.glrlm) (in module MEDimage.biomarkers.glszm) (in module MEDimage.biomarkers.ngldm) GreyLevelDependenceMatrix (class in MEDimage.biomarkers.ngldm)

H

hde() (in module MEDimage.biomarkers.ngldm) hdhge() (in module MEDimage.biomarkers.ngldm) hdlge() (in module MEDimage.biomarkers.ngldm) hgce() (in module MEDimage.biomarkers.ngldm)

hgre() (in module MEDimage.biomarkers.glrlm) hgze() (in module MEDimage.biomarkers.gldzm) (in module MEDimage.biomarkers.glszm) hist_grad_calc() (in module MEDimage.biomarkers.intensity_histogram)

I

i10() (in module MEDimage.biomarkers.int_vol_hist) i10_minus_i90() (in module MEDimage.biomarkers.int_vol_hist) i90() (in module MEDimage.biomarkers.int_vol_hist) image_reader_SITK() (in module MEDimage.utils.image_reader_SITK) image_volume_obj (class in MEDimage.utils.image_volume_obj) ImageExtentInWorld() (MEDimage.utils.imref.imref3d method) ImageExtentInWorldX (MEDimage.utils.imref.imref3d attribute) ImageExtentInWorldY (MEDimage.utils.imref.imref3d attribute) ImageExtentInWorldZ (MEDimage.utils.imref.imref3d attribute) ImageSize (MEDimage.utils.imref.imref3d attribute) img_slice (MEDimage.biomarkers.glcm.CooccurrenceMatrix attribute) (MEDimage.biomarkers.glrlm.RunLengthMatrix attribute) impute_missing() (MEDimage.learning.DataCleaner.DataCleaner method) imref3d (class in MEDimage.utils.imref) info_corr1() (in module MEDimage.biomarkers.glcm) info_corr2() (in module MEDimage.biomarkers.glcm) init_IH() (in module MEDimage.biomarkers.intensity_histogram)

init_ivh() (in module MEDimage.biomarkers.int_vol_hist) initialize_features_names() (in module MEDimage.utils.initialize_features_names) inpolygon() (in module MEDimage.utils.inpolygon) integ_int() (in module MEDimage.biomarkers.morph) interp3() (in module MEDimage.utils.interp3) interp_volume() (in module MEDimage.processing.interpolation) IntrinsicLimits() (MEDimage.utils.imref.imref3d method) intrinsicToWorld() (in module MEDimage.utils.imref) (MEDimage.utils.imref.imref3d method) inv_diff() (in module MEDimage.biomarkers.glcm) inv_diff_mom() (in module MEDimage.biomarkers.glcm) inv_diff_mom_norm() (in module MEDimage.biomarkers.glcm) inv_diff_norm() (in module MEDimage.biomarkers.glcm) inv_var() (in module MEDimage.biomarkers.glcm) iqrange() (in module MEDimage.biomarkers.intensity_histogram) (in module MEDimage.biomarkers.stats) is_list_all_none() (in module MEDimage.utils.textureTools)

J

joint_avg() (in module MEDimage.biomarkers.glcm) joint_entr() (in module MEDimage.biomarkers.glcm)

joint_max() (in module MEDimage.biomarkers.glcm) joint_var() (in module MEDimage.biomarkers.glcm)

K

kurt() (in module MEDimage.biomarkers.intensity_histogram) (in module MEDimage.biomarkers.stats)

L

LaplacianOfGaussian (class in MEDimage.filters.log) Laws (class in MEDimage.filters.laws) lde() (in module MEDimage.biomarkers.gldzm) (in module MEDimage.biomarkers.ngldm) ldhge() (in module MEDimage.biomarkers.gldzm) (in module MEDimage.biomarkers.ngldm) ldlge() (in module MEDimage.biomarkers.gldzm) (in module MEDimage.biomarkers.ngldm) lgce() (in module MEDimage.biomarkers.ngldm)

lgre() (in module MEDimage.biomarkers.glrlm) lgze() (in module MEDimage.biomarkers.gldzm) (in module MEDimage.biomarkers.glszm) load_json() (in module MEDimage.utils.json_utils) lre() (in module MEDimage.biomarkers.glrlm) lrhge() (in module MEDimage.biomarkers.glrlm) lrlge() (in module MEDimage.biomarkers.glrlm) lze() (in module MEDimage.biomarkers.glszm) lzhge() (in module MEDimage.biomarkers.glszm) lzlge() (in module MEDimage.biomarkers.glszm)

M

mad() (in module MEDimage.biomarkers.intensity_histogram) (in module MEDimage.biomarkers.stats) matrix (MEDimage.biomarkers.glcm.CooccurrenceMatrix attribute) (MEDimage.biomarkers.glrlm.RunLengthMatrix attribute) max() (in module MEDimage.biomarkers.intensity_histogram) (in module MEDimage.biomarkers.stats) max_grad() (in module MEDimage.biomarkers.intensity_histogram) max_grad_gl() (in module MEDimage.biomarkers.intensity_histogram) Mean (class in MEDimage.filters.mean) mean() (in module MEDimage.biomarkers.intensity_histogram) (in module MEDimage.biomarkers.stats) medad() (in module MEDimage.biomarkers.intensity_histogram) (in module MEDimage.biomarkers.stats) median() (in module MEDimage.biomarkers.intensity_histogram) (in module MEDimage.biomarkers.stats) MEDimage.biomarkers.BatchExtractor module MEDimage.biomarkers.diagnostics module MEDimage.biomarkers.get_oriented_bound_box module MEDimage.biomarkers.glcm module MEDimage.biomarkers.gldzm module MEDimage.biomarkers.glrlm module MEDimage.biomarkers.glszm module MEDimage.biomarkers.int_vol_hist module MEDimage.biomarkers.intensity_histogram module MEDimage.biomarkers.local_intensity module MEDimage.biomarkers.morph module MEDimage.biomarkers.ngldm module MEDimage.biomarkers.ngtdm module MEDimage.biomarkers.stats module MEDimage.biomarkers.utils module MEDimage.filters.apply_filter module MEDimage.filters.gabor module MEDimage.filters.laws module MEDimage.filters.log module MEDimage.filters.mean module MEDimage.filters.utils module MEDimage.filters.wavelet module MEDimage.learning.DataCleaner module MEDimage.learning.DesignExperiment module MEDimage.learning.FSR module MEDimage.learning.Normalization module MEDimage.learning.RadiomicsLearner module MEDimage.learning.Results module MEDimage.processing.compute_suv_map module MEDimage.processing.discretisation module MEDimage.processing.interpolation module MEDimage.processing.resegmentation module MEDimage.processing.segmentation module MEDimage.utils.batch_patients module MEDimage.utils.create_radiomics_table module MEDimage.utils.data_frame_export module MEDimage.utils.find_process_names module MEDimage.utils.get_file_paths module MEDimage.utils.get_institutions_from_ids module MEDimage.utils.get_patient_id_from_scan_name module MEDimage.utils.get_patient_names module MEDimage.utils.get_radiomic_names module MEDimage.utils.get_scan_name_from_rad_name module MEDimage.utils.image_reader_SITK module

MEDimage.utils.image_volume_obj module MEDimage.utils.imref module MEDimage.utils.initialize_features_names module MEDimage.utils.inpolygon module MEDimage.utils.interp3 module MEDimage.utils.json_utils module MEDimage.utils.mode module MEDimage.utils.parse_contour_string module MEDimage.utils.save_MEDscan module MEDimage.utils.strfind module MEDimage.utils.textureTools module MEDimage.utils.write_radiomics_csv module MEDimage.wrangling.DataManager module MEDimage.wrangling.ProcessDICOM module merge_feature() (in module MEDimage.biomarkers.glrlm) merge_method (MEDimage.biomarkers.glcm.CooccurrenceMatrix attribute) (MEDimage.biomarkers.glrlm.RunLengthMatrix attribute) min() (in module MEDimage.biomarkers.intensity_histogram) (in module MEDimage.biomarkers.stats) min_grad() (in module MEDimage.biomarkers.intensity_histogram) min_grad_gl() (in module MEDimage.biomarkers.intensity_histogram) min_oriented_bound_box() (in module MEDimage.biomarkers.morph) min_vol_ellipse() (in module MEDimage.biomarkers.morph) ml_run() (MEDimage.learning.RadiomicsLearner.RadiomicsLearner method) mode() (in module MEDimage.biomarkers.intensity_histogram) (in module MEDimage.utils.mode) model_dict (MEDimage.learning.Results.Results attribute) model_id (MEDimage.learning.Results.Results attribute) module MEDimage.biomarkers.BatchExtractor MEDimage.biomarkers.diagnostics MEDimage.biomarkers.get_oriented_bound_box MEDimage.biomarkers.glcm MEDimage.biomarkers.gldzm MEDimage.biomarkers.glrlm MEDimage.biomarkers.glszm MEDimage.biomarkers.int_vol_hist MEDimage.biomarkers.intensity_histogram MEDimage.biomarkers.local_intensity MEDimage.biomarkers.morph MEDimage.biomarkers.ngldm MEDimage.biomarkers.ngtdm MEDimage.biomarkers.stats MEDimage.biomarkers.utils MEDimage.filters.apply_filter MEDimage.filters.gabor MEDimage.filters.laws MEDimage.filters.log MEDimage.filters.mean MEDimage.filters.utils MEDimage.filters.wavelet MEDimage.learning.DataCleaner MEDimage.learning.DesignExperiment MEDimage.learning.FSR MEDimage.learning.Normalization MEDimage.learning.RadiomicsLearner MEDimage.learning.Results MEDimage.processing.compute_suv_map MEDimage.processing.discretisation MEDimage.processing.interpolation MEDimage.processing.resegmentation MEDimage.processing.segmentation MEDimage.utils.batch_patients MEDimage.utils.create_radiomics_table MEDimage.utils.data_frame_export MEDimage.utils.find_process_names MEDimage.utils.get_file_paths MEDimage.utils.get_institutions_from_ids MEDimage.utils.get_patient_id_from_scan_name MEDimage.utils.get_patient_names MEDimage.utils.get_radiomic_names MEDimage.utils.get_scan_name_from_rad_name MEDimage.utils.image_reader_SITK MEDimage.utils.image_volume_obj MEDimage.utils.imref MEDimage.utils.initialize_features_names MEDimage.utils.inpolygon MEDimage.utils.interp3 MEDimage.utils.json_utils MEDimage.utils.mode MEDimage.utils.parse_contour_string MEDimage.utils.save_MEDscan MEDimage.utils.strfind MEDimage.utils.textureTools MEDimage.utils.write_radiomics_csv MEDimage.wrangling.DataManager MEDimage.wrangling.ProcessDICOM moran_i() (in module MEDimage.biomarkers.morph)

N

n_v (MEDimage.biomarkers.glcm.CooccurrenceMatrix attribute) (MEDimage.biomarkers.glrlm.RunLengthMatrix attribute)

Normalization (class in MEDimage.learning.Normalization)

O

outlier_re_seg() (in module MEDimage.processing.resegmentation)

P

p10() (in module MEDimage.biomarkers.intensity_histogram) (in module MEDimage.biomarkers.stats) p90() (in module MEDimage.biomarkers.intensity_histogram) (in module MEDimage.biomarkers.stats) pad_imgs() (in module MEDimage.filters.utils) padding() (in module MEDimage.biomarkers.morph) parse_contour_string() (in module MEDimage.utils.parse_contour_string) parse_feature_names() (MEDimage.biomarkers.ngldm.GreyLevelDependenceMatrix method) pca_elongation() (in module MEDimage.biomarkers.morph) pca_flatness() (in module MEDimage.biomarkers.morph) pca_least() (in module MEDimage.biomarkers.morph) pca_major() (in module MEDimage.biomarkers.morph) pca_minor() (in module MEDimage.biomarkers.morph) peak_global() (in module MEDimage.biomarkers.local_intensity) peak_local() (in module MEDimage.biomarkers.local_intensity) perform_ct_imaging_summary() (MEDimage.wrangling.DataManager.DataManager method) perform_imaging_summary() (MEDimage.wrangling.DataManager.DataManager method) perform_mr_imaging_summary() (MEDimage.wrangling.DataManager.DataManager method) PixelExtentInWorld() (MEDimage.utils.imref.imref3d method) PixelExtentInWorldX (MEDimage.utils.imref.imref3d attribute)

PixelExtentInWorldY (MEDimage.utils.imref.imref3d attribute) PixelExtentInWorldZ (MEDimage.utils.imref.imref3d attribute) plot_fda_analysis_heatmap() (MEDimage.learning.Results.Results method) plot_feature_analysis() (MEDimage.learning.Results.Results method) plot_features_importance_histogram() (MEDimage.learning.Results.Results method) plot_heatmap() (MEDimage.learning.Results.Results method) plot_lf_level_tree() (MEDimage.learning.Results.Results method) plot_original_level_tree() (MEDimage.learning.Results.Results method) plot_radiomics_starting_percentage() (MEDimage.learning.Results.Results method) plot_tf_level_tree() (MEDimage.learning.Results.Results method) posix_to_string() (in module MEDimage.utils.json_utils) pre_process_radiomics_table() (MEDimage.learning.RadiomicsLearner.RadiomicsLearner method) pre_process_variables() (MEDimage.learning.RadiomicsLearner.RadiomicsLearner method) pre_radiomics_checks() (MEDimage.wrangling.DataManager.DataManager method) predict_xgb() (MEDimage.learning.RadiomicsLearner.RadiomicsLearner method) process_all() (MEDimage.wrangling.DataManager.DataManager method) process_all_dicoms() (MEDimage.wrangling.DataManager.DataManager method) process_all_niftis() (MEDimage.wrangling.DataManager.DataManager method) process_files() (MEDimage.wrangling.ProcessDICOM.ProcessDICOM method) ProcessDICOM (class in MEDimage.wrangling.ProcessDICOM)

Q

qcod() (in module MEDimage.biomarkers.intensity_histogram) (in module MEDimage.biomarkers.stats)

R

r_perc() (in module MEDimage.biomarkers.glrlm) RadiomicsLearner (class in MEDimage.learning.RadiomicsLearner) range() (in module MEDimage.biomarkers.intensity_histogram) (in module MEDimage.biomarkers.stats) range_re_seg() (in module MEDimage.processing.resegmentation) rep() (in module MEDimage.utils.textureTools) Results (class in MEDimage.learning.Results) results_dict (MEDimage.learning.Results.Results attribute) rl_entr() (in module MEDimage.biomarkers.glrlm)

rl_var() (in module MEDimage.biomarkers.glrlm) rlnu() (in module MEDimage.biomarkers.glrlm) rlnu_norm() (in module MEDimage.biomarkers.glrlm) rmad() (in module MEDimage.biomarkers.intensity_histogram) (in module MEDimage.biomarkers.stats) rms() (in module MEDimage.biomarkers.stats) roi_extract() (in module MEDimage.processing.segmentation) rot_matrix() (in module MEDimage.biomarkers.get_oriented_bound_box) run_experiment() (MEDimage.learning.RadiomicsLearner.RadiomicsLearner method) RunLengthMatrix (class in MEDimage.biomarkers.glrlm)

S

save_json() (in module MEDimage.utils.json_utils) save_MEDscan() (in module MEDimage.utils.save_MEDscan) sde() (in module MEDimage.biomarkers.gldzm) sdhge() (in module MEDimage.biomarkers.gldzm) sdlge() (in module MEDimage.biomarkers.gldzm) set_empty() (MEDimage.biomarkers.ngldm.GreyLevelDependenceMatrix method) sig_proc_find_peaks() (in module MEDimage.biomarkers.get_oriented_bound_box) sig_proc_segmentise() (in module MEDimage.biomarkers.get_oriented_bound_box) sizes_match() (in module MEDimage.utils.imref) skewness() (in module MEDimage.biomarkers.intensity_histogram) (in module MEDimage.biomarkers.stats) spatial_method (MEDimage.biomarkers.glcm.CooccurrenceMatrix attribute) (MEDimage.biomarkers.glrlm.RunLengthMatrix attribute) spatial_to_voxel() (in module MEDimage.processing.segmentation) spatialRef (MEDimage.utils.image_volume_obj.image_volume_obj attribute) sph_dispr() (in module MEDimage.biomarkers.morph) sphericity() (in module MEDimage.biomarkers.morph)

sre() (in module MEDimage.biomarkers.glrlm) srhge() (in module MEDimage.biomarkers.glrlm) srlge() (in module MEDimage.biomarkers.glrlm) stack_frame_rs (MEDimage.wrangling.DataManager.DataManager.DICOM attribute) stack_path_all (MEDimage.wrangling.DataManager.DataManager.NIfTI attribute) stack_path_images (MEDimage.wrangling.DataManager.DataManager.NIfTI attribute) stack_path_roi (MEDimage.wrangling.DataManager.DataManager.NIfTI attribute) stack_path_rs (MEDimage.wrangling.DataManager.DataManager.DICOM attribute) stack_series_rs (MEDimage.wrangling.DataManager.DataManager.DICOM attribute) strength() (in module MEDimage.biomarkers.ngtdm) strfind() (in module MEDimage.utils.strfind) sum_avg() (in module MEDimage.biomarkers.glcm) sum_entr() (in module MEDimage.biomarkers.glcm) sum_var() (in module MEDimage.biomarkers.glcm) summarize() (MEDimage.wrangling.DataManager.DataManager method) sze() (in module MEDimage.biomarkers.glszm) szhge() (in module MEDimage.biomarkers.glszm) szlge() (in module MEDimage.biomarkers.glszm)

T

test_xgb_model() (MEDimage.learning.RadiomicsLearner.RadiomicsLearner method)

to_json() (MEDimage.learning.Results.Results method) train_xgboost_model() (MEDimage.learning.RadiomicsLearner.RadiomicsLearner method)

U

uniformity() (in module MEDimage.biomarkers.intensity_histogram)

update_from_csv() (MEDimage.wrangling.DataManager.DataManager method)

V

v10() (in module MEDimage.biomarkers.int_vol_hist) v10_minus_v90() (in module MEDimage.biomarkers.int_vol_hist) v90() (in module MEDimage.biomarkers.int_vol_hist) v_dens_aabb() (in module MEDimage.biomarkers.morph) v_dens_aee() (in module MEDimage.biomarkers.morph) v_dens_conv_hull() (in module MEDimage.biomarkers.morph)

v_dens_mvee() (in module MEDimage.biomarkers.morph) v_dens_ombb() (in module MEDimage.biomarkers.morph) var() (in module MEDimage.biomarkers.intensity_histogram) (in module MEDimage.biomarkers.stats) vol() (in module MEDimage.biomarkers.morph) voxel_to_spatial() (in module MEDimage.processing.segmentation)

W

Wavelet (class in MEDimage.filters.wavelet) WorldLimits() (MEDimage.utils.imref.imref3d method)

worldToIntrinsic() (in module MEDimage.utils.imref) (MEDimage.utils.imref.imref3d method) write_radiomics_csv() (in module MEDimage.utils.write_radiomics_csv)

X

XIntrinsicLimits (MEDimage.utils.imref.imref3d attribute)

xWorldLimits (MEDimage.utils.imref.imref3d attribute)

Y

YIntrinsicLimits (MEDimage.utils.imref.imref3d attribute)

yWorldLimits (MEDimage.utils.imref.imref3d attribute)

Z

z_perc() (in module MEDimage.biomarkers.gldzm) (in module MEDimage.biomarkers.glszm) zd_entr() (in module MEDimage.biomarkers.gldzm) zd_var() (in module MEDimage.biomarkers.gldzm) zdnu() (in module MEDimage.biomarkers.gldzm) zdnu_norm() (in module MEDimage.biomarkers.gldzm)

ZIntrinsicLimits (MEDimage.utils.imref.imref3d attribute) zs_entr() (in module MEDimage.biomarkers.glszm) zs_var() (in module MEDimage.biomarkers.glszm) zsnu() (in module MEDimage.biomarkers.glszm) zsnu_norm() (in module MEDimage.biomarkers.glszm) zWorldLimits (MEDimage.utils.imref.imref3d attribute)