Getting started
Installation
Configuration Files
CSV File
Input Data
Tutorials
Instructions
DataManager
MEDscan Class
Single-scan demo
BatchExtractor
Learning
Contents
MEDiml
Developer section
License
FAQs
MEDiml
Index
Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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X
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Y
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Z
_
__init__() (MEDiml.biomarkers.BatchExtractor.BatchExtractor method)
(MEDiml.biomarkers.glcm.CooccurrenceMatrix method)
(MEDiml.biomarkers.glrlm.RunLengthMatrix method)
(MEDiml.biomarkers.ngldm.GreyLevelDependenceMatrix method)
(MEDiml.filters.gabor.Gabor method)
(MEDiml.filters.laws.Laws method)
(MEDiml.filters.log.LaplacianOfGaussian method)
(MEDiml.filters.mean.Mean method)
(MEDiml.filters.wavelet.Wavelet method)
(MEDiml.learning.DataCleaner.DataCleaner method)
(MEDiml.learning.DesignExperiment.DesignExperiment method)
(MEDiml.learning.FSR.FSR method)
(MEDiml.learning.Normalization.CombatNormalization method)
(MEDiml.learning.RadiomicsLearner.RadiomicsLearner method)
(MEDiml.learning.Results.Results method)
(MEDiml.processing.PETSUVConverter.PETSUVConverter method)
(MEDiml.wrangling.DataManager.DataManager method)
(MEDiml.wrangling.ProcessDICOM.ProcessDICOM method)
_apply_imputation() (MEDiml.learning.DataCleaner.DataCleaner method)
_copy() (MEDiml.biomarkers.glcm.CooccurrenceMatrix method)
(MEDiml.biomarkers.glrlm.RunLengthMatrix method)
_fit_imputer() (MEDiml.learning.DataCleaner.DataCleaner method)
_is_jsonable() (in module MEDiml.utils.json_utils)
_pad_imgs() (MEDiml.filters.wavelet.Wavelet method)
_parse_feature_names() (MEDiml.biomarkers.glrlm.RunLengthMatrix method)
_parse_names() (MEDiml.biomarkers.glcm.CooccurrenceMatrix method)
_parse_time() (MEDiml.processing.PETSUVConverter.PETSUVConverter static method)
_parse_to_ndarray() (MEDiml.utils.imref.imref3d method)
_process_institutions() (MEDiml.learning.Normalization.CombatNormalization method)
_set_empty() (MEDiml.biomarkers.glrlm.RunLengthMatrix method)
_validate_input() (MEDiml.learning.DataCleaner.DataCleaner method)
A
a_dens_aabb() (in module MEDiml.biomarkers.morph)
a_dens_aee() (in module MEDiml.biomarkers.morph)
a_dens_conv_hull() (in module MEDiml.biomarkers.morph)
a_dens_mvee() (in module MEDiml.biomarkers.morph)
a_dens_ombb() (in module MEDiml.biomarkers.morph)
apply_fda() (MEDiml.learning.FSR.FSR method)
apply_fda_balanced() (MEDiml.learning.FSR.FSR method)
apply_fda_one_space() (MEDiml.learning.FSR.FSR method)
apply_filter() (in module MEDiml.filters.apply_filter)
apply_fsr() (MEDiml.learning.FSR.FSR method)
apply_gabor() (in module MEDiml.filters.gabor)
apply_laws() (in module MEDiml.filters.laws)
apply_log() (in module MEDiml.filters.log)
apply_mean() (in module MEDiml.filters.mean)
apply_random_fsr() (MEDiml.learning.FSR.FSR method)
apply_random_fsr_one_space() (MEDiml.learning.FSR.FSR method)
apply_wavelet() (in module MEDiml.filters.wavelet)
approx_vol() (in module MEDiml.biomarkers.morph)
area() (in module MEDiml.biomarkers.morph)
asphericity() (in module MEDiml.biomarkers.morph)
auc() (in module MEDiml.biomarkers.int_vol_hist)
auto_corr() (in module MEDiml.biomarkers.glcm)
av() (in module MEDiml.biomarkers.morph)
average_results() (MEDiml.learning.Results.Results method)
B
batch_patients() (in module MEDiml.utils.batch_patients)
BatchExtractor (class in MEDiml.biomarkers.BatchExtractor)
bootstrap_metrics() (MEDiml.learning.Results.Results method)
busyness() (in module MEDiml.biomarkers.ngtdm)
C
calculate_cm_features() (MEDiml.biomarkers.glcm.CooccurrenceMatrix method)
calculate_cm_matrix() (MEDiml.biomarkers.glcm.CooccurrenceMatrix method)
calculate_feature() (MEDiml.biomarkers.glrlm.RunLengthMatrix method)
calculate_ngldm_matrix() (MEDiml.biomarkers.ngldm.GreyLevelDependenceMatrix method)
calculate_rlm_features() (MEDiml.biomarkers.glrlm.RunLengthMatrix method)
calculate_rlm_matrix() (MEDiml.biomarkers.glrlm.RunLengthMatrix method)
cell_frame_id (MEDiml.wrangling.DataManager.DataManager.DICOM attribute)
cell_frame_rs (MEDiml.wrangling.DataManager.DataManager.DICOM attribute)
cell_path_images (MEDiml.wrangling.DataManager.DataManager.DICOM attribute)
cell_path_rs (MEDiml.wrangling.DataManager.DataManager.DICOM attribute)
cell_series_id (MEDiml.wrangling.DataManager.DataManager.DICOM attribute)
clust_prom() (in module MEDiml.biomarkers.glcm)
clust_shade() (in module MEDiml.biomarkers.glcm)
clust_tend() (in module MEDiml.biomarkers.glcm)
coarseness() (in module MEDiml.biomarkers.ngtdm)
com() (in module MEDiml.biomarkers.morph)
CombatNormalization (class in MEDiml.learning.Normalization)
combine_matrices() (in module MEDiml.biomarkers.glcm)
combine_ngldm_matrices() (in module MEDiml.biomarkers.ngldm)
combine_rlm_matrices() (in module MEDiml.biomarkers.glrlm)
combine_slices() (MEDiml.wrangling.ProcessDICOM.ProcessDICOM method)
comp_1() (in module MEDiml.biomarkers.morph)
comp_2() (in module MEDiml.biomarkers.morph)
complexity() (in module MEDiml.biomarkers.ngtdm)
compute() (MEDiml.processing.PETSUVConverter.PETSUVConverter method)
compute_bounding_box() (in module MEDiml.processing.segmentation)
compute_box() (in module MEDiml.processing.segmentation)
compute_ngldm_features() (MEDiml.biomarkers.ngldm.GreyLevelDependenceMatrix method)
compute_radiomics() (MEDiml.biomarkers.BatchExtractor.BatchExtractor method)
compute_roi() (in module MEDiml.processing.segmentation)
contains_point() (MEDiml.utils.imref.imref3d method)
contrast() (in module MEDiml.biomarkers.glcm)
(in module MEDiml.biomarkers.ngtdm)
convolve() (in module MEDiml.filters.utils)
(MEDiml.filters.gabor.Gabor method)
(MEDiml.filters.laws.Laws method)
(MEDiml.filters.log.LaplacianOfGaussian method)
(MEDiml.filters.mean.Mean method)
(MEDiml.filters.wavelet.Wavelet method)
CooccurrenceMatrix (class in MEDiml.biomarkers.glcm)
coord2index() (in module MEDiml.utils.textureTools)
copy() (MEDiml.biomarkers.ngldm.GreyLevelDependenceMatrix method)
corr() (in module MEDiml.biomarkers.glcm)
cov() (in module MEDiml.biomarkers.intensity_histogram)
(in module MEDiml.biomarkers.stats)
create_experiment() (MEDiml.learning.DesignExperiment.DesignExperiment method)
create_kernel() (MEDiml.filters.gabor.Gabor method)
(MEDiml.filters.laws.Laws method)
(MEDiml.filters.log.LaplacianOfGaussian method)
(MEDiml.filters.mean.Mean method)
(MEDiml.filters.wavelet.Wavelet method)
create_radiomics_table() (in module MEDiml.utils.create_radiomics_table)
crop_box() (in module MEDiml.processing.segmentation)
crop_nifti_box() (in module MEDiml.processing.segmentation)
D
data (MEDiml.utils.image_volume_obj.image_volume_obj attribute)
DataCleaner (class in MEDiml.learning.DataCleaner)
DataManager (class in MEDiml.wrangling.DataManager)
DataManager.DICOM (class in MEDiml.wrangling.DataManager)
DataManager.NIfTI (class in MEDiml.wrangling.DataManager)
DataManager.Paths (class in MEDiml.wrangling.DataManager)
dc_energy() (in module MEDiml.biomarkers.ngldm)
dc_entr() (in module MEDiml.biomarkers.ngldm)
dc_var() (in module MEDiml.biomarkers.ngldm)
dcnu() (in module MEDiml.biomarkers.ngldm)
dcnu_norm() (in module MEDiml.biomarkers.ngldm)
DesignExperiment (class in MEDiml.learning.DesignExperiment)
diam() (in module MEDiml.biomarkers.morph)
diff_avg() (in module MEDiml.biomarkers.glcm)
diff_entr() (in module MEDiml.biomarkers.glcm)
diff_var() (in module MEDiml.biomarkers.glcm)
direction (MEDiml.biomarkers.glcm.CooccurrenceMatrix attribute)
(MEDiml.biomarkers.glrlm.RunLengthMatrix attribute)
direction_id (MEDiml.biomarkers.glcm.CooccurrenceMatrix attribute)
(MEDiml.biomarkers.glrlm.RunLengthMatrix attribute)
discretize() (in module MEDiml.processing.discretisation)
dissimilarity() (in module MEDiml.biomarkers.glcm)
distance (MEDiml.biomarkers.glcm.CooccurrenceMatrix attribute)
E
energy() (in module MEDiml.biomarkers.glcm)
(in module MEDiml.biomarkers.stats)
entropy() (in module MEDiml.biomarkers.intensity_histogram)
equalization() (in module MEDiml.processing.discretisation)
export_table() (in module MEDiml.utils.data_frame_export)
extract_all() (in module MEDiml.biomarkers.diagnostics)
(in module MEDiml.biomarkers.glcm)
(in module MEDiml.biomarkers.gldzm)
(in module MEDiml.biomarkers.glrlm)
(in module MEDiml.biomarkers.glszm)
(in module MEDiml.biomarkers.int_vol_hist)
(in module MEDiml.biomarkers.intensity_histogram)
(in module MEDiml.biomarkers.local_intensity)
(in module MEDiml.biomarkers.morph)
(in module MEDiml.biomarkers.ngldm)
(in module MEDiml.biomarkers.ngtdm)
(in module MEDiml.biomarkers.stats)
F
find_i_x() (in module MEDiml.biomarkers.utils)
find_spacing() (in module MEDiml.processing.segmentation)
find_v_x() (in module MEDiml.biomarkers.utils)
fit() (MEDiml.learning.DataCleaner.DataCleaner method)
(MEDiml.learning.Normalization.CombatNormalization method)
FSR (class in MEDiml.learning.FSR)
G
Gabor (class in MEDiml.filters.gabor)
geary_c() (in module MEDiml.biomarkers.morph)
generate_experiment() (MEDiml.learning.DesignExperiment.DesignExperiment method)
get_area_dens_approx() (in module MEDiml.biomarkers.morph)
(in module MEDiml.biomarkers.utils)
get_axis_lengths() (in module MEDiml.biomarkers.morph)
(in module MEDiml.biomarkers.utils)
get_cm_data() (MEDiml.biomarkers.glcm.CooccurrenceMatrix method)
get_cm_features() (in module MEDiml.biomarkers.glcm)
get_com() (in module MEDiml.biomarkers.morph)
(in module MEDiml.biomarkers.utils)
get_conversion_factors() (MEDiml.processing.PETSUVConverter.PETSUVConverter method)
get_dict() (in module MEDiml.biomarkers.ngldm)
get_file_paths() (in module MEDiml.utils.get_file_paths)
get_geary_c() (in module MEDiml.biomarkers.morph)
get_glcm_cross_diag_prob() (in module MEDiml.biomarkers.utils)
get_glcm_diag_prob() (in module MEDiml.biomarkers.utils)
get_glcm_matrices() (in module MEDiml.biomarkers.glcm)
get_glob_peak() (in module MEDiml.biomarkers.utils)
get_hold_out_set_table() (MEDiml.learning.RadiomicsLearner.RadiomicsLearner method)
get_institutions_from_ids() (in module MEDiml.utils.get_institutions_from_ids)
get_loc_peak() (in module MEDiml.biomarkers.utils)
get_matrix() (in module MEDiml.biomarkers.glcm)
(in module MEDiml.biomarkers.gldzm)
(in module MEDiml.biomarkers.glrlm)
(in module MEDiml.biomarkers.glszm)
(in module MEDiml.biomarkers.ngldm)
(in module MEDiml.biomarkers.ngtdm)
get_mesh() (in module MEDiml.biomarkers.morph)
(in module MEDiml.biomarkers.utils)
get_mesh_area() (in module MEDiml.biomarkers.morph)
get_mesh_volume() (in module MEDiml.biomarkers.morph)
get_model_performance() (MEDiml.learning.Results.Results method)
get_moran_i() (in module MEDiml.biomarkers.morph)
get_neighbour_direction() (in module MEDiml.utils.textureTools)
get_ngldm_features() (in module MEDiml.biomarkers.ngldm)
get_optimal_level() (MEDiml.learning.Results.Results method)
get_patient_id_from_scan_name() (in module MEDiml.utils.get_patient_id_from_scan_name)
get_patient_names() (in module MEDiml.utils.get_patient_names)
get_polygon_mask() (in module MEDiml.processing.segmentation)
get_process_names() (in module MEDiml.utils.find_process_names)
get_radiomic_names() (in module MEDiml.utils.get_radiomic_names)
get_rlm_features() (in module MEDiml.biomarkers.glrlm)
get_roi() (in module MEDiml.processing.segmentation)
get_roi_from_indexes() (in module MEDiml.processing.segmentation)
get_scan_name_from_rad_name() (in module MEDiml.utils.get_scan_name_from_rad_name)
get_sep_roi_names() (in module MEDiml.processing.segmentation)
get_single_matrix() (in module MEDiml.biomarkers.gldzm)
(in module MEDiml.biomarkers.glszm)
(in module MEDiml.biomarkers.ngtdm)
get_value() (in module MEDiml.utils.textureTools)
get_variables() (in module MEDiml.biomarkers.morph)
gl_var() (in module MEDiml.biomarkers.gldzm)
(in module MEDiml.biomarkers.glrlm)
(in module MEDiml.biomarkers.glszm)
(in module MEDiml.biomarkers.ngldm)
glnu() (in module MEDiml.biomarkers.gldzm)
(in module MEDiml.biomarkers.glrlm)
(in module MEDiml.biomarkers.glszm)
(in module MEDiml.biomarkers.ngldm)
glnu_norm() (in module MEDiml.biomarkers.gldzm)
(in module MEDiml.biomarkers.glrlm)
(in module MEDiml.biomarkers.glszm)
(in module MEDiml.biomarkers.ngldm)
GreyLevelDependenceMatrix (class in MEDiml.biomarkers.ngldm)
H
hde() (in module MEDiml.biomarkers.ngldm)
hdhge() (in module MEDiml.biomarkers.ngldm)
hdlge() (in module MEDiml.biomarkers.ngldm)
hgce() (in module MEDiml.biomarkers.ngldm)
hgre() (in module MEDiml.biomarkers.glrlm)
hgze() (in module MEDiml.biomarkers.gldzm)
(in module MEDiml.biomarkers.glszm)
hist_grad_calc() (in module MEDiml.biomarkers.intensity_histogram)
I
i10() (in module MEDiml.biomarkers.int_vol_hist)
i10_minus_i90() (in module MEDiml.biomarkers.int_vol_hist)
i90() (in module MEDiml.biomarkers.int_vol_hist)
image_reader_SITK() (in module MEDiml.utils.image_reader_SITK)
image_volume_obj (class in MEDiml.utils.image_volume_obj)
ImageExtentInWorld() (MEDiml.utils.imref.imref3d method)
ImageExtentInWorldX (MEDiml.utils.imref.imref3d attribute)
ImageExtentInWorldY (MEDiml.utils.imref.imref3d attribute)
ImageExtentInWorldZ (MEDiml.utils.imref.imref3d attribute)
ImageSize (MEDiml.utils.imref.imref3d attribute)
img_slice (MEDiml.biomarkers.glcm.CooccurrenceMatrix attribute)
(MEDiml.biomarkers.glrlm.RunLengthMatrix attribute)
imref3d (class in MEDiml.utils.imref)
info_corr1() (in module MEDiml.biomarkers.glcm)
info_corr2() (in module MEDiml.biomarkers.glcm)
init_IH() (in module MEDiml.biomarkers.intensity_histogram)
init_ivh() (in module MEDiml.biomarkers.int_vol_hist)
initialize_features_names() (in module MEDiml.utils.initialize_features_names)
inpolygon() (in module MEDiml.utils.inpolygon)
integ_int() (in module MEDiml.biomarkers.morph)
interp3() (in module MEDiml.utils.interp3)
interp_volume() (in module MEDiml.processing.interpolation)
IntrinsicLimits() (MEDiml.utils.imref.imref3d method)
intrinsicToWorld() (in module MEDiml.utils.imref)
(MEDiml.utils.imref.imref3d method)
inv_diff() (in module MEDiml.biomarkers.glcm)
inv_diff_mom() (in module MEDiml.biomarkers.glcm)
inv_diff_mom_norm() (in module MEDiml.biomarkers.glcm)
inv_diff_norm() (in module MEDiml.biomarkers.glcm)
inv_var() (in module MEDiml.biomarkers.glcm)
iqrange() (in module MEDiml.biomarkers.intensity_histogram)
(in module MEDiml.biomarkers.stats)
is_list_all_none() (in module MEDiml.utils.textureTools)
J
joint_avg() (in module MEDiml.biomarkers.glcm)
joint_entr() (in module MEDiml.biomarkers.glcm)
joint_max() (in module MEDiml.biomarkers.glcm)
joint_var() (in module MEDiml.biomarkers.glcm)
K
kurt() (in module MEDiml.biomarkers.intensity_histogram)
(in module MEDiml.biomarkers.stats)
L
LaplacianOfGaussian (class in MEDiml.filters.log)
Laws (class in MEDiml.filters.laws)
lde() (in module MEDiml.biomarkers.gldzm)
(in module MEDiml.biomarkers.ngldm)
ldhge() (in module MEDiml.biomarkers.gldzm)
(in module MEDiml.biomarkers.ngldm)
ldlge() (in module MEDiml.biomarkers.gldzm)
(in module MEDiml.biomarkers.ngldm)
lgce() (in module MEDiml.biomarkers.ngldm)
lgre() (in module MEDiml.biomarkers.glrlm)
lgze() (in module MEDiml.biomarkers.gldzm)
(in module MEDiml.biomarkers.glszm)
load_json() (in module MEDiml.utils.json_utils)
lre() (in module MEDiml.biomarkers.glrlm)
lrhge() (in module MEDiml.biomarkers.glrlm)
lrlge() (in module MEDiml.biomarkers.glrlm)
lze() (in module MEDiml.biomarkers.glszm)
lzhge() (in module MEDiml.biomarkers.glszm)
lzlge() (in module MEDiml.biomarkers.glszm)
M
mad() (in module MEDiml.biomarkers.intensity_histogram)
(in module MEDiml.biomarkers.stats)
matrix (MEDiml.biomarkers.glcm.CooccurrenceMatrix attribute)
(MEDiml.biomarkers.glrlm.RunLengthMatrix attribute)
max() (in module MEDiml.biomarkers.intensity_histogram)
(in module MEDiml.biomarkers.stats)
max_grad() (in module MEDiml.biomarkers.intensity_histogram)
max_grad_gl() (in module MEDiml.biomarkers.intensity_histogram)
Mean (class in MEDiml.filters.mean)
mean() (in module MEDiml.biomarkers.intensity_histogram)
(in module MEDiml.biomarkers.stats)
medad() (in module MEDiml.biomarkers.intensity_histogram)
(in module MEDiml.biomarkers.stats)
median() (in module MEDiml.biomarkers.intensity_histogram)
(in module MEDiml.biomarkers.stats)
MEDiml.biomarkers.BatchExtractor
module
MEDiml.biomarkers.diagnostics
module
MEDiml.biomarkers.get_oriented_bound_box
module
MEDiml.biomarkers.glcm
module
MEDiml.biomarkers.gldzm
module
MEDiml.biomarkers.glrlm
module
MEDiml.biomarkers.glszm
module
MEDiml.biomarkers.int_vol_hist
module
MEDiml.biomarkers.intensity_histogram
module
MEDiml.biomarkers.local_intensity
module
MEDiml.biomarkers.morph
module
MEDiml.biomarkers.ngldm
module
MEDiml.biomarkers.ngtdm
module
MEDiml.biomarkers.stats
module
MEDiml.biomarkers.utils
module
MEDiml.filters.apply_filter
module
MEDiml.filters.gabor
module
MEDiml.filters.laws
module
MEDiml.filters.log
module
MEDiml.filters.mean
module
MEDiml.filters.utils
module
MEDiml.filters.wavelet
module
MEDiml.learning.DataCleaner
module
MEDiml.learning.DesignExperiment
module
MEDiml.learning.FSR
module
MEDiml.learning.Normalization
module
MEDiml.learning.RadiomicsLearner
module
MEDiml.learning.Results
module
MEDiml.processing.discretisation
module
MEDiml.processing.interpolation
module
MEDiml.processing.PETSUVConverter
module
MEDiml.processing.resegmentation
module
MEDiml.processing.segmentation
module
MEDiml.utils.batch_patients
module
MEDiml.utils.create_radiomics_table
module
MEDiml.utils.data_frame_export
module
MEDiml.utils.find_process_names
module
MEDiml.utils.get_file_paths
module
MEDiml.utils.get_institutions_from_ids
module
MEDiml.utils.get_patient_id_from_scan_name
module
MEDiml.utils.get_patient_names
module
MEDiml.utils.get_radiomic_names
module
MEDiml.utils.get_scan_name_from_rad_name
module
MEDiml.utils.image_reader_SITK
module
MEDiml.utils.image_volume_obj
module
MEDiml.utils.imref
module
MEDiml.utils.initialize_features_names
module
MEDiml.utils.inpolygon
module
MEDiml.utils.interp3
module
MEDiml.utils.json_utils
module
MEDiml.utils.mode
module
MEDiml.utils.parse_contour_string
module
MEDiml.utils.save_MEDscan
module
MEDiml.utils.strfind
module
MEDiml.utils.textureTools
module
MEDiml.utils.write_radiomics_csv
module
MEDiml.wrangling.DataManager
module
MEDiml.wrangling.ProcessDICOM
module
merge_feature() (in module MEDiml.biomarkers.glrlm)
merge_method (MEDiml.biomarkers.glcm.CooccurrenceMatrix attribute)
(MEDiml.biomarkers.glrlm.RunLengthMatrix attribute)
min() (in module MEDiml.biomarkers.intensity_histogram)
(in module MEDiml.biomarkers.stats)
min_grad() (in module MEDiml.biomarkers.intensity_histogram)
min_grad_gl() (in module MEDiml.biomarkers.intensity_histogram)
min_oriented_bound_box() (in module MEDiml.biomarkers.morph)
min_vol_ellipse() (in module MEDiml.biomarkers.morph)
ml_run() (MEDiml.learning.RadiomicsLearner.RadiomicsLearner method)
mode() (in module MEDiml.biomarkers.intensity_histogram)
(in module MEDiml.utils.mode)
model_dict (MEDiml.learning.Results.Results attribute)
model_id (MEDiml.learning.Results.Results attribute)
module
MEDiml.biomarkers.BatchExtractor
MEDiml.biomarkers.diagnostics
MEDiml.biomarkers.get_oriented_bound_box
MEDiml.biomarkers.glcm
MEDiml.biomarkers.gldzm
MEDiml.biomarkers.glrlm
MEDiml.biomarkers.glszm
MEDiml.biomarkers.int_vol_hist
MEDiml.biomarkers.intensity_histogram
MEDiml.biomarkers.local_intensity
MEDiml.biomarkers.morph
MEDiml.biomarkers.ngldm
MEDiml.biomarkers.ngtdm
MEDiml.biomarkers.stats
MEDiml.biomarkers.utils
MEDiml.filters.apply_filter
MEDiml.filters.gabor
MEDiml.filters.laws
MEDiml.filters.log
MEDiml.filters.mean
MEDiml.filters.utils
MEDiml.filters.wavelet
MEDiml.learning.DataCleaner
MEDiml.learning.DesignExperiment
MEDiml.learning.FSR
MEDiml.learning.Normalization
MEDiml.learning.RadiomicsLearner
MEDiml.learning.Results
MEDiml.processing.discretisation
MEDiml.processing.interpolation
MEDiml.processing.PETSUVConverter
MEDiml.processing.resegmentation
MEDiml.processing.segmentation
MEDiml.utils.batch_patients
MEDiml.utils.create_radiomics_table
MEDiml.utils.data_frame_export
MEDiml.utils.find_process_names
MEDiml.utils.get_file_paths
MEDiml.utils.get_institutions_from_ids
MEDiml.utils.get_patient_id_from_scan_name
MEDiml.utils.get_patient_names
MEDiml.utils.get_radiomic_names
MEDiml.utils.get_scan_name_from_rad_name
MEDiml.utils.image_reader_SITK
MEDiml.utils.image_volume_obj
MEDiml.utils.imref
MEDiml.utils.initialize_features_names
MEDiml.utils.inpolygon
MEDiml.utils.interp3
MEDiml.utils.json_utils
MEDiml.utils.mode
MEDiml.utils.parse_contour_string
MEDiml.utils.save_MEDscan
MEDiml.utils.strfind
MEDiml.utils.textureTools
MEDiml.utils.write_radiomics_csv
MEDiml.wrangling.DataManager
MEDiml.wrangling.ProcessDICOM
moran_i() (in module MEDiml.biomarkers.morph)
N
n_v (MEDiml.biomarkers.glcm.CooccurrenceMatrix attribute)
(MEDiml.biomarkers.glrlm.RunLengthMatrix attribute)
O
outlier_re_seg() (in module MEDiml.processing.resegmentation)
P
p10() (in module MEDiml.biomarkers.intensity_histogram)
(in module MEDiml.biomarkers.stats)
p90() (in module MEDiml.biomarkers.intensity_histogram)
(in module MEDiml.biomarkers.stats)
pad_imgs() (in module MEDiml.filters.utils)
padding() (in module MEDiml.biomarkers.morph)
parse_contour_string() (in module MEDiml.utils.parse_contour_string)
parse_feature_names() (MEDiml.biomarkers.ngldm.GreyLevelDependenceMatrix method)
patient_height_cm (MEDiml.processing.PETSUVConverter.PETSUVConverter property)
patient_sex (MEDiml.processing.PETSUVConverter.PETSUVConverter property)
patient_weight_g (MEDiml.processing.PETSUVConverter.PETSUVConverter property)
pca_elongation() (in module MEDiml.biomarkers.morph)
pca_flatness() (in module MEDiml.biomarkers.morph)
pca_least() (in module MEDiml.biomarkers.morph)
pca_major() (in module MEDiml.biomarkers.morph)
pca_minor() (in module MEDiml.biomarkers.morph)
peak_global() (in module MEDiml.biomarkers.local_intensity)
peak_local() (in module MEDiml.biomarkers.local_intensity)
perform_ct_imaging_summary() (MEDiml.wrangling.DataManager.DataManager method)
perform_imaging_summary() (MEDiml.wrangling.DataManager.DataManager method)
perform_mr_imaging_summary() (MEDiml.wrangling.DataManager.DataManager method)
PETSUVConverter (class in MEDiml.processing.PETSUVConverter)
PixelExtentInWorld() (MEDiml.utils.imref.imref3d method)
PixelExtentInWorldX (MEDiml.utils.imref.imref3d attribute)
PixelExtentInWorldY (MEDiml.utils.imref.imref3d attribute)
PixelExtentInWorldZ (MEDiml.utils.imref.imref3d attribute)
plot_fda_analysis_heatmap() (MEDiml.learning.Results.Results method)
plot_feature_analysis() (MEDiml.learning.Results.Results method)
plot_features_importance_histogram() (MEDiml.learning.Results.Results method)
plot_heatmap() (MEDiml.learning.Results.Results method)
plot_lf_level_tree() (MEDiml.learning.Results.Results method)
plot_original_level_tree() (MEDiml.learning.Results.Results method)
plot_radiomics_starting_percentage() (MEDiml.learning.Results.Results method)
plot_tf_level_tree() (MEDiml.learning.Results.Results method)
posix_to_string() (in module MEDiml.utils.json_utils)
pre_process_radiomics_table() (MEDiml.learning.RadiomicsLearner.RadiomicsLearner method)
pre_process_variables() (MEDiml.learning.RadiomicsLearner.RadiomicsLearner method)
pre_radiomics_checks() (MEDiml.wrangling.DataManager.DataManager method)
process_all() (MEDiml.wrangling.DataManager.DataManager method)
process_all_dicoms() (MEDiml.wrangling.DataManager.DataManager method)
process_all_niftis() (MEDiml.wrangling.DataManager.DataManager method)
process_files() (MEDiml.wrangling.ProcessDICOM.ProcessDICOM method)
process_one_nifti() (MEDiml.wrangling.DataManager.DataManager method)
ProcessDICOM (class in MEDiml.wrangling.ProcessDICOM)
Q
qcod() (in module MEDiml.biomarkers.intensity_histogram)
(in module MEDiml.biomarkers.stats)
R
r_perc() (in module MEDiml.biomarkers.glrlm)
RadiomicsLearner (class in MEDiml.learning.RadiomicsLearner)
range() (in module MEDiml.biomarkers.intensity_histogram)
(in module MEDiml.biomarkers.stats)
range_re_seg() (in module MEDiml.processing.resegmentation)
rep() (in module MEDiml.utils.textureTools)
Results (class in MEDiml.learning.Results)
results_dict (MEDiml.learning.Results.Results attribute)
rl_entr() (in module MEDiml.biomarkers.glrlm)
rl_var() (in module MEDiml.biomarkers.glrlm)
rlnu() (in module MEDiml.biomarkers.glrlm)
rlnu_norm() (in module MEDiml.biomarkers.glrlm)
rmad() (in module MEDiml.biomarkers.intensity_histogram)
(in module MEDiml.biomarkers.stats)
rms() (in module MEDiml.biomarkers.stats)
roi_extract() (in module MEDiml.processing.segmentation)
rot_matrix() (in module MEDiml.biomarkers.get_oriented_bound_box)
run_experiment() (MEDiml.learning.RadiomicsLearner.RadiomicsLearner method)
RunLengthMatrix (class in MEDiml.biomarkers.glrlm)
S
save_json() (in module MEDiml.utils.json_utils)
save_MEDscan() (in module MEDiml.utils.save_MEDscan)
sde() (in module MEDiml.biomarkers.gldzm)
sdhge() (in module MEDiml.biomarkers.gldzm)
sdlge() (in module MEDiml.biomarkers.gldzm)
set_empty() (MEDiml.biomarkers.ngldm.GreyLevelDependenceMatrix method)
sig_proc_find_peaks() (in module MEDiml.biomarkers.get_oriented_bound_box)
sig_proc_segmentise() (in module MEDiml.biomarkers.get_oriented_bound_box)
sizes_match() (in module MEDiml.utils.imref)
skewness() (in module MEDiml.biomarkers.intensity_histogram)
(in module MEDiml.biomarkers.stats)
spatial_method (MEDiml.biomarkers.glcm.CooccurrenceMatrix attribute)
(MEDiml.biomarkers.glrlm.RunLengthMatrix attribute)
spatial_to_voxel() (in module MEDiml.processing.segmentation)
spatialRef (MEDiml.utils.image_volume_obj.image_volume_obj attribute)
sph_dispr() (in module MEDiml.biomarkers.morph)
sphericity() (in module MEDiml.biomarkers.morph)
sre() (in module MEDiml.biomarkers.glrlm)
srhge() (in module MEDiml.biomarkers.glrlm)
srlge() (in module MEDiml.biomarkers.glrlm)
stack_frame_rs (MEDiml.wrangling.DataManager.DataManager.DICOM attribute)
stack_path_all (MEDiml.wrangling.DataManager.DataManager.NIfTI attribute)
stack_path_images (MEDiml.wrangling.DataManager.DataManager.NIfTI attribute)
stack_path_roi (MEDiml.wrangling.DataManager.DataManager.NIfTI attribute)
stack_path_rs (MEDiml.wrangling.DataManager.DataManager.DICOM attribute)
stack_series_rs (MEDiml.wrangling.DataManager.DataManager.DICOM attribute)
strength() (in module MEDiml.biomarkers.ngtdm)
strfind() (in module MEDiml.utils.strfind)
sum_avg() (in module MEDiml.biomarkers.glcm)
sum_entr() (in module MEDiml.biomarkers.glcm)
sum_var() (in module MEDiml.biomarkers.glcm)
summarize() (MEDiml.wrangling.DataManager.DataManager method)
sze() (in module MEDiml.biomarkers.glszm)
szhge() (in module MEDiml.biomarkers.glszm)
szlge() (in module MEDiml.biomarkers.glszm)
T
to_json() (MEDiml.learning.Results.Results method)
transform() (MEDiml.learning.DataCleaner.DataCleaner method)
(MEDiml.learning.Normalization.CombatNormalization method)
U
uniformity() (in module MEDiml.biomarkers.intensity_histogram)
unit (MEDiml.processing.PETSUVConverter.PETSUVConverter property)
update_from_csv() (MEDiml.wrangling.DataManager.DataManager method)
V
v10() (in module MEDiml.biomarkers.int_vol_hist)
v10_minus_v90() (in module MEDiml.biomarkers.int_vol_hist)
v90() (in module MEDiml.biomarkers.int_vol_hist)
v_dens_aabb() (in module MEDiml.biomarkers.morph)
v_dens_aee() (in module MEDiml.biomarkers.morph)
v_dens_conv_hull() (in module MEDiml.biomarkers.morph)
v_dens_mvee() (in module MEDiml.biomarkers.morph)
v_dens_ombb() (in module MEDiml.biomarkers.morph)
var() (in module MEDiml.biomarkers.intensity_histogram)
(in module MEDiml.biomarkers.stats)
vol() (in module MEDiml.biomarkers.morph)
voxel_to_spatial() (in module MEDiml.processing.segmentation)
W
Wavelet (class in MEDiml.filters.wavelet)
WorldLimits() (MEDiml.utils.imref.imref3d method)
worldToIntrinsic() (in module MEDiml.utils.imref)
(MEDiml.utils.imref.imref3d method)
write_radiomics_csv() (in module MEDiml.utils.write_radiomics_csv)
X
XIntrinsicLimits (MEDiml.utils.imref.imref3d attribute)
xWorldLimits (MEDiml.utils.imref.imref3d attribute)
Y
YIntrinsicLimits (MEDiml.utils.imref.imref3d attribute)
yWorldLimits (MEDiml.utils.imref.imref3d attribute)
Z
z_perc() (in module MEDiml.biomarkers.gldzm)
(in module MEDiml.biomarkers.glszm)
zd_entr() (in module MEDiml.biomarkers.gldzm)
zd_var() (in module MEDiml.biomarkers.gldzm)
zdnu() (in module MEDiml.biomarkers.gldzm)
zdnu_norm() (in module MEDiml.biomarkers.gldzm)
ZIntrinsicLimits (MEDiml.utils.imref.imref3d attribute)
zs_entr() (in module MEDiml.biomarkers.glszm)
zs_var() (in module MEDiml.biomarkers.glszm)
zsnu() (in module MEDiml.biomarkers.glszm)
zsnu_norm() (in module MEDiml.biomarkers.glszm)
zWorldLimits (MEDiml.utils.imref.imref3d attribute)