Index

_

__init__() (dosma.models.IWOAIOAIUnet2D method) (dosma.models.IWOAIOAIUnet2DNormalized method) (dosma.models.OAIUnet2D method) (dosma.scan_sequences.Cones method) (dosma.scan_sequences.CubeQuant method) (dosma.scan_sequences.Mapss method) (dosma.scan_sequences.QDess method) (dosma.tissues.FemoralCartilage method) (dosma.tissues.Meniscus method) (dosma.tissues.PatellarCartilage method) (dosma.tissues.TibialCartilage method)

A

ACP_BOUNDARY (dosma.tissues.femoral_cartilage.FemoralCartilage attribute) (dosma.tissues.FemoralCartilage attribute) ActionWrapper (class in dosma.utils.cmd_line_utils) add_additional_volume() (dosma.quant_vals.QuantitativeValue method) add_quantitative_value() (dosma.tissues.tissue.Tissue method) affine() (dosma.data_io.med_volume.MedicalVolume property) (dosma.data_io.MedicalVolume property) ALIASES (dosma.models.IWOAIOAIUnet2D attribute) (dosma.models.IWOAIOAIUnet2DNormalized attribute) (dosma.models.OAIUnet2D attribute) (dosma.models.oaiunet2d.IWOAIOAIUnet2D attribute) (dosma.models.oaiunet2d.IWOAIOAIUnet2DNormalized attribute) (dosma.models.oaiunet2d.OAIUnet2D attribute) (dosma.models.seg_model.SegModel attribute)

aliases() (dosma.utils.cmd_line_utils.ActionWrapper property) apply_warp() (in module dosma.utils.registration)

B

biexponential() (in module dosma.utils.fits)

build_model() (dosma.models.seg_model.KerasSegModel method) (dosma.models.seg_model.SegModel method)

C

calc_quant_vals() (dosma.tissues.tissue.Tissue method) calc_rms() (dosma.scan_sequences.QDess method) (dosma.scan_sequences.qdess.QDess method) cart2pol() (in module dosma.utils.geometry_utils) circle_fit() (in module dosma.utils.geometry_utils) clone() (dosma.data_io.med_volume.MedicalVolume method) (dosma.data_io.MedicalVolume method) cmd_line_actions() (dosma.scan_sequences.Cones class method) (dosma.scan_sequences.cones.Cones class method) (dosma.scan_sequences.cube_quant.CubeQuant class method) (dosma.scan_sequences.CubeQuant class method) (dosma.scan_sequences.Mapss class method) (dosma.scan_sequences.mapss.Mapss class method) (dosma.scan_sequences.QDess class method) (dosma.scan_sequences.qdess.QDess class method)

Cones (class in dosma.scan_sequences), [1] (class in dosma.scan_sequences.cones) convert_image_data_format() (in module dosma.data_io) (in module dosma.data_io.format_io_utils) CubeQuant (class in dosma.scan_sequences), [1] (class in dosma.scan_sequences.cube_quant) curve_fit() (in module dosma.utils.fits)

D

data_format_code (dosma.data_io.DataReader attribute) (dosma.data_io.DataWriter attribute) (dosma.data_io.dicom_io.DicomReader attribute) (dosma.data_io.dicom_io.DicomWriter attribute) (dosma.data_io.DicomReader attribute) (dosma.data_io.DicomWriter attribute) (dosma.data_io.format_io.DataReader attribute) (dosma.data_io.format_io.DataWriter attribute) (dosma.data_io.nifti_io.NiftiReader attribute) (dosma.data_io.nifti_io.NiftiWriter attribute) (dosma.data_io.NiftiReader attribute) (dosma.data_io.NiftiWriter attribute) DataReader (class in dosma.data_io) (class in dosma.data_io.format_io) DataWriter (class in dosma.data_io) (class in dosma.data_io.format_io) dicom (dosma.data_io.format_io.ImageDataFormat attribute) (dosma.data_io.ImageDataFormat attribute) DicomReader (class in dosma.data_io) (class in dosma.data_io.dicom_io) DicomWriter (class in dosma.data_io) (class in dosma.data_io.dicom_io) dosma module dosma.data_io module dosma.data_io.dicom_io module dosma.data_io.format_io module dosma.data_io.format_io_utils module dosma.data_io.med_volume module dosma.data_io.nifti_io module dosma.data_io.orientation module, [1] dosma.defaults module dosma.file_constants module dosma.models module, [1] dosma.models.oaiunet2d module dosma.models.seg_model module

dosma.models.util module dosma.msk module dosma.msk.knee module dosma.quant_vals module dosma.scan_sequences module, [1] dosma.scan_sequences.cones module dosma.scan_sequences.cube_quant module dosma.scan_sequences.mapss module dosma.scan_sequences.qdess module dosma.scan_sequences.scans module dosma.tissues module, [1] dosma.tissues.femoral_cartilage module dosma.tissues.meniscus module dosma.tissues.patellar_cartilage module dosma.tissues.tibial_cartilage module dosma.tissues.tissue module dosma.utils module dosma.utils.cmd_line_utils module dosma.utils.fits module, [1] dosma.utils.geometry_utils module dosma.utils.img_utils module dosma.utils.io_utils module dosma.utils.registration module, [1] downsample_slice() (in module dosma.utils.img_utils)

F

FemoralCartilage (class in dosma.tissues), [1] (class in dosma.tissues.femoral_cartilage) find_weights() (dosma.tissues.tissue.Tissue method) fit() (dosma.utils.fits.MonoExponentialFit method) from_sitk() (dosma.data_io.med_volume.MedicalVolume class method) (dosma.data_io.MedicalVolume class method) FULL_NAME (dosma.tissues.femoral_cartilage.FemoralCartilage attribute) (dosma.tissues.FemoralCartilage attribute) (dosma.tissues.Meniscus attribute) (dosma.tissues.meniscus.Meniscus attribute) (dosma.tissues.patellar_cartilage.PatellarCartilage attribute) (dosma.tissues.PatellarCartilage attribute) (dosma.tissues.tibial_cartilage.TibialCartilage attribute) (dosma.tissues.TibialCartilage attribute) (dosma.tissues.tissue.Tissue attribute)

G

generate_mask() (dosma.models.IWOAIOAIUnet2D method) (dosma.models.OAIUnet2D method) (dosma.models.oaiunet2d.IWOAIOAIUnet2D method) (dosma.models.oaiunet2d.OAIUnet2D method) (dosma.models.seg_model.SegModel method) generate_t1_rho_map() (dosma.scan_sequences.cube_quant.CubeQuant method) (dosma.scan_sequences.CubeQuant method) (dosma.scan_sequences.Mapss method) (dosma.scan_sequences.mapss.Mapss method) generate_t2_map() (dosma.scan_sequences.Mapss method) (dosma.scan_sequences.mapss.Mapss method) (dosma.scan_sequences.QDess method) (dosma.scan_sequences.qdess.QDess method) generate_t2_star_map() (dosma.scan_sequences.Cones method) (dosma.scan_sequences.cones.Cones method) generic_load() (in module dosma.data_io) (in module dosma.data_io.format_io_utils)

get_alternative_param_names() (dosma.utils.cmd_line_utils.ActionWrapper method) get_dimensions() (dosma.scan_sequences.scans.ScanSequence method) get_filepath_variations() (in module dosma.data_io) (in module dosma.data_io.format_io_utils) get_flip_inds() (in module dosma.data_io.orientation) get_image_data_format() (dosma.data_io.format_io.ImageDataFormat class method) (dosma.data_io.ImageDataFormat class method) get_mask() (dosma.tissues.tissue.Tissue method) get_model() (in module dosma.models) (in module dosma.models.util) get_param_help() (dosma.utils.cmd_line_utils.ActionWrapper method) get_qv() (dosma.quant_vals.QuantitativeValue static method) get_reader() (in module dosma.data_io) (in module dosma.data_io.format_io_utils) get_transpose_inds() (in module dosma.data_io.orientation) get_writer() (in module dosma.data_io) (in module dosma.data_io.format_io_utils)

H

handle_knee() (in module dosma.msk.knee) headers() (dosma.data_io.med_volume.MedicalVolume property) (dosma.data_io.MedicalVolume property)

help() (dosma.utils.cmd_line_utils.ActionWrapper property)

I

ID (dosma.quant_vals.QuantitativeValue attribute) (dosma.quant_vals.T1Rho attribute) (dosma.quant_vals.T2 attribute) (dosma.quant_vals.T2Star attribute) (dosma.tissues.femoral_cartilage.FemoralCartilage attribute) (dosma.tissues.FemoralCartilage attribute) (dosma.tissues.Meniscus attribute) (dosma.tissues.meniscus.Meniscus attribute) (dosma.tissues.patellar_cartilage.PatellarCartilage attribute) (dosma.tissues.PatellarCartilage attribute) (dosma.tissues.tibial_cartilage.TibialCartilage attribute) (dosma.tissues.TibialCartilage attribute) (dosma.tissues.tissue.Tissue attribute) ImageDataFormat (class in dosma.data_io) (class in dosma.data_io.format_io)

interregister() (dosma.scan_sequences.Cones method) (dosma.scan_sequences.cones.Cones method) (dosma.scan_sequences.cube_quant.CubeQuant method) (dosma.scan_sequences.CubeQuant method) (dosma.scan_sequences.scans.NonTargetSequence method) is_filetype() (dosma.data_io.format_io.ImageDataFormat method) (dosma.data_io.ImageDataFormat method) is_identical() (dosma.data_io.med_volume.MedicalVolume method) (dosma.data_io.MedicalVolume method) is_same_dimensions() (dosma.data_io.med_volume.MedicalVolume method) (dosma.data_io.MedicalVolume method) IWOAIOAIUnet2D (class in dosma.models), [1] (class in dosma.models.oaiunet2d) IWOAIOAIUnet2DNormalized (class in dosma.models), [1] (class in dosma.models.oaiunet2d)

K

KerasSegModel (class in dosma.models.seg_model)

knee_parser() (in module dosma.msk.knee)

L

load() (dosma.data_io.DataReader method) (dosma.data_io.dicom_io.DicomReader method) (dosma.data_io.DicomReader method) (dosma.data_io.format_io.DataReader method) (dosma.data_io.nifti_io.NiftiReader method) (dosma.data_io.NiftiReader method) load_data() (dosma.quant_vals.QuantitativeValue method) (dosma.scan_sequences.Cones method) (dosma.scan_sequences.cones.Cones method) (dosma.scan_sequences.cube_quant.CubeQuant method) (dosma.scan_sequences.CubeQuant method) (dosma.scan_sequences.Mapss method) (dosma.scan_sequences.mapss.Mapss method) (dosma.scan_sequences.QDess method) (dosma.scan_sequences.qdess.QDess method) (dosma.scan_sequences.scans.ScanSequence method) (dosma.tissues.tissue.Tissue method)

load_h5() (in module dosma.utils.io_utils) load_pik() (in module dosma.utils.io_utils) load_qvs() (dosma.quant_vals.QuantitativeValue static method)

M

Mapss (class in dosma.scan_sequences), [1] (class in dosma.scan_sequences.mapss) match_orientation() (dosma.data_io.med_volume.MedicalVolume method) (dosma.data_io.MedicalVolume method) match_orientation_batch() (dosma.data_io.med_volume.MedicalVolume method) (dosma.data_io.MedicalVolume method) MedicalVolume (class in dosma.data_io) (class in dosma.data_io.med_volume) Meniscus (class in dosma.tissues), [1] (class in dosma.tissues.meniscus) mkdirs() (in module dosma.utils.io_utils) ML_BOUNDARY (dosma.tissues.femoral_cartilage.FemoralCartilage attribute) (dosma.tissues.FemoralCartilage attribute) module dosma dosma.data_io dosma.data_io.dicom_io dosma.data_io.format_io dosma.data_io.format_io_utils dosma.data_io.med_volume dosma.data_io.nifti_io dosma.data_io.orientation, [1] dosma.defaults dosma.file_constants dosma.models, [1] dosma.models.oaiunet2d dosma.models.seg_model dosma.models.util dosma.msk dosma.msk.knee dosma.quant_vals dosma.scan_sequences, [1] dosma.scan_sequences.cones dosma.scan_sequences.cube_quant dosma.scan_sequences.mapss dosma.scan_sequences.qdess dosma.scan_sequences.scans dosma.tissues, [1] dosma.tissues.femoral_cartilage dosma.tissues.meniscus dosma.tissues.patellar_cartilage dosma.tissues.tibial_cartilage dosma.tissues.tissue dosma.utils dosma.utils.cmd_line_utils dosma.utils.fits, [1] dosma.utils.geometry_utils dosma.utils.img_utils dosma.utils.io_utils dosma.utils.registration, [1]

monoexponential() (in module dosma.utils.fits) MonoExponentialFit (class in dosma.utils.fits)

N

NAME (dosma.quant_vals.QuantitativeValue attribute) (dosma.quant_vals.T1Rho attribute) (dosma.quant_vals.T2 attribute) (dosma.quant_vals.T2Star attribute) (dosma.scan_sequences.Cones attribute) (dosma.scan_sequences.cones.Cones attribute) (dosma.scan_sequences.cube_quant.CubeQuant attribute) (dosma.scan_sequences.CubeQuant attribute) (dosma.scan_sequences.Mapss attribute) (dosma.scan_sequences.mapss.Mapss attribute) (dosma.scan_sequences.QDess attribute) (dosma.scan_sequences.qdess.QDess attribute) (dosma.scan_sequences.scans.ScanSequence attribute)

name() (dosma.utils.cmd_line_utils.ActionWrapper property) nifti (dosma.data_io.format_io.ImageDataFormat attribute) (dosma.data_io.ImageDataFormat attribute) NiftiReader (class in dosma.data_io) (class in dosma.data_io.nifti_io) NiftiWriter (class in dosma.data_io) (class in dosma.data_io.nifti_io) NonTargetSequence (class in dosma.scan_sequences.scans)

O

OAIUnet2D (class in dosma.models), [1] (class in dosma.models.oaiunet2d) orientation() (dosma.data_io.med_volume.MedicalVolume property) (dosma.data_io.MedicalVolume property)

orientation_nib_to_standard() (in module dosma.data_io.orientation) orientation_standard_to_nib() (in module dosma.data_io.orientation)

P

PatellarCartilage (class in dosma.tissues), [1] (class in dosma.tissues.patellar_cartilage)

pixel_spacing() (dosma.data_io.med_volume.MedicalVolume property) (dosma.data_io.MedicalVolume property)

Q

QDess (class in dosma.scan_sequences), [1] (class in dosma.scan_sequences.qdess) QuantitativeValue (class in dosma.quant_vals) QuantitativeValueType (class in dosma.quant_vals)

qv_type() (dosma.quant_vals.QuantitativeValue property) (dosma.quant_vals.T1Rho property) (dosma.quant_vals.T2 property) (dosma.quant_vals.T2Star property)

R

reformat() (dosma.data_io.med_volume.MedicalVolume method) (dosma.data_io.MedicalVolume method)

reformat_as() (dosma.data_io.med_volume.MedicalVolume method) (dosma.data_io.MedicalVolume method) register() (in module dosma.utils.registration)

S

save() (dosma.data_io.DataWriter method) (dosma.data_io.dicom_io.DicomWriter method) (dosma.data_io.DicomWriter method) (dosma.data_io.format_io.DataWriter method) (dosma.data_io.nifti_io.NiftiWriter method) (dosma.data_io.NiftiWriter method) save_data() (dosma.quant_vals.QuantitativeValue method) (dosma.scan_sequences.Cones method) (dosma.scan_sequences.cones.Cones method) (dosma.scan_sequences.cube_quant.CubeQuant method) (dosma.scan_sequences.CubeQuant method) (dosma.scan_sequences.Mapss method) (dosma.scan_sequences.mapss.Mapss method) (dosma.scan_sequences.QDess method) (dosma.scan_sequences.qdess.QDess method) (dosma.scan_sequences.scans.ScanSequence method) (dosma.tissues.femoral_cartilage.FemoralCartilage method) (dosma.tissues.FemoralCartilage method) (dosma.tissues.tissue.Tissue method) save_h5() (in module dosma.utils.io_utils) save_pik() (in module dosma.utils.io_utils) save_qvs() (dosma.quant_vals.QuantitativeValue static method) save_tables() (in module dosma.utils.io_utils) save_volume() (dosma.data_io.med_volume.MedicalVolume method) (dosma.data_io.MedicalVolume method) scanner_origin() (dosma.data_io.med_volume.MedicalVolume property) (dosma.data_io.MedicalVolume property) ScanSequence (class in dosma.scan_sequences.scans) segment() (dosma.scan_sequences.Mapss method) (dosma.scan_sequences.mapss.Mapss method) (dosma.scan_sequences.QDess method) (dosma.scan_sequences.qdess.QDess method) (dosma.scan_sequences.scans.TargetSequence method)

SegModel (class in dosma.models.seg_model) set_debug() (in module dosma.file_constants) set_mask() (dosma.tissues.femoral_cartilage.FemoralCartilage method) (dosma.tissues.FemoralCartilage method) (dosma.tissues.Meniscus method) (dosma.tissues.meniscus.Meniscus method) (dosma.tissues.patellar_cartilage.PatellarCartilage method) (dosma.tissues.PatellarCartilage method) (dosma.tissues.tibial_cartilage.TibialCartilage method) (dosma.tissues.TibialCartilage method) (dosma.tissues.tissue.Tissue method) shape() (dosma.data_io.med_volume.MedicalVolume property) (dosma.data_io.MedicalVolume property) sigmoid_threshold (dosma.models.OAIUnet2D attribute) (dosma.models.oaiunet2d.OAIUnet2D attribute) split_regions() (dosma.tissues.femoral_cartilage.FemoralCartilage method) (dosma.tissues.FemoralCartilage method) (dosma.tissues.Meniscus method) (dosma.tissues.meniscus.Meniscus method) (dosma.tissues.patellar_cartilage.PatellarCartilage method) (dosma.tissues.PatellarCartilage method) (dosma.tissues.tibial_cartilage.TibialCartilage method) (dosma.tissues.TibialCartilage method) (dosma.tissues.tissue.Tissue method) STR_ID (dosma.tissues.femoral_cartilage.FemoralCartilage attribute) (dosma.tissues.FemoralCartilage attribute) (dosma.tissues.Meniscus attribute) (dosma.tissues.meniscus.Meniscus attribute) (dosma.tissues.patellar_cartilage.PatellarCartilage attribute) (dosma.tissues.PatellarCartilage attribute) (dosma.tissues.tibial_cartilage.TibialCartilage attribute) (dosma.tissues.TibialCartilage attribute) (dosma.tissues.tissue.Tissue attribute) symlink_elastix() (in module dosma.utils.registration)

T

T1_EXPECTED (dosma.tissues.femoral_cartilage.FemoralCartilage attribute) (dosma.tissues.FemoralCartilage attribute) (dosma.tissues.Meniscus attribute) (dosma.tissues.meniscus.Meniscus attribute) (dosma.tissues.patellar_cartilage.PatellarCartilage attribute) (dosma.tissues.PatellarCartilage attribute) (dosma.tissues.tibial_cartilage.TibialCartilage attribute) (dosma.tissues.TibialCartilage attribute) (dosma.tissues.tissue.Tissue attribute) T1_RHO (dosma.quant_vals.QuantitativeValueType attribute) T1Rho (class in dosma.quant_vals)

T2 (class in dosma.quant_vals) (dosma.quant_vals.QuantitativeValueType attribute) T2_STAR (dosma.quant_vals.QuantitativeValueType attribute) T2Star (class in dosma.quant_vals) TargetSequence (class in dosma.scan_sequences.scans) TibialCartilage (class in dosma.tissues), [1] (class in dosma.tissues.tibial_cartilage) Tissue (class in dosma.tissues.tissue) to_metrics() (dosma.quant_vals.QuantitativeValue method) to_sitk() (dosma.data_io.med_volume.MedicalVolume method) (dosma.data_io.MedicalVolume method)

U

unlink_elastix() (in module dosma.utils.registration) unroll() (dosma.tissues.femoral_cartilage.FemoralCartilage method) (dosma.tissues.FemoralCartilage method) unroll_axial() (dosma.tissues.Meniscus method) (dosma.tissues.meniscus.Meniscus method) (dosma.tissues.tibial_cartilage.TibialCartilage method) (dosma.tissues.TibialCartilage method)

unroll_coronal() (dosma.tissues.patellar_cartilage.PatellarCartilage method) (dosma.tissues.PatellarCartilage method)

V

volume() (dosma.data_io.med_volume.MedicalVolume property) (dosma.data_io.MedicalVolume property)

W

whiten_volume() (in module dosma.models.seg_model)

write_regions() (in module dosma.utils.img_utils)