cobra_db
Tutorial: Create a database from scratch
Tutorial: Group Series, Studies, and Patients.
How to: Connect your python script
How to: Sumarize ImageMetadata
Changelog
Contributing
Code of Conduct
API Reference
cobra_db
Index
Edit on GitHub
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
_
__eq__() (cobra_db.model.Patient method)
(cobra_db.model.RadiologicalSeries method)
(cobra_db.model.RadiologicalStudy method)
__post_init__() (cobra_db.model.Entity method)
(cobra_db.model.EntitySource method)
(cobra_db.model.FileSource method)
__repr__() (cobra_db.model.Entity method)
(cobra_db.model.ImageMetadata method)
(cobra_db.model.Patient method)
(cobra_db.model.RadiologicalSeries method)
(cobra_db.model.RadiologicalStudy method)
__str__() (cobra_db.mongo_dao.Connector method)
__version__ (in module cobra_db)
_deid_hash_func() (cobra_db.deid.Deider method)
_ensure_index_exists() (cobra_db.mongo_dao.ImageMetadataDao method)
(cobra_db.mongo_dao.PatientDao method)
(cobra_db.mongo_dao.SeriesDao method)
(cobra_db.mongo_dao.StudyDao method)
_entity_type (cobra_db.model.EntitySource attribute)
_get_collection() (cobra_db.mongo_dao.EntityDao method)
_get_uri() (cobra_db.mongo_dao.Connector static method)
_id (cobra_db.model.Entity attribute)
(cobra_db.model.EntitySource attribute)
_metadata (cobra_db.model.Entity attribute)
_remove_day() (cobra_db.deid.Deider static method)
_replace_dict() (cobra_db.dataset_mod.DatasetMod static method)
_replace_name() (cobra_db.deid.Deider static method)
_round_AS_to_nearest_5y() (cobra_db.deid.Deider static method)
_round_DS_to_nearest_0_05() (cobra_db.deid.Deider static method)
_round_DS_to_nearest_5() (cobra_db.deid.Deider static method)
_round_to_nearest() (cobra_db.deid.Deider static method)
_to_dict() (cobra_db.model.BaseObj method)
A
accession_number (cobra_db.model.RadiologicalStudy attribute)
add_aka() (cobra_db.mongo_dao.ImageMetadataDao method)
add_args_to_iterable() (in module cobra_db.scripts.utils)
AFDL (cobra_db.enums.PatientPosition attribute)
AFDR (cobra_db.enums.PatientPosition attribute)
aggregation_level (cobra_db.model.Annotation attribute)
aka_file_sources (cobra_db.model.ImageMetadata attribute)
Annotation (class in cobra_db.model)
annotation_type (cobra_db.model.Annotation attribute)
Annotator (class in cobra_db.model)
annotator_email (cobra_db.model.Annotation attribute)
anon_id (cobra_db.model.Patient attribute)
anon_id_to_mongo_id() (cobra_db.mongo_dao.PatientDao method)
AX (cobra_db.enums.View attribute)
B
base_recipe_path (in module cobra_db.deid)
BaseObj (class in cobra_db.model)
batcher() (in module cobra_db.scripts.utils)
BILATERAL (cobra_db.enums.Laterality attribute)
birth_date (cobra_db.model.Patient attribute)
Box (in module cobra_db.types)
breast_implant_present (cobra_db.model.RadiologicalStudy attribute)
ByEnumName (class in cobra_db.enums)
C
CC (cobra_db.enums.View attribute)
CHARS (cobra_db.enums.PersonalNumberValidity attribute)
check_mount_paths() (in module cobra_db.scripts.pseudonymize_image_metadata)
CHECKSUM (cobra_db.enums.PersonalNumberValidity attribute)
choose_first() (cobra_db.model.DicomEntity static method)
cli() (in module cobra_db.scripts.stage_1_ingest_images)
(in module cobra_db.scripts.stage_2)
close() (cobra_db.mongo_dao.Connector method)
cobra_db
module
cobra_db.dataset_mod
module
cobra_db.deid
module
cobra_db.encrypt
module
cobra_db.enums
module
cobra_db.filesystem
module
cobra_db.model
module
cobra_db.mongo_dao
module
cobra_db.scripts
module
cobra_db.scripts.pseudonymize_image_metadata
module
cobra_db.scripts.stage_1_ingest_images
module
cobra_db.scripts.stage_2
module
cobra_db.scripts.stage_2_group_patients
module
cobra_db.scripts.stage_2_group_series
module
cobra_db.scripts.stage_2_group_studies
module
cobra_db.scripts.utils
module
cobra_db.types
module
cobra_db.utils
module
connect() (cobra_db.mongo_dao.Connector method)
Connector (class in cobra_db.mongo_dao)
COR (cobra_db.enums.View attribute)
CR (cobra_db.enums.Modality attribute)
create() (cobra_db.model.Metadata class method)
created (cobra_db.model.Metadata attribute)
CT (cobra_db.enums.Modality attribute)
Cube (in module cobra_db.types)
D
DataFormat (class in cobra_db.enums)
DatasetMod (class in cobra_db.dataset_mod)
DATE (cobra_db.enums.PersonalNumberValidity attribute)
date (cobra_db.model.Annotation attribute)
(cobra_db.model.RadiologicalSeries attribute)
(cobra_db.model.RadiologicalStudy attribute)
date_of_last_detector_calibration (cobra_db.model.RadiologicalStudy attribute)
DEFINETLY_PREGNANT (cobra_db.enums.PregnancyStatus attribute)
deid_logging_levels (in module cobra_db.deid)
Deider (class in cobra_db.deid)
delete_by_id() (cobra_db.mongo_dao.EntityDao method)
description (cobra_db.model.EntitySource attribute)
(cobra_db.model.RadiologicalSeries attribute)
(cobra_db.model.RadiologicalStudy attribute)
detector_id (cobra_db.model.RadiologicalStudy attribute)
detector_type (cobra_db.model.RadiologicalStudy attribute)
device_serial_number (cobra_db.model.RadiologicalStudy attribute)
DICOM (cobra_db.enums.DataFormat attribute)
dicom_tags (cobra_db.model.DicomEntity attribute)
(cobra_db.model.ImageMetadata attribute)
DicomEntity (class in cobra_db.model)
drive_name (cobra_db.model.FileSource attribute)
DX (cobra_db.enums.Modality attribute)
E
email (cobra_db.model.Annotator attribute)
Embedded (class in cobra_db.model)
Entity (class in cobra_db.model)
EntityDao (class in cobra_db.mongo_dao)
EntitySource (class in cobra_db.model)
exists() (cobra_db.mongo_dao.PatientDao method)
expand() (cobra_db.model.BaseObj static method)
F
FFDL (cobra_db.enums.PatientPosition attribute)
FFDR (cobra_db.enums.PatientPosition attribute)
FFP (cobra_db.enums.PatientPosition attribute)
FFS (cobra_db.enums.PatientPosition attribute)
file_format (cobra_db.model.Annotation attribute)
file_source (cobra_db.model.Annotation attribute)
(cobra_db.model.ImageMetadata attribute)
filename (cobra_db.model.FileSource attribute)
FileSource (class in cobra_db.model)
find() (cobra_db.mongo_dao.EntityDao method)
find_dcm() (in module cobra_db.utils)
find_files() (in module cobra_db.utils)
first_name (cobra_db.model.Annotator attribute)
from_dataset() (cobra_db.model.DicomEntity class method)
(cobra_db.model.ImageMetadata class method)
(cobra_db.model.Patient class method)
(cobra_db.model.RadiologicalSeries class method)
(cobra_db.model.RadiologicalStudy class method)
from_dict() (cobra_db.model.BaseObj class method)
(cobra_db.model.Embedded class method)
(cobra_db.model.Entity class method)
(cobra_db.model.RadiologicalStudy class method)
from_image_laterality() (cobra_db.enums.Laterality class method)
from_images_metadata() (cobra_db.model.RadiologicalSeries class method)
from_mount_paths() (cobra_db.model.FileSource class method)
from_nkbc_a_pat_sida() (cobra_db.enums.Laterality class method)
from_view_position() (cobra_db.enums.View class method)
G
get_acquisition_datetime() (cobra_db.model.DicomEntity method)
get_all_ids() (cobra_db.mongo_dao.ImageMetadataDao method)
(cobra_db.mongo_dao.SeriesDao method)
(cobra_db.mongo_dao.StudyDao method)
get_by_id() (cobra_db.mongo_dao.EntityDao method)
(cobra_db.mongo_dao.ImageMetadataDao method)
(cobra_db.mongo_dao.PatientDao method)
(cobra_db.mongo_dao.SeriesDao method)
(cobra_db.mongo_dao.StudyDao method)
get_checksum() (cobra_db.encrypt.PersonalNumberValidator static method)
(cobra_db.model.ImageMetadata method)
get_env_pass() (cobra_db.mongo_dao.Connector class method)
get_file_size() (cobra_db.model.ImageMetadata method)
get_instance_path() (in module cobra_db.filesystem)
get_local_filepath() (cobra_db.model.FileSource method)
(cobra_db.model.ImageMetadata method)
get_obj_id() (in module cobra_db.mongo_dao)
get_pass() (cobra_db.mongo_dao.Connector class method)
get_patient() (cobra_db.mongo_dao.PatientDao method)
get_patient_by_anon_id() (cobra_db.mongo_dao.PatientDao method)
get_patient_by_id() (cobra_db.mongo_dao.PatientDao method)
get_patient_path() (in module cobra_db.filesystem)
get_pixel_data() (cobra_db.model.ImageMetadata method)
get_required_drive_names() (in module cobra_db.scripts.pseudonymize_image_metadata)
get_series_path() (in module cobra_db.filesystem)
get_study_path() (in module cobra_db.filesystem)
get_tag() (cobra_db.model.DicomEntity method)
(in module cobra_db.scripts.stage_2_group_studies)
group_study() (in module cobra_db.scripts.stage_2_group_studies)
H
hash() (cobra_db.encrypt.Hasher method)
hash_personal_number() (cobra_db.encrypt.Hasher method)
Hasher (class in cobra_db.encrypt)
HFDL (cobra_db.enums.PatientPosition attribute)
HFDR (cobra_db.enums.PatientPosition attribute)
HFP (cobra_db.enums.PatientPosition attribute)
HFS (cobra_db.enums.PatientPosition attribute)
hidden (cobra_db.model.Patient attribute)
I
Id (in module cobra_db.types)
im_meta_from_virtual_dataset() (in module cobra_db.scripts.pseudonymize_image_metadata)
im_meta_generator() (in module cobra_db.scripts.pseudonymize_image_metadata)
image_count (cobra_db.model.RadiologicalSeries attribute)
image_shape (cobra_db.model.RadiologicalSeries attribute)
ImageMetadata (class in cobra_db.model)
ImageMetadataDao (class in cobra_db.mongo_dao)
ingest_metadata() (in module cobra_db.scripts.stage_1_ingest_images)
insert_one() (cobra_db.mongo_dao.EntityDao method)
(cobra_db.mongo_dao.ImageMetadataDao method)
(cobra_db.mongo_dao.PatientDao method)
(cobra_db.mongo_dao.SeriesDao method)
(cobra_db.mongo_dao.StudyDao method)
intersect_dicts() (in module cobra_db.utils)
intersect_dicts_allow_empty_minority() (in module cobra_db.utils)
J
JPEG (cobra_db.enums.DataFormat attribute)
K
keyword_for_tag_wrapper() (cobra_db.dataset_mod.DatasetMod static method)
keywords_to_tags() (cobra_db.dataset_mod.DatasetMod static method)
L
last_name (cobra_db.model.Annotator attribute)
Laterality (class in cobra_db.enums)
LEFT (cobra_db.enums.Laterality attribute)
LENGTH (cobra_db.enums.PersonalNumberValidity attribute)
LFP (cobra_db.enums.PatientPosition attribute)
LFS (cobra_db.enums.PatientPosition attribute)
list_dirs() (in module cobra_db.utils)
list_files() (in module cobra_db.utils)
M
main() (in module cobra_db.scripts.pseudonymize_image_metadata)
(in module cobra_db.scripts.stage_1_ingest_images)
(in module cobra_db.scripts.stage_2)
(in module cobra_db.scripts.stage_2_group_patients)
(in module cobra_db.scripts.stage_2_group_series)
(in module cobra_db.scripts.stage_2_group_studies)
main_multiproc() (in module cobra_db.scripts.stage_2_group_patients)
(in module cobra_db.scripts.stage_2_group_series)
(in module cobra_db.scripts.stage_2_group_studies)
MAMMOAI (cobra_db.enums.ProjectName attribute)
manufacturer (cobra_db.model.RadiologicalStudy attribute)
manufacturer_model_name (cobra_db.model.RadiologicalStudy attribute)
Metadata (class in cobra_db.model)
MG (cobra_db.enums.Modality attribute)
MLO (cobra_db.enums.View attribute)
Modality (class in cobra_db.enums)
modality (cobra_db.model.RadiologicalStudy attribute)
model_version (cobra_db.model.Metadata attribute)
modified (cobra_db.model.Metadata attribute)
module
cobra_db
cobra_db.dataset_mod
cobra_db.deid
cobra_db.encrypt
cobra_db.enums
cobra_db.filesystem
cobra_db.model
cobra_db.mongo_dao
cobra_db.scripts
cobra_db.scripts.pseudonymize_image_metadata
cobra_db.scripts.stage_1_ingest_images
cobra_db.scripts.stage_2
cobra_db.scripts.stage_2_group_patients
cobra_db.scripts.stage_2_group_series
cobra_db.scripts.stage_2_group_studies
cobra_db.scripts.utils
cobra_db.types
cobra_db.utils
MR (cobra_db.enums.Modality attribute)
mr_recipe_path (in module cobra_db.deid)
multi_proc() (in module cobra_db.scripts.pseudonymize_image_metadata)
multiproc() (in module cobra_db.scripts.stage_1_ingest_images)
multiproc_drive() (in module cobra_db.scripts.stage_1_ingest_images)
N
name (cobra_db.model.EntitySource attribute)
non_alphanumeric (in module cobra_db.filesystem)
NOT_PREGNANT (cobra_db.enums.PregnancyStatus attribute)
NOT_VALID (cobra_db.enums.PersonalNumberValidity attribute)
O
opt (in module cobra_db.filesystem)
optional() (cobra_db.model.DicomEntity static method)
OTHER (cobra_db.enums.Modality attribute)
P
parse_arguments() (in module cobra_db.scripts.pseudonymize_image_metadata)
(in module cobra_db.scripts.stage_1_ingest_images)
(in module cobra_db.scripts.stage_2)
parse_AS_as_int() (in module cobra_db.utils)
parse_DA_as_datetime() (in module cobra_db.utils)
parse_DA_TM_as_datetime() (in module cobra_db.utils)
Patient (class in cobra_db.model)
patient_age (cobra_db.model.RadiologicalStudy attribute)
patient_anon_id (cobra_db.model.Annotation attribute)
patient_height (cobra_db.model.RadiologicalStudy attribute)
patient_id (cobra_db.model.RadiologicalStudy attribute)
patient_pregnancy_status (cobra_db.model.RadiologicalStudy attribute)
patient_weight (cobra_db.model.RadiologicalStudy attribute)
PatientDao (class in cobra_db.mongo_dao)
PatientPosition (class in cobra_db.enums)
PersonalNumberValidator (class in cobra_db.encrypt)
PersonalNumberValidity (class in cobra_db.enums)
PFDL (cobra_db.enums.PatientPosition attribute)
PFDR (cobra_db.enums.PatientPosition attribute)
PNG (cobra_db.enums.DataFormat attribute)
Point2D (in module cobra_db.types)
Point3D (in module cobra_db.types)
possible_labels (cobra_db.model.Annotation attribute)
POSSIBLY_PREGNANT (cobra_db.enums.PregnancyStatus attribute)
PregnancyStatus (class in cobra_db.enums)
process_batch() (in module cobra_db.scripts.pseudonymize_image_metadata)
process_files_batch() (in module cobra_db.scripts.stage_1_ingest_images)
process_im_meta() (in module cobra_db.scripts.pseudonymize_image_metadata)
process_patient_batch() (in module cobra_db.scripts.stage_2_group_patients)
process_series() (in module cobra_db.scripts.stage_2_group_series)
process_series_batch() (in module cobra_db.scripts.stage_2_group_series)
process_study_batch() (in module cobra_db.scripts.stage_2_group_studies)
project_name (cobra_db.model.Annotation attribute)
(cobra_db.model.Metadata attribute)
ProjectName (class in cobra_db.enums)
proto_patient_generator() (in module cobra_db.scripts.stage_2_group_patients)
proto_series_generator() (in module cobra_db.scripts.stage_2_group_series)
proto_study_generator() (in module cobra_db.scripts.stage_2_group_studies)
protocol_name (cobra_db.model.RadiologicalSeries attribute)
pseudonymize() (cobra_db.deid.Deider method)
PT (cobra_db.enums.Modality attribute)
Q
query_mux() (in module cobra_db.scripts.pseudonymize_image_metadata)
R
RadiologicalSeries (class in cobra_db.model)
RadiologicalStudy (class in cobra_db.model)
recipe_mux() (in module cobra_db.scripts.pseudonymize_image_metadata)
Rectangle (in module cobra_db.types)
referenced_entity_uid (cobra_db.model.Annotation attribute)
rel_path (cobra_db.model.FileSource attribute)
RFP (cobra_db.enums.PatientPosition attribute)
RFS (cobra_db.enums.PatientPosition attribute)
RIGHT (cobra_db.enums.Laterality attribute)
S
SAG (cobra_db.enums.View attribute)
sanity_check() (in module cobra_db.scripts.stage_2_group_series)
series_count (cobra_db.model.RadiologicalStudy attribute)
series_id (cobra_db.model.ImageMetadata attribute)
series_uid (cobra_db.model.RadiologicalSeries attribute)
SeriesDao (class in cobra_db.mongo_dao)
set_union() (in module cobra_db.scripts.stage_2_group_studies)
single_proc() (in module cobra_db.scripts.pseudonymize_image_metadata)
(in module cobra_db.scripts.stage_1_ingest_images)
Size2D (in module cobra_db.types)
Size3D (in module cobra_db.types)
software_versions (cobra_db.model.RadiologicalStudy attribute)
sop_class (cobra_db.model.RadiologicalStudy attribute)
Source (class in cobra_db.model)
specialization (cobra_db.model.Annotator attribute)
SR (cobra_db.enums.Modality attribute)
StrEnum (class in cobra_db.enums)
study_date (cobra_db.model.Annotation attribute)
study_id (cobra_db.model.ImageMetadata attribute)
(cobra_db.model.RadiologicalSeries attribute)
study_uid (cobra_db.model.RadiologicalStudy attribute)
StudyDao (class in cobra_db.mongo_dao)
T
tag_for_keyword_wrapper() (cobra_db.dataset_mod.DatasetMod static method)
tags_to_keywords() (cobra_db.dataset_mod.DatasetMod static method)
TIFF (cobra_db.enums.DataFormat attribute)
to_dataset() (cobra_db.model.ImageMetadata method)
to_dict() (cobra_db.model.BaseObj method)
(cobra_db.model.EntitySource method)
U
UNKNOWN (cobra_db.enums.PregnancyStatus attribute)
update_patient_id() (cobra_db.mongo_dao.StudyDao method)
update_series_id() (cobra_db.mongo_dao.ImageMetadataDao method)
update_study_id() (cobra_db.mongo_dao.ImageMetadataDao method)
(cobra_db.mongo_dao.SeriesDao method)
US (cobra_db.enums.Modality attribute)
V
VAIB (cobra_db.enums.ProjectName attribute)
VALID (cobra_db.enums.PersonalNumberValidity attribute)
validate() (cobra_db.encrypt.PersonalNumberValidator static method)
View (class in cobra_db.enums)
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