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Title: Client for the Cancer Imaging Archive REST API
Version: 1.0.6
Description: A wrapper for The Cancer Imaging Archive's REST API. The Cancer Imaging Archive (TCIA) hosts de-identified medical images of cancer available for public download, as well as rich metadata for each image series. TCIA provides a REST API for programmatic access to the data. This package provides simple functions to access each API endpoint. For more information, see https://github.com/pamelarussell/TCIApathfinder and TCIA's website.
Depends: R (≥ 3.4.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: httr, jsonlite
RoxygenNote: 6.1.1
Suggests: knitr, rmarkdown, oro.dicom, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-09-21 11:06:07 UTC; pamela.russell
Author: Pamela Russell [aut, cre]
Maintainer: Pamela Russell <pamela.russell@gmail.com>
Repository: CRAN
Date/Publication: 2019-09-21 11:20:03 UTC

Get body part names

Description

Get body part names

Usage

get_body_part_names(collection = NULL, modality = NULL)

Arguments

collection

TCIA collection name. If collection is NULL, body part names from all collections will be returned. To get a list of available collection names, call get_collection_names.

modality

Modality name. If modality is NULL, body part names from all modalities will be returned. To get a list of available modality names, call get_modality_names or see DICOM Modality Abbreviations.

Value

List containing elements:

See Also

get_collection_names, get_modality_names, DICOM Modality Abbreviations, TCIA REST API Usage Guide, TCIA API object definitions

Examples

## Not run: 
get_body_part_names()
get_body_part_names(collection = "TCGA-BRCA")
get_body_part_names(modality = "MR")
get_body_part_names(collection = "TCGA-BRCA", modality = "MR")

## End(Not run)


Get the names of all TCIA collections

Description

Get the names of all TCIA collections

Usage

get_collection_names()

Value

List containing elements:

See Also

TCIA REST API Usage Guide, TCIA API object definitions

Examples

## Not run: 
get_collection_names()

## End(Not run)


Get manufacturer names

Description

Get manufacturer names

Usage

get_manufacturer_names(collection = NULL, modality = NULL,
  body_part = NULL)

Arguments

collection

TCIA collection name. If collection is NULL, manufacturer names from all collections will be returned. To get a list of available collection names, call get_collection_names.

modality

Modality name. If modality is NULL, manufacturer names for all modalities will be returned. To get a list of available modality names, call get_modality_names or see DICOM Modality Abbreviations.

body_part

Body part name. If body_part is NULL, manufacturer names for all body parts will be returned. To get a list of available body part names, call get_body_part_names.

Value

List containing elements:

See Also

get_collection_names, get_modality_names, get_body_part_names, DICOM Modality Abbreviations, TCIA REST API Usage Guide, TCIA API object definitions

Examples

## Not run: 
get_manufacturer_names()
get_manufacturer_names(collection = "TCGA-BRCA")
get_manufacturer_names(collection = "TCGA-BRCA", modality = "MR", body_part = "BREAST")

## End(Not run)


Get modality names

Description

Get modality names

Usage

get_modality_names(collection = NULL, body_part = NULL)

Arguments

collection

TCIA collection name. If collection is NULL, modality names from all collections will be returned. To get a list of available collection names, call get_collection_names.

body_part

Body part name. If body_part is NULL, modality names for all body parts will be returned. To get a list of available body part names, call get_body_part_names.

Value

List containing elements:

See Also

get_collection_names, get_body_part_names, TCIA REST API Usage Guide, TCIA API object definitions

Examples

## Not run: 
get_modality_names()
get_modality_names(collection = "TCGA-BRCA")
get_modality_names(body_part = "BREAST")
get_modality_names(collection = "TCGA-BRCA", body_part = "BREAST")

## End(Not run)


Get IDs of patients that have been added to a collection since a specified date

Description

Get IDs of patients that have been added to a collection since a specified date

Usage

get_new_patients_in_collection(collection, date)

Arguments

collection

TCIA collection name. To get a list of available collection names, call get_collection_names.

date

Date in format "YYYY-MM-DD"

Value

List containing elements:

See Also

get_collection_names, TCIA REST API Usage Guide, TCIA API object definitions

Examples

## Not run: 
get_new_patients_in_collection("TCGA-BRCA", "2014-01-01")

## End(Not run)


Get studies that have been added to a collection and optionally to a patient since a specified date

Description

Get studies that have been added to a collection and optionally to a patient since a specified date

Usage

get_new_studies_in_collection(collection, date, patient_id = NULL)

Arguments

collection

TCIA collection name. To get a list of available collection names, call get_collection_names.

date

Date in format "YYYY-MM-DD"

patient_id

Patient ID. To get a list of available patient IDs, call get_patient_info. If patient_id is NULL, relevant studies for all patients in the collection will be returned.

Value

List containing elements:

See Also

get_collection_names, get_patient_info, TCIA REST API Usage Guide, TCIA API object definitions

Examples

## Not run: 
get_new_studies_in_collection("TCGA-BRCA", "2014-01-01")
get_new_studies_in_collection("TCGA-BRCA", "2014-01-01", "TCGA-OL-A66O")

## End(Not run)


Get patient information

Description

Get patient information

Usage

get_patient_info(collection = NULL)

Arguments

collection

TCIA collection name. If collection is NULL, patients from all collections will be returned. To get a list of available collection names, call get_collection_names.

Value

List containing elements:

See Also

get_collection_names, TCIA REST API Usage Guide, TCIA API object definitions

Examples

## Not run: 
get_patient_info()
get_patient_info("TCGA-BRCA")

## End(Not run)


Get patient study information

Description

Get patient study information

Usage

get_patient_studies(collection = NULL, patient_id = NULL,
  study_instance_uid = NULL)

Arguments

collection

TCIA collection name. To get a list of available collection names, call get_collection_names. If collection is NULL, information for all relevant collections will be returned.

patient_id

Patient ID. To get a list of available patient IDs, call get_patient_info. If patient_id is NULL, information for all relevant patients will be returned.

study_instance_uid

Study instance UID. If study_instance_uid is NULL, information for all relevant study instance UIDs will be returned. To get available study instance UIDs, call get_studies_in_collection, get_patient_studies, or get_new_studies_in_collection.

Value

List containing elements:

See Also

get_collection_names, get_patient_info, get_studies_in_collection, get_patient_studies, get_new_studies_in_collection, TCIA REST API Usage Guide, TCIA API object definitions

Examples

## Not run: 
get_patient_studies()
get_patient_studies(collection = "TCGA-BRCA")
get_patient_studies(patient_id = "TCGA-OL-A6VO")
get_patient_studies(patient_id = "TCGA-OL-A5DA",
     study_instance_uid = "1.3.6.1.4.1.14519.5.2.1.5382.4002.104582989590517557856962159716")

## End(Not run)


Get patient IDs given a collection name and modality

Description

Get patient IDs given a collection name and modality

Usage

get_patients_by_modality(collection, modality)

Arguments

collection

TCIA collection name. To get a list of available collection names, call get_collection_names.

modality

Modality name. To get a list of available modality names, call get_modality_names or see DICOM Modality Abbreviations.

Value

List containing elements:

See Also

get_collection_names, get_modality_names, DICOM Modality Abbreviations, TCIA REST API Usage Guide, TCIA API object definitions

Examples

## Not run: 
get_patients_by_modality("TCGA-BRCA", "MR")

## End(Not run)


Get image series information

Description

Get image series information

Usage

get_series_info(collection = NULL, patient_id = NULL,
  study_instance_uid = NULL, series_instance_uid = NULL,
  modality = NULL, body_part_examined = NULL,
  manufacturer_model_name = NULL, manufacturer = NULL)

Arguments

collection

TCIA collection name. To get a list of available collection names, call get_collection_names. If collection is NULL, information for all relevant collections will be returned.

patient_id

Patient ID. To get a list of available patient IDs, call get_patient_info. If patient_id is NULL, information for all relevant patients will be returned.

study_instance_uid

Study instance UID. If study_instance_uid is NULL, information for all relevant study instance UIDs will be returned. To get available study instance UIDs, call get_studies_in_collection, get_patient_studies, or get_new_studies_in_collection.

series_instance_uid

Series instance UID. To get a list of available series instance UIDs, call this function leaving out parameter series_instance_uid. If series_instance_uid is NULL, information for all relevant series will be returned.

modality

Modality name. To get a list of available modality names, call get_modality_names or see DICOM Modality Abbreviations. If modality is NULL, information for all relevant modalities will be returned.

body_part_examined

Body part name. To get a list of available body part names, call get_body_part_names. If body_part_examined is NULL, information for all relevant body parts will be returned. IMPORTANT: a bug in this query key has been observed in the TCIA API. If queries using this key return zero results, try removing this parameter.

manufacturer_model_name

Manufacturer model name. To get a list of available model names, call this function leaving out parameter manufacturer_model_name. If manufacturer_model_name is NULL, information for all relevant model names will be returned.

manufacturer

Manufacturer name. To get a list of available manufacturer names, call get_manufacturer_names. If manufacturer is NULL, information for all relevant manufacturers will be returned.

Value

List containing elements:

See Also

get_collection_names, get_patient_info, get_studies_in_collection, get_patient_studies, get_new_studies_in_collection, get_modality_names, get_body_part_names, get_manufacturer_names, TCIA REST API Usage Guide, TCIA API object definitions

Examples

## Not run: 
get_series_info()
get_series_info(collection = "TCGA-BRCA")
get_series_info(patient_id = "TCGA-OL-A6VO")
get_series_info(modality = "MR", manufacturer = "GE MEDICAL SYSTEMS")

## End(Not run)


Get size of image series

Description

Get size of image series

Usage

get_series_size(series_instance_uid)

Arguments

series_instance_uid

Series instance UID. To get a list of available series instance UIDs, call get_series_info.

Value

List containing elements:

See Also

get_series_info, TCIA REST API Usage Guide, TCIA API object definitions

Examples

## Not run: 
get_series_size("1.3.6.1.4.1.14519.5.2.1.5382.4002.272234209223992578700978260744")

## End(Not run)


Get SOP instance UIDs (individual DICOM image IDs) for an image series

Description

Get SOP instance UIDs (individual DICOM image IDs) for an image series

Usage

get_sop_instance_uids(series_instance_uid)

Arguments

series_instance_uid

Series instance UID. To get a list of available series instance UIDs, call get_series_info.

Value

List containing elements:

See Also

get_series_info, TCIA REST API Usage Guide, TCIA API object definitions

Examples

## Not run: 
get_sop_instance_uids("1.3.6.1.4.1.14519.5.2.1.5382.4002.272234209223992578700978260744")

## End(Not run)


Get studies in a collection and optionally for a specific patient

Description

Get studies in a collection and optionally for a specific patient

Usage

get_studies_in_collection(collection, patient_id = NULL)

Arguments

collection

TCIA collection name. To get a list of available collection names, call get_collection_names.

patient_id

Patient ID. To get a list of available patient IDs, call get_patient_info. If patient_id is NULL, studies for all patients in the collection will be returned.

Value

List containing elements:

See Also

get_collection_names, get_patient_info, TCIA REST API Usage Guide, TCIA API object definitions

Examples

## Not run: 
get_studies_in_collection("TCGA-BRCA")
get_studies_in_collection("TCGA-BRCA", "TCGA-OL-A66O")

## End(Not run)


Save a series of DICOM image files to a directory

Description

Save a series of DICOM image files to a directory

Usage

save_extracted_image_series(series_instance_uid, out_dir = NULL,
  verbose = TRUE)

extract_image_series(zip_file, out_dir = NULL)

Arguments

series_instance_uid

Series instance UID. To get a list of available series instance UIDs, call get_series_info. Note: if series_instance_uid is invalid, the API may still successfully return an empty zip file.

out_dir

Directory to write zip file to

verbose

print diagnostic messages

zip_file

downloaded zip file, usually output of save_image_series

Value

List containing elements:

Examples

## Not run: 
save_extracted_image_series(
     series_instance_uid = "1.3.6.1.4.1.14519.5.2.1.5382.4002.806935685832642465081499816867")

## End(Not run)


Save a series of DICOM image files as a zip file

Description

Save a series of DICOM image files as a zip file

Usage

save_image_series(series_instance_uid, out_dir = NULL,
  out_file_name = NULL)

Arguments

series_instance_uid

Series instance UID. To get a list of available series instance UIDs, call get_series_info. Note: if series_instance_uid is invalid, the API may still successfully return an empty zip file.

out_dir

Directory to write zip file to

out_file_name

Name of zip file to write. If out_file_name is NULL, the original file name will be used.

Value

List containing elements:

See Also

get_series_info, TCIA REST API Usage Guide, TCIA API object definitions

Examples

## Not run: 
save_image_series(
     series_instance_uid = "1.3.6.1.4.1.14519.5.2.1.5382.4002.806935685832642465081499816867",
     out_dir = "~/Desktop")
save_image_series(
     series_instance_uid = "1.3.6.1.4.1.14519.5.2.1.5382.4002.806935685832642465081499816867",
     out_dir = "~/Desktop", out_file_name = "file.zip")

## End(Not run)


Save a single DICOM image file

Description

Save a single DICOM image file

Usage

save_single_image(series_instance_uid, sop_instance_uid, out_dir = NULL,
  out_file_name = NULL)

Arguments

series_instance_uid

Series instance UID. To get a list of available series instance UIDs, call get_series_info.

sop_instance_uid

SOP instance UID. To get a list of SOP instance UIDs for an image series, call get_sop_instance_uids.

out_dir

Directory to write DICOM file to

out_file_name

Name of DICOM file to write, with .dcm extension. If out_file_name is NULL, the original file name will be used.

Value

List containing elements:

See Also

get_series_info, get_sop_instance_uids, TCIA REST API Usage Guide, TCIA API object definitions

Examples

## Not run: 
save_single_image(
     series_instance_uid = "1.3.6.1.4.1.14519.5.2.1.5382.4002.806935685832642465081499816867",
     sop_instance_uid = "1.3.6.1.4.1.14519.5.2.1.5382.4002.257663256941568276393774062283")
save_single_image(
     series_instance_uid = "1.3.6.1.4.1.14519.5.2.1.5382.4002.806935685832642465081499816867",
     sop_instance_uid = "1.3.6.1.4.1.14519.5.2.1.5382.4002.257663256941568276393774062283",
     out_file_name = "file.dcm")

## End(Not run)

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They may not be fully stable and should be used with caution. We make no claims about them.
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