Nothing
## ----echo = FALSE, message = FALSE---------------------------------------
api_key <- Sys.getenv("TCIA_API_KEY")
if (identical(api_key, "")) {
knitr::opts_chunk$set(eval = FALSE)
message("Note: code examples will not be evaluated because the system does not have a valid API key installed.")
}
## ----eval = FALSE--------------------------------------------------------
# install.packages("TCIApathfinder")
## ----eval = FALSE--------------------------------------------------------
# # install.packages("devtools")
# devtools::install_github("pamelarussell/TCIApathfinder")
## ------------------------------------------------------------------------
# library(TCIApathfinder)
## ------------------------------------------------------------------------
# collections <- get_collection_names()
# head(collections$collection_names)
## ------------------------------------------------------------------------
# modalities <- get_modality_names()
# head(modalities$modalities)
## ------------------------------------------------------------------------
# body_parts <- get_body_part_names()
# head(body_parts$body_parts)
## ------------------------------------------------------------------------
# patients_tcga_brca <- get_patient_info(collection = "TCGA-BRCA")
# head(patients_tcga_brca$patients)
## ------------------------------------------------------------------------
# series <- get_series_info(patient_id = "TCGA-AR-A1AQ")
# head(series$series)
## ------------------------------------------------------------------------
# studies <- get_patient_studies(patient_id = "TCGA-AR-A1AQ")
# head(studies$patient_studies)
## ------------------------------------------------------------------------
# studies_tcga_brca <- get_studies_in_collection(collection = "TCGA-BRCA")
# head(studies_tcga_brca$studies)
## ------------------------------------------------------------------------
# sop_uids <- get_sop_instance_uids(
# series_instance_uid = "1.3.6.1.4.1.14519.5.2.1.3344.4002.298037359751562809791703106256")
# head(sop_uids$sop_instance_uids)
## ------------------------------------------------------------------------
# im <- save_single_image(series_instance_uid = "1.3.6.1.4.1.14519.5.2.1.3344.4002.298037359751562809791703106256",
# sop_instance_uid = "1.3.6.1.4.1.14519.5.2.1.3344.4002.113224119964450170072494597907")
# im$out_file
## ------------------------------------------------------------------------
# ser <- save_image_series(series_instance_uid = "1.3.6.1.4.1.14519.5.2.1.3344.4002.298037359751562809791703106256",
# out_file_name = "series.zip")
# zip <- ser$out_file
# extracted <- extract_image_series(zip)
# extracted$dirs
## ------------------------------------------------------------------------
# ser <- save_extracted_image_series(series_instance_uid = "1.3.6.1.4.1.14519.5.2.1.5382.4002.806935685832642465081499816867")
# ser$dirs
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