Functions
This page briefly describes the functions exported by the package.
The function names in this module are in lowercase letters and sometimes underscores are used for longer function names. Most functions require keyword arguments, i.e. tcia_bodyparts(collection = collection_name) will work but tcia_bodyparts(collection_name) will not.
Index
CancerImagingArchive.dataframe_to_csvCancerImagingArchive.dictionary_to_jsonCancerImagingArchive.download_seriesCancerImagingArchive.download_seriesCancerImagingArchive.download_seriesCancerImagingArchive.remove_empty!CancerImagingArchive.tcia_bodypartsCancerImagingArchive.tcia_collectionsCancerImagingArchive.tcia_imagesCancerImagingArchive.tcia_manufacturersCancerImagingArchive.tcia_modalitiesCancerImagingArchive.tcia_newstudiesCancerImagingArchive.tcia_patientsCancerImagingArchive.tcia_patients_by_modalityCancerImagingArchive.tcia_seriesCancerImagingArchive.tcia_series_sizeCancerImagingArchive.tcia_single_imageCancerImagingArchive.tcia_sopCancerImagingArchive.tcia_studies
Public functions
CancerImagingArchive.dataframe_to_csv — Methoddataframe_to_csv(; dataframe, file)Writes the information in a DataFrame object (dataframe) into a csv file (file).
CancerImagingArchive.dictionary_to_json — Methoddictionary_to_json(; dictionary, file)Writes the information in a Dictionary Array (dictionary) into a json file (file).
CancerImagingArchive.download_series — Functiondownload_series(series_id::AbstractString, destination::AbstractString = "./", overwrite::Boolean = true)Downloads images belonging to series with series_id and extracts them to destination folder. If the destination folder already exists, then it will be overwritten by default unless overwrite = false.
CancerImagingArchive.download_series — Functiondownload_series(arr::Array, destination::AbstractString = "./"; append_desc::Boolean = true, overwrite::Boolean = true)Downloads all images from the series in the array arr and then extracts them to destination folder. The arr can be obtained through the tcia_series(..., format = "json") command. By default, the series description will be appended to the path unless append_desc = false. If the destination folder already exists, then it will be overwritten by default unless overwrite = false.
CancerImagingArchive.download_series — Functiondownload_series(df::DataFrame, destination::AbstractString = "./"; append_desc::Boolean = true, overwrite::Boolean = true)Downloads all images from the series in the dataframe df and then extracts them to destination folder. The df can be obtained through the tcia_series() function. By default, the series description will be appended to the path unless append_desc = false. If the destination folder already exists, then it will be overwritten by default unless overwrite = false.
CancerImagingArchive.remove_empty! — Methodremove_empty!(dictionary::Dict)Removes dictionary keys with empty values. Used internally to remove empty queries.
CancerImagingArchive.tcia_bodyparts — Methodtcia_bodyparts(; collection, modality, format = "csv")Returns the body parts examined in a given collection and/or by a given modality.
CancerImagingArchive.tcia_collections — Methodtcia_collections(; format = "csv")Provides names of all the collections on TCIA.
CancerImagingArchive.tcia_images — Methodtcia_images(; series, file)Downloads the images for the given SeriesInstanceUID series as the given zip-file file.
CancerImagingArchive.tcia_manufacturers — Methodtcia_manufacturers(; collection, modality, bodypart, format = "csv")Returns the hardware manufacturers for a given collection and/or modality and/or bodypart.
CancerImagingArchive.tcia_modalities — Methodtcia_modalities(; collection, bodypart, format = "csv")Returns the modalities used in a given collection and/or for a given bodypart.
CancerImagingArchive.tcia_newstudies — Methodtcia_newstudies(; date, collection, patient, format = "csv")Returns new studies for a given collection that were added after a given date formatted as YYYY-MM-DD. The patient ID can be optionally given.
CancerImagingArchive.tcia_patients — Methodtcia_patients(; collection, format = "csv")Returns the patients in a given collection.
CancerImagingArchive.tcia_patients_by_modality — Methodtcia_patients(; collection, modality, format = "csv")Returns the patients in a given collection and modality (both inputs required).
CancerImagingArchive.tcia_series — Methodtcia_series(; collection, bodypart, manufacturer, modality, model, patient, series, study, format = "csv")Returns series information for a given collection, bodypart,manufactuer,modality, manufacturermodel, patient, SeriesInstanceUID series, or StudyInstanceUID study.
CancerImagingArchive.tcia_series_size — Methodtcia_series_size(; series, format = "csv")Returns the total byte size and the number of objects in the given SeriesInstanceUID series.
CancerImagingArchive.tcia_single_image — Methodtcia_single_image(; series, sop, file)Downloads a single DICOM image for the given SeriesInstanceUID series and SOPInstanceUID sop. The DICOM file is saved as file.
CancerImagingArchive.tcia_sop — Methodtcia_sop(; series, format = "csv")Returns the SOPInstanceUIDs for the given SeriesInstanceUID series.
CancerImagingArchive.tcia_studies — Methodtcia_studies(; collection, patient, study, format = "csv")Returns the patient studies for a given collection and/or patient and/or study.