Add download_series() function

src/CancerImagingArchive.jl

@@ -2,6 +2,9 @@ module CancerImagingArchive
 
 using HTTP, CSV, DataFrames, JSON
 
+include("download_series.jl")
+export download_series
+
 export tcia_collections, tcia_modalities, tcia_bodyparts, tcia_manufacturers, tcia_studies, tcia_series, tcia_series_size
 export tcia_patients, tcia_patients_by_modality, tcia_newpatients, tcia_newstudies, tcia_sop
 export tcia_single_image, tcia_images

src/download_series.jl

@@ -0,0 +1,43 @@
+function _initialize_destination(destination, overwrite)
+    if overwrite
+        rm(destination; force = true, recursive = true)
+    end
+    if !isdir(destination)
+        mkpath(destination)
+    end
+    return destination
+end
+
+function download_series(series_id::AbstractString, destination = "./", overwrite = true)
+    _initialize_destination(destination, overwrite)
+    zip_file = joinpath(destination, "downloaded.zip")
+    tcia_images(series = series_id, file = zip_file)
+    unzip_command = `unzip -o $zip_file -d $destination`
+    run(unzip_command)
+    rm(zip_file)
+    return destination
+end
+
+function download_series(series_df::DataFrames.DataFrame, destination = "./"; append_desc = true, overwrite = true)
+    return [download_series(row, destination; append_desc=append_desc, overwrite=overwrite) for row in eachrow(series_df)]
+end
+
+function download_series(series::DataFrames.DataFrameRow, destination = "./"; append_desc = true, overwrite = true)
+    series_id = series.SeriesInstanceUID
+    if append_desc 
+        destination = joinpath(destination, series.SeriesDescription)
+    end
+    return download_series(series_id, destination, overwrite)
+end
+
+function download_series(series::Dict, destination = "./"; append_desc = true, overwrite = true)
+    series_id = series["SeriesInstanceUID"]
+    if append_desc 
+        destination = joinpath(destination, series["SeriesDescription"])
+    end
+    return download_series(series_id, destination, overwrite)
+end
+
+function download_series(series_array::Array, destination = "./"; append_desc = true, overwrite = true)
+    return [download_series(series, destination; append_desc=append_desc, overwrite=overwrite) for series in series_array]
+end

test/runtests.jl

@@ -173,6 +173,15 @@ end
     @test filesize(dicom_file) == 980794
 end
 
+@testset "Download series" begin
+  series = tcia_series(collection = "AAPM-RT-MAC", patient = "RTMAC-LIVE-001")
+  seriesjs = tcia_series(collection = "AAPM-RT-MAC", patient = "RTMAC-LIVE-001", format="json") 
+  download_series(series, "./testdf")
+  download_series(seriesjs, "./testjs")
+  download_series(series, "./testdf"; overwrite = false)
+end
+
+
 @testset "Utilities - remove_empty!()" begin
     dict_potentialy_empty_values = Dict(1 => "", 2 => "hello", 3 => "b", 4 => "", 5 => "ye")
     CancerImagingArchive.remove_empty!(dict_potentialy_empty_values)