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ygidtu / NBIA_data_retriever_CLI

command line version of NBIA data retriever
Apache License 2.0
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Does not download dicom files #10

Closed ArnolFokam closed 3 years ago

ArnolFokam commented 3 years ago

Hello, I tried to download the LIDC-IDRI dataset for CT scans with your script but all I get are JSON in the path where I expect these the dicom files of scans to be located.

Command ./nbia_cli_linux_amd64 -i /storage/notebooks/rv4mxifbqgdq5zy/manifest-1628944440778.tcia -o /storage -p 4

Output


2021-08-14T16:42:30Z | INFO   | Download 1.3.6.1.4.1.14519.5.2.1.6279.6001.179049373636438705059720603192 to /storage/yo/LIDC-IDRI/LIDC-IDRI-0001/1.3.6.1.4.1.14519.5.2.1.6279.6001.298806137288633453246975630178/01-01-2000/1.3.6.1.4.1.14519.5.2.1.6279.6001.179049373636438705059720603192
2021-08-14T16:42:47Z | INFO   | Getting https://public.cancerimagingarchive.net/nbia-download/servlet/DownloadServletV3?numberOfSeries=1&series1=1.3.6.1.4.1.14519.5.2.1.6279.6001.272348349298439120568330857680
2021-08-14T16:42:48Z | INFO   | Download 1.3.6.1.4.1.14519.5.2.1.6279.6001.272348349298439120568330857680 to /storage/yo/LIDC-IDRI/LIDC-IDRI-0007/1.3.6.1.4.1.14519.5.2.1.6279.6001.280315210397549164238230581781/01-01-2000/1.3.6.1.4.1.14519.5.2.1.6279.6001.272348349298439120568330857680
2021-08-14T16:43:04Z | INFO   | Getting https://public.cancerimagingarchive.net/nbia-download/servlet/DownloadServletV3?numberOfSeries=1&series1=1.3.6.1.4.1.14519.5.2.1.6279.6001.619372068417051974713149104919
2021-08-14T16:43:04Z | INFO   | Download 1.3.6.1.4.1.14519.5.2.1.6279.6001.619372068417051974713149104919 to /storage/yo/LIDC-IDRI/LIDC-IDRI-0002/1.3.6.1.4.1.14519.5.2.1.6279.6001.490157381160200744295382098329/01-01-2000/1.3.6.1.4.1.14519.5.2.1.6279.6001.619372068417051974713149104919```
ygidtu commented 3 years ago

Hi there,

I try the LIDC-IDRI dataset by TCIA_LIDC-IDRI_20200921.tcia from https://wiki.cancerimagingarchive.net/display/Public/LIDC-IDRI.

image

Every thing seems to be fine, please check your network environment, and maybe just try using proxy

❯ ./nbia_cli_darwin -i TCIA_LIDC-IDRI_20200921.tcia -o test
2021-08-16T16:10:01+08:00 | INFO   | Getting https://public.cancerimagingarchive.net/nbia-download/servlet/DownloadServletV3?numberOfSeries=1&series1=1.3.6.1.4.1.14519.5.2.1.6279.6001.141365756818074696859567662357
2021-08-16T16:10:03+08:00 | INFO   | Download 1.3.6.1.4.1.14519.5.2.1.6279.6001.141365756818074696859567662357 to test/LIDC-IDRI/LIDC-IDRI-0001/1.3.6.1.4.1.14519.5.2.1.6279.6001.175012972118199124641098335511/01-01-2000/1.3.6.1.4.1.14519.5.2.1.6279.6001.141365756818074696859567662357
- Ctrl+C pressed in Terminal

image

ArnolFokam commented 3 years ago

Tested it again. It worked!!! Do you know I can prevent the script from generating these meta JSON files?

ygidtu commented 3 years ago

Well, It cannot be removed automatically for now, you have to delete it manually.