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ImagingDataCommons / CloudSegmentator

Medical imaging segmentation workflows for FireCloud (Terra) and Seven Bridges Cancer Genomics Cloud
Apache License 2.0
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Eliminate an entire series not just slices with inconsistent geometry #38

Closed vkt1414 closed 8 months ago

vkt1414 commented 8 months ago

The previous query was removing localizers at the slice level while the expectation was to remove the entire series. The modified query filters the series containing localizer. In addition, the s5cmd urls are now generated from aws_urls.

fedorov commented 8 months ago

Is it a good idea to have --show-progress here? I thought it is better to not use it in the manifest, and instead (only if needed) add it to s5cmd run.

I always use --show-progress in the notebooks as it is the only way to know how many slices were downloaded and at what speed.

To confirm I understand correctly: are you saying that passing --show-progress to s5cmd run has a different effect from passing this flag to every cp command inside the manifest?

vkt1414 commented 8 months ago

Is it a good idea to have --show-progress here? I thought it is better to not use it in the manifest, and instead (only if needed) add it to s5cmd run.

I always use --show-progress in the notebooks as it is the only way to know how many slices were downloaded and at what speed.

To confirm I understand correctly: are you saying that passing --show-progress to s5cmd run has a different effect from passing this flag to every cp command inside the manifest?

Sorry I did not mean any effect but as far I understand, unlike --endpoint-url argument that can be set at the global level, we must pass --show-progress with every cp command.

fedorov commented 8 months ago

You are right! I thought I ran it with that flag passed to run, but I was mistaken.