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EOGrady21 / VPR_viewer

A shiny app to visualize plankton data and images from the Video Plankton Recorder
MIT License
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Testing with varied file directory structures #1

Open EOGrady21 opened 2 years ago

EOGrady21 commented 2 years ago

I suspect that there are some internal dependencies on file structure that I am not fully remembering, either within vprr functions or within the app code itself. I have done my best to test using different directories and structures but it should be tested in isolation or on a new machine to ensure nothing will break.

@kevinsorochan can you remind me of the directory structure output from autodeck? I would like to test to make sure I am not relying on VP structure

kevinsorochan commented 2 years ago

I think it makes sense to use the VP structure, not necessarily because we will use VP, but it seems like a good organizational structure. This is from the VPR manual (DAVPR Manual Rev 2) page 79:

The output path choice is open to the user but if the user is planning to use Visual Plankton (VP) for further processing, VP will expect the data to be stored in the following format: (drive):\data\cruise\rois\vprxxx\dxxx\hxx (drive) can be any drive available on the computer at hand \data should be there, no freedom \cruise is the cruise name during which the data was collected, is user specified. \rois should be there, no freedom \vprxxx should be there where xxx is a cast number (no leading zeros) \dxxx\hxx are automatically generated in the proper format with dxxx being the day of the year and hxx the hour of the day as computed from the date information contained in the input file name. If you want these day and hour value to be consistent between data collection and data processing, you need to make sure that both the VPR and the processing computer are set to the same time zone, GMT being our preferred setting.

In the day folder ((drive):\data\cruise\rois\vprxxx\dxxx), JpegLS_ADeck will also create ctd data files with names hxxctd.dat.

EOGrady21 commented 2 years ago

Thanks for that info Kevin.

So it seems the directory structure output from autodeck is the same as the VP structure anyway.

I think it would still be worth running some tests to be sure the app works with any file structure but maybe this is lower priority than I thought.