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dptools / dplocatej

GPS analysis pipeline with option to exclude encryption
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Input PHOENIX structure #4

Open tashrifbillah opened 3 years ago

tashrifbillah commented 3 years ago

Hello @hre80 ,

Does this structure look okay for dplocate0?

Deleted to avoid future confusion

hre80 commented 3 years ago

Hi, it is good up to A(subject). Then device (phone here). It branches to: raw and processed. Under raw gps and the .json file. The results go to processed later.

hre80 commented 3 years ago

1- under raw "gps" and then the .json 2- the "processed" folder branches out after phone in Both GENERAL and PROTECTED. Some results we decided that needs to be protected and some could go to GENERAL, i.e. the output of dplocate4-plot

tashrifbillah commented 3 years ago

Some results we decided that needs to be protected and some could go to GENERAL, i.e. the output of dplocate4-plot

So should I be providing different --output-dir for different submodules?

hre80 commented 3 years ago

No, already set in the pipeline. The --output-dir changes the main folders not this structure.

tashrifbillah commented 3 years ago

I manually created all the directories assuming the pipeline won't create any. Let me know if the assumption is not right.

dplocate-test/
├── GENERAL
│   └── BWH
│       ├── A
│       │   └── phone
│       │       └── processed
│       └── BWH_metadata.csv
└── PROTECTED
    └── BWH
        └── A
            └── phone
                ├── processed
                └── raw
                    └── gps
                        └── sensor_HRE.json
hre80 commented 3 years ago

This is great. Under processed you don't need to build gps. The pipeline creates what is needed. Please make the "processed" folder w/r to the group (770) but the raw is only readable to others (710).

tashrifbillah commented 3 years ago

Under processed you don't need to build gps.

Deleting them to test the pipeline.

Update: Test succeeded.

hre80 commented 3 years ago

And yes needs to be done before the pipeline is applied. I thought it was part of the standard structure that lochness produces. If anything has been changed in this project, let me know and I can revise the defaults accordingly.

tashrifbillah commented 3 years ago

What is the _HRE suffix at the end of sensor_HRE.json by the way? Is it appended by user's phone/collecting software?

hre80 commented 3 years ago

No, this is my initials. the collecting software (lochness I guess) can have any output format.

tashrifbillah commented 3 years ago
tashrifbillah commented 2 years ago

Hi Habib,

We have created as much as https://github.com/dptools/dplocate/issues/4#issuecomment-906523854 for dplocate.

Now Kevin @kcho has pointed out that: https://github.com/AMP-SCZ/lochness/pull/49#issuecomment-926869020

lochness.mindlamp does not creat gps subfolder.

  1. Given that, how can we run dplocate based on lochness pulled data?
  2. Is dplocate capable of obtaining input from BIDS PHOENIX structure?
tashrifbillah commented 2 years ago

gps folder name comes from Bewie API historically. It is yet to be determined for Mindlamp.