Actigraphy Merger

[pmanko]

• Update Actigraphy Merger
• Create UI for merging actigraphy files

Relevant commit: https://github.com/bwhsleepamu/access/commit/2120fcc96a4718db2848779752d5e8ba7df83661

[pmanko]

• [x] Merge lu-actigraphy into master
• [ ] Create a feature branch for actigraphy enhancement
• [ ] Add functionality to create merged AWD file in parallel with the output CSV file
• [ ] Using Access UI, create a subject group for the subjects that need to be run for the new analysis.
• Update the Rake taks (https://github.com/bwhsleepamu/access/blob/e6e3315a132d6aaa98fa7071cd79914addeeaf71/lib/tasks/etl.rake#L115) to use this new Subject group
  • [ ] Pass in subject_group name as a CLI argument (https://stackoverflow.com/questions/825748/how-to-pass-command-line-arguments-to-a-rake-task)
  • [ ] Pass in paths as a CLI argument
  • [ ] Update the subject lists in the rake taks to coincide with the lists created in the actigraphy merger

[pmanko]

A great starting place would be to get a complete grasp on the input and output file formats. Let's do this in this issue chain.

The file formats (example file with either column names or heading information) that we need are:

Note: all of these files can be found in the IPM/Projects/Database Project/Data Sources/Actigraphy folder

Actigraphy Input Files - for example

Master Files that Scott put together:

Example Columns: -``` "SUBJECT_CODE","FILE_PATH","START_TIME","END_TIME","EPOCH_LENGTH","CONDITION","NOTES" "1425MX72","/X/People/Research Staff/Beckett_Scott/Actigraphy/FD Actigraphy_11.30.2012/1425MX72/LUC712.txt",1997-02-05 10:55:00,1997-02-12 21:58:00,1,"S1","NO LIGHT DATA Pre and Post admit times established from study protocol .RPJ file" "1425MX72","/X/People/Research Staff/Beckett_Scott/Actigraphy/FD Actigraphy_11.30.2012/1425MX72/LUC03167.txt",1997-03-03 11:29:00,1997-03-16 11:20:00,1,"S2","NO LIGHT DATA Pre and Post admit times established from study protocol .RPJ file" "1425MX72","/X/People/Research Staff/Beckett_Scott/Actigraphy/FD Actigraphy_11.30.2012/1425MX72/LUC04037.txt",1997-03-21 15:23:00,1997-04-03 15:20:00,1,"S3","NO LIGHT DATA Pre and Post admit times established from study protocol .RPJ file" "1425MX72","/X/People/Research Staff/Beckett_Scott/Actigraphy/FD Actigraphy_11.30.2012/1425MX72/LUC04097.txt",1997-04-03 16:13:00,1997-04-10 13:07:00,1,"L1","NO LIGHT DATA Pre and Post admit times established from study protocol .RPJ file" "1425MX72","/X/People/Research Staff/Beckett_Scott/Actigraphy/FD Actigraphy_11.30.2012/1425MX72/LUC04237.txt",1997-04-10 13:22:00,1997-04-20 22:24:00,1,"L2","NO LIGHT DATA Pre and Post admit times established from study protocol .RPJ file"

# Actigraphy files used as input 
For example:
`smb://cifs2/dscd_t$/IPM`

24B7GXT3_L1 07-Aug-2007 15:22 4 34 P6307330451000 F 187 , 73.5 94 , 74.5 115 , 22.2 711 , 10.2 1609 , 11.6 280 , 2.7 271 , 1.2 104 , 0.6 833 , 16.6 689 , 27.9

# Merged Output Files:

subject_code,labtime_decimal,labtime_year,labtime_hour,labtime_min,labtime_sec,activity_count,light_level,epoch_length
1425MX72,1911.3833333333334,1997,1911,23,0,242.0,"",60
1425MX72,1911.4,1997,1911,24,0,114.0,"",60
1425MX72,1911.4166666666667,1997,1911,25,0,224.0,"",60
1425MX72,1911.4333333333334,1997,1911,26,0,260.0,"",60
1425MX72,1911.45,1997,1911,27,0,180.0,"",60
1425MX72,1911.4666666666667,1997,1911,28,0,54.0,"",60
1425MX72,1911.4833333333333,1997,1911,29,0,60.0,"",60
1425MX72,1911.5,1997,1911,30,0,152.0,"",60
1425MX72,1911.5166666666667,1997,1911,31,0,154.0,"",60
1425MX72,1911.5333333333333,1997,1911,32,0,192.0,"",60
1425MX72,1911.55,1997,1911,33,0,200.0,"",60
1425MX72,1911.5666666666666,1997,1911,34,0,216.0,"",60
1425MX72,1911.5833333333333,1997,1911,35,0,216.0,"",60
1425MX72,1911.6,1997,1911,36,0,164.0,"",60