added atriumdb benchmark code

[tcpan]

Quick, possible unoptimized implementation of atriumdb format. Uses SQLite for now. Requires installation of "atriumdb" python package.

[tompollard]

This is great, thanks! Please could you add the atriumdb dependency to requirements.txt?

[github-actions]

Benchmark results:

________________________________________________________________
Format: waveform_benchmark.formats.atriumdb.AtriumDB
         (Example format using NPY)
Record: ./data/waveforms/mimic_iv/waves/p100/p10079700/85594648/85594648
         214981 seconds x 6 channels
         255177600 timepoints, 199126720 samples (78.0%)
________________________________________________________________
Channel summary information:
 signal       fs(Hz)     Bit resolution       Channel length(s)   
 II           249.89     0.005(mV)            212497              
 III          249.89     0.005(mV)            5                   
 V            249.89     0.005(mV)            212497              
 aVR          249.89     0.005(mV)            212492              
 Pleth        124.94     0.000244(NU)         212486              
 Resp         62.47      0.000244(Ohm)        212497              
________________________________________________________________
Output size:    119740 KiB (4.93 bits/sample)
Time to output: 790 sec
________________________________________________________________
Fidelity check:

Chunk		 Numeric Samples		  NaN Samples
	# Errors  /  Total	  % Eq  	NaN Values Match
Signal: II
  0  	         0/  51212896	100.000		    Y (7584)    
  1  	         0/     58944	100.000		    Y (1216)    
  2  	         0/   1818752	100.000		    Y (1408)    
Signal: III
  0  	         0/       960	100.000		    Y (320)     
Signal: V
  0  	         0/  51213248	100.000		    Y (7232)    
  1  	         0/     58944	100.000		    Y (1216)    
  2  	         0/   1818752	100.000		    Y (1408)    
Signal: aVR
  0  	         0/   3982176	100.000		    Y (1184)    
  1  	         0/  47229696	100.000		    Y (6144)    
  2  	         0/     58944	100.000		    Y (1216)    
  3  	         0/   1818752	100.000		    Y (1408)    
Signal: Pleth
  0  	         0/  25610240	100.000		     Y (0)      
  1  	         0/     29440	100.000		     Y (0)      
  2  	         0/    909440	100.000		     Y (0)      
Signal: Resp
  0  	         0/  12805120	100.000		     Y (0)      
  1  	         0/     15040	100.000		     Y (0)      
  2  	         0/    455040	100.000		     Y (0)      
________________________________________________________________
Read performance (median of N trials):
 #seek  #read      KiB      sec     [N]
     0     -1   119492   3.3138     [6] read 1 x 214981s, all channels
     0     -1     4896   0.1491   [115] read 5 x 500s, all channels
     0     -1    31924   1.3312    [14] read 50 x 50s, all channels
     0     -1   287840  13.3495     [3] read 500 x 5s, all channels
     0     -1    20076   0.6044    [38] read 1 x 214981s, one channel
     0     -1      940   0.0448   [352] read 5 x 500s, one channel
     0     -1     5078   0.4084    [46] read 50 x 50s, one channel
     0     -1    47668   2.0427     [5] read 500 x 5s, one channel
________________________________________________________________

[tompollard]

Thanks @tcpan!