ephy_testing_data/neuroscope/dataset_1/YutaMouse42-151117.xml

<?xml version='1.0'?>
<parameters version="1.0" creator="ndManager-">
 <generalInfo>
  <date>2015-08-31</date>
  <experimenters>yuta</experimenters>
  <description/>
  <notes/>
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   <isolationDistance/>
   <quality/>
   <notes/>
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 </neuroscope>
 <programs>
  <program>
   <name>process_calcThreshold</name>
   <parameters>
    <parameter>
     <name>executeScriptBool</name>
     <value>1</value>
     <status>Mandatory</status>
    </parameter>
    <parameter>
     <name>rmsWindowLength</name>
     <value>2</value>
     <status>Mandatory</status>
    </parameter>
   </parameters>
   <help>useage:
process_calcThreshold fileBaseName electrodeNumber

This script calculates the spike detection threshold and puts it in the file fileBaseName.threshold.electrodeNumber

parameters:
- executeScriptBool determines whether the script should be run with the next batch process.
- rmsWindowLength represents the  root mean square (rms) integration window for detection.
</help>
  </program>
  <program>
   <name>process_detectSpikes</name>
   <parameters>
    <parameter>
     <name>executeScriptBool</name>
     <value>1</value>
     <status>Mandatory</status>
    </parameter>
    <parameter>
     <name>thresholdFactor</name>
     <value>7</value>
     <status>Mandatory</status>
    </parameter>
    <parameter>
     <name>refractoryPeriod</name>
     <value>8</value>
     <status>Mandatory</status>
    </parameter>
    <parameter>
     <name>rmsWindowLength</name>
     <value>2</value>
     <status>Mandatory</status>
    </parameter>
    <parameter>
     <name>peakWindowLength</name>
     <value>10</value>
     <status>Mandatory</status>
    </parameter>
    <parameter>
     <name>windowPeakAlign</name>
     <value>5</value>
     <status>Mandatory</status>
    </parameter>
    <parameter>
     <name>spikesFromDatBool</name>
     <value>1</value>
     <status>Mandatory</status>
    </parameter>
   </parameters>
   <help>This script does the following:

* detects the spikes (creates the .res.# file),
* aligns the peaks,
* gets the waveforms (creates the .spk.# file),

The variables used by the different programs called in this script depend on the sampling rate. The default is for a sampling rate of 10khz.
All the script  parameters are multiplifaction factor of 10khz except the thresholdFactor.

parameters:
- executeScriptBool determines whether the script should be run with the next batch process.
- refractoryPeriod represents the after detection, how many samples to skip before detecting a new spike if one is detected.
- rmsWindowLength represents the  root mean square (rms) integration window for detection.
- peakWindowLength represents the window (number of samples to test) to search for spike peak, seams to be used for eigen calculation or finding of the true spike peak.
- windowPeakAlign represents the middle of the peakWindowLength, where to take the spike peak in peakWindowLength.
- thresholdFactor is a factor to compute the detection threshold: 
threshold = thresholdFactor  * baseline
- spikesFromDatBool: set to 1 if you want detrended spikes from wideband dat file; set to 0 if from high-passed fil file
</help>
  </program>
  <program>
   <name>process_findCommonThreshold</name>
   <parameters>
    <parameter>
     <name>executeScriptBool</name>
     <value>1</value>
     <status>Mandatory</status>
    </parameter>
    <parameter>
     <name>maxThreshold</name>
     <value/>
     <status>Mandatory</status>
    </parameter>
   </parameters>
   <help>useage:
process_findCommonThreshold fileBaseName [fileBaseName ...]

for each electrodeGroup in fileBaseName.xml
the value in fileBaseName.threshold.electrodeGroup is replaced by the minimum threshold value across passed fileBaseNames.
 
parameters:
- executeScriptBool determines whether the script should be run with the next batch process.
- maxThreshold default = 500</help>
  </program>
  <program>
   <name>process_merge</name>
   <parameters>
    <parameter>
     <name>executeScriptBool</name>
     <value>1</value>
     <status>Mandatory</status>
    </parameter>
    <parameter>
     <name>mergeBaseName</name>
     <value>YutaMouse42-151117</value>
     <status>Mandatory</status>
    </parameter>
   </parameters>
   <help>process_merge

usage:
process_merge -n $mergeBaseName $fileBaseNames

merges .spk .res etc for multi-file clustering.

parameters:
- executeScriptBool determines whether the script should be run with the next batch process.
- mergeBaseName designates the fileBaseName of the merged files.

*** Requirements ***
* calls process_pca_light : to do pca without presence of .fil file
* calls pproc
* each fileBaseName.* must be in a directory fileBaseName - which can be performed by process_dirFiles
</help>
  </program>
  <program>
   <name>process_mhipass</name>
   <parameters>
    <parameter>
     <name>executeScriptBool</name>
     <value>1</value>
     <status>Mandatory</status>
    </parameter>
    <parameter>
     <name>frequency</name>
     <value>800</value>
     <status>Mandatory</status>
    </parameter>
    <parameter>
     <name>libraryPath</name>
     <value>/u16/local/matlab6.5/extern/lib/glnx86:/u16/local/matlab6.5/bin/glnx86:/u16/local/matlab6.5/sys/os/glnx86</value>
     <status>Mandatory</status>
    </parameter>
   </parameters>
   <help>This script does the high-pass filtering for subsequent spike extraction. The .fil file is created by the program called in this script.
The frequency parameter is the lowest frequency cut off.
The highest frequency is computed based on the sampling rate as 0.95 % of the Nyquist frequency:
sampling rate * 0.5 * 0.95

The program called in this script is currently a matlab program, therefore this part of the process relies on Matlab until this program is rewritten.

parameters:
- executeScriptBool determines whether the script should be run with the next batch process.
- libraryPath is the path for Matlab.</help>
  </program>
  <program>
   <name>process_mlopass</name>
   <parameters>
    <parameter>
     <name>executeScriptBool</name>
     <value>1</value>
     <status>Mandatory</status>
    </parameter>
    <parameter>
     <name>libraryPath</name>
     <value>/u16/local/matlab6.5/extern/lib/glnx86:/u16/local/matlab6.5/bin/glnx86:/u16/local/matlab6.5/sys/os/glnx86</value>
     <status>Mandatory</status>
    </parameter>
   </parameters>
   <help>This script does the low-pass filtering (for local field potentials). The .eeg file is created by the program called in this script.
It calls a resampling program which first apply an anti aliasing low pass filter to the data and then samples down to the local field potential sampling rate provided in the parameter file.

The resampling program is currently a matlab program, therefore this part of the process relies on Matlab until this program is rewritten.

parameters:
- executeScriptBool determines whether the script should be run with the next batch process.
- libraryPath is the path for Matlab.</help>
  </program>
  <program>
   <name>process_multi_start</name>
   <parameters>
    <parameter>
     <name>cpFirstXmlBool</name>
     <value>1</value>
     <status>Mandatory</status>
    </parameter>
    <parameter>
     <name>rmFilFileBool</name>
     <value>1</value>
     <status>Mandatory</status>
    </parameter>
   </parameters>
   <help>This script starts eeg and spike data processing on a list of input fileBaseNames

This script is called by:
process_multi_start fileBaseName [fileBaseNames]

Parameters:
- rmFilFileBool
 1 = remove the high pass filtered .fil file to save space
- cpFirstXmlBool
 1 = copy the xml file from the first fileBaseName to all other fileBaseNames to save time


* Note that ideally the common threshold would be for single channels rather than single electrodes (may be a problem of process_baseline)</help>
  </program>
  <program>
   <name>process_mvFiles2Dirs</name>
   <parameters>
    <parameter>
     <name>executeScriptBool</name>
     <value>1</value>
     <status>Mandatory</status>
    </parameter>
   </parameters>
   <help>This script organizes files in preparation for process_merge by moving fileBaseName.* into a directory fileBaseName
useage:
process_mvFiles2Dirs fileBaseName

parameters:
- executeScriptBool determines whether the script should be run with the next batch process.
</help>
  </program>
  <program>
   <name>process_pca</name>
   <parameters>
    <parameter>
     <name>executeScriptBool</name>
     <value>1</value>
     <status>Mandatory</status>
    </parameter>
    <parameter>
     <name>beforePeak</name>
     <value>4</value>
     <status>Mandatory</status>
    </parameter>
    <parameter>
     <name>afterPeak</name>
     <value>4</value>
     <status>Mandatory</status>
    </parameter>
    <parameter>
     <name>nSamplesInPCA</name>
     <value>16</value>
     <status>Mandatory</status>
    </parameter>
   </parameters>
   <help>This script performs the principle component analysis (PCA ). It computes the variance (creates the .m1m2.# file) and creates the  .fet.# and .mm.# files.
The variables used to compute the PCA depend on the sampling rate. The default is for a sampling rate of 10khz.
The parameters in the parameter file are multiplifaction factor of 10khz.

parameters:
- executeScriptBool determines whether the script should be run with the next batch process.
- beforePeak represents the number of samples before peak to be used for the PCA. There is one value for all the electrodes.
- afterPeak represents the number of samples after peak to be used for the PCA. There is one value for all the electrodes.
- nSamplesInPCA represents the number of samples used for PCA.  There is one value for all the electrodes.
</help>
  </program>
  <program>
   <name>updateParFile</name>
   <parameters>
    <parameter>
     <name>executeScriptBool</name>
     <value>1</value>
     <status>Mandatory</status>
    </parameter>
    <parameter>
     <name>samplesInWaveform</name>
     <value>16</value>
     <status>Mandatory</status>
    </parameter>
    <parameter>
     <name>peakSample</name>
     <value>8</value>
     <status>Mandatory</status>
    </parameter>
   </parameters>
   <help>This script updates the parameter file. 
It adds for each spike group, the number of samples in each waveform, the sample index of the peak in a waveform and the number of feaures to use to do the PCA.

The variables used by the different programs depend on the sampling rate. The default is for a sampling rate of 10khz.
All the script parameters are multiplifaction factor of 10khz.

parameters:
- executeScriptBool determines whether the script should be run with the next batch process.
- The parameter samplesInWaveform represents the number of samples in each waveform .
- The parameter peakSample represents the sample index of the peak in a waveform.
</help>
  </program>
 </programs>
 <multiFileProcessing>
  <commonThresholdBool>1</commonThresholdBool>
  <files>
   <fileBaseName>YutaMouse42-151117-01</fileBaseName>
   <fileBaseName>YutaMouse42-151117-02</fileBaseName>
   <fileBaseName>YutaMouse42-151117-03</fileBaseName>
  </files>
 </multiFileProcessing>
</parameters>