The Dir command queues all of the files that match a template for processing. The files are not actually processed until the Process command is encountered. The template should include the full path to the files.

Syntax: Dir template

e.g. Dir c:\myfiles\*.plx will queue all of the .plx files in the c:\myfiles directory for processing.

Note: It is not mandatory to specify any input data files using the File or Dir commands in a batch command file. When a batch file that does not specify any input data files is executed from within the software, it will execute on the currently-open data file.

The ForEachFile command specifies an action to be done for each file being processed. For some commands the action is performed before the channels are processed, for others it is only performed after all channels have been processed (See Notes below)

Syntax: ForEachFile sub-command

e.g. ForEachFile ExportToNex

A list of the sub-commands for the ForEachFile command follows:

• Save – Saves the file. The saved file name is the same as the input file name with a numeric suffix added on to the original filename (same as File | Save menu option).
• ExportToPlx or SaveToPlx – Saves the file as a new plx file (same as File | Export to New .PLX menu option), possibly with a numeric suffix.
• ExportToPl2 or SaveToPl2 – Saves the file as a new pl2 file (same as File | Export to New .PL2 menu option), possibly with a numeric suffix. Note that this option is only available if the file being processed is a .PL2 file.
• ExportToNex or SaveToNex – Saves the timestamps etc. to a .NEX file, possibly with a numeric suffix added on to the original filename.
• ExportToNex5 or SaveToNex5 – Saves the timestamps etc. to a .NEX5 file, possibly with a numeric suffix added on to the original filename. SaveTpl – Saves a sorting template, which is specified by the Set TplFileName command
• SortUsingTpl – Applies a sorting template, which is specified by the Set TplFileName command
• InvalidateArtifacts – Applies cross-channel artifact removal the current file, using parameters specified by the Set ArtifactXXX commands.
• InvalidateArtifactsAfter – Applies cross-channel artifact removal to the current file after the ForEachChannel commands are processed. See the Notes section below.
• ExportWaveformInfo – Writes out selectable information about each waveform in all channels to text files, a MATLAB® file or an Excel® spreadsheet. The information to be written and other controlling parameters must be specified in the File | Export Per-Waveform Data dialog.
• ExportUnitInfo – Writes out selectable information about each unit in all channels to either text files, a MATLAB file or an Excel spreadsheet. The information to be written and other controlling parameters must be specified in the File | Export Per-Unit Data dialog.
• ExportChannelInfo – Writes out selectable information about each channel to either a text file, a MATLAB file or an Excel spreadsheet. The information to be written and other controlling parameters must be specified in the File | Export Per-Channel Data dialog.

The ForEachChannel command specifies an action to be done on each channel of each file.

Syntax: ForEachChannel sub-command

e.g. ForEachChannel ValleySeek Sub-commands for the ForEachChannel command are:

• Upsample – Performs interpolation to upsample each channel of continuous data, as configured with the Set UpSampleXXX commands.
• Filter – Applies a low-cut filter to each channel of continuous data. The filter cutoff frequency is specified with the Set FilterFreq command.
• Detect – Performs waveform detection for each continuous channel, as configured with the Set DetectXXX commands.
• Align – Runs waveform alignment, using the currently set alignment parameters set via the Set AlignXXX commands.
• DeleteAllUnits – Removes all existing units
• Sort – Performs sorting that has been specified via the Set SortType command.
• ValleySeek, ValleySeek2d – Runs Valley Seeking sorting on each channel, using 2D feature space
• ValleySeek3d – Runs Valley Seeking sorting on each channel, using 3D feature space.
• TDist, TDist2d – Runs T-Distribution E-M sorting on each channel, using 2D feature space.
• TDist3d – Runs T-Distribution E-M sorting on each channel, using 3D feature space.
• RemoveOutliers2d, RemoveOutlier3d – After sorting, runs the Remove Outliers tool in either 2D or 3D feature space, using the currently set Outlier Threshold.
• RemoveShortISI – Runs the Remove Short ISI tool, using the currently set Refractory Period.
• AssignUnsorted2d, AssignUnsorted3d – Runs the Assign Unsorted tool in either 2D or 3D feature space, using the currently set Outlier Threshold.
• KeepWfsBetweenEvents – Runs an interval filter that keeps only the waveforms between two specified events, with an optional time offset from each event.
• KeepWfsInSpan – Runs an interval filter that keeps only the waveforms within a time range around a specified event.
• KeepWfsOutsideSpan – Runs an interval filter that keeps only the waveforms that are outside of a time range around a specified event.
• KeepWfsBetweenTimes – Runs an interval filter that keeps only the waveforms within a specified time range.
• InvalidateWfsBetweenTimes – Runs an interval filter that invalidates the waveforms within a specified time range.
• InvalidateUnsorted– Invalidates any waveforms that are unsorted.
• SortSummaryToPP – After sorting, dumps the sort summary to PowerPoint for each channel.
• LogStats2d, LogStats3d – After sorting, dumps the 2D or 3D sort quality stats to the log file.
• Scan – Performs a parameter scan as configured with the Set ScanXXX commands.
• SaveScanResults – Saves the results of a previous ForEachChannel Scan command to a file that can be later inspected in the software.

The Set command changes a parameter, immediately.

Syntax: Set parameterName parameterValue

e.g Set ParzenRadiusMult 2.0

The available parameters are:

• OutputDir – Specifies the directory in which the software will write all output files.
• OptionsFromFile – Immediately sets all options to the values in the specified options file. The options file can be created using the Tools | All Options | Save To File menu command. Note that this can reset the values of any previous Set commands, so it generally should come before any other Set commands. This command is useful for making sure that all parameters are set to known values before executing a batch file.
• IgnoreSrc – Specifies a Source ID that will be completely skipped by the batch operation. No channels from the specified Source ID will be processed or saved into output files. This command can be issued more than once to ignore multiple Sources. This can be useful if for example the batch job is to re-extract and sort spikes from continuous data, and there may be an original spike Source in the file that should just be ignored – otherwise the channels from that Source would be re-sorted and written to the output file.
• SuppressOutputSrc – Specifies a Source ID that will be processed but not written out to any output files. This is useful for example if you want to do filtering, thresholding, and sorting of a wideband Source (so it cannot be Ignored), but you don’t want to export the original wideband continuous data (it can be Suppressed).
• ChanMap – Specifies a filename that contains a channel map to apply. Having this command present will force the named channel map file to be applied to each loaded file.
• TplFileName – Sets the sorting template filename to use for ForEachFile SortUsingTpl.
• DefaultFileType – Specifies the file type to assume when the data file extension does not match any known extension. The argument uses a numeric code from the following table to specify the file type ImportParameters – Specifies a filename for import parameters (.ofi file) to be used for binary file import.
• ContMinFreq, ContMaxFreq – Specifies a min and max frequency in Hz for any continuous channel filtering and thresholding done during the batch operation. Any continuous channels with sampling frequencies less than the minimum or greater than the maximum will not be processed. Those channels will be saved to output files though. This is useful to avoid performing filtering and thresholding on low-frequency slow data channels.
• LowPassFilter – If on (or 1 or true) filtering will perform low pass filtering instead of high-pass filtering.
• FilterFreq – Sets the filtering cutoff frequency in Hz to use with ForEachChannel Filter.
• FilterType – Sets the type of the filter to apply, can be Butterworth, Bessel or Elliptic
• FilterPoles – Sets the number of poles to use for the filter, can be 2,4,6,8,10 or 12
• UpSampleType – Sets the type of interpolation to do for upsampling; 0=None, 1=Linear, 2=Spline.
• UpSampleFactor – Sets the interpolation factor for upsampling (e.g. 2 means 2x interpolation).
• UpSampleMinFreq, UpSampleMaxFreq – Can be used to select which continuous channels will be upsampled (e.g. if a file contains some continuous channels sampled at 1000 Hz and others sampled at 4000 Hz, setting a UpSampleMinFreq of 30000 will ensure that only the 40000 Hz channels are upsampled).
• DetectNPW – Sets the number of points per waveform to use for ForEachChannel Detect.
• DetectNPre – Sets the number of pre-threshold samples to use for ForEachChannel Detect.
• DetectSigmas – Sets the detection threshold as a number of sigmas away from the mean of the peak heights histogram; the value can be negative for negative thresholds.
• DetectMicrovolts – Sets the detection threshold in microvolts
• Detect2Sigmas – Enables dual thresholding and sets the second detection threshold as a number of sigmas away from the mean of the peak heights histogram; the value can be negative for negative thresholds.
• Detect2Microvolts – Enables dual thresholding and sets the second detection threshold in microvolts
• ContPreampGain – Allows setting the preamp gain to be used for all continuous channels
• SpikePreampGain – Allows setting the preamp gain to be used for all spike channels
• DetectDead – Sets the number of samples to ignore following a detection (the dead time) to use for ForEachChannel Detect.
• AlignType – Determines how the waveforms will be aligned; 0=first local max, 1=first local min, 2=first local extremum, 3=global max, 4=global min.
• AlignMaxShift – The maximum amount a waveform will be shifted (in clock ticks).
• AlignDuringDetect – Toggles the align during detection feature on/off
• ArtifactWidth – The number of samples used to detect coincidence for ForEachFile InvalidateArtifacts.
• ArtifactPercentage – The percentage of channels that must have coincident spikes for ForEachFile InvalidateArtifacts.
• BetweenEvent1, BetweenEvent2 – Event names to use for KeepWfsBetweenEvents interval filter.
• BetweenEvent1Offset, BetweenEvent2Offset – Time offsets in msec to use for KeepWfsBetweenEvents interval filter. Filter will invalidate waveforms outside of the time interval between (time of BetweenEvent1 + BetweenEvent1Offset) to (time of BetweenEvent2 + BetweenEvent2Offset).
• SpanEvent – Event name to use for KeepWfsInSpan interval filter.
• SpanEventStartOffset, SpanEventEndOffset – Time offsets in msec to use for SpanEvent interval filter. Filter will invalidate waveforms outside of the time interval (time of SpanEvent + SpanEventStartOffset) to (time of SpanEvent + SpanEventEndOffset).
• TimeStart, TimeEnd – Defines the time interval in msec to use for the KeepWfsBetweenTimes and InvalidateWaveformsBetweenTimes interval filters.
• SortType – Sets the sorting type to use for the ForEachChannel Sort command. The argument values are: ValleySeek, TDist, ScanKMeans, ScanStdEM, ScanValleySeek, ScanTDist.
• SortDim – Either 2 or 3 to select the dimension of the feature space used for sorting.
• SortStart, SortEnd – Sets the range of samples within each waveform to use during sorting. Specified as sample positions within the waveforms (between 0 and NPW).
• ParzenRadiusMult – Sets the parzen radius multiplier for Valley Seeking sorting to the specified value.
• DOFMult – Sets the degrees of freedom multiplier for T-Distribution E-M sorting to the specified value.
• OutlierThreshold – Sets the outlier threshold to the specified value.
• RefractoryPeriod – Sets the refractory period to the specified value, for the RemoveShortISI channel command.
• WaveformLimit – Sets the limit for the number of waveforms used in Valley Seeking and T-Distribution E-M sorting. For more details, see Section 4.5.10, “Automatic Clustering using Valley Seeking Method” on page 189.
• AssignUnsortedAfterSort, RemoveOutliersAfterSort – Controls whether or not the ‘Following Sort’ actions described in Section 4.5.10, “Automatic Clustering using Valley Seeking Method” on page 189 are performed following Valley Seeking or T-Distribution E-M batch sorting operations. • FeatureX, FeatureY, FeatureZ – Sets the feature for each dimension of feature space. See the following table for numerical values for the features. Slice1,Slice2,Slice3,Slice4 – Sets the slice position (in ticks) for the Slice n features.
• ScanType – Sets the type of scan to perform for the ForEachChannel Scan command. The argument values are: ParzenMult, DOFMult, KMEans, StdEM, OutlierThresh, WfLimit, PCAMax, KMeansSeed, StdEMSeed, StdEMBeta, TDistSeed.
• ScanStart, ScanEnd, ScanStep – Sets the scan range for the ForEachChannel Scan command, and the amount to increment the scan parameter for each step.
• ScanNormalize – Set to 1 to use normalize the sort quality metrics calculated during the scan and used to determine the ‘best’ sorting.
• ScanStat – The sort quality metric to use for Scan Sorting, from among p, J3, PsF, DB, Dn, Lr, ID.
• UseRangeStart, UseRangeEnd – Only consider the portion of the file with timestamps between the Start and End values, with the times specified in seconds. This range is used for sorting operations and for exporting to PLX, PL2 and NEX files. Set either the start or the end value to a negative number to cancel a sort range and use the entire file.
• SaveCont – Set to 1 to have ExportToPLX save the continuous data, set to 0 to save only the spike data.
• SaveProcessedCont – Set to 1 to have ExportToPLX save the upsampled and filtered version of the continuous data, set to 0 to save the ‘raw’ continuous data.
• SaveInvalidated, SaveUnsorted – Set to 1 to have ExportToPLX save invalidated or unsorted waveforms, set to 0 to ignore them.
• SaveNexCont – Set to 1 to have ExportToNex or ExportToNex5 save the continuous data, set to 0 to ignore continuous data.
• SaveNexProcessedCont – Set to 1 to have ExportToNex or ExportToNex5 save the unsampled and filtered version of the continuous data, set to 0 to save the ‘raw’ continuous data.
• SaveNexWaveforms – Set to 1 to have ExportToNex or ExportToNex5 save waveforms, set to 0 to ignore them and just save the timestamps.
• SaveNexUnsorted – Set to 1 to have ExportToNex or ExportToNex5 save unsorted waveforms, set to 0 to ignore them.
• SaveNexUnitTemplates – Set to 1 to have ExportToNex or ExportToNex5 save the unit templates to a waveform variable in the exported .NEX file.
• ExportWaveformsFileType, ExportChannelsFileType, ExportUnitsFileType – Set to either txt, mat, or xls to have the ForEachFile ExportWave-forms/Channels/UnitsInfo export functions write to text files, a MATLAB file or an Excel spreadsheet, respectively.

The Process command processes all queued files. Resets the queued files list.

Syntax: Process