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Laboratory of Neuropsychology

MatOFF Commands
(In alphabetical order)


Ana2 [ANA2]

Control display of data from the second analog channel

Ana2command controls the channel selection and display features of the second analog channel. (The second analog channel is plotted as Y in X-Y plots.) Choosing an analog channel of zero, or setting the analog channel off, disables all processing of the second analog channel. The display feature options are for the trial-by trial display of the second analog data.

ana2 show enable display of 2nd analog traces on plots
ana2 noshow disable display of 2nd analog traces on plot
ana2 off set channel number to 0, this disables the analog channel
ana2 line <type> line type for analog traces
ana2 ypos <y> vertical position the first trace (see separation)
ana2 separation <value> separation between traces on the plot, a negative value reverses the order of display
ana2 size <value> vertical size (gain) of each trace
ana2 <n> select input channel for 2nd analog, a value of 0 disables the 2nd analog

Example: ana2 size 30


Analog [ANAL]

Control display of the primary analog data channel.Analog command controls the primary analog channel. The primary channel is the channel used as X for X-Y displays. The options are:

analog show turn trace on
analog noshow turn trace off
analog off set channel number to 0, this disables the analog channel
analog line <type> line type for analog trace
analog ypos <y> y position of 1st analog trace in percent
analog separation <value> separation between traces on the plot, a negative value reverses the order of display
analog size <value> vertical size (gain) of each trace
analog <n> select input channel for 1st analog trace, a value of 0 disables the 1st analog

Example: analog show


Append

Open an existing ASCII data file for use with theWritecommand.

Appendopens an existing file for writing with theWritecommand. Data written to the file is added to the file after the existing data. See the section onProtocolscripting filesfor more details.

Example: append stats.txt


AutoUpdate [AUT]

Forces an update of the current plot each time a parameter is changed

AutoUpdate forces MatOFFto update the current plot each time a parameter is changed. It does not matter if the parameter is changed by a typed command or via the GUI. Commands that would not change the graph do not cause the graph to update.AutoUpdatestays in effect until theManualUpdatecommand is given.

Example:

auto
window 2000 Plot will update immediately after this command


AvAnalog [AVAN]

Control calculation and display of average analog trace

AvAnalogcreates and controls the display of a single trace that is an equally-weighted average of all the first analog channel data. Only the trials currently selected for display are included in the average. The options are:

avanalog show turn trace on
avanalog noshow turn trace off
avanalog line <type> line type for average analog trace
avanalog ypos <y> y position of average analog trace
avanalog size <value> vertical size (gain) of average analog trace

Example: avanalog show


Av2Analog [AV2A]

Control calculation and display of average 2nd analog trace

Av2Analogcreates and controls the display of a single trace that is an equally-weighted average of all the first analog channel data. Only the trials currently selected for display are included in the average. The options are:

av2analog show turn trace on
av2analog noshow turn trace off
av2analog line <type> line type for average of second analog
av2analog ypos <y> y position of average of second analog
av2analog size <value> vertical size (gain) of average analog trace

Example: av2analog show


AvFirstDx[AVF]

Control calculation and display of the average of the first derivatives of analog data

AvFirstDxlayout command controls the calculation and display of a single trace that is an average of the first derivative of each trial of analog data. The options are:

avfirstdx show turn trace on
avfirstdx noshow turn trace off
avfirstdx line <type> line type for averaged derivative of first analog channel
avfirstdx ypos <y> y position for averaged derivative of first analog
avfirstdx size <value> vertical size (gain) for averaged derivative of first analog

Example: avfirstdx show


AvSmooth(not implemented)

Control calculation and display of an average of the smoothed analog traces

Avsmooth command controls the calculation and display of a single trace that is an average of the smoothed analog trials for the first analog channel. Only the trials that meet all display criteria are included in the average. The options are:

avsmooth show turn trace on
avsmooth noshow turn trace off
avsmooth line <type> line type for average of smoothed first analog traces
avsmooth ypos <y> y position for average of smoothed first analog traces
avsmooth size <value> vertical size (gain) for average of smoothed first analog traces

Example: avsmooth show


Axis [AX]

Rescale X axis with 0 as first time value

TheAxiscommand controls the X axis of the plot. It has saveral main parameters: xatzero, units, multiplot, subplot.Xatzerocontrols the zero of the x axis. Normally, zero time is aligned on the centering code. When xatzero is turned on, zero time is aligned on the left edge of the plot. All times become positive.Multiplotallows up to 72 graphs on one plot. Use thesubplotparameter to choose which position the next graph will be placed.

The options are:

axis on show the x axis on the plot
axis off do not show the x axis on the plot (see 'hide x axis' in the Layout Menu)
axis show show the x axis on the plot (same as axis on)
axis noshow show the x axis on the plot (same as axis off)
axis xatzero on rescale x axis with zero on the left side of plot window
axis xatzero off normal scaling, with zero aligned on the centering code
axis units pcoff no longer supported, all units are absolute
axis units absolute no longer supported, all units are absolute
axis multiplot <graphs per page> set the number of graphs on one plot (plots per page)
axis subplot <subplot number> choose which location on the page the next graph will be plotted

subplot position numbering scheme:

2 plots/page

1

2

3 or 4 plots/page

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5, 6, 7, or 8 plots/page

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9, 10, 11 or 12 plots/page

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13 to 24 plots/page

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25 to 48 plots/page

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49 to 78 plots/page

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Example: axis xatzero on


Batch [BAT]

Process a DOS batch file

TheBatchcommand simulates the DOS batch command for processing many different data files. It recognizes a few special commands and sends all unrecognized commands to the DOS interpreter.Batchsupports DOS "replaceable parameters" (e.g., %1, %2, etc.). It can also issue aCallto another batch file, but cannot be nested beyond the firstCallcommand. See theProtocolscripting filessection for more details.

Commands processed byBatch:

Pcoff Load a protocol file, load a data file, and set up a series of replacement parameters
Set Execute aSetenvMatOFFcommand using the traditional DOS SET command format
Call Simulate a DOS Call command, which calls another batch file

Example:

batch monday.bat

The file "monday.bat" contains:

set makdat=8o
pcoff daily_recoding.pro day25 unit3 dummy [23-24] d25


Bell [BEL]

Send a beep sound to the operator

Bellsends a beep sound to the operator. It is most useful in aprotocolscripting files.

bell beep using the current parameters
bell <frequency> <duration> beep using new parameters. Both parameters must be specified.
<frequency> is in hertz
<duration> is in second

Example: bell


Break

Pause a protocol file and wait for the operator

TheBreakis strictly a protocol file command. It pauses protocol file execution and waits for the operator to enter commands. The operator can issue anyMatOFFcommands. Then, the protocol file can be continued. TheContinuecommand is used to return to the pending protocol file.

Example:

file rgb
unit rgb10
break
show

This is a protocol file to open a file, set the unit and discontinue processing. TheContinuecommand will resume processing with aShowcommand.


BinWidth [BIN]

Select the number of pixels per bin for histograms

The width of the histogram bins are set by theBinWidthcommand. TheBinWidthvalue is either the number of pixels per bin or the number of milliseconds per bin, as set by theAxiscommand.

Example:

axis units absolute
histogram show
win 6000
bin 30
show

Display 6 seconds of histogram data with 30 ms bins.


Calculator [CAL]

Activate Windows calculator

The Windows pop-up calculator can be accessed with theCalculatorcommand.

Example: calc


Cd

Change directory

Cdacts like the DOS change directory command.

Example: cd ..

Take one step down the directory tree.


Center [CEN]

Select event for alignment of all data trials

One of the primary functions ofMatOFFis to search through the data and find trials that are related to each another based on the search criteria. The selected trials must be aligned in time on some common event. TheCentercommand identifies the event for alignment. Actually, it does not identify an event,per se. It identifies which bracketed group of events in the search sequence to use for alignment. Alternatively, the value can identify a history class that contains the absolute time (in milliseconds) in each trial to use as the alignment point for that trial.

The center value indicates a event code group when the value is less than or equal to the number of groups in the sequence:

Example:

seq [14][3][28-30][33]
center 3
mark 4
show

The above sequence has 4 groups of event codes. The command "center 3" indicates that the third sequence element ([28-30]) will be used for centering. All trials will be aligned on whichever code (28, 29, or 30) was found when a trial matched the search criteria. In this case 28 was a "go left", 29 was a "go right", and 30 was a "go down". All trials will be centered on the "go" signal, regardless of the direction of the "go" signal. The operator must be careful not to confuse event codes with the ordinal number used in theCenterspecification. Thus, "center 3"does notmean to center on code "3"; it means to center on the third group of codes.

If the center value is above 99 (and if there are fewer than 99 groups), then the center value indicates a history class. The class value for each trial will be used as the centering time (in milliseconds). Centering on a class is one of the many advanced features ofhistory scripting.

Example:

seq [14][3][28-30][33]
center 200
mark 4
history file centering_script.m
history on
scan
show

The above example uses history class 200 for the centering values. The history script "centering_script.m" sets the centering time for each trial and saves that value (in milliseconds from the start of the trial) in class 200. The plot will reflect the new centering times.


CenterLine [CEN]

Control display of a center line

CenterLinelayout command controls the display of a vertical line centered at the centering code.

centerline show turn center line on
centerline noshow turn center line off
centerline line <type> set line type
centerline ypos <y> y position of top of center line in percent (0 to 100%)
centerline size <vs> vertical size (0 to 100%)

If an abbreviated form of theCenterLinecommand (e.g., center) is accidentally used without including any parameters,MatOFFwill interpret the command as aCentercommand.

Example:center show


Clean

Close open files after aMatOFFcrash

TheCleancommand closes all openMatOFFfiles (protocol, metafiles, data files, etc.). It is used primarily for debugging after aMatOFFerror leads to a MATLAB prompt.

Example: clean


Close [CLO]

Close a data file that was opened with theFile,OpenorAppendcommands

Close will close a currently open ASCII text file or data file.

close close ASCII file if one is open, otherwise close the data file if one is open
close ascii close ASCII file if one is open, otherwise do nothing
close datafile close data file if one is open, otherwise do nothing
close append closeallopenSET <process> APPENDfiles

Close with no parameter will look for an open ASCII text file and close it. If there is no ASCII file open, it will close the currently open data file.Close asciiwill close a file that was opened with eitherOpenorAppendcommands.Close datafilewill only try to close a currently open data file.Close appendwill close all openSET <process> APPENDfiles.

Example:

set epoch keep
append stats.txt
show
close ascii


Cmd

Switch to theMatOFFcommand line

Cmdleaves the MATLAB command line and returns control toMatOFF. Return to the MATLAB command prompt by entering theMatlabcommand.

Example:

>matlab
!copy koflay.dat oldlayout.dat
cmd
>

In this example we use MATLAB to make a backup of the koflay.dat layout file, then return toMatOFF.


Continue

Resume processing of the protocol file after aBreakstatement

When a protocol file issues aBreakcommand, control ofMatOFFgoes to the user's keyboard. the user may resume the protocol file at any time with theContinuecommand. If a new protocol file is loaded, theContinuecommand becomes invalid until a newBreakcommand occurs. If File errorhas been issued with the break option, then any error caused by aFilecommand will mimic aBreakcommand. TheContinuecommand can then be used to resume processing.

Example: continue

Continue processing the protocol file.


Copy[COP]

Duplicate layout specifications from one layout to another

A layout is a detailed description of the elements to place on a plot. Ten layouts reside inMatOFFat any one time; only one layout is in use at any given time. The parameters of one layout can be copied to another layout using theCopycommand. The origin and destination are simply the layout numbers (1..10). Text is handled separately. To copy text theCopycommand must include the "text" keyword. Line numbers after the text keyword indicate which lines of text to copy. Omitting the "text lines" parameter will cause all text lines to be copied.

Example:

copy 4 5

Copy all parameters from layout 4 to layout 5.

copy 1 2 text

Copy only the text from layout 1 to layout 2.


Date

Get the date

TheDatecommand prints the current date. In a protocol you can use the variable %10 for the current date.

Example: date


Directory [DIR]

List the contents of a disk directory

Directory is similar to the DOS DIR command. It will display the contents of a disk directory. If no path is specified, the current default path is used (notthe DEFAULTPATH environmental variable value). If no file extension is given, none is assumed.Lsis a synonym.

Example: dir c:\matoff


Display [DISP]

Specify the set of layouts to use for graphical display after eachShowcommand

Whenever theShow,New plot, orOld plotcommand is given without parameters, the display list is used to select which layout(s) will be used for graphical display. If the display list has only one number, that layout will be used. If the display list is larger, the same data set will be displayed once for each layout. Note that theDisplaycommand does not initiate the display of data, it only sets the layout list for theShowcommand. The list may include ranges (e.g. 1-3), but it must be limited to values between 1 and 10. The display list can also be changed by theShowcommand.

Example: display 1,3

Use layouts 1 and 3 next time theShowcommand is issued without parameters.


Dump

Create ASCII file of internalMatOFFvalues

Dumpwill print or save to disk information that has been gathered, organized, or calculated byMatOFF. The general form of theDumpcommand is:

dump <datatype> [OUTPUT] <filename>

The data types are listed below. "OUTPUT" is a keyword. It indicates that the data should be sent to the printer or a file. OUTPUT is always followed by the filename. TheDumpcommand is a simplified way to get internal values fromMatOFF. However, see theSetcommand, which is the primary method for moving data to other programs. Both are detailed inExporting results.

Data types:

spikes spike times for each trial on plot
index same asIndexcommand, butDumpcan output to a printer or file
setstats list the status of allSetcommand options
events event codes found (for each search sequence group) for every trial found
history trial numbers and class values for each history class

Dump spikes

Spike times are listed for the trials that match the sequence, and in the order based on current sort option. The spike times are all in milliseconds relative to the centering code. On the screen, spikes are dumped as one spike time per line. With the [OUTPUT] option, spike times are listed this way:

sorted trial number :unsorted trial number :time,time,time

1 :15 :1336,1427,1430,1693
2 :21 :720,1752,1754,1916,3260,3514,3528,3530,3561,3573,3574,3593,3608,3611,3655,3657,3694,3976,3978,4214,
3 :24 :1450,1498,1512,1571
4 :23 :776,1732,1734,1781,1793,1857,5074,5471
5 :25 :768,785,1777,1785,1813,1838,6104,6106,6213,6215,6572,6573,7179,7199,7201,7248,7249

Dump spikesuses three environmental variables:

DUMPMODE Controls the output file write method. Use APPEND or NOAPPEND to determine if any existing file is overwritten.
DUMPPATH Path forDumpcommand output files
DUMPTEXT This text string will be placed before each line created by theDump spikescommand.

Example:

dump index OUTPUT index.txt
Print the index of the currently opened file to a text file.

dump set

Show the current settings of all theSetcommand options.


Edit

Edit a text file

Editopens a windows text editor. The editor is specified in the EDIT environmental variable.

edit <file name> open a windows editor to edit specified file

The environmental variable EDITOR must be set before using this command.Example:

setenv editor c:\windows\notpad.exe
edit listfile.lst


End

Exit the current protocol file

Endterminates the execution of a current protocol file. It will also terminate the execution of the current metafile. If the metafile is called by a protocol file, usingEndin the metafile does not affect the execution of the protocol file.

Example:

file darby
unit db0001a
end <---- terminate the protocol file early (for testing)
sequence [12][22][35-38][42][44]
show


ENDIF

Conditional END for a protocol file

TheENDIFcommand terminates a protocol file if the condition is met. TheENDIFcommand can only be used in a protocol file. It will be echoed, but have no effect in a metafile or on the command line.

endif noanalog Exit the current protocol file if there is no data on the primary analog channel
endif nounit Exit the current protocol file if the lastUnitcommand failed

Example:

This is in a protocol file:
file RY001_2a
unit RY2a
ENDIF NOUNIT <---- end the protocol file if no unit was found
analog 3
ENDIF NOANALOG <--- end the protocol file if there is no analog data
ana2 4
sequence [14][18][22-26][29][33]
show


Erase

Clear the graphics screen

Eraseclears the graphics screen. It can be used withAxis multiplotto clear the plot for a new group of graphs.

erase <figure number> erase current figure or optional figure number

Example: erase


ErrorLevel

Control the reporting of errors and warnings

ErrorLevelcontrols the reporting of errors and warnings.

errorlevel debug print out debugging information as well as all other messages
errorlevel warning print out warnings, and error messages, this is the default error level
errorlevel serious inhibit warnings and do not echo most commands
errorlevel fatal print a message only if program cannot proceed

The debug level of error messages provides the most information. The fatal level of error messages prevents all messages except for program failures. The serious level of error messages can be used with batch files to suppress long lists of commands (e.g. layout commands), since errors are often missed when many commands are send to the screen. All of these messages can be sent to a log file. See theLogcommand.History scriptingcan make use of the sameErrorLevelcontrol by using the issue_message() support function.

TheMakdatcommand has a separate set of message reporting options.

Example: error serious

Turn off warnings.


Exit

ExitMatOFFand MATLAB

ExitMatOFFand MATLAB immediately, without confirmation. It is different from theQuitcommand, which keeps MATLAB running.

WhenMatOFFexits, it saves the current set of layouts to the file koflay.dat.

Example: exit


File [FI]

Open a new file for analysis

Fileopens a new data file for analysis. If no path is specified, the DATAPATH environmental variable is used. If DATAPATH is not assigned, DEFAULTPATH is used.If theFilecommand is issued with no arguments,MatOFFwill print the file name of the currently open file. If theFilecommand is issued with the same name as the currently open file,MatOFFwill just issue a warning message. Otherwise, theFilecommand will close the currently open file and attempt to open the new one. To close and open files of the same name, issue theClosecommand first. A file cannot be opened unless it is aMatOFFfile. UseMakdatto process Cortex files for use withMatOFF. SeeImportingfor more information.

Example: file indy


Fileerror [FILERR]

Control error handling when a data file open attempt fails

FileerrortellsMatOFFwhat action to take if aFilecommand fails during the execution of script (protocol or metafile) file. If aFilecommand is issued from the command line, or with a mouse, an error message is printed on the users screen. If aFilecommand is issued in a script, there are three possible actions depending upon the most recentFileerrorcommand. TheFileerrorcommand options are:

fileerror current fileerror state is printed on the users screen
fileerror break issue aBreakcommand if a file open error occurs
fileerror continue display error message and continue processing if a file open error occurs
fileerror exit continue to next batch file entry if a file open error occurs

TheFileerror exitform of the command is intended to be used with thePcoffcommand. The Pcoff command can only used inside a batch file using theBatchcommand.Fileerror exitcauses an abort of the currentPcoffcommand, which allows the batch file to continue. IfFileerror breakis used and a file error occurs, then theContinuecommand can be used to resume processing of the protocol file.

Example:

fileerror exit
batch indyunits.bat

IfMatOFFcannot find a data file during aPcoffcommand within the indyunits.bat file,MatOFFwill move to the next batch command in that file.


FirstDx

Control calculation and display of derivative traces for the analog data from each trial

FirstDxlayout command controls the calculation and display of traces that are first derivatives of the analog data for each trial. The options are:

firstdx show turn trace on
firstdx noshow turn trace off
firstdx line <type> line type for trace
firstdx ypos <y> y position of trace in percent (0 to 100%).
firstdx separation <sep> distance between traces in percent. Negative value reverses the order of display
firstdx size <vs> vertical size of each trace, in percent

FirstDxonly operates on the primary analog channel.

Example: firstdx show


Found [FOU]

List the sequences that matched the search criteria

Foundprints a list of the sequences that matched the search criteria during the most recent scan. Each matching sequence is listed once. The sequence list is preceded by a number that indicates how many trials were found with that exact sequence.

Example:

>found
Qty Sequence
6 65 98 65 44 87 47 41
6 65 99 65 42 87 46 41
5 65 98 65 44 87 46 41
1 65 98 65 43 87 47 41


Frequency[FREQ]

TellMatOFFthe frequency at which the A/D (analog) data were collected

If analog data are included in any analysis, it is essential to tellMatOFFthe frequency that the analog data were collected. Any integer value can be entered, but it must match the frequency of the data for the selected analog channel. If two channels have been selected by theAnalogcommand, both channels are assumed to be digitized at the same rate.

freq <value> value is an integer in samples/second
freq auto MatOFFwill look at the data file and try to calculate an A/D frequency
freq auto <list> MatOFFwill look at the data file, calculate an approximate A/D frequency, then select any value from the list that is within 5% of the calculated A/D frequency

Example:

analog 1
freq 250

analog 1
seq [198][100][20][40][101]
glo auto 1-500
scan
freq auto 250 500 1000

The first example tellsMatOFFto use analog channel 1, and to indicate that channel 1 was recorded at a frequency of 250 Hz. The second example tellsMatOFFto select an A/D rate of 250, 500, or 1000, based on the calculated A/D rate. Before you can use the auto option, you must have a successful scan. The sequence must include the A/D start and stop event codes (default are 100 and 101). The A/D rate estimate is best when at least 20 trials are found.

If you are using Cortex to collect the data, the A/D storage rate setting in Cortex corresponds to the following sampling frequencies listed below. The table assumes only 2 channels of A/D data are being collected (i.e., EOG but not EPP data).

A/D storage rate setting

Sample rate (Hz)

0

undefined?

1

1000

2

500

3

333

4

250

5

200

6

167

7

143

8

125

9

111

10

100

GlobalIgnore[GLO]

Identify event codes that should not be considered while searching for event code sequences

GlobalIgnoreidentifies event codes that are to be completely ignored during the event search and all subsequent analyses.

globalignore [list] Ignore the listed codes. The codes in the list must not be in the sequence.
globalignore auto [list] Automatically prune globalignore list by removing any codes currently in the sequence.

Example:

global [1-10,12-15,33]

InstructsMatOFFto act as if the listed event codes do not exist in the data file.

sequence [23][30][45][46]
global auto [10-300]

These two commands will automatically create a global ignore list that looks like:
[10-22,24-29,31-44,47-300]


Hair

Read a time value from a plot using the mouse

TheHaircommand enables the mouse to precisely measure time values in a plot window. Left click the mouse to drag a marker within the plot window. Let up on the mouse button to measure the precise time location of the marker. Time is given in PCOFF pixels or in absolute time dependend on theAxis unitscommand setting.

Example:

hair
Locate a position on the plot with the mouse.
781 milliseconds


Heading

Control display of heading: 6 standardized text lines that describe a graphics display

MatOFFwill include six lines of information on the graphics display as a heading. The information includes the file, unit name, search sequence, globalignore list, etc.

heading show turn heading on
heading noshow turn heading off
heading ypos <y> y position of bottom left corner in pixels
heading size <points> font size for heading in point size

Example: heading show


Help

On-line help forMatOFFcommands

TheHelpcommand is available for on-line assistance. A list of topics can be obtained by entering "help". The HTML documentation is more complete.

Example: help sequence

Find out more about theSequencecommand.


Hide Plot

Synonym forSet plot noshow

TheHide Plotcommand inhibits the screen drawings (plots) when theShowcommand is given. This command is most useful during batch file operation when statistical outputs are of interest, but drawings are not. The reverse command isShow plot(a synonym forSet plot show).

Example:

hide plot
load bigjob.pro


Histogram [HIS]

Control the display of a histogram of spike data

Histogramlayout command controls the display of a cumulative histogram of spike data. The histogram displayed byMatOFFis based on those trials that meet all the search and display criteria. That is, all trials that would be shown if aRaster Showcommand is issued.Histogram values can be further restricted to specific parts of each trial using theValidateSpikescommand. The bin sizing of the histogram is controlled by theBinWidthcommand. TheMatOFFScalecommand is the same as theHistogram scalecommand. Normally, the scaling of the histogram is relative to the bin width and the number of trials to provide a normalized pulses-per-second value. IfHistogram rawcommand is used, scaling is calculated from the number of counts in each bin independent of the bin width or number of trials.Histogram referencecommands will draw three horizontal reference lines on the histogram. One line will be the average firing rate for all bins that fall completely within Segment A (see >Segmentcommand). The other two lines will be above and below this mean based on the reference value. The reference value is the number of standard deviations above and below the mean for these two lines.

histogram show turn histogram on
histogram noshow turn histogram off
histogram on same as histogram show
historgram off same as histogram noshow
histogram scale show turn histogram scale on
histogram scale noshow turn histogram scale off
histogram scale auto automatic scaling of histogram
histogram scale <n> set range of histogram scale in pulses per second (PPS)
histogram line <type> selects color of bars and fill style for histogram
histogram size <size> vertical size in percent (100 = fill plot window)
histogram ypos <position> vertical position of baseline, in percent (0=bottom, 100=top)
histogram rawcounts scale histogram to raw counts, ignore bin width and number of trials
histogram normal scale histogram in spikes/second
histogram reference show turn on reference lines
histogram reference noshow turn off reference lines
histogram reference on same as histogram reference show
histogram reference off same as histogram reference noshow
histogram reference <value> number of standard deviations above and below the mean for reference lines
histogram reference color <value> color for reference lines (1=black, 2=green, 3=red, 4=blue)

Example: histogram show


History

Make decisions based on entire history of behavioral data

Thehistorycommand provides is a powerful method to make decisions about behavioral events. SeeHistory Scriptingfor details.

history clear remove all history data from memory, does not affect the file
history data <list> supply a numeric list of values or single string to the history script, list items must be separated with commas
history file <filename> load a history script
history off skip history processing
history on process the user's history script and use the result to keep/reject trials
history rewrite <all> save history to disk, use "all" to update all units with the same behavioral trials as the current unit.
history rewrite delete delete history of the current unit.
history spot firstclass first class to use for history spots (valid class numbers are 1 to 20,000)
history spot lastclass last class to use for history spots (valid class numbers are 1 to 20,000)
history spot noshow do not display history spot times
history spot show display history spot times

Example:
history file myscript.m
history on
show


Index [IND]

List units available in current file

Indexlists the data file index, which contains a list of what units are contained in the current file.

Example:

>file sparky25
>index

Find out what units are in file "sparky25".


Initialize [INIT]

Reset current layout to default values

Initializeresets all layout parameters of the currently-selected layout to a standard default set. It is used primarily in protocol files to set the layout to a known state. SeeLayoutssection for more details.

Example: >init


Layout [LAY]

Choose a new layout or a layout file

Ten layouts reside inMatOFFat any one time. A plot is drawn based on the currently selected layout. The current layout can be modified using either typed commands or through the layout menus. TheLayoutcommand allows the user to select which layout is current. A new set of 10 layouts can be loaded from a file usingLayout fileform of the command. If theLayout filecommand opens a new file, all layouts will be initialized to default values. The existing layouts can be saved using Layout save . The current set of layouts is automatically stored as koflay.dat whenMatOFFis exited. This file may be copied and loaded with theLayout filecommand. The currently selected layout can be preserved as a protocol file using theSave layoutcommand.

layout <n> choose layout number n to be the current layout
layout file <filename> load a group of 10 layouts from the specified file
layout save <filename> save current group of 10 layouts to the specified file

Example:

layout file indylay.dat
layout 5
avanalog show
show 5

This example opens a layout file, makes layout 5 current, turns on the average analog trace, then displays the current search data using that layout.


Load [LOA]

Startup a protocol scripting file

Load reads and executesMatOFFcommands from a text file. The text file is referred to as a protocol file, and usually has a.proextension. If the PROTOCOLPATH environmental variable is set, it used to determine the directory of the requested protocol file. Files created with theSave command have the format of a protocol file. The protocol file STARTUP.PRO is automatically executed whenMatOFFis first started. Protocol files must follow certain rules described in the section onProtocol scripting files.

Example: load rgb

Opens the protocol fileRGB.PROand executes eachMatOFFcommand in the file.


Log [LOG]

Echo output window messages to a disk file

Log sends error, warning, debugging and other information to a text file. When logging, errors, warnings, and debugging messages do not reach the console, but all other messages do.Logalways appends to any existing file. The file is placed in the default path.

log file <filename> Open a file for logging. Actual logging depends on thelog oncommand. There are no file naming restrictions.
log on Start logging. A logging file must be open.
log off Stop logging.
log close Close the logging file. If not properly closed, the data will be lost. Logging is turned off if it was on.

Example:

open output.log
close ascii
log file output.log
errorlevel debug
log on
show
log off
log close

First two lines are a trick to erase an old log file "output.log" if it exists. Next line opens the log file.Log onstarts the logging. All error, warning, and debug messages will be appended to output.log and will not be displayed on the user’s screen. Other user screen messages will be sent to both the user screen and log file. Set [process] show output will not go to the log file.Log offis not really necessary here, sincelog closewill also turn off logging.Log closeis essential to save the data.


Ls

List directory

Lsacts like the DOS DIR directory listing command. TheDirectorycommand is a synonym.

Example:

ls ..

List contents of the current directory.


Makdat [MAKD]

Stops updating plot each time a parameter is changed

Makdatmust be run on a CORTEX data before the data in that file can be processed byMatOFF. SeeThe Makdat Command.


ManualUpdate [MAN]

Turns off the AutoUpdate feature

ManualUpdateends the effects ofAutoUpdate.AutoUpdatemakesMatOFFupdate the current plot each time a parameter is changed. It does not matter if the parameter is changed by a typed command or via the graphical menus. Commands that would not change the current plot do not cause an update.

Example:

auto
window 2000 Plot will update immediately after this command
shift 500
manual


Map [MAP]

Start the mapping process

Usually theShowcommand is used to start or reprocess data after making a change to the search strategy.Showrelies on context to determine where in the process sequence to begin.Mapoverrides the context sensitivity ofShowand forces a new data mapping. TheMapcommand is rarely used.

Example: Map


Mark [MAR]

Identify the "mark" event group for sorting and statistics

Markis used in conjunction with theCentercommand to identify two events in each trial that can be used for sorting of trials and for some trial-by-trial statistics. A square marker is placed immediately under each raster at the point in the raster that the marked code occurred. If rasters are not displayed, the marked event can still be used for sorting, e.g. sorting of analog traces.

Example:

seq [4][3][28-30][33]
center 3
mark 4
show

The above sequence has 4 groups of event codes. The command "mark 4" indicates that the fourth sequence element ([33]) will be marked. In the graphics display a solid square below each raster is used to identify the exact moment that the marked code occurred. Note that theMarkspecification follows the same rules as theCenterspecification. The operator must be careful not to confuse event codes with the ordinal number used in theMarkspecification. Thus, "mark 4"does notmean to mark code "4" in this case.


Matlab [MAT]

Switch to the MATLAB command line

Matlableaves theMatOFFcommand line and returns control to MATLAB.MatOFFcommands issued via theMatOFFmenus will still execute properly. Return to theMatOFFcommand prompt by entering theCmd command.

Example:

>matlab
!copy koflay.dat oldlayout.dat
cmd

In this example we use MATLAB to make a backup of the koflay.dat layout file.


MenuPosition [MENU]

Save and load the positions of the main menus

MenuPosition savesaves the current screen arrangement of the mainMatOFFmenus. The menu arrangement can be recalled using theMenuPosition loadversion of the command. The user can save many different menu layouts and choose the most convenient arrangement as needed.MenuPositionis also helpful for users who use different screen resolutions at different times.

The menu arrangement is saved to the current default directory. No file suffix is assumed. The main menus are: File Menu, Sequence Menu, Plot & Print Menu, Layout Menu 1, Layout Menu 2, Layout Menu 3, and Text Menu.

Example:

>menu save best_for_search.mnu
>menu load best_for_layouts.mnu

In this example the menus were optimized for searching and that layout was saved to a file using the .mnu suffix. In the following statement a previously saved arrangement (best_for_layouts) was loaded. The main menus were automatically reorganized and repositioned.


mgplx2ctx

Convert Plexon MAP data file to Cortex format

mgplx2ctxis a stand-alone, graphical MATLAB program for converting Plexon ".plx" files to Cortex data files. It requires a recent version of MATLAB (R13 or later).

See themgplx2ctxpage for details.SeePlx2ctxif you are using an older version of MATLAB.

Example: mgplx2ctx


MWFiles

Perform Mann Whitney U-statistical test on two .MWU files

he Wilcoxon Mann Whitney Statistic is a powerful nonparametric test. It is useful when the statistical assumptions inherent in t-tests are violated. The null hypothesis tested by this test is that the medians of the two groups are equal. A z-value that is large enough so that the null hypothesis is rejected indicates that the chance of the medians being from a common distribution is sufficiently small. The statistic is obtained by first ranking two sets of data as a combined set and then comparing the sum of the ranks in the two individual sets.

MWFilescompares two sets of pulse data. Pulse (spike) data are saved each time aShowcommand is issued after theSet MWU Keepcommand is given. The pulse data are always stored in two files: Ax.MWU and Bx.MWU. A and B represent the two time segments of thecurrently displayeddata, specified with theSegmentcommand. The value of x in the file names is from 0 to 9999. These values start at 0 and are incremented once each time a new pair of files are generated. The starting value can be changed with theSet MWU Filenumbercommand. TheMWFilescommand tests any two MWU files against each other. MWU files are saved to and recalled from the directory assigned to the STATPATH environmental variable, if set; otherwise, the DEFAULTPATHenvironmental variableis used.

The commandsSet MWU ShowandSet MWU NoShowcontrol whether the results of testing the most recent Ax.MWU file with the most recent Bx.MWU file are displayed on the screen each time theShowcommand is executed.

Example:

axis units absolute
segment a -200 100
segment b 300 600
set mwu filenumber 0
set mwu keep
sort off
trials 1-10
show
trials 81-90
show
mwfiles a0 b0
mwfiles b0 b1

In this example a time window (segment a) is created that covers 200 ms before to 200 ms after the centering code. This period is used as a control period in this experiment. A second time window (segment b) is created to cover 300 ms to 600 ms after the centering code. This period is the test period in this experiment. The rasters are placed in chronological order usingSort Off. The first 10 trials are selected withTrials1-10.Show displays these 10 trials and generates files A0.MWU and B0.MWU. A0.MWU is the statistic for segement a, B0.MWU is the statistic for segement b. The second 10 trials of the same recording are selected by using theTrials81-90 command. This second group is viewed and two additional files A1.MWU and B1.MWU are created. A Mann Whitney U-test is performed first between the control and test periods for the first 10 trials. This checks for significant firing rate change between the control period and the test period early in the recording. A Mann Whitney U-test is then performed between the test period for the first 10 trials and the same period for the second 10 trials. This looks for a change in the test period between trials recorded early and trials recorded later in the same file.

Typical output display:

Significant= 0 m= 10 n= 21 z= 1.315

"Significant" will equal 1 if the null hypothesis can be rejected with a probability greater than 0.05 (two-tailed test).


New plot [NEW PLO]

Generate a new graphical display based on the currentMatOFFsettings

New plotis a synonym of theShowcommand, except it will always make the plot in a new window.Showuses the current window.New plotwill create multiple plots if the "display list" has more than one value. See theShowcommand for details.

Example: new plot

Reprocess if necessary, then draw a plot in a new window.


Nextplot [NEX]

Generate a new graphical display based on the currentMatOFFsettings

Nextplotsets the plot number without generating a plot.

Example:

nextplot 14
show

Reprocess if necessary, then draw a plot in figure window 14. Create figure 14 if it does not already exist.


Old plot [OLD PLO]

Generate a graphical display based on the currentMatOFFsettings in the current plot window

Old plotis a synonym forShow, except it can be used to specify which graphics output window to use for display.Old plotwith no parameters has the same action asShowwith no parameters. See theShowcommand for more details. SeeOverplotfor drawing twice on the same display.

Old plot <figure number> Make plot with explicit selection of the figure window. <figure number> is optional.
Old plot next Add + 1 to current plot number, then make a plot

Example:

axis subplot 1
axis multiplot 1
old plot 11
axis multiplot 2
old plot 12
axis subplot 2
shift 1500
show

Draw a plot in window 11. Draw the same plot in window 12 side-by-side with another view of the same data (shifted 1.5 seconds).


Open

Create and open a file for writing to with theWritecommand

Opencreates and opens a file for writing. TheWritecommand moves ASCII data to that file. If a file with the same filename already exists on the disk, the file is overwritten by theOpencommand. UseAppendto add to an existing file. See the section onProtocolscripting filesfor more details.

Example: open stats.txt


Overplot [OVER]

Plot on top of an existing plot

Overplotplots on top of an existing plot. Normally, any existing plot is cleared first. Overplot leaves the current drawing on the figure and adds to that drawing.Overplotwill only work properly if used on the most-recently created figure. SeeShowfor more details on what happens when a new drawing is requested.

Example:

center 2
show 1
display 2
center 5
overplot

This sequence will make a plot using layout 1. A second graph, based on layout 2, is overlaid on the first. The second plot has a different centering code and uses a different layout (layout 2).


Pcoff [PCOFF]

Load protocol and execute a protocol file in batch mode

ThePcoffcommand is used with theBatchcommand. TheBatchcommand simulates DOS batch file processing.ThePcoffcommand is used in a batch file to load a data file, a protocol file, a unit, and a group of parameters in one batch file command line.

pcoff <protocol file> <data file> <unit> <pcoff param1> <pcoff param2> ...

<protocol file> file name of a file that has a list ofMatOFFcommands
<data file> name of the data file to process
<unit> name of the unit to process
<pcoff param1> the value placed in thePcoffcommand line replaces "$1" in the protocol file
<pcoff param2> the value placed in thePcoffcommand line replaces "$2" in the protocol file

See the section onProtocol scripting filesfor more details.

Example:

batch monday.bat

The file "monday.bat" contains:

pcoff daily_recoding.pro day25 unit3 [23-24] d25

This command runs the "daily_recording.pro" protocol script file using data from "day25". It loads unit "unit3" and everywhere the parameter $1 occurs in "daily_recording.pro" the character string "[23-24]" is inserted (in this case, in aSequencecommand). Also, the character string "d25" is inserted wherever parameter $2 occurs in the protocol file.


Plx2ctx

Convert Plexon MAP data file to Cortex format

Plx2ctxis a stand-alone, command-line Windows program for converting Plexon ".plx" files to Cortex data files.

See thePlx2ctxpage for details. If you are using a recent version of MATLAB (R13 or later), usemgplx2ctx.

Example:

plx2ctx -mplx2ctx.map m01.plx m01 (This is done in a DOS Window)

Convert m01.plx Plexon file to one or more Cortex files using the plx2ctx.map mapping scheme.


Plot [PLO]

Create plot file from the current graphics screen display

Plotstores a figure (plot) to disk. Plot name can be fixed or numeric and automatically incremented.

plot save the current graphics screen to disk
plot <figure number> save an arbitrary graphics screen to disk

The figure number is the MATLAB figure number. It is the same figure number as specified in theOld plotcommand. TheSet plotcommand and the GRAPHICSFORMATenvironmental variablecontrol the destination file and file format of thePlotcommand.

Automatic generation of plot files

TheSet plot keepcommand will save a plot to the hard disk each time a plot is created.Set plot nokeepturns off this automatic process.

Naming the plot file

TheSet plot name <filename>command sets the name of all subsequent plot files. Plot file creation is destructive. That is, it erases any existing file of the same name.

Automatic naming of the plot file

If the plot file has not been named, then the plot file names are numeric and generated automatically. The first plot file is named 0.png. Subsequent file names are 1.png, 2.png, etc. The ".png" suffix depends on the graphics file type (see below). If the plot file has been named, use theSet plot name <filename>with a blank filename to enable automatic naming.

Controlling the number used in automatic file naming

TheSet plot filenumber <#> command sets the number of the next file saved automatically.

Controlling the graphics file type that is saved to disk

The commandSetenv GRAPHICSFORMAT <graphics type>sets the type of graphics file save to disk. The available graphics types are:

tiff compressed Tag Image File Format (TIFF)
tiffn uncompressed Tag Image File Format TIFF
hpgl HP Graphics Language (HPGL)
jpeg Joint Photographic Experts Group (JPEG)
eps Encapsulated PostScript
ai Adobe Illustrator
png Portable Network Graphics (PNG)

Creating a web page from a plot

See the secton onProtocolscripting filesfor an example of how to automatically create a HTML files from plots.

Example:

set plot filename best_unit
setenv graphicsformat jpeg
plot


Print [PRI]

Print the current graphics screen display

Printsends a copy of the graphics screen to the current default Windows printer. It can optionally choose a different graphics screen.

print print the current graphics screen
print <figure number> print an arbitrary graphics screen
print orientation <orientation> portrait or landscape
print papertype <paper type> letter, legal, or A4

Example:

new plot
print orientation landscape
print papertype a4
print


PulseChannel [PUL]

Specify which pulse (spike) channel to analyze

Single-unit (spike) data can be collected on up to 25 different pulse channels (numbered 0 through 24). Only one channel of data can be studied at a time.PulseChannelspecifies which channel to analyze. If an unused pulse channel is specified and aShowcommand is given,MatOFFwill tell the user which channels have data. Also, theIndexcommand can be used to list the available pulse channels. Note that theMakdatcommand controls which pulse channels are converted from other file formats. If you expect data from a pulse channel, but no data is there, see if that channel was properly requested in theMakdat"list" file.

Example:

pulse 1 Indicates pulse channel 1 will be used for analysis

pulse off Indicates no pulse data will be studied. This is useful for studying only the behavioral aspects of an experiment.


Pwd [PWD]

Print the working directory

Pwdacts like the DOS pwd command.

Example: pwd


Q(not implemented)

Interrupt the current process or calculation

ManyMatOFFprocesses are time-consuming.Qallows the user to interrupt a process.Qwill interrupt a protocol file with prejudice.

Example:

show
q

Regardless of whereMatOFFis in theShowprocess, theQwill interrupt the process and return control to the console.


Quit [QUIT]

ExitMatOFFand MATLAB

QuitexitsMatOFF, but keeps MATLAB running. It is different fromExit, which terminates MATLAB.

WhenMatOFFexits, it saves the current set of layouts to the file koflay.dat.

Example: quit


Raster [RAS]

Control display of spike rasters

TheRasterlayout command controls the display of spike rasters. When active, there is one spike raster for each trial of data. Spike rasters are composed of two horizontal lines of information. The first line has vertical tick marks, one for each spike. The second horizontal line has squares("o") or plus signs ("+") under them. A single square marks when in the trial the "mark" code occurs (see theMarkcommand). Plus signs indicate when in the trial a spot code was encountered (see theSpotcommand). There can be multiple spots in a trial. mark and spot marker sizes are controlled by the "labels" option value. The size of the vertical tick marks for each spike is controlled by the "size" option value. The varioussort commandscontrol the order in which the rasters are displayed. TheSet sortcommand can reverse that order.

raster show turn trace on
raster noshow turn trace off
raster labels <size> set size of raster markers
raster line <type> line type for vertical tick marks (spikes)
raster separation <percent> distance between traces in percent. Negative value reverses the order of display
raster ypos <y> location of first raster display line, in percent.

Example: raster show


Read [REA]

Examine or save raw data in current data file

Readdisplays or saves detailed information about the current unit.

read <options> out=<filename>
read <options> append=<filename>

Any number of options may be included in the command. Only the first 3 characters of an option are necessary. Using 'out=' will create an ASCII file to the device listed under <filename> instead of displaying the results on the user's screen. The 'out=' option will destroy the contents of an existing file with the same file name. Using 'append=' will also write to a file, but will append to an existing file.

options:

all synonym for 'events pulses analog'
analog include analog values
codes synonym for 'events'
events include event codes and event code times
page pause at the end of each page
pulses include pulses and pulse times
relevant list event codes without times, and omit those event codes listed inGlobalIgnore. This option operates independently and overrides the others.
spikes synonym for the 'pulses' option
which make summary listing of all channels and codes found in the unit's data

Example:

read all out=mydump.txt

Creates a file with all event codes, pulses, marks, and analog data.

read relevant out=events.txt

124,1,198,204,40,64,34,152,50,90,92,96,143,139,14,80,25,28,56,77,84,100,78,64,60,21,55,30,35,161,29,19
125,2,198,205,40,65,31,152,50,90,92,96,144,140,14,81,23,28,56,77,84,100,78,65,60,21,55,30,35,160,29,164,19
126,3,198,205,40,65,31,152,51,91,93,95,98,145,139,14,81,24,28,56,77,84,100,78,65,60,21,55,158,162,30,35,158,29,19
127,4,198,203,40,63,33,152,50,91,92,96,145,137,14,82,24,28,56,77,84,100,78,63,60,21,55,30,35,160,29,19,20,44,87,88
128,5,198,201,40,61,31,152,50,90,92,96,143,139,14,81,23,28,56,77,84,100,78,61,60,21,55,30,35,158,29,19,20,42,87,88
129,6,198,205,40,65,31,152,50,90,92,96,141,137,14,82,23,28,56,77,84,100,78,65,60,21,55,158,162,30,35,160,164,158,29

This is the output file from read relevant. The first value is the source trial number for the file (seeSourceTrials). The second number is the ordinal number of the trial in this unit. The remaining numbers in each line are the event codes (in order) for that trial. Any code included in theGlobalIgnorelist will not be included in the output file.


RIP(not implemented)

Control display of a reciprocal interval plot of spike data

RIPlayout command controls the display of a cumulative reciprocal interval plot of spike data.

rip show turn rip on
rip noshow turn rip off
rip fill connect rip points
rip nofill do not connect rip points
rip labels <label> scale labeling
rip ypos <position> y position of lower left corner in percent
rip size <size> vertical size in pixels for rip

Example: rip show


Save [SAV]

Create a protocol file with currentMatOFFsettings

TheSavecommand creates a protocol file. The file it creates is a snapshot of all the current settings. Execution of the saved file using theLoad command will returnMatOFFto the same state it was in when theSavecommand was issued. The graphical layout settings can be saved independently of the other settings depending upon with form of theSavecommand is used.Saveuses the default extension of .PRO. If the PROTOCOLPATH environmental variable is set,Saveuses that path to determine the target directory.

save<filename> save everything but the graphical layout information
save <filename> layout save everything
save <filename> only save only the layout information

Example: save rgb layout

Saves all the current settings, including layout information, to the file RGB.PRO.


Scale

Set the vertical range of the histogram display

Whenever a histogram is specified in the current layout, the current value ofScaleis used to set its vertical range in impulses per second (ips).ScaleAutoinstructsMatOFFto use the maximum histogram bin value to set the scale range. TheScalecommand is the same as theHistogram scalecommand.

scale show turn histogram scale on
scale noshow turn histogram scale off
scale auto automatic scaling of histogram
scale <n> set range of histogram scale in pulses per second (PPS)

Example:

window 6000
binwidth 120
scale 50
histogram show
show

InstructMatOFFto plot histogram data for current data. Histogram will have 120 bins of 50 ms each (= 6 seconds of data), and have a full-scale firing rate of 50 pps


Scan [SCA]

Start the scan process

TheShow,Old plotandNew plotcommands are normally used to start or reprocess data after making a change to the search strategy. These commands automatically decide which processing steps are required before a plot can be drawn. The Scan command overrides the automatic decision-making and forces a new scan for trials that match the search criteria. TheScancommand is used to trigger the processing ofHistory scripting.

Example: scan


SecondDx

Control calculation and display of a second derivative trace for the analog data from each trial

SecondDxlayout command controls the calculation and display of a traces that are second derivatives of the analog data for each trial.

seconddx show turn trace on
seconddx noshow turn trace off
seconddx labels <size> choose label size

seconddx line <type> line type for trace
seconddx xpos x x position of trace in pixels
seconddx ypos y y position of trace in pixels
seconddx separation x number of pixels between traces. A negative value reverses the order of display
seconddx size x vertical size in pixels for trace

SecondDxonly operates on the primary analog channel (seeAnalogChannelcommand).

Example: seconddx show


Segment [SEG]

Choose the trial time range for certain statistical tests

There are several statistical calculations which can be made byMatOFF. Two of them, segment statistics and Mann Whitney U are based upon comparison of spike density between the two raster segments, "A" and "B". These segments are time periods marked-off on the graphics display. Their boundaries are specified in pixels using theSegmentcommand. The time scale on the graphics display can be mapped onto 600 screen pixels for backwords compatibility with the old PCOFF program. Otherwise, values are specified in absolute time (milliseconds) across the X axis. The units are selected by theAxiscommand. Two different segments can be defined simultaneously to make intra-trial calculations easier. Once segments are set the user can extract information about those segments using theDump segmentscommand, or theSet segmentstatscommand.

segment show display segements on the graph
segment noshow do not display segments on graph
segment a1 <value> set the start of the time range for segment a. <value> can be "m" for mouse selection
segment a2 <value> set the end of the time range for segment a. <value> can be "m" for mouse selection
segment b1 <value> set the start of the range for segment b. <value> can be "m" for mouse selection
segment b2 <value> set the end of the time range for segment b. <value> can be "m" for mouse selection
segment a <value> <value> set the whole time range for segment a
segment b <value> <value> set the whole time range for segment b

The format <value>-<value>, (e.g., 300-400) is allowed ifAxis units<is set to PCOFF. This form of the command is for backwards compatibility, but cannot work with absolute units. With absolute units the dash would be interpreted as a minus sign. The mouse can be used to select the segment value in the a1, a2, b1, and b2 versions of the command.

Example:

shift 0
window 3000
axis pcoff
seg a 200 300
seg b 300 320
set segstats show
show

Using the old PCOFF mapping, define segment A as the 500 ms period before the centering code, and segment B as the first 100 ms after the centering code. After theShowcommand, spike counts for each trial, and descriptive statistics for these two window periods, will be listed on the console.


Sequence [SEQ]

Defines the event code sequence necessary to accept an epoch of data for further analysis

Sequenceis one of the most important commands inMatOFF. It sets the search strategy for identifying trials (epochs) of interest. The sequence is composed of a series of event codes based on the event codes inserted into the data stream by the data collection or data conversion program. Event codes are grouped in brackets. Within a bracket, codes are logically ORed. Between brackets, codes are logically ANDed in temporal sequence. Thus the sequence: [23,24][25][26] means to search for a 23 or a 24, followed by a 25, then a 26. Two difference code sequences can satisfy this requirement: 23 25 26 and 24 25 26. Note that the sequence 23 15 25 26 is not acceptable. The code 15 interrupts the specified sequence and thus the trial would be rejected. Likewise, the sequence 23 24 25 26 would also be rejected, because code 24 interrupts the sequence. It is possible to "ignore" an intervening code. The way to ignore a code is to "globally" ignore it using theGlobalIgnorecommand.

Example: seq [1][2,3][15-19][9]

MatOFFwill look through the data for each sequence of codes which satisfy this specification. For example, if the codes 1 3 17 9 were encountered in the data stream in that order, uninterrupted by other codes, data for the trial will be accepted for analysis and display.

To ease typing,MatOFFtries to be as "open-minded" as possible when it comes to entering theSequencecommand. The above sequence can be entered with:

seq 1] 2,3] 15-19] 9]


Set [SET]

Control a variety of program functions

General operations of theSetcommand

TheSetcommand is a powerful method for saving data after each search. This is the primary methodMatOFFuses for exporting data to other programs.Setis also used to enable or disable some built-in features ofMatOFF. When used for saving data, theSetcommand prints or saves onto the disk each time aShow,Old plot, orNew plotcommand is issued. Thus, theSetcommand automatically stores results each time a plot is created. Set is a rather complex command with multiple options and special files to define the ASCII format of any files that are saved. SeeExporting results for important details on using theSetcommand.Dump Setscan be used to display the status of many set "processes".

TheSetcommands for moving data to the screen have the general form:

set <process> show Enable automatic data dump to screen
set <process> noshow Disable automatic data dump to screen
The Setcommands for moving data to the hard disk have the general form:
set <process> name <filename> Set the disk file name for the process, disable the automatic file numbering system.
set <process> keep Enable automatic data dump to disk
set <process> nokeep Disable automatic data dump to disk
set <process> append Each new data dump is appended to the current data file
set <process> noappend Each new data dump erases any existing data in the file

The standard Set processes
epochstats Statistics on the number of pulses between the center and mark event codes
segmentstats Statistics on the number of pulses between two segment markers
sort Statistics on the values used to in the current sort. Values depend upon theSortoption
mwu Spike counts. Can be used with theMWFilescommand to do non-parametric statistical tests
histogram Bin data used for the current spike histogram(not yet implemented)
events The list of event codes that matched the sequence for each trial

Special Setcommand for controlling other MatOFFfeatures
set sort reverse Reverse the order of raster and analog traces on the plot
set sort noreverse Use the normal order of raster and analog traces
set plot noshow
set plot show
Set plot noshow will inhibit plotting the data. It is used to generate statistical files without the additional delay of making plots on the screen. Set plot show returnsMatOFFto normal operation.
set segmentstats pcoff
set segmentstats absolute
Set segmentstats pcoff will makeMatOFFscale nearly all x-axis values to the range of 0 to 599. This range provide backwards compatibility with the legacyPCOFFsystem. Set segementstats absolute returnsMatOFFto normal operations, where x-axis units are in milliseconds.
set print color
set print nocolor
Enable color printing
Print only in black and white

Output formats of ASCII files

The ASCII files generated by theSetcommand have a format that can be controlled using special format files. SeeExporting Resultsfor detailed information on how to control the output file formats. See also the DUMPLABEL environmental variable.

Automatic file numbering and the Append/Overwrite modes

When using theSet <option> Keepform of the instruction,MatOFFgenerates files with numeric names. For example:

set histogram keep

This statement will generate files named 0.HST, 1.HST, etc., incrementing each time a newShowcommand is issued. The numbering can be controlled by setting the current number with:

set histogram filenumber <n>

<n> is the starting number of the sequential file names.

Alternatively, the numbering scheme can be disabled withSet <process> Name <filename>. When this form of theSetcommand is used, every Showcommand write data to the specified file. The file name is no longer incremented. Any existing data in the file is overwritten with each new Show, unless theSet <process> Appendcommand is used or the user renames the output file for the process just before eachShowcommand. To turn off the append mode and return to the default overwrite mode, use theSet <process> NoAppendcommand. After appending to a file, use the Close appendcommand to close all files that have been opened with the Set <process> Append command. To return to the default (file number) naming use theSet <process> Namecommand with no file name. After writing to a file withSet <process> Append, useClose appendto close it. Files written withSet <process> NoAppendare closed automatically. Here are some examples.

Example 1, change the name of the output file before eachShowcommand.

set histogram keep
sequence [21][31][33][39]
set histogram name rb101_left
show
sequence [22][32][33][39]
set histogram name rb101_right
show

Example 2, save all results to one file

set histogram keep
set histogram append
set histogram name rb101_all
sequence [21][31][33][39]
show
sequence [22][32][33][39]
show
close append

Checking the status of all the Set processes

To check status of the set processes use theDump Setcommand.

Specific Set Processes

Set epochstatslists trial-by-trial information for the data that fall between the center code and the mark code. The information listed includes: unsorted trial number, number of spikes between the center and mark codes, elapse time between center and mark codes, and number if impulses per second (spikes / time) for that same period. Only the trials in the trial list (from theTrialscommand) are included. The output is in the same order as the plot. That is, the current sort function is applied. The unsorted trial numbers are the trial numbers before the sort function is applied. If a disk file is created using the Keep option, file format is controlled by the EPOCH.FMT file. The "dump label" is controlled by anEnvironmental variable. SeeExporting Resultsfor more information on formatting the output. The default file extension for disk files is .EPK.

Example epochstats output:

>set epoch show
>show
layout 1

DUMP LABEL
15-Sep-2000 14:45:25

TRIAL DELTA T COUNT IPS
1 0.721 0 0.0
2 0.721 0 0.0
6 0.721 2 2.8
8 0.721 1 1.4
20 0.721 0 0.0
21 0.721 0 0.0


TRIALS AVE SUM AVE
-------------------------------------
6 4.326 3 0.7

Set events lists the specific sequence of events for each trial that matched the sequence.A file created with the bySet events keepcan be used to evaluate behavioral measures.

In this example, the event list can be used to see which stimuli (events 80-89) evoke event 41 and which stimuli evoke event 42.

Example events output:

>set events show
>sequence [80-89][15][16][41-42]
>show
layout 1

TRIAL EVENTS
1 81 15 16 42
2 85 15 16 41
3 85 15 16 41
4 80 15 16 41
5 88 15 16 42

Set segmentstatslists trial-by-trial information for the data that fall within segment A and within segment B. See theSegmentcommand for instructions on how to select segements. The information listed includes the unsorted trial number and number if impulses per second (spikes / time) for each segment. For each segment the "Trailer" includes: number of samples (N), sum of all the samples, mean of the samples, sum of squares (SSq) for the samples, and standard deviation (SD). Only the trials in the trial list (from theTrialscommand) are included. The output is in the same order as the plot. That is, the current sort function is applied. The unsorted trial numbers are the trial numbers before the sort function is applied. If a disk file is created using the Keep option, file format is controlled by the SEGSTAT.FMT file. SeeExporting Resultsfor more information on formatting the output. The default file extension for disk files is .SEG.

Example segstats output:

>set seg show
>show
layout 1
DUMP LABEL
15-Sep-2000 14:45:25

TRIAL SEG-A SEG-B
1 1 3
2 1 0
6 0 2
8 1 0
20 1 0
21 0 1

IPS | Segment-1 Segment-2
--------+------------------------
N | 6 6
Sum | 4.000 6.000
Mean | 0.667 1.000
SSq | 4.000 14.000
S.D. | 0.402 0.784

Set sortlists trial-by-trial information for the data that were the criteria used for sorting. The information depends on the type of sort selected with theSortcommand. The sorted trial number and unsorted trial number are listed, along with a value that was used to determine the sort order (sort criterion):

Type of sort

Data listed by Set sort

Sort center centering code
Sort delta(not implemented) difference between analog values at the two test points
Sort epoch number of spikes between center and mark codes
Sort integral(not implemented) area under the analog trace in the selected time interval
Sort maximum maximum value of analog data between two time values
Sort minimum minimum value of analog data between two time values
Sort off unsorted trial number
Sort peak time to maximum value of analog data between two time values
Sort pit time to minimum value of analog data between two time values
Sort pulse number of spikes between two time values
Sort time time between center and mark codes
Sort zero(not implemented) time to first zero value of analog data between two time values

Only the trials in the trial list (from theTrialscommand) are included. The output is in the same order as the plot. That is, the current sort function is applied. The unsorted trial numbers are the trial numbers before the sort function is applied. If a disk file is created using the Keep option, file format is controlled by the SORT.FMT file. SeeExporting Resultsfor more information on formatting the output. The default file extension for disk files is .SRT.

Example sort output:

DUMP LABEL
15-Sep-2000 14:45:25
UNSORTED SORTED CRITERION VALUE
1 108 0
2 117 1
3 135 2
4 148 2
5 157 2
6 190 3
7 10 3
8 15 4
9 60 4
10 67 4
11 70 5

Set mwulists trial-by-trial information for the data that fall within segment A and within segment B. See theSegmentcommand for instructions on how to select segements. The information listed includes the unsorted trial number and number if impulses per second (spikes / time) for each segment. For each segment the "Trailer" includes: number of samples (N). Only the trials in the trial list (from theTrialscommand) are included. The output is in the same order as the plot. That is, the current sort function is applied. The unsorted trial numbers are the trial numbers before the sort function is applied. If a disk file is created using the Keep option, file format is controlled by the MWU.FMT file. SeeExporting Resultsfor more information on formatting the output. The default file extension for disk files is .MWU. If the default numeric file naming scheme is used, and the append mode is off (Set mwu noappend), thenSet mwu keepwill produce two files with eachShowcommand. The files will be named: A<number>.SEG and B<number>.SEG. These files are designed to be used with theMWFilescommand for non-parametric statistal testing. If the above defaults are not used, only one disk file is created each time and that file has the segment data as specified in the MWU.FMT format file.

Example mwu output to screen:

DUMP LABEL

15-Sep-2000 15:27:41

TRIAL SEG-A SEG-B

108 8 30

117 12 13

135 10 22

148 20 23

157 12 28

190 24 7

10 21 22

15 22 26

60 20 5

67 18 24

| SEG-A SEG-B

-----+------------------------

N | 10 10

Example mwu output to disk (default format):

A0001.MWU B0001.MWU
8
12
10
20
12
24
21
22
20
18
30
13
22
23
28
7
22
26
5
24

Set histogram output the (normalized) histogram data.(not yet implemented)


Setenv [SETENV]

Modify environment

MatOFFhas environmental variables that can be set with either the DOS SET command or theMatOFFSetenvcommand. Each environmental variable controls a different aspect ofMatOFFbehavior.

Variable Default value Purpose
datapath '.' default location of data files if no path given
defaultpath '.' default location of any files if no variable or other path defined
displayunits 'pcoff' default for units setting x axis units. SeeAxiscommand
dumplabel '' text inserted in the header ofSet<process> keep/show commands
dumpmode 'NOAPPEND' set to APPEND for appending spike times in theDump spikescommand
dumppath '.' default location to place files created withDumpcommand
dumptext '' text inserted before each line of data inDump spikescommand
editor 'c:\windows\notepad.exe default editor to open when editing text files
eventcodefile 'default.evc' file that describes each event code. used byMakdatwhen listing events.
formatpath '.' default location to find .fmt format files
graphicsformat 'png' graphics file format used withPlotcommand orSet plot keep. SeePlotcommand.
layoutpath '.' default path for storing layouts, including koflay.dat. SeeLayout command.
makdat '' default option list forMakdatcommand
makdump '' If a file is defined here, allMakdatcommand debugging information will be dumped to that file.
metachar1 '$' prefix for protocol file replacement parameters withPcoffcommand
metachar2 '%' prefix for protocol file replacment parameters in a metafile. SeeProtocol scripting files.
metapath '.' default location to find metafiles
plotpath '.' default path forPlotcommand
protocolpath '.' default location to find protocol files. SeeProtocol scripting filesand the Load command.
remapfile 'default.rmp' default spike mapping file forMakdatcommand
statpath '.' default location to put statistical output files
maxinputtrials 5000 Makdatwill quit after this number of trials in each file. This command is used only for debugging.
maxtrialsfound 250 Makdatwill stop looking for a sequence match after this number of trials.

Example: setenv datapath c:\data\


Shift

Reposition time 0 on the x axis

All data on the graphics display are aligned on the centering code. With aShift> value of 0, the centering code is in the center of the time scale. TheShiftcommand allows the user to reposition the location of the centering code with respect to the time scale on the display. The rasters, analog data, histogram, and RIP move with the centering code, which effectively "slides" all the data forward or backwards in time.

Shift values are in milliseconds. A positive shift value will move the centering point to theleft. Negative shift values move the centering code to the right.

shift <shift value (milliseconds)>

Example:

sequence [4][5][7][29]
center 4
mark 3
window 1500
shift -250
show

Center on the last code in the sequence ([29]). Look at the trials starting from 500 millisecondsbeforethe last code, and ending 1 secondafterthe last code.


Show [SHO]

Generate a graphical display based on the currentMatOFFsettings

Showcreates a graphics display. It is context sensitive in that it will do whatever processing is necessary to create a display based on what parametric changes have been made since the lastShowcommand. For example, if the search sequence was modified since the lastShowcommand,MatOFFwill search the data again for matching sequences, then do all necessary processing to plot the current data.Showis also used to display the status of certainMatOFFparameters. Many of the same parameters can be displayed using the associated command with no parameters. For example theUnitnamecommand (with no parameters) is the same as theShow unitnamecommand.

show Start processing and generate plots and data files
show binwidth Display histogram bin width
show center Display center group number
show filename Display name of current file
show frequency Display A/D sampling frequency setting
show globalignore Display globalingore list
show mark Display mark group number
show plot Enable display of plots (same as Plot show)
show pulsechannel Display spike channel number
show segment Display segment ranges
show sequence Display sequence list
show source Display source trial list
show span Display span range
show spikecounts Display each pulse channel and the number of spikes it has
show trials Display list of display trials
show unitname Display name of current unit
show window Display size of raster display window

TheShowcommand with no parameters is theMatOFF"go" command. It tellsMatOFFto build a plot from the currently open file using all the parameters that have been specified. Normally,Showis used to generate a single plot. If the user is making multiple plots on a page (see the multiplot option of theAxiscommand) oneShowcommand is used for each plot on the page.

It is possible to generate a whole group of plots with oneShowcommand.MatOFFis able to store up to 10 simultaneous "layouts". Each layout is a description of how to arrange a plot on the page. For example, one layout could be a set of rasters with matching analog data, and another layout could be rasters with a histogram. TheLayoutcommand selects which layout is currently selected for editing. But, regardless of which layout is currently selected, theDisplaycommand controls which layout to use for plotting the data. TheDisplaycommand can specify a list of layouts (layout list), andShowwill create one plot for each layout. This way, you can get several views of the same data with oneShowcommand. With the development of powerful scripting (seeMatOFF Scripting Language) the use of layout lists is less common.

In addition to creating a plot, theShowcommand tellsMatOFFto generate any statistical and other numerical data that have been specified by theSet <process>commands.

Show Plotis a special variant of theShowcommand. It is a synonym forSet plot show.Set plot noshowinhibits screen plots and is used for batch files that save results to disk and are only slowed down by the screen display.Set plot showreturnsMatOFFto normal operation.

Each plot is a numbered MATLAB window. Numbering begins at 11. (The first 10 windows are reserved for menus.)Showalways uses the current window. If a display list is used,Showwill increment by one for each new plot in the display list.Showcan be used to put multiple plots on the current page as described above. The commandNew plotis a synonym forShow, except it will find an unused plot number and create a new windows before plotting. The commandErasewill erase the current plot window. If you use only one plot window for all plots, useEraseto clear that window just before making a new plot. When writing scripts, you sometimes want very explicit control of which plot number is being used. TheOld plotcommand is another synonym for Show, except that it specifies explicitly which plot window to use. Despite the name "Old," it can be used to create a new plot by specifying a currently unused plot window number.

Example: show 1-3

Reprocess if necessary, then shows current data using layouts 1, 2, and 3. Also, makes the current display list [1,2,3].


Smooth(not implemented)

Control display of smoothed analog data

Smoothlayout command controls the display of smoothed analog for the first analog trace.

smooth show turn trace on
smooth noshow turn trace off
smooth line <type> line type for smooth trace
smooth ypos <y> y position of smoothed analog trace
smooth separation <sep> vertical space between traces. A negative value reverses the order of display
smooth size <size> vertical size of each trace

Example: smooth show


Smo2(not implemented)

Control display of smoothed second analog data

Smo2 layout command controls the display of smoothed second analog for the first analog trace.

smo2 show turn trace on
smo2 noshow turn trace off
smo2 line <type> line type for smooth 2nd analog trace
smo2 ypos <y> y position of smoothed 2nd analog trace
smo2 separation <sep> vertical space between traces. A negative value reverses the order of display
smo2 size <size> vertical size of each trace

Example: smo2 show


Sort [SORT xx]

Order the display of trials based on specified criteria

The data trials that match a specified sequence can be reordered for display or analysis. Raster and analog displays are ordered by selecting a sorting criteria.

Sort options:

Sort center Order the display of trials based on the centering code
Sort delta<start> <stop>
(not implemented)
Order the display of trials based on the magnitude of the difference between two values in the analog data
Sort epoch Order the display of trials according to the number of spikes between the center and mark codes
Sort history<class> Order the display of trials according to the values stored in a history class
Sort integral<start> <stop>
(not implemented)
Order the display of trials according to the area under the analog trace in a selected time interval
Sort maximum<start> <stop> Order the display of trials according to the maximum value of each analog trace between two interval values
Sort minimum<start> <stop> Order the display of trials according to the minimum value of each analog trace between two interval value
Sort off Force a chronological sorting of trials
Sort peak<start> <stop> Order the display of trials based on the time between a user-defined starting point and the occurrence of the peak value of the analog data
Sort pit<start> <stop> Order the display of trials based on the time between a user-defined starting point and the occurrence of the minimum value of the analog data
Sort pulse<start> <stop> or <[no]show> Order the display of trials according to the number of spikes between two interval values
Sort time Order the display of raster and analog data trials by the time between the center and mark codes
Sort zero<start>
(not implemented)
Order the display of trials based on the time between a user-defined starting point and the occurrence of a zero analog data value



General features of the Sort options:

1) <start> and <stop> are times along the X axis. Times are expressed either in absolute time on the current graph (in milliseconds) or in the old PCOFF display units. PCOFF display units map the current window value to 600 points. See theAxiscommand for details.

2) Sorting based on analog data use only the first analog channel. See theAnalogcommand for details.

3) Sorting affects all spike rasters and all analog trial-by-trial analog displays (including XY).

4) The sort order can be reversed two ways. One way is selective for the data type. You can use a negative value of separation between raster or analog traces in the graphics display menu, e.g.Raster sep -5. The other way affects all sorted traces: using theSet sort reversecommand.

Individual descriptions and examples of theSortoptions:

Sort centersorts the trials based on the centering code. This can be very useful for comparing unit responses to different experimental conditions. The lower number codes are plotted first. Suppose the experiment includes 3 different GO signals, corresponding to movements to 3 different targets. Each GO signal is coded as a different event code, in this example codes 10, 11, and 12:

sequence [4][5][10,11,12][33]
center 3
mark 2
sort center
show

Centering is on the third set of codes, which will be code 10, 11, or 12 depending on the trial.Sort Centerwill cause all the trials associated with one target (for code 10) to be displayed together, all the trials for the second target (code 11) to be displayed together next, and all the trials for the third target (code 12) to be displayed last.

Sort Deltameasures the analog value between two points in time along the graphics display. The trials are ordered from lowest difference to the highest difference. In this example trials with the smallest analog value difference, between the value at time 0 and the value 1000 ms after the center code, will be displayed first.

analog 1
frequency 250
window 5000
sequence [4][5][10][33]
center 3
mark 2
sort delta 0 1000
show

Sort epochcounts the number of spikes (impulses) between the center and mark codes, and orders the trials from fewest to most. In this example trials with the fewest spikes between code "5" and code "10" will be displayed on rasters or analog traces first.

sequence [4][5][10][33]
center 3
mark 2
sort epoch
show

Sort historyuse the history class values to sort trials. Trials that are not included in the class have the lowest value. In this example, the trials will be sorted based on the values in history class 201.

sequence [4][5][10][33]
center 3
mark 2
sort history 201
show

Sort integralintegrates the analog values between two raster segment numbers. The trials are ordered from least area under the curve in the defined interval, to the most. In this example trials with the fewest spikes between time 0 and 500 ms later, will be displayed on rasters and analog traces first.

window 5000
sequence [4][5][10][33]
center 3
mark 2
sort pulse 0 500
show

Sort maximumuses the highest analog value between two raster segment numbers to determine the order of the trials. The trials are ordered from lowest minimum to the highest minimum.

sequence [4][5][10][33]
window 5000
center 3
mark 2
sort minimum -500 500
show

Trials with the highest maximum analog value that is between 500ms before and 500ms after the centering code, will be displayed on rasters or analog traces first.

Sort minimumis likeSort maximum, but uses the minimum analog value that occurs between two time values.

Sort offis used to turn off the other sorting features. Trials are displayed in chronological order.

Sort peakrequires analog data.MatOFFfinds the highest analog value between the two time markers, then measures the period from the first marker to the peak value. This period is used to sort the trials from the shortest interval time to the longest.

Sort pitis likeSort peak, except thatMatOFFfinds the lowest analog value between the two time markers.

Sort pulsecounts the number of spikes between two times along the time axis. The trials are ordered from fewest impulses in the defined interval, to the most pulses. In this example trials with the fewest spikes between the centering code and 1 sec after the centering code, will be displayed on raster or analog traces first:

sequence [4][5][10][33]
window 5000
center 3
mark 2
sort pulse 0 1000
show

A special form of theSort pulsecommand places markers on the plot to indicate the sort pulse interval:

sort pulse show shows markers on the plot,Sort pulsemust be selected from the sort menu for the markers to appear
sort pulse noshow hides markers from the plot

Sort timeuses the time between the center and mark codes as the criteria for sorting. The trials with the smallest amount of time between these codes is plotted first. The order of the plotting can be reversed by selecting a negative value of separation between raster or analog traces in the graphics display menu.

Sort zerorequires analog data.MatOFFmeasures the time from the time given to the first time the analog value reaches zero This time period is used to sort the trials from the shortest period to the longest period. In this example trials with the shortest time period from -100 ms before the centering code to the first zero crossing will be displayed first.

analog 1
frequency 250
sequence [4][5][10][33]
center 3
mark 2
sort pit -100 200
show


SourceTrials [SOU]

Defines where, within the currently selected unit, to start collecting epochs (trials) of data that match the sequence search string

MatOFFsearches the current unit for code sequences that match a predefined sequence. The defaultSourceTrialsvalue is 1-200, which indicates thatMatOFFwill look chronologically at the the first 200 trials of data to find trials that match the search criteria. The sourcetrials list is a list of values separated by commas, which may include ranges (using the dash "-") notation. TheSourceTrialscommand can be used to skip bad data in a unit or to select different segments of the data without having to use theTrialscommand.

Example:

source 10-200

Skip the first 10 trials in the data set.

source 1-15

See if any matching trials occured early in the dataset.


Span [SPA]

Define the time window for scanning

Spanis an optional parameter. If a span value is set, it sets a limit on the time between the first element of the search sequence and the last element of the search sequence. Thus, a sequence will match the search string only if all the events all occured within the time limit set bySpan. Span can be turned off with theSpan allcommand.

span <time window> Set a time limit for the search sequence
span all No time limit for the search sequence

Example:

sequence [25][32][33][40]
span 5000

Code [40] must occur within 5 seconds of code [25] in any give trial to accept that trial for further processing.


Spot [SPO]

Place a marker on the graphics screen indicating the times of specific events

The user lists a set of event codes with theSpotcommand. The exact time of these codes will be marked under each raster with a plus ("+") sign. Any number of codes can be spotted on a given raster. Codes listed in the GlobalIgnore command cannot be spotted; only codes appearing in the sequence can be spotted.

spot <code list>

Example:

seq [4][3][28-30][33]
center 3
mark 4
spot 3,4
show

This set of commands will center on codes 28-30, mark on code 33, and spot codes 3 and 4. This example points out an important difference between specification of center and mark codes, and the specification of the spot codes.CenterandMarkuse ordinal numbers referring to one of the sequence elements. TheSpotcommand refers to the actual code values.


Taint

Debugging command. Controls the taint level

Each processing step is assigned a taint level. Each processing step cannot procede until lower taint level processes are complete. Thus, the taint level is used internally to determine how early in the processing pipeline the program must start to properly excecute a requested command.

taint with no parameters the taint value is printed
taint <taint value> set the taint value. meaningful values for <taint value> are:
10 no file open, 20 need to scan, 30 need to accumulate,
40 need to map, 50 ready to plot

Example: taint

This will print the current taint level.


Text

Control the placement of text on the graphical display

Each of the tenMatOFFlayouts can have up to 9 lines of text associated with the graphical display. These 9 lines are independent of theHeading. TheTextcommand controls the content, size and placement of the text. Note that the origin of a text line for placement begins at the left edge and center of the height of the first character in the line. SeeLayout parametersfor more information on x and y positioning. WithText frame on, the text is positioned relative to thesubplot. WithText frame off, the text is positioned relative to the entire page.

text show / noshow Turnalltext on or off
text line n Select a text line to change. n = 1 to 9. This command must be given before any of the command below.
text on / off Turn the current text line on or off.
text angle x Change the current text angle to: 0, 45, 90, -45, or -90 degrees. Positive is clockwise.
text position x,y Set the x and y positions of the beginning of the current text line.
text xpos x Set only the x position of the beginning of the current text line.
text ypos y Set onnly the y position of the beginning of the current text line.
text string <string> The <string> is the text you want to display.
text size x Set the font size of the text. The value of x is in points.
text frame on / off Frame 'on' means the text position is restricted to the current subplot. 'Off' means the text can go anywhere on the page.

Example:

text show Make sure text display is enabled
text line 1 Select text line 1 (must do this before entering or positioning text)
text position 1,10 Choose a position
text string THIS IS AN EXAMPLE TEXT STRING Write some text
text on Make sure that text line will show up
show

Place a line of text on the screen using layout 5.


Thin

Reduce the number of spikes by some factor

Thinis aMakdatlist file parameter that reduces the frequency of occurrence of an event or spike. See theMakdatcommand for details.


Time [TI]

Report time-of-day and elapse time

MatOFFwill report the current time-of-day and the elapse time sinceMatOFFwas first started. In a protocol file the variable %11 can be used to get a time-of-day string.

Example:

log rbtime.log
time
load rb117
time

See how long it takes to run protocol file rb117.pro.


Trials [TRI]

Select which matching trials to display

It is often advantageous to display only some of the trials found after searching for trials that match theSequence.Trialsselects which trials will be displayed; the same selected trials are also used in statistical analysis, histograms, etc. The order that selected trials are displayed are determined by theSortcommand and theSet sort reversecommand. When a sort is in effect the trial number refers to a trials positionafterthe trials have been sorted.

The list used in theTrialscommand is a list of values separated by commas, which may include ranges (using the dash "-") notation.

Example: trials 1-15,17-20

Display the first 20 trials, excluding trial 16.


TrialFunction [TRI]

Select which matching trials to display using a linear function

It is often advantageous to display only some of the trials found after searching for trials that match a sequence.TrialFunctionselects which trials will be displayed; the same selected trials are also used in statistical analysis, histograms, etc.TrialFunctioncommand enables the user to display trends in sorted data more dramatically and with a smaller number of rasters.

TheTrialFunctionselects trials based on a linear function Ax+B. The equation is useful to select every second, or every third trial, etc. A is the step size, B is the starting point. For example, the user can display every third sorted trial after trial number 49 using the example below.

Example: trialfunction 3,50

MatOFFstarts with x=0 and increments x until the result of the function exceeds the number of "trials found". In this case every third trial starting with trial #50: 50, 53, 56, 59, 62, 65, 68, 71, 74...


Trim

Remove every occurrence of an event code after the first one in each trial.

Trimis aMakdatlist file parameter that removed all but the first occurrence of an event or spike in each trial. See theMakdatcommand for details.


Type [TYP]

List an ASCII file on the command screen

Type is similar to the DOS "type" command. It will print the contents of a text file to the screen. It is useful for examining protocol files and the output ofMatOFFASCII dumps. If no path is specified, the DEFAULTPATH environmental variable is used.

Example: type c:\pcoff\andy\andy.pro

View the file "andy.pro".


Unit [UNI]

Identify which unit in the data file to analyze

Data sets within a data file are broken into units.Unitcommand identified which unit to analyze. Use theIndexcommand to see which units are available in a file. TheUnitcommand is case sensitive. Thus, unit A is different from unit a. Unit names can have a maximum of 12 characters. If the unit name '*" is used, all units in the data file will be combined together as a single unit.

Example: unit in121

Opens unit in121 for analysis.


ValidateSpikes [VALID]

Control which spikes are included in the histogram

When ValidateSpikes is on, only valid spikes are included in histograms, and the raster tick marks for spikes that are not valid are drawn in a different color. Each trial has a period of time (epoch) where spikes occurring in the epoch are valid. Valid spikes are spikes in between a start time and end time for each trial. The start and end times are stored in history classes. For example, if history classes 10 and 11 are the start and end classes, respectively, in any given trial spikes are valid if they occur between the timestamps saved in classes 10 and 11. For ValidateSpikes to be useful, the user must write a history script that fills the two classes with meaniful timestamps.

validatespikes start <value> History class of the timestamps that mark the beginning of valid spikes (for each trial)
validspikes end <value> History class of the timestamps that mark the end of valid spikes (for each trial)
validatespikes on Enable the ValidateSpikes function
validatespikes off Disable the ValidateSpikes function
validatespikes color <value> Set the color of spikes that are NOT valid. Color values:: yellow, magenta, cyan, red, green, blue, white or black

Example:

history file history_validate.m
history on
validate on
validate start 10
validate end 11
validate color white
show
invalid color blue
valid on
show


Version [VER]

Print version number on screen

Display the current version number ofMatOFF.

Example: version


Walk [WALK]

Pause printing to screen during long printouts

CertainMatOFFcommands, e.g. Read, can produce long printouts.Walkwill makeMatOFFpause screen printouts at regular intervals.

walk <speed> <speed> is a number between 1 and 10 that determines the number of lines that will be printed to the screen before printing is paused

Example:

walk 5
read codes

Set the walk speed to 5 before requesting a dump of the event codes in the current unit.


Why [WHY]

Trys to explain why the results are not as expected

New users can use theWhycommand to see if there is some obvious reason the data were not plotted..

Example: no trials found
why
Data file appears to be empty.


Window [WIN]

Set how many milliseconds of data are displayed on the graphics terminal

TheWindowcommand controls the graphics display. It determines how many milliseconds of analog, raster, RIP, or histogram data will be displayed across the screen.

Example: window 3000

InstructsMatOFFto display 3 seconds of data for each trial.


Write [WRI]

Write ASCII data to a file opened with theOpenorAppendcommand

MatOFFcan create ASCII (text) files.OpenandAppendare used to create a new ASCII file or append to an existing one. Once a file is open, theWritecommand is used to insert text into the file. Text is entered line-by-line. All text after theWritecommand (after skipping any blank spaces) is written to the ASCII file. Note that HTML (web pages) can be created with these commands. The section onProtocol scripting filesdiscusses ASCII files greater detail.

Example: write print $2,tabular

Put an ASCII string in the text file. $2 refers to a replaceable parameter. SeeProtocol scripting filesfor the use of replaceable parameters.


XY[XY]

Control the XY plot of the two analog channels

TheXYcommand controls an XY plot of the two analog channels on the graphical display. The primary channel is the X axis and the secondary channel is the Y axis. The size of the plot is determined by the size option.

xy show turn trace on
xy noshow turn trace off
xy line <type> line type for analog trace
xy ypos <y> y position of XY trace in percent of plot window
xy xpos <x> x position of XY trace in percet of plot window
xy separation <value> separation between XY traces on the plot, a negative value reverses the order of display
xy size <value> vertical size (gain) of each trace
xy time <value> select how much of the trial to display on the XY trace (see below)
xy start <value> start time, start event, or start class
xy stop <value> stop time, stop event, or stop class
xy overlap on XY traces fill same workspace as raster/histogram drawings
xy overlap off XY traces in a separate panel to the left of the raster/histogram drawings
The xy time function determines how much of each trial will be displayed in the XY trace:
xy time all display all analog XY points from the start to the end of the window
xy time time truncate each XY trace to just the time range specified by the start and stop values
xy time events truncate each XY trace to just the time range specified by start and stop events
xy time classes truncate each XY trace to a time range specified by the values stored in the start and stop history classes
xy time time <start time> <stop time> xy time time command with start and stop times specified
xy time events <start event> <stop event> xy time events command with start and stop events specified
xy time classes <start class> <stop_class> xy time classes with start and stop classes specified