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Laboratory of Neuropsychology

MatOFF Commands (In alphabetical order)

This page includes a list of commands for MatOff.

Related pages:

Ana2 [ANA2]

Control display of data from the second analog channel

Ana2 command 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.

Command Option Description
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, Layout Parameters for MatOFF  )
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

See Also

Creating, Printing and Saving Plots | Analog [ANAL] | Av2Analog [AV2A] | Frequency [FREQ] | Layout [LAY] | Set [SET] | Smo2 (not implemented) | Trials [TRI] | XY [XY]

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:

Command Option Description
analog show turn trace on
analog noshow turn trace on
analog off set channel number to 0, this disables the analog channel
analog line <type> line type for analog traces
analog <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

See Also

Creating, Printing and Saving Plots | Ana2 [ANA2] | AvAnalog [AVAN] | AvFirstDx [AVF] | AvSmooth (not implemented) | FirstDx | Layout Parameters for MatOFF | Set [SET] | Smooth (not implemented) | Trials [TRI] | XY [XY]

Append

Open an existing ASCII data file for use with the Write command.

Append opens an existing file for writing with the Write [WRI]  command. Data written to the file is added to the file after the existing data. See the section on Protocol scripting files( MatOFF Scripting Language  ) for more details.

Example

append stats.txt

See Also

Close [CLO] | Exporting Results | Open | Write [WRI] | MatOFF Scripting Language

AutoUpdate [AUT]

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

AutoUpdate forces MatOFF to 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. AutoUpdate stays in effect until the ManualUpdate command is given.

Example

Command Option Description
auto
window 2000
Plot will update immediately after this command

See Also

ManualUpdate [MAN]

AvAnalog [AVAN]

Control calculation and display of average analog trace

AvAnalog creates 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:

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

Example

avanalog show

See Also

Creating, Printing and Saving Plots | Analog [ANAL] | Layout Parameters for MatOFF | Trials [TRI]

Av2Analog [AV2A]

Control calculation and display of average 2nd analog trace

Av2Analog creates 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:

Command Option Description
av2analog show turn trace on
av2analog noshow turn trace off
av2analog line <type> line type for average analog trace
av2analog ypos <y> line type for analog traces
av2analog size <value> vertical size (gain) of average analog trace

Example

av2analog show

See Also

Creating, Printing and Saving Plots | Analog [ANAL] | Layout Parameters for MatOFF | Trials [TRI]

AvFirstDx [AVF]

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

AvFirstDx layout 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:

Command Option Description
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

See Also

Creating, Printing and Saving Plots | Analog [ANAL] | AvAnalog [AVAN] | FirstDx | Layout Parameters for MatOFF | Trials [TRI]

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:

Command Option Description
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

See Also

Creating, Printing and Saving Plots | Analog [ANAL] | AvAnalog [AVAN] | FirstDx | Layout Parameters for MatOFF | Trials [TRI]

Axis [AX]

Rescale X axis with 0 as first time value

The Axis command controls the X axis of the plot. It has several main parameters: xatzero, units, multiplot, subplot. Xatzero controls 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. Multiplot allows up to 72 graphs on one plot. Use the subplot parameter to choose which position the next graph will be placed.

Command Option Description
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)

subplot position numbering scheme:

2 plots/page

1 2

3 or 4 plots/page

1 2
3 4

5, 6, 7, or 8 plots/page

1 2 3 4
5 6 7 8

9, 10, 11 or 12 plots/page

1 2 3 4
5 6 7 8
9 10 11 12

13 to 24 plots/page

1 2 3 4 5 6
7 8 9 10 11 12
13 14 15 16 17 18
19 20 21 22 23 24

25 to 48 plots/page

1 2 3 4 5 6 7 8
9 10 11 12 13 14 15 16
17 18 19 20 21 22 23 24
25 26 27 28 29 30 31 32
33 34 35 36 37 38 39 40
41 42 43 44 45 46 47 48

49 to 78 plots/page

1 2 3 4 5 6 7 8
9 10 11 12 13 14 15 16
17 18 19 20 21 22 23 24
25 26 27 28 29 30 31 32
33 34 35 36 37 38 39 40
41 42 43 44 45 46 47 48
49 50 51 52 53 54 55 56
57 58 59 60 61 62 63 64
65 66 67 68 69 70 71 72

Example

axis xatzero on

See Also

Creating, Printing and Saving Plots | BinWidth [BIN] | Segment [SEG] | Plot [PLO]

Batch [BAT]

Process a DOS batch file

The Batch command 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.Batch supports DOS "replaceable parameters" (e.g., %1, %2, etc.). It can also issue a Call to another batch file, but cannot be nested beyond the first Call command. See the Protocol scripting files ( MatOFF Scripting Language  ) section for more details.

Commands processed by Batch:

Command Option Description
Pcoff Load a protocol file, load a data file, and set up a series of replacement parameters
Set Execute a Setenv MatOFF command 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

See Also

Pcoff [PCOFF] | Setenv [SETENV] | MatOFF Scripting Language

Bell [BEL]

Send a beep sound to the operator

Bell sends a beep sound to the operator. It is most useful in a protocol scripting files( MatOFF Scripting Language  ).

Command Option Description
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 seconds

Example

bell

See Also

Load [LOA] | MatOFF Scripting Language

BinWidth [BIN]

Select the number of pixels per bin for histograms

The width of the histogram bins are set by the BinWidth command. The BinWidth value is either the number of pixels per bin or the number of milliseconds per bin, as set by the Axis [AX]  command.

Example

axis units absolute
histogram show
win 6000
bin 30
show

Display 6 seconds of histogram data with 30 ms bins.

See Also

Axis [AX] | Histogram [HIS] | Window [WIN]

Break

Pause a protocol file and wait for the operator

The Break is strictly a protocol file command. It pauses protocol file execution and waits for the operator to enter commands. The operator can issue any MatOFF commands. Then, the protocol file can be continued. The Continue command 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. The Continue  command will resume processing with a Show [SHO]  command.

See Also

Continue | Quit [QUIT] | MatOFF Scripting Language

Calculator [CAL]

Activate Windows calculator

The Windows pop-up calculator can be accessed with the Calculator command.

Example

calc

See Also

Creating, Printing and Saving Plots | Analog [ANAL]

Cd

Change directory

Cd acts like the DOS change directory command.

Example

cd ..

Take one step down the directory tree.

See Also

Directory [DIR] | Pwd [PWD]

Center [CEN]

Select event for alignment of all data trials

One of the primary functions of MatOFF is 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. The Center command 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 the Center specification. Thus, "center 3" does not mean 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 of MatOFF History Scripts .

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.

See Also

GlobalIgnore [GLO] | MatOFF History Scripts | Mark [MAR] | Sequence [SEQ] | Shift | Sort [SORT xx] | Spot [SPO]

CenterLine [CEN]

Control display of a center line

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

Command Option Description
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 the CenterLine command (e.g., center) is accidentally used without including any parameters, MatOFF will interpret the command as a Center command.

Example

center show

See Also

Center [CEN] | Layout Parameters for MatOFF

Clean

Close open files after a MatOFF crash

The Clean command closes all open MatOFF files (protocol, metafiles, data files, etc.). It is used primarily for debugging after a MatOFF error leads to a MATLAB prompt.

Example

clean

See Also

ErrorLevel

Close [CLO]

Close a data file that was opened with the File, Open or Append commands

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

Command Option Description
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 close all open Set [SET]  <process> APPEND files

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 ascii will close a file that was opened with either Open or Append commands. Close datafile will only try to close a currently open data file. Close append will close all open Set [SET] <process> APPEND files.

Example

set epoch keep
append stats.txt
show
close ascii

See Also

Append | File [FI] | Open | Set [SET] | Write [WRI] | MatOFF Scripting Language

Cmd

Switch to the MatOFF command line

Cmd leaves the MATLAB command line and returns control to MatOFF. Return to the MATLAB command prompt by entering the Matlab [MAT] 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, then return to MatOFF.

See Also

Matlab [MAT]

Continue

Resume processing of the protocol file after a Break statement

When a protocol file issues a Break  command, control of MatOFF goes to the user's keyboard. the user may resume the protocol file at any time with the Continue command. If a new protocol file is loaded, the Continue command becomes invalid until a new Break command occurs. If Fileerror [FILERR] has been issued with the break option, then any error caused by a File [FI] command will mimic a Break command. The Continue command can then be used to resume processing.

Example

continue

Continue processing the protocol file.

See Also

Break | File [FI] | Fileerror [FILERR] | Load [LOA] | MatOFF Scripting Language

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 in MatOFF at 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 the Copy command. The origin and destination are simply the layout numbers (1..10). Text is handled separately. To copy text the Copy command 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.

See Also

Creating, Printing and Saving Plots | Layout [LAY] | Display [DISP] | Show [SHO] | Text

Data types

Command Option Description
spikes spike times for each trial on plot
index same as Index command, but Dump can output to a printer or file
setstats list the status of all Set command options
events event codes found (for each search sequence group) for every trial found
history trial numbers and class values for each history class

See Also

Creating, Printing and Saving Plots | Analog [ANAL]

Date [CAL]

Get the date

The Date command prints the current date. In a protocol you can use the variable %10 for the current date.

Example

date

See Also

Time [TI]

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 (not the DEFAULTPATH environmental variable value). If no file extension is given, none is assumed. Ls is a synonym.

Example

dir c:\matoff

See Also

Cd | Pwd [PWD]

Display [DISP]

Specify the set of layouts to use for graphical display after each Show command

Whenever the Show [SHO] , New plot [NEW PLO] , or Old plot [OLD PLO]  command 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 the Display command does not initiate the display of data, it only sets the layout list for the Show [SHO]  command. 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 the Show [SHO]  command.

Example

display 1,3

Use layouts 1 and 3 next time the Show [SHO]  command is issued without parameters.

See Also

Show [SHO] | Layout [LAY]

Dump

Create ASCII file of internal MatOFF values

Dump will print or save to disk information that has been gathered, organized, or calculated by MatOFF. The general form of the Dump command 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. The Dump command is a simplified way to get internal values from MatOFF. However, see the Set command, which is the primary method for moving data to other programs. Both are detailed in Exporting Results .

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 spikes uses three environmental variables:

Command Option Description
DUMPMODE Controls the output file write method. Use APPEND or NOAPPEND to determine if any existing file is overwritten.
DUMPPATH Path for Dump command output files
DUMPTEXT This text string will be placed before each line created by the Dump spikes command.

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 the Set [SET]  command options.

See Also

Exporting Results | Found [FOU] | MatOFF History Scripts | Index [IND] | Segment [SEG] | Set [SET] | Environmental Variables

Edit

Edit a text file

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

Command Option Description
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

See Also

Axis [AX] | Environmental Variables

End

Exit the current protocol file

End terminates 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, using End in 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

See Also

ENDIF | MatOFF Scripting Language

ENDIF

Conditional END for a protocol file

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

Command Option Description
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 last Unit [UNI]  command 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

See Also

End | MatOFF Scripting Language

Erase

Clear the graphics screen

Erase clears the graphics screen. It can be used with Axis [AX] multiplot to clear the plot for a new group of graphs.

Command Option Description
erase <figure number> erase current figure or optional figure number

Example

erase

See Also

Creating, Printing and Saving Plots | Axis [AX]

ErrorLevel

Control the reporting of errors and warnings

ErrorLevel controls the reporting of errors and warnings.

Command Option Description
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 the Log [LOG]]  command. MatOFF History Scripts  can make use of the same ErrorLevel control by using the issue_message() support function.

The Makdat [MAKD]  command has a separate set of message reporting options.

Example

error serious

Turn off warnings.

See Also

Log [LOG]] | Makdat [MAKD]

Exit

Exit MatOFF and MATLAB

Exit MatOFF and MATLAB immediately, without confirmation. It is different from the Quit [QUIT]  command, which keeps MATLAB running.

When MatOFF exits, it saves the current set of layouts to the file koflay.dat.

Example

exit

See Also

Quit [QUIT] | Break | MatOFF Scripting Language | Layout Parameters for MatOFF

File [FI]

Open a new file for analysis

File opens 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 the File command is issued with no arguments, MatOFF will print the file name of the currently open file. If the File command is issued with the same name as the currently open file, MatOFF will just issue a warning message. Otherwise, the File command will close the currently open file and attempt to open the new one. To close and open files of the same name, issue the Close [CLO]  command first. A file cannot be opened unless it is a MatOFF file. Use The MatOFF Makdat Command to process Cortex files for use with MatOFF. See Importing Data  for more information.

Example

file indy

See Also

Close [CLO] | Fileerror [FILERR] | Index [IND] | The MatOFF Makdat Command | Read [REA] | Unit [UNI]

Fileerror [FILERR]

Control error handling when a data file open attempt fails

Fileerror tells MatOFF what action to take if a File [FI] command fails during the execution of script ( MatOFF Scripting Language  ) file. If a File [FI] command is issued from the command line, or with a mouse, an error message is printed on the user's screen. If a File [FI] command is issued in a script, there are three possible actions depending upon the most recent Fileerror command. The Fileerror command options are:

Command Option Description
fileerror current fileerror state is printed on the user's screen
fileerror break issue a Break command 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

The Fileerror exit form of the command is intended to be used with the Pcoff [PCOFF]  command. The Pcoff [PCOFF]  command can only used inside a batch file using the Batch command. Fileerror exit causes an abort of the current Pcoff [PCOFF]  command, which allows the batch file to continue. If Fileerror break is used and a file error occurs, then the Continue command can be used to resume processing of the protocol file.

Example

fileerror exit
batch indyunits.bat

If MatOFF cannot find a data file during a Pcoff [PCOFF]  command within the indyunits.bat file, MatOFF will move to the next batch command in that file.

See Also

Creating, Printing and Saving Plots | Analog [ANAL]

FirstDx

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

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

Command Option Description
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

FirstDx only operates on the primary analog channel.

Example

firstdx show

See Also

Creating, Printing and Saving Plots | Analog [ANAL] | Layout Parameters for MatOFF

Found [FOU]

List the sequences that matched the search criteria

Found prints 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
Quantity 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]

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

If analog data are included in any analysis, it is essential to tell MatOFF the 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 the Analog [ANAL] command, both channels are assumed to be digitized at the same rate.

Command Option Description
freq <value> value is an integer in samples/second
freq auto MatOFF will look at the data file and try to calculate an A/D frequency
freq auto <list> MatOFF will 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 tells MatOFF to use analog channel 1, and to indicate that channel 1 was recorded at a frequency of 250 Hz. The second example tells MatOFF to 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

See Also

Analog [ANAL]

GlobalIgnore [GLO]

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

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

Command Option Description
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]

Instructs MatOFF to act as if the listed event codes do not exist in the data file.

Example

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]

See Also

Sequence [SEQ]

Hair

Read a time value from a plot using the mouse

The Hair command 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 the Axis [AX] command setting.

Example

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

See Also

Axis [AX]

Heading

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

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

Command Option Description
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

See Also

Creating, Printing and Saving Plots | Text | Layout Parameters for MatOFF

Help

On-line help for MatOFF commands

The Help command 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 the Sequence [SEQ]  command.

Hide Plot

Synonym for Set plot noshow

The Hide Plot command inhibits the screen drawings (plots) when the Show [SHO]  command is given. This command is most useful during batch file operation when statistical outputs are of interest, but drawings are not. The reverse command is Show [SHO]  (a synonym for Set [SET]  plot show).

Example

hide plot
load bigjob.pro

See Also

Set [SET]

Histogram [HIS]

Control the display of a histogram of spike data

Histogram layout command controls the display of a cumulative histogram of spike data. The histogram displayed by MatOFF is based on those trials that meet all the search and display criteria. That is, all trials that would be shown if a Raster [RAS]  command is issued.Histogram values can be further restricted to specific parts of each trial using the ValidateSpikes [VALID] command. The bin sizing of the histogram is controlled by the BinWidth [BIN]  command. The MatOFF Scale  command is the same as the Histogram scale command. 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. If Histogram raw command is used, scaling is calculated from the number of counts in each bin independent of the bin width or number of trials. Histogram reference commands 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 > Segment [SEG]  command). 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.

Command Option Description
histogram show turn histogram on
histogram noshow turn histogram off
histogram on same as histogram show
histogram 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
ana2 <n> select input channel for 2nd analog, a value of 0 disables the 2nd analog
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

See Also

BinWidth [BIN] | Layout Parameters for MatOFF | Scale | Segment [SEG] | RIP (not implemented)

History

Make decisions based on entire history of behavioral data

The history command provides is a powerful method to make decisions about behavioral events. See History Scripting for details.

Command Option Description
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

See Also

Dump | MatOFF History Scripts

Index [IND]

List units available in current file

Index lists 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".

See Also

Dump | File [FI] | The MatOFF Makdat Command | Show [SHO] | Unit [UNI]

Initialize [INIT]

Reset current layout to default values

Initialize resets 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. See Layout Parameters for MatOFF section for more details.

Example

>init

See Also

Display [DISP] | Layout Parameters for MatOFF

Layout [LAY]

Choose a new layout or a layout file

Ten layouts reside in MatOFF at 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. The Layout command allows the user to select which layout is current. A new set of 10 layouts can be loaded from a file using Layout file form of the command. If the Layout file command 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 when MatOFF is exited. This file may be copied and loaded with the Layout file command. The currently selected layout can be preserved as a protocol file using the Save [SAV]  command.

Command Option Description
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.

See Also

Copy [COP] | Initialize [INIT] | Layout Parameters for MatOFF | Save [SAV] | Display [DISP]

Load [LOA]

Startup a protocol scripting file

Load reads and executes MatOFF commands from a text file. The text file is referred to as a protocol file, and usually has a .pro extension. If the PROTOCOLPATH environmental variable is set, it used to determine the directory of the requested protocol file. Files created with the Save [SAV]  command have the format of a protocol file. The protocol file STARTUP.PRO is automatically executed when MatOFF is first started. Protocol files must follow certain rules described in the section on   MatOFF Scripting Language  .

Example

load rgb

Opens the protocol file RGB.PRO and executes each MatOFF command in the file.

See Also

Break | End | Continue | Save [SAV] | MatOFF Scripting Language | Environmental Variables

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. Log always appends to any existing file. The file is placed in the default path.

Command Option Description
log file <filename> Open a file for logging. Actual logging depends on the log on command. 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 on starts 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 off is not really necessary here, since log close will also turn off logging. Log close is essential to save the data.

See Also

ErrorLevel | Environmental Variables

Ls

List directory

Ls acts like the DOS DIR directory listing command. The Directory [DIR] command is a synonym.

Example

ls ..

List contents of the current directory.

See Also

Cd | Pwd [PWD]

Makdat [MAKD]

Stops updating plot each time a parameter is changed

Makdat must be run on a CORTEX data before the data in that file can be processed by MatOFF. See The MatOFF Makdat Command.

See Also

Importing Data

ManualUpdate [MAN]

Turns off the AutoUpdate feature

ManualUpdate ends the effects of AutoUpdate [AUT]. AutoUpdate [AUT] makes MatOFF 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 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

See Also

AutoUpdate [AUT]

Map [MAP]

Start the mapping process

Usually the Show command is used to start or reprocess data after making a change to the search strategy. Show relies on context to determine where in the process sequence to begin. Map overrides the context sensitivity of Show and forces a new data mapping. The Map command is rarely used.

Example

map

See Also

Scan [SCA] | Show [SHO] | Taint

Mark [MAR]

Identify the "mark" event group for sorting and statistics

Mark is used in conjunction with the Center [CEN] command 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 the Mark specification follows the same rules as the Center [CEN] specification. The operator must be careful not to confuse event codes with the ordinal number used in the Mark specification. Thus, "mark 4" does not mean to mark code "4" in this case.

See Also

Center [CEN] | GlobalIgnore [GLO] | Sequence [SEQ] | Shift | Sort [SORT xx] | Sort [SORT xx] | Spot [SPO]

Matlab [MAT]

Switch to the MATLAB command line

Matlab leaves the MatOFF command line and returns control to MATLAB. MatOFF commands issued via the MatOFF menus will still execute properly. Return to the MatOFF command prompt by entering the Cmd command.

Example

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

See Also

Cmd

MenuPosition [MENU]

Save and load the positions of the main menus

MenuPosition save saves the current screen arrangement of the main MatOFF menus. The menu arrangement can be recalled using the MenuPosition load version of the command. The user can save many different menu layouts and choose the most convenient arrangement as needed. MenuPosition is 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

mgplx2ctx

Convert Plexon MAP data file to Cortex format

mgplx2ctx is 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 the Plexon to Cortex file conversion program: mgplx2ctx page for details. See Plexon to Cortex file conversion program: mgplx2ctx if you are using an older version of MATLAB.

Example

mgplx2ctx

See Also

Makdat [MAKD]

MWFiles

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

The 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.

MWFiles compares two sets of pulse data. Pulse (spike) data are saved each time a Show [SHO]  command is issued after the Set [SET] command 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 the currently displayed data, specified with the Segment [SEG]  command. 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 the Set [SET]  command. The MWFiles command tests any two MWU files against each other. MWU files are saved to and recalled from the directory assigned to the STATPATH Environmental Variables , if set; otherwise, the DEFAULTPATH environmental variable is used.

The commands Set [SET] MWU Show and Set [SET] MWU NoShow control 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 the Show [SHO] command 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 using Sort [SORT xx] . The first 10 trials are selected with Trials [TRI]  1-10. 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 the Trials [TRI]  81-90 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).

See Also

Segment [SEG] | Set [SET] | Environmental Variables

New plot [NEW PLO]

Generate a new graphical display based on the current MatOFF settings

New plot is a synonym of the Show [SHO]  command, except it will always make the plot in a new window. Show [SHO]  uses the current window. New plot will create multiple plots if the "display list" has more than one value. See the Show [SHO]  command for details.

Example

new plot

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

See Also

Creating, Printing and Saving Plots | Display [DISP] | Erase | MatOFF Scripting Language | Nextplot [NEX] | Old plot [OLD PLO] | Overplot [OVER] | Show [SHO]

Nextplot [NEX]

Generate a new graphical display based on the current MatOFF settings

Nextplot sets 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.

See Also

Creating, Printing and Saving Plots | Display [DISP] | Erase | MatOFF Scripting Language | Nextplot [NEX] | Old plot [OLD PLO] | Overplot [OVER] | Show [SHO]

Old plot [OLD PLO]

Generate a graphical display based on the current MatOFF settings in the current plot window

Old plot is a synonym for Show [SHO] , except it can be used to specify which graphics output window to use for display. Old plot with no parameters has the same action as Show [SHO]  with no parameters. See the Show [SHO]  command for more details. See Overplot [OVER]  for drawing twice on the same display.

Command Option Description
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).

See Also

Creating, Printing and Saving Plots | Display [DISP] | Erase | MatOFF Scripting Language | Overplot [OVER] | Show [SHO] | Nextplot [NEX] | New plot [NEW PLO]

Open

Create and open a file for writing to with the Write command

Open creates and opens a file for writing. The Write [WRI]  command moves ASCII data to that file. If a file with the same filename already exists on the disk, the file is overwritten by the Open command. Use Append to add to an existing file. See the section on Protocol scripting files ( MatOFF Scripting Language ) for more details.

Example

open stats.txt

Overplot [OVER]

Plot on top of an existing plot

Overplot plots 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. Overplot will only work properly if used on the most-recently created figure. See Show [SHO]  for 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).

See Also

Creating, Printing and Saving Plots | Display [DISP] | Erase | Old plot [OLD PLO] | Show [SHO] | New plot [NEW PLO]

Pcoff [PCOFF]

Load protocol and execute a protocol file in batch mode

The Pcoff command is used with the Batch [BAT] command. The Batch [BAT] command simulates DOS batch file processing. The Pcoff command 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> ...

Command Option Description
<protocol file> file name of a file that has a list of MatOFF commands
<data file> name of the data file to process
<unit> name of the unit to process
<pcoff param1> the value placed in the Pcoff command line replaces "$1" in the protocol file
<pcoff param2> the value placed in the Pcoff command line replaces "$2" in the protocol file

See the section on MatOFF Scripting Language   for 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 a Sequence [SEQ]  command). Also, the character string "d25" is inserted wherever parameter $2 occurs in the protocol file.

See Also

Batch [BAT] | Load [LOA] | Setenv [SETENV] | MatOFF Scripting Language

Plot [PLO]

Create plot file from the current graphics screen display

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

Command Option Description
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 the Old plot [OLD PLO]  command. The Set [SET]  command and the GRAPHICSFORMAT Environmental Variables  control the destination file and file format of the Plot [PLO]  command.

Automatic generation of plot files

The Set [SET]  plot keep command will save a plot to the hard disk each time a plot is created. Set [SET]  plot nokeep turns off this automatic process.

Naming the plot file

The Set [SET]  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 the Set [SET]  plot name <filename> with a blank filename to enable automatic naming.

Controlling the number used in automatic file naming

The Set [SET]  plot filenumbercommand 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 the Set plot name <filename> with a blank filename to enable automatic naming.

Controlling the number used in automatic file naming

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

Controlling the graphics file type that is saved to disk

The command Setenv [SETENV]  GRAPHICSFORMAT <graphics type> sets the type of graphics file save to disk. The available graphics types are:

Command Option Description
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 on Protocol scripting files ( MatOFF Scripting Language  ) for an example of how to automatically create a HTML files from plots.

Example

set plot filename best_unit
setenv graphicsformat jpeg
plot

See Also

Creating, Printing and Saving Plots | Print [PRI] | Set [SET] | Environmental Variables

Plx2ctx

Convert Plexon MAP data file to Cortex format

Plx2ctx is a stand-alone, command-line Windows program for converting Plexon ".plx" files to Cortex data files.

See the Plx2ctx page for details. If you are using a recent version of MATLAB (R13 or later), use mgplx2ctx.

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.

See Also

Makdat [MAKD]

Print [PRI]

Print the current graphics screen display

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

Command Option Description
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

See Also

Creating, Printing and Saving Plots | Plot [PLO] | Set [SET]

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. PulseChannel specifies which channel to analyze. If an unused pulse channel is specified and a Show [SHO] command is given, MatOFF will tell the user which channels have data. Also, the Index [IND] command can be used to list the available pulse channels. Note that the Makdat [MAKD] command 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 the Makdat [MAKD] "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.

See Also

Index [IND] | Makdat [MAKD]

Pwd [PWD]

Print the working directory

Pwd acts like the DOS pwd command.

Example

pwd

See Also

Cd | Directory [DIR]

Q (not implemented)

Interrupt the current process or calculation

Many MatOFF processes are time-consuming. Q allows the user to interrupt a process. Q will interrupt a protocol file with prejudice.

Example

show
q

Regardless of where MatOFF is in the Show [SHO]  process, the Q will interrupt the process and return control to the console.

See Also

Break

Quit [QUIT]

Exit MatOFF and MATLAB

Quit exits MatOFF, but keeps MATLAB running. It is different from Exit, which terminates MATLAB.

When MatOFF exits, it saves the current set of layouts to the file koflay.dat.

Example

quit

See Also

Exit | Quit [QUIT] | Save [SAV] | Layout Parameters for MatOFF

Raster [RAS]

Control display of spike rasters

The Raster layout 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 the Mark [MAR] command). Plus signs indicate when in the trial a spot code was encountered (see the Spot [SPO]  command). 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 various Sort [SORT xx]  commands control the order in which the rasters are displayed. The Set [SET]  sort command can reverse that order.

Command Option Description
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

See Also

Layout Parameters for MatOFF | Mark [MAR] | Spot [SPO] | Trials [TRI] | Sort [SORT xx] | Set [SET]

Read [REA]

Examine or save raw data in current data file

Read displays 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 Description
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 in GlobalIgnore [GLO]. 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 (see SourceTrials [SOU] ). 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 the GlobalIgnore [GLO] list will not be included in the output file.

See Also

Dump | Exporting Results | File [FI] | GlobalIgnore [GLO] | Sequence [SEQ] | Set [SET] | Unit [UNI]

RIP (not implemented)

Control display of a reciprocal interval plot of spike data

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

Command Option Description
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

See Also

Histogram [HIS] | Layout [LAY]

Save [SAV]

Create a protocol file with current MatOFF settings

The Save command creates a protocol file. The file it creates is a snapshot of all the current settings. Execution of the saved file using the Load [LOA] command will return MatOFF to the same state it was in when the Save command was issued. The graphical layout settings can be saved independently of the other settings depending upon with form of the Save command is used. Save uses the default extension of .PRO. If the PROTOCOLPATH environmental variable is set, Save uses that path to determine the target directory.

Command Option Description
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.

See Also

Load [LOA] | Setenv [SETENV]

Scale

Set the vertical range of the histogram display

Whenever a histogram is specified in the current layout, the current value of Scale is used to set its vertical range in impulses per second (ips). Scale Auto instructs MatOFF to use the maximum histogram bin value to set the scale range. The Scale command is the same as the Histogram [HIS]  scale command.

Command Option Description
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

Instruct MatOFF to 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

See Also

BinWidth [BIN] | Histogram [HIS] | Window [WIN]

Scan [SCA]

Start the scan process

The Show, Old plot [OLD PLO] and New plot [NEW PLO] commands 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. The Scan command is used to trigger the processing of History scripting.

Example

scan

See Also

MatOFF History Scripts | Map [MAP] | Show [SHO]

SecondDx

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

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

Command Option Description
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
 

SecondDx only operates on the primary analog channel (see AnalogChannel command).

Example

seconddx show

See Also

Analog [ANAL] | Creating, Printing and Saving Plots | Layout Parameters for MatOFF | Trials [TRI]

Segment [SEG]

Choose the trial time range for certain statistical tests

There are several statistical calculations which can be made by MatOFF. 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 the Segment command. 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 the Axis [AX] command. 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 the Dump segments command, or the Set [SET]  segmentstats command.

Command Option Description
segment show display segments 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 if Axis [AX] 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 the Show command, spike counts for each trial, and descriptive statistics for these two window periods, will be listed on the console.

See Also

Axis [AX] | Dump | MWFiles | Set [SET]

Sequence [SEQ]

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

Sequence is one of the most important commands in MatOFF. 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 the GlobalIgnore [GLO] command.

Example

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

MatOFF will 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, MatOFF tries to be as "open-minded" as possible when it comes to entering the Sequence command. The above sequence can be entered with:

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

See Also

Center [CEN] | GlobalIgnore [GLO] | Mark [MAR] | Span [SPA] | Spot [SPO]

Set [SET]

Control a variety of program functions

General operations of the Set command

The Set command is a powerful method for saving data after each search. This is the primary method MatOFF uses for exporting data to other programs. Set is also used to enable or disable some built-in features of MatOFF. When used for saving data, the Set command prints or saves onto the disk each time a Show, Old plot [OLD PLO], or New plot [NEW PLO] command is issued. Thus, the Set command 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. See Exporting Results for important details on using the Set command. Dump Sets can be used to display the status of many set "processes".

The Set commands for moving data to the screen have the general form:

Command Option Description
set <process> show Enable automatic data dump to screen
set <process> noshow Disable automatic data dump to screen
The Set commands for moving data to the hard disk have the general form:
Command Option Description
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
Command Option Description
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 the Sort [SORT xx] option
mwu Spike counts. Can be used with the MWFiles command 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 Set command for controlling other MatOFF features
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 returns MatOFF to normal operation.
set segmentstats pcoff
set segmentstats absolute
Set segmentstats pcoff will make MatOFF scale nearly all x-axis values to the range of 0 to 599. This range provide backwards compatibility with the legacy PCOFF system. Set segementstats absolute returns MatOFF to normal operations, where x-axis units are in milliseconds.
set print color Enable color printing
set print nocolor Print only in black and white

Output formats of ASCII files

The ASCII files generated by the Set command have a format that can be controlled using special format files. See Exporting Results  for 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 the Set <option> Keep form of the instruction, MatOFF generates files with numeric names. For example:

set histogram keep

This statement will generate files named 0.HST, 1.HST, etc., incrementing each time a new Show [SHO] command 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 with Set <process> Name <filename>. When this form of the Set command is used, every Show [SHO] command 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 [SHO] , unless the Set <process> Append command is used or the user renames the output file for the process just before each Show [SHO] command. To turn off the append mode and return to the default overwrite mode, use the Set <process> NoAppend command. After appending to a file, use the Close [CLO]  append command to close all files that have been opened with the Set <process> Append command. To return to the default (filenumber) naming use the Set <process> Name command with no file name. After writing to a file with Set <process> Append, use Close [CLO]  append to close it. Files written with Set <process> NoAppend are closed automatically. Here are some examples.

Example 1, change the name of the output file before each Show [SHO]  command.

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 the Dump Set command.

Specific Set Processes

Set epochstats lists 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 the Trials command) 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 an Environmental variable. See Exporting Results for 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

 

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 .7

Set events lists the specific sequence of events for each trial that matched the sequence. A file created with the by Set events keep can 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 81 15 16 41
3 81 15 16 41
4 81 15 16 41
5 81 15 16 42

Set segmentstats lists trial-by-trial information for the data that fall within segment A and within segment B. See the Segment command 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 the Trials command) 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. See Exporting Results for 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 the Sort [SORT xx] command. 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 the Trials [TRI] command) 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. See Exporting Results for more information on formatting the output. The default file extension for disk files is .SRT.

Example

ana2 size 30

Setenv [SETENV]

Modify environment

MatOFF has environmental variables that can be set with either the DOS SET command or the MatOFF Setenv command. Each environmental variable controls a different aspect of MatOFF behavior.

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. See  Axis [AX] command
dumplabel " text inserted in the header of  Set [SET] <process> keep/show commands
dumpmode 'NOAPPEND' set to APPEND for appending spike times in the  Dump spikes command
dumppath '.' default location to place files created with  Dump command
dumptext " text inserted before each line of data in  Dump spikes  command
editor 'c:\windows\notepad.exe default editor to open when editing text files
formatpath 'default.evc' file that describes each event code. used by Makdat when listing events
graphicsformat '.' default location to find .fmt format files
layoutpath 'png' graphics file format used with  Plot [PLO] command or  Set [SET] plot keep. See  Plot [PLO] command
makdat '' default option list for  Makdat [MAKD] command
makdump '' If a file is defined here, all  Makdat [MAKD] command debugging information will be dumped to that file.
metachar1 '$' prefix for protocol file replacement parameters with  Pcoff [PCOFF] command
metachar2 '%' prefix for protocol file replacment parameters in a metafile.  See Protocol scripting files MatOFF Scripting Language  .
metapath '.' default location to find metafiles
plotpath '.' default path for  Plot [PLO] command
protocolpath '.' default location to find protocol files. See Protocol scripting files (  MatOFF Scripting Language  ) and the Load [LOA] command.
remapfile 'default.rmp' default spike mapping file for  Makdat [MAKD] command
statpath '.' default location to put statistical output files
maxinputtrials 5000 Makdat [MAKD] will quit after this number of trials in each file. This command is used only for debugging.
maxtrialsfound 250 Makdat [MAKD] will stop looking for a sequence match after this number of trials.

Example

setenv datapath c:\data\

See Also

Environmental Variables | MatOFF Scripting Language

Set histogram

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

Shift

Reposition time 0 on the x axis

All data on the graphics display are aligned on the centering code. With a Shift> value of 0, the centering code is in the center of the time scale. The Shift command 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 the left. 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 milliseconds before the last code, and ending 1 second after the last code.

See Also

Center [CEN] | CenterLine [CEN] | Sequence [SEQ] | Window [WIN]

Show [SHO]

Generate a graphical display based on the current MatOFF settings

Show creates 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 last Show command. For example, if the search sequence was modified since the last Show command, MatOFF will search the data again for matching sequences, then do all necessary processing to plot the current data. Show is also used to display the status of certain MatOFF parameters. Many of the same parameters can be displayed using the associated command with no parameters. For example the Unitname command (with no parameters) is the same as the Show unitname command.

Command Option Description
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

The Show command with no parameters is the MatOFF "go" command. It tells MatOFF to build a plot from the currently open file using all the parameters that have been specified. Normally, Show is used to generate a single plot. If the user is making multiple plots on a page (see the multiplot option of the Axis command) one Show command is used for each plot on the page.

It is possible to generate a whole group of plots with one Show command. MatOFF is 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. The Layout command selects which layout is currently selected for editing. But, regardless of which layout is currently selected, the Display command controls which layout to use for plotting the data. The Display command can specify a list of layouts (layout list), and Show will create one plot for each layout. This way, you can get several views of the same data with one Show command. With the development of powerful scripting (see MatOFF Scripting Language) the use of layout lists is less common.

In addition to creating a plot, the Show command tells MatOFF to generate any statistical and other numerical data that have been specified by the Set <process>commands.

Show Plot is a special variant of the Show command. It is a synonym for Set plot show. Set plot noshow inhibits screen plots and is used for batch files that save results to disk and are only slowed down by the screen display. Set plot show returns MatOFF to normal operation.

Each plot is a numbered MATLAB window. Numbering begins at 11. (The first 10 windows are reserved for menus.) Show always uses the current window. If a display list is used, Show will increment by one for each new plot in the display list. Show can be used to put multiple plots on the current page as described above. The command New plot is a synonym for Show, except it will find an unused plot number and create a new windows before plotting. The command Erase will erase the current plot window. If you use only one plot window for all plots, use Erase to 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. The Old plot command 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].

See Also

Creating, Printing and Saving Plots | Display [DISP] | Erase | MatOFF Scripting Language | Old plot [OLD PLO] | Overplot [OVER] | Set [SET] | Nextplot [NEX]

Smo2 (not implemented)

Control display of smoothed second analog data

Smo2 layout command controls the display of smo2ed second analog for the first analog trace.

Command Option Description
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

See Also

Creating, Printing and Saving Plots | Ana2 [ANA2] | Layout Parameters for MatOFF | Set [SET] | Trials [TRI]

Smooth (not implemented)

Control display of smoothed analog data

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

Command Option Description
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

See Also

Creating, Printing and Saving Plots | Analog [ANAL] | Layout Parameters for MatOFF | Trials [TRI]

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.

Command Option Description
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 the  Axis [AX]  command for details.

2) Sorting based on analog data use only the first analog channel.  See the  Analog [ANAL]  command 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 [RAS] .  The other way affects all sorted traces: using the  Set [SET]  sort reverse command.

Individual descriptions and examples of the  Sort options:

Sort center sorts 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 Center will 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 Delta measures 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 epoch counts 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 history use 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 integral integrates 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 maximum uses 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 minimum is like Sort maximum, but uses the minimum analog value that occurs between two time values.

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

Sort peak requires analog data.  MatOFF finds 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 pit is like Sort peak, except that MatOFF finds the lowest analog value between the two time markers.

Sort pulse counts 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 the Sort pulse command places markers on the plot to indicate the sort pulse interval:

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

Sort time uses 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 zero requires analog data. MatOFF measures 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

MatOFF searches the current unit for code sequences that match a predefined sequence. The default SourceTrials value is 1-200, which indicates that MatOFF will 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. The SourceTrials command can be used to skip bad data in a unit or to select different segments of the data without having to use the  Trials [TRI]  command.

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.

See Also

Trials [TRI]

Span [SPA]

Define the time window for scanning
Span is 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 by  Span.  Span can be turned off with the  Span all command.
Command Option Description
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.

See Also

Sequence [SEQ] | Window [WIN]

Spot [SPO]

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

The user lists a set of event codes with the Spot command. 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.  Center [CEN]  and  Mark [MAR]  use ordinal numbers referring to one of the sequence elements. The Spot command refers to the actual code values.

See Also

Center [CEN] | GlobalIgnore [GLO] | Mark [MAR] | Sequence [SEQ]

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. 

Command Option Description
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.

See Also

Scan [SCA] | Map [MAP] | Show [SHO]

Text

Control the placement of text on the graphical display

Each of the ten MatOFF layouts can have up to 9 lines of text associated with the graphical display. These 9 lines are independent of the  Heading . The Text command 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. See  Layout Parameters for MatOFF  for more information on x and y positioning.  With Text frame on, the text is positioned relative to the  Axis [AX] .  With Text frame off, the text is positioned relative to the entire page.  

Command Option Description
text show / noshow Turn all text 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 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

Command Purpose
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 xpos x Set only the x position of the beginning of the current text line.
text string THIS IS AN EXAMPLE TEXT STRING Write some text
text size x Set the font size of the text.  The value of x is in points.
text on
show 
Make sure that text line will show up

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

See Also

Creating, Printing and Saving Plots | Copy [COP] | Heading | Layout [LAY] | Layout Parameters for MatOFF

Thin

Reduce the number of spikes by some factor

Thin is a  Makdat [MAKD]  list file parameter that reduces the frequency of occurrence of an event or spike. See the  Makdat [MAKD]  command for details.

Time [TI]

Report time-of-day and elapse time

MatOFF will report the current time-of-day and the elapse time since MatOFF was 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.

See Also

Date [CAL]

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. TrialFunction selects which trials will be displayed; the same selected trials are also used in statistical analysis, histograms, etc. TrialFunction command enables the user to display trends in sorted data more dramatically and with a smaller number of rasters.

The TrialFunction selects 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

MatOFF starts 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...

See Also

Trials [TRI] | SourceTrials [SOU]

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 the  Sequence [SEQ] . Trials selects 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 the  Sort [SORT xx]  command and the  Set [SET] sort reverse command.  When a sort is in effect the trial number refers to a trial's position after the trials have been sorted.

The list used in the Trials command 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.

See Also

TrialFunction [TRI] | SourceTrials [SOU] | Sort [SORT xx] | Set [SET]

Trim

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

Trim is a  Makdat [MAKD]  list file parameter that removed all but the first occurrence of an event or spike in each trial. See the  Makdat [MAKD] command 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 of MatOFF ASCII dumps. If no path is specified, the DEFAULTPATH environmental variable is used.

Example

type c:\pcoff\andy\andy.pro

View the file "andy.pro".

See Also

Directory [DIR] | Save [SAV] | Environmental Variables

Unit [UNI]

Identify which unit in the data file to analyze

Data sets within a data file are broken into units. Unit command identified which unit to analyze. Use the  Index [IND]  command to see which units are available in a file.  The Unit command 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.

See Also

File [FI] | Index [IND] | Read [REA]

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.

Command Option Description
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

See Also

Histogram [HIS] | MatOFF History Scripts

Version [VER]

Print version number on screen

Display the current version number of MatOFF.

Example

version

Walk [WALK]

Pause printing to screen during long printouts

Certain MatOFF commands, e.g. Read, can produce long printouts.  Walk will make MatOFF pause screen printouts at regular intervals.   

Command Option Description
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 the Why command to see if there is some obvious reason the data were not plotted.

Example

no trials found
why
Data file appears to be empty.

See Also

Getting Started with MatOFF

Window [WIN]

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

The Window command 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

Instructs MatOFF to display 3 seconds of data for each trial.

See Also

BinWidth [BIN] | Center [CEN] | Shift

Write [WRI]

Write ASCII data to a file opened with the Open or Append command

MatOFF can create ASCII (text) files.  Open and Append are used to create a new ASCII file or append to an existing one.  Once a file is open, the Write command is used to insert text into the file.  Text is entered line-by-line.  All text after the Write command (after skipping any blank spaces) is written to the ASCII file. Note that HTML (web pages) can be created with these commands.  The section on Protocol scripting files discusses ASCII files greater detail.

Example

write print $2,tabular

Put an ASCII string in the text file. $2 refers to a replaceable parameter.  See  MatOFF Scripting Language   for the use of replaceable parameters.

See Also

Append | Close [CLO] | Open | Exporting Results | MatOFF Scripting Language

XY [XY]

Control the XY plot of the two analog channels

The XY command 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. 

Command Option Description
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:

Command Option Description
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