/* ophys commandCATEGORY: ABF InspectionUSAGE: getTTLDisplay every TTL and indicate which are active in the protocol of the currently-loaded ABF.`setTTL` can be used to update the TTL used by evoked stats as an alternative to clicking through the settings dialogue.*/

/* ophys commandCATEGORY: ABFGraph OperationsUSAGE: DetectEventsRun event detection (same thing as clicking the _run current_ button in the CJFmini section of the ABF Graph)*/

/* ophys commandCATEGORY: ABFGraph OperationsUSAGE: extractAllSweepsRun `extractData` on every sweep of the currently-loaded ABF.*/

/* ophys commandCATEGORY: ABFGraph OperationsUSAGE: extractdataCreates a new worksheet containing the data between the markers.This command is the same as clicking the "extract data" button on the ABF graph.To run this on several consecutive sweeps, use the `extractSweeps` or `ExtractAllSweeps` commands.*/

/* ophys commandCATEGORY: ABFGraph OperationsUSAGE: MarkerStatsRun marker stats (same thing as clicking the _M Stats_ button in the marker stats section of the ABF Graph)*/

/* ophys commandCATEGORY: ABFGraph OperationsUSAGE: memtestThis command runs the memtest analysis sequence on the currently-loaded ABF.Output is one row per sweep.To reduce output to a single row (suitable for comparison across cells) follow this command with `raved` and `rave`, or use the `memtestave` command.*/

/* ophys commandCATEGORY: ABFGraph OperationsUSAGE: memtestaveThis command calls `memtest` then forces the first row of the output sheet to contain the average of all rows of the same column.This is one way of reducing several sweeps of membrane tests into a single number suitable for comparison across cells.An alternative to this command is `memtest` followed by `raved` and `rave`.*/

/* ophys commandCATEGORY: ABFGraph OperationsUSAGE: pave [first sweep] [last sweep]Plot a sweep representing the average of all sweeps between (and including) the given sweep numbers.If the last sweep is `-1` it will average all sweeps between the first given sweep and the end of the ABF.EXAMPLE: `pave 10 20` _display an average of sweep 10 through sweep 20_EXAMPLE: `pave 10 -1` _display an average of sweep 10 and every subsequent sweep_*/

/* ophys commandCATEGORY: ABFGraph OperationsUSAGE: pavetime [start time] [stop time]Plot the average of all sweeps between the two given times (in minutes).*/

/* ophys commandCATEGORY: ABFGraph OperationsUSAGE: phaseplotRun this on a current-clamp sweep with the markers shown.This command gets the data between the markers and creates a workbook with  voltage (V) vs velocity (dV/dT)*/

/* ophys commandCATEGORY: ABFGraph OperationsUSAGE: prave [rangeNumber]USAGE: prave [range number] [range type]Plot the average sweep from the specified range in the rave dialogue (set by `raved`)EXAMPLE: `prave 1` - plot the mean sweep from the first range defined by `raved`EXAMPLE: `prave 1 bySweep` - plot each individual sweep in the first range defined by `raved`*/

/* ophys commandCATEGORY: ABFGraph SettingsUSAGE: alignByTag [tag] [minutes]Automatic tag alignment causes output sheets to be automatically shifted in time so the first ABF tag whose comment contains the given string will occur at the given time.EXAMPLE: `alignByTag` _disable automatic tag alignment_ EXAMPLE: `alignByTag TGOT 10` _tags containing 'TGOT' will be aligned to 10 minutes_ */

/* ophys commandCATEGORY: ABFGraph SettingsThis command enables, disables, or sets the range for automatic baseline subtractionEXAMPLE: `autobase on`EXAMPLE: `autobase off`EXAMPLE: `autobase 500 600`EXAMPLE: `autobase wks`*/

/* ophys commandCATEGORY: ABFGraph SettingsUSAGE: getpathCopy the path of the currently-loaded ABF to the clipboard.This is ideal for quickly loading an ABF in clampfit.*/

/* ophys commandCATEGORY: ABFGraph SettingsUSAGE: gsOpen the graph settings dialog.This is the same as clicking the "settings" button.*/

/* ophys commandCATEGORY: ABFGraph SettingsUSAGE: LPF [filter type] [size]Customize low-pass filter settings from the command window.EXAMPLE: `LPF Gaussian 5`EXAMPLE: `LPF FFT 1`EXAMPLE: `LPF Exponential 2`EXAMPLE: `LPF Off`EXAMPLE: `LPF On`EXAMPLE: `LPF wks` applies LPF settings from the active worksheet to the ABFGraph*/

/* ophys commandCATEGORY: ABFGraph SettingsUSAGE: m1 [time]moves marker 1 (the left marker) to a time point on the sweep (in milliseconds).When placing both markers, `markerSpan` may be faster.*/

/* ophys commandCATEGORY: ABFGraph SettingsUSAGE: m2 [time]moves marker 2 (the right marker) to a time point on the sweep (in milliseconds).When placing both markers, `markerSpan` may be faster.*/

/* ophys commandCATEGORY: ABFGraph SettingsUSAGE: miniConfigUSAGE: miniConfig [parameter] [value]This command sets event detection parameters from the command window.Run `miniConfig` without arguments for usage information.*/

/* ophys commandCATEGORY: ABFGraph SettingsUSAGE: minipUSAGE: minip wksUSAGE: minip wks-silentUSAGE: minip save [name]USAGE: minip load [name]USAGE: minip load-silent [name]USAGE: minip del [name]USAGE: minip listLaunch the CJFmini settings window (to set parameters for event detection).Use `minip wks` to load the event detection paramaters used to generate data of the currently-selected output sheet.Saving and loading settings: If you frequently hop between settings (e.g., analyzing downward and upward events in the same file) it is useful to save and load cjfmini settings from the command window.A few special save/load commands exist: `minip del *` deletes all user defined parameter sets with project scope via single command.*/

/* ophys commandCATEGORY: ABFGraph SettingsUSAGE: modifyNamesUSAGE: modifyNames [group]This command appends a group name to all output workbooks.Run this after loading a new ABF but before performing any analysis which outputs a workbook.People usually use this command to define the groups most often directly compared to one another (less-frequently-compared groups are organized by folders).Note that in the `gs` dialog the names appended to output workbooks are referred to as _tags_.Do not be confused with the names appended to worksheets which are also called tags.`modifyNames` stets the names of workbooks, while `modifyTags` sets the names of worksheets.Use of `modifyTags` is discouraged.EXAMPLE: `modifyNames young;`EXAMPLE: `modifyNames aged;`EXAMPLE: `modifyNames tatNeg;`EXAMPLE: `modifyNames tatPos;`*/

/* ophys commandCATEGORY: ABFGraph SettingsUSAGE: modifyTagsUSAGE: modifyTags [group]This command changes modifies the output tags in the global settings dialog without ever exposing the dialog to users.In contrast with commands like `AddTag` and `ChangeTags` which modify _existing_ sheet names, this command configures how _new_ sheets will be named when they are created.The "tag" (the second half of a sheet name separated from the base name by a period) is set with this command, or removed if no argument is given.EXAMPLE: `modifyTags aged;` _turns `_MT` into `_MT.aged` (and `_eStats.aged`, `_mStats.aged`, etc.)_EXAMPLE: `modifyTags;` _removes all tags from output sheet names, reverting to `_MT`, `_eStats`, etc._*/

/* ophys commandCATEGORY: ABFGraph SettingsUSAGE: minip wksRun this command on an active output sheet to apply its autobase settings to the ABFGraph*/

/* ophys commandCATEGORY: ABFGraph SettingsUSAGE: setmarks [time 1] [time 2]USAGE: setmarks epoch [epoch index]USAGE: setmarks epoch [epoch index] [padding]Move markers to specific times or around an epoch.EXAMPLE: `setmarks 10 100` _sets markers at 10 ms and 100 ms_EXAMPLE: `setmarks epoch 2` _sets markers around the third epoch_EXAMPLE: `setmarks epoch 2 10` _sets markers around the third epoch with 10 ms padding_EXAMPLE: `setmarks firststep` _sets markers around the first epoch where command deviates from holding_EXAMPLE: `setmarks firststep 10` _same as before, with 10 ms padding_*/

/* ophys commandCATEGORY: ABFGraph SettingsUSAGE: setMarksEpoch [epoch]USAGE: setMarksEpoch [epoch] [padding]Place markers around the given epoch (zero-indexed).*/

/* ophys commandCATEGORY: ABFGraph SettingsUSAGE: setMarksIndex [index 1] [index 2]Place markers at two sweep index positions (not millisecond positions).This function is required because setmarks uses floating point math.For example, setmarks is incapable of setting markers to index 2350*/

/* ophys commandCATEGORY: ABFGraph SettingsUSAGE: setmarks [index 1] [index 2]Place markers at two sweep index positions (not millisecond positions)*/

/* ophys commandCATEGORY: ABFGraph SettingsUSAGE: setTTL [digital out number]This command can be used to update the TTL used by evoked stats as an alternative to clicking through the settings dialogue.*/

/* ophys commandCATEGORY: AutomationUSAGE: activateByLongName [longName]Raises the workbook or graph in the current folder whose long name matches that given (cap-insensitive).This can be used to switch between output sheets and ABFGraph windows when scripts use sheet-specific commands (like "getcols") or ABFGraph-specific commands (like "m1" and "m2").*/

/* ophys commandCATEGORY: AutomationUSAGE: activateLastBookSheetRaises the most recently updated output workbook/worksheet, even if they are in another folder.This command is intended to be used when scripting to raise the output worksheet to commands like "getcols" after an analysis is finished and the ABFGraph may be selected.*/

/* ophys commandCATEGORY: AutomationUSAGE: cjfloop [first iterator] [last iterator] "commands to run"Run a command (wrapped in double-quotes) for each column in the given range.EXAMPLE: A number sign (#) in the command will be replaced with the iterator.EXAMPLE: **WARNING:** If iterating columns, remember that columns indices in Origin are base 1 (index value of first column is 1). EXAMPLE: `cjfloop 3 5 "col(#) = col(#) * 2"` _double the value in columns C, D, and E_*/

/* ophys commandCATEGORY: AutomationUSAGE: ListABFs [-all] [SearchString_protocolName]USAGE: ListABFs [-byTag] [SearchString_TagContents]ListABFs displays a list of ABFs and protocols associated with the ABF currently loaded in the ABFGraph window.By default only ABFs with the same parent are displayed, and the SearchString, if present, is used to filter results based on protocol name.Optional user flags (-all, -byTag) can be used to change defaults to list all cells in active folder and to use search string to search within ABF tags, respectively. Flags can be used alone or togehter, and in any order. Search string if present, must always be the last paramater entered.EXAMPLE: `ListAbfs` lists all ABFs with the same parentEXAMPLE: `ListABFs -all` lists all ABFs in the folderEXAMPLE: `ListABFs 0201` lists all ABFs with the same parent with a protocol containing "0201"EXAMPLE: `ListABFs -all 0201` lists all ABFs in the folder with a protocol containing "0201"EXAMPLE: `ListABFs -byTag TGOT` lists all ABFs in the folder with any tag containing the string "TGOT"*/

/* ophys commandCATEGORY: AutomationExample: RunOnCells "nextAbfProtocol 0110; MarkerStats;"Modifynames, setpath, then run the given command on every parent ABF.Parent ABFs are identified from memtests located in an adjacent folder.*/

/* ophys commandCATEGORY: Column OperationsUSAGE: addx [distance]USAGE: addx [distance] [column] [offset]Replaces the first column of the selected worksheet with an ascending series of numbers.If an argument is given, each number is multiplied by the argument.EXAMPLE: `addx 100` _fills the first column with 100, 200, 300..._ EXAMPLE: `addx 10 0 -110` _fills the first column with -110, -100, -90, -80..._ */

/* ophys commandCATEGORY: Column OperationsUSAGE: ZeroOffsetMaxWhen run with a evenly-sampled column selected (e.g., output of ExtractData), this command adjusts the offset time so the peak value occurs at time zero.*/

/* ophys commandCATEGORY: CPHUSAGE: byEventCPH [startTime] [stopTime]USAGE: byEventCPH [startTime] [stopTime] [sheetsMatching]Calculate the CPH for amplitude (Amp) and interevent interval (ii) as described on "byEvent" sheets.Only events within the supplied time range (in minutes) are included.This command may be run multiple times for multiple time ranges.EXAMPLE: `bcph 5 10` - Calculates CPH for events from 5-10 minutes only for the selected byEvent sheetEXAMPLE: `bcph 5 10 _byEvent` - Calculates CPH for events from 5-10 minutes from events across all byEvents sheets*/

/* ophys commandCATEGORY: Data LinkingActivates the link target workbook.*/

/* ophys commandCATEGORY: Data LinkingUSAGE: ActivateLinkTargetActivates workbook indicated as linkTarget, if it exists.Alias is `alt`.*/

/* ophys commandCATEGORY: Data LinkingUSAGE: LinkData [column]Links the specified column with that previously defined using `SetLinkTarget`.If `SetLinkTarget` was not run, will link data to a `LinkedData` workbook / `Main` worksheet.Alias is `ld`.**Recommendations:**EXAMPLE: Always link data to a workbook named `LinkedData`EXAMPLE: To separate different kinds of data:EXAMPLE: * Use `SetLinkTarget` to indicate where new linked data will goEXAMPLE: * Target multiple `LinkedData` workbooks in different foldersEXAMPLE: * Target multiple named worksheets in the `LinkedData` workbookEXAMPLE: `LinkData B`*/

/* ophys commandCATEGORY: Data LinkingUSAGE: masterLink [bookMatch] [sheetMatch] [columnMatch]Create a new workbook filled with columns linked to the matching source columns.**Examples**EXAMPLE: `masterLink "MarkerStats.Ep." "_Rave" "r1_"` _creates a new workbook containing linked `r1` output columns of rave sheets_*/

/* ophys commandCATEGORY: Data LinkingUSAGE: masterLinkRave [bookMatch]A simple version of `masterLink` just for creating workbooks of rave data.The rave range 1 column is always used.**Examples**EXAMPLE: `masterLinkRave "MarkerStats.Ep."`*/

/* ophys commandCATEGORY: Data LinkingUSAGE: pastelink [column index] [update method]Pastes a column (set using the `copyLink` command) into the selected column (or one identified by an argument).If the update method argument is "manual" the link will not auto-update.Alias for this command is `pl`.*/

/* ophys commandCATEGORY: Data Linking`SetLinkTarget`, `SetLinkTarget [column]`Sets the active worksheet (and optionally a column) as the target for future `LinkData` commands.Alias is `slt`.EXAMPLE: `SetLinkTarget` - sets the active worksheet as the targetEXAMPLE: `SetLinkTarget D` - sets the active worksheet column D as the target*/

/* ophys commandCATEGORY: Graph Axis ManipulationUSAGE: autoxUSAGE: autox [padding]Automatically adjusts the limits of the X axis to fit the data.Optionally an additional padding is added.EXAMPLE: `autox` _automatically scales X axis to fit data_ EXAMPLE: `autox 10` _fit X to data, then zoom out 10 units on each side_ */

/* ophys commandCATEGORY: Graph Axis ManipulationUSAGE: autoyUSAGE: autoy [padding]Automatically adjusts the limits of the Y axis to fit the data.Optionally an additional padding is added.EXAMPLE: `autoy` _automatically scales Y axis to fit data_ EXAMPLE: `autoy 10` _fit Y to data, then zoom out 10 units on each side_ */

/* ophys commandCATEGORY: Graph Axis ManipulationUSAGE: axisPan [axis] [amount]Pan the axis for the selected graph layer.This is similar to holding down Z and click-draging, but you can be confident you are only panning one axis at a time.EXAMPLE: `axisPan x 5` _pans the X axis to the right 5 units_ EXAMPLE: `axisPan y -25` _pans the Y axis down 25 units_ */

/* ophys commandCATEGORY: Graph Axis ManipulationUSAGE: axisSet [axis] [lower] [upper]USAGE: axisSetSet the axis range for the selected graph layer.This is a command window alternative to double-clicking the graph to manually define axis limits.EXAMPLE: `axisset x 5 15` _sets horizontal axis to span from 5 to 15_ EXAMPLE: `axisset y -25 5` _sets vertical axis to span from -25 to +5_ EXAMPLE: `axisSet` _shows current axis limits_*/

/* ophys commandCATEGORY: Graph Axis ManipulationUSAGE: axisSpan [axis] [span]Zoom an axis (x or y) so its axis limits are at the given span amount.The center of the axis will not change.Use this after autox or autoy to ensure your data is centered (as an alternative to cscale, which won't work if there's a large shift in the data)EXAMPLE: `axisSpan x 10` _zooms the X axis so it spans 10 units without changing the center_ */

/* ophys commandCATEGORY: Graph Axis ManipulationUSAGE: setx [layer] [lower] [upper]Manually set the horizontal axis limits for a graph of the given layer.This is an alternative to `axisSet` which acts on the currently selected graph layer.*/

/* ophys commandCATEGORY: Graph Axis ManipulationUSAGE: sety [layer] [lower] [upper]Manually set the vertical axis limits for a graph of the given layer.This is an alternative to `axisSet` which acts on the currently selected graph layer.*/

/* ophys commandCATEGORY: Graph MarkupUSAGE: hline [value on the vertical axis]Draw a horizontal line at a given point on the vertical axis*/

/* ophys commandCATEGORY: Graph MarkupUSAGE: hmark [y] [x1] [x2]Draw a horizontal line between two X positions at a specified Y locationEXAMPLE: `hmark 50 10 15` _Draw a horizontal line between 10 and 15 minutes placed at Y=50_*/

/* ophys commandCATEGORY: Graph MarkupUSAGE: hSpan [y1] [y2]USAGE: hSpan [y1] [y2] [colorIndex]Add a horizontally-infinite rectangle to shade the range between two vertical positions on the active graph.EXAMPLE: `hspan 20 25` _shades the region between Y=20 and Y=25_EXAMPLE: `hspan 20 25 3` _shades the region between Y=20 and Y=25 using a different color_*/

/* ophys commandCATEGORY: Graph MarkupStyles the selected graph using settings typical for our laboratory.This command changes axis tick label size, axis tick length, axis line width, axis title font size, legend font size, symbol size, and sets display scaling to fixed at 1.*/

/* ophys commandCATEGORY: Graph MarkupRuns `styleGraph` on every graph of the active page*/

/* ophys commandCATEGORY: Graph MarkupUSAGE: vline [value on the horizontal axis]Draw a vertical line at a given point on the horizontal axis*/

/* ophys commandCATEGORY: Graph MarkupUSAGE: vlines [x1] [x2] [x3]...Draw an arbitrary number of vertical lines at the given X positions**Example:**EXAMPLE: `vlines 7 9 12 14`*/

/* ophys commandCATEGORY: Graph MarkupUSAGE: vmark [x] [y1] [y2]Draw a vertical line between two Y positions at a specified X locationEXAMPLE: `vmark 0 -70 40` _Draw a vertical line between -70 and +40 placed at X=0_*/

/* ophys commandCATEGORY: Graph MarkupUSAGE: vSpan [x1] [x2]USAGE: vSpan [x1] [x2] [colorIndex]Add a vertically-infinite rectangle to shade the range between two horizontal positions on the active graph.EXAMPLE: `vSpan 5 10` _shades the region between X=5 and X=10_EXAMPLE: `vSpan 5 10 3` _shades the region between X=5 and X=10 using a different color_*/

/* ophys commandCATEGORY: Graph ScalingUSAGE: centModify properties of every graph layer in the selected graph window to use centimeter units.`inch` is a similar command.*/

/* ophys commandCATEGORY: Graph ScalingUSAGE: cscale [laer to copy from] [layer to copy to]When run with a graph object, this command copies the scale dimensions (axis limits) from one layer and pastes them onto another layer.Similar to `CSize`.EXAMPLE: `cscale 1 2;` _copies the axis limits of layer 1 and pastes them onto layer 2_*/

/* ophys commandCATEGORY: Graph ScalingUSAGE: csize [laer to copy from] [layer to copy to]When run with a graph object, this command copies the dimensions (size of the graph on the page) from one layer and pastes them onto another layer.Similar to `CScale`.EXAMPLE: `csize 1 2;` _copies the dimensions of layer 1 and pastes them onto layer 2_*/

/* ophys commandCATEGORY: Graph ScalingUSAGE: inchModify properties of every graph layer in the selected graph window to use inch units.`cent` is a similar command.*/

/* ophys commandCATEGORY: Graph ScalingUSAGE: scale [layer]Display information (namely axis limits) about the given graph layer.This is an alternative to `axisSet` which displays the axis limits of the currently selected graph layer when it is called without arguments.*/

/* ophys commandCATEGORY: Graph ScalingUSAGE: scaling offUSAGE: scaling onControls whether point size of fonts and other graph elements scales automatically with the size of the graph layer that contains them.EXAMPLE: `scaling off` - no effective scaling. Final point sizes of fonts and other graph objects, relative to the graph page (or when printed), are exactly as set in Origin dialogs.EXAMPLE: `scaling on` - automatially scale point size for fonts and other graph objects with the size of the layer that contains them.*/

/* ophys commandCATEGORY: Image AnalysisUSAGE: dffSheet [startTime] [endTime]USAGE: dffSheet [startTime] [endTime] [xColumnIndex]Simultaneously apply baseline subtraction and normalization to every Y column in the workbook convert fluorescence intensity (F) to dF/F.This command is an alternative to `ntrSheet` and `btrSheet` which cannot be combined and also do not support unevenly-spaced X data.EXAMPLE: `dffSheet 7 9.5` _applies dF/F using the baseline range (7-9.5) from the first column_EXAMPLE: `dffSheet 7 9.5 1` _applies dF/F using the baseline range (7-9.5) from the second column_*/

/* ophys commandCATEGORY: Image AnalysisUSAGE: LoadLinescanCSVUSAGE: LoadLinescanCSV [csv path]USAGE: LoadLinescanCSV [csv path] [book] [sheet]This command loads a CSV file as a worksheet and populates its metadata from an adjacent JSON file.The JSON file must have the same base filename but end with `.csv.json` for it to be loaded automatically.*/

/* ophys commandCATEGORY: Image AnalysisUSAGE: LoadLinescanCSVUSAGE: LoadLinescanCSV [path]USAGE: LoadLinescanCSV [path] [book] [sheet]Load a CSV file created by ScanAGator.If the CSV has an adjacent JSON file, load its contents as metadata for the new worksheet.Additional argumentsEXAMPLE: `LoadLinescanCSV` launches CSV file select dialogEXAMPLE: `LoadLinescanCSV X:/example/scan.csv` loads a specific CSV fileEXAMPLE: `LoadLinescanCSV X:/example/scan.csv Proximal Cell3` loads CSV into a target book/sheet*/

/* ophys commandCATEGORY: Image AnalysisUSAGE: RoiLoadImport XLS/CSV files containing ROI (region of interest) results created by ImageJ into Origin.Although features are frequently added and changed to support evolving types of analysis command, running `RoiLoad` without arguments will always tell you what ROI analysis commands are available and how to use them.*/

/* ophys commandCATEGORY: Internal ToolsUSAGE: cjfHelpLaunch oPhys command documentation in a web browser*/

/* ophys commandCATEGORY: Internal ToolsUSAGE: FixAbfPathsIf ABF files are moved then `setpath wks` may fail because the worksheet remembers the old file path.The `FixAbfPaths` command identifies all worksheets in the project with broken file paths and fixes them by locating the ABF file and replacing the file path in the worksheet.Contact Jason if this command fails to fix all paths in an Origin project.*/

/* ophys commandCATEGORY: Internal ToolsHotmods are LabTalk variables that change program behavior when set to 1 (enabled) or 0 (disabled).  * `deltaTTL` - Get new ttl times every sweep (useful for variable inter pulse interval protocols).  * `BasePerTTL` - Baseline subtract each evoked signal from a period just before the TTL.  * `bGetLastEvent` - Controls whether to get first or last event per sweep from byEvent sheets.  * `bIgnoreByEvent` - Treat byEvent sheets like normal sheets.  * `R2Out` - Output whole-cell capacitive transient fits (AdjR2) to extra column on memtest sheets.  * `HotMod04` - Show step command current on byEvent sheets when AP mode is enabled.  * `biphasicEvents` - Reduce event detection false positives when traces have positive and negative events.  * `HotMod03` - Report AP amplitude as peak-to-threshold voltage and AP threshold time the start time on byEvent sheets.  * `NoiseThreshold` - Blanks sweeps where 60hz noise is above the specified threshold.*/

/* ophys commandCATEGORY: Internal ToolsUSAGE: webCellLaunch a web browser to the individual cell page for the cell described by the active worksheet or ABFGraph*/

/* ophys commandCATEGORY: Internal ToolsUSAGE: webExpLaunch a web browser to the top-level experiment page for the cell described by the active worksheet or ABFGraph*/

/* ophys commandCATEGORY: Origin Project OperationsUSAGE: dABFDelete every ABFBook in the entire project to reduce the OPJ file size.Settings in the ABFGraph are preserved, and `setpath wks` can be used to re-load the ABF from any output sheet.*/

/* ophys commandCATEGORY: Origin Project OperationsUSAGE: FixAppendFixes ABFGraph and ABFBook long names.Run this after appending an OPJ into the current project.*/

/* ophys commandCATEGORY: Output Sheet OperationsUSAGE: ExtractSweepsUSAGE: ExtractSweeps [first sweep] [last sweep]Runs `extractData` on multiple sweeps.If the first and last sweeps are both unspecificed, this will get last 10 sweeps in file (orevery sweep if fewer than 10 sweeps exist).To extract all sweeps, use the `ExtractAllSweeps` command._Note: It is generally not a good idea to store tons of extracted data in an OPJ, espeically without decimation._*/

/* ophys commandCATEGORY: Output Sheet OperationsUSAGE: FreqInBinHistUSAGE: FreqInBinHist [bin size]Converts every Y column of a summary sheet into a histogram using a given bin size.To generate freuqency histograms from AP event times, run event detection and generate AP byEvent sheets, then use GetCols to get the event times (in file), then run this command on the summary sheet.The optional argument defines the bin size (in X units), with smaller numbers resulting in histograms with more bars.EXAMPLE: `FreqInBinHist` _bins AP times using the default bin size (5 seconds)_EXAMPLE: `FreqInBinHist 1` _bins AP times using 1 second bins_*/

/* ophys commandCATEGORY: Output Sheet OperationsUSAGE: getInactivationUSAGE: getInactivation [sweeps] [minimum percent]Calculate actional potential inactivation by sweep.Inactivation is the time between the last action potential and the second marker.Run on an active byEvent sheet and the output will be created as a new worksheet.For sweeps without APs inactivation is 0% or 100% if it occursbefore or after the first sweep containing an AP.Markers must be placed around the step.Use a command like: `setmarks epoch 1` to place markers around the step.*/

/* ophys commandCATEGORY: Output Sheet OperationsUSAGE: KeepFirstEventPerSweepRun on a byEvent output sheet to delete every row that isn't the first event per sweep.This can be used to isolate byEvent parameters for the first AP in every sweep.*/

/* ophys commandCATEGORY: Output Sheet OperationsUSAGE: renameByABFRun this on an output sheet (e.g., a memtest output sheet) and the sheet will be renamed by its original ABF file name.This is the traditional naming system, and this command can reverse the functionality of `renameByABF`.*/

/* ophys commandCATEGORY: Output Sheet OperationsUSAGE: renameByParentRun this on an output sheet (e.g., a memtest output sheet) and the sheet will be renamed by its _parent_ ABF.This makes it easy to compare data from multiple ABFs which all came from the same cell.Reverse this functionality with `renameByABF`.Run `renameByABF` to do the opposite.You can rapidly convert your project to a parent-named project with `runonsheets _MT renameByParent`.*/

/* ophys commandCATEGORY: Output Sheet OperationsUSAGE: ShowAbfPathDisplay the path for the ABF analyzed in the active worksheet*/

/* ophys commandCATEGORY: Output Sheet OperationsUSAGE: ShowAbfPathsDisplay the path for every ABF analyzed across all sheets of the active workbook*/

/* ophys commandCATEGORY: StatisticsUSAGE: ks2boot [columnIndexA] [columnIndexB]Run a bootstrapped two-sample Kolmogorov-Smirnov distribution test (KS test) on data from two columns.CPH data can be created using `ByEventCPH`.EXAMPLE: `ks2boot 0 1 1000` _Run the KS test (on columns 0 and 1) 1000 times_EXAMPLE: `ks2boot 0 1 1000 5` _Run the KS test (on columns 0 and 1) 1000 times with a sample size sufficient to show a 5 unit difference_*/

/* ophys commandCATEGORY: StatisticsUSAGE: sendToANOVA [group name]Run this on a summary sheet (once per group) to create a workbook suitable for using Origin's ANOVA tools.After running, manually rename column A to "group" and label columns B and C to reflect the metrics being compared.Then click Statistics, Anova, Two-Way Repeated Measures ANOVA, and point the input data fields to the 4 columns of the ANOVA workbook.*/

/* ophys commandCATEGORY: StatisticsUSAGE: std1 [column]Tell Origin that you intend to use a specific column of the selected worksheet in a ttest calculation later when `tt2` is run.This is an alternative to `tdata` designed for situations where the source columns are in two different worksheets.*/

/* ophys commandCATEGORY: StatisticsUSAGE: std2 [column]Tell Origin that you intend to use a specific column of the selected worksheet in a ttest calculation later when `tt2` is run.This is an alternative to `tdata` designed for situations where the source columns are in two different worksheets.*/

/* ophys commandCATEGORY: StatisticsUSAGE: tdata [column] [column]USAGE: tdata [column] [column] pairedEXAMPLE: `tdata C D` runs an unpaired t-test on columns C and DEXAMPLE: `tdata E F paired` runs a paired t-test on columns E and FDisplays t-test information comparing two columns in the same worksheet.To compare columns from different worksheets use `std1`, `std2`, and `tt2`.*/

/* ophys commandCATEGORY: StatisticsUSAGE: tt2USAGE: tt2 [pair type]Display two-sample T-test results comparing of data from columns previously defined by `std1` and `std2`.Pair type can be `unpaired` (default) or `paired`.A variance check is performed when this command is run, and a little arrow `->` points to the P-value that should be used (Welch's correction if variance is high).EXAMPLE: `tt2` runs an unpaired two-sample T-testEXAMPLE: `tt2 paired` runs a paired two-sample T-test*/

/* ophys commandCATEGORY: StatisticsUSAGE: tt2sets [firstColumnDatasetA] [firstColumnDatasetB] [columnsPerDataset]Run a series of t-tests on pairs of column data.*/

/* ophys commandCATEGORY: StatisticsUSAGE: vStats [column]USAGE: vStats [column] [start] [end]USAGE: vStats [column] [start] [end] asXCalculate population statistics for a column.If start and end rows are given, only report stats for the given column between those rows.Start and end rows may be defined by index (row number plus one, default) or by x value.Values can later be accessed from the command window using variables like `vStats.mean`.This may be useful in combination with range stats (see `rng` or `letters`) to run commands like `rC = rC / vStats.mean`.EXAMPLE: `vStats c` _calculate statistics for column C_EXAMPLE: `vStats c 5 10` _run stats on column C from rows 6-11_EXAMPLE: `vStats c 5 10 asX` _run stats on column C rows where where X is 6-11_*/

/* ophys commandCATEGORY: Summary and Rave SheetsUSAGE: btr [start] [end], btr [start] [end] [asX]Baseline subtract data to the mean of a range.If run on a summary sheet this command will act on all columns.If run on a regular sheet it will act on a single (specified) column.The ranges used can be defined by row numbers (asIndex) or times (asX, default).This command is similar to NormToRange.An alias for `BaseToRange` is `btr`.EXAMPLE: `btr 3 4` _on a summary sheet: baseline subtracts all columns to minutes 3-4_EXAMPLE: `btr 3 4 asIndex` _on a summary sheet: baseline subtracts all columns to rows 3-4_*/

/* ophys commandCATEGORY: Summary and Rave SheetsUSAGE: BaseToRangeSlope [start] [end]WARNING: This command is not recommended for summary sheets.Use `SlopeCorrect` instead.Subtract a sloping baseline from every Y column of the active worksheet.The baseline is calculated as a linear regression fitted to the X/Y pairs within the given range (X values, inclusive).EXAMPLE: `BaseToRangeSlope 5 10` - subtracts the baseline (linear fit of data where X is 5-10) from every Y column*/

/* ophys commandCATEGORY: Summary and Rave SheetsUSAGE: getAllColsUSAGE: getAllCols [custom match]Run `GetCols` on every Y column of the active worksheet.The sheet match is whatever comes after the last underscore (_MT, _EVN, _mStats, etc) unless it is explicitly givenEXAMPLE: `getAllCols`EXAMPLE: `getAllCols ROI`*/

/* ophys commandCATEGORY: Summary and Rave SheetsUSAGE: getCellsUSAGE: getCells meanUSAGE: getCells maxUSAGE: getCells minUSAGE: getCells firstThis command creates a summary sheet with the mean (or max, min, or first) column value from every column of every cell.The output becomes one row per cell.This command accomplishes what used to be done using getcols and raved/rave with the limits set from 0 to infinity.A "group" column is automatically created to facilitate use of Origin's grouping tools.*/

/* ophys commandCATEGORY: Summary and Rave SheetsUSAGE: getCols [column] [sheets matching] [output sheet]This command cycles through every sheet in a workbook (matching the search string) and locates the specified column, then copies all of that column's data into a single output sheet (called a summary sheet).Summary sheet names start with S.**GetCols on byEvent sheets:**GetCols has a different behavior when run on byEvent sheets.Instead of returning every value in a column, it only returns the first value for each sweep.This is desirable for some analyses (e.g., repeated AP ramps) but undesirable for others (e.g., CPH).To disable this alternate behavior and force getcols to perform normally on byEvent sheets, run `bIgnoreByEvent = 1` in the command window.**GetCols across multiple workbooks:**If a 4th argument is given, getcols is not restricted to the selected workbook.The 4th argument is a search string, and all workbooks in the current folder containing this string will be searched.It is recommended that a new workbook be created just to house getcols commands of this type.Getcols then never needs to be run on individual workbooks.However, in most cases it is better to use `LinkData` instead of creating multi-workbook getcols commands.EXAMPLE: `getcols Ih` _gets "Ih" column from every worksheet with an underscore in its name_EXAMPLE: `getcols Ih _MT` _gets "Ih" column from every worksheet matching "MT"_EXAMPLE: `getcols Ih _MT S.Ih` _gets "Ih" column from every worksheet matching "MT" and names the output sheet "S.Ih"_EXAMPLE: `getcols 3 _MT S.Rm` _gets the 4th column (numbers start at 0) from every worksheet matching "MT" and names the output sheet "S.Rm"_EXAMPLE: `getcols 3 _MT S.Rm MemTests` _runs on every workbook with "MemTests" in its name_*/

/* ophys commandCATEGORY: Summary and Rave SheetsUSAGE: GetColsXY [X column index] [Y column index] [sheet match] [output sheet name]Create a new worksheet containing pairs of X/Y columns sourced from each worksheet matching the given search string.EXAMPLE: `GetColsXY 1 2 _MT S.IhVsRa` _Creates a summary sheet with two columns from every memtest sheet_EXAMPLE: `GetColsXY 24 2 _EVN S.GainXY` _Creates an AP gain summary sheet with command current and AP count_*/

/* ophys commandCATEGORY: Summary and Rave SheetsUSAGE: getGroups [column] [sheets matching] [output sheet]This command is identical to `getcols` except that if there are output sheets with group tags (i.e., `_MT.aged`) it will separately run getcols on each group.EXAMPLE: `getgroups 1 _mStats mean.S` _runs getcols 1 using `_mStats.young` and `_mStats.aged` as search strings_*/

/* ophys commandCATEGORY: Summary and Rave SheetsUSAGE: ntr [start] [end], ntr [start] [end] [asX or asIndex]Normalize data to the mean of a range.If run on a summary sheet this command will act on all columns.If run on a regular sheet it will act on a single (specified) column.The ranges used can be defined by row numbers (asIndex) or times (asX, default).This command is similar to BaseToRange.An alias for `NormToRange` is `ntr`.EXAMPLE: `NormToRange 3 4` _on a summary sheet: normalizes all columns to minutes 3-4_EXAMPLE: `NormToRange 3 4 asIndex` _on a summary sheet: normalizes all columns to rows 3-4_*/

/* ophys commandCATEGORY: Summary and Rave SheetsUSAGE: raveThe rave command only acts on the selected worksheet.It produces a new worksheet with the same name except with `_RAVE` at the end.In this new worksheet has only two columns: the first column is the name of each column in the original sheet, and the second column is the average values for each original column between the time points specified by `raved`.Rave output sheets remember the name of the input sheet they were produced from.A rave sheet can be updated by `rave` while the rave output sheet is selected.All rave sheets in a workbook can be updated with:After you have a workbook containing many rave sheets, you can use `getcols` to collect all of the data into a single sheet.Since rave sheets only have two columns, the arguments for this command never change:EXAMPLE: `runonsheets _RAVE rave`EXAMPLE: `getCols 1 _RAVE S.RAVE`*/

/* ophys commandCATEGORY: Summary and Rave SheetsUSAGE: ravedUSAGE: raved wksUSAGE: raved wks-silentUSAGE: raved save [name]USAGE: raved load [name]USAGE: raved load-silent [name]USAGE: raved del [name]USAGE: raved listLaunch a dialog box which customizes the ranges to use for the range average.See `rave` for details.Note: you can save multiple raved parameter sets using tools nearly identical to those for minip.raved del * - will delete all stored raved parameters with project scope.*/

/* ophys commandCATEGORY: Summary and Rave SheetsUSAGE: reject columnIndex "reason for rejection"When run on a summary sheet (created by getcols) this command identifies the sheet corresponding to the given column index, applies a `_rej` tag, then adds the reason to the worksheet's notes.That sheet will no longer be included in the summary sheet when getcols is re-run.EXAMPLE: `reject 3 "cell died"`*/

/* ophys commandCATEGORY: Summary and Rave SheetsUSAGE: Resample [width]USAGE: Resample [width] [step]Down-sample the data using a moving window average.By default the window step size is the window size (for a moving window with no overlap), but this can be customized to achieve data smoothing.Setting `width` to `1` results in data smoothing with no down-sampling.Resampling can be combined with `NormToRange`, `BaseToRange`, etc.This command only works on summary sheets.Use `decimate` and `decimateWks` on non-summary sheets.EXAMPLE: `resample 2` _Downsample by 2 so 100 points becomes 50_EXAMPLE: `resample 10` _Downsample by 10 so 100 points becomes 10_EXAMPLE: `resample 10 1` _Apply data smoothing with a window size of one and no down-sampling_EXAMPLE: `resample off` _Disable resampling_*/

/* ophys commandCATEGORY: Summary and Rave SheetsUSAGE: SlopeCorrect [start] [end] [asX (default) / asIndex]USAGE: SlopeCorrect on/off (toggle only works after initial run).Run this command on a summary sheet to fit a linear line to each data column (confined to rows defined by the start and end times) then subtract the slope from the original data.The result are data columns with the same Y offset from 0 but slope removed.This command can be combined with other commands like `BaseToRange` and `NormToRange` in any order.An optional third argument `asIndex` can be given indiacting start and ends values row indexes.EXAMPLE: `SlopeCorrect 5 10` _Remove the slope (over x-axis values 5-10) from all Y columns_EXAMPLE: `SlopeCorrect 10 30 asIndex` _Remove the slope (over rows 10-30) from all Y columns_*/

/* ophys commandCATEGORY: Summary and Rave SheetsUSAGE: UpdateAllSheetsRe-runs `rave` or `getcols` on all the summary sheets using the same input parameters originally used to create those sheets.*/

/* ophys commandCATEGORY: Summary and Rave SheetsUSAGE: UpdateRaveSheetRe-runs `rave` on the active summary sheet using the same input parameters originally used to create that sheet.*/

/* ophys commandCATEGORY: Summary and Rave SheetsUSAGE: UpdateRaveSheetsRuns `UpdateRaveSheet` on every worksheet of the active workbook.*/

/* ophys commandCATEGORY: Summary and Rave SheetsUSAGE: UpdateSummarySheetRe-runs `getcols` on the active summary sheet using the same input parameters originally used to create that sheet.*/

/* ophys commandCATEGORY: Summary and Rave SheetsUSAGE: UpdateSummarySheetsRuns `UpdateSummarySheet` on every worksheet of the active workbook.*/

/* ophys commandCATEGORY: Summary and Rave SheetsUSAGE: UTSUSAGE: UpdateThisSheetre-run getcols or rave on the active worksheet*/

/* ophys commandCATEGORY: Summary and Rave SheetsUSAGE: wksUSAGE: wks columnIndexWhen run on a summary sheet (created by getcols) this command will go to the source sheet corresponding to the highlighted (or specified) column.*/

/* ophys commandCATEGORY: USAGE: ExtractEvents [start] [end]Run this command on a byEvent sheet to create an average trace of all events which occur between `start` and `end`.Arguments are sweep numbers for episodic files and minutes for gap-free files.This command can create an average AP, IPSC, or EPSC shape between two time points.EXAMPLE: `extractevents 10 30;` _averages events between sweeps 10 and 30_EXAMPLE: `getgroups 1 _mStats mean.S` _runs getcols 1 using `_mStats.young` and `_mStats.aged` as search strings_*/

/* ophys commandCATEGORY: Workbook OperationsUSAGE: dsheets [match]Delete worksheets whose name contains the matching text.*/

/* ophys commandCATEGORY: Workbook OperationsUSAGE: extractByString [match]USAGE: extractByTag [match] [destination workbook]Move all worksheets whose name matches the given string into a new workbook (or an existing workbook if specified)*/

/* ophys commandCATEGORY: Workbook OperationsUSAGE: extractByTag [tag]USAGE: extractByTag [tag] [destination workbook]Move all worksheets with the given tag into a new workbook (or an existing workbook if specified)*/

/* ophys commandCATEGORY: Workbook OperationsUSAGE: mergeSheets [tag]Vertically merges rows from all sheets whose names match the given tag into a new sheet.*/

/* ophys commandCATEGORY: Workbook OperationsUSAGE: MoveSheet [bookName]Move the active worksheet to the given bookname.If the book doesn't exist, it will be created.EXAMPLE: `runOnSheets _eStats "copySheet allStats;"` _use in combination with runOnSheets_*/

/* ophys commandCATEGORY: Workbook OperationsUSAGE: runonbooks [match phrase] "[command]"Run a labtalk command on every workbook in the current folder.The command must be inside double quotes.EXAMPLE: `runonbooks Events "getcols 3 _EVN S.FreqInBin"` _runs getcols on every events workbook_EXAMPLE: `runonbooks Events "runonsheets S. rave"` _runs rave on every summary sheet of every events workbook_*/

/* ophys commandCATEGORY: Workbook OperationsUSAGE: runonsheets [match phrase] "[command]"Run a labtalk command on every sheet of the selected workbook.The command must be inside double quotes.An optional third argument silences output if set to zero.EXAMPLE: `runonsheets _MT "setpath wks; memtest;"` _re-run membrane test on every sheet_EXAMPLE: `runonsheets _eStats "wks.ncols = 6;"` _ensure every sheet has 6 columns_EXAMPLE: `runonsheets _eStats "csetvalue formula:=[A*100] col:=6;"` _set formula for column 6 (column A * 100)_EXAMPLE: `runonsheets mStats "wks.Name$=" silent` _show the names of all worksheets_*/

/* ophys commandCATEGORY: Workbook OperationsUSAGE: sortsheetsRe-arranges all worksheets in the selected workbook according to alphabetical order.Run `sortsheets -1` to reverse-sort them.*/

/* ophys commandCATEGORY: Worksheet OperationsUSAGE: AddStatsRowsAdds mean and standard deviation rows to the active worksheet*/

/* ophys commandCATEGORY: Worksheet OperationsGiven a sheet with pairs of X/Y columns, shift data down so all X columns are aligned.This command is typically followed by `DeleteXColumns`*/

/* ophys commandCATEGORY: Worksheet OperationsUSAGE: btrsheet [start] [end]Baseline subtract all columns of data (not for summary sheets).Optionally add "false" to the end to force asIndex (not asX).*/

/* ophys commandCATEGORY: Worksheet OperationsUSAGE: ccaveUSAGE: ccave SEUSAGE: ccave SDWhen run on a worksheet, all Y columns are averaged together (horizontally) and two new columns are made (or updated): average and error.The default error is standard error (SE), but if "SD" is given as an argument the error is standard deviation (SD).*/

/* ophys commandCATEGORY: Worksheet OperationsUSAGE: decimatewks [decimate by]Reduces data vertically by making each cell the average of a given number of rows.This is non-destructive, as it creates a new copy of the current worksheet.EXAMPLE: `decimatewks 5` _makes each row the average of 5 original rows_ */

/* ophys commandCATEGORY: Worksheet OperationsUSAGE: deleteColumns [first column index], [last column index]Delete all rows between (and including) the given column index numbers.*/

/* ophys commandCATEGORY: Worksheet OperationsUSAGE: deleterows [first row] [last row]Delete all rows between (and including) the given row numbers.If the second row is not given, everything between the first row and the end of the worksheet is deleted.The `drows` command does the same thing and takes the same arguments.EXAMPLE: `deleteRows 10` _deletes row 10 and all rows after it_ EXAMPLE: `deleteRows 10 13` _deletes row 10, 11, 12, and 13. Row 14 is preserved._ */

/* ophys commandCATEGORY: Worksheet OperationsUSAGE: deleteRowsBandpass [columnIndex] [lowestAllowedValue] [highestAllowedValue]Delete rows where the value of a given column is outside an allowable range.On bySweep sheets this can be used to discard all sweeps outside an allowable time range, or whose data is outside of an allowable range.On byEvent sheets this can be used to discard all events outside an allowable time range or outside the range of expected values for events.*/

/* ophys commandCATEGORY: Worksheet OperationsFor each Y column in the active worksheet, identify the first peak, then blank all cells after it.Run on AP gain summary sheets to isolate sweeps before hyperexcitation causes reduced firing (e.g., AP block).*/

/* ophys commandCATEGORY: Worksheet OperationsDelete all X columns (except for the first one)*/

/* ophys commandCATEGORY: Worksheet OperationsUSAGE: lettersRename every column as a series of double-letters (AA, BB, CC, etc)*/

/* ophys commandCATEGORY: Worksheet OperationsUSAGE: mergeColsMerges all values from all Y columns into a column named "MERGED".This command can be re-run on the same sheet multiple times.Masked columns are ignored.*/

/* ophys commandCATEGORY: Worksheet OperationsUSAGE: nanum_to_ZeroReplace all `--` cells in the selected worksheet with the number `0`.I use this to correct instananeous frequency for gain functions.When no APs are detected (frequency should be 0 instead of NANUM)*/

/* ophys commandCATEGORY: Worksheet OperationsUSAGE: ntrsheet [start] [end]Normalize all columns of data (not for summary sheets).Optionally add "false" to the end to use asIndex (instead of asX).*/

/* ophys commandCATEGORY: Worksheet OperationsUSAGE: numbersRename every column as a series of numbers starting at 0.*/

/* ophys commandCATEGORY: Worksheet OperationsUSAGE: renameSheet [new name]Set the name of the active worksheet*/

/* ophys commandCATEGORY: Worksheet OperationsUSAGE: rngUSAGE: rng [prefix]This command allows columns of the current worksheet to be addressed from the command window.An optional prefix can be given to make it easier to do math on columns from different worksheets.EXAMPLE: `rng` - columns on the active sheet can be modified like `rA = 5`, `rB += 9`, etc.EXAMPLE: `rng sheet1` - columns on the active sheet can be modified from anywhere like `sheet1C += 3`*/

/* ophys commandCATEGORY: Worksheet OperationsUSAGE: sortColsSort columns alphabetically by their long name (skipping the first column).*/

/* ophys commandCATEGORY: Worksheet OperationsUSAGE: wksAddNote "note contents"Adds the a note to the metadata of the selected worksheet.*/

/* ophys commandCATEGORY: Worksheet TaggingUSAGE: addtag [match] [addition]When run with a workbook selected, it finds any sheet with `match` in its name and appends `addition` to its name.You could match `_` so the command works on all sheets, or you could specifically match just `_MT`.Also see `ChangeTags` and `modifyTags`.There is no problem if sheet names already contain multiple underscores.EXAMPLE: `addtag _MT .aged;` _turns `1234_123_MT` into `1234_123_MT.aged`_EXAMPLE: `addtag _MT .aged;` _run again becomes `1234_123_MT.aged.aged`_*/

/* ophys commandCATEGORY: Worksheet TaggingUSAGE: changetags [search] [replace]When run with a workbook selected, it performs a search/replace on the tail end of every sheet name in the workbook.Also see `AddTag` and `modifyTags`.EXAMPLE: `changetags _MT _MT.aged;` _turns `1234_123_MT` into `1234_123_MT.aged`_EXAMPLE: `changetags _MT.aged _MT.young;` _turns `1234_123_MT.aged` into `1234_123_MT.young`_*/