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Chapter 11
Advanced Topic: Scripting

A script is a small program that you can use to automate repetitive tasks in Delta2D. Here we show briefly the available commands. See also the example script file example.script in the Delta2D directory, this is a script that processes files in the samples directory.

The best way to learn about scripting is to use Delta2D's remote control. The remote control lets you type commands that will be immediately executed by Delta2D. Later you can combine these commands into a script. A complete list of available commands is shown with the command help or in this document in 11.1.

To start the remote control, open a Windows command prompt. Go to the program directory where you have installed Delta2D. Then start the remote control from the command line using one of the commands below. Note that these commands have to be typed in one line.

Interactive mode
– starts the remote control and waits for commands 
      Dual2DGelCompareRemoteControl.bat

Under unix-like systems you start it with 

      ./Dual2DGelCompareRemoteControl.sh
Interactive mode with initial script
– starts the remote control and immediately executes the given script file. Unless your script ends with the command exit, Delta2D will stay open after the script is finished. 
      Dual2DGelCompareRemoteControl.bat -f script-file-name

respectively 

      ./Dual2DGelCompareRemoteControl.sh -f script-file-name
Interactive mode with initial commands
– starts the remote control and immediately executes the given commands. Use exit as the last command to close Delta2D after executing the commands. 
      Dual2DGelCompareRemoteControl.bat command1 command2 ...

respectively 

      ./Dual2DGelCompareRemoteControl.sh command1 command2 ...

11.1 File Commands

Table 11.1 shows the commands that correspond to the entries in the File menu. You may need to provide a file name, telling which file to open or where to save results.

clear Clear master and sample images.
openImageAsMaster File Open an image file as the master image.
openImageAsSample File Open an image file as the sample image.
openMatchmap File Open a match map.
saveSampleImageAs File Save the sample image..
saveDualImageAs File Save the dual channel image.
saveMasterTableAs File Save the quantitation table for the master gel image.
saveSampleTableAs File Save the quantitation table for the sample gel.
saveDualTableAs File Save the quantitation table for the gel pair.

Table 11.1: File commands.

11.2 Image Processing Commands

Table 11.2 shows commands that correspond to some entries in the View and Warp menus.

disableAutoWarp Disable automatic warping.
enableAutoWarp Enable automatic warping.
warp Warp the sample image according to the current match map and automatic warp settings.
warpAuto Warp the sample image automatically, taking the current match map into account.
warpExact Warp the sample image exactly.
warpGlobal Warp the sample image globally.
unwarp Unwarp the sample image.
quantify Quantify both images.
quantifyMaster Quantify the master image.
quantifySample Quantify the sample image.
processSample File Warp and quantify the sample image, using a match map with canonical name.

Table 11.2: Image processing commands.

11.3 Commands for Controlling Windows

You can use the commands shown in Table 11.3 to control the display of the gel image view and the pairwise quantitation table.

show Show the gel image view.
hide Hide the gel image view.
showTable Show the quantitation table.
hideTable Hide the quantitation table.
zoomIn, zoomOut, unzoom Control the zoom of the gel image view.
pageDown, pageUp, pageLeft, pageRight Scroll the gel image view.

Table 11.3: Commands for controlling windows.

11.4 Remote Control Commands

Table 11.4 shows available commands for the remote control itself.

exit Exit the remote control program.
help Print a list of available commands.

Table 11.4: Commands for the remote control.

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