How to Customize Amira-Avizo with moduleExtender
Are there module settings you always need to change during your daily work? This Xtra describes how you can permanently change default settings of modules in Amira-Avizo.
Using the attached file, "modified_module_behaviour.rc2", the settings of a number of modules are changed by executing the Tcl-code inside the "proc" section on instantiation of the module.
The changes affect the following modules in the described ways:
- Generate Surface: Normally, if you try to create a surface from a not very small label data-set, a warning window pops up. By setting the "setInteractive" port to 0, that window is no longer shown.
- Volren:
- In Amira-Avizo, the default colormap for Volren is "volrenRed". That default is changed to "volrenWhite".
- With version 2021.1, the "Auto adjust range" option of the colormap has been activated by default. This results in a re-adjustment of the range-values of colormap whenever Volren is re-connected to another data-object. After running the Tcl code, that behavior is changed such that "Auto adjust range" is only activated on right-click instantiation on a data-object, and immediately deactivated afterwards.
- Volume Rendering:
- In Amira-Avizo, the default colormap for Volume Rendering is "volrenWhite". That default is changed to "grayScale".
- With version 2021.1, the option "Auto adjust range" of the colormap has been activated by default. This results in a re-adjustment of the range-values of colormap whenever Volume Rendering is re-connected to another data-object. After running the Tcl code, that behavior is changed such that "Auto adjust range" is only activated on right-click instantiation on a data-object, and immediately deactivated afterwards.
- The default for the "Sampling Quality" setting is 0.5, which becomes too slow for interactive use for larger data-sets on medium-sized GPUs. That setting is changed to 0.2.
- Surface Cross Contour: The default setting of "epsilon" might cause doubled contour-lines in certain circumstances. By reducing that value to 1e-10, that no longer occurs.
- Ortho Slice: With version 2021.1, the option "Auto adjust range" of the colormap has been activated by default. This results in a re-adjustment of the range-values of colormap whenever Ortho Slice is re-connected to another data-object. After running the Tcl code, that behavior is changed such that "Auto adjust range" is only activated on right-click instantiation on a data-object, and immediately deactivated afterwards.
You can modify the "modified_module_behaviour.rc2" file. Here are a few hints:
- Putting a "#" as first character in a line marks that line as a comment, and it is not interpreted.
- Be careful that you have the backslash ("\") at the end of each line within one call of moduleExtender, because those calls are in principle one-line commands, but for readability they have been split into multiple lines. The backslash is telling the interpreter that the command is continued in the next line.
- You have to use the semicolons (";"), which are, in Tcl, separators of commands within one line.
- The "$this fire;" command forces a refresh of the module using the parameters set earlier. In some cases this is necessary before you can set other parameters.
- If you want to use the modified file, you have to restart Amira-Avizo, because resource-files are only sourced on start-up.
Usage
Download the "modified_module_behaviour.rc2" resource file, and put it into the sub-directory "share\resources" of either the installation directory or your AVIZO_LOCAL directory.
Background information
moduleExtender
- In Amira-Avizo it is possible to customize the behavior of modules by using the "moduleExtender" internal Tcl-command.
- With "moduleExtender", an already registered module is replaced by a modified version.
- The changes demonstrated here are done by executing the Tcl-code inside the "-proc { ... }" block whenever the module is instantiated.
- Some of the changes are after "if"-blocks like this:
if { [exists $PRIMARY] } { \
$this data connect $PRIMARY \
}; \
$this fire; \That "if"-block forces the connection of the data-object before the modified settings defined afterwards are applied.
Resource-files
Resource-files in Amira-Avizo are special files containing code in the Tcl scripting-language. They are used, for example, to register modules and data-types.
Resource files are sourced (read and interpreted) at start-up of Amira-Avizo. They have to be located in one of the specific sub-directories:
- share\resources
- share\script-objects
- share\python_script_objects
of either the installation directory (i.e. AVIZO_ROOT or AMIRA_ROOT) or the user-defined "local" directory (AVIZO_LOCAL or AMIRA_LOCAL, see here for instructions).
Resource files must have either an ".rc" or ".rc2" file extension. Depending on the extension, they are sourced at different stages of the start-up procedure. Resource files in AVIZO_LOCAL are sourced after those in AVIZO_ROOT, and ".rc2"-files are sourced after all the ".rc"-files.