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The plan optimization parameters are defined in a configuration file at the YAML format. An example of configuration file is available in the git repository: scripts/flashopt/config_MIROpt.yaml. The file contains comments that describe the meaning of the different fields. Some fields are described in more details in this wiki.
The first step is to define all the optimization parameters in the YAML file.
This file has the same fields as the configuration file of the standard MIROPT version which are described on this page. In addition, for the the ConformalFLASH library, there are new fields which are described in more details in this wiki.
The YAML file has a hierarchical structure. The number of space characters at the beginning of a line defines the hierarchy level of the field. Make sure to always use the same number of spaces for a given hierarchy level. Any text after the '#' character is a comment. It is ignored by MIROPT.
The high level modules in the YAML file are:
- Data : Defines the folder containing the input data, the name of the input CT scan and the name of the RT struct file. Same description as for the standard MIROPT.
- Plan : Plan parameters to be optimized. This module contains all the new parameters specifically applicable to ConformalFLASH. The fields are defined in more details on this page.
- OptConfig : Define the parameters of the optimization function. Same description as for the standard MIROPT.
- Outputs : Define the output of the computation. Same description as for the standard MIROPT.
- Rtest : Define the parameters for robust optimization. For ConformalFLASH, the robust optimization is not available. The field robust should be set to 0 for all the objective functions. Therefore, the data of the Rtest section is not used by ConformalFLASH.
The parameters specific to ConformalFLASH are defined in the Plan field. The field are defined in more details on this page.
Once the YAML file is written, to start the optimization, at the Matlab command line, type:
start_MIROpt_workflow('/fullpath/param.yaml')
where /fullpath/param.yaml is the full path to the YAML file.
A description of the sequence of operations carried out by the ConformalFLASH library is described here. The results of the computation are described in the next section.
When the script has finished running, the results are stored on disk in the folder output_path specified in the YAML file.
A detailed description of the results can ber found on this page.
Sometime one wants to restart the simulation but does not wish to restart from scratch because that would take to much time. ConformalFLASH saves the partial results on disk. When restarting the computation, if some partial results are found on disk, the computation of these intermediate results is skipped and the previous results are loaded from disk. The parameter PlanExistentFile must contain the name of the folder containing the intermediate results. This chapter describes how to restart a simulation from a specific step of the process.