rabayliss
commented
4 years ago (StructureOperations: planning_structure_preferences, AutoLoadPlan.py, BeamOperations.py, OptimizationOperations.py, FiducialsPlacement.py):
StructureOperations: planning_structure_preferences Build: added properties to store underdose and uniform dose structures and standoffs Build: added optional argument to exists_roi that returns only existing rois sent to the function Build: Add a Levenshtein match of aliases to search. Fix: Levenshtein match tuning of aliases Fix: Regex expression for laterality at beginning, middle, and end of terms Fix: More exception structures to match filter FieldOfView, All_PTVs,UnderDose Cleanup: Eliminating obsolete lines Incorporated reviewer suggestions
AutoLoadPlan.py Build: Added a test of input commands for planning structures. It will make sure all appropriate elements are present in the xml input and parse the input data from the csv file Build: Moved planning structure generation to its own function, removed testing elements from it Build: Added optimize plan to automation.
- Imported optimize function
- Convert xml to dict to dataframe
- populate the kwargs for optimize plan
- embed optimization in a try/except Build: Added setting of CT-Density if needed - patient save needed, along with update structures Build: Added testing of targets to make sure they are present in the case Build: Added a stub for testing optimization inputs. To be expanded fix: unresolved reference to OptimizationOperations fix: incorrect xml to dict on optimizatio fix: bug in dataframe call firx: close script status upon report fix: Adding more checks to the ending optimization to keep correct reporting of optimization status completion. Is there dose? Clean: Output header Clean: Code clea:nup main
OptimizationOperations: build: created an xml to dict method for optimization configuration build: added an optional "close" to automatically shut down status upon finish fix: optimization does not seem to define the dose grid for a new plan. Explicitly doing this. fix: added new SBRT names for lung to the list of names searched for "Treat Settings" UWHeadNeck.xml Build: added optimization_configuration Build: added check on CT imaging system defined. Required examination as parameter Fix: Missing tag Fix: Added a check to see if structures should be created (no workflow specified in input file
TG-263.xml -Added aliases for Globes -Added aliases for posterior blocks -Reformat lines with pycharm TODO: Delete the planning structure definitions from main. TODO: Move all element populations to dataframes TODO: Test with Tomo, SMLC, and VMAT
UWLung.xml Fix: Modified the hypofractionated lung protocol with goals for Lungs, changed to Lungs-ITV per MD
UWHeadNeck.xml Bilateral Neck objectives: reduce the Parotid and Submand Weights Bilateral/Right/Left: Increased contralateral weighting, included DFO limits on all side-specific organs, reduced penalty on cochlea. Increased brain penalty. Build: Added 8 warmstart optimization, reduced iterations before final dose calc to eliminate vertical threading Build: Continue improvements for lower dose target coverage (PTV's3,4,5)
UWBrainCNS.xml Build: Adding the WBHA optimization template and objectives Build: Adding the planning structure strategy Build: Added a TomoBeamset and lens goals Fix: Improve WBHA solution (reduce lens/eye dose) FIX: Max Time factor is 60
FiducialPlancement.py -Changed seed length to 5 mm to reflect the correct seed length. -Changed prv radius to 0.2 cm -Renamed PRV contours as PRV02 PostReview Modifications. All suggested revisions implements
BeamOperations.py Build: Loading the tomo-specific optimization limits on treatment time
OptimizationOperations.py Fix: Adding logic for non-varying dose grid
CODEOWNERS -Added rabayliss as exclusive for now...
(StructureOperations: planning_structure_preferences, AutoLoadPlan.py, BeamOperations.py, OptimizationOperations.py, FiducialsPlacement.py):
StructureOperations: planning_structure_preferences Build: added properties to store underdose and uniform dose structures and standoffs Build: added optional argument to exists_roi that returns only existing rois sent to the function Build: Add a Levenshtein match of aliases to search. Fix: Levenshtein match tuning of aliases Fix: Regex expression for laterality at beginning, middle, and end of terms Fix: More exception structures to match filter FieldOfView, All_PTVs,UnderDose Cleanup: Eliminating obsolete lines Incorporated reviewer suggestions
AutoLoadPlan.py Build: Added a test of input commands for planning structures. It will make sure all appropriate elements are present in the xml input and parse the input data from the csv file Build: Moved planning structure generation to its own function, removed testing elements from it Build: Added optimize plan to automation.
OptimizationOperations: build: created an xml to dict method for optimization configuration build: added an optional "close" to automatically shut down status upon finish fix: optimization does not seem to define the dose grid for a new plan. Explicitly doing this. fix: added new SBRT names for lung to the list of names searched for "Treat Settings" UWHeadNeck.xml Build: added optimization_configuration Build: added check on CT imaging system defined. Required examination as parameter Fix: Missing tag Fix: Added a check to see if structures should be created (no workflow specified in input file
TG-263.xml -Added aliases for Globes -Added aliases for posterior blocks -Reformat lines with pycharm TODO: Delete the planning structure definitions from main. TODO: Move all element populations to dataframes TODO: Test with Tomo, SMLC, and VMAT
UWLung.xml Fix: Modified the hypofractionated lung protocol with goals for Lungs, changed to Lungs-ITV per MD
UWHeadNeck.xml Bilateral Neck objectives: reduce the Parotid and Submand Weights Bilateral/Right/Left: Increased contralateral weighting, included DFO limits on all side-specific organs, reduced penalty on cochlea. Increased brain penalty. Build: Added 8 warmstart optimization, reduced iterations before final dose calc to eliminate vertical threading Build: Continue improvements for lower dose target coverage (PTV's3,4,5)
UWBrainCNS.xml Build: Adding the WBHA optimization template and objectives Build: Adding the planning structure strategy Build: Added a TomoBeamset and lens goals Fix: Improve WBHA solution (reduce lens/eye dose) FIX: Max Time factor is 60
FiducialPlancement.py -Changed seed length to 5 mm to reflect the correct seed length. -Changed prv radius to 0.2 cm -Renamed PRV contours as PRV02 PostReview Modifications. All suggested revisions implements
BeamOperations.py Build: Loading the tomo-specific optimization limits on treatment time
OptimizationOperations.py Fix: Adding logic for non-varying dose grid
CODEOWNERS -Added rabayliss as exclusive for now...