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dosimetry:userguide:userguide [2015/07/02 15:34] – created dpatenaudedosimetry:userguide:userguide [2021/07/29 18:23] (current) – external edit 127.0.0.1
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 Access to the astroid Dosimetry App is provided by the thinknode™ framework using http json formatted requests. thinknode™ provides the 'backbone' used to send and receive requests, maintain users, realms and organizations, and provide data storage and management. Access to the astroid Dosimetry App is provided by the thinknode™ framework using http json formatted requests. thinknode™ provides the 'backbone' used to send and receive requests, maintain users, realms and organizations, and provide data storage and management.
  
 +The [[http://docs.apps.dotdecimal.com/dosimetry|Dosimetry Manifest Guide]] contains a complete list of all functions and types supported by the astroid Dosimetry App through API calls.
 ===== Purpose ===== ===== Purpose =====
  
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 ==== Instructions for Use ==== ==== Instructions for Use ====
  
-The [[instructions_for_use:instructions_for_use|Instructions for Use]] outlines the intended use of the Dosimetry App. Refer to each section below for more detail: +The [[dosimetry:instructions_for_use:instructions_for_use|Instructions for Use]] outlines the intended use of the Dosimetry App. Refer to each section below for more detail: 
-  * **[[instructions_for_use:instructions_for_use#overview|Overview]]** +  * **[[dosimetry:instructions_for_use:instructions_for_use#overview|Overview]]** 
-  * **[[instructions_for_use:instructions_for_use#warning|Warning]]** +  * **[[dosimetry:instructions_for_use:instructions_for_use#warning|Warning]]** 
-  * **[[instructions_for_use:instructions_for_use#user_profile|User Profile]]** +  * **[[dosimetry:instructions_for_use:instructions_for_use#user_profile|User Profile]]** 
-  * **[[instructions_for_use:instructions_for_use#product_features|Product Features]]** +  * **[[dosimetry:instructions_for_use:instructions_for_use#product_features|Product Features]]** 
-    - [[instructions_for_use:instructions_for_use#function_access_and_data_storage|Function Access and Data Storage]] +    - [[dosimetry:instructions_for_use:instructions_for_use#function_access_and_data_storage|Function Access and Data Storage]] 
-    - [[instructions_for_use:instructions_for_use#proton_dose_calculations|Proton Dose Calculations]] +    - [[dosimetry:instructions_for_use:instructions_for_use#proton_dose_calculations|Proton Dose Calculations]] 
-    - [[instructions_for_use:instructions_for_use#proton_aperture_designs|Proton Aperture Designs]] +    - [[dosimetry:instructions_for_use:instructions_for_use#proton_aperture_designs|Proton Aperture Designs]] 
-    - [[instructions_for_use:instructions_for_use#proton_range_compensator_designs|Proton Range Compensator Designs]] +    - [[dosimetry:instructions_for_use:instructions_for_use#proton_range_compensator_designs|Proton Range Compensator Designs]] 
-    - [[instructions_for_use:instructions_for_use#patient_specific_model|Patient Specific Data Model]] +    - [[dosimetry:instructions_for_use:instructions_for_use#patient_specific_model|Patient Specific Data Model]] 
-    - [[instructions_for_use:instructions_for_use#proton_treatment_delivery_machine_model|Proton Treatment Delivery Machine Model]]+    - [[dosimetry:instructions_for_use:instructions_for_use#proton_treatment_delivery_machine_model|Proton Treatment Delivery Machine Model]]
  
 ==== Precautions ==== ==== Precautions ====
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 ===== Proton Delivery System Conventions ===== ===== Proton Delivery System Conventions =====
  
-(this section could also be named Geometric and Beamline Conventions)+==== Geometric and Beamline Conventions ====
  
-The [[userguide:proton_delivery_system_conventions|Proton Delivery System Conventions]] page details definitions about the following topics: 
  
-  * **[[userguide:proton_delivery_system_conventions|Proton Delivery System Conventions:]]** +The [[dosimetry:userguide:proton_delivery_system_conventions|Proton Delivery System Conventions]] page details definitions about the following topics: 
-    * [[userguide:proton_delivery_system_conventions#coordinate_systems|Coordinate Systems]] + 
-    * [[userguide:proton_delivery_system_conventions#beam_representation|Beam Representation]]+  * **[[dosimetry:userguide:proton_delivery_system_conventions|Proton Delivery System Conventions:]]** 
 +    * [[dosimetry:userguide:proton_delivery_system_conventions#coordinate_systems|Coordinate Systems]] 
 +    * [[dosimetry:userguide:proton_delivery_system_conventions#beam_representation|Beam Representation]]
 ===== Function Categories ===== ===== Function Categories =====
  
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     * Details of each function, argument parameters, and return values are provided at the [[http://docs.apps.dotdecimal.com/dosimetry|Dosimetry Manifest Guide]].     * Details of each function, argument parameters, and return values are provided at the [[http://docs.apps.dotdecimal.com/dosimetry|Dosimetry Manifest Guide]].
     * Notes about manifest documentation:     * Notes about manifest documentation:
-      - Previous versions of the dosimetry documentation can be found at the [[:dosimetry_versions|Dosimetry Versions]] page.+      - Previous versions of the dosimetry documentation can be found at the [[dosimetry:dosimetry_versions|Dosimetry Versions]] page.
       - If a manifest is manually pulled down from the thinknode framework, that manifest will not match the one outlined in the [[http://docs.apps.dotdecimal.com/dosimetry|Dosimetry Manifest Guide]]. Only the functions and types detailed in the dosimetry manifest guide have been tested and approved for release for customer use (use of any other functions is beyond the intend scope of this product and is done at your own risk).       - If a manifest is manually pulled down from the thinknode framework, that manifest will not match the one outlined in the [[http://docs.apps.dotdecimal.com/dosimetry|Dosimetry Manifest Guide]]. Only the functions and types detailed in the dosimetry manifest guide have been tested and approved for release for customer use (use of any other functions is beyond the intend scope of this product and is done at your own risk).
 ==== Design Task Functions ==== ==== Design Task Functions ====
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 Detailed function and data type definitions can be found at [[http://docs.apps.dotdecimal.com/dosimetry|Dosimetry Manifest Guide]]. Below are basic examples of using design task functions for aperture and range compensator designs. Detailed function and data type definitions can be found at [[http://docs.apps.dotdecimal.com/dosimetry|Dosimetry Manifest Guide]]. Below are basic examples of using design task functions for aperture and range compensator designs.
  
-  * **[[userguide:design_task_functions:dtf#aperture_design|Aperture Design]]**: Explanation and sample process for aperture geometric design functions +  * **[[dosimetry:userguide:design_task_functions:dtf#aperture_design|Aperture Design]]**: Explanation and sample process for aperture geometric design functions 
-    * [[userguide:design_task_functions:dtf#computing_an_aperture_shape|Compute Aperture]] +    * [[dosimetry:userguide:design_task_functions:dtf#computing_an_aperture_shape|Compute Aperture]] 
-    * [[userguide:design_task_functions:dtf#point_vs_dual_source|Point vs Dual Source]] +    * [[dosimetry:userguide:design_task_functions:dtf#point_vs_dual_source|Point vs Dual Source]] 
-    * [[userguide:design_task_functions:dtf#aperture_mill_radius_and_smoothing|Aperture Mill Radius and Smoothing]] +    * [[dosimetry:userguide:design_task_functions:dtf#aperture_mill_radius_and_smoothing|Aperture Mill Radius and Smoothing]] 
-    * [[userguide:design_task_functions:dtf#aperture_shape_manipulation|Aperture Shape Manipulation]]+    * [[dosimetry:userguide:design_task_functions:dtf#aperture_shape_manipulation|Aperture Shape Manipulation]]
  
  
-  * **[[userguide:design_task_functions:dtf#range_compensator_design|Range Compensator Design ]]**: Explanation and sample process for range compensator degrader functions +  * **[[dosimetry:userguide:design_task_functions:dtf#range_compensator_design|Range Compensator Design ]]**: Explanation and sample process for range compensator degrader functions 
-    * [[userguide:design_task_functions:dtf#compute_an_optimized_range_compensator|Compute an Optimized Range Compensator]]  +    * [[dosimetry:userguide:design_task_functions:dtf#compute_an_optimized_range_compensator|Compute an Optimized Range Compensator]]  
-    * [[userguide:design_task_functions:dtf#patch_field_range_compensator|Patch Field Range Compensator]] +    * [[dosimetry:userguide:design_task_functions:dtf#patch_field_range_compensator|Patch Field Range Compensator]]  
 + 
 + 
 +  * **[[dosimetry:userguide:design_task_functions:dtf#pbs_fluence_optimization|PBS Fluence Optimization ]]**: Explanation and sample process for PBS plan optimization functions 
 +    * [[dosimetry:userguide:design_task_functions:dtf#optimize_pbs_plan|Compute an Optimized PBS Plan]]
 ==== Dose Calculation Functions ==== ==== Dose Calculation Functions ====
  
-Detailed function and data type definitions can be found at [[http://docs.apps.dotdecimal.com/dosimetry|Dosimetry Manifest Guide]]. Below are basic descriptions and details about the Dose Calculation Functions, dose modeling, and dose construction. +Detailed function and data type definitions can be found at [[http://docs.apps.dotdecimal.com/dosimetry|Dosimetry Manifest Guide]]. Below are basic descriptions of the available dose functions and details about the dose calculation algorithm and dose modeling.
- +
-  * **[[userguide:dose_calculation_functions:dcf#sobp_dose_functions| SOBP Dose Functions]]**  +
-    * [[userguide:dose_calculation_functions:dcf#dose_calculation_modeling|Dose Calculation Modeling]] +
-    * [[userguide:dose_calculation_functions:dcf#construction_and_modeling|Construction and Modeling]]+
  
 +  * [[dosimetry:userguide:dose_calculation_functions:dcf#pbs_dose_functions| PBS Dose Functions]] 
 +  * [[dosimetry:userguide:dose_calculation_functions:dcf#sobp_dose_functions| SOBP Dose Functions]]
 +  * [[dosimetry:userguide:dose_calculation_functions:dcf#dose_calculation_modeling|Dose Calculation & Modeling]]
 ==== Radiotherapy Support Functions ==== ==== Radiotherapy Support Functions ====
  
 Detailed function and data type definitions can be found at [[http://docs.apps.dotdecimal.com/dosimetry|Dosimetry Manifest Guide]]. Below are basic descriptions and details about common Radiotherapy Support Functions. Detailed function and data type definitions can be found at [[http://docs.apps.dotdecimal.com/dosimetry|Dosimetry Manifest Guide]]. Below are basic descriptions and details about common Radiotherapy Support Functions.
  
-  * **[[userguide:radiotherapy_support_functions:rsf|Radiotherapy Support Functions]]** +  * **[[dosimetry:userguide:radiotherapy_support_functions:rsf|Radiotherapy Support Functions]]** 
-    * [[userguide:radiotherapy_support_functions:rsf#image_processing|Image Processing]] +    * [[dosimetry:userguide:radiotherapy_support_functions:rsf#image_processing|Image Processing]] 
-    * [[userguide:radiotherapy_support_functions:rsf#contour_and_structure_modification|Contour and Structure Modification]] +    * [[dosimetry:userguide:radiotherapy_support_functions:rsf#contour_and_structure_modification|Contour and Structure Modification]] 
-    * [[userguide:radiotherapy_support_functions:rsf#degrader_manipulation|Degrader Manipulation]]+    * [[dosimetry:userguide:radiotherapy_support_functions:rsf#degrader_manipulation|Degrader Manipulation]] 
 +    * [[dosimetry:userguide:radiotherapy_support_functions:rsf#pbs_layers|PBS Energy Layer Determinations]]
  
  
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 Some more complex data types have detailed descriptions and example usages shown below: Some more complex data types have detailed descriptions and example usages shown below:
  
-  * [[userguide:datatypes#dij_matrix|Dij Matrix]]+  * [[dosimetry:userguide:datatypes#dij_matrix|Dij Matrix]]
  
-===== Examples =====+===== Calc Provider Examples =====
  
 ==== thinknode™ ==== ==== thinknode™ ====
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 Official thinknode™ user guide documentation can be found at [[https://developers.thinknode.com|https://developers.thinknode.com]]. Below are basic examples of communicating with thinknode™ calculation providers. Official thinknode™ user guide documentation can be found at [[https://developers.thinknode.com|https://developers.thinknode.com]]. Below are basic examples of communicating with thinknode™ calculation providers.
  
-  * **[[userguide:thinknode#c++|C++]]:** Sample C++ project (note: this example requires third party libraries) that details the following thinknode™ api functions: +  * **[[dosimetry:userguide:thinknode#python|Python]]:** Sample Python project (note: this example requires third party libraries) that details the following thinknode™ api functions: 
-    * [[userguide:thinknode#c++:_immutable_storage|C++: Post to Immutable Storage]] +    * [[dosimetry:userguide:thinknode#python:_immutable_storage|Python: Post to Immutable Storage]] 
-    * [[userguide:thinknode#c++:_calculation_request|C++: Post a Calculation Request]] +    * [[dosimetry:userguide:thinknode#python:_calculation_request|Python: Post a Calculation Request]]
- +
- +
-  * **[[userguide:thinknode#python|Python]]:** Sample Python project (note: this example requires third party libraries) that details the following thinknode™ api functions: +
-    * [[userguide:thinknode#python:_immutable_storage|Python: Post to Immutable Storage]] +
-    * [[userguide:thinknode#python:_calculation_request|Python: Post a Calculation Request]] +
- +
-  * **[[userguide:thinknode#node.js|Node.js]]:** Sample node.js scripts +
-    * [[userguide:thinknode#node:_decrypt_base64_blob_data|Node: Decrypt Base 64 Blob Data]]+
  
 ==== DTFs, DCFs, & RSFs ==== ==== DTFs, DCFs, & RSFs ====
  
-Refer to the [[userguide:userguide#function_categories|Function Categories]] section for explanation and usages for each function type.+Refer to the [[dosimetry:userguide:userguide#function_categories|Function Categories]] section for explanation and usages for each function type.
 ===== System Usage =====  ===== System Usage ===== 
  
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 === Grid and Image Data Interpretation === === Grid and Image Data Interpretation ===
  
-The difference between the grid and image origin definitions can easily result in image or grid data being misinterpreted. Image origins are defined at the top left most corner of the image, while grid origins are defined as the position of the upper-left most point as shown below.+The difference between the grid and image origin definitions can result in image or grid data being misinterpreted. Image origins are defined at the corner of the image, while grid origins are defined directly as the position of the corner point as shown below.
  
 For images, it's important to remember that the location of the pixel value is at the pixel center point, so the position of the first cell, for example, should be shifted by 1/2 of the pixel spacing. Grids however typically contain point data (not cell centered), so data and position correspond directly with a shift. For images, it's important to remember that the location of the pixel value is at the pixel center point, so the position of the first cell, for example, should be shifted by 1/2 of the pixel spacing. Grids however typically contain point data (not cell centered), so data and position correspond directly with a shift.
  
-{{:userguide:grid_image_origin.png?400&nolink|}}+{{dosimetry:userguide:grid_image_origin.png?400&nolink|}}
  
  
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 It's important to remember there are multiple coordinate systems being used simultaneously for dosimetry planning that are all very dependent on each other.  It's important to remember there are multiple coordinate systems being used simultaneously for dosimetry planning that are all very dependent on each other. 
  
-For a more detailed look at the coordinate systems refer to [[userguide:proton_delivery_system_conventions#coordinate_systems| Proton Delivery System Coordinate Systems]]+For a more detailed look at the coordinate systems refer to [[dosimetry:userguide:proton_delivery_system_conventions#coordinate_systems| Proton Delivery System Coordinate Systems]]
  
 ===== Known Application Limitations ===== ===== Known Application Limitations =====
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   - **Large array_types of number_types** create issues with uploading to the ISS provider if the points are too dense.   - **Large array_types of number_types** create issues with uploading to the ISS provider if the points are too dense.
     - Consider keeping arrays of numbers from being overly large.     - Consider keeping arrays of numbers from being overly large.
 +  - **PBS Dose Calculation Functions** accept the input type of proton_degrader, which allows for the use of a variable thickness range-compensator.
 +    - Currently only constant thickness range-shifters are validated for clinical use.
  
 Should you discover or suspect any additional errors or limitations not noted above, please contact the .decimal astroid Dosimetry App development lead, Kevin, Erhart, at kerhart@dotdecimal.com with details of your concerns. All concerns will be addressed as quickly as possible and follow up with the submitter will occur throughout the inquire and correction process. Should you discover or suspect any additional errors or limitations not noted above, please contact the .decimal astroid Dosimetry App development lead, Kevin, Erhart, at kerhart@dotdecimal.com with details of your concerns. All concerns will be addressed as quickly as possible and follow up with the submitter will occur throughout the inquire and correction process.
dosimetry/userguide/userguide.1435851292.txt.gz · Last modified: 2021/07/29 18:21 (external edit)