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grzankagrzanka
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Fix for Bortfeld model (#1199)
* compilation * fixes
1 parent adcd3a9 commit ab5f36b

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2 files changed

+108
-88
lines changed

2 files changed

+108
-88
lines changed

‎recompile_wasm.sh

+33
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,33 @@
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#!/bin/bash
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# Define key paths
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WORKDIR="/workspaces/web/library/distributions/JavaScript"
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OUTPUT_DIR="$WORKDIR/output"
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DEST_DIR1="/workspaces/web/src"
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DEST_DIR2="$DEST_DIR1/static/js"
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# Define GSL paths
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GSL_INCLUDE_DIRS="$HOME/usr/include"
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GSL_LIBRARY="$HOME/usr/lib/libgsl.a"
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GSL_CBLAS_LIBRARY="$HOME/usr/lib/libgslcblas.a"
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# Print status
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echo "Changing directory to: $WORKDIR"
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# Navigate to working directory and compile
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echo "Compiling JavaScript distribution..."
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cd "$WORKDIR" && GSL_INCLUDE_DIRS=$GSL_INCLUDE_DIRS GSL_LIBRARY=$GSL_LIBRARY GSL_CBLAS_LIBRARY=$GSL_CBLAS_LIBRARY ./compile_to_js.sh
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echo "Compilation complete. Copying output files..."
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# Copy compiled files to destination directories
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echo "Copying libat.js to $DEST_DIR1"
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cp "$OUTPUT_DIR/libat.js" "$DEST_DIR1"
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echo "Copying libat.js to $DEST_DIR2"
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cp "$OUTPUT_DIR/libat.js" "$DEST_DIR2"
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echo "Copying libat.wasm to $DEST_DIR1"
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cp "$OUTPUT_DIR/libat.wasm" "$DEST_DIR1"
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echo "Copying libat.wasm to $DEST_DIR2"
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cp "$OUTPUT_DIR/libat.wasm" "$DEST_DIR2"
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echo "All files copied successfully."

‎src/functionsFromC/AT_dose_Bortfeld_Gy.js

+75-88
Original file line numberDiff line numberDiff line change
@@ -1,93 +1,80 @@
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export default function AT_dose_Bortfeld_Gy(parameters) {
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let at_dose_bortfeld_gy_multi = Module.cwrap('AT_dose_Bortfeld_Gy_multi', 'null', ['number', 'array', 'number', 'number', 'number', 'number', 'number', 'number']);
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let at_dose_bortfeld_gy_single = Module.cwrap('AT_dose_Bortfeld_Gy_single', 'number', ['number', 'number', 'number', 'number', 'number', 'number']);
4-
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let at_range_bortfeld_cm = Module.cwrap('AT_range_Bortfeld_cm', 'number', ['number', 'number', 'number', 'number', 'number', 'undefined']);
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let at_fwhm_bortfeld_cm = Module.cwrap('AT_fwhm_Bortfeld_cm', 'number', ['number', 'number', 'number', 'number', 'number', 'undefined']);
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let at_max_plateau_bortfeld = Module.cwrap('AT_max_plateau_Bortfeld', 'number', ['number', 'number', 'number', 'number', 'number', 'undefined']);
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/*********************STANDARD PARAMETER*************************/
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if(typeof parameters.n === "undefined"){
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alert("MESSAGE TO DEVELOPER: NO PARAMETER n IN OBJECT PASSED TO THIS FUNCTIONS");
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return "error";
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// Validate required parameters
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if (!parameters) {
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throw new Error("Parameters object is required.");
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}
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let n = parameters.n;
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/*********************INPUT ARRAY********************************/
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if(typeof parameters.z_cm === "undefined"){
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alert("MESSAGE TO DEVELOPER: NO PARAMETER z_cm IN OBJECT PASSED TO THIS FUNCTIONS");
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return "error";
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const requiredParams = ['n', 'z_cm', 'E_MeV', 'entrance_dose_Gy', 'sigma_E_MeV', 'material_no', 'eps'];
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for (const param of requiredParams) {
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if (typeof parameters[param] === "undefined") {
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throw new Error(`Missing parameter: ${param}`);
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}
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}
22-
let z_cm = parameters.z_cm;
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let z_cmData = new Float64Array(z_cm);
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let z_cmDataBytesNumber = z_cmData.length * z_cmData.BYTES_PER_ELEMENT;
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let z_cmDataPointer = Module._malloc(z_cmDataBytesNumber);
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let z_cmHeap = new Uint8Array(Module.HEAPF64.buffer, z_cmDataPointer, z_cmDataBytesNumber);
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z_cmHeap.set(new Uint8Array(z_cmData.buffer));
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/*********************STANDARD PARAMETER*************************/
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if(typeof parameters.E_MeV === "undefined"){
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alert("MESSAGE TO DEVELOPER: NO PARAMETER E_MeV IN OBJECT PASSED TO THIS FUNCTIONS");
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return "error";
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}
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let E_MeV = parameters.E_MeV;
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/*********************STANDARD PARAMETER*************************/
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if(typeof parameters.entrance_dose_Gy === "undefined"){
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alert("MESSAGE TO DEVELOPER: NO PARAMETER entrance_dose_Gy IN OBJECT PASSED TO THIS FUNCTIONS");
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return "error";
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}
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let entrance_dose_Gy = parameters.entrance_dose_Gy;
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/*********************STANDARD PARAMETER*************************/
44-
if(typeof parameters.sigma_E_MeV === "undefined"){
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alert("MESSAGE TO DEVELOPER: NO PARAMETER sigma_E_MeV IN OBJECT PASSED TO THIS FUNCTIONS");
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return "error";
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const n = parameters.n;
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const z_cm = parameters.z_cm;
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if (!Array.isArray(z_cm)) {
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throw new Error("Parameter 'z_cm' must be an array.");
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}
48-
let sigma_E_MeV = parameters.sigma_E_MeV;
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/*********************STANDARD PARAMETER*************************/
51-
if(typeof parameters.material_no === "undefined"){
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alert("MESSAGE TO DEVELOPER: NO PARAMETER material_no IN OBJECT PASSED TO THIS FUNCTIONS");
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return "error";
54-
}
55-
let material_no = parameters.material_no;
56-
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/*********************STANDARD PARAMETER*************************/
58-
if(typeof parameters.eps === "undefined"){
59-
alert("MESSAGE TO DEVELOPER: NO PARAMETER eps IN OBJECT PASSED TO THIS FUNCTIONS");
60-
return "error";
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const E_MeV = parameters.E_MeV;
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const entrance_dose_Gy = parameters.entrance_dose_Gy;
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const sigma_E_MeV = parameters.sigma_E_MeV;
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const material_no = parameters.material_no;
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const eps = parameters.eps;
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// Setup wasm functions
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// Note: Change second argument from 'array' to 'number'
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const at_dose_bortfeld_gy_multi = Module.cwrap('AT_dose_Bortfeld_Gy_multi', null,
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['number', 'number', 'number', 'number', 'number', 'number', 'number', 'number']);
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const at_dose_bortfeld_gy_single = Module.cwrap('AT_dose_Bortfeld_Gy_single', 'number',
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['number', 'number', 'number', 'number', 'number', 'number']);
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const at_range_bortfeld_cm = Module.cwrap('AT_range_Bortfeld_cm', 'number',
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['number', 'number', 'number', 'number', 'number', 'undefined']);
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const at_fwhm_bortfeld_cm = Module.cwrap('AT_fwhm_Bortfeld_cm', 'number',
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['number', 'number', 'number', 'number']);
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const at_max_plateau_bortfeld = Module.cwrap('AT_max_plateau_Bortfeld', 'number',
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['number', 'number', 'number', 'number']);
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// Allocate memory for the input array z_cm and the output array dose_Gy
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const z_cmData = new Float64Array(z_cm);
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const z_cmDataBytesNumber = z_cmData.length * z_cmData.BYTES_PER_ELEMENT;
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const z_cmDataPointer = Module._malloc(z_cmDataBytesNumber);
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const z_cmHeap = new Uint8Array(Module.HEAPF64.buffer, z_cmDataPointer, z_cmDataBytesNumber);
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z_cmHeap.set(new Uint8Array(z_cmData.buffer));
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// Create output array with proper size
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const dose_GyReturnData = new Float64Array(n);
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const dose_GyReturnDataBytesNumber = dose_GyReturnData.length * dose_GyReturnData.BYTES_PER_ELEMENT;
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const dose_GyReturnDataPointer = Module._malloc(dose_GyReturnDataBytesNumber);
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// const dose_GyReturnHeap = new Uint8Array(Module.HEAPF64.buffer, dose_GyReturnDataPointer, dose_GyReturnDataBytesNumber);
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50+
try {
51+
// Calculate entrance dose for unit fluence at depth z_cm = 0
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const entrance_dose_for_unit_fluence_Gy = at_dose_bortfeld_gy_single(0.0, 1.0, E_MeV, sigma_E_MeV, material_no, eps);
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const fluence_cm2 = entrance_dose_Gy / entrance_dose_for_unit_fluence_Gy;
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// Compute dose over all depths: pass pointer instead of typed array view
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at_dose_bortfeld_gy_multi(n, z_cmDataPointer, fluence_cm2, E_MeV, sigma_E_MeV, material_no, eps, dose_GyReturnDataPointer);
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const resultFromArray = new Float64Array(Module.HEAPF64.buffer, dose_GyReturnDataPointer, n);
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// Compute additional metadata
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const dose_drop = -1;
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const search_direction = 1;
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const range_cm = at_range_bortfeld_cm(E_MeV, sigma_E_MeV, material_no, eps, dose_drop, search_direction);
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const fwhm_cm = at_fwhm_bortfeld_cm(E_MeV, sigma_E_MeV, material_no, eps);
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const max_plateau = at_max_plateau_bortfeld(E_MeV, sigma_E_MeV, material_no, eps);
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return {
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data: Array.from(resultFromArray),
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metadata: {
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range_cm: range_cm,
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fwhm_cm: fwhm_cm,
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max_plateau: max_plateau
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}
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};
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} finally {
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// Free allocated memory to avoid memory leaks
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// Module._free(z_cmDataPointer);
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// Module._free(dose_GyReturnDataPointer);
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}
62-
let eps = parameters.eps;
63-
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/*********************OUTPUT ARRAY*******************************/
65-
let dose_GyReturnData = new Float64Array(new Array(n));
66-
let dose_GyReturnDataBytesNumber = dose_GyReturnData.length * dose_GyReturnData.BYTES_PER_ELEMENT;
67-
let dose_GyReturnDataPointer = Module._malloc(dose_GyReturnDataBytesNumber);
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let dose_GyReturnHeap = new Uint8Array(Module.HEAPF64.buffer, dose_GyReturnDataPointer, dose_GyReturnDataBytesNumber);
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70-
/*********************CALL FUNCTION******************************/
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// dose calculated at depth z_cm = 0 (entrance) and fluence_cm = 1 (unit fluence)
73-
let entrance_dose_for_unit_fluence_Gy = at_dose_bortfeld_gy_single(0.0, 1.0, E_MeV, sigma_E_MeV, material_no, eps);
74-
let fluence_cm2 = entrance_dose_Gy / entrance_dose_for_unit_fluence_Gy;
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76-
let result = at_dose_bortfeld_gy_multi(n, z_cmHeap, fluence_cm2, E_MeV, sigma_E_MeV, material_no, eps, dose_GyReturnHeap.byteOffset);
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let resultFromArray = new Float64Array(dose_GyReturnHeap.buffer, dose_GyReturnHeap.byteOffset, dose_GyReturnData.length);
78-
79-
/*********************STANDARD PARAMETER*************************/
80-
let dose_drop = -1;
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/*********************STANDARD PARAMETER*************************/
83-
let search_direction = 1;
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/*********************CALL FUNCTION******************************/
86-
let range_cm = at_range_bortfeld_cm(E_MeV, sigma_E_MeV, material_no, eps, dose_drop, search_direction);
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let fwhm_cm = at_fwhm_bortfeld_cm(E_MeV, sigma_E_MeV, material_no, eps, dose_drop, search_direction);
88-
let max_plateau = at_max_plateau_bortfeld(E_MeV, sigma_E_MeV, material_no, eps, dose_drop, search_direction);
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90-
let combined ={'data' : [].slice.call(resultFromArray) , 'metadata' : [range_cm,fwhm_cm,max_plateau] };
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return combined;
93-
}
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}
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