ml-spectra-fitting - npm Package Compare versions

Comparing version 4.1.1 to 4.2.0

lib-esm/index.d.ts

@@ -38,2 +38,26 @@ import { DataXY, DoubleArray } from 'cheminfo-types';
 declare type OptimizationParameter = number | ((peak: Peak) => number);
+interface GeneralAlgorithmOptions {
+    /** number of max iterations
+     * @default 100
+     */
+    maxIterations?: number;
+}
+export interface LMOptimizationOptions extends GeneralAlgorithmOptions {
+    /** maximum time running before break in seconds */
+    timeout?: number;
+    /** damping factor
+     * @default 1.5
+     */
+    damping?: number;
+    /** error tolerance
+     * @default 1e-8
+     */
+    errorTolerance?: number;
+}
+export interface DirectOptimizationOptions extends GeneralAlgorithmOptions {
+    epsilon?: number;
+    tolerance?: number;
+    tolerance2?: number;
+    initialState?: any;
+}
 export interface OptimizationOptions {
@@ -43,20 +67,5 @@ /**
      */
-    kind?: 'lm' | 'levenbergMarquardt';
+    kind?: 'lm' | 'levenbergMarquardt' | 'direct';
     /** options for the specific kind of algorithm */
-    options?: {
-        /** maximum time running before break in seconds */
-        timeout?: number;
-        /** damping factor
-         * @default 1.5
-         */
-        damping?: number;
-        /** number of max iterations
-         * @default 100
-         */
-        maxIterations?: number;
-        /** error tolerance
-         * @default 1e-8
-         */
-        errorTolerance?: number;
-    };
+    options?: DirectOptimizationOptions | LMOptimizationOptions;
 }
@@ -63,0 +72,0 @@ export interface OptimizeOptions {

lib-esm/shapes/getSumOfShapes.js

@@ -13,3 +13,3 @@ /**
                 const y = parameters[peak.fromIndex + 1];
-                for (let i = 2; i <= peak.toIndex; i++) {
+                for (let i = 2; i < parameters.length; i++) {
                     //@ts-expect-error Not simply to solve the issue
@@ -16,0 +16,0 @@ peak.shapeFct[peak.parameters[i]] = parameters[peak.fromIndex + i];

lib-esm/util/selectMethod.d.ts

 import { levenbergMarquardt } from 'ml-levenberg-marquardt';
 import { OptimizationOptions } from '../index';
+import { directOptimization } from './wrappers/directOptimization';
 /** Algorithm to select the method.
@@ -10,8 +11,46 @@ * @param optimizationOptions - Optimization options
     optimizationOptions: {
+        damping: number;
+        maxIterations: number;
+        errorTolerance: number;
+    } | {
+        epsilon?: number | undefined;
+        tolerance?: number | undefined;
+        tolerance2?: number | undefined;
+        initialState?: any;
+        maxIterations: number;
+        damping: number;
+        errorTolerance: number;
+    } | {
         timeout?: number | undefined;
         damping: number;
+        errorTolerance: number;
         maxIterations: number;
-        errorTolerance: number;
     };
+} | {
+    algorithm: typeof directOptimization;
+    optimizationOptions: {
+        iterations: number;
+        epsilon: number;
+        tolerance: number;
+        tolerance2: number;
+        initialState: {};
+    } | {
+        epsilon: number;
+        tolerance: number;
+        tolerance2: number;
+        initialState: any;
+        maxIterations?: number | undefined;
+        iterations: number;
+    } | {
+        timeout?: number | undefined;
+        damping?: number | undefined;
+        errorTolerance?: number | undefined;
+        maxIterations?: number | undefined;
+        iterations: number;
+        epsilon: number;
+        tolerance: number;
+        tolerance2: number;
+        initialState: {};
+    };
 };
 //# sourceMappingURL=selectMethod.d.ts.map

lib-esm/util/selectMethod.js

 import { levenbergMarquardt } from 'ml-levenberg-marquardt';
+import { directOptimization } from './wrappers/directOptimization';
 /** Algorithm to select the method.
@@ -20,2 +21,15 @@ * @param optimizationOptions - Optimization options
             };
+        case 'direct': {
+            return {
+                algorithm: directOptimization,
+                optimizationOptions: {
+                    iterations: 20,
+                    epsilon: 1e-4,
+                    tolerance: 1e-16,
+                    tolerance2: 1e-12,
+                    initialState: {},
+                    ...options,
+                },
+            };
+        }
         default:
@@ -22,0 +36,0 @@ throw new Error(`Unknown fitting algorithm`);

lib/index.d.ts

@@ -38,2 +38,26 @@ import { DataXY, DoubleArray } from 'cheminfo-types';
 declare type OptimizationParameter = number | ((peak: Peak) => number);
+interface GeneralAlgorithmOptions {
+    /** number of max iterations
+     * @default 100
+     */
+    maxIterations?: number;
+}
+export interface LMOptimizationOptions extends GeneralAlgorithmOptions {
+    /** maximum time running before break in seconds */
+    timeout?: number;
+    /** damping factor
+     * @default 1.5
+     */
+    damping?: number;
+    /** error tolerance
+     * @default 1e-8
+     */
+    errorTolerance?: number;
+}
+export interface DirectOptimizationOptions extends GeneralAlgorithmOptions {
+    epsilon?: number;
+    tolerance?: number;
+    tolerance2?: number;
+    initialState?: any;
+}
 export interface OptimizationOptions {
@@ -43,20 +67,5 @@ /**
      */
-    kind?: 'lm' | 'levenbergMarquardt';
+    kind?: 'lm' | 'levenbergMarquardt' | 'direct';
     /** options for the specific kind of algorithm */
-    options?: {
-        /** maximum time running before break in seconds */
-        timeout?: number;
-        /** damping factor
-         * @default 1.5
-         */
-        damping?: number;
-        /** number of max iterations
-         * @default 100
-         */
-        maxIterations?: number;
-        /** error tolerance
-         * @default 1e-8
-         */
-        errorTolerance?: number;
-    };
+    options?: DirectOptimizationOptions | LMOptimizationOptions;
 }
@@ -63,0 +72,0 @@ export interface OptimizeOptions {

lib/shapes/getSumOfShapes.js

@@ -16,3 +16,3 @@ "use strict";
                 const y = parameters[peak.fromIndex + 1];
-                for (let i = 2; i <= peak.toIndex; i++) {
+                for (let i = 2; i < parameters.length; i++) {
                     //@ts-expect-error Not simply to solve the issue
@@ -19,0 +19,0 @@ peak.shapeFct[peak.parameters[i]] = parameters[peak.fromIndex + i];

lib/util/selectMethod.d.ts

 import { levenbergMarquardt } from 'ml-levenberg-marquardt';
 import { OptimizationOptions } from '../index';
+import { directOptimization } from './wrappers/directOptimization';
 /** Algorithm to select the method.
@@ -10,8 +11,46 @@ * @param optimizationOptions - Optimization options
     optimizationOptions: {
+        damping: number;
+        maxIterations: number;
+        errorTolerance: number;
+    } | {
+        epsilon?: number | undefined;
+        tolerance?: number | undefined;
+        tolerance2?: number | undefined;
+        initialState?: any;
+        maxIterations: number;
+        damping: number;
+        errorTolerance: number;
+    } | {
         timeout?: number | undefined;
         damping: number;
+        errorTolerance: number;
         maxIterations: number;
-        errorTolerance: number;
     };
+} | {
+    algorithm: typeof directOptimization;
+    optimizationOptions: {
+        iterations: number;
+        epsilon: number;
+        tolerance: number;
+        tolerance2: number;
+        initialState: {};
+    } | {
+        epsilon: number;
+        tolerance: number;
+        tolerance2: number;
+        initialState: any;
+        maxIterations?: number | undefined;
+        iterations: number;
+    } | {
+        timeout?: number | undefined;
+        damping?: number | undefined;
+        errorTolerance?: number | undefined;
+        maxIterations?: number | undefined;
+        iterations: number;
+        epsilon: number;
+        tolerance: number;
+        tolerance2: number;
+        initialState: {};
+    };
 };
 //# sourceMappingURL=selectMethod.d.ts.map

lib/util/selectMethod.js

@@ -5,2 +5,3 @@ "use strict";
 const ml_levenberg_marquardt_1 = require("ml-levenberg-marquardt");
+const directOptimization_1 = require("./wrappers/directOptimization");
 /** Algorithm to select the method.
@@ -24,2 +25,15 @@ * @param optimizationOptions - Optimization options
             };
+        case 'direct': {
+            return {
+                algorithm: directOptimization_1.directOptimization,
+                optimizationOptions: {
+                    iterations: 20,
+                    epsilon: 1e-4,
+                    tolerance: 1e-16,
+                    tolerance2: 1e-12,
+                    initialState: {},
+                    ...options,
+                },
+            };
+        }
         default:
@@ -26,0 +40,0 @@ throw new Error(`Unknown fitting algorithm`);

package.json

 {
   "name": "ml-spectra-fitting",
-  "version": "4.1.1",
+  "version": "4.2.0",
   "description": "Fit spectra using gaussian or lorentzian",
@@ -64,2 +64,3 @@ "main": "./lib/index.js",
     "ml-array-max": "^1.2.4",
+    "ml-direct": "^0.1.1",
     "ml-levenberg-marquardt": "^4.1.0",
@@ -66,0 +67,0 @@ "ml-peak-shape-generator": "^4.1.2",

src/index.ts

@@ -45,2 +45,28 @@ import { DataXY, DoubleArray } from 'cheminfo-types';
 
+interface GeneralAlgorithmOptions {
+  /** number of max iterations
+   * @default 100
+   */
+  maxIterations?: number;
+}
+export interface LMOptimizationOptions extends GeneralAlgorithmOptions {
+  /** maximum time running before break in seconds */
+  timeout?: number;
+  /** damping factor
+   * @default 1.5
+   */
+  damping?: number;
+  /** error tolerance
+   * @default 1e-8
+   */
+  errorTolerance?: number;
+}
+
+export interface DirectOptimizationOptions extends GeneralAlgorithmOptions {
+  epsilon?: number;
+  tolerance?: number;
+  tolerance2?: number;
+  initialState?: any;
+}
+
 export interface OptimizationOptions {
@@ -50,21 +76,6 @@ /**
    */
-  kind?: 'lm' | 'levenbergMarquardt';
+  kind?: 'lm' | 'levenbergMarquardt' | 'direct';
 
   /** options for the specific kind of algorithm */
-  options?: {
-    /** maximum time running before break in seconds */
-    timeout?: number;
-    /** damping factor
-     * @default 1.5
-     */
-    damping?: number;
-    /** number of max iterations
-     * @default 100
-     */
-    maxIterations?: number;
-    /** error tolerance
-     * @default 1e-8
-     */
-    errorTolerance?: number;
-  };
+  options?: DirectOptimizationOptions | LMOptimizationOptions;
 }
@@ -71,0 +82,0 @@

src/shapes/getSumOfShapes.ts

@@ -16,3 +16,3 @@ import { InternalPeak } from '../util/internalPeaks/getInternalPeaks';
         const y = parameters[peak.fromIndex + 1];
-        for (let i = 2; i <= peak.toIndex; i++) {
+        for (let i = 2; i < parameters.length; i++) {
           //@ts-expect-error Not simply to solve the issue
@@ -19,0 +19,0 @@ peak.shapeFct[peak.parameters[i]] = parameters[peak.fromIndex + i];

src/util/selectMethod.ts

@@ -5,2 +5,4 @@ import { levenbergMarquardt } from 'ml-levenberg-marquardt';
 
+import { directOptimization } from './wrappers/directOptimization';
+
 /** Algorithm to select the method.
@@ -25,2 +27,15 @@ * @param optimizationOptions - Optimization options
       };
+    case 'direct': {
+      return {
+        algorithm: directOptimization,
+        optimizationOptions: {
+          iterations: 20,
+          epsilon: 1e-4,
+          tolerance: 1e-16,
+          tolerance2: 1e-12,
+          initialState: {},
+          ...options,
+        },
+      };
+    }
     default:
@@ -27,0 +42,0 @@ throw new Error(`Unknown fitting algorithm`);

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Improved metrics

Total package byte prevSize

117912

increased by14.02%

Number of package files

73

increased by15.87%

Lines of code

2369

increased by16.47%

Worsened metrics

Dependency count

6

increased by20%

Dependency changes

• + Addedml-direct@^0.1.1

• + Addedml-direct@0.1.3(transitive)

• + Addedml-spectra-processing@12.11.0(transitive)