ml-gsd - npm Package Compare versions

Comparing version 10.0.0 to 10.1.0

lib-esm/gsd.d.ts

@@ -24,3 +24,7 @@ import type { DataXY } from 'cheminfo-types';
     /**
-     * Threshold to determine if a given peak should be considered as a noise
+     * Peak under the noiseLevel (or over in case of maxCriteria=false) are ignored.
+     */
+    noiseLevel?: number;
+    /**
+     * Minimal height of small peaks based on the ratio between min and max
      * @default 0.00025
@@ -27,0 +31,0 @@ */

lib-esm/gsd.js

 import { sgg } from 'ml-savitzky-golay-generalized';
-import { xIsEquallySpaced, xIsMonotoneIncreasing, xMinValue, xMaxValue, } from 'ml-spectra-processing';
+import { xIsEquallySpaced, xIsMonotoneIncreasing, xMinValue, xMaxValue, xNoiseStandardDeviation, } from 'ml-spectra-processing';
 import { optimizeTop } from './utils/optimizeTop';
@@ -15,3 +15,3 @@ /**
         polynomial: 3,
-    }, smoothY = false, maxCriteria = true, minMaxRatio = 0.00025, realTopDetection = false, } = options;
+    }, noiseLevel, smoothY = false, maxCriteria = true, minMaxRatio = 0.00025, realTopDetection = false, } = options;
     let { x, y } = data;
@@ -25,2 +25,21 @@ if (!xIsMonotoneIncreasing(x)) {
     let equallySpaced = xIsEquallySpaced(x);
+    if (noiseLevel === undefined) {
+        if (equallySpaced) {
+            const noiseInfo = xNoiseStandardDeviation(y);
+            if (maxCriteria) {
+                noiseLevel = noiseInfo.median + 1.5 * noiseInfo.sd;
+            }
+            else {
+                noiseLevel = -noiseInfo.median + 1.5 * noiseInfo.sd;
+            }
+        }
+        else {
+            noiseLevel = 0;
+        }
+    }
+    else {
+        if (maxCriteria === false) {
+            noiseLevel *= -1;
+        }
+    }
     if (maxCriteria === false) {
@@ -31,2 +50,9 @@ for (let i = 0; i < y.length; i++) {
     }
+    if (noiseLevel) {
+        for (let i = 0; i < y.length; i++) {
+            if (y[i] < noiseLevel) {
+                y[i] = noiseLevel;
+            }
+        }
+    }
     let yData = y;
@@ -33,0 +59,0 @@ let dY, ddY;

lib-esm/index.d.ts

 export * from './gsd';
 export * from './post/optimizePeaks';
 export * from './post/broadenPeaks';
+export * from './GSDBroadenPeak';
+export * from './GSDPeak';
+export * from './GSDPeakOptimized';
 //# sourceMappingURL=index.d.ts.map

lib-esm/index.js

@@ -6,2 +6,5 @@ export * from './gsd';
 export * from './post/broadenPeaks';
+export * from './GSDBroadenPeak';
+export * from './GSDPeak';
+export * from './GSDPeakOptimized';
 //# sourceMappingURL=index.js.map

lib/gsd.d.ts

@@ -24,3 +24,7 @@ import type { DataXY } from 'cheminfo-types';
     /**
-     * Threshold to determine if a given peak should be considered as a noise
+     * Peak under the noiseLevel (or over in case of maxCriteria=false) are ignored.
+     */
+    noiseLevel?: number;
+    /**
+     * Minimal height of small peaks based on the ratio between min and max
      * @default 0.00025
@@ -27,0 +31,0 @@ */

lib/gsd.js

@@ -18,3 +18,3 @@ "use strict";
         polynomial: 3,
-    }, smoothY = false, maxCriteria = true, minMaxRatio = 0.00025, realTopDetection = false, } = options;
+    }, noiseLevel, smoothY = false, maxCriteria = true, minMaxRatio = 0.00025, realTopDetection = false, } = options;
     let { x, y } = data;
@@ -28,2 +28,21 @@ if (!(0, ml_spectra_processing_1.xIsMonotoneIncreasing)(x)) {
     let equallySpaced = (0, ml_spectra_processing_1.xIsEquallySpaced)(x);
+    if (noiseLevel === undefined) {
+        if (equallySpaced) {
+            const noiseInfo = (0, ml_spectra_processing_1.xNoiseStandardDeviation)(y);
+            if (maxCriteria) {
+                noiseLevel = noiseInfo.median + 1.5 * noiseInfo.sd;
+            }
+            else {
+                noiseLevel = -noiseInfo.median + 1.5 * noiseInfo.sd;
+            }
+        }
+        else {
+            noiseLevel = 0;
+        }
+    }
+    else {
+        if (maxCriteria === false) {
+            noiseLevel *= -1;
+        }
+    }
     if (maxCriteria === false) {
@@ -34,2 +53,9 @@ for (let i = 0; i < y.length; i++) {
     }
+    if (noiseLevel) {
+        for (let i = 0; i < y.length; i++) {
+            if (y[i] < noiseLevel) {
+                y[i] = noiseLevel;
+            }
+        }
+    }
     let yData = y;
@@ -36,0 +62,0 @@ let dY, ddY;

lib/index.d.ts

 export * from './gsd';
 export * from './post/optimizePeaks';
 export * from './post/broadenPeaks';
+export * from './GSDBroadenPeak';
+export * from './GSDPeak';
+export * from './GSDPeakOptimized';
 //# sourceMappingURL=index.d.ts.map

lib/index.js

@@ -18,2 +18,5 @@ "use strict";
 __exportStar(require("./post/broadenPeaks"), exports);
+__exportStar(require("./GSDBroadenPeak"), exports);
+__exportStar(require("./GSDPeak"), exports);
+__exportStar(require("./GSDPeakOptimized"), exports);
 //# sourceMappingURL=index.js.map

package.json

 {
   "name": "ml-gsd",
-  "version": "10.0.0",
+  "version": "10.1.0",
   "description": "Global Spectra Deconvolution",
@@ -66,7 +66,7 @@ "main": "./lib/index.js",
     "eslint-config-cheminfo-typescript": "^10.3.0",
-    "eslint-plugin-jest": "^26.1.0",
+    "eslint-plugin-jest": "^26.1.1",
     "esm": "^3.2.25",
     "jest": "^27.5.1",
     "jest-matcher-deep-close-to": "^3.0.2",
-    "mf-global": "^1.4.20",
+    "mf-global": "^1.4.22",
     "ml-stat": "^1.3.3",
@@ -76,3 +76,3 @@ "nodemon": "^2.0.15",
     "rimraf": "^3.0.2",
-    "spectrum-generator": "^6.0.4",
+    "spectrum-generator": "^7.0.0",
     "ts-jest": "^27.1.3",
@@ -87,4 +87,4 @@ "typescript": "^4.5.5",
     "ml-spectra-fitting": "^3.0.4",
-    "ml-spectra-processing": "^10.0.0"
+    "ml-spectra-processing": "^10.1.2"
   }
 }

README.md

@@ -15,2 +15,3 @@ # global-spectral-deconvolution and peak optimizer
 - `maxCriteria`: search either for maxima or minima. We will invert the data and the results if searching for a minima
+- `noiseLevel`: specifies the noise level. All the peaks bellow this value (or above in case of maxCriteria=false) are ignored. By default the noiseLevel will be set to the median + 3 x sd. This is a good value when not too many peaks are present in the spectrum.
 - `sgOptions`: Savitzky-Golay filter that is used to smooth the data for the calculation of the derivatives
@@ -17,0 +18,0 @@ - `smoothY`: If this value is true the SG filter is not only applied during the calculation of the derivatives but also on the original data

src/__tests__/zero.test.ts

@@ -9,3 +9,3 @@ import { gsd } from '../gsd';
       gsd({ x, y });
-    }).toThrow('Window size is higher than the data length 9>0');
+    }).toThrow('input must not be empty');
   });
@@ -12,0 +12,0 @@

src/gsd.ts

@@ -8,2 +8,3 @@ import type { DataXY } from 'cheminfo-types';
   xMaxValue,
+  xNoiseStandardDeviation,
 } from 'ml-spectra-processing';
@@ -34,7 +35,10 @@
   /**
-   * Threshold to determine if a given peak should be considered as a noise
+   * Peak under the noiseLevel (or over in case of maxCriteria=false) are ignored.
+   */
+  noiseLevel?: number;
+  /**
+   * Minimal height of small peaks based on the ratio between min and max
    * @default 0.00025
    */
   minMaxRatio?: number;
-
   /**
@@ -61,2 +65,3 @@ * Use a quadratic optimizations with the peak and its 3 closest neighbors
     },
+    noiseLevel,
     smoothY = false,
@@ -78,2 +83,19 @@ maxCriteria = true,
 
+  if (noiseLevel === undefined) {
+    if (equallySpaced) {
+      const noiseInfo = xNoiseStandardDeviation(y);
+      if (maxCriteria) {
+        noiseLevel = noiseInfo.median + 1.5 * noiseInfo.sd;
+      } else {
+        noiseLevel = -noiseInfo.median + 1.5 * noiseInfo.sd;
+      }
+    } else {
+      noiseLevel = 0;
+    }
+  } else {
+    if (maxCriteria === false) {
+      noiseLevel *= -1;
+    }
+  }
+
   if (maxCriteria === false) {
@@ -84,2 +106,9 @@ for (let i = 0; i < y.length; i++) {
   }
+  if (noiseLevel) {
+    for (let i = 0; i < y.length; i++) {
+      if (y[i] < noiseLevel) {
+        y[i] = noiseLevel;
+      }
+    }
+  }
 
@@ -86,0 +115,0 @@ let yData = y;

src/index.ts

@@ -6,1 +6,5 @@ export * from './gsd';
 export * from './post/broadenPeaks';
+
+export * from './GSDBroadenPeak';
+export * from './GSDPeak';
+export * from './GSDPeakOptimized';

Fixed alerts

Major refactor

Supply chain risk

Package has recently undergone a major refactor. It may be unstable or indicate significant internal changes. Use caution when updating to versions that include significant changes.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

2607374

0.33%

Number of package files

135

1.5%

Lines of code

9757

2.53%

Number of lines in readme file

126

0.8%

Number of medium supply chain risk alerts

0

-100%

Dependency changes

• Updated

  ml-spectra-processing@^10.1.2