diff --git a/functions/addMissingShape.html b/functions/addMissingShape.html index f41e35c..d5b4e62 100644 --- a/functions/addMissingShape.html +++ b/functions/addMissingShape.html @@ -3,4 +3,4 @@ window.addEventListener('load', () => window.renderMathInElement(document.body, window.__typeDocPluginKatexOptions));

Function addMissingShape

  • addMissingShape<T>(peaks, options?): (T & {
        shape: Shape1D;
    })[]

  • add missing property if it does not exist in the peak, if shape exists but fwhm doesn't, it will be calculated from peak.width

    -

    Type Parameters

    • T extends {
          width: number;
      }

    Parameters

    • peaks: T[]
    • options: {
          output?: T[];
          shape?: Shape1D;
      } = {}
      • Optional output?: T[]
      • Optional shape?: Shape1D

    Returns (T & {
        shape: Shape1D;
    })[]

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Type Parameters

Parameters

Returns (T & {
    shape: Shape1D;
})[]

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\ No newline at end of file diff --git a/functions/broadenPeaks.html b/functions/broadenPeaks.html index 5215b5c..42ce22b 100644 --- a/functions/broadenPeaks.html +++ b/functions/broadenPeaks.html @@ -11,4 +11,4 @@

Default

false

Returns WithIDOrShape<T>[]

peakList

-

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Function gsd

  • gsd(data, options?): GSDPeakID[]

  • Global spectra deconvolution

    -

    Parameters

    • data: DataXY<DoubleArray>

      Object data with x and y arrays. Values in x has to be growing

      -
    • options: GSDOptions = {}

    Returns GSDPeakID[]

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Parameters

Returns GSDPeakID[]

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\ No newline at end of file diff --git a/functions/joinBroadPeaks.html b/functions/joinBroadPeaks.html index 9fbeec3..be3655c 100644 --- a/functions/joinBroadPeaks.html +++ b/functions/joinBroadPeaks.html @@ -1,4 +1,4 @@ joinBroadPeaks | ml-gsd

Function joinBroadPeaks

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Function joinBroadPeaks

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\ No newline at end of file diff --git a/functions/optimizePeaks.html b/functions/optimizePeaks.html index 34948b1..31f8251 100644 --- a/functions/optimizePeaks.html +++ b/functions/optimizePeaks.html @@ -3,6 +3,6 @@ window.addEventListener('load', () => window.renderMathInElement(document.body, window.__typeDocPluginKatexOptions));

Function optimizePeaks

  • optimizePeaks<T>(data, peakList, options?): GSDPeakOptimizedIDOrNot<T>[]

  • Optimize the position (x), max intensity (y), full width at half maximum (fwhm) and the ratio of gaussian contribution (mu) if it's required. It currently supports three kind of shapes: gaussian, lorentzian and pseudovoigt

    -

    Type Parameters

    Parameters

    • data: DataXY<DoubleArray>

      An object containing the x and y data to be fitted.

      +

      Type Parameters

      Parameters

      • data: DataXY<NumberArray>

        An object containing the x and y data to be fitted.

      • peakList: T[]

        A list of initial parameters to be optimized. e.g. coming from a peak picking [{x, y, width}].

        -
      • options: OptimizePeaksOptions = {}

      Returns GSDPeakOptimizedIDOrNot<T>[]

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  • options: OptimizePeaksOptions = {}

    • Returns GSDPeakOptimizedIDOrNot<T>[]

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    \ No newline at end of file diff --git a/functions/optimizePeaksWithLogs.html b/functions/optimizePeaksWithLogs.html index e028e81..8c777fa 100644 --- a/functions/optimizePeaksWithLogs.html +++ b/functions/optimizePeaksWithLogs.html @@ -3,6 +3,6 @@ window.addEventListener('load', () => window.renderMathInElement(document.body, window.__typeDocPluginKatexOptions));

    Function optimizePeaksWithLogs

    • optimizePeaksWithLogs<T>(data, peakList, options?): {
          logs: any[];
          optimizedPeaks: GSDPeakOptimizedIDOrNot<T>[];
      }

    • Optimize the position (x), max intensity (y), full width at half maximum (fwhm) and the ratio of gaussian contribution (mu) if it's required. It currently supports three kind of shapes: gaussian, lorentzian and pseudovoigt

      -

      Type Parameters

      Parameters

      • data: DataXY<DoubleArray>

        An object containing the x and y data to be fitted.

        +

        Type Parameters

        Parameters

        • data: DataXY<NumberArray>

          An object containing the x and y data to be fitted.

        • peakList: T[]

          A list of initial parameters to be optimized. e.g. coming from a peak picking [{x, y, width}].

          -
        • options: OptimizePeaksOptions = {}

        Returns {
            logs: any[];
            optimizedPeaks: GSDPeakOptimizedIDOrNot<T>[];
        }

        • logs: any[]
        • optimizedPeaks: GSDPeakOptimizedIDOrNot<T>[]

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  • options: OptimizePeaksOptions = {}

    • Returns {
        logs: any[];
        optimizedPeaks: GSDPeakOptimizedIDOrNot<T>[];
    }

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    \ No newline at end of file diff --git a/functions/setShape.html b/functions/setShape.html index 0cf67fd..59d47cb 100644 --- a/functions/setShape.html +++ b/functions/setShape.html @@ -5,4 +5,4 @@

    Type Parameters

    Parameters

    Returns (T & {
        shape: Shape1D;
    })[]

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    Returns (T & {
        shape: Shape1D;
    })[]

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    \ No newline at end of file diff --git a/interfaces/GSDBroadenPeak.html b/interfaces/GSDBroadenPeak.html index 794aad0..571a10f 100644 --- a/interfaces/GSDBroadenPeak.html +++ b/interfaces/GSDBroadenPeak.html @@ -1,7 +1,7 @@ GSDBroadenPeak | ml-gsd

    Interface GSDBroadenPeak

    interface GSDBroadenPeak {
        from: {
            x: number;
        };
        id?: string;
        index: number;
        shape?: Shape1D;
        to: {
            x: number;
        };
        width: number;
        x: number;
        y: number;
    }

    Properties

    from +

    Interface GSDBroadenPeak

    interface GSDBroadenPeak {
        from: {
            x: number;
        };
        id?: string;
        index: number;
        shape?: Shape1D;
        to: {
            x: number;
        };
        width: number;
        x: number;
        y: number;
    }

    Properties

    from id? index shape? @@ -9,4 +9,4 @@ width x y -

    Properties

    from

    from: {
        x: number;
    }

    Type declaration

    • x: number

    Optional id

    id?: string

    index

    index: number

    Optional shape

    shape?: Shape1D

    to

    to: {
        x: number;
    }

    Type declaration

    • x: number

    width

    width: number

    x

    x: number

    y

    y: number

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    Properties

    from

    from: {
        x: number;
    }

    Type declaration

    • x: number

    Optional id

    id?: string

    index

    index: number

    Optional shape

    shape?: Shape1D

    to

    to: {
        x: number;
    }

    Type declaration

    • x: number

    width

    width: number

    x

    x: number

    y

    y: number

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    \ No newline at end of file diff --git a/interfaces/GSDOptions.html b/interfaces/GSDOptions.html index 47fdbab..2a4c67e 100644 --- a/interfaces/GSDOptions.html +++ b/interfaces/GSDOptions.html @@ -1,7 +1,7 @@ GSDOptions | ml-gsd

    Interface GSDOptions

    interface GSDOptions {
        maxCriteria?: boolean;
        minMaxRatio?: number;
        noiseLevel?: number;
        realTopDetection?: boolean;
        sgOptions?: SGGOptions;
        smoothY?: boolean;
    }

    Properties

    maxCriteria? +

    Interface GSDOptions

    interface GSDOptions {
        maxCriteria?: boolean;
        minMaxRatio?: number;
        noiseLevel?: number;
        realTopDetection?: boolean;
        sgOptions?: SGGOptions;
        smoothY?: boolean;
    }

    Properties

    maxCriteria? minMaxRatio? noiseLevel? realTopDetection? @@ -10,20 +10,20 @@

    Properties

    Optional maxCriteria

    maxCriteria?: boolean

    Peaks are local maxima (true) or minima (false)

    Default

    true
    -

    Optional minMaxRatio

    minMaxRatio?: number

    Minimal height of small peaks based on the ratio between min and max

    +

    Optional minMaxRatio

    minMaxRatio?: number

    Minimal height of small peaks based on the ratio between min and max

    Default

    0.00025
    -

    Optional noiseLevel

    noiseLevel?: number

    Peak under the noiseLevel (or over in case of maxCriteria=false) are ignored.

    -

    Optional realTopDetection

    realTopDetection?: boolean

    Use a quadratic optimizations with the peak and its 3 closest neighbors

    +

    Optional noiseLevel

    noiseLevel?: number

    Peak under the noiseLevel (or over in case of maxCriteria=false) are ignored.

    +

    Optional realTopDetection

    realTopDetection?: boolean

    Use a quadratic optimizations with the peak and its 3 closest neighbors

    Default

    false
    -

    Optional sgOptions

    sgOptions?: SGGOptions

    Options for the Savitzky-Golay generalised algorithm. This algorithm is used +

    Optional sgOptions

    sgOptions?: SGGOptions

    Options for the Savitzky-Golay generalised algorithm. This algorithm is used to calculate the first ans second derivative. It is also used when smoothY:true to smooth the spectrum for peak picking. The Y values in case of smoothY is true will therefore be lower.

    Default

    {windowSize:9,polynomial:3}
    -

    Optional smoothY

    smoothY?: boolean

    Select the peak intensities from a smoothed version of the independent variables

    +

    Optional smoothY

    smoothY?: boolean

    Select the peak intensities from a smoothed version of the independent variables

    Default

    false
    -

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    \ No newline at end of file diff --git a/interfaces/GSDPeak.html b/interfaces/GSDPeak.html index ed0b405..09d80da 100644 --- a/interfaces/GSDPeak.html +++ b/interfaces/GSDPeak.html @@ -1,7 +1,7 @@ GSDPeak | ml-gsd

    Interface GSDPeak

    interface GSDPeak {
        ddY: number;
        id?: string;
        index: number;
        inflectionPoints: {
            from: {
                index: number;
                x: number;
            };
            to: {
                index: number;
                x: number;
            };
        };
        width: number;
        x: number;
        y: number;
    }

    Properties

    ddY +

    Interface GSDPeak

    interface GSDPeak {
        ddY: number;
        id?: string;
        index: number;
        inflectionPoints: {
            from: {
                index: number;
                x: number;
            };
            to: {
                index: number;
                x: number;
            };
        };
        width: number;
        x: number;
        y: number;
    }

    Properties

    ddY id? index inflectionPoints @@ -10,6 +10,6 @@ y

    Properties

    ddY

    ddY: number

    second derivative at the level of the peak This allows to determine if a peak is soft or not

    -

    Optional id

    id?: string

    index

    index: number

    index in the 'x' and 'y' array of the peak

    -

    inflectionPoints

    inflectionPoints: {
        from: {
            index: number;
            x: number;
        };
        to: {
            index: number;
            x: number;
        };
    }

    Type declaration

    • from: {
          index: number;
          x: number;
      }
      • index: number
      • x: number
    • to: {
          index: number;
          x: number;
      }
      • index: number
      • x: number

    width

    width: number

    Width at the level of the inflection points

    -

    x

    x: number

    y

    y: number

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    Optional id

    id?: string

    index

    index: number

    index in the 'x' and 'y' array of the peak

    +

    inflectionPoints

    inflectionPoints: {
        from: {
            index: number;
            x: number;
        };
        to: {
            index: number;
            x: number;
        };
    }

    Type declaration

    • from: {
          index: number;
          x: number;
      }
      • index: number
      • x: number
    • to: {
          index: number;
          x: number;
      }
      • index: number
      • x: number

    width

    width: number

    Width at the level of the inflection points

    +

    x

    x: number

    y

    y: number

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    \ No newline at end of file diff --git a/interfaces/GSDPeakOptimized.html b/interfaces/GSDPeakOptimized.html index 9225177..99651f7 100644 --- a/interfaces/GSDPeakOptimized.html +++ b/interfaces/GSDPeakOptimized.html @@ -1,9 +1,9 @@ GSDPeakOptimized | ml-gsd

    Interface GSDPeakOptimized

    interface GSDPeakOptimized {
        id?: string;
        shape: Shape1D;
        width: number;
        x: number;
        y: number;
    }

    Properties

    id? +

    Interface GSDPeakOptimized

    interface GSDPeakOptimized {
        id?: string;
        shape: Shape1D;
        width: number;
        x: number;
        y: number;
    }

    Properties

    id? shape width x y -

    Properties

    Optional id

    id?: string

    shape

    shape: Shape1D

    width

    width: number

    x

    x: number

    y

    y: number

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    Properties

    Optional id

    id?: string

    shape

    shape: Shape1D

    width

    width: number

    x

    x: number

    y

    y: number

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    \ No newline at end of file diff --git a/interfaces/JoinBroadPeaksOptions.html b/interfaces/JoinBroadPeaksOptions.html index b128522..8e0f276 100644 --- a/interfaces/JoinBroadPeaksOptions.html +++ b/interfaces/JoinBroadPeaksOptions.html @@ -1,16 +1,16 @@ JoinBroadPeaksOptions | ml-gsd

    Interface JoinBroadPeaksOptions

    interface JoinBroadPeaksOptions {
        broadRatio?: number;
        broadWidth?: number;
        optimization?: OptimizationOptions;
        shape?: Shape1D;
    }

    Properties

    broadRatio? +

    Interface JoinBroadPeaksOptions

    interface JoinBroadPeaksOptions {
        broadRatio?: number;
        broadWidth?: number;
        optimization?: OptimizationOptions;
        shape?: Shape1D;
    }

    Properties

    broadRatio? broadWidth? optimization? shape?

    Properties

    Optional broadRatio

    broadRatio?: number

    broadRatio

    Default

    0.0025
    -

    Optional broadWidth

    broadWidth?: number

    width limit to join peaks.

    +

    Optional broadWidth

    broadWidth?: number

    width limit to join peaks.

    Default

    0.25
    -

    Optional optimization

    optimization?: OptimizationOptions

    it's specify the kind and options of the algorithm use to optimize parameters.

    -

    Optional shape

    shape?: Shape1D

    it's specify the kind of shape used to fitting.

    -

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    Optional optimization

    optimization?: OptimizationOptions

    it's specify the kind and options of the algorithm use to optimize parameters.

    +

    Optional shape

    shape?: Shape1D

    it's specify the kind of shape used to fitting.

    +

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    \ No newline at end of file diff --git a/interfaces/OptimizePeaksOptions.html b/interfaces/OptimizePeaksOptions.html index f22734f..4c73b88 100644 --- a/interfaces/OptimizePeaksOptions.html +++ b/interfaces/OptimizePeaksOptions.html @@ -1,22 +1,22 @@ OptimizePeaksOptions | ml-gsd

    Interface OptimizePeaksOptions

    interface OptimizePeaksOptions {
        baseline?: number;
        factorLimits?: number;
        fromTo?: Partial<FromTo>;
        groupingFactor?: number;
        optimization?: OptimizationOptions;
        shape?: Shape1D;
    }

    Properties

    baseline? +

    Interface OptimizePeaksOptions

    interface OptimizePeaksOptions {
        baseline?: number;
        factorLimits?: number;
        fromTo?: Partial<FromTo>;
        groupingFactor?: number;
        optimization?: OptimizationOptions;
        shape?: Shape1D;
    }

    Properties

    baseline? factorLimits? fromTo? groupingFactor? optimization? shape?

    Properties

    Optional baseline

    baseline?: number

    baseline

    -

    Optional factorLimits

    factorLimits?: number

    Define the min / max values

    +

    Optional factorLimits

    factorLimits?: number

    Define the min / max values

    Default

    2
    -

    Optional fromTo

    fromTo?: Partial<FromTo>

    range to apply the optimization

    -

    Optional groupingFactor

    groupingFactor?: number

    Number of times we should multiply the width determining if the peaks have to be grouped and therefore optimized together

    +

    Optional fromTo

    fromTo?: Partial<FromTo>

    range to apply the optimization

    +

    Optional groupingFactor

    groupingFactor?: number

    Number of times we should multiply the width determining if the peaks have to be grouped and therefore optimized together

    Default

    1
    -

    Optional optimization

    optimization?: OptimizationOptions

    it's specify the kind and options of the algorithm use to optimize parameters.

    -

    Optional shape

    shape?: Shape1D

    Shape to use for optimization

    +

    Optional optimization

    optimization?: OptimizationOptions

    it's specify the kind and options of the algorithm use to optimize parameters.

    +

    Optional shape

    shape?: Shape1D

    Shape to use for optimization

    Default

    {kind:'gaussian'}
    -

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    \ No newline at end of file diff --git a/interfaces/Peak.html b/interfaces/Peak.html index 38883d8..9df0cb2 100644 --- a/interfaces/Peak.html +++ b/interfaces/Peak.html @@ -1,8 +1,8 @@ Peak | ml-gsd

    Interface Peak

    interface Peak {
        id?: string;
        width: number;
        x: number;
        y: number;
    }

    Hierarchy

    • PeakXYWidth
      • Peak

    Properties

    id? +

    Interface Peak

    interface Peak {
        id?: string;
        width: number;
        x: number;
        y: number;
    }

    Hierarchy

    • PeakXYWidth
      • Peak

    Properties

    id? width x y -

    Properties

    Optional id

    id?: string

    width

    width: number

    x

    x: number

    y

    y: number

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    Properties

    Optional id

    id?: string

    width

    width: number

    x

    x: number

    y

    y: number

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    \ No newline at end of file diff --git a/types/GSDPeakID.html b/types/GSDPeakID.html index 4d90380..acf1db5 100644 --- a/types/GSDPeakID.html +++ b/types/GSDPeakID.html @@ -1,4 +1,4 @@ GSDPeakID | ml-gsd

    Type alias GSDPeakID

    GSDPeakID: MakeMandatory<GSDPeak, "id">

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    Type alias GSDPeakID

    GSDPeakID: MakeMandatory<GSDPeak, "id">

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    \ No newline at end of file diff --git a/types/GSDPeakOptimizedID.html b/types/GSDPeakOptimizedID.html index db7d9e9..52d49da 100644 --- a/types/GSDPeakOptimizedID.html +++ b/types/GSDPeakOptimizedID.html @@ -1,4 +1,4 @@ GSDPeakOptimizedID | ml-gsd

    Type alias GSDPeakOptimizedID

    GSDPeakOptimizedID: MakeMandatory<GSDPeakOptimized, "id">

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    Type alias GSDPeakOptimizedID

    GSDPeakOptimizedID: MakeMandatory<GSDPeakOptimized, "id">

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    \ No newline at end of file diff --git a/types/GSDPeakOptionalShape.html b/types/GSDPeakOptionalShape.html index ad42c28..c9d69e8 100644 --- a/types/GSDPeakOptionalShape.html +++ b/types/GSDPeakOptionalShape.html @@ -2,4 +2,4 @@ window.__typeDocPluginKatexOptions={"delimiters":[{"left":"$","right":"$","display":true}],"fleqn":"true","leqno":"false"}; window.addEventListener('load', () => window.renderMathInElement(document.body, window.__typeDocPluginKatexOptions));

    Type alias GSDPeakOptionalShape

    GSDPeakOptionalShape: GSDPeak & {
        shape?: Shape1D;
    }

    This function tries to join the peaks that seems to belong to a broad signal in a single broad peak.

    -

    Type declaration

    • Optional shape?: Shape1D

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    Type declaration

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    \ No newline at end of file diff --git a/types/WithIDOrShape.html b/types/WithIDOrShape.html index a6c6b4f..3f73048 100644 --- a/types/WithIDOrShape.html +++ b/types/WithIDOrShape.html @@ -1,4 +1,4 @@ WithIDOrShape | ml-gsd

    Type alias WithIDOrShape<T>

    WithIDOrShape<T>: T extends {
            id: string;
        }
        ? WithOrWithout<T, GSDPeak, GSDBroadenPeakWithShapeID, GSDBroadenPeakWithID>
        : WithOrWithout<T, GSDPeak, GSDBroadenPeakWithShape, GSDBroadenPeak>

    Type Parameters

    • T

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    Type alias WithIDOrShape<T>

    WithIDOrShape<T>: T extends {
            id: string;
        }
        ? WithOrWithout<T, GSDPeak, GSDBroadenPeakWithShapeID, GSDBroadenPeakWithID>
        : WithOrWithout<T, GSDPeak, GSDBroadenPeakWithShape, GSDBroadenPeak>

    Type Parameters

    • T

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    \ No newline at end of file diff --git a/types/WithOrWithout.html b/types/WithOrWithout.html index 089df2b..492f4aa 100644 --- a/types/WithOrWithout.html +++ b/types/WithOrWithout.html @@ -1,4 +1,4 @@ WithOrWithout | ml-gsd

    Type alias WithOrWithout<T, ToExtends, TrueType, FalseType>

    WithOrWithout<T, ToExtends, TrueType, FalseType>: T extends ToExtends
        ? TrueType
        : FalseType

    Type Parameters

    • T

    • ToExtends

    • TrueType

    • FalseType

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    Type alias WithOrWithout<T, ToExtends, TrueType, FalseType>

    WithOrWithout<T, ToExtends, TrueType, FalseType>: T extends ToExtends
        ? TrueType
        : FalseType

    Type Parameters

    • T

    • ToExtends

    • TrueType

    • FalseType

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