3.2.0Construct the object from the given sd object(output of the jcampconverter or brukerconverter filter)
(SD)
Fills a zone of the spectrum with the given value. If value is undefined it will suppress the elements
(any
= this.activeElement)
Get the maximum peak the spectrum
[x, y]:
This function performs a simple peak detection in a spectraData. The parameters that can be specified are: Returns a two dimensional array of double specifying [x,y] of the detected peaks.
Return the amount of sub-spectra in this object
any:
Get the noise threshold level of the current spectrum. It uses median instead of the mean
number:
This function returns the units of the independent dimension.
(xUnit | any | M.xUnit):
(yUnit | any | M.yUnit):
Is this a XY spectrum?
any:
Set a new parameter to this spectrum
Update min max values of X and Y axis.
Set the firstX for this spectrum. You have to force and update of the xAxis after!!!
Set the first value of the indirect dimension. Only valid for 2D spectra.
Set the last value of the direct dimension. You have to force and update of the xAxis after!!!
Return the first value of the indirect dimension
This function scales the values of Y between the min and max parameters
Set the title of this spectrum.
This function suppress a zone from the given spectraData within the given x range. Returns a spectraData of type PEAKDATA without peaks in the given region
This function creates a String that represents the given spectraData in the format JCAMP-DX 5.0 The X,Y data can be compressed using one of the methods described in: "JCAMP-DX. A STANDARD FORMAT FOR THE EXCHANGE OF ION MOBILITY SPECTROMETRY DATA", http://www.iupac.org/publications/pac/pdf/2001/pdf/7311x1765.pdf
(object
= {})
some options are availables:
any:
a string containing the jcamp-DX file
SD.toJcamp(spectraData,{encode:'DIFDUP',yfactor:0.01,type:"SIMPLE",keep:['#batchID','#url']});
Return the normalization value. It is not set check the molfile and guess it from the number of atoms.
number:
Returns the index-value for the data array corresponding to a X-value in units for the element of spectraData to which it is linked (spectraNb). This method makes use of spectraData.getFirstX(), spectraData.getLastX() and spectraData.getNbPoints() to derive the return value if it of data class XY It performs a binary search if the spectrum is a peak table
(number)
value in Units to be converted
number:
An integer representing the index value of the inValue
This function return the integral values for certains ranges at specific SD instance .
Extends SD
This filter applies a circular shift(phase 1 correction in the time domain) to an NMR FID spectrum that have been obtained on spectrometers using the Bruker digital filters. The amount of shift depends on the parameters DECIM and DSPFVS. This spectraData have to be of type NMR_FID
NMR:
this object
Applies a baseline correction as described in J Magn Resonance 183 (2006) 145-151 10.1016/j.jmr.2006.07.013 The needed parameters are the Wavelet scale and the lambda used in the Whittaker smoother.
(any)
To be described
(any)
To be described
(any)
A string containing the ranges of no signal.
NMR:
this object
Applies a baseline correction as described in J Magn Resonance 183 (2006) 145-151 10.1016/j.jmr.2006.07.013 The needed parameters are the wavelet scale and the lambda used in the whittaker smoother.
(any)
To be described
(any)
To be described
NMR:
this object
This function compute again the process of the given spectraData and tries to determine the NMR signals. Returns an NMRSignal1D array containing all the detected 1D-NMR Signals
(object)
A JSONObject containing the optional parameters:
(null | any):
This filter applies a circular shift(phase 1 correction in the time domain) to an NMR FID spectrum that have been obtained on spectrometers using the Bruker digital filters. The amount of shift depends on the parameters DECIM and DSPFVS. This spectraData have to be of type NMR_FID
(object)
->
nbPoints: The number of points to shift. Positive values will shift the values to the rigth
and negative values will do to the left.
NMR:
this object
Change the intensities of a respective impurities signals based on peak picking and solvent impurities
(string)
solvent name
(object
= {})
object may have the peak picking options if this.peaks does not exist.
| Name | Description |
|---|---|
options.impurity string
(default null)
|
options to fill a particular impurity of the solvent some thing like 'solvent_residual_peak' |
options.value number
(default 0)
|
value to fill |
options.error number
(default 0.025)
|
tolerance to find the chemical shift of the impurities. |
This filter performs a linear combination of two spectraDatas. A=spec1 B=spec2 After to apply this filter you will get: A=Afactor1+Bfactor2 if autoscale is set to 'true' then you will obtain: A=Afactor1+Bk*factor2 Where the k is a factor such that the maximum peak in A is equal to the maximum peak in spectraData2
(any)
spectraData2
(any)
linear factor for spec1
(any)
linear factor for spec2
(any)
Auto-adjust scales before combine the spectraDatas
NMR:
this object
spec1 = addSpectraDatas(spec1,spec2,1,-1, false) This subtract spec2 from spec1
This function correlates the given spectraData with the given vector func. The correlation operation (*) is defined as:
__ inf
c(x)=f(x)()g(x)= \ f(x)g(x+i) ./ -- i=-inf
(any)
(any)
(any)
A double array containing the function to correlates the spectraData
any:
this object
var smoothedSP = SD.correlationFilter(spectraData,[1,1]) returns a smoothed version of the
given spectraData.
This function applies a log to all the Y values.
If the spectrum has negative or zero values, it will be shifted so that the lowest value is 1
(any)
(any)
(any)
The base to use
any:
this object
This filter makes an phase 1 correction that corrects the problem of the spectra that has been obtained on spectrometers using the Bruker digital filters. This method is used in cases when the BrukerSpectra filter could not find the correct number of points to perform a circular shift. The actual problem is that not all of the spectra has the necessary parameters for use only one method for correcting the problem of the Bruker digital filters.
(number)
Phase 1 correction value in radians.
NMR:
this object
This function increase the size of the spectrum, filling the new positions with zero values. Doing it one could increase artificially the spectral resolution.
(number)
Number of new zero points in the direct dimension
(number)
Number of new zero points in the indirect dimension
NMR:
this object
This filter applies a circular shift(phase 1 correction in the time domain) to an NMR FID spectrum that have been obtained on spectrometers using the Bruker digital filters. The amount of shift depends on the parameters DECIM and DSPFVS. This spectraData have to be of type NMR_FID
NMR2D:
this object
This filter applies a circular shift(phase 1 correction in the time domain) to an NMR FID spectrum that have been obtained on spectrometers using the Bruker digital filters. The amount of shift depends on the parameters DECIM and DSPFVS. This spectraData have to be of type NMR_FID
(object)
some options are availables:
NMR2D:
this object
Fourier transforms the given spectraData (Note. no 2D handling yet) this spectraData have to be of type NMR_FID or 2DNMR_FID
NMR2D:
this object
Return the separation between 2 consecutive points in the indirect domain
number:
Return the min value in the indirect dimension.
sd.minMax.minY:
Return the min value in the indirect dimension.
sd.minMax.maxY:
Return the maximum value of the independent variable
number:
Return the minimum value of the independent variable
number:
Return the noise factor depending on the nucleus.
(string)
number:
Return the observed nucleus in the specified dimension
(number)
string:
Return the solvent name.
(string | XML):
This function Return the units of the direct dimension. It overrides the SD getXUnits function
(ntuples.units | any | b.units):
This function Return the units of the indirect dimension. It overrides the SD getYUnits function
(ntuples.units | any | b.units):
This function process the given spectraData and tries to determine the NMR signals. Return an NMRSignal2D array containing all the detected 2D-NMR Signals
(object)
Object containing the options.
any:
set of NMRSignal2D.
Return the units of the dependent variable
(ntuples.units | any | b.units):
Return true if the it is an homo-nuclear experiment
boolean:
Return the observe frequency in the direct dimension
number:
Return the observe frequency in the indirect dimension
number:
This filter makes an phase 1 correction that corrects the problem of the spectra that has been obtained on spectrometers using the Bruker digital filters. This method is used in cases when the BrukerSpectra filter could not find the correct number of points to perform a circular shift. The actual problem is that not all of the spectra has the necessary parameters for use only one method for correcting the problem of the Bruker digital filters.
(number)
Phase 1 correction value in radians.
NMR2D:
this object
This function increase the size of the spectrum, filling the new positions with zero values. Doing it one could increase artificially the spectral resolution.
(number)
Number of new zero points in the direct dimension
(number)
Number of new zero points in the indirect dimension
NMR2D:
this object
This function return a NMR instance from Array of folders or zip file with folders
(Array)
spectra data in two possible input
(object)
the options dependent on brukerFile input, but some parameter are permanents like:
any:
This function creates a 2D spectrum from a matrix containing the independent values of the spectrum and a set of options...
any:
This function creates a SD instance from the given 2D prediction
SD:
This class converts a SpectraData object into a String that can be stored as a jcamp file. The string reflects the current state of the object and not the raw data from where this spectrum was initially loaded.
This function creates a String that represents the given spectraData, in the format JCAM-DX 5.0 The X,Y data can be compressed using one of the methods described in: "JCAMP-DX. A STANDARD FORMAT FOR THE EXCHANGE OF ION MOBILITY SPECTROMETRY DATA", http://www.iupac.org/publications/pac/pdf/2001/pdf/7311x1765.pdf
(SD)
string:
This function clustering peaks and calculate the integral value for each range from the peak list returned from extractPeaks function.
(SD)
SD instance
(Object)
nmr signals
(Object)
options object with some parameter for GSD, detectSignal functions.
| Name | Description |
|---|---|
options.nH number
(default 100)
|
Number of hydrogens or some number to normalize the integral data. If it's zero return the absolute integral value |
options.integralType string
(default 'sum')
|
option to chose between approx area with peaks or the sum of the points of given range ('sum', 'peaks') |
options.frequencyCluster number
(default 16)
|
distance limit to clustering peaks. |
options.clean number?
|
If exits it remove all the signals with integral < clean value |
options.compile boolean
(default true)
|
If true, the Janalyzer function is run over signals to compile the patterns. |
options.keepPeaks boolean
(default false)
|
If true each signal will contain an array of peaks. |
Array:
Implementation of the peak picking method described by Cobas in: A new approach to improving automated analysis of proton NMR spectra through Global Spectral Deconvolution (GSD) http://www.spectroscopyeurope.com/images/stories/ColumnPDFs/TD_23_1.pdf
(SD)
SD instance.
(Object)
nmr signals.
(Object)
options object with some parameter for GSD.
| Name | Description |
|---|---|
options.compile boolean
(default true)
|
If true, the Janalyzer function is run over signals to compile the patterns. |
options.minMaxRatio number
(default 0.01)
|
Threshold to determine if a given peak should be considered as a noise, bases on its relative height compared to the highest peak. |
options.broadRatio number
(default 0.00025)
|
If broadRatio is higher than 0, then all the peaks which second derivative smaller than broadRatio * maxAbsSecondDerivative will be marked with the soft mask equal to true. |
options.smoothY boolean
(default true)
|
Select the peak intensities from a smoothed version of the independent variables? |
options.nL number
(default 4)
|
factor to determine the width at the moment to group the peaks in signals in 'GSD.optimizePeaks' function. |
options.optimize boolean
(default true)
|
if it's true adjust an train of gaussian or lorentzian shapes to spectrum. |
options.functionType string
(default 'gaussian')
|
This option allows us choose between 'gaussian' or 'lorentzian' function when options.optimize is true. |
options.broadWidth number
(default 0.25)
|
Threshold to determine if some peak is candidate to clustering into range. |
Array:
This function encodes the given vector. The encoding format is specified by the encoding option
(Array)
(number)
(number)
(string)
: ('FIX','SQZ','DIF','DIFDUP','CVS','PAC') Default 'DIFDUP'
string:
This function make a fourier transformation to each FID withing a SD instance
(SD)
SD instance
SD:
return SD with spectrum and FID
class encodes a integer vector as a String in order to store it in a text file. The algorithms used to encode the data are describe in: http://www.iupac.org/publications/pac/pdf/2001/pdf/7311x1765.pdf Created by acastillo on 3/2/16.
Type: string
Phase correction filter
SD:
returns the modified spectraData
This function performs a circular shift of the input object without realocating memory. Positive values of shifts will shift to the right and negative values will do to the left
rotate([1,2,3,4],1) -> [4,1,2,3]
rotate([1,2,3,4],-1) -> [2,3,4,1]
This function make a zero filling to each Active element in a SD instance.
(SD)
instance.
(number)
number of points that FID will have, if is it lower
than initial number of points, the FID will be spliced
SD: