Attribute VB_Name = "INTEGRAT"
'****************************************************************************************
'
'   File:       INTEGRAT.BAS
'
'   Author:     Roberto Raso
'   Date:       2nd February 1994
'
'****************************************************************************************
'
'   Purpose:    Provide peak detection, integration and smooth functions.
'
'****************************************************************************************

'****************************************************************************************
'
'  Constant/Global declarations.
'
'****************************************************************************************

Global Const CHR_INT_PARA = "ChrIntegrate"

'Interference Peak flags
Public Enum InterferenceFlags
    PKD_NONE
    PKD_POSITIVE
    PKD_NEGATIVE
End Enum

'****************************************************************************************
'
'   Data type declarations.
'
'****************************************************************************************

'***
'*** SMO_PARAMS ***
'*** Smoothing parameters ***
'***
Type SMO_PARAMS
  nMethod As Long  'Smoothing method
  nSGPoly As Long  'Order of SG polynomial
  nSGDeriv As Long 'Order of SG derivative
  nWidth As Long 'Width of smoothing window
  nIterates As Long  'No of iterations
  bMedianConv As Long  'Median smooth to convergence ?
  bAllowMedian As Long 'Median smooth allowed ?
  fPeakWidth As Single  'Spectrum peak width
  fFactor As Single 'Chromatogram smooth factor
  bUsePeakWidth As Long 'Use peak width parameter
End Type

'***
'*** PKDSTATS
'*** Peak statistics ***
'***
Type PKDSTATS
    lfWidth As Double       'Width at 5% height
    lfMean As Double        'Mean
    lfSigma As Double       'Standard deviation
    lfSkew As Double        'Skewness
    lfKurtosis As Double    'Kurtosis
End Type

'***
'*** PKD_FULL_PEAK
'*** Full peak structure ***
'***
Type PKD_FULL_PEAK
    fStart As Single            'Baseline start X
    fStartHt As Single          'Baseline start Y
    nStartType As Long          'Baseline start type
    fEnd As Single              'Baseline end X
    fEndHt As Single            'Baseline end Y
    nEndType As Long            'Baseline end type
    fTop As Single              'Peaktop X
    fHeight As Single           'Peaktop Y
    fCent As Single             'Centroid X
    fCentHt As Single           'Centroid Y
    fArea As Single             'Peak area
    nFlags As Long              'Flags
    fPurityMean As Single       'Purity index
    fPuritySigma As Single      'Purity standard deviation
    nInterferenceFlag As Long   'Can be PKD_NONE, PKD_POSITIVE or PKD_NEGATIVE.
    nPack1 As Long              'Structure packing variable, not used
    dInterferencePercentage As Double   'Percentage difference between secondary traces.
    sStats As PKDSTATS          'Peak statistics
End Type

'***
'*** PKD_THRESH
'***
Type PKD_THRESH
    nPack1 As Long              'Structure packing variable, not used
    wRespThreshold As Integer
    fRespAreaRel As Single
    fRespAreaAbs As Single
    fRespHeightRel As Single
    fRespHeightAbs As Single
End Type


'***
'*** PKD_PARAMS
'*** Parameters for Peak Detection ***
'***
Type PKD_PARAMS

    nPack1 As Long                  'Structure packing variable, not used
    nMode As Long                   'Standard centroid, fast centroid, QTOF centroid
    nHalfWidth As Long              'Min peak width at half height
    bShldrDetect As Long            'Detect shoulders (True/False)
    nShldrWidth As Long             'Min shoulder width
    fBalance As Single              'Min peak balance (percent)
                                    '100% = Not balanced
    fShldrThresh As Single          'Shoulder flatness threshold
    fSkim As Single                 'Peak skim threshold (percent)
                                    '100% = All skimmed
    fMinEdge As Single              'Edge threshold
    fReduceTail As Single           'Reduce peak tailing by...
    fMaxReduceHt As Single          'Move baseline by no more than
    nCntrMethod As Long             'Centre method
    fCentTop As Single              'Topmost percentage of peak to
                                    'use for centroid
    bMakeSticks As Long             'Centre only - make sticks?
    nSticks As Long                 'Centre only - stick type
    nWindow As Long                 'Centre only - add/replace/new
    fBaseWidth As Single            'Peak width at baseline (fast centroid only)
    fBaseThresh As Single           'Baseline threshold (fast centroid only)
    sWatParams As PKD_WAT_PARAMS    'Waters peak detection parameters
    sQTOFParams As PKD_QTOF_PARAMS
    bEnableTOFCentroid As Long      'Allow TOF centroid mode
    
    'Accurate Mass
    bEnableAccMassCentroid As Long  'Use centroiding with uncertainty estimation
    bAccMassScan As Long            'OUTPUT: Accurate mass scan if true
    wAccMassDiagnostic As Integer   'OUTPUT: Bits set on accurate mass failure according to RawIntrf.h
    bDoAdaptiveSubtract As Long     'Do adaptive background subtract
  
End Type

'***
'*** INTEGRATE_CHRO_PARAMS ***
'*** Chromatogram Integration parameters ***
'*** Maps to INTEGRATE_PARAMS in VC++ ***
'***
Type INTEGRATE_CHRO_PARAMS
  bSmooth As Long           'Smoothing on / off
  sSmoParams As SMO_PARAMS  'Smooth parameters
  sPkdParams As PKD_PARAMS  'Peak detect parameters
  sThreshold As PKD_THRESH  'Threshold parameters
  sChroStats As CHRO_STATS  'Chromatogram stats
End Type

'***
'*** INTEGRATE_SPEC_PARAMS ***
'*** Spectrum Integration parameters ***
'*** Maps to INTEGRATE_PARAMS in VC++ ***
'***
Type INTEGRATE_SPEC_PARAMS
  bSmooth As Long           'Smoothing on / off
  sSmoParams As SMO_PARAMS  'Smooth parameters
  sPkdParams As PKD_PARAMS  'Peak detect parameters
  sThreshold As PKD_THRESH  'Threshold parameters
  sSpecStats As SPEC_STATS  'Spectrum stats
End Type

'****************************************************************************************
'
'   Function declarations.
'
'****************************************************************************************

Declare Function IntegrateChromatogramRange Lib "integr32.dll" _
    Alias "_IntegrateChromatogramRange@40" (ByVal hWnd As Long, lpRawFile As VGRAWFILE, _
    lpChroType As DMRAWCHRTYPE, hPeaks As Long, wNumPeaks As Long, hDm As Long, _
    lpIntParams As INTEGRATE_CHRO_PARAMS, ByVal dwScanStart As Long, _
    ByVal dwScanEnd As Long, ByVal wTraceNumber As Integer) As Integer
Declare Function IntegrateGetIniFile Lib "integr32.dll" Alias "_IntegrateGetIniFile@8" (ByVal lpName As String, lpIntParams As INTEGRATE_CHRO_PARAMS) As Integer
Declare Sub IntegrateEditParams Lib "integr32.dll" Alias "_IntegrateEditParams@16" (ByVal hWnd As Long, sVGRawFile As Any, sDMRawChroType As Any, sIntegrateParams As INTEGRATE_CHRO_PARAMS)
Declare Function IntegrateDialogClosed Lib "integr32.dll" Alias "_IntegrateDialogClosed@4" (sIntegrateParams As INTEGRATE_CHRO_PARAMS) As Integer

'****************************************************************************************
'
'   Purpose:    Integrate chromatogram over requested range.
'               Prototype.
'
'****************************************************************************************
Function IntegrateChro() As Integer
Dim hWnd As Long
Dim hResults As Long
Dim wNumPeaks As Long
Dim hDmRaw As Long
Dim wBytes As Integer
Dim wPeak As Integer
Dim dwStartScan As Long
Dim dwEndScan As Long
Dim dwStartOfResults As Long
Dim lpIniPara As String
Dim lpRawFile As VGRAWFILE
Dim lpChroType As DMRAWCHRTYPE
Dim lpIntParams As INTEGRATE_CHRO_PARAMS
Dim lpIntResult As PKD_FULL_PEAK

lpIniPara = "ChrIntegrate"

If IntegrateGetIniFile(lpIniPara, lpIntParams) Then
  Debug.Print ChroDescToChroType("91", lpChroType)
  'lpChroType.nChroType = 1
  'lpChroType.afMasses(0) = 91
  'lpChroType.afMasses(32) = 0

  If GetMLFileInfo("RAW", lpRawFile.lpVGFile) Then
    lpRawFile.wFunc = 1
    hWnd = FindWindow(vbNullString, "OpenLynx MS Station")

    If IntegrateChromatogramRange(hWnd, lpRawFile, lpChroType, hResults, wNumPeaks, _
                                    CLng(hDmRaw), lpIntParams, 1, 953, 0) Then
      dwStartOfResults = GlobalLock(hResults)
      wBytes = Len(lpIntResult)
      
      For wPeak = 1 To wNumPeaks
        Call hmemcpyTolp(lpIntResult, dwStartOfResults + wBytes * (wPeak - 1), wBytes)
        Debug.Print "Peak #"; wPeak; lpIntResult.fTop; lpIntResult.fHeight; lpIntResult.fArea; lpIntResult.fStart; lpIntResult.fEnd; lpIntResult.fStartHt; lpIntResult.fEndHt
      Next wPeak

      Debug.Print "Unlock"; GlobalUnlock(hResults)
      Debug.Print "Free"; GlobalFree(hResults)
      DmRawClose
      IntegrateChro = wNumPeaks
    Else
      IntegrateChro = False
    End If

  Else
    IntegrateChro = False
  End If

Else
  IntegrateChro = False
End If

End Function

'****************************************************************************************
'
'   Purpose:    Integrate chromatogram over requested range.
'               Returns the handle of the integrated trace
'               Returns number of peaks and fills array of PKD_FULL_PEAK
'
'****************************************************************************************
Function IntegrateChromatogramProcess(lpWindowCaption As String, sRawFile As VGRAWFILE, _
    wFunc As Integer, lpChroDesc As String, fStart As Single, fEnd As Single, _
    wScans As Integer, lpResults() As PKD_FULL_PEAK, sIntParams As INTEGRATE_CHRO_PARAMS, _
    bUseIni As Integer, hDm As Long, Optional nrTraceNumber As Long = 0) As Integer
    
Dim wFuncOK As Integer
Dim hWnd As Long
Dim hResults As Long
Dim wNumPeaks As Long
Dim hDmRaw As Long
Dim wBytes As Integer
Dim wPeak As Integer
Dim dwStartScan As Long
Dim dwEndScan As Long
Dim dwStartOfResults As Long
Dim lpIniPara As String
Dim lpChroType As DMRAWCHRTYPE
Dim lpIntParams As INTEGRATE_CHRO_PARAMS
Dim lpIntResult As PKD_FULL_PEAK

wFuncOK = True
wFuncOK = ChroExit()
lpIniPara = CHR_INT_PARA
If Asc(lpWindowCaption) <> 0 Then
    hWnd = FindWindow(vbNullString, lpWindowCaption)
Else
    hWnd = GetActiveWindow()
End If
lpIniPara = "ChrIntegrate"

If bUseIni <> False Then
    wFuncOK = IntegrateGetIniFile(lpIniPara, lpIntParams)
Else
    lpIntParams = sIntParams
End If

If DMCheckFunction(wFunc, sRawFile) Then

  If wScans Then
    dwStartScan = DMCheckScan(wFunc, CInt(fStart), sRawFile)
    dwEndScan = DMCheckScan(wFunc, CInt(fEnd), sRawFile)
  Else
    dwStartScan = DMCheckRT(wFunc, CInt(fStart), sRawFile)
    dwEndScan = DMCheckRT(wFunc, CInt(fEnd), sRawFile)
  End If

  If dwStartScan = False Or fStart = 0 Then
    dwStartScan = 1
  End If

  If dwEndScan = False Or fEnd = 0 Then
    dwEndScan = DmRawScansInFunction(sRawFile)
  End If

Else
  wFuncOK = False
End If

If Not ChroDescToChroType(lpChroDesc, lpChroType) Then
  wFuncOK = False
End If

If wFuncOK Then

    If IntegrateChromatogramRange(hWnd, sRawFile, lpChroType, hResults, wNumPeaks, hDm, _
                                    lpIntParams, dwStartScan, dwEndScan, nrTraceNumber) Then
      dwStartOfResults = GlobalLock(hResults)
      wBytes = Len(lpIntResult)

      If wNumPeaks Then
        ReDim lpResults(wNumPeaks - 1)
        
        For wPeak = 1 To wNumPeaks
          Call hmemcpyTolp(lpIntResult, dwStartOfResults + wBytes * (wPeak - 1), wBytes)
          lpResults(wPeak - 1) = lpIntResult
        Next wPeak

      End If

      wFuncOK = GlobalUnlock(hResults)
      wFuncOK = GlobalFree(hResults)
      DmRawClose
      IntegrateChromatogramProcess = wNumPeaks
    Else
      IntegrateChromatogramProcess = False
    End If

End If

End Function

'________________________________________________________________________________________
'
'   Process:    IntegrateParsEdit
'
'   Author:     Roberto Raso
'   Date:       21st June 1995
'
'   Purpose:    Brings up the integrate editor and sets an INTEGRATE_CHRO_PARAMS structure.
'
'   Parameters: hWnd is the window handle that will be used to position the
'                   editor dialogue box to.
'               sIntegrateParams is the set of parameters that will be used by
'                   the dialogue box and set.
'
'   Return:     True if parameters have been changed.
'________________________________________________________________________________________
Function IntegrateParsEdit(hWnd As Long, sIntegrateParams As INTEGRATE_CHRO_PARAMS) As Integer
    Dim strIntegrateParamsCur As String
    Dim strIntegrateParamsNew As String

    IntegrateParsEdit = False
    strIntegrateParamsCur = String$(Len(sIntegrateParams), 0)
    Call hmemcpy(ByVal strIntegrateParamsCur, sIntegrateParams, Len(sIntegrateParams))

    If GetGlobalDialogWnd(GD_CHRO_INTEGRATE) Then
        Exit Function
    End If

    Call IntegrateEditParams(hWnd, 0&, 0&, sIntegrateParams)

    Do Until GetGlobalDialogWnd(GD_CHRO_INTEGRATE)
        DoEvents
    Loop

    Do While GetGlobalDialogWnd(GD_CHRO_INTEGRATE)
        DoEvents
    Loop

    If IntegrateDialogClosed(sIntegrateParams) = 0 Then
        Exit Function
    End If

    strIntegrateParamsNew = String$(Len(sIntegrateParams), 0)
    Call hmemcpy(ByVal strIntegrateParamsNew, sIntegrateParams, Len(sIntegrateParams))
    
    If strIntegrateParamsNew <> strIntegrateParamsCur Then
        IntegrateParsEdit = True
    End If
    
End Function