FindPeaksMD v1¶

FindPeaksMD dialog.

Table of Contents

Summary
Properties
Description
Usage
Source

Summary ¶

Find peaks in reciprocal space in a MDEventWorkspace or a MDHistoWorkspace.

Properties ¶

Name	Direction	Type	Default	Description
InputWorkspace	Input	IMDWorkspace	Mandatory	An input MDEventWorkspace or MDHistoWorkspace with at least 3 dimensions.
PeakDistanceThreshold	Input	number	0.1	Threshold distance for rejecting peaks that are found to be too close from each other. This should be some multiple of the radius of a peak. Default: 0.1.
MaxPeaks	Input	number	500	Maximum number of peaks to find. Default: 500.
DensityThresholdFactor	Input	number	10	The overall signal density of the workspace will be multiplied by this factor to get a threshold signal density below which boxes are NOT considered to be peaks. See the help. Default: 10.0
OutputWorkspace	Output	PeaksWorkspace		An output PeaksWorkspace with the peaks’ found positions.
AppendPeaks	Input	boolean	False	If checked, then append the peaks in the output workspace if it exists. If unchecked, the output workspace is replaced (Default).
EdgePixels	Input	number	0	Remove peaks that are at pixels this close to edge.

This algorithm is used to find single-crystal peaks in a multi-dimensional workspace (MDEventWorkspace or MDHistoWorkspace). It looks for high signal density areas, and is based on an algorithm designed by Dennis Mikkelson for ISAW.

The algorithm proceeds in this way:

Sorts all the boxes in the workspace by decreasing order of signal density (total weighted event sum divided by box volume).
- It will skip any boxes with a density below a threshold. The threshold is $TotalSignal / TotalVolume * DensityThresholdFactor$ .
The centroid of the strongest box is considered a peak.
The centroid of the next strongest box is calculated.
- We look through all the peaks that have already been found. If the box is too close to an existing peak, it is rejected. This distance is PeakDistanceThreshold.
This is repeated until we find up to MaxPeaks peaks.

Each peak created is placed in the output PeaksWorkspace, which can be a new workspace or replace the old one.

This algorithm works on a MDHistoWorkspace resulting from the BinMD v1 algorithm also. It works in the same way, except that the center of each bin is used since the centroid is not accessible. It may give better results on Workspace2D‘s that were converted to MDWorkspaces.

Usage ¶

Example - IntegratePeaks:

The code iteslef works but disabled from doc tests as takes too long to complete. User should provide its own event nexus file instead of TOPAZ_3132_event.nxs used within this example. The original TOPAZ_3132_event.nxs file is availible in Mantid system tests repository.

#.. testcode:: exFindPeaksMD


def print_tableWS(pTWS,nRows):
    ''' Method to print part of the table workspace '''
    tab_names=pTWS.keys();

    for name in tab_names:
        if len(name)>8:
           name= name[0:8];
        print "| {0:8} ".format(name),
    print "|\n",

    for i in xrange(0,nRows):
        for name in tab_names:
              col = pTWS.column(name);
              data2pr=col[i]
              if type(data2pr) is float:
                   print "| {0:>8.2f} ".format(data2pr),
              else:
                  print "| {0:>8} ".format(data2pr),
        print "|\n",


# load test workspace
Load(Filename=r'TOPAZ_3132_event.nxs',OutputWorkspace='TOPAZ_3132_event',LoadMonitors='1')

# build peak workspace necessary for IntegrateEllipsoids algorithm to work
ConvertToMD(InputWorkspace='TOPAZ_3132_event',QDimensions='Q3D',dEAnalysisMode='Elastic',Q3DFrames='Q_sample',LorentzCorrection='1',OutputWorkspace='TOPAZ_3132_md',\
MinValues='-25,-25,-25',MaxValues='25,25,25',SplitInto='2',SplitThreshold='50',MaxRecursionDepth='13',MinRecursionDepth='7')
peaks=FindPeaksMD(InputWorkspace='TOPAZ_3132_md',PeakDistanceThreshold='0.37680',MaxPeaks='50',DensityThresholdFactor='100',OutputWorkspace='TOPAZ_3132_peaks')

# print 10 rows of table workspace
print_tableWS(peaks,10)

Output:

#.. testoutput:: exFindPeaksMD

| RunNumbe  | DetID     | h         | k         | l         | Waveleng  | Energy    | TOF       | DSpacing  | Intens    | SigInt    | BinCount  | BankName  | Row       | Col       | QLab      | QSample   |
|     3132  |  1124984  |     0.00  |     0.00  |     0.00  |     3.10  |     8.49  | 14482.29  |     2.02  |     0.00  |     0.00  |  1668.00  |   bank17  |   120.00  |    42.00  | [1.57771,1.21779,2.37854]  | [2.99396,0.815958,0.00317344]  |
|     3132  |  1156753  |     0.00  |     0.00  |     0.00  |     2.08  |    18.82  |  9725.74  |     1.30  |     0.00  |     0.00  |  1060.00  |   bank17  |   145.00  |   166.00  | [2.48964,1.45725,3.88666]  | [4.52618,1.71025,0.129461]  |
|     3132  |  1141777  |     0.00  |     0.00  |     0.00  |     1.71  |    28.09  |  7963.17  |     1.05  |     0.00  |     0.00  |    96.00  |   bank17  |    17.00  |   108.00  | [2.60836,2.31423,4.86391]  | [5.69122,1.79492,-0.452799]  |
|     3132  |  1125241  |     0.00  |     0.00  |     0.00  |     1.55  |    33.86  |  7252.16  |     1.01  |     0.00  |     0.00  |    83.00  |   bank17  |   121.00  |    43.00  | [3.15504,2.42573,4.75121]  | [5.97829,1.63473,0.0118744]  |
|     3132  |  1170598  |     0.00  |     0.00  |     0.00  |     1.55  |    34.12  |  7224.59  |     0.95  |     0.00  |     0.00  |    73.00  |   bank17  |   166.00  |   220.00  | [3.43363,1.70178,5.39301]  | [6.07726,2.59962,0.281759]  |
|     3132  |  1214951  |     0.00  |     0.00  |     0.00  |     1.89  |    22.79  |  8839.55  |     1.68  |     0.00  |     0.00  |   719.00  |   bank18  |   231.00  |   137.00  | [2.73683,1.43808,2.11574]  | [3.5786,0.470838,1.00329]  |
|     3132  |  1207827  |     0.00  |     0.00  |     0.00  |     1.71  |    27.89  |  7991.70  |     1.32  |     0.00  |     0.00  |   447.00  |   bank18  |    19.00  |   110.00  | [2.80324,2.29519,3.09134]  | [4.71517,0.554412,0.37714]  |
|     3132  |  1232949  |     0.00  |     0.00  |     0.00  |     1.24  |    53.28  |  5782.14  |     0.93  |     0.00  |     0.00  |    45.00  |   bank18  |    53.00  |   208.00  | [4.29033,2.63319,4.46168]  | [6.52658,1.27985,1.00646]  |
|     3132  |  1189484  |     0.00  |     0.00  |     0.00  |     1.14  |    63.42  |  5299.28  |     0.96  |     0.00  |     0.00  |    31.00  |   bank18  |   108.00  |    38.00  | [4.02414,3.39659,3.83664]  | [6.4679,0.298896,0.726133]  |
|     3132  |  1218337  |     0.00  |     0.00  |     0.00  |     1.01  |    79.81  |  4724.05  |     0.77  |     0.00  |     0.00  |    15.00  |   bank18  |    33.00  |   151.00  | [4.96622,3.61607,5.32554]  | [7.99244,1.19363,0.892655]  |