This algorithm sums, bin-by-bin, multiple spectra into a single spectra. The errors are summed in quadrature and the algorithm checks that the bin boundaries in X are the same. The new summed spectra are created at the start of the output workspace and have spectra index numbers that start at zero and increase in the order the groups are specified. All detectors from the grouped spectra will be moved to belong to the new spectrum.
Not all spectra in the input workspace have to be copied to a group. If KeepUngroupedSpectra is set to true any spectra not listed will be copied to the output workspace after the groups in order. If KeepUngroupedSpectra is set to false only the spectra selected to be in a group will be used.
To create a single group the list of spectra can be identified using a list of either spectrum numbers, detector IDs or workspace indices. The list should be set against the appropriate property.
An input file allows the specification of many groups. The file has the following format:
[number of groups in file]
[first group's number]
[number of spectra in first group]
[spectrum 1] [spectrum 2] [spectrum 3] [...] [spectrum n]
[second group's number]
[number of spectra in second group]
[spectrum 1] [spectrum 2] [spectrum 3] [...] [spectrum n]
[repeat as necessary]Mantid will still work if the number of groups specified at the start is incorrect, but other software may not. Mantid will warn you if the value given is incorrect.
Each group's spectrum number is determined by the group's number. This behaviour can be overriden by enabling the IgnoreGroupNumber property, in which case the first group will be numbered 1, and the second 2, and so on.
Blank lines and whitespace in the map file are ignored. Comments may be entered using a #, like in a Python script.
An example of an input file follows:
2
1
64
1 2 3 4 5 6 7 8 9 10
11 12 13 14 15 16 17 18 19 20
21 22 23 24 25 26 27 28 29 30
31 32 33 34 35 36 37 38 39 40
41 42 43 44 45 46 47 48 49 50
51 52 53 54 55 56 57 58 59 60
61 62 63 64
2
60
65 66 67 68 69 70 71 72 73 74
75 76 77 78 79 80 81 82 83 84
85 86 87 88 89 90 91 92 93 94
95 96 97 98 99 100 101 102 103 104
105 106 107 108 109 110 111 112 113 114
115 116 117 118 119 120 121 122 123 124In addition the following XML grouping format is also supported
<?xml version="1.0" encoding="UTF-8" ?>
<detector-grouping>
<group name="fwd1"> <ids val="1-32"/> </group>
<group name="bwd1"> <ids val="33,36,38,60-64"/> </group>
<group name="fwd2"><detids val="1,2,17,32"/></group>
<group name="bwd2"><detids val="33,36,38,60,64"/> </group>
</detector-grouping>where is used to specify spectra IDs and detector IDs.
Grouping can also be specified using the GroupingPattern property. Its syntax is as follows:
The pattern consists of a list of numbers that refer to workspace indexes and various operators: ,:+-.
To remove spectra, you list the workspace indexes that you want to keep. The : operator indicates a continuous range, sparing you the need to list every one. For example if you have 100 spectra (with workspace indexes from 0 to 99) and want to remove the first and last 10 spectra along with the 12th, you would use the pattern 10,13:89. This says keep workspace indices 10 along with 13 to 89 inclusive.
To add spectra, use + to add two spectra or - to add a range. For example you may with to add 10 to 12 and ignore the rest, you would use 10+12. If you were adding five groups of 20, you would use 0-19,20-39,40-59,60-79,80-99.
One could combine the two, for example 10+12,13:89 would list the sum of 10 and 12 followed by 13 to 89.
The set of spectra to be grouped can be given as a list of either spectrum numbers, detector IDs or workspace indices. The new, summed spectrum will appear in the workspace at the first workspace index of the pre-grouped spectra (which will be given by the ResultIndex property after execution). The detectors for all the grouped spectra will be moved to belong to the first spectrum. A technical note: the workspace indices previously occupied by summed spectra will have their data zeroed and their spectrum number set to a value of -1. See page for version 1 here.
Example 1: specifying a map file
ExMapFile
import os
# Create a grouping file from the example above. # It makes 2 groups of 64 and 60 detectors respectively. groupingFileContent = """ 2 1 64 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 2 60 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 """ # Save the data to a file groupingFilePath = os.path.expanduser('~/MantidUsageExample_GroupDetectorsGrouping.txt') f = open(groupingFilePath, 'w') f.write( groupingFileContent ) f.close()
# Create a workspace filled with a constant value = 0.3 ws=CreateSampleWorkspace() # Group detectors according to the created file. grouped = GroupDetectors( ws, MapFile = groupingFilePath )
# Check the result print 'Number of groups is', grouped.getNumberHistograms() print 'First grouped spectrum is a sum 64 input spectra:' print grouped.readY(0)[0],'== 64 * 0.3 ==', 64 * 0.3 print 'Second grouped spectrum is a sum 60 input spectra:' print grouped.readY(1)[0],'== 60 * 0.3 ==', 60 * 0.3 # Get detector IDs of the first group grp0_ids = grouped.getSpectrum(0).getDetectorIDs() print 'Number of grouped detectors is',len(grp0_ids) print '5 first detectors in group:', [ grp0_ids[i] for i in range(5) ] print '5 last detectors in group:', [ grp0_ids[i] for i in range(59,64) ] # Get detector IDs of the second group grp1_ids = grouped.getSpectrum(1).getDetectorIDs() print 'Number of grouped detectors is',len(grp1_ids) print '5 first detectors in group:', [ grp1_ids[i] for i in range(5) ] print '5 last detectors in group:', [ grp1_ids[i] for i in range(55,60) ]
ExMapFile
Number of groups is 2 First grouped spectrum is a sum 64 input spectra: 19.2 == 64 * 0.3 == 19.2 Second grouped spectrum is a sum 60 input spectra: 18.0 == 60 * 0.3 == 18.0 Number of grouped detectors is 64 5 first detectors in group: [100, 101, 102, 103, 104] 5 last detectors in group: [159, 160, 161, 162, 163] Number of grouped detectors is 60 5 first detectors in group: [164, 165, 166, 167, 168] 5 last detectors in group: [219, 220, 221, 222, 223]
ExMapFile
os.remove( groupingFilePath )
Example 2: specifying spectrum numbers
ExSpectra
# Create a workspace filled with a constant value = 0.3 ws=CreateSampleWorkspace() # Group detectots using a list of spectrum numbers grouped = GroupDetectors(ws,SpectraList=[1,3,5])
# Check the result print 'Number of groups is', grouped.getNumberHistograms() print 'The grouped spectrum is a sum 3 input spectra:' print grouped.readY(0)[0],'== 3 * 0.3 ==',3 * 0.3
# Get detector IDs in the group grp_ids = grouped.getSpectrum(0).getDetectorIDs() print 'Number of grouped detectors is',len(grp_ids) print 'Detector IDs:', grp_ids
ExSpectra
Number of groups is 1 The grouped spectrum is a sum 3 input spectra: 0.9 == 3 * 0.3 == 0.9 Number of grouped detectors is 3 Detector IDs: set(100,102,104)
Example 3: specifying detctor IDs
ExDet
# Create a workspace filled with a constant value = 0.3 ws=CreateSampleWorkspace() # Group detectots using a list of detctor IDs grouped = GroupDetectors(ws,DetectorList=[100,102,104])
# Check the result print 'Number of groups is', grouped.getNumberHistograms() print 'The grouped spectrum is a sum 3 input spectra:' print grouped.readY(0)[0],'== 3 * 0.3 ==',3 * 0.3
# Get detector IDs in the group grp_ids = grouped.getSpectrum(0).getDetectorIDs() print 'Number of grouped detectors is',len(grp_ids) print 'Detector IDs:', grp_ids
ExDet
Number of groups is 1 The grouped spectrum is a sum 3 input spectra: 0.9 == 3 * 0.3 == 0.9 Number of grouped detectors is 3 Detector IDs: set(100,102,104)
Example 4: specifying workspace indices
ExWii
# Create a workspace filled with a constant value = 0.3 ws=CreateSampleWorkspace() # Group detectots using a list of workspace indices grouped = GroupDetectors(ws,WorkspaceIndexList=[0,2,4])
# Check the result print 'Number of groups is', grouped.getNumberHistograms() print 'The grouped spectrum is a sum 3 input spectra:' print grouped.readY(0)[0],'== 3 * 0.3 ==',3 * 0.3
# Get detector IDs in the group grp_ids = grouped.getSpectrum(0).getDetectorIDs() print 'Number of grouped detectors is',len(grp_ids) print 'Detector IDs:', grp_ids
ExWii
Number of groups is 1 The grouped spectrum is a sum 3 input spectra: 0.9 == 3 * 0.3 == 0.9 Number of grouped detectors is 3 Detector IDs: set(100,102,104)
Example 5: keeping ungrouped spectra
ExKeep
import os
# Create a grouping file from the example above. # It makes 2 groups of 64 and 60 detectors respectively. groupingFileContent = """ 2 1 64 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 2 60 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 """ # Save the data to a file groupingFilePath = os.path.expanduser('~/MantidUsageExample_GroupDetectorsGrouping.txt') f = open(groupingFilePath, 'w') f.write( groupingFileContent ) f.close()
# Create a workspace filled with a constant value = 0.3 ws=CreateSampleWorkspace() # Group detectors according to the created file. grouped = GroupDetectors( ws, MapFile=groupingFilePath, KeepUngroupedSpectra=True )
# Check the result print 'Number of spectra in grouped workspace is', grouped.getNumberHistograms() print 'It includes 2 groups + ',ws.getNumberHistograms() - (64 + 60),'remaining ungrouped spectra'
print 'First spectrum is grouped, it has',len(grouped.getSpectrum(0).getDetectorIDs()),'detectors' print 'Second spectrum is grouped, it has',len(grouped.getSpectrum(1).getDetectorIDs()),'detectors' print 'Spectrum 2 is ungrouped, it has ',len(grouped.getSpectrum(2).getDetectorIDs()),'detector' print 'Spectrum 3 is ungrouped, it has ',len(grouped.getSpectrum(3).getDetectorIDs()),'detector' print '...' print 'Spectrum 77 is ungrouped, it has ',len(grouped.getSpectrum(77).getDetectorIDs()),'detector'
ExKeep
Number of spectra in grouped workspace is 78 It includes 2 groups + 76 remaining ungrouped spectra First spectrum is grouped, it has 64 detectors Second spectrum is grouped, it has 60 detectors Spectrum 2 is ungrouped, it has 1 detector Spectrum 3 is ungrouped, it has 1 detector ... Spectrum 77 is ungrouped, it has 1 detector
ExKeep
os.remove( groupingFilePath )
Example 6: Group detectors using spectra list
ExGroupDetectorsWithSpectra
# Create test input xx=range(0,10)10; # create spectra with signal equal to spectra number yy=[] for i in xrange(1,11): yy=yy+[i]10
ws=CreateWorkspace(DataX=xx,DataY=yy,NSpec=10); # Group detectors wsg0 = GroupDetectors(ws,SpectraList=[1,2,3],KeepUngroupedSpectra=True,Behaviour='Sum') print "Grouped first 3 spectra results in workspace with {0} spectra and the grouped spectra is spectrum 0:".format(wsg0.getNumberHistograms()) print wsg0.dataY(0); print "First unaffected spectrum is now spectrum 1, former spectrum 4:" print wsg0.dataY(1); print "*********************************************************"
# Group detectors differently wsg1 = GroupDetectors(ws,SpectraList=[2,3,4],KeepUngroupedSpectra=True,Behaviour='Sum') print "Grouped 3 spectra starting with second results in workspace with {0} spectra and the grouped spectra is spectrum 0:".format(wsg1.getNumberHistograms()) print wsg1.dataY(0); print "First unaffected spectrum is now spectrum 1, former spectrum 0:" print wsg1.dataY(1); print "*********************************************************"
# Group detectors in a chain: wsg2 = GroupDetectors(wsg0,SpectraList=[4,5,6],KeepUngroupedSpectra=True,Behaviour='Sum') print "Grouped 6 spectra 3x3 twice results in workspace with {0} spectra and the grouped spectra is spectrum 0 and 1:".format(wsg2.getNumberHistograms()) print wsg2.dataY(0); print wsg2.dataY(1); print "First unaffected spectrum is now spectrum 3, former spectrum 7:" print wsg2.dataY(2); print "*********************************************************"
Output:
ExGroupDetectorsWithSpectra
Grouped first 3 spectra results in workspace with 8 spectra and the grouped spectra is spectrum 0: [ 6. 6. 6. 6. 6. 6. 6. 6. 6. 6.] First unaffected spectrum is now spectrum 1, former spectrum 4: [ 4. 4. 4. 4. 4. 4. 4. 4. 4. 4.] ******************************************************* Grouped 3 spectra starting with second results in workspace with 8 spectra and the grouped spectra is spectrum 0: [ 9. 9. 9. 9. 9. 9. 9. 9. 9. 9.] First unaffected spectrum is now spectrum 1, former spectrum 0: [ 1. 1. 1. 1. 1. 1. 1. 1. 1. 1.]***************************************************** Grouped 6 spectra 3x3 twice results in workspace with 6 spectra and the grouped spectra is spectrum 0 and 1: [ 15. 15. 15. 15. 15. 15. 15. 15. 15. 15.] [ 6. 6. 6. 6. 6. 6. 6. 6. 6. 6.] First unaffected spectrum is now spectrum 3, former spectrum 7: [ 7. 7. 7. 7. 7. 7. 7. 7. 7. 7.]*******************************************************
Example 7: Group detectors using map file:
ExGroupDetectorsWithMap
import os # Create test input xx=range(0,10)10; # create spectra with signal equal to spectrum number yy=[] for i in xrange(1,11): yy=yy+[i]10
ws=CreateWorkspace(DataX=xx,DataY=yy,NSpec=10);
# Create map file file_name = os.path.join(config["defaultsave.directory"], "TestMapFile.map") f=open(file_name,'w'); f.write('4n'); # header, four groups f.write('1n3n'); # header group 1 f.write('1 2 3n'); # group 1 f.write('2n3n'); # header group 2 f.write('4 5 6n'); # group 2 f.write('3n2n'); # header group 3 f.write('7 8n'); # group 3 f.write('4n2n'); # header group 4 f.write('9 10n'); # group 4 f.close()
# Group detectors wsg = GroupDetectors(ws,MapFile=file_name,KeepUngroupedSpectra=True,Behaviour='Sum')
print "Grouped workspace has {0} spectra".format(wsg.getNumberHistograms()) print "spectrum 1 (sum of spectra 1-3):",wsg.dataY(0) print "spectrum 2 (sum of spectra 4-6):",wsg.dataY(1) print "spectrum 3 (sum of spectra 7-8):",wsg.dataY(2) print "spectrum 4 (sum of spectra 9-10):",wsg.dataY(3)
ExGroupDetectorsWithMap
os.remove(file_name)
Output:
ExGroupDetectorsWithMap
Grouped workspace has 4 spectra spectrum 1 (sum of spectra 1-3): [ 6. 6. 6. 6. 6. 6. 6. 6. 6. 6.] spectrum 2 (sum of spectra 4-6): [ 15. 15. 15. 15. 15. 15. 15. 15. 15. 15.] spectrum 3 (sum of spectra 7-8): [ 15. 15. 15. 15. 15. 15. 15. 15. 15. 15.] spectrum 4 (sum of spectra 9-10): [ 19. 19. 19. 19. 19. 19. 19. 19. 19. 19.]
Example 8: Group detectors using grouping pattern:
ExGroupDetectorsWithPattern
# Create Workspace of 5 spectra each with two entries. ws = CreateWorkspace(DataX=[1,2], DataY=[11,12,21,22,31,32,41,42,51,52], NSpec=5)
# Run algorithm adding first two spectra and then keeping last two spectra ws2 = GroupDetectors(ws, GroupingPattern="0+1,3,4")
#print result print ws2.readY(0) print ws2.readY(1) print ws2.readY(2)
Output:
ExGroupDetectorsWithPattern
[ 32. 34.] [ 41. 42.] [ 51. 52.]