Ticket #7011 (closed: fixed)

Opened 7 years ago

Last modified 5 years ago

SelectCellOfType and SelectCellOfForm change HKLs incorrectly in some cases.

Reported by: Dennis Mikkelson Owned by: Dennis Mikkelson
Priority: blocker Milestone: Release 2.5
Component: Mantid Keywords:
Cc: petersonpf@…, owen.arnold@…, mikkelsonr@… Blocked By:
Blocking: Tester: Andrei Savici

Description

Xiaoping reported a problem with the conventional cell indexing for a sample. The problem was traced to an incorrect transformation applied to the HKLs in this case. The most robust fix is to actually re-index the peaks with the new UB.

Attachments

SelectCellBugTest.peaks​ (84.2 KB) - added by Dennis Mikkelson 7 years ago.
The problem occurs with this peaks file.

Change History

Changed 7 years ago by Dennis Mikkelson

The problem occurs with this peaks file.

comment:1 Changed 7 years ago by Dennis Mikkelson

RE 7011 Fixes select cell bug

The SelectCellOfType and SelectCellWithForm algorithms now actually re-index the peaks with the new UB matrix, if the Apply parameter is true. Previously, a transformation was applied to the previously calculated hkl values, however, in some cases the transformation applied was not correct.

refs #7011

Changeset: 94011033a1b5a48f5533511485782e1818b7577a

comment:2 Changed 7 years ago by Dennis Mikkelson

  • Status changed from new to accepted

This is fixed by the modifications to the following two files in branch bugfix/7011select_cell_bug:

Framework/Crystal/src/SelectCellOfType.cpp Framework/Crystal/src/SelectCellWithForm.cpp

Unfortunately, I currently can't check them in develop, since after checking out the current develop branch I get the error: git merge --no-ff bugfix/7011_select_cell_bug Auto-merging Code/Mantid/CMakeLists.txt Auto-merging Code/Mantid/Framework/Crystal/src/SelectCellOfType.cpp Auto-merging Code/Mantid/Framework/Crystal/src/SelectCellWithForm.cpp Auto-merging Code/Mantid/MantidPlot/src/ApplicationWindow.cpp Auto-merging Code/Mantid/MantidPlot/src/Mantid/MantidUI.cpp Auto-merging Code/Mantid/docs/qtassistant/CMakeLists.txt Auto-merging Code/Mantid/docs/qtassistant/mediawiki.py CONFLICT (content): Merge conflict in Code/Mantid/docs/qtassistant/mediawiki.py Automatic merge failed; fix conflicts and then commit the result.

comment:3 Changed 7 years ago by Dennis Mikkelson

To test

  1. load the attached file: SelectCellBugTest.peaks into a peaks workspace using LoadIsawPeaks.
  1. Run FindUBUsingFFT with MinD = 4, MaxD = 15, Tolerance = 0.12 on the peaks workspace to get a UB set corresponding to a Niggli reduced cell.
  1. Run IndexPeaks, with Tolerance = 0.12 and Round HKL false. The first peak in the peaks workspace should index as 1,-3,-6.
  1. Run SelectCellOfType with CellType = Tetragonal and Centering = I, Apply = True, Tolerance = 0.12. If the first peak is now indexed as -1,3,-10, the problem is fixed.
  1. To test SelectCellWithForm, repeat steps 2 and 3, then run SelectCellWithForm with FormNumber = 15, Apply = True and Tolerance = 0.12. The first peak should again be indexed as -1,3,-10.

Prior to fixing this problem, the first peak was incorrectly indexed as -1,3,14 by both SelectCellOfType and SelectCelWithForm.

comment:4 Changed 7 years ago by Dennis Mikkelson

RE 7011 Fixes select cell bug

The SelectCellOfType and SelectCellWithForm algorithms now actually re-index the peaks with the new UB matrix, if the Apply parameter is true. Previously, a transformation was applied to the previously calculated hkl values, however, in some cases the transformation applied was not correct.

refs #7011 Changeset: 2fae3e4398b769699dd989d195df8035a1f39952

comment:5 Changed 7 years ago by Dennis Mikkelson

RE 7011 Fixes select cell bug

The SelectCellOfType and SelectCellWithForm algorithms now actually re-index the peaks with the new UB matrix, if the Apply parameter is true. Previously, a transformation was applied to the previously calculated hkl values, however, in some cases the transformation applied was not correct.

refs #7011 Changeset: 2fae3e4398b769699dd989d195df8035a1f39952

comment:6 Changed 7 years ago by Dennis Mikkelson

  • Status changed from accepted to verify
  • Resolution set to fixed

This bug is fixed in branch bugfix/7011_select_cell_bug. Instructions for testing using the file attached to this ticket are in the trac comment from 12 hours previous to this comment.

comment:7 Changed 7 years ago by Andrei Savici

  • Status changed from verify to verifying
  • Tester set to Andrei Savici

comment:8 Changed 7 years ago by Dennis Mikkelson

RE 7011 Fixes select cell bug

The SelectCellOfType and SelectCellWithForm algorithms now actually re-index the peaks with the new UB matrix, if the Apply parameter is true. Previously, a transformation was applied to the previously calculated hkl values, however, in some cases the transformation applied was not correct.

refs #7011 Changeset: 2fae3e4398b769699dd989d195df8035a1f39952

comment:9 Changed 7 years ago by Andrei Savici

  • Status changed from verifying to closed

comment:10 Changed 7 years ago by Dennis Mikkelson

RE 7011 Fixes select cell bug

The SelectCellOfType and SelectCellWithForm algorithms now actually re-index the peaks with the new UB matrix, if the Apply parameter is true. Previously, a transformation was applied to the previously calculated hkl values, however, in some cases the transformation applied was not correct.

refs #7011 Changeset: 2fae3e4398b769699dd989d195df8035a1f39952

comment:11 Changed 7 years ago by Dennis Mikkelson

RE 7011 Fixes select cell bug

The SelectCellOfType and SelectCellWithForm algorithms now actually re-index the peaks with the new UB matrix, if the Apply parameter is true. Previously, a transformation was applied to the previously calculated hkl values, however, in some cases the transformation applied was not correct.

refs #7011 Changeset: 2fae3e4398b769699dd989d195df8035a1f39952

comment:12 Changed 5 years ago by Stuart Campbell

This ticket has been transferred to github issue ​7857

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