36863 find global b matrix warnings #38574

andy-bridger · 2025-01-08T14:07:50Z

Description of work

Summary of work

Reworking of the algorithm to incorporate some 'quality of life' changes. Mainly code refactoring and updating of error/ warning messaging.

Fixes #36863 .

Further detail of work

As per the comment on the issue (#36863 (comment)) the following changes have been made:

Single wrapper function around calling a child algorithm added and replacing individual function calls
Update to the find_initial_indexing function:

If no UB on any table then call FindUBUsingLatticeParameters on tables until successful then break
If there are UBs, copy UB to each workspace to get NUB x NUB triangular matrix of nindexed peaks - find best UB to use as a reference (currently: find UB which gives the most ws with n_peaks >= thresh. Tie-breaks by choosing the UB which indexes the most peaks across all ws).
Once a reference UB has been found, index peaks in each table using this UB - if a table doesn't have enough indexed peaks then try and call FindUBUsingLatticeParameters and make_UB_consistent - if still not successful gives warning and excludes this table from optimisation.

After optimisation completed, loop over workspaces, call IndexPeaks and print warning for any runs which n_peaks < MIN_NUM_INDEXED
Move try/except to be around the call to CalculateUMatrix in calcResiduals, so we can throw error telling user which workspace/run is problematic
Relax MIN_NUM_INDEXED = 2
In validateInputs require each table to have a minimum of 2 indexed peaks if a UB is present, or 6 peaks (don't need to be indexed) if no UB is present (atm just requires total of 6 peaks).
Updated the tests to cover the change of validateInputs and the exclusion of peak tables with fewer than thresh peaks

To test:

Following script has been use for developing:

# import mantid algorithms, numpy and matplotlib
from mantid.simpleapi import *
import matplotlib.pyplot as plt
import numpy as np

# generate peak table
ws = LoadEmptyInstrument(InstrumentName='SXD', OutputWorkspace='ws')
axis = ws.getAxis(0)
axis.setUnit("TOF")  # need this to add peak to table

SetGoniometer(Workspace=ws, Axis0='-5,0,1,0,1')
peaks = CreatePeaksWorkspace(InstrumentWorkspace='ws', NumberOfPeaks=0)
UB = np.diag([0.3333, 0.25, 0.09091])  # alatt = [3,4,11] 
SetUB(peaks, UB=UB)

peaks2 = CreatePeaksWorkspace(InstrumentWorkspace='ws', NumberOfPeaks=0)
UB = np.diag([0.30, 0.25, 0.1])  # alatt = [3.3,4,10] 
SetUB(peaks2, UB=UB)

SetGoniometer(Workspace=ws, Axis0='5,0,1,0,1')
peaks3 = CreatePeaksWorkspace(InstrumentWorkspace='ws', NumberOfPeaks=0)
UB = np.diag([0.3333, 0.25, 0.09091])  # alatt = [3,4,11] 
SetUB(peaks3, UB=UB)

peaks_list = [peaks, peaks2, peaks3]
for k in range(1,6):
    for l in range(1,6):
        for peak_ws in peaks_list:
            pk = peak_ws.createPeakHKL([2, k, l])
            if pk.getDetectorID() > 0:
               peak_ws.addPeak(pk)

#ClearUB(peaks2)

FindGlobalBMatrix(PeakWorkspaces = peaks_list,
    a=3, b=4,c=11,alpha=90,beta=90,gamma=90)
    
for ws in peaks_list:
    nindexed, *_ = IndexPeaks(ws, Tolerance=0.15, CommonUBForAll=True, EnableLogging=False)
    print(f"{ws.name()} has {nindexed} indexed peaks")

Changing UB = np.diag([0.30, 0.25, 0.1]) for peaks2 to UB = np.diag([0.33, 0.25, 0.1]) should see peaks2 included within the refinement.

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sf1919 · 2025-01-13T09:00:02Z

Can we get a milestone on this please?

RichardWaiteSTFC

Thanks for taking this on, it looks like this will be an improvement and provide more informative troubleshooting warnings to the user. Thanks for adding tests for these warnings as well!
I have some suggested improvements (feel free to push back), I think in particular find_initial_indexing could be made a bit clearer (I'm aware the same could probably be said of the original function!). Perhaps if there are no UBs found initially the loop over workspaces with the call to FindUBUsingLatticeParameters could be put in a separate function e.g. find_intial_ub_using_latt_param?

RichardWaiteSTFC · 2025-01-14T10:12:54Z

Framework/PythonInterface/plugins/algorithms/FindGlobalBMatrix.py

+            # require PeakWorkspaces with different req for those with/without UBs
+            # with: to have the more relaxed, n_peaks is at least _MIN_NUM_INDEXED_PEAKS
+            # without UBs: must have at least _MIN_NUM_PEAKS
+            if isinstance(ws, IPeaksWorkspace) and n_peaks >= (_MIN_NUM_PEAKS, _MIN_NUM_INDEXED_PEAKS)[has_UB]:


This isn't quite what I had in mind, I think if there is a UB set then we will need to call IndexPEaks.
Something like this (not tested, no warranty)

def validateInputs(self): issues = dict() ws_list = self.getProperty("PeakWorkspaces").value for ws_name in self.getProperty("PeakWorkspaces").value: ws = AnalysisDataService.retrieve(wsname) if not isinstance(ws, IPeaksWorkspace): issues["PeakWorkspaces"] = f"{ws_name} is not a PeaksWorkspace." break if ws.getOrientedLattice(): nindexed, *_ = self.exec_child_alg("IndexPeaks", PeaksWorkspace=ws_name, RoundHKLs=True, CommonUBForAll=True) if nindexed < MIN_NUM_INDEXED_PEAKS: issues["PeakWorkspaces"] = f"{ws_name} has a UB set, therefore it must contain at least {_MIN_NUM_INDEXED_PEAKS} peaks that can be indexed." elif ws.getNumberPeaks() < _MIN_NUM_PEAKS: issues["PeakWorkspaces"] = f"{ws_name} does not have a UB set, therefore it must contain at least {_MIN_NUM_PEAKS} peaks." return issues

Sure, I've also incorporated the check that at least 2 ws provided are valid

RichardWaiteSTFC · 2025-01-14T14:29:34Z

Framework/PythonInterface/plugins/algorithms/FindGlobalBMatrix.py

+            self.exec_child_alg("IndexPeaks", PeaksWorkspace=cws, RoundHKLs=True, CommonUBForAll=False)
+
+        # for the ws with fewer peaks than threshold, try and find some more by adjusting U slightly
+        for iws in np.where(n_indexed_by_ref < _MIN_NUM_INDEXED_PEAKS)[0]:


I think this loop can be combined with the one above

mantid/Framework/PythonInterface/plugins/algorithms/FindGlobalBMatrix.py

Lines 188 to 190 in 870856d

for iws, cws in enumerate(ws_list):

SetUB(cws, UB=ref_ub)

self.exec_child_alg("IndexPeaks", PeaksWorkspace=cws, RoundHKLs=True, CommonUBForAll=False)

If indexed more than minimum number then set reference UB, otherwise then call FindUBUsingLatticeParameter

RichardWaiteSTFC · 2025-01-14T14:30:59Z

Framework/PythonInterface/plugins/algorithms/FindGlobalBMatrix.py

+        total_indexed_peaks = np.sum(indexed_peaks, axis=1)
+
+        # find which UBs give the most over threshold and then, of these, which fit the most peaks
+        max_over_thresh = np.argwhere(n_ws_over_thresh == np.max(n_ws_over_thresh))


I think it would be good to throw a warning if none of the UBs can index enough peaks in any of the other runs, this might indicate an error in the goniometer angles or axes.

Would it make sense to use np.argmax instead? https://numpy.org/doc/stable/reference/generated/numpy.argmax.html

I think in this case there could be multiple runs indexing the same number of peaks.
I wondered about using np.lexsort e.g.

best_iub = np.lexsort(( -total_indexed_peaks, -n_ws_over_thresh))[0] # sort by nws_indexed then total number peaks indexed

then thought sorting would be wasteful! But need to remeber only <~10 peak tables typically so this stuff won't be a performance bottleneck! Probably readability is most important thing here!

Framework/PythonInterface/plugins/algorithms/FindGlobalBMatrix.py

RichardWaiteSTFC · 2025-01-14T14:33:11Z

Framework/PythonInterface/plugins/algorithms/FindGlobalBMatrix.py

+            if nindexed < _MIN_NUM_INDEXED_PEAKS:
+                logger.warning(f"Fewer than the desired {_MIN_NUM_INDEXED_PEAKS} peaks were indexed for Workspace {iws}")
+                ws_list.pop(iws)
+                logger.warning(f"Workspace {iws} removed")


I think better to combine the warning messages together in a single call to logger.warning

Framework/PythonInterface/plugins/algorithms/FindGlobalBMatrix.py

RichardWaiteSTFC · 2025-01-14T14:58:31Z

Framework/PythonInterface/plugins/algorithms/FindGlobalBMatrix.py

-            if foundUB:
-                iws_unindexed.remove(iws)
+        # iterate over the potential reference UBs to find the best one
+        potential_ref_UBs = [


I think potential_ref_UBs doesn't need to be stored in a variable in find_initial_indexing - it's only useful inside evaluate_best_ref_UB which could return the UB rather than the index of the best UB

RichardWaiteSTFC · 2025-01-14T15:05:22Z

Framework/PythonInterface/plugins/algorithms/FindGlobalBMatrix.py

@@ -129,66 +138,110 @@ def find_initial_indexing(self, a, b, c, alpha, beta, gamma, ws_list):
        # check if a UB exists on any run and if so whether it indexes a sufficient number of peaks
        foundUB = False
        ws_with_UB = [


It's difficult to come up with a variable name that infers the object contains iws, nindexed pairs. I might be tempted just to store nindexed in a list and have something like

iws_have_ub = [iws, for iws, ws in enumerate(ws_list) if AnalysisDataService.retrieve(ws).sample().hasOrientedLattice()] nindexed = np.array([self.exec_child_alg("IndexPeaks", PeaksWorkspace=ws_list[iws], RoundHKLs=True, CommonUBForAll=False)[0] for iws in iws_have_ub]) iws_potential_ref_ub = iws_have_ub[np.flatnonzero(nindexed > _MIN_NUM_INDEXED_PEAKS)] foundUB = len(iws_potential_ref_ub) > 0

what do you think?

If the list comprehensions are getting a bit much, there is also:

def _index_workspace_peaks(workspace_index: int) -> int: """whatever the heck this does""" return self.exec_child_alg( "IndexPeaks", PeaksWorkspace=ws_list[workspace_index], RoundHKLs=True, CommonUBForAll=False, )[0] nindexed = np.fromiter(map(_index_workspace_peaks, iws_have_ub), dtype=int)

List comprehension might be slightly faster though 😅

yeh, I agree, I've done this along with the change above (#38574 (comment)) and some other little bits to generally reduce the number of repeated loops and some of the repeated/unnecessary data storing

RichardWaiteSTFC · 2025-01-14T15:18:52Z

For my reference when testing, on main the example script produces
For np.diag([0.30, 0.25, 0.1])

Lattice parameters successfully refined for workspaces: ['peaks', 'peaks2', 'peaks3']
Lattice Parameters: [ 3.001757  4.006301 11.020517 89.848446 89.904955 90.009059]
Parameter Errors  : [1.552047e-08 7.713167e-02 1.503726e+00 4.947268e+00 4.130064e+00
 1.757921e+00]
peaks has 10 indexed peaks
peaks2 has 4 indexed peaks
peaks3 has 9 indexed peaks

and for np.diag([0.33, 0.25, 0.1])

Lattice parameters successfully refined for workspaces: ['peaks', 'peaks2', 'peaks3']
Lattice Parameters: [ 2.992984  4.008921 10.873919 89.542916 89.187807 90.773892]
Parameter Errors  : [0.035323 0.045496 0.3641   3.065943 1.982192 1.249527]
peaks has 10 indexed peaks
peaks2 has 8 indexed peaks
peaks3 has 9 indexed peaks

andy-bridger · 2025-01-15T16:00:43Z

All those comments should now have changes made, plus an extra handling and test of make_ub_consistent

for more information, see https://pre-commit.ci

RichardWaiteSTFC

Nice work, almost there! Just some minor changes to wording of warnings.
I have tried this on some real runs (WISH, Fe2Me3O8) and it does seem like a better reference UB is now found - it seems there are now only 2 runs in the sequence of 9 we can't index post global B optimisation, and the angle between the U matrices are much more consistent. Previously there were at least 3 runs we couldn't index.

I think there's some extra debug info we could give the user post optimisation but happy to leave that for a later PR.

Here are some results from Fe2Me3O8 runs, mostly for my reference!

# New with UB from FindUBUsingLatticeParameters and CalculateUMatrix
####################################################################
Lattice Parameters: [  5.776435   5.787138  10.074228  89.919849  90.012372 119.975833]
Parameter Errors  : [0.003698 0.006794 0.009006 0.111621 0.071437 0.076058]
# angles between UBs
[[ 0.   9.4  8.3  8.7  2.3 57.8  7.2  7.8  5.1]
 [ 0.   0.   8.5  2.3  9.3 48.9  3.8  8.7  4.9]
 [ 0.   0.   0.   6.7  8.7 51.7  9.4 10.5  7.7]
 [ 0.   0.   0.   0.   8.4 49.3  4.   7.6  4.3]
 [ 0.   0.   0.   0.   0.  57.6  6.5  5.7  4.4]
 [ 0.   0.   0.   0.   0.   0.  52.1 54.8 53.4]
 [ 0.   0.   0.   0.   0.   0.   0.   5.7  2.4]
 [ 0.   0.   0.   0.   0.   0.   0.   0.   5.1]
 [ 0.   0.   0.   0.   0.   0.   0.   0.   0. ]]
WISH00057712_peaks_int: indexed 1 out of 94 peaks within 0.15
WISH00057713_peaks_int: indexed 94 out of 94 peaks within 0.15
WISH00057714_peaks_int: indexed 98 out of 98 peaks within 0.15
WISH00057715_peaks_int: indexed 5 out of 91 peaks within 0.15
WISH00057716_peaks_int: indexed 100 out of 100 peaks within 0.15
WISH00057718_peaks_int: indexed 90 out of 91 peaks within 0.15
WISH00057719_peaks_int: indexed 97 out of 98 peaks within 0.15
WISH00057720_peaks_int: indexed 94 out of 94 peaks within 0.15
WISH00057721_peaks_int: indexed 79 out of 79 peaks within 0.15

# New with no intial UB
######################
Lattice Parameters: [  5.782949   5.779583  10.072472  90.062373  90.019683 119.970795]
Parameter Errors  : [0.005746 0.005422 0.00805  0.082286 0.090764 0.084685]
# angles between UBs
[[ 0.  24.9 48.1 55.3 23.5  5.7 19.1 22.   7.2]
 [ 0.   0.  60.  74.6  9.2 20.2 17.7  8.7 21.2]
 [ 0.   0.   0.  24.6 52.7 51.7 43.  56.1 52.4]
 [ 0.   0.   0.   0.  68.1 60.4 58.6 69.9 60.8]
 [ 0.   0.   0.   0.   0.  20.6 13.6  5.8 22.4]
 [ 0.   0.   0.   0.   0.   0.  17.4 18.9  2.8]
 [ 0.   0.   0.   0.   0.   0.   0.  17.3 18.2]
 [ 0.   0.   0.   0.   0.   0.   0.   0.  20.9]
 [ 0.   0.   0.   0.   0.   0.   0.   0.   0. ]]
WISH00057712_peaks_int: indexed 94 out of 94 peaks within 0.15
WISH00057713_peaks_int: indexed 94 out of 94 peaks within 0.15
WISH00057714_peaks_int: indexed 98 out of 98 peaks within 0.15
WISH00057715_peaks_int: indexed 91 out of 91 peaks within 0.15
WISH00057716_peaks_int: indexed 100 out of 100 peaks within 0.15
WISH00057718_peaks_int: indexed 90 out of 91 peaks within 0.15
WISH00057719_peaks_int: indexed 5 out of 98 peaks within 0.15
WISH00057720_peaks_int: indexed 94 out of 94 peaks within 0.15
WISH00057721_peaks_int: indexed 5 out of 79 peaks within 0.15

# Old with UB from FindUBUsingLatticeParameters and CalculateUMatrix
#####################################################################
Lattice Parameters: [  5.780991   5.77608   10.075893  89.975613  90.028252 120.230395]
Parameter Errors  : [0.008211 0.012893 0.016293 0.171744 0.165701 0.150146]
# angles between UBs
[[  0.   21.2 105.9  41.3  39.6  90.9  88.4  41.2   5.9]
 [  0.    0.   91.4  33.2  26.1  81.3  75.9  27.3  20.9]
 [  0.    0.    0.   65.5  67.8  27.2  20.3  65.2 103.3]
 [  0.    0.    0.    0.   14.   50.   47.5  11.8  38.7]
 [  0.    0.    0.    0.    0.   57.6  50.8   5.7  36.5]
 [  0.    0.    0.    0.    0.    0.   17.3  54.6  88.3]
 [  0.    0.    0.    0.    0.    0.    0.   48.8  85.3]
 [  0.    0.    0.    0.    0.    0.    0.    0.   38.7]
 [  0.    0.    0.    0.    0.    0.    0.    0.    0. ]]
WISH00057712_peaks_int: indexed 9 out of 94 peaks within 0.15
WISH00057713_peaks_int: indexed 2 out of 94 peaks within 0.15
WISH00057714_peaks_int: indexed 98 out of 98 peaks within 0.15
WISH00057715_peaks_int: indexed 2 out of 91 peaks within 0.15
WISH00057716_peaks_int: indexed 100 out of 100 peaks within 0.15
WISH00057718_peaks_int: indexed 90 out of 91 peaks within 0.15
WISH00057719_peaks_int: indexed 6 out of 98 peaks within 0.15
WISH00057720_peaks_int: indexed 94 out of 94 peaks within 0.15
WISH00057721_peaks_int: indexed 2 out of 79 peaks within 0.15

# Old with no intial UB
#######################
Lattice Parameters: [  5.782866   5.779128  10.072993  90.067975  90.037199 119.936395]
Parameter Errors  : [0.00565  0.004945 0.009092 0.078644 0.098838 0.095805]
# angles between UBs
[[ 0.  24.9 48.1 45.1 23.5  5.7 19.1 22.  23.3]
 [ 0.   0.  60.  63.4  9.2 20.2 17.7  8.7  4.9]
 [ 0.   0.   0.  17.  52.7 51.7 43.  56.1 56.1]
 [ 0.   0.   0.   0.  56.9 49.9 47.2 58.8 59.7]
 [ 0.   0.   0.   0.   0.  20.6 13.6  5.8  4.4]
 [ 0.   0.   0.   0.   0.   0.  17.4 18.9 19.5]
 [ 0.   0.   0.   0.   0.   0.   0.  17.3 15.1]
 [ 0.   0.   0.   0.   0.   0.   0.   0.   5.2]
 [ 0.   0.   0.   0.   0.   0.   0.   0.   0. ]]
WISH00057712_peaks_int: indexed 94 out of 94 peaks within 0.15
WISH00057713_peaks_int: indexed 94 out of 94 peaks within 0.15
WISH00057714_peaks_int: indexed 98 out of 98 peaks within 0.15
WISH00057715_peaks_int: indexed 2 out of 91 peaks within 0.15
WISH00057716_peaks_int: indexed 100 out of 100 peaks within 0.15
WISH00057718_peaks_int: indexed 90 out of 91 peaks within 0.15
WISH00057719_peaks_int: indexed 5 out of 98 peaks within 0.15
WISH00057720_peaks_int: indexed 94 out of 94 peaks within 0.15
WISH00057721_peaks_int: indexed 79 out of 79 peaks within 0.15

RichardWaiteSTFC · 2025-01-16T14:36:16Z

Framework/PythonInterface/plugins/algorithms/FindGlobalBMatrix.py

                ws = AnalysisDataService.retrieve(wsname)
                ws.sample().getOrientedLattice().setError(*err)
+                if n_peaks[iws] < _MIN_NUM_INDEXED_PEAKS:
+                    logger.warning(
+                        f"Workspace: {wsname}, has only {n_peaks[iws]} indexed peaks, fewer than the desired {_MIN_NUM_INDEXED_PEAKS}"


Can you make this clearee that this is the number of peaks indexed after global B matrix optimisation?

RichardWaiteSTFC · 2025-01-16T14:49:22Z

Framework/PythonInterface/plugins/algorithms/FindGlobalBMatrix.py

+                        # otherwise warn the user
+                        else:
+                            logger.warning(
+                                f"Fewer than the desired {_MIN_NUM_INDEXED_PEAKS} peaks were indexed for Workspace {iws}. "


Can we make this clearer that this is prior to the global B optimisation?

RichardWaiteSTFC

Great, thanks for the hard work getting this into release!

andy-bridger added 16 commits January 8, 2025 10:43

Added a parent function to call child algs

f3b15ca

replaced child_IndexPeaks

b92824f

replaced getUBMatrix

f257439

replaced calculateUMatrix

500d15b

replaced transformHKL

1d8cd52

replaced copySample

0c8760b

added error catching for CalcUMatrix

8e7d8b7

fixed IndexPeaks: only return npeaks

edfc14c

Updated find_initial_indexing loop

fe9fae7

updated the find_initial_indexing

5d2094b

fixed optimisation bug

576d0ca

relax MIN_NUM_INDEXED_PEAKS to 2

00ab5ab

updated input validation and improved err msg

ee16d28

updated warning logging after refinement

76e254a

updated test coverage

020af37

added release note

870856d

andy-bridger marked this pull request as ready for review January 10, 2025 13:07

RichardWaiteSTFC self-assigned this Jan 10, 2025

RichardWaiteSTFC added this to the Release 6.12 milestone Jan 13, 2025

RichardWaiteSTFC added Diffraction Issues and pull requests related to diffraction Single Crystal Issues and pull requests related to single crystal ISIS Team: Diffraction Issue and pull requests managed by the Diffraction subteam at ISIS labels Jan 13, 2025

RichardWaiteSTFC requested changes Jan 14, 2025

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andy-bridger added 5 commits January 15, 2025 09:35

updated validateInputs and its tests

820aecc

reduced num repeated loops and calcs

76d314b

removed redundant IndexPeaks call

e5a7d5a

moved SetUB call to exec_child_alg

c790f57

made final treatment of refUB into one loop

c98ff40

andy-bridger added 4 commits January 15, 2025 11:32

collapse removal warning into one message

a516873

improved readability of find_initial_indexing

80a7c63

added check and test for num_ws indexed by ref_ub

7a9e55c

added check and test for make_ub_consistent

5f4ec8c

andy-bridger and others added 2 commits January 16, 2025 12:30

replace in-place popping with new list appending

413294e

[pre-commit.ci] auto fixes from pre-commit.com hooks

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jclarkeSTFC requested review from RichardWaiteSTFC and ajjackson January 16, 2025 14:52

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jclarkeSTFC changed the base branch from main to release-next January 16, 2025 15:42

amend clarity of warnings when too few peaks

23abc08

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SilkeSchomann enabled auto-merge January 16, 2025 16:54

SilkeSchomann merged commit 61bccff into release-next Jan 16, 2025
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SilkeSchomann deleted the 36863-FindGlobalBMatrix-warnings branch January 16, 2025 18:20

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FindGlobalBMatrix should throw warning if no peaks indexed in a run #36863

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36863 find global b matrix warnings #38574

36863 find global b matrix warnings #38574

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	for iws, cws in enumerate(ws_list):
	SetUB(cws, UB=ref_ub)
	self.exec_child_alg("IndexPeaks", PeaksWorkspace=cws, RoundHKLs=True, CommonUBForAll=False)

36863 find global b matrix warnings #38574

36863 find global b matrix warnings #38574

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andy-bridger commented Jan 8, 2025

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RichardWaiteSTFC Jan 15, 2025 • edited Loading

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RichardWaiteSTFC Jan 14, 2025 • edited Loading

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RichardWaiteSTFC commented Jan 14, 2025

andy-bridger commented Jan 15, 2025

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RichardWaiteSTFC Jan 15, 2025 •

edited

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RichardWaiteSTFC Jan 14, 2025 •

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