Cannot extract single peak

[czhao9]

I met a problem when I am trying the first example in the tutorial (i.e., single-peak extraction). The PDF of Ag can be successfully plotted without extracting peak. However, when I execute

srmise data/Ag_nyquist_qmax30.gr --plot --range 2 3.5 --baseline "Polynomial(degree=1)"

on my PC, following warning appears:

The input PDF appears to be missing information: The sampling interval of the input PDF (0.10471976036) is larger than the Nyquist interval (0.10471975512) defined by qmax=30.0. This information is irretrievable.
Traceback (most recent call last):
File "c:\programdata\anaconda2\lib\runpy.py", line 174, in _run_module_as_main
"main", fname, loader, pkg_name)
File "c:\programdata\anaconda2\lib\runpy.py", line 72, in run_code
exec code in run_globals
File "C:\ProgramData\Anaconda2\Scripts\srmise.exe_main.py", line 9, in
File "c:\programdata\anaconda2\lib\site-packages\diffpy\srmise\applications\extract.py", line 388, in main
cov = ext.extract()
File "c:\programdata\anaconda2\lib\site-packages\diffpy\srmise\pdfpeakextraction.py", line 386, in extract
ext.fit() # Clean up parameters after resampling.
File "c:\programdata\anaconda2\lib\site-packages\diffpy\srmise\modelcluster.py", line 878, in fit
orig_qual = self.quality()
File "c:\programdata\anaconda2\lib\site-packages\diffpy\srmise\modelcluster.py", line 1112, in quality
evaluator_inst.evaluate(self, **kwds)
File "c:\programdata\anaconda2\lib\site-packages\diffpy\srmise\modelevaluators\aic.py", line 71, in evaluate
self.chisq = self.chi_squared(fit.value(), fit.y_cluster, fit.error_cluster)
File "c:\programdata\anaconda2\lib\site-packages\diffpy\srmise\modelcluster.py", line 1067, in value
return self.valuebl(r)+(self.model.value(self.r_data, self.slice)[self.slice])
File "c:\programdata\anaconda2\lib\site-packages\diffpy\srmise\modelparts.py", line 272, in value
total += p.value(r, range)
File "c:\programdata\anaconda2\lib\site-packages\diffpy\srmise\modelparts.py", line 468, in value
return self._owner.value(self, r, range)
File "c:\programdata\anaconda2\lib\site-packages\diffpy\srmise\peaks\terminationripples.py", line 226, in value
output[rng] = value[ext_slice][::segments]
TypeError: slice indices must be integers or None or have an index method

Can anyone help with this problem?

Thanks!

[JMSkelton]

This error appears to be due to a bug on line 216 in terminationripples.py:

segments = np.ceil(dr/dr_super)

At least in newer versions of NumPy, np.ceil() returns a floating-point value, which cannot be used as an array index.

An easy solution is to edit terminationripples.py and change the line to e.g. the following:

segments = int(np.ceil(dr/dr_super))

[stevenhua0320]

@sbillinge Maybe we could move this issue later or close this one and open another one since the code might be refactored at some moment and I did a global search on the repo, which I didn't find the line that these users report that might be the culprit of the issue.

[sbillinge]

I think we should maybe try and close this. Can you do a search for part of the code, like dr/dr_super or segments? I doubt we refactored names of variables

[stevenhua0320]

Yes, I tried all the possible way to pinpoint it, but there is no such code on the global search.

[sbillinge]

Is that dataset in the repo as an example one? In that case can you run that command and see if it works? We may have renamed the file....

[stevenhua0320]

The issue might still exist... I run the command but still the issue persists. Let me dive into the issue tonight and see if I can find it out...

(diffpy.srmise_env) huarundong@Stevens-MacBook-Pro-405 diffpy.srmise % srmise docs/examples/data/Ag-nyquist-qmax30.gr --plot --range 2 3.5 --baseline "Polynomial(degree=1)"
The input PDF appears to be missing information: The sampling interval of the input PDF (0.10471976036036036) is larger than the Nyquist interval (0.10471975511965977) defined by qmax=30.0.  This information is irretrievable.
Traceback (most recent call last):
  File "/opt/miniconda3/envs/diffpy.srmise_env/bin/srmise", line 10, in <module>
    sys.exit(main())
             ~~~~^^
  File "/opt/miniconda3/envs/diffpy.srmise_env/lib/python3.14/site-packages/diffpy/srmise/applications/extract.py", line 537, in main
    cov = ext.extract()
  File "/opt/miniconda3/envs/diffpy.srmise_env/lib/python3.14/site-packages/diffpy/srmise/pdfpeakextraction.py", line 417, in extract
    pe.extract_single()
    ~~~~~~~~~~~~~~~~~^^
  File "/opt/miniconda3/envs/diffpy.srmise_env/lib/python3.14/site-packages/diffpy/srmise/peakextraction.py", line 829, in extract_single
    y = self.y[rangeslice] - bl.value(x) - ip.value(x)
                             ^^^^^^^^
AttributeError: 'str' object has no attribute 'value'

[sbillinge]

thanks! It is an easy fix if you can find it, we just have to int the ceil

[stevenhua0320]

thanks! It is an easy fix if you can find it, we just have to int the ceil

To tell the truth, it is not a quite easy thing to fix it. Because of the property of python 2 legacy issue (since this package is lack of test as we found out in 2024, there are still quite a lot py2 legacy in the code). So, it takes me some time to fix it 😂
But I somewhat fixes the bug, the only issue is I'm not quite sure whether it is really behaving properly. So, I would now open a PR for this and I would also attach the plot that it produces.