IndexError: index 3 is out of bounds for size 0 #267

picca · 2016-03-24T14:54:04Z

Hello

I am playing with the calib method, but I get this error message

ipython-input-7-32280c4943ab> in ()
----> 1 calibration.calibration(img, "CeO2", "Xpad_flat", 1.54)

/usr/lib/python2.7/dist-packages/sida/pyfai/calibration.pyc in calibration(img, calibrant_name, detector_name, wavelength)
14 calibrant.wavelength = wavelength
15 detector = get_detector(detector_name)
---> 16 calib(img, calibrant, detector)

/usr/lib/python2.7/dist-packages/pyFAI/calibration.pyc in calib(img, calibrant, detector, basename, reconstruct, dist, gaussian, interactive)
2360 c.peakPicker.gui(log=True, maximize=True, pick=True)
2361 update_fig(c.peakPicker.fig)
-> 2362 c.gui_peakPicker()
2363 c.ai.setPyFAI(**c.geoRef.getPyFAI())
2364 c.ai.wavelength = c.geoRef.wavelength

/usr/lib/python2.7/dist-packages/pyFAI/calibration.pyc in gui_peakPicker(self)
1478 update_fig(self.peakPicker.fig)
1479 # self.peakPicker.finish(self.pointfile, callback=self.set_data)
-> 1480 self.set_data(self.peakPicker.finish(self.pointfile))
1481 # input("Please press enter when you are happy with your selection" + os.linesep)
1482 # while self.data is None:

/usr/lib/python2.7/dist-packages/pyFAI/calibration.pyc in set_data(self, data)
1297 if not self.weighted:
1298 self.data = numpy.array(self.data)[:, :-1]
-> 1299 self.refine()
1300
1301 def reset_geometry(self, how="center", refine=False):

/usr/lib/python2.7/dist-packages/pyFAI/calibration.pyc in refine(self)
1517 calibrant=self.calibrant,
1518 **defaults)
-> 1519 self.geoRef.refine2(1000000, fix=self.fixed)
1520 scor = self.geoRef.chi2()
1521 pars = [getattr(self.geoRef, p) for p in self.PARAMETERS]

/usr/lib/python2.7/dist-packages/pyFAI/geometryRefinement.pyc in refine2(self, maxiter, fix)
284 bounds=bounds,
285 acc=1.0e-12,
--> 286 iprint=(logger.getEffectiveLevel() <= logging.INFO))
287
288 elif self.data.shape[-1] == 4:

/usr/lib/python2.7/dist-packages/scipy/optimize/slsqp.pyc in fmin_slsqp(func, x0, eqcons, f_eqcons, ieqcons, f_ieqcons, bounds, fprime, fprime_eqcons, fprime_ieqcons, args, iter, acc, iprint, disp, full_output, epsilon, callback)
204
205 res = _minimize_slsqp(func, x0, args, jac=fprime, bounds=bounds,
--> 206 constraints=cons, **opts)
207 if full_output:
208 return res['x'], res['fun'], res['nit'], res['status'], res['message']

/usr/lib/python2.7/dist-packages/scipy/optimize/slsqp.pyc in _minimize_slsqp(func, x0, args, jac, bounds, constraints, maxiter, ftol, iprint, disp, eps, callback, **unknown_options)
358
359 # Compute objective function
--> 360 fx = func(x)
361 # Compute the constraints
362 if cons['eq']:

/usr/lib/python2.7/dist-packages/scipy/optimize/optimize.pyc in function_wrapper(_wrapper_args)
279 def function_wrapper(_wrapper_args):
280 ncalls[0] += 1
--> 281 return function(*(wrapper_args + args))
282
283 return ncalls, function_wrapper

/usr/lib/python2.7/dist-packages/pyFAI/geometryRefinement.pyc in residu2(self, param, d1, d2, rings)
221 #dot product is faster ...
222 # return (self.residu1(param, d1, d2, rings) ** 2).sum()
--> 223 t = self.residu1(param, d1, d2, rings)
224 return numpy.dot(t, t)
225

/usr/lib/python2.7/dist-packages/pyFAI/geometryRefinement.pyc in residu1(self, param, d1, d2, rings)
213
214 def residu1(self, param, d1, d2, rings):
--> 215 return self.tth(d1, d2, param) - self.calc_2th(rings, self.wavelength)
216
217 def residu1_wavelength(self, param, d1, d2, rings):

/usr/lib/python2.7/dist-packages/pyFAI/geometryRefinement.pyc in calc_2th(self, rings, wavelength)
210 if wavelength != self.calibrant.wavelength:
211 self.calibrant.setWavelength_change2th(wavelength)
--> 212 return numpy.array(self.calibrant.get_2th(), dtype=numpy.float64)[rings]
213
214 def residu1(self, param, d1, d2, rings):

IndexError: index 3 is out of bounds for size 0

kif · 2016-03-24T16:26:35Z

On Thu, 24 Mar 2016 07:54:05 -0700
picca [email protected] wrote:

Hello

I am playing with the calib method, but I get this error message

IndexError: index 3 is out of bounds for size 0

did you refine the wavelength (together with the distance) ?
if so, there is a "bug" when wavelength runs-away, the 2theta angle
hits the pi (180°) value and there are less rings possible than
requested.

One should define an upper limit on the wavelength to prevent this.

Do you have the test images ?

Cheers

Jérôme Kieffer
tel +33 476 882 445

picca · 2016-03-24T16:59:15Z

Hello Jerome,

I just used the calib method. so it use your default :)

Yes I have the test image I can send it to you tomorrow if you want.

kif · 2016-03-24T19:14:38Z

On Thu, 24 Mar 2016 09:59:16 -0700
picca [email protected] wrote:

Hello Jerome,

I just used the calib method. so it use your default :)

Yes I have the test image I can send it to you tomorrow if you want.

Si it is actually a bug as the wl should be fixed by default.

picca · 2016-03-25T09:14:34Z

to reproduce the problem

here the code, I am using

import sys
import numpy

from pyFAI.calibration import calib, get_detector
from pyFAI.calibrant import ALL_CALIBRANTS

def get_calibrant(calibrant_name):
    return ALL_CALIBRANTS[calibrant_name]

def calibration(img, calibrant_name, detector_name, wavelength):
    calibrant = get_calibrant(calibrant_name)
    calibrant.wavelength = wavelength
    detector = get_detector(detector_name)
    calib(img, calibrant, detector)

picca · 2016-03-25T09:27:57Z

Just for information,

I obtained the same issue using directly the pyFAI-calib command line of the debian package

mine is the jessie-backports

picca · 2016-03-25T09:28:51Z

In fact the error is not the same

Modify parameters (or ? for help)? done
Traceback (most recent call last):
File "/usr/bin/pyFAI-calib", line 59, in
c.gui_peakPicker()
File "/usr/lib/python2.7/dist-packages/pyFAI/calibration.py", line 1480, in gui_peakPicker
self.set_data(self.peakPicker.finish(self.pointfile))
File "/usr/lib/python2.7/dist-packages/pyFAI/calibration.py", line 1299, in set_data
self.refine()
File "/usr/lib/python2.7/dist-packages/pyFAI/calibration.py", line 1575, in refine
AbstractCalibration.refine(self)
File "/usr/lib/python2.7/dist-packages/pyFAI/calibration.py", line 761, in refine
finished = self.prompt()
File "/usr/lib/python2.7/dist-packages/pyFAI/calibration.py", line 943, in prompt
self.postProcess()
File "/usr/lib/python2.7/dist-packages/pyFAI/calibration.py", line 1163, in postProcess
all=True)
File "/usr/lib/python2.7/dist-packages/pyFAI/azimuthalIntegrator.py", line 3132, in integrate2d
normalization_factor=normalization_factor)
File "/usr/lib/python2.7/dist-packages/pyFAI/azimuthalIntegrator.py", line 3384, in save2D
header_keys=header_keys)
TypeError: init() got an unexpected keyword argument 'header_keys'

kif · 2016-03-25T18:52:01Z

On Fri, 25 Mar 2016 02:28:51 -0700
picca [email protected] wrote:

In fact the error is not the same
header_keys=header_keys)
TypeError: init() got an unexpected keyword argument 'header_keys'

This issue is not the same ...
it is related to a change of signature in fabio (edfimage.save) and has been already fixed in pyFAI.

Two options: downgrade fabio or upgrade pyFAI.
The latest verisons of pyFAI have build-deb8.sh scripts which produces "proper" packages, so I would suggest to upgrade pyFAI.

Sorry it is too much work to maintain branches and backport bug-fixes for relaeases

Cheers,

Jerome

picca · 2016-03-26T09:11:42Z

In Debian I can not downgrad fabio :((.

Is it possible to release a new pyFAI with the fix ?

if not can you point me to the right commit fix in order to patch the current release.

picca · 2016-03-26T09:12:37Z

I fount this 4328534 right ?

actually it runs on my computer.

vallsv · 2018-02-06T12:05:40Z

Can we close this one?

kif · 2018-02-12T07:22:59Z

The initial bug arose from a failing calibration and the wavelength increased ... higher wavelength -> higher 2theta and some rings hit 180° (and disappear). I did smth to limit this but cannot remember if it was completely fixed.

An idea would be to take the largest ring number which has to be <180° and define the upper bound for the wavelength in the refinement.

kif added a commit that referenced this issue Mar 31, 2016

related to #267

bf553cc

actually it runs on my computer.

vallsv added the bug Serious issue, to be addressed in priority ! label Jun 10, 2016

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IndexError: index 3 is out of bounds for size 0 #267

IndexError: index 3 is out of bounds for size 0 #267

picca commented Mar 24, 2016

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picca commented Mar 24, 2016

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picca commented Mar 25, 2016

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picca commented Mar 26, 2016

picca commented Mar 26, 2016

vallsv commented Feb 6, 2018

kif commented Feb 12, 2018

IndexError: index 3 is out of bounds for size 0 #267

IndexError: index 3 is out of bounds for size 0 #267

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picca commented Mar 24, 2016

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picca commented Mar 26, 2016

picca commented Mar 26, 2016

vallsv commented Feb 6, 2018

kif commented Feb 12, 2018