Rebinning in 2_x-ray-analysis: Method '__array__' is not supported.

[sayantanghosh]

Hello, I am having trouble running the 2_x-ray-analysis notebook: link on the line
chandra.rebin_on_background(1)

where I get the following error:

~/anaconda3/envs/astro/bin/python3 /Users/ghosh/work/cds_tutorial/x-ray-analyse-threeml.py 
~/anaconda3/envs/astro/lib/python3.9/site-packages/numba/core/decorators.py:262: NumbaDeprecationWarning: numba.generated_jit is deprecated. Please see the documentation at: https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-generated-jit for more information and advice on a suitable replacement.
  warnings.warn(msg, NumbaDeprecationWarning)
~/anaconda3/envs/astro/lib/python3.9/site-packages/numba/core/decorators.py:262: NumbaDeprecationWarning: numba.generated_jit is deprecated. Please see the documentation at: https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-generated-jit for more information and advice on a suitable replacement.
  warnings.warn(msg, NumbaDeprecationWarning)
19:42:53 INFO      Starting 3ML!                                  __init__.py:35
         WARNING   WARNINGs here are NOT errors                   __init__.py:36
         WARNING   but are inform you about optional packages     __init__.py:37
                  that can be installed                                         
         WARNING    to disable these messages, turn off           __init__.py:40
                  start_warning in your config file                             
         WARNING   ROOT minimizer not available             minimization.py:1345
         WARNING   Multinest minimizer not available        minimization.py:1357
19:42:54 WARNING   PyGMO is not available                   minimization.py:1369
19:42:54 WARNING   The cthreeML package is not installed. You     __init__.py:94
                  will not be able to use plugins which require                 
                  the C/C++ interface (currently HAWC)                          
         WARNING   Could not import plugin HAWCLike.py. Do you   __init__.py:144
                  have the relative instrument software                         
                  installed and configured?                                     
         WARNING   Could not import plugin FermiLATLike.py. Do   __init__.py:144
                  you have the relative instrument software                     
                  installed and configured?                                     
19:42:55 WARNING   No fermitools installed           lat_transient_builder.py:44
19:42:55 WARNING   Env. variable OMP_NUM_THREADS is not set.     __init__.py:387
                  Please set it to 1 for optimal performances in                
                  3ML                                                           
         WARNING   Env. variable MKL_NUM_THREADS is not set.     __init__.py:387
                  Please set it to 1 for optimal performances in                
                  3ML                                                           
         WARNING   Env. variable NUMEXPR_NUM_THREADS is not set. __init__.py:387
                  Please set it to 1 for optimal performances in                
                  3ML                                                           
         INFO      Auto-probed noise models:                 SpectrumLike.py:469
         INFO      - observation: poisson                    SpectrumLike.py:470
         INFO      - background: poisson                     SpectrumLike.py:471
Chandra significance: 83.866613
Chandra Significance by channel:
 [-0.78657315  0.53715615 -0.         ... -0.         -0.
 -0.        ]
Chandra Exposure: 1.000000
19:42:56 INFO      Range 0.2-10 translates to channels      SpectrumLike.py:1210
                  13-684                                                        

WARNING UserWarning: Attempt to set non-positive ylim on a log-scaled axis will be ignored.

Traceback (most recent call last):
  File "~/work/cds_tutorial/x-ray-analyse-threeml.py", line 45, in <module>
    main()
  File "~/work/cds_tutorial/x-ray-analyse-threeml.py", line 42, in main
    chandra.rebin_on_background(1)
  File "~/anaconda3/envs/astro/lib/python3.9/site-packages/threeML/plugins/SpectrumLike.py", line 1608, in rebin_on_background
    self._apply_rebinner(rebinner)
  File "~/anaconda3/envs/astro/lib/python3.9/site-packages/threeML/plugins/SpectrumLike.py", line 1650, in _apply_rebinner
    (self._current_observed_counts,) = self._rebinner.rebin(self._observed_counts)
  File "~/anaconda3/envs/astro/lib/python3.9/site-packages/threeML/utils/binner.py", line 186, in rebin
    _rebin_vector_int(
  File "~/anaconda3/envs/astro/lib/python3.9/site-packages/numba/core/dispatcher.py", line 468, in _compile_for_args
    error_rewrite(e, 'typing')
  File "~/anaconda3/envs/astro/lib/python3.9/site-packages/numba/core/dispatcher.py", line 409, in error_rewrite
    raise e.with_traceback(None)
numba.core.errors.TypingError: Failed in nopython mode pipeline (step: nopython frontend)
- Resolution failure for literal arguments:
Failed in nopython mode pipeline (step: native lowering)
Method '__array__' is not supported.
- Resolution failure for non-literal arguments:
None

During: resolving callee type: BoundFunction((<class 'numba.core.types.misc.ClassInstanceType'>, 'append') for instance.jitclass._Vector#12bc136d0<n:uint64,m:uint64,full_arr:array(int64, 1d, A)>)
During: typing of call at /Users/ghosh/anaconda3/envs/astro/lib/python3.9/site-packages/threeML/utils/binner.py (679)


File "../../anaconda3/envs/astro/lib/python3.9/site-packages/threeML/utils/binner.py", line 679:
def _rebin_vector_int(vector, start, stop, mask, N):
    <source elided>

        rebinned_vector.append(np.sum(vector[start[n] : stop[n]]))
        ^


Process finished with exit code 1

To reproduce:

import threeML as tml
import os

tml.update_logging_level("INFO")
tml.silence_warnings()

import numpy as np
import matplotlib.pyplot as plt
import astropy.units as u

def main():
    chandra = tml.OGIPLike(name="chandra",
                           observation="c_data/obs.pha",

                           background="c_data/obs_bak.pha",
                           response="c_data/acis.rmf",
                           arf_file="c_data/acis.arf",
                           spectrum_number=1)

    # Check chandra significance
    print('Chandra significance: {0:f}'.format(chandra.significance))

    # Get chandra significance by channel
    print('Chandra Significance by channel:\n', chandra.significance_per_channel)

    # Display rsp
    chandra.display_rsp()

    # Get chandra exposure
    print('Chandra Exposure: {0:f}'.format(chandra.exposure))

    # Display count spectrum
    chandra.view_count_spectrum(scale_background=True)

    # Set the active energy range
    chandra.set_active_measurements('0.2-10')

    # Plot the count spectrum after setting the energy range
    chandra.view_count_spectrum()

    # Rebin
    chandra.rebin_on_background(1)

if __name__ == '__main__':
    main()
    plt.show()

SYSTEM INFORMATION
OS: macOS 13.4.1 (22F82)
conda version: conda 23.5.0
3ML version: threeml 2.4.0 pyhd8ed1ab_0 conda-forge