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thomasorb / orbs

ORBS is the data reduction pipeline for SITELLE
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Failure in running 'orbs sitelle laser.job start --laser' #10

Open darioflute opened 2 years ago

darioflute commented 2 years ago

Hi, I was interested in reducing some SITELLE data. So I installed successfully all the packages you created (ORB, ORBS, and ORC) and I tried to compute a comparison. After figuring out that the 'orbs' script is in the orbs/scripts directory, I created a laser.job input file and tried to run the command: orbs sitelle laser.job start --laser

It seemed to run well at the beginning, but then it stopped with a series of errors. This is the log: laser2.job.log

And this is the output with errors: unknown|INFO| Init of the parallel processing server with 8 threads unknown|INFO| loading quad 1/9 unknown|INFO| processing quad 1/9 [ ] [0%] [quad 1/9, column : 0] [remains: unknown]<function _find_max_in_column at 0x7fde24b3e050>: Traceback (most recent call last): File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/utils/parallel.py", line 35, in run_dill_encoded return fun(*args) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orbs-master.12f7-py3.7.egg/orbs/process.py", line 674, in _find_max_in_column poly_order=0, signal_range=signal_range_cm1) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fft.py", line 975, in fit lines, fmodel=fmodel, nofilter=nofilter, kwargs) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fft.py", line 824, in prepare_fit kwargs) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fit.py", line 2662, in _prepare_input_params kwargs = ip.add_lines_model(lines, *kwargs) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fit.py", line 2179, in add_lines_model sigma_cov_vel = self._get_sigma_cov_vel(fwhm_guess_cm1, lines_cm1) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fit.py", line 2153, in _get_sigma_cov_vel fwhm_guess_cm1.mean) / self.axis_step, File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/utils/fft.py", line 262, in apod2sigma return broadening fwhm TypeError: unsupported operand type(s) for *: 'float' and 'builtin_function_or_method'

Traceback (most recent call last): File "/home/dario/Python/orb-stable/orbs/scripts/orbs", line 249, in start flux_calibration=not args.noflux) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orbs-master.12f7-py3.7.egg/orbs/orbs.py", line 933, in start_reduction f(*args, *kwargs_dict) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orbs-master.12f7-py3.7.egg/orbs/orbs.py", line 1356, in compute_calibration_laser_map get_calibration_laser_spectrum=get_calibration_laser_spectrum) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orbs-master.12f7-py3.7.egg/orbs/process.py", line 754, in create_calibration_laser_map fitparams[x_min + ii + ijob, y_min:y_max,:]) = job() TypeError: cannot unpack non-iterable NoneType object <function _find_max_in_column at 0x7fde24b3bf80>: Traceback (most recent call last): File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/utils/parallel.py", line 35, in run_dill_encoded return fun(args) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orbs-master.12f7-py3.7.egg/orbs/process.py", line 674, in _find_max_in_column poly_order=0, signal_range=signal_range_cm1) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fft.py", line 975, in fit lines, fmodel=fmodel, nofilter=nofilter, kwargs) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fft.py", line 824, in prepare_fit kwargs) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fit.py", line 2662, in _prepare_input_params kwargs = ip.add_lines_model(lines, *kwargs) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fit.py", line 2179, in add_lines_model sigma_cov_vel = self._get_sigma_cov_vel(fwhm_guess_cm1, lines_cm1) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fit.py", line 2153, in _get_sigma_cov_vel fwhm_guess_cm1.mean) / self.axis_step, File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/utils/fft.py", line 262, in apod2sigma return broadening fwhm TypeError: unsupported operand type(s) for *: 'float' and 'builtin_function_or_method'

<function _find_max_in_column at 0x7fde24b3bf80>: Traceback (most recent call last): File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/utils/parallel.py", line 35, in run_dill_encoded return fun(*args) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orbs-master.12f7-py3.7.egg/orbs/process.py", line 674, in _find_max_in_column poly_order=0, signal_range=signal_range_cm1) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fft.py", line 975, in fit lines, fmodel=fmodel, nofilter=nofilter, kwargs) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fft.py", line 824, in prepare_fit kwargs) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fit.py", line 2662, in _prepare_input_params kwargs = ip.add_lines_model(lines, *kwargs) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fit.py", line 2179, in add_lines_model sigma_cov_vel = self._get_sigma_cov_vel(fwhm_guess_cm1, lines_cm1) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fit.py", line 2153, in _get_sigma_cov_vel fwhm_guess_cm1.mean) / self.axis_step, File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/utils/fft.py", line 262, in apod2sigma return broadening fwhm TypeError: unsupported operand type(s) for *: 'float' and 'builtin_function_or_method'

<function _find_max_in_column at 0x7fde24b3bf80>: Traceback (most recent call last): File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/utils/parallel.py", line 35, in run_dill_encoded return fun(*args) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orbs-master.12f7-py3.7.egg/orbs/process.py", line 674, in _find_max_in_column poly_order=0, signal_range=signal_range_cm1) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fft.py", line 975, in fit lines, fmodel=fmodel, nofilter=nofilter, kwargs) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fft.py", line 824, in prepare_fit kwargs) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fit.py", line 2662, in _prepare_input_params kwargs = ip.add_lines_model(lines, *kwargs) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fit.py", line 2179, in add_lines_model sigma_cov_vel = self._get_sigma_cov_vel(fwhm_guess_cm1, lines_cm1) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fit.py", line 2153, in _get_sigma_cov_vel fwhm_guess_cm1.mean) / self.axis_step, File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/utils/fft.py", line 262, in apod2sigma return broadening fwhm TypeError: unsupported operand type(s) for *: 'float' and 'builtin_function_or_method'

<function _find_max_in_column at 0x7fde24b3bf80>: Traceback (most recent call last): File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/utils/parallel.py", line 35, in run_dill_encoded return fun(*args) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orbs-master.12f7-py3.7.egg/orbs/process.py", line 674, in _find_max_in_column poly_order=0, signal_range=signal_range_cm1) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fft.py", line 975, in fit lines, fmodel=fmodel, nofilter=nofilter, kwargs) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fft.py", line 824, in prepare_fit kwargs) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fit.py", line 2662, in _prepare_input_params kwargs = ip.add_lines_model(lines, *kwargs) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fit.py", line 2179, in add_lines_model sigma_cov_vel = self._get_sigma_cov_vel(fwhm_guess_cm1, lines_cm1) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fit.py", line 2153, in _get_sigma_cov_vel fwhm_guess_cm1.mean) / self.axis_step, File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/utils/fft.py", line 262, in apod2sigma return broadening fwhm TypeError: unsupported operand type(s) for *: 'float' and 'builtin_function_or_method'

<function _find_max_in_column at 0x7fde24b3e050>: Traceback (most recent call last): File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/utils/parallel.py", line 35, in run_dill_encoded return fun(*args) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orbs-master.12f7-py3.7.egg/orbs/process.py", line 674, in _find_max_in_column poly_order=0, signal_range=signal_range_cm1) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fft.py", line 975, in fit lines, fmodel=fmodel, nofilter=nofilter, kwargs) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fft.py", line 824, in prepare_fit kwargs) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fit.py", line 2662, in _prepare_input_params kwargs = ip.add_lines_model(lines, *kwargs) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fit.py", line 2179, in add_lines_model sigma_cov_vel = self._get_sigma_cov_vel(fwhm_guess_cm1, lines_cm1) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fit.py", line 2153, in _get_sigma_cov_vel fwhm_guess_cm1.mean) / self.axis_step, File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/utils/fft.py", line 262, in apod2sigma return broadening fwhm TypeError: unsupported operand type(s) for *: 'float' and 'builtin_function_or_method'

<function _find_max_in_column at 0x7fde24b3bf80>: Traceback (most recent call last): File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/utils/parallel.py", line 35, in run_dill_encoded return fun(*args) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orbs-master.12f7-py3.7.egg/orbs/process.py", line 674, in _find_max_in_column poly_order=0, signal_range=signal_range_cm1) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fft.py", line 975, in fit lines, fmodel=fmodel, nofilter=nofilter, kwargs) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fft.py", line 824, in prepare_fit kwargs) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fit.py", line 2662, in _prepare_input_params kwargs = ip.add_lines_model(lines, *kwargs) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fit.py", line 2179, in add_lines_model sigma_cov_vel = self._get_sigma_cov_vel(fwhm_guess_cm1, lines_cm1) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fit.py", line 2153, in _get_sigma_cov_vel fwhm_guess_cm1.mean) / self.axis_step, File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/utils/fft.py", line 262, in apod2sigma return broadening fwhm TypeError: unsupported operand type(s) for *: 'float' and 'builtin_function_or_method'

<function _find_max_in_column at 0x7fde24b3bf80>: Traceback (most recent call last): File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/utils/parallel.py", line 35, in run_dill_encoded return fun(*args) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orbs-master.12f7-py3.7.egg/orbs/process.py", line 674, in _find_max_in_column poly_order=0, signal_range=signal_range_cm1) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fft.py", line 975, in fit lines, fmodel=fmodel, nofilter=nofilter, kwargs) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fft.py", line 824, in prepare_fit kwargs) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fit.py", line 2662, in _prepare_input_params kwargs = ip.add_lines_model(lines, *kwargs) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fit.py", line 2179, in add_lines_model sigma_cov_vel = self._get_sigma_cov_vel(fwhm_guess_cm1, lines_cm1) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fit.py", line 2153, in _get_sigma_cov_vel fwhm_guess_cm1.mean) / self.axis_step, File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/utils/fft.py", line 262, in apod2sigma return broadening fwhm TypeError: unsupported operand type(s) for *: 'float' and 'builtin_function_or_method'

Please, let me know if you have a clue of what I am doing wrong. Thanks, Dario

darioflute commented 2 years ago

It seems that the problem was in: anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fit.py line 2153. I changed to fwhm_guess_cm1.mean to fwhm_guess_cm1.mean() to obtain a number. So, the problem in the apod2sigma of multiplying a 'float' and a 'builtin_function_or_method'.

Nevertheless, I have now a lot of WARNING, which I doubt are normal. Any advice is welcome:

WARNING:root:Exception occured during fit: ratio must be strictly between 0 and 1 Traceback (most recent call last): File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fft.py", line 885, in prepared_fit **kwargs) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fit.py", line 2596, in _fit_lines_in_spectrum vector_err=vector_err) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fit.py", line 162, in init self.models.append(models[i]0) File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fit.py", line 733, in init self.check_input() File "/home/dario/anaconda3/envs/orb3/lib/python3.7/site-packages/orb_kernel-3.0-py3.7-linux-x86_64.egg/orb/fit.py", line 1486, in check_input raise ValueError('ratio must be strictly between 0 and 1') ValueError: ratio must be strictly between 0 and 1