search

SBC-Utrecht / pytom-match-pick

GPU-accelerated template matching for cryo-ET
https://sbc-utrecht.github.io/pytom-match-pick/
GNU General Public License v2.0
28 stars 9 forks source link

TypeError in match_template #191

Closed Phaips closed 4 months ago

Phaips commented 4 months ago

Hi, I am trying out the new version release with the phase randomization. I am running this command:

pytom_match_template.py -t tmpl.mrc --mask mask.mrc -v tomos/bin4_novactf/115.rec -d /scicore/home/engel0006/GROUP/pool-engel/Philippe/rbcPipeline/pytom/current/PyTOM/115/ -a temp/115.tlt --particle-diameter 70.0 -g 0 1 2 3 --voxel-size-angstrom 7.84 --non-spherical-mask --tomogram-ctf-model phase-flip --random-phase-correction --rng-seed 42 --per-tilt-weighting --amplitude-contrast 0.07 --dose-accumulation temp/115_exposure.txt --defocus temp/115_defocus.txt --voltage 300.0 --spherical-aberration 2.7

and it seems something is wrong with the --random-phase-correction --rng-seed 42 because it runs fine when I leave out the two flags. Maybe I am parsing this wrong since the type error is between a str and a float (42.0 doesn't fix it). Thanks for the help!

the error: Traceback (most recent call last): File "/scicore/projects/scicore-p-structsoft/ubuntu/software/Miniconda3/miniconda3_python3.12.1/envs/pytom-tm-ub/bin/pytom_match_template.py", line 8, in sys.exit(match_template()) ^^^^^^^^^^^^^^^^ File "/scicore/projects/scicore-p-structsoft/ubuntu/software/Miniconda3/miniconda3_python3.12.1/envs/pytom-tm-ub/lib/python3.12/site-packages/pytom_tm/entry_points.py", line 813, in match_template args = parser.parse_args(argv) ^^^^^^^^^^^^^^^^^^^^^^^ File "/scicore/projects/scicore-p-structsoft/ubuntu/software/Miniconda3/miniconda3_python3.12.1/envs/pytom-tm-ub/lib/python3.12/argparse.py", line 1891, in parse_args args, argv = self.parse_known_args(args, namespace) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/scicore/projects/scicore-p-structsoft/ubuntu/software/Miniconda3/miniconda3_python3.12.1/envs/pytom-tm-ub/lib/python3.12/argparse.py", line 1924, in parse_known_args namespace, args = self._parse_known_args(args, namespace) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/scicore/projects/scicore-p-structsoft/ubuntu/software/Miniconda3/miniconda3_python3.12.1/envs/pytom-tm-ub/lib/python3.12/argparse.py", line 2136, in _parse_known_args start_index = consume_optional(start_index) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/scicore/projects/scicore-p-structsoft/ubuntu/software/Miniconda3/miniconda3_python3.12.1/envs/pytom-tm-ub/lib/python3.12/argparse.py", line 2076, in consume_optional take_action(action, args, option_string) File "/scicore/projects/scicore-p-structsoft/ubuntu/software/Miniconda3/miniconda3_python3.12.1/envs/pytom-tm-ub/lib/python3.12/argparse.py", line 2000, in take_action action(self, namespace, argument_values, option_string) File "/scicore/projects/scicore-p-structsoft/ubuntu/software/Miniconda3/miniconda3_python3.12.1/envs/pytom-tm-ub/lib/python3.12/site-packages/pytom_tm/io.py", line 75, in call if values <= 0.0: ^^^^^^^^^^^^^ TypeError: '<=' not supported between instances of 'str' and 'float'

McHaillet commented 4 months ago

Hi @Phaips, glad to see you are trying the new version and thanks for the bug report!

I notice that I did not specify the type of the argument, i.e. that it should be interpreted as an integer. It should be a very easy bug fix, but we should add a unit test for it to prevent something like this in the future.

Without explicitly setting a seed, a random seed will be generated based on system time and this one is correctly set as integer. So without supplying a seed, I suspect it works fine. The seed is always annotated in the job file, so once this is fixed you should be able to reproduce your results.

Cheers!

McHaillet commented 4 months ago

It has been fixed with version 0.7.1 👍