EuanPyle
commented
12 months ago Hi James, Thanks for the report - I think I know what the bug is: PickTomo will look for rlnTomoReconstructedTomogram in your tomogram.star file, but you don't have that header as you have generated tomograms for denoising, and generated denoised tomograms but not generated tomograms not for denoising which is a slightly convoluted requirement from us!...I will fix this soon so pick tomo reads the denoised tomo or one of the half tomograms, but for now, you just rename the header 'rlnTomoReconstructedTomogramDenoised' in the tomogram.star file to 'rlnTomoReconstructedTomogram' and that should fix it. Let me know how it goes. Thanks Euan
james-vincent
dhaselb
Relion 5 Job type - PickTomo
Key global throws error in pandas. Appears to be coming from:
│ 26 │ star = starfile.read(tilt_series_star_file) │ │ ❱ 27 │ global_table = star['global'].set_index('rlnTomoName') │
╭───────────────────── Traceback (most recent call last) ──────────────────────╮ │ /programs/x86_64-linux/relion/5.0-beta_cu11.6/relion_extlib/miniconda3-4.10. │ │ 3-orl6/envs/relion-5.0/lib/python3.10/site-packages/pandas/core/indexes/base │ │ .py:3790 in get_loc │ │ │ │ 3787 │ │ """ │ │ 3788 │ │ casted_key = self._maybe_cast_indexer(key) │ │ 3789 │ │ try: │ │ ❱ 3790 │ │ │ return self._engine.get_loc(casted_key) │ │ 3791 │ │ except KeyError as err: │ │ 3792 │ │ │ if isinstance(casted_key, slice) or ( │ │ 3793 │ │ │ │ isinstance(casted_key, abc.Iterable) │ │ │ │ ╭───────────────────────────────── locals ─────────────────────────────────╮ │ │ │ casted_key = 'global' │ │ │ │ key = 'global' │ │ │ │ self = Index(['rlnTomoName', 'rlnVoltage', │ │ │ │ 'rlnSphericalAberration', │ │ │ │ │ 'rlnAmplitudeContrast', │ │ │ │ 'rlnMicrographOriginalPixelSize', 'rlnTomoHand', │ │ │ │ │ 'rlnTomoTiltSeriesPixelSize', │ │ │ │ 'rlnTomoTiltSeriesStarFile', │ │ │ │ │ 'rlnTomoTomogramBinning', 'rlnTomoSizeX', │ │ │ │ 'rlnTomoSizeY', │ │ │ │ │ 'rlnTomoSizeZ', 'rlnTomoReconstructedTomogramHalf1', │ │ │ │ │ 'rlnTomoReconstructedTomogramHalf2', │ │ │ │ │ 'rlnTomoReconstructedTomogramDenoised'], │ │ │ │ │ dtype='object') │ │ │ ╰──────────────────────────────────────────────────────────────────────────╯ │ │ │ │ in pandas._libs.index.IndexEngine.get_loc:152 │ │ │ │ in pandas._libs.index.IndexEngine.get_loc:181 │ │ │ │ in pandas._libs.hashtable.PyObjectHashTable.get_item:7080 │ │ │ │ in pandas._libs.hashtable.PyObjectHashTable.get_item:7088 │ ╰──────────────────────────────────────────────────────────────────────────────╯ KeyError: 'global'
The above exception was the direct cause of the following exception:
╭───────────────────── Traceback (most recent call last) ──────────────────────╮ │ in combine_particle_annotations:2 │ │ ╭──────────────────────────────── locals ────────────────────────────────╮ │ │ │ annotations_directory = PosixPath('PickTomo/job034/annotations') │ │ │ │ output_directory = PosixPath('PickTomo/job034') │ │ │ │ pipeline_control = PosixPath('PickTomo/job034') │ │ │ │ tilt_series_star_file = PosixPath('DenoiseTomo/job033/tomograms.star') │ │ │ ╰────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /programs/x86_64-linux/relion/5.0-beta_cu11.6/relion_extlib/miniconda3-4.10. │ │ 3-orl6/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_progra │ │ ms/_utils/relion.py:75 in pipeline_job │ │ │ │ 72 │ │ │ job_directory.mkdir(parents=True, exist_ok=True) │ │ 73 │ │ try: │ │ 74 │ │ │ pipeline_directory = kwargs.pop(PIPELINE_CONTROL_KEYWORD_AR │ │ ❱ 75 │ │ │ func(*args, *kwargs) │ │ 76 │ │ │ if job_directory is not None and pipeline_directory is not │ │ 77 │ │ │ │ write_job_success_file(job_directory) │ │ 78 │ │ except BaseException: │ │ │ │ ╭───────────────────────────────── locals ─────────────────────────────────╮ │ │ │ args = () │ │ │ │ func = <function combine_particle_annotations at │ │ │ │ 0x7f85db938430> │ │ │ │ job_directory = PosixPath('PickTomo/job034') │ │ │ │ kwargs = { │ │ │ │ │ 'tilt_series_star_file': │ │ │ │ PosixPath('DenoiseTomo/job033/tomograms.star'), │ │ │ │ │ 'annotations_directory': │ │ │ │ PosixPath('PickTomo/job034/annotations'), │ │ │ │ │ 'output_directory': │ │ │ │ PosixPath('PickTomo/job034') │ │ │ │ } │ │ │ │ pipeline_directory = PosixPath('PickTomo/job034') │ │ │ ╰──────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /programs/x86_64-linux/relion/5.0-beta_cu11.6/relion_extlib/miniconda3-4.10. │ │ 3-orl6/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_progra │ │ ms/get_particle_poses/particles.py:27 in combine_particle_annotations │ │ │ │ 24 │ ) │ │ 25 ): │ │ 26 │ star = starfile.read(tilt_series_star_file) │ │ ❱ 27 │ global_table = star['global'].set_index('rlnTomoName') │ │ 28 │ annotation_files = annotations_directory.glob('_particles.star') │ │ 29 │ dfs = [] │ │ 30 │ for file in annotation_files: │ │ │ │ ╭───────────────────────────────── locals ─────────────────────────────────╮ │ │ │ annotations_directory = PosixPath('PickTomo/job034/annotations') │ │ │ │ output_directory = PosixPath('PickTomo/job034') │ │ │ │ star = │ rlnTomoName ... │ │ │ │ rlnTomoReconstructedTomogramDenoised │ │ │ │ 0 9x9_ts_65_sort ... │ │ │ │ DenoiseTomo/job033/tomograms/rec_9x9_ts_65_sor.… │ │ │ │ │ │ │ │ [1 rows x 15 columns] │ │ │ │ tilt_series_star_file = PosixPath('DenoiseTomo/job033/tomograms.star') │ │ │ ╰──────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /programs/x86_64-linux/relion/5.0-beta_cu11.6/relion_extlib/miniconda3-4.10. │ │ 3-orl6/envs/relion-5.0/lib/python3.10/site-packages/pandas/core/frame.py:389 │ │ 3 in getitem │ │ │ │ 3890 │ │ if is_single_key: │ │ 3891 │ │ │ if self.columns.nlevels > 1: │ │ 3892 │ │ │ │ return self._getitem_multilevel(key) │ │ ❱ 3893 │ │ │ indexer = self.columns.get_loc(key) │ │ 3894 │ │ │ if is_integer(indexer): │ │ 3895 │ │ │ │ indexer = [indexer] │ │ 3896 │ │ else: │ │ │ │ ╭───────────────────────────────── locals ─────────────────────────────────╮ │ │ │ is_mi = False │ │ │ │ is_single_key = True │ │ │ │ key = 'global' │ │ │ │ self = │ rlnTomoName ... │ │ │ │ rlnTomoReconstructedTomogramDenoised │ │ │ │ 0 9x9_ts_65_sort ... │ │ │ │ DenoiseTomo/job033/tomograms/rec_9x9_ts_65_sor... │ │ │ │ │ │ │ │ [1 rows x 15 columns] │ │ │ ╰──────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /programs/x86_64-linux/relion/5.0-beta_cu11.6/relion_extlib/miniconda3-4.10. │ │ 3-orl6/envs/relion-5.0/lib/python3.10/site-packages/pandas/core/indexes/base │ │ .py:3797 in get_loc │ │ │ │ 3794 │ │ │ │ and any(isinstance(x, slice) for x in casted_key) │ │ 3795 │ │ │ ): │ │ 3796 │ │ │ │ raise InvalidIndexError(key) │ │ ❱ 3797 │ │ │ raise KeyError(key) from err │ │ 3798 │ │ except TypeError: │ │ 3799 │ │ │ # If we have a listlike key, _check_indexing_error will r │ │ 3800 │ │ │ # InvalidIndexError. Otherwise we fall through and re-ra │ │ │ │ ╭───────────────────────────────── locals ─────────────────────────────────╮ │ │ │ casted_key = 'global' │ │ │ │ key = 'global' │ │ │ │ self = Index(['rlnTomoName', 'rlnVoltage', │ │ │ │ 'rlnSphericalAberration', │ │ │ │ │ 'rlnAmplitudeContrast', │ │ │ │ 'rlnMicrographOriginalPixelSize', 'rlnTomoHand', │ │ │ │ │ 'rlnTomoTiltSeriesPixelSize', │ │ │ │ 'rlnTomoTiltSeriesStarFile', │ │ │ │ │ 'rlnTomoTomogramBinning', 'rlnTomoSizeX', │ │ │ │ 'rlnTomoSizeY', │ │ │ │ │ 'rlnTomoSizeZ', 'rlnTomoReconstructedTomogramHalf1', │ │ │ │ │ 'rlnTomoReconstructedTomogramHalf2', │ │ │ │ │ 'rlnTomoReconstructedTomogramDenoised'], │ │ │ │ │ dtype='object') │ │ │ ╰──────────────────────────────────────────────────────────────────────────╯ │ ╰──────────────────────────────────────────────────────────────────────────────╯ KeyError: 'global'