Unrecognized field name "use_symmetrie".

Issue type

Bug

TomoBEAR source

source code (via interactive MATLAB session)

TomoBEAR version

v0.6.0

Computing system

Standalone GPU workstation

Issue description

when I'm dealing with the module "dynamoalignmentproject' the error that 'use_symmetrie' file not exist came out.

Input configuration (JSON) file

{ "general": { "project_name": "Ribosome", "project_description": "Ribosome from plasma-FIB-milled data from EMPIAR-11306", "data_path": "/home/cs/Desktop/JH/TomoBEAR-main/tutorials/empiar11306_ribo_pfib/empiar11306.raw/*.eer", "processing_path": "/home/cs/Desktop/JH/TomoBEAR-main/tutorials/empiar11306_ribo_pfib", "expected_symmetrie": "C1", "apix": 1.85, "gpu": [1,2], "binnings": [4, 8, 16], "rotation_tilt_axis": 80, "template_matching_binning": 8, "reconstruction_thickness": 2000, "as_boxes": false, "mask_bandpass": [0, 4, 4] }, "MetaData": { }, "SortFiles": { }, "MotionCor2": { "gain": "/home/cs/Desktop/JH/TomoBEAR-main/tutorials/empiar11306_ribo_pfib/empiar11306.raw/20220406_175020_EER_GainReference.gain", "eer_sampling": 2, "eer_total_number_of_fractions": 343, "eer_fraction_grouping": 34, "eer_exposure_per_fraction": 0.5, "ft_bin": 2 }, "CreateStacks": { }, "BatchRunTomo": { "ending_step": 6, "skip_steps": [5], "directives": { "comparam.xcorr.tiltxcorr.FilterRadius2": 0.07, "comparam.xcorr.tiltxcorr.FilterSigma1": 0.00, "comparam.xcorr.tiltxcorr.FilterSigma2": 0.02, "comparam.xcorr.tiltxcorr.CumulativeCorrelation": 1, "comparam.xcorr_pt.tiltxcorr.FilterRadius2": 0.07, "comparam.xcorr_pt.tiltxcorr.FilterSigma1": 0.00, "comparam.xcorr_pt.tiltxcorr.FilterSigma2": 0.02, "comparam.xcorr_pt.tiltxcorr.IterateCorrelations": 1, "comparam.xcorr_pt.tiltxcorr.SizeOfPatchesXandY": "250 250", "comparam.xcorr_pt.tiltxcorr.OverlapOfPatchesXandY": "0.33 0.33", "comparam.xcorr_pt.tiltxcorr.BordersInXandY": "51 51", "runtime.Fiducials.any.trackingMethod": 1, "runtime.AlignedStack.any.eraseGold": 0, "comparam.align.tiltalign.RotOption": -1, "comparam.align.tiltalign.MagOption": 0, "comparam.align.tiltalign.TiltOption": 0, "comparam.align.tiltalign.ProjectionStretch": 0 } }, "StopPipeline": { }, "BatchRunTomo": { "starting_step": 8, "ending_step": 8 }, "GCTFCtfphaseflipCTFCorrection": { "ctf_estimation_method":"ctffind", "use_rawtlt": false }, "BatchRunTomo": { "starting_step": 11, "skip_steps": [12], "ending_step": 13 }, "BinStacks": { }, "Reconstruct": { "generate_exact_filtered_tomograms": true, "exact_filter_size": 1000, "use_rawtlt": false, "correct_angles": "none"

},
"EMDTemplateGeneration": {
    "template_emd_number": "15636",
    "mask_emd_filename": "emd_15636_msk_1.map",
    "template_pixel_size_A": 1.85
},
"DynamoTemplateMatching": {
    "size_of_chunk": [512, 512, 375],
    "sampling": 15
},
"TemplateMatchingPostProcessing": {
    "particle_count": 500,
    "cc_std":2.5
},
"GenerateParticles": {
},
"DynamoAlignmentProject":{
}

}

Additional info

I was doing tutorial 3 and this problem came out.

This is error :

Unrecognized field name "use_symmetrie".

GPU model and memory

NVIDA geforce RTX 4090

CUDA version(s)

cuda-11.8

Software setup

MATLAB R2021a

KudryashevLab / TomoBEAR