xmipp3 package

Subpackages

• xmipp3.convert package
  • Submodules
    • xmipp3.convert.convert module
    • xmipp3.convert.dataimport module
    • xmipp3.convert.io_coordinates module
  • Module contents
• xmipp3.protocols package
  • Subpackages
    • xmipp3.protocols.protocol_preprocess package
      • Submodules
      • Module contents
    • xmipp3.protocols.protocol_projmatch package
      • Submodules
      • Module contents
  • Submodules
    • xmipp3.protocols.protocol_align_volume module
    • xmipp3.protocols.protocol_align_volume_and_particles module
    • xmipp3.protocols.protocol_analyze_local_ctf module
    • xmipp3.protocols.protocol_angular_graph_consistency module
    • xmipp3.protocols.protocol_apply_alignment module
    • xmipp3.protocols.protocol_apply_tilt_to_ctf module
    • xmipp3.protocols.protocol_apply_transformation_matrix module
    • xmipp3.protocols.protocol_apply_zernike3d module
    • xmipp3.protocols.protocol_assignment_tilt_pair module
    • xmipp3.protocols.protocol_break_symmetry module
    • xmipp3.protocols.protocol_center_particles module
    • xmipp3.protocols.protocol_cl2d module
    • xmipp3.protocols.protocol_cl2d_align module
    • xmipp3.protocols.protocol_cl2d_clustering module
    • xmipp3.protocols.protocol_classes_2d_mapping module
    • xmipp3.protocols.protocol_classify_pca module
    • xmipp3.protocols.protocol_classify_pca_streaming module
    • xmipp3.protocols.protocol_compare_angles module
    • xmipp3.protocols.protocol_compare_reprojections module
    • xmipp3.protocols.protocol_consensus_classes module
    • xmipp3.protocols.protocol_consensus_local_ctf module
    • xmipp3.protocols.protocol_convert_pdb module
    • xmipp3.protocols.protocol_core_analysis module
    • xmipp3.protocols.protocol_create_gallery module
    • xmipp3.protocols.protocol_ctf_consensus module
    • xmipp3.protocols.protocol_ctf_correct_wiener2d module
    • xmipp3.protocols.protocol_ctf_defocus_group module
    • xmipp3.protocols.protocol_ctf_micrographs module
    • xmipp3.protocols.protocol_deep_center module
    • xmipp3.protocols.protocol_deep_center_predict module
    • xmipp3.protocols.protocol_deep_hand module
    • xmipp3.protocols.protocol_deep_micrograph_screen module
    • xmipp3.protocols.protocol_denoise_particles module
    • xmipp3.protocols.protocol_eliminate_empty_images module
    • xmipp3.protocols.protocol_enrich module
    • xmipp3.protocols.protocol_extract_asymmetric_unit module
    • xmipp3.protocols.protocol_extract_particles module
    • xmipp3.protocols.protocol_extract_particles_movies module
    • xmipp3.protocols.protocol_extract_particles_pairs module
    • xmipp3.protocols.protocol_flexalign module
    • xmipp3.protocols.protocol_generate_reprojections module
    • xmipp3.protocols.protocol_helical_parameters module
    • xmipp3.protocols.protocol_kerdensom module
    • xmipp3.protocols.protocol_local_ctf module
    • xmipp3.protocols.protocol_mics_defocus_balancer module
    • xmipp3.protocols.protocol_ml2d module
    • xmipp3.protocols.protocol_movie_alignment_consensus module
    • xmipp3.protocols.protocol_movie_dose_analysis module
    • xmipp3.protocols.protocol_movie_gain module
    • xmipp3.protocols.protocol_movie_max_shift module
    • xmipp3.protocols.protocol_movie_split_frames module
    • xmipp3.protocols.protocol_multiple_fscs module
    • xmipp3.protocols.protocol_multireference_alignability module
    • xmipp3.protocols.protocol_normalize_strain module
    • xmipp3.protocols.protocol_particle_pick module
    • xmipp3.protocols.protocol_particle_pick_automatic module
    • xmipp3.protocols.protocol_particle_pick_consensus module
    • xmipp3.protocols.protocol_particle_pick_pairs module
    • xmipp3.protocols.protocol_particle_pick_remove_duplicates module
    • xmipp3.protocols.protocol_phantom_create module
    • xmipp3.protocols.protocol_pick_noise module
    • xmipp3.protocols.protocol_postProcessing_deepPostProcessing module
    • xmipp3.protocols.protocol_preprocess_micrographs module
    • xmipp3.protocols.protocol_random_conical_tilt module
    • xmipp3.protocols.protocol_ransac module
    • xmipp3.protocols.protocol_reconstruct_fourier module
    • xmipp3.protocols.protocol_reconstruct_highres module
    • xmipp3.protocols.protocol_reconstruct_significant module
    • xmipp3.protocols.protocol_reconstruct_swarm module
    • xmipp3.protocols.protocol_resolution3d module
    • xmipp3.protocols.protocol_resolution_bfactor module
    • xmipp3.protocols.protocol_resolution_deepres module
    • xmipp3.protocols.protocol_resolution_directional module
    • xmipp3.protocols.protocol_resolution_fso module
    • xmipp3.protocols.protocol_resolution_monogenic_signal module
    • xmipp3.protocols.protocol_rotate_volume module
    • xmipp3.protocols.protocol_rotational_symmetry module
    • xmipp3.protocols.protocol_screen_deepConsensus module
    • xmipp3.protocols.protocol_screen_deeplearning module
    • xmipp3.protocols.protocol_screen_particles module
    • xmipp3.protocols.protocol_shift_particles module
    • xmipp3.protocols.protocol_shift_volume module
    • xmipp3.protocols.protocol_simulate_ctf module
    • xmipp3.protocols.protocol_structure_map module
    • xmipp3.protocols.protocol_structure_map_zernike3d module
    • xmipp3.protocols.protocol_subtract_projection module
    • xmipp3.protocols.protocol_tilt_analysis module
    • xmipp3.protocols.protocol_trigger_data module
    • xmipp3.protocols.protocol_validate_fscq module
    • xmipp3.protocols.protocol_validate_nontilt module
    • xmipp3.protocols.protocol_validate_overfitting module
    • xmipp3.protocols.protocol_volume_adjust_sub module
    • xmipp3.protocols.protocol_volume_consensus module
    • xmipp3.protocols.protocol_volume_deform_zernike3d module
    • xmipp3.protocols.protocol_volume_local_adjust module
    • xmipp3.protocols.protocol_volume_local_sharpening module
    • xmipp3.protocols.protocol_volume_strain module
    • xmipp3.protocols.protocol_write_testC module
    • xmipp3.protocols.protocol_write_testP module
  • Module contents
• xmipp3.viewers package
  • Submodules
    • xmipp3.viewers.plotter module
    • xmipp3.viewers.viewer module
    • xmipp3.viewers.viewer_analyze_local_ctf module
    • xmipp3.viewers.viewer_apply_tilt_to_ctf module
    • xmipp3.viewers.viewer_cl2d module
    • xmipp3.viewers.viewer_cl2d_clustering module
    • xmipp3.viewers.viewer_consensus_classes module
    • xmipp3.viewers.viewer_ctf_consensus module
    • xmipp3.viewers.viewer_deepEMHancer module
    • xmipp3.viewers.viewer_deep_consensus module
    • xmipp3.viewers.viewer_deep_micrograph_cleaner module
    • xmipp3.viewers.viewer_dose_analysis module
    • xmipp3.viewers.viewer_eliminate_empty_images module
    • xmipp3.viewers.viewer_extract_asymmetric_unit module
    • xmipp3.viewers.viewer_local_sharpening module
    • xmipp3.viewers.viewer_ml2d module
    • xmipp3.viewers.viewer_movie_alignment module
    • xmipp3.viewers.viewer_normalize_strain module
    • xmipp3.viewers.viewer_pdb_deform_zernike3d module
    • xmipp3.viewers.viewer_projmatch module
    • xmipp3.viewers.viewer_ransac module
    • xmipp3.viewers.viewer_reconstruct_highres module
    • xmipp3.viewers.viewer_resolution3d module
    • xmipp3.viewers.viewer_resolution_bfactor module
    • xmipp3.viewers.viewer_resolution_deepres module
    • xmipp3.viewers.viewer_resolution_directional module
    • xmipp3.viewers.viewer_resolution_fso module
    • xmipp3.viewers.viewer_resolution_monogenic_signal module
    • xmipp3.viewers.viewer_structure_map module
    • xmipp3.viewers.viewer_subtract_projection module
    • xmipp3.viewers.viewer_swarm module
    • xmipp3.viewers.viewer_validate_fscq module
    • xmipp3.viewers.viewer_validate_nontilt module
    • xmipp3.viewers.viewer_validate_overfitting module
    • xmipp3.viewers.viewer_volume_consensus module
    • xmipp3.viewers.viewer_volume_deform_zernike3d module
    • xmipp3.viewers.viewer_volume_strain module
    • xmipp3.viewers.viewer_volume_subtraction module
  • Module contents

Submodules

• xmipp3.base module
• xmipp3.bibtex module
• xmipp3.checkProtocolsConf module
• xmipp3.constants module
• xmipp3.programs module
• xmipp3.utils module
• xmipp3.version module
• xmipp3.wizards module

Module contents

class xmipp3.Plugin

Bases: Plugin

ctypes = <module 'ctypes' from '/home/buildbot/miniconda3/envs/develEnv/lib/python3.8/ctypes/__init__.py'>

classmethod defineBinaries(env)

Define the Xmipp binaries/source available tgz. In addition, define extra software needed by some Xmipp methods such as deepLearningToolkit. Scipion-defined software can be used as dependencies by using its name as string.

frameInfo = FrameInfo(frame=<frame at 0x2590160, file '/home/buildbot/miniconda3/envs/develEnv/lib/python3.8/runpy.py', line 194, code _run_module_as_main>, filename='/home/buildbot/miniconda3/envs/develEnv/lib/python3.8/runpy.py', lineno=194, function='_run_module_as_main', code_context=['    return _run_code(code, main_globals, None,\n'], index=0)

classmethod getEnviron(xmippFirst=True)

Create the needed environment for Xmipp programs.

classmethod getMatlabEnviron(*toolPaths)

Return an Environment prepared for launching Matlab scripts using the Xmipp binding.

inspect = <module 'inspect' from '/home/buildbot/miniconda3/envs/develEnv/lib/python3.8/inspect.py'>

classmethod runXmippProgram(program, args='')

Internal shortcut function to launch a Xmipp program.

xmipp3.installDeepLearningToolkit(plugin, env)