API
- em_workflows
- Config module
setup_pytools_log()
SLURM_exec()
Config
Config.imod_root
Config.bioformats2raw
Config.brt_binary
Config.header_loc
Config.mrc2tif_loc
Config.newstack_loc
Config.HIGH_SLURM_EXECUTOR
Config.SLURM_EXECUTOR
Config.user
Config.tmp_dir
Config.local_storage
Config.pickle_serializer
Config.proj_dir()
Config.assets_dir()
Config.repo_dir
Config.template_dir
- File_path module
log()
FilePath
FilePath.assets_dir
FilePath.working_dir
FilePath.get_environment()
FilePath.make_work_dir()
FilePath.make_assets_dir()
FilePath.copy_to_assets_dir()
FilePath.gen_output_fp()
FilePath.gen_asset()
FilePath.gen_prim_fp_elt()
FilePath.copy_workdir_to_assets()
FilePath.copy_workdir_logs_to_assets()
FilePath.rm_workdir()
FilePath.run()
- Utils
- DM Conversion
- BRT
- BRT flow
- Batchruntomo pipeline overview:
gen_dimension_command()
gen_ali_x()
gen_ali_asmbl()
gen_mrc2tiff()
gen_thumbs()
gen_tilt_movie()
gen_recon_movie()
gen_clip_avgs()
consolidate_ave_mrcs()
gen_ave_8_vol()
gen_ave_jpgs_from_ave_mrc()
cleanup_files()
gen_dimension_command()
gen_ali_x()
gen_ali_asmbl()
gen_mrc2tiff()
gen_clip_avgs()
consolidate_ave_mrcs()
gen_ave_jpgs_from_ave_mrc()
cleanup_files()
- BRT constants
- BRT flow
- SEM Tomo
- CZI
- Config module