Index

A

ali_file (em_workflows.utils.utils.BrtOutput attribute)

assets_dir (file_path.FilePath property) assets_dir() (config.Config static method)

B

bioformats2raw (config.Config attribute) bioformats_gen_zarr() (in module em_workflows.utils.neuroglancer) bioformats_gen_zarr_dup() (in module em_workflows.utils.neuroglancer) brt_binary (config.Config attribute)

BRT_DEPTH (in module em_workflows.brt.constants) BRT_HEIGHT (in module em_workflows.brt.constants) BRT_WIDTH (in module em_workflows.brt.constants) BrtOutput (class in em_workflows.utils.utils)

C

callback_with_cleanup() (in module em_workflows.utils.utils) cleanup_files() (in module em_workflows.brt.flow), [1] collect_exception_task_hook() (in module em_workflows.utils.utils) config module Config (class in config) consolidate_ave_mrcs() (in module em_workflows.brt.flow), [1] convert_2d_mrc_to_tiff() (in module em_workflows.dm_conversion.flow) convert_dm_mrc_to_jpeg() (in module em_workflows.dm_conversion.flow) convert_dms_to_mrc() (in module em_workflows.dm_conversion.flow)

convert_if_int16_tiff() (in module em_workflows.dm_conversion.flow) convert_tif_to_mrc() (in module em_workflows.sem_tomo.flow) copy_template() (in module em_workflows.utils.utils) copy_tg_to_working_dir() (in module em_workflows.utils.utils) copy_to_assets_dir() (file_path.FilePath method) copy_workdir_logs_to_assets() (file_path.FilePath method) copy_workdir_to_assets() (file_path.FilePath method) copy_workdirs_and_cleanup_hook() (in module em_workflows.utils.utils) copy_zarr_to_assets_dir() (in module em_workflows.czi.flow) create_stretch_file() (in module em_workflows.sem_tomo.flow)

D

DMS_EXT (in module em_workflows.dm_conversion.constants)

E

em_workflows.brt.constants module em_workflows.brt.flow module em_workflows.czi.constants module em_workflows.czi.flow module em_workflows.dm_conversion.constants module

em_workflows.dm_conversion.flow module em_workflows.sem_tomo.constants module em_workflows.sem_tomo.flow module em_workflows.utils.neuroglancer module em_workflows.utils.utils module

F

FIBSEM_DEPTH (in module em_workflows.sem_tomo.constants) FIBSEM_HEIGHT (in module em_workflows.sem_tomo.constants) FIBSEM_WIDTH (in module em_workflows.sem_tomo.constants)

file_path module FilePath (class in file_path) find_thumb_idx() (in module em_workflows.czi.flow)

G

gen_ali_asmbl() (in module em_workflows.brt.flow), [1] gen_ali_x() (in module em_workflows.brt.flow), [1] gen_align_xg() (in module em_workflows.sem_tomo.flow) gen_asset() (file_path.FilePath method) gen_ave_8_vol() (in module em_workflows.brt.flow) gen_ave_jpgs_from_ave_mrc() (in module em_workflows.brt.flow), [1] gen_clip_avgs() (in module em_workflows.brt.flow), [1] gen_dimension_command() (in module em_workflows.brt.flow), [1] gen_keyimg() (in module em_workflows.sem_tomo.flow) gen_keyimg_small() (in module em_workflows.sem_tomo.flow) gen_mrc2tiff() (in module em_workflows.brt.flow), [1] gen_newstack_mid_mrc_command() (in module em_workflows.sem_tomo.flow) gen_ng_metadata() (in module em_workflows.sem_tomo.flow)

gen_output_fp() (file_path.FilePath method) gen_prim_fp_elt() (file_path.FilePath method) gen_recon_movie() (in module em_workflows.brt.flow) gen_thumb() (in module em_workflows.czi.flow), [1] gen_thumbs() (in module em_workflows.brt.flow) gen_tilt_movie() (in module em_workflows.brt.flow) gen_xfalign_comand() (in module em_workflows.sem_tomo.flow) generate_czi_imageset() (in module em_workflows.czi.flow) generate_flow_run_name() (in module em_workflows.utils.utils) generate_imageset() (in module em_workflows.czi.flow) generate_zarr() (in module em_workflows.czi.flow) get_environment() (file_path.FilePath method) (in module em_workflows.utils.utils)

H

Header (class in em_workflows.utils.utils)

header_loc (config.Config attribute) HIGH_SLURM_EXECUTOR (config.Config attribute)

I

imod_root (config.Config attribute)

J

JPGS_EXT (in module em_workflows.dm_conversion.constants)

K

KEYIMG_EXTS (in module em_workflows.dm_conversion.constants)

L

LARGE_2D (in module em_workflows.dm_conversion.constants) local_storage (config.Config attribute)

log() (in module em_workflows.utils.utils) (in module file_path) lookup_dims() (in module em_workflows.utils.utils)

M

make_assets_dir() (file_path.FilePath method) make_work_dir() (file_path.FilePath method) module config em_workflows.brt.constants em_workflows.brt.flow em_workflows.czi.constants em_workflows.czi.flow em_workflows.dm_conversion.constants em_workflows.dm_conversion.flow em_workflows.sem_tomo.constants em_workflows.sem_tomo.flow em_workflows.utils.neuroglancer em_workflows.utils.utils file_path

mrc2tif_loc (config.Config attribute) MRCS_EXT (in module em_workflows.dm_conversion.constants)

N

newstack_loc (config.Config attribute)

notify_api_completion() (in module em_workflows.utils.utils)

P

pickle_serializer (config.Config attribute)

PNGS_EXT (in module em_workflows.dm_conversion.constants) proj_dir() (config.Config static method)

R

rec_file (em_workflows.utils.utils.BrtOutput attribute) rechunk_zarr() (in module em_workflows.czi.flow) (in module em_workflows.utils.neuroglancer)

repo_dir (config.Config attribute) rm_workdir() (file_path.FilePath method) run() (file_path.FilePath static method)

S

scale_jpegs() (in module em_workflows.dm_conversion.flow) setup_pytools_log() (in module config) SITK_COMPRESSION_LVL (in module em_workflows.czi.constants)

SLURM_exec() (in module config) SLURM_EXECUTOR (config.Config attribute) SMALL_2D (in module em_workflows.dm_conversion.constants)

T

template_dir (config.Config attribute) THUMB_X_DIM (in module em_workflows.czi.constants) THUMB_Y_DUM (in module em_workflows.czi.constants)

TIFS_EXT (in module em_workflows.dm_conversion.constants) TILE_SIZE (in module em_workflows.czi.constants) tmp_dir (config.Config attribute)

U

update_adoc() (in module em_workflows.utils.utils)

update_file_metadata() (in module em_workflows.czi.flow) user (config.Config attribute)

V

VALID_2D_INPUT_EXTS (in module em_workflows.dm_conversion.constants)

VALID_CZI_INPUTS (in module em_workflows.czi.constants)

W

working_dir (file_path.FilePath property)

X

x (em_workflows.utils.utils.Header attribute)

Y

y (em_workflows.utils.utils.Header attribute)

Z

z (em_workflows.utils.utils.Header attribute)

zarr_build_multiscales() (in module em_workflows.utils.neuroglancer) zarr_build_multiscales2() (in module em_workflows.utils.neuroglancer)