Index

A

annotate_heatmap() (in module core.saving)

args_to_str() (core.run_args.RunArgs method)

B

BlockAlignmentFile (class in core.data_file)

BothImgRbgFile (class in core.data_file)

C

check_blocksize() (in module toolbox.parameter_file.function_parameters) check_brightest() (in module toolbox.parameter_file.function_parameters) check_dict() (in module toolbox.parameter_file.function_parameters) check_settings() (in module toolbox.parameter_file.function_parameters) convert_dic_to_string() (in module toolbox.parameter_file.function_parameters) convert_list_to_string() (in module toolbox.parameter_file.function_parameters) convert_string_to_dictionnary() (in module toolbox.parameter_file.function_parameters) core module core.dask_cluster module

core.data_file module core.pyhim_logging module core.run_args module core.saving module create_distributed_client() (core.dask_cluster.DaskCluster method) creates_user_mask() (in module postProcessing.mask_manual)

D

DaskCluster (class in core.dask_cluster) DataFile (class in core.data_file) delete_data() (core.data_file.BlockAlignmentFile method) (core.data_file.BothImgRbgFile method) (core.data_file.DataFile method) (core.data_file.EqualizationHistogramsFile method) (core.data_file.RefDiff3DSlicesFile method) (core.data_file.RefDiffFile method)

display_3d_assembled() (in module core.saving)

E

EcsvFile (class in core.data_file)

EqualizationHistogramsFile (class in core.data_file)

F

find_label_in_path() (in module postProcessing.mask_cellpose) (in module postProcessing.mask_manual)

find_roi_name_in_path() (in module postProcessing.mask_cellpose) (in module postProcessing.mask_manual) FocalPlaneMatrixFile (class in core.data_file)

G

get_2d_commands() (core.run_args.RunArgs static method) get_3d_commands() (core.run_args.RunArgs static method) get_available_commands() (core.run_args.RunArgs static method) get_dict_shifts() (in module postProcessing.mask_cellpose) (in module postProcessing.mask_manual)

get_image_filename() (imageProcessing.imageProcessing.Image method) get_root() (core.data_file.NpyFile method) (core.data_file.TifFile method)

H

heatmap() (in module core.saving)

I

Image (class in imageProcessing.imageProcessing) image_adjust() (in module imageProcessing.imageProcessing) image_show_with_values() (in module core.saving) image_show_with_values_single() (in module core.saving) imageProcessing module

imageProcessing.imageProcessing module import_parameters() (in module toolbox.parameter_file.function_parameters) initialize_cluster() (core.dask_cluster.DaskCluster method) is_float() (in module toolbox.parameter_file.function_parameters) is_integer() (in module toolbox.parameter_file.function_parameters)

J

JsonFile (class in core.data_file)

L

lauch_dask_scheduler() (in module toolbox.imagePreProcessing) load() (core.data_file.NpyFile method) (core.data_file.TifFile method) load_image() (imageProcessing.imageProcessing.Image method) load_image_2d() (imageProcessing.imageProcessing.Image method)

load_json() (in module postProcessing.mask_cellpose) (in module postProcessing.mask_manual) load_params() (in module postProcessing.mask_cellpose) (in module postProcessing.mask_manual) Logger (class in core.pyhim_logging)

M

main() (in module postProcessing.mask_cellpose) (in module postProcessing.mask_manual) (in module postProcessing.npy_to_tiff) (in module toolbox.file_handling.cleanHiM_run) (in module toolbox.file_handling.lndir) (in module toolbox.file_handling.unzipHiM_run) (in module toolbox.file_handling.zipHiM_run) (in module toolbox.imagePreProcessing) (in module toolbox.parameter_file.pyhim_parameters) match_name() (in module toolbox.parameter_file.function_parameters) matrixOperations module module core core.dask_cluster core.data_file core.pyhim_logging core.run_args core.saving imageProcessing imageProcessing.imageProcessing matrixOperations postProcessing postProcessing.mask_cellpose postProcessing.mask_manual postProcessing.npy_to_tiff toolbox toolbox.file_handling toolbox.file_handling.cleanHiM_run toolbox.file_handling.lndir toolbox.file_handling.unzipHiM_run toolbox.file_handling.zipHiM_run toolbox.imagePreProcessing toolbox.parameter_file toolbox.parameter_file.function_parameters toolbox.parameter_file.info_parameters toolbox.parameter_file.pyhim_parameters

N

NpyFile (class in core.data_file)

P

parse_arguments() (in module toolbox.imagePreProcessing) parse_cmd() (core.run_args.RunArgs class method) parseArguments() (in module postProcessing.mask_cellpose) plot_3d_shift_matrices() (in module core.saving) plot_4_images() (in module core.saving) plot_raw_images_and_labels() (in module core.saving) Png2DFile (class in core.data_file) postProcessing module postProcessing.mask_cellpose module postProcessing.mask_manual module

postProcessing.npy_to_tiff module preprocess_3d_image() (in module imageProcessing.imageProcessing) print_analyzing_label() (in module core.pyhim_logging) print_dashes() (in module core.pyhim_logging) print_framed_text() (in module core.pyhim_logging) print_log() (in module core.pyhim_logging) print_section() (in module core.pyhim_logging) print_session_name() (in module core.pyhim_logging) print_title() (in module core.pyhim_logging) print_unknown_params() (in module core.pyhim_logging) process_images() (in module postProcessing.mask_cellpose)

R

reassemble_3d_image() (in module imageProcessing.imageProcessing) RefDiff3DSlicesFile (class in core.data_file) RefDiffFile (class in core.data_file)

run_cellpose() (in module postProcessing.mask_cellpose) run_cellpose_api() (in module postProcessing.mask_cellpose) RunArgs (class in core.run_args)

S

save() (core.data_file.BlockAlignmentFile method) (core.data_file.BothImgRbgFile method) (core.data_file.DataFile method) (core.data_file.EcsvFile method) (core.data_file.EqualizationHistogramsFile method) (core.data_file.FocalPlaneMatrixFile method) (core.data_file.JsonFile method) (core.data_file.NpyFile method) (core.data_file.Png2DFile method) (core.data_file.RefDiff3DSlicesFile method) (core.data_file.RefDiffFile method)

save_image_2d() (imageProcessing.imageProcessing.Image method) save_image_2d_cmd() (in module core.saving) save_image_as_blocks() (in module core.saving) save_json() (in module core.data_file) scatter_3d_image() (in module imageProcessing.imageProcessing) setup_logger() (core.pyhim_logging.Logger method) setup_md_file() (core.pyhim_logging.Logger method) shift_3d_mask() (in module postProcessing.mask_cellpose) (in module postProcessing.mask_manual) show_image() (imageProcessing.imageProcessing.Image method) (in module postProcessing.mask_manual)

T

TifFile (class in core.data_file) toolbox module toolbox.file_handling module toolbox.file_handling.cleanHiM_run module toolbox.file_handling.lndir module toolbox.file_handling.unzipHiM_run module toolbox.file_handling.zipHiM_run module

toolbox.imagePreProcessing module toolbox.parameter_file module toolbox.parameter_file.function_parameters module toolbox.parameter_file.info_parameters module toolbox.parameter_file.pyhim_parameters module try_get_client() (in module core.dask_cluster)

U

update_parameters() (in module toolbox.parameter_file.function_parameters)

W

write_string_to_file() (in module core.pyhim_logging)