hdf5_utils

Functions that handle hdf5 files

pysmFISH.hdf5_utils.create_loompy_raw_counting(hybridizations_infos, converted_positions, hybridization, flt_rawcnt_config, hyb_dir, processing_hyb, counting_gene_dirs)

Function used to write the counting results in a loom file

hybridizations_infos: dict

Parsed information on the experiment.

converted_positions: dict

coords of the images for all hybridization.

hybridization: str

hybridization processed (ex. Hybridization2)

flt_rawcnt_config: dict

Parsed filtering a raw counting configuration file (Filtering_raw_counting.config.yaml)

counting_gene_dirs: list

List of the directories containing the counts

pysmFISH.hdf5_utils.hdf5_create_preprocessing_file(hybridizations_infos, processing_hyb, hybridization, analysis_name, hyb_dir, converted_positions, image_properties)

Create the hdf5 file that will contain the preprocessed images for one hybridization. The preprocessing .hdf5 file must have a .ppf.hdf5 extension The file will be created for serial writing of the hdf5 file. After creation the file is closed. Remember that the ‘lzf’ compression do not accept extra items

hybridizations_infos: dict

Parsed Hybridizations metadata

processing_hyb: str

Hybridization to process. The function will create an hdf5 file for the hybridization only

hybridization: str

Hybridization name

analysis_name: str

Analysis name

hyb_dir: str

Path of the dir where to save the file

converted_positions: dict

Parsed positions