silx convert ============ Purpose ------- The *silx convert* command is provided to help with archiving legacy file formats into HDF5 files. You can refer to following tutorials for additional information about the output format: - :doc:`../Tutorials/io` - :doc:`../Tutorials/convert` - :doc:`../Tutorials/specfile_to_hdf5` Usage ----- :: silx convert [-h] [--file-pattern FILE_PATTERN] [-o OUTPUT_URI] [-m MODE] [--begin BEGIN] [--end END] [--add-root-group] [--overwrite-data] [--min-size MIN_SIZE] [--chunks [CHUNKS]] [--compression [COMPRESSION]] [--compression-opts COMPRESSION_OPTS] [--shuffle] [--fletcher32] [--debug] [input_files [input_files ...]] Options ------- :: input_files Input files (EDF, TIFF, SPEC...). When specifying multiple files, you cannot specify both fabio images and SPEC files. Multiple SPEC files will simply be concatenated, with one entry per scan. Multiple image files will be merged into a single entry with a stack of images. -h, --help show this help message and exit --file-pattern FILE_PATTERN File name pattern for loading a series of indexed image files (toto_%04d.edf). This argument is incompatible with argument input_files. If an output URI with a HDF5 path is provided, only the content of the NXdetector group will be copied there. If no HDF5 path, or just "/", is given, a complete NXdata structure will be created. -o OUTPUT_URI, --output-uri OUTPUT_URI Output file name (HDF5). An URI can be provided to write the data into a specific group in the output file: /path/to/file::/path/to/group. If not provided, the filename defaults to a timestamp: YYYYmmdd- HHMMSS.h5 -m MODE, --mode MODE Write mode: "r+" (read/write, file must exist), "w" (write, existing file is lost), "w-" (write, fail if file exists) or "a" (read/write if exists, create otherwise) --begin BEGIN First file index, or first file indices to be considered. This argument only makes sense when used together with --file-pattern. Provide as many start indices as there are indices in the file pattern, separated by commas. Examples: "--filepattern toto_%d.edf --begin 100", "--filepattern toto_%d_%04d_%02d.edf --begin 100,2000,5". --end END Last file index, or last file indices to be considered. The same rules as with argument --begin apply. Example: "--filepattern toto_%d_%d.edf --end 199,1999" --add-root-group This option causes each input file to be written to a specific root group with the same name as the file. When merging multiple input files, this can help preventing conflicts when datasets have the same name (see --overwrite-data). This option is ignored when using --file-pattern. --overwrite-data If the output path exists and an input dataset has the same name as an existing output dataset, overwrite the output dataset (in modes "r+" or "a"). --min-size MIN_SIZE Minimum number of elements required to be in a dataset to apply compression or chunking (default 500). --chunks Chunk shape. Provide an argument that evaluates as a python tuple (e.g. "(1024, 768)"). If this option is provided without specifying an argument, the h5py library will guess a chunk for you. Note that if you specify an explicit chunking shape, it will be applied identically to all datasets with a large enough size (see --min-size). --compression Compression filter. By default, the datasets in the output file are not compressed. If this option is specified without argument, the GZIP compression is used. Additional compression filters may be available, depending on your HDF5 installation. --compression-opts COMPRESSION_OPTS Compression options. For "gzip", this may be an integer from 0 to 9, with a default of 4. This is only supported for GZIP. --shuffle Enables the byte shuffle filter. This may improve the compression ratio for block oriented compressors like GZIP or LZF. --fletcher32 Adds a checksum to each chunk to detect data corruption. --debug Set logging system in debug mode Examples of usage ----------------- Simple single file conversion to new output file:: silx convert 31oct98.dat -o 31oct98.h5 Concatenation of all SPEC files in the current directory:: silx convert *.dat -o all_SPEC.h5 Appending a file to an existing output file:: silx convert ch09__mca_0005_0000_0008.edf -o archive.h5::/ch09__mca_0005_0000_0008 -m a --compression Merging a list of single frame EDF files into a multiframe HDF5 file:: silx convert --file-pattern ch09__mca_0005_0000_%d.edf -o ch09__mca_0005_0000_multiframe.h5