AFNI file: README.compression

Compressed Dataset .BRIK Files ============================== AFNI now supports the use of compressed .BRIK files. The routines that open and read these files detect the compression mode using the filename suffix, and will use the correct decompression program to read them in from disk. The character 'z' is added to the end of a dataset's listing in the AFNI menus if the .BRIK is compressed; for example, "elvis [epan]z". No other files used by AFNI can be compressed and still be readable by the software. This includes the .HEAD files, timeseries (.1D) files, etc. Note also that the programs 2swap and 4swap don't do compression or decompression, so that if you need to do byte swapping on a compressed .BRIK file, you must manually decompress it, swap the bytes, and (optionally) recompress the file. How to Compress =============== You can compress the .BRIK files manually. The following 3 programs are supported: Name Suffix Compression Command Uncompress Command -------- ------ ------------------- ------------------- compress .Z compress -v *.BRIK uncompress *.BRIK.Z gzip .gz gzip -1v *.BRIK gzip -d *.BRIK.gz bzip2 .bz2 bzip2 -1v *.BRIK bzip2 -d *.BRIK.bz2 "compress" is available on almost all Unix systems. "gzip" is available on many Unix systems, and can also be ftp-ed from the AFNI distribution site. "bzip2" is included in the AFNI distribution. It generally compresses more than the other two programs, but is much slower at both compression and uncompression. (See the file README.bzip2 for details about this program.) For large MR image datasets, "compress" and "gzip" have about the same compression factor and take about the same CPU time (at least in the samples I've tried here.) Do NOT compress the .HEAD files! AFNI will not be able to read them. Automatic Compression ===================== If you set the environment variable AFNI_COMPRESSOR to one of the strings "COMPRESS", "GZIP", or "BZIP2", then most programs will automatically pass .BRIK data through the appropriate compression program as it is written to disk. Note that this will slow down dataset write operations. Penalties for Using Compression =============================== Datasets must be uncompressed when they are read into AFNI (or other programs), which takes time. In AFNI itself, a dataset .BRIK file is only read into the program when its values are actually needed -- when an image or graph window is opened. When this happens, or when you "Switch" to a compressed dataset, there can be a noticeable delay. For "compress" and "gzip", this may be a few seconds. For "bzip2", the delays will generally be longer. The speed penalty means that it is probably best to keep the datasets you are actively using in uncompressed form. This can be done by compressing datasets manually, and avoiding the use of AFNI_COMPRESSOR (which will compress all .BRIKs). Datasets that you want to keep on disk, but don't think you will use often, can be compressed. They can still be viewed when the need arises without manual decompression. Large .BRIK files are normally directly mapped to memory. This technique saves system swap space, but isn't useful with compressed files. Compressed .BRIK files are read into "malloc" allocated memory, which will take up swap space. This may limit the number of datasets that can be used at once. AFNI will try to purge unused datasets from memory if a problem arises, but it may not succeed. If necessary, the "-purge" option can be used when starting AFNI. Very large datasets (larger than the amount of RAM on your system) should not be compressed, since it will be impossible to read such an object into memory in its entirety. It is better to rely on the memory mapping facility in such cases. Effect on Plugins and Other Programs ==================================== If you use the AFNI supplied routines to read in a dataset, then everything should work well with compressed .BRIK files. You can tell if a dataset is compressed after you open it by using the DSET_COMPRESSED(dset) macro -- it returns 1 if "dset" is compressed, 0 otherwise. How it Works ============ Using Unix pipes. Files are opened with COMRESS_fopen_read or COMPRESS_fopen_write, and closed with COMPRESS_fclose. The code is in files thd_compress.[ch], if you want to have fun. If you have a better compression utility that can operate as a filter, let me know and I can easily include it in the AFNI package. ================================= | Robert W. Cox, PhD | | Biophysics Research Institute | | Medical College of Wisconsin | =================================

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