File names of diffraction image files

Many of the collect programs read one or more diffraction image files. Often, the names of the files that are to be read can be specified on the command line. The type of file to be read/written is determined from the file extension.

extension type can read can write
.kcd KappaCCD yes yes
.syn Synthetic yes n.a.
.spe Roper Sci yes no
.mar MAR345 yes yes
.mar???? MAR345 yes n.a.
.img FAST yes no
.ipf DIP yes yes
.bmp graphic yes no
.jpg graphic yes no
.gif graphic yes no
.pgm graphic yes no
.tif graphic yes no
.ppm graphic yes no
Notes:

extension	type	can read	can write
.kcd	KappaCCD	yes	yes
.syn	Synthetic	yes	n.a.
.spe	Roper Sci	yes	no
.mar	MAR345	yes	yes
.mar????	MAR345	yes	n.a.
.img	FAST	yes	no
.ipf	DIP	yes	yes
.bmp	graphic	yes	no
.jpg	graphic	yes	no
.gif	graphic	yes	no
.pgm	graphic	yes	no
.tif	graphic	yes	no
.ppm	graphic	yes	no

MAR345 images are always written as .mar, not including the image size in the file name.
.syn images are so far only written by the "precession" program. This was turned into a separate extension because the precession geometry is so different, but the file type is very similar to the .kcd file.

Compression

Diffraction image data is very well compressible (to approximately one third to one quarter of the size). Some of the image formats (like e.g. the MAR345) are always written in compressed form. Many of the others can be compressed using unix tools:

compress, giving .Z files; this is fast and gives good compression.
gzip, giving .gz files; this is much slower than compress and gives worse compression of image files (most other files compress better using gzip than using compress!)
bzip2, giving .bz2 files; this is even slower than gzip, but generally gives even smaller files than compress.

For all image types except DIP images, the programs in the collect suite accept the .Z, .gz, and .bz2 compressed images and can read them on the fly.

Please note that "denzo" can not read images compressed with one of these three external compression programs. Before data processing using denzo can start, all images must be uncompressed.

More than one file

If a 'collect suite' program accepts more than one image via the command line, the images are not required to be of the same type. Images can be used in any desirable combination.

The only exception are programs that work on whole "scans" of images (e.g. s01f001.kcd through s01f090.kcd). It is not possible to have part of such a scan compressed and another part uncompressed. All image files in a scan must always be using the same compression program.

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