Use idiffdisp instead.
This program allows the display of images from a variety of sources. The primary assumption is that the image file consists either of a known (currently MAR) format, or of an array of pixel values expressed as unsigned short integers (integer*2), with an optional header (which is ignored except for MAR images): this second class includes unpacked images from most detector systems. The image file is described in a so-called spdfil, which is specified on the command line.
Historically, this program was a stand-alone version of a display level from Madnes, so follows a few Madnes ideas.
The program is run by
ipdisp [option] Examples: ipdisp my_image.mar2000 ipdisp -Mo -f image.img ipdisp -M -t image_###.img -d 120 -w 0.88The first [option] defines the appropriate image type, and may be followed by options to set an image filename and to set parameters which may otherwise be set interactively from the screen menu. In the case of Mar IP files with extensions of the form ".marXXXX" (where XXXX is a number eg 2000), the filename name itself (or template name following -t) is sufficient
-h gives a list of the image type options -s defines spdfil; not needed if one of the above options is given -f image filename: if this is given, it will be displayed immediately -t template name -i image increment (nearly always = 1,the default) -d detector distance (mm) -a swing angle theta (degrees) -w wavelength (A)
If the filename or template name have extensions of the form ".marXXXX", the type will be set automatically and the distance and wavelength will be read from the header.
The following define the image type (ie which spdfil to read) - if used, they MUST come before any other option: either version may be used for unix, only the second for VMS ( in which case only the first two characters are needed):
-ab -AB 2x2 ADSC scanned binned mode -a -A 2x2 ADSC scanned -m -MAr MAR scanner (small plate, SGI) -mc -MC MAR CCD scanner 130mm -md -MD MAR CCD scanner 165mm -M -BMar MAR scanner (large plate, SGI, squashed data) -Mo -BOmar MAR scanner (large plate, SGI, original format with overflow) -V -MVaxmar MAR scanner (large plate, Vax) -v -MVax MAR scanner (small plate, Vax) -r -R RAXIS II scanner -rc -RC RAXIS II scanner (coarse scan) -r4 -R4 RAXIS 4 scanner (100 micron scan) -pf -PF Photon Factory Weissenberg plate -c -C Mac Science 2500x2500 -d3 -D3 MAC Science DIP2030 -d4 -D4 MAC Science DIP2040 -dc -DC D2AM CCD scanner [Obsolete? -e -EMbl EMBL scanner (prototype) -g -GEl gel -o -OLmb Optronics film scan (LMB scan size) -O -OOlmb Optronics film scan (LMB scan size, original file) -y -Ylmb Molecular Dynamics off-line scanner at LMB -Y -BYlmb Molecular Dynamics large scanner at LMB -z -XLmb Molecular Dynamics small scanner at LMB -i2 -TIffgel TIFF file translated from a GEL file] or the spdfil filename can be given (full path not needed).The complete list of supported detectors and their associated spdfils is given below (see "List of distributed spdfils") (see the ipdisp script or COM file on VMS for details)
The left mouse button is the main pointer, the middle button is used on the image area to control the magnify window, the right button for sub-menu options in the image area
The middle mouse button controls the magnify window (top left). Clicking the middle button on the magnify window toggles a double size display. Clicking the middle button on the image display freezes the magnify window, allowing pixels in the magnify window to be picked (but not rectangles).
The top right panel contains:-
This is 800 x 800 pixels. Large images are sampled as necessary (e.g. 1 in 2, 1 in 3, or 1 in 4) on reading in. Use of Zoom allows the display of all data pixels for a part of any larger image.
The spatial distortion files (spdfil for short) contain information which characterises the image file which is to be viewed - in turn these characteristics are determined by 1. detector, 2. collection software/hardware, 3. site specific setup.
The spdfils are short text files which can be viewed e.g. using the unix command 'more'. A typical spdfil will contain several lines of comments and two lines of data. The data lines look like:
# IMGTYP NHEAD LRECL NPIXEL NPXREC IMGDRC ENDED #.......#.......#.......#.......#.......#.......#....... RAX 1 1024 950 950 +y+x litend # # YPXMAX ZPXMAX YBEAM ZBEAM YPXSIZ ZPXSIZ ROFF TOFF #.........#.........#.........#.........#.........#.........#.........#......... 950. 950. 425.0 425.0 0.2034 0.210 0.0 0.0
Lines beginning with # are comments and are ignored by IPDISP when reading the file. The following sections describe the meaning of the different items in the data lines, and how to customise existing spdfils or create new ones.
Line 1: imgtyp, nhead, lrecl, npixel, npxrec, imgdrc, ended
These entries have the following fixed fortran format: (A8, 4I8, 2A8), i.e. imgtyp (string, 8 character field), nhead/lrecl/npixel/npxrec (integers, each with an 8 character field), imgdrc/ended (strings, each with 8 character field).
Line 2: YPXMAX, ZPXMAX, YBEAM, ZBEAM, YPXSIZ, ZPXSIZ, ROFF, TOFF
These entries have the following fixed fortran format: (8F10.4) i.e. each of the entries are reals with a 10 character field and 4 decimal places.
Of these, NPIXEL, NPXREC, YPXSIZ and ZPXSIZ are detector properties. IMGDRC, ENDED are collection characteristics. YBEAM and ZBEAM are site specific.
ROFF and TOFF are corrections to do with scanning errors (the detectors are scanned in a spiral and the data are then converted to a rectangular grid for storage in the image file - these are corrections for the case when the spiral is off-centre ... they should in any case be small so set them both to zero if you don't have any better estimates).
Customisation may be necessary to correct for the alignment of the main beam (YBEAM, ZBEAM), or if the detector operates in different scan modes or with different pixel resolutions (NPIXEL, NPXREC, YPXSIZ, ZPXSIZ). New detectors may require that you write your own spdfil, with the caveat that some recent detectors (e.g. Mar345) write the image file in a packed format, which IPDISP cannot read without coding changes. In these cases it is not sufficient to write a new spdfil.
e.g. ADSC Quantum-4 CCD has an active area of 2304x2304 pixels with pixels being 81.6x81.6 microns. This gives IMGTYP = 'ADSC' (used only for reference), NPIXEL and NPXREC = 2304 and YPXSIZ and ZPXSIX = 0.0816.
Then: NRECL should be at least as big as NPIXEL (should be okay if they are equal). YPXMAX and ZPXMAX can be set equal to NPIXEL and NPXREC respectively, as defaults (not sure what these do).
YBEAM and ZBEAM together define the position of the main beam, and ideally this would be at the centre of the image, i.e. YBEAM = (YPXMAX/2) and ZBEAM = (ZPXMAX/2). In fact this is unlikely to be exactly true for a real experimental setup, and these numbers will have to be adjusted slightly. This can be done either by editing the spdfil or from within IPDISP. Similarly, ROFF and TOFF are corrections for the deviation for ideality of the radial scan, and are setup-specific. Default to 0.0.
IPDISP will look for the spdfils in the directory $CCP4/x-windows/ipdisp If you wish to have them elsewhere, you will have to edit the ipdisp script.
This is the complete list of spdfils available at present; not all spdfils have associated ipdisp options. Not all detectors are represented and it will be necessary to create new spdfils for these (see above). Otherwise MOSFLM will view images from most detectors, e.g. Mar345.
|-Y||-BYlmb||spdfil.Mld||LMB Molecular Dynamics scanner, 1400x1400 pixel scan|
|-Mo||-BOmar||spdfil.Sbigmar||MAR scanner (large plate, SGI, original format with overflow)|
|-z||-ZLmb||spdfil.Smld||LMB Molecular Dynamics scanner, 512x456 pixel scan|
|-ab||-AB||spdfil.adsc_binned||2x2 ADSC scanned binned mode (*)|
|-a||-A||spdfil.adsc_unbinned||2x2 ADSC scanned (*)|
|-M||-BMar||spdfil.bigmar||MAR scanner (large plate, SGI, squashed data)|
|-V||-BVaxmar||spdfil.bigvax||MAR scanner (large plate, Vax)|
|-o||-OLmb||spdfil.film||Optronics film scan (LMB scan size)|
|-O||-OOlmb||spdfil.film2560||Optronics film scan (LMB scan size, original file)|
|-i2||-TIffgel||spdfil.lcl||TIFF file translated from a GEL file|
|-e||-EMbl||spdfil.lmb||EMBL scanner (prototype)|
|-m||-MAr||spdfil.mar||MAR scanner (small plate, SGI)|
|-mc||-MCcd||spdfil.marccd||130mm MAR CCD scanner (*)|
|-md||-MD||spdfil.marccd165||165mm MAR CCD scanner (*)|
|-v||-MVax||spdfil.marvax||MAR scanner (small plate, Vax)|
|-c||-C||spdfil.mcs||Mac Science 2500x2500|
|-d3||-D3||spdfil.dip2030||Mac Science DIP2030 (*)|
|-d4||-D4||spdfil.dip2040||Mac Science DIP2040 (*)|
|-y||-YLmb||spdfil.mld||LMB Molecular Dynamics off-line scanner, 700x700 pixel scan|
|-pf||-PF||spdfil.pf||Photon Factory Weissenberg plate|
|-r||-R||spdfil.rax||RAXIS II scanner|
|-r4||-R4||spdfil.rax4100||RAXIS 4 scanner with 100 micron scan (*)|
|-rc||-RC||spdfil.raxc||RAXIS II scanner (coarse scan)|
|-dc||-DC||spdfil.d2amccd||D2AM CCD scanner (*)|
Files for Mar345-style images, loaded automatically by ipdisp script:-
spdfil.mar1200, spdfil.mar1600, spdfil.mar1800, spdfil.mar2000, spdfil.mar2300, spdfil.mar2400, spdfil.mar3000, spdfil.mar3450
N.B.: spdfils marked with (*) are new and have not been widely tested. Thanks to Dave Lawson for the RAXIS 4 spdfil, Sean McSweeney for the Mar CCD and ADSC spdfils, Jean-Luc Ferrer for the D2AM CCD spdfil, and to Atsushi Nakagawa for the MAC science DIP2030 and DIP2040 spdfils.