IPDISP (CCP4: Supported Program)

NAME

SYNOPSIS

DESCRIPTION

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 0.88

Contents:

1. Options for ipdisp
2. Description of the display window
3. Details of the display window
   1. Display parameter area
   2. Output area
   3. Main menu
   4. Image display area
4. Description of spatial distortion files (spdfils)
   1. Description of data items
   2. Creating or customising spdfils
5. List of distributed spdfils

Options for ipdisp

      -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).

DISPLAY WINDOW

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

1) Display parameters

This allows a number of parameters affecting the display & other options to be changed. Yes/No toggles can be changed by clicking the left mouse button on the Yes/No button. Numbers can be changed by clicking on the number with the left button, then typing the number, terminated by <cr>

2) Output area

This area reports the results of clicking on the image, etc. No input is accepted

3) Main menu

Click left button to select an option

4) Image display area

In the window area, the left mouse button can be used to select a rectangle by dragging. The average value, rms deviation & number of points are reported in the Output area. A selected rectangle may be zoomed to fill the display area by the menu option Zoom: click Zoom again to restore the full image.

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:-

1. Min & Max image values for the grey level scaling (equivalent to Scale low & high in the parameter area, but less permanent)
2. cursor position in pixels (REVERSED in order, i.e. x==Zms, y==Yms). In zoomed images, this is the pixel position in the ZOOMED image, not in the whole image. See output area after clicking for correct pixel values in the whole image.
3. Overlay On/Off/Offset menu, toggles display of circle and spot overlays (right button to select)
4. Contrast slider: controls display contrast (left button)
5. Colour table selection: probably only Black on white & White on black are useful (N.B. "Yellow if >Max" option makes pixels yellow if they are greater than scale-high (=Max) value)
6. Mag menu: controls magnification in magnify window
7. PS button: sends image to a Postscript file (after a little dialogue)

1) Display parameter area

1. Signed image: raw images are Unsigned (=No, default). Selecting Yes will set negatives = 0 for the displayed image (but picked values are still correct)
2. Scale low, high: define scaling range, i.e. the values of an image pixel to be displayed as white or black. The first image displayed will be scaled automatically, and the range may also be recalculated with the Scale image option in the menu, but you may wish to change this. These numbers are exactly equivalent the the Min/Max numbers on the image panel, but numbers set here will carry over to all images. Use Current image option to redisplay image with altered scaling.
3. Pick area: controls number of pixels displayed by Pick
4. Whole range: not relevant at present
5. Add: controls the Add images & Overlay images options, but these parameters are also prompted for by these options. Define first image number & number of images to add together or overlay.
6. Distance, Theta, Wavelength: these must be set before resolution or measure calculations are sensible
7. Beam pixel Y, Z: these are the pixel coordinates of the main beam along fast & slow directions. Normally they will be picked up from the spdfil (which should be edited for your site), but they can be changed here. Click on the beam centre to get the pixel coordinates in the output area, then click on menu item Set Main Beam, or alternatively type them in to these slots.
8. Outer circle: define resolution for the outer circle drawn by the Circles option. Default to edge of detector. The actual resolutions of the circles are given in the output area.

2) Output area

1. Pixel: last pixel hit (Yms, Zms) or 1st corner of rectangle
2. Pixel coordinates expressed in Mosflm scanner frame in mm (as in the BEAM command to Mosflm)
3. Resolution: of last pixel hit (in Angstrom)
4. Spacing: result of Measure option
5. Average, RMS, number: average, RMS deviation & number of pixels in the last selected rectangle
6. Zoom factor: if Zoom option used
7. Circle resolution: resolution of circles drawn by Circles option

(3) Main menu

1. Current image: display whatever is in the current image array. Also useful for redrawing image if Scale High & low are changed
2. Read file: give name of file to be read & displayed
3. Read image: give image number to be displayed. The file name will be constructed using the template
4. Read next image: increment the image number by the image increment (noramlly = +1), display next image in series
5. Read prev image: decrement image number, display previous image
6. Set template: set filename template, as in Madnes (i.e. filename with # characters which will be replaced by an image number). Must be done before Read image, Add images, or Overlay images options can be used.
7. Scale image: set high & low image values to display as black or white. You may need to change the scale limits to improve the appearance the display.
8. Add images: add together a series of images (actually average them). You may wish to subtract a dark image from the sum. The Write image option may be used to save the result.
9. Overlay images: for a series of images, choose the largest value at each pixel. The Write image option may be used to save the result.
10. Correct image: apply various corrections (not usually useful). Click off the sub-menu to cancel
11. Write image: write the current image to disk. Useful with Add or Overlay. The written image can be read back by ipdisp but may not be acceptable to other programs like mosflm.
12. Set Main Beam: set main beam pixel coordinates to last picked point, replace values in parameter table.
13. Fit circle: click on a series of points defining a circle centred on the main beam (e.g. a powder ring), then click this menu option again to fit a circle to the points. Determines the centre and radius of the best-fitting circle, allowing for a scale factor between the pixel size in the 2 directions. If the result is accepted, the main beam position is set to the centre of the circle, and the pixel size in the Yms (==Yc) direction is changed. Useful for determining main beam position from powder rings (e.g. wax). N.B. this fit is done in pixel coordinates multiplied by the pixel size: it does not take into account any spatial distortion (e.g. Roff & Toff), nor of detector tilt (theta)
14. Pick: toggle display of figure field around picked point on image.
15. Measure: toggle measurement of reciprocal lattice spacing. Pick two spots on a reciprocal lattice row (left button), then type number of orders, & the lattice spacing is output in the Output area. Beware skew cells, this gives you 1/a* etc, not a!
16. Circles: toggle display of resolution circles. The resolution of the outer circle is defined in the parameter table, the resolutions of all the circles is given in the output area. Note that for the Fast, the display is distorted (pixels are displayed as if they were square), so the circles are not circular.
17. Zoom: zoom a part of the image. Select an area by dragging a rectangle on the image (left button), then click Zoom. A square area enclosing the selected rectangle will be displayed. Zooming may be repeated. To restore full image, click Zoom when no rectangle is selected.
18. Exit: exit program

4) Image display area

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.

Description of Spatial Distortion Files (spdfils)

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 cutomise existing spdfils or create new ones.

Descriptions of spdfil data items

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).

IMGTYP

Image type, eg 'MAR', EMBL', 'RAX', 'MLDS', 'GEL' etc. Only used for reference purposes for the user.

NHEAD

number of header records. (1 for MAR, 0 otherwise?)

LRECL

record length (may be longer than real size; mustn't be smaller than NPIXEL)

NPIXEL

number of pixels to read from each record; this corresponds to the number of pixels along the 'fast' axis.

NPXREC

number of records to read; this corresponds to the number of pixels along the 'slow' axis.

IMGDRC

image direction; string of the form e.g. -x+y which corresponds to the mosflm convention for the order and direction of the axes stored in the image file.

ENDED

endedness of machine that wrote the image file:

1. 'litend' (little-ended, ie least significant bit written first - this is the default) (Vax- or PC-like)
2. 'bigend' (big-ended, ie most significant bit written first) (SGI, ESV, Sun, etc)

This may also contain the string sqt (eg 'bigsqt') indicating squashed data above 32767, or ovf (e.g. 'bigovf') indicating Mar-style overflow table.

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.

YPXMAX

maximum usable pixel along Yms (i.e. fast axis)

ZPXMAX

maximum usable pixel along Zms (i.e. slow axis)

YBEAM

Yms coordinate of main beam (i.e. along fast axis, guess at YPXMAX/2)

ZBEAM

Zms coordinate of main beam (i.e. along slow axis, guess at ZPXMAX/2)

YPXSIZ

pixel size in mm along Yms

ZPXSIZ

pixel size in mm along Zms

ROFF

radial offset correction

TOFF

tangential offset correction

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).

Creating or customising spdfils

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.

List of distributed spdfils

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.

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.

AUTHOR