Precession

Generate precession-like images from datasets.

Examples
Commands
How it works

Examples

The following files must exists in the current directory:

detalign.vic
distorpol.vic
goniostat.vic

and they can be overruled later.

single scan
A single φ-scan, images from Apex
This will create projections 0kl h0l hk0
```
size 512 512
rmat first
reso 0.7
all s01f*.sfrm
write prec-
exit
```

single scan

A single φ-scan, images from Apex, add zone=1 projections

size 512 512
rmat first
reso 0.7
proj 1kl h1l hk1
all s01f*.sfrm
write prec-
exit

multiple scans
Multiple φ- and ω-scans, single rmat, images from Apex
```
size 512 512
rmat first
reso 0.7
all s*.sfrm
write prec-
exit
```

multiple scans, different detaligns, rmats

Multiple φ- and ω-scans, images from Apex
An rmat-file per scan, and detaligns per scan

size 512 512
rmat ../s01f
@../postref-s01f.vic
reso 0.7
all ../s01f*.sfrm

rmat ../s02f
@../postref-s02f.vic
all ../s02f*.sfrm

rmat ../s03f
@../postref-s03f.vic
all ../s03f*.sfrm

write prec-
exit

Commands

activateproj

Syntax: activateproj nr
Activates a specific projection.

Syntax: badresponsthreshold n
Sets the threshold for bad respons pixels to n.
If badresponsthreshold is active (for ADSC and MARCCD detectors by default, or by an explicit invocation) the pixels below this threshold will not be used during the processing of images.

bg

Syntax: bg colour
Default: bg black
Sets the background colour.

clear

Syntax: clear
Clears the target array. The results of processed images will be lost.

correct

Syntax: correct none/normal/full/debug
Default: correct normal
Allows command and option corrections. Commands and options are only corrected if input originates from the keyboard, and output is sent to the screen.

none
No correction will be applied
normal
Commands and options will be corrected.
full
As before plus possible corrections are printed
debug
As before plus all available commands/options are printed

delta

Syntax: delta n
Default: delta 0
Sets the number of extra pixels for the plot command

dist

Syntax: dist f
Sets the detector distance. Normally, this information is extracted from the header of the first image.

exit

Syntax: exit
Finish program.

fg

Syntax: fg colour
Default: fg white
Sets the foreground colour.

go

Syntax: go
Process the image.

goniostat

Syntax: goniostat a1 a2 a3
Set the goniostat angles to a1 a2 a3 degrees. These values are normallty extracted from the image header

goniostatchange

Syntax: goniostatchange
Change one or more attributes of the goniostat. See the goniostat page for more information.

gridcolour

Syntax: gridcolour colour
Default: gridcolour red
Sets the grid colour.

header

Syntax: header
Show the image header

help

Syntax: help [command]
Start webbrowser with help on precession. The following browsers are tried: (GETENV BROWSER), iceweasel, firefox, mozilla, netscape. You may add the optional command; if possible, the browser will jump to the appropriate section.

hkl

Syntax: hkl h k l

hor

Syntax: hor h1 h2
Limit the horizontal pixels in the original image.

inspect

Syntax: inspect ph pv
Print the accumulated intensity value and the normalization of target pixel ph pv.

loglevel

Syntax: loglevel [0-7]
Default: loglevel 4
Set (graphics) loglevel.

mapstat

Syntax: mapstat
Print extreme values of the accumulated intensities in the various projections.

monitor

Syntax: monitor ph pv
Sets a monitor on target pixel ph pv. When this pixel is hit, the program will print the image coordinates leading to the hit.

mode

Syntax: mode n
Default: mode 1
Every pixel in the original image has four corners. Each corner maps to a point in the projection (horizontal, vertical) and a (hkl)-value for the along-axis.

mode 1 Take the average of the four corner points, map this average to the projection, and transfer the intensity. This is the fastest mode. It is possible that pixels in the projection will not receive any intensity.
mode 2 Map the four corner points to the projection, and round the result to the nearest pixel. Distribute the intensity over the resulting pixels.
mode 3 Map the four corner points to the projection. Take the int-value for for the lower (horizontal and vertical) pixels, and 1+int-value for the upper pixels. Distribute the intensity over the resulting pixels.
mode 4 Map the four corner points to the projection. Calculate the partial contribution to every projection pixel, taking into account the partial surface. This is very slow.

Syntax: next

output

Syntax: output none/normal/full/debug
Default: output normal

p2m

Syntax: p2m ph pv

plot

Syntax: plot hor ver

plotlevel

Syntax: plotlevel none/nrmal/full/debug

plotperc

Syntax: plotperc state
Default: plotperc on

proj

Syntax: proj s

projclear

Syntax: projclear

ps

Syntax: ps

read

Syntax: read image

reso

Syntax: reso f

rmat

Syntax: rmat rmatfile

scale

Syntax: scale

size

Syntax: size n1 n2

status

Syntax: status

step

Syntax: step n

swing

Syntax: swing a

thick

Syntax: thick f

title

Syntax: title s

ver

Syntax: ver v1 v2
Limit the vertical pixels in the original image.

window

Syntax: window

write

Syntax: write prefix

How it works

Every pixel in a diffraction image corresponds to an outray from the crystal.
In combination with the primary beam, this outray can be converted to a c-vector in laboratory space.
This c-vector can be rotated to a c000 vector in 000-position (all goniostat angles zero).
The c000 vector can be transformed to the reciprocal space (hkl) using the orientation matrix.
Define a view-matrix (along an axis in hkl-space)
Rotate all c000-vectors using this view-matrix to c-view.
Ignore the third component of c-view (this correspons to projection along the view axis
Test if the hkl-component of the c-view vector is within limits of the requested projection zone.
map the original pixel intensity to the target projection.

Create outray

convert the pixel coordinates (ph,pv) in the diffraction image to mm-coordinates (mmh,mmv) using distorpol.vic.
construct an outray from (mmh,mmv) using the detector distance, the detector swing angle, and the detector offsets and tilt angles detalign.vic.

Create c000

normalyze outray (length 1.0)
add inray = (1,0,0)
divide the result by λ. This leads to c-diffr
rotate c-diffr over all goniostat axes to c000. This involves the goniostat angles (from the image header), and the goniostat description from goniostat.vic

View matrix 1

This rotates to a view along an reciprocal axis.

View matrix 2

This rotates to a view perpendicular to a direct plane

Map intensity

Every pixel in the diffraction image has four corners (LowerLeft, LowerRight, UpperRight and UpperLeft) By applying all transformations, this leads to 4 corner points in the projection system. If one of the four points is within zone-limits, the diffraxtion intensity will be mapped to the projection image.
The red grid is the projection image. In yellow the transformed four corners of the diffraction-image-pixel are drawn.

mode 1

Calculate the average positon of the four corners, convert to the projection pixel and accumulate the intensity into that one pixel.
mode 2

convert every corner point to projection pixels. When necessary, add intermediate pixels. Divide the intensity ver the selected pixels
mode 3

convert every corner point to projection pixels. Calculate the horizontal/vertical extremes, and divide the intensity over all pixels within these extremes
mode 4

convert every corner point to projection pixels. Calculate partial surfaces and divide the intensity over the pixels, using the surfaces

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