ImageSum

Image manipulation program. The program can be used for:

Adding images
Subtracting images
Determining minimum/maximum values
etc.....

Use read to read images. With various manipulation commands images can be modified, added, subtracted, divided. Use write to write output files. Different formats are available.

Commands

Actions	Image	Manipulations	Constants	Input/Output	Misc
add dezinger div left low monitor right sub	adczero dark nodark zinger	abs addsave clear covar norm posrescale rescale restore save setcolumn setrow sigma subbg zero	alert logfile monitorfile poissonfile scale sigfac	fix monitorclose next nofix read rotoffset wait write	cc display header help list monitorinit output poisson status

abs

Syntax: abs
Changes al the stored values by their absolute value.

adczero

Syntax: adczero state
If set to on, an ADCZERO value will be subtracted from each image.

add

Syntax: add
New images will be added.

map_i,j = map_i,j + scale*newmap_i,j

sets also NFILES to NFILES + 1 See subbg and addsave to make use of nfiles

Syntax: addsave
This commands adds the saved values (see save) to the current results. If the total exposure time in the saved array is different from the total exposure time in the current result, a scale factor will be applied to correct for this difference.
Example
Suppose you have 10 background images d*.bg with exposure time 30 and 100 'normal' images d*.kbd with exposure time 60
Use the following sequence to subtract all background images:

clear     clear result array
sub       start subtracting
d*.bg     subtract all (10) images. (resulting values are negative!!!)
save      save the subtracted sum
clear     clear result array
add       start adding
d*.kcd    add all (100) images
addsave   multiply the save array with 20 [ (100*60)/(10*30) ] and add to the current result array

alert

Syntax: alert n
Syntax: alert 10
Sets the maximum number of alert messages to n. Alert messages can be given in dezinger mode.

cc

Syntax: cc h v
Default:cc Nx/2 Ny/2
Sets the central pixelcoordinates for mean intensity calculations. Sum1 is a 11*11 box around this centre. sum2 is a 301*301 box around this centre. The defaults are the centre of the image. Used by poisson.

clear

Syntax: clear
Sets the current image to all zero

covar

Syntax: covar dx dy

map_i,j = Σ (new_i,j-save_i,j)*(new_i+dx,j+dy-save_i+dx,j+dy)

You should store the mean image in save. The whole procedure is:

add                  (start adding)
read all images      (add all the images)
norm                 (divide sumvalues by nImages)
save                 (store it)
clear                (fresh start)
covar 1 0            (start calculations of covariance, pixel i,j times i+1,j)
read all images      (sum the covariances)
norm                 (divide by (nImages-1) )

dark

Syntax: dark imagename
Default: nodark
Specify a dark image. This image will be subtracted from all new images. Use nodark to disable the dark subtraction

dezinger

Syntax: dezinger
Sets dezinger mode. In this mode, zingers are detected using all the images. You should read the images frame by frame. The dezinger procedure is:

zinger 1
Read and store first frame
Read second frame. Then for each pixel:
- Calculate the mean value (m) until now.
- Determine the minimum of this mean value and the current value (c). If we interpret this value as counts, then sigma(min) = sqrt(min).
- Set delta (d) to abs(c-m) and compare this with the sigma(min).
- If d is greater than sigfac*sqrt(min) there is a zinger detected.
  - If this is the second frame, store 2 * min
  - If c > m ignore c
  - If c < m use c as the mean value until now
Repeat for all remaining frames.
zinger 2
Repeat for all frames again

If a zinger is detected in multiple frames, an alert message will be given. The maximum number of alert messages can be set by alert.

display

Syntax: display h v
Prints the (accumulated) value at pixel position h v

div

Syntax: div
The current image will be divided by next image

if map_i,j > 0 and new_i,j > 0 then
  map_i,j = 1000.0*map_i,j / new_i,j
else
  map_i,j = 0

header

Syntax: header
Print the header of the last image.

help

Syntax: help
Start (this) help

fix

Syntax: fix lambda/rot/target
Changes header values. Use this command to change some header values.

fix lambda alpha1 alpha2 ratio
If you want to set the final wavelength to a specific value, set alpha1 to this value, set alpha2 to anything and set ratio to a negative number. Use fix lambda just before you write an output file.
fix rot
The values of Rotation Start and Rotation End of the first image will be used in the output file. Normally, these values are updated for every input image to include the whole rotation range. Use fix rot before reading the second image.
fix target material
Sets the target material. material is one of mo/cu/ag. Use fix target just before you write an output file.

Use unfix to disable. (Use rotoffset to change the values of rotstart and rotend in the image header)

left

Syntax: left
Add the left part of the new image to the current image.

list

Syntax: list h v
Shows part of the data. A box of 11*11 pixels is printed on the screen. h v are the horizontal and vertical pixel coordinate of the lower left of the displayed box.

logfile

Syntax: logfile filename
Default: logfile imagesum
Specifies the logfile name. Errors will be written to the logfile.

low

Syntax: low
Store the minimum value of the current and new images.

map_i,j = MIN( map_i,j, scale*new_i,j)

monitor

Syntax: monitor x y
Adds the pixel coordinate x y to the list of monitored pixels. For each frame the value of the pixel [x y] will be written to a monitorfile. The name of the file can be set with monitorfile. This allows you to analyse the change of one or more pixels over a set of frames. The maximum number of monitors is 10. Remove the monitors with monitorinit.

monitorclose

Syntax: monitorclose
Closes the monitor file. If you leave the monitors intact, a new file will be created after reading the next image. Disable the monitors with monitorinit.

monitorfile

Syntax: monitorfile filename
Default:monitorfile monitor.lis
Sets the name of the monitorfile. Use monitor to define pixels to be monitored.

monitorinit

Syntax: monitorinit
Sets the number of monitors to zero.

Syntax: next
Reads next image and apply manipulation (ADD,SUB...)

nodark

Syntax: nodark
Disable dark image subtraction. Enable subtration with the dark command.

norm

Syntax: norm
Normalise map after processing N images

If sigma is active: divide by (N-1) and take the squareroot,
If covar is active: divide by (N-1)
Otherwise: divide by N

See also scale, rescale and posrescale for different scaling procedures.

output

Syntax: output none/normal/full/debug
Syntax: output normal
Controls the amount of output while reading images.

poisson

Syntax: poisson
A file poisson.lis is created. For each image file read, a line is written to this file containing:sum1 sum2 sum3.
sum1 = sum of all pixels.
sum2 = sum of the central 11*11 pixels.
sum3 = sum of central 301*301 box pixels.
A second call to poisson will close the file. The pixel coordinates of the used centre can be changed with cc. Specify the filename with with poissonfile.
The file will be closed if you invoke poisson a second time.

poissonfile

Syntax: poissonfile filename
Default:poissonfile poisson.lis
Sets the name of the poissonfile. Use poisson to start/stop writing data to this file.

posrescale

Syntax: posrescale n
Default: posrescale 25000
Scale all values between 0 and n. See also scale, rescale and norm for different scaling procedures.

read

Syntax: read filename(s)
Read filename(s) and apply manipulation (ADD,SUB...) Wildcharacters are allowed.

rescale

Syntax: rescale n
Default: rescale 25000
Scale all values between -n and +n. See also scale, posrescale and norm for different scaling procedures.

restore

Syntax: restore
Restore the values from a previous save. The current values are lost.

right

Syntax: right
Add the right part of the new image to the current image

rotoffset

Syntax: rotoffset a
Change the rotstart and rotend value in the imageheader. The value of a will be added to the current rotstart and rotend values. This offset is only used when you write a new image.
(See also fix).

save

Syntax: save
Save the current results into a different array. You may use these saved values with the commands restore and addsave. The saved data are implicitly used by sigma and covar.

scale

Syntax: scale f
Default: scale 1.0
Set scale factor to f. This scale factor is applied to each image when it is read. See also rescale, posrescale and norm for different scaling procedures.

setcolumn

Syntax: setcolumn x v
Sets the values of the pixels in column x to v.

setrow

Syntax: setrow y v
Sets the values of the pixels in row y to v.

sigfac

Syntax: sigfac f
Default: sigfac 3.0
In the dezinger procedure a difference is compared with the sigma of a value. A difference will be too large if it is greater than f*sigma.

sigma

Syntax: sigma

map_i,j = (new_i,j-save_i,j)²

You should store the mean image with save. The whole procedure is:

add                  (start adding)
read all images      (add all the images)
norm                 (divide sumvalues by nImages)
save                 (store it)
clear                (fresh start)
sigma                (start determining sigma)
read all images      (add squares of differences)
norm                 (divide by (nImages-1) and take square root)

status

Syntax: status
Show information

sub

Syntax: sub

map_i,j = map_i,j - scale*new_i,j

Sets also NFILES to NFILES - 1 See subbg for the use of NFILES

subbg

Syntax: subbg

map_i,j = map_i,j - scale*new_i,j

Sets also NFILES to NFILES - 1. The program will continue to read maps until NFILES=0 See also addsave for a different approach.
Example
You have created 5 background files (d1.dark, d2.dark ... d5.dark) and 12 data files (d01.kcd, d02.kcd, .... d12.kcd) To add up all data files and subtract the same number of background files use the command sequence:

add d*.kcd subbg d*.dark rescale write kcd output.kcd

A different approach is:

clear sub d*.dark save clear add d*.kcd addsave write kcd output.kcd

Here the dark images are accumulated in SAVE. After reading the kcd images, the command addsave will add the save array with a correction for the (different) exposure times.

unfix

Syntax: unfix lambda/rot/target
Disable the effects of the fix command.

wait

Syntax: wait filename
Wait for filename, read the images file and apply manipulation (ADD,SUB...).

write

Syntax: write format name
format is one of cnt, list, pgm or the current image format (which is the default).
name is the new filename. Default is the concatenation of sum and the last (wildcharactered) filename read.
The following formats can be written:

cnt
Syntax: write cnt filename
Contour file

Record1: Nx,Ny,title
Record2: (float(map(1,j)),j=1,nx)
Record3: (float(map(2,j)),j=1,nx)
etc....

.....
Syntax: write . filename
Writes according the the current input format. If the absolute value of the minimum or the maximum is greater than rescale (default=25000) the image is rescaled before writing to disk. See posrescale to limit the result to 0-RESCALE.
list
Syntax: write list filename
A Runtime format is constructed. File is ASCII.

pgm
Syntax: write pgm filename
Use rescale first.

Format = i3 (hexadecimal) 26 items on one row
Line  1: P2
Line  2: 512 512
line  3: 99
line  4: (map(j,0), j=  0, 25)
line  5: (map(j,0), j= 26, 51)
etc

zero

Syntax: zero

if map_i,j < 0 then map_i,j = 0

zinger

Syntax: zinger n
Sets dezinger option while reading an image.

n	description
0	use dezingered value.
-1	use mean value
-2	use minimum value
n	use frame number n

Input/Output files

Input Files

imagesum.init
images

Output files

written images

EVPY Suite Overview