All data are stored internally as 32 bits signed integer, this choice has been done in order to reach a good dynamic without losing the counting accuracy. When the image are read they are corrected from dark current (if a dark image has been set) and from flatfield (if set). Then various operation can be done on the 32 bits image. When writing an output file, the dynamic is only modified on the resulting file not on the inernel image. If you rescale the image, remember that integer operations are order dependent.
A reduced view of a SAXS image can be seen below. In the central part it shows a small angle scattering image using 2*2 binning. To show the influence of the correction on 8 bit .gif images, intensities higher than 3 times the image average have been truncated; this occurs near the beamstop and/or on cosmic rays. When an images has been stored in edf format, it is alaways assumed that this image is made by only one frame, then it is mandatory to use the U parameter to correct this if the dark file contains more than one frame.
The following images show the transformation of the data. In the central
part they show a small angle scattering image using the same binning as
for the above flatfield. To display the influence of the flatfield correction
on 8 bit .gif images, intensities higher than 3 times the image mean have
been truncated : this occurs near the beamstop and/or on cosmic ray spots,
that have not be fully cleaned.
bm2img D=dark F=flat.edf,X dani10 %X
| dark corrected | dark and flatfield corected |
| bm2img D=dark dani10 %X | bm2img D=dark F=flat.edf,X dani10 %X |
|
|
|
| command | %X | %Y | %Z |
| dynamic | 32 bits | 16 bits | 8 bits |
| default | name.edf | name.edf | name.edf |
| .edf | name.edf | name.edf | name.edf |
| .gel | name.gel | name.gel | name.gel |
| .tif | name.tif | name.tif | name.tif |
| .txt | name.txt | ||
The txt output can be used to extract some binded rows or columns of the images, it does not depend on the selected dynamic. Obviously trying to output a full image using this mode may produces some disk full error!!!
STDIN=inputfile in the bm2img.ini
file and fill this file with all the order you need. Do not forget
to clean the memory (%F) between each image to process
or they will be added together.
The following lines show an example of inputfile.
D=v2zr51.edf,U5,X img39 %X %R %F img40 %X %R %F img41 ...
bm2img -h will display its principal key words.
....
## bm2img : extracting info/preprocessing image
## bm2img_1.3 (20Jun02_0750)
## berar@esrf.fr (d2am), Jul 23 2002
usage : bm2img [D=|F=]img_file[,Bb,Ee,X,Aa|Mm,Uu] [img...] [%M=val] [%[X] [img...]]
example D=dark3,B2,A5 add frame starting at 2 in dark_files dark3 to dark8, U force used frames to u
D=dark_file to substract, F=flatfield_file (must be defined before image
Begin at frame b, End at frame e, X don't correct
Add a files with increasing number (or Merge them, DMI specific)
Inside the program the image are kept as integer with 32 bits
%M=val (%A=val) multiply current image by val (or add to) before reading next arguments
val can be expressed as %M=1.0e6/SPEC (call wspec2xl.pl ... to get real value)
%C=vah[,val] cut counts higher (lower) than vah*mean before reading next arguments
%S=val rescalling dynamics to val
%X[[name].edf|.gel|.tif|.txt] produce outfile (edf default with 32bits)
%Y[[name].edf|.gel|.tif|.txt] produce 16bits outfile (gel default) rescalling the output if mandatory
%Z[[name].edf|.gel|.tif|.txt] produce 8bits outfile (tif default) rescalling the output if mandatory
%R produce radial distribution file (.rad), one angular sector is the default
%P[=m[,o],v]]] produce peak list file (.pks), m=5 peaks is the default, omega osc if not 0, sum>v*max, v=1.5
%H produce an ascii map (h, k, l) of the file using the UB matrix
%F clean current image (but keeps dark and flat)
%G apply grid correction as defined by GRID_DCOR, GRID_XCOR, GRID_YCOR in ini file (see bm2grid)
%T="rule" transform according rule
a specific statistic routine is called when the program name contains the string 'stat'
previous keys are not valid in this case
see also prameters in bm2img.ini file
valid options in .ini files are :
Items used in the .ini file
X_MIN =
Y_MIN =
X_MAX =
Y_MAX =
X_BIND =
Y_BIND =
BEG_FRAME =
END_FRAME =
MULT =
P_EXCLUDED = x1 y1 [v] [QUIET]
C_EXCLUDED = x1 y1 r [v] [QUIET]
R_EXCLUDED = x1 y1 x2 y2 [v] [QUIET]
T_EXCLUDED = x1 y1 x2 y2 x3 y3 [v] [QUIET]
C_ROI = x1 y1 r [v] [QUIET]
R_ROI = x1 y1 x2 y2 [v] [QUIET]
DIR = full path to search for data file
OUT = full path for result (.res) file
DEF = default file extension :'.gel' or 'gel' (if not default according prg_name : spe2img, edf2img, gel2img)
CR = 0, set to 1 if you wish cr in rad file
DFORMAT = size of ineger field in output name, default same as entry
STDIN = full path for redirecting stdin
SPEC = full path to spec file for collecting info
WSPEC2XL = script (and args) to extract normation, use * for file name
XL_COL = pos of the selected column in WSPEC2XL
FLAT_NAME = full path of the flatfield file to use
DARK_NAME = full path of the dark file to use
SCA_DARK = scale factor to apply on dark
ADD_DARK = offset to add to dark curent
O_COSMIC = file_name, STDOUT or default to image_name.cosmic
T_COSMIC = used for time removal
S_COSMIC = used for space removal
R_COSMIC = ratio on the standard deviation used for time and space removal
H_COSMIC = lower cosmics on one frame for time removal
P_COSMIC = lower cosmics on the frame sum for spacial removal
SET_LIMIT = remove values lower than LOW_LIMIT if not zero
LOW_LIMIT = values are replaced mean of surrounding values (SET_LIMIT=1), by LOW_LIMIT (SET_LIMIT=2)
ADD_DARK = offset to add to dark curent
REALTIME = 0 or waiting time in secs to ensure data completion
PRINT = ... +64 cosmics, +128 cor, +256 sum, +512 raw
T_DATA = output mode (float...) for edf file
ORIG = pixel_x(=0) pixel_y(=0) center of detector
MAT_UB = values according spec
LAMBDA = 1 (if not given)
GONIO = 0.00 th chi phi
DETEC = alpha tth Rx(=1) Ry(=0) Rz(=0)
SCALE = scal_xx(=1) scal_xy(=0) scal_yx(=0) scal_yy(=1) matrix form pixel to detector
ORIG = pixel_x(=0) pixel_y(=0) center of detector
PLANE = a x+ b y+ c z= d e ecart
GRID_AUTO = NONE (default),AUTO apply grid correction
GRID_MODE = NONE (default, surface corrected), FLUX is constant, no surface correction\n");
GRID_DCOR ... see bm2grid
following group only concerns radial distribution
RADIUS = radius binning
RAD_LIM = low limit value in radial distribution (not set is no limit)
N_SECTOR = number of angular sectors (num 0 to N_SECTOR-1)
A_SECTOR = origin (degree) of the first sector
P_SECTOR = if not empty, binning specifications without space
RAD_X = if not empty, X geometrical transformation, RAD_Y
RAD_DX = if not empty, X geometrical density related to RAD_X, RAD_DY
radial distribution example, N=8,A=-22.5,P=0+4,2+6,1+3+5+7 print 3 curves
Then the following line can be used in many cases, this line can be included in a shell script for processing a lot of images when processing conditions are defined.
bm2img D=dark F=flat.edf,X dani10 %R
An ascii output file is created with the extension ".rad"
| key | expected | default | |
| ORIG= | x y | CCD center | float values to define the center of the image |
|---|---|---|---|
| N_SECTOR= | n | 1 | number of sectors : angular resolution for anisotropic images
(one sector is obviously isotropic) |
| A_SECTOR= | n | 0 | if anisotropic, angular origin of the first sector
(the origin is the lower side of the sector related to the X axis) |
| P_SECTOR= | string | empty | print statement for binning sectors, see examples below |
| RADIUS= | n | 1 | binding radius parameter |
| RAD_LIM= | f | -Inf | allow to avoid Zero or Negative values in radial distribution
(values below rad_lim are set to rad_lim |
# ./00jan147df.rad (400-900)/1*(400-800)/1 (00jan147df.gel)
# center 545.90 626.80 -> 145.90 226.80, r_max 420.51
# 16 sectors with origine at 0.00 deg
# r s/n e(s/n) n ...
0 0.00 -1.00 0.0 19.75 -1.00 0.1 0.00 -1.00 0.0 0.00 -1.00 0.0 0.00 -1.00 0.0 86.57 -1.00 0.3 0.00 -1.00 0.0 0.00 -1.00 0.0 0.00 -1.00 0.0 0.00 -1.00 0.0 120.00 -1.00 0.5 0.00 -1.00 0.0 0.00 -1.00 0.0 0.00 -1.00 0.0 49.61 -1.00 0.2 0.00 -1.00 0.0
1 47.73 -1.00 0.2 233.25 -1.00 0.9 62.13 -1.00 0.3 0.00 -1.00 0.0 94.52 -1.00 0.4 176.43 -1.00 0.7 142.05 -1.00 0.6 0.00 -1.00 0.0 164.44 -1.00 0.6 0.00 -1.00 0.0 141.03 -1.00 0.6 141.49 -1.00 0.6 0.00 -1.00 0.0 109.12 -1.00 0.4 206.39 -1.00 0.8 64.66 -1.00 0.3
2 243.13 -1.00 1.0 182.34 -1.00 0.7 182.87 -1.00 0.7 85.77 -1.00 0.3 262.33 -1.00 1.0 246.62 -1.00 1.0 157.70 -1.00 0.6 169.46 -1.00 0.6 254.40 -1.00 1.0 80.24 -1.00 0.3 241.18 -1.00 1.2 255.89 -1.00 1.0 140.50 -1.00 0.5 156.90 -1.00 0.6 203.42 -1.00 0.8 261.12 -1.00 1.0
3 253.68 -1.00 1.0 268.60 -1.00 1.4 231.71 -1.00 0.9 277.05 -1.00 1.0 271.35 -1.00 1.2 255.20 -1.00 1.5 246.90 -1.00 1.1 254.32 -1.00 1.0 260.36 -1.00 1.0 259.13 -1.00 1.1 258.15 -1.00 1.4 273.01 -1.00 1.4 282.03 -1.00 1.0 260.58 -1.00 1.1 267.47 -1.00 1.5 277.58 -1.00 1.1
4 279.85 -1.00 1.0 280.01 4.29 2.3 293.07 -1.00 1.6 281.30 -1.00 1.1 265.20 4.30 2.1 249.44 -1.00 1.3 257.70 -1.00 1.5 244.29 -1.00 1.4 255.63 -1.00 1.5 254.01 -1.00 1.6 270.05 -1.00 1.5 276.85 9.92 2.1 281.49 -1.00 1.3 294.67 -1.00 1.5 286.19 -1.00 1.2 271.42 5.35 2.1
5 289.64 5.37 2.1 304.81 16.00 2.1 300.79 -1.00 1.3 302.34 13.46 2.1 287.04 27.20 2.0 267.82 17.94 2.4 251.79 -1.00 1.7 268.03 18.86 2.1 242.62 20.99 2.0 259.82 -1.00 1.7 279.27 11.21 2.4 288.04 20.69 2.0 301.69 22.29 2.1 318.00 -1.00 1.4 288.49 6.81 2.3 274.35 9.72 2.0
6 297.29 13.17 2.0 315.34 9.24 2.9 333.89 10.67 2.3 336.10 24.43 2.0 329.26 13.30 3.0 294.24 20.22 2.0 249.00 1.66 2.1 260.46 15.27 2.2 252.05 14.14 2.3 263.75 14.57 2.1 284.13 11.89 3.0 314.98 5.94 2.2 355.74 36.16 2.0 338.35 20.64 2.4 320.42 13.93 2.8 295.34 36.50 2.0
7 333.05 26.76 2.8 331.37 31.35 2.7 372.27 27.82 2.1 378.13 14.81 2.9 352.68 8.67 3.1 325.46 23.81 2.8 257.67 8.26 2.3 258.64 10.90 3.1 257.92 7.65 3.1 294.31 15.25 2.3 316.24 15.00 2.9 363.37 34.69 3.1 401.71 28.77 2.2 390.97 31.50 3.0 356.85 36.73 2.7 362.83 24.98 2.9
in which
| r | stand for the radius of the ring |
|---|---|
| s | is the sector number |
| s/n | is the counting per pixel |
| e(s/n) | is the standard deviation on the counting |
| n | is the pixel number taken in account in the ring |
# ./00jan147df.rad (400-900)/1*(400-800)/1 (00jan147df.gel)
# center 545.90 626.80 -> 145.90 226.80, r_max 420.51
# 16 sectors with origine at 0.00 deg
# print sectors binned according : '0+8,4+12'
# 4 used sectors (of 16) are binned in 2 group : 0 ( 0 8) , 1 ( 4 12)
# r s/n e(s/n) n ...
0 0.00 -1.00 0.0 0.00 -1.00 0.0
1 212.17 -1.00 0.8 94.52 -1.00 0.4
2 248.74 5.80 2.1 268.51 -1.00 1.5
3 257.01 9.49 2.0 276.33 6.17 2.2
4 265.64 13.20 2.5 271.52 7.71 3.3
5 266.17 16.05 4.1 294.42 15.03 4.1
6 273.35 14.83 4.3 340.04 15.23 5.0
SPEC=/mat_dsk4/visit/xx...xx/fourc.26Oct01 WSPEC2XL=wspec2xl.pl -M XL_COL=5the command bm2img alpdre33.edf %M=1e7/SPEC does...
# command : %M=1e7/SPEC spec2xl 1e7/SPEC running wspec2xl.pl -Malpdre33 /mat_dsk2/lcontact/berar/Spec/fourc.26Oct01 >bm2img.SPEC using 1e+07/1.404e+07=0.712 as coefficient # alpdre33.edf : 1 frame(s), mean 16742.1 sigma 60758.2 [0@0*0 - 466609@13*58] 5220!=0It is obvious that if you wish to keep some statistical meaning, the efficient coeffficient must be of some order of magnitude (100 by example) as data are integers inside bm2img. If you wish to avoid scanning the specfile at each image, you can process like the following:
wspec2xl.pl -malpdre /mat_dsk2/lcontact/berar/Spec/fourc.26Oct01 >summary.file
SPEC=summary.file WSPEC2XL=grep " * " XL_COL=5
# command : %M=1e7/SPEC spec2xl 1e7/SPEC running grep " alpdre33 " summary.file >bm2img.SPEC using 1e+07/1.404e+07=0.712 as coefficient # alpdre33.edf : 1 frame(s), mean 16742.1 sigma 60758.2 [0@0*0 - 466609@13*58] 5220!=0