Dear Crystallographers,
I've been trying to view diffraction images in ImageJ. I can read the images through a raw import, but the parameters seem a little off. ImageJ asks for the following parameters (I just list the questionable ones):
-Image type (8-bit, 32-bit signed, etc.)
-Width,Height (seems to be, from the header, 1042 x 1042, but this gives four images in one; 521 x 521 gives one image, but which is truncated halfway down)
-Offset to first image (bytes) (seems to be 3584 from the header, but looks like wrong offset.)
The header of the images in question is pasted below.
Can anyone point to what is going on here? Is this impossibly complicated, or is there an easy way to do this, like I am just missing something? I've played around a bit, but cannot get it right.
Would it be so horrible, btw, to use tif or some other easy universal format? I think at least some of these formats can accommodate metadata...
All the best,
Jacob Keller
{
HEADER_BYTES= 3584;
BYTE_ORDER=little_endian;
BitmapSize=4274;
BitmapType=BitmapRLE;
CCD_DETECTOR_DESCRIPTION=Saturn944+ (2x2 bin mode);
CCD_DETECTOR_DIMENSIONS=1042 1042;
CCD_DETECTOR_IDENTIFICATION=MSC_REIT_Saturn944+_SN012110304;
CCD_DETECTOR_OPTIONS=imagekind:2 dezingermode:off dezingertype:average subtractclosed:on transform:on simulator:immediate trigger:on;
CCD_DETECTOR_SERVER_VERSION=MSCServCCDCamera 7.6.2.4;
CCD_DETECTOR_SIZE=93.7800 93.7800;
CCD_DETECTOR_TEMPERATURE=-45.0 deg C;
CCD_DETECTOR_VECTORS=1 0 0 0 1 0;
CCD_FIELD_OF_VIEW=Square;
CCD_GONIO_COLLISION_OFFSET=0.0 0 0.0 0.0 0.0 0;
CCD_GONIO_DESCRIPTION=AFC11 (Right): 2theta arm;
CCD_GONIO_NAMES=RotAboutBeam 2Theta RotY XShift YShift Distance;
CCD_GONIO_NUM_VALUES=6;
CCD_GONIO_UNITS=deg deg deg mm mm mm;
CCD_GONIO_VALUES=0.0000 0.0000 0.0000 0.0000 0.0000 45.0000;
CCD_GONIO_VALUES_MAX=0.0 5 0.0 0.0 0.0 300.9;
CCD_GONIO_VALUES_MIN=0.0 -110 0.0 0.0 0.0 40;
CCD_GONIO_VECTORS=0.0000 0.0000 1.0000 1.0000 0.0000 0.0000 0.0000 1.0000 0.0000 1.0000 0.0000 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 -1.0000;
CCD_NONUNF_INFO=FirstScanImage;
CCD_NONUNF_TYPE=Simple_mask;
CCD_SERIAL_NUMBER=12110304;
CCD_SPATIAL_BEAM_POSITION=508.0750 522.2700;
CCD_SPATIAL_DISTORTION_INFO=508.0750 522.2700 0.0900 0.0900;
CCD_SPATIAL_DISTORTION_TYPE=Simple_spatial;
CCD_SPATIAL_DISTORTION_VECTORS=0 -1 1 0;
CCD_TAPER_ORIENTATION=+x+y;
CCD_UNBINNED_BEAM_POSITION=1016.1500 1044.5400;
CCD_UNBINNED_DIMENSIONS=2084 2084;
CCD_VACUUM_PRESSURE=CCD: 2.67 Phosphor: 27.48;
COLLISION_INFO=C:/Rigaku/MSCServDetCCD/Collision.xml;
COMPRESSION=None;
CRYSTAL_GONIO_COLLISION_OFFSET=0 0 0;
CRYSTAL_GONIO_DESCRIPTION=AFC11 (Right): Eulerian 3 circle;
CRYSTAL_GONIO_NAMES=Omega Chi Phi;
CRYSTAL_GONIO_NUM_VALUES=3;
CRYSTAL_GONIO_SCAN_AXES=Omega Phi ;
CRYSTAL_GONIO_SERVER_VERSION=MSCServDetCCD 5.5.2.7;
CRYSTAL_GONIO_UNITS=deg deg deg;
CRYSTAL_GONIO_VALUES=0.0000 0.0000 0.0000;
CRYSTAL_GONIO_VALUES_MAX=100 60 3600;
CRYSTAL_GONIO_VALUES_MIN=-200 0 -3600;
CRYSTAL_GONIO_VECTORS=1.0000 0.0000 0.0000 0.0000 -1.0000 0.0000 1.0000 0.0000 0.0000;
DARK_PEDESTAL=20;
DETECTOR_NAMES=CCD_;
DETECTOR_NUMBER=1;
DIM=2;
DTDISPLAY_ORIENTATION=+X+Y;
DTINTEGRATE_OBLIQUE=0;
DTREK_DATE_TIME=26-Jan-2015 20:49:06;
DTREK_MODULE=d*TREK;
DTREK_VERSION=d*TREK version 9.9.9.4 W9RSSI -- Mar 27 2012;
Data_type=unsigned short int;
FILENAME=hex_lozAinv_1_0006.img;
HEADER_VERSION=1.2;
RAXIS_COMPRESSION_RATIO=128;
ROTATION=-89.500 -89.400 0.100 5.000 0.000 0.000 0.000 100.000 0.000 0.000;
ROTATION_AXIS_NAME=Omega;
ROTATION_LIMITS=0.000 360.000 1000.000;
ROTATION_VECTOR=1.000 0.000 0.000;
SATURATED_VALUE=4194176;
SCAN_CRYS_RELZERO=3.000 0.000 0.000 0.000;
SCAN_DETECTOR_OPTIONS=None;
SCAN_DET_RELZERO=2.000 0.000 45.000;
SCAN_MODE=Scan_Open;
SCAN_ROTATION=-89.500 -89.400 0.100 5.000 0.000 0.000 0.000 100.000 0.000 0.000;
SCAN_ROTATION_AXIS_NAME=Omega;
SCAN_ROTATION_LIMITS=0.000 360.000 1000.000;
SCAN_ROTATION_VECTOR=1.000 0.000 0.000;
SCAN_SEQ_INFO=6 1 1800;
SCAN_TEMPLATE=C:\Rigaku\MSCServDetCCD\hex_lozAinv_1_????.img;
SCAN_WAVELENGTH=1.541800;
SCAN_WAVELENGTH_OPTIONS=0 0;
SIZE1=1042;
SIZE2=1042;
SOURCE_CROSSFIRE=0.0002 0.0002 0.0000 0.0000;
SOURCE_POLARZ=0.5000 1.0000 0.0000 0.0000;
SOURCE_SIZE=0.0000 0.0000 0.0000 0.0000;
SOURCE_SPECTRAL_DISPERSION=0.0002 0.0002;
SOURCE_VALUES=0.0000 0.0000;
SOURCE_VECTORS=0.0000 0.0000 1.0000 0.0000 1.0000 0.0000 1.0000 0.0000 0.0000;
SOURCE_WAVELENGTH=1.0000 1.5418;
}
*******************************************
Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: [log in to unmask]
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