Okay, that is a major improvement--thanks very much! Apparently, however, it seems that that images have different offsets or some other non-uniformity from time to time, making the animation have periodic glitches (sudden reversible sideways shifts).
JPK
-----Original Message-----
From: Hattne, Johan
Sent: Thursday, July 14, 2016 12:05 PM
To: Keller, Jacob
Cc: [log in to unmask]
Subject: Re: [ccp4bb] View Images in Non-Crystallographic Software (ImageJ/FIJI)
> On Jul 14, 2016, at 10:59, Keller, Jacob <[log in to unmask]> wrote:
>
> 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.
The image type should be “16-bit Unsigned”; the Data_type item in the header indicates that this is the case and according to http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/SMV_file_format this is the data type used by all known SMV images. I would think that this explains the duplication you see. You may also need to check the “Little-endian byte order” (see the BYTE_ORDER item in the header).
> 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…
You’re right: TIFF is used by some manufacturers, and the format can accommodate metadata in different forms. However, the way the metadata is encoded in the file appears to differ from manufacturer to manufacturer, and I would think general-purposes software like ImageJ might not have the resources nor the interest to keep up with all possible variations. If you just want to look at the image and don’t care what the resolution of the pixels under your cursor is, this does not matter.
// Cheers; Johan
> 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]
> *******************************************
Research Specialist @ Gonen Lab ____________________________________________________
Janelia Research Campus * 19700 Helix Drive Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376
