Hi David, thanks for the tip—a good reason to take the plunge into ccp4 7. As for pre-tuning the images, ImageJ actually has a very impressive set of tools for all sorts of image processing, coloring, etc. And PNG is no problem for imagej either.
Jacob
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of David Waterman
Sent: Monday, July 18, 2016 7:30 AM
To: [log in to unmask]
Subject: Re: [ccp4bb] View Images in Non-Crystallographic Software (ImageJ/FIJI)
Hi Jacob,
Another option is to use dials.export_bitmaps, available in CCP4 7.0. If you pass a datablock.json created by dials.import (or taken from a xia2 run) this will create PNG format bitmaps for each of the diffraction images in your dataset. A diffraction experiment movie could then be created by e.g. convert. There are command-line options to dials.export_bitmaps for setting the brightness, colour scheme and so on. You can experiment interactively using the dials.image_viewer to get the images looking how you want first.
Cheers
-- David
On 14 July 2016 at 19:03, Tim Gruene <[log in to unmask]<mailto:[log in to unmask]>> wrote:
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Dear Jacob,
adxv can convert the images it can read into tiff or jpg on the command line.
And adxv can read a wide variety of formats. Would this help your objective?
Cheers,
Tim
On Thursday, July 14, 2016 02:59:51 PM Keller, Jacob 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.
>
> 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]<mailto:[log in to unmask]>
> *******************************************
- --
- --
Paul Scherrer Institut
Tim Gruene
- - persoenlich -
OFLC/102
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297<tel:%2B41%20%280%2956%20310%205297>
GPG Key ID = A46BEE1A
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