Programs to convert X-ray diffraction image file formats to graphics file formats: Difference between revisions
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=== Considerations and programs to convert X-ray diffraction images into a graphics file format === | |||
<nowiki> The following information was compiled from a series of responses to a post on the CCP4bb on October 21, 2009 by Andrew Torelli who asked about free utilities/programs that could convert X-ray diffraction image file formats to a graphics file format that could be edited by programs such as Photoshop. The specific responses are worthwhile to read and can be searched in the CCP4bb archives using the subject query "X-ray diffraction image --> .jpg". The summary is below: | <nowiki> The following information was compiled from a series of responses to a post on the CCP4bb on October 21, 2009 by Andrew Torelli who asked about free utilities/programs that could convert X-ray diffraction image file formats to a graphics file format that could be edited by programs such as Photoshop. The specific responses are worthwhile to read and can be searched in the CCP4bb archives using the subject query "X-ray diffraction image --> .jpg". The summary is below: | ||
</nowiki> | </nowiki> | ||
<nowiki> A notable consideration (provided by Jim Pflugrath) is that "A JPEG has fixed colors for the pixel values. A diffraction image has to use a viewer to convert the pixel values (counts) to a color. One problem with just using a converter to jpeg is how to convert intensities to color (i.e. computer display values)." | |||
</nowiki> | |||
<nowiki> Additionally, Morten Kjeldgaard noted that opening saved images (particularly TIFF images) in Photoshop will require "Image -> Adjustments -> Equalize" to see anything other than black. | |||
</nowiki> | |||
Specific program suggestions: | Specific program suggestions: | ||
* [http://legacy.ccp4.ac.uk/html/DiffractionImage.html diff2jpeg] - a CCP4 utility within the "DiffractionImage" library for handling different diffraction file formats. | |||
* [http://www.ysbl.york.ac.uk/~cowtan/ccp4wiki/wiki25.html idiffdisp] - a CCP4 utility. | |||
* [http://legacy.ccp4.ac.uk/dist/html/ipdisp.html. ipdisp] - a CCP4 utility. | |||
* [http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ Mosflm] has capability including control over grayscale. See FAQ section for details. | |||
* [http://www.scripps.edu/~arvai/adxv.html ADXV] - reportedly easy to install and can save in TIFF format. Also will save image to match coloring in view window. | |||
b) | * [http://www.marresearch.com/download.html#Utilities Marview] - can be installed using Linux_glibc-2.3.3 (RedHat9, WS3, etc). Just download it, unpack (gunzip marView.gz). | ||
first: chmod a+x marView | |||
a) to run the program from terminal: | |||
./marView | |||
or make an alias (.bashrc): alias marview=/home/user/Desktop/marview/./marView | |||
b) alternatively, place the program in the Desktop and just double-click to start it up. | |||
* demo version of [http://www.rigaku.com/downloads/software/index.html#free|''d*TREK''] is freely available from Rigaku and has dtdisplay for this purpose. | |||
* [http://cci.lbl.gov/labelit Labelit] | |||
- labelit.png <filename> <output.png> [-large] | - labelit.png <filename> <output.png> [-large] | ||
* [http://www.imagemagick.org/script/index.php ImageMagick] - part of most linux distros. See also [https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0910&L=CCP4BB&D=0&X=2FA4086DA38435B93C&Y=att29%40cornell.edu&P=196309|''James Holton's helpful and detailed reply''] made to the CCP4bb on October 21, 2009 to the original post. | |||
- convert -depth 16 -type Grayscale -colorspace GRAY -endian LSB -size 3072x3072+512 GRAY:test_0_001.img test_0_001.jpg | - convert -depth 16 -type Grayscale -colorspace GRAY -endian LSB -size 3072x3072+512 GRAY:test_0_001.img test_0_001.jpg | ||
Latest revision as of 12:54, 30 April 2021
Considerations and programs to convert X-ray diffraction images into a graphics file format[edit | edit source]
The following information was compiled from a series of responses to a post on the CCP4bb on October 21, 2009 by Andrew Torelli who asked about free utilities/programs that could convert X-ray diffraction image file formats to a graphics file format that could be edited by programs such as Photoshop. The specific responses are worthwhile to read and can be searched in the CCP4bb archives using the subject query "X-ray diffraction image --> .jpg". The summary is below:
A notable consideration (provided by Jim Pflugrath) is that "A JPEG has fixed colors for the pixel values. A diffraction image has to use a viewer to convert the pixel values (counts) to a color. One problem with just using a converter to jpeg is how to convert intensities to color (i.e. computer display values)."
Additionally, Morten Kjeldgaard noted that opening saved images (particularly TIFF images) in Photoshop will require "Image -> Adjustments -> Equalize" to see anything other than black. Specific program suggestions:
- diff2jpeg - a CCP4 utility within the "DiffractionImage" library for handling different diffraction file formats.
- idiffdisp - a CCP4 utility.
- ipdisp - a CCP4 utility.
- Mosflm has capability including control over grayscale. See FAQ section for details.
- ADXV - reportedly easy to install and can save in TIFF format. Also will save image to match coloring in view window.
- Marview - can be installed using Linux_glibc-2.3.3 (RedHat9, WS3, etc). Just download it, unpack (gunzip marView.gz).
first: chmod a+x marView
a) to run the program from terminal:
./marView
or make an alias (.bashrc): alias marview=/home/user/Desktop/marview/./marView
b) alternatively, place the program in the Desktop and just double-click to start it up.
- demo version of d*TREK is freely available from Rigaku and has dtdisplay for this purpose.
- labelit.png <filename> <output.png> [-large]
- ImageMagick - part of most linux distros. See also James Holton's helpful and detailed reply made to the CCP4bb on October 21, 2009 to the original post.
- convert -depth 16 -type Grayscale -colorspace GRAY -endian LSB -size 3072x3072+512 GRAY:test_0_001.img test_0_001.jpg