Re: [ccp4bb] X-ray diffraction image --> .jpg
Hi Andy, As well as the other alternatives, ADXV can output high resolution graphics files (1:1 if you choose 100% scale) with colouring that matches what you see in the Image window. Go to File -> Save for this function. As you're working with ADSC images you might be used to viewing with ADXV anyway (though it can view other formats too). If you don't have the software away from your favourite beamline, you can download it for various X-windows systems from http://www.scripps.edu/~arvai/adxv.html. Cheers David -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Morten Kjeldgaard Sent: 22 October 2009 10:33 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] X-ray diffraction image --> .jpg On 21/10/2009, at 16.53, Andy Torelli wrote: > Is there a free utility that can convert an x-ray diffraction image > collected with an ADSC detector to a standard image file format e.g. > .jpg, png, etc.? I'm looking for something more elegant than a > screen-capture that will yield a higher (graphics) resolution image. > I'm sure someone must have done this, but I haven't been able to find > one. It's not free, but with Photoshop you can do anything you want with TIFF based diffraction images. To be able to see anything, though, you need to do "Image -> Adjustments -> Equalize", otherwise all you'll see is black. Cheers, Morten -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
Re: [ccp4bb] X-ray diffraction image --> .jpg
On 21/10/2009, at 16.53, Andy Torelli wrote: Is there a free utility that can convert an x-ray diffraction image collected with an ADSC detector to a standard image file format e.g. .jpg, png, etc.? I'm looking for something more elegant than a screen-capture that will yield a higher (graphics) resolution image. I'm sure someone must have done this, but I haven't been able to find one. It's not free, but with Photoshop you can do anything you want with TIFF based diffraction images. To be able to see anything, though, you need to do "Image -> Adjustments -> Equalize", otherwise all you'll see is black. Cheers, Morten
Re: [ccp4bb] X-ray diffraction image --> .jpg
Believe it or not, you can do this with ImageMagick, which is already part of most linux distros: convert -depth 16 -type Grayscale -colorspace GRAY -endian LSB -size 3072x3072+512 \ GRAY:test_0_001.img test_0_001.jpg where this example turns a binned Q315 image (3072x3072 pixels) with a 512-byte header (almost always the case) that has "BYTE_ORDER=little_endian" into a jpg image. For a big_endian image, you change LSB to HSB in the above command. You may notice that the image above compresses incredibly well (about 300 fold), but if you look at it, you will be very disappointed as it is almost totally black. This is because JPEG only uses the high-order byte of a 16-bit image. One could argue that this is perhaps the "right" way to look at diffraction patterns since the most important information is in the bright spots and not the noisy background, but if you want to render your *.img file in the "ADXV way", then this command is close: convert -depth 16 -type Grayscale -colorspace GRAY -endian LSB -size 3072x3072+512 \ GRAY:test_0_001.img -negate -crop 1024x1024+512+512 -equalize test_0_001.jpg The "-negate" flag will make the spots black and the background grey, and the "-equalize" filter will throw out all the "outlier pixels" (spots) so you can look at the background. You may also want to use the "-crop" option to focus in on just one part of the image. There are other "enhancement" flags like -normalize, and -contrast-stretch or -brightness and -contrast, but the exact behavior of these flags will depend on the version of ImageMagick you have. There is probably also a way to "colorize" the data the way ADXV does with the "heat" or "rainbow" options, but I don't know how to do that in ImageMagick. In such cases, I do use screen capture, but again ImageMagick's "import" program is convenient for this. Coupled with the -autoload flag in ADXV, you can set the environment variable $XFORMSTATUSFILE to something like ./temp.txt and write a script to echo "$n $filename" into this file (where $n is an ever-increasing number), wait a few seconds (sleep 2), and then run "import -w root -crop ..." to capture the screen and crop out the part you want. This will work for the formats supported by ADXV, but obviously other formats will need another program. The central problem is that every program (ADXV, MOSFLM, HKL, D*trek, etc.) has different ways of crushing the 16-bit pixels into 8 bits for the display, and we all have our "favorite" (the one that we think makes weak spots show up better), but almost none of the GUI displays have command-line-with-options equivalents. ImageMagick has enough features that you can usually figure out how to "replicate" a given display program's algorithm, but some file formats (like the "packed" Mar files) will never be readable by ImageMagick. It is perhaps worth pointing out that the "ADSC format" is actually called "SMV" since this file format was originally created about 30 years ago for a program called "Super Marty View", (written by Martin Stanton, now at SomaLogic). It has evolved somewhat since then. The taxonomy of image file formats is something of a hobby of mine. There seems to be no less than a hundred different species of them floating around in the world. Some are rare, some are locally prevalent, but they appear to all be highly territorial and you will almost never find more than one varietal populating a given lab, synchrotron or even a given country. Someday I hope to collect specimens of each and every one of them (perhaps even filling out the "fossil record" or history of different beamlines and detectors) but documentation and particularly "example lysozyme datasets" are surprisingly hard to come by. For example, I once had a crinkly old paper document that defined the "R-axis format", but recent sitings of files from R-axis detectors seem to be a new species descended from an SMV-like ancestor, and yet nowhere on the Rigaku website is there a document describing this new format, much less an example. Most crystallographers do not have "good" data sets on hand (it is the bad ones that stay on disk forever), and many beamline scientists do not have any "test" data sets available either (for some reason). Currently, my meager "museum" is here: http://bl831.als.lbl.gov/example_data_sets/ If anyone would care to donate, I prefer data sets that are "easy" to process and that have anomalous differences (to clarify the hand of the spindle), but in cases where I have no examples, any data set will do. -James Holton MAD Scientist Andy Torelli wrote: Hi everyone, Is there a free utility that can convert an x-ray diffraction image collected with an ADSC detector to a standard image file format e.g. .jpg, png, etc.? I'm looking for something more elegant than a screen-capture that will yield a higher (graphics) resolution image. I'm sure someone must have done thi
Re: [ccp4bb] X-ray diffraction image --> .jpg
Andy, Why not try labelit.png [-large]? Labelit is availale at http://cci.lbl.gov/labelit Nick Sauter On 10/21/2009 7:53 AM, Andy Torelli wrote: Hi everyone, Is there a free utility that can convert an x-ray diffraction image collected with an ADSC detector to a standard image file format e.g. .jpg, png, etc.? I'm looking for something more elegant than a screen-capture that will yield a higher (graphics) resolution image. I'm sure someone must have done this, but I haven't been able to find one. Thanks, Andy Torelli
Re: [ccp4bb] X-ray diffraction image --> .jpg
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). A demo version of d*TREK is freely available. It contains dtdisplay which can display most known diffraction image formats (including Rigaku and ADSC) and allow you to get what you want to see. Then you can use a screen capture. I guess that one should have an option to output a TIFF or JPEG in full-resolution of the detector for use with pixel peeping photo programs like Photoshop. There has not been much demand for such a program, but maybe times have changed. Jim -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Andy Torelli Sent: Wednesday, October 21, 2009 9:53 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] X-ray diffraction image --> .jpg Hi everyone, Is there a free utility that can convert an x-ray diffraction image collected with an ADSC detector to a standard image file format e.g. .jpg, png, etc.? I'm looking for something more elegant than a screen-capture that will yield a higher (graphics) resolution image. I'm sure someone must have done this, but I haven't been able to find one. Thanks, Andy Torelli
Re: [ccp4bb] X-ray diffraction image --> .jpg
Try MarView: http://www.marresearch.com/download.html#Utilities I use the Linux_glibc-2.3.3 (RedHat9, WS3, etc). Just download it, unpack (gunzip marView.gz) # chmod a+x marView a) to run the program from terminal # ./marView or # kate .bashrc: alias marview=/home/user/Desktop/marview/./marView b) alternativelly, place the program in the Desktop and just double-click to start it up. Mauricio On Wed, Oct 21, 2009 at 12:53 PM, Andy Torelli wrote: > Hi everyone, > > Is there a free utility that can convert an x-ray diffraction image > collected with an ADSC detector to a standard image file format e.g. .jpg, > png, etc.? I'm looking for something more elegant than a screen-capture > that will yield a higher (graphics) resolution image. I'm sure someone must > have done this, but I haven't been able to find one. > > > Thanks, > Andy Torelli >
Re: [ccp4bb] X-ray diffraction image --> .jpg
Hi Mosflm has done this for years - there's a recipe on the Mosflm FAQ pages (well, the questions were asked frequently when I originally wrote them about 7 or 8 year ago!). Someone called Graeme Winter (now at Diamond) wrote this code originally...) On 21 Oct 2009, at 15:53, Andy Torelli wrote: Hi everyone, Is there a free utility that can convert an x-ray diffraction image collected with an ADSC detector to a standard image file format e.g. .jpg, png, etc.? I'm looking for something more elegant than a screen-capture that will yield a higher (graphics) resolution image. I'm sure someone must have done this, but I haven't been able to find one. Thanks, Andy Torelli Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] X-ray diffraction image --> .jpg
Hi Andy, If you have a recent CCP4 installation (i.e. 6.something I think) there's diff2jpeg, which does exactly what you want. Otherwise there are also spells to use Mosflm for this which allows a little more control over the greyscale settings. Cheers, Graeme 2009/10/21 Andy Torelli : > Hi everyone, > > Is there a free utility that can convert an x-ray diffraction image > collected with an ADSC detector to a standard image file format e.g. .jpg, > png, etc.? I'm looking for something more elegant than a screen-capture > that will yield a higher (graphics) resolution image. I'm sure someone must > have done this, but I haven't been able to find one. > > > Thanks, > Andy Torelli >
