Package: x2goclient Version: 4.0.1.4
My users have an application[1] that when run under x2go inverts the image it is displaying. There is a comparative screen shot e2boxer-inverted.png at https://drive.google.com/folderview?id=0B-6ks0UHchgjTUpxSkRwd1FLa2s&usp=sharing
The window on the left is through x2go and on the right is native. (I've added the red boxes and text to clarify what appears to be random splodges.)
We've reproduced this discrepancy on Scientific Linux 6.7, MacOS 10.6 and MacOS 10.9. When run natively, the image is displayed correctly.
x2goserver is version 4.0.1.19 running on Scientific Linux 6.7
[1] EMAN2 from http://ncmi.bcm.tmc.edu/ncmi/software/software_details?selected_software=cou...
The downloadable EMAN2 gzip file contains all the software required to run e2boxer.py - the program that exhibits this problem, no build or config is necessary. The sample input file Falcon_2016_02_02-09_10_45_cor.mrc is at the same link as the screen shot. Once EMAN2 is unpacked run:
#-- 8< --#
#!/bin/bash
EMAN2DIR=<inst_dir>/EMAN2
export EMAN2DIR export PATH=$EMAN2DIR/bin:$PATH export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$EMAN2DIR/lib export PYTHONPATH=$PYTHONPATH:$EMAN2DIR/lib
echo "******************" which e2boxer.py echo "******************"
e2boxer.py Falcon_2016_02_02-09_10_45_cor.mrc
#-- 8< --#
Many thanks for the awesome work you do keeping this software going!
Cheers Toby
Toby Darling, Scientific Computing (2N249) MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge CB2 0QH Phone 01223 267070
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Am 09.02.2016 um 17:47 schrieb Toby Darling:
Toby Darling, Scientific Computing (2N249) MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus
Toby,
are you aware that X2Go has several compression settings for images, and some of them are "lossy", i.e. they may show artifacts where in reality there is nothing, or show nothing where in reality there is a minuscule spot?
If you're using images displayed through X2Go for clinical purposes (deciding whether a certain patient requires a surgery etc.), you should absolutely make sure that you're using a lossless compression or no compression at all, or else you might be seeing things that aren't actually there, or missing things that are there. (This isn't specific to X2Go - it's something to keep in mind with all remote desktop/remote application solutions.)
For your actual bug report, it would be helpful to know if the "flipped image" (it's not color-inverted, it's mirrored along the X axis) issue only occurs with one, or with all available algorithms.
<shameless plug> X2Go also has a commercial side, where various companies - including my own - offer support contracts with guaranteed response times as well as consultancy and paid-for development work if someone wants to see a bug fixed or a new feature added in a certain time frame.
What makes my company special is, IMHO:
- I'm the current X2Go Project/Community Coordinator, so the development lead and the developers tend to listen to me.
- As far as I know, we are the only company providing X2Go support that isn't a one-man-show.
- We sub-contract other developers from the X2Go community on demand, so you only have one person you need to talk to - me - and you will only receive one invoice, even if the task involved several freelance or part-time X2Go developers.
Our hourly rate for consultancy work and fixing issues outside of a support contract is 110 EUR. With a support contract, you get guaranteed response times (starting at 400 EUR/month for 24h response time during business hours in the CET/CEST time zone from Monday to Friday, German holidays excluded) and lower hourly rates if you buy a certain amount of hours in advance. </shameless plug>
Kind Regards, Stefan
BAUR-ITCS UG (haftungsbeschränkt) Geschäftsführer: Stefan Baur Eichenäckerweg 10, 89081 Ulm | Registergericht Ulm, HRB 724364 Fon/Fax 0731 40 34 66-36/-35 | USt-IdNr.: DE268653243 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2
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Hi Stefan
Many thanks for your reply.
If you're using images displayed through X2Go for clinical purposes
No worries on that score, it's just [not so] simple biology.
For your actual bug report, it would be helpful to know if the "flipped image" (it's not color-inverted, it's mirrored along the X axis) issue only occurs with one, or with all available algorithms.
You are correct that the image inversion is is along the x-axis. The colour/shading is correct.
I've not been able to fix the inversion having tried with 16m, 16m-png, 16m-rdp, 16m-tight, 8-tight, 8 and 8-png (I hope that's enough for a representative sample)
What I have now found is that an earlier version of the software (EMAN2 2.0) *does* get displayed correctly through x2go. I've narrowed this further to version 2.07 is OK when displayed via x2go, while version 2.1 exhibits the inversion.
http://ncmi.bcm.tmc.edu/ncmi/software/software_details?selected_software=cou...
Cheers Toby
Toby Darling, Scientific Computing (2N249) MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge CB2 0QH Phone 01223 267070
Hi Toby,
On Do 11 Feb 2016 16:20:12 CET, Toby Darling wrote:
Hi Stefan
Many thanks for your reply.
If you're using images displayed through X2Go for clinical purposes
No worries on that score, it's just [not so] simple biology.
For your actual bug report, it would be helpful to know if the "flipped image" (it's not color-inverted, it's mirrored along the X axis) issue only occurs with one, or with all available algorithms.
You are correct that the image inversion is is along the x-axis. The
colour/shading is correct.I've not been able to fix the inversion having tried with 16m,
16m-png, 16m-rdp, 16m-tight, 8-tight, 8 and 8-png (I hope that's
enough for a representative sample)What I have now found is that an earlier version of the software
(EMAN2 2.0) *does* get displayed correctly through x2go. I've
narrowed this further to version 2.07 is OK when displayed via x2go,
while version 2.1 exhibits the inversion.http://ncmi.bcm.tmc.edu/ncmi/software/software_details?selected_software=cou...
Cheers Toby
Is the source code of the referenced software online? Is it free
software? If yes, there is a chance we can look at changes in that
software.
Also, does the software dynamically link in shared libraries? Or has
it been built statically?
I guess that there is a flaw in nx-libs that gets triggered by your
application. If we could generate diffs of the different EMAN2 2.0
versions, we might be able to track down the cause for the mirroring
effect.
Mike
DAS-NETZWERKTEAM mike gabriel, herweg 7, 24357 fleckeby fon: +49 (1520) 1976 148
GnuPG Key ID 0x25771B31 mail: mike.gabriel@das-netzwerkteam.de, http://das-netzwerkteam.de
freeBusy: https://mail.das-netzwerkteam.de/mailxchange/kronolith/fb.php?u=m.gabriel%40...
Hi Mike
For your actual bug report, it would be helpful to know if the "flipped image" (it's not color-inverted, it's mirrored along the X axis) issue only occurs with one, or with all available algorithms.
You are correct that the image inversion is is along the x-axis. The colour/shading is correct.
I've not been able to fix the inversion having tried with 16m, 16m-png, 16m-rdp, 16m-tight, 8-tight, 8 and 8-png (I hope that's enough for a representative sample)
What I have now found is that an earlier version of the software (EMAN2 2.0) *does* get displayed correctly through x2go. I've narrowed this further to version 2.07 is OK when displayed via x2go, while version 2.1 exhibits the inversion.
http://ncmi.bcm.tmc.edu/ncmi/software/software_details?selected_software=cou...
Cheers Toby
Is the source code of the referenced software online? Is it free software? If yes, there is a chance we can look at changes in that software.
Fortunately, it is.
2.1 : http://ncmi.bcm.edu/ncmi/software/counter_222/software_129 2.07: http://ncmi.bcm.edu/ncmi/software/counter_222/software_122
Also, does the software dynamically link in shared libraries? Or has it been built statically?
It's all python code and it ships with its own python 2.7.x
I guess that there is a flaw in nx-libs that gets triggered by your application. If we could generate diffs of the different EMAN2 2.0 versions, we might be able to track down the cause for the mirroring effect.
I did have a look, unfortunately, my python-fu is weak. I do notice that the python version went from 2.7.2 -> 2.7.3.
Cheers Toby
Toby Darling, Scientific Computing (2N249) MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge CB2 0QH Phone 01223 267070
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Mike Gabriel -
Stefan Baur -
Toby Darling