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From: Thomas H. <th...@gm...> - 2017-07-26 15:46:32
|
Hi Kenny, Haixin, Thank you for the trace. The user interface is old and written at times where I must admit had little experience with web technologies. It needs a major overhaul - anyone interested :D …? I suggest to use the command line tools to create an alignment job instead. Please try pytom/bin/alignJob.py Please let us know if it works. Cheers, Thomas > Am 24.07.2017 um 16:48 schrieb Haixin Sui <su...@ho...>: > > Hi Tom, > > Thank you very much for your response. > > I tried to repeat Kenny's test. The full stack trace and the screenshots, before and after the error message showed up, have been been included in the end of this email. > > What we did was to generate a new Alignment job with the GI. This is the first job we have tested, i.e. no previous reconstruction or localization was carried out with pytom. We assumed we could start with running an Alignment job. > > After I input the parameters and files. When clicked on the green button "create Job", a window popped up showing" InvildStateError: XMLHttpRequest state must not be LOADING or DONE." > It is where we stopped. > > Please help to identify the possible reasons of the error message. > > Thank you > > Haixin > > > The full stack trace list: > ================== > vb@dalian:/DvbWork1/rv1265rec/KM_20161216_rec/Pytom_test$ pytom /usr/local/pytom/frontend/pytomServer.py -h "dalian" & > [1] 26708 > vb@dalian:/DvbWork1/rv1265rec/KM_20161216_rec/Pytom_test$ cat: Command not found. > ---------------------------------------------------------------------------------------- > Starting Pytom Webserver on hostname dalian and port 8080 > Paste the following line into your browser to start > http://dalian:8080 <http://dalian:8080/> > Starting browser: firefox > > ---------------------------------------------------------------------------------------- > firefox http://dalian:8080/index.html <http://dalian:8080/index.html> > 127.0.0.1 - - [24/Jul/2017 09:40:27] "GET / HTTP/1.1" 200 - > /usr/local/pytom/frontend/html// > /usr/local/pytom/frontend/html/javascript/javascript/functions.js > 127.0.0.1 - - [24/Jul/2017 09:40:27] "GET /javascript/functions.js HTTP/1.1" 200 - > /usr/local/pytom/frontend/html/javascript/javascript/functions.js > /usr/local/pytom/frontend/html/javascript/javascript/reconstructionFunctions.js > 127.0.0.1 - - [24/Jul/2017 09:40:27] "GET /javascript/reconstructionFunctions.js HTTP/1.1" 200 - > /usr/local/pytom/frontend/html/javascript/javascript/reconstructionFunctions.js > /usr/local/pytom/frontend/html/javascript/javascript/mcoEXMXFunctions.js > 127.0.0.1 - - [24/Jul/2017 09:40:27] "GET /javascript/mcoEXMXFunctions.js HTTP/1.1" 200 - > /usr/local/pytom/frontend/html/javascript/javascript/mcoEXMXFunctions.js > /usr/local/pytom/frontend/html/javascript/javascript/localizationFunctions.js > 127.0.0.1 - - [24/Jul/2017 09:40:27] "GET /javascript/localizationFunctions.js HTTP/1.1" 200 - > /usr/local/pytom/frontend/html/javascript/javascript/localizationFunctions.js > /usr/local/pytom/frontend/html/javascript/javascript/alignmentFunctions.js > 127.0.0.1 - - [24/Jul/2017 09:40:27] "GET /javascript/alignmentFunctions.js HTTP/1.1" 200 - > /usr/local/pytom/frontend/html/javascript/javascript/alignmentFunctions.js > /usr/local/pytom/frontend/html/javascript/javascript/mcoACFunctions.js > 127.0.0.1 - - [24/Jul/2017 09:40:27] "GET /javascript/mcoACFunctions.js HTTP/1.1" 200 - > /usr/local/pytom/frontend/html/javascript/javascript/mcoACFunctions.js > /usr/local/pytom/frontend/html/javascript/javascript/cookies.js > 127.0.0.1 - - [24/Jul/2017 09:40:27] "GET /javascript/cookies.js HTTP/1.1" 200 - > /usr/local/pytom/frontend/html/javascript/javascript/cookies.js > /usr/local/pytom/frontend/html/images/images/pytom_logo.png > 127.0.0.1 - - [24/Jul/2017 09:40:27] "GET /images/pytom_logo.png HTTP/1.1" 200 - > /usr/local/pytom/frontend/html/images/images/pytom_logo.png > /usr/local/pytom/frontend/html/css/css/pytomMainCSS.css > 127.0.0.1 - - [24/Jul/2017 09:40:27] "GET /css/pytomMainCSS.css HTTP/1.1" 200 - > /usr/local/pytom/frontend/html/css/css/pytomMainCSS.css > /usr/local/pytom/frontend/html/images/images/pytom_logo.png > 127.0.0.1 - - [24/Jul/2017 09:40:27] "GET /images/pytom_logo.png HTTP/1.1" 200 - > /usr/local/pytom/frontend/html/images/images/pytom_logo.png > /usr/local/pytom/frontend/html/css/css/cssMainMenu.css > 127.0.0.1 - - [24/Jul/2017 09:40:27] "GET /css/cssMainMenu.css HTTP/1.1" 200 - > /usr/local/pytom/frontend/html/css/css/cssMainMenu.css > /usr/local/pytom/frontend/html/../serverpages/apiDocumentationURL.py > 127.0.0.1 - - [24/Jul/2017 09:40:27] "GET /apiDocumentationURL.py HTTP/1.1" 200 - > /usr/local/pytom/frontend/html/../serverpages/apiDocumentationURL.py > /usr/local/pytom/frontend/html/pages/pages/newAlignmentJob.html > 127.0.0.1 - - [24/Jul/2017 09:40:34] "GET /pages/newAlignmentJob.html HTTP/1.1" 200 - > /usr/local/pytom/frontend/html/pages/pages/newAlignmentJob.html > /usr/local/pytom/frontend/html/../serverpages/loadParticleList.py > 127.0.0.1 - - [24/Jul/2017 09:41:27] "GET /loadParticleList.py?DIR=/DvbWork1/rv1265rec/KM_20161216_rec/Pytom_test/KM_NS_A_sybvol HTTP/1.1" 200 - > /usr/local/pytom/frontend/html/../serverpages/loadParticleList.py > /usr/local/pytom/frontend/html/../serverpages/imageSlice.py > 127.0.0.1 - - [24/Jul/2017 09:44:24] "GET /imageSlice.py?File=/DvbWork1/rv1265rec/KM_20161216_rec/Pytom_test/Reference/Reference.mrc HTTP/1.1" 200 - > /usr/local/pytom/frontend/html/../serverpages/imageSlice.py > /usr/local/pytom/frontend/html/images/DvbWork1/rv1265rec/KM_20161216_rec/Pytom_test/Reference/Reference.png > 127.0.0.1 - - [24/Jul/2017 09:44:24] "GET /DvbWork1/rv1265rec/KM_20161216_rec/Pytom_test/Reference/Reference.png HTTP/1.1" 200 - > /usr/local/pytom/frontend/html/images/DvbWork1/rv1265rec/KM_20161216_rec/Pytom_test/Reference/Reference.png > /usr/local/pytom/frontend/html/../serverpages/imageSlice.py > 127.0.0.1 - - [24/Jul/2017 09:44:57] "GET /imageSlice.py?File=/DvbWork1/rv1265rec/KM_20161216_rec/Pytom_test/Mask/Mask.mrc HTTP/1.1" 200 - > /usr/local/pytom/frontend/html/../serverpages/imageSlice.py > /usr/local/pytom/frontend/html/images/DvbWork1/rv1265rec/KM_20161216_rec/Pytom_test/Mask/Mask.png > 127.0.0.1 - - [24/Jul/2017 09:44:57] "GET /DvbWork1/rv1265rec/KM_20161216_rec/Pytom_test/Mask/Mask.png HTTP/1.1" 200 - > /usr/local/pytom/frontend/html/images/DvbWork1/rv1265rec/KM_20161216_rec/Pytom_test/Mask/Mask.png > /usr/local/pytom/frontend/html/../serverpages/imageSlice.py > 127.0.0.1 - - [24/Jul/2017 09:46:58] "GET /imageSlice.py?File=/DvbWork1/rv1265rec/KM_20161216_rec/Pytom_test/Mask/rmask125_r70G2.mrc HTTP/1.1" 200 - > /usr/local/pytom/frontend/html/../serverpages/imageSlice.py > /usr/local/pytom/frontend/html/images/DvbWork1/rv1265rec/KM_20161216_rec/Pytom_test/Mask/rmask125_r70G2.png > 127.0.0.1 - - [24/Jul/2017 09:46:58] "GET /DvbWork1/rv1265rec/KM_20161216_rec/Pytom_test/Mask/rmask125_r70G2.png HTTP/1.1" 200 - > /usr/local/pytom/frontend/html/images/DvbWork1/rv1265rec/KM_20161216_rec/Pytom_test/Mask/rmask125_r70G2.png > > ------------ > The above has completed listing of the full stack trace. > > Before we clicked the "Create Job", the screen-shot is following. (does it look right?) > > <pastedImage.png> > > After I clicked on the green "Create Job", the screen-shot is following. When it happened, no additional information was triggers in the stack trace window. > > > <pastedImage.png> > From: Thomas Hrabe <th...@gm...> > Sent: Monday, July 24, 2017 8:52 AM > To: Kenny Chen > Cc: pyt...@li... > Subject: Re: [Pytom-mail] Error message when creating job file > > Hi Kenny, > > Thank you for the error report. > Could you please send the full stack trace to identify your problem in more detail? > > Thanks, > Thomas > > > On Jul 20, 2017, at 11:24 PM, Kenny Chen <kec...@gm...> wrote: > > > > Hi, > > > > I get an error message "InvalidStateError: XMLHttpRequest state must not be LOADING or DONE." when I create the alignment job xml file from the web server front end. > > > > I am using firefox. > > > > > > > > Thank you for your help! > > > > > > Kenny > > ------------------------------------------------------------------------------ > > Check out the vibrant tech community on one of the world's most > > engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________ <http://sdm.link/slashdot_______________________________________________> > > Pytom-mail mailing list > > Pyt...@li... > > https://lists.sourceforge.net/lists/listinfo/pytom-mail <https://lists.sourceforge.net/lists/listinfo/pytom-mail> > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org <http://slashdot.org/>! http://sdm.link/slashdot <http://sdm.link/slashdot> > _______________________________________________ > Pytom-mail mailing list > Pyt...@li... <mailto:Pyt...@li...> > https://lists.sourceforge.net/lists/listinfo/pytom-mail <https://lists.sourceforge.net/lists/listinfo/pytom-mail> |
|
From: Thomas H. <th...@gm...> - 2017-07-24 12:52:45
|
Hi Kenny, Thank you for the error report. Could you please send the full stack trace to identify your problem in more detail? Thanks, Thomas > On Jul 20, 2017, at 11:24 PM, Kenny Chen <kec...@gm...> wrote: > > Hi, > > I get an error message "InvalidStateError: XMLHttpRequest state must not be LOADING or DONE." when I create the alignment job xml file from the web server front end. > > I am using firefox. > > > > Thank you for your help! > > > Kenny > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________ > Pytom-mail mailing list > Pyt...@li... > https://lists.sourceforge.net/lists/listinfo/pytom-mail |
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From: Haixin S. <su...@ho...> - 2017-07-21 19:57:40
|
Hi Dustin This the first time our people tried the Pytom I installed. What do you think about the error message? Any advice? Haixin Sui (518)474-4235 (office) http://www.wadsworth.org/resnres/bios/sui.html ________________________________ From: Kenny Chen <kec...@gm...> Sent: Thursday, July 20, 2017 5:24 PM To: pyt...@li... Subject: [Pytom-mail] Error message when creating job file Hi, I get an error message "InvalidStateError: XMLHttpRequest state must not be LOADING or DONE." when I create the alignment job xml file from the web server front end. I am using firefox. Thank you for your help! Kenny |
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From: Dustin M. <dus...@gm...> - 2017-07-21 08:57:58
|
Hi Zheng, You could check to see if you are using maybe too strong of a lowpass filter, which is turning your ribosomes "into" gold, and then maybe letting more signal in could help boost true ribosome scores. But, false positives are always a problem with template matching, and so you can always just move forward to the CPCA-EXMX routines as described in the tutorial to remove them. I've also found that you can generate 2D projections of your subvolumes and use any SPA 2D classification routine to also remove false positives a little faster. Hope that Helps, Dustin ___ Cheers, Dustin M. On Fri, Jul 21, 2017 at 7:42 AM, 纪正 <jz...@ma...> wrote: > Hi, > > I adopted Template Matching when localizing ribosomes, finding out Gold > markers got HIGHer score than some ribosome particles. > > How can I get rid of these "awesome" markers? (@^@) > > I localized particles using localizaiton.py and normalized every volume > after getting out from Tomo. > > Thanks for your help. > > Zheng > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Pytom-mail mailing list > Pyt...@li... > https://lists.sourceforge.net/lists/listinfo/pytom-mail > > |
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From: 纪正 <jz...@ma...> - 2017-07-21 06:42:13
|
Hi, I adopted Template Matching when localizing ribosomes, finding out Gold markers got HIGHer score than some ribosome particles. How can I get rid of these "awesome" markers? (@^@) I localized particles using localizaiton.py and normalized every volume after getting out from Tomo. Thanks for your help. Zheng |
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From: Kenny C. <kec...@gm...> - 2017-07-20 21:24:59
|
Hi, I get an error message "InvalidStateError: XMLHttpRequest state must not be LOADING or DONE." when I create the alignment job xml file from the web server front end. I am using firefox. Thank you for your help! Kenny |
|
From: Ortiz, J. O. <or...@bi...> - 2017-03-30 20:44:35
|
Dear Emmanuel, I found in my records, some matlab procedures that I wrote exactly for your purpose, but I can not garantee that they are working with your list. I would start with the version 3 (_v3.m) which should be the latest. Sorry for not given you more details. Since a while I don't use these tools. Saludos, Julio ________________________________ Von: Emmanuel Moebel [emm...@in...] Gesendet: Donnerstag, 30. März 2017 16:37 An: pyt...@li... Betreff: [Pytom-mail] converting particlelists into motivelists Dear Pytom community, I would like to convert particle lists (.xml file) produced by pytom into "motive lists" (.em file), as used in the matlab TOM and AV3 toolboxes (see https://www.biochem.mpg.de/tom ). I started writing a pytom script in order to do that: -------------------------------------------------------------------- from pytom.basic.structures import ParticleList partlFile = 'aligned_pl_iter9.xml' motlFile = 'motl_aligned_iter9.em' pl = ParticleList() pl.fromXMLFile(partlFile) # read particle list pl.toMOTL(motlFile) # save as motive list -------------------------------------------------------------------- This script transfers most informations from the particle list into the motive list, except for the particle IDs, which is annoying. In the motive list row where should be the particle IDs, I just have 0,1,2,3,4,5 .... But this IDs don't correspond to the particle infos (position, orientation etc) Is there something I missed? Or maybe someone already wrote a script and is willing to share it? Best regards, Emmanuel Moebel PhD student at Inria Rennes (France) Member of team Serpico |
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From: Thomas H. <th...@gm...> - 2017-03-30 17:33:30
|
Hi Emanuel, Yes, the documentation of toMOTL states that the result may not be consistent with the particle index, it enumerates the index from 1:numberParticles. http://pytom.org/doc/epydoc/index.html <http://pytom.org/doc/epydoc/index.html> However, you can copy your files into a new folder with copyFiles(self, destinationDirectory, particlePrefix) and this way the new particles would be consistent to a new MOTL list. Hope it helps, Thomas > On Mar 30, 2017, at 7:37 AM, Emmanuel Moebel <emm...@in...> wrote: > > Dear Pytom community, > > I would like to convert particle lists (.xml file) produced by pytom into "motive lists" (.em file), as used in the matlab TOM and AV3 toolboxes (see https://www.biochem.mpg.de/tom <https://www.biochem.mpg.de/tom> ). > I started writing a pytom script in order to do that: > > -------------------------------------------------------------------- > from pytom.basic.structures import ParticleList > > partlFile = 'aligned_pl_iter9.xml' > motlFile = 'motl_aligned_iter9.em' > > pl = ParticleList() > pl.fromXMLFile(partlFile) # read particle list > pl.toMOTL(motlFile) # save as motive list > -------------------------------------------------------------------- > > This script transfers most informations from the particle list into the motive list, except for the particle IDs, which is annoying. > In the motive list row where should be the particle IDs, I just have 0,1,2,3,4,5 .... But this IDs don't correspond to the particle infos (position, orientation etc) > > Is there something I missed? Or maybe someone already wrote a script and is willing to share it? > > Best regards, > Emmanuel Moebel > PhD student at Inria Rennes (France) > Member of team Serpico > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________ > Pytom-mail mailing list > Pyt...@li... > https://lists.sourceforge.net/lists/listinfo/pytom-mail |
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From: Emmanuel M. <emm...@in...> - 2017-03-30 14:37:49
|
Dear Pytom community, I would like to convert particle lists (.xml file) produced by pytom into "motive lists" (.em file), as used in the matlab TOM and AV3 toolboxes (see https://www.biochem.mpg.de/tom ). I started writing a pytom script in order to do that: -------------------------------------------------------------------- from pytom.basic.structures import ParticleList partlFile = 'aligned_pl_iter9.xml' motlFile = 'motl_aligned_iter9.em' pl = ParticleList() pl.fromXMLFile(partlFile) # read particle list pl.toMOTL(motlFile) # save as motive list -------------------------------------------------------------------- This script transfers most informations from the particle list into the motive list, except for the particle IDs, which is annoying. In the motive list row where should be the particle IDs, I just have 0,1,2,3,4,5 .... But this IDs don't correspond to the particle infos (position, orientation etc) Is there something I missed? Or maybe someone already wrote a script and is willing to share it? Best regards, Emmanuel Moebel PhD student at Inria Rennes (France) Member of team Serpico |
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From: Dustin M. <dus...@gm...> - 2016-10-27 23:08:26
|
Hi all,
I get an error with calculate_correlation_matrix.py when I try to use binning.
Traceback (most recent call last):
File "/share/apps/pytom/classification/calculate_correlation_matrix.py", line 246, in <module>
worker.start(job, verbose)
File "/share/apps/pytom/classification/calculate_correlation_matrix.py", line 54, in start
self.run(verbose)
File "/share/apps/pytom/classification/calculate_correlation_matrix.py", line 110, in run
vf = f.getTransformedVolume(binning)
File "/share/apps/pytom/basic/structures.py", line 1863, in getTransformedVolume
volumeTransformed = vol(volume.sizeX(),volume.sizeY(),volume.sizeZ())
AttributeError: tuple object has no attribute sizeX
I traced the error to pytom.basic.structure.Particle.getVolume and at line 1631 the call to resize
actually returns a tuple of the resized volume and the Fourier volume. This patch seems to fix things.
1631c1631
< volume, fvolume = resize(volume=volume, factor=1./binning, interpolation='Fourier')
---
> volume = resize(volume=volume, factor=1./binning, interpolation='Fourier')
Hope this helps anyone who runs into the same problem.
--
Cheers,
Dustin
|
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From: Thomas H. <th...@gm...> - 2016-09-13 18:03:04
|
Hi Kanika,
EM is currently still the format PyTom was tested on exhaustively. MRC is supported, but there are be some issue still as you see.
If the conversion works for you, I suggest to keep it up for your project and not change your protocols for such minor issues.
However, I agree that MRC support should be improved in the future.
Cheers,
Thomas
> On Sep 8, 2016, at 1:48 PM, Kanika Khanna <kk...@uc...> wrote:
>
> Thank you!
>
> I had another quick question. When I am trying to run localization jobs, I am only able to run if I convert my .rec files (which are essentially mrc format) to em format using mrc2em.py . If I try to run the localization with .rec or .mrc format, I get the following error:
> Traceback (most recent call last):
>
> File "/usr/local/pytom/bin/localization.py", line 82, in <module>
> startLocalizationJob(jobName, splitX, splitY, splitZ, doSplitAngles=False)
> File "/usr/local/pytom/bin/localization.py", line 21, in startLocalizationJob
> leader.parallelRun(job, splitX, splitY, splitZ, verbose)
> File "/usr/local/pytom/localization/parallel_extract_peaks.py", line 1046, in parallelRun
> result = self.run(verbose)
> File "/usr/local/pytom/localization/parallel_extract_peaks.py", line 83, in run
> v = self.volume.getVolume(self.volume.subregion)
> File "/usr/local/pytom/localization/structures.py", line 55, in getVolume
> binning[0], binning[1], binning[2])
> File "/usr/local/pytom/pytomc/swigModules/pytom_volume.py", line 378, in read
> return _pytom_volume.read(*args)
> RuntimeError: Reading CCP4 file: the datatype in the file is not supported!
>
> For information, both my pdb and mask are in em format as well.
>
>
> On Wed, Sep 7, 2016 at 12:06 PM, Thomas Hrabe <th...@gm... <mailto:th...@gm...>> wrote:
> Hi Kanika,
>
> Code between the lines. When you try to access information from a ParticleList, you must read it first from disk. You were trying to read the wrong type - PickPosition - instead of ParticleList
>
> Replace PickPosition with ParticleList
>
> Hope it helps solving your problem,
> Thomas
>
>> On Sep 7, 2016, at 12:00 PM, Kanika Khanna <kk...@uc... <mailto:kk...@uc...>> wrote:
>>
>> Hello all,
>>
>> I have been trying to get coordinates of X,Y,Z from particle list using the function 'PickPosition' from ipytom as follows:
>> ipytom
>> from pytom.basic.structures import PickPosition
>
> from pytom.basic.structures import ParticleList
>
>> pl=PickPosition()
>> pl.fromXMLFile(pl.xml’)
>
> for i,p in enumerate(pl):
> p.getPickPosition()
>
> or
>
> pl[i].getPickPosition()
>
>
>
>
>> But I run into the following error:
>> UnboundLocalError Traceback (most recent call last)
>> <ipython-input-5-71b11edb47f3> in <module>()
>> ----> 1 pl.fromXMLFile ('pl.xml')
>>
>> /usr/local/pytom/basic/structures.py in fromXMLFile(self, filename)
>> 72 lines = readStringFile(filename)
>> 73
>> ---> 74 self.fromStr(lines)
>> 75
>> 76 def toXMLFile(self,filename):
>>
>> /usr/local/pytom/basic/structures.py in fromStr(self, string)
>> 45 root = etree.fromstring(string)
>> 46
>> ---> 47 self.fromXML(root)
>> 48
>> 49 def __str__(self):
>>
>> /usr/local/pytom/basic/structures.py in fromXML(self, xmlObj)
>> 3674 TypeError('PickPosition: You must provide a valid PickPosition XML object.')
>> 3675
>> -> 3676 self._x = float(shift_element.get('X'))
>> 3677 self._y = float(shift_element.get('Y'))
>> 3678 self._z = float(shift_element.get('Z'))
>>
>> UnboundLocalError: local variable 'shift_element' referenced before assignment
>>
>>
>> Am I doing it right? How can I get the X,Y,Z coordinates of particles in a matrix from particle file?
>>
>> Thanks!
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> Pytom-mail mailing list
>> Pyt...@li... <mailto:Pyt...@li...>
>> https://lists.sourceforge.net/lists/listinfo/pytom-mail <https://lists.sourceforge.net/lists/listinfo/pytom-mail>
>
>
|
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From: Kanika K. <kk...@uc...> - 2016-09-08 20:49:33
|
Thank you!
I had another quick question. When I am trying to run localization jobs, I
am only able to run if I convert my .rec files (which are essentially mrc
format) to em format using mrc2em.py . If I try to run the localization
with .rec or .mrc format, I get the following error:
Traceback (most recent call last):
File "/usr/local/pytom/bin/localization.py", line 82, in <module>
startLocalizationJob(jobName, splitX, splitY, splitZ,
doSplitAngles=False)
File "/usr/local/pytom/bin/localization.py", line 21, in
startLocalizationJob
leader.parallelRun(job, splitX, splitY, splitZ, verbose)
File "/usr/local/pytom/localization/parallel_extract_peaks.py", line
1046, in parallelRun
result = self.run(verbose)
File "/usr/local/pytom/localization/parallel_extract_peaks.py", line 83,
in run
v = self.volume.getVolume(self.volume.subregion)
File "/usr/local/pytom/localization/structures.py", line 55, in getVolume
binning[0], binning[1], binning[2])
File "/usr/local/pytom/pytomc/swigModules/pytom_volume.py", line 378, in
read
return _pytom_volume.read(*args)
RuntimeError: Reading CCP4 file: the datatype in the file is not supported!
For information, both my pdb and mask are in em format as well.
On Wed, Sep 7, 2016 at 12:06 PM, Thomas Hrabe <th...@gm...> wrote:
> Hi Kanika,
>
> Code between the lines. When you try to access information from a
> ParticleList, you must read it first from disk. You were trying to read the
> wrong type - PickPosition - instead of ParticleList
>
> Replace PickPosition with ParticleList
>
> Hope it helps solving your problem,
> Thomas
>
> On Sep 7, 2016, at 12:00 PM, Kanika Khanna <kk...@uc...> wrote:
>
> Hello all,
>
> I have been trying to get coordinates of X,Y,Z from particle list using
> the function 'PickPosition' from ipytom as follows:
> ipytom
> from pytom.basic.structures import PickPosition
>
>
> from pytom.basic.structures import ParticleList
>
> pl=PickPosition()
> pl.fromXMLFile(pl.xml’)
>
>
> for i,p in enumerate(pl):
> p.getPickPosition()
>
> or
> pl[i].getPickPosition()
>
>
>
>
> But I run into the following error:
> UnboundLocalError Traceback (most recent call last)
> <ipython-input-5-71b11edb47f3> in <module>()
> ----> 1 pl.fromXMLFile ('pl.xml')
>
> /usr/local/pytom/basic/structures.py in fromXMLFile(self, filename)
> 72 lines = readStringFile(filename)
> 73
> ---> 74 self.fromStr(lines)
> 75
> 76 def toXMLFile(self,filename):
>
> /usr/local/pytom/basic/structures.py in fromStr(self, string)
> 45 root = etree.fromstring(string)
> 46
> ---> 47 self.fromXML(root)
> 48
> 49 def __str__(self):
>
> /usr/local/pytom/basic/structures.py in fromXML(self, xmlObj)
> 3674 TypeError('PickPosition: You must provide a valid
> PickPosition XML object.')
> 3675
> -> 3676 self._x = float(shift_element.get('X'))
> 3677 self._y = float(shift_element.get('Y'))
> 3678 self._z = float(shift_element.get('Z'))
>
> UnboundLocalError: local variable 'shift_element' referenced before
> assignment
>
>
> Am I doing it right? How can I get the X,Y,Z coordinates of particles in a
> matrix from particle file?
>
> Thanks!
> ------------------------------------------------------------
> ------------------
> _______________________________________________
> Pytom-mail mailing list
> Pyt...@li...
> https://lists.sourceforge.net/lists/listinfo/pytom-mail
>
>
>
|
|
From: Thomas H. <th...@gm...> - 2016-09-07 19:07:11
|
Hi Kanika,
Code between the lines. When you try to access information from a ParticleList, you must read it first from disk. You were trying to read the wrong type - PickPosition - instead of ParticleList
Replace PickPosition with ParticleList
Hope it helps solving your problem,
Thomas
> On Sep 7, 2016, at 12:00 PM, Kanika Khanna <kk...@uc...> wrote:
>
> Hello all,
>
> I have been trying to get coordinates of X,Y,Z from particle list using the function 'PickPosition' from ipytom as follows:
> ipytom
> from pytom.basic.structures import PickPosition
from pytom.basic.structures import ParticleList
> pl=PickPosition()
> pl.fromXMLFile(pl.xml’)
for i,p in enumerate(pl):
p.getPickPosition()
or
pl[i].getPickPosition()
> But I run into the following error:
> UnboundLocalError Traceback (most recent call last)
> <ipython-input-5-71b11edb47f3> in <module>()
> ----> 1 pl.fromXMLFile ('pl.xml')
>
> /usr/local/pytom/basic/structures.py in fromXMLFile(self, filename)
> 72 lines = readStringFile(filename)
> 73
> ---> 74 self.fromStr(lines)
> 75
> 76 def toXMLFile(self,filename):
>
> /usr/local/pytom/basic/structures.py in fromStr(self, string)
> 45 root = etree.fromstring(string)
> 46
> ---> 47 self.fromXML(root)
> 48
> 49 def __str__(self):
>
> /usr/local/pytom/basic/structures.py in fromXML(self, xmlObj)
> 3674 TypeError('PickPosition: You must provide a valid PickPosition XML object.')
> 3675
> -> 3676 self._x = float(shift_element.get('X'))
> 3677 self._y = float(shift_element.get('Y'))
> 3678 self._z = float(shift_element.get('Z'))
>
> UnboundLocalError: local variable 'shift_element' referenced before assignment
>
>
> Am I doing it right? How can I get the X,Y,Z coordinates of particles in a matrix from particle file?
>
> Thanks!
> ------------------------------------------------------------------------------
> _______________________________________________
> Pytom-mail mailing list
> Pyt...@li...
> https://lists.sourceforge.net/lists/listinfo/pytom-mail
|
|
From: Kanika K. <kk...@uc...> - 2016-09-07 19:01:22
|
Hello all,
I have been trying to get coordinates of X,Y,Z from particle list using the
function 'PickPosition' from ipytom as follows:
ipytom
from pytom.basic.structures import PickPosition
pl=PickPosition()
pl.fromXMLFile(pl.xml')
But I run into the following error:
UnboundLocalError Traceback (most recent call last)
<ipython-input-5-71b11edb47f3> in <module>()
----> 1 pl.fromXMLFile ('pl.xml')
/usr/local/pytom/basic/structures.py in fromXMLFile(self, filename)
72 lines = readStringFile(filename)
73
---> 74 self.fromStr(lines)
75
76 def toXMLFile(self,filename):
/usr/local/pytom/basic/structures.py in fromStr(self, string)
45 root = etree.fromstring(string)
46
---> 47 self.fromXML(root)
48
49 def __str__(self):
/usr/local/pytom/basic/structures.py in fromXML(self, xmlObj)
3674 TypeError('PickPosition: You must provide a valid
PickPosition XML object.')
3675
-> 3676 self._x = float(shift_element.get('X'))
3677 self._y = float(shift_element.get('Y'))
3678 self._z = float(shift_element.get('Z'))
UnboundLocalError: local variable 'shift_element' referenced before
assignment
Am I doing it right? How can I get the X,Y,Z coordinates of particles in a
matrix from particle file?
Thanks!
|
|
From: Dustin M. <dus...@gm...> - 2016-06-22 22:23:30
|
Hey Thomas,
Sorry I didn't want to be overly verbose in case it was something simple. Here were the changes I made so far:
+++ /home/dustin/pytom_0.971/angles/localSampling.py
--- /share/apps/pytom/angles/localSampling.py
290c290
< class ExtendedInplaneSampling(AngleList):
---
> class ExtendedInplaneSampling(AngleList, LocalSampling):
438c438
< if angleList_element.get('ShellIncrement') is None:
---
> if angleListElement.get('ShellIncrement') is None:
The change at 290 was to get rid of an error with the super call in nextRotation at line 452:
super(type, obj): obj must be an instance or subtype of type
The change at 438 was fixing what looked to be typo.
But after making both of these changes I still get another error and I gave up:
>>>>>>>>> MPI rank: 0, Iteration: 0
>>>>>>>>> Aligning Even ....
This is a virtual class and thus virtual member function
<class 'pytom.angles.localSampling.ExtendedInplaneSampling'>
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 0.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
'NoneType' object has no attribute '__getitem__'
Thanks for the help.
--
Cheers,
Dustin
>
> Hi Dustin,
>
> can you please be more specific about your problems?
>
> Thanks,
> Thomas
>
>
>> On Jun 21, 2016, at 8:27 AM, Dustin Morado <dus...@gm...> wrote:
>>
>> Hi all,
>>
>> Does anybody have any experience using ExtendedInplaneSampling in GLocal alignment jobs? I'm trying to get a job to run with it and running into a few problems. Just want to check if I'm missing something simple or obvious.
>>
>> --
>> Cheers,
>> Dustin Morado
>>
>>
>> ------------------------------------------------------------------------------
>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
>> present their vision of the future. This family event has something for
>> everyone, including kids. Get more information and register today.
>> http://sdm.link/attshape
>> _______________________________________________
>> Pytom-mail mailing list
>> Pyt...@li...
>> https://lists.sourceforge.net/lists/listinfo/pytom-mail
>
|
|
From: Thomas H. <th...@gm...> - 2016-06-22 21:19:16
|
Hi Dustin, can you please be more specific about your problems? Thanks, Thomas > On Jun 21, 2016, at 8:27 AM, Dustin Morado <dus...@gm...> wrote: > > Hi all, > > Does anybody have any experience using ExtendedInplaneSampling in GLocal alignment jobs? I'm trying to get a job to run with it and running into a few problems. Just want to check if I'm missing something simple or obvious. > > -- > Cheers, > Dustin Morado > > > ------------------------------------------------------------------------------ > Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San > Francisco, CA to explore cutting-edge tech and listen to tech luminaries > present their vision of the future. This family event has something for > everyone, including kids. Get more information and register today. > http://sdm.link/attshape > _______________________________________________ > Pytom-mail mailing list > Pyt...@li... > https://lists.sourceforge.net/lists/listinfo/pytom-mail |
|
From: Dustin M. <dus...@gm...> - 2016-06-21 15:27:13
|
Hi all, Does anybody have any experience using ExtendedInplaneSampling in GLocal alignment jobs? I'm trying to get a job to run with it and running into a few problems. Just want to check if I'm missing something simple or obvious. -- Cheers, Dustin Morado |
|
From: Dustin M. <dus...@gm...> - 2016-06-06 15:50:46
|
Hi all, I solved my own problem, but it pointed out a different problem. I had made my mask with Chimera and then converted the MRC file to EM using EMAN2. This EM file was the problem and the EM format output from EMAN2 is not compatible for some reason with pytom_volume read. Once I converted the mask from MRC to EM using pytom, everything works again. -- Cheers, Dustin |
|
From: Dustin M. <dus...@gm...> - 2016-06-04 02:49:54
|
Hi all, I am running into a weird error trying to run a classification. I generate the 0 round cluster averages, but then immediately the job terminates with an error about the mask not existing. There's got to be something I'm missing in my job file but I can't seem to find any significant difference between my job file and the job file from the tutorial which runs successfully besides my mask being non-spherical. I've attached the job script for the mcoemmx job, the output from it, and the job file for the refinement that's causing the crash. I've truncated the particle lists so that the attachments aren't unwieldy. Any advice or help would be gratefully appreciated. -- Cheers, Dustin |
|
From: Dustin M. <dus...@gm...> - 2016-05-10 22:10:17
|
Hi Kanika, Are you also not getting any output? The output your talking about is just a warning. sigma is generated by sqrt in the cmath module and so it can return a complex number, but “a” is calculated using exp from the math module which doesn’t work on complex numbers to it just discards the imaginary part and that’s what you’re seeing here. FWIW from our experience with lots of different samples and data collected a lot of different ways, we never found a consistent way to estimate the number using a gaussian fit, and so we just extract more than we expect by a factor of about 5 and then remove false positives by classification. HTH — Cheers, Dustin > On May 10, 2016, at 4:57 PM, Kanika Khanna <kk...@uc...> wrote: > > Hi, > > Can someone help me with the questions above. I am still trying to figure things out > > Thanks! I appreciate your help. > > On Sat, Apr 23, 2016 at 4:37 AM, Kanika Khanna <kk...@uc... <mailto:kk...@uc...>> wrote: > The reason I ask this is I get this runtime error : /usr/local/pytom/tools/maths.py:652: ComplexWarning: Casting complex values to real discards the imaginary part > a=exp(a0+mu**2/(2*sigma**2)), whatever parameters I enter. > > On Fri, Apr 22, 2016 at 4:03 PM, Kanika Khanna <kk...@uc... <mailto:kk...@uc...>> wrote: > Hello all, > > I am trying to estimate the no. of particles in tomogram by plotting the Gaussian plot. I extracted for instance, 1000 particles. What is the best way to optimize and determine the values of n (no. of bins), p (peak) and c (ccc value) in this case? > > Thanks! > > > ------------------------------------------------------------------------------ > Mobile security can be enabling, not merely restricting. Employees who > bring their own devices (BYOD) to work are irked by the imposition of MDM > restrictions. Mobile Device Manager Plus allows you to control only the > apps on BYO-devices by containerizing them, leaving personal data untouched! > https://ad.doubleclick.net/ddm/clk/304595813;131938128;j_______________________________________________ > Pytom-mail mailing list > Pyt...@li... > https://lists.sourceforge.net/lists/listinfo/pytom-mail |
|
From: Kanika K. <kk...@uc...> - 2016-05-10 21:58:08
|
Hi, Can someone help me with the questions above. I am still trying to figure things out Thanks! I appreciate your help. On Sat, Apr 23, 2016 at 4:37 AM, Kanika Khanna <kk...@uc...> wrote: > The reason I ask this is I get this runtime error : > /usr/local/pytom/tools/maths.py:652: ComplexWarning: Casting complex values > to real discards the imaginary part > a=exp(a0+mu**2/(2*sigma**2)), whatever parameters I enter. > > On Fri, Apr 22, 2016 at 4:03 PM, Kanika Khanna <kk...@uc...> wrote: > >> Hello all, >> >> I am trying to estimate the no. of particles in tomogram by plotting the >> Gaussian plot. I extracted for instance, 1000 particles. What is the best >> way to optimize and determine the values of n (no. of bins), p (peak) and c >> (ccc value) in this case? >> >> Thanks! >> > > |
|
From: Kanika K. <kk...@uc...> - 2016-04-22 23:38:27
|
Hello all, I am trying to estimate the no. of particles in tomogram by plotting the Gaussian plot. I extracted for instance, 1000 particles. What is the best way to optimize and determine the values of n (no. of bins), p (peak) and c (ccc value) in this case? Thanks! |
|
From: Kanika K. <kk...@uc...> - 2016-04-22 23:20:00
|
The reason I ask this is I get this runtime error : /usr/local/pytom/tools/maths.py:652: ComplexWarning: Casting complex values to real discards the imaginary part a=exp(a0+mu**2/(2*sigma**2)), whatever parameters I enter. On Fri, Apr 22, 2016 at 4:03 PM, Kanika Khanna <kk...@uc...> wrote: > Hello all, > > I am trying to estimate the no. of particles in tomogram by plotting the > Gaussian plot. I extracted for instance, 1000 particles. What is the best > way to optimize and determine the values of n (no. of bins), p (peak) and c > (ccc value) in this case? > > Thanks! > |
|
From: Thomas H. <th...@gm...> - 2016-03-24 19:28:26
|
Hi Kanika, sorry for the delay but I was traveling. I think Friedrich and Dustin may be right. Since your localization does not write out the score and angle files, it may be that your MRC file formats are not understood for some reason. If you don’t mind, you could send me a sample and I will have a look at your filetype and whether there’s a technical problem. Do you remember what you changed when the program ran? Does pytom still process the tutorial files correctly? Best, Thomas > On Mar 17, 2016, at 8:56 AM, Kanika Khanna <kk...@uc...> wrote: > > Hi, > > @Thomas, no scores and angles were generated as the process did not run. When I run the commands in ipytom, I get the following error: > > <pytom_volume.vol_comp; proxy of <Swig Object of type 'swigTom::swigVolume< std::complex< float >,float > *' at 0x1a4aed0> > > > @Dustin and Friedrich, the memory of my system as I see is 32.64 GB which I think is pretty good (Is it?) My tomogram is binned 2 times. I have actually run the mpi command sometime back when it worked and now it no longer with the same job. > > I converted the mrc to em format (using mrc2em.py). The problem persists. On that note, are all the volume, template, reference files supposed to be in the same format (all mrc or all em?). I tried playing around with that and using the smallest no. of rotations (angle file), still nothing. > > Can you please explain what exactly would be reading the files interactively in pytom? > > Thanks! > > > > On Wed, Mar 16, 2016 at 8:40 PM, Dustin Morado <dus...@gm... <mailto:dus...@gm...>> wrote: > Anything with alloc in the error is usually a memory error. Do you have enough RAM to fit everything? If you use binning does it work? > > -- > Cheers, > Dustin > > > On Mar 16, 2016, at 7:47 PM, Kanika Khanna <kk...@uc... <mailto:kk...@uc...>> wrote: > > > > Hello > > > > I have been trying endlessly to run the localization job with parallel processing, but it is always giving an error. > > > > Traceback (most recent call last): > > File "/usr/local/pytom/bin/localization.py", line 82, in <module> > > startLocalizationJob(jobName, splitX, splitY, splitZ, doSplitAngles=False) > > File "/usr/local/pytom/bin/localization.py", line 21, in startLocalizationJob > > leader.parallelRun(job, splitX, splitY, splitZ, verbose) > > File "/usr/local/pytom/localization/parallel_extract_peaks.py", line 1046, in parallelRun > > result = self.run(verbose) > > File "/usr/local/pytom/localization/parallel_extract_peaks.py", line 104, in run > > [resV, orientV, sumV, sqrV] = extractPeaks(v, ref, rot, scoreFnc, m, mIsSphere, wedg, nodeName=self.name <http://self.name/>, verboseMode=verbose, moreInfo=moreInfo) > > File "/usr/local/pytom/localization/extractPeaks.py", line 130, in extractPeaks > > meanV = meanUnderMask(volume, maskV, p); > > File "/usr/local/pytom/basic/correlation.py", line 244, in meanUnderMask > > result = iftshift(ifft(fMask*fft(volume)))/(size*p) > > File "/usr/local/pytom/basic/fourier.py", line 122, in fft > > returnValue = pytom_volume.vol_comp(theTuple.complexVolume.sizeX(),theTuple.complexVolume.sizeY(),theTuple.complexVolume.sizeZ()) > > File "/usr/local/pytom/pytomc/swigModules/pytom_volume.py", line 234, in __init__ > > this = _pytom_volume.new_vol_comp(*args) > > RuntimeError: std::bad_alloc > > -------------------------------------------------------------------------- > > mpirun detected that one or more processes exited with non-zero status, thus causing > > the job to be terminated. The first process to do so was: > > > > Process name: [[6894,1],0] > > Exit code: 1 > > > > > > On Fri, Mar 11, 2016 at 12:00 PM, Kanika Khanna <kk...@uc... <mailto:kk...@uc...>> wrote: > > Hi > > > > I am sorry but the job did start running and it gave this weird error then and aborted again! :( > > Primary job terminated normally, but 1 process returned > > a non-zero exit code.. Per user-direction, the job has been aborted. > > > > node_0: send number of 50 rotations to node 2 > > node_0: send number of 25 rotations to node 1 > > node_2: send number of 25 rotations to node 3 > > node_0: starting to calculate 25 rotations > > node_3: starting to calculate 25 rotations > > node_1: starting to calculate 25 rotations > > node_2: starting to calculate 25 rotations > > Traceback (most recent call last): > > File "/usr/local/pytom/bin/localization.py", line 82, in <module> > > startLocalizationJob(jobName, splitX, splitY, splitZ, doSplitAngles=False) > > File "/usr/local/pytom/bin/localization.py", line 21, in startLocalizationJob > > leader.parallelRun(job, splitX, splitY, splitZ, verbose) > > File "/usr/local/pytom/localization/parallel_extract_peaks.py", line 1046, in parallelRun > > result = self.run(verbose) > > File "/usr/local/pytom/localization/parallel_extract_peaks.py", line 104, in run > > [resV, orientV, sumV, sqrV] = extractPeaks(v, ref, rot, scoreFnc, m, mIsSphere, wedg, nodeName=self.name <http://self.name/>, verboseMode=verbose, moreInfo=moreInfo) > > File "/usr/local/pytom/localization/extractPeaks.py", line 130, in extractPeaks > > meanV = meanUnderMask(volume, maskV, p); > > File "/usr/local/pytom/basic/correlation.py", line 244, in meanUnderMask > > result = iftshift(ifft(fMask*fft(volume)))/(size*p) > > File "/usr/local/pytom/pytomc/swigModules/pytom_volume.py", line 342, in __mul__ > > return _pytom_volume.vol_comp___mul__(self, *args) > > RuntimeError: std::bad_alloc > > ------------------------------------------------------- > > Primary job terminated normally, but 1 process returned > > a non-zero exit code.. Per user-direction, the job has been aborted. > > > > > > On Fri, Mar 11, 2016 at 11:56 AM, Kanika Khanna <kk...@uc... <mailto:kk...@uc...>> wrote: > > Hi Thomas, > > > > I have been able to resolve issue 1. I just killed all the processes and started again. It worked that time. > > > > On Sat, Mar 12, 2016 at 1:05 AM, Thomas Hrabe <th...@gm... <mailto:th...@gm...>> wrote: > > Hi Kanika, > > > > > > 1. > > to me, it looks like that you are trying to open a file called > > > > > <Volume Binning="[0, 0, 0]" Filename="PY79.mrc" Sampling="[0, 0, 0]" Subregion="[0, 0, 0, 0, 0, 0]"/> > > > > > > Can you please attach the xml file? > > > > 2. > > I have to look into the script as well. I must re-install it before I can advice about how to use it. > > > > Cheers, > > Thomas > > > > > On Mar 11, 2016, at 11:15 AM, Kanika Khanna <kk...@uc... <mailto:kk...@uc...>> wrote: > > > > > > Hello all, > > > > > > 1. When I try to execute my job using the following command > > > mpirun --host HostName -c 4 pytom localization.py PathToJobFile 2 2 2 > > > > > > I get the following error: > > > Traceback (most recent call last): > > > File "/usr/local/pytom/bin/localization.py", line 82, in <module> > > > startLocalizationJob(jobName, splitX, splitY, splitZ, doSplitAngles=False) > > > File "/usr/local/pytom/bin/localization.py", line 11, in startLocalizationJob > > > job.check() > > > File "/usr/local/pytom/localization/peak_job.py", line 184, in check > > > Traceback (most recent call last): > > > File "/usr/local/pytom/bin/localization.py", line 82, in <module> > > > raise IOError('File: ' + str(self.volume) + ' not found!') > > > IOError: File: <Volume Binning="[0, 0, 0]" Filename="PY79.mrc" Sampling="[0, 0, 0]" Subregion="[0, 0, 0, 0, 0, 0]"/> > > > not found! > > > startLocalizationJob(jobName, splitX, splitY, splitZ, doSplitAngles=False) > > > File "/usr/local/pytom/bin/localization.py", line 11, in startLocalizationJob > > > job.check() > > > File "/usr/local/pytom/localization/peak_job.py", line 184, in check > > > raise IOError('File: ' + str(self.volume) + ' not found!') > > > IOError: File: <Volume Binning="[0, 0, 0]" Filename="PY79.mrc" Sampling="[0, 0, 0]" Subregion="[0, 0, 0, 0, 0, 0]"/> > > > not found! > > > Traceback (most recent call last): > > > File "/usr/local/pytom/bin/localization.py", line 82, in <module> > > > startLocalizationJob(jobName, splitX, splitY, splitZ, doSplitAngles=False) > > > File "/usr/local/pytom/bin/localization.py", line 11, in startLocalizationJob > > > job.check() > > > File "/usr/local/pytom/localization/peak_job.py", line 184, in check > > > raise IOError('File: ' + str(self.volume) + ' not found!') > > > IOError: File: <Volume Binning="[0, 0, 0]" Filename="PY79.mrc" Sampling="[0, 0, 0]" Subregion="[0, 0, 0, 0, 0, 0]"/> > > > not found! > > > ------------------------------------------------------- > > > Primary job terminated normally, but 1 process returned > > > a non-zero exit code.. Per user-direction, the job has been aborted. > > > ------------------------------------------------------- > > > Traceback (most recent call last): > > > File "/usr/local/pytom/bin/localization.py", line 82, in <module> > > > startLocalizationJob(jobName, splitX, splitY, splitZ, doSplitAngles=False) > > > File "/usr/local/pytom/bin/localization.py", line 11, in startLocalizationJob > > > job.check() > > > File "/usr/local/pytom/localization/peak_job.py", line 184, in check > > > raise IOError('File: ' + str(self.volume) + ' not found!') > > > IOError: File: <Volume Binning="[0, 0, 0]" Filename="PY79.mrc" Sampling="[0, 0, 0]" Subregion="[0, 0, 0, 0, 0, 0]"/> > > > not found! > > > -------------------------------------------------------------------------- > > > mpirun detected that one or more processes exited with non-zero status, thus causing > > > the job to be terminated. The first process to do so was: > > > > > > Process name: [[27852,1],3] > > > Exit code: 1 > > > > > > > > > Any idea how I can circumvent this? Or what exactly might be going wrong? > > > > > > 2. Once you have the pl.xml file generated after extraction of particles, we have the script VolumeDialog.py for viewing it in Chimera. I already installed it in the Volume Viewer folder. How exactly are we suppose to use it? Also, there were a couple of existing files of the same name in the folder existing previously (is that the case with everyone here?). Anything to do with them? > > > > > > Thanks! > > > > > > > > > > > > > > > ------------------------------------------------------------------------------ > > > Transform Data into Opportunity. > > > Accelerate data analysis in your applications with > > > Intel Data Analytics Acceleration Library. > > > Click to learn more. > > > http://pubads.g.doubleclick.net/gampad/clk?id=278785111&iu=/4140_______________________________________________ <http://pubads.g.doubleclick.net/gampad/clk?id=278785111&iu=/4140_______________________________________________> > > > Pytom-mail mailing list > > > Pyt...@li... <mailto:Pyt...@li...> > > > https://lists.sourceforge.net/lists/listinfo/pytom-mail <https://lists.sourceforge.net/lists/listinfo/pytom-mail> > > > > > > > > > > ------------------------------------------------------------------------------ > > Transform Data into Opportunity. > > Accelerate data analysis in your applications with > > Intel Data Analytics Acceleration Library. > > Click to learn more. > > http://pubads.g.doubleclick.net/gampad/clk?id=278785231&iu=/4140_______________________________________________ <http://pubads.g.doubleclick.net/gampad/clk?id=278785231&iu=/4140_______________________________________________> > > Pytom-mail mailing list > > Pyt...@li... <mailto:Pyt...@li...> > > https://lists.sourceforge.net/lists/listinfo/pytom-mail <https://lists.sourceforge.net/lists/listinfo/pytom-mail> > > > ------------------------------------------------------------------------------ > Transform Data into Opportunity. > Accelerate data analysis in your applications with > Intel Data Analytics Acceleration Library. > Click to learn more. > http://pubads.g.doubleclick.net/gampad/clk?id=278785231&iu=/4140_______________________________________________ > Pytom-mail mailing list > Pyt...@li... > https://lists.sourceforge.net/lists/listinfo/pytom-mail |
|
From: Kanika K. <kk...@uc...> - 2016-03-17 15:57:32
|
Hi,
@Thomas, no scores and angles were generated as the process did not run.
When I run the commands in ipytom, I get the following error:
<pytom_volume.vol_comp; proxy of <Swig Object of type 'swigTom::swigVolume<
std::complex< float >,float > *' at 0x1a4aed0> >
@Dustin and Friedrich, the memory of my system as I see is 32.64 GB which I
think is pretty good (Is it?) My tomogram is binned 2 times. I have
actually run the mpi command sometime back when it worked and now it no
longer with the same job.
I converted the mrc to em format (using mrc2em.py). The problem persists.
On that note, are all the volume, template, reference files supposed to be
in the same format (all mrc or all em?). I tried playing around with that
and using the smallest no. of rotations (angle file), still nothing.
Can you please explain what exactly would be reading the files
interactively in pytom?
Thanks!
On Wed, Mar 16, 2016 at 8:40 PM, Dustin Morado <dus...@gm...>
wrote:
> Anything with alloc in the error is usually a memory error. Do you have
> enough RAM to fit everything? If you use binning does it work?
>
> --
> Cheers,
> Dustin
>
> > On Mar 16, 2016, at 7:47 PM, Kanika Khanna <kk...@uc...> wrote:
> >
> > Hello
> >
> > I have been trying endlessly to run the localization job with parallel
> processing, but it is always giving an error.
> >
> > Traceback (most recent call last):
> > File "/usr/local/pytom/bin/localization.py", line 82, in <module>
> > startLocalizationJob(jobName, splitX, splitY, splitZ,
> doSplitAngles=False)
> > File "/usr/local/pytom/bin/localization.py", line 21, in
> startLocalizationJob
> > leader.parallelRun(job, splitX, splitY, splitZ, verbose)
> > File "/usr/local/pytom/localization/parallel_extract_peaks.py", line
> 1046, in parallelRun
> > result = self.run(verbose)
> > File "/usr/local/pytom/localization/parallel_extract_peaks.py", line
> 104, in run
> > [resV, orientV, sumV, sqrV] = extractPeaks(v, ref, rot, scoreFnc, m,
> mIsSphere, wedg, nodeName=self.name, verboseMode=verbose,
> moreInfo=moreInfo)
> > File "/usr/local/pytom/localization/extractPeaks.py", line 130, in
> extractPeaks
> > meanV = meanUnderMask(volume, maskV, p);
> > File "/usr/local/pytom/basic/correlation.py", line 244, in
> meanUnderMask
> > result = iftshift(ifft(fMask*fft(volume)))/(size*p)
> > File "/usr/local/pytom/basic/fourier.py", line 122, in fft
> > returnValue =
> pytom_volume.vol_comp(theTuple.complexVolume.sizeX(),theTuple.complexVolume.sizeY(),theTuple.complexVolume.sizeZ())
> > File "/usr/local/pytom/pytomc/swigModules/pytom_volume.py", line 234,
> in __init__
> > this = _pytom_volume.new_vol_comp(*args)
> > RuntimeError: std::bad_alloc
> >
> --------------------------------------------------------------------------
> > mpirun detected that one or more processes exited with non-zero status,
> thus causing
> > the job to be terminated. The first process to do so was:
> >
> > Process name: [[6894,1],0]
> > Exit code: 1
> >
> >
> > On Fri, Mar 11, 2016 at 12:00 PM, Kanika Khanna <kk...@uc...>
> wrote:
> > Hi
> >
> > I am sorry but the job did start running and it gave this weird error
> then and aborted again! :(
> > Primary job terminated normally, but 1 process returned
> > a non-zero exit code.. Per user-direction, the job has been aborted.
> >
> > node_0: send number of 50 rotations to node 2
> > node_0: send number of 25 rotations to node 1
> > node_2: send number of 25 rotations to node 3
> > node_0: starting to calculate 25 rotations
> > node_3: starting to calculate 25 rotations
> > node_1: starting to calculate 25 rotations
> > node_2: starting to calculate 25 rotations
> > Traceback (most recent call last):
> > File "/usr/local/pytom/bin/localization.py", line 82, in <module>
> > startLocalizationJob(jobName, splitX, splitY, splitZ,
> doSplitAngles=False)
> > File "/usr/local/pytom/bin/localization.py", line 21, in
> startLocalizationJob
> > leader.parallelRun(job, splitX, splitY, splitZ, verbose)
> > File "/usr/local/pytom/localization/parallel_extract_peaks.py", line
> 1046, in parallelRun
> > result = self.run(verbose)
> > File "/usr/local/pytom/localization/parallel_extract_peaks.py", line
> 104, in run
> > [resV, orientV, sumV, sqrV] = extractPeaks(v, ref, rot, scoreFnc, m,
> mIsSphere, wedg, nodeName=self.name, verboseMode=verbose,
> moreInfo=moreInfo)
> > File "/usr/local/pytom/localization/extractPeaks.py", line 130, in
> extractPeaks
> > meanV = meanUnderMask(volume, maskV, p);
> > File "/usr/local/pytom/basic/correlation.py", line 244, in
> meanUnderMask
> > result = iftshift(ifft(fMask*fft(volume)))/(size*p)
> > File "/usr/local/pytom/pytomc/swigModules/pytom_volume.py", line 342,
> in __mul__
> > return _pytom_volume.vol_comp___mul__(self, *args)
> > RuntimeError: std::bad_alloc
> > -------------------------------------------------------
> > Primary job terminated normally, but 1 process returned
> > a non-zero exit code.. Per user-direction, the job has been aborted.
> >
> >
> > On Fri, Mar 11, 2016 at 11:56 AM, Kanika Khanna <kk...@uc...>
> wrote:
> > Hi Thomas,
> >
> > I have been able to resolve issue 1. I just killed all the processes and
> started again. It worked that time.
> >
> > On Sat, Mar 12, 2016 at 1:05 AM, Thomas Hrabe <th...@gm...> wrote:
> > Hi Kanika,
> >
> >
> > 1.
> > to me, it looks like that you are trying to open a file called
> >
> > > <Volume Binning="[0, 0, 0]" Filename="PY79.mrc" Sampling="[0, 0, 0]"
> Subregion="[0, 0, 0, 0, 0, 0]"/>
> >
> >
> > Can you please attach the xml file?
> >
> > 2.
> > I have to look into the script as well. I must re-install it before I
> can advice about how to use it.
> >
> > Cheers,
> > Thomas
> >
> > > On Mar 11, 2016, at 11:15 AM, Kanika Khanna <kk...@uc...> wrote:
> > >
> > > Hello all,
> > >
> > > 1. When I try to execute my job using the following command
> > > mpirun --host HostName -c 4 pytom localization.py PathToJobFile 2 2 2
> > >
> > > I get the following error:
> > > Traceback (most recent call last):
> > > File "/usr/local/pytom/bin/localization.py", line 82, in <module>
> > > startLocalizationJob(jobName, splitX, splitY, splitZ,
> doSplitAngles=False)
> > > File "/usr/local/pytom/bin/localization.py", line 11, in
> startLocalizationJob
> > > job.check()
> > > File "/usr/local/pytom/localization/peak_job.py", line 184, in check
> > > Traceback (most recent call last):
> > > File "/usr/local/pytom/bin/localization.py", line 82, in <module>
> > > raise IOError('File: ' + str(self.volume) + ' not found!')
> > > IOError: File: <Volume Binning="[0, 0, 0]" Filename="PY79.mrc"
> Sampling="[0, 0, 0]" Subregion="[0, 0, 0, 0, 0, 0]"/>
> > > not found!
> > > startLocalizationJob(jobName, splitX, splitY, splitZ,
> doSplitAngles=False)
> > > File "/usr/local/pytom/bin/localization.py", line 11, in
> startLocalizationJob
> > > job.check()
> > > File "/usr/local/pytom/localization/peak_job.py", line 184, in check
> > > raise IOError('File: ' + str(self.volume) + ' not found!')
> > > IOError: File: <Volume Binning="[0, 0, 0]" Filename="PY79.mrc"
> Sampling="[0, 0, 0]" Subregion="[0, 0, 0, 0, 0, 0]"/>
> > > not found!
> > > Traceback (most recent call last):
> > > File "/usr/local/pytom/bin/localization.py", line 82, in <module>
> > > startLocalizationJob(jobName, splitX, splitY, splitZ,
> doSplitAngles=False)
> > > File "/usr/local/pytom/bin/localization.py", line 11, in
> startLocalizationJob
> > > job.check()
> > > File "/usr/local/pytom/localization/peak_job.py", line 184, in check
> > > raise IOError('File: ' + str(self.volume) + ' not found!')
> > > IOError: File: <Volume Binning="[0, 0, 0]" Filename="PY79.mrc"
> Sampling="[0, 0, 0]" Subregion="[0, 0, 0, 0, 0, 0]"/>
> > > not found!
> > > -------------------------------------------------------
> > > Primary job terminated normally, but 1 process returned
> > > a non-zero exit code.. Per user-direction, the job has been aborted.
> > > -------------------------------------------------------
> > > Traceback (most recent call last):
> > > File "/usr/local/pytom/bin/localization.py", line 82, in <module>
> > > startLocalizationJob(jobName, splitX, splitY, splitZ,
> doSplitAngles=False)
> > > File "/usr/local/pytom/bin/localization.py", line 11, in
> startLocalizationJob
> > > job.check()
> > > File "/usr/local/pytom/localization/peak_job.py", line 184, in check
> > > raise IOError('File: ' + str(self.volume) + ' not found!')
> > > IOError: File: <Volume Binning="[0, 0, 0]" Filename="PY79.mrc"
> Sampling="[0, 0, 0]" Subregion="[0, 0, 0, 0, 0, 0]"/>
> > > not found!
> > >
> --------------------------------------------------------------------------
> > > mpirun detected that one or more processes exited with non-zero
> status, thus causing
> > > the job to be terminated. The first process to do so was:
> > >
> > > Process name: [[27852,1],3]
> > > Exit code: 1
> > >
> > >
> > > Any idea how I can circumvent this? Or what exactly might be going
> wrong?
> > >
> > > 2. Once you have the pl.xml file generated after extraction of
> particles, we have the script VolumeDialog.py for viewing it in Chimera. I
> already installed it in the Volume Viewer folder. How exactly are we
> suppose to use it? Also, there were a couple of existing files of the same
> name in the folder existing previously (is that the case with everyone
> here?). Anything to do with them?
> > >
> > > Thanks!
> > >
> > >
> > >
> > >
> > >
> ------------------------------------------------------------------------------
> > > Transform Data into Opportunity.
> > > Accelerate data analysis in your applications with
> > > Intel Data Analytics Acceleration Library.
> > > Click to learn more.
> > >
> http://pubads.g.doubleclick.net/gampad/clk?id=278785111&iu=/4140_______________________________________________
> > > Pytom-mail mailing list
> > > Pyt...@li...
> > > https://lists.sourceforge.net/lists/listinfo/pytom-mail
> >
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > Transform Data into Opportunity.
> > Accelerate data analysis in your applications with
> > Intel Data Analytics Acceleration Library.
> > Click to learn more.
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=278785231&iu=/4140_______________________________________________
> > Pytom-mail mailing list
> > Pyt...@li...
> > https://lists.sourceforge.net/lists/listinfo/pytom-mail
>
>
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