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|
From: Jose M. de la R. T. <del...@gm...> - 2016-08-24 20:05:30
|
Hi Jonathan, In Scipion the output of any 2D classification method should generate a SetOfClasses2D as output. Independently of the package used (EMAN, Xmipp, Relion, Spider, etc). You should be able to open classes and the particles associated to each classes. In the 2D case, these particles should contain the 2D alignment. Could you provide more details about your specific problem? (in order to detect if the is some bug over there). First, what version of Scipion are you using? Second, if you browse in the ML2D run folder, and go to the extra, can you find the generated .xmd files for each iteration? They looks like having the correct alignment parameters in Xmipp? (MDL_SHIFTX, etc) We are happy to help to overcome this issue and continue with your processing. Bests, Jose Miguel. On Wed, Aug 24, 2016 at 12:39 PM, List, Jonathan <jon...@ph...> wrote: > Hi > > we are currently using scipion for generating class averages of DNA > origami structures. We optained best result with the xmipp ml2d algorithm. > Sadly we were not able to access the single particles for the classes in > the aligned state (it worked for other algorithms). The "aply > gemometry" checkbox charged something but did not result in the correct > alignmet like in the class average image. Also clicking on > summary/ouput/classes insted of "analyse results" which sometimes did the > trick for the old xmipp did not work. Do you know a way to generate this > correctly aligned particle stack from ml2d runs? > > Greetings and thanks > > Jonathan List > > ------------------------------------------------------------ > ------------------ > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
|
From: List, J. <jon...@ph...> - 2016-08-24 10:54:07
|
Hi we are currently using scipion for generating class averages of DNA origami structures. We optained best result with the xmipp ml2d algorithm. Sadly we were not able to access the single particles for the classes in the aligned state (it worked for other algorithms). The "aply gemometry" checkbox charged something but did not result in the correct alignmet like in the class average image. Also clicking on summary/ouput/classes insted of "analyse results" which sometimes did the trick for the old xmipp did not work. Do you know a way to generate this correctly aligned particle stack from ml2d runs? Greetings and thanks Jonathan List |
|
From: Pablo C. <pc...@cn...> - 2016-08-11 12:53:34
|
Dear users,
We don't want to distract you from your research, but we want to share
(monthly) our progress with you.
Hope you find it useful, all the best,
Scipion team.
August 2016
<https://github.com/I2PC/scipion/wiki/Newsletters#graphical-interface-improvements>Graphical
interface improvements
We are always working to improve the graphical tools in order to enhance
the user experience. Two new improvements are planned for the next release:
*
Now you can label your protocols in the Project Window!
<https://github.com/I2PC/scipion/wiki/labels>.
*
Need to pick helix or filaments? linear picking implemented.
<https://github.com/I2PC/scipion/wiki/Linear-picking>
<https://github.com/I2PC/scipion/wiki/Newsletters#new-web-tools-released>New
web tools released
Last month we have released two new web tools, but the paper is not out
yet…Shhh!! The*My reliability tool*will assess the reliability of your
images compared to your map, using"Phantom in the noise"
<http://dx.doi.org/10.3934/biophy.2015.1.21>and the"alignment
reliability" <https://doi.org/10.1038/srep21626>. The*protein
interaction tool*will analyze the domain-domain interactions of your
protein.Do not dare to check them out!
<http://scipion.cnb.csic.es/m/services/>
<https://github.com/I2PC/scipion/wiki/Newsletters#localized-reconstruction-in-scipion>Localized
Reconstruction in Scipion
During the first week of July we received the visit of Serban Ilca
andJuha Huiskonen
<https://www.strubi.ox.ac.uk/research/juha-huiskonen>from the Oxford
Particle Imaging Centre <http://www.opic.ox.ac.uk/>to integrate their
recentLocalized Reconstruction
<https://github.com/OPIC-Oxford/localrec/wiki>method into Scipion. Now
the steps proposed into the method are smoothly integrated into the
whole Scipion framework.
/Same info can be found online //here
<https://github.com/I2PC/scipion/wiki/Newsletters#august-2016>/
|
|
From: Jose M. de la R. T. <del...@gm...> - 2016-07-15 10:33:52
|
Dear Alfonso,
The errors that you are having are very weird, we have never seem before.
Could you provide more information about the installation? What OS and
compiler versions are you using?
What problems did you have when installing external libraries and how did
you solve it?
Best regards,
Jose Miguel.
On Fri, Jul 15, 2016 at 11:53 AM, Alfonso Avino <aa...@ib...> wrote:
> Hi there.
> I'm writing because I had several problem compiling your software.
> After fixing some problem had during the installation of the external
> softwares, now I'm having this error.
>
> Any idea to fix it it and go ahead with the installation?
> Thanks in advance for your help.
>
>
>
> g++ -o
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.o
> -c -Isoftware/em/xmipp/external -Isoftware/em/xmipp/libraries
> -Isoftware/em/xmipp/libraries -Isoftware/include
> -Isoftware/include/python2.7
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:31:
> error: expected constructor, destructor, or type conversion before string
> constant
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:48:
> error: expected class-name before '{' token
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:51:
> error: 'FileName' does not name a type
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:52:
> error: 'FileName' does not name a type
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:53:
> error: ISO C++ forbids declaration of 'MultidimArray' with no type
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:53:
> error: expected ';' before '<' token
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:54:
> error: 'Matrix1D' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:54:
> error: template argument 1 is invalid
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:54:
> error: template argument 2 is invalid
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:54:
> error: expected unqualified-id before '>' token
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:55:
> error: 'MetaData' does not name a type
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:116:
> error: ISO C++ forbids declaration of 'string' with no type
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:116:
> error: expected ',' or '...' before '&' token
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:151:
> error: ISO C++ forbids declaration of 'string' with no type
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:151:
> error: expected ',' or '...' before '&' token
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:202:
> error: ISO C++ forbids declaration of 'MultidimArray' with no type
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:202:
> error: expected ',' or '...' before '<' token
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:212:
> error: ISO C++ forbids declaration of 'cv' with no type
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:212:
> error: expected ',' or '...' before '::' token
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:222:
> error: 'cv' has not been declared
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:222:
> error: expected ',' or '...' before 'opencvDoubleMat'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:230:
> error: ISO C++ forbids declaration of 'FileName' with no type
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:230:
> error: expected ',' or '...' before '&' token
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:261:
> error: ISO C++ forbids declaration of 'cv' with no type
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:261:
> error: expected ',' or '...' before '::' token
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
> In member function 'void ProgOpticalAligment::defineParams()':
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:63:
> error: 'addUsageLine' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:64:
> error: 'addParamsLine' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
> In member function 'void ProgOpticalAligment::readParams()':
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:83:
> error: 'fname' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:83:
> error: 'getParam' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:84:
> error: 'foname' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:85:
> error: 'checkParam' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:87:
> error: 'gianRefFilename' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:89:
> error: 'checkParam' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:91:
> error: 'darkRefFilename' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:93:
> error: 'checkParam' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:95:
> error: 'globalShiftFilename' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:97:
> error: 'getIntParam' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:101:
> error: 'checkParam' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
> In member function 'int ProgOpticalAligment::saveMat(int)':
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:118:
> error: 'M' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:122:
> error: 'ofstream' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:122:
> error: expected ';' before 'out'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:123:
> error: 'out' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:126:
> error: 'M' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:132:
> error: 'out' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
> In member function 'int ProgOpticalAligment::readMat(int)':
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:153:
> error: 'ifstream' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:153:
> error: expected ';' before 'in'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:154:
> error: 'in' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:165:
> error: 'in' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:175:
> error: 'CV_8UC' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:178:
> error: 'CV_32FC' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:181:
> error: 'CV_64FC' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:186:
> error: 'M' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:186:
> error: 'cv' has not been declared
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:186:
> error: 'cv' has not been declared
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
> In member function 'void ProgOpticalAligment::xmipp2Opencv(int)':
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:204:
> error: 'xmippArray' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:204:
> error: 'YSIZE' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:205:
> error: 'XSIZE' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:206:
> error: 'opencvMat' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:206:
> error: 'cv' has not been declared
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:206:
> error: 'CV_32FC1' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:207:
> error: 'FOR_ALL_DIRECT_ELEMENTS_IN_ARRAY2D' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:208:
> error: expected ';' before 'opencvMat'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
> In member function 'void ProgOpticalAligment::opencv2Xmipp(int)':
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:214:
> error: 'opencvMat' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:216:
> error: 'xmippArray' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:217:
> error: 'FOR_ALL_DIRECT_ELEMENTS_IN_ARRAY2D' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:218:
> error: expected ';' before 'DIRECT_A2D_ELEM'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
> In member function 'void ProgOpticalAligment::convert2Uint8(int)':
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:225:
> error: 'cv' has not been declared
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:225:
> error: 'opencvDoubleMat' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:226:
> error: 'opencvUintMat' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:226:
> error: 'CV_8U' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
> In member function 'void ProgOpticalAligment::computeAvg(int)':
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:232:
> error: 'ImageGeneric' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:232:
> error: expected ';' before 'movieStack'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:233:
> error: 'MultidimArray' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:233:
> error: expected primary-expression before 'double'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:233:
> error: expected ';' before 'double'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:234:
> error: 'Matrix1D' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:234:
> error: expected primary-expression before 'double'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:234:
> error: expected ';' before 'double'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:235:
> error: 'end' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:235:
> error: 'begin' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:239:
> error: 'movieStack' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:239:
> error: 'movieFile' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:240:
> error: 'frameImage' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:242:
> error: 'avgImg' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:242:
> error: 'YSIZE' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:242:
> error: 'XSIZE' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:244:
> error: 'darkImage' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:246:
> error: 'gainImage' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:249:
> error: 'shiftMatrix' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:249:
> error: 'XX' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:249:
> error: 'shiftVector' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:250:
> error: 'YY' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:251:
> error: 'LINEAR' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:251:
> error: 'shiftedFrame' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:251:
> error: 'WRAP' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:251:
> error: 'translate' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:252:
> error: 'avgImg' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:255:
> error: 'avgImg' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:257:
> error: 'avgImg' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:258:
> error: 'frameImage' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:259:
> error: 'movieStack' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
> In member function 'void ProgOpticalAligment::std_dev2(int)':
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:267:
> error: 'flowx' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:273:
> error: 'planes' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:273:
> error: expected primary-expression before 'float'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:273:
> error: expected ';' before 'float'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:275:
> error: 'abs' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:277:
> error: expected primary-expression before 'float'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:277:
> error: expected ';' before 'float'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:284:
> error: 'meanStdDev' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:285:
> error: 'sqrt' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
> In member function 'int ProgOpticalAligment::main2()':
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:293:
> error: 'MultidimArray' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:293:
> error: expected primary-expression before 'double'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:293:
> error: expected ';' before 'double'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:294:
> error: expected primary-expression before 'double'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:294:
> error: expected ';' before 'double'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:295:
> error: 'Matrix1D' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:295:
> error: expected primary-expression before 'double'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:295:
> error: expected ';' before 'double'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:296:
> error: 'ImageGeneric' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:296:
> error: expected ';' before 'movieStack'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:297:
> error: 'Image' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:297:
> error: expected primary-expression before 'double'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:297:
> error: expected ';' before 'double'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:298:
> error: 'MetaData' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:298:
> error: expected ';' before 'MD'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:299:
> error: 'FileName' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:299:
> error: expected ';' before 'motionInfFile'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:300:
> error: 'ArrayDim' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:300:
> error: expected ';' before 'aDim'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:312:
> error: 'cv' has not been declared
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:312:
> error: expected ';' before 'flow'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:313:
> error: 'cv' has not been declared
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:313:
> error: expected ';' before 'flowxPre'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:314:
> error: 'cv' has not been declared
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:314:
> error: expected ';' before 'avgcurr'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:315:
> error: 'cv' has not been declared
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:315:
> error: expected ';' before 'planes'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:320:
> error: 'motionInfFile' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:320:
> error: 'foname' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:321:
> error: 'fname' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:324:
> error: 'movieStack' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:324:
> error: 'HEADER' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:325:
> error: 'aDim' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:331:
> error: 'II' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:331:
> error: 'darkRefFilename' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:332:
> error: 'darkImage' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:336:
> error: 'II' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:336:
> error: 'gianRefFilename' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:337:
> error: 'gainImage' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:339:
> error: 'meanStdev' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:341:
> error: 'avgCurr' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:342:
> error: 'flowxPre' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:342:
> error: 'cv' has not been declared
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:342:
> error: 'CV_32FC1' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:343:
> error: 'flowyPre' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:343:
> error: 'cv' has not been declared
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:362:
> error: 'outputMovie' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:366:
> error: expected primary-expression before 'double'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:366:
> error: expected ';' before 'double'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:367:
> error: 'shiftVector' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:368:
> error: 'shiftMD' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:368:
> error: 'globalShiftFilename' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:369:
> error: 'FOR_ALL_OBJECTS_IN_METADATA' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:370:
> error: expected ';' before '{' token
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:383:
> error: 'sqrt' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:388:
> error: 'II' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:392:
> error: 'avgcurr' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:393:
> error: 'cout' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:398:
> error: 'avgstep' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:398:
> error: 'cv' has not been declared
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:415:
> error: expected primary-expression before 'double'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:415:
> error: expected ';' before 'double'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:416:
> error: expected primary-expression before 'double'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:416:
> error: expected ';' before 'double'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:418:
> error: 'frameImage' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:420:
> error: 'darkImage' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:422:
> error: 'gainImage' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:423:
> error: 'shiftMatrix' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:423:
> error: 'XX' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:423:
> error: 'shiftVector' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:424:
> error: 'YY' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:425:
> error: 'BSPLINE3' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:425:
> error: 'preImg' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:425:
> error: 'WRAP' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:425:
> error: 'translate' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:430:
> error: 'preImg' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:432:
> error: 'darkImage' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:434:
> error: 'gainImage' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:436:
> error: 'preImg' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:436:
> error: 'preimg' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:441:
> error: 'preImg' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:443:
> error: 'preImg' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:445:
> error: 'preImg' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:445:
> error: 'preimg' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:447:
> error: 'avgcurr8' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:448:
> error: 'preimg8' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:475:
> error: 'flow' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:475:
> error: 'calcOpticalFlowFarneback' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:478:
> error: 'flowFileName' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:478:
> error: 'formatString' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:479:
> error: 'flow' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:480:
> error: 'cv' has not been declared
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:480:
> error: 'calcOpticalFlowFarneback' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:482:
> error: 'flow' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:482:
> error: 'planes' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:482:
> error: 'split' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:491:
> error: 'MD' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:492:
> error: 'MDL_OPTICALFLOW_MEANX' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:493:
> error: 'MDL_OPTICALFLOW_MEANY' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:494:
> error: 'MDL_OPTICALFLOW_STDX' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:495:
> error: 'MDL_OPTICALFLOW_STDY' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:496:
> error: 'MD_APPEND' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:510:
> error: 'flowFileName' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:510:
> error: 'formatString' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:520:
> error: expected primary-expression before 'float'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:520:
> error: expected ';' before 'float'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:521:
> error: expected primary-expression before 'float'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:521:
> error: expected ';' before 'float'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:523:
> error: 'cv' has not been declared
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:523:
> error: 'dest' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:523:
> error: 'cv' has not been declared
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:526:
> error: 'mappedImg' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:526:
> error: 'outputMovie' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:538:
> error: 'II' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:543:
> error: 'outputMovie' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:548:
> error: 'avgstep' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:549:
> error: 'preimg' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:550:
> error: 'avgcurr8' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:551:
> error: 'preimg8' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:552:
> error: 'flow' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:553:
> error: 'planes' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:558:
> error: 'preImg' was not declared in this scope
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
> In function 'int main(int, char**)':
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:568:
> error: 'class ProgOpticalAligment' has no member named 'read'
> software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:569:
> error: 'class ProgOpticalAligment' has no member named 'tryRun'
> scons: ***
> [software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.o]
> Error 1
> scons: building terminated because of errors.
>
> --
> Alfonso Avino
> Informatica
> IBMB-CSIC
> C/ Baldiri Reixac 15, 3 A17
> 08028, Barcelona, España
> Tel. (+34)934020194
>
>
>
> ------------------------------------------------------------------------------
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> J-Flow, sFlow and other flows. Make informed decisions using capacity
> planning
> reports.http://sdm.link/zohodev2dev
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>
|
|
From: Alfonso A. <aa...@ib...> - 2016-07-15 10:20:00
|
Hi there.
I'm writing because I had several problem compiling your software.
After fixing some problem had during the installation of the external
softwares, now I'm having this error.
Any idea to fix it it and go ahead with the installation?
Thanks in advance for your help.
g++ -o
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.o
-c -Isoftware/em/xmipp/external -Isoftware/em/xmipp/libraries
-Isoftware/em/xmipp/libraries -Isoftware/include
-Isoftware/include/python2.7
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:31:
error: expected constructor, destructor, or type conversion before string
constant
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:48:
error: expected class-name before '{' token
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:51:
error: 'FileName' does not name a type
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:52:
error: 'FileName' does not name a type
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:53:
error: ISO C++ forbids declaration of 'MultidimArray' with no type
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:53:
error: expected ';' before '<' token
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:54:
error: 'Matrix1D' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:54:
error: template argument 1 is invalid
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:54:
error: template argument 2 is invalid
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:54:
error: expected unqualified-id before '>' token
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:55:
error: 'MetaData' does not name a type
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:116:
error: ISO C++ forbids declaration of 'string' with no type
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:116:
error: expected ',' or '...' before '&' token
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:151:
error: ISO C++ forbids declaration of 'string' with no type
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:151:
error: expected ',' or '...' before '&' token
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:202:
error: ISO C++ forbids declaration of 'MultidimArray' with no type
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:202:
error: expected ',' or '...' before '<' token
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:212:
error: ISO C++ forbids declaration of 'cv' with no type
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:212:
error: expected ',' or '...' before '::' token
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:222:
error: 'cv' has not been declared
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:222:
error: expected ',' or '...' before 'opencvDoubleMat'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:230:
error: ISO C++ forbids declaration of 'FileName' with no type
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:230:
error: expected ',' or '...' before '&' token
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:261:
error: ISO C++ forbids declaration of 'cv' with no type
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:261:
error: expected ',' or '...' before '::' token
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
In member function 'void ProgOpticalAligment::defineParams()':
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:63:
error: 'addUsageLine' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:64:
error: 'addParamsLine' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
In member function 'void ProgOpticalAligment::readParams()':
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:83:
error: 'fname' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:83:
error: 'getParam' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:84:
error: 'foname' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:85:
error: 'checkParam' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:87:
error: 'gianRefFilename' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:89:
error: 'checkParam' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:91:
error: 'darkRefFilename' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:93:
error: 'checkParam' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:95:
error: 'globalShiftFilename' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:97:
error: 'getIntParam' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:101:
error: 'checkParam' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
In member function 'int ProgOpticalAligment::saveMat(int)':
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:118:
error: 'M' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:122:
error: 'ofstream' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:122:
error: expected ';' before 'out'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:123:
error: 'out' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:126:
error: 'M' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:132:
error: 'out' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
In member function 'int ProgOpticalAligment::readMat(int)':
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:153:
error: 'ifstream' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:153:
error: expected ';' before 'in'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:154:
error: 'in' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:165:
error: 'in' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:175:
error: 'CV_8UC' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:178:
error: 'CV_32FC' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:181:
error: 'CV_64FC' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:186:
error: 'M' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:186:
error: 'cv' has not been declared
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:186:
error: 'cv' has not been declared
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
In member function 'void ProgOpticalAligment::xmipp2Opencv(int)':
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:204:
error: 'xmippArray' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:204:
error: 'YSIZE' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:205:
error: 'XSIZE' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:206:
error: 'opencvMat' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:206:
error: 'cv' has not been declared
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:206:
error: 'CV_32FC1' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:207:
error: 'FOR_ALL_DIRECT_ELEMENTS_IN_ARRAY2D' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:208:
error: expected ';' before 'opencvMat'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
In member function 'void ProgOpticalAligment::opencv2Xmipp(int)':
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:214:
error: 'opencvMat' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:216:
error: 'xmippArray' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:217:
error: 'FOR_ALL_DIRECT_ELEMENTS_IN_ARRAY2D' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:218:
error: expected ';' before 'DIRECT_A2D_ELEM'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
In member function 'void ProgOpticalAligment::convert2Uint8(int)':
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:225:
error: 'cv' has not been declared
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:225:
error: 'opencvDoubleMat' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:226:
error: 'opencvUintMat' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:226:
error: 'CV_8U' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
In member function 'void ProgOpticalAligment::computeAvg(int)':
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:232:
error: 'ImageGeneric' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:232:
error: expected ';' before 'movieStack'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:233:
error: 'MultidimArray' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:233:
error: expected primary-expression before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:233:
error: expected ';' before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:234:
error: 'Matrix1D' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:234:
error: expected primary-expression before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:234:
error: expected ';' before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:235:
error: 'end' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:235:
error: 'begin' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:239:
error: 'movieStack' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:239:
error: 'movieFile' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:240:
error: 'frameImage' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:242:
error: 'avgImg' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:242:
error: 'YSIZE' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:242:
error: 'XSIZE' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:244:
error: 'darkImage' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:246:
error: 'gainImage' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:249:
error: 'shiftMatrix' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:249:
error: 'XX' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:249:
error: 'shiftVector' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:250:
error: 'YY' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:251:
error: 'LINEAR' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:251:
error: 'shiftedFrame' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:251:
error: 'WRAP' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:251:
error: 'translate' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:252:
error: 'avgImg' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:255:
error: 'avgImg' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:257:
error: 'avgImg' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:258:
error: 'frameImage' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:259:
error: 'movieStack' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
In member function 'void ProgOpticalAligment::std_dev2(int)':
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:267:
error: 'flowx' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:273:
error: 'planes' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:273:
error: expected primary-expression before 'float'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:273:
error: expected ';' before 'float'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:275:
error: 'abs' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:277:
error: expected primary-expression before 'float'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:277:
error: expected ';' before 'float'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:284:
error: 'meanStdDev' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:285:
error: 'sqrt' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
In member function 'int ProgOpticalAligment::main2()':
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:293:
error: 'MultidimArray' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:293:
error: expected primary-expression before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:293:
error: expected ';' before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:294:
error: expected primary-expression before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:294:
error: expected ';' before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:295:
error: 'Matrix1D' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:295:
error: expected primary-expression before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:295:
error: expected ';' before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:296:
error: 'ImageGeneric' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:296:
error: expected ';' before 'movieStack'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:297:
error: 'Image' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:297:
error: expected primary-expression before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:297:
error: expected ';' before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:298:
error: 'MetaData' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:298:
error: expected ';' before 'MD'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:299:
error: 'FileName' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:299:
error: expected ';' before 'motionInfFile'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:300:
error: 'ArrayDim' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:300:
error: expected ';' before 'aDim'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:312:
error: 'cv' has not been declared
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:312:
error: expected ';' before 'flow'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:313:
error: 'cv' has not been declared
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:313:
error: expected ';' before 'flowxPre'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:314:
error: 'cv' has not been declared
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:314:
error: expected ';' before 'avgcurr'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:315:
error: 'cv' has not been declared
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:315:
error: expected ';' before 'planes'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:320:
error: 'motionInfFile' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:320:
error: 'foname' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:321:
error: 'fname' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:324:
error: 'movieStack' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:324:
error: 'HEADER' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:325:
error: 'aDim' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:331:
error: 'II' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:331:
error: 'darkRefFilename' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:332:
error: 'darkImage' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:336:
error: 'II' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:336:
error: 'gianRefFilename' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:337:
error: 'gainImage' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:339:
error: 'meanStdev' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:341:
error: 'avgCurr' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:342:
error: 'flowxPre' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:342:
error: 'cv' has not been declared
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:342:
error: 'CV_32FC1' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:343:
error: 'flowyPre' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:343:
error: 'cv' has not been declared
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:362:
error: 'outputMovie' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:366:
error: expected primary-expression before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:366:
error: expected ';' before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:367:
error: 'shiftVector' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:368:
error: 'shiftMD' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:368:
error: 'globalShiftFilename' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:369:
error: 'FOR_ALL_OBJECTS_IN_METADATA' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:370:
error: expected ';' before '{' token
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:383:
error: 'sqrt' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:388:
error: 'II' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:392:
error: 'avgcurr' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:393:
error: 'cout' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:398:
error: 'avgstep' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:398:
error: 'cv' has not been declared
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:415:
error: expected primary-expression before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:415:
error: expected ';' before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:416:
error: expected primary-expression before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:416:
error: expected ';' before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:418:
error: 'frameImage' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:420:
error: 'darkImage' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:422:
error: 'gainImage' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:423:
error: 'shiftMatrix' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:423:
error: 'XX' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:423:
error: 'shiftVector' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:424:
error: 'YY' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:425:
error: 'BSPLINE3' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:425:
error: 'preImg' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:425:
error: 'WRAP' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:425:
error: 'translate' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:430:
error: 'preImg' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:432:
error: 'darkImage' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:434:
error: 'gainImage' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:436:
error: 'preImg' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:436:
error: 'preimg' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:441:
error: 'preImg' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:443:
error: 'preImg' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:445:
error: 'preImg' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:445:
error: 'preimg' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:447:
error: 'avgcurr8' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:448:
error: 'preimg8' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:475:
error: 'flow' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:475:
error: 'calcOpticalFlowFarneback' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:478:
error: 'flowFileName' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:478:
error: 'formatString' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:479:
error: 'flow' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:480:
error: 'cv' has not been declared
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:480:
error: 'calcOpticalFlowFarneback' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:482:
error: 'flow' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:482:
error: 'planes' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:482:
error: 'split' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:491:
error: 'MD' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:492:
error: 'MDL_OPTICALFLOW_MEANX' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:493:
error: 'MDL_OPTICALFLOW_MEANY' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:494:
error: 'MDL_OPTICALFLOW_STDX' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:495:
error: 'MDL_OPTICALFLOW_STDY' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:496:
error: 'MD_APPEND' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:510:
error: 'flowFileName' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:510:
error: 'formatString' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:520:
error: expected primary-expression before 'float'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:520:
error: expected ';' before 'float'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:521:
error: expected primary-expression before 'float'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:521:
error: expected ';' before 'float'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:523:
error: 'cv' has not been declared
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:523:
error: 'dest' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:523:
error: 'cv' has not been declared
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:526:
error: 'mappedImg' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:526:
error: 'outputMovie' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:538:
error: 'II' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:543:
error: 'outputMovie' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:548:
error: 'avgstep' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:549:
error: 'preimg' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:550:
error: 'avgcurr8' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:551:
error: 'preimg8' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:552:
error: 'flow' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:553:
error: 'planes' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:558:
error: 'preImg' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
In function 'int main(int, char**)':
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:568:
error: 'class ProgOpticalAligment' has no member named 'read'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:569:
error: 'class ProgOpticalAligment' has no member named 'tryRun'
scons: ***
[software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.o]
Error 1
scons: building terminated because of errors.
--
Alfonso Avino
Informatica
IBMB-CSIC
C/ Baldiri Reixac 15, 3 A17
08028, Barcelona, España
Tel. (+34)934020194
|
|
From: Juha H. <juh...@gm...> - 2016-07-11 17:45:47
|
Dear Jose Miguel, I prefer to collect movies as stacks instead of single frames but I would say both scenarios are pretty common. Best wishes, Juha -- Juha T. Huiskonen, PhD Associate Professor Principal Investigator Oxford Particle Imaging Centre Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford http://www.strubi.ox.ac.uk/strubi/research/huiskonen/ Email: ju...@st... Tel.: +44 1865 287 844 Mob.: +44 7576 505 422 On Mon, Jul 11, 2016 at 5:25 PM, Jose Miguel de la Rosa Trevin < del...@gm...> wrote: > Indeed, the # has an special meaning, because it mark the ID of the item > (either Micrograph or Movie) that will be used > inside the set. The % character can do the work here. In a general case I > think that should be combined with the > movies since the most common case is to have a dataset with more than one > movie. > > I will let you know when you do any progress in this direction. I'm > thinking that it can a bit more complicated when using > this in an streaming mode. By the way, how do you usually collect movies, > in a single stack or in separate frames, or both? > > Bests, > Jose Miguel. > > > On Mon, Jul 11, 2016 at 5:51 PM, Juha Huiskonen <juh...@gm...> > wrote: > >> Dear Jose Miguel, >> >> May I suggest that wildcards "*" and "?" are reserved for general use and >> "#" for digits [0-9], and "%" for specifying the pattern for all the frames >> in one movie. >> >> So in my case >> >> movie_%%%%.mrc >> >> or >> >> mov*_%%%%.mrc >> >> would work. I hope that makes sense and would not be too complicated. >> >> Alternatively, a >> >> Best wishes, >> Juha >> >> >> >> -- >> Juha T. Huiskonen, PhD >> Associate Professor >> Principal Investigator >> >> Oxford Particle Imaging Centre >> Division of Structural Biology >> Wellcome Trust Centre for Human Genetics >> University of Oxford >> >> http://www.strubi.ox.ac.uk/strubi/research/huiskonen/ >> Email: ju...@st... >> Tel.: +44 1865 287 844 >> Mob.: +44 7576 505 422 >> >> On Mon, Jul 11, 2016 at 4:24 PM, Jose Miguel de la Rosa Trevin < >> del...@gm...> wrote: >> >>> Dear Juha, >>> >>> Right now it is only possible to import frames contained in a single >>> stack (mrcs or any other EM format). >>> I have started a modification to support frames in individual frames, >>> but it is in a development branch >>> and is not ready yet. Something that we still have not clear is how we >>> could allow to specify both the movie part >>> and the frame part in the pattern without complicating things too >>> much....so any suggestion about this is >>> welcome. >>> >>> We have pending to generate some documentation pages about the types and >>> options for each import case. >>> >>> Hope this helps, >>> Jose Miguel. >>> >>> >>> On Mon, Jul 11, 2016 at 4:37 PM, Juha Huiskonen < >>> juh...@gm...> wrote: >>> >>>> Hi all, >>>> >>>> I am trying to import one movie, that is stored as separate frames, >>>> called >>>> >>>> movie_0001.mrc >>>> movie_0002.mrc >>>> ... >>>> movie_0020.mrc >>>> >>>> For import, I tried using pattern movie_####.mrc which I was hoping >>>> would do exactly what I wanted. However, it seems I got out 20 single frame >>>> 'movies', instead of one 20-frame movie (SetOfMovies has 20 items). >>>> >>>> What am I doing wrong? >>>> >>>> Best wishes, >>>> Juha >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> 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 >>>> _______________________________________________ >>>> scipion-users mailing list >>>> sci...@li... >>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>> >>>> >>> >> >> >> ------------------------------------------------------------------------------ >> 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 >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> > |
|
From: Jose M. de la R. T. <del...@gm...> - 2016-07-11 16:25:59
|
Indeed, the # has an special meaning, because it mark the ID of the item (either Micrograph or Movie) that will be used inside the set. The % character can do the work here. In a general case I think that should be combined with the movies since the most common case is to have a dataset with more than one movie. I will let you know when you do any progress in this direction. I'm thinking that it can a bit more complicated when using this in an streaming mode. By the way, how do you usually collect movies, in a single stack or in separate frames, or both? Bests, Jose Miguel. On Mon, Jul 11, 2016 at 5:51 PM, Juha Huiskonen <juh...@gm...> wrote: > Dear Jose Miguel, > > May I suggest that wildcards "*" and "?" are reserved for general use and > "#" for digits [0-9], and "%" for specifying the pattern for all the frames > in one movie. > > So in my case > > movie_%%%%.mrc > > or > > mov*_%%%%.mrc > > would work. I hope that makes sense and would not be too complicated. > > Alternatively, a > > Best wishes, > Juha > > > > -- > Juha T. Huiskonen, PhD > Associate Professor > Principal Investigator > > Oxford Particle Imaging Centre > Division of Structural Biology > Wellcome Trust Centre for Human Genetics > University of Oxford > > http://www.strubi.ox.ac.uk/strubi/research/huiskonen/ > Email: ju...@st... > Tel.: +44 1865 287 844 > Mob.: +44 7576 505 422 > > On Mon, Jul 11, 2016 at 4:24 PM, Jose Miguel de la Rosa Trevin < > del...@gm...> wrote: > >> Dear Juha, >> >> Right now it is only possible to import frames contained in a single >> stack (mrcs or any other EM format). >> I have started a modification to support frames in individual frames, but >> it is in a development branch >> and is not ready yet. Something that we still have not clear is how we >> could allow to specify both the movie part >> and the frame part in the pattern without complicating things too >> much....so any suggestion about this is >> welcome. >> >> We have pending to generate some documentation pages about the types and >> options for each import case. >> >> Hope this helps, >> Jose Miguel. >> >> >> On Mon, Jul 11, 2016 at 4:37 PM, Juha Huiskonen <juh...@gm... >> > wrote: >> >>> Hi all, >>> >>> I am trying to import one movie, that is stored as separate frames, >>> called >>> >>> movie_0001.mrc >>> movie_0002.mrc >>> ... >>> movie_0020.mrc >>> >>> For import, I tried using pattern movie_####.mrc which I was hoping >>> would do exactly what I wanted. However, it seems I got out 20 single frame >>> 'movies', instead of one 20-frame movie (SetOfMovies has 20 items). >>> >>> What am I doing wrong? >>> >>> Best wishes, >>> Juha >>> >>> >>> ------------------------------------------------------------------------------ >>> 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 >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >>> >> > > > ------------------------------------------------------------------------------ > 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 > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
|
From: Juha H. <juh...@gm...> - 2016-07-11 15:52:14
|
Dear Jose Miguel, May I suggest that wildcards "*" and "?" are reserved for general use and "#" for digits [0-9], and "%" for specifying the pattern for all the frames in one movie. So in my case movie_%%%%.mrc or mov*_%%%%.mrc would work. I hope that makes sense and would not be too complicated. Alternatively, a Best wishes, Juha -- Juha T. Huiskonen, PhD Associate Professor Principal Investigator Oxford Particle Imaging Centre Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford http://www.strubi.ox.ac.uk/strubi/research/huiskonen/ Email: ju...@st... Tel.: +44 1865 287 844 Mob.: +44 7576 505 422 On Mon, Jul 11, 2016 at 4:24 PM, Jose Miguel de la Rosa Trevin < del...@gm...> wrote: > Dear Juha, > > Right now it is only possible to import frames contained in a single stack > (mrcs or any other EM format). > I have started a modification to support frames in individual frames, but > it is in a development branch > and is not ready yet. Something that we still have not clear is how we > could allow to specify both the movie part > and the frame part in the pattern without complicating things too > much....so any suggestion about this is > welcome. > > We have pending to generate some documentation pages about the types and > options for each import case. > > Hope this helps, > Jose Miguel. > > > On Mon, Jul 11, 2016 at 4:37 PM, Juha Huiskonen <juh...@gm...> > wrote: > >> Hi all, >> >> I am trying to import one movie, that is stored as separate frames, called >> >> movie_0001.mrc >> movie_0002.mrc >> ... >> movie_0020.mrc >> >> For import, I tried using pattern movie_####.mrc which I was hoping would >> do exactly what I wanted. However, it seems I got out 20 single frame >> 'movies', instead of one 20-frame movie (SetOfMovies has 20 items). >> >> What am I doing wrong? >> >> Best wishes, >> Juha >> >> >> ------------------------------------------------------------------------------ >> 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 >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> > |
|
From: Jose M. de la R. T. <del...@gm...> - 2016-07-11 15:24:28
|
Dear Juha, Right now it is only possible to import frames contained in a single stack (mrcs or any other EM format). I have started a modification to support frames in individual frames, but it is in a development branch and is not ready yet. Something that we still have not clear is how we could allow to specify both the movie part and the frame part in the pattern without complicating things too much....so any suggestion about this is welcome. We have pending to generate some documentation pages about the types and options for each import case. Hope this helps, Jose Miguel. On Mon, Jul 11, 2016 at 4:37 PM, Juha Huiskonen <juh...@gm...> wrote: > Hi all, > > I am trying to import one movie, that is stored as separate frames, called > > movie_0001.mrc > movie_0002.mrc > ... > movie_0020.mrc > > For import, I tried using pattern movie_####.mrc which I was hoping would > do exactly what I wanted. However, it seems I got out 20 single frame > 'movies', instead of one 20-frame movie (SetOfMovies has 20 items). > > What am I doing wrong? > > Best wishes, > Juha > > > ------------------------------------------------------------------------------ > 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 > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
|
From: Juha H. <juh...@gm...> - 2016-07-11 14:38:28
|
Hi all, I am trying to import one movie, that is stored as separate frames, called movie_0001.mrc movie_0002.mrc ... movie_0020.mrc For import, I tried using pattern movie_####.mrc which I was hoping would do exactly what I wanted. However, it seems I got out 20 single frame 'movies', instead of one 20-frame movie (SetOfMovies has 20 items). What am I doing wrong? Best wishes, Juha |
|
From: Jose M. de la R. T. <del...@gm...> - 2016-07-04 11:56:17
|
Dear Scipion users, We are pleased to announce a new bug-fixing release of Scipion, version v1.0.1!!! Several small bugs have been fixed in Spider, Relion, Frealign, Resmap and Xmipp protocols inside Scipion. Moreover, some improvements and fixes were done also in some graphical interfaces. For more details see: https://github.com/I2PC/scipion/releases/tag/v1.0.1 The new version is already available for download here: http://scipion.cnb.csic.es/m/download_form Some instructions about how to upgrade from v1.0.0 are provided here: https://github.com/I2PC/scipion/wiki/Update-from-v1.0.0-to-v1.0.1 As usual, do not hesitate to contact us if you need any help, have any questions or feedback. Cheers, Scipion Development Team |
|
From: Jose M. de la R. T. <del...@gm...> - 2016-06-30 11:54:09
|
Dear Lei, I'm really sorry for taking so long to answer your mail. We were really busy with some workshops and recently with a new Scipion bug-fixing release (v1.0.1) that will be out in the next days. When you mention estimation and correction for anisotropic magnication distortion, are you referring to a particular method? I have seen a recent one in ScienceDirect: http://www.sciencedirect.com/science/article/pii/S1047847716301095 Or a previous one (end of last year): http://www.sciencedirect.com/science/article/pii/S1047847715300186 We will add your petition for the list of requested feature in our roadmap, but I'm not sure when we can work on it. Do you have some kind of scripts for doing this estimation and correction? You are welcome if you want to contribute with them to the Scipion code. We would be very happy to assist you with the knowledge required for adding new protocols into Scipion. Kind regards and sorry again for the delay, Bests, Jose Miguel. On Tue, Jun 7, 2016 at 2:51 PM, 王雷 <wan...@16...> wrote: > Dear developers, > Thanks very much for your Scipion software, as it's convenient for me to > use tools from different cryo-EM programs. And it would be better if you > could incorporate the function to estimation and correction of anisotropic > magnification distortion in EM. Thanks for your attention. > Regards, > Lei > > > > > > > > > ------------------------------------------------------------------------------ > What NetFlow Analyzer can do for you? Monitors network bandwidth and > traffic > patterns at an interface-level. Reveals which users, apps, and protocols > are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity > planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
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From: 王雷 <wan...@16...> - 2016-06-07 12:51:26
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Dear developers, Thanks very much for your Scipion software, as it's convenient for me to use tools from different cryo-EM programs. And it would be better if you could incorporate the function to estimation and correction of anisotropic magnification distortion in EM. Thanks for your attention. Regards, Lei |
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From: Jose M. de la R. T. <del...@gm...> - 2016-05-26 19:36:08
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Dear Ian, In this case it seems that our installation script did not detected where your MPI folders are, even if they are properly installed in your system. You should edit config/scipion.conf and modify the values for: MPI_LIBDIR (the place where the mpi librares are, usually the libmpi*.so should be there) MPI_BINDIR (the folder where mpi programs are, mpiCC and mpicc MPI_INCLUDE (the folder where the header files are, usually mpi.h) Please let us know if you could fix that and the installation proceed or do you find any other issue. Bests, Jose Miguel. On Thu, May 26, 2016 at 6:34 PM, Ian Tickle <Ian...@as...> wrote: > > Hello, I'm having some problems with the initial installation, this is > what I get: > > cluster_user@master:/software/scipion$ scipion config > > Scipion v1.0.0 (2016-02-20) Augusto > > >>>>> python /software/scipion/pyworkflow/apps/pw_config.py > All the expected sections and options found in > /software/scipion/config/scipion.conf > All the expected sections and options found in > /software/scipion/config/protocols.conf > All the expected sections and options found in > /software/scipion/config/hosts.conf > All the expected sections and options found in > /home/cluster_user/.config/scipion/scipion.conf > Checking paths in /software/scipion/config/scipion.conf ... > Path to MPI_LIBDIR (/usr/lib64/openmpi/lib) should exist but it doesn't. > Path to MPI_INCLUDE (/usr/include/openmpi-x86_64) should exist but it > doesn't. > Path to MPI_BINDIR (/usr/lib64/openmpi/bin) should exist but it doesn't. > Cannot find file: /usr/lib64/openmpi/bin/mpicc > Cannot find file: /usr/lib64/openmpi/bin/mpiCC > Cannot find file: /usr/lib64/openmpi/bin/mpiCC > Cannot find file: /usr/include/openmpi-x86_64/mpi.h > Errors found. > Please edit /software/scipion/config/scipion.conf and check again. > To regenerate the config files trying to guess the paths, you can run: > scipion config --overwrite > > cluster_user@master:/software/scipion$ which scipion > ./scipion > > > AFAICS all the dependencies are installed: > > root@master:~# sudo apt-get install openjdk-7-jdk libopenmpi-dev > openmpi-bin gfortran > Reading package lists... Done > Building dependency tree > Reading state information... Done > openjdk-7-jdk is already the newest version. > openmpi-bin is already the newest version. > libopenmpi-dev is already the newest version. > gfortran is already the newest version. > 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. > > > I tried changing /usr/lib64 to /usr/lib but it made no difference, so now > I'm stuck. > > Any ideas? > > Thanks > > -- Ian > > > ******************************************** > Ian J. Tickle MA, DPhil. > X-ray Technology Consultant > Astex Pharmaceuticals > 436 Science Park > Milton Road > Cambridge > CB4 0QA, UK > Tel: +44(0)1223 435071 > Fax: +44(0)1223 226201 > WWW: astx.com > > > This email and any attachments thereto may contain private, confidential, > and privileged material for the sole use of the intended recipient. Any > review, copying or distribution of this email (or any attachments thereto) > by others is strictly prohibited. If you are not the intended recipient, > please delete the original and any copies of this email and any attachments > thereto and notify the sender immediately. > > > > ------------------------------------------------------------------------------ > 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 > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Ian T. <Ian...@as...> - 2016-05-26 16:50:24
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Hello, I'm having some problems with the initial installation, this is what I get: cluster_user@master:/software/scipion$ scipion config Scipion v1.0.0 (2016-02-20) Augusto >>>>> python /software/scipion/pyworkflow/apps/pw_config.py All the expected sections and options found in /software/scipion/config/scipion.conf All the expected sections and options found in /software/scipion/config/protocols.conf All the expected sections and options found in /software/scipion/config/hosts.conf All the expected sections and options found in /home/cluster_user/.config/scipion/scipion.conf Checking paths in /software/scipion/config/scipion.conf ... Path to MPI_LIBDIR (/usr/lib64/openmpi/lib) should exist but it doesn't. Path to MPI_INCLUDE (/usr/include/openmpi-x86_64) should exist but it doesn't. Path to MPI_BINDIR (/usr/lib64/openmpi/bin) should exist but it doesn't. Cannot find file: /usr/lib64/openmpi/bin/mpicc Cannot find file: /usr/lib64/openmpi/bin/mpiCC Cannot find file: /usr/lib64/openmpi/bin/mpiCC Cannot find file: /usr/include/openmpi-x86_64/mpi.h Errors found. Please edit /software/scipion/config/scipion.conf and check again. To regenerate the config files trying to guess the paths, you can run: scipion config --overwrite cluster_user@master:/software/scipion$ which scipion ./scipion AFAICS all the dependencies are installed: root@master:~# sudo apt-get install openjdk-7-jdk libopenmpi-dev openmpi-bin gfortran Reading package lists... Done Building dependency tree Reading state information... Done openjdk-7-jdk is already the newest version. openmpi-bin is already the newest version. libopenmpi-dev is already the newest version. gfortran is already the newest version. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I tried changing /usr/lib64 to /usr/lib but it made no difference, so now I'm stuck. Any ideas? Thanks -- Ian ******************************************** Ian J. Tickle MA, DPhil. X-ray Technology Consultant Astex Pharmaceuticals 436 Science Park Milton Road Cambridge CB4 0QA, UK Tel: +44(0)1223 435071 Fax: +44(0)1223 226201 WWW: astx.com This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient. Any review, copying or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please delete the original and any copies of this email and any attachments thereto and notify the sender immediately. |
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From: David B. <Dav...@ut...> - 2016-05-25 18:06:19
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Jose Miguel, Thank you for getting back to me. I don’t think anything unusual happened, but I’ve copied my student on this message, and he can reply if he thinks of anything strange that happened. I think he successfully opened the file in the morning but couldn’t when he came to see me later in the day. I attached the project.sqlite and settings.sqlite files in a compressed tar file. David ======================================= David M. Belnap Electron Microscopy Core Laboratory Department of Biochemistry Department of Biology 2501 SMBB University of Utah Salt Lake City, Utah 84112 USA Phone 801.585.1242 FAX 801.587.3077 Dav...@ut... ======================================= > On May 25, 2016, at 2:39 AM, Jose Miguel de la Rosa Trevin <del...@gm...> wrote: > > Dear David, > > Do you have any clue have this happened? Maybe an interrupted copy of the project files? > We haven't experienced this problem until now. I must say that .sqlite database files are quite robust. > > Anyway, could you send us the corrupted file to take a look? All runs make a copy of the db at the > moment they started, so, if we do not succeed in recovering the db file, we could use the last > run db as a kind of "backup". > > Kind regards, > Jose Miguel. > > > On Wed, May 25, 2016 at 12:42 AM, David Belnap <Dav...@ut...> wrote: > I have a data set that is all of a sudden giving the error "database disk image is malformed” when I try to open it. It didn’t give this error this morning, but does this afternoon! What does that error mean? > > Thanks. > > David > > ======================================= > David M. Belnap > Electron Microscopy Core Laboratory > Department of Biochemistry > Department of Biology > 2501 SMBB > University of Utah > Salt Lake City, Utah 84112 USA > Phone 801.585.1242 > FAX 801.587.3077 > Dav...@ut... > ======================================= > > > > > > > ------------------------------------------------------------------------------ > 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 > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Jose M. de la R. T. <del...@gm...> - 2016-05-25 08:39:28
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Dear David, Do you have any clue have this happened? Maybe an interrupted copy of the project files? We haven't experienced this problem until now. I must say that .sqlite database files are quite robust. Anyway, could you send us the corrupted file to take a look? All runs make a copy of the db at the moment they started, so, if we do not succeed in recovering the db file, we could use the last run db as a kind of "backup". Kind regards, Jose Miguel. On Wed, May 25, 2016 at 12:42 AM, David Belnap <Dav...@ut...> wrote: > I have a data set that is all of a sudden giving the error "database disk > image is malformed” when I try to open it. It didn’t give this error this > morning, but does this afternoon! What does that error mean? > > Thanks. > > David > > ======================================= > David M. Belnap > Electron Microscopy Core Laboratory > Department of Biochemistry > Department of Biology > 2501 SMBB > University of Utah > Salt Lake City, Utah 84112 USA > Phone 801.585.1242 > FAX 801.587.3077 > Dav...@ut... > ======================================= > > > > > > > > ------------------------------------------------------------------------------ > 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 > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: David B. <Dav...@ut...> - 2016-05-24 22:42:17
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I have a data set that is all of a sudden giving the error "database disk image is malformed” when I try to open it. It didn’t give this error this morning, but does this afternoon! What does that error mean? Thanks. David ======================================= David M. Belnap Electron Microscopy Core Laboratory Department of Biochemistry Department of Biology 2501 SMBB University of Utah Salt Lake City, Utah 84112 USA Phone 801.585.1242 FAX 801.587.3077 Dav...@ut... ======================================= |
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From: Pablo C. <pc...@cn...> - 2016-04-19 06:18:59
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Thanks Jose! Now I know I was missing even more things than Jagan. ;-) On 19/04/16 08:08, Jose Miguel de la Rosa Trevin wrote: > Pablo, > > I think you has pointed out to an out-of-date Xmipp page. I think the > new one for *xmipp_phantom_create *is: > http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Phantom_create_v31 > > Additional information about the input metadata format can be found here: > http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/FileFormats > > Jagan, euler angles are always tricky. In Xmipp, the convention is > ZYZ, this means: > - rotate first around the Z axis (this single rotation does not change > the case of the cylinder volume) > - rotate around the new Y axis, and > - rotate around the new Z axis (again, this makes no distinction in > the particular case of the cylinder) > > I think you can use for the last values: 90 90 0 and this will give > you a different oriented volume than 0 90 0. As I said, *in the > cylinder case*, if rot and tilt angles are the same, the psi (last > in-plane rotation around Z) will not change the volume orientation. > > Hope this helps, > Jose Miguel. > > > > > On Mon, Apr 18, 2016 at 7:43 PM, Pablo Conesa <pc...@cn... > <mailto:pc...@cn...>> wrote: > > Hi, Jagan...I'm probably not the right person to answer since I > couldn't run the phanton_create last week!! > > Wait I've tried today and now I can generate a volume > > > I might be missing something too but format in the wiki and in my > local working file looks different: > > wiki: http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Create_phantom > > My file has (this generate a cylinder in the center (circular base): > > This: > > 65 65 65 0 > cyl = 1 -30 0 0 5 10 30 0 0 0 > cyl = 1 -10 0 0 5 10 30 0 0 90 > cyl = 1 10 0 0 5 10 30 0 90 0 > cyl = 1 30 0 0 5 10 30 90 0 0 > > > generates this (front view -z): > > > > > To me, what seems to be wrong th the last one, unless I'm not > getting it right, which it's very likely. > > > Which version are you working with? > > Sorry for not being resolutive!! > > All the best, Pablo. > > > On 18/04/16 11:20, Jagan Mohan wrote: >> Dear All, >> >> I have been trying to use xmipp_phantom_create to create a >> cylinder using the following description file contents - >> >> >> # XMIPP_STAR_1 * >> # Phantom description file, (generated with phantom help) >> data_block1 >> _dimensions3D '232 232 232' >> _phantomBGDensity 0 >> _scale 1 >> data_block2 >> loop_ >> _featureType >> _featureOperation >> _featureDensity >> _featureCenter >> _featureSpecificVector >> cyl + 1 '0 0 0' '40 40 232 0 90 0' >> >> >> However, when I change the last line to >> >> cyl + 1 '0 0 0' '40 40 232 0 90 90' >> >> I get the same volume in both cases meaning that the last >> rotation around Z is not being applied. Am I missing something >> here? Is it something to do with the center of rotation? >> >> >> Regards, >> Jagan >> >> >> >> >> -- >> -{[O]}- >> >> >> ------------------------------------------------------------------------------ >> Find and fix application performance issues faster with Applications Manager >> Applications Manager provides deep performance insights into multiple tiers of >> your business applications. It resolves application problems quickly and >> reduces your MTTR. Get your free trial! >> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users > > > ------------------------------------------------------------------------------ > Find and fix application performance issues faster with > Applications Manager > Applications Manager provides deep performance insights into > multiple tiers of > your business applications. It resolves application problems > quickly and > reduces your MTTR. Get your free trial! > https://ad.doubleclick.net/ddm/clk/302982198;130105516;z > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
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From: Jose M. de la R. T. <del...@gm...> - 2016-04-19 06:08:50
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Pablo, I think you has pointed out to an out-of-date Xmipp page. I think the new one for *xmipp_phantom_create *is: http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Phantom_create_v31 Additional information about the input metadata format can be found here: http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/FileFormats Jagan, euler angles are always tricky. In Xmipp, the convention is ZYZ, this means: - rotate first around the Z axis (this single rotation does not change the case of the cylinder volume) - rotate around the new Y axis, and - rotate around the new Z axis (again, this makes no distinction in the particular case of the cylinder) I think you can use for the last values: 90 90 0 and this will give you a different oriented volume than 0 90 0. As I said, *in the cylinder case*, if rot and tilt angles are the same, the psi (last in-plane rotation around Z) will not change the volume orientation. Hope this helps, Jose Miguel. On Mon, Apr 18, 2016 at 7:43 PM, Pablo Conesa <pc...@cn...> wrote: > Hi, Jagan...I'm probably not the right person to answer since I couldn't > run the phanton_create last week!! > > Wait I've tried today and now I can generate a volume > > > I might be missing something too but format in the wiki and in my local > working file looks different: > > wiki: http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Create_phantom > > My file has (this generate a cylinder in the center (circular base): > > This: > > 65 65 65 0 > cyl = 1 -30 0 0 5 10 30 0 0 0 > cyl = 1 -10 0 0 5 10 30 0 0 90 > cyl = 1 10 0 0 5 10 30 0 90 0 > cyl = 1 30 0 0 5 10 30 90 0 0 > > > generates this (front view -z): > > > > > To me, what seems to be wrong th the last one, unless I'm not getting it > right, which it's very likely. > > > Which version are you working with? > > Sorry for not being resolutive!! > > All the best, Pablo. > > > On 18/04/16 11:20, Jagan Mohan wrote: > > Dear All, > > I have been trying to use xmipp_phantom_create to create a cylinder using > the following description file contents - > > > # XMIPP_STAR_1 * > # Phantom description file, (generated with phantom help) > data_block1 > _dimensions3D '232 232 232' > _phantomBGDensity 0 > _scale 1 > data_block2 > loop_ > _featureType > _featureOperation > _featureDensity > _featureCenter > _featureSpecificVector > cyl + 1 '0 0 0' '40 40 232 0 90 0' > > > However, when I change the last line to > > cyl + 1 '0 0 0' '40 40 232 0 90 90' > > I get the same volume in both cases meaning that the last rotation around > Z is not being applied. Am I missing something here? Is it something to do > with the center of rotation? > > > Regards, > Jagan > > > > > -- > -{[O]}- > > > ------------------------------------------------------------------------------ > Find and fix application performance issues faster with Applications Manager > Applications Manager provides deep performance insights into multiple tiers of > your business applications. It resolves application problems quickly and > reduces your MTTR. Get your free trial!https://ad.doubleclick.net/ddm/clk/302982198;130105516;z > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > > ------------------------------------------------------------------------------ > Find and fix application performance issues faster with Applications > Manager > Applications Manager provides deep performance insights into multiple > tiers of > your business applications. It resolves application problems quickly and > reduces your MTTR. Get your free trial! > https://ad.doubleclick.net/ddm/clk/302982198;130105516;z > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
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From: Pablo C. <pc...@cn...> - 2016-04-18 17:44:20
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Hi, Jagan...I'm probably not the right person to answer since I couldn't run the phanton_create last week!! Wait I've tried today and now I can generate a volume I might be missing something too but format in the wiki and in my local working file looks different: wiki: http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Create_phantom My file has (this generate a cylinder in the center (circular base): This: 65 65 65 0 cyl = 1 -30 0 0 5 10 30 0 0 0 cyl = 1 -10 0 0 5 10 30 0 0 90 cyl = 1 10 0 0 5 10 30 0 90 0 cyl = 1 30 0 0 5 10 30 90 0 0 generates this (front view -z): To me, what seems to be wrong th the last one, unless I'm not getting it right, which it's very likely. Which version are you working with? Sorry for not being resolutive!! All the best, Pablo. On 18/04/16 11:20, Jagan Mohan wrote: > Dear All, > > I have been trying to use xmipp_phantom_create to create a cylinder > using the following description file contents - > > > # XMIPP_STAR_1 * > # Phantom description file, (generated with phantom help) > data_block1 > _dimensions3D '232 232 232' > _phantomBGDensity 0 > _scale 1 > data_block2 > loop_ > _featureType > _featureOperation > _featureDensity > _featureCenter > _featureSpecificVector > cyl + 1 '0 0 0' '40 40 232 0 90 0' > > > However, when I change the last line to > > cyl + 1 '0 0 0' '40 40 232 0 90 90' > > I get the same volume in both cases meaning that the last rotation > around Z is not being applied. Am I missing something here? Is it > something to do with the center of rotation? > > > Regards, > Jagan > > > > > -- > -{[O]}- > > > ------------------------------------------------------------------------------ > Find and fix application performance issues faster with Applications Manager > Applications Manager provides deep performance insights into multiple tiers of > your business applications. It resolves application problems quickly and > reduces your MTTR. Get your free trial! > https://ad.doubleclick.net/ddm/clk/302982198;130105516;z > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Jagan M. <o....@gm...> - 2016-04-18 09:20:42
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Dear All,
I have been trying to use xmipp_phantom_create to create a cylinder using
the following description file contents -
# XMIPP_STAR_1 *
# Phantom description file, (generated with phantom help)
data_block1
_dimensions3D '232 232 232'
_phantomBGDensity 0
_scale 1
data_block2
loop_
_featureType
_featureOperation
_featureDensity
_featureCenter
_featureSpecificVector
cyl + 1 '0 0 0' '40 40 232 0 90 0'
However, when I change the last line to
cyl + 1 '0 0 0' '40 40 232 0 90 90'
I get the same volume in both cases meaning that the last rotation around Z
is not being applied. Am I missing something here? Is it something to do
with the center of rotation?
Regards,
Jagan
--
-{[O]}-
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From: Jose M. de la R. T. <del...@gm...> - 2016-03-18 11:56:09
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Hi Wolfgang, Thanks for your feedback. There was a bug where the LD_LIBRARY_PATH was overwritten for all Python modules that we think is related to the problem you mention. It was fixed here: https://github.com/I2PC/scipion/pull/364/files We should release that in the next bug-fix release (v1.0.1). Bests, Jose Miguel. On Fri, Mar 18, 2016 at 12:14 PM, Wolfgang Lugmayr <w.l...@uk...> wrote: > hi, > > the default scipion 1.0 installation mixes up the mpi4py installation (in > our case). > > so first you must put the mpicc etc. in your path and then > extract (from the original homepage) mpi4py-1.3.1.tar.gz > an reinstall the package with the scipion python executable. > > then mpi will work. > > cheers, > wolfgang > > > > > On 03/18/2016 11:21 AM, Pablo Conesa wrote: > > Thanks, Grigory. > > Here a colleague told me that eman must run using Threads (it fails with > MPI). > > On 17/03/16 15:12, Grigory Sharov wrote: > > Hi Pablo, > > I have not tried EMAN2 with mpi in Scipion yet, but my guess is that > scratchdir does not exist.. > > Best regards, > Grigory > > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > Institute of Genetics and Molecular and Cellular Biology > Integrated Structural Biology Department (CBI) > 1, rue Laurent Fries > 67404 Illkirch, France > tel. 03 69 48 51 00 > e-mail: sh...@ig... > > On Thu, Mar 17, 2016 at 2:44 PM, Pablo <p.c...@gm...> wrote: > >> Hi! Does anyone know why this might be happening? (Running eman initial >> volume.) >> >> Must say this is a special setup (not the standard Scipion one) but from >> source code, using web-develop branch (but that protocol runs fine in my >> machine, same source code) >> >> Is it some setup problem? >> >> >> Exception in thread Thread-1: >> 00048: Traceback (most recent call last): >> 00049: File >> ".../scipion/software/em/eman2.12/Python/lib/python2.7/threading.py", line >> 551, in __bootstrap_inner >> 00050: self.run() >> 00051: File >> ".../scipion/software/em/eman2.12/Python/lib/python2.7/threading.py", line >> 504, in run >> 00052: self.__target(*self.__args, **self.__kwargs) >> 00053: File ".../scipion/software/em/eman2.12/lib/EMAN2PAR.py", line 577, >> in run >> 00054: >> proc=subprocess.Popen(["e2parallel.py","localclient","--taskin=%s/%07d"%(self.scratchdir,self.nextid),"--taskout=%s/%07d.out"%(self.scratchdir,self.nextid)]) >> >> 00055: File >> ".../scipion/software/em/eman2.12/Python/lib/python2.7/subprocess.py", line >> 679, in __init__ >> 00056: errread, errwrite) >> 00057: File >> ".../scipion/software/em/eman2.12/Python/lib/python2.7/subprocess.py", line >> 1249, in execute child >> 00058: raise child_exception >> 00059: OSError: [Errno 2] No such file or directory >> >> (Have replaced actual path in the log with "...", but those paths >> exists.). >> >> >> All the best, Pablo. >> >> >> ------------------------------------------------------------------------------ >> 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 >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> > > > ------------------------------------------------------------------------------ > 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 > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > > ------------------------------------------------------------------------------ > 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 > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > -- > Universitätsklinikum Hamburg-Eppendorf (UKE) > @ Centre for Structral Systems Biology (CSSB) > @ Institute of Molecular Biotechnology (IMBA) > Dr. Bohr-Gasse 3-7 (Room 6.14) > 1030 Vienna, Austria > Tel.: +43 (1) 790 44-4649 > Email: w.l...@uk...http://www.cssb-hamburg.de/ > > > ------------------------------ > > Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen > Rechts; Gerichtsstand: Hamburg | www.uke.de > Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. > Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik > ------------------------------ > > SAVE PAPER - THINK BEFORE PRINTING > > > ------------------------------------------------------------------------------ > 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 > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
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From: Wolfgang L. <w.l...@uk...> - 2016-03-18 11:50:14
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hi, the default scipion 1.0 installation mixes up the mpi4py installation (in our case). so first you must put the mpicc etc. in your path and then extract (from the original homepage) mpi4py-1.3.1.tar.gz an reinstall the package with the scipion python executable. then mpi will work. cheers, wolfgang On 03/18/2016 11:21 AM, Pablo Conesa wrote: > Thanks, Grigory. > > Here a colleague told me that eman must run using Threads (it fails > with MPI). > > On 17/03/16 15:12, Grigory Sharov wrote: >> Hi Pablo, >> >> I have not tried EMAN2 with mpi in Scipion yet, but my guess is that >> scratchdir does not exist.. >> >> Best regards, >> Grigory >> >> -------------------------------------------------------------------------------- >> Grigory Sharov, Ph.D. >> Institute of Genetics and Molecular and Cellular Biology >> Integrated Structural Biology Department (CBI) >> 1, rue Laurent Fries >> 67404 Illkirch, France >> tel. 03 69 48 51 00 >> e-mail: sh...@ig... >> >> On Thu, Mar 17, 2016 at 2:44 PM, Pablo <p.c...@gm... >> <mailto:p.c...@gm...>> wrote: >> >> Hi! Does anyone know why this might be happening? (Running eman >> initial volume.) >> >> Must say this is a special setup (not the standard Scipion one) >> but from source code, using web-develop branch (but that protocol >> runs fine in my machine, same source code) >> >> Is it some setup problem? >> >> >> Exception in thread Thread-1: >> 00048: Traceback (most recent call last): >> 00049: File >> ".../scipion/software/em/eman2.12/Python/lib/python2.7/threading.py", >> line 551, in __bootstrap_inner >> 00050: self.run() >> 00051: File >> ".../scipion/software/em/eman2.12/Python/lib/python2.7/threading.py", >> line 504, in run >> 00052: self.__target(*self.__args, **self.__kwargs) >> 00053: File ".../scipion/software/em/eman2.12/lib/EMAN2PAR.py", >> line 577, in run >> 00054: >> proc=subprocess.Popen(["e2parallel.py","localclient","--taskin=%s/%07d"%(self.scratchdir,self.nextid),"--taskout=%s/%07d.out"%(self.scratchdir,self.nextid)]) >> >> 00055: File >> ".../scipion/software/em/eman2.12/Python/lib/python2.7/subprocess.py", >> line 679, in __init__ >> 00056: errread, errwrite) >> 00057: File >> ".../scipion/software/em/eman2.12/Python/lib/python2.7/subprocess.py", >> line 1249, in execute child >> 00058: raise child_exception >> 00059: OSError: [Errno 2] No such file or directory >> >> (Have replaced actual path in the log with "...", but those paths >> exists.). >> >> >> All the best, Pablo. >> >> ------------------------------------------------------------------------------ >> 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 >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> >> >> >> ------------------------------------------------------------------------------ >> 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 >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > ------------------------------------------------------------------------------ > 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 > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Universitätsklinikum Hamburg-Eppendorf (UKE) @ Centre for Structral Systems Biology (CSSB) @ Institute of Molecular Biotechnology (IMBA) Dr. Bohr-Gasse 3-7 (Room 6.14) 1030 Vienna, Austria Tel.: +43 (1) 790 44-4649 Email: w.l...@uk... http://www.cssb-hamburg.de/ -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING |
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From: Pablo C. <pc...@cn...> - 2016-03-18 10:21:36
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Thanks, Grigory. Here a colleague told me that eman must run using Threads (it fails with MPI). On 17/03/16 15:12, Grigory Sharov wrote: > Hi Pablo, > > I have not tried EMAN2 with mpi in Scipion yet, but my guess is that > scratchdir does not exist.. > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > Institute of Genetics and Molecular and Cellular Biology > Integrated Structural Biology Department (CBI) > 1, rue Laurent Fries > 67404 Illkirch, France > tel. 03 69 48 51 00 > e-mail: sh...@ig... <mailto:sh...@ig...> > > On Thu, Mar 17, 2016 at 2:44 PM, Pablo <p.c...@gm... > <mailto:p.c...@gm...>> wrote: > > Hi! Does anyone know why this might be happening? (Running eman > initial volume.) > > Must say this is a special setup (not the standard Scipion one) > but from source code, using web-develop branch (but that protocol > runs fine in my machine, same source code) > > Is it some setup problem? > > > Exception in thread Thread-1: > 00048: Traceback (most recent call last): > 00049: File > ".../scipion/software/em/eman2.12/Python/lib/python2.7/threading.py", > line 551, in __bootstrap_inner > 00050: self.run() > 00051: File > ".../scipion/software/em/eman2.12/Python/lib/python2.7/threading.py", > line 504, in run > 00052: self.__target(*self.__args, **self.__kwargs) > 00053: File ".../scipion/software/em/eman2.12/lib/EMAN2PAR.py", > line 577, in run > 00054: > proc=subprocess.Popen(["e2parallel.py","localclient","--taskin=%s/%07d"%(self.scratchdir,self.nextid),"--taskout=%s/%07d.out"%(self.scratchdir,self.nextid)]) > > 00055: File > ".../scipion/software/em/eman2.12/Python/lib/python2.7/subprocess.py", > line 679, in __init__ > 00056: errread, errwrite) > 00057: File > ".../scipion/software/em/eman2.12/Python/lib/python2.7/subprocess.py", > line 1249, in execute child > 00058: raise child_exception > 00059: OSError: [Errno 2] No such file or directory > > (Have replaced actual path in the log with "...", but those paths > exists.). > > > All the best, Pablo. > > ------------------------------------------------------------------------------ > 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 > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > > ------------------------------------------------------------------------------ > 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 > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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