Activity

From 09 Oct 2013 to 07 Nov 2013

07 Nov 2013

19:05 Revision 6ade0868: Merge branch 'develop' of apps.jcns.fz-juelich.de:BornAgain into develop
wuttke
18:21 Support #460: Create git repository for user related info
and use common JCNS fileserver for data exchange wuttke
14:29 Support #460 (Resolved): Create git repository for user related info
Redmine subproject created. Git repository will only be created if needed. herck
16:32 Documentation #487 (Rejected): Provide screenshots for project homepage
A screenshot section is standard for a project homepage, and for good reason: potential users want to get a first imp... wuttke
16:25 Feature #300: Investigate alternatives to Monte-Carlo computation of non-analytic form factors
For license reasons, we will not be able to copy the solution from HipGisas.
Open-source libraries that may help for...
wuttke
15:46 Feature #486 (Archived): Implement/review Spheroid formfactor
* validation of formula
* check for complex qx, qy
* comparison with IsGISAXS
* integration in UnitTests (getVolu...
pospelov
15:45 Feature #485 (Archived): Implement/review Anisotropic hemi-spheroid formfactor
* validation of formula
* check for complex qx, qy
* comparison with IsGISAXS
* integration in UnitTests (getVolu...
pospelov
15:45 Feature #484 (Archived): Implement/review Ellipsoid formfactor
* validation of formula
* check for complex qx, qy
* comparison with IsGISAXS
* integration in UnitTests (getVolu...
pospelov
15:45 Feature #483 (Archived): Implement/review Anisotropic pyramid formfactor

* validation of formula
* check for complex qx, qy
* comparison with IsGISAXS
* integration in UnitTests (getVo...
pospelov
15:44 Feature #482 (Archived): Implement/review Full spheroid formfactor
* validation of formula
* check for complex qx, qy
* comparison with IsGISAXS
* integration in UnitTests (getVolu...
pospelov
15:44 Feature #481 (Archived): Implement/review Cybooctaedron formfactor

* validation of formula
* check for complex qx, qy
* comparison with IsGISAXS
* integration in UnitTests (getVo...
pospelov
15:43 Feature #480 (Archived): Implement/review Cone6 formfactor

* validation of formula
* check for complex qx, qy
* comparison with IsGISAXS
* integration in UnitTests (getVo...
pospelov
15:42 Feature #479 (Archived): Implement/review Prism6 formfactor

* validation of formula
* check for complex qx, qy
* comparison with IsGISAXS
* integration in UnitTests (getVo...
pospelov
15:42 Feature #478 (Archived): Implement/review Tethraedron formfactor

* validation of formula
* check for complex qx, qy
* comparison with IsGISAXS
* integration in UnitTests (getVo...
pospelov
15:41 Feature #477 (Archived): Implement/review Cone formfactor

* validation of formula
* check for complex qx, qy
* comparison with IsGISAXS
* integration in UnitTests (get...
pospelov
15:32 Documentation #475 (Archived): Create prototype of latex (pdf) page representing form factor
* name and parameters
* 2d sketches of shape, isometric view of shape
* 1d and 2d histograms for ff .vs. qx,qy,qz ...
pospelov
15:30 Feature #474 (Rejected): Implement functional test to run through all defined form factors
* should compare with IsGISAXS form factors in BA
* also script is required to run IsGISAXS in batch mode and prod...
pospelov
15:23 Bug #473 (Resolved): Simulation fails at zero abundance in particle_decoration.addParticle
pospelov
15:17 Bug #473 (Sprint): Simulation fails at zero abundance in particle_decoration.addParticle
pospelov
15:23 Revision 9e9bf306: Protection againss zero abundance
pospelov
15:12 Revision b4ed5326: User manual now can be compiled with cmake in standalone mode (without whole B...
pospelov
14:02 Bug #470 (Resolved): fitting example failure
pospelov
14:00 Revision 5306fa52: Fitting example data included in the cmake installation
pospelov
11:37 Bug #447 (Resolved): Our minimum required cmake version 2.8.0 doesn't contain PARSE_MACRO
Minimum required CMake now 2.8.3 pospelov
11:36 Revision 2a396f0d: Minimum required CMake version is increased till 2.8.3
pospelov
11:07 Revision 5f032054: Changes in fitting manual (local minima trap section)
pospelov

06 Nov 2013

18:02 Revision d8ca6f19: Finalizing fitting manual
pospelov
13:38 Feature #333 (Rejected): PythonAPI: provide convertion of eigen matrix to numpy array

Lets drop this issue. For the moment we are able to read polarized output data from python, no need to try to bin...
pospelov
13:32 Documentation #448 (Resolved): Examples: prepare FitCylindersAndPrism_detailed example
New example python/fitting/FitCylindersPrism_detailed.py with graphics showing the iteration progress pospelov
13:26 Revision d6fc92aa: Merge branch 'FittingManual'
pospelov
13:26 Revision b71d37bc: Detailed fitting example with vizualization
pospelov
12:39 Bug #473 (Archived): Simulation fails at zero abundance in particle_decoration.addParticle
The error message does not describe the problem:... ganeva
11:10 Revision 14b81288: FitCylindersPrisms got interactive matplotlib graphics to display fit progress.
pospelov

05 Nov 2013

18:19 Revision 1c85da7f: IObservable exposed to python
pospelov
16:17 Revision 47d50b2d: Refactoring in fitting to get nicer python interface
pospelov
14:32 Revision 1a201fc7: Merge branch 'FittingManual'
pospelov
14:31 Revision d9bdc487: ForFactorBox fix, now DEPRECATED_NUMPY warning, Layer::setDecoration is protec...
pospelov
12:10 Bug #470 (Sprint): fitting example failure
pospelov
09:22 Bug #470: fitting example failure
Refdata_fitcylinderprisms.txt is provided in the source package, but not in the binary package. ganeva
09:18 Bug #470 (Archived): fitting example failure
Examples/python/fitting/ex002_FitCylindersAndPrisms/FitCylindersPrisms_advanced.py and FitCylindersPrisms.py fail be... ganeva
12:09 Feature #437 (Resolved): Provide OutputData with ExportToNumpy function for PythonAPI

Finally, in python we have IntensityData == OutputData<double> and couple of new functions defined
* simulation....
pospelov
12:04 Revision d0489888: New method Simulation:::getPolarizeIntensityData(i,j) for Python
pospelov
11:51 Revision c537b618: Access to AxisDouble vector and changes in intensitydata unittest
pospelov
11:22 Documentation #471 (Archived): Write down formalism for polarized DWBA on embedded particles
And communicate this to E.Kentzinger.
He will provide the theory for DWBA on domains and roughness for polarized neu...
herck
11:15 Revision 5a6f0d24: Merge branch 'PyOutputData' into develop
pospelov
11:07 Revision 8336f6c1: Merge branch 'develop' of apps.jcns.fz-juelich.de:BornAgain into develop
pospelov
10:22 Support #460 (Sprint): Create git repository for user related info
herck

04 Nov 2013

19:13 Revision 1bb8425c: New Python unittest for testing IntensityData from CMake, all py examples/test...
pospelov
17:43 Bug #469 (Archived): Review form factor calculation for big particle dimensions
In one dimension, the correct integral for a shape of 'radius' L is:
2(Si(q_2L)-Si(q_1L))
herck
17:31 Feature #55 (Rejected): PythonAPI: implement python unit tests infrastructure
No need to set up additional infrastructure. I started to use elements of Python's unittest in TestPyCore (see new in... pospelov
17:30 Revision b89cf8d0: Fixed dubious parametrization in FormFactorBox
herck
15:34 Revision e9feab3c: AxisDouble, getIntensityData are exposed into Python
pospelov

31 Oct 2013

15:08 Bug #468 (Archived): Make use of python interpreter to guess libpython location
CMake can be puzzled if more then one python is present on the system.
To avoid mixing of different version of inter...
pospelov
15:04 Feature #431 (Sprint): Build: provide thisbornagain.sh to set system PATHs to the installation di...
pospelov

30 Oct 2013

17:40 Bug #466 (Rejected): Our CMake gets confused when there are boost 1.46 and 1.48 present on the sy...
It finds boost 1.46 and then complains, that version is too old.
Was nnoticed on Alice's ubuntu.
pospelov

29 Oct 2013

16:44 Documentation #448 (Sprint): Examples: prepare FitCylindersAndPrism_detailed example
pospelov
16:42 Feature #465 (Archived): Organize BornAgain mail list with subscription
pospelov
16:41 Feature #464 (Rejected): Investigate running TeamCity build agent on Windows server
pospelov
16:39 Documentation #449 (Sprint): Review manual's simulation python example section to conform changes...
pospelov
16:23 Bug #447 (Sprint): Our minimum required cmake version 2.8.0 doesn't contain PARSE_MACRO
pospelov
16:18 Bug #463 (Archived): Provide compilation under Jülich CentOS 5.10
Josef Heinen reported build failure on Jülich CentOS due to static version of libpython.a (thread issue) pospelov
16:16 Bug #462 (Archived): Provide compilation on Jülich MacOS server
Josef Heinen observed build failure on Jülich MacOS server.
CMake gets tangled between different versions of Python ...
pospelov
16:13 Bug #461 (Archived): Provide compilation on latest MacOS Maverick
Josef Heinen found out build failure on latest MacOS Maverick.
Apparently new MacOS clang is too strict with our code.
pospelov
11:38 Support #460 (Archived): Create git repository for user related info
* should be protected
* kind of database of users and they requests
* among other things, will contain scripts with...
pospelov
11:34 Documentation #455 (Sprint): Add demos into Examples/python section
pospelov
11:32 Documentation #441 (Resolved): Prepare talk for Koordinierungstreffen
pospelov
11:32 Feature #444 (Resolved): Prepare talk for ILL
herck
11:25 Documentation #459 (Archived): Review installation section
* Describe installation on Windows if the user already has Python installed
* Recommend PyCharm
* Explain thisborna...
pospelov

26 Oct 2013

18:15 Documentation #456 (Resolved): Prepare talk "Data Analysis in HEP" for ILL
pospelov
18:15 Documentation #458 (Resolved): Prepare talk about Python bindings for ILL
pospelov

25 Oct 2013

14:59 Revision f7e649cb: Merge branch 'develop' of apps.jcns.fz-juelich.de:BornAgain into develop
pospelov
14:59 Revision e66d9a7f: Picture with number of lines of code
pospelov
14:58 Revision 58c72b97: Merge branch 'develop' of apps.jcns.fz-juelich.de:BornAgain into develop
herck
14:58 Revision 1bd36ac0: Added demos
herck

21 Oct 2013

10:51 Documentation #458 (Archived): Prepare talk about Python bindings for ILL
pospelov
10:13 Testing #457 (Resolved): Implement unit tests for form factors
celine

19 Oct 2013

11:17 Documentation #456 (Archived): Prepare talk "Data Analysis in HEP" for ILL
pospelov

18 Oct 2013

11:15 Revision 839502ca: Merge branch 'develop' of apps.jcns.fz-juelich.de:BornAgain into develop
pospelov
11:15 Revision 8466c669: Another qmake fix
pospelov
11:03 Revision 2f0daf30: Merge branch 'develop' of apps.jcns.fz-juelich.de:BornAgain into develop
herck
11:02 Revision ff13037e: Added python demos to git
herck
10:59 Revision f33c1b6e: Fix for qmake
pospelov
10:05 Revision ae0fe894: Bug fix in fitting introduced with the last refactoring fixed.
pospelov
10:03 Documentation #455 (Archived): Add demos into Examples/python section
Those demos which Walter has prepared for Hamburg/ILL.
With short README.
pospelov
09:39 Feature #454 (Archived): Change behavior of setParameterValue
If there is '*' in the parameter name, then setMatchedParametersValue should be used instead of setParameterValue
Up...
pospelov
09:19 Revision b167db30: Merge branch 'FitManual'
Conflicts:
CMakeLists.txt
Core/PythonAPI/src/FormFactorGauss.pypp.cpp
pospelov
09:13 Revision 71731a1e: Manual: gentle introduction to the data fitting
pospelov

17 Oct 2013

14:43 Revision 3090132c: New TestToyFitting to illustrate the manual
pospelov
11:34 Feature #450 (Resolved): Provide python function to retrieve polarized output data
herck
10:06 Feature #450 (Archived): Provide python function to retrieve polarized output data
herck
11:34 Revision 097bd31f: Merge branch 'python_pol_outputdata' into develop
herck
11:34 Revision ed71125c: Added global function to retrieve polarized output data in python
herck
09:42 Documentation #449 (Archived): Review manual's simulation python example section to conform chang...
pospelov
09:38 Refactoring #443 (Resolved): Refactor IMinimizer for better control of minimizer option
pospelov

16 Oct 2013

17:59 Revision 50e5e38f: Fitting example explained + lots of changes in fitting PythonAPI
pospelov
17:51 Revision 3e41c917: Reset python & app building to defaults
herck
17:47 Revision 5356e3bd: Merge branch 'mc_ff2' into develop
herck
17:43 Revision 38c10873: Found Gaussian FormFactor problem: height was much bigger than layer thickness...
herck
17:42 Documentation #448 (Archived): Examples: prepare FitCylindersAndPrism_detailed example
It has to contain access to Simulated data with optimal parameters from the fit and simple matplotlib visualization
...
pospelov
13:49 Revision 969f7742: Use Gauss form factor for mesocrystal simulation
herck
13:49 Revision b903250e: Add getVolume() to FormFactorGauss
herck
13:49 Revision 6061c84a: Changed lattice calculations
herck
13:49 Revision 85c0495c: Refactored FormFactorGauss
herck
13:49 Revision c601a047: Updated Xcode project
herck
10:58 Revision c30bb52c: UserManual section: associating model and reference in the fit
pospelov
10:38 Revision 0c260094: Put back hardcoded BAVersion.h file to fix quake build
herck

15 Oct 2013

17:42 Revision e8c823e1: Minimizer setting parts in User manual and corresponding refactoring (Minimize...
pospelov
15:51 Bug #447 (Archived): Our minimum required cmake version 2.8.0 doesn't contain PARSE_MACRO
Add another minimum required version 2.8.10(?) or add own version of PARSE_MACRO pospelov
13:31 Revision bf82b22e: Adapt release script
herck
13:12 Refactoring #236: multi-line comment style
In 'modern' IDE's, the symmetric version can also be collapsed :) herck
12:59 Refactoring #236 (Backlog): multi-line comment style
libBornAgainFit should be equipped with correct header too
pospelov
11:44 Revision 3b3bd5ba: New method printSampleTree for python users comfort
pospelov
11:11 Feature #446 (Archived): Repair broken Genetic minimizer after we get rid from ROOT dependency
pospelov
11:06 Revision ba8aab07: Merge branch 'iss417' into develop
Conflicts:
CMakeLists.txt
herck
11:02 Testing #445 (Archived): Implement BornAgainFit unit test infrastructure
pospelov
11:01 Revision c6f0846c: IParameterized::setParameterValue behavior changed to the global pool
pospelov
10:06 Feature #444 (Archived): Prepare talk for ILL
herck
09:14 Refactoring #443 (Archived): Refactor IMinimizer for better control of minimizer option
pospelov

14 Oct 2013

17:07 Revision 612408ff: Some other minor changes to the release script.
ganeva
16:29 Documentation #439 (Resolved): Explain sample parameters paradigm in simulation examples section
pospelov
16:28 Revision 2958ce78: Sample parameter pool is explained
pospelov
16:23 Revision df10fcfb: Some small corrections to the release script.
ganeva
15:41 Revision dc0c1b1a: Added menu to the release script.
ganeva

11 Oct 2013

18:44 Revision 200a314f: Manual: fitting implementation details in BornAgain
pospelov
18:03 Documentation #442 (Rejected): Review SoftwareDesignOverview section

Walter?
pospelov
16:22 Documentation #441 (Archived): Prepare talk for Koordinierungstreffen
pospelov
15:58 Documentation #440 (Resolved): Create svg plot representing minimization flow
pospelov
13:47 Documentation #440 (Archived): Create svg plot representing minimization flow
pospelov
15:58 Feature #438 (Resolved): Adjust existing python examples to conform PEP8 style
pospelov
09:36 Feature #438 (Archived): Adjust existing python examples to conform PEP8 style
pospelov
15:56 Revision 03f11a41: New plot with minimization workflow
pospelov
13:48 Refactoring #436 (Sprint): Refactor ISample, IParameterized and ParameterPool for better access t...
pospelov
13:47 Feature #437 (Sprint): Provide OutputData with ExportToNumpy function for PythonAPI
pospelov
12:34 Documentation #439 (Archived): Explain sample parameters paradigm in simulation examples section
pospelov
11:24 Revision 6d300e37: Added graphics in SampleParametersIntro.py, all other python examples modified...
pospelov

10 Oct 2013

16:06 Feature #437 (Archived): Provide OutputData with ExportToNumpy function for PythonAPI
This has to be discussed. We need some general approach to access OutputData in Python,
including the cases when Out...
pospelov
15:59 Feature #287 (Backlog): IntensityData campaign
pospelov
15:57 Refactoring #436 (Archived): Refactor ISample, IParameterized and ParameterPool for better access...
Refactor ISample, IParameterized and ParameterPool for better access to global ISample's parameter pool and natural i... pospelov
15:54 Feature #34: Implement different types of detector scans

This must be the part of some other activity, not OutputData
pospelov
14:59 Feature #434 (Rejected): User Requests campaign
pospelov
14:33 Feature #434 (Rejected): User Requests campaign
This is the issue to group different user requests pospelov
14:39 Feature #435 (Archived): Request: provide JFM with the python script simulating the sample_jfm1
sample_jfm1 means two homogeneous layers with spheres 50nm at hexagonal lattice.
There will be probably other reques...
pospelov
09:43 Revision 098c64d0: New example SampleParametersIntro
pospelov

09 Oct 2013

23:05 Documentation #432: Examples: prepare example with correlated roughness interface
Also provide one example with just a single rough interface herck
 

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