Activity

From 29 Nov 2016 to 28 Dec 2016

23 Dec 2016

14:08 Refactoring #1744 (Sprint): resolve mutual directory dependence Aggregate <-> Multilayer
wuttke
14:07 Refactoring #1744 (Rejected): resolve mutual directory dependence Aggregate <-> Multilayer
Recent refactoring (introducing FormFactorCoherentPart) broke the directed-graph structure of Core subdirectories: Ag... wuttke
14:08 Refactoring #1743 (Sprint): resolve mutual directory dependence Parametrization <-> Scattering
wuttke
14:05 Refactoring #1743 (Resolved): resolve mutual directory dependence Parametrization <-> Scattering
Recent refactoring (introducing INode) broke the directed-graph structure of Core subdirectories: Parametrization/ an... wuttke

20 Dec 2016

15:17 Documentation #1742 (Rejected): Website should provide link to GitHub issue tracker. Close forum ...
The Website should invite users to submit bug reports to the GitHub issue tracker.
The forum entitled »Bug reports...
wuttke

19 Dec 2016

20:11 Feature #1741 (Rejected): Wavelength/radiatio independent way to define material parameters
It would be helpful and for time of flight modeling necessary to have other possibilities to define the material para... a.glavic
20:09 Bug #1636: Unexpected wavelength depent intensity Roughness vs. ParticleLayout
I will have to test this again, but I think I found my mistake now. I did not define the materials correctly using SL... a.glavic

16 Dec 2016

11:29 Feature #1740 (Resolved): Implement polarized scattering on magnetic nanoparticles using the magn...
Following some email conversations with A. Glavic, it has become clear that we need to calculate the polarized scatte... herck

12 Dec 2016

17:23 Refactoring #1732: Optimization in innermost loop in RT computation
Solved in 2baf9d, pull request 122. wuttke
15:15 Refactoring #1732: Optimization in innermost loop in RT computation
Implemented in branch bisectRT+test. wuttke
08:48 Refactoring #1732 (Rejected): Optimization in innermost loop in RT computation
SpecularMatrix::calculateUpFromLayer contains an innermost loop.
For thick multilayer system with few scattering lay...
wuttke
17:19 Refactoring #1735 (Resolved): remove include guards from unit tests
Resolved in 38845bca. wuttke
13:08 Refactoring #1735: remove include guards from unit tests
-> pull request 121 wuttke
09:43 Refactoring #1735 (Resolved): remove include guards from unit tests
There is no reason why a unit test h file should be included twice, therefore there is no reason to have include guar... wuttke
16:40 Feature #1738 (Rejected): Rename files and classes in Multilayer to resolve ambiguity about "Matrix"
Currently:... wuttke
13:08 Bug #1734 (Resolved): Investigate numerical stability of multilayer RT computation
Cannot confirm.
Tests supplied in pull request 121.
wuttke
09:12 Bug #1734 (Resolved): Investigate numerical stability of multilayer RT computation
Details will follow. I'm investigating. wuttke
09:15 Feature #1103: extend simulation to transmission geometry (detector images with z<0)
Probably this requires a renaming of variables or functions at some places: R and T will become Up and Down. wuttke
09:06 Feature #1706 (Resolved): Profile simulation with multilayers containing large amount of layers
For proposed solution see #1732 and #1733. wuttke
09:02 Refactoring #1733 (Resolved): Avoid multiple calculations of same RT coefficients
Currently, SpecularMatrix::calculateUpFromLayer is called within loops... wuttke
08:44 Refactoring #1673 (Resolved): Design proposal for all subtasks under #1645
No comments received, so proposal is accepted. wuttke

09 Dec 2016

14:05 Feature #31: Implement x-ray polarization factor
For a multilayer, it's not just one polarization factor.
Rather, polarization must be taken into account at each int...
wuttke

07 Dec 2016

15:50 Feature #1670 (Sprint): Provide interface for adding particle shapes in different layers that are...
herck
14:54 Refactoring #1731 (Backlog): Reduce number of TODOs in code
Currently counting 105. herck
14:01 Configuration #1496 (Rejected): Switch Windows10 buildslave from virtual box to vagrant box
Currently, the VM is always on (thanks to Jan). This should resolve many of the problems we experience with the Windo... herck
12:33 Refactoring #1730 (Sprint): Refactor ICompositeSample hierarchy
Then I start slowly via focused pull requests to have only few changes at a time. pospelov
10:39 Refactoring #1730 (Rfc): Refactor ICompositeSample hierarchy
pospelov
12:13 Configuration #1729 (Resolved): Fix centos7 CI build on buildbot
herck
10:52 Bug #1641 (Resolved): histogram2d test fails under certain configurations

Test was fixed by requiring numpy array to be of type dtype=float64.
Also we've discovered, that there is no 'a...
pospelov
10:35 Bug #1674 (Resolved): Possible bug introduced in Polygon in Python context
pospelov

06 Dec 2016

17:44 Refactoring #1730 (Resolved): Refactor ICompositeSample hierarchy
To implement #1624 (#1562 is also related), we might have to provide the following
* Turn lots of ISample into ICo...
pospelov
17:21 Feature #1667 (Resolved): Read DESY/dpdak tiff files to BornAgain GUI
TiffHandler now reads TIFF files with IEEE float sample format. Anonymous
16:54 Configuration #1729 (Resolved): Fix centos7 CI build on buildbot
herck
15:04 Configuration #1544: require libcerf instead of providing ThirdParty/Fadeeva
It might be advantageous to first provide a C++ version of the library (using C++ std::complex instead of C complex t... herck
12:39 Refactoring #1659 (Resolved): rename PixelMap -> Pixel
herck
10:49 Refactoring #1407 (Rejected): rotate the sample, not Q
Not worth a separate refactoring, but will be done when implementing graded layers, as explained in design proposal. wuttke

05 Dec 2016

17:27 Refactoring #1659 (Sprint): rename PixelMap -> Pixel
herck
17:26 Feature #1669 (Resolved): Allow for multiple form factors (dwba or not) in FromFactorWrapper and ...
herck
17:25 Bug #1705 (Rejected): Py Fit crashes for zero fit parameters
Duplicate of #1664, which is resolved. herck
17:15 Bug #1633 (Resolved): Possible memory leakage in LayerStrategyBuilder.
herck
12:35 Feature #1680 (Resolved): Provide 1.7.1 hotfix
pospelov
09:33 Feature #1722 (Long Term Idea): self-absorption correction
Optional correction for extinction along the incoming and outgoing ray, due to scattering. wuttke
09:30 Feature #1721 (Rejected): Scattered intensity should depend on beam size and sample size
The 1/sin(alpha_i) dependence of the scattered intensity is only correct if the beam footprint is smaller than the sa... wuttke

02 Dec 2016

20:38 Refactoring #1693: Make consequential use of default values in initializer lists.
Particle also has four constructors (but may be more onerous to refactor):... wuttke
20:35 Refactoring #1720 (Rejected): Vacuum() instead of HomogeneousMaterial("Air", 0.0, 0.0)
For accuracy, let's not call it air if the refractive index is zero. Change all examples.
For convenience, provide...
wuttke
19:32 Refactoring #1673: Design proposal for all subtasks under #1645
started writing, gisas/internal_reports/1611_design_gradedLayers.tex wuttke
15:33 Documentation #1719 (Rejected): Manual: avoid the word "matrix" for embedding, ambient bulk material
at few places, confusion with mathematical matrix is not entirely impossible wuttke
15:15 Configuration #1718 (New): Provide Windows installer with debug info in it

Might be an intermediate solution on the way to crash handling.
* We already know how to compile under Windows i...
pospelov
14:57 Documentation #1523 (Resolved): explain numeric value of HomogeneousMagneticMaterial::m_magnetic_...
Added comment in my current feature branch explaining the numeric value of this prefactor. herck
14:30 Documentation #1523 (Sprint): explain numeric value of HomogeneousMagneticMaterial::m_magnetic_pr...
wuttke
14:46 Bug #1717 (Rejected): GISASSimulation: setBeamParameters and setDetectorParameters have opposite ...
For each choice I can guess a reason. Nonetheless it's confusing and potentially misleading.
One solution could be...
wuttke
14:41 Feature #1716 (New): GISASSimulation::setBeamParameter: default value 0 for third parameter phi_i
and simplify examples accordingly wuttke
14:02 Feature #1715 (Rejected): start sample construction with SlabSample() or FilmSample()
The semi-infinite bottom and top layers are special. This should be reflected in the API.
Instead of...
wuttke
13:40 Feature #1714 (Rejected): == Enhance functionality ==
wuttke
13:39 Refactoring #1581 (Backlog): get... -> create... if new pointer is returned
wuttke
13:37 Refactoring #1713 (Rejected): light refactoring proposals
While reading code. Please ignore this for the moment, as I will add more.
* "override" -> "final" in FormFactorDW...
wuttke
13:36 Feature #1712 (Rejected): == Code maintenance ==
Refactorings that leave functionality invariant. To be done preferably at the beginning of a sprint. wuttke

01 Dec 2016

17:41 Documentation #1710 (Backlog): Manual: explain particle density
wuttke
17:03 Bug #1633 (Sprint): Possible memory leakage in LayerStrategyBuilder.
herck
16:48 Refactoring #1707 (Resolved): refactor LayerStrategyBuilder, DecoratedLayerComputation -> LayoutS...
These two classes are concerned with a single Layout, not with all layouts in a layer. Therefore:
* Rename them
* T...
wuttke
16:43 Feature #1706 (Resolved): Profile simulation with multilayers containing large amount of layers
Simulation of multilayer structures with more then 30 layers is very slow. It is would be very helpful to find a poss... ganeva
16:05 Refactoring #1549 (Rejected): rename class FitSuite
will come up automatically with #1469, no need for action till then wuttke
15:09 Refactoring #1469 (Long Term Idea): Package Multifit-Suite as separate library
wuttke
14:41 Feature #1653 (Resolved): Outcome of BornAgain user meetings in November
Resolved into issues #1694 - #1705. Transcribed everything except for
* IPython matplotlib problem (if somebodey can...
wuttke
14:40 Bug #1705 (Sprint): Py Fit crashes for zero fit parameters
Assigned to sprint since it sounds easy and important. wuttke
14:40 Bug #1705 (Rejected): Py Fit crashes for zero fit parameters
If no fit parameters are defined, Python fit crashes. On Windows, it does this without any clear message. So we need ... wuttke
14:38 Feature #1704 (New): Revise chi squared module
Provide examples/functional tests to create custom chi2 module from python. Provide log10, sqrt amplitude function in... wuttke
14:37 Feature #1703 (Rejected): GUI: provide convenient way to set min,max for relative difference map.
And probably all other properties of plot on FitView wuttke
14:35 Feature #1702 (Resolved): Fit: Provide extended print output for fit parameters during iterations.
Artur pointed out, that we do not have a way to see how many sample parameters are steered by given fit parameter. wuttke
14:34 Feature #1701 (Rejected): import real-space sample configuration, e.g. from molecular dynamics (m...
wuttke
14:32 Refactoring #1700 (Rejected): Implement FitSuite::printParameters (or ::parametersToString.)
Now GISASSimulation::printParameters() reports parameter names which are different from what FitSuite has.... wuttke
14:31 Feature #1699 (Rejected): functional tests: Improve MinimizerCatalogue::toString
While preparing advanced fitting tutorial realized that the existing MinimizerCatalogue::toString provide too little ... wuttke
14:14 Bug #1681 (Resolved): Fitting GUI: free parameter error
pospelov
13:55 Bug #1681 (Sprint): Fitting GUI: free parameter error
pospelov
14:07 Feature #1698 (New): GUI: save/load detector mask
wuttke
14:06 Feature #1697 (New): Save/load detector mask
Define data format, and implement save and load functions for a detector mask. wuttke
14:04 Feature #1696 (Sprint): GUI: Improve drag-and-drop construction of a MultiLayer.
I suspect there is a deeper reason for the observed problem, namely the mixed nature of the current sample constructi... wuttke
13:53 Feature #1696 (Resolved): GUI: Improve drag-and-drop construction of a MultiLayer.
At the Hamburg and Garching tutorials, many users have been experiencing problems while dropping Layer on top of a Mu... wuttke
13:52 Bug #1661 (Resolved): FitSuite doesn't know about TestMinimizer
Fixed, but without providing functional test. Later will be created as separate issue pospelov
13:51 Feature #1082: GUI: provide unddo/redo functionality
This can be done first for sample construction. I think that we have to implement the full fledged "Command" pattern.... wuttke
13:44 Feature #1695 (Rejected): GUI: Implement crash handler, and restoration of state before crash
During Hamburg and Garching tutorials, there were quite some number of GUI's crashes (about 10-20 per 8 hours of tuto... wuttke
13:37 Feature #1694 (Rejected): GUI: Provide a way to save fitted image into the file.
In FitView there is no any button (or right mouse click action) to save fitted image into the file.
wuttke
13:16 Configuration #1635 (Resolved): update to gtest-1.8
resolved in 9de8f297de wuttke
13:10 Bug #1674: Possible bug introduced in Polygon in Python context
Fixed in hotfix. Unit tests still have to be created.
pospelov
13:09 Bug #1662 (Resolved): CMake: require Qt version 5.4
pospelov
13:09 Bug #1692 (Resolved): GUI and Py: simulation crash when sample contains undefined material
pospelov
10:43 Bug #1692: GUI and Py: simulation crash when sample contains undefined material
Python problem is different one (which I was not aware of, thanks). Should be solved in different way, than in GUI. B... pospelov
10:33 Bug #1692: GUI and Py: simulation crash when sample contains undefined material
It's not only a GUI problem.
Take any python example, and change the line...
wuttke
09:33 Bug #1692 (Resolved): GUI and Py: simulation crash when sample contains undefined material

How to reproduce:
* Drag and drop sample from the list of standard samples
* Go to material editor ('m'), remov...
pospelov
13:08 Bug #1658 (Resolved): add qt5-svg as a dependency
pospelov
12:58 Bug #1639 (Resolved): GUI: crash if fitting parameter removed
herck
11:46 Refactoring #1693: Make consequential use of default values in initializer lists.
I think such sequence of constructors with growing list of parameters was because of boost-python bindings. Probably ... pospelov
11:13 Refactoring #1693 (Backlog): Make consequential use of default values in initializer lists.
For example, in ParticleLayout.h we currently have three constructors, and four versions of @addParticle@:... wuttke

30 Nov 2016

13:04 Bug #1689 (Resolved): memory leak in ParameterSample
ganeva
09:43 Bug #1689: memory leak in ParameterSample
I believe that due to API changes @wl_distr.generateSamples(nsamples, xmin, xmax)@ should instead be something like @... jmfisher
11:07 Feature #1691 (Resolved): Decrease number of warnings produced by Windows build

Currently number of Windows warnings is tremendous, makes it difficult to analyze logs.
* In Release 1.8 Appveyo...
pospelov

29 Nov 2016

16:44 Bug #1689: memory leak in ParameterSample
It appears that the template @std::vector< ParameterSample > >@ is not being exported by swig. So it should be a simp... jmfisher
16:28 Bug #1689 (Sprint): memory leak in ParameterSample
ganeva
16:14 Bug #1689 (Resolved): memory leak in ParameterSample
The following simple script... ganeva
15:03 Documentation #1141: Manual: describe multi layers
will come back to it later wuttke
11:38 Bug #1658: add qt5-svg as a dependency
Resolved in f1de40e, pull request #93.f1de40e
Can be transfered to hotfix branch using git cherry-pick f1de40e.
wuttke
11:22 Bug #1662: CMake: require Qt version 5.4
In hotfix branch, apply git cherry-pick b4f148 wuttke
11:20 Bug #1662: CMake: require Qt version 5.4
Solved in b4f14 (pull request #93). wuttke
10:40 Configuration #1615: in each third-party source directory, provide information about used downloa...
The information file shall be called 00_PROVENANCE.
Work on this issue started with gtest-1.8.0.
wuttke
10:39 Configuration #1635: update to gtest-1.8
Done in 2ff998fba, pull request #92. wuttke
09:37 Refactoring #1660 (Resolved): remove global functions
Learned from Walter that not all global functions are bad. Unnecessary globals are mostly removed with pull request #88. wuttke
09:27 Refactoring #1479 (Rejected): presence of some boost components not checked by cmake
Rejected for two reasons:
* CMake and Boost are changing so quickly that there is no way for us to provide a lasting...
wuttke
09:00 Feature #1688 (Rejected): == Roughness ==
wuttke
 

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