HoloPy

HoloPy 2.0 "Dennis"

HoloPy 2.0 is a full rework of the HoloPy code to be much more flexible and extensible. Nothing is coupled that does not need to be coupled, and to the greatest extent possible you can mix and match different peices build up a calculation. It also makes it easy to plug in new minimizers, a capability we demonstrate by adding support for the OpenOpt minimizer package.

Holopy 2.0 also contains a preview of calculation of holograms from arbitrary objects using the discrete diploe approximtion (dda). It works and you can use it, but it may be subject to change as we continue developing.

Milestone information

Project:
HoloPy
Series:
dev
Version:
2.0
Code name:
Dennis
Released:
 
Registrant:
Tom Dimiduk
Release registered:
Active:
No. Drivers cannot target bugs and blueprints to this milestone.  

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Assigned to you:
No blueprints or bugs assigned to you.
Assignees:
3 Anna Wang, 5 Jerome Fung, 1 Jesse W Collins, 3 Rebecca W. Perry, 17 Tom Dimiduk, 3 Vinothan N. Manoharan
Blueprints:
20 Implemented, 1 Informational
Bugs:
2 Invalid, 1 Won't Fix, 31 Fix Released

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Release notes 

A complete rewrite of HoloPy. The 2.0 release focuses on the core functionality of HoloPy on a firm footing to work from. This release consists of a large number of loosely coupled components that you can use to build up a sophisticated calculation. This loosely coupled nature should also make it fairly easy for us to add new features without affecting the core functionality

Changelog 

View the full changelog

A changelong would be kind of meaningless since almost no one outside our group has seen the code in any earlier state. Go look at the docs instead, they do a pretty good job of describing everything you should be interested in.

21 blueprints and 34 bugs targeted

Blueprint Priority Assignee Delivery
Provide Binary Builds Provide Binary Builds 5 Essential Jesse W Collins  11 Implemented
Alternate Minimizer Alternate Minimizer 4 High Tom Dimiduk  11 Implemented
Fit Timeseries Fit Timeseries 4 High Rebecca W. Perry  11 Implemented
Improved Output/object saving Improved Output/object saving 4 High   11 Implemented
Make fortran calculation functions accept spherical coordinates as input Make fortran calculation functions accept spherical coordinates as input 4 High Tom Dimiduk  11 Implemented
N particle fitting N particle fitting 4 High Tom Dimiduk  11 Implemented
New class structure for scattering theories New class structure for scattering theories 4 High Vinothan N. Manoharan  11 Implemented
New object-based fitting framework New object-based fitting framework 4 High Tom Dimiduk  11 Implemented
Split scatterer discription from scattering theory Split scatterer discription from scattering theory 4 High Vinothan N. Manoharan  11 Implemented
Tmatrix for Arbitrary clusters Tmatrix for Arbitrary clusters 4 High Jerome Fung  11 Implemented
Unify related scatterpy classes Unify related scatterpy classes 4 High   11 Implemented
Add option to calculate Radial component of scattering Add option to calculate Radial component of scattering 4 High Jerome Fung  11 Implemented
DDA scattering theory DDA scattering theory 3 Medium Tom Dimiduk  11 Implemented
Cleanup Load and save functions Cleanup Load and save functions 3 Medium   11 Implemented
Introduce new package for things both scatterpy and holopy need Introduce new package for things both scatterpy and holopy need 3 Medium   11 Implemented
Make Scattering theory Accept Volume Schema Make Scattering theory Accept Volume Schema 3 Medium Tom Dimiduk  11 Implemented
Easier Description of general scatterers Easier Description of general scatterers 1 Undefined   11 Implemented
Investigate Simplifying Marray inheritance Heirarchy Investigate Simplifying Marray inheritance Heirarchy 1 Undefined   11 Implemented
Network Delivery of Test Binary Data Network Delivery of Test Binary Data 1 Undefined   11 Implemented
Remove Defaults specific to our setup Remove Defaults specific to our setup 1 Undefined   11 Implemented
Multi Stage Fitting Multi Stage Fitting Informational 0 Not   12 Informational
Bug report Importance Assignee Status
1012727 #1012727 multisphere fortran does not work with gfortran 4.6 1 Undecided   3 Invalid
1098271 #1098271 scattering tests, non-convergence 1 Undecided Rebecca W. Perry  3 Invalid
953092 #953092 Holopy does not have 100% test coverage 4 Medium Tom Dimiduk  4 Won't Fix
953097 #953097 Documentation is out of date 2 Critical   10 Fix Released
1008643 #1008643 how to handle overlaping spheres ("non-physical") 3 High   10 Fix Released
1010206 #1010206 new_fit.py doesn't catch guesses that are out of bounds 3 High Tom Dimiduk  10 Fix Released
1037207 #1037207 fit.fit fails when minimizer doesn't converge 3 High Jerome Fung  10 Fix Released
1099612 #1099612 schema without polarization should fail in a more helpful way 3 High Anna Wang  10 Fix Released
1100039 #1100039 holopy.save() on Windows saves inaccurate image 3 High   10 Fix Released
887253 #887253 returned chi square is wrong (when overlap encountered) 4 Medium Tom Dimiduk  10 Fix Released
1007711 #1007711 Holopy breaks compatibility with python 2.6 4 Medium Vinothan N. Manoharan  10 Fix Released
1008648 #1008648 Holopy cannot calculate hologram values at an arbitrary set of pixels 4 Medium Rebecca W. Perry  10 Fix Released
1011205 #1011205 test_mie.test_Mie_construction fails 4 Medium Tom Dimiduk  10 Fix Released
1094582 #1094582 Tests involving loading example data fail on Windows 4 Medium Tom Dimiduk  10 Fix Released
1094589 #1094589 test_basics.test_calc_field() fails 4 Medium   10 Fix Released
1099520 #1099520 multisphere doesn't handle layered spheres in any graceful way 4 Medium Jerome Fung  10 Fix Released
1099572 #1099572 sphere with no center, exception 4 Medium Anna Wang  10 Fix Released
1100902 #1100902 test_yaml_output fails on 32-bit Ubuntu 12.04 4 Medium   10 Fix Released
1102617 #1102617 hp.load() on a .yaml file uses the spacing and optics saved in the yaml blindly 4 Medium Tom Dimiduk  10 Fix Released
834756 #834756 superposition fits get slightly wrong alpha 5 Low   10 Fix Released
962433 #962433 minmizer_info in FitResult is inside an unnecessary list 5 Low Tom Dimiduk  10 Fix Released
1000938 #1000938 reconstruction fails with 0 distance 5 Low Tom Dimiduk  10 Fix Released
1007030 #1007030 fit output yaml has unexpected text 5 Low Tom Dimiduk  10 Fix Released
1007176 #1007176 process.center_find intermittently fails with index error 5 Low Jerome Fung  10 Fix Released
1015395 #1015395 Parameter object cannot handle imaginary numbers 1 Undecided   10 Fix Released
1042399 #1042399 error relating to specifying pixel_scale shows when inapplicable 1 Undecided   10 Fix Released
1042929 #1042929 static light scattering of single sphere 1 Undecided Tom Dimiduk  10 Fix Released
1046042 #1046042 setting maxiter for nmpfit from fit() does not work 1 Undecided   10 Fix Released
1046045 #1046045 tieing parameters for two spheres doesn't work 1 Undecided   10 Fix Released
1046096 #1046096 fitting with guesses given as integers does not converge well 1 Undecided   10 Fix Released
1046522 #1046522 can't fix alpha to a constant value in a fit 1 Undecided   10 Fix Released
1072505 #1072505 false error when importing holopy 1 Undecided Tom Dimiduk  10 Fix Released
1097072 #1097072 Random subset fitting test fails randomly 1 Undecided   10 Fix Released
1099608 #1099608 model.scatterer.guess can't handle ComplexParameters 1 Undecided Anna Wang  10 Fix Released
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