source: sasview/docs/sphinx-docs/source/user/RELEASE.rst @ 67ed543

magnetic_scattrelease-4.2.2ticket-1009ticket-1094-headlessticket-1242-2d-resolutionticket-1243ticket-1249unittest-saveload
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Issue with spinodal scale added to release notes. Addresses #1191

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[8ac05a5]1Release Notes
2=============
3
4.. note:: In Windows use [Alt]-[Cursor left] to return to the previous page
5
6.. toctree::
7   :maxdepth: 1
8
9Features
10========
11
12New in Version 4.2.0
13--------------------
14This release heralds many improvements and a host of bug fixes, along with
15some significant changes from previous versions. Further, as promised, it
16marks the end of support for 32 bit operating systems and is only
17available for 64 bit operating systems.
18
19With this version the change to the new model API and plugins infrastructure
[1d2a4aa]20begun with 4.0 is essentially complete (though extensions are in the works,
21and more are likely, they should remain backwardly compatible with previous
[8ac05a5]22versions of SasView).
23
[1d2a4aa]24.. warning:: Old-style plugin models, including old sum|multiply models, continue
25             to be supported (i.e. SasView will run them) in 4.x, although our
26             automatic on-the-fly translation may not cope in all use cases (see
27             Known Issues below). However, this backward compatibility will be
28             removed in 5.0 and users are therefore strongly encouraged to
29             convert their custom models to the new API.
[8ac05a5]30
31Finally, the changes to orientation angles and orientational distribution
32definitions are now also complete.
33
34Changes
35^^^^^^^
36* The infrastucture for calculating 2D patterns from 3D orientated objects
37  has been totally re-factored. It is now more accurate and consistent
38  across models.
39* The way that SasView defines the orientation of anisometric and
40  aligned objects has been completely overhauled. It now differs from
41  previous versions.
42* Plugin models, including sum|multiply models, have completely migrated
43  to the new infrastructure. NOTE that 3.x type models as well as early,
44  intermediate 4.x type models, including those generated by sum|multiply
45  will continue to be supported in 4.x but will likely no longer be
46  supported after the move to 5.0.  Users are strongly encouraged to
47  migrate any custom models.
48* The NeXus loader has been removed as it is superseded by the NXcanSAS
49  standard loader and SasView does not support the treatment of raw
50  data.
51
52Improvements
53^^^^^^^^^^^^
54* The accuracy/speed of some numerical integrations have been improved.
55* An orientation viewer tool has been introduced to assist in
56  understanding the new orientation framework.
57* Problems with the computation of magnetic scattering from some
58  objects have been rectified. Some questions remain however.
59* The known issue with the core_shell_parallelepiped model is now fixed.
[1d2a4aa]60* An error in the be_polyelectrolyte model was identified and rectified, but
61  the fix is yet to be validated.
[67ed543]62* (Added post-release) An error with the reporting of the scale parameter
63  from the spinodal model was rectified.
[8ac05a5]64* A number of issues and inconsistencies with the creation of
65  sum|multiply models have been rectified.
66* A Boltzmann distribution has been added for polydispersity/orientational
67  distributions.
68* Some batch slicing options have been introduced.
69* Correlation function analysis now computes both the 1D and 3D functions.
70* There are several data loading improvements.
71* There are several improvements to Save/Load Project.
[1d2a4aa]72* The SasView version number now appears in Reports.
73* The Release Notes are now available from the program Help menu.
[8ac05a5]74* There have been numerous other bug fixes.
75
76Documentation
77^^^^^^^^^^^^^
78Several sections of the help documentation have undergone significant
79checking and updating, particularly those relating to orientation,
[1d2a4aa]80magnetic scattering, and polydispersity distributions.
81
82Detailed advanced instructions for plugin writing and some scripting
83instructions have also been added.
84
85Concerns about the intended versus implemented meaning of some parameters
86in the bcc_paracrystal, fcc_paracrystal, and sc_paracrystal models have
87been brought to our attention. These have yet to be resolved and so a
88Warning has been placed on each of these models. Anyone who feels they
89may have the requisite expertise to investigate these concerns is strongly
90encouraged to contact the Developers!
[8ac05a5]91
92Other Work
93^^^^^^^^^^
94* A Third-Party initiative has recently succeeded in getting SasView to
95  run on Debian. More details at
96  http://trac.sasview.org/wiki/DevNotes/Projects/Debian
97* With this release we have started to prepare for the inevitable move
98  to Python 3, which will occur with the release of 5.0
99* SasView 5.0 is currently in development. The two most significant
100  features of this version will be (i) a move away from the present
101  WxPython GUIs to new, completely rewritten, Qt5 GUIs, and
102  (ii)implementation of the Beta-approximation for S(Q). Subject to
103  resources, some limited access to the latter functionality may be
104  available in a future SasView 4.x release.
105
106Bug Fixes
107^^^^^^^^^
[1d2a4aa]108* Fixes #  14: Loading a saved project is really really slow
[8ac05a5]109* Fixes # 260: Box integration does not update when entering values in dialog
110* Fixes # 446: Saving plot as PGF (not PDF!) format throws error
111* Fixes # 467: Extend batch functionality to slicer
112* Fixes # 489: ABS reader (NIST 1D) does not handle negative dx properly (USANS slit smearing)
113* Fixes # 499: create sin(x)/x, 2*J1(x)/x and 3*j1(x)/x functions
114* Fixes # 510: Build PDF documentation along with HTML
115* Fixes # 525: Add GUI category defaults to models in sasmodels
116* Fixes # 579: clean up sasview directory
117* Fixes # 597: Need to document Combine Batch Fit
118* Fixes # 645: GUI logic problem in Batch vs single fit mode
119* Fixes # 648: Need to allow user input background value in Pr perspective
120* Fixes # 685: Fix data upload to marketplace
121* Fixes # 695: linear slope in onion model
122* Fixes # 735: Review new Corfunc documentation
123* Fixes # 741: Recalculate P(Q) and S(Q) components on model update.
124* Fixes # 767: Sum/Product Models don't do what they should
125* Fixes # 776: angular dispersity
126* Fixes # 784: Add 3D integral to Correlation Function analysis
127* Fixes # 786: core_shell_parallelepiped 1-D model is incorrect
[1d2a4aa]128* Fixes # 818: “report button” followed by “save” makes an empty pdf file???
129* Fixes # 830: Check compliance of loader against NXcanSAS-1.0 release
[8ac05a5]130* Fixes # 838: Fix model download from marketplace
131* Fixes # 848: can't save analysis when only one fit page
[1d2a4aa]132* Fixes # 849: Load Folder should ignore files starting with .
[8ac05a5]133* Fixes # 852: More unit tests, especially for oriented or 2d models
134* Fixes # 854: remove unnecessary sleep() in fitting perspective
135* Fixes # 856: Reading SAS_OPENCL from custom_config sometimes raises an ERROR
136* Fixes # 861: cannot defined a structure factor plugin
137* Fixes # 864: New Model Editor (simple plugin editor) error parsing parameter line
138* Fixes # 865: Plugin live discovery issues
139* Fixes # 866: inform user when NaN is returned from compute
140* Fixes # 869: fit page computation thread cleanup
141* Fixes # 875: Possible weirdness with 1D NXcanSAS data
142* Fixes # 876: Add check for HDF5 format in dataloader
143* Fixes # 887: reorganize tree, separating the installed source from the build source
144* Fixes # 889: Refactor dataloader error handling infrastructure
145* Fixes # 890: use new orientation definition for asymmetric shapes
146* Fixes # 891: update docs for oriented shapes with new orientation definition
147* Fixes # 896: equations in core shell parallelepiped docs do not match code
148* Fixes # 898: Image Viewer Tool file selector issue
149* Fixes # 899: Igor Reader q calculation
150* Fixes # 902: IgorReader Q calculation needs fixing/improving
151* Fixes # 903: sasview - all non-gui tests should be converted to run in Python 3
152* Fixes # 906: polydispersity not showing up in tabulated results
153* Fixes # 912: About box points to misleading contributors page on Github
[1d2a4aa]154* Fixes # 913: Need to add Diamond developer and logo in relevant places
[8ac05a5]155* Fixes # 915: load project issues
156* Fixes # 916: Proper Logging
157* Fixes # 920: Logarithmic binning option in the slice viewer
158* Fixes # 921: Improve developer communication methods
159* Fixes # 922: Remove support for all data formats that are not in q space
160* Fixes # 923: Add CI and trac integrations to Slack
161* Fixes # 930: fitting help says chisq is normalized to number of points
162* Fixes # 931: Allow admins to edit all models and upload data etc on marketplace
163* Fixes # 932: Need to fix upload of data files to marketplace
164* Fixes # 934: Slurp tutorial repo for tutorials
165* Fixes # 935: Build new tutorials as PDF
166* Fixes # 943: Deep copy error on setting model after data is selected
167* Fixes # 950: Most of the readers don't close files properly.
168* Fixes # 954: cross check dll/opencl/python polydispersity and orientation results
169* Fixes # 956: Possible problem with new doc build process
170* Fixes # 961: sasmodels tests should fail if the parameter name does not exist
171* Fixes # 962: star polymer typo in docs
[1d2a4aa]172* Fixes # 966: Inconsistent chi2 reporting
[8ac05a5]173* Fixes # 967: no uncertainties errors on fitting parameters
174* Fixes # 969: About Box not picking up dls_logo.png
175* Fixes # 970: ASCII loader doesn't handle ISIS 2D ASCII
176* Fixes # 974: blacklist Intel HD 620/630 for double precision
177* Fixes # 978: load project fails for pages which have not been defined
178* Fixes # 983: Remove Nexus Loader
179* Fixes # 984: PDF reports are not being properly generated on Windows
180* Fixes # 985: Saving Project Fails
181* Fixes # 986: Send to fitting overwrites theory page even if blank FitPage has focus
182* Fixes # 990: utest_sasview.py giving different results than run_one.py
183* Fixes # 993: Windows x64 versions not installing to correct folder
184* Fixes # 994: Error changing fit engine
185* Fixes # 995: OpenCL required on Linux even if turned off in GUI
186* Fixes #1006: multiplicity models don't work with SQ
187* Fixes #1007: spherical_sld model freezes SasView
[1d2a4aa]188* Fixes #1008: plugin model scaling not working?
[8ac05a5]189* Fixes #1010: Win64 build script not creating working executable
190* Fixes #1011: sld_test failing on ubuntu
191* Fixes #1013: FileReaderBaseClass output[] not reset - same file loaded multiple times
192* Fixes #1018: add Boltzmann distribution
193* Fixes #1021: add PDF documentation to website and document in wiki release process
194* Fixes #1024: Update version numbers in master
195* Fixes #1025: Sum/multiply editor hangs
[1d2a4aa]196* Fixes #1030: volume normalization for hollow shapes is different from solvent-filled shapes
[8ac05a5]197* Fixes #1032: convert C++ modules to C
198* Fixes #1035: Order of combining P(Q) and S(Q) in Plugins seems to matter
199* Fixes #1037: data loader crop not working? & all fits crashing
200* Fixes #1043: problem compiling marketplace models
[1d2a4aa]201* Fixes #1044: Unable to upload c file to marketplace
202* Fixes #1046: convert non builtin models in the marketplace to new API
[8ac05a5]203* Fixes #1050: fix appveyor test for sasmodels win 64 python 3
204* Fixes #1052: Can't use a user-created plugin model in a plugin model
[1d2a4aa]205* Fixes #1054: Check plugin & orientation descriptions in full docs once SasModels PR #57 is merged
[8ac05a5]206* Fixes #1057: phi rotation issue for elliptical cylinder
207* Fixes #1060: incorrect default for rectangle dispersion
208* Fixes #1062: win32 build not installing correctly
[1d2a4aa]209* Fixes #1064: "Fitting did not converge!!!" error with a Sum|Multi plugin model
210* Fixes #1068: 2d data (from NG7) not loadiing - strange format?
[8ac05a5]211* Fixes #1069: GUI problem when using polydispersity/orientation distributions
212* Fixes #1070: Parameter error boxes should not be editable
[1d2a4aa]213* Fixes #1072: Orientation distributions seem to depend on initial angle
[8ac05a5]214* Fixes #1079: Remove save button in report dialog on Mac
215* Fixes #1081: GUI problem with new orientation distribution
216* Fixes #1083: Magnetic models not being computed
217* Fixes #1099: Erratic behaviour of Sum|Multi model in 4.1.2
218* Fixes #1101: Batch results page not displaying polydispersity values
[1d2a4aa]219* Fixes #1128: AutoPlot generation for model documentation does not include background
[8ac05a5]220* Fixes #1131: OpencCl dialog does not open
221* Fixes #1132: Slit Size Calculator Tool not working
222* Fixes #1139: Missing Docs and Help for new Batch Slicing
223* Fixes #1141: Intro to scripting.rst needs improvement
224* Fixes #1142: Plugin framework is broken
225* Fixes #1145: Update models in model marketplace to 4.2 when 4.2 is released.
[1d2a4aa]226* Fixes #1155: BE Polyelectrolyte errors
227* Fixes #1160: fix VR for core_shell_cylinder, fractal_core_shell and hollow_cylinder
228* Fixes #1163: Fix help note in sum of sum|multiply interface
229* Fixes #1164: Sphinx doc build does not support superscript or substitution
230* Fixes #1166: No longer able to report from multiple fit pages
231* Fixes #1167: Clarify the documentation for the Spinodal Model
232* Fixes #1173: more problems with math in plugins
233* Fixes #1176: Make Release Notes/Known Issues available from Help in Menu Bar
234* Fixes #1179: PDF Report should contain SasView Version Number
235* Fixes #1183: Test from creating new model reset all parameters to default in all open FitPages
[fa053ff7]236* Fixes #1188: fitpage hangs if change model while magnetism is on
[67ed543]237* Fixes #1191: Correct erroneous Scale reported by Spinodal model
[1d2a4aa]238
239**It is recommended that all users upgrade to this version, but your
240attention is drawn to the Changes section above.**
[8ac05a5]241
242
243New in Version 4.2.0-Beta
244-------------------------
245This is a beta pre-release version of 4.2.0.  A number of fixes and changes
246have been made in the year since the previous release. Full release notes
247will be compiled prior to the full release 4.2.0.
248
249Highlights are:
250
251* Infrastucture for calculating 2D patterns from 3D orientated objects
252  has now been totally refactored
253* Plugins have completely migrated to the new infrastructure now,
254  including sum/multiply models
255* Some batch slicing options have been introduced
256* The known issue with the core_shell_parallelepiped is now fixed
257* Several data loading improvements
258* Several save Project improvements (though there are more to come)
259* Numerous bug fixes
260* Lots of documentation enhancement
261
262In the meantime please report any bugs or issues found while using this beta
263
264
265New in Version 4.1.2
266--------------------
267This point release is a bug-fix release addressing:
268
269* Fixes #984: PDF Reports Generate Empty PDFs
270* Fixes a path typo
271* 64 bit and 32 bit Windows executables now available
272
273It is recommended that all users upgrade to this version
274
275
276New in Version 4.1.1
277--------------------
278This point release is a bug-fix release addressing:
279
280* Fixes #948: Mathjax CDN is going away
281* Fixes #938: Cannot read canSAS1D file output by SasView
282* Fixes #960: Save project throws error if empty fit page
283* Fixes #929: Problem deleting data in first fit page
284* Fixes #918: Test folders not bundled with release
285* Fixes an issue with the live discovery of plugin models
286* Fixes an issue with the NXcanSAS data loader
287* Updated tutorials for SasView 4.x.y
288
289
290New in Version 4.1.0
291--------------------
292This incremental release brings a series of new features and improvements,
293and a host of bug fixes. Of particular note are:
294
295Correlation Function Analysis (Corfunc)
296^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
297This performs a correlation function analysis of one-dimensional SAXS/SANS data,
298or generates a model-independent volume fraction profile from the SANS from an
299adsorbed polymer/surfactant layer.
300
301A correlation function may be interpreted in terms of an imaginary rod moving
302through the structure of the material. G1(R) is the probability that a rod of
303length R moving through the material has equal electron/neutron scattering
304length density at either end. Hence a frequently occurring spacing within a
305structure manifests itself as a peak.
306
307A volume fraction profile \Phi(z) describes how the density of polymer
308segments/surfactant molecules varies with distance from an (assumed locally flat)
309interface. *This is not yet implemented*.
310
311Fitting of SESANS Data
312^^^^^^^^^^^^^^^^^^^^^^
313Data from Spin-Echo SANS measurements can now be loaded and fitted. The data will
314be plotted against the correct axes and models will automatically perform a Hankel
315transform in order to calculate SESANS from a SANS model.
316
317Documentation
318^^^^^^^^^^^^^
319The documentation has undergone significant checking and updating.
320
321Improvements
322^^^^^^^^^^^^
323* Correlation function (corfunc) analysis of 1D SAS data added from CCP13
324* File converter tool for multi-file single column data sets
325* SESANS data loading and direct fitting using the Hankel transformation
326* Saving and loading of simultaneous and constrained fits now supported
327* Save states from SasView v3.x.y now loaded using sasmodel model names
328* Saving and loading of projects with 2D fits now supported
329* Loading a project removes all existing data, fits, and plots
330* Structure factor and form factor can be plotted independently
331* OpenCL is disabled by default and can be enabled through a fit menu
332* Data and theory fields are now independently expandable
333
334Bug Fixes
335^^^^^^^^^
336* Fixes #667: Models computed multiple times on parameters changes
337* Fixes #673: Custom models override built in models of same name
338* Fixes #678: Hard crash when running complex models on GPU
339* Fixes $774: Old style plugin models unloadable
340* Fixes #789: stacked disk scale doesn't match cylinder model
341* Fixes #792: core_shell_fractal uses wrong effective radius
342* Fixes #800: Plot range reset on plot redraws
343* Fixes #811 and #825: 2D smearing broken
344* Fixes #815: Integer model parameter handling
345* Fixes #824: Cannot apply sector averaging when no detector data present
346* Fixes #830: Cansas HDF5 reader fully compliant with NXCanSAS v1.0 format
347* Fixes #835: Fractal model breaks with negative Q values
348* Fixes #843: Multilayer vesicle does not define effective radius
349* Fixes #858: Hayter MSA S(Q) returns errors
350* Numerous grammatical and contexual errors in documention
351
352
353New in Version 4.0.1
354--------------------
355This release fixes the critical bug #750 in P(Q)xS(Q).  Most damaging
356it appears that the background term was being added to S(Q) prior to
357multiplication by P(Q).
358
359
360New in Version 4.0
361------------------
362This release fixes the various bugs found during the alpha and beta testing
363
364Improvements
365^^^^^^^^^^^^
366* Support for reading data files from Anton Paar Saxess instruments
367* Adds documentation on how to write custom models in the new framework
368
369Bug Fixes
370^^^^^^^^^
371* Fixes #604: Pringle model questions
372* Fixes #472: Reparameterize Teubner-Strey
373* Fixes #530: Numerical instabilities in Teubner Strey model
374* Fixes #658: ASCII reader very broken
375
376
377New in Version 4.0 beta 1
378-------------------------
379This beta adds support for the magnetic and multilevel models of 3.1.2
380and along with a host of bug fixes found in the alpha.
381
382Model package changes and improvements
383^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
384* All 3.1.2 models now available in new interface
385* Old custom models should now still work
386* Custom model editor now creates new style models
387* Custom model editor supports better error checking
388 
389.. note:: Old custom models should be converted to the new model format
390          which is now the same as the built-in models and offers much
391          better support. The old custom model format will be deprecated
392          in a future version.
393
394Documentation improvements
395^^^^^^^^^^^^^^^^^^^^^^^^^^
396* Continued general cleanup
397
398Other improvements/additions
399^^^^^^^^^^^^^^^^^^^^^^^^^^^^
400* Support for new canSAS 2D data files added
401* Plot axes range can now be set manually as well as by zooming
402* Plot annotations can now be moved around after being placed on plot.
403* The active optimizer is now listed on the top of the fit panel.
404* Linear fits now update qmin and max when the x scale limits are
405  changed.  Also the plot range no longer resets after a fit.
406
407Bug fixes
408^^^^^^^^^
409* Fixes #511: Errors in linearized fits and clean up of interface
410  including Kratky representation
411* Fixes #186: Data operation Tool now executes when something is
412  entered in the text box and does not wait for the user to hit enter
413* Fixes #459: plot context menu bug
414* Fixes #559: copy to clipboard in graph menu broken
415* Fixes #466: cannot remove a linear fit from graph
416* Numerous bugs introduced in the alpha
417
418
419New in Version 4.0.0-alpha
420--------------------------
421This alpha release brings a major overhaul of the model system. The new model
422package allows rapid integration of custom models and access to polydispersity
423without requiring a compiler.
424
425Model package changes and improvements
426^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
427* Separation of GUI and calculations for future GUI enhancements
428* Model interface moved to independent sasmodels package.
429* Most models converted to new interface.
430* Allows rapid integration of user-written models.
431* OpenCL GPU utilization for faster fitting.
432* Improved numerical integration of Bessel functions.
433
434SESANS integration and implementation
435^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
436* Scripting interface added for analysis of SESANS data.
437* Hankel transformation now accepts finite acceptance angles.
438* 2D cosine transformation added for TOF SESANS analysis.
439
440Documentation improvements
441^^^^^^^^^^^^^^^^^^^^^^^^^^
442* The documentation tree was restructured for a better end user experience.
443* The documentation for each model was revamped and verified by at least
444  two people following the conversion of the model.
445* Theoretical 1D (and 2D if applicable) scattering curves are auto-generated
446  and added to the model documentation for each model.
447   
448Bug fixes
449^^^^^^^^^
450* Fixes #411: No stop button on simultaneous fit page
451* Fixes #410: Error with raspberry model
452* Fixes #364: Possible inconsistency in Poly_GausCoil model
453* Fixes #439: Hayter Penfold MSA code needs checking
454* Fixes #484: lammellerPC is precision limited
455* Fixes #498: $HOME/.matplotlib conflicts
456* Fixes #348: Control order in which fit parameters appear in the gui
457* Fixes #456: Provide DREAM Results Panel with something to identify
458  data and age of results
459* Fixes #556: Build script improvements for developers
460
461
462New in Version 3.1.2
463--------------------
464This release is a major stability improvement, having fixed a serious bug
465that came to light since release 3.1.1. All users should upgrade.
466
467* Fixes #468: broken remove constraint buttons in
468  simultaneous/constrained fitting panel
469* Fixes #474: resulting from changes in 3.1.1 that had
470  introduced an error in the high-Q of slit-smeared models.
471* Fixes #478: which would cause wx to run out of IDs and result
472  in SasView crashing even if left alone.
473* Fixes #479: missing help button on simultaneous/constrained fit page
474* Fixes #480: GUI resizing issues on simultaneous fit page
475* Fixes #486: broken Report Results
476* Fixes #488: redraw issues in fit page
477
478
479New in Version 3.1.1
480--------------------
481Fixes #457 that prevented SasView from starting if the user was not
482connected to the internet, or was behind a proxy server.
483
484
485New in Version 3.1.0
486--------------------
487The documentation/help has had a complete overhaul including:
488
489* A completely new presentation interface (Sphinx).
490* Proof reading!
491* Updating for latest features.
492* A Help (or sometimes ?) button has been added to every panel, and some
493  sub panels if appropriate, linking to the appropriate section in the
494  documentation.
495* The model help has been split so that the Details button now brings up
496  a very short pop-up giving the equation being used while HELP goes to
497  the section in the full documentation describing the model.
498* Extensive help has also been added for the new optimizer engine (see
499  below) including rules of thumb on how and when to choose a given
500  optimizer and what the parameters do.
501
502The optimizer engine has been completely replaced. The new optimizer
503still defaults to the standard Levenberg-Marquardt algorithm. However 4
504other optimizers are now also available. Each starts with a set of default
505parameters which can be tuned. The DREAM optimizer takes the longest but
506is the most powerful and yields rich information including full parameter
507correlation and uncertainty plots. A results panel has been added to
508accommodate this. The five new optimizers are:
509
510* A Levenberg-Marquardt optimizer
511* A Quasi-Newton BFGS optimizer
512* A Nelder-Mead Simplex optimizer
513* A Differential Evolution optimizer
514* A Monte Carlo optimizer (DREAM)
515
516New models were added:
517
518* MicelleSphCoreModel (currently residing in the Uncategorized category)
519
520Existing models were updated:
521
522* LamellarPS (bug in polydispersity integration fixed)
523* RectangularPrismModel
524* RectangularHollowPrismModel
525* RectangularHollowPrismInfThinWallsModel
526
527Other work:
528
529* Infrastructure to allow SESANS data to be fit with models was added. This
530  will become available in a future release but can currently be used from
531  the command line with some caveats.
532* A number of bugs were fixed including a thread crashing issue and an
533  incorrect slit smearing resolution calculation.
534* Implemented much more robust error logging to enable much easier
535  debugging in general but particularly the debugging of issues reported by
536  SasView users.
537* A number of infrastructure tasks under the hood to enhance maintainability
538* Upgrade from Wx 2.8 to Wx 3.0.2 which allows several new features but
539  required significant additional rework as well.
540* Fully implemented Sphinx to the build process to produce both better
541  user documentation and developer documentation.
542* Restructuring of the code base to more unified nomenclature and structure
543  so that the source installation tree more closely matches the installer
544  version tree.
545* Code cleanup (an ongoing task).
546* Migration of the repository to github simplifying contributions from
547  non-project personnel through pull requests.
548
549
550New in Version 3.0.0
551--------------------
552* The GUI look and feel has been refactored to be more familiar for
553  Windows users by using MDI frames. Graph windows are also now free-
554  floating.
555* Five new models have been added: PringlesModel, CoreShellEllipsoidXTModel,
556  RectangularPrismModel, RectangularHollowPrismModel and
557  RectangularHollowPrismInfThinWallsModel.
558* The data loader now supports ILL DAT data files and reads the full meta
559  information from canSAS file formats.
560* Redefined convention for specifying angular parameters for anisotropic
561  models.
562* A number of minor features have been added such as permitting a log
563  distribution of points when using a model to simulate data, and the
564  addition of a Kratky plot option to the linear plots.
565* A number of bugs have also been fixed.
566* Save Project and Save Analysis now work more reliably.
567* BETA: Magnetic contrast supporting full polarization analysis has been
568  implemented for some spherical and cylindrical models.
569* BETA: Two new tools have been added:
570
571  * A generic scattering calculator which takes an atomic, magnetic or
572    SLD distribution in space and generates the appropriate 2D
573    scattering pattern. In some cases the orientationally averaged
574    (powder) 1D scattering can also be computed. Supported formats
575    include: SLD or text, PDB, and OMF magnetic moment distribution
576    file.
577  * An image viewer/converter for data in image format; this reads in
578    an image file and will attempt to convert the image pixels to
579    data. Supported formats include: TIFF, TIF, PNG, BMP, JPG.
580
581
582New in Version 2.2.1
583--------------------
584* Minor patch to support CanSAS XML v1.1 file format
585* Added DataInfo for data in the DataExplorer and plots
586* Added Maximize/Restore button in the title bar of the graphs
587* Added a hide button in the toolbar of the graph panel
588* The 'x' button now deletes a graph
589* Edit SUM Model from the menubar can now generate and save more than one sum model
590* Reports can now be saved in pdf format on WIN and MAC
591* Made significant improvements to the batch/grid panel and fixed several bugs
592* Fixed a number of other minor bugs
593
594
595New in Version 2.2.0
596--------------------
597* Application name changed to SasView
598* New fully customizable Category Manager added for better management of
599  increasing number of models
600* Improved the Grid Window functionality in the batch fitting mode
601* Added a simpler Graph/Plot modification interface
602* Added a new 'Data Operation' tool for addition, subtraction, multiplication,
603  division, of two data sets.
604* The 'Sum Model' editor was extended and renamed 'Summation and Multiplication'
605  editor
606* Added more plot symbols options for 1d plots
607* Added improved trapping of compiling errors to the 'New model editor'
608* Added some intelligent outputs (e.g., Rg, background, or rod diameter
609  depending on the choice of axis scale of the plot) to the linear fits
610* Added more models
611
612
613Feature set from previous versions
614-----------------------------------
615Perspectives Available
616^^^^^^^^^^^^^^^^^^^^^^
617* Invariant calculator: Calculates the invariant, volume fraction, and
618  specific surface area.
619* P(r) inversion calculator: Indirect Fourier transformation method.
620* Fitting: the tool used for modeling and fitting 1D and 2D data to
621  analytical model functions
622* Tools: provides a number of useful supplementary tools such as SLD
623  calculation
[a98c55a]624
[8ac05a5]625Fitting
626^^^^^^^
627* Includes a large number of model functions, both form factors and structure factors.
628* Support P(Q)*S(Q) for form factors that flag they can be so multiplied.
629* Supports Gaussian, lognormal, Shulz, rectangular and custom distribution
630  functions for models that need to include polydispersity or for orientational
631  distributions if appropriate.
632* Anisotropic shapes and magnetic moment modeling in 2D allow for a non-uniform
633  distribution of orientations of a given axis leading to modeling and fitting
634  capabilities of non azimuthaly symmetric data.
635* User can choose to weight fits or not. If using weights, the user can choose
636  the error bar on each point if provided in the file, the square root
637  of the intensity or the intensity itself.
638* Instrumental resolution smearing of model or fits is provided with several
639  options: read the resolution/point fromt he file. Input a pinhole resolution
640  or a slit resolution.
641* Users can define the Qrange (Qmin and Qmax) for both 1D and 2D data for
642  fitting and modeling, but not graphically.  The range can be reset to the
643  defaults (limits of q in data set for a fit) with the reset button.
644* A mask can be applied to 2D calculation and fitting.
645* Normalized residual plots are provided with every fit.
646* Model function help available through detail button or from the fitting panel.
647* Simultaneous/(advanced)constrained fitting allows for fitting a single
648  data set or several different sets simultaneously with the application
649  of advanced constraints relating fit parameters to functions of other
650  parameters (including from a different set). For example thickness of
651  shell = sin(30) times the length.
652* Models that are the sum of two other models can be easily generated through the
653  SUM Model menubar item.
654* New Python models can be added on the fly by creating an appropriate Python
655  file in the model plugin directory. Two tools are provided to help:
656  An easy to use custom model editor allows the quick generation of new Python
657  models by supplying only the parameters and their default value (box 1)
658  and the mathematical function of the model (box 2) and generating the
659  necessary .py file.  A separate advanced model editor provides a full Python
660  file editor.  Either way once saved the model becomes immediately available
661  to the application.
662* A batch fitting capability allows for the analysis of a series of data sets to
663  a single model and provides the results in a tabular form suitable for saving
664  or plotting the evolution of the fit parameters with error bars (from within
665  the application).
[a98c55a]666
[8ac05a5]667Tools
668^^^^^
669* A scattering length density calculator,including some X-ray information
670  is provided.
671* A density to vol. fraction converter is provided
672* In application access to a Python shell/editor (PyCrust) is provided
673* An instrument resolution calculator, including possible gravitational and
674  TOF effects is provided
675* A slit size calculator optimized for Anton Paar Saxess is provided.
676* A kiessig fringe thickness calculator is provided
[a98c55a]677
[8ac05a5]678Plots and plot management
679^^^^^^^^^^^^^^^^^^^^^^^^^
680* A 3D graphing option (for 2d data/results) is provided with the view
681  controlled by the mouse
682* 2D plots are shown with an intensity color bar. 2D Color map can be user
683  adjusted.
684* Supports output of plot to a variety of graphic formats. Supported formats
685  include: png, eps, emf, jpg/jpeg, pdf, ps, tif/tiff, rawRGBbitmap(raw, rgba),
686  and scalable vector graphic (svg/svgz)
687* Supports ouput of data in plot (1 or 2D) to limited data formats
688* Multiple data sets can be loaded into a single graph for viewing (but a fit
689  plot can currently only have a single plot).
690* Extensive context sensitive plot/fitting/manipulation options are available
691  through a right mouse click pop-up menu on plots.
[a98c55a]692
[8ac05a5]693Data management
694^^^^^^^^^^^^^^^
695* Supports 2 + column 1D ASCII data, NIST 1D and 2D data, and canSAS data
696  via plug-in mechanism which can easily allow other readers as appropriate.
697* 2D data is expected in Q space but for historical reasons accepts the
698  NIST 2D raw pixel format and will do conversion internally.
699* The full data and metadata available to SasView is viewable in ASCII via
700  right clicking on a data set and choosing Data Info in the DataExplorer
701  or on the plots
702* Supports loading a single file, multiple files, or a whole folder
703* An optional Data Explorer is provided (default) which simplifies managing,
704  plotting, deleting, or setup for computation. Most functions however do
705  not require access to the explorer/manager and can be accessed through
706  right click menus and the toolbar.  The data explorer can be re-started
707  from the menu bar.
[a98c55a]708
[8ac05a5]709Data manipulation
710^^^^^^^^^^^^^^^^^
711* Support various 2D averaging methods : Circular, sectors, annular,
712  boxsum, boxQx and boxQy.
713* A 2D data maks editor is provided
714* 2D mask can be applied to the circular averaging.
[a98c55a]715
[8ac05a5]716Miscellaneous features
717^^^^^^^^^^^^^^^^^^^^^^
718* Limited reports can be generated in pdf format
719* Provides multiprocessor support(Windows only)
720* Limited startup customization currently includes default startup
721  data folder and choice of default starting with data manager
722* Limited support for saving(opening) a SasView project or a SasView analysis
723  (subproject) is provided.
724* SasView can be launched and loaded with a file of interesty by double-clicking
725  on that file (recognized extension)
726* A data file or data folder can be passed to SasView when launched from
727  the command line.
728* Limited bookmarking capability to later recall the results of a fit calculation
729  is provided.
730* Extensive help is provided through context sensitive mouse roll-over,
731  information bar (at the bottom of the panel), the console menu, and
732  access to the help files in several different ways.
733
734
735Downloading and Installing
736==========================
737
738.. note:: If you have a SasView installer (.EXE or .MSI), you do not need to
739          worry about any of the following.  However, it is highly recommended
740          that any previous versions of SasView are uninstalled prior to
741          installing the new version UNLESS you are installing SasView to
742          versioned folders.
743
744.. note:: The easiest approach to setting up the proper environment to
745          build from source is to use Conda.  Instructions for setting up
746          and using Conda can be found at http://trac.sasview.org/wiki/DevNotes/CondaDevSetup
747                   
748.. note:: Much more information is available at www.sasview.org under
749          links/downloads. In particular, look in the 'For Developers' section.
750          Also have a look at http://trac.sasview.org/
751
752System Requirements
753-------------------
754* Python version >= 2.5 and < 3.0 should be running on the system
755* We currently use Python 2.7
756
757Package Dependencies
758--------------------
759* Ensure the required dependencies are installed
760* For the latest list of dependencies see the appropriate yml file in
761  the SasView repo at sasview/build_tools/conda/ymls
762
763Installing from Source
764----------------------
765* Get the source code
766* Create a folder to contain the source code; if working with
767  multiple versions you might want to use versioned folder names
768  like 'sasview-x.x.x'
769* Open a command line window in the source code folder
770* To get the CURRENT DEVELOPMENT VERSION from source control use
771  git clone https://github.com/SasView/sasview.git sasview
772  git clone https://github.com/Sasview/sasmodels.git sasmodels
773  git clone https://github.com/bumps/bumps.git bumps
774* To get a SPECIFIC RELEASE VERSION from source control go to
775  https://github.com/SasView/sasview/releases
776  and download the required zip or tar.gz file. Unzip/untar it
777  to the source code folder.
778
779Building and Installing
780-----------------------
781* To build the code
782  use 'python setup.py build'
783* To build the documentation
784  use'python setup.py docs'
785
786Running SasView
787---------------
788* use 'python run.py'; this runs from the source directories, so you
789  don't have to rebuild every time you make a change, unless you are
790  changing the C model files.
791* if using Conda the above command will also build SasView, but you
792  must issue 'activate sasview' first.
793
794
795Known Issues
796============
[2ae8579]797
798A full list of known bugs and feature requests by release version that
799users may wish to be aware of can be viewed at http://trac.sasview.org/report/3
[8ac05a5]800
[2ae8579]8014.2.0 - All systems
802-------------------
803The refactoring of the plugin model architecture means that some issues
804may be encountered if Save Project/Analysis files using plugin models
805created in earlier versions of SasView are loaded in version 4.2.0.
806
807For example:
808
809* on loading an old project file an error window appears with the error
810  *This model state has missing or outdated information* or *dictionary changed size during iteration*.
811
812   * if this occurs, try restarting SasView and reloading the project.
813   
814* on loading an old project file all the FitPages and Graphs appear, but
815  only the SasView default model parameters appear in the FitPages.
816
817  * this has happened because plugin model parameter names have changed.
818    There are two possible workarounds:
819   
820   * Install the version of SasView that the project was created in,
821     recreate the plugin in that version, then run 4.2.0 and re-load
822     the project. All being well, 4.2.0 will still compile the old
823     plugin.
824
825   * If 4.2.0 cannot compile the old plugin, the more tedious solution
826     is to use a text editor to do global search & replace operations
827     to change all the parameter names in the project file by hand. The
828     quickest way to see the *existing* parameter names is simply to
829     scroll to the bottom of the project file. To see what the *new* 
830     parameter names should be, simply create the equivalent plugin in
831     SasView 4.2.0. In most instances, what was *p1_parameter* will
832     become *A_parameter*, *p2_parameter* will become *B_parameter*,
833     and so on.
834
[8ac05a5]8354.1.x- All systems
836------------------
837The conversion to sasmodels infrastructure is ongoing and should be
838completed in the next release. In the meantime this leads to a few known
839issues:
840
841* The way that orientation is defined is being refactored to address
842  long standing issues and comments.  In release 4.1 however only models
843  with symmetry (e.g. a=b) have been converted to the new definitions.
844  The rest (a <> b <> c - e.g. parellelepiped) maintain the same
845  definition as before and will be converted in 4.2.  Note that
846  orientational distribution also makes much more sense in the new
847  framework.  The documentation should indicate which definition is being
848  used for a given model.
849* The infrastructure currently handles internal conversion of old style
850  models so that user created models in previous versions should continue
851  to work for now. At some point in the future such support will go away.
852  Everyone is encouraged to convert to the new structure which should be
853  relatively straight forward and provides a number of benefits.
854* In that vein, the distributed models and those generated by the new
855  plugin model editor are in the new format, however those generated by
856  sum|multiply models are the old style sum|multiply models. This should
857  also disappear in the near future
858* The on the fly discovery of plugin models and changes thereto behave
859  inconsistently.  If a change to a plugin model does not seem to
860  register, the Load Plugin Models (under fitting -> Plugin Model
861  Operations) can be used.  However, after calling Load Plugin Models, the
862  active plugin will no longer be loaded (even though the GUI looks like
863  it is) unless it is a sum|multiply model which works properly.  All
864  others will need to be recalled from the model dropdown menu to reload
865  the model into the calculation engine.  While it might be annoying it
866  does not appear to prevent SasView from working..
867* The model code and documentation review is ongoing. At this time the
868  core shell parellelepiped is known to have the C shell effectively fixed
869  at 0 (noted in documentation) while the triaxial ellipsoid does not seem
870  to reproduce the limit of the oblate or prolate ellipsoid. If errors are
871  found and corrected, corrected versions will be uploaded to the
872  marketplace.
[67ed543]873* (Added after Release 4.2.0) The scale parameter reported from the spinodal
874  model is the square root of the true value.
[8ac05a5]875
8763.1- All systems
877----------------
878* The documentation window may take a few seconds to load the first time
879  it is called. Also, an internet connection is required before
880  equations will render properly. Until then they will show in their
881  original TeX format.
882* If the documentation window remains stubbornly blank, try installing a
883  different browser and set that as your default browser. Issues have
884  been noted with Internet Explorer 11.
885* Check for Updates may fail (with the status bar message ' Cannot
886  connect to the application server') if your internet connection uses
887  a proxy server. Tested resolutions for this are described on the
888  website FAQ.
889* The copy and paste functions (^C, ^V) in the batch mode results grid
890  require two clicks: one to select the cell and a second to select the
891  contents of the cell.
892* The tutorial has not yet been updated and is somewhat out of date
893* Very old computers may struggle to run the 3.x and later releases
894* Polydispersity on multiple parameters included in a simultaneous/
895  constrained fit will likely not be correct
896* Constrained/simultaneous fit page does not have a stop button
897* Constrained/simultaneous fit do not accept min/max limits
898* Save project does not store the state of all the windows
899* Loading projects can be very slow
900* Save Project only works once a data set has been associated with
901  a model.  Error is reported on status bar.
902* There is a numerical precision problem with the multishell model when
903  the inner radius gets large enough (ticket #288)
904* The angular distribution angles are not clearly defined and may in
905  some cases lead to incorrect calculations(ticket #332)
906
9073.1 - Windows
908-------------
909* If installed to same directory as old version without first removing
910  the old version, the old desktop icon will remain but point to the
911  new exe version. Likewise all the start menu folders and items will
912  have the old name even though pointing to the new version.  Usually
913  safest to uninstall old version prior to installing new version anyway.
914
9153.1 - MAC
916---------
917* Application normally starts up hidden. Click icon in Dock to view/use
918  application.
919* Multiprocessing does not currently work on MAC OS
920
9213.1 - Linux
922-----------
923* Not well tested
924
925
926SasView Website
927===============
928http://www.sasview.org
929
930This main project site is the gateway to all information about the sasview
931project.  It includes information about the project, a FAQ page and links
932to all developer and user information, tools and resources.
933
934
935Frequently Asked Questions
936==========================
937http://www.sasview.org/faq.html
938
939
940Installer Download Website
941==========================
942Latest release Version
943https://github.com/SasView/sasview/releases
944
945Latest developer builds
946https://jenkins.esss.dk/sasview/view/Master-Builds/
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