Changes in / [e2663b7:3bfcd9e] in sasview

Files:

• installers/README-next-release.txt (modified) (1 diff)
• src/sas/sascalc/dataloader/readers/abs_reader.py (modified) (1 diff)
• src/sas/sascalc/fit/pagestate.py (modified) (2 diffs)
• src/sas/sasgui/guiframe/local_perspectives/plotting/parameters_panel_slicer.py (modified) (2 diffs)
• src/sas/sasgui/guiframe/media/graph_help.rst (modified) (3 diffs)
• test/sasdataloader/test/utest_abs_reader.py (modified) (1 diff)

installers/README-next-release.txt

@@ -1 @@
-   - New in Version 3.?.?
+Release Notes
+=============
+    
+1- Features
+===========
+    - New in Version 4.2.0
+      --------------------
+      This point release heralds many improvements and a host of bug fixes. But there are also some significant changes from previous versions.
+      
+      - Changes
+         - The infrastucture for calculating 2D patterns from 3D orientated objects has been totally re-factored. It is now more accurate and consistent across models.
+         - The way that SasView defines the orientation of anisometric and aligned objects has been completely overhauled. It now differs from previous versions.
+         - Plugin models, including sum/multiply models, have completely migrated to the new infrastructure. ???DO WE NEED TO SAY SOMETHING ABOUT BACKWARD COMPATIBILITY OR LEGACY SUPPORT HERE???
+         - The NeXus loader has been removed (as it is superseded by the NXcanSAS loader).
+      - Improvements
+         - The accuracy/speed of some numerical integrations have been improved. ???CHECK WITH PAULK???
+         - An orientation viewer tool has been introduced (to assist in understanding the new orientation framework).
+         - Problems with the computation of magnetic scattering from some objects have been rectified.
+         - The known issue with the core_shell_parallelepiped model is now fixed.
+         - A number of issues and inconsistencies with the creation of sum|product models have been rectified (and more work is in progress).
+         - A Boltzmann distribution has been added for polydispersity/orientational distributions.
+         - Some batch slicing options have been introduced.
+         - Correlation function analysis now computes both the 1D and 3D functions.
+         - There are several data loading improvements.
+         - There are several improvements to Save/Load Project (with more to come).
+         - There have been numerous other bug fixes.
+      - Documentation
+         Several sections of the help documentation have undergone significant checking and updating, particularly those relating to orientation, magnetic scattering, and polydispersity distributions.
+      - Other work
+         - A Third-Party initiative has recently succeeded in getting SasView to run on Debian. More details at http://trac.sasview.org/wiki/DevNotes/Projects/Debian
+         - With this release we have started to prepare for the inevitable move to Python 3.
+         - SasView 5.0 is already in development. The two most significant features of this version will be (i) a move away from the present WxPython GUIs to new Qt5 GUIs, and (ii) implementation of the Beta-approximation for S(Q). Subject to resources, the latter functionality may be released (in a non-GUI form) in an interim SasView 4.3.0.
+      - Bug Fixes
+         Fixes #  14: Loading a saved project is really really slow  
+         Fixes # 260: Box integration does not update when entering values in dialog  
+         Fixes # 379: Need to make the BUMPS output page more more obvious  
+         Fixes # 446: Saving plot as PGF (not PDF!) format throws error  
+         Fixes # 467: Extend batch functionality to slicer  
+         Fixes # 489: ABS reader (NIST 1D) does not handle negative dx properly (USANS slit smearing)  
+         Fixes # 499: create sin(x)/x, 2*J1(x)/x and 3*j1(x)/x functions  
+         Fixes # 510: Build PDF documentation along with HTML  
+         Fixes # 525: Add GUI category defaults to models in sasmodels  
+         Fixes # 579: clean up sasview directory  
+         Fixes # 597: Need to document Combine Batch Fit  
+         Fixes # 645: GUI logic problem in Batch vs single fit mode  
+         Fixes # 648: Need to allow user input background value in Pr perspective  
+         Fixes # 685: Fix data upload to marketplace  
+         Fixes # 695: linear slope in onion model  
+         Fixes # 735: Review new Corfunc documentation  
+         Fixes # 741: Recalculate P(Q) and S(Q) components on model update.  
+         Fixes # 767: Sum/Product Models don't do what they should  
+         Fixes # 776: angular dispersity  
+         Fixes # 784: Add 3D integral to Correlation Function analysis  
+         Fixes # 786: core_shell_parallelepiped 1-D model is incorrect  
+         Fixes # 818: “report button” followed by “save” makes an empty pdf file???  
+         Fixes # 830: Check compliance of loader against NXcanSAS-1.0 release  
+         Fixes # 838: Fix model download from marketplace  
+         Fixes # 848: can't save analysis when only one fit page  
+         Fixes # 849: Load Folder should ignore files starting with .  
+         Fixes # 852: More unit tests, especially for oriented or 2d models  
+         Fixes # 854: remove unnecessary sleep() in fitting perspective  
+         Fixes # 856: Reading SAS_OPENCL from custom_config sometimes raises an ERROR  
+         Fixes # 861: cannot defined a structure factor plugin  
+         Fixes # 864: New Model Editor (simple plugin editor) error parsing parameter line  
+         Fixes # 865: Plugin live discovery issues  
+         Fixes # 866: inform user when NaN is returned from compute  
+         Fixes # 869: fit page computation thread cleanup  
+         Fixes # 875: Possible weirdness with 1D NXcanSAS data  
+         Fixes # 876: Add check for HDF5 format in dataloader  
+         Fixes # 887: reorganize tree, separating the installed source from the build source  
+         Fixes # 889: Refactor dataloader error handling infrastructure  
+         Fixes # 890: use new orientation definition for asymmetric shapes  
+         Fixes # 891: update docs for oriented shapes with new orientation definition  
+         Fixes # 896: equations in core shell parallelepiped docs do not match code  
+         Fixes # 898: Image Viewer Tool file selector issue  
+         Fixes # 899: Igor Reader q calculation  
+         Fixes # 902: IgorReader Q calculation needs fixing/improving  
+         Fixes # 903: sasview - all non-gui tests should be converted to run in Python 3  
+         Fixes # 906: polydispersity not showing up in tabulated results  
+         Fixes # 912: About box points to misleading contributors page on Github  
+         Fixes # 913: Need to add Diamond developer and logo in relevant places  
+         Fixes # 915: load project issues  
+         Fixes # 916: Proper Logging  
+         Fixes # 920: Logarithmic binning option in the slice viewer  
+         Fixes # 921: Improve developer communication methods  
+         Fixes # 922: Remove support for all data formats that are not in q space  
+         Fixes # 923: Add CI and trac integrations to Slack  
+         Fixes # 930: fitting help says chisq is normalized to number of points  
+         Fixes # 931: Allow admins to edit all models and upload data etc on marketplace  
+         Fixes # 932: Need to fix upload of data files to marketplace  
+         Fixes # 934: Slurp tutorial repo for tutorials  
+         Fixes # 935: Build new tutorials as PDF  
+         Fixes # 943: Deep copy error on setting model after data is selected  
+         Fixes # 950: Most of the readers don't close files properly.  
+         Fixes # 954: cross check dll/opencl/python polydispersity and orientation results  
+         Fixes # 956: Possible problem with new doc build process  
+         Fixes # 961: sasmodels tests should fail if the parameter name does not exist  
+         Fixes # 962: star polymer typo in docs  
+         Fixes # 966: Inconsistent chi2 reporting  
+         Fixes # 967: no uncertainties errors on fitting parameters  
+         Fixes # 969: About Box not picking up dls_logo.png  
+         Fixes # 970: ASCII loader doesn't handle ISIS 2D ASCII  
+         Fixes # 974: blacklist Intel HD 620/630 for double precision  
+         Fixes # 978: load project fails for pages which have not been defined  
+         Fixes # 980: Inconsistent results between Igor & SasView using Fractal Core-Shell model  
+         Fixes # 983: Remove Nexus Loader  
+         Fixes # 984: PDF reports are not being properly generated on Windows  
+         Fixes # 985: Saving Project Fails  
+         Fixes # 986: Send to fitting overwrites theory page even if blank FitPage has focus  
+         Fixes # 990: utest_sasview.py giving different results than run_one.py  
+         Fixes # 993: Windows x64 versions not installing to correct folder  
+         Fixes # 994: Error changing fit engine  
+         Fixes # 995: OpenCL required on Linux even if turned off in GUI  
+         Fixes #1006: multiplicity models don't work with SQ  
+         Fixes #1007: spherical_sld model freezes SasView  
+         Fixes #1008: plugin model scaling not working? S 
+         Fixes #1010: Win64 build script not creating working executable  
+         Fixes #1011: sld_test failing on ubuntu  
+         Fixes #1012: ESS GUI not updating after fitting  
+         Fixes #1013: FileReaderBaseClass output[] not reset - same file loaded multiple times  
+         Fixes #1018: add Boltzmann distribution  
+         Fixes #1021: add PDF documentation to website and document in wiki release process  
+         Fixes #1024: Update version numbers in master  
+         Fixes #1025: Sum/multiply editor hangs  
+         Fixes #1032: convert C++ modules to C  
+         Fixes #1035: Order of combining P(Q) and S(Q) in Plugins seems to matter  
+         Fixes #1037: data loader crop not working? & all fits crashing  
+         Fixes #1043: problem compiling marketplace models  
+         Fixes #1050: fix appveyor test for sasmodels win 64 python 3  
+         Fixes #1052: Can't use a user-created plugin model in a plugin model  
+         Fixes #1054: Check plugin & orientation descriptions in full docs once SasModels PR #57 is merged  
+         Fixes #1057: phi rotation issue for elliptical cylinder  
+         Fixes #1060: incorrect default for rectangle dispersion  
+         Fixes #1062: win32 build not installing correctly  
+         Fixes #1064: Fitting did not converge!!! error with a Sum|Multi plugin model  
+         Fixes #1068: 2d data (from NG7) not loadiing - strange format?  
+         Fixes #1069: GUI problem when using polydispersity/orientation distributions  
+         Fixes #1070: Parameter error boxes should not be editable  
+         Fixes #1072: Orientation distributions seem to depend on initial angle  
+         Fixes #1079: Remove save button in report dialog on Mac  
+         Fixes #1081: GUI problem with new orientation distribution  
+         Fixes #1083: Magnetic models not being computed  
+         Fixes #1099: Erratic behaviour of Sum|Multi model in 4.1.2  
+         Fixes #1101: Batch results page not displaying polydispersity values  
+         Fixes #1103: Problem with plugin models on mac when using ER  
+         Fixes #1134: sum/multi scale factor in 4.2 seems incorrect?  
+         Fixes #1139: Missing Docs and Help for new Batch Slicing  
+         Fixes #1145: Update models in model marketplace to 4.2 when 4.2 is released.  
+         Fixes #1146: Need to add Release notes for 4.2 
+      - Current Known Issues
+         Listed here are known issues that users should be aware of. A full list of known bugs and feature requests is available at http://trac.sasview.org/report/3
+      - Blocker
+         Ticket #1131: OpencCl dialog does not open                                              assigned wojciech defect blocker
+         Ticket #1132: Slit Size Calculator Tool not working                                     assigned krzywon defect blocker
+         Ticket #1133: Reference in Acknowledging SasView box will need updating for release     assigned ajj task blocker
+         Ticket #1142: Plugin framework is broken                                                reopened pkienzle defect blocker
+      - Critical
+         Ticket #1148: Documentation for S(Q) models need updating SasView 4.2.0                 assigned butler defect critical
+      - Other Significant
+         Ticket #1046: convert non builtin models in the marketplace to new API                  assigned butler task major
+         Ticket #1128: AutoPlot generation for model documentation does not include background   assigned pkienzle defect major
+         Ticket #1140: Batch Slicer requires plotting of all 2D data sets to use in batch        assigned krzywon enhancement major
+         Ticket #1141: Intro to scripting.rst needs improvement                                  new pkienzle enhancement major
+         Ticket #1143: Validate new orientation distribution                                     assigned butler task major
+         Ticket #1144: Redundant MultiplicationModel class                                       new pkienzle defect major
+      - Model Issues
+         Corrections will be posted to Marketplace as available (and fixed in following release)
+         Ticket #1044: Unable to upload c file to marketplace                                    assigned tim defect major
+
+      It is recommended that all users upgrade to this version, but your attention is drawn to the Changes section above.
+
+
+    - New in Version 4.1.2
+      --------------------
+      This point release is a bug-fix release addressing:
+
+       - Fixes #984: PDF Reports Generate Empty PDFs
+       - Fixes a path typo
+       - 64 bit and 32 bit Windows executables now available
+
+      It is recommended that all users upgrade to this version
+
+
+    - New in Version 4.1.1
+      --------------------
+      This point release is a bug-fix release addressing:
+
+       - Fixes #948: Mathjax CDN is going away
+       - Fixes #938: Cannot read canSAS1D file output by SasView
+       - Fixes #960: Save project throws error if empty fit page
+       - Fixes #929: Problem deleting data in first fit page
+       - Fixes #918: Test folders not bundled with release
+       - Fixes an issue with the live discovery of plugin models
+       - Fixes an issue with the NXcanSAS data loader
+       - Updated tutorials for SasView 4.x.y
+
+
+    - New in Version 4.1.0
+      ------------------
+      This incremental release brings a series of new features and improvements,
+      and a host of bug fixes. Of particular note are:
+      
+      - Correlation Function Analysis (Corfunc)
+        This performs a correlation function analysis of one-dimensional SAXS/SANS data, 
+            or generates a model-independent volume fraction profile from the SANS from an 
+            adsorbed polymer/surfactant layer.
+
+            A correlation function may be interpreted in terms of an imaginary rod moving 
+            through the structure of the material. Γ1D(R) is the probability that a rod of 
+            length R moving through the material has equal electron/neutron scattering 
+            length density at either end. Hence a frequently occurring spacing within a 
+            structure manifests itself as a peak.
+
+            A volume fraction profile \Phi(z) describes how the density of polymer 
+            segments/surfactant molecules varies with distance from an (assumed locally flat)
+            interface.
+
+      - Fitting of SESANS Data
+        Data from Spin-Echo SANS measurements can now be loaded and fitted. The data will 
+            be plotted against the correct axes and models will automatically perform a Hankel 
+            transform in order to calculate SESANS from a SANS model.
+
+      - Documentation
+        The documentation has undergone significant checking and updating.
+
+      - Improvements
+        - Correlation function (corfunc) analysis of 1D SAS data added from CCP13
+        - File converter tool for multi-file single column data sets
+        - SESANS data loading and direct fitting using the Hankel transformation
+        - Saving and loading of simultaneous and constrained fits now supported
+        - Save states from SasView v3.x.y now loaded using sasmodel model names
+        - Saving and loading of projects with 2D fits now supported
+        - Loading a project removes all existing data, fits, and plots
+        - Structure factor and form factor can be plotted independently
+        - OpenCL is disabled by default and can be enabled through a fit menu
+        - Data and theory fields are now independently expandable
+      - Bug Fixes
+        - Fixes #667: Models computed multiple times on parameters changes
+        - Fixes #673: Custom models override built in models of same name
+        - Fixes #678: Hard crash when running complex models on GPU
+        - Fixes $774: Old style plugin models unloadable
+        - Fixes #789: stacked disk scale doesn't match cylinder model
+        - Fixes #792: core_shell_fractal uses wrong effective radius
+        - Fixes #800: Plot range reset on plot redraws
+        - Fixes #811 and #825: 2D smearing broken
+        - Fixes #815: Integer model parameter handling
+        - Fixes #824: Cannot apply sector averaging when no detector data present
+        - Fixes #830: Cansas HDF5 reader fully compliant with NXCanSAS v1.0 format
+        - Fixes #835: Fractal model breaks with negative Q values
+        - Fixes #843: Multilayer vesicle does not define effective radius
+        - Fixes #858: Hayter MSA S(Q) returns errors
+        - Numerous grammatical and contexual errors in documention
+
+
+    - New in Version 4.0.1
+      ------------------
+      This release fixes the critical bug #750 in P(Q)*S(Q).  Most damaging
+      it appears that the background term was being added to S(Q) prior to
+      multiplication by P(Q).
+
+
+    - New in Version 4.0
+      ------------------
+      This release fixes the various bugs found during the alpha and beta testing
+      - Improvements
+        - Support for reading data files from Anton Paar Saxess instruments
+        - Adds documentation on how to write custom models in the new framework
+      - Bug Fixes
+        - Fixes bug #604 Pringle model questions
+        - Fixes bug #472 Reparameterize Teubner-Strey
+        - Fixes bug #530 Numerical instabilities in Teubner Strey model
+        - Fixes bug #658 ASCII reader very broken
+
+
+    - New in Version 4.0 beta 1
+      --------------------
+      This beta adds support for the magnetic and multilevel models of 3.1.2
+      and along with a host of bug fixes found in the alpha.
+
+      - Model package changes and improvements
+         - All 3.1.2 models now available in new interface
+         - Old custom models should now still work
+            - '''NOTE:''' These will be deprecated in a future version. Old
+            custom models should be converted to the new model format which
+            is now the same as the built in models and offers much better
+            support.
+         - Custom model editor now creates new style models
+         - Custom model editor supports better error checking
+      - Documentation improvements
+        - Continued general cleanup
+      - Other improvements/additions
+         - Support for new canSAS 2D data files added
+         - Plot axes range can now be set manually as well as by zooming
+         - Plot annotations can now be moved around after being placed on plot.
+         - The active optimizer is now listed on the top of the fit panel.
+         - Linear fits now update qmin and max when the x scale limits are
+         changed.  Also the plot range no longer resets after a fit.
+      - Bug fixes
+         - Fixes bug #511 Errors in linearized fits and clean up of interface
+         including Kratky representation
+         - Fixes bug #186 Data operation Tool now executes when something is
+         entered in the text box and does not wait for the user to hit enter
+         - Fixes bug #459 plot context menu bug
+         - Fixes bug #559 copy to clipboard in graph menu broken
+         - Fixes bug #466 cannot remove a linear fit from graph
+         - Numerous bugs introduced in the alpha
+
+
+    - New in Version 4.0.0-alpha
+      --------------------
+      This alpha release brings a major overhaul of the model system. The new model
+      package allows rapid integration of custom models and access to polydispersity
+      without requiring a compiler.
+
+      - Model package changes and improvements
+         - Model interface moved to independent sasmodels package.
+         - Most models converted to new interface.
+         - Allows rapid integration of user-written models.
+         - OpenCL GPU utilization for faster fitting.
+         - Improved numerical integration of Bessel functions.
+      - SESANS integration and implementation
+         - Scripting interface added for analysis of SESANS data.
+         - Hankel transformation now accepts finite acceptance angles.
+         - 2D cosine transformation added for TOF SESANS analysis.
+      - Documentation improvements
+         - The documentation tree was restructured for a better end user experience.
+         - The documentation for each model was revamped and verified by at least
+           two people following the conversion of the model.
+         - Theoretical 1D (and 2D if applicable) scattering curves are auto-generated
+           and added to the model documentation for each model.
+      - Separation of GUI and calculations for future GUI enhancements
+      - Bug fixes
+         - Fixes bug #411 No stop button on simultaneous fit page
+         - Fixes bug #410 Error with raspberry model
+         - Fixes bug #364 Possible inconsistency in Poly_GausCoil model
+         - Fixes bug #439 Hayter Penfold MSA code needs checking
+         - Fixes bug #484 lammellerPC is precision limited
+         - Fixes bug #498 $HOME/.matplotlib conflicts
+         - Fixes bug #348 Control order in which fit parameters appear in the gui
+         - Fixes bug #456 Provide DREAM Results Panel with something to identify
+           data and age of results
+         - Fixes bug #556 Build script improvements for developers
+
+
+   - New in Version 3.1.2
      --------------------
-
+     This release is a major stability improvement, having fixed a serious bug
+     that came to light since release 3.1.1. All users should upgrade.
+
+     - Fixes bug #468 broken remove constraint buttons in
+       simultaneous/constrained fitting panel
+     - Fixes bug #474 resulting from changes in 3.1.1 that had
+       introduced an error in the high-Q of slit-smeared models.
+     - Fixes bug #478 which would cause wx to run out of IDs and result
+       in SasView crashing even if left alone.
+     - Fixes bug #479 missing help button on simultaneous/constrained fit page
+     - Fixes bug #480 GUI resizing issues on simultaneous fit page
+     - Fixes bug #486 broken Report Results
+     - Fixes bug #488 redraw issues in fit page
+
+
+   - New in Version 3.1.1
+     --------------------
+     - Fixes bug #457 that prevented SasView from starting if the user was not
+       connected to the internet, or was behind a proxy server.
+
+
+   - New in Version 3.1.0
+     --------------------
+     - The documentation/help has had a complete overhaul including:
+       - A completely new presentation interface (Sphinx).
+       - Proof reading!
+       - Updating for latest features.
+       - A Help (or sometimes ?) button has been added to every panel, and some
+         sub panels if appropriate, linking to the appropriate section in the
+         documentation.
+       - The model help has been split so that the Details button now brings up
+         a very short pop-up giving the equation being used while HELP goes to
+         the section in the full documentation describing the model.
+       - Extensive help has also been added for the new optimizer engine (see
+         below) including rules of thumb on how and when to choose a given
+         optimizer and what the parameters do.
+     - The optimizer engine has been completely replaced. The new optimizer
+       still defaults to the standard Levenberg-Marquardt algorithm. However 4
+       other optimizers are now also available. Each starts with a set of default
+       parameters which can be tuned. The DREAM optimizer takes the longest but
+       is the most powerful and yields rich information including full parameter
+       correlation and uncertainty plots. A results panel has been added to
+       accommodate this.
+       - The five new optimizers are:
+         - A Levenberg-Marquardt optimizer
+         - A Quasi-Newton BFGS optimizer
+         - A Nelder-Mead Simplex optimizer
+         - A Differential Evolution optimizer
+         - A Monte Carlo optimizer (DREAM)
      - New models were added:
-       - LamellarPolLz
-
+         - MicelleSphCoreModel (currently residing in the Uncategorized category)
      - Existing models were updated:
-       - LamellarPS and LamellarPSHG have been changed to LamellarCaille and 
-         LamellarCailleHG
-       
+         - LamellarPS (bug in polydispersity integration fixed)
+         - RectangularPrismModel
+         - RectangularHollowPrismModel
+         - RectangularHollowPrismInfThinWallsModel
+     - Infrastructure to allow SESANS data to be fit with models was added. This
+       will become available in a future release but can currently be used from
+       the command line with some caveats.
+     - A number of bugs were fixed including a thread crashing issue and an
+       incorrect slit smearing resolution calculation.
+     - Implemented much more robust error logging to enable much easier
+       debugging in general but particularly the debugging of issues reported by
+       SasView users.
+     - A number of infrastructure tasks under the hood to enhance maintainability
+     - Upgrade from Wx 2.8 to Wx 3.0.2 which allows several new features but
+       required significant additional rework as well.
+     - Fully implemented Sphinx to the build process to produce both better
+       user documentation and developer documentation.
+     - Restructuring of the code base to more unified nomenclature and structure
+       so that the source installation tree more closely matches the installer
+       version tree.
+     - Code cleanup (an ongoing task) .
+     - Migration of the repository to github simplifying contributions from
+       non-project personnel through pull requests.
+
+
+   - New in Version 3.0.0
+     --------------------
+     - The GUI look and feel has been refactored to be more familiar for
+       Windows users by using MDI frames. Graph windows are also now free-
+       floating.
+     - Five new models have been added: PringlesModel, CoreShellEllipsoidXTModel,
+       RectangularPrismModel, RectangularHollowPrismModel and
+       RectangularHollowPrismInfThinWallsModel.
+     - The data loader now supports ILL DAT data files and reads the full meta
+       information from canSAS file formats.
+     - Redefined convention for specifying angular parameters for anisotropic
+       models.
+     - A number of minor features have been added such as permitting a log
+       distribution of points when using a model to simulate data, and the
+       addition of a Kratky plot option to the linear plots.
+     - A number of bugs have also been fixed.
+     - Save Project and Save Analysis now work more reliably.
+     - BETA: Magnetic contrast supporting full polarization analysis has been
+       implemented for some spherical and cylindrical models.
+     - BETA: Two new tools have been added:
+       - A generic scattering calculator which takes an atomic, magnetic or
+         SLD distribution in space and generates the appropriate 2D
+         scattering pattern. In some cases the orientationally averaged
+         (powder) 1D scattering can also be computed. Supported formats
+         include: SLD or text, PDB, and OMF magnetic moment distribution
+         file.
+       - An image viewer/converter for data in image format; this reads in
+         an image file and will attempt to convert the image pixels to
+         data. Supported formats include: TIFF, TIF, PNG, BMP, JPG.
+
+
+   - New in Version 2.2.1
+     --------------------
+     - Minor patch to support CanSAS XML v1.1 file format
+     - Added DataInfo for data in the DataExplorer and plots
+     - Added Maximize/Restore button in the title bar of the graphs
+     - Added a hide button in the toolbar of the graph panel
+     - The 'x' button now deletes a graph
+     - Edit SUM Model from the menubar can now generate and save more than one sum model
+     - Reports can now be saved in pdf format on WIN and MAC
+     - Made significant improvements to the batch/grid panel and fixed several bugs
+     - Fixed a number of other minor bugs
+
+
+   - New in Version 2.2.0
+     --------------------
+     - Application name changed to SasView
+     - New fully customizable Category Manager added for better management of
+       increasing number of models
+     - Improved the Grid Window functionality in the batch fitting mode
+     - Added a simpler Graph/Plot modification interface
+     - Added a new 'Data Operation' tool for addition, subtraction, multiplication,
+       division, of two data sets.
+     - The 'Sum Model' editor was extended and renamed 'Summation and Multiplication'
+       editor
+     - Added more plot symbols options for 1d plots
+     - Added improved trapping of compiling errors to the 'New model editor'
+     - Added some intelligent outputs (e.g., Rg, background, or rod diameter
+       depending on the choice of axis scale of the plot) to the linear fits
+     - Added more models
+
+   - Feature set from previous versions
+     -----------------------------------
+     - Perspectives Available
+       - Invariant calculator: Calculates the invariant, volume fraction, and
+         specific surface area.
+       - P(r) inversion calculator: Indirect Fourier transformation method.
+       - Fitting: the tool used for modeling and fitting 1D and 2D data to
+         analytical model functions
+       - Tools: provides a number of useful supplementary tools such as SLD
+         calculation
+
+     - Fitting
+       - Includes a large number of model functions, both form factors and structure factors.
+       - Support P(Q)*S(Q) for form factors that flag they can be so multiplied.
+       - Supports Gaussian, lognormal, Shulz, rectangular and custom distribution
+         functions for models that need to include polydispersity or for orientational
+         distributions if appropriate.
+       - Anisotropic shapes and magnetic moment modeling in 2D allow for a non-uniform
+         distribution of orientations of a given axis leading to modeling and fitting
+         capabilities of non azimuthaly symmetric data.
+       - User can choose to weight fits or not. If using weights, the user can choose
+         the error bar on each point if provided in the file, the square root
+         of the intensity or the intensity itself.
+       - Instrumental resolution smearing of model or fits is provided with several
+         options: read the resolution/point fromt he file. Input a pinhole resolution
+         or a slit resolution.
+       - Users can define the Qrange (Qmin and Qmax) for both 1D and 2D data for
+         fitting and modeling, but not graphically.  The range can be reset to the
+         defaults (limits of q in data set for a fit) with the reset button.
+       - A mask can be applied to 2D calculation and fitting.
+       - Normalized residual plots are provided with every fit.
+       - Model function help available through detail button or from the fitting panel.
+       - Simultaneous/(advanced)constrained fitting allows for fitting a single
+         data set or several different sets simultaneously with the application
+         of advanced constraints relating fit parameters to functions of other
+         parameters (including from a different set). For example thickness of
+         shell = sin(30) times the length.
+       - Models that are the sum of two other models can be easily generated through the
+         SUM Model menubar item.
+       - New Python models can be added on the fly by creating an appropriate Python
+         file in the model plugin directory. Two tools are provided to help:
+         An easy to use custom model editor allows the quick generation of new Python
+         models by supplying only the parameters and their default value (box 1)
+         and the mathematical function of the model (box 2) and generating the
+         necessary *.py file.  A separate advanced model editor provides a full Python
+         file editor.  Either way once saved the model becomes immediately available
+         to the application.
+       - A batch fitting capability allows for the analysis of a series of data sets to
+         a single model and provides the results in a tabular form suitable for saving
+         or plotting the evolution of the fit parameters with error bars (from within
+         the application).
+
+     - Tools
+       - A scattering length density calculator,including some X-ray information
+         is provided.
+       - A density to vol. fraction converter is provided
+       - In application access to a Python shell/editor (PyCrust) is provided
+       - An instrument resolution calculator, including possible gravitational and
+         TOF effects is provided
+       - A slit size calculator optimized for Anton Paar Saxess is provided.
+       - A kiessig fringe thickness calculator is provided
+
+     - Plots and plot management
+       - A 3D graphing option (for 2d data/results) is provided with the view
+         controlled by the mouse
+       - 2D plots are shown with an intensity color bar. 2D Color map can be user
+         adjusted.
+       - Supports output of plot to a variety of graphic formats. Supported formats
+         include: png, eps, emf, jpg/jpeg, pdf, ps, tif/tiff, rawRGBbitmap(raw, rgba),
+         and scalable vector graphic (svg/svgz)
+       - Supports ouput of data in plot (1 or 2D) to limited data formats
+       - Multiple data sets can be loaded into a single graph for viewing (but a fit
+         plot can currently only have a single plot).
+       - Extensive context sensitive plot/fitting/manipulation options are available
+         through a right mouse click pop-up menu on plots.
+
+     - Data management
+       - Supports 2 + column 1D ASCII data, NIST 1D and 2D data, and canSAS data
+         via plug-in mechanism which can easily allow other readers as appropriate.
+       - 2D data is expected in Q space but for historical reasons accepts the
+         NIST 2D raw pixel format and will do conversion internally.
+       - The full data and metadata available to SasView is viewable in ASCII via
+         right clicking on a data set and choosing Data Info in the DataExplorer
+         or on the plots
+       - Supports loading a single file, multiple files, or a whole folder
+       - An optional Data Explorer is provided (default) which simplifies managing,
+         plotting, deleting, or setup for computation. Most functions however do
+         not require access to the explorer/manager and can be accessed through
+         right click menus and the toolbar.  The data explorer can be re-started
+         from the menu bar.
+
+     - Data manipulation
+       - Support various 2D averaging methods : Circular, sectors, annular,
+         boxsum, boxQx and boxQy.
+       - A 2D data maks editor is provided
+       - 2D mask can be applied to the circular averaging.
+
+     - Miscellaneous features
+       - limited reports can be generated in pdf format
+       - Provides multiprocessor support(Windows only)
+       - Limited startup customization currently includes default startup
+         data folder and choice of default starting with data manager
+       - Limited support for saving(opening) a SasView project or a SasView analysis
+         (subproject) is provided.
+       - SasView can be launched and loaded with a file of interesty by double-clicking
+         on that file (recognized extension)
+       - A data file or data folder can be passed to SasView when launched from
+         the command line.
+       - Limited bookmarking capability to later recall the results of a fit calculation
+         is provided.
+       - Extensive help is provided through context sensitive mouse roll-over,
+         information bar (at the bottom of the panel), the console menu, and
+         access to the help files in several different ways.
+
+
+2- Downloading and Installing
+=============================
+
+   *** Note 1:  Much more information is available at www.sasview.org under links.
+                    Look in the 'For Developers' section and particularly the wiki at
+                www.sasview.org/trac/wiki.
+   *** Note 2:  If you have EXE or ZIP SasView installer, you won't need any of
+                the following.  However it is highly recommended that any
+                previous versions be un-installed prior to installing the
+                new version.
+
+   2.1- System Requirements
+        - Python version >= 2.5 and < 3.0 should be running on the system
+        - We currently use Python 2.7
+
+   2.2- Installing from source
+        - Get the source code
+          - to follow the current development version from source control use
+              git clone https://github.com/SasView/sasview.git
+              git clone https://github.com/bumps/bumps.git
+          - to install a specific version
+
+        - Build, install and run a specific release
+          - make sure the requirements below are already installed
+          - retrieve the source from https://github.com/SasView/sasview/releases
+          - open a command line window in the 'sasview-x.x.x' directory
+          - run 'python setup.py install'
+          - run 'python sasview.py' under the 'sasview' folder.
+
+        - Build, install and run the current development version
+          - clone the source from git; also clone bumps, which is developed in parallel
+              git clone https://github.com/SasView/sasview.git
+              git clone https://github.com/bumps/bumps.git
+          - open a command line window in the 'sasview' directory
+          - run 'python setup.py build'
+          - run 'python run.py'; this runs from the source directories, so you
+            don't have to rebuild every time you make a change, unless you are
+            changing the C++ model files
+
+        - The following modules are required (version numbers are what are used
+          in the windows release build):
+
+          - Common Packages
+            - reportlab 3.1.44
+            - lxml 3.4.4.0 (MAC 3.4.2.0)
+            - PIL 1.1.7
+            - xhtml2pdf 3.0.33 (MAC = not installed on build server)
+            - unittest-xml-reporting 1.12.0 (MAC 1.10.0)
+            - matplotlib Version Installed: 1.4.3 (MAC 1.1.1)
+            - bumps Version Installed: 0.7.5.9
+            - scipy Version Installed: 0.16.0b2 (MAC 0.11.0)
+            - periodictable Version Installed: 1.4.1
+            - setuptools Version Installed: 7.0 (MAC 12.0.5)
+            - sphinx Version Installed: 1.3.1 (MAC 1.3b2)
+            - pyparsing Version Installed: 2.0.3
+            - numpy Version Installed: 1.9.2 (MAC 1.6.2)
+            - html5lib Version Installed: 0.99999
+            - wx Version Installed: 3.0.2.0
+
+          - Windows Specific Packages
+            - pywin 219
+            - py2exe 0.6.9
+            - comtypes 1.1.1
+            - MinGW w/ gcc version 4.6.1 (WIN)
+            - vcredist_x86.exe (version 9.0.21022.8  -microsoft visual C 2008
+              re-distributable)
+            - Innosetup (WIN - isetup 5.4.2-unicode) - used to create distributable
+
+            *** Note: Windows build dependencies can be set up using anaconda. Instructions
+                can be found at http://trac.sasview.org/wiki/AnacondaSetup
+
+          - MAC Specifc Packages
+            - py2app 0.7.1
+
+
+3- Known Issues
+===============
+
+   4.1- All systems:
+      The conversion to sasmodels infrastructure is ongoing and should be
+      completed in the next release. In the meantime this leads to a few known
+      issues:
+        - The way that orientation is defined is being refactored to address
+        long standing issues and comments.  In release 4.1 however only models
+        with symmetry (e.g. a=b) have been converted to the new definitions.
+        The rest (a <> b <> c - e.g. parellelepiped) maintain the same
+        definition as before and will be converted in 4.2.  Note that
+        orientational distribution also makes much more sense in the new
+        framework.  The documentation should indicate which definition is being
+        used for a given model.
+        - The infrastructure currently handles internal conversion of old style
+        models so that user created models in previous versions should continue
+        to work for now. At some point in the future such support will go away.
+        Everyone is encouraged to convert to the new structure which should be
+        relatively straight forward and provides a number of benefits. 
+        - In that vein, the distributed models and those generated by the new
+        plugin model editor are in the new format, however those generated by
+        sum|multiply models are the old style sum|multiply models. This should
+        also disappear in the near future 
+        - The on the fly discovery of plugin models and changes thereto behave
+        inconsistently.  If a change to a plugin model does not seem to
+        register, the Load Plugin Models (under fitting -> Plugin Model
+        Operations) can be used.  However, after calling Load Plugin Models, the
+        active plugin will no longer be loaded (even though the GUI looks like
+        it is) unless it is a sum|multiply model which works properly.  All
+        others will need to be recalled from the model dropdown menu to reload
+        the model into the calculation engine.  While it might be annoying it
+        does not appear to prevent SasView from working..
+        - The model code and documentation review is ongoing. At this time the
+        core shell parellelepiped is known to have the C shell effectively fixed
+        at 0 (noted in documentation) while the triaxial ellipsoid does not seem
+        to reproduce the limit of the oblate or prolate ellipsoid. If errors are
+        found and corrected, corrected versions will be uploaded to the
+        marketplace. 
+   
+   3.1- All systems:
+        - The documentation window may take a few seconds to load the first time
+          it is called. Also, an internet connection is required before
+          equations will render properly. Until then they will show in their
+          original TeX format.
+        - If the documentation window remains stubbornly blank, try installing a
+          different browser and set that as your default browser. Issues have
+          been noted with Internet Explorer 11.
+        - Check for Updates may fail (with the status bar message ' Cannot
+          connect to the application server') if your internet connection uses
+          a proxy server. Tested resolutions for this are described on the
+          website FAQ.
+        - The copy and paste functions (^C, ^V) in the batch mode results grid
+          require two clicks: one to select the cell and a second to select the
+          contents of the cell.
+        - The tutorial has not yet been updated and is somewhat out of date
+        - Very old computers may struggle to run the 3.x and later releases
+        - Polydispersity on multiple parameters included in a simultaneous/
+          constrained fit will likely not be correct
+        - Constrained/simultaneous fit page does not have a stop button
+        - Constrained/simultaneous fit do not accept min/max limits
+        - Save project does not store the state of all the windows
+        - Loading projects can be very slow
+        - Save Project only works once a data set has been associated with
+          a model.  Error is reported on status bar.
+        - There is a numerical precision problem with the multishell model when
+          the iner radius gets large enough (ticket #288)
+        - The angular distribution angles are not clearly defined and may in
+          some cases lead to incorrect calculations(ticket #332)
+
+   3.2- Windows:
+        - If installed to same directory as old version without first removing
+          the old version, the old desktop icon will remain but point to the
+          new exe version. Likewise all the start menu folders and items will
+          have the old name even though pointing to the new version.  Usually
+          safest to uninstall old version prior to installing new version anyway.
+
+   3.3- MAC:
+        - Application normally starts up hidden. Click icon in Dock to view/use
+          application.
+        - Multiprocessing does not currently work on MAC OS
+
+   3.4- Linux:
+        - Not well tested
+
+
+4- SasView website
+==================
+
+   - www.sasview.org.  This main project site is the gateway to all
+     information about the sasview project.  It includes information
+     about the project, a FAQ page and links to all developer and user
+     information, tools and resources.
+
+
+5- Frequently Asked Questions
+=============================
+
+   - www.sasview.org/faq.html
+
+
+6- Installer download website
+=============================
+
+   - Latest release Version
+     - https://github.com/SasView/sasview/releases
+   - Latest developer builds
+     - https://jenkins.esss.dk/sasview/view/Master-Builds/

src/sas/sascalc/dataloader/readers/abs_reader.py

@@ -171 +171 @@
 
                 try:
-                    _x = float(toks[0])
+                    _x = float(toks[4])
                     _y = float(toks[1])
                     _dy = float(toks[2])

src/sas/sascalc/fit/pagestate.py

@@ -13 +13 @@
 ################################################################################
 import time
+import re
 import os
 import sys
@@ -962 +963 @@
         if node.get('version'):
             # Get the version for model conversion purposes
-            self.version = tuple(int(e) for e in
-                                 str.split(node.get('version'), "."))
+            x = re.sub('[^\d.]', '', node.get('version'))
+            self.version = tuple(int(e) for e in str.split(x, "."))
             # The tuple must be at least 3 items long
             while len(self.version) < 3:

src/sas/sasgui/guiframe/local_perspectives/plotting/parameters_panel_slicer.py

@@ -251 +251 @@
             self.bck.Add(self.batch_slicer_button, (iy, ix), (1, 1),
                          wx.LEFT | wx.EXPAND | wx.ADJUST_MINSIZE, 15)
+            # Help button
+
+            self.bt_help = wx.Button(self, wx.NewId(), "HELP")
+            self.bt_help.SetToolTipString(
+                "Help for the slicer parameters and batch slicing.")
+            self.bck.Add(self.bt_help, (iy, 1), (1, 1),
+                         wx.ALIGN_RIGHT | wx.ADJUST_MINSIZE, 15)
+            wx.EVT_BUTTON(self, self.bt_help.GetId(), self.on_help)
+
             iy += 1
             self.bck.Add((5, 5), (iy, ix), (1, 1),
                          wx.LEFT | wx.EXPAND | wx.ADJUST_MINSIZE, 5)
+
         self.bck.Layout()
         self.bck.Fit(self)
@@ -535 +545 @@
             self.default_value += "_{0}".format(key).split(" [")[0]
             self.default_value += "-{:.2f}".format(params[key])
+
+    def on_help(self, event=None):
+        """
+        Opens a help window for the slicer parameters/batch slicing window
+        :param event:
+        :return:
+        """
+        from sas.sasgui.guiframe.documentation_window import DocumentationWindow
+
+        _TreeLocation = "user/sasgui/guiframe/graph_help.html"
+        _doc_viewer = DocumentationWindow(self, wx.ID_ANY, _TreeLocation,
+                                          "#d-data-averaging",
+                                          "Data Explorer Help")

src/sas/sasgui/guiframe/media/graph_help.rst

@@ -266 +266 @@
 
 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+.. _d_data_averaging:
 
 2D data averaging
@@ -301 +302 @@
 Alternatively, once a 'slicer' is active you can also select the region to
 average by bringing back the *Dataset Menu* and selecting *Edit Slicer
-Parameters*. A dialog window will appear in which you can enter values to
-define a region or select the number of points to plot (*nbins*).
+Parameters and Batch Fitting*. A dialog window will appear in which you can
+enter values to define a region, select the number of points to plot (*nbins*),
+or apply the slicer to any or all other 2D data plots.
 
 A separate plot window will also have appeared, displaying the requested
@@ -315 +317 @@
 
 To remove a 'slicer', bring back the *Dataset menu* and select *Clear Slicer*.
+
+Batch Slicing
+^^^^^^^^^^^^^
+
+A slicer can be applied to any or all existing 2D data plots using the 'Slicer
+Parameters' window. To open the window, select *Edit Slicer Parameters and Batch
+Fitting* in the *Dataset Menu* (see Invoking_the_dataset_menu_). Batch slicing
+options are available at the bottom of the window.
+
+Select the 2D plots you want to apply the slicer to. All 2D plots are selected
+by default. The resulting 1D data for all slicers can be saved as a text file
+and then sent to fitting by selecting the *Auto save generated 1D* check box.
+Sending data to the fitting perspective requires the data be saved.
+
+Once the auto save check box is selected, you can select where the files are
+saved. The file name for the saved data is the slicer name plus the file name
+of the original data set, plus what is in the *Append to file name* field. The
+default value in the append to field includes the names and values for all of
+the slicer parameters.
+
+The batch of slices can be sent to fitting if desired, with three options
+available. The first is to not fit the data, the second is to send the
+slices to individual fit pages, and the third is to send all sliced data to a
+single batch fit window.
+
+Clicking *Apply Slicer to Selected Plots* will create a slicer for each selected
+plot with the parameters entered in the 'Slicer Parameters' window. Depending on
+the options selected the data may then be saved, loaded as separate data sets in
+the data manager panel, and finally sent to fitting.
 
 Unmasked circular average

test/sasdataloader/test/utest_abs_reader.py

@@ -53 +53 @@
 
         self.assertEqual(self.data.y_unit, 'cm^{-1}')
-        self.assertEqual(self.data.x[0], 0.002618)
-        self.assertEqual(self.data.x[1], 0.007854)
-        self.assertEqual(self.data.x[2], 0.01309)
+        self.assertEqual(self.data.x[0], 0.008082)
+        self.assertEqual(self.data.x[1], 0.0275)
+        self.assertEqual(self.data.x[2], 0.02762)
         self.assertEqual(self.data.x[126], 0.5828)