source: sasview/sasview/README.txt @ c62e5eb

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1Release Notes
2=============
3
41- Features
5===========
6    - New in Version 4.1.0
7      ------------------
8      This incremental release brings a series of new features and improvements,
9      and a host of bug fixes.
10
11      - Improvements
12        - Correlation function (corfunc) analysis of 1D SAS data added from CCP13
13        - File converter tool for multi-file single column data sets
14        - SESANS data loading and direct fitting using the Hankel transformation
15        - Saving and loading of simultaneous and constrained fits now supported
16        - Save states from SasView v3.x.y now loaded using sasmodel model names
17        - Saving and loading of projects with 2D fits now supported
18        - Loading a project removes all existing data, fits, and plots
19        - Structure factor and form factor can be plotted independently
20        - OpenCL is disabled by default and can be enabled through a fit menu
21        - Data and theory fields are now independently expandable
22      - Bug Fixes
23        - Fixes #667: Models computed multiple times on parameters changes
24        - Fixes #673: Custom models override built in models of same name
25        - Fixes #678: Hard crash when running complex models on GPU
26        - Fixes $774: Old style plugin models unloadable
27        - Fixes #789: stacked disk scale doesn't match cylinder model
28        - Fixes #792: core_shell_fractal uses wrong effective radius
29        - Fixes #800: Plot range reset on plot redraws
30        - Fixes #811 and #825: 2D smearing broken
31        - Fixes #815: Integer model parameter handling
32        - Fixes #824: Cannot apply sector averaging when no detector data present
33        - Fixes #830: Cansas HDF5 reader fully compliant with NXCanSAS v1.0 format
34        - Fixes #835: Fractal model breaks with negative Q values
35        - Fixes #843: Multilayer vesicle does not define effective radius
36        - Fixes #858: Hayter MSA S(Q) returns errors
37        - Numerous grammatical and contexual errors in documention
38
39
40    - New in Version 4.0.1
41      ------------------
42      This release fixes the critical bug #750 in P(Q)*S(Q).  Most damaging
43      it appears that the background term was being added to S(Q) prior to
44      multiplication by P(Q).
45
46
47    - New in Version 4.0
48      ------------------
49      This release fixes the various bugs found during the alpha and beta testing
50      - Improvements
51        - Support for reading data files from Anton Paar Saxess instruments
52        - Adds documentation on how to write custom models in the new framework
53      - Bug Fixes
54        - Fixes bug #604 Pringle model questions
55        - Fixes bug #472 Reparameterize Teubner-Strey
56        - Fixes bug #530 Numerical instabilities in Teubner Strey model
57        - Fixes bug #658 ASCII reader very broken
58
59
60    - New in Version 4.0 beta 1
61      --------------------
62      This beta adds support for the magnetic and multilevel models of 3.1.2
63      and along with a host of bug fixes found in the alpha.
64
65      - Model package changes and improvements
66         - All 3.1.2 models now available in new interface
67         - Old custom models should now still work
68            - '''NOTE:''' These will be deprecated in a future version. Old
69            custom models should be converted to the new model format which
70            is now the same as the built in models and offers much better
71            support.
72         - Custom model editor now creates new style models
73         - Custom model editor supports better error checking
74      - Documentation improvements
75        - Continued general cleanup
76      - Other improvements/additions
77         - Support for new canSAS 2D data files added
78         - Plot axes range can now be set manually as well as by zooming
79         - Plot annotations can now be moved around after being placed on plot.
80         - The active optimizer is now listed on the top of the fit panel.
81         - Linear fits now update qmin and max when the x scale limits are
82         changed.  Also the plot range no longer resets after a fit.
83      - Bug fixes
84         - Fixes bug #511 Errors in linearized fits and clean up of interface
85         including Kratky representation
86         - Fixes bug #186 Data operation Tool now executes when something is
87         entered in the text box and does not wait for the user to hit enter
88         - Fixes bug #459 plot context menu bug
89         - Fixes bug #559 copy to clipboard in graph menu broken
90         - Fixes bug #466 cannot remove a linear fit from graph
91         - Numerous bugs introduced in the alpha
92
93
94
95    - New in Version 4.0.0-alpha
96      --------------------
97      This alpha release brings a major overhaul of the model system. The new model
98      package allows rapid integration of custom models and access to polydispersity
99      without requiring a compiler.
100
101      - Model package changes and improvements
102         - Model interface moved to independent sasmodels package.
103         - Most models converted to new interface.
104         - Allows rapid integration of user-written models.
105         - OpenCL GPU utilization for faster fitting.
106         - Improved numerical integration of Bessel functions.
107      - SESANS integration and implementation
108         - Scripting interface added for analysis of SESANS data.
109         - Hankel transformation now accepts finite acceptance angles.
110         - 2D cosine transformation added for TOF SESANS analysis.
111      - Documentation improvements
112         - The documentation tree was restructured for a better end user experience.
113         - The documentation for each model was revamped and verified by at least
114           two people following the conversion of the model.
115         - Theoretical 1D (and 2D if applicable) scattering curves are auto-generated
116           and added to the model documentation for each model.
117      - Separation of GUI and calculations for future GUI enhancements
118      - Bug fixes
119         - Fixes bug #411 No stop button on simultaneous fit page
120         - Fixes bug #410 Error with raspberry model
121         - Fixes bug #364 Possible inconsistency in Poly_GausCoil model
122         - Fixes bug #439 Hayter Penfold MSA code needs checking
123         - Fixes bug #484 lammellerPC is precision limited
124         - Fixes bug #498 $HOME/.matplotlib conflicts
125         - Fixes bug #348 Control order in which fit parameters appear in the gui
126         - Fixes bug #456 Provide DREAM Results Panel with something to identify
127           data and age of results
128         - Fixes bug #556 Build script improvements for developers
129
130
131
132   - New in Version 3.1.2
133     --------------------
134     This release is a major stability improvement, having fixed a serious bug
135     that came to light since release 3.1.1. All users should upgrade.
136
137     - Fixes bug #468 broken remove constraint buttons in
138       simultaneous/constrained fitting panel
139     - Fixes bug #474 resulting from changes in 3.1.1 that had
140       introduced an error in the high-Q of slit-smeared models.
141     - Fixes bug #478 which would cause wx to run out of IDs and result
142       in SasView crashing even if left alone.
143     - Fixes bug #479 missing help button on simultaneous/constrained fit page
144     - Fixes bug #480 GUI resizing issues on simultaneous fit page
145     - Fixes bug #486 broken Report Results
146     - Fixes bug #488 redraw issues in fit page
147
148
149
150   - New in Version 3.1.1
151     --------------------
152     - Fixes bug #457 that prevented SasView from starting if the user was not
153       connected to the internet, or was behind a proxy server.
154
155   - New in Version 3.1.0
156     --------------------
157     - The documentation/help has had a complete overhaul including:
158       - A completely new presentation interface (Sphinx).
159       - Proof reading!
160       - Updating for latest features.
161       - A Help (or sometimes ?) button has been added to every panel, and some
162         sub panels if appropriate, linking to the appropriate section in the
163         documentation.
164       - The model help has been split so that the Details button now brings up
165         a very short pop-up giving the equation being used while HELP goes to
166         the section in the full documentation describing the model.
167       - Extensive help has also been added for the new optimizer engine (see
168         below) including rules of thumb on how and when to choose a given
169         optimizer and what the parameters do.
170     - The optimizer engine has been completely replaced. The new optimizer
171       still defaults to the standard Levenberg-Marquardt algorithm. However 4
172       other optimizers are now also available. Each starts with a set of default
173       parameters which can be tuned. The DREAM optimizer takes the longest but
174       is the most powerful and yields rich information including full parameter
175       correlation and uncertainty plots. A results panel has been added to
176       accommodate this.
177       - The five new optimizers are:
178         - A Levenberg-Marquardt optimizer
179         - A Quasi-Newton BFGS optimizer
180         - A Nelder-Mead Simplex optimizer
181         - A Differential Evolution optimizer
182         - A Monte Carlo optimizer (DREAM)
183     - New models were added:
184         - MicelleSphCoreModel (currently residing in the Uncategorized category)
185     - Existing models were updated:
186         - LamellarPS (bug in polydispersity integration fixed)
187         - RectangularPrismModel
188         - RectangularHollowPrismModel
189         - RectangularHollowPrismInfThinWallsModel
190     - Infrastructure to allow SESANS data to be fit with models was added. This
191       will become available in a future release but can currently be used from
192       the command line with some caveats.
193     - A number of bugs were fixed including a thread crashing issue and an
194       incorrect slit smearing resolution calculation.
195     - Implemented much more robust error logging to enable much easier
196       debugging in general but particularly the debugging of issues reported by
197       SasView users.
198     - A number of infrastructure tasks under the hood to enhance maintainability
199     - Upgrade from Wx 2.8 to Wx 3.0.2 which allows several new features but
200       required significant additional rework as well.
201     - Fully implemented Sphinx to the build process to produce both better
202       user documentation and developer documentation.
203     - Restructuring of the code base to more unified nomenclature and structure
204       so that the source installation tree more closely matches the installer
205       version tree.
206     - Code cleanup (an ongoing task) .
207     - Migration of the repository to github simplifying contributions from
208       non-project personnel through pull requests.
209
210   - New in Version 3.0.0
211     --------------------
212     - The GUI look and feel has been refactored to be more familiar for
213       Windows users by using MDI frames. Graph windows are also now free-
214       floating.
215     - Five new models have been added: PringlesModel, CoreShellEllipsoidXTModel,
216       RectangularPrismModel, RectangularHollowPrismModel and
217       RectangularHollowPrismInfThinWallsModel.
218     - The data loader now supports ILL DAT data files and reads the full meta
219       information from canSAS file formats.
220     - Redefined convention for specifying angular parameters for anisotropic
221       models.
222     - A number of minor features have been added such as permitting a log
223       distribution of points when using a model to simulate data, and the
224       addition of a Kratky plot option to the linear plots.
225     - A number of bugs have also been fixed.
226     - Save Project and Save Analysis now work more reliably.
227     - BETA: Magnetic contrast supporting full polarization analysis has been
228       implemented for some spherical and cylindrical models.
229     - BETA: Two new tools have been added:
230       - A generic scattering calculator which takes an atomic, magnetic or
231         SLD distribution in space and generates the appropriate 2D
232         scattering pattern. In some cases the orientationally averaged
233         (powder) 1D scattering can also be computed. Supported formats
234         include: SLD or text, PDB, and OMF magnetic moment distribution
235         file.
236       - An image viewer/converter for data in image format; this reads in
237         an image file and will attempt to convert the image pixels to
238         data. Supported formats include: TIFF, TIF, PNG, BMP, JPG.
239
240   - New in Version 2.2.1
241     --------------------
242     - Minor patch to support CanSAS XML v1.1 file format
243     - Added DataInfo for data in the DataExplorer and plots
244     - Added Maximize/Restore button in the title bar of the graphs
245     - Added a hide button in the toolbar of the graph panel
246     - The 'x' button now deletes a graph
247     - Edit SUM Model from the menubar can now generate and save more than one sum model
248     - Reports can now be saved in pdf format on WIN and MAC
249     - Made significant improvements to the batch/grid panel and fixed several bugs
250     - Fixed a number of other minor bugs
251
252   - New in Version 2.2.0
253     --------------------
254     - Application name changed to SasView
255     - New fully customizable Category Manager added for better management of
256       increasing number of models
257     - Improved the Grid Window functionality in the batch fitting mode
258     - Added a simpler Graph/Plot modification interface
259     - Added a new 'Data Operation' tool for addition, subtraction, multiplication,
260       division, of two data sets.
261     - The 'Sum Model' editor was extended and renamed 'Summation and Multiplication'
262       editor
263     - Added more plot symbols options for 1d plots
264     - Added improved trapping of compiling errors to the 'New model editor'
265     - Added some intelligent outputs (e.g., Rg, background, or rod diameter
266       depending on the choice of axis scale of the plot) to the linear fits
267     - Added more models
268
269   - Feature set from previous versions
270     -----------------------------------
271     - Perspectives Available
272       - Invariant calculator: Calculates the invariant, volume fraction, and
273         specific surface area.
274       - P(r) inversion calculator: Indirect Fourier transformation method.
275       - Fitting: the tool used for modeling and fitting 1D and 2D data to
276         analytical model functions
277       - Tools: provides a number of useful supplementary tools such as SLD
278         calculation
279
280     - Fitting
281       - Includes a large number of model functions, both form factors and structure factors.
282       - Support P(Q)*S(Q) for form factors that flag they can be so multiplied.
283       - Supports Gaussian, lognormal, Shulz, rectangular and custom distribution
284         functions for models that need to include polydispersity or for orientational
285         distributions if appropriate.
286       - Anisotropic shapes and magnetic moment modeling in 2D allow for a non-uniform
287         distribution of orientations of a given axis leading to modeling and fitting
288         capabilities of non azimuthaly symmetric data.
289       - User can choose to weight fits or not. If using weights, the user can choose
290         the error bar on each point if provided in the file, the square root
291         of the intensity or the intensity itself.
292       - Instrumental resolution smearing of model or fits is provided with several
293         options: read the resolution/point fromt he file. Input a pinhole resolution
294         or a slit resolution.
295       - Users can define the Qrange (Qmin and Qmax) for both 1D and 2D data for
296         fitting and modeling, but not graphically.  The range can be reset to the
297         defaults (limits of q in data set for a fit) with the reset button.
298       - A mask can be applied to 2D calculation and fitting.
299       - Normalized residual plots are provided with every fit.
300       - Model function help available through detail button or from the fitting panel.
301       - Simultaneous/(advanced)constrained fitting allows for fitting a single
302         data set or several different sets simultaneously with the application
303         of advanced constraints relating fit parameters to functions of other
304         parameters (including from a different set). For example thickness of
305         shell = sin(30) times the length.
306       - Models that are the sum of two other models can be easily generated through the
307         SUM Model menubar item.
308       - New Python models can be added on the fly by creating an appropriate Python
309         file in the model plugin directory. Two tools are provided to help:
310         An easy to use custom model editor allows the quick generation of new Python
311         models by supplying only the parameters and their default value (box 1)
312         and the mathematical function of the model (box 2) and generating the
313         necessary *.py file.  A separate advanced model editor provides a full Python
314         file editor.  Either way once saved the model becomes immediately available
315         to the application.
316       - A batch fitting capability allows for the analysis of a series of data sets to
317         a single model and provides the results in a tabular form suitable for saving
318         or plotting the evolution of the fit parameters with error bars (from within
319         the application).
320
321     - Tools
322       - A scattering length density calculator,including some X-ray information
323         is provided.
324       - A density to vol. fraction converter is provided
325       - In application access to a Python shell/editor (PyCrust) is provided
326       - An instrument resolution calculator, including possible gravitational and
327         TOF effects is provided
328       - A slit size calculator optimized for Anton Paar Saxess is provided.
329       - A kiessig fringe thickness calculator is provided
330
331     - Plots and plot management
332       - A 3D graphing option (for 2d data/results) is provided with the view
333         controlled by the mouse
334       - 2D plots are shown with an intensity color bar. 2D Color map can be user
335         adjusted.
336       - Supports output of plot to a variety of graphic formats. Supported formats
337         include: png, eps, emf, jpg/jpeg, pdf, ps, tif/tiff, rawRGBbitmap(raw, rgba),
338         and scalable vector graphic (svg/svgz)
339       - Supports ouput of data in plot (1 or 2D) to limited data formats
340       - Multiple data sets can be loaded into a single graph for viewing (but a fit
341         plot can currently only have a single plot).
342       - Extensive context sensitive plot/fitting/manipulation options are available
343         through a right mouse click pop-up menu on plots.
344
345     - Data management
346       - Supports 2 + column 1D ASCII data, NIST 1D and 2D data, and canSAS data
347         via plug-in mechanism which can easily allow other readers as appropriate.
348       - 2D data is expected in Q space but for historical reasons accepts the
349         NIST 2D raw pixel format and will do conversion internally.
350       - The full data and metadata available to SasView is viewable in ASCII via
351         right clicking on a data set and choosing Data Info in the DataExplorer
352         or on the plots
353       - Supports loading a single file, multiple files, or a whole folder
354       - An optional Data Explorer is provided (default) which simplifies managing,
355         plotting, deleting, or setup for computation. Most functions however do
356         not require access to the explorer/manager and can be accessed through
357         right click menus and the toolbar.  The data explorer can be re-started
358         from the menu bar.
359
360     - Data manipulation
361       - Support various 2D averaging methods : Circular, sectors, annular,
362         boxsum, boxQx and boxQy.
363       - A 2D data maks editor is provided
364       - 2D mask can be applied to the circular averaging.
365
366     - Miscellaneous features
367       - limited reports can be generated in pdf format
368       - Provides multiprocessor support(Windows only)
369       - Limited startup customization currently includes default startup
370         data folder and choice of default starting with data manager
371       - Limited support for saving(opening) a SasView project or a SasView analysis
372         (subproject) is provided.
373       - SasView can be launched and loaded with a file of interesty by double-clicking
374         on that file (recognized extension)
375       - A data file or data folder can be passed to SasView when launched from
376         the command line.
377       - Limited bookmarking capability to later recall the results of a fit calculation
378         is provided.
379       - Extensive help is provided through context sensitive mouse roll-over,
380         information bar (at the bottom of the panel), the console menu, and
381         access to the help files in several different ways.
382
383
3842- Downloading and Installing
385=============================
386
387   *** Note 1:  Much more information is available at www.sasview.org under links.
388                    Look in the 'For Developers' section and particularly the wiki at
389                www.sasview.org/trac/wiki.
390   *** Note 2:  If you have EXE or ZIP SasView installer, you won't need any of
391                the following.  However it is highly recommended that any
392                previous versions be un-installed prior to installing the
393                new version.
394
395   2.1- System Requirements
396        - Python version >= 2.5 and < 3.0 should be running on the system
397        - We currently use Python 2.7
398
399   2.2- Installing from source
400        - Get the source code
401          - to follow the current development version from source control use
402              git clone https://github.com/SasView/sasview.git
403              git clone https://github.com/bumps/bumps.git
404          - to install a specific version
405
406        - Build, install and run a specific release
407          - make sure the requirements below are already installed
408          - retrieve the source from https://github.com/SasView/sasview/releases
409          - open a command line window in the 'sasview-x.x.x' directory
410          - run 'python setup.py install'
411          - run 'python sasview.py' under the 'sasview' folder.
412
413        - Build, install and run the current development version
414          - clone the source from git; also clone bumps, which is developed in parallel
415              git clone https://github.com/SasView/sasview.git
416              git clone https://github.com/bumps/bumps.git
417          - open a command line window in the 'sasview' directory
418          - run 'python setup.py build'
419          - run 'python run.py'; this runs from the source directories, so you
420            don't have to rebuild every time you make a change, unless you are
421            changing the C++ model files
422
423        - The following modules are required (version numbers are what are used
424          in the windows release build):
425
426          - Common Packages
427            - reportlab 3.1.44
428            - lxml 3.4.4.0 (MAC 3.4.2.0)
429            - PIL 1.1.7
430            - xhtml2pdf 3.0.33 (MAC = not installed on build server)
431            - unittest-xml-reporting 1.12.0 (MAC 1.10.0)
432            - matplotlib Version Installed: 1.4.3 (MAC 1.1.1)
433            - bumps Version Installed: 0.7.5.9
434            - scipy Version Installed: 0.16.0b2 (MAC 0.11.0)
435            - periodictable Version Installed: 1.4.1
436            - setuptools Version Installed: 7.0 (MAC 12.0.5)
437            - sphinx Version Installed: 1.3.1 (MAC 1.3b2)
438            - pyparsing Version Installed: 2.0.3
439            - numpy Version Installed: 1.9.2 (MAC 1.6.2)
440            - html5lib Version Installed: 0.99999
441            - wx Version Installed: 3.0.2.0
442
443          - Windows Specific Packages
444            - pywin 219
445            - py2exe 0.6.9
446            - comtypes 1.1.1
447            - MinGW w/ gcc version 4.6.1 (WIN)
448            - vcredist_x86.exe (version 9.0.21022.8  -microsoft visual C 2008
449              re-distributable)
450            - Innosetup (WIN - isetup 5.4.2-unicode) - used to create distributable
451
452            *** Note: Windows build dependencies can be set up using anaconda. Instructions
453                can be found at http://trac.sasview.org/wiki/AnacondaSetup
454
455          - MAC Specifc Packages
456            - py2app 0.7.1
457
458
4593- Known Issues
460===============
461
462   3.1- All systems:
463        - The documentation window may take a few seconds to load the first time
464          it is called. Also, an internet connection is required before
465          equations will render properly. Until then they will show in their
466          original TeX format.
467        - If the documentation window remains stubbornly blank, try installing a
468          different browser and set that as your default browser. Issues have
469          been noted with Internet Explorer 11.
470        - Check for Updates may fail (with the status bar message ' Cannot
471          connect to the application server') if your internet connection uses
472          a proxy server. Tested resolutions for this are described on the
473          website FAQ.
474        - The copy and paste functions (^C, ^V) in the batch mode results grid
475          require two clicks: one to select the cell and a second to select the
476          contents of the cell.
477        - The tutorial has not yet been updated and is somewhat out of date
478        - Very old computers may struggle to run the 3.x and later releases
479        - Polydispersity on multiple parameters included in a simultaneous/
480          constrained fit will likely not be correct
481        - Constrained/simultaneous fit page does not have a stop button
482        - Constrained/simultaneous fit do not accept min/max limits
483        - Save project does not store the state of all the windows
484        - Loading projects can be very slow
485        - Save Project only works once a data set has been associated with
486          a model.  Error is reported on status bar.
487        - There is a numerical precision problem with the multishell model when
488          the iner radius gets large enough (ticket #288)
489        - The angular distribution angles are not clearly defined and may in
490          some cases lead to incorrect calculations(ticket #332)
491
492   3.2- Windows:
493        - If installed to same directory as old version without first removing
494          the old version, the old desktop icon will remain but point to the
495          new exe version. Likewise all the start menu folders and items will
496          have the old name even though pointing to the new version.  Usually
497          safest to uninstall old version prior to installing new version anyway.
498
499   3.3- MAC:
500        - Application normally starts up hidden. Click icon in Dock to view/use
501          application.
502        - Multiprocessing does not currently work on MAC OS
503
504   3.4- Linux:
505        - Not well tested
506
507
5084- SasView website
509==================
510
511   - www.sasview.org.  This main project site is the gateway to all
512     information about the sasview project.  It includes information
513     about the project, a FAQ page and links to all developer and user
514     information, tools and resources.
515
516
5175- Frequently Asked Questions
518=============================
519
520   - www.sasview.org/faq.html
521
522
5236- Installer download website
524=============================
525
526   - Latest release Version
527     - https://github.com/SasView/sasview/releases
528   - Latest developer builds
529     - https://jenkins.esss.dk/sasview/view/Master-Builds/
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