source: sasview/sasview/README.txt @ 9a182b2

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalccostrafo411magnetic_scattrelease-4.1.1release-4.1.2release-4.2.2release_4.0.1ticket-1009ticket-1094-headlessticket-1242-2d-resolutionticket-1243ticket-1249ticket885unittest-saveload
Last change on this file since 9a182b2 was 9a182b2, checked in by ajj, 6 years ago

Updating version numbers for 4.0 release and making some release notes

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1Release Notes
2=============
3
41- Features
5===========
6    - New in Version 4.0
7      ------------------
8      This release fixes the various bugs found during the alpha and beta testing
9      - Improvements
10        - Support for reading data files from Anton Paar Saxess instruments
11        - Adds documentation on how to write custom models in the new framework
12      - Bug Fixes
13        - Fixes bug #604 Pringle model questions
14        - Fixes bug #472 Reparameterize Teubner-Strey
15        - Fixes bug #530 Numerical instabilities in Teubner Strey model
16        - Fixes bug #658 ASCII reader very broken
17
18
19    - New in Version 4.0 beta 1
20      --------------------
21      This beta adds support for the magnetic and multilevel models of 3.1.2
22      and along with a host of bug fixes found in the alpha.
23
24      - Model package changes and improvements
25         - All 3.1.2 models now available in new interface
26         - Old custom models should now still work
27            - '''NOTE:''' These will be deprecated in a future version. Old
28            custom models should be converted to the new model format which
29            is now the same as the built in models and offers much better
30            support.
31         - Custom model editor now creates new style models
32         - Custom model editor supports better error checking
33      - Documentation improvements
34        - Continued general cleanup
35      - Other improvements/additions
36         - Support for new canSAS 2D data files added
37         - Plot axes range can now be set manually as well as by zooming
38         - Plot annotations can now be moved around after being placed on plot.
39         - The active optimizer is now listed on the top of the fit panel.
40         - Linear fits now update qmin and max when the x scale limits are
41         changed.  Also the plot range no longer resets after a fit.
42      - Bug fixes
43         - Fixes bug #511 Errors in linearized fits and clean up of interface
44         including Kratky representation
45         - Fixes bug #186 Data operation Tool now executes when something is
46         entered in the text box and does not wait for the user to hit enter
47         - Fixes bug #459 plot context menu bug
48         - Fixes bug #559 copy to clipboard in graph menu broken
49         - Fixes bug #466 cannot remove a linear fit from graph
50         - Numerous bugs introduced in the alpha
51
52
53
54    - New in Version 4.0.0-alpha
55      --------------------
56      This alpha release brings a major overhaul of the model system. The new model
57      package allows rapid integration of custom models and access to polydispersity
58      without requiring a compiler.
59
60      - Model package changes and improvements
61         - Model interface moved to independent sasmodels package.
62         - Most models converted to new interface.
63         - Allows rapid integration of user-written models.
64         - OpenCL GPU utilization for faster fitting.
65         - Improved numerical integration of Bessel functions.
66      - SESANS integration and implementation
67         - Scripting interface added for analysis of SESANS data.
68         - Hankel transformation now accepts finite acceptance angles.
69         - 2D cosine transformation added for TOF SESANS analysis.
70      - Documentation improvements
71         - The documentation tree was restructured for a better end user experience.
72         - The documentation for each model was revamped and verified by at least
73           two people following the conversion of the model.
74         - Theoretical 1D (and 2D if applicable) scattering curves are auto-generated
75           and added to the model documentation for each model.
76      - Separation of GUI and calculations for future GUI enhancements
77      - Bug fixes
78         - Fixes bug #411 No stop button on simultaneous fit page
79         - Fixes bug #410 Error with raspberry model
80         - Fixes bug #364 Possible inconsistency in Poly_GausCoil model
81         - Fixes bug #439 Hayter Penfold MSA code needs checking
82         - Fixes bug #484 lammellerPC is precision limited
83         - Fixes bug #498 $HOME/.matplotlib conflicts
84         - Fixes bug #348 Control order in which fit parameters appear in the gui
85         - Fixes bug #456 Provide DREAM Results Panel with something to identify
86           data and age of results
87         - Fixes bug #556 Build script improvements for developers
88
89
90
91   - New in Version 3.1.2
92     --------------------
93     This release is a major stability improvement, having fixed a serious bug
94     that came to light since release 3.1.1. All users should upgrade.
95
96     - Fixes bug #468 broken remove constraint buttons in
97       simultaneous/constrained fitting panel
98     - Fixes bug #474 resulting from changes in 3.1.1 that had
99       introduced an error in the high-Q of slit-smeared models.
100     - Fixes bug #478 which would cause wx to run out of IDs and result
101       in SasView crashing even if left alone.
102     - Fixes bug #479 missing help button on simultaneous/constrained fit page
103     - Fixes bug #480 GUI resizing issues on simultaneous fit page
104     - Fixes bug #486 broken Report Results
105     - Fixes bug #488 redraw issues in fit page
106
107
108
109   - New in Version 3.1.1
110     --------------------
111     - Fixes bug #457 that prevented SasView from starting if the user was not
112       connected to the internet, or was behind a proxy server.
113
114   - New in Version 3.1.0
115     --------------------
116     - The documentation/help has had a complete overhaul including:
117       - A completely new presentation interface (Sphinx).
118       - Proof reading!
119       - Updating for latest features.
120       - A Help (or sometimes ?) button has been added to every panel, and some
121         sub panels if appropriate, linking to the appropriate section in the
122         documentation.
123       - The model help has been split so that the Details button now brings up
124         a very short pop-up giving the equation being used while HELP goes to
125         the section in the full documentation describing the model.
126       - Extensive help has also been added for the new optimizer engine (see
127         below) including rules of thumb on how and when to choose a given
128         optimizer and what the parameters do.
129     - The optimizer engine has been completely replaced. The new optimizer
130       still defaults to the standard Levenberg-Marquardt algorithm. However 4
131       other optimizers are now also available. Each starts with a set of default
132       parameters which can be tuned. The DREAM optimizer takes the longest but
133       is the most powerful and yields rich information including full parameter
134       correlation and uncertainty plots. A results panel has been added to
135       accommodate this.
136       - The five new optimizers are:
137         - A Levenberg-Marquardt optimizer
138         - A Quasi-Newton BFGS optimizer
139         - A Nelder-Mead Simplex optimizer
140         - A Differential Evolution optimizer
141         - A Monte Carlo optimizer (DREAM)
142     - New models were added:
143         - MicelleSphCoreModel (currently residing in the Uncategorized category)
144     - Existing models were updated:
145         - LamellarPS (bug in polydispersity integration fixed)
146         - RectangularPrismModel
147         - RectangularHollowPrismModel
148         - RectangularHollowPrismInfThinWallsModel
149     - Infrastructure to allow SESANS data to be fit with models was added. This
150       will become available in a future release but can currently be used from
151       the command line with some caveats.
152     - A number of bugs were fixed including a thread crashing issue and an
153       incorrect slit smearing resolution calculation.
154     - Implemented much more robust error logging to enable much easier
155       debugging in general but particularly the debugging of issues reported by
156       SasView users.
157     - A number of infrastructure tasks under the hood to enhance maintainability
158     - Upgrade from Wx 2.8 to Wx 3.0.2 which allows several new features but
159       required significant additional rework as well.
160     - Fully implemented Sphinx to the build process to produce both better
161       user documentation and developer documentation.
162     - Restructuring of the code base to more unified nomenclature and structure
163       so that the source installation tree more closely matches the installer
164       version tree.
165     - Code cleanup (an ongoing task) .
166     - Migration of the repository to github simplifying contributions from
167       non-project personnel through pull requests.
168
169   - New in Version 3.0.0
170     --------------------
171     - The GUI look and feel has been refactored to be more familiar for
172       Windows users by using MDI frames. Graph windows are also now free-
173       floating.
174     - Five new models have been added: PringlesModel, CoreShellEllipsoidXTModel,
175       RectangularPrismModel, RectangularHollowPrismModel and
176       RectangularHollowPrismInfThinWallsModel.
177     - The data loader now supports ILL DAT data files and reads the full meta
178       information from canSAS file formats.
179     - Redefined convention for specifying angular parameters for anisotropic
180       models.
181     - A number of minor features have been added such as permitting a log
182       distribution of points when using a model to simulate data, and the
183       addition of a Kratky plot option to the linear plots.
184     - A number of bugs have also been fixed.
185     - Save Project and Save Analysis now work more reliably.
186     - BETA: Magnetic contrast supporting full polarization analysis has been
187       implemented for some spherical and cylindrical models.
188     - BETA: Two new tools have been added:
189       - A generic scattering calculator which takes an atomic, magnetic or
190         SLD distribution in space and generates the appropriate 2D
191         scattering pattern. In some cases the orientationally averaged
192         (powder) 1D scattering can also be computed. Supported formats
193         include: SLD or text, PDB, and OMF magnetic moment distribution
194         file.
195       - An image viewer/converter for data in image format; this reads in
196         an image file and will attempt to convert the image pixels to
197         data. Supported formats include: TIFF, TIF, PNG, BMP, JPG.
198
199   - New in Version 2.2.1
200     --------------------
201     - Minor patch to support CanSAS XML v1.1 file format
202     - Added DataInfo for data in the DataExplorer and plots
203     - Added Maximize/Restore button in the title bar of the graphs
204     - Added a hide button in the toolbar of the graph panel
205     - The 'x' button now deletes a graph
206     - Edit SUM Model from the menubar can now generate and save more than one sum model
207     - Reports can now be saved in pdf format on WIN and MAC
208     - Made significant improvements to the batch/grid panel and fixed several bugs
209     - Fixed a number of other minor bugs
210
211   - New in Version 2.2.0
212     --------------------
213     - Application name changed to SasView
214     - New fully customizable Category Manager added for better management of
215       increasing number of models
216     - Improved the Grid Window functionality in the batch fitting mode
217     - Added a simpler Graph/Plot modification interface
218     - Added a new 'Data Operation' tool for addition, subtraction, multiplication,
219       division, of two data sets.
220     - The 'Sum Model' editor was extended and renamed 'Summation and Multiplication'
221       editor
222     - Added more plot symbols options for 1d plots
223     - Added improved trapping of compiling errors to the 'New model editor'
224     - Added some intelligent outputs (e.g., Rg, background, or rod diameter
225       depending on the choice of axis scale of the plot) to the linear fits
226     - Added more models
227
228   - Feature set from previous versions
229     -----------------------------------
230     - Perspectives Available
231       - Invariant calculator: Calculates the invariant, volume fraction, and
232         specific surface area.
233       - P(r) inversion calculator: Indirect Fourier transformation method.
234       - Fitting: the tool used for modeling and fitting 1D and 2D data to
235         analytical model functions
236       - Tools: provides a number of useful supplementary tools such as SLD
237         calculation
238
239     - Fitting
240       - Includes a large number of model functions, both form factors and structure factors.
241       - Support P(Q)*S(Q) for form factors that flag they can be so multiplied.
242       - Supports Gaussian, lognormal, Shulz, rectangular and custom distribution
243         functions for models that need to include polydispersity or for orientational
244         distributions if appropriate.
245       - Anisotropic shapes and magnetic moment modeling in 2D allow for a non-uniform
246         distribution of orientations of a given axis leading to modeling and fitting
247         capabilities of non azimuthaly symmetric data.
248       - User can choose to weight fits or not. If using weights, the user can choose
249         the error bar on each point if provided in the file, the square root
250         of the intensity or the intensity itself.
251       - Instrumental resolution smearing of model or fits is provided with several
252         options: read the resolution/point fromt he file. Input a pinhole resolution
253         or a slit resolution.
254       - Users can define the Qrange (Qmin and Qmax) for both 1D and 2D data for
255         fitting and modeling, but not graphically.  The range can be reset to the
256         defaults (limits of q in data set for a fit) with the reset button.
257       - A mask can be applied to 2D calculation and fitting.
258       - Normalized residual plots are provided with every fit.
259       - Model function help available through detail button or from the fitting panel.
260       - Simultaneous/(advanced)constrained fitting allows for fitting a single
261         data set or several different sets simultaneously with the application
262         of advanced constraints relating fit parameters to functions of other
263         parameters (including from a different set). For example thickness of
264         shell = sin(30) times the length.
265       - Models that are the sum of two other models can be easily generated through the
266         SUM Model menubar item.
267       - New Python models can be added on the fly by creating an appropriate Python
268         file in the model plugin directory. Two tools are provided to help:
269         An easy to use custom model editor allows the quick generation of new Python
270         models by supplying only the parameters and their default value (box 1)
271         and the mathematical function of the model (box 2) and generating the
272         necessary *.py file.  A separate advanced model editor provides a full Python
273         file editor.  Either way once saved the model becomes immediately available
274         to the application.
275       - A batch fitting capability allows for the analysis of a series of data sets to
276         a single model and provides the results in a tabular form suitable for saving
277         or plotting the evolution of the fit parameters with error bars (from within
278         the application).
279
280     - Tools
281       - A scattering length density calculator,including some X-ray information
282         is provided.
283       - A density to vol. fraction converter is provided
284       - In application access to a Python shell/editor (PyCrust) is provided
285       - An instrument resolution calculator, including possible gravitational and
286         TOF effects is provided
287       - A slit size calculator optimized for Anton Paar Saxess is provided.
288       - A kiessig fringe thickness calculator is provided
289
290     - Plots and plot management
291       - A 3D graphing option (for 2d data/results) is provided with the view
292         controlled by the mouse
293       - 2D plots are shown with an intensity color bar. 2D Color map can be user
294         adjusted.
295       - Supports output of plot to a variety of graphic formats. Supported formats
296         include: png, eps, emf, jpg/jpeg, pdf, ps, tif/tiff, rawRGBbitmap(raw, rgba),
297         and scalable vector graphic (svg/svgz)
298       - Supports ouput of data in plot (1 or 2D) to limited data formats
299       - Multiple data sets can be loaded into a single graph for viewing (but a fit
300         plot can currently only have a single plot).
301       - Extensive context sensitive plot/fitting/manipulation options are available
302         through a right mouse click pop-up menu on plots.
303
304     - Data management
305       - Supports 2 + column 1D ASCII data, NIST 1D and 2D data, and canSAS data
306         via plug-in mechanism which can easily allow other readers as appropriate.
307       - 2D data is expected in Q space but for historical reasons accepts the
308         NIST 2D raw pixel format and will do conversion internally.
309       - The full data and metadata available to SasView is viewable in ASCII via
310         right clicking on a data set and choosing Data Info in the DataExplorer
311         or on the plots
312       - Supports loading a single file, multiple files, or a whole folder
313       - An optional Data Explorer is provided (default) which simplifies managing,
314         plotting, deleting, or setup for computation. Most functions however do
315         not require access to the explorer/manager and can be accessed through
316         right click menus and the toolbar.  The data explorer can be re-started
317         from the menu bar.
318
319     - Data manipulation
320       - Support various 2D averaging methods : Circular, sectors, annular,
321         boxsum, boxQx and boxQy.
322       - A 2D data maks editor is provided
323       - 2D mask can be applied to the circular averaging.
324
325     - Miscellaneous features
326       - limited reports can be generated in pdf format
327       - Provides multiprocessor support(Windows only)
328       - Limited startup customization currently includes default startup
329         data folder and choice of default starting with data manager
330       - Limited support for saving(opening) a SasView project or a SasView analysis
331         (subproject) is provided.
332       - SasView can be launched and loaded with a file of interesty by double-clicking
333         on that file (recognized extension)
334       - A data file or data folder can be passed to SasView when launched from
335         the command line.
336       - Limited bookmarking capability to later recall the results of a fit calculation
337         is provided.
338       - Extensive help is provided through context sensitive mouse roll-over,
339         information bar (at the bottom of the panel), the console menu, and
340         access to the help files in several different ways.
341
342
3432- Downloading and Installing
344=============================
345
346   *** Note 1:  Much more information is available at www.sasview.org under links.
347                    Look in the 'For Developers' section and particularly the wiki at
348                www.sasview.org/trac/wiki.
349   *** Note 2:  If you have EXE or ZIP SasView installer, you won't need any of
350                the following.  However it is highly recommended that any
351                previous versions be un-installed prior to installing the
352                new version.
353
354   2.1- System Requirements
355        - Python version >= 2.5 and < 3.0 should be running on the system
356        - We currently use Python 2.7
357
358   2.2- Installing from source
359        - Get the source code
360          - to follow the current development version from source control use
361              git clone https://github.com/SasView/sasview.git
362              git clone https://github.com/bumps/bumps.git
363          - to install a specific version
364
365        - Build, install and run a specific release
366          - make sure the requirements below are already installed
367          - retrieve the source from https://github.com/SasView/sasview/releases
368          - open a command line window in the 'sasview-x.x.x' directory
369          - run 'python setup.py install'
370          - run 'python sasview.py' under the 'sasview' folder.
371
372        - Build, install and run the current development version
373          - clone the source from git; also clone bumps, which is developed in parallel
374              git clone https://github.com/SasView/sasview.git
375              git clone https://github.com/bumps/bumps.git
376          - open a command line window in the 'sasview' directory
377          - run 'python setup.py build'
378          - run 'python run.py'; this runs from the source directories, so you
379            don't have to rebuild every time you make a change, unless you are
380            changing the C++ model files
381
382        - The following modules are required (version numbers are what are used
383          in the windows release build):
384
385          - Common Packages
386            - reportlab 3.1.44
387            - lxml 3.4.4.0 (MAC 3.4.2.0)
388            - PIL 1.1.7
389            - xhtml2pdf 3.0.33 (MAC = not installed on build server)
390            - unittest-xml-reporting 1.12.0 (MAC 1.10.0)
391            - matplotlib Version Installed: 1.4.3 (MAC 1.1.1)
392            - bumps Version Installed: 0.7.5.9
393            - scipy Version Installed: 0.16.0b2 (MAC 0.11.0)
394            - periodictable Version Installed: 1.4.1
395            - setuptools Version Installed: 7.0 (MAC 12.0.5)
396            - sphinx Version Installed: 1.3.1 (MAC 1.3b2)
397            - pyparsing Version Installed: 2.0.3
398            - numpy Version Installed: 1.9.2 (MAC 1.6.2)
399            - html5lib Version Installed: 0.99999
400            - wx Version Installed: 3.0.2.0
401
402          - Windows Specific Packages
403            - pywin 219
404            - py2exe 0.6.9
405            - comtypes 1.1.1
406            - MinGW w/ gcc version 4.6.1 (WIN)
407            - vcredist_x86.exe (version 9.0.21022.8  -microsoft visual C 2008
408              re-distributable)
409            - Innosetup (WIN - isetup 5.4.2-unicode) - used to create distributable
410
411            *** Note: Windows build dependencies can be set up using anaconda. Instructions
412                can be found at http://trac.sasview.org/wiki/AnacondaSetup
413
414          - MAC Specifc Packages
415            - py2app 0.7.1
416
417
4183- Known Issues
419===============
420
421   3.1- All systems:
422        - The documentation window may take a few seconds to load the first time
423          it is called. Also, an internet connection is required before
424          equations will render properly. Until then they will show in their
425          original TeX format.
426        - If the documentation window remains stubbornly blank, try installing a
427          different browser and set that as your default browser. Issues have
428          been noted with Internet Explorer 11.
429        - Check for Updates may fail (with the status bar message ' Cannot
430          connect to the application server') if your internet connection uses
431          a proxy server. Tested resolutions for this are described on the
432          website FAQ.
433        - The copy and paste functions (^C, ^V) in the batch mode results grid
434          require two clicks: one to select the cell and a second to select the
435          contents of the cell.
436        - The tutorial has not yet been updated and is somewhat out of date
437        - Very old computers may struggle to run the 3.x and later releases
438        - Polydispersity on multiple parameters included in a simultaneous/
439          constrained fit will likely not be correct
440        - Constrained/simultaneous fit page does not have a stop button
441        - Constrained/simultaneous fit do not accept min/max limits
442        - Save project does not store the state of all the windows
443        - Loading projects can be very slow
444        - Save Project only works once a data set has been associated with
445          a model.  Error is reported on status bar.
446        - There is a numerical precision problem with the multishell model when
447          the iner radius gets large enough (ticket #288)
448        - The angular distribution angles are not clearly defined and may in
449          some cases lead to incorrect calculations(ticket #332)
450
451   3.2- Windows:
452        - If installed to same directory as old version without first removing
453          the old version, the old desktop icon will remain but point to the
454          new exe version. Likewise all the start menu folders and items will
455          have the old name even though pointing to the new version.  Usually
456          safest to uninstall old version prior to installing new version anyway.
457
458   3.3- MAC:
459        - Application normally starts up hidden. Click icon in Dock to view/use
460          application.
461        - Multiprocessing does not currently work on MAC OS
462
463   3.4- Linux:
464        - Not well tested
465
466
4674- SasView website
468==================
469
470   - www.sasview.org.  This main project site is the gateway to all
471     information about the sasview project.  It includes information
472     about the project, a FAQ page and links to all developer and user
473     information, tools and resources.
474
475
4765- Frequently Asked Questions
477=============================
478
479   - www.sasview.org/faq.html
480
481
4826- Installer download website
483=============================
484
485   - Latest release Version
486     - https://github.com/SasView/sasview/releases
487   - Latest developer builds
488     - https://jenkins.esss.dk/sasview/view/Master-Builds/
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