source: sasview/sasview/README.txt @ 220b1e7

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-4.2.2ticket-1009ticket-1094-headlessticket-1242-2d-resolutionticket-1243ticket-1249ticket885unittest-saveload
Last change on this file since 220b1e7 was 220b1e7, checked in by butler, 3 years ago

update version number to 4.1 in init and sphinx. Also updated readme
for 4.0.1 which was missing. Changes for 4.1 will need to be added once
all changes are final

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1Release Notes
2=============
3
41- Features
5===========
6    - New in Version 4.0.1
7      ------------------
8      This release fixes the critical bug #750 in P(Q)*S(Q).  Most damaging
9      it appears that the background term was being added to S(Q) prior to
10      multiplication by P(Q).
11
12
13    - New in Version 4.0
14      ------------------
15      This release fixes the various bugs found during the alpha and beta testing
16      - Improvements
17        - Support for reading data files from Anton Paar Saxess instruments
18        - Adds documentation on how to write custom models in the new framework
19      - Bug Fixes
20        - Fixes bug #604 Pringle model questions
21        - Fixes bug #472 Reparameterize Teubner-Strey
22        - Fixes bug #530 Numerical instabilities in Teubner Strey model
23        - Fixes bug #658 ASCII reader very broken
24
25
26    - New in Version 4.0 beta 1
27      --------------------
28      This beta adds support for the magnetic and multilevel models of 3.1.2
29      and along with a host of bug fixes found in the alpha.
30
31      - Model package changes and improvements
32         - All 3.1.2 models now available in new interface
33         - Old custom models should now still work
34            - '''NOTE:''' These will be deprecated in a future version. Old
35            custom models should be converted to the new model format which
36            is now the same as the built in models and offers much better
37            support.
38         - Custom model editor now creates new style models
39         - Custom model editor supports better error checking
40      - Documentation improvements
41        - Continued general cleanup
42      - Other improvements/additions
43         - Support for new canSAS 2D data files added
44         - Plot axes range can now be set manually as well as by zooming
45         - Plot annotations can now be moved around after being placed on plot.
46         - The active optimizer is now listed on the top of the fit panel.
47         - Linear fits now update qmin and max when the x scale limits are
48         changed.  Also the plot range no longer resets after a fit.
49      - Bug fixes
50         - Fixes bug #511 Errors in linearized fits and clean up of interface
51         including Kratky representation
52         - Fixes bug #186 Data operation Tool now executes when something is
53         entered in the text box and does not wait for the user to hit enter
54         - Fixes bug #459 plot context menu bug
55         - Fixes bug #559 copy to clipboard in graph menu broken
56         - Fixes bug #466 cannot remove a linear fit from graph
57         - Numerous bugs introduced in the alpha
58
59
60
61    - New in Version 4.0.0-alpha
62      --------------------
63      This alpha release brings a major overhaul of the model system. The new model
64      package allows rapid integration of custom models and access to polydispersity
65      without requiring a compiler.
66
67      - Model package changes and improvements
68         - Model interface moved to independent sasmodels package.
69         - Most models converted to new interface.
70         - Allows rapid integration of user-written models.
71         - OpenCL GPU utilization for faster fitting.
72         - Improved numerical integration of Bessel functions.
73      - SESANS integration and implementation
74         - Scripting interface added for analysis of SESANS data.
75         - Hankel transformation now accepts finite acceptance angles.
76         - 2D cosine transformation added for TOF SESANS analysis.
77      - Documentation improvements
78         - The documentation tree was restructured for a better end user experience.
79         - The documentation for each model was revamped and verified by at least
80           two people following the conversion of the model.
81         - Theoretical 1D (and 2D if applicable) scattering curves are auto-generated
82           and added to the model documentation for each model.
83      - Separation of GUI and calculations for future GUI enhancements
84      - Bug fixes
85         - Fixes bug #411 No stop button on simultaneous fit page
86         - Fixes bug #410 Error with raspberry model
87         - Fixes bug #364 Possible inconsistency in Poly_GausCoil model
88         - Fixes bug #439 Hayter Penfold MSA code needs checking
89         - Fixes bug #484 lammellerPC is precision limited
90         - Fixes bug #498 $HOME/.matplotlib conflicts
91         - Fixes bug #348 Control order in which fit parameters appear in the gui
92         - Fixes bug #456 Provide DREAM Results Panel with something to identify
93           data and age of results
94         - Fixes bug #556 Build script improvements for developers
95
96
97
98   - New in Version 3.1.2
99     --------------------
100     This release is a major stability improvement, having fixed a serious bug
101     that came to light since release 3.1.1. All users should upgrade.
102
103     - Fixes bug #468 broken remove constraint buttons in
104       simultaneous/constrained fitting panel
105     - Fixes bug #474 resulting from changes in 3.1.1 that had
106       introduced an error in the high-Q of slit-smeared models.
107     - Fixes bug #478 which would cause wx to run out of IDs and result
108       in SasView crashing even if left alone.
109     - Fixes bug #479 missing help button on simultaneous/constrained fit page
110     - Fixes bug #480 GUI resizing issues on simultaneous fit page
111     - Fixes bug #486 broken Report Results
112     - Fixes bug #488 redraw issues in fit page
113
114
115
116   - New in Version 3.1.1
117     --------------------
118     - Fixes bug #457 that prevented SasView from starting if the user was not
119       connected to the internet, or was behind a proxy server.
120
121   - New in Version 3.1.0
122     --------------------
123     - The documentation/help has had a complete overhaul including:
124       - A completely new presentation interface (Sphinx).
125       - Proof reading!
126       - Updating for latest features.
127       - A Help (or sometimes ?) button has been added to every panel, and some
128         sub panels if appropriate, linking to the appropriate section in the
129         documentation.
130       - The model help has been split so that the Details button now brings up
131         a very short pop-up giving the equation being used while HELP goes to
132         the section in the full documentation describing the model.
133       - Extensive help has also been added for the new optimizer engine (see
134         below) including rules of thumb on how and when to choose a given
135         optimizer and what the parameters do.
136     - The optimizer engine has been completely replaced. The new optimizer
137       still defaults to the standard Levenberg-Marquardt algorithm. However 4
138       other optimizers are now also available. Each starts with a set of default
139       parameters which can be tuned. The DREAM optimizer takes the longest but
140       is the most powerful and yields rich information including full parameter
141       correlation and uncertainty plots. A results panel has been added to
142       accommodate this.
143       - The five new optimizers are:
144         - A Levenberg-Marquardt optimizer
145         - A Quasi-Newton BFGS optimizer
146         - A Nelder-Mead Simplex optimizer
147         - A Differential Evolution optimizer
148         - A Monte Carlo optimizer (DREAM)
149     - New models were added:
150         - MicelleSphCoreModel (currently residing in the Uncategorized category)
151     - Existing models were updated:
152         - LamellarPS (bug in polydispersity integration fixed)
153         - RectangularPrismModel
154         - RectangularHollowPrismModel
155         - RectangularHollowPrismInfThinWallsModel
156     - Infrastructure to allow SESANS data to be fit with models was added. This
157       will become available in a future release but can currently be used from
158       the command line with some caveats.
159     - A number of bugs were fixed including a thread crashing issue and an
160       incorrect slit smearing resolution calculation.
161     - Implemented much more robust error logging to enable much easier
162       debugging in general but particularly the debugging of issues reported by
163       SasView users.
164     - A number of infrastructure tasks under the hood to enhance maintainability
165     - Upgrade from Wx 2.8 to Wx 3.0.2 which allows several new features but
166       required significant additional rework as well.
167     - Fully implemented Sphinx to the build process to produce both better
168       user documentation and developer documentation.
169     - Restructuring of the code base to more unified nomenclature and structure
170       so that the source installation tree more closely matches the installer
171       version tree.
172     - Code cleanup (an ongoing task) .
173     - Migration of the repository to github simplifying contributions from
174       non-project personnel through pull requests.
175
176   - New in Version 3.0.0
177     --------------------
178     - The GUI look and feel has been refactored to be more familiar for
179       Windows users by using MDI frames. Graph windows are also now free-
180       floating.
181     - Five new models have been added: PringlesModel, CoreShellEllipsoidXTModel,
182       RectangularPrismModel, RectangularHollowPrismModel and
183       RectangularHollowPrismInfThinWallsModel.
184     - The data loader now supports ILL DAT data files and reads the full meta
185       information from canSAS file formats.
186     - Redefined convention for specifying angular parameters for anisotropic
187       models.
188     - A number of minor features have been added such as permitting a log
189       distribution of points when using a model to simulate data, and the
190       addition of a Kratky plot option to the linear plots.
191     - A number of bugs have also been fixed.
192     - Save Project and Save Analysis now work more reliably.
193     - BETA: Magnetic contrast supporting full polarization analysis has been
194       implemented for some spherical and cylindrical models.
195     - BETA: Two new tools have been added:
196       - A generic scattering calculator which takes an atomic, magnetic or
197         SLD distribution in space and generates the appropriate 2D
198         scattering pattern. In some cases the orientationally averaged
199         (powder) 1D scattering can also be computed. Supported formats
200         include: SLD or text, PDB, and OMF magnetic moment distribution
201         file.
202       - An image viewer/converter for data in image format; this reads in
203         an image file and will attempt to convert the image pixels to
204         data. Supported formats include: TIFF, TIF, PNG, BMP, JPG.
205
206   - New in Version 2.2.1
207     --------------------
208     - Minor patch to support CanSAS XML v1.1 file format
209     - Added DataInfo for data in the DataExplorer and plots
210     - Added Maximize/Restore button in the title bar of the graphs
211     - Added a hide button in the toolbar of the graph panel
212     - The 'x' button now deletes a graph
213     - Edit SUM Model from the menubar can now generate and save more than one sum model
214     - Reports can now be saved in pdf format on WIN and MAC
215     - Made significant improvements to the batch/grid panel and fixed several bugs
216     - Fixed a number of other minor bugs
217
218   - New in Version 2.2.0
219     --------------------
220     - Application name changed to SasView
221     - New fully customizable Category Manager added for better management of
222       increasing number of models
223     - Improved the Grid Window functionality in the batch fitting mode
224     - Added a simpler Graph/Plot modification interface
225     - Added a new 'Data Operation' tool for addition, subtraction, multiplication,
226       division, of two data sets.
227     - The 'Sum Model' editor was extended and renamed 'Summation and Multiplication'
228       editor
229     - Added more plot symbols options for 1d plots
230     - Added improved trapping of compiling errors to the 'New model editor'
231     - Added some intelligent outputs (e.g., Rg, background, or rod diameter
232       depending on the choice of axis scale of the plot) to the linear fits
233     - Added more models
234
235   - Feature set from previous versions
236     -----------------------------------
237     - Perspectives Available
238       - Invariant calculator: Calculates the invariant, volume fraction, and
239         specific surface area.
240       - P(r) inversion calculator: Indirect Fourier transformation method.
241       - Fitting: the tool used for modeling and fitting 1D and 2D data to
242         analytical model functions
243       - Tools: provides a number of useful supplementary tools such as SLD
244         calculation
245
246     - Fitting
247       - Includes a large number of model functions, both form factors and structure factors.
248       - Support P(Q)*S(Q) for form factors that flag they can be so multiplied.
249       - Supports Gaussian, lognormal, Shulz, rectangular and custom distribution
250         functions for models that need to include polydispersity or for orientational
251         distributions if appropriate.
252       - Anisotropic shapes and magnetic moment modeling in 2D allow for a non-uniform
253         distribution of orientations of a given axis leading to modeling and fitting
254         capabilities of non azimuthaly symmetric data.
255       - User can choose to weight fits or not. If using weights, the user can choose
256         the error bar on each point if provided in the file, the square root
257         of the intensity or the intensity itself.
258       - Instrumental resolution smearing of model or fits is provided with several
259         options: read the resolution/point fromt he file. Input a pinhole resolution
260         or a slit resolution.
261       - Users can define the Qrange (Qmin and Qmax) for both 1D and 2D data for
262         fitting and modeling, but not graphically.  The range can be reset to the
263         defaults (limits of q in data set for a fit) with the reset button.
264       - A mask can be applied to 2D calculation and fitting.
265       - Normalized residual plots are provided with every fit.
266       - Model function help available through detail button or from the fitting panel.
267       - Simultaneous/(advanced)constrained fitting allows for fitting a single
268         data set or several different sets simultaneously with the application
269         of advanced constraints relating fit parameters to functions of other
270         parameters (including from a different set). For example thickness of
271         shell = sin(30) times the length.
272       - Models that are the sum of two other models can be easily generated through the
273         SUM Model menubar item.
274       - New Python models can be added on the fly by creating an appropriate Python
275         file in the model plugin directory. Two tools are provided to help:
276         An easy to use custom model editor allows the quick generation of new Python
277         models by supplying only the parameters and their default value (box 1)
278         and the mathematical function of the model (box 2) and generating the
279         necessary *.py file.  A separate advanced model editor provides a full Python
280         file editor.  Either way once saved the model becomes immediately available
281         to the application.
282       - A batch fitting capability allows for the analysis of a series of data sets to
283         a single model and provides the results in a tabular form suitable for saving
284         or plotting the evolution of the fit parameters with error bars (from within
285         the application).
286
287     - Tools
288       - A scattering length density calculator,including some X-ray information
289         is provided.
290       - A density to vol. fraction converter is provided
291       - In application access to a Python shell/editor (PyCrust) is provided
292       - An instrument resolution calculator, including possible gravitational and
293         TOF effects is provided
294       - A slit size calculator optimized for Anton Paar Saxess is provided.
295       - A kiessig fringe thickness calculator is provided
296
297     - Plots and plot management
298       - A 3D graphing option (for 2d data/results) is provided with the view
299         controlled by the mouse
300       - 2D plots are shown with an intensity color bar. 2D Color map can be user
301         adjusted.
302       - Supports output of plot to a variety of graphic formats. Supported formats
303         include: png, eps, emf, jpg/jpeg, pdf, ps, tif/tiff, rawRGBbitmap(raw, rgba),
304         and scalable vector graphic (svg/svgz)
305       - Supports ouput of data in plot (1 or 2D) to limited data formats
306       - Multiple data sets can be loaded into a single graph for viewing (but a fit
307         plot can currently only have a single plot).
308       - Extensive context sensitive plot/fitting/manipulation options are available
309         through a right mouse click pop-up menu on plots.
310
311     - Data management
312       - Supports 2 + column 1D ASCII data, NIST 1D and 2D data, and canSAS data
313         via plug-in mechanism which can easily allow other readers as appropriate.
314       - 2D data is expected in Q space but for historical reasons accepts the
315         NIST 2D raw pixel format and will do conversion internally.
316       - The full data and metadata available to SasView is viewable in ASCII via
317         right clicking on a data set and choosing Data Info in the DataExplorer
318         or on the plots
319       - Supports loading a single file, multiple files, or a whole folder
320       - An optional Data Explorer is provided (default) which simplifies managing,
321         plotting, deleting, or setup for computation. Most functions however do
322         not require access to the explorer/manager and can be accessed through
323         right click menus and the toolbar.  The data explorer can be re-started
324         from the menu bar.
325
326     - Data manipulation
327       - Support various 2D averaging methods : Circular, sectors, annular,
328         boxsum, boxQx and boxQy.
329       - A 2D data maks editor is provided
330       - 2D mask can be applied to the circular averaging.
331
332     - Miscellaneous features
333       - limited reports can be generated in pdf format
334       - Provides multiprocessor support(Windows only)
335       - Limited startup customization currently includes default startup
336         data folder and choice of default starting with data manager
337       - Limited support for saving(opening) a SasView project or a SasView analysis
338         (subproject) is provided.
339       - SasView can be launched and loaded with a file of interesty by double-clicking
340         on that file (recognized extension)
341       - A data file or data folder can be passed to SasView when launched from
342         the command line.
343       - Limited bookmarking capability to later recall the results of a fit calculation
344         is provided.
345       - Extensive help is provided through context sensitive mouse roll-over,
346         information bar (at the bottom of the panel), the console menu, and
347         access to the help files in several different ways.
348
349
3502- Downloading and Installing
351=============================
352
353   *** Note 1:  Much more information is available at www.sasview.org under links.
354                    Look in the 'For Developers' section and particularly the wiki at
355                www.sasview.org/trac/wiki.
356   *** Note 2:  If you have EXE or ZIP SasView installer, you won't need any of
357                the following.  However it is highly recommended that any
358                previous versions be un-installed prior to installing the
359                new version.
360
361   2.1- System Requirements
362        - Python version >= 2.5 and < 3.0 should be running on the system
363        - We currently use Python 2.7
364
365   2.2- Installing from source
366        - Get the source code
367          - to follow the current development version from source control use
368              git clone https://github.com/SasView/sasview.git
369              git clone https://github.com/bumps/bumps.git
370          - to install a specific version
371
372        - Build, install and run a specific release
373          - make sure the requirements below are already installed
374          - retrieve the source from https://github.com/SasView/sasview/releases
375          - open a command line window in the 'sasview-x.x.x' directory
376          - run 'python setup.py install'
377          - run 'python sasview.py' under the 'sasview' folder.
378
379        - Build, install and run the current development version
380          - clone the source from git; also clone bumps, which is developed in parallel
381              git clone https://github.com/SasView/sasview.git
382              git clone https://github.com/bumps/bumps.git
383          - open a command line window in the 'sasview' directory
384          - run 'python setup.py build'
385          - run 'python run.py'; this runs from the source directories, so you
386            don't have to rebuild every time you make a change, unless you are
387            changing the C++ model files
388
389        - The following modules are required (version numbers are what are used
390          in the windows release build):
391
392          - Common Packages
393            - reportlab 3.1.44
394            - lxml 3.4.4.0 (MAC 3.4.2.0)
395            - PIL 1.1.7
396            - xhtml2pdf 3.0.33 (MAC = not installed on build server)
397            - unittest-xml-reporting 1.12.0 (MAC 1.10.0)
398            - matplotlib Version Installed: 1.4.3 (MAC 1.1.1)
399            - bumps Version Installed: 0.7.5.9
400            - scipy Version Installed: 0.16.0b2 (MAC 0.11.0)
401            - periodictable Version Installed: 1.4.1
402            - setuptools Version Installed: 7.0 (MAC 12.0.5)
403            - sphinx Version Installed: 1.3.1 (MAC 1.3b2)
404            - pyparsing Version Installed: 2.0.3
405            - numpy Version Installed: 1.9.2 (MAC 1.6.2)
406            - html5lib Version Installed: 0.99999
407            - wx Version Installed: 3.0.2.0
408
409          - Windows Specific Packages
410            - pywin 219
411            - py2exe 0.6.9
412            - comtypes 1.1.1
413            - MinGW w/ gcc version 4.6.1 (WIN)
414            - vcredist_x86.exe (version 9.0.21022.8  -microsoft visual C 2008
415              re-distributable)
416            - Innosetup (WIN - isetup 5.4.2-unicode) - used to create distributable
417
418            *** Note: Windows build dependencies can be set up using anaconda. Instructions
419                can be found at http://trac.sasview.org/wiki/AnacondaSetup
420
421          - MAC Specifc Packages
422            - py2app 0.7.1
423
424
4253- Known Issues
426===============
427
428   3.1- All systems:
429        - The documentation window may take a few seconds to load the first time
430          it is called. Also, an internet connection is required before
431          equations will render properly. Until then they will show in their
432          original TeX format.
433        - If the documentation window remains stubbornly blank, try installing a
434          different browser and set that as your default browser. Issues have
435          been noted with Internet Explorer 11.
436        - Check for Updates may fail (with the status bar message ' Cannot
437          connect to the application server') if your internet connection uses
438          a proxy server. Tested resolutions for this are described on the
439          website FAQ.
440        - The copy and paste functions (^C, ^V) in the batch mode results grid
441          require two clicks: one to select the cell and a second to select the
442          contents of the cell.
443        - The tutorial has not yet been updated and is somewhat out of date
444        - Very old computers may struggle to run the 3.x and later releases
445        - Polydispersity on multiple parameters included in a simultaneous/
446          constrained fit will likely not be correct
447        - Constrained/simultaneous fit page does not have a stop button
448        - Constrained/simultaneous fit do not accept min/max limits
449        - Save project does not store the state of all the windows
450        - Loading projects can be very slow
451        - Save Project only works once a data set has been associated with
452          a model.  Error is reported on status bar.
453        - There is a numerical precision problem with the multishell model when
454          the iner radius gets large enough (ticket #288)
455        - The angular distribution angles are not clearly defined and may in
456          some cases lead to incorrect calculations(ticket #332)
457
458   3.2- Windows:
459        - If installed to same directory as old version without first removing
460          the old version, the old desktop icon will remain but point to the
461          new exe version. Likewise all the start menu folders and items will
462          have the old name even though pointing to the new version.  Usually
463          safest to uninstall old version prior to installing new version anyway.
464
465   3.3- MAC:
466        - Application normally starts up hidden. Click icon in Dock to view/use
467          application.
468        - Multiprocessing does not currently work on MAC OS
469
470   3.4- Linux:
471        - Not well tested
472
473
4744- SasView website
475==================
476
477   - www.sasview.org.  This main project site is the gateway to all
478     information about the sasview project.  It includes information
479     about the project, a FAQ page and links to all developer and user
480     information, tools and resources.
481
482
4835- Frequently Asked Questions
484=============================
485
486   - www.sasview.org/faq.html
487
488
4896- Installer download website
490=============================
491
492   - Latest release Version
493     - https://github.com/SasView/sasview/releases
494   - Latest developer builds
495     - https://jenkins.esss.dk/sasview/view/Master-Builds/
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