source: sasview/sasview/README.txt @ 153ee77

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalc
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1Release Notes
2=============
3
41- Features
5===========
6
7    - New in Version 4.0 beta 1
8      --------------------
9      This beta adds support for the magnetic and multilevel models of 3.1.2
10      and along with a host of bug fixes found in the alpha.
11
12      - Model package changes and improvements
13         - All 3.1.2 models now available in new interface
14         - Old custom models should now still work
15            - '''NOTE:''' These will be deprecated in a future version. Old
16            custom models should be converted to the new model format which
17            is now the same as the built in models and offers much better
18            support.
19         - Custom model editor now creates new style models
20         - Custom model editor supports better error checking
21      - Documentation improvements
22        - Continued general cleanup
23      - Other improvements/additions
24         - Support for new canSAS 2D data files added
25         - Plot axes range can now be set manually as well as by zooming
26         - Plot annotations can now be moved around after being placed on plot.
27         - The active optimizer is now listed on the top of the fit panel.
28         - Linear fits now update qmin and max when the x scale limits are
29         changed.  Also the plot range no longer resets after a fit.
30      - Bug fixes
31         - Fixes bug #511 Errors in linearized fits and clean up of interface
32         including Kratky representation
33         - Fixes bug #186 Data operation Tool now executes when something is
34         entered in the text box and does not wait for the user to hit enter
35         - Fixes bug #459 plot context menu bug
36         - Fixes bug #559 copy to clipboard in graph menu broken
37         - Fixes bug #466 cannot remove a linear fit from graph
38         - Numerous bugs introduced in the alpha
39
40
41
42    - New in Version 4.0.0-alpha
43      --------------------
44      This alpha release brings a major overhaul of the model system. The new model
45      package allows rapid integration of custom models and access to polydispersity
46      without requiring a compiler.
47
48      - Model package changes and improvements
49         - Model interface moved to independent sasmodels package.
50         - Most models converted to new interface.
51         - Allows rapid integration of user-written models.
52         - OpenCL GPU utilization for faster fitting.
53         - Improved numerical integration of Bessel functions.
54      - SESANS integration and implementation
55         - Scripting interface added for analysis of SESANS data.
56         - Hankel transformation now accepts finite acceptance angles.
57         - 2D cosine transformation added for TOF SESANS analysis.
58      - Documentation improvements
59         - The documentation tree was restructured for a better end user experience.
60         - The documentation for each model was revamped and verified by at least
61           two people following the conversion of the model.
62         - Theoretical 1D (and 2D if applicable) scattering curves are auto-generated
63           and added to the model documentation for each model.
64      - Separation of GUI and calculations for future GUI enhancements
65      - Bug fixes
66         - Fixes bug #411 No stop button on simultaneous fit page
67         - Fixes bug #410 Error with raspberry model
68         - Fixes bug #364 Possible inconsistency in Poly_GausCoil model
69         - Fixes bug #439 Hayter Penfold MSA code needs checking
70         - Fixes bug #484 lammellerPC is precision limited
71         - Fixes bug #498 $HOME/.matplotlib conflicts
72         - Fixes bug #348 Control order in which fit parameters appear in the gui
73         - Fixes bug #456 Provide DREAM Results Panel with something to identify
74           data and age of results
75         - Fixes bug #556 Build script improvements for developers
76
77
78
79   - New in Version 3.1.2
80     --------------------
81     This release is a major stability improvement, having fixed a serious bug
82     that came to light since release 3.1.1. All users should upgrade.
83
84     - Fixes bug #468 broken remove constraint buttons in
85       simultaneous/constrained fitting panel
86     - Fixes bug #474 resulting from changes in 3.1.1 that had
87       introduced an error in the high-Q of slit-smeared models.
88     - Fixes bug #478 which would cause wx to run out of IDs and result
89       in SasView crashing even if left alone.
90     - Fixes bug #479 missing help button on simultaneous/constrained fit page
91     - Fixes bug #480 GUI resizing issues on simultaneous fit page
92     - Fixes bug #486 broken Report Results
93     - Fixes bug #488 redraw issues in fit page
94
95
96
97   - New in Version 3.1.1
98     --------------------
99     - Fixes bug #457 that prevented SasView from starting if the user was not
100       connected to the internet, or was behind a proxy server.
101
102   - New in Version 3.1.0
103     --------------------
104     - The documentation/help has had a complete overhaul including:
105       - A completely new presentation interface (Sphinx).
106       - Proof reading!
107       - Updating for latest features.
108       - A Help (or sometimes ?) button has been added to every panel, and some
109         sub panels if appropriate, linking to the appropriate section in the
110         documentation.
111       - The model help has been split so that the Details button now brings up
112         a very short pop-up giving the equation being used while HELP goes to
113         the section in the full documentation describing the model.
114       - Extensive help has also been added for the new optimizer engine (see
115         below) including rules of thumb on how and when to choose a given
116         optimizer and what the parameters do.
117     - The optimizer engine has been completely replaced. The new optimizer
118       still defaults to the standard Levenberg-Marquardt algorithm. However 4
119       other optimizers are now also available. Each starts with a set of default
120       parameters which can be tuned. The DREAM optimizer takes the longest but
121       is the most powerful and yields rich information including full parameter
122       correlation and uncertainty plots. A results panel has been added to
123       accommodate this.
124       - The five new optimizers are:
125         - A Levenberg-Marquardt optimizer
126         - A Quasi-Newton BFGS optimizer
127         - A Nelder-Mead Simplex optimizer
128         - A Differential Evolution optimizer
129         - A Monte Carlo optimizer (DREAM)
130     - New models were added:
131         - MicelleSphCoreModel (currently residing in the Uncategorized category)
132     - Existing models were updated:
133         - LamellarPS (bug in polydispersity integration fixed)
134         - RectangularPrismModel
135         - RectangularHollowPrismModel
136         - RectangularHollowPrismInfThinWallsModel
137     - Infrastructure to allow SESANS data to be fit with models was added. This
138       will become available in a future release but can currently be used from
139       the command line with some caveats.
140     - A number of bugs were fixed including a thread crashing issue and an
141       incorrect slit smearing resolution calculation.
142     - Implemented much more robust error logging to enable much easier
143       debugging in general but particularly the debugging of issues reported by
144       SasView users.
145     - A number of infrastructure tasks under the hood to enhance maintainability
146     - Upgrade from Wx 2.8 to Wx 3.0.2 which allows several new features but
147       required significant additional rework as well.
148     - Fully implemented Sphinx to the build process to produce both better
149       user documentation and developer documentation.
150     - Restructuring of the code base to more unified nomenclature and structure
151       so that the source installation tree more closely matches the installer
152       version tree.
153     - Code cleanup (an ongoing task) .
154     - Migration of the repository to github simplifying contributions from
155       non-project personnel through pull requests.
156
157   - New in Version 3.0.0
158     --------------------
159     - The GUI look and feel has been refactored to be more familiar for
160       Windows users by using MDI frames. Graph windows are also now free-
161       floating.
162     - Five new models have been added: PringlesModel, CoreShellEllipsoidXTModel,
163       RectangularPrismModel, RectangularHollowPrismModel and
164       RectangularHollowPrismInfThinWallsModel.
165     - The data loader now supports ILL DAT data files and reads the full meta
166       information from canSAS file formats.
167     - Redefined convention for specifying angular parameters for anisotropic
168       models.
169     - A number of minor features have been added such as permitting a log
170       distribution of points when using a model to simulate data, and the
171       addition of a Kratky plot option to the linear plots.
172     - A number of bugs have also been fixed.
173     - Save Project and Save Analysis now work more reliably.
174     - BETA: Magnetic contrast supporting full polarization analysis has been
175       implemented for some spherical and cylindrical models.
176     - BETA: Two new tools have been added:
177       - A generic scattering calculator which takes an atomic, magnetic or
178         SLD distribution in space and generates the appropriate 2D
179         scattering pattern. In some cases the orientationally averaged
180         (powder) 1D scattering can also be computed. Supported formats
181         include: SLD or text, PDB, and OMF magnetic moment distribution
182         file.
183       - An image viewer/converter for data in image format; this reads in
184         an image file and will attempt to convert the image pixels to
185         data. Supported formats include: TIFF, TIF, PNG, BMP, JPG.
186
187   - New in Version 2.2.1
188     --------------------
189     - Minor patch to support CanSAS XML v1.1 file format
190     - Added DataInfo for data in the DataExplorer and plots
191     - Added Maximize/Restore button in the title bar of the graphs
192     - Added a hide button in the toolbar of the graph panel
193     - The 'x' button now deletes a graph
194     - Edit SUM Model from the menubar can now generate and save more than one sum model
195     - Reports can now be saved in pdf format on WIN and MAC
196     - Made significant improvements to the batch/grid panel and fixed several bugs
197     - Fixed a number of other minor bugs
198
199   - New in Version 2.2.0
200     --------------------
201     - Application name changed to SasView
202     - New fully customizable Category Manager added for better management of
203       increasing number of models
204     - Improved the Grid Window functionality in the batch fitting mode
205     - Added a simpler Graph/Plot modification interface
206     - Added a new 'Data Operation' tool for addition, subtraction, multiplication,
207       division, of two data sets.
208     - The 'Sum Model' editor was extended and renamed 'Summation and Multiplication'
209       editor
210     - Added more plot symbols options for 1d plots
211     - Added improved trapping of compiling errors to the 'New model editor'
212     - Added some intelligent outputs (e.g., Rg, background, or rod diameter
213       depending on the choice of axis scale of the plot) to the linear fits
214     - Added more models
215     
216   - Feature set from previous versions         
217     -----------------------------------
218     - Perspectives Available
219       - Invariant calculator: Calculates the invariant, volume fraction, and
220         specific surface area.
221       - P(r) inversion calculator: Indirect Fourier transformation method.
222       - Fitting: the tool used for modeling and fitting 1D and 2D data to
223         analytical model functions
224       - Tools: provides a number of useful supplementary tools such as SLD
225         calculation 
226   
227     - Fitting
228       - Includes a large number of model functions, both form factors and structure factors.
229       - Support P(Q)*S(Q) for form factors that flag they can be so multiplied.
230       - Supports Gaussian, lognormal, Shulz, rectangular and custom distribution
231         functions for models that need to include polydispersity or for orientational
232         distributions if appropriate.
233       - Anisotropic shapes and magnetic moment modeling in 2D allow for a non-uniform
234         distribution of orientations of a given axis leading to modeling and fitting
235         capabilities of non azimuthaly symmetric data. 
236       - User can choose to weight fits or not. If using weights, the user can choose
237         the error bar on each point if provided in the file, the square root
238         of the intensity or the intensity itself.
239       - Instrumental resolution smearing of model or fits is provided with several
240         options: read the resolution/point fromt he file. Input a pinhole resolution
241         or a slit resolution.
242       - Users can define the Qrange (Qmin and Qmax) for both 1D and 2D data for
243         fitting and modeling, but not graphically.  The range can be reset to the
244         defaults (limits of q in data set for a fit) with the reset button.
245       - A mask can be applied to 2D calculation and fitting.
246       - Normalized residual plots are provided with every fit.
247       - Model function help available through detail button or from the fitting panel.
248       - Simultaneous/(advanced)constrained fitting allows for fitting a single
249         data set or several different sets simultaneously with the application
250         of advanced constraints relating fit parameters to functions of other
251         parameters (including from a different set). For example thickness of
252         shell = sin(30) times the length. 
253       - Models that are the sum of two other models can be easily generated through the
254         SUM Model menubar item.
255       - New Python models can be added on the fly by creating an appropriate Python
256         file in the model plugin directory. Two tools are provided to help:
257         An easy to use custom model editor allows the quick generation of new Python
258         models by supplying only the parameters and their default value (box 1)
259         and the mathematical function of the model (box 2) and generating the
260         necessary *.py file.  A separate advanced model editor provides a full Python
261         file editor.  Either way once saved the model becomes immediately available
262         to the application.
263       - A batch fitting capability allows for the analysis of a series of data sets to
264         a single model and provides the results in a tabular form suitable for saving
265         or plotting the evolution of the fit parameters with error bars (from within
266         the application).
267 
268     - Tools
269       - A scattering length density calculator,including some X-ray information
270         is provided.
271       - A density to vol. fraction converter is provided
272       - In application access to a Python shell/editor (PyCrust) is provided
273       - An instrument resolution calculator, including possible gravitational and
274         TOF effects is provided
275       - A slit size calculator optimized for Anton Paar Saxess is provided.
276       - A kiessig fringe thickness calculator is provided
277         
278     - Plots and plot management
279       - A 3D graphing option (for 2d data/results) is provided with the view
280         controlled by the mouse
281       - 2D plots are shown with an intensity color bar. 2D Color map can be user
282         adjusted.
283       - Supports output of plot to a variety of graphic formats. Supported formats
284         include: png, eps, emf, jpg/jpeg, pdf, ps, tif/tiff, rawRGBbitmap(raw, rgba),
285         and scalable vector graphic (svg/svgz)
286       - Supports ouput of data in plot (1 or 2D) to limited data formats
287       - Multiple data sets can be loaded into a single graph for viewing (but a fit
288         plot can currently only have a single plot).
289       - Extensive context sensitive plot/fitting/manipulation options are available
290         through a right mouse click pop-up menu on plots.
291           
292     - Data management
293       - Supports 2 + column 1D ASCII data, NIST 1D and 2D data, and canSAS data
294         via plug-in mechanism which can easily allow other readers as appropriate.
295       - 2D data is expected in Q space but for historical reasons accepts the
296         NIST 2D raw pixel format and will do conversion internally.
297       - The full data and metadata available to SasView is viewable in ASCII via
298         right clicking on a data set and choosing Data Info in the DataExplorer
299         or on the plots
300       - Supports loading a single file, multiple files, or a whole folder   
301       - An optional Data Explorer is provided (default) which simplifies managing,
302         plotting, deleting, or setup for computation. Most functions however do
303         not require access to the explorer/manager and can be accessed through
304         right click menus and the toolbar.  The data explorer can be re-started
305         from the menu bar.
306           
307     - Data manipulation
308       - Support various 2D averaging methods : Circular, sectors, annular,
309         boxsum, boxQx and boxQy.
310       - A 2D data maks editor is provided
311       - 2D mask can be applied to the circular averaging.
312         
313     - Miscellaneous features
314       - limited reports can be generated in pdf format
315       - Provides multiprocessor support(Windows only)
316       - Limited startup customization currently includes default startup
317         data folder and choice of default starting with data manager
318       - Limited support for saving(opening) a SasView project or a SasView analysis
319         (subproject) is provided.
320       - SasView can be launched and loaded with a file of interesty by double-clicking
321         on that file (recognized extension)
322       - A data file or data folder can be passed to SasView when launched from
323         the command line.
324       - Limited bookmarking capability to later recall the results of a fit calculation
325         is provided.
326       - Extensive help is provided through context sensitive mouse roll-over,
327         information bar (at the bottom of the panel), the console menu, and
328         access to the help files in several different ways.
329
330
3312- Downloading and Installing
332=============================
333       
334   *** Note 1:  Much more information is available at www.sasview.org under links.
335                    Look in the 'For Developers' section and particularly the wiki at
336                www.sasview.org/trac/wiki.
337   *** Note 2:  If you have EXE or ZIP SasView installer, you won't need any of
338                the following.  However it is highly recommended that any
339                previous versions be un-installed prior to installing the
340                new version.
341
342   2.1- System Requirements
343        - Python version >= 2.5 and < 3.0 should be running on the system
344        - We currently use Python 2.7
345
346   2.2- Installing from source
347        - Get the source code
348          - to follow the current development version from source control use
349              git clone https://github.com/SasView/sasview.git
350              git clone https://github.com/bumps/bumps.git
351          - to install a specific version
352
353        - Build, install and run a specific release
354          - make sure the requirements below are already installed
355          - retrieve the source from https://github.com/SasView/sasview/releases
356          - open a command line window in the 'sasview-x.x.x' directory
357          - run 'python setup.py install'
358          - run 'python sasview.py' under the 'sasview' folder.
359
360        - Build, install and run the current development version
361          - clone the source from git; also clone bumps, which is developed in parallel
362              git clone https://github.com/SasView/sasview.git
363              git clone https://github.com/bumps/bumps.git
364          - open a command line window in the 'sasview' directory
365          - run 'python setup.py build'
366          - run 'python run.py'; this runs from the source directories, so you
367            don't have to rebuild every time you make a change, unless you are
368            changing the C++ model files
369
370        - The following modules are required (version numbers are what are used
371          in the windows release build):
372         
373          - Common Packages
374            - reportlab 3.1.44
375            - lxml 3.4.4.0 (MAC 3.4.2.0)
376            - PIL 1.1.7
377            - xhtml2pdf 3.0.33 (MAC = not installed on build server)
378            - unittest-xml-reporting 1.12.0 (MAC 1.10.0)
379            - matplotlib Version Installed: 1.4.3 (MAC 1.1.1)
380            - bumps Version Installed: 0.7.5.9
381            - scipy Version Installed: 0.16.0b2 (MAC 0.11.0)
382            - periodictable Version Installed: 1.4.1
383            - setuptools Version Installed: 7.0 (MAC 12.0.5)
384            - sphinx Version Installed: 1.3.1 (MAC 1.3b2)
385            - pyparsing Version Installed: 2.0.3
386            - numpy Version Installed: 1.9.2 (MAC 1.6.2)
387            - html5lib Version Installed: 0.99999
388            - wx Version Installed: 3.0.2.0
389         
390          - Windows Specific Packages
391            - pywin 219
392            - py2exe 0.6.9
393            - comtypes 1.1.1
394            - MinGW w/ gcc version 4.6.1 (WIN)
395            - vcredist_x86.exe (version 9.0.21022.8  -microsoft visual C 2008
396              re-distributable)
397            - Innosetup (WIN - isetup 5.4.2-unicode) - used to create distributable
398
399            *** Note: Windows build dependencies can be set up using anaconda. Instructions
400                can be found at http://trac.sasview.org/wiki/AnacondaSetup
401           
402          - MAC Specifc Packages
403            - py2app 0.7.1
404         
405
4063- Known Issues
407===============
408
409   3.1- All systems:
410        - The documentation window may take a few seconds to load the first time
411          it is called. Also, an internet connection is required before
412          equations will render properly. Until then they will show in their
413          original TeX format.
414        - If the documentation window remains stubbornly blank, try installing a
415          different browser and set that as your default browser. Issues have
416          been noted with Internet Explorer 11.
417        - Check for Updates may fail (with the status bar message ' Cannot
418          connect to the application server') if your internet connection uses
419          a proxy server. Tested resolutions for this are described on the
420          website FAQ.
421        - The copy and paste functions (^C, ^V) in the batch mode results grid
422          require two clicks: one to select the cell and a second to select the
423          contents of the cell.
424        - The tutorial has not yet been updated and is somewhat out of date
425        - Very old computers may struggle to run the 3.x and later releases
426        - Polydispersity on multiple parameters included in a simultaneous/
427          constrained fit will likely not be correct
428        - Constrained/simultaneous fit page does not have a stop button
429        - Constrained/simultaneous fit do not accept min/max limits
430        - Save project does not store the state of all the windows
431        - Loading projects can be very slow
432        - Save Project only works once a data set has been associated with
433          a model.  Error is reported on status bar.
434        - There is a numerical precision problem with the multishell model when
435          the iner radius gets large enough (ticket #288)
436        - The angular distribution angles are not clearly defined and may in
437          some cases lead to incorrect calculations(ticket #332)
438         
439   3.2- Windows:
440        - If installed to same directory as old version without first removing
441          the old version, the old desktop icon will remain but point to the
442          new exe version. Likewise all the start menu folders and items will
443          have the old name even though pointing to the new version.  Usually
444          safest to uninstall old version prior to installing new version anyway.
445               
446   3.3- MAC:
447        - Application normally starts up hidden. Click icon in Dock to view/use
448          application.
449        - Multiprocessing does not currently work on MAC OS
450               
451   3.4- Linux:
452        - Not well tested
453
454
4554- SasView website
456==================
457
458   - www.sasview.org.  This main project site is the gateway to all
459     information about the sasview project.  It includes information
460     about the project, a FAQ page and links to all developer and user
461     information, tools and resources.
462
463
4645- Frequently Asked Questions
465=============================
466
467   - www.sasview.org/faq.html
468
469
4706- Installer download website
471=============================
472
473   - Latest release Version
474     - https://github.com/SasView/sasview/releases
475   - Latest developer builds
476     - https://jenkins.esss.dk/sasview/view/Master-Builds/
477
478   
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