source: sasview/sasview/README.txt @ f9fbe99

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 f9fbe99 was 243fbc0, checked in by Paul Kienzle <pkienzle@…>, 7 years ago

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1Release Notes
2=============
3
41- Features
5===========
6
7    - New in Version 4.0.0-alpha
8      --------------------
9      This alpha release brings a major overhaul of the model system. The new model
10      package allows rapid integration of custom models and access to polydispersity
11      without requiring a compiler.
12
13      - Model package changes and improvements
14         - Model interface moved to independent sasmodels package.
15         - Most models converted to new interface.
16         - Allows rapid integration of user-written models.
17         - OpenCL GPU utilization for faster fitting.
18         - Improved numerical integration of Bessel functions.
19      - SESANS integration and implementation
20         - Scripting interface added for analysis of SESANS data.
21         - Hankel transformation now accepts finite acceptance angles.
22         - 2D cosine transformation added for TOF SESANS analysis.
23      - Documentation improvements
24         - The documentation tree was restructured for a better end user experience.
25         - The documentation for each model was revamped and verified by at least
26           two people following the conversion of the model.
27         - Theoretical 1D (and 2D if applicable) scattering curves are auto-generated
28           and added to the model documentation for each model.
29      - Separation of GUI and calculations for future GUI enhancements
30      - Bug fixes
31         - Fixes bug #411 No stop button on simultaneous fit page
32         - Fixes bug #410 Error with raspberry model
33         - Fixes bug #364 Possible inconsistency in Poly_GausCoil model
34         - Fixes bug #439 Hayter Penfold MSA code needs checking
35         - Fixes bug #484 lammellerPC is precision limited
36         - Fixes bug #498 $HOME/.matplotlib conflicts
37         - Fixes bug #348 Control order in which fit parameters appear in the gui
38         - Fixes bug #456 Provide DREAM Results Panel with something to identify
39           data and age of results
40         - Fixes bug #556 Build script improvements for developers
41
42
43
44   - New in Version 3.1.2
45     --------------------
46     This release is a major stability improvement, having fixed a serious bug
47     that came to light since release 3.1.1. All users should upgrade.
48
49     - Fixes bug #468 broken remove constraint buttons in
50       simultaneous/constrained fitting panel
51     - Fixes bug #474 resulting from changes in 3.1.1 that had
52       introduced an error in the high-Q of slit-smeared models.
53     - Fixes bug #478 which would cause wx to run out of IDs and result
54       in SasView crashing even if left alone.
55     - Fixes bug #479 missing help button on simultaneous/constrained fit page
56     - Fixes bug #480 GUI resizing issues on simultaneous fit page
57     - Fixes bug #486 broken Report Results
58     - Fixes bug #488 redraw issues in fit page
59
60
61
62   - New in Version 3.1.1
63     --------------------
64     - Fixes bug #457 that prevented SasView from starting if the user was not
65       connected to the internet, or was behind a proxy server.
66
67   - New in Version 3.1.0
68     --------------------
69     - The documentation/help has had a complete overhaul including:
70       - A completely new presentation interface (Sphinx).
71       - Proof reading!
72       - Updating for latest features.
73       - A Help (or sometimes ?) button has been added to every panel, and some
74         sub panels if appropriate, linking to the appropriate section in the
75         documentation.
76       - The model help has been split so that the Details button now brings up
77         a very short pop-up giving the equation being used while HELP goes to
78         the section in the full documentation describing the model.
79       - Extensive help has also been added for the new optimizer engine (see
80         below) including rules of thumb on how and when to choose a given
81         optimizer and what the parameters do.
82     - The optimizer engine has been completely replaced. The new optimizer
83       still defaults to the standard Levenberg-Marquardt algorithm. However 4
84       other optimizers are now also available. Each starts with a set of default
85       parameters which can be tuned. The DREAM optimizer takes the longest but
86       is the most powerful and yields rich information including full parameter
87       correlation and uncertainty plots. A results panel has been added to
88       accommodate this.
89       - The five new optimizers are:
90         - A Levenberg-Marquardt optimizer
91         - A Quasi-Newton BFGS optimizer
92         - A Nelder-Mead Simplex optimizer
93         - A Differential Evolution optimizer
94         - A Monte Carlo optimizer (DREAM)
95     - New models were added:
96         - MicelleSphCoreModel (currently residing in the Uncategorized category)
97     - Existing models were updated:
98         - LamellarPS (bug in polydispersity integration fixed)
99         - RectangularPrismModel
100         - RectangularHollowPrismModel
101         - RectangularHollowPrismInfThinWallsModel
102     - Infrastructure to allow SESANS data to be fit with models was added. This
103       will become available in a future release but can currently be used from
104       the command line with some caveats.
105     - A number of bugs were fixed including a thread crashing issue and an
106       incorrect slit smearing resolution calculation.
107     - Implemented much more robust error logging to enable much easier
108       debugging in general but particularly the debugging of issues reported by
109       SasView users.
110     - A number of infrastructure tasks under the hood to enhance maintainability
111     - Upgrade from Wx 2.8 to Wx 3.0.2 which allows several new features but
112       required significant additional rework as well.
113     - Fully implemented Sphinx to the build process to produce both better
114       user documentation and developer documentation.
115     - Restructuring of the code base to more unified nomenclature and structure
116       so that the source installation tree more closely matches the installer
117       version tree.
118     - Code cleanup (an ongoing task) .
119     - Migration of the repository to github simplifying contributions from
120       non-project personnel through pull requests.
121
122   - New in Version 3.0.0
123     --------------------
124     - The GUI look and feel has been refactored to be more familiar for
125       Windows users by using MDI frames. Graph windows are also now free-
126       floating.
127     - Five new models have been added: PringlesModel, CoreShellEllipsoidXTModel,
128       RectangularPrismModel, RectangularHollowPrismModel and
129       RectangularHollowPrismInfThinWallsModel.
130     - The data loader now supports ILL DAT data files and reads the full meta
131       information from canSAS file formats.
132     - Redefined convention for specifying angular parameters for anisotropic
133       models.
134     - A number of minor features have been added such as permitting a log
135       distribution of points when using a model to simulate data, and the
136       addition of a Kratky plot option to the linear plots.
137     - A number of bugs have also been fixed.
138     - Save Project and Save Analysis now work more reliably.
139     - BETA: Magnetic contrast supporting full polarization analysis has been
140       implemented for some spherical and cylindrical models.
141     - BETA: Two new tools have been added:
142       - A generic scattering calculator which takes an atomic, magnetic or
143         SLD distribution in space and generates the appropriate 2D
144         scattering pattern. In some cases the orientationally averaged
145         (powder) 1D scattering can also be computed. Supported formats
146         include: SLD or text, PDB, and OMF magnetic moment distribution
147         file.
148       - An image viewer/converter for data in image format; this reads in
149         an image file and will attempt to convert the image pixels to
150         data. Supported formats include: TIFF, TIF, PNG, BMP, JPG.
151
152   - New in Version 2.2.1
153     --------------------
154     - Minor patch to support CanSAS XML v1.1 file format
155     - Added DataInfo for data in the DataExplorer and plots
156     - Added Maximize/Restore button in the title bar of the graphs
157     - Added a hide button in the toolbar of the graph panel
158     - The 'x' button now deletes a graph
159     - Edit SUM Model from the menubar can now generate and save more than one sum model
160     - Reports can now be saved in pdf format on WIN and MAC
161     - Made significant improvements to the batch/grid panel and fixed several bugs
162     - Fixed a number of other minor bugs
163
164   - New in Version 2.2.0
165     --------------------
166     - Application name changed to SasView
167     - New fully customizable Category Manager added for better management of
168       increasing number of models
169     - Improved the Grid Window functionality in the batch fitting mode
170     - Added a simpler Graph/Plot modification interface
171     - Added a new 'Data Operation' tool for addition, subtraction, multiplication,
172       division, of two data sets.
173     - The 'Sum Model' editor was extended and renamed 'Summation and Multiplication'
174       editor
175     - Added more plot symbols options for 1d plots
176     - Added improved trapping of compiling errors to the 'New model editor'
177     - Added some intelligent outputs (e.g., Rg, background, or rod diameter
178       depending on the choice of axis scale of the plot) to the linear fits
179     - Added more models
180     
181   - Feature set from previous versions         
182     -----------------------------------
183     - Perspectives Available
184       - Invariant calculator: Calculates the invariant, volume fraction, and
185         specific surface area.
186       - P(r) inversion calculator: Indirect Fourier transformation method.
187       - Fitting: the tool used for modeling and fitting 1D and 2D data to
188         analytical model functions
189       - Tools: provides a number of useful supplementary tools such as SLD
190         calculation 
191   
192     - Fitting
193       - Includes a large number of model functions, both form factors and structure factors.
194       - Support P(Q)*S(Q) for form factors that flag they can be so multiplied.
195       - Supports Gaussian, lognormal, Shulz, rectangular and custom distribution
196         functions for models that need to include polydispersity or for orientational
197         distributions if appropriate.
198       - Anisotropic shapes and magnetic moment modeling in 2D allow for a non-uniform
199         distribution of orientations of a given axis leading to modeling and fitting
200         capabilities of non azimuthaly symmetric data. 
201       - User can choose to weight fits or not. If using weights, the user can choose
202         the error bar on each point if provided in the file, the square root
203         of the intensity or the intensity itself.
204       - Instrumental resolution smearing of model or fits is provided with several
205         options: read the resolution/point fromt he file. Input a pinhole resolution
206         or a slit resolution.
207       - Users can define the Qrange (Qmin and Qmax) for both 1D and 2D data for
208         fitting and modeling, but not graphically.  The range can be reset to the
209         defaults (limits of q in data set for a fit) with the reset button.
210       - A mask can be applied to 2D calculation and fitting.
211       - Normalized residual plots are provided with every fit.
212       - Model function help available through detail button or from the fitting panel.
213       - Simultaneous/(advanced)constrained fitting allows for fitting a single
214         data set or several different sets simultaneously with the application
215         of advanced constraints relating fit parameters to functions of other
216         parameters (including from a different set). For example thickness of
217         shell = sin(30) times the length. 
218       - Models that are the sum of two other models can be easily generated through the
219         SUM Model menubar item.
220       - New Python models can be added on the fly by creating an appropriate Python
221         file in the model plugin directory. Two tools are provided to help:
222         An easy to use custom model editor allows the quick generation of new Python
223         models by supplying only the parameters and their default value (box 1)
224         and the mathematical function of the model (box 2) and generating the
225         necessary *.py file.  A separate advanced model editor provides a full Python
226         file editor.  Either way once saved the model becomes immediately available
227         to the application.
228       - A batch fitting capability allows for the analysis of a series of data sets to
229         a single model and provides the results in a tabular form suitable for saving
230         or plotting the evolution of the fit parameters with error bars (from within
231         the application).
232 
233     - Tools
234       - A scattering length density calculator,including some X-ray information
235         is provided.
236       - A density to vol. fraction converter is provided
237       - In application access to a Python shell/editor (PyCrust) is provided
238       - An instrument resolution calculator, including possible gravitational and
239         TOF effects is provided
240       - A slit size calculator optimized for Anton Paar Saxess is provided.
241       - A kiessig fringe thickness calculator is provided
242         
243     - Plots and plot management
244       - A 3D graphing option (for 2d data/results) is provided with the view
245         controlled by the mouse
246       - 2D plots are shown with an intensity color bar. 2D Color map can be user
247         adjusted.
248       - Supports output of plot to a variety of graphic formats. Supported formats
249         include: png, eps, emf, jpg/jpeg, pdf, ps, tif/tiff, rawRGBbitmap(raw, rgba),
250         and scalable vector graphic (svg/svgz)
251       - Supports ouput of data in plot (1 or 2D) to limited data formats
252       - Multiple data sets can be loaded into a single graph for viewing (but a fit
253         plot can currently only have a single plot).
254       - Extensive context sensitive plot/fitting/manipulation options are available
255         through a right mouse click pop-up menu on plots.
256           
257     - Data management
258       - Supports 2 + column 1D ASCII data, NIST 1D and 2D data, and canSAS data
259         via plug-in mechanism which can easily allow other readers as appropriate.
260       - 2D data is expected in Q space but for historical reasons accepts the
261         NIST 2D raw pixel format and will do conversion internally.
262       - The full data and metadata available to SasView is viewable in ASCII via
263         right clicking on a data set and choosing Data Info in the DataExplorer
264         or on the plots
265       - Supports loading a single file, multiple files, or a whole folder   
266       - An optional Data Explorer is provided (default) which simplifies managing,
267         plotting, deleting, or setup for computation. Most functions however do
268         not require access to the explorer/manager and can be accessed through
269         right click menus and the toolbar.  The data explorer can be re-started
270         from the menu bar.
271           
272     - Data manipulation
273       - Support various 2D averaging methods : Circular, sectors, annular,
274         boxsum, boxQx and boxQy.
275       - A 2D data maks editor is provided
276       - 2D mask can be applied to the circular averaging.
277         
278     - Miscellaneous features
279       - limited reports can be generated in pdf format
280       - Provides multiprocessor support(Windows only)
281       - Limited startup customization currently includes default startup
282         data folder and choice of default starting with data manager
283       - Limited support for saving(opening) a SasView project or a SasView analysis
284         (subproject) is provided.
285       - SasView can be launched and loaded with a file of interesty by double-clicking
286         on that file (recognized extension)
287       - A data file or data folder can be passed to SasView when launched from
288         the command line.
289       - Limited bookmarking capability to later recall the results of a fit calculation
290         is provided.
291       - Extensive help is provided through context sensitive mouse roll-over,
292         information bar (at the bottom of the panel), the console menu, and
293         access to the help files in several different ways.
294
295
2962- Downloading and Installing
297=============================
298       
299   *** Note 1:  Much more information is available at www.sasview.org under links.
300                    Look in the 'For Developers' section and particularly the wiki at
301                www.sasview.org/trac/wiki.
302   *** Note 2:  If you have EXE or ZIP SasView installer, you won't need any of
303                the following.  However it is highly recommended that any
304                previous versions be un-installed prior to installing the
305                new version.
306
307   2.1- System Requirements
308        - Python version >= 2.5 and < 3.0 should be running on the system
309        - We currently use Python 2.7
310
311   2.2- Installing from source
312        - Get the source code
313          - to follow the current development version from source control use
314              git clone https://github.com/SasView/sasview.git
315              git clone https://github.com/bumps/bumps.git
316          - to install a specific version
317
318        - Build, install and run a specific release
319          - make sure the requirements below are already installed
320          - retrieve the source from https://github.com/SasView/sasview/releases
321          - open a command line window in the 'sasview-x.x.x' directory
322          - run 'python setup.py install'
323          - run 'python sasview.py' under the 'sasview' folder.
324
325        - Build, install and run the current development version
326          - clone the source from git; also clone bumps, which is developed in parallel
327              git clone https://github.com/SasView/sasview.git
328              git clone https://github.com/bumps/bumps.git
329          - open a command line window in the 'sasview' directory
330          - run 'python setup.py build'
331          - run 'python run.py'; this runs from the source directories, so you
332            don't have to rebuild every time you make a change, unless you are
333            changing the C++ model files
334
335        - The following modules are required (version numbers are what are used
336          in the windows release build):
337         
338          - Common Packages
339            - reportlab 3.1.44
340            - lxml 3.4.4.0 (MAC 3.4.2.0)
341            - PIL 1.1.7
342            - xhtml2pdf 3.0.33 (MAC = not installed on build server)
343            - unittest-xml-reporting 1.12.0 (MAC 1.10.0)
344            - matplotlib Version Installed: 1.4.3 (MAC 1.1.1)
345            - bumps Version Installed: 0.7.5.9
346            - scipy Version Installed: 0.16.0b2 (MAC 0.11.0)
347            - periodictable Version Installed: 1.4.1
348            - setuptools Version Installed: 7.0 (MAC 12.0.5)
349            - sphinx Version Installed: 1.3.1 (MAC 1.3b2)
350            - pyparsing Version Installed: 2.0.3
351            - numpy Version Installed: 1.9.2 (MAC 1.6.2)
352            - html5lib Version Installed: 0.99999
353            - wx Version Installed: 3.0.2.0
354         
355          - Windows Specific Packages
356            - pywin 219
357            - py2exe 0.6.9
358            - comtypes 1.1.1
359            - MinGW w/ gcc version 4.6.1 (WIN)
360            - vcredist_x86.exe (version 9.0.21022.8  -microsoft visual C 2008
361              re-distributable)
362            - Innosetup (WIN - isetup 5.4.2-unicode) - used to create distributable
363
364            *** Note: Windows build dependencies can be set up using anaconda. Instructions
365                can be found at http://trac.sasview.org/wiki/AnacondaSetup
366           
367          - MAC Specifc Packages
368            - py2app 0.7.1
369         
370
3713- Known Issues
372===============
373
374   3.1- All systems:
375        - The documentation window may take a few seconds to load the first time
376          it is called. Also, an internet connection is required before
377          equations will render properly. Until then they will show in their
378          original TeX format.
379        - If the documentation window remains stubbornly blank, try installing a
380          different browser and set that as your default browser. Issues have
381          been noted with Internet Explorer 11.
382        - Check for Updates may fail (with the status bar message ' Cannot
383          connect to the application server') if your internet connection uses
384          a proxy server. Tested resolutions for this are described on the
385          website FAQ.
386        - The copy and paste functions (^C, ^V) in the batch mode results grid
387          require two clicks: one to select the cell and a second to select the
388          contents of the cell.
389        - The tutorial has not yet been updated and is somewhat out of date
390        - Very old computers may struggle to run the 3.x and later releases
391        - Polydispersity on multiple parameters included in a simultaneous/
392          constrained fit will likely not be correct
393        - Constrained/simultaneous fit page does not have a stop button
394        - Constrained/simultaneous fit do not accept min/max limits
395        - Save project does not store the state of all the windows
396        - Loading projects can be very slow
397        - Save Project only works once a data set has been associated with
398          a model.  Error is reported on status bar.
399        - There is a numerical precision problem with the multishell model when
400          the iner radius gets large enough (ticket #288)
401        - The angular distribution angles are not clearly defined and may in
402          some cases lead to incorrect calculations(ticket #332)
403         
404   3.2- Windows:
405        - If installed to same directory as old version without first removing
406          the old version, the old desktop icon will remain but point to the
407          new exe version. Likewise all the start menu folders and items will
408          have the old name even though pointing to the new version.  Usually
409          safest to uninstall old version prior to installing new version anyway.
410               
411   3.3- MAC:
412        - Application normally starts up hidden. Click icon in Dock to view/use
413          application.
414        - Multiprocessing does not currently work on MAC OS
415               
416   3.4- Linux:
417        - Not well tested
418
419
4204- SasView website
421==================
422
423   - www.sasview.org.  This main project site is the gateway to all
424     information about the sasview project.  It includes information
425     about the project, a FAQ page and links to all developer and user
426     information, tools and resources.
427
428
4295- Frequently Asked Questions
430=============================
431
432   - www.sasview.org/faq.html
433
434
4356- Installer download website
436=============================
437
438   - Latest release Version
439     - https://github.com/SasView/sasview/releases
440   - Latest developer builds
441     - https://jenkins.esss.dk/sasview/view/Master-Builds/
442
443   
Note: See TracBrowser for help on using the repository browser.