source: sasview/sasview/README.txt @ 42dbcfb

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
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1Release Notes
2=============
3
4SasView 3.1.0
5    -The documentation/help has had a complete overhaul including
6      - A completely new interface.
7      - The text has had a clean-up and been brought up to date with the latest
8        features.
9      - A Help (or sometimes ?) button has been added to every panel, and some
10        sub panels if appropriate, linking to the appropriate section in the
11        documentation.
12      - The model help has been split so that the details button now brings up
13        a very short pop-up giving the equation being used while HELP goes to
14        the section in the full documentation describing the model.
15      - Extensive help has also been added for the new optimizer engine (see
16        below) including rules of thumb on how and when to choose a given
17        optimizer and what the parameter do.
18    - The optimizer package has been completely replaced.  The new optimizer
19      still defaults to the standard Levenberg-Marquardt algorithm.  However 4
20      other optimizers are now available. Each starts with a set of default
21      parameters which can be tuned.  The DREAM optimizer takes the longest but
22      is the most powerful and yields rich information including full parameter
23      correlation and uncertainty plots.  A results panel has been added to
24      accommodate this.  The five optimizers are:
25      - A Levenberg-Marquardt optimizer
26      - A Quasi-Newton BFGS optimizer
27      - A Nelder-Mead Simplex optimizer
28      - A Differential Evolution optimizer
29      - A Monte Carlo optimizer DREAM optimizer
30    - Several new models added (what are they)
31    - Infrastructure to allow SESANS data to bit fit with models in a future
32      release was added and can currently be used from command line with some
33      caveats.
34    - A number of bugs were fixed including a thread crashing issue and a
35      incorrect resolution slit smearing.
36    - Implemented much more robust error logging to better enable much easier
37      debugging in general and particularly debugging an issue reported by
38      SasView user.
39    - A number of infrastructure tasks under the hood to enhance maintainability
40      - Upgrade from Wx 2.9 to 3.0.2 which allows several new features but
41        required significant other rework as well.
42      - Fully implemented Sphinx to the build process to produce both better
43        user documentation and developer documentation.
44      - Restructuring of code base to more unified nomenclature and structure
45        so that source installation tree more closely matches the installer
46        version tree.
47      - Code cleanup (an ongoing task)
48      - Migration of repository to github simplifying contributions from
49        non-project personnel through pull requests
50
51
52    - New in Version 3.0.0
53      - The GUI look and feel has been refactored to be more familiar for
54        Windows users by using MDI frames. Graph windows are also now free-
55        floating.
56      - Five new models have been added: PringlesModel, CoreShellEllipsoidXTModel,
57        RectangularPrismModel, RectangularHollowPrismModel and
58        RectangularHollowPrismInfThinWallsModel.
59      - The data loader now supports ILL DAT data files and reads the full meta
60        information from canSAS file formats.
61      - Redefined convention for specifying angular parameters for anisotropic
62        models.
63      - A number of minor features have been added such as permitting a log
64        distribution of points when using a model to simulate data, and the
65        addition of a Kratky plot option to the linear plots.
66      - A number of bugs have also been fixed.
67      - Save Project and Save Analysis now work more reliably.
68      - BETA: Magnetic contrast supporting full polarization analysis has been
69            implemented for some spherical and cylindrical models.
70      - BETA: Two new tools have been added:
71            * A generic scattering calculator which takes an atomic, magnetic or
72              SLD distribution in space and generates the appropriate 2D
73              scattering pattern. In some cases the orientationally averaged
74              (powder) 1D scattering can also be computed. Supported formats
75              include: SLD or text, PDB, and OMF magnetic moment distribution
76              file.
77            * An image viewer/converter for data in image format; this reads in
78              an image file and will attempt to convert the image pixels to
79              data. Supported formats include: TIFF, TIF, PNG, BMP, JPG.
80
81    - New in Version 2.2.1
82      - Minor patch to support CanSAS XML v1.1 file format
83      - Added DataInfo for data in the DataExplorer and plots
84      - Added Maximize/Restore button in the title bar of the graphs
85      - Added a hide button in the toolbar of the graph panel
86      - The 'x' button now deletes a graph
87      - Edit SUM Model from the menubar can now generate and save more than one sum model
88      - Reports can now be saved in pdf format on WIN and MAC
89      - Made significant improvements to the batch/grid panel and fixed several bugs
90      - Fixed a number of other minor bugs
91
92    - New in Version 2.2.0
93      - Application name changed to SasView
94      - New fully customizable Category Manager added for better management of
95        increasing number of models
96      - Improved the Grid Window functionality in the batch fitting mode
97      - Added a simpler Graph/Plot modification interface
98      - Added a new 'Data Operation' tool for addition, subtraction, multiplication,
99        division, of two data sets.
100      - The 'Sum Model' editor was extended and renamed 'Summation and Multiplication'
101        editor
102      - Added more plot symbols options for 1d plots
103      - Added improved trapping of compiling errors to the 'New model editor'
104      - Added some intelligent outputs (e.g., Rg, background, or rod diameter depending on the choice of axis scale of the plot) to the linear fits
105      - Added more models
106
107    - Feature set from Previous Versions:       
108   
109    - Perspectives Available
110      - Invariant calculator: Calculates the invariant, volume fraction, and
111        specific surface area.
112      - P(r) inversion calculator: Indirect Fourier transformation method.
113      - Fitting: the tool used for modeling and fitting 1D and 2D data to
114        analytical model functions
115      - Tools: provides a number of useful supplementary tools such as SLD
116        calculation 
117   
118    - Fitting
119      - Includes a large number of model functions, both form factors and structure factors.
120      - Support P(Q)*S(Q) for form factors that flag they can be so multiplied.
121      - Supports Gaussian, lognormal, Shulz, rectangular and custom distribution
122        functions for models that need to include polydispersity or for orientational
123        distributions if appropriate.
124      - Anisotropic shapes and magnetic moment modeling in 2D allow for a non-uniform
125        distribution of orientations of a given axis leading to modeling and fitting
126        capabilities of non azimuthaly symmetric data. 
127      - User can choose to weight fits or not. If using weights, the user can choose
128        the error bar on each point if provided in the file, the square root
129        of the intensity or the intensity itself.
130      - Instrumental resolution smearing of model or fits is provided with several
131        options: read the resolution/point fromt he file. Input a pinhole resolution
132        or a slit resolution.
133      - Users can define the Qrange (Qmin and Qmax) for both 1D and 2D data for
134        fitting and modeling, but not graphically.  The range can be reset to the
135        defaults (limits of q in data set for a fit) with the reset button.
136      - A mask can be applied to 2D calculation and fitting.
137      - Normalized residual plots are provided with every fit.
138      - Model function help available through detail button or from the fitting panel.
139      - Simultaneous/(advanced)constrained fitting allows for fitting a single
140        data set or several different sets simultaneously with the application
141        of advanced constraints relating fit parameters to functions of other
142        parameters (including from a different set). For example thickness of
143        shell = sin(30) times the length. 
144      - Models that are the sum of two other models can be easily generated through the
145        SUM Model menubar item.
146      - New Python models can be added on the fly by creating an appropriate Python
147        file in the model plugin directory. Two tools are provided to help:
148        An easy to use custom model editor allows the quick generation of new Python
149        models by supplying only the parameters and their default value (box 1)
150        and the mathematical function of the model (box 2) and generating the
151        necessary *.py file.  A separate advanced model editor provides a full Python
152        file editor.  Either way once saved the model becomes immediately available
153        to the application.
154      - A batch fittng capability allows for the analysis of a series of data sets to
155        a sinble model and provides the results in a tabular form suitable for saving
156        or plotting the evolution of the fit parameters with error bars (from within
157        the application).
158 
159    - Tools
160      - A scattering length density calculator,including some X-ray information
161        is provided.
162      - A density to vol. fraction converter is provided
163      - In application access to a Python shell/editor (PyCrust) is provided
164      - An instrument resolution calculator, including possible gravitational and
165        TOF effects is provided
166      - A slit size calculator optimized for Anton Paar Saxess is provided.
167      - A kiessig fringe thickness calculator is provided
168    - Plots and plot management
169      - A 3D graphing option (for 2d data/results) is provided with the view
170        controlled by the mouse
171      - 2D plots are shown with an intensity color bar. 2D Color map can be user
172        adjusted.
173      - Supports output of plot to a variety of graphic formats. Supported formats
174        include: png, eps, emf, jpg/jpeg, pdf, ps, tif/tiff, rawRGBbitmap(raw, rgba),
175        and scalable vector graphic (svg/svgz)
176      - Supports ouput of data in plot (1 or 2D) to limited data formats
177      - Multiple data sets can be loaded into a single graph for viewing (but a fit
178        plot can currently only have a single plot).
179      - Extensive context sensitive plot/fitting/manipulation options are available
180        through a right mouse click pop-up menu on plots. 
181    - Data management
182      - Supports 2 + column 1D ASCII data, NIST 1D and 2D data, and canSAS data
183        via plug-in mechanism which can easily allow other readers as appropriate.
184      - 2D data is expected in Q space but for historical reasons accepts the
185        NIST 2D raw pixel format and will do conversion internally.
186      - The full data and metadata available to SasView is viewable in ASCII via
187        right clicking on a data set and choosing Data Info in the DataExplorer
188        or on the plots
189      - Supports loading a single file, multiple files, or a whole folder   
190      - An optional Data Explorer is provided (default) which simplifies managing,
191        plotting, deleting, or setup for computation. Most functions however do
192        not require access to the explorer/manager and can be accessed through
193        right click menus and the toolbar.  The data explorer can be re-started
194        from the menu bar.
195    - Data manipulation
196      - Support various 2D averaging methods : Circular, sectors, annular,
197        boxsum, boxQx and boxQy.
198      - A 2D data maks editor is provided
199      - 2D mask can be applied to the circular averaging.
200    - Miscellaneous features
201      - limited reports can be generated in pdf format
202      - Provides multiprocessor support(Windows only)
203      - Limited startup customization currently includes default startup
204        data folder and choice of default starting with data manager
205      - Limited support for saving(opening) a SasView project or a SasView analysis
206        (subproject) is provided.
207      - SasView can be launched and loaded with a file of interesty by double-clicking
208        on that file (recognized extension)
209      - A data file or data folder can be passed to SasView when launched from
210        the command line.
211      - Limited bookmarking capability to later recall the results of a fit calculation
212        is provided.
213      - Extensive help is provided through context sensitive mouse roll-over,
214        information bar (at the bottom of the panel), the console menu, and
215        access to the help files in several different ways.
216
217
218
2192- Downloading and Installing
220       
221    *** Note 1:  Much more information is available at www.sasview.org under links.
222                     Look in the 'For Developers' section and particularly the wiki at
223                     www.sasview.org/trac/wiki.
224    *** Note 2:  If you have EXE or ZIP SasView installer, you won't need any of
225                 the following.  However it is highly recommended that any
226                 previous versions be un-installed prior to installing the
227                 new version.
228
229    2.1- System Requirements:
230        - Python version >= 2.5 and < 3.0 should be running on the system
231        - We currently use Python 2.7
232
233    2.2- Installing from source:
234        - Get the code from GitHub at https://github.com/SasView/sasview.git
235          for this release version use: https://github.com/SasView/sasview/releases
236            - run 'python setup.py install' under the 'sasview-x.x.x' folder
237            - run 'python sasview.py' under the 'sasview' folder.
238        - The following modules are required (version numbers are what are used
239          in the windows release build):
240        - Common Packages
241          - reportlab 3.1.44
242          - lxml 3.4.4.0 (MAC 3.4.2.0)
243          - PIL 1.1.7
244          - xhtml2pdf 3.0.33 (MAC = not installed on build server)
245          - unittest-xml-reporting 1.12.0 (MAC 1.10.0)
246          - matplotlib Version Installed: 1.4.3 (MAC 1.1.1)
247          - bumps Version Installed: 0.7.5.6
248          - scipy Version Installed: 0.16.0b2 (MAC 0.11.0)
249          - periodictable Version Installed: 1.4.1
250          - setuptools Version Installed: 7.0 (MAC 12.0.5)
251          - sphinx Version Installed: 1.3.1 (MAC 1.3b2)
252          - pyparsing Version Installed: 2.0.3
253          - numpy Version Installed: 1.9.2 (MAC 1.6.2)
254          - html5lib Version Installed: 0.99999
255          - wx Version Installed: 3.0.2.0
256         
257
258        - Windows Specific Packages:
259          - pywin 219
260          - py2exe 0.6.9
261          - comtypes 1.1.1
262          - MinGW w/ gcc version 4.6.1 (WIN)
263          - vcredist_x86.exe (version 9.0.21022.8  -microsoft visual C 2008
264              re-distributable)
265          - Innosetup (WIN - isetup 5.4.2-unicode) - used to create distributable
266           
267        - MAC Specifci Packages:
268          - py2app 0.7.1
269        - Windows build dependencies can be set up using anaconda. Instructions
270          can be found at http://trac.sasview.org/wiki/AnacondaSetup
271
272
2733- Known Issues
274
275    3.1- All systems:
276        - Documentation Window may take a few seconds to load the first time
277          it i called.  Also, an internet connection is required before
278          equations will render properly. Until then they will show in their
279          original TeX format.
280        - The copy and paste functions (^C, ^V) in the batch mode results grid
281          require two clicks: one to select the cell and a second to select the
282          contents of the cell.
283        - Tutorial has not yet been updated and is somewhat out of date
284        - Very old computers may not be able to run
285        - Polydispersity on multiple parameters included in a simultaneous/
286          constrained fit will likely not be correct
287        - Constrained/simultaneous fit page does not have a stop button
288        - Constrained/simultaneous fit do not accept min/max limits
289        - Save project does not store the state of all the windows
290        - Loading projects can be very slow
291        - Save Project only works once a data set has been associated with
292          a model.  Error is reported on status bar.
293        - There is a numerical precision problem with the multishell model when
294          the iner radius gets large enough (ticket #288)
295        - The angular distribution angles are not clearly defined and may in
296          some cases lead to incorrect calculations(ticket #332)
297         
298
299    3.2- Windows:
300        - If installed to same directory as old version without first removing
301          the old version, the old desktop icon will remain but point to the
302          new exe version. Likewise all the start menu folders and items will
303          have the old name even though pointing to the new version.  Usually
304          safest to uninstall old version prior to installing new version anyway.
305               
306    3.3- MAC:
307        - Application normally starts up hidden. Click icon in Dock to view/use
308          application.
309        - multiprocessing does not currently work on MAC OS
310               
311    3.4- Linux:
312        - Not well tested
313
3144- SasView website
315
316    - www.sasview.org.  This main project site is the gateway to all
317      information about the sasview project.  It includes information
318      about the project, a FAQ page and links to all developer and user
319      information, tools and resources.
320
3215- Frequently Asked Questions
322
323    - www.sasview.org/faq.html
324
3256- Installer download website
326
327    - Latest release Version
328        - https://github.com/SasView/sasview/releases
329    - Latest developer builds
330        - https://jenkins.esss.dk/sasview/view/Master-Builds/
331
332   
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