Changeset 786685e in sasview for sansview


Ignore:
Timestamp:
May 15, 2014 7:08:38 PM (11 years ago)
Author:
pkienzle
Branches:
master, ESS_GUI, ESS_GUI_Docs, ESS_GUI_batch_fitting, ESS_GUI_bumps_abstraction, ESS_GUI_iss1116, ESS_GUI_iss879, ESS_GUI_iss959, ESS_GUI_opencl, ESS_GUI_ordering, ESS_GUI_sync_sascalc, costrafo411, magnetic_scatt, release-4.1.1, release-4.1.2, release-4.2.2, release_4.0.1, ticket-1009, ticket-1094-headless, ticket-1242-2d-resolution, ticket-1243, ticket-1249, ticket885, unittest-saveload
Children:
4a0dc427
Parents:
4e9f227 (diff), bb1b892 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.
Message:

merge from trunk

Location:
sansview
Files:
3 edited

Legend:

Unmodified
Added
Removed

  • sansview/README.txt

    r10be315 r7a67f4da  
    44SasView 3.0.0 
    55 
    6     - Implemented Polarization and magnetic SANS parameters in some models. 
    7     - New Tool: Generic SANS / PDB reader & atomic scattering calculator 
    8     - New Tool: Image viewer 
     6    - The GUI look and feel has been refactored to be more familiar for Windows 
     7      users by using MDI frames. Graph windows are also now free-floating 
     8    - Four new models have been added: CoreShellEllipsoidXTModel, 
     9      RectangularPrismModel, RectangularHollowPrismModel and  
     10      RectangularHollowPrismInfThinWallsModel 
     11    - The data loader now supports ILL DAT data files and reads the full meta  
     12      information from canSAS file formats 
    913    - Redefined angles of angular parameters for anisotropic models 
    10     - Use MDI frames in GUI 
    11  
    12         - Previous Versions:  
    13          
    14         - Changed the application name to 'SasView'. 
    15         - Model category can be modified via (Category Manager). 
    16         - Improved Grid/Batch window functionality. 
    17         - Added a new tool; Data operation for addition, subtraction, multiplication, division, and combination of two data sets. 
    18         - Extended Sum Model Editor to Summation and Multiplication Editor. 
    19         - Better compiling error captures in the 'New' model editor. 
    20         - More outputs (e.g., Rg, background, or rod diameter) on LinearFit in certain axis scales. 
    21         - Added DataInfo for data in the DataExplorer and plots 
    22         - Added Maximize/Restore button in the title bar of the graphs 
    23         - The 'x' button now works as deleting the graph 
    24         - Added a hide button in the toolbar of the graph panel 
    25         - Fixed some bugs and improved some behaviors in the batch/grid panel. 
    26         - Edit SUM Model from the menubar can now generate more than one sum model. 
    27         - Report can now be saved as a pdf format on WIN and MAC. 
    28         - Multiprocessor support(Windows) 
    29         - Simple custom model editor 
    30         - Advanced model editor 
    31         - Sum model editing panel  
    32         - 3D graphic (for 2d data/results) and legend moves with mouse 
    33         - New Tool: density to vol fraction calculator and Python file editor 
    34         - Batch Fit included. 
    35         - More Graph modifications. 
    36         - More options for the fit weighting. 
    37         - Added a Python (PyCrust) shell in the 'Tool' menu. 
    38         - The 'Startup Setting' in the View menu can remember the last data file folder. 
    39         - Updated the resolution computation for the gravitational effect and added TOF estimation  capability. 
    40         - Fixed the problem of displaying the fit results in the wrong parameter (with ParkMC FitEngine). 
    41         - Pr Inversion: Fixed a missing Rg output 
    42         - Startup Setting: fixed a problem with DataExplorer ON/OFF 
    43         - Fixed a bug w/ 2D color map dialog 
    44         - Minor feature added: Enable to load a data folder from the command line        
    45         - Much easier graphical user interface 
    46         - Optimized for the speed and accuracy of the computations 
    47         - Added Many shape, polymer, and other models including SphericalSLD, OnionExponetialShell, and even ReflectivityModels 
    48         - Added Data Explorer to manage, plot, delete, or setup for computation 
    49         - Added Instrumental resolution estimator (as a Tool) 
    50         - Customizable Startup appearance 
    51         - More functionalities on plot panels 
    52         - Combined Modeling and Fitting 
    53         - Save/open a SasView project or SasView analysis (subproject) 
    54         - Start the SasView application from a data file by double-clicking or from command line 
    55         - Easy manipulation of data and plot 
    56         - Provides Normalized residual plot 
    57         - Added useful key-combinations to copy (fitpage), paste (fitpage), change fit-tolerance, etc. 
    58         - Report 
    59         - 2D masked circular averaging 
    60         - 2D smearing calculation now uses dQ_parrellel and dQ_perpendicular 
    61         - Improved the speed of loading 2D data. 
    62         - Improved the speed of P*S calculations. 
    63         - Added 2D smearing calculation for dQx and dQy given along the x-y axes. 
    64         - MAC release 
    65         - Implemented the invariant, volume fraction, and specific surface area computation. 
    66         - Implemented the scattering length density calculator. 
    67         - Re-structured 2D calculation to 2D reduced(Q) data rather than raw pixel data 
    68         - Capable of Mask enhanced 2D calculation and fitting. 
    69         - Added a 2D mask data editor. 
    70         - Added inputs for the slit and pinhole resolution. 
    71         - Added a slit size calculator. 
    72         - Support more format options to save a graph. 
    73         - Enable to display multiple data sets in one graph by loading a data into the graph. 
    74         - Added a tool bar in a plot panel. 
    75         - Implemented P(r) inversion (Indirect Fourier transformations). 
    76         - Improved fitting and model calculation speed by a factor of ten. 
    77         - Supporting many more model functions. 
    78         - Supporting P(Q)*S(Q) for most of the shape based form factors. 
    79         - Added more distribution functions for the polydispersion calculations. 
    80         - Added a bookmark feature so that the results of the calculation can be recalled later. 
    81         - Q range reset button is added. 
    82         - Added a color bar in 2D data plots. 
    83         - Added a model function detail button for an easy access to the model help from the fitting panel. 
    84         - Simultaneous fit of a number of different sets of data with/without the constraints.  
    85         - Loading and displaying 1D and 2D data of various formats. 
    86         - 1D and 2D data fitting using Scipy or Park (a MC fitting optimizer) fit engine.  
    87         - 2D data manipulation and modeling.  
    88         - Supporting a number of standard model and model-independent functions including form factor and structure factor functions and their multiplications.   
    89         - Plug-in mechanism for data readers.  
    90         - Easy pop-up menu by mouse clicking on a given plot.  
    91         - Users arrange the various windows.  
    92         - Supporting varius 2D averaging methods : Circular, sectorslicer, annulus, boxsum, boxQx and boxQy.   
    93         - User defined Qrange (Qmin and Qmax) for both 1D and 2D data for fitting and modeling.   
    94         - The user can toggle between a number of different scales on all plots. 
    95         - Support saving data in the formats of ASCII and xml. 
     14    - A number of minor features have been added such as permitting a log  
     15      distribution of points when using a model to simulate data, and the  
     16      addition of a Kratky plot option to the linear plots 
     17    - a number of bugs have also been fixed       
     18    - BETA: Magnetic contrast supporting full polarization analysis has been  
     19            implemented for some spherical and cylindrical models 
     20    - BETA: Two new tools have been added: 
     21            * A generic scattering calculator which takes an atomic, magnetic or  
     22              SLD distribution in space and generates the appropriate 2D  
     23              scattering pattern. In some cases the orientationally averaged  
     24              (powder) 1D scattering can also be computed. Supported formats  
     25              include: SLD or text, PDB, and OMF magnetic moment distribution  
     26              file. 
     27            * An image viewer/converter for data in image format; this reads in  
     28              an image file and will attempt to convert the image pixels to  
     29              data. Supported formats include: TIFF, TIF, PNG, BMP, JPG 
     30 
     31    - New in Version 2.2.1 
     32      - Minor patch to support CanSAS XML v1.1 file format 
     33 
     34    - New in Version 2.2.0 
     35      - Application name changed to SasView 
     36      - New fully customizable Category Manager added for better management of 
     37        increasing number of models 
     38      - Improved the Grid Window functionality in the batch fitting mode 
     39      - Added a simpler Graph/Plot modification interface 
     40      - Added a new 'Data Operation' tool for addition, subtraction, multiplication, 
     41        division, of two data sets. 
     42      - The 'Sum Model' editor was extended and renamed 'Summation and Multiplication' 
     43        editor 
     44      - Added more plot symbols options for 1d plots 
     45      - Added improved trapping of compiling errors to the 'New model editor' 
     46      - 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 
     47      - Added more models 
     48 
     49    - Feature set from Previous Versions:        
     50     
     51    - Perspectives Available 
     52      - Invariant calculator: Calculates the invariant, volume fraction, and 
     53        specific surface area. 
     54      - P(r) inversion calculator: Indirect Fourier transformation method. 
     55      - Fitting: the tool used for modeling and fitting 1D and 2D data to  
     56        analytical model functions 
     57      - Tools: provides a number of useful supplementary tools such as SLD 
     58        calculation   
     59     
     60    - Fitting  
     61      - Includes a large number of model functions, both form factors and structure factors. 
     62      - Support P(Q)*S(Q) for form factors that flag they can be so multiplied. 
     63      - Supports Gaussian, lognormal, Shulz, rectangular and custom distribution 
     64        functions for models that need to include polydispersity or for orientational 
     65        distributions if appropriate. 
     66      - Anisotropic shapes and magnetic moment modeling in 2D allow for a non-uniform 
     67        distribution of orientations of a given axis leading to modeling and fitting 
     68        capabilities of non azimuthaly symmetric data.   
     69      - User can choose to weight fits or not. If using weights, the user can choose 
     70        the error bar on each point if provided in the file, the square root 
     71        of the intensity or the intensity itself.  
     72      - Instrumental resolution smearing of model or fits is provided with several 
     73        options: read the resolution/point fromt he file. Input a pinhole resolution 
     74        or a slit resolution. 
     75      - Users can define the Qrange (Qmin and Qmax) for both 1D and 2D data for 
     76        fitting and modeling, but not graphically.  The range can be reset to the 
     77        defaults (limits of q in data set for a fit) with the reset button. 
     78      - A mask can be applied to 2D calculation and fitting. 
     79      - Normalized residual plots are provided with every fit. 
     80      - Model function help available through detail button or from the fitting panel. 
     81      - Simultaneous/(advanced)constrained fitting allows for fitting a single 
     82        data set or several different sets simultaneously with the application 
     83        of advanced constraints relating fit parameters to functions of other 
     84        parameters (including from a different set). For example thickness of  
     85        shell = sin(30) times the length.   
     86      - Models that are the sum of two other models can be easily generated through the 
     87        SUM Model menubar item. 
     88      - New Python models can be added on the fly by creating an appropriate Python 
     89        file in the model plugin directory. Two tools are provided to help: 
     90        An easy to use custom model editor allows the quick generation of new Python 
     91        models by supplying only the parameters and their default value (box 1) 
     92        and the mathematical function of the model (box 2) and generating the 
     93        necessary *.py file.  A separate advanced model editor provides a full Python 
     94        file editor.  Either way once saved the model becomes immediately available  
     95        to the application.  
     96      - A batch fittng capability allows for the analysis of a series of data sets to 
     97        a sinble model and provides the results in a tabular form suitable for saving 
     98        or plotting the evolution of the fit parameters with error bars (from within 
     99        the application). 
     100  
     101    - Tools 
     102      - A scattering length density calculator,including some X-ray information 
     103        is provided. 
     104      - A density to vol. fraction converter is provided 
     105      - In application access to a Python shell/editor (PyCrust) is provided 
     106      - An instrument resolution calculator, including possible gravitational and 
     107        TOF effects is provided 
     108      - A slit size calculator optimized for Anton Paar Saxess is provided. 
     109      - A kiessig fringe thickness calculator is provided 
     110    - Plots and plot management 
     111      - A 3D graphing option (for 2d data/results) is provided with the view 
     112        controlled by the mouse 
     113      - 2D plots are shown with an intensity color bar. 2D Color map can be user 
     114        adjusted. 
     115      - Supports output of plot to a variety of graphic formats. Supported formats 
     116        include: png, eps, emf, jpg/jpeg, pdf, ps, tif/tiff, rawRGBbitmap(raw, rgba), 
     117        and scalable vector graphic (svg/svgz) 
     118      - Supports ouput of data in plot (1 or 2D) to limited data formats 
     119      - Multiple data sets can be loaded into a single graph for viewing (but a fit 
     120        plot can currently only have a single plot). 
     121      - Extensive context sensitive plot/fitting/manipulation options are available 
     122        through a right mouse click pop-up menu on plots.   
     123    - Data management 
     124      - Supports 2 + column 1D ASCII data, NIST 1D and 2D data, and canSAS data 
     125        via plug-in mechanism which can easily allow other readers as appropriate.  
     126      - 2D data is expected in Q space but for historical reasons accepts the 
     127        NIST 2D raw pixel format and will do conversion internally. 
     128      - The full data and metadata available to SasView is viewable in ASCII via 
     129        right clicking on a data set and choosing Data Info in the DataExplorer 
     130        or on the plots 
     131      - Supports loading a single file, multiple files, or a whole folder    
     132      - An optional Data Explorer is provided (default) which simplifies managing, 
     133        plotting, deleting, or setup for computation. Most functions however do 
     134        not require access to the explorer/manager and can be accessed through 
     135        right click menus and the toolbar.  The data explorer can be re-started 
     136        from the menu bar. 
     137    - Data manipulation 
     138      - Support various 2D averaging methods : Circular, sectors, annular, 
     139        boxsum, boxQx and boxQy. 
     140      - A 2D data maks editor is provided 
     141      - 2D mask can be applied to the circular averaging. 
     142    - Miscellaneous features 
     143      - limited reports can be generated in pdf format 
     144      - Provides multiprocessor support(Windows only) 
     145      - Limited startup customization currently includes default startup 
     146        data folder and choice of default starting with data manager 
     147      - Limited support for saving(opening) a SasView project or a SasView analysis 
     148        (subproject) is provided. 
     149      - SasView can be launched and loaded with a file of interesty by double-clicking 
     150        on that file (recognized extension) 
     151      - A data file or data folder can be passed to SasView when launched from 
     152        the command line. 
     153      - Limited bookmarking capability to later recall the results of a fit calculation 
     154        is provided. 
     155      - Extensive help is provided through context sensitive mouse roll-over, 
     156        information bar (at the bottom of the panel), the console menu, and 
     157        access to the help files in several different ways. 
     158 
    96159 
    97160 
    981612- Downloading and Installing 
    99162         
    100         *** Note: If you have EXE or ZIP SasView installer, you don't need any of the following. 
    101          
    102         2.1- System Requirements: 
    103                 - Python version >= 2.5 and < 3.0 should be running on the system 
    104                 - We currently use Python 2.6 
    105  
    106         2.2- Installing from source: 
    107                 - Get the code from https://sasviewproject.svn.sourceforge.net/svnroot/sansviewproject/releases/sasview-x.x.x 
    108                         - run 'python setup.py install' under the 'sasview-x.x.x' folder 
    109                         - run 'python sasview.py' under the 'sasview' folder. 
    110                 - The following modules are required (version numbers are what are used in the release build): 
    111                         - wxPython 2.8.12.1 (NOTE: do NOT use version 2.9) 
    112                         - matplotlib 1.1.0  (NOTE: Mac build is using version 1.0.1) 
    113                         - SciPy 0.10.1 
    114                         - pisa 3.0.27 (NOTE Mac Version uses 3.0.33 BUT -- DO NOT USE ver 3.0.33 on windows: it will not work!) 
    115                         - setuptools 0.6c11 
    116  
    117                         (The following three are easily installed using easy_install) 
    118                         - lxml 2.3.0 
    119                         - numpy 1.6.1 (NOTE: Mac build is using version 1.5.1) 
    120                         - periodictable 1.3.0 
    121  
    122                         (The following are additional dependencies for Mac) 
    123                         - py2app 
    124  
    125                         (The following are additional dependencies for Windows) 
    126                         - comtypes 0.6.2 (for PDF support on windows systems) 
    127                         - pywin32 build 217 (to read ms office) 
    128                         - pyPdf 1.13 
    129                         - html5lib 0.95 
    130                         - reportlab 2.5 
    131                         - pyparsing 1.5.5 (required for periodictable and bundling) 
    132                         - PIL 1.1.7 (Python Image Library) 
    133                         - py2exe 0.6.9 (WIN) 
    134                         - svn 
    135                         - MinGW w/ gcc version 4.6.1 (WIN) 
    136                         - Innosetup (WIN). 
    137  
    138                         (On Windows, the following site has all the dependencies nicely packaged) 
    139                         http://www.lfd.uci.edu/~gohlke/pythonlibs/ 
     163        *** Note 1:  Much more information is available at www.sasview.org under links. 
     164                     Look in the 'For Developers' section and particularly the wiki at 
     165                     www.sasview.org/trac/wiki. 
     166    *** Note 2:  If you have EXE or ZIP SasView installer, you won't need any of 
     167                 the following. 
     168 
     169    2.1- System Requirements: 
     170        - Python version >= 2.5 and < 3.0 should be running on the system 
     171        - We currently use Python 2.6 
     172 
     173    2.2- Installing from source: 
     174        - Get the code from sourceforge at https://svn.code.sf.net/p/sasview/code/ 
     175          for trunk end with code/trunk for a this release version end in  
     176          code/releases/sasview-3.0.0 
     177            - run 'python setup.py install' under the 'sasview-x.x.x' folder 
     178            - run 'python sasview.py' under the 'sasview' folder. 
     179        - The following modules are required (version numbers are what are used in the release build): 
     180            - wxPython 2.8.12.1 (NOTE: do NOT use version 2.9) 
     181            - matplotlib 1.1.0 
     182            - SciPy 0.10.1 (NOTE: Mac build uses 0.10.0) 
     183            - pisa 3.0.27 (DO NOT USE ver 3.0.33 on windows: it will not work!) 
     184            - setuptools 0.6c11 
     185 
     186            (The following three are easily installed using easy_install) 
     187            - lxml 2.3.0.0 (NOTE: Mac build uses 3.1.0.0) 
     188            - numpy 1.6.1 (NOTE: Mac build uses version 1.6.2) 
     189            - periodictable 1.3.0 
     190             
     191            (The following are additional dependencies for Mac) 
     192            - py2app 0.7.1 
     193             
     194            (The following are additional dependencies for Windows) 
     195            - comtypes 0.6.2 (for PDF support on windows systems) 
     196            - pywin32 build 217 (to read ms office) 
     197            - html5lib 0.95-dev 
     198            - reportlab 2.5 (NOTE: Mab build uses 2.6 though should not be needed) 
     199            - pyparsing 1.5.5 (required for periodictable and bundling 
     200              NOTE: is ALSO present on Mac Build) 
     201            - PIL 1.1.7 (Python Image Library - NOTE: is also present on Mac build) 
     202            - py2exe 0.6.9 (WIN) 
     203            - vcredist_x86.exe (version 9.0.21022.8  -microsoft visual C 2008  
     204              re-distributable) 
     205            - subversion -1.6.0 (<1.6.1) 
     206            - MinGW w/ gcc version 4.6.1 (WIN) 
     207            - Innosetup (WIN - isetup 5.4.2-unicode). 
     208             
     209            (On Windows, the following site has all the dependencies nicely packaged) 
     210            http://www.lfd.uci.edu/~gohlke/pythonlibs/ 
    140211 
    141212 
    1422133- Known Issues 
    143214 
    144         3.1- All systems: 
    145                 - very old computers may not be able to run  
    146  
    147         3.2- Windows: 
    148                 - None 
     215    3.1- All systems: 
     216        - very old computers may not be able to run 
     217        - polydispersity on multiple parameters included in a simultaneous/ 
     218          constrained fit will likely not be correct 
     219        - Save project does not store the state of all the windows 
     220 
     221    3.2- Windows: 
     222        - None 
    149223                 
    150         3.3- MAC: 
    151                 - None 
     224    3.3- MAC: 
     225        - multiprocessing does not currently work on MAC OS 
    152226                 
    153         3.4- Linux: 
    154                 - None 
    155  
    156 4- Troubleshooting 
    157  
    158         - None 
     227    3.4- Linux: 
     228        - None 
     229 
     2304- SasView website 
     231 
     232    - www.sasview.org.  This main project site is the gateway to all  
     233      information about the sasview project.  It includes information 
     234      about the project, a FAQ page and links to all developer and user 
     235      information, tools and resources. 
    159236 
    1602375- Frequently Asked Questions 
    161238 
    162         - None 
     239    - www.sasview.org/faq.html 
    163240 
    1642416- Installer download website 
    165242 
    166         - http://sourceforge.net/projects/sansviewproject/files/ 
     243    - Latest release Version 
     244        - http://sourceforge.net/projects/sasview/files/ 
     245    - Latest developer Windows or Ubuntu build 
     246        - http://build.sasview.org/ 
     247    - Latest developer Mac OS build 
     248        - http://download.mantidproject.org/jenkins/view/All/job/sasview_snowleopard_32bit/ 
     249 
     250     

  • sansview/sansview.py

    re2271c5 r6fe5100  
    3636PLUGIN_MODEL_DIR = 'plugin_models' 
    3737APP_NAME = 'SasView' 
    38 def run(): 
    39     sys.path.append(os.path.join("..","..","..")) 
    40     from multiprocessing import freeze_support 
    41     freeze_support() 
    42     sasview = SasView() 
    43          
     38 
    4439class SasViewApp(gui_manager.ViewApp): 
    4540    """ 
    … …  
    113108        self.gui.clean_plugin_models(PLUGIN_MODEL_DIR) 
    114109        # Start the main loop 
    115         self.gui.MainLoop()   
    116         
     110        self.gui.MainLoop() 
    117111 
    118112 
    119 if __name__ == "__main__":  
     113def run(): 
    120114    from multiprocessing import freeze_support 
    121115    freeze_support() 
    122     #Process(target=SasView).start() 
    123     sasview = SasView() 
     116    if len(sys.argv) > 1: 
     117        thing_to_run = sys.argv[1] 
     118        sys.argv = sys.argv[1:] 
     119        import runpy 
     120        if os.path.exists(thing_to_run): 
     121            runpy.run_path(thing_to_run) 
     122        else: 
     123            runpy.run_module(thing_to_run) 
     124    else: 
     125        SasView() 
    124126 
    125     
     127if __name__ == "__main__": 
     128    run() 
     129 

  • sansview/setup_exe.py

    r27b7acc r6fe5100  
    319319'reportlab.platypus', 
    320320]) 
     321packages.append('IPython') 
    321322includes = ['site'] 
    322323 
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