Changes in / [4fea1df:cb823f0] in sasview


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  • .gitignore

    rdf332d8 r5dd7499  
    4141 
    4242/docs/sphinx-docs/build 
     43/docs/sphinx-docs/source-temp 
    4344/docs/sphinx-docs/source/dev/api 
    4445/docs/sphinx-docs/source/user/guiframe 
    4546/docs/sphinx-docs/source/user/models 
    4647/docs/sphinx-docs/source/user/perspectives 
     48/docs/sphinx-docs/source/user/sasgui 
     49 
    4750 
    4851# test outputs 

  • .travis.yml

    r58918de red8f27e7  
    1212  system_site_packages: true 
    1313before_install: 
    14   - 'if [ $TRAVIS_PYTHON_VERSION == "2.7" ]; then sudo apt-get update;sudo apt-get install python-numpy python-scipy python-matplotlib libhdf5-serial-dev python-h5py fglrx opencl-headers python-pyopencl; fi' 
     14  - 'if [ $TRAVIS_PYTHON_VERSION == "2.7" ]; then sudo apt-get update;sudo apt-get install python-matplotlib libhdf5-serial-dev python-h5py fglrx opencl-headers python-pyopencl gfortran libblas-dev liblapack-dev libatlas-dev; fi' 
    1515 
    1616install: 

  • build_tools/requirements.txt

    rbe4cb41 r0ff9e1f  
    77reportlab==2.5 
    88lxml==2.3 
    9 PIL==1.1.7 
     9#PIL==1.1.7 
    1010periodictable==1.3.0 
    1111bumps==0.7.5.9 
    12 # numpy==1.6.1 
     12numpy>=1.7.1 
    1313scipy>=0.18.0 
    1414# wx==2.8.12.1 

  • docs/sphinx-docs/build_sphinx.py

    r578a11d r5dd7499  
    3030SASVIEW_DOCS = os.path.join(SASVIEW_BUILD, "doc") 
    3131SASVIEW_TEST = os.path.join(SASVIEW_SRC, "..", "sasview", "test", "media") 
     32SASVIEW_TOC_SOURCE = os.path.join(CURRENT_SCRIPT_DIR, "source") 
    3233 
    3334# Need to slurp in the new sasmodels model definitions to replace the old model_functions.rst 
    … …  
    4243SASMODELS_SOURCE_IMG = os.path.join(CURRENT_SCRIPT_DIR, "..", "..", "..", "sasmodels", "doc", "model", "img") 
    4344SASMODELS_SOURCE_AUTOIMG = os.path.join(CURRENT_SCRIPT_DIR, "..", "..", "..", "sasmodels", "doc", "_build", "html","_images") 
    44 SASMODELS_DEST_PROLOG = os.path.join(CURRENT_SCRIPT_DIR, "source") 
    45 SASMODELS_DEST_REF_MODELS = os.path.join(CURRENT_SCRIPT_DIR, "source", "user") 
    46 SASMODELS_DEST_MODELS = os.path.join(CURRENT_SCRIPT_DIR, "source", "user", "models") 
    47 SASMODELS_DEST_IMG = os.path.join(CURRENT_SCRIPT_DIR,  "source", "user", "model-imgs", "new-models") 
    48 SASMODELS_DEST_MAGIMG = os.path.join(CURRENT_SCRIPT_DIR,  "source", "user", "mag_img") 
    49 SASMODELS_DEST_BUILDIMG = os.path.join(CURRENT_SCRIPT_DIR,  "source", "user", "models", "img") 
     45## Don't do assemble-in-place 
     46## Assemble the docs in a temporary folder 
     47SASMODELS_DEST_PROLOG = os.path.join(CURRENT_SCRIPT_DIR, "source-temp") 
     48SASMODELS_DEST_REF_MODELS = os.path.join(SASMODELS_DEST_PROLOG, "user") 
     49SASMODELS_DEST_MODELS = os.path.join(SASMODELS_DEST_PROLOG, "user", "models") 
     50SASMODELS_DEST_IMG = os.path.join(SASMODELS_DEST_PROLOG, "user", "model-imgs", "new-models") 
     51SASMODELS_DEST_MAGIMG = os.path.join(SASMODELS_DEST_PROLOG, "user", "mag_img") 
     52SASMODELS_DEST_BUILDIMG = os.path.join(SASMODELS_DEST_PROLOG, "user", "models", "img") 
    5053 
    5154#if os.path.exists(SASMODELS_SOURCE_PROLOG): 
    … …  
    6669 
    6770SPHINX_BUILD = os.path.join(CURRENT_SCRIPT_DIR, "build") 
    68 SPHINX_SOURCE = os.path.join(CURRENT_SCRIPT_DIR, "source") 
     71SPHINX_SOURCE = os.path.join(CURRENT_SCRIPT_DIR, "source-temp") 
    6972SPHINX_SOURCE_API = os.path.join(SPHINX_SOURCE, "dev", "api") 
    7073SPHINX_SOURCE_GUIFRAME = os.path.join(SPHINX_SOURCE, "user", "sasgui", "guiframe") 
    … …  
    104107    _remove_dir(SASVIEW_DOCS) 
    105108    _remove_dir(SPHINX_BUILD) 
    106     _remove_dir(SPHINX_SOURCE_GUIFRAME) 
    107     _remove_dir(SPHINX_SOURCE_MODELS) 
    108     _remove_dir(SPHINX_SOURCE_PERSPECTIVES) 
    109     _remove_dir(SPHINX_SOURCE_TEST) 
    110  
     109    _remove_dir(SPHINX_SOURCE) 
     110    #_remove_dir(SPHINX_SOURCE_GUIFRAME) 
     111    #_remove_dir(SPHINX_SOURCE_MODELS) 
     112    #_remove_dir(SPHINX_SOURCE_PERSPECTIVES) 
     113    #_remove_dir(SPHINX_SOURCE_TEST) 
     114 
     115def setup_source_temp(): 
     116    """ 
     117    Copy the source toctrees to new folder for assembling the sphinx-docs 
     118    """ 
     119    print "=== Copying Source toctrees ===" 
     120    if os.path.exists(SASVIEW_TOC_SOURCE): 
     121       print "Found docs folder at ", SASVIEW_TOC_SOURCE 
     122       shutil.copytree(SASVIEW_TOC_SOURCE, SPHINX_SOURCE) 
    111123 
    112124def retrieve_user_docs(): 
    … …  
    336348def rebuild(): 
    337349    clean() 
     350    setup_source_temp() 
    338351    retrieve_user_docs() 
    339352    retrieve_bumps_docs() 

  • sasview/local_config.py

    rc1fdf84 r06707b6  
    4444'''This work benefited from the use of the SasView application, originally developed under NSF Award  
    4545DMR-0520547. SasView also contains code developed with funding from the EU Horizon 2020 research  
    46 and innovation programme under the SINE2020 project Grant No 654000.''' 
     46and innovation programme under the SINE2020 project Grant No 654000 and by Adam Washington.''' 
    4747 
    4848_acknowledgement =  \ 
    4949'''This work was originally developed as part of the DANSE project funded by the US NSF under Award DMR-0520547, but is currently maintained by a  
    5050collaboration between UTK, UMD, NIST, ORNL, ISIS, ESS, ILL and ANSTO. SasView also contains code developed with funding from the EU Horizon 2020  
    51 research and innovation programme under the SINE2020 project (Grant No 654000).''' 
     51research and innovation programme under the SINE2020 project (Grant No 654000) and by Adam Washington (corfunc-py).''' 
    5252 
    5353_homepage = "http://www.sasview.org" 

  • sasview/test/media/testdata_help.rst

    ra32aa3e rda456fb  
    77sub-folder in your SasView installation folder. 
    88 
    9 The data sets are organized based on their data structure; 1D data, 2D data,  
    10 SASVIEW saved states, and data in formats that are not yet implemented but  
    11 which are in the works for future versions. 
     9The test data sets are organized based on their data structure: 
    1210 
    13 1D data sets have at least two columns of data with Intensity (assumed  
    14 absolute units) on the Y-axis and Q on the X-axis.  
    15  
    16 2D data sets are data sets that give the deduced intensity for each detector  
    17 pixel. Depending on the file extension, uncertainty and meta data may also be  
    18 available. 
    19  
    20 Saved states are projects and analyses saved by the SasView program. A single  
    21 analysis file contains the data and parameters for a single fit (.fit), p(r)  
    22 inversion (.pr), or invariant calculation (.inv). A project file (.svs) contains  
    23 the results for every active analysis. 
    24  
    25 Some of the available test data is described below. 
     11- *1D data* 
     12- *2D data* 
     13- *coordinate data* 
     14- *image data* 
     15- *SESANS data* 
     16- *save states* 
     17- *upcoming formats* 
    2618 
    2719.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    2820 
     211D Data 
     22^^^^^^^ 
     231D data sets EITHER have: 
     24 
     25- at least two columns of data with I(Q) (assumed to be in absolute units) on the y-axis and Q on the x-axis. And additional columns of data may carry uncertainty data, resolution data, or other metadata. 
     26 
     27OR: 
     28 
     29- the I(Q) and Q data in separate files *with no other information*. 
     30 
     31Data in the latter format need to be converted to a single file format with the :ref:`File_Converter_Tool` before they can be analysed in SasView. 
     32 
    29331D Test Data 
    30 ^^^^^^^^^^^^ 
     34............ 
     3533837rear_1D_1.75_16.5 
     36  - Data from a magnetically-oriented surfactant liquid crystal output by the Mantid framework. The data was collected on the SANS2D instrument at ISIS. 
    3137 
     3810wtAOT_Reline_120_reduced / Anton-Paar_PDH / saxsess_example 
     39  - Data from Anton-Paar SAXSess instruments saved in Otto Glatter's PDH format. 
     40   
    3241AOT_Microemulsion 
    3342  - Aerosol-OT surfactant stabilised oil-in-water microemulsion data at three  
    … …  
    3544    (surfactant layer). 
    3645  - Suitable for testing simultaneous fitting. 
    37    
     46 
     47APS_DND-CAT 
     48  - ASCII data from the DND-CAT beamline at the APS. 
     49 
     50APS_X / APS_Y 
     51  - ASCII data output by a reduction software package at the APS. 
     52  - Suitable for testing the :ref:`File_Converter_Tool` . 
     53 
     54FIT2D_I / FIT2D_Q 
     55  - ASCII data output by the FIT2D software package at the ESRF. 
     56  - Suitable for testing the :ref:`File_Converter_Tool` . 
     57 
    3858hSDS_D2O 
    3959  - h25-sodium dodecyl sulphate solutions at two concentrations: 0.5wt% (just  
    … …  
    4262  - Suitable for testing charged S(Q) models. 
    4363 
    44 P123_D2O 
    45   - Lyotropic liquid crystalline solutions of non-ionic ABA block copolymer  
    46     Pluronic P123 in water at three concentrations: 10wt%, 30wt%, and 40wt%. 
    47   - Suitable for testing paracrystal models. 
     64ISIS_83404 / ISIS_98929 
     65  - Polyamide-6 fibres hydrated in D2O exhibiting a broad lamellar peak from the semi-crystalline nanostructure. 
     66  - This is the *same data* as that in Z8300* / Z9800* but in an amalgamated ASCII format! 
     67  - Suitable for testing :ref:`Correlation_Function_Analysis` . 
    4868 
    4969ISIS_Polymer_Blend_TK49 
    … …  
    5272  - Suitable for testing Poly_GaussCoil and RPA10 models. 
    5373 
     74P123_D2O 
     75  - Lyotropic liquid crystalline solutions of non-ionic ABA block copolymer  
     76    Pluronic P123 in water at three concentrations: 10wt%, 30wt%, and 40wt%. 
     77  - Suitable for testing paracrystal models. 
     78 
     79Z8300*.I1D / Z8300*.QAX / Z9800*.I1D / Z9800*.QAX 
     80  - BSL/OTOKO data from polyamide-6 fibres hydrated in D2O exhibiting a broad lamellar peak from the semi-crystalline nanostructure. 
     81  - This is the *same data* as that in ISIS_83404 / ISIS_98929 but in an older separated format! 
     82  - Suitable for testing the :ref:`File_Converter_Tool` . 
     83  - Suitable for testing :ref:`Correlation_Function_Analysis` . 
     84 
    5485.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    5586 
     872D Data 
     88^^^^^^^ 
     892D data sets are data sets that give the reduced intensity for each Qx-Qy bin. Depending on the file format, uncertainty data and metadata may also be available. 
     90 
    56912D Test Data 
    57 ^^^^^^^^^^^^ 
     92............ 
     9333837rear_2D_1.75_16.5 
     94  - Data from a magnetically-oriented surfactant liquid crystal output by the Mantid framework. The data was collected on the SANS2D instrument at ISIS. 
    5895 
    5996P123_D2O 
    … …  
    64101.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    65102 
     103Coordinate Data 
     104^^^^^^^^^^^^^^^ 
     105Coordinate data sets, such as PDB or OMF files, and which describe a specific structure, are designed to be read and viewed in the :ref:`SANS_Calculator_Tool` . 
     106 
     107Coordinate Test Data 
     108.................... 
     109A_Raw_Example-1 
     110  - OMF format data file from a simulation of magnetic spheres. 
     111 
     112diamond 
     113  - PDB format data file for diamond. 
     114 
     115dna 
     116  - PDB format data file for DNA. 
     117 
     118sld_file 
     119  - Example SLD format data file. 
     120 
     121.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
     122 
     123Image Data 
     124^^^^^^^^^^ 
     125Image data sets are designed to be read by the :ref:`Image_Viewer_Tool` . They can be converted into synthetic 2D data. 
     126 
     127Image Test Data 
     128............... 
     129ISIS_98940 
     130  - Polyamide-6 fibres hydrated in D2O exhibiting a broad lamellar peak from the semi-crystalline nanostructure. 
     131  - Data is presented in Windows Bitmap (BMP), GIF, JPEG (JPG), PNG, and TIFF (TIF) formats. 
     132 
     133.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
     134 
     135SESANS Data 
     136^^^^^^^^^^^ 
     137SESANS (Spin-Echo SANS) data sets primarily contain the neutron polarisation as a function of the spin-echo length. Also see :ref:`SESANS` . 
     138 
     139SESANS Test Data 
     140................ 
     141spheres2micron 
     142  - SESANS data from 2 micron polystyrene spheres in 53% H2O / 47% D2O. 
     143 
     144.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
     145 
     146Save States 
     147^^^^^^^^^^^ 
     148Saved states are projects and analyses saved by the SasView program. A single  
     149analysis file contains the data and parameters for a single fit (.fit), p(r)  
     150inversion (.prv), or invariant calculation (.inv). A project file (.svs) contains  
     151the results for every active analysis in a SasView session. 
     152 
    66153Saved State Test Data 
    67 ^^^^^^^^^^^^^^^^^^^^^ 
     154..................... 
     155fitstate.fitv 
     156  - a saved fitting analysis. 
    68157 
    69 _phi_weights.txt 
     158test.inv 
     159  - a saved invariant analysis. 
    70160 
    71 _radius_dist.txt 
     161test002.inv 
     162  - a saved invariant analysis. 
    72163 
    73 _THETA_weights.txt 
    74  
    75 fitstate.fitv 
     164prstate.prv 
     165  - a saved P(r) analysis. 
    76166 
    77167newone.svs 
     168  - a saved SasView project. 
    78169 
    79 prstate.prv 
     170.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    80171 
    81 sld_file.sld 
    82  
    83 test.inv 
    84  
    85 test002.inv 
     172Upcoming Formats 
     173^^^^^^^^^^^^^^^^ 
     174Data in this folder are in formats that are not yet implemented in SasView but which might be in future versions of the program. 
    86175 
    87176.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    … …  
    89178Other Test Data 
    90179^^^^^^^^^^^^^^^ 
     180phi_weights.txt 
    91181 
    92 1000A_sphere_sm.xml 
     182radius_dist.txt 
    93183 
    94 diamond.pdb 
    95  
    96 dna.pdb 
     184THETA_weights.txt 
    97185 
    98186.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    99187 
    100 .. note::  This help document was last changed by Steve King, 26Jun2015 
     188.. note::  This help document was last changed by Steve King, 06Oct2016 

  • src/sas/sasgui/perspectives/calculator/media/image_viewer_help.rst

    rd85c194 rda456fb  
    33.. This is a port of the original SasView html help file to ReSTructured text 
    44.. by S King, ISIS, during SasView CodeCamp-III in Feb 2015. 
     5 
     6.. _Image_Viewer_Tool: 
    57 
    68Image Viewer Tool 

  • src/sas/sasgui/perspectives/calculator/media/sas_calculator_help.rst

    r7805458 rda456fb  
    33.. This is a port of the original SasView html help file to ReSTructured text 
    44.. by S King, ISIS, during SasView CodeCamp-III in Feb 2015. 
     5 
     6.. _SANS_Calculator_Tool: 
    57 
    68Generic SANS Calculator Tool 

  • src/sas/sasgui/perspectives/corfunc/media/corfunc_help.rst

    rf56770ef rda456fb  
    11.. corfunc_help.rst 
     2 
     3.. _Correlation_Function_Analysis: 
    24 
    35Correlation Function Analysis 

  • src/sas/sasgui/perspectives/file_converter/media/file_converter_help.rst

    r97e90b7 rda456fb  
    11.. file_converter_help.rst 
     2 
     3.. _File_Converter_Tool: 
    24 
    35File Converter Tool 
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