Changeset c22b621 in sasview


Ignore:
Timestamp:
Sep 28, 2017 6:40:02 PM (8 weeks ago)
Author:
Paul Kienzle <pkienzle@…>
Branches:
master, ESS_GUI, ESS_GUI_Pr, ESS_GUI_corf, ESS_GUI_py2_OLD, SVCC-1, docs, ticket-1032-sldi, ticket-776-orientation, ticket-873, ticket1007, true
Children:
749b715
Parents:
df72475 (diff), 2b538cd (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 branch 'py3' into ticket-947-sasmodels-docs

Files:
55 deleted
22 edited

Legend:

Unmodified
Added
Removed
  • src/sas/sascalc/dataloader/readers/cansas_reader.py

    r9e6aeaf r2b538cd  
    589589            try: 
    590590                unit = attr['unit'] 
     591                # Split the units to retain backwards compatibility with 
     592                # projects, analyses, and saved data from v4.1.0 
    591593                unit_list = unit.split("|") 
    592594                if len(unit_list) > 1: 
    593                     self.current_dataset.xaxis(unit_list[0].strip(), 
    594                                                unit_list[1].strip()) 
    595595                    local_unit = unit_list[1] 
    596596                else: 
     
    12371237            if units is not None: 
    12381238                toks = variable.split('.') 
    1239                 # TODO: why split() when accessing unit, but not when setting value? 
    12401239                local_unit = getattr(storage, toks[0]+"_unit") 
    12411240                if local_unit is not None and units.lower() != local_unit.lower(): 
  • src/sas/sascalc/dataloader/readers/cansas_reader_HDF5.py

    r7b50f14 r2b538cd  
    226226 
    227227                for data_point in data_set: 
    228                     if data_point.dtype.char == 'S': 
    229                         data_point = decode(bytes(data_point)) 
     228                    if isinstance(data_point, np.ndarray): 
     229                        if data_point.dtype.char == 'S': 
     230                            data_point = decode(bytes(data_point)) 
     231                    else: 
     232                        data_point = decode(data_point) 
    230233                    # Top Level Meta Data 
    231234                    if key == u'definition': 
  • docs/sphinx-docs/build_sphinx.py

    r6e546f8 rdf72475  
    1010import subprocess 
    1111import os 
     12from os.path import join as joinpath, abspath, dirname, isdir, exists, relpath 
    1213import sys 
    1314import fnmatch 
     
    2526platform = '.%s-%s'%(get_platform(),sys.version[:3]) 
    2627 
    27 CURRENT_SCRIPT_DIR = os.path.dirname(os.path.abspath(__file__)) 
    28  
    29 run = imp.load_source('run', os.path.join(CURRENT_SCRIPT_DIR, '..', '..', 'run.py')) 
     28# sphinx paths 
     29SPHINX_ROOT = dirname(abspath(__file__)) 
     30SPHINX_BUILD = joinpath(SPHINX_ROOT, "build") 
     31SPHINX_SOURCE = joinpath(SPHINX_ROOT, "source-temp") 
     32SPHINX_PERSPECTIVES = joinpath(SPHINX_SOURCE, "user", "sasgui", "perspectives") 
     33 
     34# sasview paths 
     35SASVIEW_ROOT = joinpath(SPHINX_ROOT, '..', '..') 
     36SASVIEW_DOCS = joinpath(SPHINX_ROOT, "source") 
     37SASVIEW_BUILD = abspath(joinpath(SASVIEW_ROOT, "build", "lib"+platform)) 
     38SASVIEW_MEDIA_SOURCE = joinpath(SASVIEW_ROOT, "src", "sas") 
     39SASVIEW_DOC_TARGET = joinpath(SASVIEW_BUILD, "doc") 
     40SASVIEW_API_TARGET = joinpath(SPHINX_SOURCE, "dev", "sasview-api") 
     41 
     42# sasmodels paths 
     43SASMODELS_ROOT = joinpath(SASVIEW_ROOT, "..", "sasmodels") 
     44SASMODELS_DOCS = joinpath(SASMODELS_ROOT, "doc") 
     45SASMODELS_BUILD = joinpath(SASMODELS_ROOT, "build", "lib") 
     46SASMODELS_MODEL_SOURCE = joinpath(SASMODELS_DOCS, "model") 
     47SASMODELS_MODEL_TARGET = joinpath(SPHINX_SOURCE, "user", "models") 
     48#SASMODELS_API_SOURCE = joinpath(SASMODELS_DOCS, "api") 
     49SASMODELS_API_TARGET = joinpath(SPHINX_SOURCE, "dev", "sasmodels-api") 
     50SASMODELS_DEV_SOURCE = joinpath(SASMODELS_DOCS, "developer") 
     51SASMODELS_DEV_TARGET = joinpath(SPHINX_SOURCE, "dev", "sasmodels-dev") 
     52SASMODELS_GUIDE_SOURCE = joinpath(SASMODELS_DOCS, "guide") 
     53SASMODELS_GUIDE_TARGET = joinpath(SPHINX_PERSPECTIVES, "fitting") 
     54SASMODELS_GUIDE_EXCLUDE = [ 
     55    "index.rst", "install.rst", "intro.rst", 
     56] 
     57 
     58# bumps paths 
     59BUMPS_DOCS = joinpath(SASVIEW_ROOT, "..", "bumps", "doc") 
     60BUMPS_SOURCE = joinpath(BUMPS_DOCS, "guide") 
     61BUMPS_TARGET = joinpath(SPHINX_PERSPECTIVES, "fitting") 
     62 
     63run = imp.load_source('run', joinpath(SASVIEW_ROOT, 'run.py')) 
    3064run.prepare() 
    31  
    32 SASVIEW_SRC = os.path.join(CURRENT_SCRIPT_DIR, "..", "..", "src") 
    33 SASVIEW_BUILD = os.path.abspath(os.path.join(CURRENT_SCRIPT_DIR, "..", "..", "build", "lib"+platform)) 
    34 SASVIEW_DOCS = os.path.join(SASVIEW_BUILD, "doc") 
    35 SASVIEW_TEST = os.path.join(SASVIEW_SRC, "..", "sasview", "test", "media") 
    36 SASVIEW_TOC_SOURCE = os.path.join(CURRENT_SCRIPT_DIR, "source") 
    37  
    38 # Need to slurp in the new sasmodels model definitions to replace the old model_functions.rst 
    39 # We are currently here: 
    40 #/sasview-local-trunk/docs/sphinx-docs/build_sphinx.py 
    41 SASMODELS_SOURCE_PROLOG = os.path.join(CURRENT_SCRIPT_DIR, "..", "..", "..", "sasmodels", "doc") 
    42 SASMODELS_SOURCE_GPU = os.path.join(CURRENT_SCRIPT_DIR, "..", "..", "..", "sasmodels", "doc", "guide", "gpu") 
    43 SASMODELS_SOURCE_SESANS = os.path.join(CURRENT_SCRIPT_DIR, "..", "..", "..", "sasmodels", "doc", "guide", "sesans") 
    44 SASMODELS_SOURCE_SESANSIMG = os.path.join(CURRENT_SCRIPT_DIR, "..", "..", "..", "sasmodels", "doc", "guide", "sesans", "sesans_img") 
    45 SASMODELS_SOURCE_MAGNETISM = os.path.join(CURRENT_SCRIPT_DIR, "..", "..", "..", "sasmodels", "doc", "guide", "magnetism") 
    46 SASMODELS_SOURCE_MAGIMG = os.path.join(CURRENT_SCRIPT_DIR, "..", "..", "..", "sasmodels", "doc", "guide", "magnetism", "mag_img") 
    47 SASMODELS_SOURCE_REF_MODELS = os.path.join(CURRENT_SCRIPT_DIR, "..", "..", "..", "sasmodels", "doc", "guide", "models") 
    48 SASMODELS_SOURCE_MODELS = os.path.join(CURRENT_SCRIPT_DIR, "..", "..", "..", "sasmodels", "doc", "model") 
    49 SASMODELS_SOURCE_IMG = os.path.join(CURRENT_SCRIPT_DIR, "..", "..", "..", "sasmodels", "doc", "model", "img") 
    50 SASMODELS_SOURCE_AUTOIMG = os.path.join(CURRENT_SCRIPT_DIR, "..", "..", "..", "sasmodels", "doc", "_build", "html","_images") 
    51 ## Don't do assemble-in-place 
    52 ## Assemble the docs in a temporary folder 
    53 SASMODELS_DEST_PROLOG = os.path.join(CURRENT_SCRIPT_DIR, "source-temp") 
    54 SASMODELS_DEST_REF_MODELS = os.path.join(SASMODELS_DEST_PROLOG, "user") 
    55 SASMODELS_DEST_MODELS = os.path.join(SASMODELS_DEST_PROLOG, "user", "models") 
    56 SASMODELS_DEST_IMG = os.path.join(SASMODELS_DEST_PROLOG, "user", "model-imgs", "new-models") 
    57 SASMODELS_DEST_MAGIMG = os.path.join(SASMODELS_DEST_PROLOG, "user", "mag_img") 
    58 SASMODELS_DEST_SESANSIMG = os.path.join(SASMODELS_DEST_PROLOG, "user", "sesans_img") 
    59 SASMODELS_DEST_BUILDIMG = os.path.join(SASMODELS_DEST_PROLOG, "user", "models", "img") 
    60  
    61  
    62 SPHINX_BUILD = os.path.join(CURRENT_SCRIPT_DIR, "build") 
    63 SPHINX_SOURCE = os.path.join(CURRENT_SCRIPT_DIR, "source-temp") 
    64 SPHINX_SOURCE_API = os.path.join(SPHINX_SOURCE, "dev", "api") 
    65 SPHINX_SOURCE_GUIFRAME = os.path.join(SPHINX_SOURCE, "user", "sasgui", "guiframe") 
    66 SPHINX_SOURCE_MODELS = os.path.join(SPHINX_SOURCE, "user", "models") 
    67 SPHINX_SOURCE_PERSPECTIVES = os.path.join(SPHINX_SOURCE, "user", "sasgui", "perspectives") 
    68 SPHINX_SOURCE_TEST = os.path.join(SPHINX_SOURCE, "test") 
    69 SPHINX_SOURCE_USER = os.path.join(SPHINX_SOURCE, "user") 
    70  
    71 BUMPS_DOCS = os.path.join(CURRENT_SCRIPT_DIR, "..", "..", "..", 
    72                           "bumps", "doc", "guide") 
    73 BUMPS_TARGET = os.path.join(SPHINX_SOURCE_PERSPECTIVES, "fitting") 
    7465 
    7566def inplace_change(filename, old_string, new_string): 
     
    8879def _remove_dir(dir_path): 
    8980    """Removes the given directory.""" 
    90     if os.path.isdir(dir_path): 
     81    if isdir(dir_path): 
    9182        print("Removing \"%s\"... " % dir_path) 
    9283        shutil.rmtree(dir_path) 
     
    9788    """ 
    9889    print("=== Cleaning Sphinx Build ===") 
    99     _remove_dir(SASVIEW_DOCS) 
     90    _remove_dir(SASVIEW_DOC_TARGET) 
    10091    _remove_dir(SPHINX_BUILD) 
    10192    _remove_dir(SPHINX_SOURCE) 
    102     #_remove_dir(SPHINX_SOURCE_GUIFRAME) 
    103     #_remove_dir(SPHINX_SOURCE_MODELS) 
    104     #_remove_dir(SPHINX_SOURCE_PERSPECTIVES) 
    105     #_remove_dir(SPHINX_SOURCE_TEST) 
    10693 
    10794def setup_source_temp(): 
     
    11097    """ 
    11198    print("=== Copying Source toctrees ===") 
    112     if os.path.exists(SASVIEW_TOC_SOURCE): 
    113        print("Found docs folder at", SASVIEW_TOC_SOURCE) 
    114        shutil.copytree(SASVIEW_TOC_SOURCE, SPHINX_SOURCE) 
     99    shutil.copytree(SASVIEW_DOCS, SPHINX_SOURCE) 
    115100 
    116101def retrieve_user_docs(): 
     
    132117    print("=== Retrieve User Docs ===") 
    133118 
    134     # Copy documentation files from their "source" to their "destination". 
    135     for root, dirnames, _ in os.walk(SASVIEW_SRC): 
    136         for dirname in fnmatch.filter(dirnames, 'media'): 
    137  
    138             docs = os.path.abspath(os.path.join(root, dirname)) 
    139             print("Found docs folder at \"%s\"." % docs) 
    140  
    141             dest_dir_part = os.path.dirname(os.path.relpath(docs, SASVIEW_SRC)) 
    142             if os.sep in dest_dir_part: 
    143                 dest_dir_part = dest_dir_part[dest_dir_part.index(os.sep) + 1:] 
    144             dest_dir = os.path.join(SPHINX_SOURCE, "user", dest_dir_part) 
    145  
    146             copy_tree(docs, dest_dir) 
    147  
    148     # Now pickup testdata_help.rst 
    149     print("=== Including Test Data Docs ===") 
    150     if os.path.exists(SASVIEW_TEST): 
    151        print("Found docs folder at", SASVIEW_TEST) 
    152        shutil.copytree(SASVIEW_TEST, SPHINX_SOURCE_TEST) 
    153  
    154     print("=== And the Sasmodels Docs ===") 
    155     # Make sure we have the relevant images for the new sasmodels documentation 
    156     # First(!) we'll make a local reference copy for SasView (/new-models will be cleaned each build) 
    157     if os.path.exists(SASMODELS_SOURCE_IMG): 
    158         print("Found img folder SASMODELS_SOURCE_IMG at", SASMODELS_SOURCE_IMG) 
    159         if not os.path.exists(SASMODELS_DEST_IMG): 
    160             print("Missing docs folder SASMODELS_DEST_IMG at", SASMODELS_DEST_IMG) 
    161             os.makedirs(SASMODELS_DEST_IMG) 
    162             print("created SASMODELS_DEST_BUILDIMG at", SASMODELS_DEST_BUILDIMG) 
    163         else: 
    164             print("Found img folder SASMODELS_DEST_IMG at", SASMODELS_DEST_IMG) 
    165         print("Copying sasmodels model image files...") 
    166         for files in os.listdir(SASMODELS_SOURCE_IMG): 
    167             fromhere=os.path.join(SASMODELS_SOURCE_IMG,files) 
    168             tohere=os.path.join(SASMODELS_DEST_IMG,files) 
    169             shutil.copy(fromhere,tohere) 
    170     else: 
    171         print("no source directory",SASMODELS_SOURCE_IMG,"was found") 
    172  
    173     if os.path.exists(SASMODELS_SOURCE_AUTOIMG): 
    174         print("Found img folder SASMODELS_SOURCE_AUTOIMG at", SASMODELS_SOURCE_AUTOIMG) 
    175         if not os.path.exists(SASMODELS_DEST_IMG): 
    176             print("Missing docs folder SASMODELS_DEST_IMG at", SASMODELS_DEST_IMG) 
    177             os.makedirs(SASMODELS_DEST_BUILDIMG) 
    178             print("created SASMODELS_DEST_BUILDIMG at", SASMODELS_DEST_BUILDIMG) 
    179         print("Copying sasmodels model auto-generated image files...") 
    180         for files in os.listdir(SASMODELS_SOURCE_AUTOIMG): 
    181             fromhere=os.path.join(SASMODELS_SOURCE_AUTOIMG,files) 
    182             tohere=os.path.join(SASMODELS_DEST_IMG,files) 
    183             shutil.copy(fromhere,tohere) 
    184     else: 
    185         print("no source directory",SASMODELS_SOURCE_AUTOIMG ,"was found") 
    186  
    187     # And the rst prolog with the unit substitutions 
    188     if os.path.exists(SASMODELS_SOURCE_PROLOG): 
    189         print("Found prolog folder SASMODELS_SOURCE_PROLOG at", SASMODELS_SOURCE_PROLOG) 
    190         if os.path.exists(SASMODELS_DEST_PROLOG): 
    191             print("Found docs folder SASMODELS_DEST_PROLOG at", SASMODELS_DEST_PROLOG) 
    192             print("Copying sasmodels rst_prolog file...") 
    193             for files in os.listdir(SASMODELS_SOURCE_PROLOG): 
    194                 if files.startswith("rst"): 
    195                     fromhere=os.path.join(SASMODELS_SOURCE_PROLOG,files) 
    196                     tohere=os.path.join(SASMODELS_DEST_PROLOG,files) 
    197                     shutil.copy(fromhere,tohere) 
    198     else: 
    199         print("no source directory",SASMODELS_SOURCE_PROLOG, "was found") 
    200  
    201     if os.path.exists(SASMODELS_SOURCE_GPU): 
    202         print("Found docs folder SASMODELS_SOURCE_GPU at", SASMODELS_SOURCE_GPU) 
    203         if os.path.exists(SPHINX_SOURCE_USER): 
    204             print("Found docs folder SPHINX_SOURCE_USER at", SPHINX_SOURCE_USER) 
    205             print("Copying sasmodels gpu files...") 
    206             for files in os.listdir(SASMODELS_SOURCE_GPU): 
    207                 if files.endswith(".rst"): 
    208                     fromhere=os.path.join(SASMODELS_SOURCE_GPU,files) 
    209                     tohere=os.path.join(SPHINX_SOURCE_USER,files) 
    210                     shutil.copy(fromhere,tohere) 
    211     else: 
    212         print("no source directory",SASMODELS_SOURCE_GPU,"was found") 
    213  
    214     if os.path.exists(SASMODELS_SOURCE_SESANS): 
    215         print("Found docs folder SASMODELS_SOURCE_SESANS at", SASMODELS_SOURCE_SESANS) 
    216         if os.path.exists(SPHINX_SOURCE_USER): 
    217             print("Found docs folder SPHINX_SOURCE_USER at", SPHINX_SOURCE_USER) 
    218             print("Copying sasmodels sesans files...") 
    219             for files in os.listdir(SASMODELS_SOURCE_SESANS): 
    220                 if files.endswith(".rst"): 
    221                     fromhere=os.path.join(SASMODELS_SOURCE_SESANS,files) 
    222                     tohere=os.path.join(SPHINX_SOURCE_USER,files) 
    223                     shutil.copy(fromhere,tohere) 
    224     else: 
    225         print("no source directory",SASMODELS_SOURCE_SESANS,"was found") 
    226  
    227     if os.path.exists(SASMODELS_SOURCE_MAGNETISM): 
    228         print("Found docs folder SASMODELS_SOURCE_MAGNETISM at", SASMODELS_SOURCE_MAGNETISM) 
    229         if os.path.exists(SASMODELS_DEST_REF_MODELS): 
    230             print("Found docs folder SASMODELS_DEST_REF_MODELS at", SASMODELS_DEST_REF_MODELS) 
    231             print("Copying sasmodels model toctree files...") 
    232             for files in os.listdir(SASMODELS_SOURCE_MAGNETISM): 
    233                 if files.endswith(".rst"): 
    234                     fromhere=os.path.join(SASMODELS_SOURCE_MAGNETISM,files) 
    235                     tohere=os.path.join(SASMODELS_DEST_REF_MODELS,files) 
    236                     shutil.copy(fromhere,tohere) 
    237     else: 
    238         print("no source directory",SASMODELS_SOURCE_MAGNETISM,"was found") 
    239  
    240     if os.path.exists(SASMODELS_SOURCE_MAGIMG): 
    241         print("Found img folder SASMODELS_SOURCE_MAGIMG   at", SASMODELS_SOURCE_MAGIMG) 
    242         if not os.path.exists(SASMODELS_DEST_MAGIMG): 
    243             print("Missing img folder SASMODELS_DEST_MAGIMG at", SASMODELS_DEST_MAGIMG) 
    244             os.makedirs(SASMODELS_DEST_MAGIMG) 
    245             print("created SASMODELS_DEST_MAGIMG at", SASMODELS_DEST_MAGIMG) 
    246         print("Copying sasmodels mag image files...") 
    247         for files in os.listdir(SASMODELS_SOURCE_MAGIMG): 
    248             fromhere=os.path.join(SASMODELS_SOURCE_MAGIMG,files) 
    249             tohere=os.path.join(SASMODELS_DEST_MAGIMG,files) 
    250             shutil.copy(fromhere,tohere) 
    251     else: 
    252         print("no source directory",SASMODELS_SOURCE_MAGIMG ,"was found") 
    253  
    254     if os.path.exists(SASMODELS_SOURCE_SESANSIMG): 
    255         print("Found img folder SASMODELS_SOURCE_SESANSIMG at", SASMODELS_SOURCE_SESANSIMG) 
    256         if not os.path.exists(SASMODELS_DEST_SESANSIMG): 
    257             print("Missing img folder SASMODELS_DEST_SESANSIMG at", SASMODELS_DEST_SESANSIMG) 
    258             os.makedirs(SASMODELS_DEST_SESANSIMG) 
    259             print("created SASMODELS_DEST_SESANSIMG at", SASMODELS_DEST_SESANSIMG) 
    260         print("Copying sasmodels sesans image files...") 
    261         for files in os.listdir(SASMODELS_SOURCE_SESANSIMG): 
    262             fromhere=os.path.join(SASMODELS_SOURCE_SESANSIMG,files) 
    263             tohere=os.path.join(SASMODELS_DEST_SESANSIMG,files) 
    264             shutil.copy(fromhere,tohere) 
    265     else: 
    266         print("no source directory",SASMODELS_SOURCE_SESANSIMG ,"was found") 
    267  
    268     if os.path.exists(SASMODELS_SOURCE_REF_MODELS): 
    269         print("Found docs folder SASMODELS_SOURCE_REF_MODELS at", SASMODELS_SOURCE_REF_MODELS) 
    270         if os.path.exists(SASMODELS_DEST_REF_MODELS): 
    271             print("Found docs folder SASMODELS_DEST_REF_MODELS at", SASMODELS_DEST_REF_MODELS) 
    272             print("Copying sasmodels model toctree files...") 
    273             for files in os.listdir(SASMODELS_SOURCE_REF_MODELS): 
    274                 if files.endswith(".rst"): 
    275                     fromhere=os.path.join(SASMODELS_SOURCE_REF_MODELS,files) 
    276                     tohere=os.path.join(SASMODELS_DEST_REF_MODELS,files) 
    277                     shutil.copy(fromhere,tohere) 
    278             # But need to change the path to the model docs in the tocs 
    279             for files in os.listdir(SASMODELS_DEST_REF_MODELS): 
    280         #        print files 
    281                 if files.startswith("shape"): 
    282                     print("Changing toc paths in", files) 
    283                     inplace_change(os.path.join(SASMODELS_DEST_REF_MODELS,files), "../../model/", "models/") 
    284                 if files.startswith("sphere"): 
    285                     print("Changing toc paths in", files) 
    286                     inplace_change(os.path.join(SASMODELS_DEST_REF_MODELS,files), "../../model/", "models/") 
    287                 if files.startswith("custom"): 
    288                     print("Changing toc paths in", files) 
    289                     inplace_change(os.path.join(SASMODELS_DEST_REF_MODELS,files), "../../model/", "models/") 
    290                 if files.startswith("structure"): 
    291                     print("Changing toc paths in", files) 
    292                     inplace_change(os.path.join(SASMODELS_DEST_REF_MODELS,files), "../../model/", "models/") 
    293     else: 
    294         print("no source directory",SASMODELS_SOURCE_REF_MODELS," was found") 
    295  
    296     if os.path.exists(SASMODELS_SOURCE_MODELS): 
    297         print("Found docs folder SASMODELS_SOURCE_MODELS at", SASMODELS_SOURCE_MODELS) 
    298         if os.path.exists(SASMODELS_DEST_MODELS): 
    299             print("Found docs folder SASMODELS_DEST_MODELS at", SASMODELS_DEST_MODELS) 
    300             print("Copying sasmodels model files...") 
    301             for files in os.listdir(SASMODELS_SOURCE_MODELS): 
    302                 if files.endswith(".rst"): 
    303                     fromhere=os.path.join(SASMODELS_SOURCE_MODELS,files) 
    304                     tohere=os.path.join(SASMODELS_DEST_MODELS,files) 
    305                     shutil.copy(fromhere,tohere) 
    306         else: 
    307             print("Missing docs folder SASMODELS_DEST_MODELS at", SASMODELS_DEST_MODELS) 
    308             os.makedirs(SASMODELS_DEST_MODELS) 
    309             if not os.path.exists(SASMODELS_DEST_BUILDIMG): 
    310                 os.makedirs(SASMODELS_DEST_BUILDIMG) 
    311             print("Created docs folder SASMODELS_DEST_MODELS at", SASMODELS_DEST_MODELS) 
    312             print("Copying model files for build...") 
    313             for files in os.listdir(SASMODELS_SOURCE_MODELS): 
    314                 if files.endswith(".rst"): 
    315                     fromhere=os.path.join(SASMODELS_SOURCE_MODELS,files) 
    316                     tohere=os.path.join(SASMODELS_DEST_MODELS,files) 
    317                     shutil.copy(fromhere,tohere) 
    318             # No choice but to do this because model files are all coded for images in /models/img 
    319             print("Copying image files for build...") 
    320             for files in os.listdir(SASMODELS_DEST_IMG): 
    321                 fromhere=os.path.join(SASMODELS_DEST_IMG,files) 
    322                 tohere=os.path.join(SASMODELS_DEST_BUILDIMG,files) 
    323                 shutil.copy(fromhere,tohere) 
    324     else: 
    325         print("no source directory",SASMODELS_SOURCE_MODELS,"was found.") 
    326         print("!!!!NO MODEL DOCS WILL BE BUILT!!!!") 
     119    # Copy documentation files from sas/.../media to the sphinx directory 
     120    for root, dirs, _ in os.walk(SASVIEW_MEDIA_SOURCE): 
     121        if 'media' in dirs: 
     122            source_dir = abspath(joinpath(root, "media")) 
     123            relative = dirname(relpath(source_dir, SASVIEW_MEDIA_SOURCE)) 
     124            dest_dir = joinpath(SPHINX_SOURCE, "user", relative) 
     125 
     126            print("Found sasview docs folder at \"%s\"." % relative) 
     127            copy_tree(source_dir, dest_dir) 
     128 
     129    print("=== Sasmodels Docs ===") 
     130    shutil.copy(joinpath(SASMODELS_DOCS, "rst_prolog"), SPHINX_SOURCE) 
     131    copy_tree(SASMODELS_MODEL_SOURCE, SASMODELS_MODEL_TARGET) 
     132    #copy_tree(SASMODELS_API_SOURCE, SASMODELS_API_TARGET) 
     133    copy_tree(SASMODELS_DEV_SOURCE, SASMODELS_DEV_TARGET) 
     134    copy_tree(SASMODELS_GUIDE_SOURCE, SASMODELS_GUIDE_TARGET) 
     135    for filename in SASMODELS_GUIDE_EXCLUDE: 
     136        os.unlink(joinpath(SASMODELS_GUIDE_TARGET, filename)) 
     137 
     138    # Model category files reference the model as ../../model/name.rst.  Since 
     139    # we are rearranging the tree, we need to update each of these links. 
     140    catdir = joinpath(SASMODELS_GUIDE_TARGET, "models") 
     141    for filename in os.listdir(catdir): 
     142        inplace_change(joinpath(catdir, filename), "../../model/", "/user/models/") 
     143 
    327144 
    328145def retrieve_bumps_docs(): 
     
    330147    Copies select files from the bumps documentation into fitting perspective 
    331148    """ 
    332     if os.path.exists(BUMPS_DOCS): 
     149    if exists(BUMPS_SOURCE): 
    333150        print("=== Retrieve BUMPS Docs ===") 
    334         filenames = [os.path.join(BUMPS_DOCS, "optimizer.rst")] 
    335         filenames += glob(os.path.join(BUMPS_DOCS, "dream-*.png")) 
    336         filenames += glob(os.path.join(BUMPS_DOCS, "fit-*.png")) 
     151        filenames = [joinpath(BUMPS_SOURCE, "optimizer.rst")] 
     152        filenames += glob(joinpath(BUMPS_SOURCE, "dream-*.png")) 
     153        filenames += glob(joinpath(BUMPS_SOURCE, "fit-*.png")) 
    337154        for f in filenames: 
    338155            print("Copying file", f) 
     
    354171 
    355172    # Clean directory before generating a new version. 
    356     _remove_dir(SPHINX_SOURCE_API) 
     173    #_remove_dir(SASVIEW_API_TARGET) 
    357174 
    358175    subprocess.call(["sphinx-apidoc", 
    359                      "-o", SPHINX_SOURCE_API, # Output dir. 
     176                     "-o", SASVIEW_API_TARGET, # Output dir. 
    360177                     "-d", "8", # Max depth of TOC. 
     178                     "-H", "SasView", # Package header 
    361179                     SASVIEW_BUILD]) 
     180 
     181    subprocess.call(["sphinx-apidoc", 
     182                     "-o", SASMODELS_API_TARGET, # Output dir. 
     183                     "-d", "8", # Max depth of TOC. 
     184                     "-H", "sasmodels", # Package header 
     185                     SASMODELS_BUILD, 
     186                     joinpath(SASMODELS_BUILD, "sasmodels", "models"), # exclude 
     187                     ]) 
    362188 
    363189def build_pdf(): 
     
    368194    subprocess.call(["sphinx-build", 
    369195                     "-b", "latex", # Builder name. TODO: accept as arg to setup.py. 
    370                      "-d", os.path.join(SPHINX_BUILD, "doctrees"), 
     196                     "-d", joinpath(SPHINX_BUILD, "doctrees"), 
    371197                     SPHINX_SOURCE, 
    372                      os.path.join(SPHINX_BUILD, "latex")]) 
    373  
    374     LATEXDIR = os.path.join(SPHINX_BUILD, "latex") 
     198                     joinpath(SPHINX_BUILD, "latex")]) 
     199 
     200    LATEXDIR = joinpath(SPHINX_BUILD, "latex") 
    375201    #TODO: Does it need to be done so many time? 
    376202    def pdflatex(): 
     
    384210 
    385211    print("=== Copy PDF to HTML Directory ===") 
    386     source = os.path.join(LATEXDIR, "SasView.pdf") 
    387     target = os.path.join(SASVIEW_DOCS, "SasView.pdf") 
     212    source = joinpath(LATEXDIR, "SasView.pdf") 
     213    target = joinpath(SASVIEW_DOC_TARGET, "SasView.pdf") 
    388214    shutil.copyfile(source, target) 
    389215 
     
    395221    subprocess.call(["sphinx-build", 
    396222                     "-b", "html", # Builder name. TODO: accept as arg to setup.py. 
    397                      "-d", os.path.join(SPHINX_BUILD, "doctrees"), 
     223                     "-d", joinpath(SPHINX_BUILD, "doctrees"), 
    398224                     SPHINX_SOURCE, 
    399                      os.path.join(SPHINX_BUILD, "html")]) 
     225                     joinpath(SPHINX_BUILD, "html")]) 
    400226 
    401227    print("=== Copy HTML Docs to Build Directory ===") 
    402     html = os.path.join(SPHINX_BUILD, "html") 
    403     copy_tree(html, SASVIEW_DOCS) 
     228    html = joinpath(SPHINX_BUILD, "html") 
     229    copy_tree(html, SASVIEW_DOC_TARGET) 
    404230 
    405231def fetch_katex(version, destination="_static"): 
     
    408234    url = "https://github.com/Khan/KaTeX/releases/download/%s/katex.zip" % version 
    409235    cache_path = "katex_%s.zip" % version 
    410     if not os.path.exists(cache_path): 
     236    if not exists(cache_path): 
    411237        try: 
    412238            fd_in = urllib2.urlopen(url) 
     
    420246def convert_katex(): 
    421247    print("=== Preprocess HTML, converting latex to html ===") 
    422     subprocess.call(["node", "convertKaTex.js", SASVIEW_DOCS]) 
     248    subprocess.call(["node", "convertKaTex.js", SASVIEW_DOC_TARGET]) 
    423249 
    424250def convert_mathjax(): 
    425251    print("=== Preprocess HTML, converting latex to html ===") 
    426     subprocess.call(["node", "convertMathJax.js", SASVIEW_DOCS]) 
     252    subprocess.call(["node", "convertMathJax.js", SASVIEW_DOC_TARGET]) 
    427253 
    428254def fetch_mathjax(): 
  • docs/sphinx-docs/source/dev/dev.rst

    r959eb01 r3bd677b  
    1010   :maxdepth: 1 
    1111 
    12    SasView API <api/modules> 
     12   SasView API <sasview-api/modules> 
     13   sasmodels overview <sasmodels-dev/index> 
     14   sasmodels API <sasmodels-api/modules> 
    1315 
    1416Indices and Search 
  • docs/sphinx-docs/source/user/marketplace.rst

    r959eb01 r59dfb53  
    33Model Marketplace 
    44================= 
    5 The Model Marketplace allows members of the SAS Community to contribute plug-in fitting models for *SasView* for all to use. 
     5The Model Marketplace allows members of the SAS Community to contribute 
     6plug-in fitting models for *SasView* for all to use. 
    67 
    78.. note:: These plug-in models require SasView version 4.0 or later. 
    89 
    9 Contributed models should be written in Python (only version 2.7.x is currently supported) or, if computational speed is an issue, in a combination of Python and C. You only need to upload the .py/.c source code files to the Marketplace! 
     10Contributed models should be written in Python (only version 2.7.x is 
     11currently supported) or, if computational speed is an issue, in a 
     12combination of Python and C. You only need to upload the .py/.c source 
     13code files to the Marketplace! 
    1014 
    11 For guidance on how to write a plugin model see :ref:`Writing_a_Plugin` . It may also be helpful to examine the library models in the */sasmodels-data/models* sub-folder of your SasView installation directory. 
     15For guidance on how to write a plugin model see :ref:`Writing_a_Plugin` . It 
     16may also be helpful to examine the library models in 
     17the */sasmodels-data/models* sub-folder of your SasView installation directory. 
    1218 
    13 The Marketplace also provides the option to upload a SasView text file of the scattering function data computed by your model. If you do this a graph of the scattering function will appear under the Marketplace entry for your model. 
     19The Marketplace also provides the option to upload a SasView text file of 
     20the scattering function data computed by your model. If you do this a graph 
     21of the scattering function will appear under the Marketplace entry for 
     22your model. 
    1423 
    15 .. note:: The SasView Development Team regret to say that they do not have the resources to fix the bugs or polish the code in every model contributed to the Marketplace! 
     24.. note:: 
     25    The SasView Development Team regret to say that they do not have the 
     26    resources to fix the bugs or polish the code in every model contributed 
     27    to the Marketplace! 
  • docs/sphinx-docs/source/user/tutorial.rst

    r2f6d340 r3bd677b  
    88.. note:: In Windows use [Alt]-[Cursor left] to return to the previous page 
    99 
    10 :download:`Getting Started with Sasview <../../../../src/sas/sasview/media/getting_started_with_sasview.pdf>` 
     10:download:`Getting Started with Sasview <sasview/getting_started_with_sasview.pdf>` 
    1111 
    12 :download:`Old Tutorial <../../../../src/sas/sasview/media/Tutorial.pdf>` 
     12:download:`Old Tutorial <sasview/Tutorial.pdf>` 
  • docs/sphinx-docs/source/user/user.rst

    r959eb01 r3bd677b  
    77   :maxdepth: 1 
    88 
    9    Model Documentation <index> 
    10     
     9   Model Documentation <sasgui/perspectives/fitting/models/index> 
     10 
    1111   Menu Bar <menu_bar> 
    1212 
    1313   Fitting & Other Analyses <analysis> 
    14     
     14 
    1515   Tools & Utilities <tools> 
    16           
     16 
    1717   Working with SasView <working> 
  • docs/sphinx-docs/source/user/working.rst

    r8cc39d6 r3bd677b  
    88 
    99   Data Formats <sasgui/guiframe/data_formats_help> 
    10     
     10 
    1111   Loading Data <sasgui/guiframe/data_explorer_help> 
    12     
     12 
    1313   Plotting Data/Models <sasgui/guiframe/graph_help> 
    14     
    15    Test Data <../test/testdata_help.rst> 
    16        
    17    Tutorials <tutorial.rst> 
    18     
    19    Writing a Plugin Model <sasgui/perspectives/fitting/plugin.rst> 
    20     
    21    Computations with a GPU <gpu_computations> 
    22     
     14 
     15   Test Data <sasview/test/testdata_help> 
     16 
     17   Tutorials <tutorial> 
     18 
     19   Writing a Plugin Model <sasgui/perspectives/fitting/plugin> 
     20 
     21   Model marketplace <marketplace> 
  • src/sas/sascalc/corfunc/corfunc_calculator.py

    rb916afa ra26f67f  
    177177        """ 
    178178        Extract the interesting measurements from a correlation function 
    179         :param transformed_data: Fourier transformation of the 
    180             extrapolated data 
     179 
     180        :param transformed_data: Fourier transformation of the extrapolated data 
    181181        """ 
    182182        # Calculate indexes of maxima and minima 
  • src/sas/sascalc/data_util/registry.py

    rdc8d1c2 ra26f67f  
    121121        Call the loader for the file type of path. 
    122122 
    123         :raise ValueError: if no loader is available. 
    124         :raise KeyError: if format is not available. 
     123        :raises ValueError: if no loader is available. 
     124        :raises KeyError: if format is not available. 
     125 
    125126        May raise a loader-defined exception if loader fails. 
    126127        """ 
  • src/sas/sascalc/file_converter/c_ext/__init__.py

    r18e7309 ra26f67f  
     1""" 
     2    Data loader for the Diamond BSL beamline. 
     3""" 
  • src/sas/sasgui/guiframe/CategoryInstaller.py

    rb963b20 ra26f67f  
    112112    def check_install(homedir = None, model_list=None): 
    113113        """ 
    114         the main method of this class 
    115         makes sure categories.json exists and if not 
    116         compile it and install 
     114        Makes sure categories.json exists and if not compile it and install. 
     115 
     116        This is the main method of this class. 
     117 
    117118        :param homefile: Override the default home directory 
    118         :param model_list: List of model names except those in Plugin Models 
    119               which are user supplied. 
     119        :param model_list: List of model names except those in 
     120            Plugin Models which are user supplied. 
    120121        """ 
    121122        _model_dict = {model.name: model for model in model_list} 
  • src/sas/sasgui/guiframe/local_perspectives/plotting/parameters_panel_slicer.py

    r47d93073 ra26f67f  
    395395        """ 
    396396        Event based parameter setting. 
     397 
    397398        :param evt: Event triggered to apply parameters to a list of plots 
    398                     evt should have attrs plot_list and params 
     399           evt should have attrs plot_list and params 
     400 
    399401        """ 
    400402        if evt is None: 
     
    467469        """ 
    468470        Send a list of data to the fitting perspective 
    469         :param fit: fit type desired  
     471        :param fit: fit type desired 
    470472        :param file_list: list of loaded file names to send to fit 
    471473        """ 
  • src/sas/sasgui/perspectives/file_converter/converter_panel.py

    r19296dc ra26f67f  
    9393        <SasData> element. 
    9494 
    95         :param frame_data: If single_file is true, an array of Data1D objects. 
    96         If single_file is false, a dictionary of the form frame_number: Data1D. 
     95        :param frame_data: If single_file is true, an array of Data1D 
     96            objects. If single_file is false, a dictionary of the 
     97            form *{frame_number: Data1D}*. 
    9798        :param filepath: Where to save the CanSAS file 
    98         :param single_file: If true, array is saved as a single file, if false, 
    99         each item in the array is saved to it's own file 
     99        :param single_file: If true, array is saved as a single file, 
     100            if false, each item in the array is saved to it's own file 
    100101        """ 
    101102        writer = CansasWriter() 
     
    192193        :return x_data: A 1D array containing all the x coordinates of the data 
    193194        :return y_data: A 1D array containing all the y coordinates of the data 
    194         :return frame_data: A dictionary of the form frame_number: data, where 
    195         data is a 2D numpy array containing the intensity data 
     195        :return frame_data: A dictionary of the form *{frame_number: data}*, where data is a 2D numpy array containing the intensity data 
    196196        """ 
    197197        loader = BSLLoader(filename) 
  • src/sas/sasgui/perspectives/fitting/basepage.py

    rd3b0c77 r3bd677b  
    28162816                                              "", name + " Help") 
    28172817        else: 
    2818             _TreeLocation = 'user/index.html' 
     2818            _TreeLocation = 'user/sasgui/perspectives/fitting/models/index.html' 
    28192819            _doc_viewer = DocumentationWindow(self, wx.ID_ANY, _TreeLocation, 
    28202820                                              "", "General Model Help") 
     
    28872887        """ 
    28882888 
    2889         _TreeLocation = "user/magnetism.html" 
     2889        _TreeLocation = "user/sasgui/perspectives/fitting/magnetism/magnetism.html" 
    28902890        _doc_viewer = DocumentationWindow(self, wx.ID_ANY, _TreeLocation, "", 
    28912891                                          "Polarized Beam/Magnetc Help") 
     
    29332933        """ 
    29342934 
    2935         _TreeLocation = "user/sasgui/perspectives/fitting/pd_help.html" 
     2935        _TreeLocation = "user/sasgui/perspectives/fitting/pd/polydispersity.html" 
    29362936        _PageAnchor = "" 
    29372937        _doc_viewer = DocumentationWindow(self, wx.ID_ANY, _TreeLocation, 
  • src/sas/sasgui/perspectives/fitting/fitpage.py

    r0315b63 r3bd677b  
    10791079        """ 
    10801080 
    1081         _TreeLocation = "user/sasgui/perspectives/fitting/sm_help.html" 
     1081        _TreeLocation = "user/sasgui/perspectives/fitting/resolution.html" 
    10821082        _doc_viewer = DocumentationWindow(self, wx.ID_ANY, _TreeLocation, "", 
    10831083                                          "Instrumental Resolution Smearing \ 
  • src/sas/sasgui/perspectives/fitting/gpu_options.py

    r73cbeec r3bd677b  
    318318        Provide help on opencl options. 
    319319        """ 
    320         TreeLocation = "user/gpu_computations.html" 
     320        TreeLocation = "user/sasgui/perspectives/fitting/gpu_setup.html" 
    321321        anchor = "#device-selection" 
    322322        DocumentationWindow(self, -1, 
  • src/sas/sasgui/perspectives/fitting/media/fitting.rst

    r46dfee9 r3bd677b  
    1313   Assessing Fit Quality <residuals_help> 
    1414 
    15    Polydispersity Distributions <pd_help> 
     15   Polydispersity Distributions <pd/polydispersity> 
    1616 
    17    Smearing Functions <sm_help> 
     17   Smearing Functions <resolution> 
    1818 
    19    Polarisation/Magnetic Scattering <mag_help> 
     19   Polarisation/Magnetic Scattering <magnetism/magnetism> 
    2020 
    21    Information on the SasView Optimisers <optimizer.rst> 
    22        
    23    Converting SANS to SESANS for Fitting <../../../sans_to_sesans> 
    24     
    25    Fitting SESANS Data <../../../sesans_fitting.rst> 
    26     
    27    Writing a Plugin Model <plugin.rst> 
    28        
    29    Computations with a GPU <../../../gpu_computations> 
    30     
     21   Information on the SasView Optimisers <optimizer> 
     22 
     23   Converting SANS to SESANS for Fitting <sesans/sans_to_sesans> 
     24 
     25   Fitting SESANS Data <sesans/sesans_fitting> 
     26 
     27   Writing a Plugin Model <plugin> 
     28 
     29   Computations with a GPU <gpu_setup> 
     30 
     31   Scripting interface to sasmodels <scripting> 
     32 
     33   References <refs> 
  • src/sas/sasgui/perspectives/fitting/media/fitting_help.rst

    rc5cfb20 r5005ae0  
    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 .. |inlineimage004| image:: sm_image004.png 
    7 .. |inlineimage005| image:: sm_image005.png 
    8 .. |inlineimage008| image:: sm_image008.png 
    9 .. |inlineimage009| image:: sm_image009.png 
    10 .. |inlineimage010| image:: sm_image010.png 
    11 .. |inlineimage011| image:: sm_image011.png 
    12 .. |inlineimage012| image:: sm_image012.png 
    13 .. |inlineimage018| image:: sm_image018.png 
    14 .. |inlineimage019| image:: sm_image019.png 
    15  
    165 
    176Fitting 
     
    3827   for example, if you have measured the same sample at different contrasts) 
    3928 
    40 *  in *Batch* fit mode - multiple data sets are fitted sequentially to the *same* model (this might be useful, for example, if you have performed a kinetic or time-resolved experiment and have *lots* of data sets!) 
     29*  in *Batch* fit mode - multiple data sets are fitted sequentially to the 
     30   *same* model (this might be useful, for example, if you have performed 
     31   a kinetic or time-resolved experiment and have *lots* of data sets!) 
    4132 
    4233.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
     
    5445*  *Lamellae* - lamellar shapes (lamellar, core shell lamellar, stacked 
    5546   lamellar, etc) 
    56 *  *Shape-Independent* - models describing structure in terms of density correlation functions, fractals, peaks, power laws, etc 
     47*  *Shape-Independent* - models describing structure in terms of density 
     48   correlation functions, fractals, peaks, power laws, etc 
    5749*  *Paracrystal* - semi ordered structures (bcc, fcc, etc) 
    5850*  *Structure Factor* - S(Q) models 
     
    143135   and/or relatively simple models) 
    144136*  By copying/editing an existing model (this can include models generated by 
    145    the New Plugin Model* dialog) in the :ref:`Python_shell` or  
     137   the New Plugin Model* dialog) in the :ref:`Python_shell` or 
    146138   :ref:`Advanced_Plugin_Editor` (suitable for all use cases) 
    147139*  By writing a model from scratch outside of SasView (only recommended for code 
     
    181173.. image:: new_model.png 
    182174 
    183 When using this feature, be aware that even if your code has errors, including  
    184 syntax errors, a model file is still generated. When you then correct the errors  
    185 and click 'Apply' again to re-compile you will get an error informing you that  
    186 the model already exists if the 'Overwrite' box is not checked. In this case you  
    187 will need to supply a new model function name. By default the 'Overwrite' box is  
     175When using this feature, be aware that even if your code has errors, including 
     176syntax errors, a model file is still generated. When you then correct the errors 
     177and click 'Apply' again to re-compile you will get an error informing you that 
     178the model already exists if the 'Overwrite' box is not checked. In this case you 
     179will need to supply a new model function name. By default the 'Overwrite' box is 
    188180*checked*\ . 
    189181 
     
    195187the :ref:`Advanced_Plugin_Editor` . 
    196188 
    197 **SasView version 4.2** made it possible to specify whether a plugin created with  
    198 the *New Plugin Model* dialog is actually a form factor P(Q) or a structure factor  
    199 S(Q). To do this, simply add one or other of the following lines under the *import*  
     189**SasView version 4.2** made it possible to specify whether a plugin created with 
     190the *New Plugin Model* dialog is actually a form factor P(Q) or a structure factor 
     191S(Q). To do this, simply add one or other of the following lines under the *import* 
    200192statements. 
    201193 
     
    203195 
    204196     form_factor = True 
    205           
     197 
    206198or for a structure factor:: 
    207199 
    208200     structure_factor = True 
    209           
    210 If the plugin is a structure factor it is *also* necessary to add two variables to  
     201 
     202If the plugin is a structure factor it is *also* necessary to add two variables to 
    211203the parameter list:: 
    212204 
    213      parameters = [  
     205     parameters = [ 
    214206                     ['radius_effective', '', 1, [0.0, numpy.inf], 'volume', ''], 
    215207                     ['volfraction', '', 1, [0.0, 1.0], '', ''], 
     
    222214     def Iqxy(x, y, radius_effective, volfraction, ...): 
    223215 
    224 Such a plugin should then be available in the S(Q) drop-down box on a FitPage (once  
     216Such a plugin should then be available in the S(Q) drop-down box on a FitPage (once 
    225217a P(Q) model has been selected). 
    226218 
     
    243235them. Finally, click the *Apply* button to generate and test the model and then click *Close*. 
    244236 
    245 Any changes to a plugin model generated in this way only become effective *after* it is re-selected  
    246 from the plugin models drop-down menu on the FitPage. If the model is not listed you can force a  
     237Any changes to a plugin model generated in this way only become effective *after* it is re-selected 
     238from the plugin models drop-down menu on the FitPage. If the model is not listed you can force a 
    247239recompilation of the plugins by selecting *Fitting* > *Plugin Model Operations* > *Load Plugin Models*. 
    248240 
    249 **SasView version 4.2** introduced a much simplified and more extensible structure for plugin models  
    250 generated through the Easy Sum/Multi Editor. For example, the code for a combination of a sphere model  
     241**SasView version 4.2** introduced a much simplified and more extensible structure for plugin models 
     242generated through the Easy Sum/Multi Editor. For example, the code for a combination of a sphere model 
    251243with a power law model now looks like this:: 
    252244 
    253245     from sasmodels.core import load_model_info 
    254246     from sasmodels.sasview_model import make_model_from_info 
    255       
     247 
    256248     model_info = load_model_info('sphere+power_law') 
    257249     model_info.name = 'MyPluginModel' 
     
    259251     Model = make_model_from_info(model_info) 
    260252 
    261 To change the models or operators contributing to this plugin it is only necessary to edit the string  
    262 in the brackets after *load_model_info*, though it would also be a good idea to update the model name  
     253To change the models or operators contributing to this plugin it is only necessary to edit the string 
     254in the brackets after *load_model_info*, though it would also be a good idea to update the model name 
    263255and description too!!! 
    264256 
    265 The model specification string can handle multiple models and combinations of operators (+ or *) which  
    266 are processed according to normal conventions. Thus 'model1+model2*model3' would be valid and would  
    267 multiply model2 by model3 before adding model1. In this example, parameters in the *FitPage* would be  
    268 prefixed A (for model2), B (for model3) and C (for model1). Whilst this might appear a little  
    269 confusing, unless you were creating a plugin model from multiple instances of the same model the parameter  
     257The model specification string can handle multiple models and combinations of operators (+ or *) which 
     258are processed according to normal conventions. Thus 'model1+model2*model3' would be valid and would 
     259multiply model2 by model3 before adding model1. In this example, parameters in the *FitPage* would be 
     260prefixed A (for model2), B (for model3) and C (for model1). Whilst this might appear a little 
     261confusing, unless you were creating a plugin model from multiple instances of the same model the parameter 
    270262assignments ought to be obvious when you load the plugin. 
    271263 
    272 If you need to include another plugin model in the model specification string, just prefix the name of  
     264If you need to include another plugin model in the model specification string, just prefix the name of 
    273265that model with *custom*. For instance:: 
    274266 
     
    278270 
    279271     sphere@hardsphere 
    280       
    281 This streamlined approach to building complex plugin models from existing library models, or models  
    282 available on the *Model Marketplace*, also permits the creation of P(Q)*\S(Q) plugin models, something  
    283 that was not possible in earlier versions of SasView.  
     272 
     273This streamlined approach to building complex plugin models from existing library models, or models 
     274available on the *Model Marketplace*, also permits the creation of P(Q)*\S(Q) plugin models, something 
     275that was not possible in earlier versions of SasView. 
    284276 
    285277.. _Advanced_Plugin_Editor: 
     
    471463 
    472464This mode is an extension of the :ref:`Single_Fit_Mode` that fits two or more data 
    473 sets *to the same model* simultaneously. If necessary it is possible to constrain  
     465sets *to the same model* simultaneously. If necessary it is possible to constrain 
    474466fit parameters between data sets (eg, to fix a background level, or radius, etc). 
    475467 
     
    689681recognises the operators +, -, \*, /, or 'pow', and allows the following 
    690682types of expression : 
    691   
     683 
    692684  1) if an axis label range is a function of 1 or more *columns*, write 
    693685     this type of expression 
     
    706698 
    707699     Example: radius [2 : 5] , radius [10 : 25] 
    708       
     700 
    709701.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    710702 
     
    756748   p#_ appended to the beginning and thus radius and p1_radius will not be 
    757749   recognized as the same parameter. 
    758     
     750 
    759751.. image:: combine_batch_grid.png 
    760752 
     
    764756time is not listed in the file but the file name contains the information. As 
    765757described in :ref:`Grid_Window`, a column can be added manually, in this case 
    766 called time, and the peak position plotted against time.  
     758called time, and the peak position plotted against time. 
    767759 
    768760.. image:: combine_batch_plot.png 
  • src/sas/sasgui/perspectives/fitting/media/residuals_help.rst

    r940d034 r99ded31  
    2626^^^^ 
    2727 
    28 Chi2 is a statistical parameter that quantifies the differences between an observed 
    29 data set and an expected dataset (or 'theory'). 
     28$\chi^2$ is a statistical parameter that quantifies the differences between 
     29an observed data set and an expected dataset (or 'theory'). 
    3030 
    31 *SasView* actually returns this parameter normalized to the number of data points, 
    32 *Npts* such that 
     31When showing the a model with the data, *SasView* displays this parameter 
     32normalized to the number of data points, $N_\mathrm{pts}$ such that 
    3333 
    3434.. math:: 
    3535 
    36   \chi^2/N_{pts} =  \sum[(Y_i - \mathrm{theory}_i)^2 / \mathrm{error}_i^2] / N_{pts} 
     36  \chi^2_N 
     37  =  \sum[(Y_i - \mathrm{theory}_i)^2 / \mathrm{error}_i^2] / N_\mathrm{pts} 
    3738 
    38 This differs slightly from what is sometimes called the 'reduced $\chi^2$' 
    39 because it does not take into account the number of fitting parameters (to 
    40 calculate the number of 'degrees of freedom'), but the 'normalized $\chi^2$ 
    41 and the 'reduced $\chi^2$ are very close to each other when $N_{pts} \gg 
    42 \text{number of parameters}. 
     39When performing a fit, *SasView* instead displays the reduced $\chi^2_R$, 
     40which takes into account the number of fitting parameters $N_\mathrm{par}$ 
     41(to calculate the number of 'degrees of freedom'). This is computed as 
    4342 
    44 For a good fit, $\chi^2/N_{pts}$ tends to 1. 
     43.. math:: 
    4544 
    46 $\chi^2/N_{pts}$ is sometimes referred to as the 'goodness-of-fit' parameter. 
     45  \chi^2_R 
     46  =  \sum[(Y_i - \mathrm{theory}_i)^2 / \mathrm{error}_i^2] 
     47  / [N_\mathrm{pts} - N_\mathrm{par}] 
     48 
     49The normalized $\chi^2_N$ and the reduced $\chi^2_R$ are very close to each 
     50other when $N_\mathrm{pts} \gg N_\mathrm{par}$. 
     51 
     52For a good fit, $\chi^2_R$ tends to 1. 
     53 
     54$\chi^2_R$ is sometimes referred to as the 'goodness-of-fit' parameter. 
    4755 
    4856.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
     
    5260 
    5361A residual is the difference between an observed value and an estimate of that 
    54 value, such as a 'theory' calculation (whereas the difference between an observed 
    55 value and its *true* value is its error). 
     62value, such as a 'theory' calculation (whereas the difference between an 
     63observed value and its *true* value is its error). 
    5664 
    5765*SasView* calculates 'normalized residuals', $R_i$, for each data point in the 
     
    6068.. math:: 
    6169 
    62   R_i = (Y_i - Y_theory_i) / (Y_err_i) 
     70  R_i = (Y_i - \mathrm{theory}_i) / \mathrm{error}_i 
    6371 
    64 For a good fit, $R_i \sim 0$. 
     72Think of each normalized residual as the number of standard deviations 
     73between the measured value and the theory.  For a good fit, 68% of $R_i$ 
     74will be within one standard deviation, which will show up in the Residuals 
     75plot as $R_i$ values between $-1$ and $+1$.  Almost all the values should 
     76be between $-3$ and $+3$. 
     77 
     78Residuals values larger than $\pm 3$ indicate that the model 
     79is not fit correctly, the wrong model was chosen (e.g., because there is 
     80more than one phase in your system), or there are problems in 
     81the data reduction.  Since the goodness of fit is calculated from the 
     82sum-squared residuals, these extreme values will drive the choice of fit 
     83parameters.  Any uncertainties calculated for the fitting parameters will 
     84be meaningless. 
    6585 
    6686.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    6787 
    68 .. note::  This help document was last changed by Steve King, 08Jun2015 
     88*Document History* 
     89 
     90| 2015-06-08 Steve King 
     91| 2017-09-28 Paul Kienzle 
  • src/sas/sasgui/perspectives/fitting/plugin_models/__init__.py

    rab0b93f r64cdb0d  
     1""" 
     2Example plugin models to be added to the SasView plugin directory on startup 
     3if no plugins are present. 
     4 
     5This is currently empty. 
     6""" 
  • src/sas/sasgui/plottools/LineModel.py

    r959eb01 ra26f67f  
    22""" 
    33Provide Line function (y= Ax + B). Until July 10, 2016 this function provided 
    4 (y= A + Bx).  This however was contrary to all the other code using it which  
     4(y= A + Bx).  This however was contrary to all the other code using it which 
    55assumed (y= mx+b) or in this nomenclature (y=Ax + B). This lead to some 
    66contortions in the code and worse incorrect calculations until now for at least 
     
    6767        Evaluate the model 
    6868 
    69         :note: This is the function called by fitDialog to calculate the 
    70         the y(xmin) and y(xmax), but the only difference between this and 
    71         runXY is when the if statement is true. I however cannot see what that 
    72         function is for.  It needs to be documented here or removed. 
    73         PDB 7/10/16  
    74  
    7569        :param x: simple value 
    7670 
    7771        :return: (Line value) 
     72 
     73        .. note:: 
     74            This is the function called by fitDialog to calculate the 
     75            the y(xmin) and y(xmax), but the only difference between this and 
     76            runXY is when the if statement is true. I however cannot see what 
     77            that function is for.  It needs to be documented here or removed. 
     78            PDB 7/10/16 
    7879        """ 
    7980        if x.__class__.__name__ == 'list': 
     
    8990        """ 
    9091        Evaluate the model. 
    91          
    92         :note: This is to be what is called by fitDialog for the actual fit 
    93         but the only difference between this and run is when the if  
    94         statement is true. I however cannot see what that function 
    95         is for.  It needs to be documented here or removed. PDB 7/10/16  
    9692 
    9793        :param x: simple value 
     
    9995        :return: Line value 
    10096 
     97        .. note:: 
     98            This is to be what is called by fitDialog for the actual fit 
     99            the only difference between this and run is when the if 
     100            statement is true. I however cannot see what that function 
     101            is for.  It needs to be documented here or removed. PDB 7/10/16 
    101102        """ 
    102103        if x.__class__.__name__ == 'list': 
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