Changes in / [61f8638:56b2687] in sasmodels


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19 edited

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  • README.rst

    r9fb92a0 r84bc3c1  
    5353in the same data set. 
    5454 
    55 `Travis-CI Build Status <https://travis-ci.org/SasView/sasmodels.svg?branch=master)](https://travis-ci.org/SasView/sasmodels>`_ 
     55|TravisStatus|_ 
     56 
     57.. |TravisStatus| image:: https://travis-ci.org/SasView/sasmodels.svg?branch=master 
     58.. _TravisStatus: https://travis-ci.org/SasView/sasmodels 

  • sascomp

    ra78bebc r6708a6a  
    44import os 
    55import glob 
     6import logging 
     7logging.basicConfig(level=logging.INFO) 
    68 
    79def main(): 
    810    sasmodels = os.path.dirname(os.path.realpath(__file__)) 
    911    root = os.path.dirname(sasmodels) 
    10     sasview=glob.glob(os.path.join(root, 'sasview', 'build', 'lib.*' )) 
     12    sasview=glob.glob(os.path.join(root, 'sasview', 'build', 'lib*' )) 
    1113    sys.path.insert(0, os.path.join(root, 'bumps')) 
    1214    sys.path.insert(0, os.path.join(root, 'periodictable')) 
     15    sys.path.insert(0, os.path.join(root, 'tinycc', 'build', 'lib')) 
    1316    if sasview:  # glob returns a list 
    1417        sys.path.insert(0, sasview[0]) 

  • sasmodels/__init__.py

    rc2c51a2 r59d94b3  
    2424    """ 
    2525    from os.path import join as joinpath 
    26     from .generate import SIBLING_DIR, DATA_PATH 
    27     data_files = {} 
    28     def add_patterns(path, patterns): 
    29         data_files[joinpath(SIBLING_DIR, *path)] \ 
    30             = [joinpath(DATA_PATH, *(path+[p])) for p in patterns] 
    31     add_patterns([], ['*.c', '*.cl', 'convert.json']) 
    32     add_patterns(['models'], ['*.c']) 
    33     add_patterns(['models', 'lib'], ['*.c']) 
     26    import glob 
    3427 
    35     return data_files 
     28    from .generate import EXTERNAL_DIR, DATA_PATH 
    3629 
     30    def expand_patterns(path, patterns): 
     31        target_path = joinpath(EXTERNAL_DIR, *path) 
     32        source_path = joinpath(DATA_PATH, *path) 
     33        files = [] 
     34        for p in patterns: 
     35            files.extend(glob.glob(joinpath(source_path, p))) 
     36        return target_path, files 
     37 
     38    # Place the source for the model tree in the distribution.  Minimally we 
     39    # need the c and cl files for running on OpenCL.  Need the py files so 
     40    # users can easily copy existing models.  Need the img files so that we 
     41    # can build model docs on the fly, including images. 
     42    return_list = [ 
     43        expand_patterns([], ['*.c', '*.cl', 'convert.json']), 
     44        expand_patterns(['models'], ['*.py', '*.c']), 
     45        expand_patterns(['models', 'lib'], ['*.c']), 
     46        expand_patterns(['models', 'img'], ['*.*']), 
     47        ] 
     48    return return_list 
     49 
     50 

  • sasmodels/core.py

    r7bf4757 rf5dde3f  
    3434    pass 
    3535 
     36try: 
     37    np.meshgrid([]) 
     38    meshgrid = np.meshgrid 
     39except Exception: 
     40    # CRUFT: np.meshgrid requires multiple vectors 
     41    def meshgrid(*args): 
     42        if len(args) > 1: 
     43            return np.meshgrid(*args) 
     44        else: 
     45            return [np.asarray(v) for v in args] 
    3646 
    3747# TODO: refactor composite model support 

  • sasmodels/custom/__init__.py

    r7ae2b7f r4bfbca2  
    2525    def load_module_from_path(fullname, path): 
    2626        module = imp.load_source(fullname, path) 
    27         os.unlink(path+"c")  # remove the automatic pyc file 
     27        #os.unlink(path+"c")  # remove the automatic pyc file 
    2828        return module 
    2929 

  • sasmodels/data.py

    re78edc4 r4e00c13  
    6262    Add a beam stop of the given *radius*.  If *outer*, make an annulus. 
    6363    """ 
    64     from sas.dataloader.manipulations import Ringcut  # type: ignore 
     64    from sas.sascalc.dataloader.manipulations import Ringcut 
    6565    if hasattr(data, 'qx_data'): 
    6666        data.mask = Ringcut(0, radius)(data) 
    … …  
    7878    Select half of the data, either "right" or "left". 
    7979    """ 
    80     from sas.dataloader.manipulations import Boxcut  # type: ignore 
     80    from sas.sascalc.dataloader.manipulations import Boxcut 
    8181    if half == 'right': 
    8282        data.mask += \ 
    … …  
    9292    Chop the top off the data, above *cutoff*. 
    9393    """ 
    94     from sas.dataloader.manipulations import Boxcut  # type: ignore 
     94    from sas.sascalc.dataloader.manipulations import Boxcut 
    9595    data.mask += \ 
    9696        Boxcut(x_min=-np.inf, x_max=np.inf, y_min=-np.inf, y_max=cutoff)(data) 

  • sasmodels/direct_model.py

    r0ff62d4 r4d8e0bb  
    133133 
    134134        if self.data_type == 'sesans': 
    135              
    136135            q = sesans.make_q(data.sample.zacceptance, data.Rmax) 
    137136            index = slice(None, None) 
    … …  
    180179                  and getattr(data, 'dxw', None) is not None): 
    181180                res = resolution.Slit1D(data.x[index], 
    182                                         qx_width=data.dxw[index], 
    183                                         qy_width=data.dxl[index]) 
     181                                        qx_width=data.dxl[index], 
     182                                        qy_width=data.dxw[index]) 
    184183            else: 
    185184                res = resolution.Perfect1D(data.x[index]) 

  • sasmodels/generate.py

    rc2c51a2 r001d9f5  
    179179    pass 
    180180 
    181 SIBLING_DIR = 'sasmodels-data' 
    182 PACKAGE_PATH = abspath(dirname(__file__)) 
    183 SIBLING_PATH = abspath(joinpath(PACKAGE_PATH, '..', 'sasmodels-data')) 
    184 DATA_PATH = SIBLING_PATH if isdir(SIBLING_PATH) else PACKAGE_PATH 
     181def get_data_path(external_dir, target_file): 
     182    path = abspath(dirname(__file__)) 
     183    if exists(joinpath(path, target_file)): 
     184        return path 
     185 
     186    # check next to exe/zip file 
     187    exepath = dirname(sys.executable) 
     188    path = joinpath(exepath, external_dir) 
     189    if exists(joinpath(path, target_file)): 
     190        return path 
     191 
     192    # check in py2app Contents/Resources 
     193    path = joinpath(exepath, '..', 'Resources', external_dir) 
     194    if exists(joinpath(path, target_file)): 
     195        return abspath(path) 
     196 
     197    raise RuntimeError('Could not find '+joinpath(external_dir, target_file)) 
     198 
     199EXTERNAL_DIR = 'sasmodels-data' 
     200DATA_PATH = get_data_path(EXTERNAL_DIR, 'kernel_template.c') 
    185201MODEL_PATH = joinpath(DATA_PATH, 'models') 
    186202 
    … …  
    657673 
    658674 
     675def make_html(model_info): 
     676    """ 
     677    Convert model docs directly to html. 
     678    """ 
     679    from . import rst2html 
     680    return rst2html.convert(make_doc(model_info), title=model_info['name']) 
     681 
    659682def demo_time(): 
    660683    # type: () -> None 

  • sasmodels/kernel_template.c

    r3832f27 r5efe850  
    1212// Note: if using a C++ compiler, then define kernel as extern "C" 
    1313#ifndef USE_OPENCL 
     14// Use SAS_DOUBLE to force the use of double even for float kernels 
     15#  define SAS_DOUBLE dou ## ble 
    1416#  ifdef __cplusplus 
    1517      #include <cstdio> 
    … …  
    3840     #if defined(__TINYC__) 
    3941         #include <math.h> 
    40          inline double trunc(double x) { return x>=0?floor(x):-floor(-x); } 
    41          inline double fmin(double x, double y) { return x>y ? y : x; } 
    42          inline double fmax(double x, double y) { return x<y ? y : x; } 
    4342         // TODO: test isnan 
    4443         inline double _isnan(double x) { return x != x; } // hope this doesn't optimize away! 
    4544         #undef isnan 
    4645         #define isnan(x) _isnan(x) 
     46         // Defeat the double->float conversion since we don't have tgmath 
     47         inline SAS_DOUBLE trunc(SAS_DOUBLE x) { return x>=0?floor(x):-floor(-x); } 
     48         inline SAS_DOUBLE fmin(SAS_DOUBLE x, SAS_DOUBLE y) { return x>y ? y : x; } 
     49         inline SAS_DOUBLE fmax(SAS_DOUBLE x, SAS_DOUBLE y) { return x<y ? y : x; } 
    4750         #define NEED_EXPM1 
    4851         #define NEED_TGAMMA 
    … …  
    7073 
    7174#if defined(NEED_EXPM1) 
    72    static double expm1(double x) { 
     75   static SAS_DOUBLE expm1(SAS_DOUBLE x_in) { 
     76      double x = (double)x_in;  // go back to float for single precision kernels 
    7377      // Adapted from the cephes math library. 
    7478      // Copyright 1984 - 1992 by Stephen L. Moshier 

  • sasmodels/kernelcl.py

    rae2b6b5 r197e41d  
    5252import os 
    5353import warnings 
     54import logging 
    5455 
    5556import numpy as np  # type: ignore 
    … …  
    6061    # Ask OpenCL for the default context so that we know that one exists 
    6162    cl.create_some_context(interactive=False) 
    62 except Exception as ocl_exc: 
    63     warnings.warn(str(ocl_exc)) 
    64     del ocl_exc 
     63except Exception as exc: 
     64    warnings.warn("OpenCL startup failed with ***"+str(exc)+"***; using C compiler instead") 
    6565    raise RuntimeError("OpenCL not available") 
    6666 
    6767from pyopencl import mem_flags as mf  # type: ignore 
    6868from pyopencl.characterize import get_fast_inaccurate_build_options  # type: ignore 
     69# CRUFT: pyopencl < 2017.1  (as of June 2016 needs quotes around include path) 
     70def _quote_path(v): 
     71    """ 
     72    Quote the path if it is not already quoted. 
     73 
     74    If v starts with '-', then assume that it is a -I option or similar 
     75    and do not quote it.  This is fragile:  -Ipath with space needs to 
     76    be quoted. 
     77    """ 
     78    return '"'+v+'"' if v and ' ' in v and not v[0] in "\"'-" else v 
     79 
     80if hasattr(cl, '_DEFAULT_INCLUDE_OPTIONS'): 
     81    cl._DEFAULT_INCLUDE_OPTIONS = [_quote_path(v) for v in cl._DEFAULT_INCLUDE_OPTIONS] 
     82 
     83from pyopencl import mem_flags as mf 
     84from pyopencl.characterize import get_fast_inaccurate_build_options 
    6985 
    7086from . import generate 
    … …  
    188204    source = "\n".join(source_list) 
    189205    program = cl.Program(context, source).build(options=options) 
     206    #print("done with "+program) 
    190207    return program 
    191208 
    … …  
    262279        Compile the program for the device in the given context. 
    263280        """ 
    264         key = "%s-%s-%s"%(name, dtype, fast) 
     281        key = "%s-%s%s"%(name, dtype, ("-fast" if fast else "")) 
    265282        if key not in self.compiled: 
     283            context = self.get_context(dtype) 
     284            logging.info("building %s for OpenCL %s" 
     285                         % (key, context.devices[0].name.strip())) 
     286            program = compile_model(context, source, np.dtype(dtype), fast) 
    266287            #print("OpenCL compile",name) 
    267288            dtype = np.dtype(dtype) 

  • sasmodels/kerneldll.py

    r5a91c6b r15e74ad  
    4949import os 
    5050from os.path import join as joinpath, split as splitpath, splitext 
     51import subprocess 
    5152import tempfile 
    5253import ctypes as ct  # type: ignore 
    5354from ctypes import c_void_p, c_int32, c_longdouble, c_double, c_float  # type: ignore 
     55import logging 
    5456 
    5557import numpy as np  # type: ignore 
    … …  
    6870    pass 
    6971 
    70 # Compiler platform details 
    71 if sys.platform == 'darwin': 
    72     #COMPILE = "gcc-mp-4.7 -shared -fPIC -std=c99 -fopenmp -O2 -Wall %s -o %s -lm -lgomp" 
    73     COMPILE = "gcc -shared -fPIC -std=c99 -O2 -Wall %(source)s -o %(output)s -lm" 
    74 elif os.name == 'nt': 
     72if os.name == 'nt': 
     73    ARCH = "" if sys.maxint > 2**32 else "x86"  # maxint=2**31-1 on 32 bit 
     74    # Windows compiler; check if TinyCC is available 
     75    try: 
     76        import tinycc 
     77    except ImportError: 
     78        tinycc = None 
    7579    # call vcvarsall.bat before compiling to set path, headers, libs, etc. 
    7680    if "VCINSTALLDIR" in os.environ: 
    … …  
    8185        # TODO: remove intermediate OBJ file created in the directory 
    8286        # TODO: maybe don't use randomized name for the c file 
    83         CC = "cl /nologo /Ox /MD /W3 /GS- /DNDEBUG /Tp%(source)s " 
    84         LN = "/link /DLL /INCREMENTAL:NO /MANIFEST /OUT:%(output)s" 
     87        # TODO: maybe ask distutils to find MSVC 
     88        CC = "cl /nologo /Ox /MD /W3 /GS- /DNDEBUG".split() 
    8589        if "SAS_OPENMP" in os.environ: 
    86             COMPILE = " ".join((CC, "/openmp", LN)) 
    87         else: 
    88             COMPILE = " ".join((CC, LN)) 
    89     elif True: 
    90         # If MSVC compiler is not available, try using mingw 
    91         # fPIC is not needed on windows 
    92         COMPILE = "gcc -shared -std=c99 -O2 -Wall %(source)s -o %(output)s -lm" 
     90            CC.append("/openmp") 
     91        LN = "/link /DLL /INCREMENTAL:NO /MANIFEST".split() 
     92        def compile_command(source, output): 
     93            return CC + ["/Tp%s"%source] + LN + ["/OUT:%s"%output] 
     94    elif tinycc: 
     95        # TinyCC compiler. 
     96        CC = [tinycc.TCC] + "-shared -rdynamic -Wall".split() 
     97        def compile_command(source, output): 
     98            return CC + [source, "-o", output] 
     99    else: 
     100        # MinGW compiler. 
     101        CC = "gcc -shared -std=c99 -O2 -Wall".split() 
    93102        if "SAS_OPENMP" in os.environ: 
    94             COMPILE += " -fopenmp" 
    95     else: 
    96         # If MSVC compiler is not available, try using tinycc 
    97         from tinycc import TCC 
    98         COMPILE = TCC + " -shared -rdynamic -Wall %(source)s -o %(output)s" 
     103            CC.append("-fopenmp") 
     104        def compile_command(source, output): 
     105            return CC + [source, "-o", output, "-lm"] 
    99106else: 
    100     COMPILE = "cc -shared -fPIC -fopenmp -std=c99 -O2 -Wall %(source)s -o %(output)s -lm" 
     107    ARCH = "" 
     108    # Generic unix compile 
     109    # On mac users will need the X code command line tools installed 
     110    #COMPILE = "gcc-mp-4.7 -shared -fPIC -std=c99 -fopenmp -O2 -Wall %s -o %s -lm -lgomp" 
     111    CC = "cc -shared -fPIC -std=c99 -O2 -Wall".split() 
     112    # add openmp support if not running on a mac 
     113    if sys.platform != "darwin": 
     114        CC.append("-fopenmp") 
     115    def compile_command(source, output): 
     116        return CC + [source, "-o", output, "-lm"] 
    101117 
    102118# Windows-specific solution 
    … …  
    112128ALLOW_SINGLE_PRECISION_DLLS = True 
    113129 
     130def compile(source, output): 
     131    command = compile_command(source=source, output=output) 
     132    command_str = " ".join('"%s"'%p if ' ' in p else p for p in command) 
     133    logging.info(command_str) 
     134    try: 
     135        # need shell=True on windows to keep console box from popping up 
     136        shell = (os.name == 'nt') 
     137        subprocess.check_output(command, shell=shell, stderr=subprocess.STDOUT) 
     138    except subprocess.CalledProcessError as exc: 
     139        raise RuntimeError("compile failed.\n%s\n%s"%(command_str, exc.output)) 
     140    if not os.path.exists(output): 
     141        raise RuntimeError("compile failed.  File is in %r"%source) 
    114142 
    115143def dll_name(model_info, dtype): 
    … …  
    120148    """ 
    121149    bits = 8*dtype.itemsize 
    122     return "sas%d_%s"%(bits, model_info.id) 
     150    basename = "sas%d_%s"%(bits, model_info.id) 
     151    basename += ARCH + ".so" 
     152 
     153    # Hack to find precompiled dlls 
     154    path = joinpath(generate.DATA_PATH, '..', 'compiled_models', basename) 
     155    if os.path.exists(path): 
     156        return path 
     157 
     158    return joinpath(DLL_PATH, basename) 
    123159 
    124160 
    … …  
    161197    if not os.path.exists(dll): 
    162198        need_recompile = True 
    163     elif getattr(sys, 'frozen', False): 
     199    elif getattr(sys, 'frozen', None) is not None: 
    164200        # TODO: don't suppress time stamp 
    165201        # Currently suppressing recompile when running in a frozen environment 
    … …  
    173209        fid, filename = tempfile.mkstemp(suffix=".c", prefix=basename) 
    174210        source = generate.convert_type(source, dtype) 
    175         os.fdopen(fid, "w").write(source) 
    176         command = COMPILE%{"source":filename, "output":dll} 
    177         status = os.system(command) 
    178         if status != 0 or not os.path.exists(dll): 
    179             raise RuntimeError("compile failed.  File is in %r"%filename) 
    180         else: 
    181             ## comment the following to keep the generated c file 
    182             os.unlink(filename) 
    183             #print("saving compiled file in %r"%filename) 
     211        fd, filename = tempfile.mkstemp(suffix=".c", prefix=tempfile_prefix) 
     212        with os.fdopen(fd, "w") as file: 
     213            file.write(source) 
     214        compile(source=filename, output=dll) 
     215        # comment the following to keep the generated c file 
     216        # Note: if there is a syntax error then compile raises an error 
     217        # and the source file will not be deleted. 
     218        os.unlink(filename) 
     219        #print("saving compiled file in %r"%filename) 
    184220    return dll 
    185221 

  • sasmodels/models/core_shell_parallelepiped.py

    rec45c4f r500128b  
    66can be different on all three (pairs) of faces.** 
    77 
    8 The form factor is normalized by the particle volume *V* such that 
     8The form factor is normalized by the particle volume $V$ such that 
    99 
    10 *I(q)* = *scale* \* <*f*\ :sup:`2`> / *V* + *background* 
     10.. math:: 
    1111 
    12 where < > is an average over all possible orientations of the rectangular solid. 
     12    I(q) = \text{scale}\frac{\langle f^2 \rangle}{V} + \text{background} 
     13 
     14where $\langle \ldots \rangle$ is an average over all possible orientations 
     15of the rectangular solid. 
    1316 
    1417An instrument resolution smeared version of the model is also provided. 
    … …  
    1922 
    2023The function calculated is the form factor of the rectangular solid below. 
    21 The core of the solid is defined by the dimensions *A*, *B*, *C* such that 
    22 *A* < *B* < *C*. 
     24The core of the solid is defined by the dimensions $A$, $B$, $C$ such that 
     25$A < B < C$. 
    2326 
    2427.. image:: img/core_shell_parallelepiped_geometry.jpg 
    2528 
    26 There are rectangular "slabs" of thickness $t_A$ that add to the *A* dimension 
    27 (on the *BC* faces). There are similar slabs on the *AC* $(=t_B)$ and *AB* 
    28 $(=t_C)$ faces. The projection in the *AB* plane is then 
     29There are rectangular "slabs" of thickness $t_A$ that add to the $A$ dimension 
     30(on the $BC$ faces). There are similar slabs on the $AC$ $(=t_B)$ and $AB$ 
     31$(=t_C)$ faces. The projection in the $AB$ plane is then 
    2932 
    3033.. image:: img/core_shell_parallelepiped_projection.jpg 
    … …  
    4346 
    4447**For the calculation of the form factor to be valid, the sides of the solid 
    45 MUST be chosen such that** *A* < *B* < *C*. 
     48MUST be chosen such that** $A < B < C$. 
    4649**If this inequality is not satisfied, the model will not report an error, 
    4750and the calculation will not be correct.** 
    … …  
    4952FITTING NOTES 
    5053If the scale is set equal to the particle volume fraction, |phi|, the returned 
    51 value is the scattered intensity per unit volume; ie, *I(q)* = |phi| *P(q)*. 
     54value is the scattered intensity per unit volume, $I(q) = \phi P(q)$. 
    5255However, **no interparticle interference effects are included in this calculation.** 
    5356 
    … …  
    5659 
    5760Constraints must be applied during fitting to ensure that the inequality 
    58 *A* < *B* < *C* is not violated. The calculation will not report an error, 
     61$A < B < C$ is not violated. The calculation will not report an error, 
    5962but the results will not be correct. 
    6063 
    … …  
    6467based on the the averaged effective radius $(=\sqrt{(A+2t_A)(B+2t_B)/\pi})$ 
    6568and length $(C+2t_C)$ values, and used as the effective radius 
    66 for *S(Q)* when *P(Q)* \* *S(Q)* is applied. 
     69for $S(Q)$ when $P(Q) * S(Q)$ is applied. 
    6770 
    6871.. Comment by Miguel Gonzalez: 
    … …  
    7174 
    7275To provide easy access to the orientation of the parallelepiped, we define the 
    73 axis of the cylinder using three angles |theta|, |phi| and |bigpsi|. 
     76axis of the cylinder using three angles $\theta$, $\phi$ and $\Psi$. 
    7477(see :ref:`cylinder orientation <cylinder-angle-definition>`). 
    75 The angle |bigpsi| is the rotational angle around the *long_c* axis against the 
    76 *q* plane. For example, |bigpsi| = 0 when the *short_b* axis is parallel to the 
     78The angle $\Psi$ is the rotational angle around the *long_c* axis against the 
     79$q$ plane. For example, $\Psi = 0$ when the *short_b* axis is parallel to the 
    7780*x*-axis of the detector. 
    7881 

  • sasmodels/models/hollow_rectangular_prism.py

    rec45c4f r117090a  
    33r""" 
    44 
    5 This model provides the form factor, *P(q)*, for a hollow rectangular 
    6 parallelepiped with a wall of thickness |bigdelta|. 
     5This model provides the form factor, $P(q)$, for a hollow rectangular 
     6parallelepiped with a wall of thickness $\Delta$. 
    77It computes only the 1D scattering, not the 2D. 
    88 
    … …  
    2424  \int_0^{\frac{\pi}{2}} A_{P\Delta}^2(q) \, \sin\theta \, d\theta \, d\phi 
    2525 
    26 where |theta| is the angle between the *z* axis and the longest axis 
    27 of the parallelepiped, |phi| is the angle between the scattering vector 
    28 (lying in the *xy* plane) and the *y* axis, and 
     26where $\theta$ is the angle between the $z$ axis and the longest axis 
     27of the parallelepiped, $\phi$ is the angle between the scattering vector 
     28(lying in the $xy$ plane) and the $y$ axis, and 
    2929 
    3030.. math:: 
    … …  
    4949  \end{align} 
    5050 
    51 where *A*, *B* and *C* are the external sides of the parallelepiped fulfilling 
    52 :math:`A \le B \le C`, and the volume *V* of the parallelepiped is 
     51where $A$, $B$ and $C$ are the external sides of the parallelepiped fulfilling 
     52$A \le B \le C$, and the volume $V$ of the parallelepiped is 
    5353 
    5454.. math:: 
    … …  
    5858 
    5959.. math:: 
    60   I(q) = \mbox{scale} \times V \times (\rho_{\mbox{p}} - 
    61   \rho_{\mbox{solvent}})^2 \times P(q) 
     60  I(q) = \text{scale} \times V \times (\rho_{\text{p}} - 
     61  \rho_{\text{solvent}})^2 \times P(q) + \text{background} 
    6262 
    63 where :math:`\rho_{\mbox{p}}` is the scattering length of the parallelepiped, 
    64 :math:`\rho_{\mbox{solvent}}` is the scattering length of the solvent, 
     63where $\rho_{\text{p}}$ is the scattering length of the parallelepiped, 
     64$\rho_{\text{solvent}}$ is the scattering length of the solvent, 
    6565and (if the data are in absolute units) *scale* represents the volume fraction 
    6666(which is unitless). 

  • sasmodels/models/lamellar.py

    rd2bb604 r500128b  
    99.. math:: 
    1010 
    11     I(q) = scale*\frac{2\pi P(q)}{q^2\delta } 
     11    I(q) = \text{scale}\frac{2\pi P(q)}{q^2\delta} + \text{background} 
    1212 
    1313 
    … …  
    1616.. math:: 
    1717 
    18    P(q) = \frac{2\Delta\rho^2}{q^2}(1-cos(q\delta)) = \frac{4\Delta\rho^2}{q^2}sin^2(\frac{q\delta}{2}) 
     18   P(q) = \frac{2\Delta\rho^2}{q^2}(1-\cos(q\delta)) 
     19        = \frac{4\Delta\rho^2}{q^2}\sin^2\left(\frac{q\delta}{2}\right) 
    1920 
    2021where $\delta$ is the total layer thickness and $\Delta\rho$ is the scattering length density difference. 

  • sasmodels/models/sc_paracrystal.py

    rec45c4f r500128b  
    1313.. math:: 
    1414 
    15     I(q) = \frac{scale}{V_p}V_{lattice}P(q)Z(q) 
     15    I(q) = \text{scale}\frac{V_\text{lattice}P(q)Z(q)}{V_p} + \text{background} 
    1616 
    1717where scale is the volume fraction of spheres, $V_p$ is the volume of 
    18 the primary particle, $V_{lattice}$ is a volume correction for the crystal 
     18the primary particle, $V_\text{lattice}$ is a volume correction for the crystal 
    1919structure, $P(q)$ is the form factor of the sphere (normalized), and 
    2020$Z(q)$ is the paracrystalline structure factor for a simple cubic structure. 
    … …  
    2828.. math:: 
    2929 
    30     V_{lattice}=\frac{4\pi}{3}\frac{R^3}{D^3} 
     30    V_\text{lattice}=\frac{4\pi}{3}\frac{R^3}{D^3} 
    3131 
    3232The distortion factor (one standard deviation) of the paracrystal is included 

  • sasmodels/models/squarewell.py

    rd2bb604 raa9e4e3  
    1414The interaction potential is: 
    1515 
    16   .. image:: img\squarewell.png 
     16  .. image:: img/squarewell.png 
    1717 
    1818.. math:: 

  • sasmodels/sasview_model.py

    rf36c1b7 rfa800e72  
    55create a sasview model class to run that kernel as follows:: 
    66 
    7     from sasmodels.sasview_model import make_class 
    8     from sasmodels.models import cylinder 
    9     CylinderModel = make_class(cylinder, dtype='single') 
    10  
    11 The model parameters for sasmodels are different from those in sasview. 
    12 When reloading previously saved models, the parameters should be converted 
    13 using :func:`sasmodels.convert.convert`. 
     7    from sasmodels.sasview_model import load_custom_model 
     8    CylinderModel = load_custom_model('sasmodels/models/cylinder.py') 
    149""" 
    1510from __future__ import print_function 
    … …  
    4944) 
    5045 
     46MODELS = {} 
     47def find_model(modelname): 
     48    # TODO: used by sum/product model to load an existing model 
     49    # TODO: doesn't handle custom models properly 
     50    if modelname.endswith('.py'): 
     51        return load_custom_model(modelname) 
     52    elif modelname in MODELS: 
     53        return MODELS[modelname] 
     54    else: 
     55        raise ValueError("unknown model %r"%modelname) 
     56 
     57 
    5158# TODO: figure out how to say that the return type is a subclass 
    5259def load_standard_models(): 
    … …  
    6168    for name in core.list_models(): 
    6269        try: 
    63             models.append(_make_standard_model(name)) 
     70            MODELS[name] = _make_standard_model(name) 
     71            models.append(MODELS[name]) 
    6472        except Exception: 
    6573            logging.error(traceback.format_exc()) 
    … …  
    7280    Load a custom model given the model path. 
    7381    """ 
     82    #print("load custom model", path) 
    7483    kernel_module = custom.load_custom_kernel_module(path) 
    75     model_info = modelinfo.make_model_info(kernel_module) 
    76     return _make_model_from_info(model_info) 
     84    try: 
     85        model = kernel_module.Model 
     86    except AttributeError: 
     87        model_info = modelinfo.make_model_info(kernel_module) 
     88        model = _make_model_from_info(model_info) 
     89    MODELS[model.name] = model 
     90    return model 
    7791 
    7892 
    … …  
    254268        self._persistency_dict = {} 
    255269        self.params = collections.OrderedDict() 
    256         self.dispersion = {} 
     270        self.dispersion = collections.OrderedDict() 
    257271        self.details = {} 
    258272        for p in self._model_info.parameters.user_parameters(): 
    … …  
    300314        :param par_name: the parameter name to check 
    301315        """ 
    302         return par_name.lower() in self.fixed 
     316        return par_name in self.fixed 
    303317        #For the future 
    304318        #return self.params[str(par_name)].is_fittable() 
    … …  
    337351        if len(toks) == 2: 
    338352            for item in self.dispersion.keys(): 
    339                 if item.lower() == toks[0].lower(): 
     353                if item == toks[0]: 
    340354                    for par in self.dispersion[item]: 
    341                         if par.lower() == toks[1].lower(): 
     355                        if par == toks[1]: 
    342356                            self.dispersion[item][par] = value 
    343357                            return 
    … …  
    345359            # Look for standard parameter 
    346360            for item in self.params.keys(): 
    347                 if item.lower() == name.lower(): 
     361                if item == name: 
    348362                    self.params[item] = value 
    349363                    return 
    … …  
    363377        if len(toks) == 2: 
    364378            for item in self.dispersion.keys(): 
    365                 if item.lower() == toks[0].lower(): 
     379                if item == toks[0]: 
    366380                    for par in self.dispersion[item]: 
    367                         if par.lower() == toks[1].lower(): 
     381                        if par == toks[1]: 
    368382                            return self.dispersion[item][par] 
    369383        else: 
    370384            # Look for standard parameter 
    371385            for item in self.params.keys(): 
    372                 if item.lower() == name.lower(): 
     386                if item == name: 
    373387                    return self.params[item] 
    374388 
    … …  
    391405        """ 
    392406        # TODO: fix test so that parameter order doesn't matter 
    393         ret = ['%s.%s' % (p.name.lower(), ext) 
     407        ret = ['%s.%s' % (p.name, ext) 
    394408               for p in self._model_info.parameters.user_parameters() 
    395409               for ext in ('npts', 'nsigmas', 'width') 
    … …  
    544558        :param dispersion: dispersion object of type Dispersion 
    545559        """ 
    546         if parameter.lower() in (s.lower() for s in self.params.keys()): 
     560        if parameter in self.params: 
    547561            # TODO: Store the disperser object directly in the model. 
    548             # The current method of creating one on the fly whenever it is 
    549             # needed is kind of funky. 
     562            # The current method of relying on the sasview GUI to 
     563            # remember them is kind of funky. 
    550564            # Note: can't seem to get disperser parameters from sasview 
    551565            # (1) Could create a sasview model that has not yet # been 

  • sasmodels/weights.py

    ra936688 rfa800e72  
    205205    v, w = obj.get_weights(value, limits[0], limits[1], relative) 
    206206    return v, w 
    207  
    208 # Hack to allow sasview dispersion objects to interoperate with sasmodels 
    209 dispersers = dict((v.__name__, k) for k, v in MODELS.items()) 
    210 dispersers['DispersionModel'] = RectangleDispersion.type 
    211  

  • setup.py

    re9d10a6 r3a161d0  
    2121    version=find_version('sasmodels'), 
    2222    description="sasmodels package", 
    23     long_description=open('README.md').read(), 
     23    long_description=open('README.rst').read(), 
    2424    author="SasView Collaboration", 
    2525    author_email="management@sasview.org", 
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