Changes in / [c1799d3:a8a1d48] in sasmodels


Ignore:
Files:
6 added
6 deleted
7 edited

Legend:

Unmodified
Added
Removed

  • README.rst

    re30d645 r2a64722  
    1010is available. 
    1111 
    12 Example 
     12Install 
    1313------- 
     14 
     15The easiest way to use sasmodels is from `SasView <http://www.sasview.org/>`_. 
     16 
     17You can also install sasmodels as a standalone package in python. Use 
     18`miniconda <https://docs.conda.io/en/latest/miniconda.html>`_ 
     19or `anaconda <https://www.anaconda.com/>`_ 
     20to create a python environment with the sasmodels dependencies:: 
     21 
     22    $ conda create -n sasmodels -c conda-forge numpy scipy matplotlib pyopencl 
     23 
     24The option ``-n sasmodels`` names the environment sasmodels, and the option 
     25``-c conda-forge`` selects the conda-forge package channel because pyopencl 
     26is not part of the base anaconda distribution. 
     27 
     28Activate the environment and install sasmodels:: 
     29 
     30    $ conda activate sasmodels 
     31    (sasmodels) $ pip install sasmodels 
     32 
     33Install `bumps <https://github.com/bumps/bumps>`_ if you want to use it to fit 
     34your data:: 
     35 
     36    (sasmodels) $ pip install bumps 
     37 
     38Usage 
     39----- 
     40 
     41Check that the works:: 
     42 
     43    (sasmodels) $ python -m sasmodels.compare cylinder 
     44 
     45To show the orientation explorer:: 
     46 
     47    (sasmodels) $ python -m sasmodels.jitter 
     48 
     49Documentation is available online as part of the SasView 
     50`fitting perspective <http://www.sasview.org/docs/index.html>`_ 
     51as well as separate pages for 
     52`individual models <http://www.sasview.org/docs/user/sasgui/perspectives/fitting/models/index.html>`_. 
     53Programming details for sasmodels are available in the 
     54`developer documentation <http://www.sasview.org/docs/dev/dev.html>`_. 
     55 
     56 
     57Fitting Example 
     58--------------- 
    1459 
    1560The example directory contains a radial+tangential data set for an oriented 
    1661rod-like shape. 
    1762 
    18 The data is loaded by sas.dataloader from the sasview package, so sasview 
    19 is needed to run the example. 
     63To load the example data, you will need the SAS data loader from the sasview 
     64package. This is not yet available on PyPI, so you will need a copy of the 
     65SasView source code to run it.  Create a directory somewhere to hold the 
     66sasview and sasmodels source code, which we will refer to as $SOURCE. 
    2067 
    21 To run the example, you need sasview, sasmodels and bumps.  Assuming these 
    22 repositories are installed side by side, change to the sasmodels/example 
    23 directory and enter:: 
     68Use the following to install sasview, and the sasmodels examples:: 
    2469 
    25     PYTHONPATH=..:../../sasview/src ../../bumps/run.py fit.py \ 
    26         cylinder --preview 
     70    (sasmodels) $ cd $SOURCE 
     71    (sasmodels) $ conda install git 
     72    (sasmodels) $ git clone https://github.com/sasview/sasview.git 
     73    (sasmodels) $ git clone https://github.com/sasview/sasmodels.git 
    2774 
    28 See bumps documentation for instructions on running the fit.  With the 
    29 python packages installed, e.g., into a virtual environment, then the 
    30 python path need not be set, and the command would be:: 
     75Set the path to the sasview source on your python path within the sasmodels 
     76environment.  On Windows, this will be:: 
    3177 
    32     bumps fit.py cylinder --preview 
     78    (sasmodels)> set PYTHONPATH="$SOURCE\sasview\src" 
     79    (sasmodels)> cd $SOURCE/sasmodels/example 
     80    (sasmodels)> python -m bumps.cli fit.py cylinder --preview 
     81 
     82On Mac/Linux with the standard shell this will be:: 
     83 
     84    (sasmodels) $ export PYTHONPATH="$SOURCE/sasview/src" 
     85    (sasmodels) $ cd $SOURCE/sasmodels/example 
     86    (sasmodels) $ bumps fit.py cylinder --preview 
    3387 
    3488The fit.py model accepts up to two arguments.  The first argument is the 
    … …  
    3892both radial and tangential simultaneously, use the word "both". 
    3993 
    40 Notes 
    41 ----- 
    42  
    43 cylinder.c + cylinder.py is the cylinder model with renamed variables and 
    44 sld scaled by 1e6 so the numbers are nicer.  The model name is "cylinder" 
    45  
    46 lamellar.py is an example of a single file model with embedded C code. 
     94See `bumps documentation <https://bumps.readthedocs.io/>`_ for detailed 
     95instructions on running the fit. 
    4796 
    4897|TravisStatus|_ 

  • explore/beta/sasfit_compare.py

    r2a12351b r119073a  
    505505    } 
    506506 
    507     Q, IQ = load_sasfit(data_file('richard_test.txt')) 
    508     Q, IQSD = load_sasfit(data_file('richard_test2.txt')) 
    509     Q, IQBD = load_sasfit(data_file('richard_test3.txt')) 
     507    Q, IQ = load_sasfit(data_file('sasfit_sphere_schulz_IQD.txt')) 
     508    Q, IQSD = load_sasfit(data_file('sasfit_sphere_schulz_IQSD.txt')) 
     509    Q, IQBD = load_sasfit(data_file('sasfit_sphere_schulz_IQBD.txt')) 
    510510    target = Theory(Q=Q, F1=None, F2=None, P=IQ, S=None, I=IQSD, Seff=None, Ibeta=IQBD) 
    511511    actual = sphere_r(Q, norm="sasfit", **pars) 
    … …  
    526526    } 
    527527 
    528     Q, IQ = load_sasfit(data_file('richard_test4.txt')) 
    529     Q, IQSD = load_sasfit(data_file('richard_test5.txt')) 
    530     Q, IQBD = load_sasfit(data_file('richard_test6.txt')) 
     528    Q, IQ = load_sasfit(data_file('sasfit_ellipsoid_shulz_IQD.txt')) 
     529    Q, IQSD = load_sasfit(data_file('sasfit_ellipsoid_shulz_IQSD.txt')) 
     530    Q, IQBD = load_sasfit(data_file('sasfit_ellipsoid_shulz_IQBD.txt')) 
    531531    target = Theory(Q=Q, F1=None, F2=None, P=IQ, S=None, I=IQSD, Seff=None, Ibeta=IQBD) 
    532532    actual = ellipsoid_pe(Q, norm="sasfit", **pars) 

  • explore/precision.py

    rfba9ca0 rcd28947  
    207207    return model_info 
    208208 
    209 # Hack to allow second parameter A in two parameter functions 
     209# Hack to allow second parameter A in the gammainc and gammaincc functions. 
     210# Create a 2-D variant of the precision test if we need to handle other two 
     211# parameter functions. 
    210212A = 1 
    211213def parse_extra_pars(): 
     214    """ 
     215    Parse the command line looking for the second parameter "A=..." for the 
     216    gammainc/gammaincc functions. 
     217    """ 
    212218    global A 
    213219 
    … …  
    333339) 
    334340add_function( 
     341    # Note: "a" is given as A=... on the command line via parse_extra_pars 
    335342    name="gammainc(x)", 
    336343    mp_function=lambda x, a=A: mp.gammainc(a, a=0, b=x)/mp.gamma(a), 
    … …  
    339346) 
    340347add_function( 
     348    # Note: "a" is given as A=... on the command line via parse_extra_pars 
    341349    name="gammaincc(x)", 
    342350    mp_function=lambda x, a=A: mp.gammainc(a, a=x, b=mp.inf)/mp.gamma(a), 

  • sasmodels/generate.py

    r39a06c9 rcd28947  
    703703    """ 
    704704    for code in source: 
    705         m = _FQ_PATTERN.search(code) 
    706         if m is not None: 
     705        if _FQ_PATTERN.search(code) is not None: 
    707706            return True 
    708707    return False 
    … …  
    712711    # type: (List[str]) -> bool 
    713712    """ 
    714     Return True if C source defines "void Fq(". 
     713    Return True if C source defines "double shell_volume(". 
    715714    """ 
    716715    for code in source: 
    717         m = _SHELL_VOLUME_PATTERN.search(code) 
    718         if m is not None: 
     716        if _SHELL_VOLUME_PATTERN.search(code) is not None: 
    719717            return True 
    720718    return False 

  • sasmodels/kernel.py

    re44432d rcd28947  
    133133        nout = 2 if self.info.have_Fq and self.dim == '1d' else 1 
    134134        total_weight = self.result[nout*self.q_input.nq + 0] 
     135        # Note: total_weight = sum(weight > cutoff), with cutoff >= 0, so it 
     136        # is okay to test directly against zero.  If weight is zero then I(q), 
     137        # etc. must also be zero. 
    135138        if total_weight == 0.: 
    136139            total_weight = 1. 

  • sasmodels/models/pearl_necklace.c

    r99658f6 r9b5fd42  
    4040    const double si = sas_sinx_x(q*A_s); 
    4141    const double omsi = 1.0 - si; 
    42     const double pow_si = pow(si, num_pearls); 
     42    const double pow_si = pown(si, num_pearls); 
    4343 
    4444    // form factor for num_pearls 
    … …  
    8181radius_from_volume(double radius, double edge_sep, double thick_string, double fp_num_pearls) 
    8282{ 
    83     const int num_pearls = (int) fp_num_pearls +0.5; 
    8483    const double vol_tot = form_volume(radius, edge_sep, thick_string, fp_num_pearls); 
    8584    return cbrt(vol_tot/M_4PI_3); 

  • sasmodels/sasview_model.py

    r5024a56 r3a1afed  
    694694            return self._calculate_Iq(qx, qy) 
    695695 
    696     def _calculate_Iq(self, qx, qy=None, Fq=False, effective_radius_type=1): 
     696    def _calculate_Iq(self, qx, qy=None): 
    697697        if self._model is None: 
    698698            self._model = core.build_model(self._model_info) 
    … …  
    714714        #print("values", values) 
    715715        #print("is_mag", is_magnetic) 
    716         if Fq: 
    717             result = calculator.Fq(call_details, values, cutoff=self.cutoff, 
    718                                    magnetic=is_magnetic, 
    719                                    effective_radius_type=effective_radius_type) 
    720716        result = calculator(call_details, values, cutoff=self.cutoff, 
    721717                            magnetic=is_magnetic) 
    … …  
    735731        Calculate the effective radius for P(q)*S(q) 
    736732 
     733        *mode* is the R_eff type, which defaults to 1 to match the ER 
     734        calculation for sasview models from version 3.x. 
     735 
    737736        :return: the value of the effective radius 
    738737        """ 
    739         Fq = self._calculate_Iq([0.1], True, mode) 
    740         return Fq[2] 
     738        # ER and VR are only needed for old multiplication models, based on 
     739        # sas.sascalc.fit.MultiplicationModel.  Fail for now.  If we want to 
     740        # continue supporting them then add some test cases so that the code 
     741        # is exercised.  We can access ER/VR using the kernel Fq function by 
     742        # extending _calculate_Iq so that it calls: 
     743        #    if er_mode > 0: 
     744        #        res = calculator.Fq(call_details, values, cutoff=self.cutoff, 
     745        #                            magnetic=False, effective_radius_type=mode) 
     746        #        R_eff, form_shell_ratio = res[2], res[4] 
     747        #        return R_eff, form_shell_ratio 
     748        # Then use the following in calculate_ER: 
     749        #    ER, VR = self._calculate_Iq(q=[0.1], er_mode=mode) 
     750        #    return ER 
     751        # Similarly, for calculate_VR: 
     752        #    ER, VR = self._calculate_Iq(q=[0.1], er_mode=1) 
     753        #    return VR 
     754        # Obviously a combined calculate_ER_VR method would be better, but 
     755        # we only need them to support very old models, so ignore the 2x 
     756        # performance hit. 
     757        raise NotImplementedError("ER function is no longer available.") 
    741758 
    742759    def calculate_VR(self): 
    … …  
    747764        :return: the value of the form:shell volume ratio 
    748765        """ 
    749         Fq = self._calculate_Iq([0.1], True, mode) 
    750         return Fq[4] 
     766        # See comments in calculate_ER. 
     767        raise NotImplementedError("VR function is no longer available.") 
    751768 
    752769    def set_dispersion(self, parameter, dispersion): 
Note: See TracChangeset for help on using the changeset viewer.