Changes in / [31d5187:cff2939] in sasmodels

Files:

• README.rst (modified) (2 diffs)
• explore/precision.py (modified) (3 diffs)
• sasmodels/compare.py (modified) (1 diff)
• sasmodels/direct_model.py (modified) (1 diff)
• sasmodels/generate.py (modified) (3 diffs)
• sasmodels/kernel.py (modified) (1 diff)
• sasmodels/modelinfo.py (modified) (6 diffs)
• sasmodels/models/hardsphere.py (modified) (1 diff)
• sasmodels/sasview_model.py (modified) (7 diffs)

README.rst

@@ -10 +10 @@
 is available.
 
-Install
+Example
 -------
-
-The easiest way to use sasmodels is from `SasView <http://www.sasview.org/>`_.
-
-You can also install sasmodels as a standalone package in python. Use
-`miniconda <https://docs.conda.io/en/latest/miniconda.html>`_
-or `anaconda <https://www.anaconda.com/>`_
-to create a python environment with the sasmodels dependencies::
-
-    $ conda create -n sasmodels -c conda-forge numpy scipy matplotlib pyopencl
-
-The option ``-n sasmodels`` names the environment sasmodels, and the option
-``-c conda-forge`` selects the conda-forge package channel because pyopencl
-is not part of the base anaconda distribution.
-
-Activate the environment and install sasmodels::
-
-    $ conda activate sasmodels
-    (sasmodels) $ pip install sasmodels
-
-Install `bumps <https://github.com/bumps/bumps>`_ if you want to use it to fit
-your data::
-
-    (sasmodels) $ pip install bumps
-
-Usage
------
-
-Check that the works::
-
-    (sasmodels) $ python -m sasmodels.compare cylinder
-
-To show the orientation explorer::
-
-    (sasmodels) $ python -m sasmodels.jitter
-
-Documentation is available online as part of the SasView
-`fitting perspective <http://www.sasview.org/docs/index.html>`_
-as well as separate pages for
-`individual models <http://www.sasview.org/docs/user/sasgui/perspectives/fitting/models/index.html>`_.
-Programming details for sasmodels are available in the
-`developer documentation <http://www.sasview.org/docs/dev/dev.html>`_.
-
-
-Fitting Example
----------------
 
 The example directory contains a radial+tangential data set for an oriented
 rod-like shape.
 
-To load the example data, you will need the SAS data loader from the sasview
-package. This is not yet available on PyPI, so you will need a copy of the
-SasView source code to run it.  Create a directory somewhere to hold the
-sasview and sasmodels source code, which we will refer to as $SOURCE.
+The data is loaded by sas.dataloader from the sasview package, so sasview
+is needed to run the example.
 
-Use the following to install sasview, and the sasmodels examples::
+To run the example, you need sasview, sasmodels and bumps.  Assuming these
+repositories are installed side by side, change to the sasmodels/example
+directory and enter::
 
-    (sasmodels) $ cd $SOURCE
-    (sasmodels) $ conda install git
-    (sasmodels) $ git clone https://github.com/sasview/sasview.git
-    (sasmodels) $ git clone https://github.com/sasview/sasmodels.git
+    PYTHONPATH=..:../../sasview/src ../../bumps/run.py fit.py \
+        cylinder --preview
 
-Set the path to the sasview source on your python path within the sasmodels
-environment.  On Windows, this will be::
+See bumps documentation for instructions on running the fit.  With the
+python packages installed, e.g., into a virtual environment, then the
+python path need not be set, and the command would be::
 
-    (sasmodels)> set PYTHONPATH="$SOURCE\sasview\src"
-    (sasmodels)> cd $SOURCE/sasmodels/example
-    (sasmodels)> python -m bumps.cli fit.py cylinder --preview
-
-On Mac/Linux with the standard shell this will be::
-
-    (sasmodels) $ export PYTHONPATH="$SOURCE/sasview/src"
-    (sasmodels) $ cd $SOURCE/sasmodels/example
-    (sasmodels) $ bumps fit.py cylinder --preview
+    bumps fit.py cylinder --preview
 
 The fit.py model accepts up to two arguments.  The first argument is the
@@ -92 +38 @@
 both radial and tangential simultaneously, use the word "both".
 
-See `bumps documentation <https://bumps.readthedocs.io/>`_ for detailed
-instructions on running the fit.
+Notes
+-----
+
+cylinder.c + cylinder.py is the cylinder model with renamed variables and
+sld scaled by 1e6 so the numbers are nicer.  The model name is "cylinder"
+
+lamellar.py is an example of a single file model with embedded C code.
 
 |TravisStatus|_

explore/precision.py

@@ -207 +207 @@
     return model_info
 
-# Hack to allow second parameter A in the gammainc and gammaincc functions.
-# Create a 2-D variant of the precision test if we need to handle other two
-# parameter functions.
+# Hack to allow second parameter A in two parameter functions
 A = 1
 def parse_extra_pars():
-    """
-    Parse the command line looking for the second parameter "A=..." for the
-    gammainc/gammaincc functions.
-    """
     global A
 
@@ -339 +333 @@
 )
 add_function(
-    # Note: "a" is given as A=... on the command line via parse_extra_pars
     name="gammainc(x)",
     mp_function=lambda x, a=A: mp.gammainc(a, a=0, b=x)/mp.gamma(a),
@@ -346 +339 @@
 )
 add_function(
-    # Note: "a" is given as A=... on the command line via parse_extra_pars
     name="gammaincc(x)",
     mp_function=lambda x, a=A: mp.gammainc(a, a=x, b=mp.inf)/mp.gamma(a),

sasmodels/compare.py

@@ -1152 +1152 @@
         'rel_err'   : True,
         'explore'   : False,
-        'use_demo'  : False,
+        'use_demo'  : True,
         'zero'      : False,
         'html'      : False,

sasmodels/direct_model.py

@@ -332 +332 @@
 
         # Need to pull background out of resolution for multiple scattering
-        default_background = self._model.info.parameters.common_parameters[1].default
-        background = pars.get('background', default_background)
+        background = pars.get('background', DEFAULT_BACKGROUND)
         pars = pars.copy()
         pars['background'] = 0.

sasmodels/generate.py

@@ -703 +703 @@
     """
     for code in source:
-        if _FQ_PATTERN.search(code) is not None:
+        m = _FQ_PATTERN.search(code)
+        if m is not None:
             return True
     return False
@@ -711 +712 @@
     # type: (List[str]) -> bool
     """
-    Return True if C source defines "double shell_volume(".
+    Return True if C source defines "void Fq(".
     """
     for code in source:
-        if _SHELL_VOLUME_PATTERN.search(code) is not None:
+        m = _SHELL_VOLUME_PATTERN.search(code)
+        if m is not None:
             return True
     return False
@@ -1006 +1008 @@
         pars = model_info.parameters.kernel_parameters
     else:
-        pars = (model_info.parameters.common_parameters
-                + model_info.parameters.kernel_parameters)
+        pars = model_info.parameters.COMMON + model_info.parameters.kernel_parameters
     partable = make_partable(pars)
     subst = dict(id=model_info.id.replace('_', '-'),

sasmodels/kernel.py

@@ -133 +133 @@
         nout = 2 if self.info.have_Fq and self.dim == '1d' else 1
         total_weight = self.result[nout*self.q_input.nq + 0]
-        # Note: total_weight = sum(weight > cutoff), with cutoff >= 0, so it
-        # is okay to test directly against zero.  If weight is zero then I(q),
-        # etc. must also be zero.
         if total_weight == 0.:
             total_weight = 1.

sasmodels/modelinfo.py

@@ -404 +404 @@
       parameters counted as n individual parameters p1, p2, ...
 
-    * *common_parameters* is the list of common parameters, with a unique
-      copy for each model so that structure factors can have a default
-      background of 0.0.
-
     * *call_parameters* is the complete list of parameters to the kernel,
       including scale and background, with vector parameters recorded as
@@ -420 +416 @@
     parameters don't use vector notation, and instead use p1, p2, ...
     """
+    # scale and background are implicit parameters
+    COMMON = [Parameter(*p) for p in COMMON_PARAMETERS]
+
     def __init__(self, parameters):
         # type: (List[Parameter]) -> None
-
-        # scale and background are implicit parameters
-        # Need them to be unique to each model in case they have different
-        # properties, such as default=0.0 for structure factor backgrounds.
-        self.common_parameters = [Parameter(*p) for p in COMMON_PARAMETERS]
-
         self.kernel_parameters = parameters
         self._set_vector_lengths()
@@ -475 +468 @@
                          if p.polydisperse and p.type not in ('orientation', 'magnetic'))
         self.pd_2d = set(p.name for p in self.call_parameters if p.polydisperse)
-
-    def set_zero_background(self):
-        """
-        Set the default background to zero for this model.  This is done for
-        structure factor models.
-        """
-        # type: () -> None
-        # Make sure background is the second common parameter.
-        assert self.common_parameters[1].id == "background"
-        self.common_parameters[1].default = 0.0
-        self.defaults = self._get_defaults()
 
     def check_angles(self):
@@ -585 +567 @@
     def _get_call_parameters(self):
         # type: () -> List[Parameter]
-        full_list = self.common_parameters[:]
+        full_list = self.COMMON[:]
         for p in self.kernel_parameters:
             if p.length == 1:
@@ -688 +670 @@
 
         # Gather the user parameters in order
-        result = control + self.common_parameters
+        result = control + self.COMMON
         for p in self.kernel_parameters:
             if not is2d and p.type in ('orientation', 'magnetic'):
@@ -788 +770 @@
 
     info = ModelInfo()
-
-    # Build the parameter table
     #print("make parameter table", kernel_module.parameters)
     parameters = make_parameter_table(getattr(kernel_module, 'parameters', []))
-
-    # background defaults to zero for structure factor models
-    structure_factor = getattr(kernel_module, 'structure_factor', False)
-    if structure_factor:
-        parameters.set_zero_background()
-
-    # TODO: remove demo parameters
-    # The plots in the docs are generated from the model default values.
-    # Sascomp set parameters from the command line, and so doesn't need
-    # demo values for testing.
     demo = expand_pars(parameters, getattr(kernel_module, 'demo', None))
-
     filename = abspath(kernel_module.__file__).replace('.pyc', '.py')
     kernel_id = splitext(basename(filename))[0]

sasmodels/models/hardsphere.py

@@ -162 +162 @@
     return pars
 
+demo = dict(radius_effective=200, volfraction=0.2,
+            radius_effective_pd=0.1, radius_effective_pd_n=40)
 # Q=0.001 is in the Taylor series, low Q part, so add Q=0.1,
 # assuming double precision sasview is correct

sasmodels/sasview_model.py

@@ -382 +382 @@
             hidden.add('scale')
             hidden.add('background')
+            self._model_info.parameters.defaults['background'] = 0.
 
         # Update the parameter lists to exclude any hidden parameters
@@ -694 +695 @@
             return self._calculate_Iq(qx, qy)
 
-    def _calculate_Iq(self, qx, qy=None):
+    def _calculate_Iq(self, qx, qy=None, Fq=False, effective_radius_type=1):
         if self._model is None:
             self._model = core.build_model(self._model_info)
@@ -714 +715 @@
         #print("values", values)
         #print("is_mag", is_magnetic)
+        if Fq:
+            result = calculator.Fq(call_details, values, cutoff=self.cutoff,
+                                   magnetic=is_magnetic,
+                                   effective_radius_type=effective_radius_type)
         result = calculator(call_details, values, cutoff=self.cutoff,
                             magnetic=is_magnetic)
@@ -731 +736 @@
         Calculate the effective radius for P(q)*S(q)
 
-        *mode* is the R_eff type, which defaults to 1 to match the ER
-        calculation for sasview models from version 3.x.
-
         :return: the value of the effective radius
         """
-        # ER and VR are only needed for old multiplication models, based on
-        # sas.sascalc.fit.MultiplicationModel.  Fail for now.  If we want to
-        # continue supporting them then add some test cases so that the code
-        # is exercised.  We can access ER/VR using the kernel Fq function by
-        # extending _calculate_Iq so that it calls:
-        #    if er_mode > 0:
-        #        res = calculator.Fq(call_details, values, cutoff=self.cutoff,
-        #                            magnetic=False, effective_radius_type=mode)
-        #        R_eff, form_shell_ratio = res[2], res[4]
-        #        return R_eff, form_shell_ratio
-        # Then use the following in calculate_ER:
-        #    ER, VR = self._calculate_Iq(q=[0.1], er_mode=mode)
-        #    return ER
-        # Similarly, for calculate_VR:
-        #    ER, VR = self._calculate_Iq(q=[0.1], er_mode=1)
-        #    return VR
-        # Obviously a combined calculate_ER_VR method would be better, but
-        # we only need them to support very old models, so ignore the 2x
-        # performance hit.
-        raise NotImplementedError("ER function is no longer available.")
+        Fq = self._calculate_Iq([0.1], True, mode)
+        return Fq[2]
 
     def calculate_VR(self):
@@ -764 +748 @@
         :return: the value of the form:shell volume ratio
         """
-        # See comments in calculate_ER.
-        raise NotImplementedError("VR function is no longer available.")
+        Fq = self._calculate_Iq([0.1], True, mode)
+        return Fq[4]
 
     def set_dispersion(self, parameter, dispersion):
@@ -930 +914 @@
     CylinderModel().evalDistribution([0.1, 0.1])
 
-def test_structure_factor_background():
-    # type: () -> None
-    """
-    Check that sasview model and direct model match, with background=0.
-    """
-    from .data import empty_data1D
-    from .core import load_model_info, build_model
-    from .direct_model import DirectModel
-
-    model_name = "hardsphere"
-    q = [0.0]
-
-    sasview_model = _make_standard_model(model_name)()
-    sasview_value = sasview_model.evalDistribution(np.array(q))[0]
-
-    data = empty_data1D(q)
-    model_info = load_model_info(model_name)
-    model = build_model(model_info)
-    direct_model = DirectModel(data, model)
-    direct_value_zero_background = direct_model(background=0.0)
-
-    assert sasview_value == direct_value_zero_background
-
-    # Additionally check that direct value background defaults to zero
-    direct_value_default = direct_model()
-    assert sasview_value == direct_value_default
-
-
 def magnetic_demo():
     Model = _make_standard_model('sphere')
@@ -978 +934 @@
     #print("rpa:", test_rpa())
     #test_empty_distribution()
-    #test_structure_factor_background()