Changeset ff7119b in sasmodels for sasmodels/bumps_model.py

Timestamp:

Aug 26, 2014 8:27:06 PM (10 years ago)

Author:

Paul Kienzle <pkienzle@…>

Branches:

master, core_shell_microgels, costrafo411, magnetic_model, release_v0.94, release_v0.95, ticket-1257-vesicle-product, ticket_1156, ticket_1265_superball, ticket_822_more_unit_tests

Children:

5d4777d

Parents:

a7684e5

Message:

docu update

File:

• sasmodels/bumps_model.py (moved) (moved from sasmodels/core.py) (9 diffs)

sasmodels/bumps_model.py

@@ -1 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
+"""
+Sasmodels core.
+"""
 import sys, os
 import datetime
-import warnings
 
 import numpy as np
 
 
-def opencl_model(kernel_module, dtype="single"):
-    from sasmodels import gen, gpu
-
-    source, info = gen.make(kernel_module)
-    ## for debugging, save source to a .cl file, edit it, and reload as model
-    #open(modelname+'.cl','w').write(source)
-    #source = open(modelname+'.cl','r').read()
-    return gpu.GpuModel(source, info, dtype)
-
-
-if sys.platform == 'darwin':
-    COMPILE = "gcc-mp-4.7 -shared -fPIC -std=c99 -fopenmp -O2 -Wall %s -o %s -lm -lgomp"
-elif os.name == 'nt':
-    COMPILE = "gcc -shared -fPIC -std=c99 -fopenmp -O2 -Wall %s -o %s -lm"
-else:
-    COMPILE = "cc -shared -fPIC -std=c99 -fopenmp -O2 -Wall %s -o %s -lm"
-DLL_PATH = "/tmp"
-
-
-def dll_path(info):
-    from os.path import join as joinpath, split as splitpath, splitext
-    basename = splitext(splitpath(info['filename'])[1])[0]
-    return joinpath(DLL_PATH, basename+'.so')
-
-
-def dll_model(kernel_module):
-    import os
-    import tempfile
-    from sasmodels import gen, dll
-
-    source, info = gen.make(kernel_module)
-    dllpath = dll_path(info)
-    if not os.path.exists(dllpath) \
-            or (os.path.getmtime(dllpath) < os.path.getmtime(info['filename'])):
-        # Replace with a proper temp file
-        srcfile = tempfile.mkstemp(suffix=".c",prefix="sas_"+info['name'])
-        open(srcfile, 'w').write(source)
-        os.system(COMPILE%(srcfile, dllpath))
-        ## comment the following to keep the generated c file
-        #os.unlink(srcfile)
-    return dll.DllModel(dllpath, info)
-
-
-TIC = None
 def tic():
-    global TIC
+    """
+    Timer function.
+
+    Use "toc=tic()" to start the clock and "toc()" to measure
+    a time interval.
+    """
     then = datetime.datetime.now()
-    TIC = lambda: (datetime.datetime.now()-then).total_seconds()
-    return TIC
-
-
-def toc():
-    return TIC()
+    return lambda: (datetime.datetime.now()-then).total_seconds()
 
 
 def load_data(filename):
+    """
+    Load data using a sasview loader.
+    """
     from sans.dataloader.loader import Loader
     loader = Loader()
@@ -73 +31 @@
 
 
+def empty_data1D(q):
+    """
+    Create empty 1D data using the given *q* as the x value.
+
+    Resolutions dq/q is 5%.
+    """
+
+    from sans.dataloader.data_info import Data1D
+
+    Iq = 100*np.ones_like(q)
+    dIq = np.sqrt(Iq)
+    data = Data1D(q, Iq, dx=0.05*q, dy=dIq)
+    data.filename = "fake data"
+    data.qmin, data.qmax = q.min(), q.max()
+    return data
+
+
 def empty_data2D(qx, qy=None):
+    """
+    Create empty 2D data using the given mesh.
+
+    If *qy* is missing, create a square mesh with *qy=qx*.
+
+    Resolution dq/q is 5%.
+    """
     from sans.dataloader.data_info import Data2D, Detector
 
@@ -114 +96 @@
 
 
-def empty_data1D(q):
-    from sans.dataloader.data_info import Data1D
-
-    Iq = 100*np.ones_like(q)
-    dIq = np.sqrt(Iq)
-    data = Data1D(q, Iq, dx=0.05*q, dy=dIq)
-    data.filename = "fake data"
-    data.qmin, data.qmax = q.min(), q.max()
-    return data
-
-
 def set_beam_stop(data, radius, outer=None):
+    """
+    Add a beam stop of the given *radius*.  If *outer*, make an annulus.
+    """
     from sans.dataloader.manipulations import Ringcut
     if hasattr(data, 'qx_data'):
@@ -138 +112 @@
 
 def set_half(data, half):
+    """
+    Select half of the data, either "right" or "left".
+    """
     from sans.dataloader.manipulations import Boxcut
     if half == 'right':
@@ -146 +123 @@
 
 def set_top(data, max):
+    """
+    Chop the top off the data, above *max*.
+    """
     from sans.dataloader.manipulations import Boxcut
     data.mask += Boxcut(x_min=-np.inf, x_max=np.inf, y_min=-np.inf, y_max=max)(data)
@@ -151 +131 @@
 
 def plot_data(data, iq, vmin=None, vmax=None, scale='log'):
+    """
+    Plot the target value for the data.  This could be the data itself,
+    the theory calculation, or the residuals.
+
+    *scale* can be 'log' for log scale data, or 'linear'.
+    """
     from numpy.ma import masked_array, masked
     import matplotlib.pyplot as plt
@@ -172 +158 @@
 
 
-def plot_result2D(data, theory, view='log'):
+def _plot_result1D(data, theory, view):
+    """
+    Plot the data and residuals for 1D data.
+    """
+    import matplotlib.pyplot as plt
+    from numpy.ma import masked_array, masked
+    #print "not a number",sum(np.isnan(data.y))
+    #data.y[data.y<0.05] = 0.5
+    mdata = masked_array(data.y, data.mask)
+    mdata[np.isnan(mdata)] = masked
+    if view is 'log':
+        mdata[mdata <= 0] = masked
+    mtheory = masked_array(theory, mdata.mask)
+    mresid = masked_array((theory-data.y)/data.dy, mdata.mask)
+
+    plt.subplot(121)
+    plt.errorbar(data.x, mdata, yerr=data.dy)
+    plt.plot(data.x, mtheory, '-', hold=True)
+    plt.yscale(view)
+    plt.subplot(122)
+    plt.plot(data.x, mresid, 'x')
+    #plt.axhline(1, color='black', ls='--',lw=1, hold=True)
+    #plt.axhline(0, color='black', lw=1, hold=True)
+    #plt.axhline(-1, color='black', ls='--',lw=1, hold=True)
+
+
+def _plot_result2D(data, theory, view):
+    """
+    Plot the data and residuals for 2D data.
+    """
     import matplotlib.pyplot as plt
     resid = (theory-data.data)/data.err_data
@@ -185 +200 @@
     plt.colorbar()
 
-
-def plot_result1D(data, theory, view='log'):
-    import matplotlib.pyplot as plt
-    from numpy.ma import masked_array, masked
-    #print "not a number",sum(np.isnan(data.y))
-    #data.y[data.y<0.05] = 0.5
-    mdata = masked_array(data.y, data.mask)
-    mdata[np.isnan(mdata)] = masked
-    if view is 'log':
-        mdata[mdata <= 0] = masked
-    mtheory = masked_array(theory, mdata.mask)
-    mresid = masked_array((theory-data.y)/data.dy, mdata.mask)
-
-    plt.subplot(121)
-    plt.errorbar(data.x, mdata, yerr=data.dy)
-    plt.plot(data.x, mtheory, '-', hold=True)
-    plt.yscale(view)
-    plt.subplot(122)
-    plt.plot(data.x, mresid, 'x')
-    #plt.axhline(1, color='black', ls='--',lw=1, hold=True)
-    #plt.axhline(0, color='black', lw=1, hold=True)
-    #plt.axhline(-1, color='black', ls='--',lw=1, hold=True)
+def plot_result(data, theory, view='log'):
+    """
+    Plot the data and residuals.
+    """
+    if hasattr(data, 'qx_data'):
+        _plot_result2D(data, theory, view)
+    else:
+        _plot_result1D(data, theory, view)
 
 
 class BumpsModel(object):
+    """
+    Return a bumps wrapper for a SAS model.
+
+    *data* is the data to be fitted.
+
+    *model* is the SAS model, e.g., from :func:`gen.opencl_model`.
+
+    *cutoff* is the integration cutoff, which avoids computing the
+    the SAS model where the polydispersity weight is low.
+
+    Model parameters can be initialized with additional keyword
+    arguments, or by assigning to model.parameter_name.value.
+
+    The resulting bumps model can be used directly in a FitProblem call.
+    """
     def __init__(self, data, model, cutoff=1e-5, **kw):
         from bumps.names import Parameter
-        from . import gpu
 
         # interpret data
-        self.is2D = hasattr(data,'qx_data')
         self.data = data
-        if self.is2D:
+        if hasattr(data, 'qx_data'):
             self.index = (data.mask==0) & (~np.isnan(data.data))
             self.iq = data.data[self.index]
@@ -294 +308 @@
 
     def plot(self, view='log'):
-        if self.is2D:
-            plot_result2D(self.data, self.theory(), view=view)
-        else:
-            plot_result1D(self.data, self.theory(), view=view)
+        plot_result(self.data, self.theory(), view=view)
 
     def save(self, basename):