Changeset 70bbb74 in sasmodels

Timestamp:

Mar 17, 2016 3:57:42 AM (8 years ago)

Author:

gonzalezm

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:

c5dadbb

Parents:

fcd7bbd

Message:

Autogenerate 1D figures for documentation

File:

• doc/genmodel.py (modified) (2 diffs)

doc/genmodel.py

@@ -1 @@
-import sys, os
+import sys, os, math, re
+import numpy as np
+import matplotlib.pyplot as plt
 sys.path.insert(0, os.path.abspath('..'))
 from sasmodels import generate, core
+from sasmodels.direct_model import DirectModel
+from sasmodels.data import empty_data1D, empty_data2D
+
 
 # Convert ../sasmodels/models/name.py to name
@@ -8 +13 @@
 # Load the doc string from the module definition file and store it in rst
 docstr = generate.make_doc(core.load_model_info(model_name))
+    
+# Generate automatically plot of the model and add it to rst documentation
+
+info = core.load_model_info(model_name)
+
+# Calculate 1D curve for default parameters
+pars = dict((p[0], p[2]) for p in info['parameters'])
+
+# Plotting ranges and options
+opts = {
+        'xscale'    : 'log',
+        'yscale'    : 'log' if not info['structure_factor'] else 'linear',
+        'qmin'      : 0.005,
+        'qmax'      : 1.0,
+        'nq'        : 1000,
+        'nq2d'      : 100,
+}
+
+qmin, qmax, nq = opts['qmin'], opts['qmax'], opts['nq']
+qmin = math.log10(qmin)
+qmax = math.log10(qmax)
+q = np.logspace(qmin, qmax, nq)
+data = empty_data1D(q)
+model = core.load_model(model_name)
+calculator = DirectModel(data, model)
+Iq1D = calculator()
+
+# TO DO: Generation of 2D plots 
+# Problem in sasmodels.direct_model._calc_theory
+# There self._kernel.q_input.nq  gets a value of 0 in the 2D case
+# and returns a 0 numpy array (it does not call the C code)
+
+# If 2D model, compute 2D image
+#if info['has_2d'] != []:
+#    qmax, nq2d = opts['qmax'], opts['nq2d']
+#    data2d = empty_data2D(np.linspace(-qmax, qmax, nq2d), resolution=0.0) 
+#    #model = core.load_model(model_name)
+#    calculator = DirectModel(data2d, model)
+#    Iq2D = calculator()
+
+# Generate image (comment IF for 1D/2D for the moment) and generate only 1D
+#if info['has_2d'] == []:
+#    fig = plt.figure()
+#    ax = fig.add_subplot(1,1,1)
+#    ax.plot(q, Iq1D, color='blue', lw=2, label=model_name)
+#    ax.set_xlabel(r'$Q \/(\AA^{-1})$')
+#    ax.set_xscale(opts['xscale'])   
+#    ax.set_ylabel(r'$I(Q) \/(\mathrm{cm}^{-1})$')
+#    ax.set_yscale(opts['yscale'])  
+#    ax.legend()
+#else:
+#    # need figure with 1D + 2D
+#    pass
+fig = plt.figure()
+ax = fig.add_subplot(1,1,1)
+ax.plot(q, Iq1D, color='blue', lw=2, label=model_name)
+ax.set_xlabel(r'$Q \/(\AA^{-1})$')
+ax.set_xscale(opts['xscale'])   
+ax.set_ylabel(r'$I(Q) \/(\mathrm{cm}^{-1})$')
+ax.set_yscale(opts['yscale'])  
+ax.legend()
+ 
+
+# Save image in model/img
+figname = model_name + '_autogenfig.png'
+filename = os.path.join('model', 'img', figname)
+plt.savefig(filename)
+
+# Auto caption for figure
+captionstr = '\n'
+captionstr += '.. figure:: img/' + model_name + '_autogenfig.png\n'
+captionstr += '\n'
+#if info['has_2d'] == []:
+#    captionstr += '    1D plot corresponding to the default parameters of the model.\n'
+#else:
+#    captionstr += '    1D and 2D plots corresponding to the default parameters of the model.\n'
+captionstr += '    1D plot corresponding to the default parameters of the model.\n'
+captionstr += '\n'
+
+# Add figure reference and caption to documentation (at end, before References)
+pattern = '\*\*REFERENCE'
+m = re.search(pattern, docstr.upper())
+
+if m:
+    docstr1 = docstr[:m.start()]
+    docstr2 = docstr[m.start():]
+    docstr = docstr1 + captionstr + docstr2
+else:
+    print 'References NOT FOUND for model: ', model_name
+    docstr = docstr + captionstr
+
 open(sys.argv[2],'w').write(docstr)