Changeset 668c38b in sasmodels for sasmodels

Timestamp:

Apr 6, 2017 5:27:16 AM (7 years ago)

Author:

Adam Washington <adam.washington@…>

Branches:

master, core_shell_microgels, costrafo411, magnetic_model, ticket-1257-vesicle-product, ticket_1156, ticket_1265_superball, ticket_822_more_unit_tests

Children:

133103b

Parents:

9f91afe (diff), 650c6d2 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'master' into sesans_tof

Location:

sasmodels

Files:

• compare.py (modified) (13 diffs)
• core.py (modified) (1 diff)
• data.py (modified) (3 diffs)
• direct_model.py (modified) (1 diff)
• generate.py (modified) (1 diff)
• models/hayter_msa.py (modified) (1 diff)
• rst2html.py (modified) (2 diffs)
• sesans.py (modified) (3 diffs)

sasmodels/compare.py

@@ -30 +30 @@
 
 import sys
+import os
 import math
 import datetime
@@ -40 +41 @@
 from . import kerneldll
 from . import exception
-from .data import plot_theory, empty_data1D, empty_data2D
+from .data import plot_theory, empty_data1D, empty_data2D, load_data
 from .direct_model import DirectModel
 from .convert import revert_name, revert_pars, constrain_new_to_old
@@ -85 +86 @@
     -html shows the model docs instead of running the model
     -title="note" adds note to the plot title, after the model name
+    -data="path" uses q, dq from the data file
 
 Any two calculation engines can be selected for comparison:
@@ -544 +546 @@
     'f32': '32',
     'f64': '64',
+    'float16': '16',
+    'float32': '32',
+    'float64': '64',
+    'float128': '128',
     'longdouble': '128',
 }
@@ -747 +753 @@
     comp = opts['engines'][1] if have_comp else None
     data = opts['data']
+    use_data = have_base ^ have_comp
 
     # Plot if requested
@@ -763 +770 @@
     if have_base:
         if have_comp: plt.subplot(131)
-        plot_theory(data, base_value, view=view, use_data=False, limits=limits)
+        plot_theory(data, base_value, view=view, use_data=use_data, limits=limits)
         plt.title("%s t=%.2f ms"%(base.engine, base_time))
         #cbar_title = "log I"
@@ -769 +776 @@
         if have_base: plt.subplot(132)
         if not opts['is2d'] and have_base:
-            plot_theory(data, base_value, view=view, use_data=False, limits=limits)
-        plot_theory(data, comp_value, view=view, use_data=False, limits=limits)
+            plot_theory(data, base_value, view=view, use_data=use_data, limits=limits)
+        plot_theory(data, comp_value, view=view, use_data=use_data, limits=limits)
         plt.title("%s t=%.2f ms"%(comp.engine, comp_time))
         #cbar_title = "log I"
@@ -784 +791 @@
             err[err>cutoff] = cutoff
         #err,errstr = base/comp,"ratio"
-        plot_theory(data, None, resid=err, view=errview, use_data=False)
+        plot_theory(data, None, resid=err, view=errview, use_data=use_data)
         if view == 'linear':
             plt.xscale('linear')
@@ -834 +841 @@
 VALUE_OPTIONS = [
     # Note: random is both a name option and a value option
-    'cutoff', 'random', 'nq', 'res', 'accuracy', 'title',
+    'cutoff', 'random', 'nq', 'res', 'accuracy', 'title', 'data',
     ]
 
@@ -951 +958 @@
         'html'      : False,
         'title'     : None,
+        'data'      : None,
     }
     engines = []
@@ -971 +979 @@
         elif arg.startswith('-cutoff='):   opts['cutoff'] = float(arg[8:])
         elif arg.startswith('-random='):   opts['seed'] = int(arg[8:])
-        elif arg.startswith('-title'):     opts['title'] = arg[7:]
+        elif arg.startswith('-title='):    opts['title'] = arg[7:]
+        elif arg.startswith('-data='):     opts['data'] = arg[6:]
         elif arg == '-random':  opts['seed'] = np.random.randint(1000000)
         elif arg == '-preset':  opts['seed'] = -1
@@ -1112 +1121 @@
 
     # Create the computational engines
-    data, _ = make_data(opts)
+    if opts['data'] is not None:
+        data = load_data(os.path.expanduser(opts['data']))
+    else:
+        data, _ = make_data(opts)
     if n1:
         base = make_engine(model_info, data, engines[0], opts['cutoff'])
@@ -1142 +1154 @@
     show html docs for the model
     """
-    import wx  # type: ignore
-    from .generate import view_html_from_info
-    app = wx.App() if wx.GetApp() is None else None
-    view_html_from_info(opts['def'][0])
-    if app: app.MainLoop()
-
+    import os
+    from .generate import make_html
+    from . import rst2html
+
+    info = opts['def'][0]
+    html = make_html(info)
+    path = os.path.dirname(info.filename)
+    url = "file://"+path.replace("\\","/")[2:]+"/"
+    rst2html.view_html_qtapp(html, url)
 
 def explore(opts):

sasmodels/core.py

@@ -250 +250 @@
         dtype = "longdouble"
     elif dtype == "half":
-        dtype = "f16"
+        dtype = "float16"
 
     # Convert dtype string to numpy dtype.

sasmodels/data.py

@@ -54 +54 @@
     if data is None:
         raise IOError("Data %r could not be loaded" % filename)
+    if hasattr(data, 'x'):
+        data.qmin, data.qmax = data.x.min(), data.x.max()
+        data.mask = (np.isnan(data.y) if data.y is not None
+                     else np.zeros_like(data.x, dtype='bool'))
     return data
 
@@ -348 +352 @@
     # data, but they already handle the masking and graph markup already, so
     # do not repeat.
-    if hasattr(data, 'lam'):
+    if hasattr(data, 'isSesans') and data.isSesans:
         _plot_result_sesans(data, None, None, use_data=True, limits=limits)
     elif hasattr(data, 'qx_data'):
@@ -376 +380 @@
     *Iq_calc* is the raw theory values without resolution smearing
     """
-    if hasattr(data, 'lam'):
+    if hasattr(data, 'isSesans') and data.isSesans:
         _plot_result_sesans(data, theory, resid, use_data=True, limits=limits)
     elif hasattr(data, 'qx_data'):

sasmodels/direct_model.py

@@ -192 +192 @@
 
         # interpret data
-        if hasattr(data, 'lam'):
+        if hasattr(data, 'isSesans') and data.isSesans:
             self.data_type = 'sesans'
         elif hasattr(data, 'qx_data'):

sasmodels/generate.py

@@ -928 +928 @@
     from . import rst2html
     url = "file://"+dirname(info.filename)+"/"
-    rst2html.wxview(make_html(info), url=url)
+    rst2html.view_html(make_html(info), url=url)
 
 def demo_time():

sasmodels/models/hayter_msa.py

@@ -74 +74 @@
     ["radius_effective", "Ang", 20.75,   [0, inf],    "volume", "effective radius of charged sphere"],
     ["volfraction",   "None",     0.0192, [0, 0.74],   "", "volume fraction of spheres"],
-    ["charge",        "e",   19.0,    [0, inf],    "", "charge on sphere (in electrons)"],
-    ["temperature",   "K",  318.16,   [0, inf],    "", "temperature, in Kelvin, for Debye length calculation"],
-    ["concentration_salt",      "M",    0.0,    [-inf, inf], "", "conc of salt, moles/litre, 1:1 electolyte, for Debye length"],
+    ["charge",        "e",   19.0,    [0, 200],    "", "charge on sphere (in electrons)"],
+    ["temperature",   "K",  318.16,   [0, 450],    "", "temperature, in Kelvin, for Debye length calculation"],
+    ["concentration_salt",      "M",    0.0,    [0, inf], "", "conc of salt, moles/litre, 1:1 electolyte, for Debye length"],
     ["dielectconst",  "None",    71.08,   [-inf, inf], "", "dielectric constant (relative permittivity) of solvent, default water, for Debye length"]
     ]

sasmodels/rst2html.py

@@ -29 +29 @@
 from docutils.writers.html4css1 import HTMLTranslator
 from docutils.nodes import SkipNode
-
-def wxview(html, url="", size=(850, 540)):
-    import wx
-    from wx.html2 import WebView
-    frame = wx.Frame(None, -1, size=size)
-    view = WebView.New(frame)
-    view.SetPage(html, url)
-    frame.Show()
-    return frame
-
-def view_rst(filename):
-    from os.path import expanduser
-    with open(expanduser(filename)) as fid:
-        rst = fid.read()
-    html = rst2html(rst)
-    wxview(html)
 
 def rst2html(rst, part="whole", math_output="mathjax"):
@@ -155 +139 @@
     assert replace_dollar(u"a (again $in parens$) a") == u"a (again :math:`in parens`) a"
 
-def view_rst_app(filename):
+def load_rst_as_html(filename):
+    from os.path import expanduser
+    with open(expanduser(filename)) as fid:
+        rst = fid.read()
+    html = rst2html(rst)
+    return html
+
+def wxview(html, url="", size=(850, 540)):
+    import wx
+    from wx.html2 import WebView
+    frame = wx.Frame(None, -1, size=size)
+    view = WebView.New(frame)
+    view.SetPage(html, url)
+    frame.Show()
+    return frame
+
+def qtview(html, url=""):
+    try:
+        from PyQt5.QtWebKitWidgets import QWebView
+        from PyQt5.QtCore import QUrl
+    except ImportError:
+        from PyQt4.QtWebkit import QWebView
+        from PyQt4.QtCore import QUrl
+    helpView = QWebView()
+    helpView.setHtml(html, QUrl(url))
+    helpView.show()
+    return helpView
+
+def view_html_wxapp(html, url=""):
     import wx  # type: ignore
     app = wx.App()
-    view_rst(filename)
+    frame = wxview(html, url)
     app.MainLoop()
 
+def view_html_qtapp(html, url=""):
+    import sys
+    try:
+        from PyQt5.QtWidgets import QApplication
+    except ImportError:
+        from PyQt4.QtGui import QApplication
+    app = QApplication([])
+    frame = qtview(html, url)
+    sys.exit(app.exec_())
+
+def view_rst_app(filename, qt=False):
+    import os
+    html = load_rst_as_html(filename)
+    url="file://"+os.path.abspath(filename)+"/"
+    if qt:
+        view_html_qtapp(html, url)
+    else:
+        view_html_wxapp(html, url)
 
 if __name__ == "__main__":
     import sys
-    view_rst_app(sys.argv[1])
+    view_rst_app(sys.argv[1], qt=True)
 

sasmodels/sesans.py

@@ -41 +41 @@
     _H0 = None # type: np.ndarray
 
-    def __init__(self, z, SElength, zaccept, Rmax):
+    def __init__(self, z, SElength, lam, zaccept, Rmax):
         # type: (np.ndarray, float, float) -> None
         #import logging; logging.info("creating SESANS transform")
         self.q = z
-        self._set_hankel(SElength, zaccept, Rmax)
+        self._set_hankel(SElength, lam, zaccept, Rmax)
 
     def apply(self, Iq):
@@ -54 +54 @@
         return P
 
-    def _set_hankel(self, SElength, zaccept, Rmax):
+    def _set_hankel(self, SElength, lam, zaccept, Rmax):
         # type: (np.ndarray, float, float) -> None
         # Force float32 arrays, otherwise run into memory problems on some machines
@@ -71 +71 @@
         H = np.float32(dq/(2*pi)) * j0(repSE*repq) * repq
 
+        replam = np.tile(lam, (q.size, 1))
+        reptheta = np.arcsin(repq*replam/2*np.pi)
+        mask = reptheta > zaccept
+        H[mask] = 0
+
         self.q_calc = q
         self._H, self._H0 = H, H0