Changes in / [34a9e4e:9ed43f4] in sasmodels

Files:

• example/latex_smeared_out_0.txt (added)
• example/latex_smeared_out_1.txt (added)
• example/oriented_usans.py (modified) (2 diffs)
• example/simul_fit.py (added)
• sasmodels/data.py (modified) (4 diffs)
• sasmodels/models/onion.py (modified) (4 diffs)
• sasmodels/models/spherical_sld.py (modified) (2 diffs)
• sasmodels/rst2html.py (modified) (3 diffs)

example/oriented_usans.py

@@ -19 +19 @@
     scale=0.08, background=0,
     sld=.291, sld_solvent=7.105,
-    r_polar=1800, r_polar_pd=0.222296, r_polar_pd_n=0,
-    r_equatorial=2600, r_equatorial_pd=0.28, r_equatorial_pd_n=0,
+    radius_polar=1800, radius_polar_pd=0.222296, radius_polar_pd_n=0,
+    radius_equatorial=2600, radius_equatorial_pd=0.28, radius_equatorial_pd_n=0,
     theta=60, theta_pd=0, theta_pd_n=0,
     phi=60, phi_pd=0, phi_pd_n=0,
@@ -26 +26 @@
 
 # SET THE FITTING PARAMETERS
-model.r_polar.range(1000, 10000)
-model.r_equatorial.range(1000, 10000)
+model.radius_polar.range(1000, 10000)
+model.radius_equatorial.range(1000, 10000)
 model.theta.range(0, 360)
 model.phi.range(0, 360)

sasmodels/data.py

@@ -450 +450 @@
             if view is 'log':
                 mtheory[mtheory <= 0] = masked
-            plt.plot(data.x, scale*mtheory, '-', hold=True)
+            plt.plot(data.x, scale*mtheory, '-')
             all_positive = all_positive and (mtheory > 0).all()
             some_present = some_present or (mtheory.count() > 0)
@@ -457 +457 @@
             plt.ylim(*limits)
 
-        plt.xscale('linear' if not some_present or non_positive_x  else view)
+        plt.xscale('linear' if not some_present or non_positive_x
+                   else view if view is not None
+                   else 'log')
         plt.yscale('linear'
                    if view == 'q4' or not some_present or not all_positive
-                   else view)
+                   else view if view is not None
+                   else 'log')
         plt.xlabel("$q$/A$^{-1}$")
         plt.ylabel('$I(q)$')
+        title = ("data and model" if use_theory and use_data
+                 else "data" if use_data
+                 else "model")
+        plt.title(title)
 
     if use_calc:
@@ -482 +489 @@
         if num_plots > 1:
             plt.subplot(1, num_plots, use_calc + 2)
-        plt.plot(data.x, mresid, '-')
+        plt.plot(data.x, mresid, '.')
         plt.xlabel("$q$/A$^{-1}$")
         plt.ylabel('residuals')
-        plt.xscale('linear' if not some_present or non_positive_x else view)
+        plt.xscale('linear')
+        plt.title('(model - Iq)/dIq')
 
 
@@ -512 +520 @@
         if theory is not None:
             if is_tof:
-                plt.plot(data.x, np.log(theory)/(data.lam*data.lam), '-', hold=True)
+                plt.plot(data.x, np.log(theory)/(data.lam*data.lam), '-')
             else:
-                plt.plot(data.x, theory, '-', hold=True)
+                plt.plot(data.x, theory, '-')
         if limits is not None:
             plt.ylim(*limits)

sasmodels/models/onion.py

@@ -1 +1 @@
 r"""
 This model provides the form factor, $P(q)$, for a multi-shell sphere where
-the scattering length density (SLD) of the each shell is described by an
+the scattering length density (SLD) of each shell is described by an
 exponential, linear, or constant function. The form factor is normalized by
 the volume of the sphere where the SLD is not identical to the SLD of the
@@ -142 +142 @@
 
 For $A = 0$, the exponential function has no dependence on the radius (so that
-$\rho_\text{out}$ is ignored this case) and becomes flat. We set the constant
+$\rho_\text{out}$ is ignored in this case) and becomes flat. We set the constant
 to $\rho_\text{in}$ for convenience, and thus the form factor contributed by
 the shells is
@@ -346 +346 @@
             # flat shell
             z.append(z_current + thickness[k])
-            rho.append(sld_out[k])
+            rho.append(sld_in[k])
         else:
             # exponential shell
@@ -357 +357 @@
                 z.append(z_current+z_shell)
                 rho.append(slope*exp(A[k]*z_shell/thickness[k]) + const)
-
+    
     # add in the solvent
     z.append(z[-1])

sasmodels/models/spherical_sld.py

@@ -199 +199 @@
 category = "shape:sphere"
 
-SHAPES = [["erf(|nu|*z)", "Rpow(z^|nu|)", "Lpow(z^|nu|)",
-           "Rexp(-|nu|z)", "Lexp(-|nu|z)"]]
+SHAPES = ["erf(|nu|*z)", "Rpow(z^|nu|)", "Lpow(z^|nu|)",
+          "Rexp(-|nu|z)", "Lexp(-|nu|z)"]
 
 # pylint: disable=bad-whitespace, line-too-long
@@ -209 +209 @@
               ["thickness[n_shells]",  "Ang",        100.0,  [0, inf],       "volume", "thickness shell"],
               ["interface[n_shells]",  "Ang",        50.0,   [0, inf],       "volume", "thickness of the interface"],
-              ["shape[n_shells]",      "",           0,      SHAPES,         "", "interface shape"],
+              ["shape[n_shells]",      "",           0,      [SHAPES],       "", "interface shape"],
               ["nu[n_shells]",         "",           2.5,    [0, inf],       "", "interface shape exponent"],
               ["n_steps",              "",           35,     [0, inf],       "", "number of steps in each interface (must be an odd integer)"],

sasmodels/rst2html.py

@@ -155 +155 @@
     return frame
 
+def view_html_wxapp(html, url=""):
+    import wx  # type: ignore
+    app = wx.App()
+    frame = wxview(html, url)
+    app.MainLoop()
+
+def view_url_wxapp(url):
+    import wx  # type: ignore
+    from wx.html2 import WebView
+    app = wx.App()
+    frame = wx.Frame(None, -1, size=(850, 540))
+    view = WebView.New(frame)
+    view.LoadURL(url)
+    frame.Show()
+    app.MainLoop()
+
 def qtview(html, url=""):
     try:
@@ -167 +183 @@
     return helpView
 
-def view_html_wxapp(html, url=""):
-    import wx  # type: ignore
-    app = wx.App()
-    frame = wxview(html, url)
-    app.MainLoop()
-
 def view_html_qtapp(html, url=""):
     import sys
@@ -183 +193 @@
     sys.exit(app.exec_())
 
-def view_rst_app(filename, qt=False):
+def view_url_qtapp(url):
+    import sys
+    try:
+        from PyQt5.QtWidgets import QApplication
+    except ImportError:
+        from PyQt4.QtGui import QApplication
+    app = QApplication([])
+    try:
+        from PyQt5.QtWebKitWidgets import QWebView
+        from PyQt5.QtCore import QUrl
+    except ImportError:
+        from PyQt4.QtWebkit import QWebView
+        from PyQt4.QtCore import QUrl
+    frame = QWebView()
+    frame.load(QUrl(url))
+    frame.show()
+    sys.exit(app.exec_())
+
+def view_help(filename, qt=False):
     import os
-    html = load_rst_as_html(filename)
-    url="file://"+os.path.abspath(filename)+"/"
-    if qt:
-        view_html_qtapp(html, url)
+    url="file:///"+os.path.abspath(filename).replace("\\","/")
+    if filename.endswith('.rst'):
+        html = load_rst_as_html(filename)
+        if qt:
+            view_html_qtapp(html, url)
+        else:
+            view_html_wxapp(html, url)
     else:
-        view_html_wxapp(html, url)
+        if qt:
+            view_url_qtapp(url)
+        else:
+            view_url_wxapp(url)
 
 if __name__ == "__main__":
     import sys
-    view_rst_app(sys.argv[1], qt=True)
-
+    view_help(sys.argv[1], qt=True)
+