Changes in / [fdd56a1:f40064d] in sasmodels

Location:

sasmodels

Files:

• models/parallelepiped.py (modified) (1 diff)
• models/spherical_sld.py (modified) (2 diffs)
• models/triaxial_ellipsoid.py (modified) (4 diffs)
• rst2html.py (modified) (3 diffs)

sasmodels/models/parallelepiped.py

@@ -22 +22 @@
 .. note::
 
-   The edge of the solid used to have to satisfy the condition that $A < B < C$.
-   After some improvements to the effective radius calculation, used with
-   an S(Q), it is beleived that this is no longer the case.
+The three dimensions of the parallelepiped (strictly here a cuboid) may be given in 
+$any$ size order. To avoid multiple fit solutions, especially
+with Monte-Carlo fit methods, it may be advisable to restrict their ranges. There may 
+be a number of closely similar "best fits", so some trial and error, or fixing of some 
+dimensions at expected values, may help.
 
 The 1D scattering intensity $I(q)$ is calculated as:

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/models/triaxial_ellipsoid.py

@@ -66 +66 @@
     r^2 &= b^2(p_a \sin^2(\phi)(1 - u^2) + 1 + p_c u^2)
 
+Though for convenience we describe the three radii of the ellipsoid as equatorial
+and polar, they may be given in $any$ size order. To avoid multiple solutions, especially
+with Monte-Carlo fit methods, it may be advisable to restrict their ranges. For typical
+small angle diffraction situations there may be a number of closely similar "best fits",
+so some trial and error, or fixing of some radii at expected values, may help.
+    
 To provide easy access to the orientation of the triaxial ellipsoid,
 we define the axis of the cylinder using the angles $\theta$, $\phi$
-and $\psi$. These angles are defined analogously to the elliptical_cylinder below
+and $\psi$. These angles are defined analogously to the elliptical_cylinder below, note that
+angle $\phi$ is now NOT the same as in the equations above.
 
 .. figure:: img/elliptical_cylinder_angle_definition.png
 
-    Definition of angles for oriented triaxial ellipsoid, where radii shown
-    here are $a < b << c$ and angle $\Psi$ is a rotation around the axis
-    of the particle.
+    Definition of angles for oriented triaxial ellipsoid, where radii are for illustration here 
+    $a < b << c$ and angle $\Psi$ is a rotation around the axis of the particle.
 
 For oriented ellipsoids the *theta*, *phi* and *psi* orientation parameters will appear when fitting 2D data, 
@@ -83 +89 @@
 .. figure:: img/triaxial_ellipsoid_angle_projection.png
 
-    Some example angles for oriented ellipsoid.
+    Some examples for an oriented triaxial ellipsoid.
 
 The radius-of-gyration for this system is  $R_g^2 = (R_a R_b R_c)^2/5$.
@@ -92 +98 @@
 
 NB: The 2nd virial coefficient of the triaxial solid ellipsoid is
-calculated based on the polar radius $R_p = R_c$ and equatorial
-radius $R_e = \sqrt{R_a R_b}$, and used as the effective radius for
+calculated after sorting the three radii to give the most appropriate
+prolate or oblate form, from the new polar radius $R_p = R_c$ and effective equatorial
+radius,  $R_e = \sqrt{R_a R_b}$, to then be used as the effective radius for
 $S(q)$ when $P(q) \cdot S(q)$ is applied.
 
@@ -125 +132 @@
 
 description = """
-   Note - fitting ensure that the inequality ra<rb<rc is not
-   violated. Otherwise the calculation may not be correct.
+   Triaxial ellipsoid - see main documentation.
 """
 category = "shape:ellipsoid"

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)
+