Changeset fa8011eb in sasmodels

Timestamp:

Feb 24, 2016 3:51:27 PM (9 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:

d51ea74

Parents:

c8dcbdf

Message:

doc cleanup

Location:

sasmodels

Files:

• generate.py (modified) (2 diffs)
• models/core_shell_bicelle.py (modified) (1 diff)
• models/core_shell_sphere.py (modified) (2 diffs)
• models/elliptical_cylinder.py (modified) (6 diffs)
• models/guinier_porod.py (modified) (1 diff)
• models/img/rpa_1d.jpg (added)
• models/line.py (modified) (1 diff)
• models/rpa.py (modified) (1 diff)
• models/vesicle.py (modified) (3 diffs)

sasmodels/generate.py

@@ -191 +191 @@
 The function :func:`make` loads the metadata from the module and returns
 the kernel source.  The function :func:`doc` extracts the doc string
-and adds the parameter table to the top.  The function :func:`sources`
+and adds the parameter table to the top.  The function :func:`model_sources`
 returns a list of files required by the model.
 """
@@ -206 +206 @@
 import numpy as np
 
-__all__ = ["make", "doc", "sources", "convert_type"]
+#__all__ = ["make", "doc", "model_sources", "convert_type"]
 
 C_KERNEL_TEMPLATE_PATH = joinpath(dirname(__file__), 'kernel_template.c')

sasmodels/models/core_shell_bicelle.py

@@ -7 +7 @@
 The form factor is normalized by the particle volume.
 
-.. _core-shell-cylinder-geometry:
+.. _core-shell-bicelle-geometry:
 
 .. figure:: img/core_shell_bicelle_geometry.png

sasmodels/models/core_shell_sphere.py

@@ -15 +15 @@
 
 .. math::
+
     F^2(q)=\frac{3}{V_s}\left[V_c(\rho_c-\rho_s)\frac{\sin(qr_c)-qr_c\cos(qr_c)}{(qr_c)^3}+
     V_s(\rho_s-\rho_{solv})\frac{\sin(qr_s)-qr_s\cos(qr_s)}{(qr_s)^3}\right]
@@ -41 +42 @@
 our model and the output of the NIST software.
 
-.. image:: img/core_shell_sphere_1d.jpg
+.. figure:: img/core_shell_sphere_1d.jpg
 
-    Figure 1: Comparison of the SasView scattering intensity for a core-shell sphere with
+    Comparison of the SasView scattering intensity for a core-shell sphere with
     the output of the NIST SANS analysis software. The parameters were set to:
     *scale* = 1.0, *radius* = 60 , *contrast* = 1e-6 |Ang^-2|, and

sasmodels/models/elliptical_cylinder.py

@@ -10 +10 @@
 to any of the orientation angles, and also for the minor radius and the ratio of the ellipse radii.
 
-.. image:: img/elliptical_cylinder_geometry.gif
+.. figure:: img/elliptical_cylinder_geometry.gif
 
-    *Figure.* *a* = *r_minor* and |nu|\ :sub:`n` = $r_ratio$ (i.e., $r_major / r_minor$).
+    *a* = *r_minor* and |nu|\ :sub:`n` = $r_ratio$ (i.e., $r_major / r_minor$).
 
 The function calculated is
 
 .. math::
+
     I(\mathbf{q})=\frac{1}{V_{cyl}}\int{d\psi}\int{d\phi}\int{p(\theta,\phi,\psi)F^2(\mathbf{q},\alpha,\psi)\sin(\theta)d\theta}
 
@@ -22 +23 @@
 
 .. math::
+
     F(\mathbf{q},\alpha,\psi)=2\frac{J_1(a)\sin(b)}{ab}
     \\
@@ -40 +42 @@
     P(q) = scale  <F^2> / V
 
-The returned value is scaled to units of |cm^-1|.
-
 To provide easy access to the orientation of the elliptical cylinder, we define the axis of the cylinder using two
 angles |theta|, |phi| and |bigpsi|. As for the case of the cylinder, the angles |theta| and |phi| are defined on
@@ -49 +49 @@
 All angle parameters are valid and given only for 2D calculation; ie, an oriented system.
 
-.. image:: img/elliptical_cylinder_geometry_2d.jpg
+.. figure:: img/elliptical_cylinder_geometry_2d.jpg
 
-    *Figure. Definition of angles for 2D*
+    Definition of angles for 2D
 
-.. image:: img/core_shell_bicelle_fig2.jpg
+.. figure:: img/core_shell_bicelle_fig2.jpg
 
-    *Figure. Examples of the angles for oriented elliptical cylinders against the detector plane.*
+    Examples of the angles for oriented elliptical cylinders against the detector plane.
 
 NB: The 2nd virial coefficient of the cylinder is calculated based on the averaged radius (= sqrt(*r_minor*\ :sup:`2` \* *r_ratio*))
@@ -61 +61 @@
 
 
-.. image:: img/elliptical_cylinder_comparison_1d.jpg
+.. figure:: img/elliptical_cylinder_comparison_1d.jpg
 
-    *Figure. 1D plot using the default values (w/1000 data point).*
+    1D plot using the default values (w/1000 data point).
 
 Validation
@@ -73 +73 @@
 and 76 degrees are taken for the angles of |theta|, |phi|, and |bigpsi| respectively).
 
-.. image:: img/elliptical_cylinder_validation_1d.gif
+.. figure:: img/elliptical_cylinder_validation_1d.gif
 
-    *Figure. Comparison between 1D and averaged 2D.*
+    Comparison between 1D and averaged 2D.
 
 In the 2D average, more binning in the angle |phi| is necessary to get the proper result. The following figure shows
 the results of the averaging by varying the number of angular bins.
 
-.. image:: img/elliptical_cylinder_averaging.gif
+.. figure:: img/elliptical_cylinder_averaging.gif
 
-    *Figure. The intensities averaged from 2D over different numbers of bins and angles.*
+    The intensities averaged from 2D over different numbers of bins and angles.
 
 Reference

sasmodels/models/guinier_porod.py

@@ -51 +51 @@
     q = \sqrt{q_x^2+q_y^2}
 
-.. image:: img/guinier_porod_model.jpg
+.. figure:: img/guinier_porod_model.jpg
 
-    Figure 1: Guinier-Porod model for $R_g=100$ |Ang|, $s=1$, $m=3$, and $background=0.1$.
+    Guinier-Porod model for $R_g=100$ |Ang|, $s=1$, $m=3$, and $background=0.1$.
 
 

sasmodels/models/line.py

@@ -13 +13 @@
 .. note::
     For 2D plots intensity has different definition than other shape independent models
+
 .. math::
     I(q) = I(qx) \cdot I(qy)
-
-.. figure:: None
 
 References

sasmodels/models/rpa.py

@@ -43 +43 @@
 component.
 
-.. figure:: img/image215.jpg
+.. figure:: img/rpa_1d.jpg
 
     1D plot using the default values (w/500 data points).

sasmodels/models/vesicle.py

@@ -24 +24 @@
 is a flat background level (due for example to incoherent scattering in the
 case of neutrons), and $j_1$ is the spherical bessel function
-$j_1 = (sin(x) - x cos(x))/ x^2$.
+$j_1 = (\sin(x) - x \cos(x))/ x^2$.
 
 The functional form is identical to a "typical" core-shell structure, except
@@ -35 +35 @@
 thickness = $R_{\text{tot}} - R_{\text{core}}$.
 
-.. figure: img/vesicle_geometry.jpg
+.. figure:: img/vesicle_geometry.jpg
+
+    Vesicle geometry.
 
 The 2D scattering intensity is the same as *P(q)* above, regardless of the
@@ -48 +50 @@
 radius for *S(Q)* when *P(Q)* \* *S(Q)* is applied.
 
-.. image:: img/vesicle_1d.jpg
+.. figure:: img/vesicle_1d.jpg
 
-*Figure. 1D plot using the default values given in the table
-(w/200 data point). Polydispersity and instrumental resolution normally
-will smear out most of the rapidly oscillating features.*
+    1D plot using the default values given in the table (w/200 data point).
+    Polydispersity and instrumental resolution normally will smear out most
+    of the rapidly oscillating features.
 
 REFERENCE