Changeset 43dc17e in sasmodels


Ignore:
Timestamp:
Mar 16, 2016 3:07:50 PM (9 years ago)
Author:
krzywon
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:
5be92e8
Parents:
092933d (diff), 2f0c07d (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 remote-tracking branch 'origin/master'

Files:
1 added
2 deleted
25 edited
23 moved

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  • sasmodels/generate.py

    r91c5fdc r2f0c07d  
    672672    * *tests* is a set of tests that must pass 
    673673    * *source* is the list of library files to include in the C model build 
    674     * *Iq*, *Iqxy*, *form_volume*, *ER*, and *VR* are python functions 
     674    * *Iq*, *Iqxy*, *form_volume*, *ER*, *VR* and *sesans* are python functions 
    675675      implementing the kernel for the module, or None if they are not 
    676676      defined in python 
    … …  
    682682      *model_info* blocks for the composition objects.  This allows us to 
    683683      build complete product and mixture models from just the info. 
     684 
    684685    """ 
    685686    # TODO: maybe turn model_info into a class ModelDefinition 
    … …  
    710711        ) 
    711712    process_parameters(model_info) 
    712     # Fill in available functions 
    713     model_info.update((k, getattr(kernel_module, k, None)) 
    714                       for k in ('ER', 'VR', 'form_volume', 'Iq', 'Iqxy')) 
     713    # Check for optional functions 
     714    functions = "ER VR form_volume Iq Iqxy shape sesans".split() 
     715    model_info.update((k, getattr(kernel_module, k, None)) for k in functions) 
    715716    return model_info 
    716717 

  • sasmodels/models/_onion.py

    rfdb1487 r2f0c07d  
    146146            \frac{j_1(qr_\text{in})}{qr_\text{in}} 
    147147 
    148 .. figure:: img/onion_annotated_profile.gif 
     148.. figure:: img/onion_geometry.gif 
    149149 
    150150    Example of an onion model profile. 
    … …  
    159159NB: The outer most radius is used as the effective radius for $S(q)$ 
    160160when $P(q) S(q)$ is applied. 
    161  
    162 .. figure:: img/onion_1d.jpg 
    163  
    164     1D plot using the default values (w/400 point) 
    165  
    166 .. figure:: img/onion_profile.jpg 
    167  
    168     SLD profile from the default values. 
    169161 
    170162References 
    … …  
    321313 
    322314 
    323 def profile(core_sld, core_radius, solvent_sld, n, in_sld, out_sld, thickness, A): 
     315def shape(core_sld, core_radius, solvent_sld, n, in_sld, out_sld, thickness, A): 
    324316    """ 
    325     Get SLD profile 
    326  
    327     Returns *(r, rho(r))* where *r* is the radius (Ang) and *rho(r)* is the 
    328     SLD (1/Ang^2). 
     317    SLD profile 
    329318    """ 
    330319 

  • sasmodels/models/adsorbed_layer.py

    rcf95788 r2f0c07d  
    2020 
    2121Note that all parameters except the |sigma| are correlated so fitting more than one of these parameters will generally fail. Also note that unlike other shape models, no volume normalization is applied to this model (the calculation is exact). 
    22  
    23 .. figure:: img/adsorbed_layer_1d.jpg 
    24  
    25     1D plot using the default values. 
    2622 
    2723References 

  • sasmodels/models/barbell.py

    r50e1e40 r2f0c07d  
    6868    up to you to restrict this during analysis. 
    6969 
    70 .. figure:: img/barbell_1d.jpg 
     70The 2D scattering intensity is calculated similar to the 2D cylinder model. 
    7171 
    72     1D plot using the default values (w/256 data point). 
    73  
    74 For 2D data, the scattering intensity is calculated similar to the 2D 
    75 cylinder model. 
    76  
    77 .. figure:: img/barbell_2d.jpg 
    78  
    79     2D plot (w/(256X265) data points) for $\theta = 45^\circ$ and 
    80     $\phi = 0^\circ$ with default values for the remaining parameters. 
    81  
    82 .. figure:: img/orientation.jpg 
     72.. figure:: img/cylinder_angle_definition.jpg 
    8373 
    8474    Definition of the angles for oriented 2D barbells. 
    8575 
    86 .. figure:: img/orientation2.jpg 
     76.. figure:: img/cylinder_angle_projection.jpg 
    8777 
    8878    Examples of the angles for oriented pp against the detector plane. 

  • sasmodels/models/bcc.py

    rad90df9 r2f0c07d  
    4545 
    4646 
    47 .. figure:: img/bcc_lattice.jpg 
     47.. figure:: img/bcc_geometry.jpg 
    4848 
    4949    Body-centered cubic lattice. 
    … …  
    7777*qmin* = 0.001 |Ang^-1|, *qmax* = 0.1 |Ang^-1| and the above default values. 
    7878 
    79 .. figure:: img/bcc_1d.jpg 
    80  
    81     1D plot in the linear scale using the default values (w/200 data point). 
    82  
    8379The 2D (Anisotropic model) is based on the reference below where $I(q)$ is 
    8480approximated for 1d scattering. Thus the scattering pattern for 2D may not 
    … …  
    8682model computation. 
    8783 
    88 .. figure:: img/crystal_orientation.png 
     84.. figure:: img/bcc_angle_definition.png 
    8985 
    9086    Orientation of the crystal with respect to the scattering plane. 
    91  
    92 .. figure:: img/bcc_2d.jpg 
    93  
    94     2D plot using the default values (w/200X200 pixels).* 
    9587 
    9688References 

  • sasmodels/models/be_polyelectrolyte.py

    r0e86967 r2f0c07d  
    3030    q = \sqrt{q_x^2 + q_y^2} 
    3131 
    32  
    33 .. figure:: img/be_polyelectrolyte_1d.jpg 
    34  
    35     1D plot using the default values (w/500 data point). 
    3632 
    3733NB: $1 barn = 10^{-24} cm^2$ 

  • sasmodels/models/broad_peak.py

    rdcdf29d r2f0c07d  
    2828    q = \sqrt{q_x^2 + q_y^2} 
    2929 
    30  
    31 .. figure:: img/broad_peak_1d.jpg 
    32  
    33     1D plot using the default values (w/200 data point). 
    3430 
    3531References 

  • sasmodels/models/capped_cylinder.py

    r50e1e40 r2f0c07d  
    6969    It is up to you to restrict this during analysis. 
    7070 
    71 :num:`Figure #capped-cylinder-1d` shows the output produced by 
    72 a running the 1D capped cylinder model, using *qmin* = 0.001 |Ang^-1|, 
    73 *qmax* = 0.7 |Ang^-1| and  the default values of the parameters. 
     71The 2D scattering intensity is calculated similar to the 2D cylinder model. 
    7472 
    75 .. _capped-cylinder-1d: 
    76  
    77 .. figure:: img/capped_cylinder_1d.jpg 
    78  
    79     1D plot using the default values (w/256 data point). 
    80  
    81 The 2D scattering intensity is calculated similar to the 2D cylinder model. 
    82 :num:`Figure #capped-cylinder-2d` shows the output for $\theta=45^\circ$ 
    83 and $\phi=0^\circ$ with default values for the other parameters. 
    84  
    85 .. _capped-cylinder-2d: 
    86  
    87 .. figure:: img/capped_cylinder_2d.jpg 
    88  
    89     2D plot (w/(256X265) data points). 
    90  
    91 .. figure:: img/orientation.jpg 
     73.. figure:: img/cylinder_angle_definition.jpg 
    9274 
    9375    Definition of the angles for oriented 2D cylinders. 
    9476 
    95 .. figure:: img/orientation2.jpg 
     77.. figure:: img/cylinder_angle_projection.jpg 
    9678 
    97     Examples of the angles for oriented pp against the detector plane. 
     79    Examples of the angles for oriented 2D cylinders against the detector plane. 
    9880 
    9981References 

  • sasmodels/models/core_shell_bicelle.py

    re7678b2 r2f0c07d  
    44---------- 
    55This model provides the form factor for a circular cylinder with a core-shell 
    6 scattering length density profile. 
    7 The form factor is normalized by the particle volume. 
     6scattering length density profile. The form factor is normalized by the 
     7particle volume. 
    88 
    99.. _core-shell-bicelle-geometry: 
    … …  
    2121use the c-library from NIST. 
    2222 
    23 .. figure:: img/core_shell_bicelle_1d.jpg 
     23.. figure:: img/cylinder_angle_definition.jpg 
    2424 
    25     1D plot using the default values (w/200 data point). 
     25    Definition of the angles for the oriented core shell bicelle tmodel. 
    2626 
    27 .. figure:: img/core_shell_bicelle_fig1.jpg 
    28  
    29     Definition of the angles for the oriented CoreShellBicelleModel. 
    30  
    31 .. figure:: img/core_shell_bicelle_fig2.jpg 
     27.. figure:: img/cylinder_angle_projection.jpg 
    3228 
    3329    Examples of the angles for oriented pp against the detector plane. 

  • sasmodels/models/core_shell_cylinder.py

    rf0aa7f8 r2f0c07d  
    6767Validation of our code was done by comparing the output of the 1D model to 
    6868the output of the software provided by the NIST (Kline, 2006). 
    69 :num:`Figure #core-shell-cylinder-1d` shows a comparison 
    70 of the 1D output of our model and the output of the NIST software. 
    71  
    72 .. _core-shell-cylinder-1d: 
    73  
    74 .. figure:: img/core_shell_cylinder_1d.jpg 
    75  
    76     Comparison of the SasView scattering intensity for a core-shell cylinder 
    77     with the output of the NIST SANS analysis software. The parameters were 
    78     set to: *scale* = 1.0 |Ang|, *radius* = 20 |Ang|, *thickness* = 10 |Ang|, 
    79     *length* =400 |Ang|, *core_sld* =1e-6 |Ang^-2|, *shell_sld* = 4e-6 |Ang^-2|, 
    80     *solvent_sld* = 1e-6 |Ang^-2|, and *background* = 0.01 |cm^-1|. 
    8169 
    8270Averaging over a distribution of orientation is done by evaluating the 
    8371equation above. Since we have no other software to compare the 
    84 implementation of the intensity for fully oriented cylinders, we can 
    85 compare the result of averaging our 2D output using a uniform 
     72implementation of the intensity for fully oriented cylinders, we 
     73compared the result of averaging our 2D output using a uniform 
    8674distribution $p(\theta,\phi) = 1.0$. 
    87 :num:`Figure #core-shell-cylinder-2d` shows the result 
    88 of such a cross-check. 
    89  
    90 .. _core-shell-cylinder-2d: 
    91  
    92 .. figure:: img/core_shell_cylinder_2d.jpg 
    93  
    94     Comparison of the intensity for uniformly distributed core-shell 
    95     cylinders calculated from our 2D model and the intensity from the 
    96     NIST SANS analysis software. The parameters used were: *scale* = 1.0, 
    97     *radius* = 20 |Ang|, *thickness* = 10 |Ang|, *length* = 400 |Ang|, 
    98     *core_sld* = 1e-6 |Ang^-2|, *shell_sld* = 4e-6 |Ang^-2|, 
    99     *solvent_sld* = 1e-6 |Ang^-2|, and *background* = 0.0 |cm^-1|. 
    10075 
    101762013/11/26 - Description reviewed by Heenan, R. 

  • sasmodels/models/core_shell_ellipsoid.py

    r177c1a1 r2f0c07d  
    1010applied over all orientations for 1D. 
    1111 
    12 .. figure:: img/core_shell_ellipsoid_fig1.gif 
     12.. figure:: img/core_shell_ellipsoid_geometry.gif 
    1313 
    1414    The returned value is in units of $cm^{-1}$, on absolute scale. 
    … …  
    3636To provide easy access to the orientation of the core-shell ellipsoid, 
    3737we define the axis of the solid ellipsoid using two angles $\theta$ and $\phi$. 
    38 These angles are defined on Figure 2 of the CylinderModel. 
     38These angles are defined as for 
     39:ref:`cylinder orientation <cylinder-angle-definition>`. 
    3940The contrast is defined as SLD(core) - SLD(shell) and SLD(shell) - SLD(solvent). 
    4041 
    … …  
    4849    and used as the effective radius for *S(Q)* when $P(Q) * S(Q)$ is applied. 
    4950 
    50 .. figure:: img/core_shell_ellipsoid_1d.jpg 
    51  
    52     1D plot using the default values (w/200 data point). 
    53  
    54 .. figure:: img/core_shell_ellipsoid_fig2.jpg 
     51.. figure:: img/core_shell_ellipsoid_angle_projection.jpg 
    5552 
    5653    The angles for oriented core_shell_ellipsoid. 

  • sasmodels/models/core_shell_ellipsoid_xt.py

    r3882eeb r2f0c07d  
    1010---------- 
    1111 
    12 .. figure:: img/core_shell_ellipsoid_fig1.gif 
    13  
     12.. figure:: img/core_shell_ellipsoid_geometry.gif 
    1413 
    1514The geometric parameters of this model are 

  • sasmodels/models/core_shell_parallelepiped.py

    r44bd2be r2f0c07d  
    2222*A* < *B* < *C*. 
    2323 
    24 .. image:: img/core_shell_parallelepiped.jpg 
     24.. image:: img/core_shell_parallelepiped_geometry.jpg 
    2525 
    2626There are rectangular "slabs" of thickness $t_A$ that add to the *A* dimension 
    … …  
    7272To provide easy access to the orientation of the parallelepiped, we define the 
    7373axis of the cylinder using three angles |theta|, |phi| and |bigpsi|. 
    74 These angles are defined on Figure 2 of the :ref:`cylinder` model. 
     74(see :ref:`cylinder orientation <cylinder-angle-definition>`). 
    7575The angle |bigpsi| is the rotational angle around the *long_c* axis against the 
    7676*q* plane. For example, |bigpsi| = 0 when the *short_b* axis is parallel to the 
    7777*x*-axis of the detector. 
    7878 
    79 .. figure:: img/parallelepiped_angles_definition.jpg 
     79.. figure:: img/parallelepiped_angle_definition.jpg 
    8080 
    8181    Definition of the angles for oriented core-shell parallelepipeds. 
    8282 
    83 .. figure:: img/parallelepiped_angles_examples.jpg 
     83.. figure:: img/parallelepiped_angle_projection.jpg 
    8484 
    8585    Examples of the angles for oriented core-shell parallelepipeds against the 

  • sasmodels/models/cylinder.py

    r50e1e40 r2f0c07d  
    3131To provide easy access to the orientation of the cylinder, we define the 
    3232axis of the cylinder using two angles $\theta$ and $\phi$. Those angles 
    33 are defined in :num:`figure #cylinder-orientation`. 
     33are defined in :num:`figure #cylinder-angle-definition`. 
    3434 
    35 .. _cylinder-orientation: 
     35.. _cylinder-angle-definition: 
    3636 
    37 .. figure:: img/orientation.jpg 
     37.. figure:: img/cylinder_angle_definition.jpg 
    3838 
    3939    Definition of the angles for oriented cylinders. 
    4040 
    41 .. figure:: img/orientation2.jpg 
     41.. figure:: img/cylinder_angle_projection.jpg 
    4242 
    4343    Examples of the angles for oriented cylinders against the detector plane. 

  • sasmodels/models/ellipsoid.py

    r431caae r2f0c07d  
    4747$S(q)$ when $P(q) \cdot S(q)$ is applied. 
    4848 
    49 .. _ellipsoid-1d: 
    50  
    51 .. figure:: img/ellipsoid_1d.jpg 
    52  
    53     The output of the 1D scattering intensity function for randomly oriented 
    54     ellipsoids given by the equation above. 
    55  
    5649 
    5750The $\theta$ and $\phi$ parameters are not used for the 1D output. 
    … …  
    5952.. _ellipsoid-geometry: 
    6053 
    61 .. figure:: img/ellipsoid_geometry.jpg 
     54.. figure:: img/ellipsoid_angle_projection.jpg 
    6255 
    6356    The angles for oriented ellipsoid. 

  • sasmodels/models/elliptical_cylinder.py

    rfa8011eb r2f0c07d  
    4343 
    4444To provide easy access to the orientation of the elliptical cylinder, we define the axis of the cylinder using two 
    45 angles |theta|, |phi| and |bigpsi|. As for the case of the cylinder, the angles |theta| and |phi| are defined on 
    46 Figure 2 of CylinderModel. The angle |bigpsi| is the rotational angle around its own long_c axis against the *q* plane. 
     45angles |theta|, |phi| and |bigpsi| (see :ref:`cylinder orientation <cylinder-angle-definition>`). 
     46The angle |bigpsi| is the rotational angle around its own long_c axis against the *q* plane. 
    4747For example, |bigpsi| = 0 when the *r_minor* axis is parallel to the *x*\ -axis of the detector. 
    4848 
    4949All angle parameters are valid and given only for 2D calculation; ie, an oriented system. 
    5050 
    51 .. figure:: img/elliptical_cylinder_geometry_2d.jpg 
     51.. figure:: img/elliptical_cylinder_angle_definition.jpg 
    5252 
    5353    Definition of angles for 2D 
    5454 
    55 .. figure:: img/core_shell_bicelle_fig2.jpg 
     55.. figure:: img/cylinder_angle_projection.jpg 
    5656 
    5757    Examples of the angles for oriented elliptical cylinders against the detector plane. 
    … …  
    6060and length values, and used as the effective radius for *S(Q)* when *P(Q)* \* *S(Q)* is applied. 
    6161 
    62  
    63 .. figure:: img/elliptical_cylinder_comparison_1d.jpg 
    64  
    65     1D plot using the default values (w/1000 data point). 
    6662 
    6763Validation 

  • sasmodels/models/fcc.py

    rad90df9 r2f0c07d  
    4343where $g$ is a fractional distortion based on the nearest neighbor distance. 
    4444 
    45 .. figure:: img/fcc_lattice.jpg 
     45.. figure:: img/fcc_geometry.jpg 
    4646 
    4747    Face-centered cubic lattice. 
    … …  
    7171integral. Very, very slow. Go get lunch! 
    7272 
    73 This example dataset is produced using 200 data points, *qmin* = 0.01 |Ang^-1|, 
    74 *qmax* = 0.1 |Ang^-1| and the above default values. 
    75  
    76 .. figure:: img/fcc_1d.jpg 
    77  
    78     1D plot in the linear scale using the default values (w/200 data point). 
    79  
    8073The 2D (Anisotropic model) is based on the reference below where $I(q)$ is 
    8174approximated for 1d scattering. Thus the scattering pattern for 2D may not 
    … …  
    83762D model computation. 
    8477 
    85 .. figure:: img/crystal_orientation.png 
     78.. figure:: img/bcc_angle_definition.png 
    8679 
    8780    Orientation of the crystal with respect to the scattering plane. 
    88  
    89 .. figure:: img/fcc_2d.jpg 
    90  
    91     2D plot using the default values (w/200X200 pixels). 
    9281 
    9382References 

  • sasmodels/models/hollow_cylinder.py

    re0fd913 r2f0c07d  
    3434Bessel function. 
    3535 
    36 To provide easy access to the orientation of the core-shell cylinder, we define 
    37 the axis of the cylinder using two angles $\theta$ and $\phi$. As for the case 
    38 of the cylinder, those angles are defined in Figure 2 of the CylinderModel. 
    39  
    4036**NB**: The 2nd virial coefficient of the cylinder is calculated 
    4137based on the radius and 2 length values, and used as the effective radius 
    … …  
    4541and the *radius* is $R_\text{shell}$ while *core_radius* is $R_\text{core}$. 
    4642 
    47 .. figure:: img/hollow_cylinder_1d.jpg 
    48  
    49     1D plot using the default values (w/1000 data point). 
    50  
    51 .. figure:: img/orientation.jpg 
    52  
    53     Definition of the angles for the oriented hollow_cylinder model. 
    54  
    55 .. figure:: img/orientation2.jpg 
    56  
    57     Examples of the angles for oriented pp against the detector plane. 
     43To provide easy access to the orientation of the core-shell cylinder, we define 
     44the axis of the cylinder using two angles $\theta$ and $\phi$ 
     45(see :ref:`cylinder model <cylinder-angle-definition>`). 
    5846 
    5947References 

  • sasmodels/models/linear_pearls.py

    r32c743d r2f0c07d  
    55The thickness of each string is assumed to be negligible. 
    66 
    7 .. figure:: img/linear_pearls_fig1.jpg 
     7.. figure:: img/linear_pearls_geometry.jpg 
    88 
    99 
    … …  
    2525The 2D scattering intensity is the same as P(q) above, 
    2626regardless of the orientation of the q vector. 
    27  
    28 .. figure:: img/linear_pearls_1d.jpg 
    29  
    30     1D plot using the default values (w/500 data point). 
    3127 
    3228References 

  • sasmodels/models/multi_shell.py

    rd51ea74 r2f0c07d  
    1919parameters fixed as possible. 
    2020 
    21 .. figure:: img/multi_shell_fig1.jpg 
     21.. figure:: img/multi_shell_geometry.jpg 
    2222 
    2323The 2D scattering intensity is the same as 1D, regardless of the orientation 
    … …  
    3333    is used as the effective radius for *S(Q)* when $P(Q) * S(Q)$ is applied. 
    3434 
    35  
    36 .. figure:: img/multi_shell_1d.jpg 
    37  
    38     1D plot using the default values (with 200 data point). 
    3935 
    4036Our model uses the form factor calculations implemented in a c-library provided 

  • sasmodels/models/parallelepiped.py

    rdeb7ee0 r2f0c07d  
    9999.. _parallelepiped-orientation: 
    100100 
    101 .. figure:: img/parallelepiped_angles_definition.jpg 
     101.. figure:: img/parallelepiped_angle_definition.jpg 
    102102 
    103103    Definition of the angles for oriented parallelepipeds. 
    104104 
    105 .. figure:: img/parallelepiped_angles_examples.jpg 
     105.. figure:: img/parallelepiped_angle_projection.jpg 
    106106 
    107107    Examples of the angles for oriented parallelepipeds against the detector plane. 
    … …  
    156156This model is based on form factor calculations implemented in a c-library 
    157157provided by the NIST Center for Neutron Research (Kline, 2006). 
    158  
    159158""" 
    160159 

  • sasmodels/models/pearl_necklace.py

    rd18582e r2f0c07d  
    66(= *A* - 2\ *R*)). *A* is the center-to-center pearl separation distance. 
    77 
    8 .. figure:: img/pearl_fig.jpg 
     8.. figure:: img/pearl_necklace_geometry.jpg 
    99 
    1010    Pearl Necklace schematic 
    … …  
    4848NB: *number_of_pearls* must be an integer. 
    4949 
    50 .. figure:: img/pearl_plot.jpg 
    51  
    52     1D plot using the default values (w/1000 data point). 
    53  
    54 REFERENCE 
     50References 
     51---------- 
    5552 
    5653R Schweins and K Huber, *Particle Scattering Factor of Pearl Necklace Chains*, 

  • sasmodels/models/sc_crystal.py

    rad90df9 r2f0c07d  
    4141The simple cubic lattice is 
    4242 
    43 .. figure:: img/sc_crystal_fig1.jpg 
     43.. figure:: img/sc_crystal_geometry.jpg 
    4444 
    4545For a crystal, diffraction peaks appear at reduced q-values given by 
    … …  
    7777    Go get lunch! 
    7878 
    79 This example dataset is produced using 200 data points, 
    80 $q_{min} = 0.01A^{-1}, q_{max} = 0.1A^{-1}$ and the above default values. 
    81  
    82 .. figure:: img/sc_crystal_1d.jpg 
    83  
    84     1D plot in the linear scale using the default values (w/200 data point). 
    85  
    8679The 2D (Anisotropic model) is based on the reference below where *I(q)* is 
    8780approximated for 1d scattering. Thus the scattering pattern for 2D may not 
    … …  
    8982model computation. 
    9083 
    91 .. figure:: img/sc_crystal_fig2.jpg 
    92 .. figure:: img/sc_crystal_fig3.jpg 
    93  
    94     2D plot using the default values (w/200X200 pixels). 
     84.. figure:: img/sc_crystal_angle_definition.jpg 
    9585 
    9686Reference 

  • sasmodels/models/stacked_disks.py

    rd507c3a r2f0c07d  
    2121---------- 
    2222 
    23 .. figure:: img/stacked_disks_fig1.gif 
     23.. figure:: img/stacked_disks_geometry.gif 
    2424 
    2525The scattered intensity $I(q)$ is calculated as 
    … …  
    6868and $\sigma_D$ = the Gaussian standard deviation of the d-spacing (sigma_d). 
    6969 
    70 To provide easy access to the orientation of the stacked disks, we define 
    71 the axis of the cylinder using two angles $\theta$ and $\varphi$. 
    72 These angles are defined on Figure 2 of cylinder_model. 
    73  
    7470.. note:: 
    7571    The 2nd virial coefficient of the cylinder is calculated based on the 
    … …  
    7874    is applied. 
    7975 
    80 .. figure:: img/stacked_disks_1d.jpg 
    81  
    82     1D plot using the default values (w/1000 data point). 
    83  
    84 .. figure:: img/stacked_disks_fig2.jpg 
     76To provide easy access to the orientation of the stacked disks, we define 
     77the axis of the cylinder using two angles $\theta$ and $\varphi$. 
     78 
     79.. figure:: img/stacked_disks_angle_definition.jpg 
    8580 
    8681    Examples of the angles for oriented stacked disks against 
    8782    the detector plane. 
    8883 
    89 .. figure:: img/stacked_disks_fig3.jpg 
     84.. figure:: img/stacked_disks_angle_projection.jpg 
    9085 
    9186    Examples of the angles for oriented pp against the detector plane. 

  • sasmodels/models/triaxial_ellipsoid.py

    r469e763 r2f0c07d  
    4343.. _triaxial-ellipsoid-angles: 
    4444 
    45 .. figure:: img/triaxial_ellipsoid_angles.jpg 
     45.. figure:: img/triaxial_ellipsoid_angle_projection.jpg 
    4646 
    4747    The angles for oriented ellipsoid. 
    … …  
    5757radius $R_e = \sqrt{R_a R_b}$, and used as the effective radius for 
    5858$S(q)$ when $P(q) \cdot S(q)$ is applied. 
    59  
    60 .. figure:: img/triaxial_ellipsoid_1d.jpg 
    61  
    62     1D plot using the default values (w/1000 data point). 
    6359 
    6460Validation 
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