Changeset f5f8553 in sasview

Timestamp:

Mar 31, 2019 7:43:12 AM (6 years ago)

Author:

GitHub <noreply@…>

Parents:

6d7b252b (diff), d4cde37 (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.

git-author:

Paul Kienzle <pkienzle@…> (03/31/19 07:43:12)

git-committer:

GitHub <noreply@…> (03/31/19 07:43:12)

Message:

Merge d4cde3775cc19e3e8ac413babb90e5015eb330e7 into 6d7b252bf3722c053065645b1afe65424979127f

Files:

• src/sas/sasgui/perspectives/fitting/fitpage.py (modified) (1 diff)
• INSTALL.txt (modified) (1 diff)
• docs/sphinx-docs/source/user/RELEASE.rst (modified) (3 diffs)
• src/sas/sasgui/perspectives/fitting/media/fitting.rst (modified) (2 diffs)
• src/sas/sasgui/perspectives/fitting/media/fitting_help.rst (modified) (4 diffs)
• src/sas/sasgui/perspectives/fitting/media/p_and_s_buttons.png (added)
• src/sas/sasview/media/getting_started_with_sasview.pdf (modified) (previous)
• src/sas/sasview/test/1d_data/AUSANS_run3_2_no_buffer.ABS (added)
• src/sas/sasview/test/1d_data/AUSANS_run4_1_with_buffer.ABS (added)
• src/sas/sasview/test/README.txt (modified) (1 diff)

src/sas/sasgui/perspectives/fitting/fitpage.py

@@ -2365 +2365 @@
                 percent = self.dx_percent/100
                 if self._is_2D():
-                    data.dqx_data[data.dqx_data == 0] = percent * data.qx_data
-                    data.dqy_data[data.dqy_data == 0] = percent * data.qy_data
+                    q = np.sqrt(data.qx_data**2 + data.qy_data**2)
+                    data.dqx_data = data.dqy_data = percent*q
                 else:
                     data.dx = percent * data.x

INSTALL.txt

@@ -47 +47 @@
 More information can be found here:
 
-http://www.sasview.org/help.html
-http://www.sasview.org/faq.html
+http://www.sasview.org/help/
+http://www.sasview.org/faq/
 http://www.sasview.org/trac/wiki/DevNotes

docs/sphinx-docs/source/user/RELEASE.rst

@@ -156 +156 @@
 * Fixes # 784: Add 3D integral to Correlation Function analysis
 * Fixes # 786: core_shell_parallelepiped 1-D model is incorrect
-* Fixes # 818: “report button” followed by “save” makes an empty pdf file???
+* Fixes # 818: "report button" followed by "save" makes an empty pdf file???
 * Fixes # 830: Check compliance of loader against NXcanSAS-1.0 release
 * Fixes # 838: Fix model download from marketplace
@@ -770 +770 @@
           that any previous versions of SasView are uninstalled prior to 
           installing the new version UNLESS you are installing SasView to 
-          versioned folders.
+          versioned folders. **We recommend you avoid using folder paths 
+          that contain spaces or characters that cannot be found on a 
+          standard keyboard (eg, characters with accents, umlauts, etc).**
 
 .. note:: The easiest approach to setting up the proper environment to
@@ -965 +967 @@
 Frequently Asked Questions
 ==========================
-http://www.sasview.org/faq.html
+http://www.sasview.org/faq/
 
 

src/sas/sasgui/perspectives/fitting/media/fitting.rst

@@ -17 +17 @@
    Smearing Functions <resolution>
 
+   Fitting Models with Structure Factors <fitting_sq>
+
+   Writing a Plugin Model <plugin>
+
    Polarisation/Magnetic Scattering <magnetism/magnetism>
-   
+
    Oriented Particles <orientation/orientation>
 
@@ -27 +31 @@
    Fitting SESANS Data <sesans/sesans_fitting>
 
-   Writing a Plugin Model <plugin>
-
    Computations with a GPU <gpu_setup>
 

src/sas/sasgui/perspectives/fitting/media/fitting_help.rst

@@ -42 +42 @@
 *  *Ellipsoid* - ellipsoidal shapes (oblate,prolate, core shell, etc)
 *  *Parellelepiped* - as the name implies
-*  *Sphere* - sheroidal shapes (sphere, core multishell, vesicle, etc)
+*  *Sphere* - spheroidal shapes (sphere, core multishell, vesicle, etc)
 *  *Lamellae* - lamellar shapes (lamellar, core shell lamellar, stacked
    lamellar, etc)
@@ -61 +61 @@
 on the *Description* button to the right.
 
+Product Models
+^^^^^^^^^^^^^^
+
+.. figure:: p_and_s_buttons.png
+
+S(Q) models can be combined with models in the other categories to generate
+what SasView calls "product models". See :ref:`Product_Models` for more
+information.
+
 Show 1D/2D
 ^^^^^^^^^^
@@ -119 +128 @@
 
 For a complete list of all the library models available in SasView, see
-the `Model Documentation <../../../index.html>`_ .
+the `Model Documentation <../../../sasgui/perspectives/fitting/models/index.html>`_ .
 
 It is also possible to add your own models.
@@ -338 +347 @@
 These optimisers form the *Bumps* package written by P Kienzle. For more information
 on each optimiser, see the :ref:`Fitting_Documentation`.
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+Fitting Integer Parameters
+--------------------------
+
+Most of the parameters in SasView models will naturally take floating point (decimal) 
+values, but there are some parameters which can only have integer values. Examples 
+include, but are not limited to, the number of shells in a multilayer vesicle, the 
+number of beads in a pearl necklace, the number of arms of a star polymer, and so on.
+Wherever possible/recognised, the integer nature of a parameter is specified in the 
+respective model documentation and/or parameter table, so read the documentation 
+carefully!
+
+Integer parameters must be fitted with care.
+
+Start with your best possible guess for the value of the parameter. And using 
+*a priori* knowledge, fix as many of the other parameters as possible.
+ 
+The SasView optimizers treat integer parameters internally as floating point 
+numbers, but the values presented to the user are truncated or rounded, as 
+appropriate.
+
+In most instances integer parameters will probably be greater than zero. A good 
+policy in such cases is to use a constraint to enforce this.
+
+Because an integer parameter should, by definition, only move in integer steps, 
+problems may be encountered if the optimizer step size is too small. Similarly, 
+be **very careful** about applying polydispersity to integer parameters.
+
+The Levenberg-Marquardt and Quasi-Newton BFGS (and other derivative-based) 
+optimizers are probably best avoided for fitting models with integer parameters.
 
 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ

src/sas/sasview/test/README.txt

@@ -1 @@
-Test data sets are included as a convenience to our users. The data sets are organized based on their data structure; 1D data (ie, I(Q)), 2D data (ie, I(Qx,Qy)), coordinate data (eg, PDB files), image data (eg, TIFF files), SasView saved states, SESANS data, and data in formats that are not yet implemented but which are in the works for future releases.
+Test data sets are included as a convenience to our users. The data sets are
+organized based on their data structure; 1D data (ie, I(Q)), 2D data
+(ie, I(Qx,Qy)), coordinate data (eg, PDB files), image data
+(eg, TIFF files), SasView saved states, SESANS data, and data in formats that
+are not yet implemented but which are in the works for future releases.
 
-1D data sets EITHER a) have at least two columns of data with I(abs. units) on the y-axis and Q on the x-axis, OR b) have I and Q in separate files. Data in the latter format (/convertible_files) need to be converted to a single file format with the File Converter tool before SasView will analyse them.
+1D data sets EITHER a) have at least two columns of data with I(abs. units) on
+the y-axis and Q on the x-axis, OR b) have I and Q in separate files. Data in
+the latter format (/convertible_files) need to be converted to a single file
+format with the File Converter tool before SasView will analyse them.
 
-2D data sets are data sets that give the deduced intensity for each detector pixel. Depending on the file extension, uncertainty and metadata may also be available.
+2D data sets are data sets that give the deduced intensity for each detector
+pixel. Depending on the file extension, uncertainty and metadata may also be
+available.
 
-Coordinate data sets are designed to be read by the Generic Scattering Calculator tool.
+Coordinate data sets are designed to be read by the Generic Scattering
+Calculator tool.
 
 Image data sets are designed to be read by the Image Viewer tool.
 
-Save states are projects and analyses saved by the SASVIEW program. A single analysis file contains the data and parameters for a single fit (.fit), p(r) inversion (.pr), or invariant calculation (.inv). A project file (.svs) contains the results for every active analysis.
+Save states are projects and analyses saved by the SASVIEW program. A single
+analysis file contains the data and parameters for a single fit (.fit), p(r)
+inversion (.pr), or invariant calculation (.inv). A project file (.svs)
+contains the results for every active analysis.
 
-SESANS data sets primarily contain the neutron polarisation as a function of the spin-echo length.
+SESANS data sets primarily contain the neutron polarisation as a function of
+the spin-echo length.