Changeset 868846b in sasview for src/sas

Timestamp:

Sep 11, 2017 5:49:05 PM (7 years ago)

Author:

GitHub <noreply@…>

Branches:

master, ESS_GUI, ESS_GUI_Docs, ESS_GUI_batch_fitting, ESS_GUI_bumps_abstraction, ESS_GUI_iss1116, ESS_GUI_iss879, ESS_GUI_iss959, ESS_GUI_opencl, ESS_GUI_ordering, ESS_GUI_sync_sascalc, costrafo411, magnetic_scatt, release-4.2.2, ticket-1009, ticket-1094-headless, ticket-1242-2d-resolution, ticket-1243, ticket-1249, ticket885, unittest-saveload

Children:

7b3f154

Parents:

e2b2473 (diff), 05b0bf6 (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 Butler <butlerpd@…> (09/11/17 17:49:05)

git-committer:

GitHub <noreply@…> (09/11/17 17:49:05)

Message:

Merge pull request #78 from SasView?/ticket-597

Ticket 597

Location:

src/sas

Files:

• sasgui/perspectives/fitting/media/combine_batch_grid.png (added)
• sasgui/perspectives/fitting/media/combine_batch_page.png (added)
• sasgui/perspectives/fitting/media/combine_batch_plot.png (added)
• sasgui/perspectives/fitting/media/fitting_help.rst (modified) (2 diffs)
• sasgui/perspectives/fitting/simfitpage.py (modified) (3 diffs)
• sascalc/dataloader/data_info.py (modified) (1 diff)
• sascalc/dataloader/file_reader_base_class.py (modified) (4 diffs)
• sascalc/dataloader/readers/cansas_reader.py (modified) (1 diff)
• sascalc/dataloader/readers/danse_reader.py (modified) (1 diff)

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

@@ -484 +484 @@
 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
 
+.. _Batch_Fit_Mode:
+
 Batch Fit Mode
 --------------
@@ -636 +638 @@
 
      Example: radius [2 : 5] , radius [10 : 25]
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-.. note::  This help document was last changed by Steve King, 10Oct2016
+     
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+Combined Batch Fit Mode
+-----------------------
+
+The purpose of the Combined Batch Fit is to allow running two or more batch
+fits in sequence without overwriting the output table of results.  This may be
+of interest for example if one is fitting a series of data sets where there is
+a shape change occurring in the series that requires changing the model part
+way through the series; for example a sphere to rod transition.  Indeed the
+regular batch mode does not allow for multiple models and requires all the
+files in the series to be fit with single model and set of parameters.  While
+it is of course possible to just run part of the series as a batch fit using
+model one followed by running another batch fit on the rest of the series with
+model two (and/or model three etc), doing so will overwrite the table of
+outputs from the previous batch fit(s).  This may not be desirable if one is
+interested in comparing the parameters: for example the sphere radius of set
+one and the cylinder radius of set two.
+
+Method
+^^^^^^
+
+In order to use the *Combined Batch Fit*, first load all the data needed as
+described in :ref:`Loading_data`. Next start up two or more *BatchPage* fits
+following the instructions in :ref:`Batch_Fit_Mode` but **DO NOT PRESS FIT**.
+At this point the *Combine Batch Fit* menu item under the *Fitting menu* should
+be active (if there is one or no *BatchPage* the menu item will be greyed out
+and inactive).  Clicking on *Combine Batch Fit* will bring up a new panel,
+similar to the *Const & Simult Fit* panel. In this case there will be a
+checkbox for each *BatchPage* instead of each *FitPage* that should be included
+in the fit.  Once all are selected, click the Fit button on
+the *BatchPage* to run each batch fit in *sequence*
+
+.. image:: combine_batch_page.png
+
+The batch table will then pop up at the end as for the case of the simple Batch
+Fitting with the following caveats:
+
+.. note::
+   The order matters.  The parameters in the table will be taken from the model
+   used in the first *BatchPage* of the list.  Any parameters from the
+   second and later *BatchPage* s that have the same name as a parameter in the
+   first will show up allowing for plotting of that parameter across the
+   models. The other parameters will not be available in the grid.
+.. note::
+   a corralary of the above is that currently models created as a sum|multiply
+   model will not work as desired because the generated model parameters have a
+   p#_ appended to the beginning and thus radius and p1_radius will not be
+   recognized as the same parameter.
+   
+.. image:: combine_batch_grid.png
+
+In the example shown above the data is a time series with a shifting peak.
+The first part of the series was fitted using the *broad_peak* model, while
+the rest of the data were fit using the *gaussian_peak* model. Unfortunately the
+time is not listed in the file but the file name contains the information. As
+described in :ref:`Grid_Window`, a column can be added manually, in this case
+called time, and the peak position plotted against time. 
+
+.. image:: combine_batch_plot.png
+
+Note the discontinuity in the peak position.  This reflects the fact that the
+Gaussian fit is a rather poor model for the data and is not actually
+finding the peak.
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. note::  This help document was last changed by Paul Butler, 10 September
+   2017

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

@@ -1 +1 @@
 """
-    Simultaneous fit page
+    Simultaneous or Batch fit page
 """
+# Note that this is used for both Simultaneous/Constrained fit AND for 
+# combined batch fit.  This is done through setting of the batch_on parameter.
+# There are the a half dozen or so places where an if statement is used as in 
+# if not batch_on:
+#     xxxx
+# else:
+#     xxxx
+# This is just wrong but dont have time to fix this go. Proper approach would be
+# to strip all parts of the code that depend on batch_on and create the top
+# level class from which a contrained/simultaneous fit page and a combined 
+# batch page inherit.
+#
+#            04/09/2017   --PDB
+
 import sys
 from collections import namedtuple
@@ -400 +414 @@
         # General Help button
         self.btHelp = wx.Button(self, wx.ID_HELP, 'HELP')
-        self.btHelp.SetToolTipString("Simultaneous/Constrained Fitting help.")
+        if self.batch_on:
+            self.btHelp.SetToolTipString("Combined Batch Fitting help.")
+        else:
+            self.btHelp.SetToolTipString("Simultaneous/Constrained Fitting help.")
         self.btHelp.Bind(wx.EVT_BUTTON, self._on_help)
 
@@ -527 +544 @@
     """
         _TreeLocation = "user/sasgui/perspectives/fitting/fitting_help.html"
-        _PageAnchor = "#simultaneous-fit-mode"
-        _doc_viewer = DocumentationWindow(self, self.ID_DOC, _TreeLocation,
+        if not self.batch_on:
+            _PageAnchor = "#simultaneous-fit-mode"
+            _doc_viewer = DocumentationWindow(self, self.ID_DOC, _TreeLocation,
                                           _PageAnchor,
                                           "Simultaneous/Constrained Fitting Help")
+        else:
+            _PageAnchor = "#combined-batch-fit-mode"
+            _doc_viewer = DocumentationWindow(self, self.ID_DOC, _TreeLocation,
+                                          _PageAnchor,
+                                          "Combined Batch Fit Help")
 
     def set_manager(self, manager):

src/sas/sascalc/dataloader/data_info.py

@@ -1161 +1161 @@
     final_dataset = None
     if isinstance(data, plottable_1D):
-        final_dataset = Data1D(data.x, data.y)
+        final_dataset = Data1D(data.x, data.y, isSesans=datainfo.isSesans)
         final_dataset.dx = data.dx
         final_dataset.dy = data.dy
         final_dataset.dxl = data.dxl
         final_dataset.dxw = data.dxw
+        final_dataset.x_unit = data._xunit
+        final_dataset.y_unit = data._yunit
         final_dataset.xaxis(data._xaxis, data._xunit)
         final_dataset.yaxis(data._yaxis, data._yunit)

src/sas/sascalc/dataloader/file_reader_base_class.py

@@ -6 +6 @@
 
 import os
+import re
 import logging
 import numpy as np
@@ -106 +107 @@
         for data in self.output:
             if isinstance(data, Data1D):
+                # Normalize the units for
+                data.x_unit = self.format_unit(data.x_unit)
+                data.y_unit = self.format_unit(data.y_unit)
                 # Sort data by increasing x and remove 1st point
                 ind = np.lexsort((data.y, data.x))
@@ -131 +135 @@
         for dataset in self.output:
             if isinstance(dataset, Data2D):
+                # Normalize the units for
+                dataset.x_unit = self.format_unit(dataset.Q_unit)
+                dataset.y_unit = self.format_unit(dataset.I_unit)
                 dataset.data = dataset.data.astype(np.float64)
                 dataset.qx_data = dataset.qx_data.astype(np.float64)
@@ -155 +162 @@
                 dataset.data = dataset.data.flatten()
 
+    def format_unit(self, unit=None):
+        """
+        Format units a common way
+        :param unit:
+        :return:
+        """
+        if unit:
+            split = unit.split("/")
+            if len(split) == 1:
+                return unit
+            elif split[0] == '1':
+                return "{0}^".format(split[1]) + "{-1}"
+            else:
+                return "{0}*{1}^".format(split[0], split[1]) + "{-1}"
+
     def set_all_to_none(self):
         """

src/sas/sascalc/dataloader/readers/cansas_reader.py

@@ -299 +299 @@
                     self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
                 elif tagname == 'dQw':
-                    if self.current_dataset.dqw is None: self.current_dataset.dqw = np.empty(0)
+                    if self.current_dataset.dxw is None:
+                        self.current_dataset.dxw = np.empty(0)
                     self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
                 elif tagname == 'dQl':
-                    if self.current_dataset.dxl is None: self.current_dataset.dxl = np.empty(0)
+                    if self.current_dataset.dxl is None:
+                        self.current_dataset.dxl = np.empty(0)
                     self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
                 elif tagname == 'Qmean':

src/sas/sascalc/dataloader/readers/danse_reader.py

@@ -189 +189 @@
         x_vals = np.tile(x_vals, (size_y, 1)).flatten()
         y_vals = np.tile(y_vals, (size_x, 1)).T.flatten()
-        if self.current_dataset.err_data == np.all(np.array(None)) or np.any(self.current_dataset.err_data <= 0):
+        if (np.all(self.current_dataset.err_data == None)
+                or np.any(self.current_dataset.err_data <= 0)):
             new_err_data = np.sqrt(np.abs(self.current_dataset.data))
         else: