Changeset 6afc14b in sasview

Timestamp:

Apr 18, 2016 12:02:01 PM (9 years ago)

Author:

gonzalezm

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:

b768e92

Parents:

70e5f97 (diff), 42585bf (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 branch 'master' of ​https://github.com/SasView/sasview

Files:

• sasview/README.txt (modified) (1 diff)
• sasview/__init__.py (modified) (1 diff)
• sasview/default_categories.json (modified) (1 diff)
• src/sas/sascalc/calculator/BaseComponent.py (modified) (1 diff)
• src/sas/sascalc/calculator/sas_gen.py (modified) (1 diff)
• src/sas/sascalc/fit/MultiplicationModel.py (modified) (3 diffs)
• src/sas/sasgui/perspectives/calculator/model_editor.py (modified) (3 diffs)
• src/sas/sasgui/perspectives/fitting/basepage.py (modified) (7 diffs)
• src/sas/sasgui/perspectives/fitting/fitpage.py (modified) (4 diffs)
• src/sas/sasgui/perspectives/fitting/models.py (modified) (2 diffs)
• src/sas/sasgui/plottools/PlotPanel.py (modified) (1 diff)

sasview/README.txt

@@ -4 +4 @@
 1- Features
 ===========
+
+    - New in Version 4.0.0-alpha
+      --------------------
+      This alpha release brings a major overhaul of the model system. The new model
+      package allows rapid integration of custom models and access to polydispersity
+      without requiring a compiler.
+
+      - Model package changes and improvements
+         - Model interface moved to independent sasmodels package.
+         - Most models converted to new interface.
+         - Allows rapid integration of user-written models.
+         - OpenCL GPU utilization for faster fitting.
+         - Improved numerical integration of Bessel functions.
+      - SESANS integration and implementation
+         - Scripting interface added for analysis of SESANS data.
+         - Hankel transformation now accepts finite acceptance angles.
+         - 2D cosine transformation added for TOF SESANS analysis.
+      - Documentation improvements
+         - The documentation tree was restructured for a better end user experience.
+         - The documentation for each model was revamped and verified by at least
+           two people following the conversion of the model.
+         - Theoretical 1D (and 2D if applicable) scattering curves are auto-generated
+           and added to the model documentation for each model.
+      - Separation of GUI and calculations for future GUI enhancements
+      - Bug fixes
+         - Fixes bug #411 No stop button on simultaneous fit page
+         - Fixes bug #410 Error with raspberry model
+         - Fixes bug #364 Possible inconsistency in Poly_GausCoil model
+         - Fixes bug #439 Hayter Penfold MSA code needs checking
+         - Fixes bug #484 lammellerPC is precision limited
+         - Fixes bug #498 $HOME/.matplotlib conflicts
+         - Fixes bug #348 Control order in which fit parameters appear in the gui
+         - Fixes bug #456 Provide DREAM Results Panel with something to identify
+           data and age of results
+         - Fixes bug #556 Build script improvements for developers
+
+
 
    - New in Version 3.1.2

sasview/__init__.py

@@ -1 @@
-__version__ = "3.1.2"
+__version__ = "4.0.0-alpha"
 __build__ = "1"

sasview/default_categories.json

@@ -1 @@
-{"Shapes": [["barbell", true], ["pearl_necklace", true], ["hollow_cylinder", true], ["CoreMultiShellModel", true], ["fcc_paracrystal", true], ["parallelepiped", true], ["fuzzy_sphere", true], ["core_shell_ellipsoid_xt", true], ["lamellarPC", true], ["bcc_paracrystal", true], ["ellptical_cylinder", true], ["hollow_rectangular_prism_infinitely_thin_walls", true], ["core_shell_parallelepiped", true], ["OnionExpShellModel", true], ["multi_shell", true], ["raspberry", true], ["core_shell_ellipsoid", true], ["capped_cylinder", true], ["cylinder", true], ["SphericalSLDModel", true], ["sc_crystal", true], ["stacked_disks", true], ["LamellarPSHGModel", true], ["core_shell_bicelle", true], ["hollow_rectangular_prism", true], ["LamellarPSModel", true], ["ellipsoid", true], ["sphere", true], ["vesicle", true], ["triaxial_ellipsoid", true], ["lamellar", true], ["pringles", true], ["rectangular_prism", true], ["core_shell_cylinder", true], ["BinaryHSModel", true], ["flexible_cylinder", true], ["lamellarFFHG", true], ["flexible_cylinder_ex", true], ["linear_pearls", true], ["core_shell_sphere", true]], "Structure Factor": [["squarewell", true], ["hayter_msa", true], ["hardsphere", true], ["stickyhardsphere", true]], "Shape-Independent": [["two_power_law", true], ["gel_fit", true], ["dab", true], ["power_law", true], ["porod", true], ["guinier", true], ["rpa", true], ["teubner_strey", true], ["star_polymer", true], ["UnifiedPowerRgModel", true], ["mass_surface_fractal", true], ["adsorbed_layer", true], ["two_lorentzian", true], ["mono_gauss_coil", true], ["mass_fractal", true], ["guinier_porod", true], ["correlation_length", true], ["polymer_excl_volume", true], ["FractalModel", true], ["peak_lorentz", true], ["broad_peak", true], ["fractal_core_shell", true], ["gaussian_peak", true], ["be_polyelectrolyte", true], ["poly_gauss_coil", true], ["surface_fractal", true], ["gauss_lorentz_gel", true], ["lorentz", true]], "Uncategorized": [["ReflectivityModel", true], ["ReflectivityIIModel", true], ["line", true], ["micell_spherical_coil", true]]}
+{"Shapes": [["cylinder", true], ["lamellar_stack_paracrystal", true], ["multilayer_vesicle", true], ["core_shell_cylinder", true], ["lamellar_hg", true], ["fuzzy_sphere", true], ["sphere", true], ["triaxial_ellipsoid", true], ["rectangular_prism", true], ["core_shell_bicelle", true], ["flexible_cylinder", true], ["flexible_cylinder_elliptical", true], ["binary_hard_sphere", true], ["core_multi_shell", true], ["sc_paracrystal", true], ["ellipsoid", true], ["capped_cylinder", true], ["core_shell_ellipsoid", true], ["fcc_paracrystal", true], ["core_shell_parallelepiped", true], ["core_shell_ellipsoid_xt", true], ["elliptical_cylinder", true], ["pringle", true], ["hollow_rectangular_prism_thin_walls", true], ["hollow_rectangular_prism", true], ["vesicle", true], ["polymer_micelle", true], ["parallelepiped", true], ["hollow_cylinder", true], ["linear_pearls", true], ["spherical_sld", true], ["raspberry", true], ["lamellar_hg_stack_caille", true], ["pearl_necklace", true], ["lamellar", true], ["onion", true], ["lamellar_stack_caille", true], ["bcc_paracrystal", true], ["core_shell_sphere", true], ["stacked_disks", true]], "Structure Factor": [["hayter_msa", true], ["squarewell", true], ["stickyhardsphere", true], ["hardsphere", true]], "Shape-Independent": [["guinier_porod", true], ["polymer_excl_volume", true], ["gel_fit", true], ["teubner_strey", true], ["mono_gauss_coil", true], ["mass_surface_fractal", true], ["mass_fractal", true], ["adsorbed_layer", true], ["two_lorentzian", true], ["fractal", true], ["fractal_core_shell", true], ["dab", true], ["poly_gauss_coil", true], ["star_polymer", true], ["broad_peak", true], ["surface_fractal", true], ["two_power_law", true], ["power_law", true], ["rpa", true], ["be_polyelectrolyte", true], ["peak_lorentz", true], ["guinier", true], ["correlation_length", true], ["line", true], ["gaussian_peak", true], ["porod", true], ["gauss_lorentz_gel", true], ["lorentz", true]]}

src/sas/sascalc/calculator/BaseComponent.py

@@ -50 +50 @@
         self.output_unit = "cm^{-1}"
 
+        self.is_multiplicity_model = False
+        self.is_structure_factor = False
+        self.is_form_factor = False
+
     def __str__(self):
         """

src/sas/sascalc/calculator/sas_gen.py

@@ -80 +80 @@
         ## Parameter details [units, min, max]
         self.details = {}
-        self.details['scale'] = ['', None, None]
-        self.details['background'] = ['[1/cm]', None, None]
-        self.details['solvent_SLD'] = ['1/A^(2)', None, None]
-        self.details['total_volume'] = ['A^(3)', None, None]
-        self.details['Up_frac_in'] = ['[u/(u+d)]', None, None]
-        self.details['Up_frac_out'] = ['[u/(u+d)]', None, None]
-        self.details['Up_theta'] = ['[deg]', None, None]
+        self.details['scale'] = ['', 0.0, numpy.inf]
+        self.details['background'] = ['[1/cm]', 0.0, numpy.inf]
+        self.details['solvent_SLD'] = ['1/A^(2)', -numpy.inf, numpy.inf]
+        self.details['total_volume'] = ['A^(3)', 0.0, numpy.inf]
+        self.details['Up_frac_in'] = ['[u/(u+d)]', 0.0, 1.0]
+        self.details['Up_frac_out'] = ['[u/(u+d)]', 0.0, 1.0]
+        self.details['Up_theta'] = ['[deg]', -numpy.inf, numpy.inf]
         # fixed parameters
         self.fixed = []

src/sas/sascalc/fit/MultiplicationModel.py

@@ +1 @@
+import copy
+
+import numpy
 
 from sas.sascalc.calculator.BaseComponent import BaseComponent
-#import numpy, math
-import copy
-from sas.sascalc.fit.pluginmodel import Model1DPlugin
+
 class MultiplicationModel(BaseComponent):
     r"""
@@ -47 +48 @@
         ## Parameter details [units, min, max]
         self._set_details()
-        self.details['scale_factor'] = ['',     None, None]
+        self.details['scale_factor'] = ['', 0.0, numpy.inf]
         
         #list of parameter that can be fitted
@@ -75 +76 @@
                 self.multiplicity_info = p_model.multiplicity_info 
                 self.fun_list = p_model.fun_list
+                self.is_multiplicity_model = True
             except:
                 pass
         else:
-            self.multiplicity_info = []
+            self.is_multiplicity_model = False
+            self.multiplicity_info = [0]
             
     def _clone(self, obj):

src/sas/sasgui/perspectives/calculator/model_editor.py

@@ -1329 +1329 @@
 SUM_TEMPLATE = """
 # A sample of an experimental model function for Sum/Multiply(Pmodel1,Pmodel2)
+import os
+import sys
 import copy
+
+import nuympy
+
 from sas.sascalc.fit.pluginmodel import Model1DPlugin
 from sasmodels.sasview_model import make_class
@@ -1339 +1344 @@
 #P2_model:
 #from %s import Model as P2
-import os
-import sys
 
 class Model(Model1DPlugin):
@@ -1385 +1388 @@
         ## Parameter details [units, min, max]
         self._set_details()
-        self.details['scale_factor'] = ['', None, None]
+        self.details['scale_factor'] = ['', 0.0, numpy.inf]
 
 

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

@@ -1896 +1896 @@
                 for model in self.model_list_box[mod_cat]:
                     if 'sasmodels.sasview_model.' in str(model):
-                        str_m = model._model_info['id']
+                        str_m = model.id
                     else:
                         str_m = str(model).split(".")[0]
@@ -1945 +1945 @@
         mlist = []
         for models in list:
-            model = models()
-            name = model.__class__.__name__
-            if models.__name__ != "NoStructure":
-                name = model.name
-                mlist.append((name, models))
+            if models.name != "NoStructure":
+                mlist.append((models.name, models))
 
         # Sort the models
@@ -2099 +2096 @@
         if form_factor != None:
             # set multifactor for Mutifunctional models
-            if form_factor().__class__ in \
-                                        self.model_list_box["Multi-Functions"]:
+            if form_factor.is_multiplicity_model:
                 m_id = self.multifactorbox.GetCurrentSelection()
-                multiplicity = form_factor().multiplicity_info[0]
+                multiplicity = form_factor.multiplicity_info[0]
                 self.multifactorbox.Clear()
                 self._set_multfactor_combobox(multiplicity)
                 self._show_multfactor_combobox()
                 #ToDo:  this info should be called directly from the model
-                text = form_factor().multiplicity_info[1]  # 'No. of Shells: '
+                text = form_factor.multiplicity_info[1]  # 'No. of Shells: '
 
                 self.mutifactor_text.SetLabel(text)
@@ -2117 +2113 @@
                 if self.multi_factor == None:
                     self.multi_factor = 0
-                form_factor = form_factor(int(self.multi_factor))
                 self.multifactorbox.SetSelection(m_id)
                 # Check len of the text1 and max_multiplicity
@@ -2131 +2126 @@
                 else:
                     self.sld_axes = ""
-
             else:
                 self._hide_multfactor_combobox()
                 self.show_sld_button.Hide()
-                form_factor = form_factor()
                 self.multi_factor = None
         else:
@@ -2147 +2140 @@
         if  struct_factor != None:
             from sas.sascalc.fit.MultiplicationModel import MultiplicationModel
-            self.model = MultiplicationModel(form_factor, struct_factor())
+            self.model = MultiplicationModel(form_factor(self.multi_factor),
+                                             struct_factor())
             # multifunctional form factor
             if len(form_factor.non_fittable) > 0:
                 self.temp_multi_functional = True
+        elif form_factor != None:
+            self.model = form_factor(self.multi_factor)
         else:
-            if form_factor != None:
-                self.model = form_factor
-            else:
-                self.model = None
-                return self.model
+            self.model = None
+            return
+
         # check if model has magnetic parameters
         if len(self.model.magnetic_params) > 0:
@@ -2286 +2280 @@
                 parameter's error of fit,
                 parameter's minimum value,
-                parrameter's maximum value ,
+                parameter's maximum value ,
                 parameter's units]
         """

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

@@ -10 +10 @@
 import math
 import time
+
+from sasmodels.weights import MODELS as POLYDISPERSITY_MODELS
+
 from sas.sasgui.guiframe.events import StatusEvent
 from sas.sasgui.guiframe.events import NewPlotEvent
@@ -621 +624 @@
         model_disp = wx.StaticText(self, wx.ID_ANY, 'Function')
         CHECK_STATE = self.cb1.GetValue()
-        #import sas.models.dispersion_models
-        #self.polydisp = sas.models.dispersion_models.models
-        import sasmodels.weights
-        self.polydisp =  sasmodels.weights.models
 
         ix = 0
@@ -784 +783 @@
                 disp_box = wx.ComboBox(self, wx.ID_ANY, size=(65, -1),
                                        style=wx.CB_READONLY, name='%s' % name1)
-                for key, value in self.polydisp.iteritems():
+                for key, value in POLYDISPERSITY_MODELS.iteritems():
                     name_disp = str(key)
                     disp_box.Append(name_disp, value)
@@ -948 +947 @@
                 disp_box = wx.ComboBox(self, wx.ID_ANY, size=(65, -1),
                                 style=wx.CB_READONLY, name='%s' % name1)
-                for key, value in self.polydisp.iteritems():
+                for key, value in POLYDISPERSITY_MODELS.iteritems():
                     name_disp = str(key)
                     disp_box.Append(name_disp, value)

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

@@ -296 +296 @@
         #Build list automagically from sasmodels package
         for model in load_standard_models():
-            self.model_dictionary[model._model_info['name']] = model
-            if model._model_info['structure_factor'] == True:
+            self.model_dictionary[model.name] = model
+            if model.is_structure_factor:
                 self.struct_list.append(model)
-            if model._model_info['variant_info'] is not None:
+            if model.is_form_factor:
+                self.multiplication_factor.append(model)
+            if model.is_multiplicity_model:
                 self.multi_func_list.append(model)
             else:
-                self.model_name_list.append(model._model_info['name'])
-            if model._model_info['ER'] is not None:
-                self.multiplication_factor.append(model)
+                self.model_name_list.append(model.name)
 
         #Looking for plugins
@@ -387 +387 @@
         Get the multifunctional models
         """
-        for item in self.plugins:
-            try:
-                # check the multiplicity if any
-                if item.multiplicity_info[0] > 1:
-                    self.multi_func_list.append(item)
-            except:
-                # pass to other items
-                pass
+        items = [item for item in self.plugins if item.is_multiplicity_model]
+        self.multi_func_list = items
 
     def get_model_list(self):

src/sas/sasgui/plottools/PlotPanel.py

@@ -1994 +1994 @@
         """
         try:
-            self.toolbar.copy_figure()
+            self.toolbar.copy_figure(self.canvas)
         except:
             print "Error in copy Image"