Changeset 4203

Timestamp:

Dec 15, 2019 1:52:48 PM (4 years ago)

Author:

toby

Message:

Add close and composition to G2scriptable; more doc updates

Location:

trunk

Files:

• GSASIIElemGUI.py (modified) (1 diff)
• GSASIIscriptable.py (modified) (17 diffs)

trunk/GSASIIElemGUI.py

@@ -59 +59 @@
 
     def __init__(self, parent,oneOnly=False,ifNone=False,ifMag=False,multiple=False):
-        'Needs a doc string'
         self.oneOnly = oneOnly
         self.ifNone = ifNone

trunk/GSASIIscriptable.py

@@ -31 +31 @@
 ==================================================
 This section of the documentation provides an overview to API, with full documentation 
-in the :ref:`API` section. The typical API use will be with a Python script, such as this:
-
-.. code-block::  python
-
-    from __future__ import division, print_function
-    import os,sys
-    sys.path.insert(0,'/Users/toby/software/G2/GSASII') # needed to "find" GSAS-II modules
-    import GSASIIscriptable as G2sc
-    datadir = "/Users/Scratch/"
-    gpx = G2sc.G2Project(os.path.join(datadir,'test2.gpx'))
-    gpx.histogram(0).add_back_peak(4.5,30000,5000,0)
-    pardict = {'set': {'Sample Parameters': ['Absorption', 'Contrast', 'DisplaceX'],
-                       'Background': {'type': 'chebyschev-1', 'refine': True,
-                                      'peaks':[[0,True]]}}}
-    gpx.set_refinement(pardict)
-
-Most functionality is provided via the objects and methods described in this section. 
+in the :ref:`API` section. The typical API use will be with a Python script, such as 
+what is found in :ref:`CodeExamples`. Most functionality is provided via the objects and methods
+summarized below.
+
+---------------------
+Overview of Classes 
+---------------------
+
+===============================    ===============================================================================================================
+class                              Encapsulates 
+===============================    ===============================================================================================================
+:class:`G2Project`                  a GSAS-II project file, provides references to objects below,
+                                    each corresponding to a tree item 
+                                    (excepting :class:`G2AtomRecord`)
+:class:`G2Phase`                    a phase
+:class:`G2PwdrData`                 a powder histogram
+:class:`G2Image`                    an image
+:class:`G2PDF`                      a PDF histogram
+:class:`G2SeqRefRes`                the sequential results table
+:class:`G2AtomRecord`               an atom within a phase
+===============================    ===============================================================================================================
 
 ---------------------
@@ -62 +66 @@
 ==================================================    ===============================================================================================================
 
----------------------
-:class:`G2Project`
----------------------
+---------------------------------
+Class :class:`G2Project`
+---------------------------------
 
   All GSASIIscriptable scripts will need to create a :class:`G2Project` object 
@@ -111 +115 @@
 ==================================================    ===============================================================================================================
 
----------------------
-:class:`G2Phase`
----------------------
+---------------------------------
+Class :class:`G2Phase`
+---------------------------------
+
 
   Another common object in GSASIIscriptable scripts is :class:`G2Phase`, used to encapsulate each phase in a project, with commonly used methods:
@@ -139 +144 @@
 ==================================================    ===============================================================================================================
 
----------------------
-:class:`G2PwdrData`
----------------------
+---------------------------------
+Class :class:`G2PwdrData`
+---------------------------------
 
   Another common object in GSASIIscriptable scripts is :class:`G2PwdrData`, which encapsulate each powder diffraction histogram in a project, with commonly used methods:
@@ -168 +173 @@
 ==================================================    ===============================================================================================================
 
----------------------
-:class:`G2Image`
----------------------
+---------------------------------
+Class :class:`G2Image`
+---------------------------------
 
   When working with images, there will be a :class:`G2Image` object for each image (also see :meth:`G2Project.add_image`  and :meth:`G2Project.images`).
@@ -192 +197 @@
 
 
----------------------
-:class:`G2PDF`
----------------------
+---------------------------------
+Class :class:`G2PDF`
+---------------------------------
 
   To work with PDF entries, object :class:`G2PDF`, encapsulates a PDF entry with methods:
@@ -210 +215 @@
 ==================================================    ===============================================================================================================
 
----------------------
-:class:`G2SeqRefRes`
----------------------
+---------------------------------
+Class :class:`G2SeqRefRes`
+---------------------------------
 
   To work with Sequential Refinement results, object :class:`G2SeqRefRes`, encapsulates the sequential refinement table with methods:
@@ -227 +232 @@
 ==================================================    ===============================================================================================================
 
-----------------------
-:class:`G2AtomRecord`
-----------------------
+---------------------------------
+Class :class:`G2AtomRecord`
+---------------------------------
 
   When working with phases, :class:`G2AtomRecord` objects provide access to the contents of each atom in a phase. This provides access to "properties" that can be 
@@ -660 +665 @@
 Note that the parameters must match the object type and method (phase vs. histogram vs. HAP).
 
+.. _CodeExamples:
+
 =================================
 Code Examples
@@ -747 +754 @@
     gpx.histogram(0).Export('PbSO4data','.csv','hist') # data
     gpx.histogram(0).Export('PbSO4refl','.csv','refl') # reflections
+
+----------------------
+Simple Refinement
+----------------------
+
+GSASIIscriptable can be used to setup and perform simple refinements. 
+This example reads in an existing project (.gpx) file, adds a background
+peak, changes some refinement flags and performs a refinement.
+
+.. code-block::  python
+
+    from __future__ import division, print_function
+    import os,sys
+    sys.path.insert(0,'/Users/toby/software/G2/GSASII') # needed to "find" GSAS-II modules
+    import GSASIIscriptable as G2sc
+    datadir = "/Users/Scratch/"
+    gpx = G2sc.G2Project(os.path.join(datadir,'test2.gpx'))
+    gpx.histogram(0).add_back_peak(4.5,30000,5000,0)
+    pardict = {'set': {'Sample Parameters': ['Absorption', 'Contrast', 'DisplaceX'],
+                       'Background': {'type': 'chebyschev-1', 'refine': True,
+                                      'peaks':[[0,True]]}}}
+    gpx.set_refinement(pardict)
 
 ----------------------
@@ -979 +1008 @@
 ============================================================
 
-The large number of classes and modules in this module are described below.
-A script will have one or more G2Project objects using :class:`G2Project` and then
+The classes and modules in this module are described below.
+A script will create one or more :class:`G2Project` objects by reading 
+a GSAS-II project (.gpx) file or creating a new one and will then
 perform actions such as adding a histogram (method :meth:`G2Project.add_powder_histogram`),
 adding a phase (method :meth:`G2Project.add_phase`),
@@ -991 +1021 @@
 
 #============================================================================
-# adding a new object type
+# Notes for adding a new object type
 # 1) add a new object class (e.g. G2PDF)
 # 2) add the wrapper into G2Project (e.g. _pdfs, pdf, pdfs)
@@ -1993 +2023 @@
         return self.histogram(histname)
 
+    def clone_powder_histogram(self, histref, newname, Y, Yerr=None):
+        '''Creates a copy of a powder diffraction histogram with new Y values.
+        The X values are not changed. The number of Y values must match the
+        number of X values.         
+
+        :param histref: The histogram object, the name of the histogram (str), or ranId 
+           or histogram index.
+        :param str newname: The name to be assigned to the new histogram
+        :param list Y: A set of intensity values
+        :param list Yerr: A set of uncertainties for the intensity values (may be None,
+           sets all weights to unity)
+        :returns: the new histogram object (type G2PwdrData)
+        '''
+        hist = self.histogram(histref)
+        for i in self.names:
+            if i[0] == hist.name:
+                subkeys = i[1:]
+                break
+        else:
+            raise Exception("error in self.names, hist not found")
+        orighist = hist.name
+        newhist = 'PWDR '+newname
+        if len(Y) != len(self[orighist]['data'][1][0]):
+            raise Exception("clone error: length of Y does not match number of X values ({})"
+                                .format(len(self[orighist]['data'][1][0])))            
+        if Yerr is not None and len(Yerr) != len(self[orighist]['data'][1][0]):
+            raise Exception("clone error: length of Yerr does not match number of X values ({})"
+                                .format(len(self[orighist]['data'][1][0])))
+        
+        self[newhist] = copy.deepcopy(self[orighist])
+        # intensities
+        yo = self[newhist]['data'][1][1] = ma.MaskedArray(Y,mask=self[orighist]['data'][1][1].mask)
+        
+        Ymin,Ymax = yo.min(),yo.max()
+        # set to zero: weights, calc, bkg, obs-calc
+        for i in [2,3,4,5]:
+            self[newhist]['data'][1][i] *= 0
+        # weights
+        if Yerr is not None:
+            self[newhist]['data'][1][2] += 1./np.array(Yerr)**2
+        else:
+            self[newhist]['data'][1][2] += 1            # set all weights to 1
+        self[newhist]['data'][0] = {'wtFactor': 1.0, 'Dummy': False,
+                  'ranId': ran.randint(0, sys.maxsize),
+                  'Offset': [0.0, 0.0], 'delOffset': 0.02*Ymax,
+                  'refOffset': -0.1*Ymax, 'refDelt': 0.1*Ymax,
+                  'Yminmax': [Ymin, Ymax]}
+        self[newhist]['Comments'].insert(0,'Cloned from '+orighist)
+        self[newhist]['Reflection Lists'] = {}
+        self[newhist]['Index Peak List'] = [[], []]
+        self[newhist]['Unit Cells List'] = []
+        self[newhist]['Peak List'] = {'peaks': [], 'sigDict': {}}
+        self.names.append([newhist]+subkeys)
+        self.update_ids()
+        return self.histogram(newhist)
+        
     def add_simulated_powder_histogram(self, histname, iparams, Tmin, Tmax, Tstep,
                                        wavelength=None, scale=None, phases=[]):
@@ -3257 +3343 @@
 
     @property
+    def element(self):
+        '''Get the associated atom's element symbol
+        '''
+        import re
+        try:
+            return re.match('^([A-Z][a-z]?)',self.data[self.ct]).group(1)
+        except:
+            raise Exception("element parse error with type {}".
+                                format(self.data[self.ct]))
+
+    @property
     def refinement_flags(self):
         '''Get or set refinement flags for the associated atom
@@ -3281 +3378 @@
         '''
         return self.data[self.cx+3]
-
+    
     @occupancy.setter
     def occupancy(self, val):
         self.data[self.cx+3] = float(val)
 
+    @property
+    def mult(self):
+        '''Get the associated atom's multiplicity value
+        '''
+        return self.data[self.cs+1]
+    
     @property
     def ranId(self):
@@ -4053 +4156 @@
         """
         ptrs = self.data['General']['AtomPtrs']
-        output = []
-        atoms = self.data['Atoms']
-        for atom in atoms:
-            output.append(G2AtomRecord(atom, ptrs, self.proj))
-        return output
+        return [G2AtomRecord(atom, ptrs, self.proj) for atom in self.data['Atoms']]
 
     def histograms(self):
@@ -4063 +4162 @@
         as they appear in the tree (see :meth:`G2Project.histograms`).
         '''
-        return [i.name for i in self.proj.histograms() if i.name in self.data.get('Histograms', {})] 
-
+        return [i.name for i in self.proj.histograms() if i.name in self.data.get('Histograms', {})]
+    
+    @property
+    def composition(self):
+        '''Returns a dict where keys are atom types and values are the number of 
+        atoms of that type in cell (such as {'H': 2.0, 'O': 1.0})
+        '''
+        out = {}
+        for a in self.atoms():
+            typ = a.element
+            if typ in out:
+                out[typ] += a.mult*a.occupancy
+            else:
+                out[typ] = a.mult*a.occupancy
+        return out
+            
+    
     @property
     def ranId(self):