Changeset 3209 for trunk/GSASIIscriptable.py

Timestamp:

Dec 28, 2017 12:50:40 PM (4 years ago)

Author:

toby

Message:

Add simulation to scriptable & add to tutorial; add sphinx index to ctrlsGUI; remove path from RunGSASII.bat

File:

• trunk/GSASIIscriptable.py (modified) (6 diffs)

trunk/GSASIIscriptable.py

@@ -563 +563 @@
         file.close()
 
-def ImportPowder(reader,filename):
-    '''Use a reader to import a powder diffraction data file
-
-    :param str reader: a scriptable reader
-    :param str filename: full name of powder data file; can be "multi-Bank" data
-
-    :returns: list rdlist: list of reader objects containing powder data, one for each
-        "Bank" of data encountered in file. Items in reader object of interest are:
-
-          * rd.comments: list of str: comments found on powder file
-          * rd.dnames: list of str: data nammes suitable for use in GSASII data tree NB: duplicated in all rd entries in rdlist
-          * rd.powderdata: list of numpy arrays: pos,int,wt,zeros,zeros,zeros as needed for a PWDR entry in  GSASII data tree.
-    '''
-    rdfile,rdpath,descr = imp.find_module(reader)
-    rdclass = imp.load_module(reader,rdfile,rdpath,descr)
-    rd = rdclass.GSAS_ReaderClass()
-    if not rd.scriptable:
-        print(u'**** ERROR: '+reader+u' is not a scriptable reader')
-        return None
-    rdlist = []
-    if rd.ContentsValidator(filename):
-        repeat = True
-        rdbuffer = {} # create temporary storage for file reader
-        block = 0
-        while repeat: # loop if the reader asks for another pass on the file
-            block += 1
-            repeat = False
-            rd.objname = ospath.basename(filename)
-            flag = rd.Reader(filename,None,buffer=rdbuffer,blocknum=block,)
-            if flag:
-                rdlist.append(copy.deepcopy(rd)) # save the result before it is written over
-                if rd.repeat:
-                    repeat = True
-        return rdlist
-    print(rd.errors)
-    return None
+# def ImportPowder(reader,filename):
+#     '''Use a reader to import a powder diffraction data file
+
+#     :param str reader: a scriptable reader
+#     :param str filename: full name of powder data file; can be "multi-Bank" data
+
+#     :returns: list rdlist: list of reader objects containing powder data, one for each
+#         "Bank" of data encountered in file. Items in reader object of interest are:
+
+#           * rd.comments: list of str: comments found on powder file
+#           * rd.dnames: list of str: data nammes suitable for use in GSASII data tree NB: duplicated in all rd entries in rdlist
+#           * rd.powderdata: list of numpy arrays: pos,int,wt,zeros,zeros,zeros as needed for a PWDR entry in  GSASII data tree.
+#     '''
+#     rdfile,rdpath,descr = imp.find_module(reader)
+#     rdclass = imp.load_module(reader,rdfile,rdpath,descr)
+#     rd = rdclass.GSAS_ReaderClass()
+#     if not rd.scriptable:
+#         print(u'**** ERROR: '+reader+u' is not a scriptable reader')
+#         return None
+#     rdlist = []
+#     if rd.ContentsValidator(filename):
+#         repeat = True
+#         rdbuffer = {} # create temporary storage for file reader
+#         block = 0
+#         while repeat: # loop if the reader asks for another pass on the file
+#             block += 1
+#             repeat = False
+#             rd.objname = ospath.basename(filename)
+#             flag = rd.Reader(filename,None,buffer=rdbuffer,blocknum=block,)
+#             if flag:
+#                 rdlist.append(copy.deepcopy(rd)) # save the result before it is written over
+#                 if rd.repeat:
+#                     repeat = True
+#         return rdlist
+#     print(rd.errors)
+#     return None
 
 def SetDefaultDData(dType,histoName,NShkl=0,NDij=0):
@@ -1166 +1166 @@
         :param list phases: Phases to link to the new histogram
         :param str fmthint: If specified, only importers where the format name
-          (reader.formatName, as shown in Import menu) containing the
+          (reader.formatName, as shown in Import menu) contains the
           supplied string will be tried as importers. If not specified, all
           importers consistent with the file extension will be tried
@@ -1196 +1196 @@
         return self.histogram(histname)
 
+    def add_simulated_powder_histogram(self, histname, iparams, Tmin, Tmax, Tstep,
+                                       wavelength=None, scale=None, phases=[]):
+        """Loads a powder data histogram into the project.
+
+        Requires an instrument parameter file. 
+        Note that in unix fashion, "~" can be used to indicate the
+        home directory (e.g. ~/G2data/data.prm). The instrument parameter file
+        will determine if the histogram is x-ray, CW neutron, TOF, etc. as well
+        as the instrument type. 
+
+        :param str histname: A name for the histogram to be created.
+        :param str iparams: The instrument parameters file, a filename.
+        :param float Tmin: Minimum 2theta or TOF (ms) for dataset to be simulated
+        :param float Tmax: Maximum 2theta or TOF (ms) for dataset to be simulated
+        :param float Tstep: Step size in 2theta or TOF (ms) for dataset to be simulated       
+        :param float wavelength: Wavelength for CW instruments, overriding the value
+           in the instrument parameters file if specified.
+        :param float scale: Histogram scale factor which multiplies the pattern. Note that
+           simulated noise is added to the pattern, so that if the maximum intensity is
+           small, the noise will mask the computed pattern. The scale 
+           needs to be a large number for CW neutrons.
+           The default, None, provides a scale of 1 for x-rays and TOF; 10,000 for CW neutrons.
+        :param list phases: Phases to link to the new histogram. Use proj.phases() to link to
+           all defined phases.
+
+        :returns: A :class:`G2PwdrData` object representing the histogram
+        """
+        LoadG2fil()
+        iparams = os.path.abspath(os.path.expanduser(iparams))
+        if not os.path.exists(iparams):
+            raise G2ScriptException("File does not exist:"+iparams)
+        rd = G2obj.ImportPowderData( # Initialize a base class reader
+            extensionlist=tuple(),
+            strictExtension=False,
+            formatName = 'Simulate dataset',
+            longFormatName = 'Compute a simulated pattern')
+        rd.powderentry[0] = '' # no filename
+        rd.powderentry[2] = 1 # only one bank
+        rd.comments.append('This is a dummy dataset for powder pattern simulation')
+        #Iparm1, Iparm2 = load_iprms(iparams, rd)
+        if Tmax < Tmin:
+            Tmin,Tmax = Tmax,Tmin
+        Tstep = abs(Tstep)
+        if 'TOF' in rd.idstring:
+                N = (np.log(Tmax)-np.log(Tmin))/Tstep
+                x = np.exp((np.arange(0,N))*Tstep+np.log(Tmin*1000.))
+                N = len(x)
+        else:            
+                N = int((Tmax-Tmin)/Tstep)+1
+                x = np.linspace(Tmin,Tmax,N,True)
+                N = len(x)
+        if N < 3:
+            raise G2ScriptException("Error: Range is too small or step is too large, <3 points")
+        rd.powderdata = [
+            np.array(x), # x-axis values
+            np.zeros_like(x), # powder pattern intensities
+            np.ones_like(x), # 1/sig(intensity)^2 values (weights)
+            np.zeros_like(x), # calc. intensities (zero)
+            np.zeros_like(x), # calc. background (zero)
+            np.zeros_like(x), # obs-calc profiles
+            ]
+        Tmin = rd.powderdata[0][0]
+        Tmax = rd.powderdata[0][-1]
+        rd.idstring = histname
+        histname, new_names, pwdrdata = load_pwd_from_reader(rd, iparams,
+                                                            [h.name for h in self.histograms()])
+        if histname in self.data:
+            print("Warning - redefining histogram", histname)
+        elif self.names[-1][0] == 'Phases':
+            self.names.insert(-1, new_names)
+        else:
+            self.names.append(new_names)
+        if scale is not None:
+            pwdrdata['Sample Parameters']['Scale'][0] = scale
+        elif pwdrdata['Instrument Parameters'][0]['Type'][0].startswith('PNC'):
+            pwdrdata['Sample Parameters']['Scale'][0] = 10000.
+        self.data[histname] = pwdrdata
+        self.update_ids()
+
+        for phase in phases:
+            phase = self.phase(phase)
+            self.link_histogram_phase(histname, phase)
+
+        return self.histogram(histname)
+    
     def add_phase(self, phasefile, phasename=None, histograms=[], fmthint=None):
         """Loads a phase into the project from a .cif file
@@ -1202 +1287 @@
         :param str phasename: The name of the new phase, or None for the default
         :param list histograms: The names of the histograms to associate with
-            this phase
+            this phase. Use proj.Histograms() to add to all histograms.
         :param str fmthint: If specified, only importers where the format name
-          (reader.formatName, as shown in Import menu) containing the
+          (reader.formatName, as shown in Import menu) contains the
           supplied string will be tried as importers. If not specified, all
           importers consistent with the file extension will be tried
@@ -1369 +1454 @@
         Gives an object representing the specified phase in this project.
 
-        :param str phasename: The name of the desired phase. Either the name
-            (str), the phase's ranId, or the phase's index
+        :param str phasename: A reference to the desired phase. Either the phase 
+            name (str), the phase's ranId, the phase's index (both int) or
+            a phase object (:class:`G2Phase`)
         :returns: A :class:`G2Phase` object
         :raises: KeyError
@@ -1379 +1465 @@
             :meth:`G2Project.phases`
             """
+        if isinstance(phasename, G2Phase):
+            if phasename.proj == self:
+                return phasename
         phases = self.data['Phases']
         if phasename in phases: