Changeset 1925

Timestamp:

Jul 10, 2015 3:50:10 PM (7 years ago)

Author:

vondreele

Message:

create AddHatomDialog? & work on OnHydAtomAdd?
allow reading of .cor images made at APS 1ID

Location:

trunk

Files:

• GSASIIIO.py (modified) (4 diffs)
• GSASIIconstrGUI.py (modified) (1 diff)
• GSASIIgrid.py (modified) (3 diffs)
• GSASIImath.py (modified) (1 diff)
• GSASIIphsGUI.py (modified) (2 diffs)

trunk/GSASIIIO.py

@@ -178 +178 @@
     if not os.path.exists(imagefile):
         dlg = wx.FileDialog(G2frame, 'Previous image file not found; open here', '.', '',\
-        'Any image file (*.edf;*.tif;*.tiff;*.mar*;*.ge*;*.avg;*.sum;*.img)\
-        |*.edf;*.tif;*.tiff;*.mar*;*.ge*;*.avg;*.sum;*.img|\
+        'Any image file (*.edf;*.tif;*.tiff;*.mar*;*.ge*;*.avg;*.sum;*.img;*.cor)\
+        |*.edf;*.tif;*.tiff;*.mar*;*.ge*;*.avg;*.sum;*.img;*.cor|\
         European detector file (*.edf)|*.edf|\
         Any detector tif (*.tif;*.tiff)|*.tif;*.tiff|\
         MAR file (*.mar*)|*.mar*|\
-        GE Image (*.ge*;*.avg;*.sum)|*.ge*;*.avg;*.sum|\
+        GE Image (*.ge*;*.avg;*.sum;*.cor)|*.ge*;*.avg;*.sum;*.cor|\
         ADSC Image (*.img)|*.img|\
         All files (*.*)|*.*',wx.OPEN|wx.CHANGE_DIR)
@@ -303 +303 @@
     elif ext in ['.mar3450','.mar2300','.mar2560']:
         Comments,Data,Npix,Image = GetMAR345Data(imagefile)
-    elif ext in ['.sum','.avg'] or 'ge' in ext:
+    elif ext in ['.sum','.avg','.cor'] or 'ge' in ext:
         Comments,Data,Npix,Image = GetGEsumData(imagefile)
     elif ext == '.G2img':
@@ -410 +410 @@
         print 'Read GE sum file: ',filename    
     File = open(filename,'rb')
-    if '.sum' in filename:
-        head = ['GE detector sum data from APS 1-ID',]
+    if '.sum' in filename or '.cor' in filename:
+        head = ['GE detector sum or cor data from APS 1-ID',]
         sizexy = [2048,2048]
     elif '.avg' in filename or '.ge' in filename:
@@ -424 +424 @@
         File.seek(pos)
     Npix = sizexy[0]*sizexy[1]
-    if '.sum' in filename:
+    if '.sum' in filename or '.cor' in filename:
         image = np.array(ar.array('f',File.read(4*Npix)),dtype=np.int32)
     elif '.avg' in filename or '.ge' in filename:

trunk/GSASIIconstrGUI.py

@@ -775 +775 @@
         Dx = np.inner(Amat,XYZ-XYZ[Orig]).T
         dist = np.sqrt(np.sum(Dx**2,axis=1))
-        sumR = AtInfo[OType]+0.5
+        sumR = AtInfo[OType]+0.5    #H-atoms only!
         IndB = ma.nonzero(ma.masked_greater(dist-0.85*sumR,0.))
         for j in IndB[0]:

trunk/GSASIIgrid.py

@@ -316 +316 @@
         parent.Raise()
         self.EndModal(wx.ID_CANCEL)
+        
+class AddHatomDialog(wx.Dialog):
+    '''H atom addition dialog. After :meth:`ShowModal` returns, the results 
+    are found in dict :attr:`self.data`, which is accessed using :meth:`GetData`.
+    :param wx.Frame parent: reference to parent frame (or None)
+    :param dict Neigh: a dict of atom names with list of atom name, dist pairs for neighboring atoms
+    :param dict phase: a dict containing the phase as defined by
+      :ref:`Phase Tree Item <Phase_table>`    
+    '''
+    def __init__(self,parent,Neigh,phase):
+        wx.Dialog.__init__(self,parent,wx.ID_ANY,'H atom add', 
+            pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
+        self.panel = wxscroll.ScrolledPanel(self)         #just a dummy - gets destroyed in Draw!
+        self.Neigh = Neigh
+        self.phase = phase
+        self.Hatoms = []
+        self.Draw(self.Neigh,self.phase)
+            
+    def Draw(self,Neigh,phase):
+        '''Creates the contents of the dialog. Normally called
+        by :meth:`__init__`.
+        '''
+        def OnHSelect(event):
+            Obj = event.GetEventObject()
+            item,i = Indx[Obj.GetId()]
+            for obj in Indx[item]:
+                obj.SetValue(False)
+            Obj.SetValue(True)
+            self.Neigh[item][2] = i
+            
+        self.panel.Destroy()
+        self.panel = wxscroll.ScrolledPanel(self,style = wx.DEFAULT_DIALOG_STYLE)
+        mainSizer = wx.BoxSizer(wx.VERTICAL)
+        mainSizer.Add(wx.StaticText(self.panel,-1,'H atom add controls for phase %s:'%(phase['General']['Name'])),
+            0,wx.LEFT|wx.TOP,10)
+        mainSizer.Add(wx.StaticText(self.panel,-1," Atom:  Add # H's          Neighbors, dist"),0,wx.TOP|wx.LEFT,5)
+        nHatms = ['0','1','2','3']
+        dataSizer = wx.FlexGridSizer(0,3,0,0)
+        Indx = {}
+        for inei,neigh in enumerate(Neigh):
+            dataSizer.Add(wx.StaticText(self.panel,-1,' %s:  '%(neigh[0])),0,WACV)
+            nH = 1      #for O atom
+            if 'C' in neigh[0] or 'N' in neigh[0]:
+                nH = 4-len(neigh[1])
+            neigh[2] = nH
+            checks = wx.BoxSizer(wx.HORIZONTAL)
+            Ids = []
+            for i in range(nH+1):
+                nHs = wx.CheckBox(self.panel,-1,label=nHatms[i])
+                if i == neigh[2]:
+                    nHs.SetValue(True)
+                Indx[nHs.GetId()] = [inei,i]
+                Ids.append(nHs)
+                nHs.Bind(wx.EVT_CHECKBOX, OnHSelect)
+                checks.Add(nHs,0,WACV)
+            Indx[inei] = Ids
+            dataSizer.Add(checks,0,WACV)
+            lineSizer = wx.BoxSizer(wx.HORIZONTAL)
+            for bond in neigh[1]:
+                lineSizer.Add(wx.StaticText(self.panel,-1,' %s, %.3f'%(bond[0],bond[1])),0,WACV)
+            dataSizer.Add(lineSizer,0,WACV)
+        mainSizer.Add(dataSizer,0,wx.LEFT,5)
+
+        CancelBtn = wx.Button(self.panel,-1,'Cancel')
+        CancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
+        OkBtn = wx.Button(self.panel,-1,'Ok')
+        OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
+        btnSizer = wx.BoxSizer(wx.HORIZONTAL)
+        btnSizer.Add((20,20),1)
+        btnSizer.Add(OkBtn)
+        btnSizer.Add((20,20),1)
+        btnSizer.Add(CancelBtn)
+        btnSizer.Add((20,20),1)
+        mainSizer.Add(btnSizer,0,wx.EXPAND|wx.BOTTOM|wx.TOP, 10)
+        self.panel.SetSizer(mainSizer)
+        self.panel.SetupScrolling()
+        
+    def GetData(self):
+        'Returns the values from the dialog'
+        return self.Neigh       #has #Hs to add for each entry
+        
+    def OnOk(self,event):
+        'Called when the OK button is pressed'
+        parent = self.GetParent()
+        parent.Raise()
+        self.EndModal(wx.ID_OK)              
+
+    def OnCancel(self,event):
+        parent = self.GetParent()
+        parent.Raise()
+        self.EndModal(wx.ID_CANCEL)
 
 class DisAglDialog(wx.Dialog):
@@ -331 +422 @@
       search ranges for each element.
     '''
-    def __init__(self,parent,data,default):
+    def __init__(self,parent,data,default,Reset=True):
         wx.Dialog.__init__(self,parent,wx.ID_ANY,
                            'Distance Angle Controls', 
             pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
         self.default = default
+        self.Reset = Reset
         self.panel = wx.Panel(self)         #just a dummy - gets destroyed in Draw!
         self._default(data,self.default)
@@ -396 +488 @@
         OkBtn = wx.Button(self.panel,-1,"Ok")
         OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
-        ResetBtn = wx.Button(self.panel,-1,'Reset')
-        ResetBtn.Bind(wx.EVT_BUTTON, self.OnReset)
         btnSizer = wx.BoxSizer(wx.HORIZONTAL)
         btnSizer.Add((20,20),1)
         btnSizer.Add(OkBtn)
-        btnSizer.Add(ResetBtn)
+        if self.Reset:
+            ResetBtn = wx.Button(self.panel,-1,'Reset')
+            ResetBtn.Bind(wx.EVT_BUTTON, self.OnReset)
+            btnSizer.Add(ResetBtn)
         btnSizer.Add((20,20),1)
         mainSizer.Add(btnSizer,0,wx.EXPAND|wx.BOTTOM|wx.TOP, 10)

trunk/GSASIImath.py

@@ -376 +376 @@
     return XYZ
 
+def FindNeighbors(phase,FrstName,AtNames):
+    General = phase['General']
+    cx,ct,cs,cia = General['AtomPtrs']
+    Atoms = phase['Atoms']
+    atNames = [atom[ct-1] for atom in Atoms]
+    Cell = General['Cell'][1:7]
+    Amat,Bmat = G2lat.cell2AB(Cell)
+    atTypes = General['AtomTypes']
+    Radii = np.array(General['BondRadii'])
+    AtInfo = dict(zip(atTypes,Radii)) #or General['BondRadii']
+    Orig = atNames.index(FrstName)
+    OType = Atoms[Orig][ct]
+    XYZ = getAtomXYZ(Atoms,cx)        
+    Neigh = []
+    Dx = np.inner(Amat,XYZ-XYZ[Orig]).T
+    dist = np.sqrt(np.sum(Dx**2,axis=1))
+    sumR = np.array([AtInfo[OType]+AtInfo[atom[ct]] for atom in Atoms])
+    IndB = ma.nonzero(ma.masked_greater(dist-0.85*sumR,0.))
+    for j in IndB[0]:
+        if j != Orig:
+            Neigh.append([AtNames[j],dist[j]])
+    return Neigh
+        
 def AtomUij2TLS(atomData,atPtrs,Amat,Bmat,rbObj):   #unfinished & not used
     '''default doc string

trunk/GSASIIphsGUI.py

@@ -1537 +1537 @@
         
     def OnHydAtomAdd(event):
-        print "Doesn't do anything yet!"
         indx = Atoms.GetSelectedRows()
         if indx:
+            DisAglCtls = {}
             generalData = data['General']
             if 'DisAglCtls' in generalData:
                 DisAglCtls = generalData['DisAglCtls']
-            dlg = G2gd.DisAglDialog(G2frame,DisAglCtls,generalData)
+                if 'H' not in DisAglCtls['AtomTypes']:
+                    DisAglCtls['AtomTypes'].append('H')
+                    DisAglCtls['AngleRadii'].append(0.5)
+                    DisAglCtls['BondRadii'].append(0.5)
+            dlg = G2gd.DisAglDialog(G2frame,DisAglCtls,generalData,Reset=False)
             if dlg.ShowModal() == wx.ID_OK:
                 DisAglCtls = dlg.GetData()
@@ -1551 +1555 @@
             dlg.Destroy()
             generalData['DisAglCtls'] = DisAglCtls
+            cx,ct,cs,cia = generalData['AtomPtrs']
             atomData = data['Atoms']
+            AtNames = [atom[ct-1] for atom in atomData]
             colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
+            Neigh = []
             for ind in indx:
                 atom = atomData[ind]
+                if atom[ct] not in ['C','N','O']:
+                    continue
+                neigh = [atom[ct-1],G2mth.FindNeighbors(data,atom[ct-1],AtNames),0]
+                if len(neigh[1]) > 3 or (atom[ct] == 'O' and len(neigh[1]) > 1):
+                    continue
+                Neigh.append(neigh)
+            if Neigh:
+                dlg = G2gd.AddHatomDialog(G2frame,Neigh,data)
+                if dlg.ShowModal() == wx.ID_OK:
+                    Neigh = dlg.GetData()
+                    for neigh in Neigh:
+                        print neigh
+                    
+                dlg.Destroy()
+            else:
+                wx.MessageBox('No candidates found',caption='Add H atom Error',style=wx.ICON_EXCLAMATION)
         
     def OnAtomMove(event):