Changeset 242

Timestamp:

Jan 26, 2011 9:38:41 AM (11 years ago)

Author:

vondreele

Message:

refactor polygon search & rendering to eliminate internal "faces". Polygon search now in FindBonds? and Faces put at end of drawAtom array. Much faster rendering of complex polygons

Location:

trunk

Files:

• GSASIIgrid.py (modified) (2 diffs)
• GSASIIphsGUI.py (modified) (8 diffs)
• GSASIIplot.py (modified) (3 diffs)

trunk/GSASIIgrid.py

@@ -19 +19 @@
 [ wxID_ATOMSEDITADD, wxID_ATOMSEDITINSERT, wxID_ATOMSEDITDELETE, wxID_ATOMSREFINE, 
     wxID_ATOMSMODIFY, wxID_ATOMSTRANSFORM, wxID_ATOMSTESTADD, wxID_ATONTESTINSERT,
-] = [wx.NewId() for _init_coll_Atom_Items in range(8)]
+    wxID_RELOADDRAWATOMS,
+] = [wx.NewId() for _init_coll_Atom_Items in range(9)]
 
 [ wxID_PWDRADD, wxID_HKLFADD, wxID_DATADELETE,
@@ -104 +105 @@
         parent.Append(id=wxID_ATOMSTRANSFORM, kind=wx.ITEM_NORMAL,text='Transform atoms',
             help='Select atoms to transform first')
+        parent.Append(id=wxID_RELOADDRAWATOMS, kind=wx.ITEM_NORMAL,text='Reload draw atoms',
+            help='Reload atom drawing list')
             
     def _init_coll_Data_Items(self,parent):

trunk/GSASIIphsGUI.py

@@ -926 +926 @@
             else:
                 Atoms.ForceRefresh()
+                
+#Structure drawing GUI stuff                
 
     def SetupDrawingData():
@@ -980 +982 @@
             else:
                 atomInfo = [atom[:2]+atom[3:6]+['1',]+['vdW balls',]+
-                    ['',]+[[255,255,255],]+atom[9:]+[[]]][0]
+                    ['',]+[[255,255,255],]+atom[9:]+[[],[]]][0]
             ct,cs = [1,8]         #type & color
         elif generalData['Type'] == 'macromolecular':
@@ -989 +991 @@
             atomInfo = [[atom[1].strip()+atom[0],]+
                 [AA1letter[oneLetter]+atom[0],]+atom[2:5]+
-                atom[6:9]+['1',]+['sticks',]+['',]+[[255,255,255],]+atom[12:]+[[]]][0]
+                atom[6:9]+['1',]+['sticks',]+['',]+[[255,255,255],]+atom[12:]+[[],[]]][0]
             ct,cs = [4,11]         #type & color
         elif generalData['Type'] == 'magnetic':
@@ -995 +997 @@
                 atomInfo = [atom[:2]+oldatom[3:]][0]
             else:
-                atomInfo = [atom[:2]+atom[3:6]+['vdW balls',]+['',]+atom[9:]+[[]]][0]
+                atomInfo = [atom[:2]+atom[3:6]+['vdW balls',]+['',]+atom[9:]+[[],[]]][0]
             ct,cs = [1,8]         #type & color
 #        elif generalData['Type'] == 'modulated':
@@ -1553 +1555 @@
             pass            
         for atom in atomData:
-            atom[-1] = []               #clear out old bonds
+            atom[-2] = []               #clear out old bonds/polyhedra
+            atom[-1] = []
         Indx = range(len(atomData))
         Atoms = []
@@ -1580 +1583 @@
                 for j in IndB[0]:
                     if Styles[i] == 'polyhedra':
-                        atomData[i][-1].append(np.inner(Amat,Dx[j]))
+                        atomData[i][-2].append(np.inner(Amat,Dx[j]))
                     elif Styles[j] != 'polyhedra' and j > i:
-                        atomData[i][-1].append(Dx[j]*Radii[i]/sumR[j])
-                        atomData[j][-1].append(-Dx[j]*Radii[j]/sumR[j])
-
+                        atomData[i][-2].append(Dx[j]*Radii[i]/sumR[j])
+                        atomData[j][-2].append(-Dx[j]*Radii[j]/sumR[j])
+                if Styles[i] == 'polyhedra':
+                    Bonds = atomData[i][-2]
+                    Faces = []
+                    if len(Bonds) > 2:
+                        FaceGen = G2lat.uniqueCombinations(Bonds,3)     #N.B. this is a generator
+                        for face in FaceGen:
+                            vol = nl.det(face)
+                            if abs(vol) > 1. or len(Bonds) == 3:
+                                if vol < 0.:
+                                    face = [face[0],face[2],face[1]]
+                                face = np.array(face)
+                                if not np.array([np.array(nl.det(face-bond))+0.0001 < 0 for bond in Bonds]).any():
+                                    norm = np.cross(face[1]-face[0],face[2]-face[0])
+                                    norm /= np.sqrt(np.sum(norm**2))
+                                    Faces.append([face,norm])
+                        atomData[i][-1] = Faces
+                        
     def DrawAtomsDelete(event):   
         indx = drawAtoms.GetSelectedRows()
@@ -1596 +1615 @@
             drawAtoms.ClearSelection()
             G2plt.PlotStructure(self,data)
+        event.StopPropagation()
+        
+    def OnReloadDrawAtoms(event):
+        data['Drawing']['Atoms'] = []
+        UpdateDrawAtoms()
+        drawAtoms.ClearSelection()
+        G2plt.PlotStructure(self,data)
         event.StopPropagation()
         
@@ -2403 +2429 @@
             self.dataFrame.Bind(wx.EVT_MENU, AtomModify, id=G2gd.wxID_ATOMSMODIFY)
             self.dataFrame.Bind(wx.EVT_MENU, AtomTransform, id=G2gd.wxID_ATOMSTRANSFORM)
+            self.dataFrame.Bind(wx.EVT_MENU, OnReloadDrawAtoms, id=G2gd.wxID_RELOADDRAWATOMS)
             FillAtomsGrid()
         elif text == 'General':

trunk/GSASIIplot.py

@@ -1769 +1769 @@
         for iat,atom in enumerate(drawingData['Atoms']):
             x,y,z = atom[cx:cx+3]
-            Bonds = atom[-1]
+            Bonds = atom[-2]
+            Faces = atom[-1]
             try:
                 atNum = generalData['AtomTypes'].index(atom[ct])
@@ -1780 +1781 @@
             radius = 0.5
             if atom[cs] != '':
-                glLoadName(atom[-2])
+                glLoadName(atom[-3])                    
             if 'balls' in atom[cs]:
                 vdwScale = drawingData['vdwScale']
@@ -1829 +1830 @@
                 RenderBonds(x,y,z,Bonds,bondR,color)
             elif atom[cs] == 'polyhedra':
-                if len(Bonds) > 2:
-                    FaceGen = G2lat.uniqueCombinations(Bonds,3)     #N.B. this is a generator
-                    Faces = []
-                    for face in FaceGen:
-                        vol = nl.det(face)
-                        if abs(vol) > 1. or len(Bonds) == 3:
-                            if vol < 0.:
-                                face = [face[0],face[2],face[1]]
-                            norm = np.cross(face[1]-face[0],face[2]-face[0])
-                            norm /= np.sqrt(np.sum(norm**2))
-                            Faces.append([face,norm])
-                    RenderPolyhedra(x,y,z,Faces,color)
+                RenderPolyhedra(x,y,z,Faces,color)
             elif atom[cs] == 'backbone':
                 if atom[ct-1].split()[0] in ['C','N']: