Changeset 1399

Timestamp:

Jun 30, 2014 10:40:05 AM (9 years ago)

Author:

vondreele

Message:

allow D (&T) for hydrogen atom types
allow ge* for image extensions (as found at APS 1ID!)
switch e11 & e22 definitions to match coordinate system (x horizontal, y vertical)
add subtraction of dark image for image display & strain fitting
skip images with no strain entries in fitallstrsta

Location:

trunk

Files:

• ElementTable.py (modified) (1 diff)
• GSASII.py (modified) (1 diff)
• GSASIIIO.py (modified) (4 diffs)
• GSASIIimage.py (modified) (2 diffs)
• GSASIIimgGUI.py (modified) (5 diffs)
• GSASIIplot.py (modified) (2 diffs)

trunk/ElementTable.py

@@ -20 +20 @@
 White = (255, 255, 255)            
 ElTable = [
-#    (["D","D-1"],                  0,0, "Deuterium",   White,           0.0000,(255,255,255)),
-#    (["T","T-1"],                  0,0, "Tritium",     White,           0.0000,(255,255,255)),
     (["H","H-1","D","D-1","T","T-1"],0,0, "Hydrogen",    White,           0.0000,(255,255,255)),
+    (["D","D-1"],                  0,0, "Deuterium",   White,           0.0000,(255,255,255)),
+    (["T","T-1"],                  0,0, "Tritium",     White,           0.0000,(255,255,255)),
     (["He",],                     17,0, "Helium",      Noblecolor,      0.0000,(217,255,255)),
     (["Li","Li+1"],                0,1, "Lithium",     Alkcolor,        0.0004,(204,128,255)),

trunk/GSASII.py

@@ -2041 +2041 @@
         dlg = wx.FileDialog(
             self, 'Choose image files', '.', '',
-            'Any supported image file (*.edf;*.tif;*.tiff;*.mar*;*.avg;*.sum;*.img;*.G2img;*.png)|'
-            '*.edf;*.tif;*.tiff;*.mar*;*.avg;*.sum;*.img;*.G2img;*.png;*.zip|'
+            'Any supported image file (*.edf;*.tif;*.tiff;*.mar*;*.ge*;*.avg;*.sum;*.img;*.G2img;*.png)|'
+            '*.edf;*.tif;*.tiff;*.mar*;*.ge*;*.avg;*.sum;*.img;*.G2img;*.png;*.zip|'
             'European detector file (*.edf)|*.edf|'
             'Any detector tif (*.tif;*.tiff)|*.tif;*.tiff|'
             'MAR file (*.mar*)|*.mar*|'
-            'GE Image (*.avg;*.sum)|*.avg;*.sum|'
+            'GE Image (*.ge*;*.avg;*.sum)|*.ge*;*.avg;*.sum|'
             'ADSC Image (*.img)|*.img|'
             'GSAS-II Image (*.G2img)|*.G2img|'

trunk/GSASIIIO.py

@@ -138 +138 @@
     if not ospath.exists(imagefile):
         dlg = wx.FileDialog(G2frame, 'Bad image file name; choose name', '.', '',\
-        'Any image file (*.edf;*.tif;*.tiff;*.mar*;*.avg;*.sum;*.img)\
-        |*.edf;*.tif;*.tiff;*.mar*;*.avg;*.sum;*.img|\
+        'Any image file (*.edf;*.tif;*.tiff;*.mar*;*.ge*;*.avg;*.sum;*.img)\
+        |*.edf;*.tif;*.tiff;*.mar*;*.ge*;*.avg;*.sum;*.img|\
         European detector file (*.edf)|*.edf|\
         Any detector tif (*.tif;*.tiff)|*.tif;*.tiff|\
         MAR file (*.mar*)|*.mar*|\
-        GE Image (*.avg;*.sum)|*.avg;*.sum|\
+        GE Image (*.ge*;*.avg;*.sum)|*.ge*;*.avg;*.sum|\
         ADSC Image (*.img)|*.img|\
         All files (*.*)|*.*',wx.OPEN|wx.CHANGE_DIR)
@@ -262 +262 @@
     elif ext == '.mar3450' or ext == '.mar2300':
         Comments,Data,Npix,Image = GetMAR345Data(imagefile)
-    elif ext in ['.sum','.avg','']:
+    elif ext in ['.sum','.avg'] or 'ge' in ext:
         Comments,Data,Npix,Image = GetGEsumData(imagefile)
     elif ext == '.G2img':
@@ -366 +366 @@
         head = ['GE detector sum data from APS 1-ID',]
         sizexy = [2048,2048]
-    elif '.avg' in filename:
-        head = ['GE detector avg data from APS 1-ID',]
+    elif '.avg' in filename or '.ge' in filename:
+        head = ['GE detector avg or ge* data from APS 1-ID',]
         sizexy = [2048,2048]
     else:
@@ -379 +379 @@
     if '.sum' in filename:
         image = np.array(ar.array('f',File.read(4*Npix)),dtype=np.int32)
-    elif '.avg' in filename:
+    elif '.avg' in filename or '.ge' in filename:
         image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
     else:

trunk/GSASIIimage.py

@@ -972 +972 @@
     for ring in StrSta['d-zero']:
         Eij = ring['Emat']
-        E = [[Eij[0],Eij[1],0],[Eij[1],Eij[2],0],[0,0,0]]
+        E = [[Eij[2],Eij[1],0],[Eij[1],Eij[0],0],[0,0,0]]
         th,azm = ring['ImtaObs']
         th0 = np.ones_like(azm)*npasind(wave/(2.*ring['Dset']))
@@ -1023 +1023 @@
         
     def strainCalc(p,xyd,dset,wave,phi,StaType):
-        E = np.array([[p[0],p[1],0],[p[1],p[2],0],[0,0,0]])
+        E = np.array([[p[2],p[1],0],[p[1],p[0],0],[0,0,0]])
         dspo,azm,dsp = xyd
         th = npasind(wave/(2.0*dspo))

trunk/GSASIIimgGUI.py

@@ -777 +777 @@
         def OnDarkImage(event):
             data['dark image'][0] = darkImage.GetValue()
+            G2plt.PlotExposedImage(G2frame,event=event)
 
         def OnBackMult(event):
@@ -793 +794 @@
                 pass
             darkMult.SetValue("%.3f" % (data['dark image'][1]))          #reset in case of error 
+            G2plt.PlotExposedImage(G2frame,event=event)
         
         backSizer = wx.FlexGridSizer(0,4,5,5)
@@ -1523 +1525 @@
                     names.append(choices[sel])
             dlg.Destroy()
-            SeqResult = {'histNames':names,}
+            SeqResult = {}
             dlg = wx.ProgressDialog('Sequential IMG Strain fit','Data set name = '+names[0],len(names), 
                 style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_REMAINING_TIME|wx.PD_CAN_ABORT)          
             wx.BeginBusyCursor()
+            goodnames = []
             try:
                 for i,name in enumerate(names):
@@ -1536 +1539 @@
                     Controls = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Image Controls'))
                     StaCtrls = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Stress/Strain'))
+                    if not len(StaCtrls['d-zero']):
+                        continue
+                    goodnames.append(name)
                     id = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, name)
                     Npix,imagefile = G2frame.PatternTree.GetItemPyData(Id)
                     image = G2IO.GetImageData(G2frame,imagefile,True)
+                    dark = Controls['dark image']
+                    if dark[0]:
+                        darkfile = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame, 
+                            G2frame.root,dark[0]))[1]
+                        darkImg = G2IO.GetImageData(G2frame,darkfile,imageOnly=True)
+                        image += dark[1]*darkImg
                     G2img.FitStrSta(image,StaCtrls,Controls)
                     G2plt.PlotStrain(G2frame,StaCtrls,newPlot=True)
@@ -1554 +1566 @@
                         'covMatrix':[],'title':name,'parmDict':parmDict}
                 else:
+                    SeqResult['histNames'] = goodnames
                     dlg.Destroy()
                     print ' ***** Sequential strain refinement successful *****'

trunk/GSASIIplot.py

@@ -2879 +2879 @@
         pass
     size,imagefile = G2frame.PatternTree.GetItemPyData(G2frame.Image)
+    dark = Data['dark image']
+    if dark[0]:
+        darkfile = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame, 
+            G2frame.root,dark[0]))[1]
     if imagefile != G2frame.oldImagefile:
         imagefile = G2IO.CheckImageFile(G2frame,imagefile)
@@ -2886 +2890 @@
         G2frame.PatternTree.SetItemPyData(G2frame.Image,[size,imagefile])
         G2frame.ImageZ = G2IO.GetImageData(G2frame,imagefile,imageOnly=True)
+        if dark[0]:
+            darkImg = G2IO.GetImageData(G2frame,darkfile,imageOnly=True)
+            G2frame.ImageZ += dark[1]*darkImg
         G2frame.oldImagefile = imagefile