bring up to date w/current master (c94f93a)

briantoby · briantoby · commit 741f916a0329 · 2025-02-09T20:55:11.000-06:00
diff --git a/GSASII/GSASIIIntPDFtool.py b/GSASII/GSASIIIntPDFtool.py
@@ -498,7 +498,7 @@ def ontblModeBtn(event):
         sizer.Add(self.readDir,1,wx.EXPAND,1)
         btn3 = wx.Button(mnpnl, wx.ID_ANY, "Browse")
         btn3.Bind(wx.EVT_BUTTON, self.SetSourceDir)
-        sizer.Add(btn3,0,wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
+        sizer.Add(btn3,0,wx.ALIGN_CENTER_VERTICAL)
         mnsizer.Add(sizer,0,wx.EXPAND,0)
         sizer = wx.BoxSizer(wx.HORIZONTAL)
         sizer.Add((-1,-1),1,wx.EXPAND,1)
@@ -522,7 +522,7 @@ def ontblModeBtn(event):
         sizer.Add(fInp3,1,wx.EXPAND)
         btn3 = wx.Button(mnpnl,  wx.ID_ANY, "Browse")
         btn3.Bind(wx.EVT_BUTTON, OnBrowse)
-        sizer.Add(btn3,0,wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
+        sizer.Add(btn3,0,wx.ALIGN_CENTER_VERTICAL)
         lblsizr.Add(sizer,0,wx.EXPAND)
         sizer = wx.BoxSizer(wx.HORIZONTAL)
         sizer.Add(wx.StaticText(mnpnl, wx.ID_ANY,'Select format(s):'))
diff --git a/GSASII/GSASIIdataGUI.py b/GSASII/GSASIIdataGUI.py
@@ -6925,7 +6925,7 @@ def _makemenu():     # routine to create menu when first used
         G2G.Define_wxId('wxID_IMCALIBRATE', 'wxID_IMRECALIBRATE', 'wxID_IMINTEGRATE', 'wxID_IMCLEARCALIB', 'wxID_IMRECALIBALL',
             'wxID_IMCOPYCONTROLS', 'wxID_INTEGRATEALL', 'wxID_IMSAVECONTROLS', 'wxID_IMLOADCONTROLS', 'wxID_IMAUTOINTEG',
             'wxID_IMCOPYSELECTED', 'wxID_SAVESELECTEDCONTROLS', 'wxID_IMXFERCONTROLS', 'wxID_IMRESETDIST', 'wxID_CALCRINGS',
-            'wxID_LOADELECTEDCONTROLS','wxID_IMDISTRECALIB', 'wxID_IMINTEGPDFTOOL')
+            'wxID_LOADELECTEDCONTROLS','wxID_IMDISTRECALIB', 'wxID_IMINTEGPDFTOOL','wxID_IMMULTGAINMAP')
         G2G.Define_wxId('wxID_IMDRWPHS')
         def _makemenu():     # routine to create menu when first used
             self.ImageMenu = wx.MenuBar()
@@ -6938,6 +6938,7 @@ def _makemenu():     # routine to create menu when first used
             self.ImageEdit.Append(G2G.wxID_CALCRINGS,'Calculate rings','Calculate rings from calibration parameters')
             self.ImageEdit.Append(G2G.wxID_IMDISTRECALIB,'Multi-distance Recalibrate','Recalibrate all images varying delta-distance and fitting wavelength')
             self.ImageEdit.Append(G2G.wxID_IMCLEARCALIB,'Clear calibration','Clear calibration data points and rings')
+            self.ImageEdit.Append(G2G.wxID_IMMULTGAINMAP,'Multiimage Gain map','Make gain map from multiple images')
             ImageIntegrate = wx.Menu(title='')
             self.ImageMenu.Append(menu=ImageIntegrate, title='Integration')
             ImageIntegrate.Append(G2G.wxID_IMINTEGRATE,'Integrate','Integrate selected image')
diff --git a/GSASII/GSASIIimage.py b/GSASII/GSASIIimage.py
@@ -707,14 +707,19 @@ def costth(xyz):
         dxyz = dxyz0
     ctth = costth(dxyz)
     tth = npacosd(ctth)
-    azm = (npatan2d(dxyz[:,:,1],dxyz[:,:,0])+data['azmthOff']+720.)%360.
-# G-calculation - use Law of sines
-    distm = data['distance']/1000.0
-    sinB2 = np.minimum(np.ones_like(tth),
-                    (data['distance']*npsind(tth))**2/(dx**2+dy**2))
-    #sinB2 = (data['distance']*npsind(tth))**2/(dx**2+dy**2)
-    C = 180.-tth-npacosd(np.sqrt(1.- sinB2))
-    G = distm**2*sinB2/npsind(C)**2
+    azm = (npatan2d(dxyz[:,:,1],dxyz[:,:,0])+data['azmthOff']+720.)%360.        
+# old G-calculation        
+    x0 = data['distance']*nptand(tilt)
+    x0x = x0*npcosd(data['rotation'])
+    x0y = x0*npsind(data['rotation'])
+    distsq = data['distance']**2
+    G = ((dx-x0x)**2+(dy-x0y)**2+distsq)/distsq       #for geometric correction = 1/cos(2theta)^2 if tilt=0.
+# # G-calculation - use Law of sines - wrong for nonzero det2theta!
+#     distm = data['distance']/1000.0
+#     sinB2 = np.minimum(np.ones_like(tth),
+#         (data['distance']*npsind(tth))**2/(dx**2+dy**2))
+#     C = 180.-tth-npacosd(np.sqrt(1.- sinB2))
+#     G = distm**2*sinB2/npsind(C)**2
     return tth,azm,G
 
 def meanAzm(a,b):
@@ -1468,7 +1473,7 @@ def MakeUseMask(data,masks,blkSize=128):
 
 def MakeGainMap(image,Ix,Iy,data,blkSize=128):
     import scipy.ndimage.filters as sdif
-    Iy *= npcosd(Ix[:-1])**3       #undo parallax
+    Iy /= npcosd(Ix[:-1])       #undo parallax
     Iy *= (1000./data['distance'])**2    #undo r^2 effect
     Iy /= np.array(G2pwd.Polarization(data['PolaVal'][0],Ix[:-1],0.)[0])    #undo polarization
     if data['Oblique'][1]:
@@ -1687,7 +1692,8 @@ def ImageIntegrate(image,data,masks,blkSize=128,returnN=False,useTA=None,useMask
         H1 = LRazm
     if 'SASD' not in data['type']:
         H0 *= np.array(G2pwd.Polarization(data['PolaVal'][0],H2[:-1],0.)[0])
-    H0 /= np.abs(npcosd(H2[:-1]-np.abs(data['det2theta'])))           #parallax correction
+    if np.abs(data['det2theta']) < 1.0:         #small angle approx only; not appropriate for detectors at large 2-theta
+        H0 /= np.abs(npcosd(H2[:-1]-np.abs(data['det2theta'])))           #parallax correction
     # H0 *= (data['distance']/1000.)**2    #remove r^2 effect - done earlier
     if 'SASD' in data['type']:
         H0 /= npcosd(H2[:-1])           #one more for small angle scattering data?
diff --git a/GSASII/GSASIIimgGUI.py b/GSASII/GSASIIimgGUI.py
@@ -362,7 +362,10 @@ def OnRecalibAll(event):
         G2frame.G2plotNB.Delete('Sequential refinement')    #clear away probably invalid plot
         G2plt.PlotExposedImage(G2frame,event=None)
         if Id: G2frame.GPXtree.SelectItem(Id)
-
+        
+    def OnMultiGainMap(event):
+        print('TBD - gain map from multiple images')
+        
     def OnCalcRings(event):
         '''Use existing calibration values to compute rings & display them
         '''
@@ -1679,6 +1682,7 @@ def computePhaseRings():
     G2frame.Bind(wx.EVT_MENU, OnCalcRings, id=G2G.wxID_CALCRINGS)
     G2frame.Bind(wx.EVT_MENU, OnDistRecalib, id=G2G.wxID_IMDISTRECALIB)
     G2frame.Bind(wx.EVT_MENU, OnClearCalib, id=G2G.wxID_IMCLEARCALIB)
+    G2frame.Bind(wx.EVT_MENU, OnMultiGainMap, id=G2G.wxID_IMMULTGAINMAP)
 #    if data.get('calibrant'):
 #        mode = True
 #    else:
diff --git a/GSASII/imports/G2img_1TIF.py b/GSASII/imports/G2img_1TIF.py
@@ -208,7 +208,7 @@ def GetTifData(filename):
     elif 270 in IFD:
         File.seek(IFD[270][2][0])
         S = File.read(IFD[273][2][0]-IFD[270][2][0])
-        if b'Pilatus3' in S:
+        if b'Pilatus3' in S or sizexy == [1475,1679]:
             tifType = 'Pilatus3'
             dataType = 0
             pixy = [172.,172.]
diff --git a/GSASII/imports/G2pwd_BrukerRAW.py b/GSASII/imports/G2pwd_BrukerRAW.py
@@ -37,12 +37,12 @@ def ContentsValidator(self, filename):
             self.formatName = 'Bruker RAW ver. 3'
         elif head == 'RAW4.00':
             self.formatName = 'Bruker RAW ver. 4'
-            self.errors += "Sorry, this is a Version 4 Bruker file. "
-            self.errors += "We need documentation for it so that it can be implemented in GSAS-II. "
-            self.errors += "Use PowDLL (http://users.uoi.gr/nkourkou/powdll/) to convert it to ASCII xy."
-            print(self.errors)
-            fp.close()
-            return False
+            # self.errors += "Sorry, this is a Version 4 Bruker file. "
+            # self.errors += "We need documentation for it so that it can be implemented in GSAS-II. "
+            # self.errors += "Use PowDLL (http://users.uoi.gr/nkourkou/powdll/) to convert it to ASCII xy."
+            # print(self.errors)
+            # fp.close()
+            # return False
         else:
             self.errors = 'Unexpected information in header: '
             if all([ord(c) < 128 and ord(c) != 0 for c in str(head)]): # show only if ASCII
@@ -161,38 +161,93 @@ def Reader(self,filename, ParentFrame=None, **kwarg):
                     self.repeat = True
             fp.close()
             
-        elif 'ver. 4' in self.formatName:   #does not work - format still elusive
+        elif 'ver. 4' in self.formatName: 
+            driveNo = 0
             fp.seek(12)   #ok
-            self.comments.append('Date='+self.Read(fp,10))
-            self.comments.append('Time='+self.Read(fp,10))
-            fp.seek(144)
-            self.comments.append('Sample='+self.Read(fp,60))
-            fp.seek(564)  # where is it?
-            radius = st.unpack('<f',fp.read(4))[0]
-            self.comments.append('Gonio. radius=%.2f'%(radius))
-            self.Sample['Gonio. radius'] = radius
-            fp.seek(516)  #ok
-            self.comments.append('Anode='+self.Read(fp,4))
-            fp.seek(472)  #ok
-            self.comments.append('Ka mean=%.5f'%(st.unpack('<d',fp.read(8))[0]))
-            self.comments.append('Ka1=%.5f'%(st.unpack('<d',fp.read(8))[0]))
-            self.comments.append('Ka2=%.5f'%(st.unpack('<d',fp.read(8))[0]))
-            self.comments.append('Kb=%.5f'%(st.unpack('<d',fp.read(8))[0]))
-            self.comments.append('Ka2/Ka1=%.5f'%(st.unpack('<d',fp.read(8))[0]))
-            fp.seek(pos)  #deliberate fail here - pos not known from file contents
-            self.idstring = os.path.basename(filename) + ' Scan '+str(1)
-            nSteps = int(st.unpack('<i',fp.read(4))[0])
-            st.unpack('<d',fp.read(8))[0]
-            start2Th = st.unpack('<d',fp.read(8))[0]
-            fp.seek(pos+176)
-            step = st.unpack('<d',fp.read(8))[0]
-            pos += headLen      #position at start of data block
-            fp.seek(pos)                                    
-            x = np.array([start2Th+i*step for i in range(nSteps)])
-            y = np.array([max(1.,st.unpack('<f',fp.read(4))[0]) for i in range(nSteps)])
-            w = 1./y
-            self.powderdata = [x,y,w,np.zeros(nSteps),np.zeros(nSteps),np.zeros(nSteps)]
-            fp.close()
+            self.comments.append('Date='+self.Read(fp,12).strip('\x00'))
+            self.comments.append('Time='+self.Read(fp,10).strip('\x00'))
+            fp.seek(61)     #start of header segments
+            while True:
+                segtype = st.unpack('<I',fp.read(4))[0]
+                if not segtype or segtype == 160:    
+                    break           # done with header
+                seglen = max(st.unpack('<I',fp.read(4))[0],8)
+                if segtype == 10:
+                    fp.read(4)    #skip these
+                    self.comments.append('%s=%s'%(self.Read(fp,24).strip('\x00'),self.Read(fp,seglen-36).strip('\x00')))
+                elif segtype == 30: #x-ray source info
+                    fp.read(64)
+                    self.comments.append('Ka mean=%.5f'%(st.unpack('<d',fp.read(8))[0]))
+                    self.comments.append('Ka1=%.5f'%(st.unpack('<d',fp.read(8))[0]))
+                    self.comments.append('Ka2=%.5f'%(st.unpack('<d',fp.read(8))[0]))
+                    self.comments.append('Kb=%.5f'%(st.unpack('<d',fp.read(8))[0]))
+                    self.comments.append('Ka2/Ka1=%.5f'%(st.unpack('<d',fp.read(8))[0]))
+                    fp.read(4)
+                    self.comments.append('Anode='+self.Read(fp,4).strip('\x00'))
+                    fp.read(seglen-120)
+                elif segtype == 60:
+                    alignFlag = st.unpack('<I',fp.read(4))[0]
+                    driveName = self.Read(fp,24).strip('\x00')
+                    fp.read(32)
+                    Delt = st.unpack('<d',fp.read(8))[0]
+                    fp.read(seglen-76)
+                    self.comments.append('Drive %s: align flag %d'%(driveName,alignFlag))
+                    self.comments.append('Drive %s: delta %f'%(driveName,Delt))
+                    driveNo += 1
+                else:
+                    fp.read(seglen-8)
+            while (segtype == 0 or segtype == 160):
+                self.idstring = os.path.basename(filename)  # + ' Scan '+str(blockNum)
+                meta = {}
+                fp.read(28)
+                meta['ScanType'] = self.Read(fp,24).strip('\x00')
+                if meta['ScanType'] not in ['Locked Coupled','Unlocked Coupled']:
+                    return False
+                fp.read(16)
+                startAngle = st.unpack('<d',fp.read(8))[0]
+                meta['startAngle'] = '%.4f'%startAngle
+                stepSize = st.unpack('<d',fp.read(8))[0]
+                meta['stepSize'] = '%.4f'%stepSize
+                Nsteps = st.unpack('<I',fp.read(4))[0]
+                meta['Nsteps'] = '%d'%Nsteps
+                meta['stepTime(ms)'] = st.unpack('<f',fp.read(4))[0]
+                fp.read(4)
+                meta['generatorVoltage(kV)'] = st.unpack('<f',fp.read(4))[0]
+                meta['generatorCurrent(mA)'] = st.unpack('<f',fp.read(4))[0]
+                fp.read(4)
+                meta['usedWave'] = st.unpack('<d',fp.read(8))[0]
+                fp.read(16)
+                datumSize = st.unpack('<I',fp.read(4))[0]
+                hdrSize = st.unpack('<I',fp.read(4))[0]
+                fp.read(16)
+                if meta['ScanType'] in ['Locked Coupled','Unlocked Coupled']:
+                    while hdrSize > 0:
+                        segtype = st.unpack('<I',fp.read(4))[0]
+                        seglen = max(st.unpack('<I',fp.read(4))[0],8)
+                        if segtype == 50:
+                            fp.read(4)
+                            segName = self.Read(fp,24).strip('\x00')
+                            if segName in ['Theta','2Theta','Chi','Phi','BeamTranslation','Z-Drive','Divergence Slit']:
+                                fp.read(20)
+                                meta['start %s'%segName] = '%.4f'%(st.unpack('<d',fp.read(8))[0])
+                                fp.read(seglen-64)
+                            else:
+                                fp.read(seglen-36)
+                        else:
+                            fp.read(seglen-8)
+                        hdrSize -= seglen
+                    #end of reading scan header   
+                    x = np.array([startAngle+i*stepSize for i in range(Nsteps)])
+                    y = np.array([max(1.,st.unpack('<f',fp.read(4))[0]) for i in range(Nsteps)])
+                    w = 1./y
+                    self.powderdata = [x,y,w,np.zeros(Nsteps),np.zeros(Nsteps),np.zeros(Nsteps)]
+                    for item in meta:
+                        self.comments.append('%s = %s'%(item,str(meta[item])))
+                    fp.close()
+                else:
+                    meta['Unknown range/scan type'] = True
+                    fp.read(hdrSize)
+                    fp.read(datumSize*Nsteps)
         else:
             return False
             
diff --git a/docs/source/packages.rst b/docs/source/packages.rst
@@ -120,14 +120,16 @@ as defined in variable :attr:`GSASIIdataGUI.versionDict`,
 but for new installations we are currently recommending the following
 interpreter/package versions: 
 
- * Python 3.11 is recommended. GSAS-II should run with any Python
+ * Python 3.11, 3.12 or 3.13 is recommended. GSAS-II should run with any Python
    version from 3.7 or later, but you will need to locate (from the
    old subversion server) or locate binaries to match that Python version. 
  * wxPython 4.2 or later is recommended, but with Python <=3.9 any
    wx4.x version should be OK. However, there may be problems with
    newer sections of the GUI with wx <4.0.
- * NumPy 1.26 recommended, but anything from 1.17 on is likely fine,
-   but does need to approximately match the GSAS-II binaries. 
+ * NumPy 1.26 recommended with Python 3.11 and 2.2 with 3.12 or 3.13,
+   but anything from 1.17 on is likely fine,
+   but if you do not match the supplied GSAS-II binaries you will
+   need to build them yourself. 
  * matplotlib 3.6 is recommended, but 3.4 or later is preferred. 
  * pyOpenGL: no version-related problems have been seen.
  * SciPy: no version-related problems have been seen, but in at least one
@@ -138,9 +140,13 @@ For more details on problems noted with specific versions of Python
 and Python packages, see comments below and details here:
 :attr:`GSASIIdataGUI.versionDict`,
    
-Note that GSAS-II is currently being developed using Python 3.11. We
-are seeing compilation problems with Python 3.12 that will be addressed
-later via the build migration to meson.  We are no longer
+Note that GSAS-II is currently being developed using Python 3.11 and 3.13. We
+have just adopted a build process using meson in place of scons for
+Python 3.12+ but this is not incorporated into the master branch and
+is not fully documented. If you need to build the GSAS-II binaries at
+this time, please contact Brian. 
+
+We are no longer
 supporting Python 2.7 and <=3.6, and strongly encourage that
 systems running GSAS-II under these older Python versions reinstall
 Python. Typically this is done by reinstalling GSAS-II from a current self-installer. 
@@ -238,6 +244,9 @@ environment this command can be used::
   
   conda env export --from-history -n <env>
 
+Note that binaries for Python 3.12 and 3.13 are also now supplied,
+with numpy=2.2. 
+  
 .. _ScriptingRequirements:
 
   
@@ -323,12 +332,17 @@ Required Binary Files
 As noted before, GSAS-II also requires that some code be compiled.
 For the following platforms, binary images are provided at
 https://github.com/AdvancedPhotonSource/GSAS-II-buildtools/releases/latest
-for Python 3.11 and NumPy 1.26:
+for Python 3.11 and NumPy 1.26, Python 3.12 and NumPy 2.2, and Python
+3.13 and NumPy 2.2 for these platforms:
 
   * Windows-10: 64-bit Intel-compatible processors.
   * MacOS: Intel processors.
   * MacOS: ARM processors, aka Apple Silicon (M1, etc). 
-  * Linux: 64-bit Intel-compatible processors. 
+  * Linux: 64-bit Intel-compatible processors.
+
+Some binaries are also supplied for Raspberry Pi, but may not be
+up-to-date. Please ask for newer if needed:
+    
   * Linux: ARM processors (64-bit and 32-bit Raspberry Pi OS and
     Ubuntu for Raspberry Pi).
 
@@ -338,6 +352,10 @@ Should one wish to run GSAS-II where binary files are not
 supplied (such as 32-bit Windows or Linux) or with other combinations of
 Python/NumPy, compilation will be need to be done by the user. See
 the `compilation information <https://advancedphotonsource.github.io/GSAS-II-tutorials/compile.html>`_ for more information. 
+We have just adopted a build process using meson in place of scons for
+Python 3.12+ but this is not incorporated into the master branch and
+is not fully documented. If you need to build the GSAS-II binaries at
+this time, please contact Brian.
 
 Supported Externally-Developed Software
 ----------------------------------------------------
