Changeset 3815

Timestamp:

Feb 11, 2019 11:26:52 AM (4 years ago)

Author:

toby

Message:

Add recalibrate & more image load/set routines

Location:

trunk

Files:

• GSASIIfiles.py (modified) (1 diff)
• GSASIIimage.py (modified) (4 diffs)
• GSASIIimgGUI.py (modified) (3 diffs)
• GSASIIscriptable.py (modified) (9 diffs)

trunk/GSASIIfiles.py

@@ -743 +743 @@
         File.write(key+':'+str(data[key])+'\n')
     File.close()
-    
+
+def RereadImageData(ImageReaderlist,imagefile,ImageTag=None,FormatName=''):
+    '''Read a single image with an image importer. This is called to 
+    reread an image after it has already been imported, so it is not 
+    necessary to reload metadata.
+
+    Based on :func:`GetImageData.GetImageData` which this can replace
+    where imageOnly=True
+
+    :param list ImageReaderlist: list of Reader objects for images
+    :param str imagefile: name of image file
+    :param int/str ImageTag: specifies a particular image to be read from a file.
+      First image is read if None (default).
+    :param str formatName: the image reader formatName
+
+    :returns: an image as a numpy array
+    '''
+    # determine which formats are compatible with this file
+    primaryReaders = []
+    secondaryReaders = []
+    for rd in ImageReaderlist:
+        flag = rd.ExtensionValidator(imagefile)
+        if flag is None: 
+            secondaryReaders.append(rd)
+        elif flag:
+            if not FormatName:
+                primaryReaders.append(rd)
+            elif FormatName == rd.formatName:
+                primaryReaders.append(rd)
+    if len(secondaryReaders) + len(primaryReaders) == 0:
+        print('Error: No matching format for file '+imagefile)
+        raise Exception('No image read')
+    errorReport = ''
+    if not imagefile:
+        return
+    for rd in primaryReaders+secondaryReaders:
+        rd.ReInitialize() # purge anything from a previous read
+        rd.errors = "" # clear out any old errors
+        if not rd.ContentsValidator(imagefile): # rejected on cursory check
+            errorReport += "\n  "+rd.formatName + ' validator error'
+            if rd.errors: 
+                errorReport += ': '+rd.errors
+                continue
+        flag = rd.Reader(imagefile,None,blocknum=ImageTag)
+        if flag: # this read succeeded
+            if rd.Image is None:
+                raise Exception('No image read. Strange!')
+            if GSASIIpath.GetConfigValue('Transpose'):
+                print ('Transposing Image!')
+                rd.Image = rd.Image.T
+            #rd.readfilename = imagefile
+            return rd.Image
+    else:
+        print('Error reading file '+imagefile)
+        print('Error messages(s)\n'+errorReport)
+        raise Exception('No image read')
+
+def readMasks(filename,masks,ignoreThreshold):
+    '''Read a GSAS-II masks file'''
+    File = open(filename,'r')
+    save = {}
+    oldThreshold = masks['Thresholds'][0]
+    S = File.readline()
+    while S:
+        if S[0] == '#':
+            S = File.readline()
+            continue
+        [key,val] = S.strip().split(':',1)
+        if key in ['Points','Rings','Arcs','Polygons','Frames','Thresholds']:
+            if ignoreThreshold and key == 'Thresholds':
+                S = File.readline() 
+                continue
+            save[key] = eval(val)
+            if key == 'Thresholds':
+                save[key][0] = oldThreshold
+                save[key][1][1] = min(oldThreshold[1],save[key][1][1])
+        S = File.readline()
+    File.close()
+    masks.update(save)
+    # CleanupMasks
+    for key in ['Points','Rings','Arcs','Polygons']:
+        masks[key] = masks.get(key,[])
+        masks[key] = [i for i in masks[key] if len(i)]

trunk/GSASIIimage.py

@@ -540 +540 @@
     return tam.T
     
-def ImageRecalibrate(G2frame,data,masks):
+def ImageRecalibrate(G2frame,ImageZ,data,masks):
     '''Called to repeat the calibration on an image, usually called after
     calibration is done initially to improve the fit.
+
+    :param G2frame: The top-level GSAS-II frame or None, to skip plotting
+    :param np.Array ImageZ: the image to calibrate
+    :param dict data: the Controls dict for the image
+    :param dict masks: a dict with masks
+    :returns: a list containing vals,varyList,sigList,parmDict
     '''
     import ImageCalibrants as calFile
@@ -580 +586 @@
     wave = data['wavelength']
     frame = masks['Frames']
-    tam = ma.make_mask_none(G2frame.ImageZ.shape)
+    tam = ma.make_mask_none(ImageZ.shape)
     if frame:
         tam = ma.mask_or(tam,MakeFrameMask(data,frame))
@@ -591 +597 @@
             break
         ellipse = GetEllipse(dsp,data)
-        Ring = makeRing(dsp,ellipse,pixLimit,cutoff,scalex,scaley,ma.array(G2frame.ImageZ,mask=tam))[0]
+        Ring = makeRing(dsp,ellipse,pixLimit,cutoff,scalex,scaley,ma.array(ImageZ,mask=tam))[0]
         if Ring:
             if iH >= skip:
@@ -621 +627 @@
         data['ellipses'].append(copy.deepcopy(ellipse+('b',)))    
     print ('calibration time = %.3f'%(time.time()-time0))
-    G2plt.PlotImage(G2frame,newImage=True)        
+    if G2frame:
+        G2plt.PlotImage(G2frame,newImage=True)        
     return [vals,varyList,sigList,parmDict]
             

trunk/GSASIIimgGUI.py

@@ -192 +192 @@
                 
     def OnRecalibrate(event):
-        G2img.ImageRecalibrate(G2frame,data,masks)
+        G2img.ImageRecalibrate(G2frame,G2frame.ImageZ,data,masks)
         wx.CallLater(100,UpdateImageControls,G2frame,data,masks)
         
@@ -217 +217 @@
                     Mid = G2gd.GetGPXtreeItemId(G2frame,G2frame.Image,'Masks')
                     Masks = G2frame.GPXtree.GetItemPyData(Mid)
-                    vals,varyList,sigList,parmDict = G2img.ImageRecalibrate(G2frame,Data,Masks)
+                    vals,varyList,sigList,parmDict = G2img.ImageRecalibrate(
+                        G2frame,G2frame.ImageZ,Data,Masks)
                     sigList = list(sigList)
                     if 'dist' not in varyList:
@@ -1436 +1437 @@
             if dlg.ShowModal() == wx.ID_OK:
                 filename = dlg.GetPath()
-                File = open(filename,'r')
-                save = {}
-                oldThreshold = data['Thresholds'][0]
-                S = File.readline()
-                while S:
-                    if S[0] == '#':
-                        S = File.readline()
-                        continue
-                    [key,val] = S.strip().split(':',1)
-                    if key in ['Points','Rings','Arcs','Polygons','Frames','Thresholds']:
-                        if ignoreThreshold and key == 'Thresholds':
-                            S = File.readline() 
-                            continue
-                        save[key] = eval(val)
-                        if key == 'Thresholds':
-                            save[key][0] = oldThreshold
-                            save[key][1][1] = min(oldThreshold[1],save[key][1][1])
-                    S = File.readline()
-                File.close()
-                data.update(save)
-                CleanupMasks(data)
+                G2fil.readMasks(filename,data,ignoreThreshold)
                 wx.CallAfter(UpdateMasks,G2frame,data)
                 G2plt.PlotExposedImage(G2frame,event=event)                

trunk/GSASIIscriptable.py

@@ -576 +576 @@
 import GSASIIElem as G2elem
 import GSASIIfiles as G2fil
+import GSASIIimage as G2img
 
 # Delay imports to not slow down small scripts that don't need them
@@ -584 +585 @@
 
 def LoadG2fil():
-    """Delay importing this module, it is slow"""
+    """Setup GSAS-II importers. Delay importing this module, it is slow"""
     if len(Readers['Pwdr']) > 0: return
     # initialize imports
@@ -1160 +1161 @@
             into[:] = from_
 
+def GetCorrImage(ImageReaderlist,proj,imageRef):
+    '''Gets image & applies dark, background & flat background corrections.
+    based on :func:`GSASIIimgGUI.GetImageZ`
+
+    :param list ImageReaderlist: list of Reader objects for images
+    :param object ImageReaderlist: list of Reader objects for images
+    :param imageRef: A reference to the desired image. Either the Image 
+      tree name (str), the image's index (int) or
+      a image object (:class:`G2Image`)
+
+    :return: array sumImg: corrected image for background/dark/flat back
+    '''
+    ImgObj = proj.image(imageRef)
+    Controls = ImgObj.data['Image Controls']
+    formatName = Controls.get('formatName','')
+    imagefile = ImgObj.data['data'][1]
+    ImageTag = None # fix this for multiimage files
+    sumImg = G2fil.RereadImageData(ImageReaderlist,imagefile,ImageTag=ImageTag,FormatName=formatName)
+    if sumImg is None:
+        return []
+    darkImg = False
+    if 'dark image' in Controls:
+        darkImg,darkScale = Controls['dark image']
+        if darkImg:
+            dImgObj = proj.image(darkImg)
+            formatName = dImgObj.data['Image Controls'].get('formatName','')
+            imagefile = dImgObj.data['data'][1]
+            ImageTag = None # fix this for multiimage files
+            darkImg = G2fil.RereadImageData(ImageReaderlist,imagefile,ImageTag=ImageTag,FormatName=formatName)
+            if darkImg is None:
+                raise Exception('Error reading dark image {}'.format(imagefile))
+            sumImg += np.array(darkImage*darkScale,dtype='int32')
+    if 'background image' in Controls:
+        backImg,backScale = Controls['background image']            
+        if backImg:     #ignores any transmission effect in the background image
+            bImgObj = proj.image(backImg)
+            formatName = bImgObj.data['Image Controls'].get('formatName','')
+            imagefile = bImgObj.data['data'][1]
+            ImageTag = None # fix this for multiimage files
+            backImg = G2fil.RereadImageData(ImageReaderlist,imagefile,ImageTag=ImageTag,FormatName=formatName)
+            if backImage is None:
+                raise Exception('Error reading background image {}'.format(imagefile))
+            if darkImg:
+                backImage += np.array(darkImage*darkScale/backScale,dtype='int32')
+            else:
+                sumImg += np.array(backImage*backScale,dtype='int32')
+    if 'Gain map' in Controls:
+        gainMap = Controls['Gain map']
+        if gainMap:
+            gImgObj = proj.image(gainMap)
+            formatName = gImgObj.data['Image Controls'].get('formatName','')
+            imagefile = gImgObj.data['data'][1]
+            ImageTag = None # fix this for multiimage files
+            GMimage = G2fil.RereadImageData(ImageReaderlist,imagefile,ImageTag=ImageTag,FormatName=formatName)
+            if GMimage is None:
+                raise Exception('Error reading Gain map image {}'.format(imagefile))
+            sumImg = sumImg*GMimage/1000
+    sumImg -= int(Controls.get('Flat Bkg',0))
+    Imax = np.max(sumImg)
+    Controls['range'] = [(0,Imax),[0,Imax]]
+    return np.asarray(sumImg,dtype='int32')
 
 class G2ObjectWrapper(object):
@@ -3123 +3185 @@
                      'DetDepthRef', 'showLines'],
         'str': ['SampleShape', 'binType', 'formatName', 'color',
-                    'type', 'calibrant'],
+                    'type', ],
         'list': ['GonioAngles', 'IOtth', 'LRazimuth', 'Oblique', 'PolaVal',
                    'SampleAbs', 'center', 'ellipses', 'linescan',
                     'pixelSize', 'range', 'ring', 'rings', 'size', ],
         'dict': ['varylist'],
-#        'image': ['background image', 'dark image', 'Gain map'],
         }
     '''Defines the items known to exist in the Image Controls tree section 
     and their data types.
     '''
+    # special handling: 'background image', 'dark image', 'Gain map',
+    #   'calibrant'
 
     def __init__(self, data, name, proj):
@@ -3206 +3269 @@
         return matchList
 
+    def setCalibrant(self,calib):
+        '''Set a calibrant for the current image
+
+        :param str calib: specifies a calibrant name which must be one of
+          the entries in file ImageCalibrants.py. This is validated.
+        '''
+        import ImageCalibrants as calFile
+        if calib in calFile.Calibrants.keys():
+            self.data['Image Controls']['calibrant'] = calib
+            return
+        print('Calibrant {} is not valid. Valid calibrants'.format(calib))
+        for i in calFile.Calibrants.keys():
+            if i: print('\t"{}"'.format(i))
+        
     def setControlFile(self,typ,imageRef,mult=None):
         '''Set a image to be used as a background/dark/gain map image
@@ -3212 +3289 @@
            'background image', 'dark image', 'gain map'; N.B. only the first
            four characters must be specified and case is ignored.
-        :param imageRef: 
-        :param float mult:
+        :param imageRef: A reference to the desired image. Either the Image 
+          tree name (str), the image's index (int) or
+          a image object (:class:`G2Image`)
+        :param float mult: a multiplier to be applied to the image (not used 
+          for 'Gain map'; required for 'background image', 'dark image'
         '''
-#        'image': ['background image', 'dark image', 'Gain map'],
         if 'back' in typ.lower():
             key = 'background image'
@@ -3237 +3316 @@
     def loadControls(self,filename):
         '''load controls from a .imctrl file
+
         :param str filename: specifies a file to be read, which should end 
           with .imctrl
@@ -3248 +3328 @@
     def saveControls(self,filename):
         '''write current controls values to a .imctrl file
+
         :param str filename: specifies a file to write, which should end 
           with .imctrl
@@ -3254 +3335 @@
         print('file {} written from {}'.format(filename,self.name))
 
+    def loadMasks(self,filename,ignoreThreshold=False):
+        '''load masks from a .immask file
+
+        :param str filename: specifies a file to be read, which should end 
+          with .immask
+        :param bool ignoreThreshold: If True, masks are loaded with
+          threshold masks. Default is False which means any Thresholds 
+          in the file are ignored.
+        '''
+        G2fil.readMasks(filename,self.data['Masks'],ignoreThreshold)
+        print('file {} read into {}'.format(filename,self.name))
+        
+    def Recalibrate(self):
+        ImageZ = GetCorrImage(Readers['Image'],self.proj,self)
+        G2img.ImageRecalibrate(None,ImageZ,self.data['Image Controls'],self.data['Masks'])
+        
 ##########################
 # Command Line Interface #