Changeset 91

Timestamp:

09/13/07 14:23:16 (12 months ago)

Author:

andrew

Message:

Added OME and TIFF image frame counting and basic comparison

Files:

• Xml/Validator/Backend/OmeValidator.py (modified) (7 diffs)

Xml/Validator/Backend/OmeValidator.py

@@ -133 +133 @@
         unresolvedList = None
         
+        """
+        Create variables used to check internal consistency
+        """
+        # count of TiffData elements founf in the XML
+        omeTiffDataCount = None
+        # count of image frames found in Tiff file
+        tiffFileFrames = None
+        
+        # count of pixels
+        omePixelsCount = None
+        # count of planes
+        omePlanesCount = None
+        # count of Z * C * T
+        ome5dPlaneCount = None
+        # count of number of times a tiff data block has asked for "all available frames" - value of more then 1 indicates an error
+        theAllFrameCount = None
+        
         def __init__(self):
                 """
@@ -144 +161 @@
                 # build the blank dom
                 self.theDom = None
+        
         
         def __str__(self):
@@ -268 +286 @@
                         if reference not in handlerContent.ids:
                                 self.unresolvedList.append(ParseMessage(None, None, None, "UnresolvedID",None, reference))
+                
+                # store the internal counters
+                self.omeTiffDataCount = handlerContent.omeTiffDataCount
+                self.omePixelsCount = handlerContent.omePixelsCount
+                self.omePlanesCount = handlerContent.omePlanesCount
+                self.ome5dPlaneCount = handlerContent.ome5dPlaneCount
+                self.omeTiffDataPlaneCount = handlerContent.omeTiffDataPlaneCount
+                self.theAllFrameCount = handlerContent.theAllFrameCount
                 
                 # store the namespace
@@ -349 +375 @@
                                         # create a file object to represent the xml string
                                         theFileString = StringIO(theXml)
+                                        # print theXml
+                                        
                                         # parse the new string/file object into the report and validate it 
                                         theTiffReport.parse(theFileString)
+                                        theTiffReport.validateTiffImageData(image)
+                                        """
+                                        print "Tiff Frames    : %s" % theTiffReport.tiffFileFrames      
+                                        print "Ome Frames     : %s" % theTiffReport.omeTiffDataCount    
+                                        print "Ome Pixels     : %s" % theTiffReport.omePixelsCount      
+                                        print "Ome Planes     : %s" % theTiffReport.omePlanesCount      
+                                        print "Ome 5dPlane    : %s" % theTiffReport.ome5dPlaneCount     
+                                        print "Ome TiffPlane  : %s" % theTiffReport.omeTiffDataPlaneCount       
+                                        print "Ome AllFrame   : %s" % theTiffReport.theAllFrameCount    
+                                        """
+                                        
                 return theTiffReport
         validateTiff = classmethod(validateTiff)
         
+        def validateTiffImageData(self, inImage, ):
+                """
+                Examines the tiff image data to compare with 
+                """
+                
+                """ code to look at the list of tiff image dimensions
+                theTiffWidth = None
+                theTiffHeight = None
+                try:
+                        #theTiffWidth = int(inImage.tag[256])
+                        print inImage.tag[256]
+                except KeyError:
+                        pass
+                except ValueError:
+                        pass
+                try:
+                        theTiffHeight = int(inImage.tag[257])
+                except KeyError:
+                        pass
+                except ValueError:
+                        pass
+                """
+                
+                #look for frames
+                self.tiffFileFrames = 0
+                try:
+                    while True:
+                        inImage.seek( self.tiffFileFrames )
+                        self.tiffFileFrames = self.tiffFileFrames + 1
+                except EOFError:
+                    inImage.seek( 0 )
+                    pass
+                
+                # compare with values from xml and tiff
+                if self.tiffFileFrames > self.ome5dPlaneCount:
+                        self.warningList.append(ParseMessage(None, None, None, "TIFF", ("Frames %s needing %s" % (self.tiffFileFrames,self.ome5dPlaneCount)) , "Extra frames are present in this Tiff file"))
+
+                if self.tiffFileFrames < self.ome5dPlaneCount:
+                        self.warningList.append(ParseMessage(None, None, None, "TIFF", ("Frames %s out of %s" % (self.tiffFileFrames,self.ome5dPlaneCount)) , "Not all possible frames are present in this Tiff file"))
+
+                # compare with values from xml TiffData and tiff
+                totalTiffDataFrames = self.omeTiffDataPlaneCount + (self.tiffFileFrames * self.theAllFrameCount)
+                if self.tiffFileFrames > totalTiffDataFrames:
+                        self.warningList.append(ParseMessage(None, None, None, "TIFF", ("Frames %s referenced %s" % (self.tiffFileFrames,totalTiffDataFrames)) , "Unreferenced frames are present in this Tiff file"))
+
+                if self.tiffFileFrames < totalTiffDataFrames:
+                        self.errorList.append(ParseMessage(None, None, None, "TIFF", ("Frames %s out of %s" % (self.tiffFileFrames,totalTiffDataFrames)) , "Not all required frames are present in this Tiff file"))
 
 # Used by sax parser to handle errors when processing Elements
@@ -392 +478 @@
                 self.inBinDataContent = False
                 self.shortFormXml = ""
+                # internal check counters
                 self.skipCount = 0
+                self.omeTiffDataCount = 0
+                self.omePixelsCount = 0
+                self.omePlanesCount = 0
+                self.ome5dPlaneCount = 0
+                self.omeTiffDataPlaneCount = 0
+                self.theAllFrameCount = 0
                 
                 # Setup the DOM chunk
@@ -474 +567 @@
                 if name[-7:] == "BinData":
                         self.inBinData = True
+                
+                if name[-8:] == "TiffData":
+                        self.omeTiffDataCount = self.omeTiffDataCount + 1
+                        # omeTiffDataPlaneCount
+                        if "NumPlanes" in attribs:
+                                # use the number of planes specified
+                                self.omeTiffDataPlaneCount = self.omeTiffDataPlaneCount + int(attribs.getValue("NumPlanes"))
+                                if self.theAllFrameCount > 0:
+                                        self.errorList.append(ParseMessage(None, None, None, "OME","", "Inconsistent use of TiffData element [Type 1]"))
+                                
+                        else:
+                                if "IFD" in attribs:
+                                        # use one frame
+                                        self.omeTiffDataPlaneCount = self.omeTiffDataPlaneCount + 1
+                                        if self.theAllFrameCount > 0:
+                                                self.errorList.append(ParseMessage(None, None, None, "OME","", "Inconsistent use of TiffData element [Type 2]"))
+                                else:
+                                        # use all the frames in the tiff
+                                        self.theAllFrameCount = self.theAllFrameCount + 1
+                                        if (self.theAllFrameCount > 1) or (self.omeTiffDataPlaneCount > 0):
+                                                self.errorList.append(ParseMessage(None, None, None, "OME","", "Inconsistent use of TiffData element [Type 3]"))
+                        
+                        """
+                        IFD: Gives the IFD(s) for which this element is applicable. Indexed from 0. Default is 0 (the first IFD).
+                        FirstZ: Gives the Z position of the image plane at the specified IFD. Indexed from 0. Default is 0 (the first Z position).
+                        FirstT: Gives the T position of the image plane at the specified IFD. Indexed from 0. Default is 0 (the first T position).
+                        FirstC: Gives the C position of the image plane at the specified IFD. Indexed from 0. Default is 0 (the first C position).
+                        NumPlanes: Gives the number of IFDs affected. Dimension order of IFDs is given by the enclosing Pixels element's DimensionOrder attribute. 
+                                           Default is the number of IFDs in the TIFF file, unless an IFD is specified, in which case the default is 1.
+                        """
+                
+                if name[-6:] == "Pixels":
+                        self.omePixelsCount = self.omePixelsCount + 1
+                        try:
+                                # total up planes needed from Z, C and T
+                                theZ = int(attribs.getValue("SizeZ"))
+                                theC = int(attribs.getValue("SizeC"))
+                                theT = int(attribs.getValue("SizeT"))
+                                # print "Z: %s, C: %s, T: %s" % (theZ, theC, theT)
+                                self.ome5dPlaneCount = self.ome5dPlaneCount + (theZ * theC * theT)
+                        except KeyError:
+                                pass
+                        except ValueError:
+                                pass
+                
+                if name[-5:] == "Plane":
+                        self.omePlanesCount = self.omePlanesCount + 1
+                
                 self.domify(name, attribs)
                         
@@ -544 +685 @@
 
 if __name__ == '__main__':
-        for aFilename in ["samples/completesamplenopre.xml","samples/completesample.xml","samples/completesamplenoenc.xml",
-                "samples/sdub.ome", "samples/sdub-fix.ome", "samples/sdub-fix-pre.ome", 
-                "samples/tiny.ome", "samples/broke.ome"]:
-                print "============ XML file %s ============ " % aFilename
-                print XmlReport.validateFile(aFilename)
+        """     for aFilename in ["samples/completesamplenopre.xml","samples/completesample.xml","samples/completesamplenoenc.xml",
+                        "samples/sdub.ome", "samples/sdub-fix.ome", "samples/sdub-fix-pre.ome", 
+                        "samples/tiny.ome", "samples/broke.ome"]:
+                        print "============ XML file %s ============ " % aFilename
+                        print XmlReport.validateFile(aFilename)
+        """
         
         for aFilename in ["samples/4d2wOME.tif", "samples/4d2wOME-fixed.tif",