fabio 0.1.1__zip

Library/Python/2.7/site-packages/fabio/GEimage_old.py

@@ -0,0 +1,501 @@
+
+#!/usr/bin/env python
+
+"""
+Reads the header from a GE a-Si Angio Detector
+
+Authors: Henning O. Sorensen & Erik Knudsen
+         Center for Fundamental Research: Metal Structures in Four Dimensions
+         Risoe National Laboratory
+         Frederiksborgvej 399
+         DK-4000 Roskilde
+         email:erik.knudsen@risoe.dk
+
+        + Jon Wright, ESRF
+
+        The header information has been taken from the script read_GEaSi_data.py
+        by
+        Antonino Miceli
+        Thu Jan  4 13:46:31 CST 2007
+
+"""
+
+import numpy
+from fabioimage import fabioimage
+
+class GEimage(fabioimage):
+
+
+    def _readheader(self, infile):
+
+        infile.seek(0)
+
+        # ADEPT
+        self.ImageFormat = infile.read(10)
+
+        # USHORT --> "=H"
+        # ULONG  --> "=L"
+        #   = means byte order is native
+
+        self.header['HeaderVersion'] = numpy.fromstring(infile.read(2), numpy.uint16)[0]
+        self.header['HeaderSizeInBytes'] = int(numpy.fromstring(infile.read(4), numpy.uint32)[0])
+        self.header['UserHeaderVersion'] = numpy.fromstring(infile.read(2), numpy.uint16)[0]
+        self.header['UserHeaderSizeInBytes'] = int(numpy.fromstring(infile.read(4), numpy.uint32)[0])
+
+        self.header['NumberOfFrames'] = numpy.fromstring(infile.read(2), numpy.uint16)[0]
+        self.header['NumberOfRowsInFrame'] = numpy.fromstring(infile.read(2), numpy.uint16)[0]
+        self.header['NumberOfColsInFrame'] = numpy.fromstring(infile.read(2), numpy.uint16)[0]
+        self.header['BitsPerPixel'] = numpy.fromstring(infile.read(2), numpy.uint16)[0]
+
+        self.header['AcquisitionDate'] = infile.read(20)
+        self.header['AcquisitionTime'] = infile.read(20)
+
+        self.DUTID = infile.read(20)
+
+        self.header['Operator'] = infile.read(50)
+
+        self.header['DetectorSignature'] = infile.read(20)
+        self.header['TestSystemName'] = infile.read(20)
+        self.header['TestStationRevision'] = infile.read(20)
+        self.header['CoreBundleRevision'] = infile.read(20)
+        self.header['AcquisitionName'] = infile.read(40)
+        self.header['AcquisitionParameterRevision'] = infile.read(20)
+
+#         self.OriginalNumberOfRows = infile.read(2)
+#         self.OriginalNumberOfRows = struct.unpack("=H",self.OriginalNumberOfRows)[0]
+
+#         self.OriginalNumberOfColumns = infile.read(2)
+#         self.OriginalNumberOfColumns = struct.unpack("=H",self.OriginalNumberOfColumns)[0]
+
+#         self.RowNumberUpperLeftPointArchiveROI = infile.read(2)
+#         self.RowNumberUpperLeftPointArchiveROI = struct.unpack("=H",self.RowNumberUpperLeftPointArchiveROI)[0]
+
+#         self.ColNumberUpperLeftPointArchiveROI = infile.read(2)
+#         self.ColNumberUpperLeftPointArchiveROI = struct.unpack("=H",self.ColNumberUpperLeftPointArchiveROI)[0]
+
+#         self.Swapped = infile.read(2) 
+#         self.Swapped = struct.unpack("=H",self.Swapped)[0]
+
+#         self.Reordered = infile.read(2) 
+#         self.Reordered = struct.unpack("=H",self.Reordered)[0]
+
+#         self.HorizontalFlipped = infile.read(2) 
+#         self.HorizontalFlipped = struct.unpack("=H",self.HorizontalFlipped)[0]
+
+#         self.VerticalFlipped = infile.read(2) 
+#         self.VerticalFlipped = struct.unpack("=H",self.VerticalFlipped)[0]
+
+#         self.WindowValueDesired = infile.read(2) 
+#         self.WindowValueDesired = struct.unpack("=H",self.WindowValueDesired)[0]
+
+#         self.LevelValueDesired = infile.read(2) 
+#         self.LevelValueDesired = struct.unpack("=H",self.LevelValueDesired)[0]
+
+#         self.AcquisitionMode = infile.read(2) 
+#         self.AcquisitionMode = struct.unpack("=H",self.AcquisitionMode)[0]
+
+#         self.AcquisitionType = infile.read(2) 
+#         self.AcquisitionType = struct.unpack("=H",self.AcquisitionType)[0]
+
+#         self.UserAcquisitionCoffFileName1 = infile.read(100) 
+#         self.UserAcquisitionCoffFileName2 = infile.read(100) 
+
+#         self.FramesBeforeExpose = infile.read(2) 
+#         self.FramesBeforeExpose = struct.unpack("=H",self.FramesBeforeExpose)[0]
+
+#         self.FramesDuringExpose = infile.read(2)  
+#         self.FramesDuringExpose = struct.unpack("=H",self.FramesDuringExpose)[0]
+
+#         self.FramesAfterExpose = infile.read(2) 
+#         self.FramesAfterExpose = struct.unpack("=H",self.FramesAfterExpose)[0]
+
+#         self.IntervalBetweenFrames = infile.read(2) 
+#         self.IntervalBetweenFrames = struct.unpack("=H",self.IntervalBetweenFrames)[0]
+
+#         self.ExposeTimeDelayInMicrosecs = infile.read(8) 
+#         self.ExposeTimeDelayInMicrosecs = struct.unpack("=d",self.ExposeTimeDelayInMicrosecs)[0]
+
+#         self.TimeBetweenFramesInMicrosecs = infile.read(8) 
+#         self.TimeBetweenFramesInMicrosecs = struct.unpack("=d",self.TimeBetweenFramesInMicrosecs)[0]
+
+#         self.FramesToSkipExpose = infile.read(2) 
+#         self.FramesToSkipExpose = struct.unpack("=H",self.FramesToSkipExpose)[0]
+
+#         # Rad --> ExposureMode = 1
+#         self.ExposureMode = infile.read(2) 
+#         self.ExposureMode = struct.unpack("=H",self.ExposureMode)[0]
+
+#         self.PrepPresetTimeInMicrosecs = infile.read(8) 
+#         self.PrepPresetTimeInMicrosecs = struct.unpack("=d",self.PrepPresetTimeInMicrosecs)[0]
+
+#         self.ExposePresetTimeInMicrosecs = infile.read(8) 
+#         self.ExposePresetTimeInMicrosecs = struct.unpack("=d",self.ExposePresetTimeInMicrosecs)[0]
+
+#         self.AcquisitionFrameRateInFps = infile.read(4) 
+#         self.AcquisitionFrameRateInFps = struct.unpack("=f",self.AcquisitionFrameRateInFps)[0]
+
+#         self.FOVSelect = infile.read(2)
+#         self.FOVSelect = struct.unpack("=H",self.FOVSelect)[0]
+
+#         self.ExpertMode = infile.read(2)
+#         self.ExpertMode = struct.unpack("=H",self.ExpertMode)[0]
+
+#         self.SetVCommon1 = infile.read(8)
+#         self.SetVCommon1 = struct.unpack("=d",self.SetVCommon1)[0]
+
+#         self.SetVCommon2 = infile.read(8)
+#         self.SetVCommon2 = struct.unpack("=d",self.SetVCommon2)[0]
+
+#         self.SetAREF = infile.read(8)
+#         self.SetAREF = struct.unpack("=d",self.SetAREF)[0]
+
+#         self.SetAREFTrim = infile.read(4)
+#         self.SetAREFTrim = struct.unpack("=L",self.SetAREFTrim)[0]
+
+#         self.SetSpareVoltageSource = infile.read(8)
+#         self.SetSpareVoltageSource = struct.unpack("=d",self.SetSpareVoltageSource)[0]
+
+#         self.SetCompensationVoltageSource = infile.read(8)
+#         self.SetCompensationVoltageSource = struct.unpack("=d",self.SetCompensationVoltageSource)[0]
+
+#         self.SetRowOffVoltage = infile.read(8)
+#         self.SetRowOffVoltage = struct.unpack("=d",self.SetRowOffVoltage)[0]
+
+#         self.SetRowOnVoltage = infile.read(8)
+#         self.SetRowOnVoltage = struct.unpack("=d",self.SetRowOnVoltage)[0]
+
+#         self.StoreCompensationVoltage = infile.read(4)
+#         self.StoreCompensationVoltage = struct.unpack("=L",self.StoreCompensationVoltage)[0]
+
+#         self.RampSelection = infile.read(2)
+#         self.RampSelection = struct.unpack("=H",self.RampSelection)[0]
+
+#         self.TimingMode = infile.read(2)
+#         self.TimingMode = struct.unpack("=H",self.TimingMode)[0]
+
+#         self.Bandwidth = infile.read(2)
+#         self.Bandwidth = struct.unpack("=H",self.Bandwidth)[0]
+
+#         self.ARCIntegrator = infile.read(2)
+#         self.ARCIntegrator = struct.unpack("=H",self.ARCIntegrator)[0]
+
+#         self.ARCPostIntegrator = infile.read(2)
+#         self.ARCPostIntegrator = struct.unpack("=H",self.ARCPostIntegrator)[0]
+
+#         self.NumberOfRows = infile.read(4)
+#         self.NumberOfRows = struct.unpack("=L",self.NumberOfRows)[0]
+
+#         self.RowEnable = infile.read(2)
+#         self.RowEnable = struct.unpack("=H",self.RowEnable)[0]
+
+#         self.EnableStretch = infile.read(2)
+#         self.EnableStretch = struct.unpack("=H",self.EnableStretch)[0]
+
+#         self.CompEnable = infile.read(2)
+#         self.CompEnable = struct.unpack("=H",self.CompEnable)[0]
+
+#         self.CompStretch = infile.read(2)
+#         self.CompStretch = struct.unpack("=H",self.CompStretch)[0]
+
+#         self.LeftEvenTristate = infile.read(2)
+#         self.LeftEvenTristate = struct.unpack("=H",self.LeftEvenTristate)[0]
+
+#         self.RightOddTristate = infile.read(2)
+#         self.RightOddTristate = struct.unpack("=H",self.RightOddTristate)[0]
+
+#         self.TestModeSelect = infile.read(4)
+#         self.TestModeSelect = struct.unpack("=L",self.TestModeSelect)[0]
+
+#         self.AnalogTestSource = infile.read(4)
+#         self.AnalogTestSource = struct.unpack("=L",self.AnalogTestSource)[0]
+
+#         self.VCommonSelect = infile.read(4)
+#         self.VCommonSelect = struct.unpack("=L",self.VCommonSelect)[0]
+
+#         self.DRCColumnSum = infile.read(4)
+#         self.DRCColumnSum = struct.unpack("=L",self.DRCColumnSum)[0]
+
+#         self.TestPatternFrameDelta = infile.read(4)
+#         self.TestPatternFrameDelta = struct.unpack("=L",self.TestPatternFrameDelta)[0]
+
+#         self.TestPatternRowDelta = infile.read(4)
+#         self.TestPatternRowDelta = struct.unpack("=L",self.TestPatternRowDelta)[0]
+
+#         self.TestPatternColumnDelta = infile.read(4)
+#         self.TestPatternColumnDelta = struct.unpack("=L",self.TestPatternColumnDelta)[0]
+
+#         self.DetectorHorizontalFlip = infile.read(2)
+#         self.DetectorHorizontalFlip = struct.unpack("=H",self.DetectorHorizontalFlip)[0]
+
+#         self.DetectorVerticalFlip = infile.read(2)
+#         self.DetectorVerticalFlip = struct.unpack("=H",self.DetectorVerticalFlip)[0]
+
+#         self.DFNAutoScrubOnOff = infile.read(2)
+#         self.DFNAutoScrubOnOff = struct.unpack("=H",self.DFNAutoScrubOnOff)[0]
+
+#         self.FiberChannelTimeOutInMicrosecs = infile.read(4)
+#         self.FiberChannelTimeOutInMicrosecs = struct.unpack("=L",self.FiberChannelTimeOutInMicrosecs)[0]
+
+#         self.DFNAutoScrubDelayInMicrosecs = infile.read(4)
+#         self.DFNAutoScrubDelayInMicrosecs = struct.unpack("=L",self.DFNAutoScrubDelayInMicrosecs)[0]
+
+#         self.StoreAECROI = infile.read(2)
+#         self.StoreAECROI = struct.unpack("=H",self.StoreAECROI)[0]
+
+#         self.TestPatternSaturationValue = infile.read(2)
+#         self.TestPatternSaturationValue = struct.unpack("=H",self.TestPatternSaturationValue)[0]
+
+#         self.TestPatternSeed = infile.read(4)
+#         self.TestPatternSeed = struct.unpack("=L",self.TestPatternSeed)[0]
+
+#         self.ExposureTimeInMillisecs = infile.read(4) 
+#         self.ExposureTimeInMillisecs = struct.unpack("=f",self.ExposureTimeInMillisecs)[0]
+
+#         self.FrameRateInFps = infile.read(4) 
+#         self.FrameRateInFps = struct.unpack("=f",self.FrameRateInFps)[0]
+
+#         self.kVp = infile.read(4) 
+#         self.kVp = struct.unpack("=f",self.kVp)[0]
+
+#         self.mA = infile.read(4) 
+#         self.mA = struct.unpack("=f",self.mA)[0]
+
+#         self.mAs = infile.read(4) 
+#         self.mAs = struct.unpack("=f",self.mAs)[0]
+
+#         self.FocalSpotInMM = infile.read(4) 
+#         self.FocalSpotInMM = struct.unpack("=f",self.FocalSpotInMM)[0]
+
+#         self.GeneratorType = infile.read(20)
+
+#         self.StrobeIntensityInFtL = infile.read(4) 
+#         self.StrobeIntensityInFtL = struct.unpack("=f",self.StrobeIntensityInFtL)[0]
+
+#         self.NDFilterSelection = infile.read(2) 
+#         self.NDFilterSelection = struct.unpack("=H",self.NDFilterSelection)[0]
+
+#         self.RefRegTemp1 = infile.read(8) 
+#         self.RefRegTemp1 = struct.unpack("=d",self.RefRegTemp1)[0]
+
+#         self.RefRegTemp2 = infile.read(8) 
+#         self.RefRegTemp2 = struct.unpack("=d",self.RefRegTemp2)[0]
+
+#         self.RefRegTemp3 = infile.read(8) 
+#         self.RefRegTemp3 = struct.unpack("=d",self.RefRegTemp3)[0]
+
+#         self.Humidity1 = infile.read(4) 
+#         self.Humidity1 = struct.unpack("=f",self.Humidity1)[0]
+
+#         self.Humidity2 = infile.read(4) 
+#         self.Humidity2 = struct.unpack("=f",self.Humidity2)[0]
+
+#         self.DetectorControlTemp = infile.read(8) 
+#         self.DetectorControlTemp = struct.unpack("=d",self.DetectorControlTemp)[0]
+
+#         self.DoseValueInmR = infile.read(8) 
+#         self.DoseValueInmR = struct.unpack("=d",self.DoseValueInmR)[0]
+
+#         self.TargetLevelROIRow0 = infile.read(2)
+#         self.TargetLevelROIRow0 = struct.unpack("=H",self.TargetLevelROIRow0)[0]
+
+#         self.TargetLevelROICol0 = infile.read(2)
+#         self.TargetLevelROICol0 = struct.unpack("=H",self.TargetLevelROICol0)[0]
+
+#         self.TargetLevelROIRow1 = infile.read(2)
+#         self.TargetLevelROIRow1 = struct.unpack("=H",self.TargetLevelROIRow1)[0]
+
+#         self.TargetLevelROICol1 = infile.read(2)
+#         self.TargetLevelROICol1 = struct.unpack("=H",self.TargetLevelROICol1)[0]
+
+#         self.FrameNumberForTargetLevelROI = infile.read(2)
+#         self.FrameNumberForTargetLevelROI = struct.unpack("=H",self.FrameNumberForTargetLevelROI)[0]
+
+#         self.PercentRangeForTargetLevel = infile.read(2)
+#         self.PercentRangeForTargetLevel = struct.unpack("=H",self.PercentRangeForTargetLevel)[0]
+
+#         self.TargetValue = infile.read(2)
+#         self.TargetValue = struct.unpack("=H",self.TargetValue)[0]
+
+#         self.ComputedMedianValue = infile.read(2)
+#         self.ComputedMedianValue = struct.unpack("=H",self.ComputedMedianValue)[0]
+
+#         self.LoadZero = infile.read(2)
+#         self.LoadZero = struct.unpack("=H",self.LoadZero)[0]
+
+#         self.MaxLUTOut = infile.read(2)
+#         self.MaxLUTOut = struct.unpack("=H",self.MaxLUTOut)[0]
+
+#         self.MinLUTOut = infile.read(2)
+#         self.MinLUTOut = struct.unpack("=H",self.MinLUTOut)[0]
+
+#         self.MaxLinear = infile.read(2)
+#         self.MaxLinear = struct.unpack("=H",self.MaxLinear)[0]
+
+#         self.Reserved = infile.read(2)
+#         self.Reserved = struct.unpack("=H",self.Reserved)[0]
+
+#         self.ElectronsPerCount = infile.read(2)
+#         self.ElectronsPerCount = struct.unpack("=H",self.ElectronsPerCount)[0]
+
+#         self.ModeGain = infile.read(2)
+#         self.ModeGain = struct.unpack("=H",self.ModeGain)[0]
+
+#         self.TemperatureInDegC = infile.read(8)
+#         self.TemperatureInDegC = struct.unpack("=d",self.TemperatureInDegC)[0]
+
+#         self.LineRepaired = infile.read(2)
+#         self.LineRepaired = struct.unpack("=H",self.LineRepaired)[0]
+
+#         self.LineRepairFileName = infile.read(100)
+
+#         self.CurrentLongitudinalInMM = infile.read(4)
+#         self.CurrentLongitudinalInMM = struct.unpack("=f",self.CurrentLongitudinalInMM)[0]
+
+#         self.CurrentTransverseInMM = infile.read(4)
+#         self.CurrentTransverseInMM = struct.unpack("=f",self.CurrentTransverseInMM)[0]
+
+#         self.CurrentCircularInMM = infile.read(4)
+#         self.CurrentCircularInMM = struct.unpack("=f",self.CurrentCircularInMM)[0]
+
+#         self.CurrentFilterSelection = infile.read(4)
+#         self.CurrentFilterSelection = struct.unpack("=L",self.CurrentFilterSelection)[0]
+
+#         self.DisableScrubAck = infile.read(2)
+#         self.DisableScrubAck = struct.unpack("=H",self.DisableScrubAck)[0]
+
+#         self.ScanModeSelect = infile.read(2)
+#         self.ScanModeSelect = struct.unpack("=H",self.ScanModeSelect)[0]
+
+#         self.DetectorAppSwVersion = infile.read(20)	
+
+#         self.DetectorNIOSVersion = infile.read(20)	
+
+#         self.DetectorPeripheralSetVersion = infile.read(20)	
+
+#         self.DetectorPhysicalAddress	 = infile.read(20)
+
+#         self.PowerDown = infile.read(2)
+#         self.PowerDown = struct.unpack("=H",self.PowerDown)[0]
+
+#         self.InitialVoltageLevel_VCOMMON = infile.read(8)
+#         self.InitialVoltageLevel_VCOMMON = struct.unpack("=d",self.InitialVoltageLevel_VCOMMON)[0]
+
+#         self.FinalVoltageLevel_VCOMMON = infile.read(8)
+#         self.FinalVoltageLevel_VCOMMON = struct.unpack("=d",self.FinalVoltageLevel_VCOMMON)[0]
+
+#         self.DmrCollimatorSpotSize	 = infile.read(10)
+
+#         self.DmrTrack	 = infile.read(5)
+
+#         self.DmrFilter	 = infile.read(5)
+
+#         self.FilterCarousel = infile.read(2)
+#         self.FilterCarousel = struct.unpack("=H",self.FilterCarousel)[0]
+
+#         self.Phantom	 = infile.read(20)
+
+#         self.SetEnableHighTime = infile.read(2)
+#         self.SetEnableHighTime = struct.unpack("=H",self.SetEnableHighTime)[0]
+
+#         self.SetEnableLowTime = infile.read(2)
+#         self.SetEnableLowTime = struct.unpack("=H",self.SetEnableLowTime)[0]
+
+#         self.SetCompHighTime = infile.read(2)
+#         self.SetCompHighTime = struct.unpack("=H",self.SetCompHighTime)[0]
+
+#         self.SetCompLowTime = infile.read(2)
+#         self.SetCompLowTime = struct.unpack("=H",self.SetCompLowTime)[0]
+
+#         self.SetSyncLowTime = infile.read(2)
+#         self.SetSyncLowTime = struct.unpack("=H",self.SetSyncLowTime)[0]
+
+#         self.SetConvertLowTime = infile.read(2)
+#         self.SetConvertLowTime = struct.unpack("=H",self.SetConvertLowTime)[0]
+
+#         self.SetSyncHighTime = infile.read(2)
+#         self.SetSyncHighTime = struct.unpack("=H",self.SetSyncHighTime)[0]
+
+#         self.SetEOLTime = infile.read(2)
+#         self.SetEOLTime = struct.unpack("=H",self.SetEOLTime)[0]
+
+#         self.SetRampOffsetTime = infile.read(2)
+#         self.SetRampOffsetTime = struct.unpack("=H",self.SetRampOffsetTime)[0]
+
+#         self.FOVStartingValue = infile.read(2)
+#         self.FOVStartingValue = struct.unpack("=H",self.FOVStartingValue)[0]
+
+#         self.ColumnBinning = infile.read(2)
+#         self.ColumnBinning = struct.unpack("=H",self.ColumnBinning)[0]
+
+#         self.RowBinning = infile.read(2)
+#         self.RowBinning = struct.unpack("=H",self.RowBinning)[0]
+
+#         self.BorderColumns64 = infile.read(2)
+#         self.BorderColumns64 = struct.unpack("=H",self.BorderColumns64)[0]
+
+#         self.BorderRows64 = infile.read(2)
+#         self.BorderRows64 = struct.unpack("=H",self.BorderRows64)[0]
+
+#         self.FETOffRows64 = infile.read(2)
+#         self.FETOffRows64 = struct.unpack("=H",self.FETOffRows64)[0]
+
+#         self.FOVStartColumn128 = infile.read(2)
+#         self.FOVStartColumn128 = struct.unpack("=H",self.FOVStartColumn128)[0]
+
+#         self.FOVStartRow128 = infile.read(2)
+#         self.FOVStartRow128 = struct.unpack("=H",self.FOVStartRow128)[0]
+
+#         self.NumberOfColumns128 = infile.read(2)
+#         self.NumberOfColumns128 = struct.unpack("=H",self.NumberOfColumns128)[0]
+
+#         self.NumberOfRows128 = infile.read(2)
+#         self.NumberOfRows128 = struct.unpack("=H",self.NumberOfRows128)[0]
+
+#         self.VFPAquisition	 = infile.read(2000)
+
+#         self.Comment	 = infile.read(200)
+
+
+
+    def read(self, fname, frame=None):
+        """
+        Read in header into self.header and
+            the data   into self.data
+        """
+        self.header = {}
+        self.resetvals()
+        infile = self._open(fname, "rb")
+        self._readheader(infile)
+        # Compute image size
+        try:
+            self.dim1 = int(self.header['NumberOfRowsInFrame'])
+            self.dim2 = int(self.header['NumberOfColsInFrame'])
+            self.bpp = int(self.header['BitsPerPixel'])
+        except:
+            raise Exception("GE  file", str(fname) + \
+                                "is corrupt, cannot read it")
+
+        # More than one image can be saved in a GE file
+        # Will only load the first one
+
+
+        # Go to the beginning of the file
+        infile.seek(0)
+        infile.seek(self.header['HeaderSizeInBytes'] + self.header['UserHeaderSizeInBytes'])
+
+        ReadBytes = self.dim1 * self.dim2 * (self.bpp / 8)
+        block = infile.read(ReadBytes)
+        block = numpy.fromstring(block, numpy.uint16)
+
+        infile.close()
+
+        try:
+            self.data = numpy.reshape(block, [self.dim2, self.dim1])
+        except:
+            print len(block), self.dim2, self.dim1
+            raise IOError, \
+              'Size spec in GE-header does not match size of image data field'
+
+        self.bytecode = self.data.dtype.type
+        self.pilimage = None
+        return self

Library/Python/2.7/site-packages/fabio/HiPiCimage.py

@@ -0,0 +1,106 @@
+
+#!/usr/bin/env python
+"""
+Authors: Henning O. Sorensen & Erik Knudsen
+         Center for Fundamental Research: Metal Structures in Four Dimensions
+         Risoe National Laboratory
+         Frederiksborgvej 399
+         DK-4000 Roskilde
+         email:erik.knudsen@risoe.dk
+
+        + Jon Wright, ESRF
+
+Information about the file format from Masakatzu Kobayashi is highly appreciated
+"""
+
+import numpy, logging
+logger = logging.getLogger("HiPiCimage")
+from fabioimage import fabioimage
+
+class HiPiCimage(fabioimage):
+    """ Read HiPic images e.g. collected with a Hamamatsu CCD camera"""
+
+
+    def _readheader(self, infile):
+        """
+        Read in a header from an already open file
+
+        """
+        Image_tag = infile.read(2)
+        print Image_tag
+        Comment_len = numpy.fromstring(infile.read(2), numpy.uint16)
+        Dim_1 = numpy.fromstring(infile.read(2), numpy.uint16)[0]
+        Dim_2 = numpy.fromstring(infile.read(2), numpy.uint16)[0]
+        Dim_1_offset = numpy.fromstring(infile.read(2), numpy.uint16)[0]
+        Dim_2_offset = numpy.fromstring(infile.read(2), numpy.uint16)[0]
+        HeaderType = numpy.fromstring(infile.read(2), numpy.uint16)[0]
+        Dump = infile.read(50)
+        Comment = infile.read(Comment_len)
+        self.header['Image_tag'] = Image_tag
+        self.header['Dim_1'] = Dim_1
+        self.header['Dim_2'] = Dim_2
+        self.header['Dim_1_offset'] = Dim_1_offset
+        self.header['Dim_2_offset'] = Dim_2_offset
+        #self.header['Comment'] = Comment
+        if Image_tag != 'IM' :
+            # This does not look like an HiPic file
+            logging.warning("no opening.  Corrupt header of HiPic file " + \
+                            str(infile.name))
+        Comment_split = Comment[:Comment.find('\x00')].split('\r\n')
+
+        for topcomment in Comment_split:
+            topsplit = topcomment.split(',')
+            for line in topsplit:
+                if '=' in line:
+                    key, val = line.split('=' , 1)
+                    # Users cannot type in significant whitespace
+                    key = key.rstrip().lstrip()
+                    self.header_keys.append(key)
+                    self.header[key] = val.lstrip().rstrip()
+                    self.header[key] = val.lstrip('"').rstrip('"')
+
+    def read(self, fname, frame=None):
+        """
+        Read in header into self.header and
+            the data   into self.data
+        """
+        self.header = {}
+        self.resetvals()
+        infile = self._open(fname, "rb")
+        self._readheader(infile)
+        # Compute image size
+        try:
+            self.dim1 = int(self.header['Dim_1'])
+            self.dim2 = int(self.header['Dim_2'])
+        except:
+            raise Exception("HiPic file", str(fname) + \
+                                "is corrupt, cannot read it")
+        bytecode = numpy.uint16
+        self.bpp = len(numpy.array(0, bytecode).tostring())
+
+        # Read image data
+        block = infile.read(self.dim1 * self.dim2 * self.bpp)
+        infile.close()
+
+        #now read the data into the array
+        try:
+            self.data = numpy.reshape(
+                numpy.fromstring(block, bytecode),
+                [self.dim2, self.dim1])
+        except:
+            print len(block), bytecode, self.bpp, self.dim2, self.dim1
+            raise IOError, \
+              'Size spec in HiPic-header does not match size of image data field'
+        self.bytecode = self.data.dtype.type
+
+        # Sometimes these files are not saved as 12 bit,
+        # But as 16 bit after bg subtraction - which results 
+        # negative values saved as 16bit. Therefore values higher 
+        # 4095 is really negative values
+        if self.data.max() > 4095:
+            gt12bit = self.data > 4095
+            self.data = self.data - gt12bit * (2 ** 16 - 1)
+
+        # ensure the PIL image is reset
+        self.pilimage = None
+        return self