# coding: utf-8 # # Project: X-ray image reader # https://github.com/silx-kit/fabio # # # Copyright (C) European Synchrotron Radiation Facility, Grenoble, France # # Principal author: Jérôme Kieffer (Jerome.Kieffer@ESRF.eu) # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program. If not, see . # """ 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 """ # Get ready for python3: from __future__ import with_statement, print_function 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.check_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 GEimage = GeImage