fabio 0.1.1__zip

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

@@ -0,0 +1,334 @@
+#!/usr/bin/env python
+
+#
+# Reads the header from a GE a-Si Angio Detector
+# Using version 8001 of the header from file:
+#     c:\adept\core\DefaultImageInfoConfig.csv
+#
+#  Antonino Miceli
+#  Thu Jan  4 13:46:31 CST 2007
+#
+
+# modifications by Jon Wright for style, pychecker and fabio
+# 
+
+import numpy
+import struct, logging
+logger = logging.getLogger("GEimage")
+from fabioimage import fabioimage
+from fabioutils import next_filename, previous_filename
+
+GE_HEADER_INFO = [
+    # Name, length in bytes, format for struct (None means string)
+    ('ImageFormat', 10, None),
+    ('VersionOfStandardHeader', 2, '=H'),
+    ('StandardHeaderSizeInBytes', 4, '=L'),
+    ('VersionOfUserHeader', 2, '=H'),
+    ('UserHeaderSizeInBytes', 4, '=L'),
+    ('NumberOfFrames', 2, '=H'),
+    ('NumberOfRowsInFrame', 2, '=H'),
+    ('NumberOfColsInFrame', 2, '=H'),
+    ('ImageDepthInBits', 2, '=H'),
+    ('AcquisitionDate', 20, None),
+    ('AcquisitionTime', 20, None),
+    ('DUTID', 20, None),
+    ('Operator', 50, None),
+    ('DetectorSignature', 20, None),
+    ('TestSystemName', 20, None),
+    ('TestStationRevision', 20, None),
+    ('CoreBundleRevision', 20, None),
+    ('AcquisitionName', 40, None),
+    ('AcquisitionParameterRevision', 20, None),
+    ('OriginalNumberOfRows', 2, '=H'),
+    ('OriginalNumberOfColumns', 2, '=H'),
+    ('RowNumberUpperLeftPointArchiveROI', 2, '=H'),
+    ('ColNumberUpperLeftPointArchiveROI', 2, '=H'),
+    ('Swapped', 2, '=H'),
+    ('Reordered', 2, '=H'),
+    ('HorizontalFlipped', 2, '=H'),
+    ('VerticalFlipped', 2, '=H'),
+    ('WindowValueDesired', 2, '=H'),
+    ('LevelValueDesired', 2, '=H'),
+    ('AcquisitionMode', 2, '=H'),
+    ('AcquisitionType', 2, '=H'),
+    ('UserAcquisitionCoffFileName1', 100, None),
+    ('UserAcquisitionCoffFileName2', 100, None),
+    ('FramesBeforeExpose', 2, '=H'),
+    ('FramesDuringExpose', 2, '=H'),
+    ('FramesAfterExpose', 2, '=H'),
+    ('IntervalBetweenFrames', 2, '=H'),
+    ('ExposeTimeDelayInMicrosecs', 8, '=d'),
+    ('TimeBetweenFramesInMicrosecs', 8, '=d'),
+    ('FramesToSkipExpose', 2, '=H'),
+    ('ExposureMode', 2, '=H'),
+    ('PrepPresetTimeInMicrosecs', 8, '=d'),
+    ('ExposePresetTimeInMicrosecs', 8, '=d'),
+    ('AcquisitionFrameRateInFps', 4, '=f'),
+    ('FOVSelect', 2, '=H'),
+    ('ExpertMode', 2, '=H'),
+    ('SetVCommon1', 8, '=d'),
+    ('SetVCommon2', 8, '=d'),
+    ('SetAREF', 8, '=d'),
+    ('SetAREFTrim', 4, '=L'),
+    ('SetSpareVoltageSource', 8, '=d'),
+    ('SetCompensationVoltageSource', 8, '=d'),
+    ('SetRowOffVoltage', 8, '=d'),
+    ('SetRowOnVoltage', 8, '=d'),
+    ('StoreCompensationVoltage', 4, '=L'),
+    ('RampSelection', 2, '=H'),
+    ('TimingMode', 2, '=H'),
+    ('Bandwidth', 2, '=H'),
+    ('ARCIntegrator', 2, '=H'),
+    ('ARCPostIntegrator', 2, '=H'),
+    ('NumberOfRows', 4, '=L'),
+    ('RowEnable', 2, '=H'),
+    ('EnableStretch', 2, '=H'),
+    ('CompEnable', 2, '=H'),
+    ('CompStretch', 2, '=H'),
+    ('LeftEvenTristate', 2, '=H'),
+    ('RightOddTristate', 2, '=H'),
+    ('TestModeSelect', 4, '=L'),
+    ('AnalogTestSource', 4, '=L'),
+    ('VCommonSelect', 4, '=L'),
+    ('DRCColumnSum', 4, '=L'),
+    ('TestPatternFrameDelta', 4, '=L'),
+    ('TestPatternRowDelta', 4, '=L'),
+    ('TestPatternColumnDelta', 4, '=L'),
+    ('DetectorHorizontalFlip', 2, '=H'),
+    ('DetectorVerticalFlip', 2, '=H'),
+    ('DFNAutoScrubOnOff', 2, '=H'),
+    ('FiberChannelTimeOutInMicrosecs', 4, '=L'),
+    ('DFNAutoScrubDelayInMicrosecs', 4, '=L'),
+    ('StoreAECROI', 2, '=H'),
+    ('TestPatternSaturationValue', 2, '=H'),
+    ('TestPatternSeed', 4, '=L'),
+    ('ExposureTimeInMillisecs', 4, '=f'),
+    ('FrameRateInFps', 4, '=f'),
+    ('kVp', 4, '=f'),
+    ('mA', 4, '=f'),
+    ('mAs', 4, '=f'),
+    ('FocalSpotInMM', 4, '=f'),
+    ('GeneratorType', 20, None),
+    ('StrobeIntensityInFtL', 4, '=f'),
+    ('NDFilterSelection', 2, '=H'),
+    ('RefRegTemp1', 8, '=d'),
+    ('RefRegTemp2', 8, '=d'),
+    ('RefRegTemp3', 8, '=d'),
+    ('Humidity1', 4, '=f'),
+    ('Humidity2', 4, '=f'),
+    ('DetectorControlTemp', 8, '=d'),
+    ('DoseValueInmR', 8, '=d'),
+    ('TargetLevelROIRow0', 2, '=H'),
+    ('TargetLevelROICol0', 2, '=H'),
+    ('TargetLevelROIRow1', 2, '=H'),
+    ('TargetLevelROICol1', 2, '=H'),
+    ('FrameNumberForTargetLevelROI', 2, '=H'),
+    ('PercentRangeForTargetLevel', 2, '=H'),
+    ('TargetValue', 2, '=H'),
+    ('ComputedMedianValue', 2, '=H'),
+    ('LoadZero', 2, '=H'),
+    ('MaxLUTOut', 2, '=H'),
+    ('MinLUTOut', 2, '=H'),
+    ('MaxLinear', 2, '=H'),
+    ('Reserved', 2, '=H'),
+    ('ElectronsPerCount', 2, '=H'),
+    ('ModeGain', 2, '=H'),
+    ('TemperatureInDegC', 8, '=d'),
+    ('LineRepaired', 2, '=H'),
+    ('LineRepairFileName', 100, None),
+    ('CurrentLongitudinalInMM', 4, '=f'),
+    ('CurrentTransverseInMM', 4, '=f'),
+    ('CurrentCircularInMM', 4, '=f'),
+    ('CurrentFilterSelection', 4, '=L'),
+    ('DisableScrubAck', 2, '=H'),
+    ('ScanModeSelect', 2, '=H'),
+    ('DetectorAppSwVersion', 20, None),
+    ('DetectorNIOSVersion', 20, None),
+    ('DetectorPeripheralSetVersion', 20, None),
+    ('DetectorPhysicalAddress', 20, None),
+    ('PowerDown', 2, '=H'),
+    ('InitialVoltageLevel_VCOMMON', 8, '=d'),
+    ('FinalVoltageLevel_VCOMMON', 8, '=d'),
+    ('DmrCollimatorSpotSize', 10, None),
+    ('DmrTrack', 5, None),
+    ('DmrFilter', 5, None),
+    ('FilterCarousel', 2, '=H'),
+    ('Phantom', 20, None),
+    ('SetEnableHighTime', 2, '=H'),
+    ('SetEnableLowTime', 2, '=H'),
+    ('SetCompHighTime', 2, '=H'),
+    ('SetCompLowTime', 2, '=H'),
+    ('SetSyncLowTime', 2, '=H'),
+    ('SetConvertLowTime', 2, '=H'),
+    ('SetSyncHighTime', 2, '=H'),
+    ('SetEOLTime', 2, '=H'),
+    ('SetRampOffsetTime', 2, '=H'),
+    ('FOVStartingValue', 2, '=H'),
+    ('ColumnBinning', 2, '=H'),
+    ('RowBinning', 2, '=H'),
+    ('BorderColumns64', 2, '=H'),
+    ('BorderRows64', 2, '=H'),
+    ('FETOffRows64', 2, '=H'),
+    ('FOVStartColumn128', 2, '=H'),
+    ('FOVStartRow128', 2, '=H'),
+    ('NumberOfColumns128', 2, '=H'),
+    ('NumberOfRows128', 2, '=H'),
+    ('VFPAquisition', 2000, None),
+    ('Comment', 200, None)
+    ]
+
+
+class GEimage(fabioimage):
+
+    _need_a_seek_to_read = True
+
+    def _readheader(self, infile):
+        """ Read a GE image header """
+
+        infile.seek(0)
+
+        self.header = {}
+        for name, nbytes, format in GE_HEADER_INFO:
+            if format is None:
+                self.header[ name ] = infile.read(nbytes)
+            else:
+                self.header[ name ] = struct.unpack(format,
+                                                     infile.read(nbytes))[0]
+
+    def read(self, fname, frame=None):
+        """
+        Read in header into self.header and
+        the data   into self.data
+        """
+        if frame is None:
+            frame = 0
+        self.header = {}
+        self.resetvals()
+        infile = self._open(fname, "rb")
+        self.sequencefilename = fname
+        self._readheader(infile)
+        self.nframes = self.header['NumberOfFrames']
+        self._readframe(infile, frame)
+        infile.close()
+        return self
+
+    def _makeframename(self):
+        """ The thing to be printed for the user to represent a frame inside
+        a file """
+        self.filename = "%s$%04d" % (self.sequencefilename,
+                                   self.currentframe)
+
+    def _readframe(self, filepointer, img_num):
+        """
+        # Load only one image from the sequence
+        #    Note: the first image in the sequence 0
+        # raises an exception if you give an invalid image
+        # otherwise fills in self.data
+        """
+        if(img_num > self.nframes or img_num < 0):
+            raise Exception("Bad image number")
+        imgstart = self.header['StandardHeaderSizeInBytes'] + \
+                   self.header['UserHeaderSizeInBytes'] + \
+                   img_num * self.header['NumberOfRowsInFrame'] * \
+                   self.header['NumberOfColsInFrame'] * \
+                   self.header['ImageDepthInBits'] / 8
+        # whence = 0 means seek from start of file
+        filepointer.seek(imgstart, 0)
+
+        self.bpp = self.header['ImageDepthInBits'] / 8 # hopefully 2        
+        imglength = self.header['NumberOfRowsInFrame'] * \
+                    self.header['NumberOfColsInFrame'] * self.bpp
+        if self.bpp != 2:
+            logging.warning("Using uint16 for GE but seems to be wrong")
+
+        # Guessing it is always unsigned int?
+        self.data = numpy.fromstring(filepointer.read(imglength), numpy.uint16)
+        self.data.shape = (self.header['NumberOfRowsInFrame'],
+                            self.header['NumberOfColsInFrame'])
+        self.dim2 , self.dim1 = self.data.shape
+        self.currentframe = int(img_num)
+        self._makeframename()
+
+
+    def write(self, fname, force_type=numpy.uint16):
+        """ Not yet implemented"""
+        raise Exception("Write is not implemented")
+
+    def getframe(self, num):
+        """
+        Returns a frame as a new fabioimage object
+        """
+        if num < 0 or num > self.nframes:
+            raise Exception("Requested frame number is out of range")
+        # Do a deep copy of the header to make a new one
+        newheader = {}
+        for k in self.header.keys():
+            newheader[k] = self.header[k]
+        frame = GEimage(header=newheader)
+        frame.nframes = self.nframes
+        frame.sequencefilename = self.sequencefilename
+        infile = frame._open(self.sequencefilename, "rb")
+        frame._readframe(infile, num)
+        infile.close()
+        return frame
+
+    def next(self):
+        """
+        Get the next image in a series as a fabio image
+        """
+        if self.currentframe < (self.nframes - 1) and self.nframes > 1:
+            return self.getframe(self.currentframe + 1)
+        else:
+            newobj = GEimage()
+            newobj.read(next_filename(
+                self.sequencefilename))
+            return newobj
+
+    def previous(self):
+        """
+        Get the previous image in a series as a fabio image
+        """
+        if self.currentframe > 0:
+            return self.getframe(self.currentframe - 1)
+        else:
+            newobj = GEimage()
+            newobj.read(previous_filename(
+                self.sequencefilename))
+            return newobj
+
+
+def demo():
+    import sys, time
+
+    if len(sys.argv) < 2:
+        print "USAGE: GE_script.py <GEaSi_raw_image_file>"
+        sys.exit()
+
+    image_file = sys.argv[1]
+
+    print "init read_GEaSi_data class and load header.."
+    sequence1 = GEimage()
+    sequence1.read(image_file)
+
+    print "TimeBetweenFramesInMicrosecs = ",
+    print sequence1.header['TimeBetweenFramesInMicrosecs']
+    print "AcquisitionTime = ",
+    print sequence1.header['AcquisitionTime']
+
+
+    print "Mean = ", sequence1.data.ravel().mean()
+
+    while 1:
+        start = time.time()
+        try:
+            sequence1 = sequence1.next()
+            print sequence1.currentframe, sequence1.data.ravel().mean(), \
+                  time.time() - start
+        except Exception, ex:
+            raise ex
+
+
+
+
+if __name__ == '__main__':
+    demo()