/usr/share/pyshared/fabio/GEimage.py is in python-fabio 0.1.4-1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 | #!/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
#
# Get ready for python3:
from __future__ import with_statement, print_function
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 as ex:
raise ex
if __name__ == '__main__':
demo()
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