def processFile(f, tests, keepGoing, resultMap):
retVal = 0
try:
logging.info('File: {:s} size: {:d}'.format(f, os.path.getsize(f)))
myFi = File.FileRead(f, theFileId=f, keepGoing=keepGoing)
#a = r'W:\LISTestData\logPassStd256MB.lis'
#myFi = File.FileRead(a, theFileId=a)
clkStart = time.clock()
myIdx = FileIndexer.FileIndex(myFi)
#print(myIdx.longDesc())
print('Index time: {:.3f}'.format(time.clock() - clkStart))
except Exception as err:
logging.error(str(err))
traceback.print_exc()
else:
#print('resultMap', resultMap)
#print('tests', tests)
for t in tests:
#print('t', t)
resultMap[t][f] = []
for aLpi in myIdx.genLogPasses():
for t in tests:
try:
myR = TEST_TYPE[t][0](myFi, aLpi.logPass)
except Exception as err:
logging.error(str(err))
traceback.print_exc()
else:
retVal = 1
if myR is not None:
resultMap[t][f].append(myR)
return retVal
def test_02(self):
"""TestIndexEflrHeadTail.test_02(): Reel head and tail."""
myFile = self._retFileFromBytes(self._retReelHead()+self._retReelTail())
myIdx = FileIndexer.FileIndex(myFile)
#print()
#print(myIdx._idx)
self.assertEqual(2, len(myIdx))
self.assertEqual([132, 133], myIdx.lrTypeS)
def test_01(self):
"""TestIndexEflrHeadTail.test_01(): Tape head and tail."""
myFile = self._retFileFromBytes(self._retTapeHead()+self._retTapeTail())
myIdx = FileIndexer.FileIndex(myFile)
#print()
#print(myIdx._idx)
self.assertEqual(2, len(myIdx))
self.assertEqual([130, 131], myIdx.lrTypeS)
def _retLisFileAndIndex(self, fpIn):
"""Returns a LisFile.LisFile() and a FileIndexer.FileIndex() from fpIn.
May raises an ExceptionTotalDepthLIS."""
assert (os.path.isfile(fpIn))
logging.info(
'ProcLISPathBase._retLisFileAndIndex(): Reading LIS file {:s}'.
format(fpIn))
myFi = File.FileRead(fpIn, theFileId=fpIn, keepGoing=self._keepGoing)
myIdx = FileIndexer.FileIndex(myFi)
return myFi, myIdx
def test_00(self):
"""TestIndexMarker.test_00(): All marker records."""
myFile = self._retFileFromBytes(
self._retSinglePr(b'\x89\x00') + self._retSinglePr(b'\x8A\x00') +
self._retSinglePr(b'\x8B\x00') + self._retSinglePr(b'\x8D\x00'))
myIdx = FileIndexer.FileIndex(myFile)
#print()
#print(myIdx._idx)
self.assertEqual(4, len(myIdx))
#print(myIdx.lrTypeS)
self.assertEqual([137, 138, 139, 141], myIdx.lrTypeS)
def dumpFrameSets(fp, keepGoing, summaryOnly):
logging.info('Index.indexFile(): {:s}'.format(fp))
assert(os.path.isfile(fp))
myFi = File.FileRead(fp, theFileId=fp, keepGoing=keepGoing)
myIdx = FileIndexer.FileIndex(myFi)
for aLp in myIdx.genLogPasses():
print(aLp)
# Load the FrameSet
if aLp.logPass.totalFrames == 0:
print('No frames to load.')
else:
aLp.logPass.setFrameSet(myFi, None, None)
myFrSet = aLp.logPass.frameSet
if not summaryOnly:
# Print the channels and units
hdrS = []
if myFrSet.isIndirectX:
hdrS.append('XAXIS [{:s}]'.format(myFrSet.xAxisDecl.depthUnits))
hdrS.extend(['{:s} [{:s}]'.format(m, u) for m,u in aLp.logPass.genFrameSetHeadings()])
#print('TRACE: len(hdrS)', len(hdrS))
print('\t'.join(hdrS))
for frIdx in range(myFrSet.numFrames):
#print('TRACE: len(frame)', len(myFrSet.frame(frIdx)))
if myFrSet.isIndirectX:
print(myFrSet.xAxisValue(frIdx), '\t', end='')
print('\t'.join(['%g' % v for v in myFrSet.frame(frIdx)]))
# Accumulate min/mean/max
myAccClasses = [
FrameSet.AccCount,
FrameSet.AccMin,
FrameSet.AccMean,
FrameSet.AccMax,
FrameSet.AccStDev,
FrameSet.AccDec,
FrameSet.AccEq,
FrameSet.AccInc,
FrameSet.AccBias,
FrameSet.AccDrift,
FrameSet.AccActivity,
]
myAcc = myFrSet.accumulate(myAccClasses)
print()
fmtStr = '{:12s} ' + (' {:>12s}'*len(myAccClasses))
print(fmtStr.format(
'Sc Name', 'Count', 'Min', 'Mean', 'Max', 'Std Dev.', '--', '==', '++', 'Bias', 'Drift', 'Activity',
)
)
schNameS = list(aLp.logPass.genFrameSetScNameUnit())
# print(schNameS)
for scIdx, aRow in enumerate(myAcc):
print('{:4s} [{:4s}]'.format(*schNameS[scIdx]),
' ',
' '.join(['{:12.5g}'.format(v) for v in aRow]))
def _retFileIndexSingleChannel(self):
myBa = bytearray(self._retFileHead())
# Add a log pass
myLp = self._retLogPassGen()
# Stick the DFSR on the array
myBa += self.retPrS(myLp.lrBytesDFSR())
# Add some logical records
for i in range(4):
myBa += self.retPrS(myLp.lrBytes(i * 100, 100))
myBa += self._retFileTail()
myFile = self._retFileFromBytes(myBa)
myIdx = FileIndexer.FileIndex(myFile)
return myFile, myIdx
def test_00(self):
"""TestIndexUnknownIntFormat.test_00(): Logical Records of unknown internal format, random lengths."""
#print()
#print(LogiRec.LR_TYPE_UNKNOWN_INTERNAL_FORMAT)
myB = b''
for aType in LogiRec.LR_TYPE_UNKNOWN_INTERNAL_FORMAT:
myB += self._retSinglePr(self._retLrRandom(aType))
myFile = self._retFileFromBytes(myB)
myIdx = FileIndexer.FileIndex(myFile)
#print(myIdx._idx)
self.assertEqual(len(LogiRec.LR_TYPE_UNKNOWN_INTERNAL_FORMAT), len(myIdx))
#print(myIdx.lrTypeS)
self.assertEqual(list(LogiRec.LR_TYPE_UNKNOWN_INTERNAL_FORMAT), myIdx.lrTypeS)
def _processFile(fp, keepGoing, tabMtch, theCntr):
assert (os.path.isfile(fp))
logging.info('PlotLogPasses._processFile(): {:s}'.format(fp))
assert (os.path.isfile(fp))
try:
myFi = File.FileRead(fp, theFileId=fp, keepGoing=keepGoing)
myIdx = FileIndexer.FileIndex(myFi)
except ExceptionTotalDepthLIS as err:
logging.error('Can not read LIS file {:s} with error: {:s}'.format(
fp, err))
else:
# print(' Index longDesc() '.center(75, '='))
# print(myIdx.longDesc())
# print(' Index longDesc() DONE '.center(75, '='))
# Iterate through the FileIndexer object
retVal = False
for anIo in myIdx.genAll():
# print('anIdxObj:', anIo)
if anIo.lrType in LogiRec.LR_TYPE_TABLE_DATA \
and tabMtch.lrTypeMatch(anIo.lrType) \
and tabMtch.nameTableMatch(anIo.name):
# Read the whole table logical record
myFi.seekLr(anIo.tell)
try:
myLrTable = LogiRec.LrTableRead(myFi)
except Exception as err:
logging.error(
'Can not create Logical Record, error: {:s}'.format(
err))
else:
# print('myLrTable', myLrTable)
for aRow in myLrTable.genRows():
theCntr.incRow(anIo.lrType, anIo.name, aRow.value)
if tabMtch.nameRowMatch(aRow.value):
for aCell in aRow.genCells():
theCntr.incCol(anIo.lrType, anIo.name,
aCell.mnem)
if tabMtch.nameColMatch(aCell.mnem):
theCntr.incAll(
tabMtch,
anIo.lrType,
anIo.name,
aRow.value,
aCell.mnem,
aCell.engVal.value,
)
# if aCell.mnem == b'TYPE' and aCell.engVal.value == b'CONS':
# retVal = True
return retVal
def test_03(self):
"""TestIndexEflrHeadTail.test_03(): Reel/Tape/File head and tail."""
myFile = self._retFileFromBytes(self._retReelHead() +
self._retTapeHead() +
self._retFileHead() +
self._retFileTail() +
self._retTapeTail() +
self._retReelTail())
myIdx = FileIndexer.FileIndex(myFile)
#print()
#print(myIdx._idx)
self.assertEqual(6, len(myIdx))
#print(myIdx.lrTypeS)
self.assertEqual([132, 130, 128, 129, 131, 133], myIdx.lrTypeS)
def dumpFrameSets(fp, keepGoing, summaryOnly, channels):
"""Dump the frame values to stdout.
keepGoing is a bool.
SummaryOnly is a bool to emit a summary only, if false all the data and the summary is written out.
Channels is a set of Mnems, if non-empty then only these channels, if present, are written out."""
logging.info('Index.indexFile(): {:s}'.format(fp))
assert (os.path.isfile(fp))
myFi = File.FileRead(fp, theFileId=fp, keepGoing=keepGoing)
myIdx = FileIndexer.FileIndex(myFi)
for aLp in myIdx.genLogPasses():
print(aLp)
# Load the FrameSet
if aLp.logPass.totalFrames == 0:
print('No frames to load.')
else:
aLp.logPass.setFrameSet(myFi, None, None)
myFrSet = aLp.logPass.frameSet
if not summaryOnly:
# Print the channels and units
hdrS = []
if myFrSet.isIndirectX:
hdrS.append('XAXIS [{!r:s}]'.format(
myFrSet.xAxisDecl.depthUnits))
indexes = []
if len(channels):
for i, (m,
u) in enumerate(aLp.logPass.genFrameSetHeadings()):
if m in channels:
hdrS.append('{!r:s} [{!r:s}]'.format(m, u))
indexes.append(i)
else:
hdrS.extend([
'{!r:s} [{!r:s}]'.format(m, u)
for m, u in aLp.logPass.genFrameSetHeadings()
])
if len(indexes) == len(channels):
logging.warning(
'Some channels you specified can not be found: indexes={!r:s} channels={!r:s}'
.format(indexes, channels))
#print('TRACE: len(hdrS)', len(hdrS))
print('\t'.join(hdrS))
for frIdx in range(myFrSet.numFrames):
#print('TRACE: len(frame)', len(myFrSet.frame(frIdx)))
if myFrSet.isIndirectX:
print(myFrSet.xAxisValue(frIdx), '\t', end='')
if len(indexes):
values = [myFrSet.frame(frIdx)[i] for i in indexes]
print('\t'.join(['%g' % v for v in values]))
else:
print('\t'.join(
['%g' % v for v in myFrSet.frame(frIdx)]))
# Accumulate min/mean/max
myAccClasses = [
FrameSet.AccCount,
FrameSet.AccMin,
FrameSet.AccMean,
FrameSet.AccMax,
FrameSet.AccStDev,
FrameSet.AccDec,
FrameSet.AccEq,
FrameSet.AccInc,
FrameSet.AccBias,
FrameSet.AccDrift,
FrameSet.AccActivity,
]
myAcc = myFrSet.accumulate(myAccClasses)
print()
fmtStr = '{:12s} ' + (' {:>12s}' * len(myAccClasses))
print(
fmtStr.format(
'Sc Name',
'Count',
'Min',
'Mean',
'Max',
'Std Dev.',
'--',
'==',
'++',
'Bias',
'Drift',
'Activity',
))
schNameS = list(aLp.logPass.genFrameSetScNameUnit())
# print(schNameS)
for scIdx, aRow in enumerate(myAcc):
print('{:4s} [{:4s}]'.format(*schNameS[scIdx]), ' ',
' '.join(['{:12.5g}'.format(v) for v in aRow]))
def _processFile(self, fpIn, fpOut):
assert (os.path.isfile(fpIn))
assert (os.path.exists(os.path.dirname(fpOut)))
logging.info(
'PlotLogPasses._processFile(): Starting on {:s}'.format(fpIn))
# Read LIS file and create index
myFi = File.FileRead(fpIn, theFileId=fpIn, keepGoing=self._keepGoing)
try:
myIdx = FileIndexer.FileIndex(myFi)
except ExceptionTotalDepthLIS as err:
logging.error(
'Can not create index: for "{:s}", error: {:s}'.format(
fpIn, err))
return
# Iterate through the PlotRecordSet objects
for lpIdx, aPrs in enumerate(myIdx.genPlotRecords()):
if len(self._lgFormatS) == 0:
# Use internal FILM/PRES plotting specification
self._plotUsingLISLogicalRecords(myFi, lpIdx, aPrs, fpOut)
else:
self._plotUsingLgFormats(myFi, lpIdx, aPrs, fpOut)
# myPlot, myLogPass, myCONSRecS = self._retPlotFromPlotRecordSet(myFi, aPrs)
# for aFilmId in myPlot.filmIdS():
# logging.info('PlotLogPasses._processFile(): FILM ID={:s}.'.format(aFilmId.pStr(strip=True)))
# if myPlot.hasDataToPlotLIS(myLogPass, aFilmId):
# myOutFilePath = '{:s}_{:04d}_{:s}.svg'.format(fpOut, lpIdx, aFilmId.pStr(strip=True))
# myFout = open(myOutFilePath, 'w')
# myCurvIDs, numPoints = myPlot.plotLogPassLIS(myFi,
# myLogPass,
# myLogPass.xAxisFirstEngVal,
# myLogPass.xAxisLastEngVal,
# aFilmId,
# myFout,
# frameStep=1,
# title="Plot: {:s} LogPass: {:d} FILM ID={:s}".format(
# os.path.abspath(myOutFilePath),
# lpIdx,
# aFilmId.pStr(strip=True),
# ),
# lrCONS=myCONSRecS,
# )
# assert(myCurvIDs is not None and numPoints is not None)
# # So here the essential data that we have to put in the index.html is:
# # Key: myOutFilePath or input file fp, lpIdx, aFilmId,
# # Value: (myPlot.xScale(aFilmId), myLogPass.xAxisFirstEngVal, myLogPass.xAxisLastEngVal, myCurvIDs)
# self.plotLogInfo.addPlotResult(
# fpIn,
# myOutFilePath,
# lpIdx,
# aFilmId.pStr(),
# myPlot.xScale(aFilmId),
# myLogPass.xAxisFirstEngVal,
# myLogPass.xAxisLastEngVal,
# theCurveS=myCurvIDs,
# ptsPlotted=numPoints)
# else:
# logging.info('PlotLogPasses._processFile(): No data to plot for FILM ID {:s}'.format(aFilmId))
# Count the number of LogPasses, files etc.
self.plotLogInfo.logPassCntr += myIdx.numLogPasses()
self.plotLogInfo.lisFileCntr += 1
logging.info(
'PlotLogPasses._processFile(): Done with {:s}'.format(fpIn))
def test_00(self):
"""TestFileIndexer.test_00(): Empty file."""
myF = self._retFileFromBytes(b'')
myIdx = FileIndexer.FileIndex(myF)
def indexFile(fp, numTimes, verbose, keepGoing, convertJson):
logging.info('Index.indexFile(): {:s}'.format(fp))
assert(os.path.isfile(fp))
retIt = IndexTimer()
try:
myLenPickle = -1
myLenJson = -1
timeS = []
for t in range(numTimes):
clkStart = time.clock()
myFi = File.FileRead(fp, theFileId=fp, keepGoing=keepGoing)
try:
myIdx = FileIndexer.FileIndex(myFi)
except ExceptionTotalDepthLIS as err:
logging.error('{:s}'.format(str(err)))
continue
timeS.append(time.clock() - clkStart)
if verbose:
print(myIdx.longDesc())
print(' All records '.center(75, '='))
for aLr in myIdx.genAll():
print(str(aLr))
print(' All records DONE '.center(75, '='))
print(' Log Passes '.center(75, '='))
for aLp in myIdx.genLogPasses():
print('LogPass', aLp.logPass.longStr())
print()
print(' Log Passes DONE '.center(75, '='))
print(' Plot Records '.center(75, '='))
for aPlotRec in myIdx.genPlotRecords():
print('Plot Record:', aPlotRec)
print()
print(' Plot Records DONE '.center(75, '='))
#print('CPU time = %8.3f (S)' % timeS[-1])
if t == 0:
pikBy = pickle.dumps(myIdx)
#print('Pickled: file={:10d} size={:10d} {:8.3f}%'.format(
# os.path.getsize(fp),
# len(pikBy),
# len(pikBy)*100/os.path.getsize(fp)
# )
#)
myLenPickle = len(pikBy)
#print('{:d}\t{:d}\t{:.3f} #Pickled'.format(os.path.getsize(fp), len(pikBy), len(pikBy)*100/os.path.getsize(fp)))
if convertJson:
jsonObj = myIdx.jsonObject()
# pprint.pprint(jsonObj)
jsonBytes = json.dumps(jsonObj, sort_keys=True, indent=4)
myLenJson = len(jsonBytes)
if verbose:
print(' JSON [{:d}] '.format(myLenJson).center(75, '='))
print(jsonBytes)
print(' JSON DONE '.center(75, '='))
if len(timeS) > 0:
refTime = sum(timeS)/len(timeS)
if verbose:
print(' Min: {:.3f} (s)'.format(min(timeS)))
print(' Max: {:.3f} (s)'.format(max(timeS)))
print(' Mean: {:.3f} (s)'.format(refTime))
if len(timeS) > 2:
timeS = sorted(timeS)
#print(timeS)
refTime = timeS[((len(timeS)+1)//2)-1]
if verbose:
print('Median: {:.3f} (s)'.format(refTime))
#print(os.path.getsize(fp), refTime)
mySiz = os.path.getsize(fp)
sizemb = mySiz / 2**20
rate = refTime * 1000 / sizemb
print('File size: {:d} ({:.3f} MB) Reference Time: {:.6f} (s), rate {:.3f} ms/MB file: {:s} pickleLen={:d} jsonLen={:d}'.format(
mySiz,
sizemb,
refTime,
rate,
fp,
myLenPickle,
myLenJson,
)
)
retIt.addSizeTime(mySiz, refTime)
except ExceptionTotalDepthLIS as err:
retIt.addErr()
traceback.print_exc()
return retIt