def pairLidarFiles(lidarFolder, skipValidate, logger):
'''For each pair of lidar files generate a double size point cloud.
We can use these later since they do not have any gaps between adjacent files.'''
logger.info('Generating lidar pairs...')
# Create the output folder
pairedFolder = icebridge_common.getPairedLidarFolder(lidarFolder)
os.system('mkdir -p ' + pairedFolder)
convLidarFile = icebridge_common.getConvertedLidarIndexFile(lidarFolder)
if not os.path.exists(convLidarFile):
raise Exception("Missing file: " + convLidarFile)
(lidarDict, dummyUrlDict) = icebridge_common.readIndexFile(convLidarFile)
lidarExt = ''
for frame in lidarDict:
lidarExt = icebridge_common.fileExtension(lidarDict[frame])
numLidarFiles = len(lidarDict.keys())
pairedDict = {}
# Loop through all pairs of csv files in the folder
badFiles = False
lidarKeys = sorted(lidarDict.keys())
for i in range(len(lidarKeys) - 1):
thisFile = lidarDict[lidarKeys[i]]
nextFile = lidarDict[lidarKeys[i + 1]]
date2, time2 = icebridge_common.parseTimeStamps(nextFile)
# Record the name with the second file
# - More useful because the time for the second file represents the middle of the file.
outputName = icebridge_common.lidar_pair_prefix(
) + date2 + '_' + time2 + lidarExt
pairedDict[lidarKeys[i]] = outputName
# Handle paths
path1 = os.path.join(lidarFolder, thisFile)
path2 = os.path.join(lidarFolder, nextFile)
outputPath = os.path.join(pairedFolder, outputName)
if not os.path.exists(path1) or not os.path.exists(path2):
logger.info("Cannot create " + outputPath +
" as we are missing its inputs")
# If the inputs are missing, but the output is there, most likely it is corrupt.
# Wipe it. Hopefully a subsequent fetch and convert step will bring it back.
if os.path.exists(outputPath):
logger.info("Wiping: " + outputPath)
os.system('rm -f ' + outputPath) # will not throw
badFiles = True
continue
# Skip existing valid files
if skipValidate:
if os.path.exists(outputPath):
logger.info("File exists, skipping: " + outputPath)
continue
else:
if icebridge_common.isValidLidarCSV(outputPath):
#logger.info("File exists and is valid, skipping: " + outputPath)
continue
# Concatenate the two files
cmd1 = 'cat ' + path1 + ' > ' + outputPath
cmd2 = 'tail -n +2 -q ' + path2 + ' >> ' + outputPath
logger.info(cmd1)
p = subprocess.Popen(cmd1, stdout=subprocess.PIPE, shell=True)
out, err = p.communicate()
logger.info(cmd2)
p = subprocess.Popen(cmd2, stdout=subprocess.PIPE, shell=True)
out, err = p.communicate()
if not icebridge_common.isValidLidarCSV(outputPath):
logger.error('Failed to generate merged LIDAR file, will wipe: ' +
outputPath)
os.system('rm -f ' + outputPath) # will not throw
badFiles = True
pairedLidarFile = icebridge_common.getPairedIndexFile(pairedFolder)
willWritePairedFile = False
if not os.path.exists(pairedLidarFile):
willWritePairedFile = True
else:
# Bugfix: Sometimes the written converted file has the wrong size, maybe
# something got interrupted earlier.
(lidarDictIn,
dummyUrlDict) = icebridge_common.readIndexFile(pairedLidarFile)
if lidarDictIn != pairedDict:
willWritePairedFile = True
if willWritePairedFile:
logger.info("Writing: " + pairedLidarFile)
icebridge_common.writeIndexFile(pairedLidarFile, pairedDict, {})
return (not badFiles)
def pairLidarFiles(lidarFolder, skipValidate, logger):
'''For each pair of lidar files generate a double size point cloud.
We can use these later since they do not have any gaps between adjacent files.'''
logger.info('Generating lidar pairs...')
# Create the output folder
pairedFolder = icebridge_common.getPairedLidarFolder(lidarFolder)
os.system('mkdir -p ' + pairedFolder)
convLidarFile = icebridge_common.getConvertedLidarIndexFile(lidarFolder)
if not os.path.exists(convLidarFile):
raise Exception("Missing file: " + convLidarFile)
(lidarDict, dummyUrlDict) = icebridge_common.readIndexFile(convLidarFile)
lidarExt = ''
for frame in lidarDict:
lidarExt = icebridge_common.fileExtension(lidarDict[frame])
numLidarFiles = len(lidarDict.keys())
pairedDict = {}
# Loop through all pairs of csv files in the folder
badFiles = False
lidarKeys = sorted(lidarDict.keys())
for i in range(len(lidarKeys)-1):
thisFile = lidarDict[lidarKeys[i ]]
nextFile = lidarDict[lidarKeys[i+1]]
date2, time2 = icebridge_common.parseTimeStamps(nextFile)
# Record the name with the second file
# - More useful because the time for the second file represents the middle of the file.
outputName = icebridge_common.lidar_pair_prefix() + date2 +'_'+ time2 + lidarExt
pairedDict[lidarKeys[i]] = outputName
# Handle paths
path1 = os.path.join(lidarFolder, thisFile)
path2 = os.path.join(lidarFolder, nextFile)
outputPath = os.path.join(pairedFolder, outputName)
if not os.path.exists(path1) or not os.path.exists(path2):
logger.info("Cannot create " + outputPath + " as we are missing its inputs")
# If the inputs are missing, but the output is there, most likely it is corrupt.
# Wipe it. Hopefully a subsequent fetch and convert step will bring it back.
if os.path.exists(outputPath):
logger.info("Wiping: " + outputPath)
os.system('rm -f ' + outputPath) # will not throw
badFiles = True
continue
# Skip existing valid files
if skipValidate:
if os.path.exists(outputPath):
logger.info("File exists, skipping: " + outputPath)
continue
else:
if icebridge_common.isValidLidarCSV(outputPath):
#logger.info("File exists and is valid, skipping: " + outputPath)
continue
# Concatenate the two files
cmd1 = 'cat ' + path1 + ' > ' + outputPath
cmd2 = 'tail -n +2 -q ' + path2 + ' >> ' + outputPath
logger.info(cmd1)
p = subprocess.Popen(cmd1, stdout=subprocess.PIPE, shell=True,
universal_newlines=True)
out, err = p.communicate()
logger.info(cmd2)
p = subprocess.Popen(cmd2, stdout=subprocess.PIPE, shell=True,
universal_newlines=True)
out, err = p.communicate()
if not icebridge_common.isValidLidarCSV(outputPath):
logger.error('Failed to generate merged LIDAR file, will wipe: ' + outputPath)
os.system('rm -f ' + outputPath) # will not throw
badFiles = True
pairedLidarFile = icebridge_common.getPairedIndexFile(pairedFolder)
willWritePairedFile = False
if not os.path.exists(pairedLidarFile):
willWritePairedFile = True
else:
# Bugfix: Sometimes the written converted file has the wrong size, maybe
# something got interrupted earlier.
(lidarDictIn, dummyUrlDict) = icebridge_common.readIndexFile(pairedLidarFile)
if lidarDictIn != pairedDict:
willWritePairedFile = True
if willWritePairedFile:
logger.info("Writing: " + pairedLidarFile)
icebridge_common.writeIndexFile(pairedLidarFile, pairedDict, {})
return (not badFiles)
def convertLidarDataToCsv(lidarFolder, startFrame, stopFrame, skipValidate,
logger):
'''Make sure all lidar data is available in a readable text format.
Returns false if any files failed to convert.'''
logger.info('Converting LIDAR files...')
lidarIndexPath = icebridge_common.csvIndexFile(lidarFolder)
(frameDict, urlDict) = icebridge_common.readIndexFile(lidarIndexPath)
if not skipValidate:
validFilesList = icebridge_common.validFilesList(
os.path.dirname(lidarFolder), startFrame, stopFrame)
validFilesSet = set()
validFilesSet = icebridge_common.updateValidFilesListFromDisk(
validFilesList, validFilesSet)
numInitialValidFiles = len(validFilesSet)
convDict = {}
# Loop through all files in the folder
badFiles = False
for frame in sorted(frameDict.keys()):
f = frameDict[frame]
extension = icebridge_common.fileExtension(f)
# Only interested in a few file types
if (extension != '.qi') and (extension != '.hdf5') and (extension !=
'.h5'):
convDict[frame] = f # these are already in plain text
continue
convDict[frame] = os.path.splitext(f)[0] + '.csv'
outputPath = os.path.join(lidarFolder, convDict[frame])
# Handle paths
fullPath = os.path.join(lidarFolder, f)
if not os.path.exists(fullPath):
logger.info("Cannot convert missing file: " + fullPath)
continue
# If the input is invalid, wipe both it, its xml, and the output
# Hopefully there will be a subsquent fetch step where it will get
# refetched.
if not icebridge_common.hasValidChkSum(fullPath, logger):
logger.info("Will wipe invalid file: " + fullPath)
xmlFile = icebridge_common.xmlFile(fullPath)
os.system('rm -f ' + fullPath) # will not throw
os.system('rm -f ' + xmlFile) # will not throw
os.system('rm -f ' + outputPath) # will not throw
badFiles = True
continue
# Skip existing valid files
if skipValidate:
if os.path.exists(outputPath):
logger.info("File exists, skipping: " + outputPath)
continue
else:
if outputPath in validFilesSet and os.path.exists(outputPath):
#logger.info('Previously validated: ' + outputPath) # verbose
continue
if icebridge_common.isValidLidarCSV(outputPath):
#logger.info("File exists and is valid, skipping: " + outputPath)
continue
# Call the conversion
logger.info("Process " + fullPath)
extract_icebridge_ATM_points.main([fullPath])
# Check the result
if not icebridge_common.isValidLidarCSV(outputPath):
logger.error('Failed to parse LIDAR file, will wipe: ' +
outputPath)
os.system('rm -f ' + outputPath) # will not throw
badFiles = True
else:
if not skipValidate:
validFilesSet.add(outputPath) # mark it as validated
convLidarFile = icebridge_common.getConvertedLidarIndexFile(lidarFolder)
willWriteConvFile = False
if not os.path.exists(convLidarFile):
willWriteConvFile = True
else:
# Bugfix: Sometimes the written converted file has the wrong size, maybe
# something got interrupted earlier.
(lidarDictIn,
dummyUrlDict) = icebridge_common.readIndexFile(convLidarFile)
if lidarDictIn != convDict:
willWriteConvFile = True
if willWriteConvFile:
logger.info("Writing: " + convLidarFile)
icebridge_common.writeIndexFile(convLidarFile, convDict, {})
if not skipValidate:
# Write to disk the list of validated files, but only if new
# validations happened. First re-read that list, in case a
# different process modified it in the meantime, such as if two
# managers are running at the same time.
numFinalValidFiles = len(validFilesSet)
if numInitialValidFiles != numFinalValidFiles:
validFilesSet = icebridge_common.updateValidFilesListFromDisk(
validFilesList, validFilesSet)
icebridge_common.writeValidFilesList(validFilesList, validFilesSet)
return (not badFiles)
def convertLidarDataToCsv(lidarFolder, startFrame, stopFrame,
skipValidate, logger):
'''Make sure all lidar data is available in a readable text format.
Returns false if any files failed to convert.'''
logger.info('Converting LIDAR files...')
lidarIndexPath = icebridge_common.csvIndexFile(lidarFolder)
(frameDict, urlDict) = icebridge_common.readIndexFile(lidarIndexPath)
if not skipValidate:
validFilesList = icebridge_common.validFilesList(os.path.dirname(lidarFolder),
startFrame, stopFrame)
validFilesSet = set()
validFilesSet = icebridge_common.updateValidFilesListFromDisk(validFilesList, validFilesSet)
numInitialValidFiles = len(validFilesSet)
convDict = {}
# Loop through all files in the folder
badFiles = False
for frame in sorted(frameDict.keys()):
f = frameDict[frame]
extension = icebridge_common.fileExtension(f)
# Only interested in a few file types
if (extension != '.qi') and (extension != '.hdf5') and (extension != '.h5'):
convDict[frame] = f # these are already in plain text
continue
convDict[frame] = os.path.splitext(f)[0] + '.csv'
outputPath = os.path.join(lidarFolder, convDict[frame])
# Handle paths
fullPath = os.path.join(lidarFolder, f)
if not os.path.exists(fullPath):
logger.info("Cannot convert missing file: " + fullPath)
continue
# If the input is invalid, wipe both it, its xml, and the output
# Hopefully there will be a subsquent fetch step where it will get
# refetched.
if not icebridge_common.hasValidChkSum(fullPath, logger):
logger.info("Will wipe invalid file: " + fullPath)
xmlFile = icebridge_common.xmlFile(fullPath)
os.system('rm -f ' + fullPath) # will not throw
os.system('rm -f ' + xmlFile) # will not throw
os.system('rm -f ' + outputPath) # will not throw
badFiles = True
continue
# Skip existing valid files
if skipValidate:
if os.path.exists(outputPath):
logger.info("File exists, skipping: " + outputPath)
continue
else:
if outputPath in validFilesSet and os.path.exists(outputPath):
#logger.info('Previously validated: ' + outputPath) # verbose
continue
if icebridge_common.isValidLidarCSV(outputPath):
#logger.info("File exists and is valid, skipping: " + outputPath)
continue
# Call the conversion
logger.info("Process " + fullPath)
extract_icebridge_ATM_points.main([fullPath])
# Check the result
if not icebridge_common.isValidLidarCSV(outputPath):
logger.error('Failed to parse LIDAR file, will wipe: ' + outputPath)
os.system('rm -f ' + outputPath) # will not throw
badFiles = True
else:
if not skipValidate:
validFilesSet.add(outputPath) # mark it as validated
convLidarFile = icebridge_common.getConvertedLidarIndexFile(lidarFolder)
willWriteConvFile = False
if not os.path.exists(convLidarFile):
willWriteConvFile = True
else:
# Bugfix: Sometimes the written converted file has the wrong size, maybe
# something got interrupted earlier.
(lidarDictIn, dummyUrlDict) = icebridge_common.readIndexFile(convLidarFile)
if lidarDictIn != convDict:
willWriteConvFile = True
if willWriteConvFile:
logger.info("Writing: " + convLidarFile)
icebridge_common.writeIndexFile(convLidarFile, convDict, {})
if not skipValidate:
# Write to disk the list of validated files, but only if new
# validations happened. First re-read that list, in case a
# different process modified it in the meantime, such as if two
# managers are running at the same time.
numFinalValidFiles = len(validFilesSet)
if numInitialValidFiles != numFinalValidFiles:
validFilesSet = icebridge_common.updateValidFilesListFromDisk(validFilesList,
validFilesSet)
icebridge_common.writeValidFilesList(validFilesList, validFilesSet)
return (not badFiles)