def testValidUnsuccessfulCommand(self):
scmd = SystemCommand('ls abc.txt')
self.assertEqual(scmd.msg,
b"ls: cannot access 'abc.txt': No such file or directory\n")
scmd = SystemCommand('gdalinfo abc.txt', logging.getLogger())
self.assertTrue(b'ERROR 4: abc.txt: No such file or' in scmd.msg)
with self.assertRaisesRegex(RuntimeError, 'A system command error'):
scmd = SystemCommand('gdalinfo abc.txt',
logging.getLogger(),
True)
def getBand(self, outputDir, bandName):
gdalBandIndex = int(self.bandNameList.index(bandName)) + 1
baseName = os.path.basename(self.fileName().replace(
self.extension, '_b{}.tif'.format(gdalBandIndex)))
tempBandFile = os.path.join(outputDir, baseName)
if not os.path.exists(tempBandFile):
cmd = 'gdal_translate' + \
' -b {}'.format(gdalBandIndex) + \
' -a_nodata 0' + \
' -strict' + \
' -mo "bandName={}"'.format(bandName) + \
' ' + self.fileName() + \
' ' + tempBandFile
sCmd = SystemCommand(cmd, self.logger)
if sCmd.returnCode:
tempBandFile = None
# Copy scene .xml to accompany the extracted .tif for dg_mosaic
shutil.copy(self.xmlFileName, tempBandFile.replace('.tif', '.xml'))
return tempBandFile
def resample(self, xScale, yScale):
cmd = self._getBaseCmd() + ' -tr ' + str(xScale) + ' ' + \
str(yScale)
# Finish the command.
outFile = tempfile.mkstemp(suffix='.nc')[1]
cmd += ' ' + self._filePath + ' ' + outFile
SystemCommand(cmd, None, True)
shutil.move(outFile, self._filePath)
# Update the dataset.
self.getDataset()
def clipReproject(self, envelope=None, outputSRS=None, dataset=None):
dataset = dataset or self._filePath
# At least one operation must be configured.
if not envelope and not outputSRS:
raise RuntimeError('Clip envelope or output SRS must be ' +
'specified.')
cmd = self._getBaseCmd()
# Clip?
if envelope:
if not isinstance(envelope, Envelope):
raise TypeError('The first parameter must be an Envelope.')
if not self.envelope().Intersection(envelope):
raise RuntimeError('The clip envelope does not intersect ' +
'the image.')
cmd += (' -te' + ' ' + str(envelope.ulx()) + ' ' +
str(envelope.lry()) + ' ' + str(envelope.lrx()) + ' ' +
str(envelope.uly()) + ' -te_srs' + ' "' +
envelope.GetSpatialReference().ExportToProj4() + '"')
# Reproject?
if outputSRS and not self._dataset.GetSpatialRef().IsSame(outputSRS):
cmd += ' -t_srs "' + outputSRS.ExportToProj4() + '"'
self._srs = outputSRS
# Finish the command.
outFile = tempfile.mkstemp()[1]
cmd += ' ' + dataset + ' ' + outFile
SystemCommand(cmd, self.logger, True)
shutil.move(outFile, self._filePath)
# ---
# Update the dataset. It would be nice to use the SRS inside the
# reprojected file; however, if it is EPSG:4326, the axis order could
# be incorrect. Passing the requested SRS keeps the axis order
# consistent.
# ---
self.__init__(self._filePath, spatialReference=outputSRS)
def runMaxEntJar(self, jarFile=MAX_ENT_JAR):
print ('Running MaxEnt.')
# Invoke maxent.jar.
baseCmd = 'java -Xmx1024m -jar ' + \
jarFile + \
' visible=false autorun -P -J writeplotdata ' + \
'"applythresholdrule=Equal training sensitivity and ' + \
'specificity" removeduplicates=false '
cmd = baseCmd + \
'-s "' + self._maxEntSpeciesFile + '" ' + \
'-e "' + self._ascDir + '" ' + \
'-o "' + self._outputDirectory + '"'
SystemCommand(cmd, None, True)
def __exit__(self, type, value, traceback):
try:
print('In ILProcessController.__exit__() {}'.format(os.getpid()))
processToKill = '\"{} worker -Q {}\"'.format(
ILProcessController.celeryConfig, os.getpid())
# Shutdown the Celery workers
shutdownWorkers = "/usr/bin/pkill -9 -f {}".format(processToKill)
SystemCommand(shutdownWorkers, None, True)
except exceptions.ConnectionError as inst:
print("Connection Error ignore: {}".format(inst))
except OSError as e:
print("Execution failed:", e, file=sys.stderr)
except Exception as inst:
print(type(inst)) # the exception instance
print(inst.args) # arguments stored in .args
print(inst) # __str__ allows args to be printed directly,
def readFile(self, dayFile, band):
outBaseName = os.path.splitext(os.path.basename(dayFile))[0]
bandName = band.split(':')[-1]
outName = os.path.join(self._outDir,
outBaseName + '-' + bandName + '.tif')
# Only bother reading, if the file does not exist.
if not os.path.exists(outName):
# 'HDF4_EOS:EOS_GRID:"' +
cmd = 'gdal_translate -tr 231.656358 231.656358 ' + \
'HDF4_EOS:EOS_GRID:"' + \
dayFile + '"' + \
band + ' ' + \
outName + ' '\
'-co "COMPRESS=LZW"'
SystemCommand(cmd, self._logger, True)
return outName
def prepareImage(image, srs, envelope, ascDir):
# ---
# First, to preserve the original files, copy the input file to the
# output directory.
# ---
baseName = os.path.basename(image.fileName())
nameNoExtension = os.path.splitext(baseName)[0]
ascImagePath = os.path.join(ascDir, nameNoExtension + '.asc')
if not os.path.exists(ascImagePath):
copyPath = os.path.join(ascDir, baseName)
print ('Processing ' + copyPath)
shutil.copy(image.fileName(), copyPath)
imageCopy = GeospatialImageFile(copyPath, srs)
imageCopy.clipReproject(envelope)
squareScale = imageCopy.getSquareScale()
imageCopy.resample(squareScale, squareScale)
# Convert to ASCII Grid.
cmd = 'gdal_translate -ot Float32 -of AAIGrid -a_nodata -9999.0' +\
' "' + imageCopy.fileName() + '"' + \
' "' + ascImagePath + '"'
SystemCommand(cmd, None, True)
# Fix NaNs.
for line in fileinput.FileInput(ascImagePath, inplace=1):
line = line.replace('nan', '-9999')
sys.stdout.write(line)
else:
print(baseName, 'was previously prepared.')
return ascImagePath
def testValidSuccessfulCommand(self):
SystemCommand('ls')
SystemCommand('ls', logging.getLogger())
SystemCommand('ls', logging.getLogger(), True)
def testInvalidCommand(self):
with self.assertRaisesRegex(RuntimeError, 'A system command error'):
SystemCommand('notA_Cmd', None, True)