def run(self):
configuration = {}
with self.input()[0].open('r') as getConfiguration:
configuration = json.load(getConfiguration)
getManifestInfo = {}
with self.input()[1].open('r') as getManifest:
getManifestInfo = json.load(getManifest)
manifestLoader = CheckFileExists(
filePath=getManifestInfo["manifestFile"])
yield manifestLoader
manifest = {}
with manifestLoader.output().open('r') as manifestFile:
manifest = manifestFile.read()
cutLine = {}
cutDemPathRoot = wc.createWorkingPath(configuration["workingRoot"],
'dem')
cutDemPath = os.path.join(cutDemPathRoot, 'cutDem.tif')
cutLinePath = os.path.join(cutDemPathRoot, "cutline.geojson")
demPath = os.path.join(self.paths["static"],
configuration["demFilename"])
boundingBoxCoords = self.getBoundingBoxCoords(manifest)
inputFilePath = configuration["inputFilePath"]
cutLine = {"type": "polygon", "coordinates": [boundingBoxCoords]}
with open(cutLinePath, "w") as cutlineFile:
cutlineFile.write(json.dumps(cutLine, use_decimal=True))
if not self.testProcessing:
try:
subprocess.check_output(
"gdalwarp -of GTiff -crop_to_cutline -overwrite --config CHECK_DISK_FREE_SPACE NO -cutline {} {} {}"
.format(cutLinePath, demPath, cutDemPath),
stderr=subprocess.STDOUT,
shell=True)
except subprocess.CalledProcessError as e:
errStr = "command '{}' return with error (code {}): {}".format(
e.cmd, e.returncode, e.output)
log.error(errStr)
raise RuntimeError(errStr)
else:
wc.createTestFile(cutDemPath)
with self.output().open("w") as outFile:
outFile.write(
json.dumps({
'cutDemPath': cutDemPath,
'cutLine': cutLine
},
use_decimal=True,
indent=4))
def run(self):
configuration = {}
with self.input().open('r') as getConfiguration:
configuration = json.load(getConfiguration)
cutLine = {}
cutDemPathRoot = wc.createWorkingPath(configuration["workingRoot"], 'dem')
cutDemPath = os.path.join(cutDemPathRoot, 'cutDem.tif')
cutLinePath = os.path.join(cutDemPathRoot, "cutline.geojson")
demPath = os.path.join(self.paths["static"], configuration["demFilename"])
inputFilePath = configuration["inputFilePath"]
if not self.testProcessing:
with zipfile.ZipFile(inputFilePath) as productZipFile:
with productZipFile.open("{}.SAFE/preview/map-overlay.kml".format(os.path.basename(inputFilePath).replace(".zip", ""))) as overlay:
# Grab first latlong element as there should only be one
coordinatesXMLElement = xml.etree.ElementTree.fromstring(overlay.read().decode("utf-8")).findall(".//Document/Folder/GroundOverlay/gx:LatLonQuad/coordinates", {"gx": "http://www.google.com/kml/ext/2.2"})[0]
coordinates = []
# Push coordinates from XML into array, converting to floats
for coord in coordinatesXMLElement.text.split(' '):
coordinates.append(list(map(lambda x: float(x), coord.split(','))))
# Copy first coordinate to end of list to complete polygon
coordinates.append(coordinates[0])
cutLine = {
"type": "polygon",
"coordinates": [coordinates]
}
with open(cutLinePath, "w") as cutlineFile:
cutlineFile.write(json.dumps(cutLine))
try:
subprocess.check_output(
"gdalwarp -of GTiff -crop_to_cutline -overwrite --config CHECK_DISK_FREE_SPACE NO -cutline {} {} {}".format(cutLinePath, demPath, cutDemPath),
stderr=subprocess.STDOUT,
shell=True)
except subprocess.CalledProcessError as e:
errStr = "command '{}' return with error (code {}): {}".format(e.cmd, e.returncode, e.output)
log.error(errStr)
raise RuntimeError(errStr)
else:
# yield CreateLocalFile(filePath=cutDemPath, content="TEST_FILE")
wc.createTestFile(cutDemPath)
with self.output().open("w") as outFile:
outFile.write(json.dumps({
'cutDemPath' : cutDemPath,
'cutLine' : cutLine
}))
def run(self):
cutDemInfo = {}
with self.input()[0].open('r') as cutDEM:
cutDemInfo = json.load(cutDEM)
copyInputFileInfo = {}
with self.input()[1].open('r') as copyInputFile:
copyInputFileInfo = json.load(copyInputFile)
configuration = {}
with self.input()[2].open('r') as getConfiguration:
configuration = json.load(getConfiguration)
tempOutputPath = wc.createWorkingPath(configuration["workingRoot"], "output")
log.info('Populating configfile params')
# todo these two options are probabably no longer needed and can be removed after code checks
configFilePath = "/app/toolchain/scripts/JNCC_S1_GRD_configfile_v.1.1.sh"
vmOptionsFilePath = "/app/snap/bin/gpt.vmoptions"
processingConfiguration = {
"scriptConfigFilePath" : configFilePath,
"vmOptionsFilePath" : vmOptionsFilePath,
"arguments" : self.spatialConfig["snapRunArguments"],
"parameters" : {
"s1_ard_main_dir" : configuration["workingRoot"],
"s1_ard_basket_dir" : copyInputFileInfo["tempInputPath"],
"s1_ard_ext_dem" : cutDemInfo["cutDemPath"],
"s1_ard_temp_output_dir" : tempOutputPath,
"s1_ard_snap_memory" : str(self.memoryLimit),
"s1_ard_utm_proj" : self.spatialConfig["snapConfigUtmProj"],
"s1_ard_central_meridian" : self.spatialConfig["snapConfigCentralMeridian"],
"s1_ard_false_northing" : self.spatialConfig["snapConfigFalseNorthing"]
}
}
if not os.path.isdir(processingConfiguration["parameters"]["s1_ard_main_dir"]):
raise Exception("Invalid working path: Check working path in paths parameter")
with self.output().open("w") as outFile:
outFile.write(json.dumps(processingConfiguration))
def run(self):
configuration = {}
with self.input().open('r') as getConfiguration:
configuration = json.load(getConfiguration)
tempManifestFile = os.path.join(
wc.createWorkingPath(configuration["workingRoot"], "manifest"),
"source_manifest.txt")
rawZip = zipfile.ZipFile(configuration["inputFilePath"], 'r')
manifestPath = os.path.join(
os.path.splitext(os.path.basename(
configuration["inputFilePath"]))[0] + ".SAFE", "manifest.safe")
manifest = rawZip.read(manifestPath).decode("utf-8")
with open(tempManifestFile, 'w') as manifestFile:
manifestFile.write(manifest)
with self.output().open('w') as out:
out.write(json.dumps({"manifestFile": tempManifestFile}))
def run(self):
configuration = {}
with self.input().open('r') as getConfiguration:
configuration = json.load(getConfiguration)
tempInputPath = wc.createWorkingPath(configuration["workingRoot"], "input")
inputSource = configuration["inputFilePath"]
tempTatget = os.path.join(tempInputPath, os.path.basename(inputSource))
try:
shutil.copy(inputSource, tempTatget)
log.info("Copied input file to {}".format(tempTatget))
except IOError as e:
raise("Unable to copy file. {}".format(e))
except:
raise("Unexpected error:", sys.exc_info())
with self.output().open('w') as out:
out.write(json.dumps({
"tempInputPath" : tempInputPath,
"tempInputFile" : tempTatget
}))