def main():
# Connect to database - ignore engine information
pds_session, pds_engine = db_connect(pds_db)
# Connect to database - ignore engine information
session, upc_engine = db_connect(upc_db)
# ***************** Set up logging *****************
logger = logging.getLogger('UPC_Process')
logger.setLevel(logging.INFO)
logFileHandle = logging.FileHandler(pds_log + 'Process.log')
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s, %(message)s')
logFileHandle.setFormatter(formatter)
logger.addHandler(logFileHandle)
PDSinfoDICT = json.load(open(pds_info, 'r'))
# Redis Queue Objects
RQ_main = RedisQueue('UPC_ReadyQueue')
logger.info("UPC Processing Queue: %s", RQ_main.id_name)
RQ_lock = RedisLock(lock_obj)
# If the queue isn't registered, add it and set it to "running"
RQ_lock.add({RQ_main.id_name: '1'})
proc_date_tid = get_tid('processdate', session)
err_type_tid = get_tid('errortype', session)
err_msg_tid = get_tid('errormessage', session)
err_flag_tid = get_tid('error', session)
isis_footprint_tid = get_tid('isisfootprint', session)
isis_centroid_tid = get_tid('isiscentroid', session)
start_time_tid = get_tid('starttime', session)
stop_time_tid = get_tid('stoptime', session)
checksum_tid = get_tid('checksum', session)
# while there are items in the redis queue
while int(RQ_main.QueueSize()) > 0 and RQ_lock.available(RQ_main.id_name):
# get a file from the queue
item = literal_eval(RQ_main.QueueGet().decode("utf-8"))
inputfile = item[0]
fid = item[1]
archive = item[2]
#inputfile = (RQ_main.QueueGet()).decode('utf-8')
if os.path.isfile(inputfile):
pass
else:
print("{} is not a file\n".format(inputfile))
if os.path.isfile(inputfile):
logger.info('Starting Process: %s', inputfile)
# @TODO refactor this logic. We're using an object to find a path, returning it,
# then passing it back to the object so that the object can use it.
recipeOBJ = Recipe()
recipe_json = recipeOBJ.getRecipeJSON(archive)
#recipe_json = recipeOBJ.getRecipeJSON(getMission(str(inputfile)))
recipeOBJ.AddJsonFile(recipe_json, 'upc')
infile = workarea + os.path.splitext(
str(os.path.basename(inputfile)))[0] + '.UPCinput.cub'
outfile = workarea + os.path.splitext(
str(os.path.basename(inputfile)))[0] + '.UPCoutput.cub'
caminfoOUT = workarea + os.path.splitext(
str(os.path.basename(inputfile)))[0] + '_caminfo.pvl'
EDRsource = inputfile.replace(
'/pds_san/PDS_Archive/',
'https://pdsimage.wr.ugs.gov/Missions/')
status = 'success'
# Iterate through each process listed in the recipe
for item in recipeOBJ.getProcesses():
# If any of the processes failed, discontinue processing
if status.lower() == 'error':
break
elif status.lower() == 'success':
processOBJ = Process()
processOBJ.ProcessFromRecipe(item, recipeOBJ.getRecipe())
# Handle processing based on string description.
if '2isis' in item:
processOBJ.updateParameter('from_', inputfile)
processOBJ.updateParameter('to', outfile)
elif item == 'thmproc':
processOBJ.updateParameter('from_', inputfile)
processOBJ.updateParameter('to', outfile)
thmproc_odd = str(workarea) + str(
os.path.splitext(os.path.basename(inputfile))
[0]) + '.UPCoutput.raw.odd.cub'
thmproc_even = str(workarea) + str(
os.path.splitext(os.path.basename(inputfile))
[0]) + '.UPCoutput.raw.even.cub'
elif item == 'handmos':
processOBJ.updateParameter('from_', thmproc_even)
processOBJ.updateParameter('mosaic', thmproc_odd)
elif item == 'spiceinit':
processOBJ.updateParameter('from_', infile)
elif item == 'cubeatt':
band_infile = infile + '+' + str(1)
processOBJ.updateParameter('from_', band_infile)
processOBJ.updateParameter('to', outfile)
elif item == 'footprintinit':
processOBJ.updateParameter('from_', infile)
elif item == 'caminfo':
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', caminfoOUT)
else:
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', outfile)
pwd = os.getcwd()
# iterate through functions listed in process obj
for k, v in processOBJ.getProcess().items():
# load a function into func
func = getattr(isis, k)
try:
os.chdir(workarea)
# execute function
func(**v)
os.chdir(pwd)
if item == 'handmos':
if os.path.isfile(thmproc_odd):
os.rename(thmproc_odd, infile)
else:
if os.path.isfile(outfile):
os.rename(outfile, infile)
status = 'success'
if '2isis' in item:
label = pvl.load(infile)
infile_bandlist = label['IsisCube']['BandBin'][
PDSinfoDICT[archive]['bandbinQuery']]
infile_centerlist = label['IsisCube'][
'BandBin']['Center']
elif item == 'thmproc':
pass
elif item == 'handmos':
label = pvl.load(infile)
infile_bandlist = label['IsisCube']['BandBin'][
PDSinfoDICT[archive]['bandbinQuery']]
infile_centerlist = label['IsisCube'][
'BandBin']['Center']
except ProcessError as e:
print(e)
status = 'error'
processError = item
# keyword definitions
keywordsOBJ = None
if status.lower() == 'success':
try:
keywordsOBJ = UPCkeywords(caminfoOUT)
except:
with open(caminfoOUT, 'r') as f:
filedata = f.read()
filedata = filedata.replace(';', '-').replace('&', '-')
filedata = re.sub(r'\-\s+', r'', filedata, flags=re.M)
with open(caminfoOUT, 'w') as f:
f.write(filedata)
keywordsOBJ = UPCkeywords(caminfoOUT)
target_Qobj = session.query(upc_models.Targets).filter(
upc_models.Targets.targetname == keywordsOBJ.getKeyword(
'TargetName').upper()).first()
instrument_Qobj = session.query(upc_models.Instruments).filter(
upc_models.Instruments.instrument ==
keywordsOBJ.getKeyword('InstrumentId')).first()
if session.query(upc_models.DataFiles).filter(
upc_models.DataFiles.isisid == keywordsOBJ.getKeyword(
'IsisId')).first() is None:
test_input = upc_models.DataFiles(
isisid=keywordsOBJ.getKeyword('IsisId'),
productid=keywordsOBJ.getKeyword('ProductId'),
edr_source=EDRsource,
edr_detached_label='',
instrumentid=instrument_Qobj.instrumentid,
targetid=target_Qobj.targetid)
session.merge(test_input)
session.commit()
Qobj = session.query(upc_models.DataFiles).filter(
upc_models.DataFiles.isisid == keywordsOBJ.getKeyword(
'IsisId')).first()
UPCid = Qobj.upcid
print(UPCid)
# block to add band information to meta_bands
if isinstance(infile_bandlist, list):
index = 0
while index < len(infile_bandlist):
B_DBinput = upc_models.MetaBands(
upcid=UPCid,
filter=str(infile_bandlist[index]),
centerwave=infile_centerlist[index])
session.merge(B_DBinput)
index = index + 1
else:
try:
# If infile_centerlist is in "Units" format, grab the value
f_centerlist = float(infile_centerlist[0])
except TypeError:
f_centerlist = float(infile_centerlist)
B_DBinput = upc_models.MetaBands(upcid=UPCid,
filter=infile_bandlist,
centerwave=f_centerlist)
session.merge(B_DBinput)
session.commit()
# Block to add common keywords
testjson = json.load(open(keyword_def, 'r'))
for element_1 in testjson['instrument']['COMMON']:
keyvalue = ""
keytype = testjson['instrument']['COMMON'][element_1][
'type']
keyword = testjson['instrument']['COMMON'][element_1][
'keyword']
keyword_Qobj = session.query(upc_models.Keywords).filter(
and_(upc_models.Keywords.typename == element_1,
upc_models.Keywords.instrumentid == 1)).first()
if keyword_Qobj is None:
continue
else:
keyvalue = keywordsOBJ.getKeyword(keyword)
if keyvalue is None:
continue
keyvalue = db2py(keytype, keyvalue)
try:
DBinput = upc_models.create_table(
keytype,
upcid=UPCid,
typeid=keyword_Qobj.typeid,
value=keyvalue)
except Exception as e:
logger.warn("Unable to enter %s into table\n\n%s",
keytype, e)
continue
session.merge(DBinput)
try:
session.flush()
except:
logger.warn("Unable to flush database connection")
session.commit()
for element_1 in testjson['instrument'][archive]:
keyvalue = ""
keytype = testjson['instrument'][archive][element_1][
'type']
keyword = testjson['instrument'][archive][element_1][
'keyword']
keyword_Qobj = session.query(upc_models.Keywords).filter(
and_(
upc_models.Keywords.typename == element_1,
upc_models.Keywords.instrumentid.in_(
(1, instrument_Qobj.instrumentid)))).first()
if keyword_Qobj is None:
continue
else:
keyvalue = keywordsOBJ.getKeyword(keyword)
if keyvalue is None:
logger.debug("Keyword %s not found", keyword)
continue
keyvalue = db2py(keytype, keyvalue)
try:
DBinput = upc_models.create_table(
keytype,
upcid=UPCid,
typeid=keyword_Qobj.typeid,
value=keyvalue)
except Exception as e:
logger.warn("Unable to enter %s into database\n\n%s",
keytype, e)
continue
session.merge(DBinput)
try:
session.flush()
except:
logger.warn("Unable to flush database connection")
session.commit()
# geometry stuff
G_centroid = 'point ({} {})'.format(
str(keywordsOBJ.getKeyword('CentroidLongitude')),
str(keywordsOBJ.getKeyword('CentroidLatitude')))
G_keyword_Qobj = session.query(
upc_models.Keywords.typeid).filter(
upc_models.Keywords.typename ==
'isiscentroid').first()
G_footprint_Qobj = session.query(
upc_models.Keywords.typeid).filter(
upc_models.Keywords.typename ==
'isisfootprint').first()
G_footprint = keywordsOBJ.getKeyword('GisFootprint')
G_DBinput = upc_models.MetaGeometry(upcid=UPCid,
typeid=G_keyword_Qobj,
value=G_centroid)
session.merge(G_DBinput)
G_DBinput = upc_models.MetaGeometry(upcid=UPCid,
typeid=G_footprint_Qobj,
value=G_footprint)
session.merge(G_DBinput)
session.flush()
session.commit()
f_hash = hashlib.md5()
with open(inputfile, "rb") as f:
for chunk in iter(lambda: f.read(4096), b""):
f_hash.update(chunk)
checksum = f_hash.hexdigest()
DBinput = upc_models.MetaString(upcid=UPCid,
typeid=checksum_tid,
value=checksum)
session.merge(DBinput)
DBinput = upc_models.MetaBoolean(upcid=UPCid,
typeid=err_flag_tid,
value=False)
session.merge(DBinput)
session.commit()
AddProcessDB(pds_session, fid, True)
os.remove(infile)
os.remove(caminfoOUT)
elif status.lower() == 'error':
try:
label = pvl.load(infile)
except Exception as e:
logger.info('%s', e)
continue
date = datetime.datetime.now(
pytz.utc).strftime("%Y-%m-%d %H:%M:%S")
if '2isis' in processError or processError == 'thmproc':
if session.query(upc_models.DataFiles).filter(
upc_models.DataFiles.edr_source ==
EDRsource.decode("utf-8")).first() is None:
target_Qobj = session.query(upc_models.Targets).filter(
upc_models.Targets.targetname == str(
label['IsisCube']['Instrument']
['TargetName']).upper()).first()
instrument_Qobj = session.query(
upc_models.Instruments).filter(
upc_models.Instruments.instrument == str(
label['IsisCube']['Instrument']
['InstrumentId'])).first()
error1_input = upc_models.DataFiles(
isisid='1', edr_source=EDRsource)
session.merge(error1_input)
session.commit()
EQ1obj = session.query(upc_models.DataFiles).filter(
upc_models.DataFiles.edr_source == EDRsource).first()
UPCid = EQ1obj.upcid
errorMSG = 'Error running {} on file {}'.format(
processError, inputfile)
DBinput = MetaTime(upcid=UPCid,
typeid=proc_date_tid,
value=date)
session.merge(DBinput)
DBinput = MetaString(upcid=UPCid,
typeid=err_type_tid,
value=processError)
session.merge(DBinput)
DBinput = MetaString(upcid=UPCid,
typeid=err_msg_tid,
value=errorMSG)
session.merge(DBinput)
DBinput = MetaBoolean(upcid=UPCid,
typeid=err_flag_tid,
value=True)
session.merge(DBinput)
DBinput = MetaGeometry(upcid=UPCid,
typeid=isis_footprint_tid,
value='POINT(361 0)')
session.merge(DBinput)
DBinput = MetaGeometry(upcid=UPCid,
typeid=isis_centroid_tid,
value='POINT(361 0)')
session.merge(DBinput)
session.commit()
else:
try:
label = pvl.load(infile)
except Exception as e:
logger.warn('%s', e)
continue
isisSerial = getISISid(infile)
if session.query(upc_models.DataFiles).filter(
upc_models.DataFiles.isisid ==
isisSerial).first() is None:
target_Qobj = session.query(upc_models.Targets).filter(
upc_models.Targets.targetname == str(
label['IsisCube']['Instrument']
['TargetName']).upper()).first()
instrument_Qobj = session.query(
upc_models.Instruments).filter(
upc_models.Instruments.instrument == str(
label['IsisCube']['Instrument']
['InstrumentId'])).first()
if target_Qobj is None or instrument_Qobj is None:
continue
error2_input = upc_models.DataFiles(
isisid=isisSerial,
productid=label['IsisCube']['Archive']
['ProductId'],
edr_source=EDRsource,
instrumentid=instrument_Qobj.instrumentid,
targetid=target_Qobj.targetid)
session.merge(error2_input)
session.commit()
try:
EQ2obj = session.query(upc_models.DataFiles).filter(
upc_models.DataFiles.isisid == isisSerial).first()
UPCid = EQ2obj.upcid
errorMSG = 'Error running {} on file {}'.format(
processError, inputfile)
DBinput = MetaTime(upcid=UPCid,
typeid=proc_date_tid,
value=date)
session.merge(DBinput)
DBinput = MetaString(upcid=UPCid,
typeid=err_type_tid,
value=processError)
session.merge(DBinput)
DBinput = MetaString(upcid=UPCid,
typeid=err_msg_tid,
value=errorMSG)
session.merge(DBinput)
DBinput = MetaBoolean(upcid=UPCid,
typeid=err_flag_tid,
value=True)
session.merge(DBinput)
DBinput = MetaGeometry(upcid=UPCid,
typeid=isis_footprint_tid,
value='POINT(361 0)')
session.merge(DBinput)
DBinput = MetaGeometry(upcid=UPCid,
typeid=isis_centroid_tid,
value='POINT(361 0)')
session.merge(DBinput)
except:
pass
try:
v = label['IsisCube']['Instrument']['StartTime']
except KeyError:
v = None
except:
continue
try:
DBinput = MetaTime(upcid=UPCid,
typeid=start_time_tid,
value=v)
session.merge(DBinput)
except:
continue
try:
v = label['IsisCube']['Instrument']['StopTime']
except KeyError:
v = None
DBinput = MetaTime(upcid=UPCid,
typeid=stop_time_tid,
value=v)
session.merge(DBinput)
session.commit()
AddProcessDB(pds_session, fid, False)
os.remove(infile)
# Disconnect from db sessions
pds_session.close()
session.close()
# Disconnect from the engines
pds_engine.dispose()
upc_engine.dispose()
logger.info("UPC processing exited successfully")
def main():
# pdb.set_trace()
DBQO = PDS_DBquery('JOBS')
Key = DBQO.jobKey()
# Key = '2d7379497fed4c092046b2a06f5471a5'
DBQO.setJobsQueued(Key)
#*************** Setup logging ******************
logger = logging.getLogger(Key)
logger.setLevel(logging.INFO)
logFileHandle = logging.FileHandler('/usgs/cdev/PDS/logs/Service.log')
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s, %(message)s')
logFileHandle.setFormatter(formatter)
logger.addHandler(logFileHandle)
logger.info('Starting Process')
xmlOBJ = jobXML(DBQO.jobXML4Key(Key))
# ********** Test if Directory exists and make it if not *******
directory = '/scratch/pds_services/' + Key
if not os.path.exists(directory):
os.makedirs(directory)
logger.info('Working Area: %s', directory)
# ******************** Setup Redis Hash for ground range *********
RedisH = RedisHash(Key + '_info')
RedisH.RemoveAll()
RedisErrorH = RedisHash(Key + '_error')
RedisErrorH.RemoveAll()
RedisH_DICT = {}
RedisH_DICT['service'] = xmlOBJ.getProcess()
RedisH_DICT['fileformat'] = xmlOBJ.getOutFormat()
RedisH_DICT['outbit'] = xmlOBJ.getOutBit()
if xmlOBJ.getRangeType() is not None:
RedisH_DICT['grtype'] = xmlOBJ.getRangeType()
RedisH_DICT['minlat'] = xmlOBJ.getMinLat()
RedisH_DICT['maxlat'] = xmlOBJ.getMaxLat()
RedisH_DICT['minlon'] = xmlOBJ.getMinLon()
RedisH_DICT['maxlon'] = xmlOBJ.getMaxLon()
if RedisH.IsInHash('service'):
pass
else:
RedisH.AddHash(RedisH_DICT)
if RedisH.IsInHash('service'):
logger.info('Redis info Hash: Success')
else:
logger.error('Redis info Hash Not Found')
# ***end ground range **
RQ_recipe = RedisQueue(Key + '_recipe')
RQ_recipe.RemoveAll()
RQ_file = RedisQueue(Key + '_FileQueue')
RQ_file.RemoveAll()
RQ_WorkQueue = RedisQueue(Key + '_WorkQueue')
RQ_WorkQueue.RemoveAll()
RQ_loggy = RedisQueue(Key + '_loggy')
RQ_loggy.RemoveAll()
RQ_zip = RedisQueue(Key + '_ZIP')
RQ_zip.RemoveAll()
if xmlOBJ.getProcess() == 'POW':
fileList = xmlOBJ.getFileListWB()
elif xmlOBJ.getProcess() == 'MAP2':
fileList = xmlOBJ.getMFileListWB()
for List_file in fileList:
######### Input and output file naming and path stuff ############
if xmlOBJ.getProcess() == 'POW':
if xmlOBJ.getInst() == 'THEMIS_IR':
Input_file = List_file.replace('odtie1_', 'odtir1_')
Input_file = Input_file.replace('xxedr', 'xxrdr')
Input_file = Input_file.replace('EDR.QUB', 'RDR.QUB')
Input_file = Input_file.replace(
'http://pdsimage.wr.usgs.gov/Missions/',
'/pds_san/PDS_Archive/')
elif xmlOBJ.getInst() == 'ISSNA':
Input_file = List_file.replace('.IMG', '.LBL')
Input_file = Input_file.replace(
'http://pdsimage.wr.usgs.gov/Missions/',
'/pds_san/PDS_Archive/')
elif xmlOBJ.getInst() == 'ISSWA':
Input_file = List_file.replace('.IMG', '.LBL')
Input_file = Input_file.replace(
'http://pdsimage.wr.usgs.gov/Missions/',
'/pds_san/PDS_Archive/')
elif xmlOBJ.getInst() == 'SOLID STATE IMAGING SYSTEM':
Input_file = List_file.replace('.img', '.lbl')
Input_file = Input_file.replace(
'http://pdsimage.wr.usgs.gov/Missions/',
'/pds_san/PDS_Archive/')
else:
Input_file = List_file.replace(
'http://pdsimage.wr.usgs.gov/Missions/',
'/pds_san/PDS_Archive/')
elif xmlOBJ.getProcess() == 'MAP2':
Input_file = List_file.replace('file://pds_san', '/pds_san')
if '+' in Input_file:
tempsplit = Input_file.split('+')
tempFile = tempsplit[0]
else:
tempFile = Input_file
label = pvl.load(tempFile)
#*********Output final file naming **************
Tbasename = os.path.splitext(os.path.basename(tempFile))[0]
splitBase = Tbasename.split('_')
labP = xmlOBJ.getProjection()
if labP == 'INPUT':
lab_proj = label['IsisCube']['Mapping']['ProjectionName'][0:4]
else:
lab_proj = labP[0:4]
if xmlOBJ.getClat() is None or xmlOBJ.getClon() is None:
basefinal = splitBase[0] + splitBase[1] + \
splitBase[2] + '_MAP2_' + lab_proj.upper()
else:
lab_clat = float(xmlOBJ.getClat())
if lab_clat >= 0:
labH = 'N'
elif lab_clat < 0:
labH = 'S'
lab_clon = float(xmlOBJ.getClon())
basefinal = splitBase[0] + splitBase[1] + splitBase[
2] + '_MAP2_' + str(lab_clat) + labH + str(
lab_clon) + '_' + lab_proj.upper()
RedisH.MAPname(basefinal)
try:
RQ_file.QueueAdd(Input_file)
logger.info('File %s Added to Redis Queue', Input_file)
except Exception as e:
logger.warn('File %s NOT Added to Redis Queue', Input_file)
print('Redis Queue Error', e)
RedisH.FileCount(RQ_file.QueueSize())
logger.info('Count of Files Queue: %s', str(RQ_file.QueueSize()))
# ************* Map Template Stuff ******************
logger.info('Making Map File')
mapOBJ = MakeMap()
if xmlOBJ.getProcess() == 'MAP2' and xmlOBJ.getProjection() == 'INPUT':
proj = label['IsisCube']['Mapping']['ProjectionName']
mapOBJ.Projection(proj)
else:
mapOBJ.Projection(xmlOBJ.getProjection())
if xmlOBJ.getClon() is not None:
mapOBJ.CLon(float(xmlOBJ.getClon()))
if xmlOBJ.getClat() is not None:
mapOBJ.CLat(float(xmlOBJ.getClat()))
if xmlOBJ.getFirstParallel() is not None:
mapOBJ.FirstParallel(float(xmlOBJ.getFirstParallel()))
if xmlOBJ.getSecondParallel() is not None:
mapOBJ.SecondParallel(float(xmlOBJ.getSecondParallel()))
if xmlOBJ.getResolution() is not None:
mapOBJ.PixelRes(float(xmlOBJ.getResolution()))
if xmlOBJ.getTargetName() is not None:
mapOBJ.Target(xmlOBJ.getTargetName())
if xmlOBJ.getERadius() is not None:
mapOBJ.ERadius(float(xmlOBJ.getERadius()))
if xmlOBJ.getPRadius() is not None:
mapOBJ.PRadius(float(xmlOBJ.getPRadius()))
if xmlOBJ.getLatType() is not None:
mapOBJ.LatType(xmlOBJ.getLatType())
if xmlOBJ.getLonDirection() is not None:
mapOBJ.LonDirection(xmlOBJ.getLonDirection())
if xmlOBJ.getLonDomain() is not None:
mapOBJ.LonDomain(int(xmlOBJ.getLonDomain()))
if xmlOBJ.getProcess() == 'MAP2':
if xmlOBJ.getMinLat() is not None:
mapOBJ.MinLat(float(xmlOBJ.getMinLat()))
if xmlOBJ.getMaxLat() is not None:
mapOBJ.MaxLat(float(xmlOBJ.getMaxLat()))
if xmlOBJ.getMinLon() is not None:
mapOBJ.MinLon(float(xmlOBJ.getMinLon()))
if xmlOBJ.getMaxLon() is not None:
mapOBJ.MaxLon(float(xmlOBJ.getMaxLon()))
mapOBJ.Map2pvl()
MAPfile = directory + "/" + Key + '.map'
mapOBJ.Map2File(MAPfile)
try:
f = open(MAPfile)
f.close
logger.info('Map File Creation: Success')
except IOError as e:
logger.error('Map File %s Not Found', MAPfile)
# ** End Map Template Stuff **
# *************************************************
logger.info('Building Recipe')
recipeOBJ = Recipe()
if xmlOBJ.getProcess() == 'POW':
recipeOBJ.AddJsonFile(recipe_dict[xmlOBJ.getInst()])
elif xmlOBJ.getProcess() == 'MAP2':
recipeOBJ.AddJsonFile(recipe_dict['MAP'])
# ************** Test for stretch and add to recipe **********************
# if MAP2 and 8 or 16 bit run stretch to set range
if xmlOBJ.getOutBit() == 'input':
testBitType = str(label['IsisCube']['Core']['Pixels']['Type']).upper()
else:
testBitType = xmlOBJ.getOutBit().upper()
if xmlOBJ.getProcess() == 'MAP2' and xmlOBJ.STR_Type() is None:
if str(label['IsisCube']['Core']['Pixels']['Type']).upper(
) != xmlOBJ.getOutBit().upper() and str(
label['IsisCube']['Core']['Pixels']['Type']).upper() != 'REAL':
if str(label['IsisCube']['Core']['Pixels']
['Type']).upper() == 'SIGNEDWORD':
strpairs = '0:-32765 0:-32765 100:32765 100:32765'
elif str(label['IsisCube']['Core']['Pixels']
['Type']).upper() == 'UNSIGNEDBYTE':
strpairs = '0:1 0:1 100:254 100:254'
STRprocessOBJ = Process()
STRprocessOBJ.newProcess('stretch')
STRprocessOBJ.AddParameter('from_', 'value')
STRprocessOBJ.AddParameter('to', 'value')
STRprocessOBJ.AddParameter('usepercentages', 'yes')
STRprocessOBJ.AddParameter('pairs', strpairs)
recipeOBJ.AddProcess(STRprocessOBJ.getProcess())
strType = xmlOBJ.STR_Type()
if strType == 'StretchPercent' and xmlOBJ.STR_PercentMin(
) is not None and xmlOBJ.STR_PercentMax(
) is not None and testBitType != 'REAL':
if float(xmlOBJ.STR_PercentMin()) != 0 and float(
xmlOBJ.STR_PercentMax()) != 100:
if testBitType == 'UNSIGNEDBYTE':
strpairs = '0:1 ' + xmlOBJ.STR_PercentMin() + ':1 ' + \
xmlOBJ.STR_PercentMax() + ':254 100:254'
elif testBitType == 'SIGNEDWORD':
strpairs = '0:-32765 ' + xmlOBJ.STR_PercentMin() + ':-32765 ' + \
xmlOBJ.STR_PercentMax() + ':32765 100:32765'
STRprocessOBJ = Process()
STRprocessOBJ.newProcess('stretch')
STRprocessOBJ.AddParameter('from_', 'value')
STRprocessOBJ.AddParameter('to', 'value')
STRprocessOBJ.AddParameter('usepercentages', 'yes')
STRprocessOBJ.AddParameter('pairs', strpairs)
recipeOBJ.AddProcess(STRprocessOBJ.getProcess())
elif strType == 'GaussStretch':
STRprocessOBJ = Process()
STRprocessOBJ.newProcess('gaussstretch')
STRprocessOBJ.AddParameter('from_', 'value')
STRprocessOBJ.AddParameter('to', 'value')
STRprocessOBJ.AddParameter('gsigma', xmlOBJ.STR_GaussSigma())
recipeOBJ.AddProcess(STRprocessOBJ.getProcess())
elif strType == 'HistogramEqualization':
STRprocessOBJ = Process()
STRprocessOBJ.newProcess('histeq')
STRprocessOBJ.AddParameter('from_', 'value')
STRprocessOBJ.AddParameter('to', 'value')
if xmlOBJ.STR_PercentMin() is None:
STRprocessOBJ.AddParameter('minper', '0')
else:
STRprocessOBJ.AddParameter('minper', xmlOBJ.STR_PercentMin())
if xmlOBJ.STR_PercentMax() is None:
STRprocessOBJ.AddParameter('maxper', '100')
else:
STRprocessOBJ.AddParameter('maxper', xmlOBJ.STR_PercentMax())
recipeOBJ.AddProcess(STRprocessOBJ.getProcess())
elif strType == 'SigmaStretch':
STRprocessOBJ = Process()
STRprocessOBJ.newProcess('sigmastretch')
STRprocessOBJ.AddParameter('from_', 'value')
STRprocessOBJ.AddParameter('to', 'value')
STRprocessOBJ.AddParameter('variance', xmlOBJ.STR_SigmaVariance())
recipeOBJ.AddProcess(STRprocessOBJ.getProcess())
# ************* Test for output bit type and add to recipe *************
if xmlOBJ.getProcess() == 'POW':
if xmlOBJ.getOutBit().upper() == 'UNSIGNEDBYTE' or xmlOBJ.getOutBit(
).upper() == 'SIGNEDWORD':
CAprocessOBJ = Process()
CAprocessOBJ.newProcess('cubeatt-bit')
CAprocessOBJ.AddParameter('from_', 'value')
CAprocessOBJ.AddParameter('to', 'value')
recipeOBJ.AddProcess(CAprocessOBJ.getProcess())
elif xmlOBJ.getProcess() == 'MAP2':
if xmlOBJ.getOutBit().upper() != 'INPUT':
if xmlOBJ.getOutBit().upper(
) == 'UNSIGNEDBYTE' or xmlOBJ.getOutBit().upper() == 'SIGNEDWORD':
if str(label['IsisCube']['Core']['Pixels']
['Type']).upper() != xmlOBJ.getOutBit().upper():
CAprocessOBJ = Process()
CAprocessOBJ.newProcess('cubeatt-bit')
CAprocessOBJ.AddParameter('from_', 'value')
CAprocessOBJ.AddParameter('to', 'value')
recipeOBJ.AddProcess(CAprocessOBJ.getProcess())
# **************** Add Grid(MAP2) *************
if xmlOBJ.getGridInterval() is not None:
GprocessOBJ = Process()
GprocessOBJ.newProcess('grid')
GprocessOBJ.AddParameter('from_', 'value')
GprocessOBJ.AddParameter('to', 'value')
GprocessOBJ.AddParameter('latinc', xmlOBJ.getGridInterval())
GprocessOBJ.AddParameter('loninc', xmlOBJ.getGridInterval())
GprocessOBJ.AddParameter('outline', 'yes')
GprocessOBJ.AddParameter('boundary', 'yes')
GprocessOBJ.AddParameter('linewidth', '3')
recipeOBJ.AddProcess(GprocessOBJ.getProcess())
# ********OUTPUT FORMAT ***************
# ************* Test for GDAL and add to recipe *************************
Oformat = xmlOBJ.getOutFormat()
if Oformat == 'GeoTiff-BigTiff' or Oformat == 'GeoJPEG-2000' or Oformat == 'JPEG' or Oformat == 'PNG':
if Oformat == 'GeoJPEG-2000':
Oformat = 'JP2KAK'
if Oformat == 'GeoTiff-BigTiff':
Oformat = 'GTiff'
GDALprocessOBJ = Process()
# GDALprocessOBJ.newProcess('/usgs/dev/contrib/bin/FWTools-linux-x86_64-3.0.3/bin_safe/gdal_translate')
GDALprocessOBJ.newProcess('/usgs/apps/anaconda/bin/gdal_translate')
if xmlOBJ.getOutBit() != 'input':
GDALprocessOBJ.AddParameter(
'-ot', GDALprocessOBJ.GDAL_OBit(xmlOBJ.getOutBit()))
GDALprocessOBJ.AddParameter('-of', Oformat)
if Oformat == 'GTiff' or Oformat == 'JP2KAK' or Oformat == 'JPEG':
GDALprocessOBJ.AddParameter('-co',
GDALprocessOBJ.GDAL_Creation(Oformat))
recipeOBJ.AddProcess(GDALprocessOBJ.getProcess())
# **************** set up pds2isis and add to recipe
elif Oformat == 'PDS':
pdsProcessOBJ = Process()
pdsProcessOBJ.newProcess('isis2pds')
pdsProcessOBJ.AddParameter('from_', 'value')
pdsProcessOBJ.AddParameter('to', 'value')
if xmlOBJ.getOutBit() == 'unsignedbyte':
pdsProcessOBJ.AddParameter('bittype', '8bit')
elif xmlOBJ.getOutBit() == 'signedword':
pdsProcessOBJ.AddParameter('bittype', 's16bit')
recipeOBJ.AddProcess(pdsProcessOBJ.getProcess())
for item in recipeOBJ.getProcesses():
processOBJ = Process()
processOBJ.ProcessFromRecipe(item, recipeOBJ.getRecipe())
if item == 'cam2map':
processOBJ.updateParameter('map', MAPfile)
if xmlOBJ.getResolution() is None:
processOBJ.updateParameter('pixres', 'CAMERA')
else:
processOBJ.updateParameter('pixres', 'MAP')
if xmlOBJ.getRangeType() is None:
processOBJ.updateParameter('defaultrange', 'MINIMIZE')
elif xmlOBJ.getRangeType() == 'smart' or xmlOBJ.getRangeType(
) == 'fill':
processOBJ.updateParameter('defaultrange', 'CAMERA')
processOBJ.AddParameter('trim', 'YES')
elif item == 'map2map':
processOBJ.updateParameter('map', MAPfile)
if xmlOBJ.getResolution() is None:
processOBJ.updateParameter('pixres', 'FROM')
else:
processOBJ.updateParameter('pixres', 'MAP')
if xmlOBJ.OutputGeometry() is not None:
processOBJ.updateParameter('defaultrange', 'MAP')
processOBJ.AddParameter('trim', 'YES')
else:
processOBJ.updateParameter('defaultrange', 'FROM')
processJSON = processOBJ.Process2JSON()
try:
RQ_recipe.QueueAdd(processJSON)
logger.info('Recipe Element Added to Redis: %s : Success', item)
except Exception as e:
logger.warn('Recipe Element NOT Added to Redis: %s', item)
# ** *************** HPC job stuff ***********************
logger.info('HPC Cluster job Submission Starting')
jobOBJ = HPCjob()
jobOBJ.setJobName(Key + '_Service')
jobOBJ.setStdOut('/usgs/cdev/PDS/output/' + Key + '_%A_%a.out')
jobOBJ.setStdError('/usgs/cdev/PDS/output/' + Key + '_%A_%a.err')
jobOBJ.setWallClock('24:00:00')
# jobOBJ.setMemory('8192')
# jobOBJ.setMemory('16384')
jobOBJ.setMemory('24576')
jobOBJ.setPartition('pds')
JAsize = RQ_file.QueueSize()
jobOBJ.setJobArray(JAsize)
logger.info('Job Array Size : %s', str(JAsize))
jobOBJ.addPath('/usgs/apps/anaconda/bin')
if xmlOBJ.getProcess() == 'POW':
cmd = '/usgs/cdev/PDS/bin/POWprocess.py ' + Key
elif xmlOBJ.getProcess() == 'MAP2':
cmd = '/usgs/cdev/PDS/bin/MAPprocess.py ' + Key
logger.info('HPC Command: %s', cmd)
jobOBJ.setCommand(cmd)
SBfile = directory + '/' + Key + '.sbatch'
jobOBJ.MakeJobFile(SBfile)
try:
sb = open(SBfile)
sb.close
logger.info('SBATCH File Creation: Success')
except IOError as e:
logger.error('SBATCH File %s Not Found', SBfile)
try:
jobOBJ.Run()
logger.info('Job Submission to HPC: Success')
DBQO.setJobsStarted(Key)
except IOError as e:
logger.error('Jobs NOT Submitted to HPC')
def main():
# pdb.set_trace()
##***************** Set up logging *****************
logger = logging.getLogger('Browse_Process')
logger.setLevel(logging.INFO)
logFileHandle = logging.FileHandler(pds_log + 'Process.log')
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s, %(message)s')
logFileHandle.setFormatter(formatter)
logger.addHandler(logFileHandle)
RQ_main = RedisQueue('Browse_ReadyQueue')
PDSinfoDICT = json.load(open(pds_info, 'r'))
pds_session, _ = db_connect(pds_db)
upc_session, _ = db_connect(upc_db)
tid = get_tid('fullimageurl', upc_session)
while int(RQ_main.QueueSize()) > 0:
item = literal_eval(RQ_main.QueueGet().decode("utf-8"))
inputfile = item[0]
fid = item[1]
archive = item[2]
if os.path.isfile(inputfile):
logger.info('Starting Process: %s', inputfile)
finalpath = makedir(inputfile)
recipeOBJ = Recipe()
recip_json = recipeOBJ.getRecipeJSON(archive)
recipeOBJ.AddJsonFile(recip_json, 'reduced')
infile = workarea + os.path.splitext(
os.path.basename(inputfile))[0] + '.Binput.cub'
outfile = workarea + os.path.splitext(
os.path.basename(inputfile))[0] + '.Boutput.cub'
status = 'success'
for item in recipeOBJ.getProcesses():
if status == 'error':
break
elif status == 'success':
processOBJ = Process()
processR = processOBJ.ProcessFromRecipe(
item, recipeOBJ.getRecipe())
if '2isis' in item:
processOBJ.updateParameter('from_', inputfile)
processOBJ.updateParameter('to', outfile)
elif item == 'spiceinit':
processOBJ.updateParameter('from_', infile)
elif item == 'cubeatt':
label = pvl.load(infile)
bands = PDSinfoDICT[archive]['bandorder']
query_bands = label['IsisCube']['BandBin'][
PDSinfoDICT[archive]['bandbinQuery']]
# Create a set from the list / single value
try:
query_band_set = set(query_bands)
except:
query_band_set = set([query_bands])
# Iterate through 'bands' and grab the first value that is present in the
# set defined by 'bandbinquery' -- if not present, default to 1
exband = next(
(band for band in bands if band in query_band_set),
1)
band_infile = infile + '+' + str(exband)
processOBJ.updateParameter('from_', band_infile)
processOBJ.updateParameter('to', outfile)
elif item == 'ctxevenodd':
label = pvl.load(infile)
SS = label['IsisCube']['Instrument']['SpatialSumming']
if SS != 1:
break
else:
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', outfile)
elif item == 'reduce':
label = pvl.load(infile)
Nline = label['IsisCube']['Core']['Dimensions'][
'Lines']
Nsample = label['IsisCube']['Core']['Dimensions'][
'Samples']
Nline = int(Nline)
Nsample = int(Nsample)
Sfactor = scaleFactor(Nline, Nsample, recip_json)
processOBJ.updateParameter('lscale', Sfactor)
processOBJ.updateParameter('sscale', Sfactor)
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', outfile)
elif item == 'isis2std':
final_outfile = finalpath + '/' + os.path.splitext(
os.path.basename(inputfile))[0] + '.browse.jpg'
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', final_outfile)
else:
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', outfile)
for k, v in processOBJ.getProcess().items():
func = getattr(isis, k)
try:
func(**v)
logger.info('Process %s :: Success', k)
if os.path.isfile(outfile):
if '.cub' in outfile:
os.rename(outfile, infile)
status = 'success'
if '2isis' in item:
isisSerial = getISISid(infile)
except ProcessError as e:
print(e)
logger.error('Process %s :: Error', k)
status = 'error'
if status == 'success':
DB_addURL(upc_session, isisSerial, final_outfile, tid)
os.remove(infile)
logger.info('Browse Process Success: %s', inputfile)
AddProcessDB(pds_session, fid, 't')
else:
logger.error('File %s Not Found', inputfile)
def main():
args = Args()
args.parse_args()
key = args.key
namespace = args.namespace
if namespace is None:
namespace = default_namespace
# Set up logging
logger = logging.getLogger(key)
logger.setLevel(logging.INFO)
logFileHandle = logging.FileHandler(pds_log + 'Service.log')
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s, %(message)s')
logFileHandle.setFormatter(formatter)
logger.addHandler(logFileHandle)
# Connect to database and access 'jobs' table
DBQO = PDS_DBquery('JOBS')
if key is None:
# If no key is specified, grab the first key
key = DBQO.jobKey()
try:
# Set the 'queued' column to current time i.e. prep for processing
DBQO.setJobsQueued(key)
except KeyError as e:
logger.error('%s', e)
exit(1)
logger.info('Starting Process')
xmlOBJ = jobXML(DBQO.jobXML4Key(key))
# Make directory if it doesn't exist
directory = scratch + key
if not os.path.exists(directory):
os.makedirs(directory)
logger.info('Working Area: %s', directory)
# Set up Redis Hash for ground range
RedisH = RedisHash(key + '_info')
RedisH.RemoveAll()
RedisErrorH = RedisHash(key + '_error')
RedisErrorH.RemoveAll()
RedisH_DICT = {}
RedisH_DICT['service'] = xmlOBJ.getProcess()
RedisH_DICT['fileformat'] = xmlOBJ.getOutFormat()
RedisH_DICT['outbit'] = xmlOBJ.getOutBit()
if xmlOBJ.getRangeType() is not None:
RedisH_DICT['grtype'] = xmlOBJ.getRangeType()
RedisH_DICT['minlat'] = xmlOBJ.getMinLat()
RedisH_DICT['maxlat'] = xmlOBJ.getMaxLat()
RedisH_DICT['minlon'] = xmlOBJ.getMinLon()
RedisH_DICT['maxlon'] = xmlOBJ.getMaxLon()
if RedisH.IsInHash('service'):
pass
else:
RedisH.AddHash(RedisH_DICT)
if RedisH.IsInHash('service'):
logger.info('Redis info Hash: Success')
else:
logger.error('Redis info Hash Not Found')
# End ground range
RQ_recipe = RedisQueue(key + '_recipe', namespace)
RQ_recipe.RemoveAll()
RQ_file = RedisQueue(key + '_FileQueue', namespace)
RQ_file.RemoveAll()
RQ_WorkQueue = RedisQueue(key + '_WorkQueue', namespace)
RQ_WorkQueue.RemoveAll()
RQ_loggy = RedisQueue(key + '_loggy', namespace)
RQ_loggy.RemoveAll()
RQ_zip = RedisQueue(key + '_ZIP', namespace)
RQ_zip.RemoveAll()
if xmlOBJ.getProcess() == 'POW':
fileList = xmlOBJ.getFileListWB()
elif xmlOBJ.getProcess() == 'MAP2':
fileList = xmlOBJ.getMFileListWB()
for List_file in fileList:
# Input and output file naming and path stuff
if xmlOBJ.getProcess() == 'POW':
if xmlOBJ.getInst() == 'THEMIS_IR':
Input_file = List_file.replace('odtie1_', 'odtir1_')
Input_file = Input_file.replace('xxedr', 'xxrdr')
Input_file = Input_file.replace('EDR.QUB', 'RDR.QUB')
Input_file = Input_file.replace(
'http://pdsimage.wr.usgs.gov/Missions/', archive_base)
elif xmlOBJ.getInst() == 'ISSNA':
Input_file = List_file.replace('.IMG', '.LBL')
Input_file = Input_file.replace(
'http://pdsimage.wr.usgs.gov/Missions/', archive_base)
elif xmlOBJ.getInst() == 'ISSWA':
Input_file = List_file.replace('.IMG', '.LBL')
Input_file = Input_file.replace(
'http://pdsimage.wr.usgs.gov/Missions/', archive_base)
elif xmlOBJ.getInst() == 'SOLID STATE IMAGING SYSTEM':
Input_file = List_file.replace('.img', '.lbl')
Input_file = Input_file.replace(
'http://pdsimage.wr.usgs.gov/Missions/', archive_base)
else:
Input_file = List_file.replace(
'http://pdsimage.wr.usgs.gov/Missions/', archive_base)
elif xmlOBJ.getProcess() == 'MAP2':
Input_file = List_file.replace('file://pds_san', '/pds_san')
if '+' in Input_file:
tempsplit = Input_file.split('+')
tempFile = tempsplit[0]
else:
tempFile = Input_file
label = pvl.load(tempFile)
# Output final file naming
Tbasename = os.path.splitext(os.path.basename(tempFile))[0]
splitBase = Tbasename.split('_')
labP = xmlOBJ.getProjection()
if labP == 'INPUT':
lab_proj = label['IsisCube']['Mapping']['ProjectionName'][0:4]
else:
lab_proj = labP[0:4]
if xmlOBJ.getClat() is None or xmlOBJ.getClon() is None:
basefinal = splitBase[0] + splitBase[1] + \
splitBase[2] + '_MAP2_' + lab_proj.upper()
else:
lab_clat = float(xmlOBJ.getClat())
if lab_clat >= 0:
labH = 'N'
elif lab_clat < 0:
labH = 'S'
lab_clon = float(xmlOBJ.getClon())
basefinal = splitBase[0] + splitBase[1] + splitBase[
2] + '_MAP2_' + str(lab_clat) + labH + str(
lab_clon) + '_' + lab_proj.upper()
RedisH.MAPname(basefinal)
try:
RQ_file.QueueAdd(Input_file)
logger.info('File %s Added to Redis Queue', Input_file)
except Exception as e:
logger.warn('File %s NOT Added to Redis Queue', Input_file)
print('Redis Queue Error', e)
RedisH.FileCount(RQ_file.QueueSize())
logger.info('Count of Files Queue: %s', str(RQ_file.QueueSize()))
# Map Template Stuff
logger.info('Making Map File')
mapOBJ = MakeMap()
if xmlOBJ.getProcess() == 'MAP2' and xmlOBJ.getProjection() == 'INPUT':
proj = label['IsisCube']['Mapping']['ProjectionName']
mapOBJ.Projection(proj)
else:
mapOBJ.Projection(xmlOBJ.getProjection())
if xmlOBJ.getClon() is not None:
mapOBJ.CLon(float(xmlOBJ.getClon()))
if xmlOBJ.getClat() is not None:
mapOBJ.CLat(float(xmlOBJ.getClat()))
if xmlOBJ.getFirstParallel() is not None:
mapOBJ.FirstParallel(float(xmlOBJ.getFirstParallel()))
if xmlOBJ.getSecondParallel() is not None:
mapOBJ.SecondParallel(float(xmlOBJ.getSecondParallel()))
if xmlOBJ.getResolution() is not None:
mapOBJ.PixelRes(float(xmlOBJ.getResolution()))
if xmlOBJ.getTargetName() is not None:
mapOBJ.Target(xmlOBJ.getTargetName())
if xmlOBJ.getERadius() is not None:
mapOBJ.ERadius(float(xmlOBJ.getERadius()))
if xmlOBJ.getPRadius() is not None:
mapOBJ.PRadius(float(xmlOBJ.getPRadius()))
if xmlOBJ.getLatType() is not None:
mapOBJ.LatType(xmlOBJ.getLatType())
if xmlOBJ.getLonDirection() is not None:
mapOBJ.LonDirection(xmlOBJ.getLonDirection())
if xmlOBJ.getLonDomain() is not None:
mapOBJ.LonDomain(int(xmlOBJ.getLonDomain()))
if xmlOBJ.getProcess() == 'MAP2':
if xmlOBJ.getMinLat() is not None:
mapOBJ.MinLat(float(xmlOBJ.getMinLat()))
if xmlOBJ.getMaxLat() is not None:
mapOBJ.MaxLat(float(xmlOBJ.getMaxLat()))
if xmlOBJ.getMinLon() is not None:
mapOBJ.MinLon(float(xmlOBJ.getMinLon()))
if xmlOBJ.getMaxLon() is not None:
mapOBJ.MaxLon(float(xmlOBJ.getMaxLon()))
mapOBJ.Map2pvl()
MAPfile = directory + "/" + key + '.map'
mapOBJ.Map2File(MAPfile)
try:
f = open(MAPfile)
f.close
logger.info('Map File Creation: Success')
except IOError as e:
logger.error('Map File %s Not Found', MAPfile)
# ** End Map Template Stuff **
logger.info('Building Recipe')
recipeOBJ = Recipe()
if xmlOBJ.getProcess() == 'POW':
recipeOBJ.AddJsonFile(recipe_base + xmlOBJ.getCleanName() + '.json',
"pow")
elif xmlOBJ.getProcess() == 'MAP2':
recipeOBJ.AddJsonFile(recipe_base + "map2_process.json", "map")
# Test for stretch and add to recipe
# if MAP2 and 8 or 16 bit run stretch to set range
if xmlOBJ.getOutBit() == 'input':
testBitType = str(label['IsisCube']['Core']['Pixels']['Type']).upper()
else:
testBitType = xmlOBJ.getOutBit().upper()
if xmlOBJ.getProcess() == 'MAP2' and xmlOBJ.STR_Type() is None:
if str(label['IsisCube']['Core']['Pixels']['Type']).upper(
) != xmlOBJ.getOutBit().upper() and str(
label['IsisCube']['Core']['Pixels']['Type']).upper() != 'REAL':
if str(label['IsisCube']['Core']['Pixels']
['Type']).upper() == 'SIGNEDWORD':
strpairs = '0:-32765 0:-32765 100:32765 100:32765'
elif str(label['IsisCube']['Core']['Pixels']
['Type']).upper() == 'UNSIGNEDBYTE':
strpairs = '0:1 0:1 100:254 100:254'
STRprocessOBJ = Process()
STRprocessOBJ.newProcess('stretch')
STRprocessOBJ.AddParameter('from_', 'value')
STRprocessOBJ.AddParameter('to', 'value')
STRprocessOBJ.AddParameter('usepercentages', 'yes')
STRprocessOBJ.AddParameter('pairs', strpairs)
recipeOBJ.AddProcess(STRprocessOBJ.getProcess())
strType = xmlOBJ.STR_Type()
if strType == 'StretchPercent' and xmlOBJ.STR_PercentMin(
) is not None and xmlOBJ.STR_PercentMax(
) is not None and testBitType != 'REAL':
if float(xmlOBJ.STR_PercentMin()) != 0 and float(
xmlOBJ.STR_PercentMax()) != 100:
if testBitType == 'UNSIGNEDBYTE':
strpairs = '0:1 ' + xmlOBJ.STR_PercentMin() + ':1 ' + \
xmlOBJ.STR_PercentMax() + ':254 100:254'
elif testBitType == 'SIGNEDWORD':
strpairs = '0:-32765 ' + xmlOBJ.STR_PercentMin() + ':-32765 ' + \
xmlOBJ.STR_PercentMax() + ':32765 100:32765'
STRprocessOBJ = Process()
STRprocessOBJ.newProcess('stretch')
STRprocessOBJ.AddParameter('from_', 'value')
STRprocessOBJ.AddParameter('to', 'value')
STRprocessOBJ.AddParameter('usepercentages', 'yes')
STRprocessOBJ.AddParameter('pairs', strpairs)
recipeOBJ.AddProcess(STRprocessOBJ.getProcess())
elif strType == 'GaussStretch':
STRprocessOBJ = Process()
STRprocessOBJ.newProcess('gaussstretch')
STRprocessOBJ.AddParameter('from_', 'value')
STRprocessOBJ.AddParameter('to', 'value')
STRprocessOBJ.AddParameter('gsigma', xmlOBJ.STR_GaussSigma())
recipeOBJ.AddProcess(STRprocessOBJ.getProcess())
elif strType == 'HistogramEqualization':
STRprocessOBJ = Process()
STRprocessOBJ.newProcess('histeq')
STRprocessOBJ.AddParameter('from_', 'value')
STRprocessOBJ.AddParameter('to', 'value')
if xmlOBJ.STR_PercentMin() is None:
STRprocessOBJ.AddParameter('minper', '0')
else:
STRprocessOBJ.AddParameter('minper', xmlOBJ.STR_PercentMin())
if xmlOBJ.STR_PercentMax() is None:
STRprocessOBJ.AddParameter('maxper', '100')
else:
STRprocessOBJ.AddParameter('maxper', xmlOBJ.STR_PercentMax())
recipeOBJ.AddProcess(STRprocessOBJ.getProcess())
elif strType == 'SigmaStretch':
STRprocessOBJ = Process()
STRprocessOBJ.newProcess('sigmastretch')
STRprocessOBJ.AddParameter('from_', 'value')
STRprocessOBJ.AddParameter('to', 'value')
STRprocessOBJ.AddParameter('variance', xmlOBJ.STR_SigmaVariance())
recipeOBJ.AddProcess(STRprocessOBJ.getProcess())
# Test for output bit type and add to recipe
if xmlOBJ.getProcess() == 'POW':
if xmlOBJ.getOutBit().upper() == 'UNSIGNEDBYTE' or xmlOBJ.getOutBit(
).upper() == 'SIGNEDWORD':
CAprocessOBJ = Process()
CAprocessOBJ.newProcess('cubeatt-bit')
CAprocessOBJ.AddParameter('from_', 'value')
CAprocessOBJ.AddParameter('to', 'value')
recipeOBJ.AddProcess(CAprocessOBJ.getProcess())
elif xmlOBJ.getProcess() == 'MAP2':
if xmlOBJ.getOutBit().upper() != 'INPUT':
if xmlOBJ.getOutBit().upper(
) == 'UNSIGNEDBYTE' or xmlOBJ.getOutBit().upper() == 'SIGNEDWORD':
if str(label['IsisCube']['Core']['Pixels']
['Type']).upper() != xmlOBJ.getOutBit().upper():
CAprocessOBJ = Process()
CAprocessOBJ.newProcess('cubeatt-bit')
CAprocessOBJ.AddParameter('from_', 'value')
CAprocessOBJ.AddParameter('to', 'value')
recipeOBJ.AddProcess(CAprocessOBJ.getProcess())
# Add Grid(MAP2)
if xmlOBJ.getGridInterval() is not None:
GprocessOBJ = Process()
GprocessOBJ.newProcess('grid')
GprocessOBJ.AddParameter('from_', 'value')
GprocessOBJ.AddParameter('to', 'value')
GprocessOBJ.AddParameter('latinc', xmlOBJ.getGridInterval())
GprocessOBJ.AddParameter('loninc', xmlOBJ.getGridInterval())
GprocessOBJ.AddParameter('outline', 'yes')
GprocessOBJ.AddParameter('boundary', 'yes')
GprocessOBJ.AddParameter('linewidth', '3')
recipeOBJ.AddProcess(GprocessOBJ.getProcess())
# OUTPUT FORMAT
# Test for GDAL and add to recipe
Oformat = xmlOBJ.getOutFormat()
if Oformat == 'GeoTiff-BigTiff' or Oformat == 'GeoJPEG-2000' or Oformat == 'JPEG' or Oformat == 'PNG':
if Oformat == 'GeoJPEG-2000':
Oformat = 'JP2KAK'
if Oformat == 'GeoTiff-BigTiff':
Oformat = 'GTiff'
GDALprocessOBJ = Process()
# @TODO remove hard-coded path in favor of using whichever utilities are found within the conda environment --
# we need more information here to ensure that whichever utilities are found are capable of supporting GeoJPEG-2000.
GDALprocessOBJ.newProcess('/usgs/apps/anaconda/bin/gdal_translate')
if xmlOBJ.getOutBit() != 'input':
GDALprocessOBJ.AddParameter(
'-ot', GDALprocessOBJ.GDAL_OBit(xmlOBJ.getOutBit()))
GDALprocessOBJ.AddParameter('-of', Oformat)
if Oformat == 'GTiff' or Oformat == 'JP2KAK' or Oformat == 'JPEG':
GDALprocessOBJ.AddParameter('-co',
GDALprocessOBJ.GDAL_Creation(Oformat))
recipeOBJ.AddProcess(GDALprocessOBJ.getProcess())
# set up pds2isis and add to recipe
elif Oformat == 'PDS':
pdsProcessOBJ = Process()
pdsProcessOBJ.newProcess('isis2pds')
pdsProcessOBJ.AddParameter('from_', 'value')
pdsProcessOBJ.AddParameter('to', 'value')
if xmlOBJ.getOutBit() == 'unsignedbyte':
pdsProcessOBJ.AddParameter('bittype', '8bit')
elif xmlOBJ.getOutBit() == 'signedword':
pdsProcessOBJ.AddParameter('bittype', 's16bit')
recipeOBJ.AddProcess(pdsProcessOBJ.getProcess())
for item in recipeOBJ.getProcesses():
processOBJ = Process()
processOBJ.ProcessFromRecipe(item, recipeOBJ.getRecipe())
if item == 'cam2map':
processOBJ.updateParameter('map', MAPfile)
if xmlOBJ.getResolution() is None:
processOBJ.updateParameter('pixres', 'CAMERA')
else:
processOBJ.updateParameter('pixres', 'MAP')
if xmlOBJ.getRangeType() is None:
processOBJ.updateParameter('defaultrange', 'MINIMIZE')
elif xmlOBJ.getRangeType() == 'smart' or xmlOBJ.getRangeType(
) == 'fill':
processOBJ.updateParameter('defaultrange', 'CAMERA')
processOBJ.AddParameter('trim', 'YES')
elif item == 'map2map':
processOBJ.updateParameter('map', MAPfile)
if xmlOBJ.getResolution() is None:
processOBJ.updateParameter('pixres', 'FROM')
else:
processOBJ.updateParameter('pixres', 'MAP')
if xmlOBJ.OutputGeometry() is not None:
processOBJ.updateParameter('defaultrange', 'MAP')
processOBJ.AddParameter('trim', 'YES')
else:
processOBJ.updateParameter('defaultrange', 'FROM')
processJSON = processOBJ.Process2JSON()
try:
RQ_recipe.QueueAdd(processJSON)
logger.info('Recipe Element Added to Redis: %s : Success', item)
except Exception as e:
logger.warn('Recipe Element NOT Added to Redis: %s', item)
# HPC job stuff
logger.info('HPC Cluster job Submission Starting')
jobOBJ = HPCjob()
jobOBJ.setJobName(key + '_Service')
jobOBJ.setStdOut(slurm_log + key + '_%A_%a.out')
jobOBJ.setStdError(slurm_log + key + '_%A_%a.err')
jobOBJ.setWallClock('24:00:00')
jobOBJ.setMemory('24576')
jobOBJ.setPartition('pds')
JAsize = RQ_file.QueueSize()
jobOBJ.setJobArray(JAsize)
logger.info('Job Array Size : %s', str(JAsize))
# @TODO replace with source activate <env>
#jobOBJ.addPath('/usgs/apps/anaconda/bin')
# Whether or not we use the default namespace, this guarantees that the POW/MAP queues will match the namespace
# used in the job manager.
if xmlOBJ.getProcess() == 'POW':
cmd = cmd_dir + "POWprocess.py -k {} -n {}".format(key, namespace)
elif xmlOBJ.getProcess() == 'MAP2':
cmd = cmd_dir + "MAPprocess.py -k {} -n {}".format(key, namespace)
logger.info('HPC Command: %s', cmd)
jobOBJ.setCommand(cmd)
SBfile = directory + '/' + key + '.sbatch'
jobOBJ.MakeJobFile(SBfile)
try:
sb = open(SBfile)
sb.close
logger.info('SBATCH File Creation: Success')
except IOError as e:
logger.error('SBATCH File %s Not Found', SBfile)
try:
jobOBJ.Run()
logger.info('Job Submission to HPC: Success')
DBQO.setJobsStarted(key)
except IOError as e:
logger.error('Jobs NOT Submitted to HPC')