fgreg commented on a change in pull request #61: SDAP-105 DOMS matchup netcdf
and csv generation
URL:
https://github.com/apache/incubator-sdap-nexus/pull/61#discussion_r243469680
##########
File path: analysis/webservice/algorithms/doms/BaseDomsHandler.py
##########
@@ -560,165 +392,245 @@ def __addNetCDFConstants(dataset):
dataset.publisher_name = "NASA PO.DAAC"
dataset.publisher_email = "[email protected]"
dataset.publisher_url = "https://podaac.jpl.nasa.gov";
- dataset.acknowledgment = "DOMS is a NASA/AIST-funded project. Grant
number ####."
-
-
-class DomsNetCDFFormatterAlt:
- @staticmethod
- def create(executionId, results, params, details):
- t = tempfile.mkstemp(prefix="doms_", suffix=".nc")
- tempFileName = t[1]
-
- dataset = Dataset(tempFileName, "w", format="NETCDF4")
-
- dataset.matchID = executionId
- dataset.Matchup_TimeWindow = params["timeTolerance"]
- dataset.Matchup_TimeWindow_Units = "hours"
-
- dataset.time_coverage_start =
datetime.fromtimestamp(params["startTime"] / 1000).strftime('%Y%m%d %H:%M:%S')
- dataset.time_coverage_end = datetime.fromtimestamp(params["endTime"] /
1000).strftime('%Y%m%d %H:%M:%S')
- dataset.depth_min = params["depthMin"]
- dataset.depth_max = params["depthMax"]
- dataset.platforms = params["platforms"]
-
- dataset.Matchup_SearchRadius = params["radiusTolerance"]
- dataset.Matchup_SearchRadius_Units = "m"
-
- dataset.bounding_box = params["bbox"]
- dataset.primary = params["primary"]
- dataset.secondary = ",".join(params["matchup"])
-
- dataset.Matchup_ParameterPrimary = params["parameter"] if "parameter"
in params else ""
-
- dataset.time_coverage_resolution = "point"
-
- bbox = geo.BoundingBox(asString=params["bbox"])
- dataset.geospatial_lat_max = bbox.north
- dataset.geospatial_lat_min = bbox.south
- dataset.geospatial_lon_max = bbox.east
- dataset.geospatial_lon_min = bbox.west
- dataset.geospatial_lat_resolution = "point"
- dataset.geospatial_lon_resolution = "point"
- dataset.geospatial_lat_units = "degrees_north"
- dataset.geospatial_lon_units = "degrees_east"
- dataset.geospatial_vertical_min = 0.0
- dataset.geospatial_vertical_max = params["radiusTolerance"]
- dataset.geospatial_vertical_units = "m"
- dataset.geospatial_vertical_resolution = "point"
- dataset.geospatial_vertical_positive = "down"
-
- dataset.time_to_complete = details["timeToComplete"]
- dataset.num_insitu_matched = details["numInSituMatched"]
- dataset.num_gridded_checked = details["numGriddedChecked"]
- dataset.num_gridded_matched = details["numGriddedMatched"]
- dataset.num_insitu_checked = details["numInSituChecked"]
-
- dataset.date_modified = datetime.now().strftime('%Y%m%d %H:%M:%S')
- dataset.date_created = datetime.now().strftime('%Y%m%d %H:%M:%S')
-
- DomsNetCDFFormatterAlt.__addNetCDFConstants(dataset)
-
- satelliteGroup = dataset.createGroup("SatelliteData")
- satelliteWriter = DomsNetCDFValueWriter(satelliteGroup)
-
- insituGroup = dataset.createGroup("InsituData")
- insituWriter = DomsNetCDFValueWriter(insituGroup)
-
- matches = DomsNetCDFFormatterAlt.__writeResults(results,
satelliteWriter, insituWriter)
-
- satelliteWriter.commit()
- insituWriter.commit()
-
- satDim = dataset.createDimension("satellite_ids", size=None)
- satVar = dataset.createVariable("satellite_ids", "i4",
("satellite_ids",), chunksizes=(2048,),
- fill_value=-32767)
-
- satVar[:] = [f[0] for f in matches]
-
- insituDim = dataset.createDimension("insitu_ids", size=None)
- insituVar = dataset.createVariable("insitu_ids", "i4",
("insitu_ids",), chunksizes=(2048,),
- fill_value=-32767)
- insituVar[:] = [f[1] for f in matches]
-
- dataset.close()
-
- f = open(tempFileName, "rb")
- data = f.read()
- f.close()
- os.unlink(tempFileName)
- return data
+ dataset.acknowledgment = "DOMS is a NASA/AIST-funded project. NRA
NNH14ZDA001N."
@staticmethod
def __writeResults(results, satelliteWriter, insituWriter):
ids = {}
matches = []
-
insituIndex = 0
for r in range(0, len(results)):
result = results[r]
- satelliteWriter.write(result)
+ satelliteWriter.addData(result)
for match in result["matches"]:
if match["id"] not in ids:
ids[match["id"]] = insituIndex
insituIndex += 1
- insituWriter.write(match)
+ insituWriter.addData(match)
matches.append((r, ids[match["id"]]))
- return matches
+ satelliteWriter.writeGroup()
+ insituWriter.writeGroup()
- @staticmethod
- def __addNetCDFConstants(dataset):
- dataset.bnds = 2
- dataset.Conventions = "CF-1.6, ACDD-1.3"
- dataset.title = "DOMS satellite-insitu machup output file"
- dataset.history = "Processing_Version = V1.0, Software_Name = DOMS,
Software_Version = 1.03"
- dataset.institution = "JPL, FSU, NCAR"
- dataset.source = "doms.jpl.nasa.gov"
- dataset.standard_name_vocabulary = "CF Standard Name Table v27", "BODC
controlled vocabulary"
- dataset.cdm_data_type = "Point/Profile, Swath/Grid"
- dataset.processing_level = "4"
- dataset.platform = "Endeavor"
- dataset.instrument = "Endeavor on-board sea-bird SBE 9/11 CTD"
- dataset.project = "Distributed Oceanographic Matchup System (DOMS)"
- dataset.keywords_vocabulary = "NASA Global Change Master Directory
(GCMD) Science Keywords"
- dataset.keywords = "Salinity, Upper Ocean, SPURS, CTD, Endeavor,
Atlantic Ocean"
- dataset.creator_name = "NASA PO.DAAC"
- dataset.creator_email = "[email protected]"
- dataset.creator_url = "https://podaac.jpl.nasa.gov/";
- dataset.publisher_name = "NASA PO.DAAC"
- dataset.publisher_email = "[email protected]"
- dataset.publisher_url = "https://podaac.jpl.nasa.gov";
- dataset.acknowledgment = "DOMS is a NASA/AIST-funded project. Grant
number ####."
+ return matches
class DomsNetCDFValueWriter:
def __init__(self, group):
- self.latVar = DomsNetCDFValueWriter.__createDimension(group, "lat",
"f4")
- self.lonVar = DomsNetCDFValueWriter.__createDimension(group, "lon",
"f4")
- self.sstVar = DomsNetCDFValueWriter.__createDimension(group,
"sea_water_temperature", "f4")
- self.timeVar = DomsNetCDFValueWriter.__createDimension(group, "time",
"f4")
+ group.createDimension("dim", size=None)
+ self.group = group
self.lat = []
self.lon = []
- self.sst = []
self.time = []
+ self.sea_water_salinity = []
+ self.wind_speed = []
+ self.wind_u = []
+ self.wind_v = []
+ self.wind_direction = []
+ self.sea_water_temperature = []
+ self.depth = []
+
+ def addData(self, value):
+ self.lat.append(value.get("y", None))
+ self.lon.append(value.get("x", None))
+ self.time.append(time.mktime(value.get("time").timetuple()))
+ self.sea_water_salinity.append(value.get("sea_water_salinity", None))
+ self.wind_speed.append(value.get("wind_speed", None))
+ self.wind_u.append(value.get("wind_u", None))
+ self.wind_v.append(value.get("wind_v", None))
+ self.wind_direction.append(value.get("wind_direction", None))
+ self.sea_water_temperature.append(value.get("sea_water_temperature",
None))
+
+ #
+ # Compress multiple depth variables into one depth array
+ #
+ if value.get("sea_water_temperature_depth") is not None:
+ self.depth.append(value.get("sea_water_temperature_depth"))
+ elif value.get("sea_water_salinity_depth") is not None:
+ self.depth.append(value.get("sea_water_salinity_depth"))
+ else:
+ self.depth.append(None)
+
+ def writeGroup(self):
+ #
+ # Create variables, enrich with attributes, and add data
+ #
+ lonVar = self.group.createVariable("lon", "f4", ("dim",),
fill_value=-32767.0)
+ latVar = self.group.createVariable("lat", "f4", ("dim",),
fill_value=-32767.0)
+ timeVar = self.group.createVariable("time", "f4", ("dim",),
fill_value=-32767.0)
+
+ self.__enrichLon(lonVar, min(self.lon), max(self.lon))
+ self.__enrichLat(latVar, min(self.lat), max(self.lat))
+ self.__enrichTime(timeVar)
+
+ latVar[:] = self.lat
+ lonVar[:] = self.lon
+ timeVar[:] = self.time
+
+ if self.sea_water_salinity.count(None) != len(self.sea_water_salinity):
+ if self.group.name == "SatelliteData":
Review comment:
Check against a variable instead of a string
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