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ql_viirs_edr.py
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ql_viirs_edr.py
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#!/usr/bin/env python
# encoding: utf-8
"""
ql_viirs_edr.py
Purpose: Create quicklook PNGs for VIIRS EDR products.
Minimum commandline...
export CSPP_EDR_HOME=$(readlink -f /path/to/EDR)
source $CSPP_EDR_HOME/cspp_edr_env.sh
python ql_viirs_edr.py -g '/path/to/files/GMTCO*.h5' -i '/path/to/files/IICMO*.h5' -p VCM
or
python ql_viirs_edr.py --geo_file=/path/to/files/GMTCO*.h5 --ip_file=/path/to/files/IICMO*.h5 -p VCM
Created by Geoff Cureton on 2012-11-13.
Copyright (c) 2012 University of Wisconsin SSEC. All rights reserved.
"""
file_Date = '$Date$'
file_Revision = '$Revision$'
file_Author = '$Author$'
file_HeadURL = '$HeadURL$'
file_Id = '$Id$'
__author__ = 'G.P. Cureton <[email protected]>'
__version__ = '$Id$'
__docformat__ = 'Epytext'
import string, sys, traceback
from glob import glob
from os import path, uname
from time import time
import traceback
import numpy as np
from numpy import ma as ma
import scipy as scipy
import matplotlib
import matplotlib.cm as cm
from matplotlib.colors import ListedColormap
from matplotlib.figure import Figure
matplotlib.use('Agg')
from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas
# This must come *after* the backend is specified.
import matplotlib.pyplot as ppl
from mpl_toolkits.basemap import Basemap
import optparse as optparse
from ViirsData import ViirsTrimTable
import viirs_edr_data
import viirs_cloud_mask as viirsCM
import viirs_cloud_products as viirsCld
import viirs_aerosol_products as viirsAero
import viirs_sst_products as viirsSST
import viirs_vi_products as viirsVI
import viirs_st_products as viirsST
import viirs_lst_products as viirsLST
import tables as pytables
from tables import exceptions as pyEx
# every module should have a LOG object
# e.g. LOG.warning('my dog has fleas')
import logging
LOG = logging.getLogger(__file__)
###################################################
# Global Data #
###################################################
# VCM dataset selection
#global cmByte,cmBit
def set_vcm_dset(newCmByte,newCmBit) :
global cmByte,cmBit
cmByte,cmBit = newCmByte,newCmBit
###################################
# Get File Lists #
###################################
def granuleFiles(geoGlob,prodGlob):
'''
Returns sorted lists of the geolocation and product files.
'''
geoDir = path.dirname(path.abspath(path.expanduser(geoGlob)))
prodDir = path.dirname(path.abspath(path.expanduser(prodGlob)))
LOG.debug("Initial geoGlob = ",geoGlob)
LOG.debug("Initial prodGlob = ",prodGlob)
geoGlob = path.basename(path.abspath(path.expanduser(geoGlob)))
prodGlob = path.basename(path.abspath(path.expanduser(prodGlob)))
geoPrefix = string.split(geoGlob,'_')[0]
LOG.debug("geoDir = ",geoDir)
LOG.debug("prodDir = ",prodDir)
LOG.debug("geoGlob = ",geoGlob)
LOG.debug("prodGlob = ",prodGlob)
LOG.debug("geoPrefix = ",geoPrefix)
geoList_in = glob("%s/%s" % (geoDir,geoGlob))
prodList_in = glob("%s/%s" % (prodDir,prodGlob))
geoList_in.sort()
prodList_in.sort()
#LOG.debug("prodList_in...")
#for prodFile in prodList_in:
#LOG.debug(prodFile)
geoList = []
prodList = []
#prodList = prodList_in
for files in prodList_in :
prod_arr = string.split(path.basename(files),"_")
#LOG.debug("prod_arr = ",prod_arr
dateStamp = prod_arr[2]
timeStamp = prod_arr[3]
geoFileGlob="%s/%s*%s_%s*.h5" % (geoDir,geoPrefix,dateStamp,timeStamp)
#LOG.debug("dateStamp = ",dateStamp)
#LOG.debug("timeStamp = ",timeStamp)
#LOG.debug("geoFileGlob = ",geoFileGlob)
geoFile = glob("%s/%s*%s_%s*.h5" % (geoDir,geoPrefix,dateStamp,timeStamp))
if (np.shape(geoFile)[0] != 0) :
geoList.append(geoFile[0])
prodList.append(files)
else :
#geoList.append(files)
LOG.debug(" ... no match found for {}, appending {}".format( geoFile, files))
pass
for geoFile,prodFile in zip(geoList,prodList):
LOG.debug("{},{}".format(geoFile,prodFile))
return geoList,prodList
###################################################
# Granulation Functions #
###################################################
def gran_VCM(geoList,cmList,shrink=1):
'''
Returns the granulated VCM
'''
global cmByte,cmBit
# Define the colourmap we want to use.
LOG.debug("Importing the CloudMaskProduct object...")
CloudMaskProduct = viirs_edr_data.CloudMaskData
LOG.debug("done")
try :
reload(viirsCM)
reload(viirs_edr_data)
del(viirsCMobj)
del(latArr)
del(lonArr)
del(cmArr)
del(qualArr)
except :
pass
LOG.debug("Creating viirsCMobj...")
viirsCMobj = viirsCM.viirsCM()
LOG.debug("done")
# Determine the correct fillValue
trimObj = ViirsTrimTable()
eps = 1.e-6
for grans in np.arange(len(geoList)):
LOG.debug("\nIngesting granule {} using cmByte={} and cmBit={} ...".format(grans,cmByte,cmBit))
retArr = viirsCMobj.ingest(geoList[grans],cmList[grans],cmByte,cmBit,shrink)
try :
latArr = np.vstack((latArr,viirsCMobj.Lat[:,:]))
lonArr = np.vstack((lonArr,viirsCMobj.Lon[:,:]))
except NameError :
latArr = viirsCMobj.Lat[:,:]
lonArr = viirsCMobj.Lon[:,:]
try :
cmArr = np.vstack((cmArr,viirsCMobj.ViirsCMaskSDS[:,:]))
qualArr = np.vstack((qualArr,viirsCMobj.ViirsCMquality[:,:]))
except NameError :
cmArr = viirsCMobj.ViirsCMaskSDS[:,:]
qualArr = viirsCMobj.ViirsCMquality[:,:]
LOG.debug("Intermediate latArr.shape = {}".format(str(latArr.shape)))
LOG.debug("Intermediate lonArr.shape = {}".format(str(lonArr.shape)))
LOG.debug("Intermediate cmArr.shape = {}".format(str(cmArr.shape)))
LOG.debug("Intermediate qualArr.shape = {}".format(str(qualArr.shape)))
lat_0 = latArr[np.shape(latArr)[0]/2,np.shape(latArr)[1]/2]
lon_0 = lonArr[np.shape(lonArr)[0]/2,np.shape(lonArr)[1]/2]
try :
# Determine masks for each fill type, for the VCM IP
cmFillMasks = {}
for fillType in trimObj.sdrTypeFill.keys() :
fillValue = trimObj.sdrTypeFill[fillType][cmArr.dtype.name]
if 'float' in fillValue.__class__.__name__ :
cmFillMasks[fillType] = ma.masked_inside(cmArr,fillValue-eps,fillValue+eps).mask
if (cmFillMasks[fillType].__class__.__name__ != 'ndarray') :
cmFillMasks[fillType] = None
elif 'int' in fillValue.__class__.__name__ :
cmFillMasks[fillType] = ma.masked_equal(cmArr,fillValue).mask
if (cmFillMasks[fillType].__class__.__name__ != 'ndarray') :
cmFillMasks[fillType] = None
else :
LOG.debug("Dataset was neither int not float... a worry")
pass
# Construct the total mask from all of the various fill values
totalMask = ma.array(np.zeros(cmArr.shape,dtype=np.bool))
for fillType in trimObj.sdrTypeFill.keys() :
if cmFillMasks[fillType] is not None :
totalMask = totalMask * ma.array(np.zeros(cmArr.shape,dtype=np.bool),\
mask=cmFillMasks[fillType])
# Define the masks, and mask the main dataset
ViirsCMqualityMask = ma.masked_equal(qualArr,0)
ViirsCMclearMask = ma.masked_equal(cmArr,1)
if cmByte==0 and cmBit==1 :
totalMask = totalMask * ViirsCMqualityMask
elif cmByte==5 and cmBit==0 :
totalMask = totalMask * ViirsCMqualityMask * ViirsCMclearMask
try :
data = ma.array(cmArr,mask=totalMask.mask)
lats = ma.array(latArr,mask=totalMask.mask)
lons = ma.array(lonArr,mask=totalMask.mask)
except ma.core.MaskError :
LOG.debug(">> error: Mask Error, probably mismatched geolocation and product array sizes, aborting...")
sys.exit(1)
except Exception, err :
LOG.debug(">> error: {}...".format(str(err)))
sys.exit(1)
return lats,lons,data,lat_0,lon_0
def gran_COP(geoList,copList,dataSet,shrink=1):
'''
Returns the granulated COP dataset
'''
try :
reload(viirsCld)
reload(viirs_edr_data)
del(viirsCldObj)
del(latArr)
del(lonArr)
del(copArr)
del(phaseArr)
except :
pass
LOG.debug("Creating viirsCldObj...")
reload(viirsCld)
viirsCldObj = viirsCld.viirsCld()
LOG.debug("done")
# Determine the correct fillValue
trimObj = ViirsTrimTable()
eps = 1.e-6
for grans in np.arange(len(geoList)):
LOG.debug("Ingesting granule {} ...".format(grans))
retArr = viirsCldObj.ingestLite(geoList[grans],copList[grans],dataSet,1)
LOG.debug("done")
try :
latArr = viirsCldObj.Lat[:,:]
lonArr = viirsCldObj.Lon[:,:]
lat_0 = latArr[np.shape(latArr)[0]/2,np.shape(latArr)[1]/2]
lon_0 = lonArr[np.shape(lonArr)[0]/2,np.shape(lonArr)[1]/2]
badGeo = False
if not (-90. <= lat_0 <= 90.) :
LOG.debug("\n>> error: Latitude of granule midpoint ({}) does not satisfy (-90. <= lat_0 <= 90.)\nfor file {}\n\taborting...".format(lat_0,geoList[grans]))
badGeo = True
if not (-180. <= lat_0 <= 180.) :
LOG.debug("\n>> error: Longitude of granule midpoint ({}) does not satisfy (-180. <= lon_0 <= 180.)\nfor file {}\n\taborting...".format(lon_0,geoList[grans]))
badGeo = True
if badGeo :
sys.exit(1)
copArr = viirsCldObj.ViirsCProdSDS[:,:]
phaseArr = viirsCldObj.ViirsCProdSDSphase[:,:]
# Determine masks for each fill type, for the COP IP
copFillMasks = {}
for fillType in trimObj.sdrTypeFill.keys() :
fillValue = trimObj.sdrTypeFill[fillType][copArr.dtype.name]
if 'float' in fillValue.__class__.__name__ :
copFillMasks[fillType] = ma.masked_inside(copArr,fillValue-eps,fillValue+eps).mask
if (copFillMasks[fillType].__class__.__name__ != 'ndarray') :
copFillMasks[fillType] = None
elif 'int' in fillValue.__class__.__name__ :
copFillMasks[fillType] = ma.masked_equal(copArr,fillValue).mask
if (copFillMasks[fillType].__class__.__name__ != 'ndarray') :
copFillMasks[fillType] = None
else :
LOG.debug("Dataset was neither int not float... a worry")
pass
# Construct the total mask from all of the various fill values
totalMask = ma.array(np.zeros(copArr.shape,dtype=np.bool))
for fillType in trimObj.sdrTypeFill.keys() :
if copFillMasks[fillType] is not None :
totalMask = totalMask * ma.array(np.zeros(copArr.shape,dtype=np.bool),\
mask=copFillMasks[fillType])
# Added the "bad data" from the COP phase quality flag.
totalMask = totalMask * ma.masked_equal(phaseArr,0)
try :
data = ma.array(copArr, mask=totalMask.mask)
phase = ma.array(phaseArr,mask=totalMask.mask)
lats = ma.array(latArr, mask=totalMask.mask)
lons = ma.array(lonArr, mask=totalMask.mask)
except ma.core.MaskError :
LOG.debug(">> error: Mask Error, probably mismatched geolocation and product array sizes, aborting...")
sys.exit(1)
except :
LOG.debug(">> error: there was an exception...")
sys.exit(1)
return lats,lons,data,phase,lat_0,lon_0
def gran_COT_EDR(geoList,cotList,shrink=1):
'''
Returns the granulated COT EDR
'''
try :
reload(viirsAero)
reload(viirs_edr_data)
del(viirsAeroObj)
del(latArr)
del(lonArr)
del(cotArr)
except :
pass
LOG.debug("Creating viirsCldObj...")
reload(viirsCld)
viirsCldObj = viirsCld.viirsCld()
LOG.debug("done")
# Determine the correct fillValue
trimObj = ViirsTrimTable()
eps = 1.e-6
for grans in np.arange(len(geoList)):
LOG.debug("Ingesting EDR granule {} ...".format(grans))
# Read in geolocation...
ViirsGeoFileName = geoList[grans]
if(pytables.isHDF5File(ViirsGeoFileName)) :
try :
ViirsGeoFileObj = pytables.openFile(ViirsGeoFileName,mode='r')
LOG.debug("Successfully opened geolocation file",ViirsGeoFileName)
except IOError :
LOG.debug(">> error: Could not open geolocation file: ",ViirsGeoFileName)
sys.exit(1)
# Detemine the geolocation group name and related information
#group = getobj(ViirsGeoFileObj,'/All_Data')
group = ViirsGeoFileObj.getNode('/All_Data')
geoGroupName = '/All_Data/'+group.__members__[0]
group._g_close()
LOG.debug("Geolocation Group : {} ".format(geoGroupName))
isEdrGeo = ('VIIRS-CLD-AGG-GEO_All' in geoGroupName)
if not isEdrGeo :
LOG.debug(">> error: {} is not an EDR resolution cloud geolocation file\n\taborting...".format(ViirsGeoFileName))
sys.exit(1)
# Get the geolocation Latitude and Longitude nodes...
try :
dataName = 'Latitude'
geoLatNode = ViirsGeoFileObj.getNode(geoGroupName+'/'+dataName)
LOG.debug("Shape of {} node is {}".format(geoGroupName+'/'+dataName,repr(geoLatNode.shape)))
dataName = 'Longitude'
geoLonNode = ViirsGeoFileObj.getNode(geoGroupName+'/'+dataName)
LOG.debug("Shape of {} node is {}".format(geoGroupName+'/'+dataName,repr(geoLonNode.shape)))
except pyEx.NoSuchNodeError :
LOG.debug("\n>> error: No required node {}/{} in {}\n\taborting...".format(geoGroupName,dataName,ViirsGeoFileName))
ViirsGeoFileObj.close()
sys.exit(1)
# Make a copy of the geolocation node data, so we can close the file
try :
dataName = 'Latitude'
LOG.debug("Reading {} dataset...".format(dataName))
latArr = geoLatNode[:,:]
geoLatNode.close()
latArr = np.squeeze(latArr)
LOG.debug("done")
dataName = 'Longitude'
LOG.debug("Reading {} dataset...".format(dataName))
lonArr = geoLonNode[:,:]
geoLonNode.close()
lonArr = np.squeeze(lonArr)
LOG.debug("done")
LOG.debug("Closing geolocation file")
ViirsGeoFileObj.close()
except :
LOG.debug("\n>> error: Could not retrieve %/% node data in {}\n\taborting...".format(geoGroupName,dataName,ViirsGeoFileName))
geoLatNode.close()
geoLonNode.close()
ViirsGeoFileObj.close()
sys.exit(1)
else :
LOG.debug("\n>> error: {} is not a HDF5 file,\n\taborting...".format(ViirsGeoFileName))
sys.exit(1)
# Read in dataSets...
ViirsEDRFileName = cotList[grans]
if(pytables.isHDF5File(ViirsEDRFileName)) :
try :
ViirsEDRFileObj = pytables.openFile(ViirsEDRFileName,mode='r')
LOG.debug("Successfully opened edr file",ViirsEDRFileName)
except IOError :
LOG.debug(">> error: Could not open edr file: ",ViirsEDRFileName)
sys.exit(1)
# Detemine the edr group name and related information
#group = getobj(ViirsEDRFileObj,'/All_Data')
group = ViirsEDRFileObj.getNode('/All_Data')
edrGroupName = '/All_Data/'+group.__members__[0]
group._g_close()
LOG.debug("Edr Group : {} ".format(edrGroupName))
isEdr = ('VIIRS-COT-EDR_All' in edrGroupName)
if not isEdr :
LOG.debug(">> error: {} is not an EDR resolution cloud file\n\taborting...".format(ViirsEDRFileName))
sys.exit(1)
# Get the edr nodes...
try :
dataName = 'AverageCloudOpticalThickness'
cotNode = ViirsEDRFileObj.getNode(edrGroupName+'/'+dataName)
LOG.debug("Shape of {} node is {}".format(edrGroupName+'/'+dataName,repr(cotNode.shape)))
dataName = 'COTFactors'
cotFactorsNode = ViirsEDRFileObj.getNode(edrGroupName+'/'+dataName)
LOG.debug("Shape of {} node is {}".format(edrGroupName+'/'+dataName,repr(cotFactorsNode.shape)))
dataName = 'QF3_VIIRSCOTAVGEDR'
QF3_VIIRSCOTAVGEDR_Node = ViirsEDRFileObj.getNode(edrGroupName+'/'+dataName)
LOG.debug("Shape of {} node is {}".format(edrGroupName+'/'+dataName,repr(QF3_VIIRSCOTAVGEDR_Node.shape)))
except pyEx.NoSuchNodeError :
LOG.debug("\n>> error: No required node {}/{} in {}\n\taborting...".format(edrGroupName,dataName,ViirsEDRFileName))
ViirsEDRFileObj.close()
sys.exit(1)
# Make a copy of the edr node data, so we can close the file
try :
dataName = 'AverageCloudOpticalThickness'
LOG.debug("Reading {} dataset...".format(dataName))
cot = cotNode[:,:]
cot = np.squeeze(cot)
cotNode.close()
LOG.debug("done")
dataName = 'COTFactors'
LOG.debug("Reading {} dataset...".format(dataName))
cotFactors = cotFactorsNode[:]
cotFactors = np.squeeze(cotFactors)
cotFactorsNode.close()
LOG.debug("done")
dataName = 'QF3_VIIRSCOTAVGEDR'
LOG.debug("Reading {} dataset...".format(dataName))
cloudConf = np.bitwise_and(QF3_VIIRSCOTAVGEDR_Node[:,:],3) >> 0
waterCldFrac = np.bitwise_and(QF3_VIIRSCOTAVGEDR_Node[:,:],12) >> 2
mixedCldFrac = np.bitwise_and(QF3_VIIRSCOTAVGEDR_Node[:,:],192) >> 6
QF3_VIIRSCOTAVGEDR_Node.close()
LOG.debug("done")
LOG.debug("Closing edr file")
ViirsEDRFileObj.close()
LOG.debug("Shape of cot is {}".format(repr(np.shape(cot))))
LOG.debug("Shape of latsArr is {}".format(repr(np.shape(latArr))))
LOG.debug("Shape of lonsArr is {}".format(repr(np.shape(lonArr))))
except :
LOG.debug("\n>> error: Could not retrieve %/% node data in {}\n\taborting...".format(edrGroupName,dataName,ViirsEDRFileName))
cotNode.close()
cotFactorsNode.close()
QF3_VIIRSCOTAVGEDR_Node.close()
ViirsEDRFileObj.close()
sys.exit(1)
else :
LOG.debug("\n>> error: {} is not a HDF5 file,\n\taborting...".format(ViirsEDRFileName))
sys.exit(1)
LOG.debug("Creating some masks")
try :
lat_0 = latArr[np.shape(latArr)[0]/2,np.shape(latArr)[1]/2]
lon_0 = lonArr[np.shape(lonArr)[0]/2,np.shape(lonArr)[1]/2]
badGeo = False
if not (-90. <= lat_0 <= 90.) :
LOG.debug("\n>> error: Latitude of granule midpoint ({}) does not satisfy (-90. <= lat_0 <= 90.)\nfor file {}\n\taborting...".format(lat_0,geoList[grans]))
badGeo = True
if not (-180. <= lat_0 <= 180.) :
LOG.debug("\n>> error: Longitude of granule midpoint ({}) does not satisfy (-180. <= lon_0 <= 180.)\nfor file {}\n\taborting...".format(lon_0,geoList[grans]))
badGeo = True
if badGeo :
sys.exit(1)
cotArr = cot[:,:]
cloudConfArr = cloudConf[:,:]
waterCldFracArr = waterCldFrac[:,:]
mixedCldFracArr = mixedCldFrac[:,:]
# Determine masks for each fill type, for the EPS EDR
cotFillMasks = {}
for fillType in trimObj.sdrTypeFill.keys() :
fillValue = trimObj.sdrTypeFill[fillType][cotArr.dtype.name]
if 'float' in fillValue.__class__.__name__ :
cotFillMasks[fillType] = ma.masked_inside(cotArr,fillValue-eps,fillValue+eps).mask
if (cotFillMasks[fillType].__class__.__name__ != 'ndarray') :
cotFillMasks[fillType] = None
elif 'int' in fillValue.__class__.__name__ :
cotFillMasks[fillType] = ma.masked_equal(cotArr,fillValue).mask
if (cotFillMasks[fillType].__class__.__name__ != 'ndarray') :
cotFillMasks[fillType] = None
else :
LOG.debug("Dataset was neither int not float... a worry")
pass
# Construct the total mask from all of the various fill values
totalMask = ma.array(np.zeros(cotArr.shape,dtype=np.bool))
for fillType in trimObj.sdrTypeFill.keys() :
if cotFillMasks[fillType] is not None :
totalMask = totalMask * ma.array(np.zeros(cotArr.shape,dtype=np.bool),\
mask=cotFillMasks[fillType])
try :
data = ma.array(cotArr, mask=totalMask.mask)
cloudConfArr = ma.array(cloudConfArr ,mask=totalMask.mask)
waterCldFracArr = ma.array(waterCldFracArr,mask=totalMask.mask)
mixedCldFracArr = ma.array(mixedCldFracArr,mask=totalMask.mask)
lats = ma.array(latArr, mask=totalMask.mask)
lons = ma.array(lonArr, mask=totalMask.mask)
except ma.core.MaskError :
LOG.debug(">> error: Mask Error, probably mismatched geolocation and product array sizes, aborting...")
sys.exit(1)
data = data * cotFactors[0] + cotFactors[1]
cldPhase = np.ones(data.shape,dtype=np.uint8) * trimObj.sdrTypeFill['NA_FILL']['uint8']
LOG.debug("cloudPhase.shape = ",cldPhase.shape)
LOG.debug("cloudConfArr.shape = ",cloudConfArr.shape)
LOG.debug("waterCldFracArr.shape = ",waterCldFracArr.shape)
LOG.debug("mixedCldFracArr.shape = ",mixedCldFracArr.shape)
cloudFracMask = (cloudConfArr>0)
waterFracMask = (waterCldFracArr>0)
mixedFracMask = (mixedCldFracArr>0)
waterMask = cloudFracMask * (waterFracMask + mixedFracMask)
iceMask = cloudFracMask * np.logical_not(waterFracMask + mixedFracMask)
LOG.debug("waterMask.shape = ",waterMask.shape)
LOG.debug("iceMask.shape = ",iceMask.shape)
LOG.debug("Number of pixels with > 25% cloudy confidence: ",cloudFracMask.sum())
LOG.debug("Number of pixels with > 25% water cloud fraction: ",waterFracMask.sum())
LOG.debug("Number of pixels with > 25% mixed cloud fraction: ",mixedFracMask.sum())
LOG.debug("Number of water pixels: ",(cloudFracMask * (waterFracMask + mixedFracMask)).sum())
LOG.debug("Number of ice pixels: ",cloudFracMask.sum() - (waterFracMask + mixedFracMask).sum())
LOG.debug("Number of water pixels: ",waterMask.sum())
LOG.debug("Number of ice pixels: ",iceMask.sum())
cldPhaseShape = cldPhase.shape
cldPhase = np.ravel(cldPhase)
wtrIdx = np.where(np.ravel(waterMask))
iceIdx = np.where(np.ravel(iceMask))
cldPhase[wtrIdx] = 3
cldPhase[iceIdx] = 5
cldPhase = np.reshape(cldPhase,cldPhaseShape)
except Exception, err :
LOG.debug(">> error: {}...".format(str(err)))
sys.exit(1)
LOG.debug("lat_0,lon_0 = {},{}".format(lat_0,lon_0))
LOG.debug("Shape of data is {}".format(repr(np.shape(data))))
LOG.debug("Shape of cldPhase is {}".format(repr(np.shape(cldPhase))))
LOG.debug("Shape of lats is {}".format(repr(np.shape(lats))))
LOG.debug("Shape of lons is {}".format(repr(np.shape(lons))))
return lats,lons,data,cldPhase,lat_0,lon_0
def gran_EPS_EDR(geoList,epsList,shrink=1):
'''
Returns the granulated EPS EDR
'''
try :
reload(viirsCld)
reload(viirs_edr_data)
del(viirsCldObj)
del(latArr)
del(lonArr)
del(epsArr)
except :
pass
LOG.debug("Creating viirsCldObj...")
reload(viirsCld)
viirsCldObj = viirsCld.viirsCld()
LOG.debug("done")
# Determine the correct fillValue
trimObj = ViirsTrimTable()
eps = 1.e-6
for grans in np.arange(len(geoList)):
LOG.debug("Ingesting EDR granule {} ...".format(grans))
# Read in geolocation...
ViirsGeoFileName = geoList[grans]
if(pytables.isHDF5File(ViirsGeoFileName)) :
try :
ViirsGeoFileObj = pytables.openFile(ViirsGeoFileName,mode='r')
LOG.debug("Successfully opened geolocation file",ViirsGeoFileName)
except IOError :
LOG.debug(">> error: Could not open geolocation file: ",ViirsGeoFileName)
sys.exit(1)
# Detemine the geolocation group name and related information
#group = getobj(ViirsGeoFileObj,'/All_Data')
group = ViirsGeoFileObj.getNode('/All_Data')
geoGroupName = '/All_Data/'+group.__members__[0]
group._g_close()
LOG.debug("Geolocation Group : {} ".format(geoGroupName))
isEdrGeo = ('VIIRS-CLD-AGG-GEO_All' in geoGroupName)
if not isEdrGeo :
LOG.debug(">> error: {} is not an EDR resolution cloud geolocation file\n\taborting...".format(ViirsGeoFileName))
sys.exit(1)
# Get the geolocation Latitude and Longitude nodes...
try :
dataName = 'Latitude'
geoLatNode = ViirsGeoFileObj.getNode(geoGroupName+'/'+dataName)
LOG.debug("Shape of {} node is {}".format(geoGroupName+'/'+dataName,repr(geoLatNode.shape)))
dataName = 'Longitude'
geoLonNode = ViirsGeoFileObj.getNode(geoGroupName+'/'+dataName)
LOG.debug("Shape of {} node is {}".format(geoGroupName+'/'+dataName,repr(geoLonNode.shape)))
except pyEx.NoSuchNodeError :
LOG.debug("\n>> error: No required node {}/{} in {}\n\taborting...".format(geoGroupName,dataName,ViirsGeoFileName))
ViirsGeoFileObj.close()
sys.exit(1)
# Make a copy of the geolocation node data, so we can close the file
try :
dataName = 'Latitude'
LOG.debug("Reading {} dataset...".format(dataName))
latArr = geoLatNode[:,:]
geoLatNode.close()
latArr = np.squeeze(latArr)
LOG.debug("done")
dataName = 'Longitude'
LOG.debug("Reading {} dataset...".format(dataName))
lonArr = geoLonNode[:,:]
geoLonNode.close()
lonArr = np.squeeze(lonArr)
LOG.debug("done")
LOG.debug("Closing geolocation file")
ViirsGeoFileObj.close()
except :
LOG.debug("\n>> error: Could not retrieve %/% node data in {}\n\taborting...".format(geoGroupName,dataName,ViirsGeoFileName))
geoLatNode.close()
geoLonNode.close()
ViirsGeoFileObj.close()
sys.exit(1)
else :
LOG.debug("\n>> error: {} is not a HDF5 file,\n\taborting...".format(ViirsGeoFileName))
sys.exit(1)
# Read in dataSets...
ViirsEDRFileName = epsList[grans]
if(pytables.isHDF5File(ViirsEDRFileName)) :
try :
ViirsEDRFileObj = pytables.openFile(ViirsEDRFileName,mode='r')
LOG.debug("Successfully opened edr file",ViirsEDRFileName)
except IOError :
LOG.debug(">> error: Could not open edr file: ",ViirsEDRFileName)
sys.exit(1)
# Detemine the edr group name and related information
#group = getobj(ViirsEDRFileObj,'/All_Data')
group = ViirsEDRFileObj.getNode('/All_Data')
edrGroupName = '/All_Data/'+group.__members__[0]
group._g_close()
LOG.debug("Edr Group : {} ".format(edrGroupName))
isEdr = ('VIIRS-CEPS-EDR_All' in edrGroupName)
if not isEdr :
LOG.debug(">> error: {} is not an EDR resolution cloud file\n\taborting...".format(ViirsEDRFileName))
sys.exit(1)
# Get the edr nodes...
try :
dataName = 'AverageCloudEffectiveParticleSize'
epsNode = ViirsEDRFileObj.getNode(edrGroupName+'/'+dataName)
LOG.debug("Shape of {} node is {}".format(edrGroupName+'/'+dataName,repr(epsNode.shape)))
dataName = 'CEPSFactors'
epsFactorsNode = ViirsEDRFileObj.getNode(edrGroupName+'/'+dataName)
LOG.debug("Shape of {} node is {}".format(edrGroupName+'/'+dataName,repr(epsFactorsNode.shape)))
dataName = 'QF3_VIIRSCEPSAVGEDR'
QF3_VIIRSCEPSAVGEDR_Node = ViirsEDRFileObj.getNode(edrGroupName+'/'+dataName)
LOG.debug("Shape of {} node is {}".format(edrGroupName+'/'+dataName,repr(QF3_VIIRSCEPSAVGEDR_Node.shape)))
except pyEx.NoSuchNodeError :
LOG.debug("\n>> error: No required node {}/{} in {}\n\taborting...".format(edrGroupName,dataName,ViirsEDRFileName))
ViirsEDRFileObj.close()
sys.exit(1)
# Make a copy of the edr node data, so we can close the file
try :
dataName = 'AverageCloudEffectiveParticleSize'
LOG.debug("Reading {} dataset...".format(dataName))
eps = epsNode[:,:]
eps = np.squeeze(eps)
epsNode.close()
LOG.debug("done")
dataName = 'CEPSFactors'
LOG.debug("Reading {} dataset...".format(dataName))
epsFactors = epsFactorsNode[:]
epsFactors = np.squeeze(epsFactors)
epsFactorsNode.close()
LOG.debug("done")
dataName = 'QF3_VIIRSCEPSAVGEDR'
LOG.debug("Reading {} dataset...".format(dataName))
cloudConf = np.bitwise_and(QF3_VIIRSCEPSAVGEDR_Node[:,:],3) >> 0
waterCldFrac = np.bitwise_and(QF3_VIIRSCEPSAVGEDR_Node[:,:],12) >> 2
mixedCldFrac = np.bitwise_and(QF3_VIIRSCEPSAVGEDR_Node[:,:],192) >> 6
QF3_VIIRSCEPSAVGEDR_Node.close()
LOG.debug("done")
LOG.debug("Closing edr file")
ViirsEDRFileObj.close()
LOG.debug("Shape of eps is {}".format(repr(np.shape(eps))))
LOG.debug("Shape of latsArr is {}".format(repr(np.shape(latArr))))
LOG.debug("Shape of lonsArr is {}".format(repr(np.shape(lonArr))))
except :
LOG.debug("\n>> error: Could not retrieve %/% node data in {}\n\taborting...".format(edrGroupName,dataName,ViirsEDRFileName))
epsNode.close()
epsFactorsNode.close()
QF3_VIIRSCEPSAVGEDR_Node.close()
ViirsEDRFileObj.close()
sys.exit(1)
else :
LOG.debug("\n>> error: {} is not a HDF5 file,\n\taborting...".format(ViirsEDRFileName))
sys.exit(1)
LOG.debug("Creating some masks")
try :
lat_0 = latArr[np.shape(latArr)[0]/2,np.shape(latArr)[1]/2]
lon_0 = lonArr[np.shape(lonArr)[0]/2,np.shape(lonArr)[1]/2]
badGeo = False
if not (-90. <= lat_0 <= 90.) :
LOG.debug("\n>> error: Latitude of granule midpoint ({}) does not satisfy (-90. <= lat_0 <= 90.)\nfor file {}\n\taborting...".format(lat_0,geoList[grans]))
badGeo = True
if not (-180. <= lat_0 <= 180.) :
LOG.debug("\n>> error: Longitude of granule midpoint ({}) does not satisfy (-180. <= lon_0 <= 180.)\nfor file {}\n\taborting...".format(lon_0,geoList[grans]))
badGeo = True
if badGeo :
sys.exit(1)
epsArr = eps[:,:]
cloudConfArr = cloudConf[:,:]
waterCldFracArr = waterCldFrac[:,:]
mixedCldFracArr = mixedCldFrac[:,:]
# Determine masks for each fill type, for the EPS EDR
epsFillMasks = {}
for fillType in trimObj.sdrTypeFill.keys() :
fillValue = trimObj.sdrTypeFill[fillType][epsArr.dtype.name]
if 'float' in fillValue.__class__.__name__ :
epsFillMasks[fillType] = ma.masked_inside(epsArr,fillValue-eps,fillValue+eps).mask
if (epsFillMasks[fillType].__class__.__name__ != 'ndarray') :
epsFillMasks[fillType] = None
elif 'int' in fillValue.__class__.__name__ :
epsFillMasks[fillType] = ma.masked_equal(epsArr,fillValue).mask
if (epsFillMasks[fillType].__class__.__name__ != 'ndarray') :
epsFillMasks[fillType] = None
else :
LOG.debug("Dataset was neither int not float... a worry")
pass
# Construct the total mask from all of the various fill values
totalMask = ma.array(np.zeros(epsArr.shape,dtype=np.bool))
for fillType in trimObj.sdrTypeFill.keys() :
if epsFillMasks[fillType] is not None :
totalMask = totalMask * ma.array(np.zeros(epsArr.shape,dtype=np.bool),\
mask=epsFillMasks[fillType])
try :
data = ma.array(epsArr, mask=totalMask.mask)
cloudConfArr = ma.array(cloudConfArr ,mask=totalMask.mask)
waterCldFracArr = ma.array(waterCldFracArr,mask=totalMask.mask)
mixedCldFracArr = ma.array(mixedCldFracArr,mask=totalMask.mask)
lats = ma.array(latArr, mask=totalMask.mask)
lons = ma.array(lonArr, mask=totalMask.mask)
except ma.core.MaskError :
LOG.debug(">> error: Mask Error, probably mismatched geolocation and product array sizes, aborting...")
sys.exit(1)
data = data * epsFactors[0] + epsFactors[1]
cldPhase = np.ones(data.shape,dtype=np.uint8) * trimObj.sdrTypeFill['NA_FILL']['uint8']
cloudFracMask = (cloudConfArr>0)
waterFracMask = (waterCldFracArr>0)
mixedFracMask = (mixedCldFracArr>0)
waterMask = cloudFracMask * (waterFracMask + mixedFracMask)
iceMask = cloudFracMask * np.logical_not(waterFracMask + mixedFracMask)
LOG.debug("Number of pixels with > 25% cloudy confidence: ",cloudFracMask.sum())
LOG.debug("Number of pixels with > 25% water cloud fraction: ",waterFracMask.sum())
LOG.debug("Number of pixels with > 25% mixed cloud fraction: ",mixedFracMask.sum())
LOG.debug("Number of water pixels: ",(cloudFracMask * (waterFracMask + mixedFracMask)).sum())
LOG.debug("Number of ice pixels: ",cloudFracMask.sum() - (waterFracMask + mixedFracMask).sum())
LOG.debug("Number of water pixels: ",waterMask.sum())
LOG.debug("Number of ice pixels: ",iceMask.sum())
cldPhaseShape = cldPhase.shape
cldPhase = np.ravel(cldPhase)
wtrIdx = np.where(np.ravel(waterMask))
iceIdx = np.where(np.ravel(iceMask))
cldPhase[wtrIdx] = 3
cldPhase[iceIdx] = 5
cldPhase = np.reshape(cldPhase,cldPhaseShape)
except Exception, err :
LOG.debug(">> error: {}...".format(str(err)))
sys.exit(1)
LOG.debug("lat_0,lon_0 = {},{}".format(lat_0,lon_0))
LOG.debug("Shape of data is {}".format(repr(np.shape(data))))
LOG.debug("Shape of cldPhase is {}".format(repr(np.shape(cldPhase))))
LOG.debug("Shape of lats is {}".format(repr(np.shape(lats))))
LOG.debug("Shape of lons is {}".format(repr(np.shape(lons))))
return lats,lons,data,cldPhase,lat_0,lon_0
def gran_CTp(geoList,ctpList,dataSet,shrink=1):
'''
Returns the granulated CTp dataset
'''
try :
reload(viirsCld)
reload(viirs_edr_data)
del(viirsCldObj)
del(latArr)
del(lonArr)
del(ctpArr)
del(phaseArr)
except :
pass
LOG.debug("Creating viirsCldObj...")
reload(viirsCld)
viirsCldObj = viirsCld.viirsCld()
LOG.debug("done")
# Determine the correct fillValue
trimObj = ViirsTrimTable()
eps = 1.e-6
for grans in np.arange(len(geoList)):
LOG.debug("Ingesting granule {} ...".format(grans))
retArr = viirsCldObj.ingestLite(geoList[grans],ctpList[grans],dataSet,1)
LOG.debug("done")
try :
latArr = viirsCldObj.Lat[:,:]
lonArr = viirsCldObj.Lon[:,:]
lat_0 = latArr[np.shape(latArr)[0]/2,np.shape(latArr)[1]/2]
lon_0 = lonArr[np.shape(lonArr)[0]/2,np.shape(lonArr)[1]/2]
badGeo = False
if not (-90. <= lat_0 <= 90.) :
LOG.debug("\n>> error: Latitude of granule midpoint ({}) does not satisfy (-90. <= lat_0 <= 90.)\nfor file {}\n\taborting...".format(lat_0,geoList[grans]))
badGeo = True
if not (-180. <= lat_0 <= 180.) :
LOG.debug("\n>> error: Longitude of granule midpoint ({}) does not satisfy (-180. <= lon_0 <= 180.)\nfor file {}\n\taborting...".format(lon_0,geoList[grans]))
badGeo = True
if badGeo :
sys.exit(1)
ctpArr = viirsCldObj.ViirsCProdSDS[:,:]
phaseArr = viirsCldObj.ViirsCProdSDSphase[:,:]
# Determine masks for each fill type, for the CTp IP
ctpFillMasks = {}
for fillType in trimObj.sdrTypeFill.keys() :
fillValue = trimObj.sdrTypeFill[fillType][ctpArr.dtype.name]
if 'float' in fillValue.__class__.__name__ :
ctpFillMasks[fillType] = ma.masked_inside(ctpArr,fillValue-eps,fillValue+eps).mask
if (ctpFillMasks[fillType].__class__.__name__ != 'ndarray') :
ctpFillMasks[fillType] = None
elif 'int' in fillValue.__class__.__name__ :
ctpFillMasks[fillType] = ma.masked_equal(ctpArr,fillValue).mask
if (ctpFillMasks[fillType].__class__.__name__ != 'ndarray') :
ctpFillMasks[fillType] = None
else :
LOG.debug("Dataset was neither int not float... a worry")
pass
# Construct the total mask from all of the various fill values
totalMask = ma.array(np.zeros(ctpArr.shape,dtype=np.bool))
for fillType in trimObj.sdrTypeFill.keys() :
if ctpFillMasks[fillType] is not None :
totalMask = totalMask * ma.array(np.zeros(ctpArr.shape,dtype=np.bool),\
mask=ctpFillMasks[fillType])
# Added the "bad data" from the CTp phase quality flag.
totalMask = totalMask * ma.masked_equal(phaseArr,0)
try :
data = ma.array(ctpArr, mask=totalMask.mask)
phase = ma.array(phaseArr,mask=totalMask.mask)
lats = ma.array(latArr, mask=totalMask.mask)
lons = ma.array(lonArr, mask=totalMask.mask)
except ma.core.MaskError :
LOG.debug(">> error: Mask Error, probably mismatched geolocation and product array sizes, aborting...")
sys.exit(1)
except :
LOG.debug(">> error: There was an exception...")
sys.exit(1)
return lats,lons,data,phase,lat_0,lon_0
def gran_CTT_EDR(geoList,cttList,shrink=1):
'''
Returns the granulated EPS EDR
'''
try :
reload(viirsCld)
reload(viirs_edr_data)
del(viirsCldObj)
del(latArr)
del(lonArr)
del(cttArr)
except :
pass
LOG.debug("Creating viirsCldObj...")
reload(viirsCld)
viirsCldObj = viirsCld.viirsCld()
LOG.debug("done")