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CSPP_VIIRS_CM-IP_blobPlots.py
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CSPP_VIIRS_CM-IP_blobPlots.py
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import numpy as np
from os import path,readlink
import string
from numpy import ma
from glob import glob
import re
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,addcyclic,shiftgrid
import adl_blob
from VIIRS import ViirsData as ViirsData
# every module should have a LOG object
# e.g. LOG.warning('my dog has fleas')
import logging
logging.basicConfig()
#dpi=200
### Moderate and Imager resolution trim table arrays. These are
### bool arrays, and the trim pixels are set to True.
trimObj = ViirsData.ViirsTrimTable()
modTrimMask = trimObj.createModTrimArray(nscans=48,trimType=bool)
xmlDir = '/home/geoffc/SSEC/sshfs/rh5b/RH5B/CSPP/EDR/common/ADL/xml/VIIRS'
def get_blob_asc_dict(xmlDir,blobDir,collShortNames):
blob_asc_Files = {}
blobDir = path.expanduser(blobDir)
if path.isdir(blobDir):
pass
else :
blobDir = path.dirname(blobDir)
for shortName in collShortNames :
#print '%s --> ' % (shortName)
fileGlob = path.join(path.expanduser(blobDir),'*.%s'%(shortName))
blobFiles = glob(fileGlob)
if blobFiles != []:
blobFiles.sort()
blobDict = {}
print '%s --> ' % (shortName)
for files in blobFiles :
blobFile = path.basename(files)
ascFile = string.replace(blobFile,shortName,'asc')
ascFullPath = path.join(blobDir,'%s'%(ascFile))
ascFileObj = open(ascFullPath,"r")
for line in ascFileObj:
if re.search("N_Granule_ID", line):
granID = string.split(line,'"')[3]
ascFileObj.close()
blobDict[granID] = [blobFile,ascFile]
blob_asc_Files[shortName] = blobDict
return blob_asc_Files
class VCMclass():
def __init__(self,xmlDir,blobPath,endian=adl_blob.LITTLE_ENDIAN):
self.xmlDir = xmlDir
self.blobPath = blobPath
self.collShortNames = [
'VIIRS-CM-IP'
]
self.xmlName = {}
self.xmlName['VIIRS-CM-IP'] = 'VIIRS_CM_IP.xml'
self.plotDescr = {}
self.plotDescr['VIIRS-CM-IP'] = r'Cloud Mask'
self.plotLims = {}
self.plotLims['VIIRS-CM-IP'] = [0, 3]
self.dataName = {}
self.dataName['VIIRS-CM-IP'] = 'vcm0'
self.blob_dict = get_blob_asc_dict(xmlDir,blobPath,self.collShortNames)
for granID in self.blob_dict['VIIRS-CM-IP'].keys() :
xmlFile = path.join(xmlDir,self.xmlName['VIIRS-CM-IP'])
blobFile = self.blob_dict['VIIRS-CM-IP'][granID][0]
blobFile = path.join(blobPath,'%s'%(blobFile))
blobObj = adl_blob.map(xmlFile,blobFile,endian=endian)
self.blob_dict['VIIRS-CM-IP'][granID].append(blobObj)
def plot_VCM_granules(self,pngDir=None,annotation='',dpi=300):
if pngDir is None :
pngDir = path.abspath(path.curdir)
plotDescr = self.plotDescr
plotLims = self.plotLims
blobDict = self.blob_dict
collShortNames = blobDict.keys()
for shortName in collShortNames :
dataName = self.dataName[shortName]
for granID in blobDict[shortName].keys() :
print '%s --> %s ' % (shortName, granID)
blobObj = blobDict[shortName][granID][2]
blobArrObj = blobObj.as_arrays()
data = getattr(blobArrObj,dataName)
pixelTrimValue = trimObj.sdrTypeFill['ONBOARD_PT_FILL'][data.dtype.name]
print "pixelTrimValue is %r" % (pixelTrimValue)
# Bit mask and shift to get the Cloud Mask
bitMask = ViirsData.CloudMaskData.ViirsCMbitMasks[0][1]
bitShift = ViirsData.CloudMaskData.ViirsCMbitShift[0][1]
data = np.bitwise_and(data ,bitMask) >> bitShift
# Apply the moderate pixel trim, so that we can properly mask them out at plot time.
data = ma.array(data,mask=modTrimMask,fill_value=trimObj.sdrTypeFill['ONBOARD_PT_FILL'][data.dtype.name])
data = data.filled()
cmap = ListedColormap(ViirsData.CloudMaskData.ViirsCMfillColours[0][1])
numCats = np.array(ViirsData.CloudMaskData.ViirsCMfillColours[0][1]).size
numBounds = numCats + 1
ViirsData.CloudMaskData.ViirsCMTickPos = np.arange(float(numBounds))/float(numCats)
ViirsData.CloudMaskData.ViirsCMTickPos = ViirsData.CloudMaskData.ViirsCMTickPos[0 :-1] + \
ViirsData.CloudMaskData.ViirsCMTickPos[1]/2.
print "numCats = ",numCats
print "ViirsCMTickPos = ",ViirsData.CloudMaskData.ViirsCMTickPos
vmin,vmax = plotLims[shortName]
plotTitle = '%s : %s %s' % (shortName,granID,annotation)
cbTitle = plotDescr[shortName]
# Create figure with default size, and create canvas to draw on
scale=1.5
fig = Figure(figsize=(scale*8,scale*3))
canvas = FigureCanvas(fig)
# Create main axes instance, leaving room for colorbar at bottom,
# and also get the Bbox of the axes instance
ax_rect = [0.05, 0.18, 0.9, 0.75 ] # [left,bottom,width,height]
ax = fig.add_axes(ax_rect)
# Granule axis title
ax_title = ppl.setp(ax,title=plotTitle)
ppl.setp(ax_title,fontsize=12)
ppl.setp(ax_title,family="sans-serif")
# Plot the data
print "%s is of kind %r" % (shortName,data.dtype.kind)
#print data
if (data.dtype.kind =='i' or data.dtype.kind =='u'):
#data = ma.masked_equal(data,pixelTrimValue)
data = ma.masked_greater(data,200)
else:
data = ma.masked_less(data,-800.)
im = ax.imshow(ma.masked_less(data,0),interpolation='nearest',vmin=vmin,vmax=vmax,cmap=cmap)
#im = ax.imshow(ma.masked_equal(data,pixelTrimValue),axes=ax,interpolation='nearest',vmin=vmin,vmax=vmax)
#im = ax.imshow(data,axes=ax,interpolation='nearest',vmin=vmin,vmax=vmax)
#im = ax.imshow(ma.masked_less(data,-800.),axes=ax,interpolation='nearest')
ppl.setp(ax.get_xticklabels(), visible=False)
ppl.setp(ax.get_yticklabels(), visible=False)
ppl.setp(ax.get_xticklines(),visible=False)
ppl.setp(ax.get_yticklines(),visible=False)
# add a colorbar axis
cax_rect = [0.05 , 0.05, 0.9 , 0.10 ] # [left,bottom,width,height]
cax = fig.add_axes(cax_rect,frameon=False) # setup colorbar axes
# Plot the colorbar.
cb = fig.colorbar(im, cax=cax, orientation='horizontal')
ppl.setp(cax.get_xticklabels(),fontsize=9)
ppl.setp(cax.get_xticklines(),visible=False)
# Set the colourbar tick locations and ticklabels
#ppl.setp(cb.ax,xticks=ViirsData.CloudMaskData.ViirsCMTickPos) # In colorbar axis coords (0..1)
cb.set_ticks(3.*ViirsData.CloudMaskData.ViirsCMTickPos) # In data coords (0..3)
ppl.setp(cb.ax,xticklabels=ViirsData.CloudMaskData.ViirsCMtickNames[0][1])
# Colourbar title
cax_title = ppl.setp(cax,title=cbTitle)
ppl.setp(cax_title,fontsize=10)
# Turn off the tickmarks on the colourbar
#ppl.setp(cb.ax.get_xticklines(),visible=False)
#ppl.setp(cb.ax.get_xticklabels(),fontsize=9)
# Redraw the figure
canvas.draw()
# Save the figure to a png file...
pngFile = path.join(pngDir,'%s_%s.png' % (shortName,granID))
canvas.print_figure(pngFile,dpi=dpi)
ppl.close('all')
def plot_VCM_tests(self,pngDir=None,annotation='',dpi=300):
if pngDir is None :
pngDir = path.abspath(path.curdir)
plotDescr = self.plotDescr
plotLims = self.plotLims
blobDict = self.blob_dict
collShortNames = blobDict.keys()
print 'collShortNames = %r' % (collShortNames)
CMD = ViirsData.CloudMaskData
for shortName in collShortNames :
print 'shortName = %s' % (shortName)
dataName = self.dataName[shortName]
for granID in blobDict[shortName].keys() :
print '%s --> %s ' % (shortName, granID)
blobObj = blobDict[shortName][granID][2]
blobArrObj = blobObj.as_arrays()
for byte in [0,1,2,3,5] :
print ""
numPlots = len(CMD.ViirsCMbitMasks[byte])
numRows = np.ceil(float(numPlots)/2.)
figWidth = 15. # inches
figHeight = 3. * numPlots/2. # inches
fig = Figure(figsize=((figWidth,figHeight)))
canvas = FigureCanvas(fig)
Ax = []
Im = []
Txt = []
Cb = []
plotIdx = 1
for dSet in range(np.shape(CMD.ViirsCMbitMasks[byte])[0]):
print 'dSet = ',dSet
dSetName = 'vcm'+str(byte)
plotTitle = '%s : %s %s (Byte %d)' % (shortName,granID,annotation,byte)
fig.text(0.5, 0.95, plotTitle, fontsize=16, color='black', ha='center', va='bottom', alpha=1.0)
if (CMD.ViirsCMbitMaskNames[byte][dSet] == 'Spare') :
print "Skipping dataset with byte = %d, dSet = %d" % (byte, dSet)
else :
print "byte = %d, dSet = %d" % (byte, dSet)
byteMask = CMD.ViirsCMbitMasks[byte][dSet]
byteShift = CMD.ViirsCMbitShift[byte][dSet]
print "byteMask = %d, byteShift = %d, dSetName = %s" % (byteMask, byteShift, dSetName)
data = np.bitwise_and(getattr(blobArrObj,dSetName)[:,:],byteMask) >> byteShift
vmin,vmax = CMD.ViirsCMvalues[byte][dSet][0], CMD.ViirsCMvalues[byte][dSet][-1]
print "vmin = %d, vmax = %d" % (vmin, vmax)
titleStr = CMD.ViirsCMbitMaskNames[byte][dSet]
print "titleStr = %s" % (titleStr)
Ax.append(fig.add_subplot(numRows,2,plotIdx))
print "data.dtype.__str__() = %s" % (data.dtype.__str__())
Im.append(Ax[dSet].imshow(data.astype('int')[::-1,::-1], vmin=vmin, vmax=vmax, interpolation='nearest'))
Txt.append(Ax[dSet].set_title(titleStr))
ppl.setp(Txt[dSet],fontsize=10)
ppl.setp(Ax[dSet].get_xticklines(), visible=False)
ppl.setp(Ax[dSet].get_yticklines(), visible=False)
ppl.setp(Ax[dSet].get_xticklabels(), visible=False)
ppl.setp(Ax[dSet].get_yticklabels(), visible=False)
Cb.append(fig.colorbar(Im[dSet], orientation='horizonal', pad=0.05))
plotIdx += 1
pngFile = path.join(pngDir,'%s_%s_%s.png' % (shortName,granID,dSetName))
print "Writing to %s..." % (pngFile)
canvas.draw()
canvas.print_figure(pngFile,dpi=dpi)
ppl.close('all')
def plot_VCM_tests_diff(VCMobj1,VCMobj2,pngDir=None,annotation='',dpi=300):
print ViirsData.__file__
CMD = ViirsData.CloudMaskData
blob_dict1 = VCMobj1.blob_dict
blob_dict2 = VCMobj2.blob_dict
for granID1,granID2 in zip(blob_dict1['VIIRS-CM-IP'].keys(),blob_dict1['VIIRS-CM-IP'].keys()) :
if granID1 != granID2 :
print "Granule IDs do not match, aborting..."
return(1)
blobObj1 = blob_dict1['VIIRS-CM-IP'][granID1][2]
blobObj2 = blob_dict2['VIIRS-CM-IP'][granID2][2]
print '%s --> %s ' % ('VIIRS-CM-IP', granID1)
blobArrObj1 = blobObj1.as_arrays()
blobArrObj2 = blobObj2.as_arrays()
#for byte in range(len(CMD.ViirsCMbitMasks)):
for byte in [0,1,2,3,5] :
#for byte in [3] :
print ""
numPlots = len(CMD.ViirsCMbitMasks[byte])
numRows = np.ceil(float(numPlots)/2.)
figWidth = 15. # inches
figHeight = 3. * numPlots/2. # inches
fig = Figure(figsize=((figWidth,figHeight)))
canvas = FigureCanvas(fig)
Ax = []
Im = []
Txt = []
Cb = []
plotIdx = 1
for dSet in range(np.shape(CMD.ViirsCMbitMasks[byte])[0]):
dSetName = 'vcm'+str(byte)
plotTitle = "%s VIIRS Cloud Mask: Byte %d" % (annotation, byte)
fig.text(0.5, 0.95, plotTitle, fontsize=16, color='black', ha='center', va='bottom', alpha=1.0)
if (CMD.ViirsCMbitMaskNames[byte][dSet] == 'Spare') :
print "Skipping dataset with byte = %d, dSet = %d" % (byte, dSet)
else :
print "byte = %d, dSet = %d" % (byte, dSet)
byteMask = CMD.ViirsCMbitMasks[byte][dSet]
byteShift = CMD.ViirsCMbitShift[byte][dSet]
print "byteMask = %d, byteShift = %d, dSetName = %s" % (byteMask, byteShift, dSetName)
data1 = np.bitwise_and(getattr(blobArrObj1,dSetName)[:,:],byteMask) >> byteShift
data2 = np.bitwise_and(getattr(blobArrObj2,dSetName)[:,:],byteMask) >> byteShift
diffData = data1 - data2
vmax = np.abs(CMD.ViirsCMvalues[byte][dSet][-1] - CMD.ViirsCMvalues[byte][dSet][0])
vmin = -1. * vmax
print "vmin = %d, vmax = %d" % (vmin, vmax)
titleStr = CMD.ViirsCMbitMaskNames[byte][dSet]
print "titleStr = %s" % (titleStr)
Ax.append(fig.add_subplot(numRows,2,plotIdx))
Im.append(Ax[dSet].imshow(diffData[::-1,::-1], vmin=vmin, vmax=vmax, interpolation='nearest'))
Txt.append(Ax[dSet].set_title(titleStr))
ppl.setp(Txt[dSet],fontsize=10)
ppl.setp(Ax[dSet].get_xticklines(), visible=False)
ppl.setp(Ax[dSet].get_yticklines(), visible=False)
ppl.setp(Ax[dSet].get_xticklabels(), visible=False)
ppl.setp(Ax[dSet].get_yticklabels(), visible=False)
Cb.append(fig.colorbar(Im[dSet], orientation='horizonal', pad=0.05))
plotIdx += 1
pngFile = path.join(pngDir,'%s_%s_diff_%s.png' % ('VIIRS-CM-IP',granID1,dSetName))
print "Writing to %s..." % (pngFile)
canvas.draw()
canvas.print_figure(pngFile,dpi=dpi)
ppl.close('all')