read_merra_aerosol_and_dump_ascii.py

#!/usr/bin/python
'''
Module: read_merra_aerosol_and_dump_ascii.py
==========================================================================================
Disclaimer: The code is for demonstration purposes only. Users are responsible to check for accuracy and revise to fit their objective.

Author: Justin Roberts-Pierel, 2015 
Organization: NASA ARSET
Purpose: To save a MERRA netCDF4 file in ASCII format. Saves lat, lon, and other SDS dependent on file.

See the README associated with this module for more information.
==========================================================================================
'''

#import necessary modules 
import numpy as np
import netCDF4 as nc4
import sys 

#This finds the user's current path so that all hdf4 files can be found
try:
	fileList=open('fileList.txt','r')
except:
	print('Did not find a text file containing file names (perhaps name does not match)')
	sys.exit()

#loops through all files listed in the text file
for FILE_NAME in fileList:
	FILE_NAME=FILE_NAME.strip()
	user_input=input('\nWould you like to process\n' + FILE_NAME + '\n\n(Y/N)')
	if(user_input == 'N' or user_input == 'n'):
		continue
	else:
		#read in the data 
		merraData = nc4.Dataset(FILE_NAME, 'r')
		variables=set(merraData.variables)
		desiredVariables=set({'AOD','RH','ps','PBLH','TA','US','VS'})
		desiredVariables=set([x.lower() for x in desiredVariables])
		var1=variables.intersection(desiredVariables)
		desiredVariables=set([x.upper() for x in desiredVariables])
		var2=variables.intersection(desiredVariables)
		fileVars=list(var1.union(var2))
		if len(fileVars)==0:
			print('This file contains none of the selected SDS. Skipping...')			
			continue
		print('Saving the following SDS from current file: \n')
		[print('(' + str(fileVars.index(x)) + ')',x) for x in fileVars]
		
		#extract lat and lon info. These are just vectors in the dataset so they're repeated to accommodate the data array  
		lats=merraData.variables['lat'][:]
		lons=merraData.variables['lon'][:]
		totalLon=np.tile(lons,len(lats))
		totalLat=lats.repeat(len(lons))
		#create a matrix the same size as the lat/lon datasets to save everything 
		output=np.zeros((totalLat.shape[0],len(fileVars)+2))
		output[:,0]=totalLat
		output[:,1]=totalLon
		#can't combine string and floats in an array, so a list of titles is made 
		tempOutput=[]
		tempOutput.append('Latitude')
		tempOutput.append('Longitude')
		index=2
		for SDS_NAME in fileVars:
			try:
				#read merra data as a vector 
				data=merraData.variables[SDS_NAME][:]
			except:
				print('There is an issue with your MERRA file (might be the wrong MERRA file type). Skipping...')
				continue
			if len(data.shape) ==4:
				level=data.shape[1]-1
				data=data[0,level,:,:]
			elif len(data.shape) == 3:
				level=data.shape[0]-1
				data=data[level,:,:]
			data=data.ravel()
			#save variable
			output[:,index]=data
			tempOutput.append(SDS_NAME)
			index+=1
		#stacks the titles on the data array to be saved to file 
		output=np.row_stack((tempOutput,output))
		#create the name of the file from the filename 
		outputName='{0}.txt'.format(FILE_NAME[:-4])
		#save the file 
		np.savetxt(outputName,output,delimiter=',',fmt='%s')
print('\nAll valid files have been saved successfully.')