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Subject: svn commit: r1517753 [11/33] - in
 /incubator/climate/branches/rcmet-2.1.1:
 ./ src/ src/main/ src/main/python/ src/main/python/bin/
 src/main/python/docs/ src/main/python/docs/_static/
 src/main/python/docs/_templates/ src/main/python/rcmes/ src/main/pyth...
Date: Tue, 27 Aug 2013 05:35:49 -0000
To: commits@climate.incubator.apache.org
From: pramirez@apache.org
Message-Id: <20130827053601.8A8852388C1C@eris.apache.org>

Added: incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/utils/misc.py
URL: http://svn.apache.org/viewvc/incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/utils/misc.py?rev=1517753&view=auto
==============================================================================
--- incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/utils/misc.py (added)
+++ incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/utils/misc.py Tue Aug 27 05:35:42 2013
@@ -0,0 +1,1376 @@
+"""Module with a collection of helper functions"""
+
+
+import ConfigParser
+import datetime
+import glob
+import json
+import os
+import sys
+
+import numpy as np
+import numpy.ma as ma
+import netCDF4
+
+import classes
+
+from fortranfile import FortranFile
+from toolkit import process
+
+def configToDict(config):
+    """
+    Helper function to parse a configuration input and return a python dictionary
+    
+    Input::  
+        config - list of ('key', 'value') tuples from ConfigParser.
+            key01 - string i.e. 'value01'
+            key-2 - string i.e. 'value02'
+    Output::
+        configDict - Dictionary of Key/Value pairs
+    """
+    configDict = {}
+    for entry in config:
+        configDict[entry[0]] = entry[1]
+
+    return configDict
+
+
+def readSubRegionsFile(regionsFile):
+    """
+    Input::
+        regionsFile - Path to a subRegion configuration file
+        
+    Output::
+        Ordered List of SubRegion Objects decoded from regionsFile
+    """
+    if os.path.exists(regionsFile):
+        regionsConfig = ConfigParser.SafeConfigParser()
+        regionsConfig.optionxform = str
+        regionsConfig.read(regionsFile)
+        regions = generateSubRegions(regionsConfig.items('REGIONS'))
+
+        return regions
+    else:
+        raise IOError
+
+def getSubRegionsInteractively(counts, workdir):
+    """
+    Purpose::
+        This function provides a commandline Q&A session to help users define 
+        SubRegion Objects.
+    Input::
+        counts - dictionary with int counts of various metric inputs
+            i.e. {'observations': 3,
+                  'models'      : 1,
+                  'times'       : 120}
+        workdir - string of the current working directory where auxillary files
+        can be found.  In this case the directory will be used to locate an 
+        existing sub_regions.txt file.
+
+    Output:: 
+        subRegions = List of Parsed SubRegion Objects based on User inputs 
+    """
+    do_timeseries = None
+    yes_no_list = ['y', 'n', '']
+    
+    while do_timeseries not in yes_no_list:
+        do_timeseries = raw_input('Calculate area-mean timeseries for subregions? y/n: [n] \n>>>')
+        if do_timeseries not in yes_no_list:
+            print("'%s' is not a valid answer please try again" % do_timeseries)
+
+    if do_timeseries == 'y':
+        interactive_subregions = None
+        while interactive_subregions not in yes_no_list:
+            interactive_subregions = raw_input('Input Sub Region info interactively? y/n: [n] \n>>>')
+            if interactive_subregions not in yes_no_list:
+                print("'%s' is not a valid answer please try again" % interactive_subregions)
+            
+        if interactive_subregions == 'y':
+            while interactive_subregions == 'y':
+                regions = []
+                region = createSubRegionObjectInteractively()
+                regions.append(region)
+                anotherRegion = None
+                while anotherRegion == None:
+                    another = raw_input("Would you like to add another sub region? y/n [n] \n>>>")
+                    if another not in yes_no_list:
+                        print("'%s' is not a valid answer please try again" % another)
+                    elif another in ['', 'n']:
+                        anotherRegion = 'n'
+                        interactive_subregions = 'n'
+                    else:
+                        anotherRegion = 'y'
+
+        else:
+            subRegionFilename = None
+            while subRegionFilename == None:
+                readDefault = raw_input('Read from a default file (workdir + "/sub_regions.txt")? y/n: [y] \n>>>')
+
+                if readDefault == 'y' or readDefault == '':
+                    subRegionFilename = workdir + "/sub_regions.txt"
+                    print("Attempting to parse %s..." % subRegionFilename)
+                    regions = readSubRegionsFile(subRegionFilename)
+
+                elif readDefault == 'n':
+                    while subRegionFilename == None:
+                        # ask about using a non default filename
+                        subRegionFilename = raw_input('Enter the full path to the Sub Region file to read from:\n>>>')
+                        print("Attempting to parse %s..." % subRegionFilename)
+                        regions = readSubRegionsFile(subRegionFilename)
+
+                elif readDefault == 'NONE':
+                    subRegionFilename = 'NONE'
+                    regions = []
+            
+                else:
+                    print("'%'s is not a valid selection.  Please try again.  To proceed without Sub Regions defined enter NONE at the prompt" % readDefault)
+
+        return regions
+
+def generateSubRegions(regions):
+    """ Takes in a list of ConfigParser tuples and returns a list of SubRegion objects
+    
+    Input::
+        regions - Config Tuple: [('Region01', '["R01", 36.5, 29, 0.0, -10]'), ('Region02',....]
+
+    Output::
+        subRegions - list of SubRegion objects
+    """
+    subRegions = []
+    for region in regions:
+        name, latMax, latMin, lonMax, lonMin = json.loads(region[1])
+        subRegion = classes.SubRegion(name, latMin, lonMin, latMax, lonMax)
+        subRegions.append(subRegion)
+
+    return subRegions
+
+def parseSubRegions(subRegionConfig):
+    """
+    Input::
+        subRegionConfig - ConfigParser object
+    
+    Output::
+        subRegions - List of SubRegion Objects.  This could return an empty List if unable to parse subRegionConfig
+    """
+    subRegions = []
+    try:
+        if os.path.exists(subRegionConfig['subRegionFile']):
+            subRegions = readSubRegionsFile(subRegionConfig['subRegionFile'])
+            
+        else:
+            print "SubRegion Filepath: [%s] does not exist.  Check your configuration file, or comment out the SUB_REGION Section." % (subRegionConfig['subRegionFile'],)
+            print "Processing without SubRegion support"
+
+
+    except IOError:
+        print "Unable to open %s.  Running without SubRegions" % (subRegionConfig['subRegionFile'],)
+    except KeyError:
+        print "subRegionFile parameter was not provided.  Processing without SubRegion support"
+
+    return subRegions
+
+
+def decode_wrf_times(xtimes, base_time):
+    '''
+      Routine to convert from WRF time ('minutes since simulation start....') 
+      into a python datetime structure
+      Input:
+          xtimes - list of wrf 'XTIME' in units of 'minutes since simulation start'
+          base_time - a python datetime object describing simulation start date/time
+      Output:
+          times  - list of python datetime objects describing model data times
+         Peter Lean August 2010
+    '''
+    times = []
+    for xtime in xtimes:
+        dt = datetime.timedelta(minutes=xtime)
+        times.append(base_time + dt)
+    return times
+
+def calc_base_time_wrf(filename):
+    '''
+      Routine to calculate base_time (i.e. model initialization time)
+       for wrf files with timestamp in their filenames.
+        NB. Only works if includes a timestamp in format 'YYYY-MM-DD_HH:MM:SS'
+        TODO: work out a more general way of doing this...
+      Input:
+          filename - full path to WRF netCDF file.
+      Output:
+          base_time  - a python datetime object describing model start time
+         Peter Lean August 2010
+    '''
+    
+    # Extract time from netCDF file (in units of 'minutes since beginning of simulation')
+    f = netCDF4.Dataset(filename, mode='r')
+    timesraw = f.variables["XTIME"]
+    model_time = timesraw[0]
+    
+    dt = datetime.timedelta(minutes=int(model_time))
+           
+    # Extract and decode timestamp from filename
+    
+    filename = os.path.basename(filename)  # strip off the filepath
+    
+    timestamp_string = filename[11:30]   # cut out the date time stamp
+    DATE_FORMAT = '%Y-%m-%d_%H:%M:%S'  
+    
+    timestamp = datetime.datetime(*time.strptime(timestamp_string, DATE_FORMAT)[:6])
+    
+    # Base Time = timestamp - 'minutes since beginning of simulation'
+    base_time = timestamp - dt
+    
+    print 'Base Time calculated as: ', base_time
+    
+    return base_time
+
+def calc_period_precip_from_running_tot(running_precip):
+    '''
+     WRF precipitation accumulations are stored as running totals from the start of the model run
+     To find out values during each output time period, you must subtract the previous total
+    
+       e.g. running tot = 0,0,1,1,1,2,2,4,7,9,9,11 
+            period accu = 0,0,1,0,0,1,0,2,3,2,0,2
+    
+      Input: 
+         running_precip   - numpy array containing precipitation data at more than one time level
+                             NB. assumes time dimension is the first one precip[time, lat, lon, level] 
+    
+      Output:
+         acc_precip       - numpy array of same dimensions as input, 
+                            but with period accumulations instead of running total.
+    
+    
+        Peter Lean August 2010
+    
+    '''
+    
+    print 'Calculating period precip accumulations from running total'
+    shifted_running_precip = np.roll(running_precip, -1, axis=0)
+    nt = running_precip.shape[0]
+    # avoid wrapping from the end time to the start time by forcing the accumulation at final time=0
+    shifted_running_precip[nt - 1, :, :] = running_precip[nt - 1, :, :]
+    acc_precip = shifted_running_precip - running_precip 
+
+    # NB. sometimes rounding errors in the model lead to very small negative period accumulations
+    #     These are removed and set to zero here.
+    acc_precip = np.maximum(acc_precip, 0)
+
+    return acc_precip
+
+def decode_eraint_surf_times(xtimes):
+    '''
+      Routine to convert from ERA-Interim time ('hours since 1900...') 
+      into a python datetime structure
+    
+      Input:
+          xtimes - list of ERA-Interim times in units of 'hours since 1900'
+    
+      Output:
+          times  - list of python datetime objects describing model data times
+    
+    
+         Peter Lean August 2010
+    
+    '''
+    base_time = datetime.datetime(1900, 1, 1, 0, 0, 0, 0)
+    times = []
+    
+    for xtime in xtimes:
+        dt = datetime.timedelta(hours=xtime)
+        times.append(base_time + dt)
+    
+    return times
+
+def read_total_precip_from_filelist(myfilelist):
+    '''
+     WRF outputs precipitation data under several variables:
+     
+         **RAINC** =  convective total precip
+         
+         **RAINNC** = large scale total precip  ("no convective")
+         
+         **SNOWC** =  convective snow
+         
+         **SNOWNC** = large scale snow  ("no convective")
+     
+     Therefore: 
+         real rain = (rainc+rainnc)-(snowc+snownc)
+         total precip = rainc+rainnc+snowc+snownc
+         
+     Input:
+         myfilelist - a list of filename (including full path)
+           
+     Output:
+         precip - a numpy array of total precip values
+         lat, lon - 2D array of latitude and longitude values
+         times    - list of times
+     
+     NB. THIS ROUTINE IS NO LONGER NEEDED... I HAD MISUNDERSTOOD HOW PRECIP DATA WAS STORED IN WRF
+     TOTAL PRECIP  = RAINNC
+     **A SIMILAR ROUTINE MAY BE REQUIRED TO FIND THE INDIVIDUAL COMPONENTS THOUGH..**
+    
+    '''
+    myfilelist.sort()
+
+    print 'Calculating total precipitation from individual rain/snow, convective/ls components'
+    lat, lon, times, rainnc = read_data_from_file_list(myfilelist, 'RAINC')
+    lat, lon, times, rainc = read_data_from_file_list(myfilelist, 'RAINNC')
+    precip = rainnc + rainc
+    # reset negative values to zero
+    precip[precip < 0] = 0.0
+
+    return lat, lon, times, precip
+
+
+def isDirGood(directory):
+    """
+    Purpose::
+        This function will check if a directory exists and is writeable.  If the directory doesn't exist it is created.
+    Input::
+        directory - Path we need to check 
+    Output::
+        directoryStatus - Boolean
+    """
+    directoryStatus = False
+    
+    if os.path.exists(directory):
+        directoryStatus = os.access(directory, os.W_OK | os.X_OK)
+        if directoryStatus:
+            pass
+        else:
+            raise OSError("Unable to access the directory: %s.  Check that you have the proper permissions to read and write to that directory." % directory)
+            #directoryStatus = False
+    else:
+        try:
+            os.mkdir(directory)
+            directoryStatus = True
+        except OSError:
+            raise
+
+    return directoryStatus
+    
+
+def read_trmm_3b42_files(filelist, latMin, latMax, lonMin, lonMax):
+    '''
+     ** Alternate method of getting TRMM data from local repository if DB not available **
+     Reads TRMM gridded precipitation data from netCDF files in local repository.
+    
+     Input:
+        filelist - list of filenames (including path)
+        latMin,latMax,lonMin,lonMax - define region to extract (in degrees)
+     Output:
+        lat, lon   - 1D array of latitude and longitude values
+        timestore  - list of python datetime objects
+        mdata      - numpy masked array containing data from all files    
+    
+      NB. written specific for TRMM netCDF output files
+    
+       Peter Lean June 2010 
+    '''
+    filelist.sort()
+
+    # Crash nicely if 'filelist' is zero length
+    if len(filelist) == 0:
+        print 'Error: no files have been passed to read_data_from_file_list()'
+        sys.exit()
+    
+    # Open the first file in the list to:
+    #    i) read in lats, lons
+    #    ii) find out how many timesteps in the file 
+    #        (assume same ntimes in each file in list)
+    #     -allows you to create an empty array to store variable data for all times
+    tmp = netCDF4.Dataset(filelist[0], mode='r')
+    latsraw = tmp.variables["latitude"]
+    lonsraw = tmp.variables["longitude"]
+    lat = latsraw[:]
+    lon = lonsraw[:]
+    print 'Lats and lons read in for first file in filelist'
+
+    # Find out how many times there are in the file (should always be 1 for these TRMM files)
+    timesraw = tmp.variables["time"]
+    ntimes = len(timesraw)
+    
+    
+    # Convert specified longitudes into 0-360 format if required
+    if(lonMin < 0):
+        lonMin = lonMin + 360
+    if(lonMax < 0):
+        lonMax = lonMax + 360
+
+    # Create mask to extract required region only
+    #  NB. longitude is slightly more complicated as can wrap the prime meridion
+    print 'Extracting for :- lats:', latMin, latMax, ' lons: ', lonMin, lonMax
+    wh_lat = np.logical_and((lat > latMin), (lat < latMax))
+    if(lonMin <= lonMax):
+        wh_lon = np.logical_and((lon > lonMin), (lon < lonMax))
+    if(lonMin > lonMax):
+        wh_lon = np.logical_or((lon > lonMin), (lon < lonMax))
+    
+    sublat = lat[wh_lat]
+    sublon = lon[wh_lon]
+    
+    wh_true1, wh_true2 = np.meshgrid(wh_lon, wh_lat)
+    wh = np.logical_and(wh_true1, wh_true2)
+    
+    # Create empty array to store data
+    t2store = np.empty((ntimes * len(filelist), sublat.size, sublon.size))
+    timestore = []
+
+    # Now load in the data for real
+    #  NB. no need to reload in the latitudes and longitudes -assume invariant
+    i = 0
+    timesaccu = 0 # a counter for number of times stored so far in t2store 
+    #  NB. this method allows for missing times in data files 
+    #      as no assumption made that same number of times in each file...
+    for ifile in filelist:
+        print 'Loading data from file: ', filelist[i]
+        f = netCDF4.Dataset(ifile, mode = 'r')
+        t2raw = f.variables['hrf']
+        
+        # Read time from filename (NB. 'time' variable in netCDF always set to zero)
+        filename = os.path.basename(ifile)  # strip off the filepath
+        timestamp_string = filename[11:23]   # cut out the date time stamp
+        DATE_FORMAT = '%Y.%m.%d.%H'  
+        mytime = datetime.datetime(*time.strptime(timestamp_string, DATE_FORMAT)[:4])
+        ntimes = 1
+        t2tmp = t2raw[0, :, :]
+        sub = t2tmp[wh].reshape(sublat.size, sublon.size)
+        t2store[timesaccu, :, :] = sub
+        timestore.append(mytime)
+        timesaccu = timesaccu + ntimes
+        i += 1 
+    
+    print 'Data read in successfully with dimensions: ', t2store.shape
+    
+    # Create masked array using missing value flag from file
+    mdi = f.variables['hrf'].missing_value[0]
+    mdata = ma.masked_array(t2store, mask=(t2store == mdi))
+    
+    return sublat, sublon, timestore, mdata
+
+def read_airs_lev3_files(filelist, myvar, latMin, latMax, lonMin, lonMax):
+    '''
+     ** For testing work before database was ready. **
+     Reads AIRS level III gridded data from netCDF files.
+    
+     Input:
+        filelist - list of filenames (including path)
+        myvar    - name of variable to load
+        latMin,latMax,lonMin,lonMax - define region to extract (in degrees)
+     Output:
+        lat, lon   - 1D array of latitude and longitude values
+        timestore  - list of python datetime objects
+        mdata      - numpy masked array containing data from all files    
+    
+      NB. written specific for AIRS level III netCDF output files
+    
+      NB. Ascending passes have local time of 1:30pm
+      NB. Descending passes have local time of 1:30am
+    
+       Peter Lean June 2010 
+    '''
+    
+    filelist.sort()
+    
+    # Crash nicely if 'filelist' is zero length
+    if len(filelist) == 0:
+        print 'Error: no files have been passed to read_data_from_file_list()'
+        sys.exit()
+
+    # Open the first file in the list to:
+    #    i) read in lats, lons
+    #    ii) find out how many timesteps in the file 
+    #        (assume same ntimes in each file in list)
+    #     -allows you to create an empty array to store variable data for all times
+    tmp = netCDF4.Dataset(filelist[0], mode = 'r')
+    latsraw = tmp.variables["lat"]
+    lonsraw = tmp.variables["lon"]
+    lat = latsraw[:]
+    lon = lonsraw[:]
+    print 'Lats and lons read in for first file in filelist'
+
+    # Only one time per file in AIRS level III data
+    ntimes = 1
+    
+    # Create mask to extract required region only
+    #  NB. longitude is slightly more complicated as can wrap the prime meridion
+    print 'Extracting for :- lats:', latMin, latMax, ' lons: ', lonMin, lonMax
+    wh_lat = np.logical_and((lat >= latMin), (lat <= latMax))
+    if(lonMin < lonMax):
+        wh_lon = np.logical_and((lon >= lonMin), (lon <= lonMax))
+    if(lonMin > lonMax):
+        wh_lon = np.logical_or((lon >= lonMin), (lon <= lonMax))
+    
+    sublat = lat[wh_lat]
+    sublon = lon[wh_lon]
+    
+    wh_true1, wh_true2 = np.meshgrid(wh_lon, wh_lat)
+    wh = np.logical_and(wh_true1, wh_true2)
+    
+    # Create empty array to store data
+    t2store = np.empty((ntimes * len(filelist), sublat.size, sublon.size))
+    timestore = []
+
+    # Now load in the data for real
+    #  NB. no need to reload in the latitudes and longitudes -assume invariant
+    i = 0
+    timesaccu = 0 # a counter for number of times stored so far in t2store 
+    #  NB. this method allows for missing times in data files 
+    #      as no assumption made that same number of times in each file...
+    for ifile in filelist:
+        print 'Loading data from file: ', filelist[i]
+        f = netCDF4.Dataset(ifile, mode='r')
+        t2raw = f.variables[myvar]
+        
+        # Read time from filename (NB. 'time' variable in netCDF always set to zero)
+        filename = os.path.basename(ifile)  # strip off the filepath
+        timestamp_string = filename[5:15]   # cut out the date time stamp
+        DATE_FORMAT = '%Y.%m.%d'  
+        mytime = datetime.datetime(*time.strptime(timestamp_string, DATE_FORMAT)[:4])
+        print mytime
+        ntimes = 1
+        t2tmp = t2raw[:, :]
+        sub = t2tmp[wh].reshape(sublat.size, sublon.size)
+        t2store[timesaccu, :, :] = sub
+        timestore.append(mytime)
+        timesaccu = timesaccu + ntimes
+        i += 1 
+
+
+    print 'Data read in successfully with dimensions: ', t2store.shape
+
+    # Create masked array using missing value flag from file
+    mdi = f.variables[myvar]._FillValue[0]
+    mdata = ma.masked_array(t2store, mask=(t2store == mdi))
+    # Rearrange array so data match lat lon values
+    mdata = np.flipud(mdata[:, ::-1])
+
+    return sublat, sublon, timestore, mdata
+
+def read_urd_files(filelist, latMin, latMax, lonMin, lonMax):
+    '''
+     Routine to load in NCEP Unified Raingauge Database binary files
+    
+      Input:
+         filelist - a list of URD data files
+    
+    
+      Output:
+         sublats, sublons: 2d arrays of latitude and longitude values for user selected region.
+         times - a list of python datetime objects
+         subdata - precipitation data for user selected region
+    
+      Peter Lean  August 2010
+    '''
+    
+    repository_path = '/nas/share1-hp/jinwonki/data/obs/pr25urd/daily/'
+    
+    # NB. Domain: 140W - 60W; 20N - 60N; Resolution: 0.25x0.25 degrees.
+    #     The grids are arranged such that
+    #     longitude is from 140W eastward to 60W and latitude from 20N northward
+    #     to 60N, so that the first grid is (140W,20N), the second is 
+    #     (139.75W,20N)......
+    
+    # Parameters specific to the URD dataset
+    nlat = 161
+    nlon = 321
+    
+    # Calculate the latitude and longitude arrays
+    lat = np.arange(20, 60.25, 0.25)  # Hard wired lat,lon extent values for URD data files
+    lon = np.arange(-140, -59.75, 0.25)
+    
+    lons, lats = np.meshgrid(lon, lat)
+
+    # Define sub-region mask 
+    #  NB. longitude is slightly more complicated as can wrap the prime meridion
+    print 'Extracting for :- lats:', latMin, latMax, ' lons: ', lonMin, lonMax
+    wh_lat = np.logical_and((lats >= latMin), (lats <= latMax))
+    if(lonMin < lonMax):
+        wh_lon = np.logical_and((lons >= lonMin), (lons <= lonMax))
+    if(lonMin > lonMax):
+        wh_lon = np.logical_or((lons >= lonMin), (lons <= lonMax))
+    
+    # count number of latitude values in subselection (for redimensioning array)
+    wh_true = np.logical_and(wh_lat, wh_lon)
+    nsublat = np.where(np.logical_and((lat >= latMin), (lat <= latMax)))[0].size
+    
+    sublats = lats[wh_true].reshape(nsublat, -1)  # infers longitude dimension given latitude dimension
+    sublons = lons[wh_true].reshape(nsublat, -1)  # infers longitude dimension given latitude dimension
+    nsublon = sublats.shape[1]
+
+    # Load in the daily data
+    datastore = []
+    for myfile in filelist:
+        f = FortranFile(repository_path + myfile)
+    
+        # Extract month and year from filename
+        yearmonth = int(myfile[7:13])
+        year = int(str(yearmonth)[0:4])
+        month = int(str(yearmonth)[4:6])
+        
+        # Find out how many days there are in that month
+        nt = calendar.monthrange(year, month)[1]
+        
+        data = np.zeros((nt, nsublat, nsublon))
+        for t in np.arange(nt):
+            precip = f.readReals()
+            precip.shape = [nlat, nlon]
+            data[t, :, :] = precip[wh_true].reshape(nsublat, nsublon) 
+        
+        datastore.append(data)
+
+    # Make a single 3d numpy array out of my list of numpy arrays
+    nt = 0
+    for i in range(len(datastore)):
+        nt = nt + datastore[i].shape[0]
+    
+    final_data = np.zeros((nt, nsublat, nsublon))
+    t = 0
+    for i in range(len(datastore)):
+        nt = datastore[i].shape[0]
+        final_data[t:t + nt, :, :] = datastore[i]
+        t = t + nt
+
+    # Load in land/sea mask
+    ls = np.fromfile("/nas/share1-hp/jinwonki/data/obs/pr25urd/s/d/lsm25.usa", sep=" ")
+    ls.shape = [nlat, nlon]
+    # Extract subregion from land/sea mask
+    subls = np.ones(final_data.shape)
+    for t in np.arange(final_data.shape[0]):
+        subls[t, :, :] = ls[wh_true].reshape(nsublat, nsublon) 
+    
+    # Construct a masked array of data i.e. only using data from land points
+    mdi = -1
+    mdata = ma.masked_array(final_data, mask=(subls == mdi))
+
+    # Construct datetime list from dates in filenames.
+    yearmonth = np.zeros(len(filelist))
+    i = 0
+    for filename in filelist:
+        # Extract month and year from filename
+        yearmonth[i] = int(filename[7:13])
+        i += 1
+    
+    # Construct a list of datetimes between the earliest and latest yearmonth
+    firstyear = int(str(yearmonth.min())[0:4])
+    firstmonth = int(str(yearmonth.min())[4:6])
+    times = []
+
+    cur_time = datetime.datetime(firstyear, firstmonth, 1, 0, 0, 0, 0)
+    
+    for i in range(final_data.shape[0]):
+        times.append(cur_time)
+        dt = datetime.timedelta(days=1)
+        cur_time = cur_time + dt
+    
+    return sublats, sublons, times, mdata
+
+def read_tmp_watershed(myfile, dom_num):
+    '''
+     Routine to read watershed weighting file mapped onto WRF model grids.
+      NB.this will be superceded by proper routines to read shape files and regrid onto any model grid.
+    
+      Input:
+         myfile - file name of the watershed ascii file to load
+         dom_num - WRF domain number (specific to this experiment)
+    
+      Output:
+         mymask - boolean mask array saying where the watershed is
+    
+       Peter Lean    September 2010
+    '''
+    
+    # Parameters specific to WRF domain setup required for these files
+    if(dom_num == 1):
+        nx = 190
+        ny = 130
+    
+    if(dom_num == 2):
+        nx = 192
+        ny = 180
+      
+    # Create an empty array to store the weights
+    myweights = np.zeros((ny, nx))
+    
+    # Load in data from the mask file
+    i, j, w = np.loadtxt("/home/plean/demo/rcmes/watersheds/" + myfile, unpack=True)
+    
+    for q in np.arange(len(i)):
+        myweights[j[q], i[q]] = w[q]
+    
+    mymask = np.empty((ny, nx))
+    mymask[:] = True
+    mymask[(myweights > 0.5)] = False
+    
+    return mymask
+
+def read_eraint_surf_files(filelist, myvar, latMin, latMax, lonMin, lonMax):
+    '''
+     ** For testing work before database was ready. **
+     Reads ERA-Interim surface netCDF files.
+    
+     Input:
+        filelist - list of filenames (including path)
+        myvar    - name of variable to load
+        latMin,latMax,lonMin,lonMax - define region to extract (in degrees)
+     Output:
+        lat, lon   - 1D array of latitude and longitude values
+        timestore  - list of python datetime objects
+        mdata      - numpy masked array containing data from all files    
+    
+       Peter Lean September 2010 
+    '''
+    
+    
+    # Crash nicely if 'filelist' is zero length
+    if len(filelist) == 0:
+        print 'Error: no files have been passed to read_data_from_file_list()'
+        sys.exit()
+
+    # Open the first file in the list to:
+    #    i) read in lats, lons
+    #    ii) find out how many timesteps in the file 
+    #        (assume same ntimes in each file in list)
+    #     -allows you to create an empty array to store variable data for all times
+    tmp = netCDF4.Dataset(filelist[0], mode='r')
+    latsraw = tmp.variables["latitude"]
+    lonsraw = tmp.variables["longitude"]
+    lat = latsraw[:]
+    lon = lonsraw[:]
+    print 'Lats and lons read in for first file in filelist'
+    
+    # Create mask to extract required region only
+    #  NB. longitude is slightly more complicated as can wrap the prime meridion
+    print 'Extracting for :- lats:', latMin, latMax, ' lons: ', lonMin, lonMax
+    wh_lat = np.logical_and((lat >= latMin), (lat <= latMax))
+    if(lonMin < lonMax):
+        wh_lon = np.logical_and((lon >= lonMin), (lon <= lonMax))
+    if(lonMin > lonMax):
+        wh_lon = np.logical_or((lon >= lonMin), (lon <= lonMax))
+    
+    sublat = lat[wh_lat]
+    sublon = lon[wh_lon]
+    
+    wh_true1, wh_true2 = np.meshgrid(wh_lon, wh_lat)
+    wh = np.logical_and(wh_true1, wh_true2)
+    
+    # Create storage lists
+    datastore = []
+    timestore = []
+
+    # Now load in the data for real
+    #  NB. no need to reload in the latitudes and longitudes -assume invariant
+    i = 0
+    timesaccu = 0 # a counter for number of times stored so far in t2store 
+    #  NB. this method allows for missing times in data files 
+    #      as no assumption made that same number of times in each file...
+    for ifile in filelist:
+        print 'Loading data from file: ', filelist[i]
+        f = netCDF4.open_file(ifile, mode='r')
+        data = f.variables[myvar][:]
+        scale = f.variables[myvar].scale_factor
+        offset = f.variables[myvar].add_offset
+        data = data * scale + offset
+        times = f.variables["time"][:]
+        ntimes = times.size
+        # Decode times into python datetime object
+        sub = data[:, wh].reshape(ntimes, sublat.size, sublon.size)
+        datastore.append(sub)
+        timestore.append(times)
+        timesaccu = timesaccu + ntimes
+        i += 1 
+
+    # move data from lists into correctly dimensioned arrays
+    final_data = np.zeros((timesaccu, sublat.size, sublon.size))
+    t = 0
+    for i in range(len(datastore)):
+        nt = datastore[i].shape[0]
+        final_data[t:t + nt, :, :] = datastore[i]
+        t = t + nt
+    
+    times = np.zeros((timesaccu))
+    t = 0
+    for i in range(len(timestore)):
+        nt = timestore[i].shape[0]
+        times[t:t + nt] = timestore[i]
+        t = t + nt
+  
+    # Decode times into python datetime objects
+    times = rcmes.process.decode_eraint_surf_times(times)
+    
+    print 'Data read in successfully with dimensions: ', final_data.shape
+    
+    # Create masked array using missing value flag from file
+    mdi = f.variables[myvar]._FillValue[0]
+    mdata = ma.masked_array(final_data, mask=(final_data == mdi))
+
+    # Rearrange array so data match lat lon values
+    mdata = np.flipud(mdata[:, ::-1])
+    
+    return sublat, sublon, times, mdata
+
+def make_list_of_wrf_files(firstTime, lastTime, ident):
+    '''
+     Routine to make list of WRF filenames given time period.
+    
+      Input:
+          firstTime - datetime object specifying start time
+          lastTime  - datetime object specifying end time
+          ident     - identifier for model run, e.g. 'd01'
+    
+      Output:
+          filelist  - list of standard format WRF filenames
+    
+          Peter Lean
+    '''
+
+    dt = datetime.timedelta(hours=6)
+    filenamelist = []
+    curTime = firstTime
+
+    while curTime <= lastTime:
+        curTimeString = curTime.strftime("%Y-%m-%d_%H:%M:%S")
+        filenamelist.append('wrfout_' + ident + '_' + curTimeString)
+        curTime += dt
+    
+    return filenamelist
+
+def make_list_of_trmm_files(firstTime, lastTime):
+    '''
+     Routine to make list of TRMM filenames given time period.
+    
+      Input:
+          firstTime - datetime object specifying start time
+          lastTime  - datetime object specifying end time
+    
+      Output:
+          filelist  - list of standard format WRF filenames
+    
+          Peter Lean
+    '''
+    trmm_repository = '/nas/share4-cf/plean/TRMM/'
+    dt = datetime.timedelta(hours=24)
+    filenamelist = []
+    curTime = firstTime
+    while curTime <= lastTime:
+        curTimeString = curTime.strftime("%Y.%m.%d")
+        filenamelist.append(trmm_repository + '3B42_daily.' + curTimeString + '.6.nc')
+        
+        curTime += dt
+    
+    return filenamelist
+
+def make_list_of_airs_files(firstTime, lastTime):
+    '''
+     Routine to make list of AIRS filenames given time period.
+    
+      Input:
+          firstTime - datetime object specifying start time
+          lastTime  - datetime object specifying end time
+    
+      Output:
+          filelist  - list of standard format WRF filenames
+    
+          Peter Lean
+    '''
+
+
+    airs_repository = '/nas/share4-cf/plean/AIRX3STD/'
+    dt = datetime.timedelta(hours=24)
+    filenamelist = []
+    curTime = firstTime
+    while curTime <= lastTime:
+        curTimeString = curTime.strftime("%Y.%m.%d")
+        filenamelist.append(glob.glob(airs_repository + 'AIRS.' + curTimeString + '.L3.*.nc')[0])
+        
+        curTime += dt
+    
+    return filenamelist
+
+def make_list_of_urd_files(firstTime, lastTime):
+    '''
+     Routine to make list of URD filenames given time period.
+    
+      Input:
+          firstTime - datetime object specifying start time
+          lastTime  - datetime object specifying end time
+    
+      Output:
+          filelist  - list of standard format WRF filenames
+    
+          Peter Lean
+    '''
+    
+    dt = datetime.timedelta(days=30)
+    filenamelist = []
+    newfirstTime = datetime.datetime(firstTime.year, firstTime.month, 15, 0, 0, 0)
+    newlastTime = datetime.datetime(lastTime.year, lastTime.month, 15, 0, 0, 0)
+    
+    curTime = newfirstTime
+    while curTime <= newlastTime:
+        curTimeString = curTime.strftime("%Y%m")
+        filenamelist.append('pr_ncep' + curTimeString)
+        if(curTime.month == 1):
+            curTime = datetime.datetime(curTime.year, curTime.month, 15, 00, 00, 00, 00)
+        
+        curTime += dt
+    
+    return filenamelist
+
+def make_list_of_era_surf_files(firstTime, lastTime):
+    '''
+     Routine to make list of ERA-Interim surface filenames given time period.
+    
+      Input:
+          firstTime - datetime object specifying start time
+          lastTime  - datetime object specifying end time
+    
+      Output:
+          filelist  - list of standard format WRF filenames
+    
+          Peter Lean
+    '''
+
+    import datetime
+    eraint_repository = '/data/plean/era-int/surf/'
+    filenamelist = []
+    dt = datetime.timedelta(days=30)
+    newfirstTime = datetime.datetime(firstTime.year, firstTime.month, 15, 0, 0, 0)
+    newlastTime = datetime.datetime(lastTime.year, lastTime.month, 15, 0, 0, 0)
+    curTime = newfirstTime
+
+    while curTime <= newlastTime:
+        curTimeString = curTime.strftime("%b%Y")
+        filenamelist.append(eraint_repository + 'sfc.' + curTimeString.lower() + '.nc')
+        if(curTime.month == 1):
+            curTime = datetime.datetime(curTime.year, curTime.month, 15, 00, 00, 00, 00)
+        
+        curTime += dt
+    
+    return filenamelist
+
+
+#
+
+def assign_subRgns_from_a_text_file(infile):
+    # Read pre-fabricated sugregion information from a text file
+    # Note: python indexing includes the beginning point but excludes the ending point
+    f = open(infile, 'r')
+    for i in np.arange(8):
+        string = f.readline()
+        print 'Line ', i, ': Content ', string
+    string = f.readline()
+    numSubRgn = int(string[20:22])
+    print 'numSubRgn = ', numSubRgn
+    for i in np.arange(3):
+        string = f.readline()
+    # Read input string and extract subRegion info (name, longs, lats) from the string
+    subRgnName = []
+    subRgnLon0 = ma.zeros((numSubRgn))
+    subRgnLon1 = ma.zeros((numSubRgn))
+    subRgnLat0 = ma.zeros((numSubRgn))
+    subRgnLat1 = ma.zeros((numSubRgn))
+    for i in np.arange(numSubRgn):
+        string = f.readline()
+        subRgnName.append(string[0:19])
+        subRgnLon0[i] = float(string[30:37])
+        subRgnLon1[i] = float(string[40:47])
+        subRgnLat0[i] = float(string[50:55])
+        subRgnLat1[i] = float(string[60:65])
+    f.close()
+    print 'subRgnName: ', subRgnName
+    print 'subRgnLon0: ', subRgnLon0
+    print 'subRgnLon1: ', subRgnLon1
+    print 'subRgnLat0: ', subRgnLat0
+    print 'subRgnLat1: ', subRgnLat1
+    return numSubRgn, subRgnName, subRgnLon0, subRgnLon1, subRgnLat0, subRgnLat1
+
+def createSubRegionObjectInteractively():
+    """
+    Purpose::
+        Mini command line program to enable users to enter SubRegion Information
+    Input::
+        None
+    Output::
+        SubRegion Object
+    """
+    rawInput = None
+    while rawInput == None:
+        userMessage = ("Enter information for 1 Sub Region using the following "
+                       "pipe '|' separated format: \n"
+                       "RegionName | Degrees North | Degrees South | Degrees East | Degrees West \n>>>")
+        userInput = raw_input(userMessage)
+        inputList = userInput.split('|')
+        if len(inputList) != 5:
+            badLengthMessage = ("Unable to parse %s.  You should have 5 inputs "
+                                "separated by 4 pipe characters. \n"
+                                "Example:  Region Name | 85 | 80 | 10 | -30" % userInput)
+            print(badLengthMessage)
+        else:
+            name = str(inputList[0]).strip()
+            latMax = str(inputList[1]).strip()
+            latMin = str(inputList[2]).strip()
+            lonMax = str(inputList[3]).strip()
+            lonMin = str(inputList[4]).strip()
+            subRegion = classes.SubRegion(name, latMin, lonMin, latMax, lonMax)
+            rawInput = True
+
+    return subRegion
+
+def selectSubRegion(subRegions):
+    # interactively select the sub-region ID for area-mean time-series evaluation
+    print '-'*59
+    columnTemplate = "|{0:2}|{1:10}|{2:10}|{3:10}|{4:10}|{5:10}|"
+    print columnTemplate.format("ID", "Name", "LonMin", "LonMax", "LatMin", "LatMax")
+    counter = 0
+    for subRegion in subRegions:
+        print columnTemplate.format(counter, subRegion.name, subRegion.lonMin, subRegion.lonMax, subRegion.latMin, subRegion.latMax)
+        counter += 1
+
+    print '-'*59
+    ask = 'Enter the sub-region ID to be evaluated. -9 for all sub-regions: \n'
+    rgnSelect = int(raw_input(ask))
+    if rgnSelect >= len(subRegions):
+        print 'sub-region ID out of range. Max = %s' % len(subRegions)
+        sys.exit()
+    return rgnSelect
+
+def getStartEndTimes(status, startOverLapTime, endOverLapTime):
+    '''
+    This function will get the start and end time from user.
+    It also check whether or not user enters the proper time for both start and end.
+    If user leaves the start and end time empty, it will get the largest time range as default (overlap).
+    '''
+
+    if status == "start":
+        try:
+            time = raw_input("Please Enter a Start Date [%s]: " % startOverLapTime.strftime('%Y-%m-%d'))
+            if not time:
+                time = startOverLapTime
+                print "Your time starts from [%s] " % time.strftime('%Y-%m-%d')
+                return time
+            time = datetime.datetime.strptime(time, '%Y-%m-%d')
+            if time < startOverLapTime:
+                print "WARNING: The time you inputted [%s] " % time.strftime('%Y-%m-%d') + " is before the minimum start time [%s]."  % startOverLapTime.strftime('%Y-%m-%d')
+                time = getStartEndTimes("start", startOverLapTime, endOverLapTime)
+                return time
+            elif time > endOverLapTime:
+                print "WARNING: The time you inputted [%s] " % time.strftime('%Y-%m-%d') + " is after the maximum end time [%s]. " % endOverLapTime.strftime('%Y-%m-%d')
+                time = getStartEndTimes("start", startOverLapTime, endOverLapTime)
+                return time
+            else:
+                return time
+        except ValueError:
+            getStartEndTimes(status, startOverLapTime, endOverLapTime)
+    
+    if status == "end":
+        try:
+            time = raw_input("Please Enter an End Date [%s]: " % endOverLapTime.strftime('%Y-%m-%d'))
+            if not time:
+                time = endOverLapTime
+                print "Your time ends by [%s] " % time.strftime('%Y-%m-%d')
+                return time
+            time = datetime.datetime.strptime(time, '%Y-%m-%d')
+            if time > endOverLapTime:
+                print "WARNING: The time you inputted [%s] " % time.strftime('%Y-%m-%d') + " is after the maximum end time [%s]. " % endOverLapTime.strftime('%Y-%m-%d')
+                time = getStartEndTimes("end", startOverLapTime, endOverLapTime)
+                return time
+            elif time < startOverLapTime:
+                print "WARNING: The time you inputted [%s] " % time.strftime('%Y-%m-%d') + " is before the minimum start time [%s]."  % startOverLapTime.strftime('%Y-%m-%d')
+                time = getStartEndTimes("end", startOverLapTime, endOverLapTime)
+                return time
+            else:
+                return time
+        except ValueError:
+            getStartEndTimes(status, startOverLapTime, endOverLapTime)
+
+
+def getDirSettings():
+    """
+    This function will collect 2 parameters from the user about the RCMET run they have started.
+    
+    Output::
+        dirs - Tuple of strings i.e. ('workDirPath', 'cacheDirPath')
+    """
+    workDir = os.path.abspath(raw_input('Please enter workDir:\n> '))
+    if os.path.isdir(workDir):
+        pass
+    else:
+        makeDirectory(workDir)
+    
+    cacheDir= os.path.abspath(raw_input('Please enter cacheDir:\n> '))
+    if os.path.isdir(cacheDir):
+        pass
+    else:
+        makeDirectory(cacheDir)
+    
+    return (workDir, cacheDir)
+
+def getModelFiles():
+    modelList = []
+    while len(modelList) < 1:
+        userInput = raw_input('Please enter model file (or specify multiple files using wildcard):\n> ')
+        modelList = glob.glob(userInput)
+        if len(modelList) == 0:
+            print("Sorry we were unable to find any files at - %s" % userInput)
+            print("Please try again, and use the asterisk * for the wildcard")
+        
+    return modelList
+
+def getTemporalGrid():
+    options = ['annual', 'monthly', 'daily']
+    print("Please select one of the following Temporal Grid Options:\n")
+    for key, option in enumerate(options):
+        print("[%s] - %s" % (key, option))
+    choice = int(raw_input(">>>"))
+    try:
+        temporalGrid = options[choice]
+    except IndexError:
+        getTemporalGrid()
+    else:
+        return temporalGrid
+
+def getSpatialGrid():
+    options = ['obs', 'model', 'user']
+    print("Please select one of the following Spatial Grid Options:\n")
+    for key, option in enumerate(options):
+        print("[%s] - %s" % (key, option))
+
+    choice = int(raw_input(">>>"))
+    try:
+        spatialGrid = options[choice]
+    except IndexError:
+        getSpatialGrid()
+
+    return spatialGrid
+
+def askUserForVariableName(variableNames, targetName):
+    if targetName == "analysis":
+        print("Select the variable you want to use for analysis/metrics:")
+    else:
+        print("Select the variable that corresponds to %s:" % targetName)
+
+    for idx, variable in enumerate(variableNames):
+        print("[%s] - %s" % (idx, variable))
+    userChoice = int(raw_input(">>>"))
+    try:
+        variableName = variableNames[userChoice]
+    except IndexError:
+        askUserForVariableName(variableNames, targetName)
+    
+    return variableName
+        
+        
+
+def getLatLonStep(settings):
+    pass
+
+def getSpatialBounds(settings):
+    pass
+
+
+def getUserSpatialSettings(settings):
+    getLatLonStep(settings)
+    getSpatialBounds(settings)
+
+def makeDirectory(directory):
+    print "%s doesn't exist.  Trying to create it now." % directory
+    try:
+        os.mkdir(directory)
+        print("Created %s successfully" % directory)
+    except OSError:
+        print "This program cannot create dir: %s due to permission issues." % directory
+        sys.exit()
+
+
+def userDefinedStartEndTimes(obsSource,obsName,obsTimeName,obsList,modelList):
+    """
+    The function will interactively ask the user to select a start and end time based on the start/end times
+    of the supplied observation and model objects
+     
+    Input::
+        obsList - List of Observation Objects
+        modelList - List of Model Objects
+    
+    Output::
+        startTime - Python datetime object from User Input
+        endTime - Python datetime object from User Input
+    """
+    startTimes = []
+    endTimes = []
+    print '='*94
+    template = "|{0:60}|{1:15}|{2:15}|"
+    print template.format('Dataset - NAME', 'START DATE', 'END DATE')
+    if obsSource == 0:                # observation from RCMED
+        for observation in obsList:
+            startTimes.append(datetime.datetime.strptime(observation['start_date'],'%Y-%m-%d'))
+            endTimes.append(datetime.datetime.strptime(observation['end_date'],'%Y-%m-%d'))
+            print template.format(observation['longname'], observation['start_date'], observation['end_date'])
+    elif obsSource == 1:              # observation from user
+        nn = 0
+        for observation in obsList:
+            times, timeStep = process.getModelTimes(observation,obsTimeName)
+            #print times, timeStep
+            startTimes.append(min(times))
+            endTimes.append(max(times))
+            print template.format(obsName[nn], min(times).strftime('%Y-%m-%d'), max(times).strftime('%Y-%m-%d'))
+            nn = +1
+    print '-'*94
+    for model in modelList:
+        startTimes.append(model.minTime)
+        endTimes.append(model.maxTime)
+        print template.format(model.name, model.minTime.strftime('%Y-%m-%d'), model.maxTime.strftime('%Y-%m-%d'))
+    print '='*94
+    
+    # Compute Overlap
+    maxstartTimes=max(startTimes)
+    minendTimes=min(endTimes)
+    # TODO:  Do we need to start on JAN and end on DEC?  Do we know someone is doing ANNUAL analysis at this point?
+#    if maxstartTimes.month != 1:
+#        maxstartTimes = datetime.datetime(maxstartTimes.year+1,1,maxstartTimes.day)
+#    if minendTimes.month != 12:
+#        minendTimes = datetime.datetime(minendTimes.year-1,12,minendTimes.day)
+    if minendTimes.year < maxstartTimes.year:
+        print 'Not enough data for overlapping years'
+        sys.exit()
+    overLap = (maxstartTimes.strftime('%Y-%m-%d'), minendTimes.strftime('%Y-%m-%d'))
+    # Present default overlap to user as default value
+    print 'Standard Overlap in the selected datasets are %s through %s' % (overLap)
+
+    startOverLapTime = datetime.datetime.strptime(overLap[0],'%Y-%m-%d')
+    endOverLapTime = datetime.datetime.strptime(overLap[1],'%Y-%m-%d')
+
+    # Enter Start Date
+    startTime = getStartEndTimes("start", startOverLapTime, endOverLapTime)    
+    # Enter End Date
+    endTime = getStartEndTimes("end", startOverLapTime, endOverLapTime)
+        
+    if startTime > endTime:
+        print "WARNING: The start time you entered [%s]" % startTime.strftime('%Y-%m-%d') + " is after the end time you entered [%s]." % endTime.strftime('%Y-%m-%d')
+        startTime = getStartEndTimes("start", startOverLapTime, endOverLapTime)
+        endTime = getStartEndTimes("end", startOverLapTime, endOverLapTime)
+
+    return startTime, endTime
+
+
+def reshapeMonthlyData(dataset1):
+    """
+    Purpose::
+       Returns a view of an array with shape (nMonth, ...)
+       reshaped to (nYR, 12, ...) in order to assist in monthly
+       calculations
+    Input::
+       dataset1 - an input array with the first dimension corresponding
+       to the number of months, which must be a multiple of 12
+    Output::
+       data - A view of dataset1 but with shape (nYR, 12, ...).
+    """
+
+    # Create a view of dataset1. This lets us change the shape
+    # without copying or modifying the original array.
+    data = dataset1[:]
+    ishape = data.shape
+    nMonth = ishape[0]
+    nshape = nMonth/12, 12
+
+    # Combine the number of years / months (nshape) with other dimensions
+    data.shape = tuple(list(nshape) + list(ishape[1:]))
+    return data
+
+
+def select_timOpt():
+    #---------------------------------------------
+    # Interacrively select the time scale to be evaluated
+    # e.g., the means over annual, seasonal, monthly, or a specified period (e.g., JJAS for Indian monsoon)
+    #------------------------------------------------------------------------------------
+    print 'Select the time-mean properties to be evaluated: Enter'
+    timeOption = \
+      int(raw_input('1=annual, 2=seasonal (define "season", e.g., JJAS for Indian monsoon), 3=monthly \n> '))
+    return timeOption
+
+def select_data(nDat, Times, List, sourceDat):
+    #---------------------------------------------
+    # Interacrively select a model or models for evaluation
+    #----------------------------------------------------------------------------
+    print '-----------------------------------------------'
+    if sourceDat == 'mdl':
+        print 'mdlID  mdlName numMOs  mdlStartTime mdlEndTime fileName'
+    elif sourceDat == 'obs':
+        print 'obsID  obsName obsMOs  obsStartTime obsEndTime fileName'
+    else:
+        print 'not valid data source: CRASH and restart'
+        sys.exit()
+    print '-----------------------------------------------'
+
+    for n in np.arange(len(List)):
+        print n, List[n], Times[0], Times[-1]
+        n += 1
+    print '-----------------------------------------------'
+    if sourceDat == 'mdl':
+        ask = 'Enter the model ID to be evaluated. -9 for all models (-9 is not active yet): \n'
+    elif sourceDat == 'obs':
+        ask = 'Enter the obs ID to be evaluated. -9 for all models (-9 is not active yet): \n'
+    datSelect = int(raw_input(ask))
+    if datSelect > nDat - 1:
+        print 'Data ID out of range: CRASH'
+        sys.exit()
+    return datSelect
+
+def select_data_combined(nDat, Times, List, datType):
+    '''
+    # Interacrively select a model or models for evaluation
+    '''
+    nT = len(Times)
+    print '-------------------------------------------------------'
+    print 'datID  datName numStp  datStartTime datEndTime dataName'
+    print '-------------------------------------------------------'
+    for n in np.arange(nDat):
+        print n, List[n], nT, Times[0], Times[nT-1], List[n]
+        n+=1
+    print '-----------------------------------------------'
+    if datType == 'ref':
+        ask = 'Enter the reference data ID.: \n'
+    elif datType == 'mdl':
+        ask = 'Enter the data ID to be evaluated. -1 for all models, -2 for all models + obs, -3 for all obs, -4 for any combinations: \n'
+    datSelect = int(raw_input(ask))
+    if datSelect > nDat-1:
+        print 'Data ID out of range: CRASH'
+        sys.exit()
+    return datSelect
+
+def select_metrics():
+    #---------------------------------------------
+    # Interacrively select an evaluation metric
+    # Input : none
+    # Output: metricOption, the indicator for selecting the metric to be calculated
+    #------------------------------------------------------------------------------
+    print 'Metric options'
+    print '[0] Bias: mean bias across full time range'
+    print '[1] Mean Absolute Error: across full time range'
+    print '[2] Spatial Pattern Correlation: results in a time series of spatial correlation coeff'
+    print '[3] Temporal Correlation: results in 2-d array of temporal correlation coefficient'
+    print '[4] Spatial Pattern Correlation between averaged fields: results in a single correlation coeff'
+    print '[5] RMSE in time: results in a 2-d array of RMSE over two time series'
+    print '[6] TODO: Probability Distribution Function similarity score'
+    print '[7] Taylor diagram for spatial variability'
+    choice = int(raw_input('Please make a selection from the options above\n> '))
+    # assign the evaluation metric to be calculated
+    if choice == 0:
+        metricOption = 'BIAS'
+    elif choice == 1:
+        metricOption = 'MAE'
+    elif choice == 2:
+        metricOption = 'PCt'
+    elif choice == 3:
+        metricOption = 'TC'
+    elif choice == 4:
+        metricOption = 'PCC'
+    elif choice == 5:
+        metricOption = 'RMSt'
+    elif choice == 6:
+        metricOption = 'pdfSkillScore'
+    elif choice == 7:
+        metricOption = 'Taylor_space'
+    print 'in subroutine metricOption = ', metricOption
+    return metricOption
+

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Added: incubator/climate/branches/rcmet-2.1.1/src/main/python/tests/files/missingSubRegionParam.cfg
URL: http://svn.apache.org/viewvc/incubator/climate/branches/rcmet-2.1.1/src/main/python/tests/files/missingSubRegionParam.cfg?rev=1517753&view=auto
==============================================================================
--- incubator/climate/branches/rcmet-2.1.1/src/main/python/tests/files/missingSubRegionParam.cfg (added)
+++ incubator/climate/branches/rcmet-2.1.1/src/main/python/tests/files/missingSubRegionParam.cfg Tue Aug 27 05:35:42 2013
@@ -0,0 +1,3 @@
+[SUB_REGION]
+# Sub Region(s) Full File Path
+

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Added: incubator/climate/branches/rcmet-2.1.1/src/main/python/tests/files/validSubRegionConfigFile.cfg
URL: http://svn.apache.org/viewvc/incubator/climate/branches/rcmet-2.1.1/src/main/python/tests/files/validSubRegionConfigFile.cfg?rev=1517753&view=auto
==============================================================================
--- incubator/climate/branches/rcmet-2.1.1/src/main/python/tests/files/validSubRegionConfigFile.cfg (added)
+++ incubator/climate/branches/rcmet-2.1.1/src/main/python/tests/files/validSubRegionConfigFile.cfg Tue Aug 27 05:35:42 2013
@@ -0,0 +1,3 @@
+[SUB_REGION]
+# Sub Region(s) Full File Path
+subRegionFile=files/validSubRegions.cfg

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Added: incubator/climate/branches/rcmet-2.1.1/src/main/python/tests/files/validSubRegions.cfg
URL: http://svn.apache.org/viewvc/incubator/climate/branches/rcmet-2.1.1/src/main/python/tests/files/validSubRegions.cfg?rev=1517753&view=auto
==============================================================================
--- incubator/climate/branches/rcmet-2.1.1/src/main/python/tests/files/validSubRegions.cfg (added)
+++ incubator/climate/branches/rcmet-2.1.1/src/main/python/tests/files/validSubRegions.cfg Tue Aug 27 05:35:42 2013
@@ -0,0 +1,7 @@
+[REGIONS]
+Region01:     ["R01", 36.5, 29, 0.0, -10]
+Region02:     ["R02", 37.5, 29, 10, 0]
+Region04:     ["R04", 32.5, 25, 33, 20]
+
+
+

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Added: incubator/climate/branches/rcmet-2.1.1/src/main/python/tests/test_files.py
URL: http://svn.apache.org/viewvc/incubator/climate/branches/rcmet-2.1.1/src/main/python/tests/test_files.py?rev=1517753&view=auto
==============================================================================
--- incubator/climate/branches/rcmet-2.1.1/src/main/python/tests/test_files.py (added)
+++ incubator/climate/branches/rcmet-2.1.1/src/main/python/tests/test_files.py Tue Aug 27 05:35:42 2013
@@ -0,0 +1,69 @@
+import os
+import unittest
+import Nio as nio
+
+import storage.files as files
+
+
+class TestGetVariableByType(unittest.TestCase):
+
+    def setUp(self):
+        self.badFilename = '/tmp/fail.txt'
+        self.missingVariable = 'missing'
+
+    def testNioRaisesException(self):
+        with self.assertRaises(Exception):
+            files.getVariableByType(self.badFilename, 'time')
+        
+    def testTimeVariableNames(self):
+        self.variableList = files.VARIABLE_NAMES['time']
+        for variable in self.variableList:
+            testFile = self.makeNioFile(variable)
+            timeVariable = files.getVariableByType(testFile, 'time')
+            os.remove(testFile)
+            self.assertEqual(timeVariable, variable)
+    
+    def testLatitudeVariableNames(self):
+        self.variableList = files.VARIABLE_NAMES['latitude']
+        for variable in self.variableList:
+            testFile = self.makeNioFile(variable)
+            timeVariable = files.getVariableByType(testFile, 'latitude')
+            os.remove(testFile)
+            self.assertEqual(timeVariable, variable)
+
+    def testLongitudeVariableNames(self):
+        self.variableList = files.VARIABLE_NAMES['longitude']
+        for variable in self.variableList:
+            testFile = self.makeNioFile(variable)
+            timeVariable = files.getVariableByType(testFile, 'longitude')
+            os.remove(testFile)
+            self.assertEqual(timeVariable, variable)
+
+    def testTimeVariableMissing(self):
+        testFile = self.make5VariableNioFile()
+        testVariable = files.getVariableByType(testFile, 'time')
+        os.remove(testFile)
+        self.assertEqual(len(testVariable), 5)
+    
+    def makeNioFile(self, variableName):
+        filename = '/tmp/good_%s.nc' % variableName
+        f = nio.open_file(filename, 'w')
+        f.create_dimension('test_dimension', 1)
+        f.create_variable(variableName,'l',('test_dimension',))
+        f.close()
+        return filename
+    
+    def make5VariableNioFile(self):
+        filename = '/tmp/5_variables.nc'
+        f = nio.open_file(filename, 'w')
+        f.create_dimension('dimension_one', 1)
+        f.create_variable('one', 'l', ('dimension_one',))
+        f.create_variable('two', 'l', ('dimension_one',))
+        f.create_variable('three', 'l', ('dimension_one',))
+        f.create_variable('four', 'l', ('dimension_one',))
+        f.create_variable('five', 'l', ('dimension_one',))
+        f.close()
+        return filename
+
+if __name__ == '__main__':
+    unittest.main()

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Added: incubator/climate/branches/rcmet-2.1.1/src/main/python/tests/test_misc.py
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==============================================================================
--- incubator/climate/branches/rcmet-2.1.1/src/main/python/tests/test_misc.py (added)
+++ incubator/climate/branches/rcmet-2.1.1/src/main/python/tests/test_misc.py Tue Aug 27 05:35:42 2013
@@ -0,0 +1,56 @@
+import os
+import unittest
+
+from utils import misc
+import ConfigParser
+
+class TestReadSubRegionsFile(unittest.TestCase):
+
+    def setUp(self):
+        self.badFilename = '/tmp/fail.txt'
+        self.validSubRegionsFile = './files/validSubRegions.cfg'
+
+    def testMissingFileException(self):
+        with self.assertRaises(Exception):
+            misc.readSubRegionsFile(self.badFilename)
+    
+class TestParseSubRegions(unittest.TestCase):
+    
+    def setUp(self):
+        self.userConfig = ConfigParser.SafeConfigParser()
+        self.userConfig.optionxform = str # This is so the case is preserved on the items in the config file
+        self.missingSubRegion = './files/missingSubRegionParam.cfg'
+    
+    def testMissingSubRegionParameter(self):
+        self.userConfig.read(self.missingSubRegion)
+        self.missingSubRegionParam = misc.configToDict(self.userConfig.items('SUB_REGION'))
+        self.assertFalse(misc.parseSubRegions(self.missingSubRegionParam))
+
+class TestIsDirGood(unittest.TestCase):
+    
+    def setUp(self):
+        self.goodDir = '/tmp'
+        self.unwriteableDir = '/usr'
+        self.unwritableMissingDir = '/usr/test_bad_direcory'
+        self.writeableMissingDir = '/tmp/test_good_directory'
+        
+    def tearDown(self):
+        if os.path.exists(self.writeableMissingDir):
+            os.rmdir(self.writeableMissingDir)
+
+    def testGoodDirExists(self):
+        self.assertTrue(misc.isDirGood(self.goodDir))
+    
+    def testGoodDirDoesNotExist(self):
+        self.assertTrue(misc.isDirGood(self.writeableMissingDir))
+
+    def testUnwriteableDir(self):
+        with self.assertRaises(OSError):
+            misc.isDirGood(self.unwriteableDir)
+    
+    def testUnwritableMissingDir(self):
+        with self.assertRaises(OSError):
+            misc.isDirGood(self.unwritableMissingDir)
+
+if __name__ == '__main__':
+    unittest.main()

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Added: incubator/climate/branches/rcmet-2.1.1/src/main/python/tests/test_process.py
URL: http://svn.apache.org/viewvc/incubator/climate/branches/rcmet-2.1.1/src/main/python/tests/test_process.py?rev=1517753&view=auto
==============================================================================
--- incubator/climate/branches/rcmet-2.1.1/src/main/python/tests/test_process.py (added)
+++ incubator/climate/branches/rcmet-2.1.1/src/main/python/tests/test_process.py Tue Aug 27 05:35:42 2013
@@ -0,0 +1,26 @@
+import unittest
+from datetime import datetime, timedelta
+
+import toolkit.process as process
+
+
+class TestNormalizeDatetimes(unittest.TestCase):
+    
+    def testMonthlyNormalize(self):
+        self.annualClean = [datetime(2000, x, 1) for x in range(1, 12)]
+        self.annualFifteenth = [datetime(2000, x, 15) for x in range(1, 12)]
+        self.monthly = 'monthly'
+        self.normalDates = process.normalizeDatetimes(self.annualFifteenth, self.monthly)
+        self.assertEqual(self.normalDates, self.annualClean)
+    
+    def testDailyNormalize(self):
+        self.dailyClean = [datetime(2000, 1, 1, 0, 0) + timedelta(days=x) for x in range(0, 5)]
+        self.dailyNoonish = [datetime(2000, 1, 1, 12, 15) + timedelta(days=x) for x in range(0, 5)]
+        self.daily = 'daily'
+        self.normalDaily = process.normalizeDatetimes(self.dailyNoonish, self.daily)
+        self.assertEqual(self.dailyClean, self.normalDaily)
+        
+        
+if __name__ == '__main__':
+    unittest.main()
+         
\ No newline at end of file

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Added: incubator/climate/branches/rcmet-2.1.1/src/main/resources/PyLintREADME.txt
URL: http://svn.apache.org/viewvc/incubator/climate/branches/rcmet-2.1.1/src/main/resources/PyLintREADME.txt?rev=1517753&view=auto
==============================================================================
--- incubator/climate/branches/rcmet-2.1.1/src/main/resources/PyLintREADME.txt (added)
+++ incubator/climate/branches/rcmet-2.1.1/src/main/resources/PyLintREADME.txt Tue Aug 27 05:35:42 2013
@@ -0,0 +1,26 @@
+OVERVIEW:
+
+The code within RCMES has been linted using a project specific set of parameters.  We have blended Python's PEP-8
+while also including some Java formatting (namely camelCase instead of underscores).
+
+You don't really need to know all the particulars, but if you are curious you can look at the pyLintRcFile.txt in 
+this directory for full details.
+
+
+HOW TO LINT THE CODE:
+
+If you are contributing to this code base then you will need to comply with the code convention standards set forth
+by the project team.  We have used PyLint to check for code correctness, and the included pyLintRcFile.txt can be
+used with PyLint (http://pypi.python.org/pypi/pylint/).
+
+After you have installed pylint follow these directions.  Happy linting!
+
+Assuming you want to lint the metrics.py file within lib/rcmes, do the following
+
+$> cd rcmes/rcmet/src/main/python/rcmes
+$> pylint --rcfile=../../resources/pyLintRcFile.txt cli/rcmet_ui.py
+
+You will be presented with a Report of any Warnings, Conventions, Errors, or Refactoring opportunities as well as
+variable name conventions, etc..  For more about the meaning of the report look up the PyLint documentation online.
+
+This will help the team keep the codebase clean and consistent as multiple team members contribute code.

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--- incubator/climate/branches/rcmet-2.1.1/src/main/resources/pyLintRcFile.txt (added)
+++ incubator/climate/branches/rcmet-2.1.1/src/main/resources/pyLintRcFile.txt Tue Aug 27 05:35:42 2013
@@ -0,0 +1,249 @@
+[MASTER]
+
+# Specify a configuration file.
+#rcfile=
+
+# Python code to execute, usually for sys.path manipulation such as
+# pygtk.require().
+#init-hook=
+
+# Profiled execution.
+profile=no
+
+# Add files or directories to the blacklist. They should be base names, not
+# paths.
+ignore=CVS
+
+# Pickle collected data for later comparisons.
+persistent=yes
+
+# List of plugins (as comma separated values of python modules names) to load,
+# usually to register additional checkers.
+load-plugins=
+
+
+[MESSAGES CONTROL]
+
+# Enable the message, report, category or checker with the given id(s). You can
+# either give multiple identifier separated by comma (,) or put this option
+# multiple time.
+#enable=
+
+# Disable the message, report, category or checker with the given id(s). You
+# can either give multiple identifier separated by comma (,) or put this option
+# multiple time (only on the command line, not in the configuration file where
+# it should appear only once).
+#disable=
+
+
+[REPORTS]
+
+# Set the output format. Available formats are text, parseable, colorized, msvs
+# (visual studio) and html
+output-format=text
+
+# Include message's id in output
+include-ids=no
+
+# Put messages in a separate file for each module / package specified on the
+# command line instead of printing them on stdout. Reports (if any) will be
+# written in a file name "pylint_global.[txt|html]".
+files-output=no
+
+# Tells whether to display a full report or only the messages
+reports=yes
+
+# Python expression which should return a note less than 10 (10 is the highest
+# note). You have access to the variables errors warning, statement which
+# respectively contain the number of errors / warnings messages and the total
+# number of statements analyzed. This is used by the global evaluation report
+# (RP0004).
+evaluation=10.0 - ((float(5 * error + warning + refactor + convention) / statement) * 10)
+
+# Add a comment according to your evaluation note. This is used by the global
+# evaluation report (RP0004).
+comment=no
+
+
+[BASIC]
+
+# Required attributes for module, separated by a comma
+required-attributes=
+
+# List of builtins function names that should not be used, separated by a comma
+bad-functions=map,filter,apply,input
+
+# Regular expression which should only match correct module names
+module-rgx=(([a-z][a-z0-9]*)|([A-Z][a-zA-Z0-9]+))$
+
+# Regular expression which should only match correct module level names
+const-rgx=(([A-Z_][A-Z0-9_]*)|(__.*__))$
+
+# Regular expression which should only match correct class names
+class-rgx=[A-Z][a-zA-Z]+$
+
+# Regular expression which should only match correct function names
+function-rgx=[a-z]+[A-Za-z0-9]{2,30}$
+
+# Regular expression which should only match correct method names
+method-rgx=(([a-z]+[A-Za-z0-9]{2,30})|(__.*__))$
+
+# Regular expression which should only match correct instance attribute names
+attr-rgx=[a-z]+[A-Za-z0-9]{2,30}$
+
+# Regular expression which should only match correct argument names
+argument-rgx=[a-z][A-Za-z0-9]{2,30}$
+
+# Regular expression which should only match correct variable names
+variable-rgx=[a-z]+[A-Za-z0-9]{2,30}$
+
+# Regular expression which should only match correct list comprehension /
+# generator expression variable names
+inlinevar-rgx=[A-Za-z][A-Za-z0-9]*$
+
+# Good variable names which should always be accepted, separated by a comma
+good-names=i,j,k,ex,Run,_
+
+# Bad variable names which should always be refused, separated by a comma
+bad-names=foo,bar,baz,toto,tutu,tata
+
+# Regular expression which should only match functions or classes name which do
+# not require a docstring
+no-docstring-rgx=__.*__
+
+
+[FORMAT]
+
+# Maximum number of characters on a single line.
+max-line-length=120
+
+# Maximum number of lines in a module
+max-module-lines=1000
+
+# String used as indentation unit. This is usually " " (4 spaces) or "\t" (1
+# tab).
+indent-string='    '
+
+
+[MISCELLANEOUS]
+
+# List of note tags to take in consideration, separated by a comma.
+notes=FIXME,XXX,TODO
+
+
+[SIMILARITIES]
+
+# Minimum lines number of a similarity.
+min-similarity-lines=4
+
+# Ignore comments when computing similarities.
+ignore-comments=yes
+
+# Ignore docstrings when computing similarities.
+ignore-docstrings=yes
+
+
+[TYPECHECK]
+
+# Tells whether missing members accessed in mixin class should be ignored. A
+# mixin class is detected if its name ends with "mixin" (case insensitive).
+ignore-mixin-members=yes
+
+# List of classes names for which member attributes should not be checked
+# (useful for classes with attributes dynamically set).
+ignored-classes=SQLObject
+
+# When zope mode is activated, add a predefined set of Zope acquired attributes
+# to generated-members.
+zope=no
+
+# List of members which are set dynamically and missed by pylint inference
+# system, and so shouldn't trigger E0201 when accessed. Python regular
+# expressions are accepted.
+generated-members=REQUEST,acl_users,aq_parent
+
+
+[VARIABLES]
+
+# Tells whether we should check for unused import in __init__ files.
+init-import=no
+
+# A regular expression matching the beginning of the name of dummy variables
+# (i.e. not used).
+dummy-variables-rgx=_|dummy
+
+# List of additional names supposed to be defined in builtins. Remember that
+# you should avoid to define new builtins when possible.
+additional-builtins=
+
+
+[CLASSES]
+
+# List of interface methods to ignore, separated by a comma. This is used for
+# instance to not check methods defines in Zope's Interface base class.
+ignore-iface-methods=isImplementedBy,deferred,extends,names,namesAndDescriptions,queryDescriptionFor,getBases,getDescriptionFor,getDoc,getName,getTaggedValue,getTaggedValueTags,isEqualOrExtendedBy,setTaggedValue,isImplementedByInstancesOf,adaptWith,is_implemented_by
+
+# List of method names used to declare (i.e. assign) instance attributes.
+defining-attr-methods=__init__,__new__,setUp
+
+# List of valid names for the first argument in a class method.
+valid-classmethod-first-arg=cls
+
+
+[DESIGN]
+
+# Maximum number of arguments for function / method
+max-args=5
+
+# Argument names that match this expression will be ignored. Default to name
+# with leading underscore
+ignored-argument-names=_.*
+
+# Maximum number of locals for function / method body
+max-locals=15
+
+# Maximum number of return / yield for function / method body
+max-returns=6
+
+# Maximum number of branch for function / method body
+max-branchs=12
+
+# Maximum number of statements in function / method body
+max-statements=50
+
+# Maximum number of parents for a class (see R0901).
+max-parents=7
+
+# Maximum number of attributes for a class (see R0902).
+max-attributes=7
+
+# Minimum number of public methods for a class (see R0903).
+min-public-methods=2
+
+# Maximum number of public methods for a class (see R0904).
+max-public-methods=20
+
+
+[IMPORTS]
+
+# Deprecated modules which should not be used, separated by a comma
+deprecated-modules=regsub,string,TERMIOS,Bastion,rexec
+
+# Create a graph of every (i.e. internal and external) dependencies in the
+# given file (report RP0402 must not be disabled)
+import-graph=
+
+# Create a graph of external dependencies in the given file (report RP0402 must
+# not be disabled)
+ext-import-graph=
+
+# Create a graph of internal dependencies in the given file (report RP0402 must
+# not be disabled)
+int-import-graph=
+
+
+[EXCEPTIONS]
+
+# Exceptions that will emit a warning when being caught. Defaults to
+# "Exception"
+overgeneral-exceptions=Exception

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+Regional Climate Modeling Evaluation Toolkit Use Case
+
+User = Scientist
+System = RCMES
+
+Goal:  Compute Metrics on a Local Climate Model
+Main Success Scenario
+1.  User logs into System
+2.  User selects a model file
+3.  User selects model latitude, longitude, time and parameter
+4.  User selects observation datasets and parameters
+5.  System returns the time range information where Obs and Model
+parameters overlap.
+6.  User selects time range.
+7.  System returns VALID re-gridding options for Space and Time.  
+(VALID meaning smaller grid to a larger grid step)
+8.  User selects the re-gridding options
+9.  Optional Processing (SEE OPEN ISSUES SECTION)
+
+
+Extensions:
+1a:  User has no account setup
+	.1:  User will create an account
+	.2:  System will create an upload directory for the account
+	and email instructions about how to FTP the model files into
+	the new directory
+	Main Success Scenario Step 1
+
+2a:  User has no models in the System to choose
+	.1:  User will FTP their model file(s) into their upload directory
+	Main Success Scenario Step 2
+
+# This could be prevented if Step 4 ONLY returns Datasets with a proper
+#  temporal overlap.  This might be an enhancement in the future.
+5a:  The Model and Observational Datasets don't have a time overlap
+	.1:  System will return a message explaining the lack of overlap
+	Main Success Scenario Step 4
+
+
+OPEN QUESTIONS/ISSUES
+
+***Optional Processing***
+Masked Region:  Does this work today?
+Seasonal Cycles:  Does this option work?
+
+User will select the Metric they want to compute.  [Should we consider limiting
+this list based on what is being selected in the model and observations]
+Metrics:
+-Bias: mean bias across full time range
+-Mean Absolute Error: across full time range  
+-Difference: calculated at each time unit
+-Anomaly Correlation
+-Pattern Correlation
+*Probability Distribution Function similarity score
+-Root Mean Square Error
+
+Customize Plots:  Does this work today?  

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+/* app css stylesheet */
+
+#map 
+{
+    height: 670px;
+    width: 80%;
+    margin-left: 10%;
+	margin-bottom: 20px;
+}
+
+#rcmetHeader
+{
+	margin-left: 10%;
+}
+
+.small-alert 
+{
+	font-size: 12px;
+	color: green;
+	margin-top: 4px;
+	margin-left: 10px;
+}
+
+ul 
+{
+	list-style-type: none;
+}

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