climate-commits mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From jo...@apache.org
Subject [02/10] climate git commit: CLIMATE-551 - Drop old RCMET toolkit from codebase
Date Mon, 10 Nov 2014 16:05:49 GMT
http://git-wip-us.apache.org/repos/asf/climate/blob/8c142c35/rcmet/src/main/python/rcmes/utils/misc.py
----------------------------------------------------------------------
diff --git a/rcmet/src/main/python/rcmes/utils/misc.py b/rcmet/src/main/python/rcmes/utils/misc.py
deleted file mode 100644
index f913104..0000000
--- a/rcmet/src/main/python/rcmes/utils/misc.py
+++ /dev/null
@@ -1,1413 +0,0 @@
-#
-# Licensed to the Apache Software Foundation (ASF) under one
-# or more contributor license agreements.  See the NOTICE file
-# distributed with this work for additional information
-# regarding copyright ownership.  The ASF licenses this file
-# to you under the Apache License, Version 2.0 (the
-# "License"); you may not use this file except in compliance
-# with the License.  You may obtain a copy of the License at
-#
-#    http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing,
-# software distributed under the License is distributed on an
-# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-# KIND, either express or implied.  See the License for the
-# specific language governing permissions and limitations
-# under the License.
-#
-"""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
-
-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 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:
-        subRegionFile = os.path.abspath(subRegionConfig['subRegionFile'])
-        if os.path.exists(subRegionFile):
-            subRegions = readSubRegionsFile(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 = ma.array(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.open_file(ifile, mode='r')
-        t2raw = ma.array(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.Dataset(ifile, mode='r')
-        data = ma.array(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):
-    '''
-    Extract subregion definitions from a text file
-    
-    Input: 
-        infile - string representing the path to the subregion definition config file
-        
-    Output:
-        numSubRgn - the number of subregion definitions extracted from the input file
-        subRgnName - a Numpy masked array of subregion names
-        subRgnLon0 - a Numpy masked array of subregion "Degrees East" values
-        subRgnLon1 - a Numpy masked array of subregion "Degrees West" values
-        subRgnLat0 - a Numpy masked array of subregion "Degrees North" values
-        subRgnLat1 - a Numpy masked array of subregion "Degrees South" values
-    '''
-    
-    # Parse subregions from provided file
-    subregions = readSubRegionsFile(infile)
-    numSubRgn  = len(subregions)
-    
-    print subregions
-    
-    # Define Numpy masked arrays to hold the subregion definition data
-    subRgnName = []
-    subRgnLon0 = ma.zeros((numSubRgn))
-    subRgnLon1 = ma.zeros((numSubRgn))
-    subRgnLat0 = ma.zeros((numSubRgn))
-    subRgnLat1 = ma.zeros((numSubRgn))
-    
-    # Populate the arrays with the data extracted from the file
-    for i in np.arange(numSubRgn):
-        parts = region_parts[i]
-        subRgnName.append(parts[0].strip('"'))
-        subRgnLon0[i] = float(parts[1])
-        subRgnLon1[i] = float(parts[2])
-        subRgnLat0[i] = float(parts[3])
-        subRgnLat1[i] = float(parts[4])
-    
-    # Return the computed arrays
-    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 (-9 is not active yet): \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):
-        # PER CLIMATE-179 a temporary print statement has been put in place
-        if option == 'obs':
-            print("[%s] - TODO: %s" % (key, option))
-        else:
-            print("[%s] - %s" % (key, option))
-
-    choice = int(raw_input(">>>"))
-    try:
-        spatialGrid = options[choice]
-    except IndexError:
-        getSpatialGrid()
-
-    # PER CLIMATE-179 a temporary guard has also been put in place
-    if spatialGrid == 'obs':
-        print 'Using an observational grid for Spatial regridding is not currently supported.'
-        print 'If you know the grid size and spacing you could use the user option instead\n'
-        return False
-    else:
-        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(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')
-    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'])
-    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 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 mean, 2=seasonal mean (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_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] TODO: 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] TODO: 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'
-    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'
-    else:
-        print("Your selection: %s is invalid, please try again\n" % choice)
-        metricOption = select_metrics()
-    
-    return metricOption
-
-
-def msg(key=None, val=None, indent=0, returnResult=False):
-    ''' Output messages to stdout, with support for indentation 
-       and formatted printing of lists and dicts
-    '''
-    if key == None:
-        message = ' '*indent
-    else:
-        message = ' '*indent + (key if val == None else key + ':\t')
-    if isinstance(val, dict):
-        values = ['{0}: {1}'.format(' '*(indent+2) + str(k),
-            msg(val=v, indent=indent+2, returnResult=True))
-            for k,v in val.items()]
-        message += '\n' + '\n'.join(values)
-    elif isinstance(val, (list, tuple)):
-        values = [' '*(indent+2) +
-            msg(val=v, indent=indent+2, returnResult=True) 
-            for v in val]
-        message += '\n' + '\n'.join(values)
-    else:
-        if val != None:
-            message += str(val)
-    if returnResult:
-        return message
-    else:
-        print message

http://git-wip-us.apache.org/repos/asf/climate/blob/8c142c35/rcmet/src/main/python/rcmes/utils/taylor.py
----------------------------------------------------------------------
diff --git a/rcmet/src/main/python/rcmes/utils/taylor.py b/rcmet/src/main/python/rcmes/utils/taylor.py
deleted file mode 100644
index a9081e6..0000000
--- a/rcmet/src/main/python/rcmes/utils/taylor.py
+++ /dev/null
@@ -1,126 +0,0 @@
-"""
-Taylor diagram (Taylor, 2001) test implementation.
- 
-http://www-pcmdi.llnl.gov/about/staff/Taylor/CV/Taylor_diagram_primer.htm
-"""
- 
-__version__ = "Time-stamp: <2012-02-17 20:59:35 ycopin>"
-__author__ = "Yannick Copin <yannick.copin@laposte.net>"
- 
-import numpy as NP
-import matplotlib.pyplot as PLT
- 
-class TaylorDiagram(object):
-    """Taylor diagram: plot model standard deviation and correlation
-    to reference (data) sample in a single-quadrant polar plot, with
-    r=stddev and theta=arccos(correlation).
-    """
- 
-    def __init__(self, refstd, radmax=1.5, fig=None, rect=111, label='_'):
-        """Set up Taylor diagram axes, i.e. single quadrant polar
-        plot, using mpl_toolkits.axisartist.floating_axes. refstd is
-        the reference standard deviation to be compared to.
-        """
- 
-        from matplotlib.projections import PolarAxes
-        import mpl_toolkits.axisartist.floating_axes as FA
-        import mpl_toolkits.axisartist.grid_finder as GF
- 
-        self.refstd = refstd            # Reference standard deviation
- 
-        tr = PolarAxes.PolarTransform()
- 
-        # Correlation labels
-        rlocs = NP.concatenate((NP.arange(10)/10.,[0.95,0.99]))
-        tlocs = NP.arccos(rlocs)        # Conversion to polar angles
-        gl1 = GF.FixedLocator(tlocs)    # Positions
-        tf1 = GF.DictFormatter(dict(zip(tlocs, map(str,rlocs))))
- 
-        # Standard deviation axis extent
-        self.smin = 0
-        self.smax = radmax*self.refstd
- 
-        ghelper = FA.GridHelperCurveLinear(tr,
-                                           extremes=(0,NP.pi/2, # 1st quadrant
-                                                     self.smin,self.smax),
-                                           grid_locator1=gl1,
-                                           tick_formatter1=tf1,
-                                           )
- 
-        if fig is None:
-            fig = PLT.figure()
- 
-        ax = FA.FloatingSubplot(fig, rect, grid_helper=ghelper)
-        fig.add_subplot(ax)
- 
-        # Adjust axes
-        ax.axis["top"].set_axis_direction("bottom")  # "Angle axis"
-        ax.axis["top"].toggle(ticklabels=True, label=True)
-        ax.axis["top"].major_ticklabels.set_axis_direction("top")
-        ax.axis["top"].label.set_axis_direction("top")
-        ax.axis["top"].label.set_text("Correlation")
- 
-        ax.axis["left"].set_axis_direction("bottom") # "X axis"
-        ax.axis["left"].label.set_text("Standard deviation")
- 
-        ax.axis["right"].set_axis_direction("top")   # "Y axis"
-        ax.axis["right"].toggle(ticklabels=True)
-        ax.axis["right"].major_ticklabels.set_axis_direction("left")
- 
-        ax.axis["bottom"].set_visible(False)         # Useless
-        
-        # Contours along standard deviations
-        ax.grid(False)
- 
-        self._ax = ax                   # Graphical axes
-        self.ax = ax.get_aux_axes(tr)   # Polar coordinates
- 
-        # Add reference point and stddev contour
-        # print "Reference std:", self.refstd
-        l, = self.ax.plot([0], self.refstd, 'k*',
-                          ls='', ms=10, label=label)
-        t = NP.linspace(0, NP.pi/2)
-        r = NP.zeros_like(t) + self.refstd
-        self.ax.plot(t,r, 'k--', label='_')
- 
-        # Collect sample points for latter use (e.g. legend)
-        self.samplePoints = [l]
- 
-    def add_sample(self, stddev, corrcoef, *args, **kwargs):
-        """Add sample (stddev,corrcoeff) to the Taylor diagram. args
-        and kwargs are directly propagated to the Figure.plot
-        command."""
- 
-        l, = self.ax.plot(NP.arccos(corrcoef), stddev,
-                          *args, **kwargs) # (theta,radius)
-        self.samplePoints.append(l)
- 
-        return l
- 
-    def add_rms_contours(self, levels=5, **kwargs):
-        """Add constant centered RMS difference contours."""
- 
-        rs,ts = NP.meshgrid(NP.linspace(self.smin,self.smax),
-                            NP.linspace(0,NP.pi/2))
-        # Compute centered RMS difference
-        rms = NP.sqrt(self.refstd**2 + rs**2 - 2*self.refstd*rs*NP.cos(ts))
-        
-        contours = self.ax.contour(ts, rs, rms, levels, **kwargs)
-    
-    def add_stddev_contours(self, std, corr1, corr2, **kwargs):
-        """Add a curved line with a radius of std between two points
-        [std, corr1] and [std, corr2]"""
-
-        t = NP.linspace(NP.arccos(corr1), NP.arccos(corr2)) 
-        r = NP.zeros_like(t) + std
-        return self.ax.plot(t,r,'red', linewidth=2)
-    
-    def add_contours(self,std1,corr1,std2,corr2, **kwargs):
-        """Add a line between two points
-        [std1, corr1] and [std2, corr2]"""
-        
-        t = NP.linspace(NP.arccos(corr1), NP.arccos(corr2)) 
-        r = NP.linspace(std1, std2)
-
-        return self.ax.plot(t,r,'red',linewidth=2)
- 

http://git-wip-us.apache.org/repos/asf/climate/blob/8c142c35/rcmet/src/main/python/tests/files/missingSubRegionParam.cfg
----------------------------------------------------------------------
diff --git a/rcmet/src/main/python/tests/files/missingSubRegionParam.cfg b/rcmet/src/main/python/tests/files/missingSubRegionParam.cfg
deleted file mode 100644
index c05f013..0000000
--- a/rcmet/src/main/python/tests/files/missingSubRegionParam.cfg
+++ /dev/null
@@ -1,3 +0,0 @@
-[SUB_REGION]
-# Sub Region(s) Full File Path
-

http://git-wip-us.apache.org/repos/asf/climate/blob/8c142c35/rcmet/src/main/python/tests/files/validSubRegionConfigFile.cfg
----------------------------------------------------------------------
diff --git a/rcmet/src/main/python/tests/files/validSubRegionConfigFile.cfg b/rcmet/src/main/python/tests/files/validSubRegionConfigFile.cfg
deleted file mode 100644
index a6fcc03..0000000
--- a/rcmet/src/main/python/tests/files/validSubRegionConfigFile.cfg
+++ /dev/null
@@ -1,3 +0,0 @@
-[SUB_REGION]
-# Sub Region(s) Full File Path
-subRegionFile=files/validSubRegions.cfg

http://git-wip-us.apache.org/repos/asf/climate/blob/8c142c35/rcmet/src/main/python/tests/files/validSubRegions.cfg
----------------------------------------------------------------------
diff --git a/rcmet/src/main/python/tests/files/validSubRegions.cfg b/rcmet/src/main/python/tests/files/validSubRegions.cfg
deleted file mode 100644
index b3c7800..0000000
--- a/rcmet/src/main/python/tests/files/validSubRegions.cfg
+++ /dev/null
@@ -1,7 +0,0 @@
-[REGIONS]
-Region01:     ["R01", 36.5, 29, 0.0, -10]
-Region02:     ["R02", 37.5, 29, 10, 0]
-Region04:     ["R04", 32.5, 25, 33, 20]
-
-
-

http://git-wip-us.apache.org/repos/asf/climate/blob/8c142c35/rcmet/src/main/python/tests/test_files.py
----------------------------------------------------------------------
diff --git a/rcmet/src/main/python/tests/test_files.py b/rcmet/src/main/python/tests/test_files.py
deleted file mode 100644
index 20a4423..0000000
--- a/rcmet/src/main/python/tests/test_files.py
+++ /dev/null
@@ -1,87 +0,0 @@
-#
-# Licensed to the Apache Software Foundation (ASF) under one
-# or more contributor license agreements.  See the NOTICE file
-# distributed with this work for additional information
-# regarding copyright ownership.  The ASF licenses this file
-# to you under the Apache License, Version 2.0 (the
-# "License"); you may not use this file except in compliance
-# with the License.  You may obtain a copy of the License at
-#
-#    http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing,
-# software distributed under the License is distributed on an
-# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-# KIND, either express or implied.  See the License for the
-# specific language governing permissions and limitations
-# under the License.
-#
-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()

http://git-wip-us.apache.org/repos/asf/climate/blob/8c142c35/rcmet/src/main/python/tests/test_metrics.py
----------------------------------------------------------------------
diff --git a/rcmet/src/main/python/tests/test_metrics.py b/rcmet/src/main/python/tests/test_metrics.py
deleted file mode 100644
index 07ac33e..0000000
--- a/rcmet/src/main/python/tests/test_metrics.py
+++ /dev/null
@@ -1,52 +0,0 @@
-#
-# Licensed to the Apache Software Foundation (ASF) under one
-# or more contributor license agreements.  See the NOTICE file
-# distributed with this work for additional information
-# regarding copyright ownership.  The ASF licenses this file
-# to you under the Apache License, Version 2.0 (the
-# "License"); you may not use this file except in compliance
-# with the License.  You may obtain a copy of the License at
-#
-#    http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing,
-# software distributed under the License is distributed on an
-# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-# KIND, either express or implied.  See the License for the
-# specific language governing permissions and limitations
-# under the License.
-#
-
-import unittest
-
-import toolkit.metrics
-
-import numpy as np
-import numpy.ma as ma
-
-
-class TestCalcPdf(unittest.TestCase):
-    
-    def testUsingSettingsKwarg(self):
-
-        # declare and initialize 1d arrays (mimick timeseries)
-        good_pdf = '0.091'
-      
-        # declare and initialize  3d(time,lat,lon) type array
-        evaluationDataset = np.arange(0, 12, 0.5)
-        evaluationDataset = evaluationDataset.reshape(4, 2, 3)
-        evaluationDataset = ma.array(evaluationDataset)
-    
-        referenceDataset = np.arange(10, 34)
-        referenceDataset = referenceDataset.reshape(4, 2, 3)
-        referenceDataset = ma.array(referenceDataset)
-
-        settings = (3, 10, 20)
-
-        pdf =  '%.3f' % toolkit.metrics.calcPdf(evaluationDataset, referenceDataset, settings)
-        # Checking accuracy to 3 decimal places using a simple string comparison
-        self.assertEqual(pdf, good_pdf)
-        
-
-if __name__ == '__main__':
-    unittest.main()

http://git-wip-us.apache.org/repos/asf/climate/blob/8c142c35/rcmet/src/main/python/tests/test_misc.py
----------------------------------------------------------------------
diff --git a/rcmet/src/main/python/tests/test_misc.py b/rcmet/src/main/python/tests/test_misc.py
deleted file mode 100644
index 266ec88..0000000
--- a/rcmet/src/main/python/tests/test_misc.py
+++ /dev/null
@@ -1,74 +0,0 @@
-#
-# Licensed to the Apache Software Foundation (ASF) under one
-# or more contributor license agreements.  See the NOTICE file
-# distributed with this work for additional information
-# regarding copyright ownership.  The ASF licenses this file
-# to you under the Apache License, Version 2.0 (the
-# "License"); you may not use this file except in compliance
-# with the License.  You may obtain a copy of the License at
-#
-#    http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing,
-# software distributed under the License is distributed on an
-# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-# KIND, either express or implied.  See the License for the
-# specific language governing permissions and limitations
-# under the License.
-#
-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()

http://git-wip-us.apache.org/repos/asf/climate/blob/8c142c35/rcmet/src/main/python/tests/test_process.py
----------------------------------------------------------------------
diff --git a/rcmet/src/main/python/tests/test_process.py b/rcmet/src/main/python/tests/test_process.py
deleted file mode 100644
index aab5957..0000000
--- a/rcmet/src/main/python/tests/test_process.py
+++ /dev/null
@@ -1,44 +0,0 @@
-#
-# Licensed to the Apache Software Foundation (ASF) under one
-# or more contributor license agreements.  See the NOTICE file
-# distributed with this work for additional information
-# regarding copyright ownership.  The ASF licenses this file
-# to you under the Apache License, Version 2.0 (the
-# "License"); you may not use this file except in compliance
-# with the License.  You may obtain a copy of the License at
-#
-#    http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing,
-# software distributed under the License is distributed on an
-# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-# KIND, either express or implied.  See the License for the
-# specific language governing permissions and limitations
-# under the License.
-#
-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

http://git-wip-us.apache.org/repos/asf/climate/blob/8c142c35/rcmet/src/main/resources/PyLintREADME.txt
----------------------------------------------------------------------
diff --git a/rcmet/src/main/resources/PyLintREADME.txt b/rcmet/src/main/resources/PyLintREADME.txt
deleted file mode 100644
index 4816a7f..0000000
--- a/rcmet/src/main/resources/PyLintREADME.txt
+++ /dev/null
@@ -1,26 +0,0 @@
-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 rcmet_ui.py file within the cli module, 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.

http://git-wip-us.apache.org/repos/asf/climate/blob/8c142c35/rcmet/src/main/resources/pyLintRcFile.txt
----------------------------------------------------------------------
diff --git a/rcmet/src/main/resources/pyLintRcFile.txt b/rcmet/src/main/resources/pyLintRcFile.txt
deleted file mode 100644
index 286dcfe..0000000
--- a/rcmet/src/main/resources/pyLintRcFile.txt
+++ /dev/null
@@ -1,249 +0,0 @@
-[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

http://git-wip-us.apache.org/repos/asf/climate/blob/8c142c35/rcmet/src/main/resources/rcmet_use_case.txt
----------------------------------------------------------------------
diff --git a/rcmet/src/main/resources/rcmet_use_case.txt b/rcmet/src/main/resources/rcmet_use_case.txt
deleted file mode 100644
index 41e8e90..0000000
--- a/rcmet/src/main/resources/rcmet_use_case.txt
+++ /dev/null
@@ -1,57 +0,0 @@
-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?  


Mime
View raw message