eddy_functions.py

'''

    A set of functions to accompany the eddy tracking software

'''

import numpy as np
import scipy as sp
import numpy.linalg as linalg
import scipy.signal as signal
import scipy.ndimage as ndimage
import scipy.interpolate as interpolate
import glob

import matplotlib
# Turn the followin on if you are running on storm sometimes - Forces matplotlib to not use any Xwindows backend.
matplotlib.use('Agg')

import matplotlib.pyplot as plt
import pandas as pd

from netCDF4 import Dataset

from itertools import repeat

import params 
import experiments as exps

import re
import os


def raw_nemo_globber_specifytpe(exp_path,return_dates=False):
    """function that globs for NEMO files from the raw experiment output looking for velocity files only.

    Parameters
    ----------
    exp_path:  path to NEMO experiment (will glob through the year directories)
    1) 'grid_T_2D' : glob all files of type grid_T_2D

    return_dates:  optional. will run find_dates function before returning and so will return a pandas DataFrame

    :returns: 

    For 'grid_T_2D' : single list of globbed files

    Will return pandas DataFrame instead if return_dates=True

    WARNING: if return_dates is true you will get one line for every new date in the pandas dataframe!
    (There will be multiple references to the same file.)

    Notes
    -------
    Runs reg_date by default.

    Typical NEMO output looks like:
    
        cordex24-ERAI01_1d_19910101_19911231_grid_T_2D.nc

    Example 
    -------

    """
    #_lg.info("We are globbing for experiment type: " + os.path.basename(exp_path))
    #_lg.info("We are globbing for the following file type: " + file_type)
    glob_pattern='*/*_grid_T_2D.nc'

    infiles=sorted(glob.glob(exp_path + glob_pattern ))
    assert(infiles!=[]),"glob didn't find anything!"

    #if isinstance(date_extraction,(list,tuple)):
        #infiles=globbed_date_remove(infiles)

    if return_dates:
        return find_dates(infiles)
    return infiles


def reg_date(string_to_find_date_in):
    """function that uses regular expressions to find start and end date from file.
    
    :string_to_find_date_in: string from NEMO netCDF file.
    :returns: string with start and end date
    """
    #really handonline regex finder: https://regex101.com/#python
    exp = re.search(r'[0-9]{8}_[0-9]{8}', string_to_find_date_in) 
    exp=exp.group()

    #print exp
    return exp

def find_dates(globbedfiles):
    """function that finds dates associated with passed list of NEMO output. Returns in pandas DataFrame.

    NB: assumes daily output on your NEMO files.

    Parameters
    ----------
    :globbedfiles: list of globbed files from raw_nemo_globber with pattern:
        */cordex24*_1d_*_grid_T_2D.nc

    :returns: dataframe of names and dates in pandas DataFrame.
    """
    
    #globbedfiles=globbedfiles[0:3]

    dates_nemo_start=[pd.to_datetime(reg_date(file)[0:8],format='%Y%m%d')\
            for file in globbedfiles]

    dates_nemo_end=[pd.to_datetime(reg_date(file)[9:],format='%Y%m%d')\
            for file in globbedfiles]

    t_steps=\
    [(end-start).days+1 for end,start in zip(dates_nemo_end,dates_nemo_start)]

    #create time_index from start and end dates
    time_index=[]
    for start,end in zip(dates_nemo_start,dates_nemo_end):
        time_index.append(pd.Series(pd.date_range(start,end,freq='D')))

    time_index=pd.concat(time_index)

    ##creates two lists:
    ##file_time_index list that tells you which time index in a file
    ##file_list list which file
    file_time_index=[]
    file_list=[]
    for idx,t in enumerate(t_steps):
        file_time_index=file_time_index+range(t)
        file_list=file_list+[globbedfiles[idx]]*t

    nemo_df=pd.DataFrame({'date':time_index,\
                          'file_time_index':file_time_index,\
                          'file_list':file_list\
                          })

    nemo_df.index=nemo_df.date
    del nemo_df['date']
    return nemo_df


def find_nearest(array, value):
    idx=(np.abs(array-value)).argmin()
    return array[idx], idx

def nanmean(array, axis=None):
    return np.mean(np.ma.masked_array(array, np.isnan(array)), axis)

def load_lonlat(run, disk='erebor'):
    '''
    Loads latitude and longitude vectors from OFAM runs or AVISO
    Assumes root is /mnt/erebor unless cerberus is specified.
    '''

    #    
    # OFAM
    #

    if run=='CTRL' or run=='A1B':

        if disk=='erebor':
            pathroot = '/mnt/erebor/data/OFAM/'
        elif disk=='cerberus':
            pathroot = '/media/cerberus/data/OFAM/'

        filename = 'ctrl_nov10/daily/ocean_tse_sfc_2003_01.nc'

        fileobj = Dataset(pathroot+filename, mode='r')
        lon = fileobj.variables['xt_ocean'][:]
        lat = fileobj.variables['yt_ocean'][:]
        fileobj.close()

    #
    # AVISO
    #

    elif run=='AVISO':

        pathroot = '/mnt/devil/data/sla/orig_qd/'

        # Find week's map
        file_header = 'dt_ref_global_merged_msla_h_qd_'
        file_list = glob.glob(pathroot + file_header + '*.nc')
        file = file_list[0]

        # load week's map
        fileobj = Dataset(file, mode='r')
        lon = fileobj.variables['NbLongitudes'][:]
        lat = fileobj.variables['NbLatitudes'][:]
        fileobj.close()

    elif run=='AVISOd':

        pathroot = '/media/DataOne/data/sla/aviso/dt_global_twosat_msla_h/'

        # Find week's map
        file_header = 'dt_global_twosat_msla_h_'
        file_list = glob.glob(pathroot + file_header + '*.nc')
        file = file_list[0]

        # load week's map
        fileobj = Dataset(file, mode='r')
        lon = fileobj.variables['lon'][:]
        lat = fileobj.variables['lat'][:]
        fileobj.close()

    elif run=='cb_AVISO':

        pathroot = './'
        pathroot=exps.pathroot

        # Find week's map
        #note slight difference in file name!
        #file_header = 'dt_ref_global_merged_madt_h_qd_'
        file_header = 'dt_global_allsat_madt_h_'
        file_list = glob.glob(pathroot + file_header + '*.nc')

        assert (len(file_list)>0),"globbing failed, exiting"

        #this is just for the lat/lon info so we only need one time step..
        file = file_list[0]

        # load week's map
        fileobj = Dataset(file, mode='r')
        #lon = fileobj.variables['NbLongitudes'][:]
        #lat = fileobj.variables['NbLatitudes'][:]
        lon = fileobj.variables['lon'][:]
        lat = fileobj.variables['lat'][:]
        fileobj.close()

    elif run=='cb_NEMO':

        pathroot=exps.pathroot

        # Find week's map
        #file_header = '*/cordex24-ERAI01_1d_*_grid_T_2D'
        #file_list = glob.glob(pathroot + file_header + '*.nc')
        file_list=raw_nemo_globber_specifytpe(exps.pathroot,return_dates=False)

        assert (len(file_list)>0),"globbing failed, exiting"

        #this is just for the lat/lon info so we only need one time step..

        filename = file_list[0]
        #print filename

        #fileobj = Dataset(filename,mode='r')
        #lon = fileobj.variables['nav_lon'][:]
        #lat = fileobj.variables['nav_lat'][:]
        #h'm need to interpolate...

        lon=np.arange(params.lon1,params.lon2,.25)
        lat=np.arange(params.lat1,params.lat2,.25)

    return lon, lat


def restrict_lonlat(lon, lat, lon1, lon2, lat1, lat2):
    '''
    Restricts latitude and longitude vectors given
    input limits.
    '''

    tmp, i1 = find_nearest(lon, lon1)
    tmp, i2 = find_nearest(lon, lon2)
    tmp, j1 = find_nearest(lat, lat1)
    tmp, j2 = find_nearest(lat, lat2)

    lon = lon[i1:i2+1]
    lat = lat[j1:j2+1]

    return lon, lat, i1, i2, j1, j2

def load_eta(run, tt, i1, i2, j1, j2, disk='erebor',getNEMOtime=False):
    """
    Loads sea surface height field from OFAM runs or Aviso or NEMO

    Parameters
    ----------
    tt: 
    i1: 
    i2: 
    j1: 
    j2: 
    disk:
    getNEMOtime: (optional) chris added so that he can return absolute time step
    exportNEMOtime: (optional) chris added so that he can habe absolute time steps in eddy_tracking

    Returns
    -------
    eta: ssh
    eta_miss: missing value in eta
    
    Notes
    -------
    Assumes root is /mnt/erebor unless cerberus is specified.
    run = 'CTRL' or 'A1B' or 'AVISO' or 'cb_AVISO' or 'cb_NEMO'
    """

    #    
    # OFAM
    #

    if run=='CTRL' or run=='A1B':

        if disk=='erebor':
            pathroot = '/mnt/erebor/data/OFAM/'
        elif disk=='cerberus':
            pathroot = '/media/cerberus/data/OFAM/'

        if run=='CTRL':
            runpath = 'ctrl_nov10/daily/'
            year0 = 1998
        elif run=='A1B':
            runpath = 'A1b_2060_oct10/daily/'
            year0 = 2065

        dpy = 365
        dpm = [31, 28, 31, 30, 31, 30, 31, 31, 30, 31, 30, 31]
        months = np.array([]).astype(int)
        for i in range(len(dpm)):
            months = np.append(months, (i+1)*np.ones(dpm[i]).astype(int))

        # which year
        year = year0 + tt/dpy

        # which month
        doy = np.mod(tt, dpy)
        month = months[doy]

        # which day
        day = doy - sum(dpm[0:month-1])

        # load day's map
        fileobj = Dataset(pathroot + runpath + 'ocean_tse_sfc_' + str(year) + '_' +str(month).zfill(2) + '.nc', mode='r')
        eta = fileobj.variables['eta_t'][:][day, j1:j2+1, i1:i2+1]
        eta_miss = fileobj.variables['eta_t']._FillValue
        fileobj.close()

    #
    # AVISO
    #

    elif run=='AVISO':

        pathroot = '/mnt/devil/data/sla/orig_qd/'

        # Find week's map
        file_header = 'dt_ref_global_merged_msla_h_qd_'
        file_list = glob.glob(pathroot + file_header + '*.nc')
        file = file_list[tt]

        # load week's map
        fileobj = Dataset(file, mode='r')
        eta = fileobj.variables['Grid_0001'][:][i1:i2+1, j1:j2+1].T / 100
        eta_miss = fileobj.variables['Grid_0001']._FillValue / 100
        fileobj.close()

    elif run=='AVISOd':

        pathroot = '/media/DataOne/data/sla/aviso/dt_global_twosat_msla_h/'

        # Find week's map
        file_header = 'dt_global_twosat_msla_h_'
        file_list = glob.glob(pathroot + file_header + '*.nc')
        file = file_list[tt]

        # load week's map
        fileobj = Dataset(file, mode='r')
        eta = fileobj.variables['sla'][:][0, j1:j2+1, i1:i2+1] * fileobj.variables['sla'].scale_factor
        eta_miss = fileobj.variables['sla']._FillValue * fileobj.variables['sla'].scale_factor
        fileobj.close()

    elif run=='cb_AVISO':

        pathroot = './'
        pathroot='/srv/ccrc/data42/z3457920/RawData/AVISO/RawData/dt_global_allsat_madt/ftp.aviso.altimetry.fr/global/delayed-time/grids/madt/all-sat-merged/h/1993/'
        pathroot=exps.pathroot

        # Find week's map
        #note slight difference in file name!
        file_header = 'dt_global_allsat_madt_h_'
        file_list = glob.glob(pathroot + file_header + '*.nc')

        assert (len(file_list)>0),"globbing failed, exiting"

        file = file_list[tt]

        # load week's map
        fileobj = Dataset(file, mode='r')
        #lon = fileobj.variables['NbLongitudes'][:]
        #lat = fileobj.variables['NbLatitudes'][:]
        lon = fileobj.variables['lon'][:]
        lat = fileobj.variables['lat'][:]

        #eta = fileobj.variables['Grid_0001'][:][i1:i2+1, j1:j2+1].T / 100
        eta = fileobj.variables['adt'][0,:,:][j1:j2+1, i1:i2+1] 

        #careful chris! Eric might be doing something different!!!
        #EO line:
        #eta_miss = fileobj.variables['Grid_0001']._FillValue / 100

        #new new cb line
        #eta_miss=[fileobj.variables['adt'][:].fill_value]
        eta_miss=[-214748]

        #################

        fileobj.close()

    elif run=='cb_NEMO':
        def nemo_fixdateline(netcdf_datasetobj):
            """function to return fixed version of netcdf nav_lon variable
            
            :netcdf_datasetobj: netCDF4 Dataset object of nemo file
            :returns: nemo_lons numpy array with fixed dateline
            """
            nemo_lons=netcdf_datasetobj.variables['nav_lon'][:]
            #fix the dateline
            for index in np.arange(np.shape(nemo_lons)[0]):
                start=np.where(np.sign(nemo_lons[index,:])==-1)[0][0]
                nemo_lons[index,start:]=nemo_lons[index,start:]+360
            return nemo_lons

        pathroot=exps.pathroot

        #this is daft because we repeat this every time step!
        file_list=raw_nemo_globber_specifytpe(exps.pathroot,return_dates=True)
        infile=file_list.iloc[tt]['file_list']
        file_time_index=file_list.iloc[tt]['file_time_index']

        if getNEMOtime:
            #return the absolute time
            return file_list.index[tt]            

        #h'm need to interpolate because of funky NEMO grid...
        fileobj = Dataset(infile,mode='r')
        loni=nemo_fixdateline(fileobj)
        #loni = fileobj.variables['nav_lon'][:]
        lati = fileobj.variables['nav_lat'][:]

        lon=np.arange(params.lon1,params.lon2,.25)
        lat=np.arange(params.lat1,params.lat2,.25)

        old_grid_data=fileobj.variables['zos'][file_time_index,:,:]
        XI, YI = np.meshgrid(lon,lat)
        
        #interp
        etamask=interpolate.griddata((loni.flatten(),lati.flatten()),old_grid_data.flatten() , (XI,YI),method='nearest')

        eta=interpolate.griddata((loni.flatten(),lati.flatten()),old_grid_data.flatten() , (XI,YI),method='cubic')

        #set mask
        eta[np.where(etamask==0)]=0
        eta_miss=[0]

        fileobj.close()

    return eta, eta_miss[0]

def load_nemo_time():
    """
    Loads time steps from NEMO experiments

    Parameters
    ----------

    Returns
    -------
    list of pandas time stamps 
    
    Notes
    -------
    """
    file_list=raw_nemo_globber_specifytpe(exps.pathroot,return_dates=True)
    return file_list.index.tolist()    

def quick_plot(field,findrange=False):
    '''
    Create quick interactive diagnostic plot to double check eddy_detection is doing what we want...
    '''
    y,x=np.meshgrid(np.arange(field.shape[1]),np.arange(field.shape[0]))
    plt.clf()

    if not findrange:
        plt.contourf(y, x, field, levels=np.arange(-2.5,2.5,0.05))
    else:
        if np.isnan(np.sum(field)):
            plotfield=np.nan_to_num(field)
            print 'range of field is:'
            print 'min',np.min(plotfield)
            print 'max',np.max(plotfield)

            plt.contourf(y, x, field,levels=np.linspace(np.min(plotfield),np.max(plotfield),50))

        else:
            print 'range of field is:'
            print 'min',np.min(field)
            print 'max',np.max(field)

            plt.contourf(y, x, field,levels=np.linspace(np.min(field),np.max(field),50))
    plt.title('diagnostic plot')
    plt.show()
    import ipdb; ipdb.set_trace()

def remove_missing(field, missing, replacement):
    '''
    Replaces all instances of 'missing' in 'field' with 'replacement'
    '''

    field[field==missing] = replacement

    return field


def interp_nans(data, indices):
    '''
    Linearly interpolates over missing values (np.nan's) in data
    Data is defined at locations in vector indices.
    '''

    not_nan = np.logical_not(np.isnan(data))

    return np.interp(indices, indices[not_nan], data[not_nan])


def match_missing(data1, data2):
    '''
    Make all locations that are missing in data2 also missing in data1
    Missing values are assumed to be np.nan.
    '''

    data1[np.isnan(data2)] = np.nan
    return data1


def spatial_filter(field, lon, lat, res, cut_lon, cut_lat):
    '''
    Performs a spatial filter, removing all features with
    wavelenth scales larger than cut_lon in longitude and
    cut_lat in latitude from field (defined in grid given
    by lon and lat).  Field has spatial resolution of res
    and land identified by np.nan's
    '''

    field_filt = np.zeros(field.shape)

    # see Chelton et al, Prog. Ocean., 2011 for explanation of factor of 1/5
    sig_lon = (cut_lon/5.) / res
    sig_lat = (cut_lat/5.) / res

    land = np.isnan(field)
    field[land] = nanmean(field)

    field_filt = field - ndimage.gaussian_filter(field, [sig_lat, sig_lon])

    field_filt[land] = np.nan

    return field_filt


def distance_matrix(lons,lats):
    '''Calculates the distances (in km) between any two cities based on the formulas
    c = sin(lati1)*sin(lati2)+cos(longi1-longi2)*cos(lati1)*cos(lati2)
    d = EARTH_RADIUS*Arccos(c)
    where EARTH_RADIUS is in km and the angles are in radians.
    Source: http://mathforum.org/library/drmath/view/54680.html
    This function returns the matrix.'''

    EARTH_RADIUS = 6378.1
    X = len(lons)
    Y = len(lats)
    assert X == Y, 'lons and lats must have same number of elements'

    d = np.zeros((X,X))

    #Populate the matrix.
    for i2 in range(len(lons)):
        lati2 = lats[i2]
        loni2 = lons[i2]
        c = np.sin(np.radians(lats)) * np.sin(np.radians(lati2)) + \
            np.cos(np.radians(lons-loni2)) * \
            np.cos(np.radians(lats)) * np.cos(np.radians(lati2))
        d[c<1,i2] = EARTH_RADIUS * np.arccos(c[c<1])

    return d


def detect_eddies(field, lon, lat, ssh_crits, res, Npix_min, Npix_max, amp_thresh, d_thresh, cyc='anticyclonic'):
    '''
    Detect eddies present in field which satisfy the criteria
    outlined in Chelton et al., Prog. ocean., 2011, App. B.2.

    Field is a 2D array specified on grid defined by lat and lon.

    ssh_crits is an array of ssh levels over which to perform
    eddy detection loop

    res is resolutin in degrees of field

    Npix_min, Npix_max, amp_thresh, d_thresh specify the constants
    used by the eddy detection algorithm (see Chelton paper for
    more details)

    cyc = 'cyclonic' or 'anticyclonic' [default] specifies type of
    eddies to be detected

    Function outputs lon, lat coordinates of detected eddies
    '''

    len_deg_lat = 111.325 # length of 1 degree of latitude [km]

    llon, llat = np.meshgrid(lon, lat)

    lon_eddies = np.array([])
    lat_eddies = np.array([])
    amp_eddies = np.array([])
    area_eddies = np.array([])
    scale_eddies = np.array([])

    # ssh_crits increasing for 'cyclonic', decreasing for 'anticyclonic'
    ssh_crits.sort()
    if cyc == 'cyclonic':
        ssh_crits = np.flipud(ssh_crits)

    # loop over ssh_crits and remove interior pixels of detected eddies from subsequent loop steps
    for ssh_crit in ssh_crits:
 
    # 1. Find all regions with eta greater (less than) than ssh_crit for anticyclonic (cyclonic) eddies (Chelton et al. 2011, App. B.2, criterion 1)
        if cyc == 'anticyclonic':
            regions, nregions = ndimage.label( (field>ssh_crit).astype(int) )
        elif cyc == 'cyclonic':
            regions, nregions = ndimage.label( (field<ssh_crit).astype(int) )

        for iregion in range(nregions):
 
    # 2. Calculate number of pixels comprising detected region, reject if not within [Npix_min, Npix_max]
            region = (regions==iregion+1).astype(int)
            region_Npix = region.sum()
            eddy_area_within_limits = (region_Npix < Npix_max) * (region_Npix > Npix_min)
 
    # 3. Detect presence of local maximum (minimum) for anticylonic (cyclonic) eddies, reject if non-existent
            interior = ndimage.binary_erosion(region)
            exterior = region.astype(bool) - interior
            if interior.sum() == 0:
                continue
            if cyc == 'anticyclonic':
                has_internal_ext = field[interior].max() > field[exterior].max()
            elif cyc == 'cyclonic':
                has_internal_ext = field[interior].min() < field[exterior].min()
 
    # 4. Find amplitude of region, reject if < amp_thresh
            if cyc == 'anticyclonic':
                amp = field[interior].max() - field[exterior].mean()
            elif cyc == 'cyclonic':
                amp = field[exterior].mean() - field[interior].min()
            is_tall_eddy = amp >= amp_thresh
 
    # 5. Find maximum linear dimension of region, reject if < d_thresh
            if np.logical_not( eddy_area_within_limits * has_internal_ext * is_tall_eddy):
                continue
 
            lon_ext = llon[exterior]
            lat_ext = llat[exterior]
            d = distance_matrix(lon_ext, lat_ext)
            is_small_eddy = d.max() < d_thresh

    # Detected eddies:
            if eddy_area_within_limits * has_internal_ext * is_tall_eddy * is_small_eddy:
                # find centre of mass of eddy
                eddy_object_with_mass = field * region
                eddy_object_with_mass[np.isnan(eddy_object_with_mass)] = 0
                j_cen, i_cen = ndimage.center_of_mass(eddy_object_with_mass)
                lon_cen = np.interp(i_cen, range(0,len(lon)), lon)
                lat_cen = np.interp(j_cen, range(0,len(lat)), lat)
                lon_eddies = np.append(lon_eddies, lon_cen)
                lat_eddies = np.append(lat_eddies, lat_cen)
                # assign (and calculated) amplitude, area, and scale of eddies
                amp_eddies = np.append(amp_eddies, amp)
                area = region_Npix * res**2 * len_deg_lat * len_deg_lon(lat_cen) # [km**2]
                area_eddies = np.append(area_eddies, area)
                scale = np.sqrt(area / np.pi) # [km]
                scale_eddies = np.append(scale_eddies, scale)
                # remove its interior pixels from further eddy detection
                eddy_mask = np.ones(field.shape)
                eddy_mask[interior.astype(int)==1] = np.nan
                field = field * eddy_mask

    return lon_eddies, lat_eddies, amp_eddies, area_eddies, scale_eddies


def detection_plot(tt,lon,lat,eta,eta_filt,anticyc_eddies,cyc_eddies,ptype,plot_dir,findrange=True,ptitle=''):
    """function to plot how the eddy detection alogirthm went
    
    :tt
    :lon
    :lat
    :eta
    :eta_filt
    :anticyc_eddies
    :cyc_eddies
    :ptype
    :plot_dir
    :findrange=True
    :returns: @todo
    """
    def plot_eddies():
        """@todo: Docstring for plot_eddies
        :returns: @todo
        """
        ax.plot(anticyc_eddies[0], anticyc_eddies[1], 'k^')
        ax.plot(cyc_eddies[0], cyc_eddies[1], 'kv')
    
        pass
    if ptype=='single':
        plt.close('all')
        fig=plt.figure()
        ax=fig.add_subplot(1, 1,1)

    elif ptype=='rawtoo':
        plt.close('all')
        fig=plt.figure()

        #width then height
        fig=plt.figure(figsize=(12.0,9.0))
        ax=fig.add_subplot(1, 2,1)

        #ecj range...
        #plt.contourf(lon, lat, eta_filt, levels=np.arange(-2.5,2.5,0.05))

        #cb NEMO range
        cs1=plt.contourf(lon, lat, eta_filt, levels=np.linspace(-.817,0.5,40))
        cbar=fig.colorbar(cs1,orientation='vertical')
        if ptitle=='':
            ax.set_title('day: ' + str(tt)+' filtered ssh')
        else:
            ax.set_title(ptitle+ '. filtered ssh')
        plot_eddies()
        
        ax=fig.add_subplot(1, 2,2)
        cs1=plt.contourf(lon, lat, eta, levels=np.linspace(-1.75,0.85,40))
        cbar=fig.colorbar(cs1,orientation='vertical')
        if ptitle=='':
            ax.set_title('day: ' + str(tt)+' raw ssh')
        else:
            ax.set_title(ptitle+ '. raw ssh')
        plot_eddies()


        #determine range to plot 
        #if np.isnan(np.sum(eta_filt)):
            #plt.contourf(lon,lat, eta_filt,levels=np.linspace(np.min(np.nan_to_num(eta_filt)),np.max(np.nan_to_num(eta_filt)),50))
            #print np.min(np.nan_to_num(eta_filt))
            #print np.max(np.nan_to_num(eta_filt))
        #else:
            #plt.contourf(lon,lat, eta_filt,levels=np.linspace(np.min(eta_filt),np.max(eta_filt),50))

        #plt.clim(-0.5,0.5)
        plt.savefig(plot_dir+'eta_filt_' + str(tt).zfill(4) + '.png', bbox_inches=0)

    pass

def eddies_list(lon_eddies_a, lat_eddies_a, amp_eddies_a, area_eddies_a, scale_eddies_a, lon_eddies_c, lat_eddies_c, amp_eddies_c, area_eddies_c, scale_eddies_c,time_eddies_a,time_eddies_c):
    '''
    Creates list detected eddies
    '''

    eddies = []

    #loop through each time step
    for ed in range(len(lon_eddies_c)):
        eddy_tmp = {}
        eddy_tmp['lon'] = np.append(lon_eddies_a[ed], lon_eddies_c[ed])
        eddy_tmp['lat'] = np.append(lat_eddies_a[ed], lat_eddies_c[ed])
        eddy_tmp['amp'] = np.append(amp_eddies_a[ed], amp_eddies_c[ed])
        eddy_tmp['area'] = np.append(area_eddies_a[ed], area_eddies_c[ed])
        eddy_tmp['scale'] = np.append(scale_eddies_a[ed], scale_eddies_c[ed])
        eddy_tmp['type'] = list(repeat('anticyclonic',len(lon_eddies_a[ed]))) + list(repeat('cyclonic',len(lon_eddies_c[ed])))
        eddy_tmp['N'] = len(eddy_tmp['lon'])
        
        #if we want the time...
        if time_eddies_a!=[] or time_eddies_c!=[]:
            eddy_tmp['date'] =  np.append(time_eddies_a[ed], time_eddies_c[ed])
        
        eddies.append(eddy_tmp)

    return eddies


def eddies_init(det_eddies):
    '''
    Initializes list of eddies. The ith element of output is
    a dictionary of the ith eddy containing information about
    position and size as a function of time, as well as type.
    '''

    eddies = []

    for ed in range(det_eddies[0]['N']):
        eddy_tmp = {}
        eddy_tmp['lon'] = np.array([det_eddies[0]['lon'][ed]])
        eddy_tmp['lat'] = np.array([det_eddies[0]['lat'][ed]])
        eddy_tmp['amp'] = np.array([det_eddies[0]['amp'][ed]])
        eddy_tmp['area'] = np.array([det_eddies[0]['area'][ed]])
        eddy_tmp['scale'] = np.array([det_eddies[0]['scale'][ed]])
        eddy_tmp['type'] = det_eddies[0]['type'][ed]
        eddy_tmp['time'] = np.array([1])
        eddy_tmp['exist_at_start'] = True
        eddy_tmp['terminated'] = False
        eddies.append(eddy_tmp)

    return eddies


def load_rossrad():
    '''
    Load first baroclinic wave speed [m/s] and Rossby radius
    of deformation [km] data from rossrad.dat (Chelton et al., 1998)

    Also calculated is the first baroclinic Rossby wave speed [m/s]
    according to the formula:  cR = -beta rossby_rad**2
    '''

    #data = np.loadtxt('data/rossrad.dat')

    #cb
    data = np.loadtxt(os.path.dirname(os.path.realpath(__file__))+'/rossrad.dat')

    rossrad = {}
    rossrad['lat'] = data[:,0]
    rossrad['lon'] = data[:,1]
    rossrad['c1'] = data[:,2] # m/s
    rossrad['rossby_rad'] = data[:,3] # km

    R = 6371.e3 # Radius of Earth [m]
    Sigma = 2 * np.pi / (24*60*60) # Rotation frequency of Earth [rad/s]
    beta = (2*Sigma/R) * np.cos(rossrad['lat']*np.pi/180) # 1 / m s
    rossrad['cR'] = -beta * (1e3*rossrad['rossby_rad'])**2

    return rossrad


def is_in_ellipse(x0, y0, dE, d, x, y):
    '''
    Check if point (x,y) is contained in ellipse given by the equation

      (x-x1)**2     (y-y1)**2
      ---------  +  ---------  =  1
         a**2          b**2

    where:

      a = 0.5 * (dE + dW)
      b = dE
      x1 = x0 + 0.5 * (dE - dW)
      y1 = y0
    '''

    dW = np.max([d, dE])

    b = dE
    a = 0.5 * (dE + dW)

    x1 = x0 + 0.5*(dE - dW)
    y1 = y0

    return (x-x1)**2 / a**2 + (y-y1)**2 / b**2 <= 1


def len_deg_lon(lat):
    '''
    Returns the length of one degree of longitude (at latitude
    specified) in km.
    '''

    R = 6371. # Radius of Earth [km]

    return (np.pi/180.) * R * np.cos( lat * np.pi/180. )


def calculate_d(dE, lon, lat, rossrad, dt):
    '''
    Calculates length of search area to the west of central point.
    This is equal to the length of the search area to the east of
    central point (dE) unless in the tropics ( abs(lat) < 18 deg )
    in which case the distance a Rossby wave travels in one time step
    (dt, days) is used instead.
    '''

    if np.abs(lat) < 18 :
        # Rossby wave speed [km/day]
        c = interpolate.griddata(np.array([rossrad['lon'], rossrad['lat']]).T, rossrad['cR'], (lon, lat), method='linear') * 86400. / 1000.
        d = np.abs(1.75 * c * dt)
    else:
        d = dE

    return d


def track_eddies(eddies, det_eddies, tt, dt, dt_aviso, dE_aviso, rossrad, eddy_scale_min, eddy_scale_max):
    '''
    Given a map of detected eddies as a function of time (det_eddies)
    this function will update tracks of individual eddies at time step
    tt in variable eddies
    '''

    # List of unassigned eddies at time tt

    unassigned = range(det_eddies[tt]['N'])

    # For each existing eddy (t<tt) loop through unassigned eddies and assign to existing eddy if appropriate

    for ed in range(len(eddies)):

        # Check if eddy has already been terminated

        if not eddies[ed]['terminated']:

            # Define search region around centroid of existing eddy ed at last known position
    
            x0 = eddies[ed]['lon'][-1] # [deg. lon]
            y0 = eddies[ed]['lat'][-1] # [deg. lat]
            dE = dE_aviso/(dt_aviso/dt) # [km]
            d = calculate_d(dE, x0, y0, rossrad, dt) # [km]
    
            # Find all eddy centroids in search region at time tt
    
            is_near = is_in_ellipse(x0, y0, dE/len_deg_lon(y0), d/len_deg_lon(y0), det_eddies[tt]['lon'][unassigned], det_eddies[tt]['lat'][unassigned])
    
            # Check if eddies' amp  and area are between 0.25 and 2.5 of original eddy
    
            amp = eddies[ed]['amp'][-1]
            area = eddies[ed]['area'][-1]
            is_similar_amp = (det_eddies[tt]['amp'][unassigned] < amp*eddy_scale_max) * (det_eddies[tt]['amp'][unassigned] > amp*eddy_scale_min)
            is_similar_area = (det_eddies[tt]['area'][unassigned] < area*eddy_scale_max) * (det_eddies[tt]['area'][unassigned] > area*eddy_scale_min)
    
            # Check if eddies' type is the same as original eddy
    
            is_same_type = np.array([det_eddies[tt]['type'][i] == eddies[ed]['type'] for i in unassigned])
    
            # Possible eddies are those which are near, of the right amplitude, and of the same type
    
            possibles = is_near * is_similar_amp * is_similar_area * is_same_type
            if possibles.sum() > 0:
    
                # Of all found eddies, accept only the nearest one
    
                dist = np.sqrt((x0-det_eddies[tt]['lon'][unassigned])**2 + (y0-det_eddies[tt]['lat'][unassigned])**2)
                nearest = dist == dist[possibles].min()
                next_eddy = unassigned[np.where(nearest * possibles)[0][0]]
    
                # Add coordinatse and properties of accepted eddy to trajectory of eddy ed
    
                eddies[ed]['lon'] = np.append(eddies[ed]['lon'], det_eddies[tt]['lon'][next_eddy])
                eddies[ed]['lat'] = np.append(eddies[ed]['lat'], det_eddies[tt]['lat'][next_eddy])
                eddies[ed]['amp'] = np.append(eddies[ed]['amp'], det_eddies[tt]['amp'][next_eddy])
                eddies[ed]['area'] = np.append(eddies[ed]['area'], det_eddies[tt]['area'][next_eddy])
                eddies[ed]['scale'] = np.append(eddies[ed]['scale'], det_eddies[tt]['scale'][next_eddy])
                eddies[ed]['time'] = np.append(eddies[ed]['time'], tt+1)
    
                # Remove detected eddy from list of eddies available for assigment to existing trajectories
    
                unassigned.remove(next_eddy)

            # Terminate eddy otherwise

            else:

                eddies[ed]['terminated'] = True

    # Create "new eddies" from list of eddies not assigned to existing trajectories

    if len(unassigned) > 0:

        for un in unassigned:

            eddy_tmp = {}
            eddy_tmp['lon'] = np.array([det_eddies[tt]['lon'][un]])
            eddy_tmp['lat'] = np.array([det_eddies[tt]['lat'][un]])
            eddy_tmp['amp'] = np.array([det_eddies[tt]['amp'][un]])
            eddy_tmp['area'] = np.array([det_eddies[tt]['area'][un]])
            eddy_tmp['scale'] = np.array([det_eddies[tt]['scale'][un]])
            eddy_tmp['type'] = det_eddies[tt]['type'][un]
            eddy_tmp['time'] = np.array([tt+1])
            eddy_tmp['exist_at_start'] = False
            eddy_tmp['terminated'] = False
            eddies.append(eddy_tmp)

    return eddies

def add_time_2tracked_eddies(eddies, nemo_tsteps):
    '''
    Given output from track_eddies, add start time
    '''
    for ed in np.arange(len(eddies)):
        #zero because we want the first time we tracked the eddy 
        eddies[ed]['start_date']=nemo_tsteps[eddies[ed]['time'][0]-1]
    return eddies