summarize_obs.py

#!/usr/bin/env python
import sys
sys.path.append('../../')
import os
import numpy as np
import string
import datetime as dt
import logging
import da.tools.io4 as io
from da.tools.general import CreateDirs

fontsize=10

def nice_lat(cls):
  #
  # Convert latitude from decimal to cardinal
  #
  if cls > 0:
     h = 'N'
  else:
     h = 'S'
  
  dec, deg = np.math.modf(cls)

  return string.strip('%2d %2d\'%s' % (abs(deg), round(abs(60 * dec), 0), h))

def nice_lon(cls):
  #
  # Convert longitude from decimal to cardinal
  #
  if cls > 0:
     h = 'E'
  else:
     h = 'W'
  
  dec, deg = np.math.modf(cls)

  return string.strip('%3d %2d\'%s' % (abs(deg), round(abs(60 * dec), 0), h))

def nice_alt(cls):
  #
  # Reformat elevation or altitude
  #
  return string.strip('%10.1f masl' % round(cls, -1))


def SummarizeObs(DaCycle,printfmt='html'):
    """***************************************************************************************
    Call example:

    python summarize_obs.py 

    Option printfmt    : [tex,scr,html] print summary table in latex, terminal, or html format 

    Other options are all those needed to create a DaCycle object

    OR:

    call directly from a python script as:

    q=SummarizeObs(DaCycle,printfmt='html')

    ***************************************************************************************"""

    sumdir=os.path.join(DaCycle['dir.analysis'],'summary')
    if not os.path.exists(sumdir):
        logging.info( "Creating new directory "+sumdir )
        os.makedirs(sumdir)

    mrdir=os.path.join(DaCycle['dir.analysis'],'data_molefractions')
    if not os.path.exists(mrdir):
        logging.error( "Input directory does not exist (%s), exiting... "%mrdir )
        return None

    mrfiles = os.listdir(mrdir)
    infiles = [os.path.join(mrdir,f) for f in mrfiles if f.endswith('.nc')]

    if printfmt == 'tex': 
        print '\\begin{tabular*}{\\textheight}{l l l l r r r r}'
        print 'Code &  Name & Lat, Lon, Elev & Lab &  N (flagged) & $\\sqrt{R}$  &Inn \\XS &Bias\\\\'
        print '\hline\\\\ \n\multicolumn{8}{ c }{Semi-Continuous Surface Samples}\\\\[3pt] '
        fmt= '%8s  & '+' %55s  & '+'%20s &'+'%6s &'+' %4d (%d)  & '+' %5.2f  & '+' %5.2f & '+'%+5.2f  \\\\'
    elif printfmt == 'html':
        tablehead = \
              "<TR>\n <TH> Site code </TH> \
                   <TH> Sampling Type </TH> \
                   <TH> Lab. </TH> \
                   <TH> Country </TH> \
                   <TH> Lat, Lon, Elev. (m ASL) </TH> \
                   <TH> No. Obs. Avail. </TH>  \
                   <TH> &#8730;R (&mu;mol mol<sup>-1</sup>) </TH>  \
                   <TH> &#8730;HPH  (&mu;mol mol<sup>-1</sup>) </TH> \
                   <TH> H(x)-y (&mu;mol mol<sup>-1</sup>) </TH> \
                   <TH> H(x)-y (JJAS) (&mu;mol mol<sup>-1</sup>) </TH>  \
                   <TH> H(x)-y (NDJFMA) (&mu;mol mol<sup>-1</sup>) </TH> \n \
               </TR>\n"

        fmt=  """<TR> \n \
                <TD><a href='javascript:LoadCO2Tseries("%s")'>%s </a></TD>\
                <TD>%s</TD>\
                <TD>%s</TD>\
                <TD>%40s</TD>\
                <TD>%s</TD>\
                <TD>%d</TD>\
                <TD>%+5.2f</TD>\
                <TD>%+5.2f</TD>\
                <TD>%+5.2f&plusmn;%5.2f</TD>\
                <TD>%+5.2f&plusmn;%5.2f</TD>\
                <TD>%+5.2f&plusmn;%5.2f</TD>\n \
               </TR>\n"""
    elif printfmt == 'scr':
        print 'Code   Site     NObs flagged  R  Inn X2'
        fmt= '%8s '+' %55s  %s %s'+' %4d '+' %4d '+' %5.2f '+' %5.2f'

    table=[]
    lons=[]
    lats=[]
    names=[]
    nobs=[]
    for infile in infiles:

            #logging.debug( infile )
            f         = io.CT_CDF(infile,'read')
            date      = f.GetVariable('time')
            obs       = f.GetVariable('value')*1e6
            mdm       = f.GetVariable('modeldatamismatch')*1e6
            simulated = f.GetVariable('modelsamplesmean')*1e6
            simulated_std = f.GetVariable('modelsamplesstandarddeviation')*1e6

            pydates = [dt.datetime(1970,1,1)+dt.timedelta(seconds=int(d)) for d in date]

            summer = [i for i,d in enumerate(pydates) if d.month in [6,7,8,9] ]
            winter = [i for i,d in enumerate(pydates) if d.month in [11,12,1,2,3,4] ]

            diff=((simulated-obs).mean())
            diffsummer=((simulated-obs).take(summer).mean())
            diffwinter=((simulated-obs).take(winter).mean())
            diffstd=((simulated-obs).std())
            diffsummerstd=((simulated-obs).take(summer).std())
            diffwinterstd=((simulated-obs).take(winter).std())
            longsitestring=f.site_name+', '+f.site_country
            location=nice_lat(f.site_latitude)+', '+ nice_lon(f.site_longitude)+', '+nice_alt(f.site_elevation)

            if printfmt == 'html':
                ss=(f.site_code.upper(),
                    f.site_code.upper(),
                    f.dataset_project,
                    f.lab_abbr,
                    f.site_country,
                    location,
                    len(mdm.compressed()),
                    mdm.mean(),
                    np.sqrt((simulated_std**2).mean()),
                    diff,diffstd,
                    diffsummer,diffsummerstd,
                    diffwinter,diffwinterstd)
            
            table.append(ss)
            lons.append(f.site_longitude)
            lats.append(f.site_latitude)
            names.append(f.site_code)
            nobs.append(len(mdm.compressed()))
            f.close()

    if printfmt == 'tex':
        saveas=os.path.join(sumdir,'site_table.tex')
        f=open(saveas,'w')
    elif printfmt == 'html':
        saveas=os.path.join(sumdir,'site_table.html')
        f=open(saveas,'w')
        txt = "<meta http-equiv='content-type' content='text/html;charset=utf-8' />\n"
        f.write(txt)
        txt="<table border=1 cellpadding=2 cellspacing=2 width='100%' bgcolor='#EEEEEE'>\n"
        f.write(txt)

    f.write(tablehead)

    for i,ss in enumerate(table):

        f.write(fmt%ss)
        if (i+1)%15 == 0:
            f.write(tablehead)

    if printfmt == 'tex': 
        f.write( '\cline{2-8}\\\\' )
        f.write( '\hline \\\\')
        f.write( '\end{tabular*}')
    else:
        txt="\n</table>"
        f.write(txt)
    f.close()

    logging.info("File written with summary: %s" % saveas)

# main body if called as script

if __name__ == '__main__':    # started as script

    from da.tools.initexit import CycleControl
    from da.ct.dasystem import CtDaSystem 
    from da.ct.statevector import CtStateVector 

    sys.path.append('../../')

    logging.root.setLevel(logging.DEBUG)

    DaCycle = CycleControl(args={'rc':'../../ctdas-od-gfed2-glb6x4-obspack.rc'})
    DaCycle.Initialize()
    DaCycle.ParseTimes()

    DaSystem    = CtDaSystem('../rc/carbontracker_ct09_op.rc')
    DaSystem.Initialize()

    DaCycle.DaSystem    = DaSystem

    q=SummarizeObs(DaCycle)

    sys.exit(0)