Ignore:
Timestamp:
Aug 28, 2012, 3:08:35 PM (12 years ago)
Author:
acolaitis
Message:

###################################################
# PYTHON / PLANETPLOT #
###################################################

# ------------------- XY plots ------------------ #

# Added a new category of plot to unidim, contour, etc... called "xy"
# - xy plots are plots that do not use time,vert,lat or lon as axis
# - variables to be plotted are stored in plot_x and plot_y, which is done in
# select_getfield. (there is no "what_I_plot" var for "wy" plots)
# - plot_x and plot_y are also subject to reduce field. A None value indicates
# the plot is not 'xy'
# - "xy" plots are used for a specific subset of plots : histograms, fourier
# transforms, hodographs
# - added option --analysis to perform certain kinds of analysis on the data
# (corresponding to xy plots).
# - One selects the fields he wants to plot (e.g. -v UV --lon 0 --lat 20) and
# chooses a kind of analysis :

--analysis fft # in the particular case given above, this mode corresponds

# to the mean of the ampitude spectrum of the vertical spatial
# fast fourier transform taken at each time index
# note that for now, fft are always done along the vertical
# axis. This could be made more flexible.
# not that the minimum wavelength you can plot depends on the
# vertical step of your simulation. THIS STEP HAS TO BE
# CONSTANT, hence you MUST use API or ZRECAST with constant
# spacing.

--analysis histo # histogram on the flattened data. If the user asks for --lon 0,20,

# the average is done before computing the histogram (contrary to the fft).
# However, if given a 2D array (with only --lon and --lat on a
# 4D field for example), the data is flattened before computation
# so that the result is still a 1D histogram.

--analysis histodensity # histogram with a kernel density estimate to a

# gaussian distribution, also giving the mean, variance,
# skewness and kurtosis. Other distributions are available in
# the scipy.stats package and could be implemented.

# - added variables "-v hodograph" and "-v hodograph_2". First one is a
# regular hodograph with "u" and "v" as axis, with labels of the local times
# (use --axtime lt). This is a "xy" plot (you must specify a vertical level
# as well, usually --vert 0 with an interpolation at 5m (-i 4 -l 0.005)).
# Second one is the variation with local time (for exemple) of the wind
# rotation (arctan(v/u)). This is not a "xy" plot but "unidim".
# For --ope plots in "xy" cases, only the operation plot is displayed.

# ------------------- Operations ------------------ #

# - For operations --ope -, the histogram (fourth plot) has been removed. To get it
# back, call --ope -_histo.
# - _only has been added to "+","-","-%" operations (eg "-_only")
# - For operations "-","+","-%","-_only","+_only","-%_only","-_histo", it is now
# possible to call multiple files (sill one variable) and compare each of them
# with the unique given reference file. Ex: -f file1,file2 --fref file3 --ope - will give 6 plots:

file1 file3 file1-file3
file2 file3 file2-file3

# In the case of "xy" plots, the multiple operation plots are regrouped on a
# single plot (using multiple lines). the title of this plot is not 'fig(2)-fig(1)'
# (default) but the argument of the --title command. Labels have to be given
# as following : --labels "dummy","dummy","file1-file3 label","dummy","dummy","file2-file3 label" (dummy can be anything. this is to be improved)
# To be able to run on multiple files and easily introduce the correct number and order of plots, these operations have been moved outside of the main loop
# on namefiles and variables. Operation of the type "add_var" or "cat" have
# been left inside the loop and are unchanged.

# ------------------- Localtime ------------------ #

# Changed the way localtime is computed. Reasons:
# - it was assuming one timestep per hour in computations mixing indices and
# actual times
# - to determine the starting date, it was using the name of the file (for Meso), instead of using the netcdf
# attribute (START_DATE)
# - it was using the computed mean longitude of the domain, which is not correct for
# hemispheric domain. => better to use the netcdf attribute CEN_LON
# - it was using this mean longitude even for profile plots at given
# longitude => better to get the local time at this given lon, especially
# important for large domains
# => new localtime() is in myplot (old one is commented). Interv is obsolete (but not removed yet). Case "Geo" has not been looked at.
# new localtime in myplot correctly account for starting date of the file in
# all cases
# accounts for local longitude of the plot
# accounts for files that do not have per hour outputs, but per timestep.
# specific cases can be added in myplot in localtime()

# ------------------ Misc ------------------ #

# - added option --xlog to get x logarithmic axis (--ylog already existed)
# - added the possibility to use 2 files of different gridding (-f
# file1,file2) although of the same type (meso for exemple). For that purpose,
# lon, lat, alt and vert arrays are now indexed with 'index_f', as for
# all_var. => all_lon, all_lat, all_lat, all_vert
# - added function teta_to_tk in myplot so that a call to pp.py on standard
# LMD mesoscale file with "-v tk" can be done without the need to call API.
# The temperature is computed from T and PTOT, knowing P0, T0 and R_CP.
# - bug correction in determineplot() that was causing wrong plot number and
# slices number when not calling averaged lon, lat, vert or times. (which is
# often !)
# - added new options to redope: --redope edge_x1, edge_x2, edge_y1, edge_y2
# which plots the boundaries of the domain. This is different compared to
# asking for a fixed longitude, because the domain boundary might not be at constant
# longitude (hemispheric domain for exemple). x1 is the western boundary, x2
# the eastern, y1 the southern and y2 the northern. x1 and x2 reduce the
# dimension along --lon, y1 and y2 reduce the dimension along --lat.
# - added control in windamplitude() to determine whether winds are staggered or
# unstaggered. This is usefull when dealing with non LMD_MMM files.
# - corrected a bug in reduce_field where the mean was computed on the wrong
# axis !!! (pretty serious bug)

# Exemple of plots you can do with these new options can be found in
$YOUR_SVN/trunk/UTIL/PYTHON/Intercomparison/Plots_MasterScript/bam.sh

# ------------------ API ------------------ #

# - changed maximum of levels from 299 to 1000 in API (interpolation on 1000 levels is
# usefull to get larger bandwidth in fourier transform)
# the following concerns users of MRAMS files.
# - API has not been modified for MRAMS files. Instead, a python script
# (ic.py) is run on MRAMS .ctl and .dat files, which automatically format those files
# to be API and pp.py compatible.
# - ic.py is in $YOUR_SVN/trunk/UTIL/PYTHON/Intercomparison/File_conversion

###################################################
# INTERCOMPARISON TOOLS: #
###################################################

#ic.py in
$YOUR_SVN/trunk/UTIL/PYTHON/Intercomparison/File_conversion
#CDO installer with import_binary in
$YOUR_SVN/trunk/UTIL/PYTHON/Intercomparison/CDO
#Plotting scripts in
$YOUR_SVN/trunk/UTIL/PYTHON/Intercomparison/Plots_MasterScript
#1D sensibility tool in
$YOUR_SVN/trunk/UTIL/PYTHON/Intercomparison/1D_sensibility_tool

# See README in each of these folders for details.

File:
1 edited

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  • trunk/UTIL/PYTHON/planetoplot.py

    r760 r763  
    2626           winds=False,\
    2727           addchar=None,\
    28            interv=[0,1],\
    2928           vmin=None,\
    3029           vmax=None,\
    … …  
    5453           yaxis=[None,None],\
    5554           ylog=False,\
     55           xlog=False,\
    5656           yintegral=False,\
    5757           blat=None,\
    … …  
    7373           facwind=1.,\
    7474           trycol=False,\
    75            streamflag=False):
     75           streamflag=False,\
     76           analysis=None):
    7677
    7778    ####################################################################################################################
    … …  
    9596    import numpy as np
    9697    from numpy.core.defchararray import find
     98    from scipy.stats import gaussian_kde,describe
    9799    from videosink import VideoSink
    98100    from times import sol2ls
    … …  
    126128### we prepare number of plot fields [zelen] and number of plot instances [numplot] according to user choices
    127129### --> we support multifile and multivar plots : files + vars separated by commas are on the same figure
    128     nlon, nlat, nvert, ntime, mapmode, nslices = determineplot(slon, slat, svert, stime)
     130    nlon, nlat, nvert, ntime, mapmode, nslices = determineplot(slon, slat, svert, stime, redope)
    129131    zelen = len(namefiles)*len(var)
     132### we correct number of plot fields for possible operation (substract, etc...)
     133    if ope is not None:
     134        if fileref is not None:       zelen = 3*len(var)*len(namefiles)
     135        elif "var" in ope:            zelen = zelen + 1
    130136    numplot = zelen*nslices
    131137    print "********** FILES, SLICES, VARS, TOTAL PLOTS: ", len(namefiles), nslices, len(var), numplot
    132138    print "********** MAPMODE: ", mapmode
    133 ### we correct number of plot fields for possible operation (substract, etc...)
    134     if ope is not None:
    135         if fileref is not None:       zelen = zelen + 2
    136         elif "var" in ope:            zelen = zelen + 1
    137139### we define the arrays for plot fields -- which will be placed within multiplot loops
    138     all_var  = [[]]*zelen ; all_var2  = [[]]*zelen
    139     all_title = [[]]*zelen ; all_varname = [[]]*zelen ; all_namefile = [[]]*zelen ; all_time = [[]]*zelen ; all_colorb = [[]]*zelen
     140    all_var  = [[]]*zelen ; all_var2  = [[]]*zelen
     141    all_title = [[]]*zelen ; all_varname = [[]]*zelen ; all_namefile = [[]]*zelen ; all_colorb = [[]]*zelen
     142    all_time = [[]]*zelen ; all_vert = [[]]*zelen ; all_lat = [[]]*zelen ; all_lon = [[]]*zelen
    140143    all_windu = [[]]*zelen ; all_windv = [[]]*zelen
    141 
     144    plot_x = [[]]*zelen ; plot_y = [[]]*zelen ; multiplot = [[]]*zelen
     145### tool (should be move to mymath)
     146    getVar = lambda searchList, ind: [searchList[i] for i in ind]
    142147#############################
    143148### LOOP OVER PLOT FIELDS ###
    144149#############################
     150   
    145151    for nnn in range(len(namefiles)):
    146152     for vvv in range(len(var)):
    … …  
    290296              ftime = np.zeros(len(time))
    291297              for i in range(len(time)):
    292                  ftime[i] = localtime ( interv[0]+time[i]*interv[1], 0.5*(wlon[0]+wlon[1]) )
     298                 ftime[i] = localtime ( time[i], slon , nc )
    293299              time=ftime
    294300              time=check_localtime(time)
    … …  
    312318      all_namefile[k] = namefile
    313319      all_time[k] = time
     320      all_vert[k] = vert
     321      all_lat[k] = lat
     322      all_lon[k] =  lon
    314323      all_colorb[k] = clb[vvv]
    315       if var2:  all_var2[k] = select_getfield(zvarname=var2,znc=nc,ztypefile=typefile,mode='getvar',ztsat=tsat,ylon=lon,ylat=lat,yalt=vert,ytime=all_time[k])
     324      if var2:  all_var2[k], plot_x[k], plot_y[k] = select_getfield(zvarname=var2,znc=nc,ztypefile=typefile,mode='getvar',ztsat=tsat,ylon=all_lon[k],ylat=all_lat[k],yalt=all_vert[k],ytime=all_time[k],analysis=analysis)
    316325      if winds: all_windu[k] = getfield(nc,uchar) ; all_windv[k] = getfield(nc,vchar)
    317326    ### we fill the arrays of fields to be plotted at the current step considered
    318       all_var[k] = select_getfield(zvarname=all_varname[k],znc=nc,ztypefile=typefile,mode='getvar',ztsat=tsat,ylon=lon,ylat=lat,yalt=vert,ytime=all_time[k])
    319     ### we inform the user about the loop then increment the loop. this is the last line of "for namefile in namefiles"
     327      all_var[k], plot_x[k], plot_y[k] = select_getfield(zvarname=all_varname[k],znc=nc,ztypefile=typefile,mode='getvar',ztsat=tsat,ylon=all_lon[k],ylat=all_lat[k],yalt=all_vert[k],ytime=all_time[k],analysis=analysis)
     328
     329      # last line of for namefile in namefiles
    320330      print "**** GOT SUBDATA:",k," NAMEFILE:",namefile," VAR:",varname, var2 ; k += 1 ; firstfile = False
    321331
    … …  
    323333
    324334    ##################################
    325     ### Operation on files
    326     if ope is not None:
    327         print "********** OPERATION: ",ope
    328         if "var" not in ope:
    329              if len(var) > 1: errormess("for this operation... please set only one var !")
    330              if ope in ["-","+","-%"]:
    331                 if fileref is not None:   
    332                    ncref = Dataset(fileref)
    333                    all_var[k] = select_getfield(zvarname=all_varname[k-1],znc=ncref,ztypefile=typefile,mode='getvar',ztsat=tsat,ylon=lon,ylat=lat,yalt=vert,ytime=all_time[k])
    334                    all_varname[k] = all_varname[k-1] ; all_time[k] = all_time[k-1] ; all_namefile[k] = all_namefile[k-1] ; all_var2[k] = all_var2[k-1] ; all_colorb[k] = all_colorb[k-1]
    335                    if winds: all_windu[k] = getfield(ncref,uchar) ; all_windv[k] = getfield(ncref,vchar)
    336                 else: errormess("fileref is missing!")
    337                 if ope == "-":     all_var[k+1]= all_var[k-1] - all_var[k]
    338                 elif ope == "+":   all_var[k+1]= all_var[k-1] + all_var[k]
    339                 elif ope == "-%":
    340                     masked = np.ma.masked_where(all_var[k] == 0,all_var[k])
    341                     masked.set_fill_value([np.NaN])
    342                     all_var[k+1]= 100.*(all_var[k-1] - masked)/masked
    343                 all_varname[k+1] = all_varname[k] ; all_time[k+1] = all_time[k] ; all_namefile[k+1] = all_namefile[k] ; all_var2[k+1] = all_var2[k] ; numplot = numplot+2
    344                 if len(clb) >= zelen:  all_colorb[k+1] = clb[-1]   # last additional user-defined color is for operation plot
    345                 else:                  all_colorb[k+1] = "RdBu_r"  # if no additional user-defined color... set a good default one
    346                 if winds: all_windu[k+1] = all_windu[k-1]-all_windu[k] ; all_windv[k+1] = all_windv[k-1] - all_windv[k]
    347              elif ope in ["cat"]:
    348                 tabtime = all_time[0];tab = all_var[0];k = 1
    349                 if var2: tab2 = all_var2[0]
    350                 while k != len(namefiles) and len(all_time[k]) != 0:
    351                     if var2: tab2 = np.append(tab2,all_var2[k],axis=0)
    352                     tabtime = np.append(tabtime,all_time[k]) ; tab = np.append(tab,all_var[k],axis=0) ; k += 1
    353                 all_time[0] = np.array(tabtime) ; all_var[0] = np.array(tab) ; numplot = 1
    354                 if var2: all_var2[0] = np.array(tab2)
    355              else: errormess(ope+" : non-implemented operation. Check pp.py --help")
    356         else:
    357              if len(namefiles) > 1: errormess("for this operation... please set only one file !") 
    358              if len(var) > 2:       errormess("not sure this works for more than 2 vars... please check.")
    359              if   "div_var" in ope: all_var[k] = all_var[k-2] / all_var[k-1] ; insert = '_div_'
    360              elif "mul_var" in ope: all_var[k] = all_var[k-2] * all_var[k-1] ; insert = '_mul_'
    361              elif "add_var" in ope: all_var[k] = all_var[k-2] + all_var[k-1] ; insert = '_add_'
    362              elif "sub_var" in ope: all_var[k] = all_var[k-2] - all_var[k-1] ; insert = '_sub_'
    363              else:                    errormess(ope+" : non-implemented operation. Check pp.py --help")
    364              numplot = numplot + 1 ; all_time[k] = all_time[k-1] ; all_namefile[k] = all_namefile[k-1]
    365              all_varname[k] = all_varname[k-2] + insert + all_varname[k-1]
    366              if len(clb) >= zelen: all_colorb[k] = clb[-1]   # last additional user-defined color is for operation plot
    367              else:                 all_colorb[k] = all_colorb[k-1]  # if no additional user-defined color... set same as var
    368              ### only the operation plot. do not mention colorb so that it is user-defined?
    369              if "only" in ope:
    370                  numplot = 1 ; all_var[0] = all_var[k]
    371                  all_time[0] = all_time[k] ; all_namefile[0] = all_namefile[k]
    372                  all_varname[0] = all_varname[k-2] + insert + all_varname[k-1]
    373 
     335    ### Operation on files (I) with _var
     336    if ope is not None and "var" in ope:
     337         print "********** OPERATION: ",ope
     338         if len(namefiles) > 1: errormess("for this operation... please set only one file !")
     339         if len(var) > 2:       errormess("not sure this works for more than 2 vars... please check.")
     340         if   "div_var" in ope: all_var[k] = all_var[k-2] / all_var[k-1] ; insert = '_div_'
     341         elif "mul_var" in ope: all_var[k] = all_var[k-2] * all_var[k-1] ; insert = '_mul_'
     342         elif "add_var" in ope: all_var[k] = all_var[k-2] + all_var[k-1] ; insert = '_add_'
     343         elif "sub_var" in ope: all_var[k] = all_var[k-2] - all_var[k-1] ; insert = '_sub_'
     344         else:                    errormess(ope+" : non-implemented operation. Check pp.py --help")
     345         plot_x[k] = None ; plot_y[k] = None
     346         all_time[k] = all_time[k-1] ; all_vert[k] = all_vert[k-1] ; all_lat[k] = all_lat[k-1] ; all_lon[k] = all_lon[k-1] ; all_namefile[k] = all_namefile[k-1]
     347         all_varname[k] = all_varname[k-2] + insert + all_varname[k-1]
     348         if len(clb) >= zelen: all_colorb[k] = clb[-1]   # last additional user-defined color is for operation plot
     349         else:                 all_colorb[k] = all_colorb[k-1]  # if no additional user-defined color... set same as var
     350         ### only the operation plot. do not mention colorb so that it is user-defined?
     351         if "only" in ope:
     352             numplot = 1 ; all_var[0] = all_var[k]
     353             all_time[0] = all_time[k] ; all_vert[0] = all_vert[k] ; all_lat[0] = all_lat[k] ; all_lon[0] = all_lon[k] ; all_namefile[0] = all_namefile[k]
     354             all_varname[0] = all_varname[k-2] + insert + all_varname[k-1]
     355
     356
     357    ##################################
     358    ### Operation on files (II) without _var
     359    # we re-iterate on the plots to set operation subplots to make it compatible with multifile (using the same ref file)
     360    # (k+1)%3==0 is the index of operation plots
     361    # (k+2)%3==0 is the index of reference plots
     362    # (k+3)%3==0 is the index of first plots
     363    opefirstpass=True
     364    if ope is not None and "var" not in ope:
     365       print "********** OPERATION: ",ope
     366       for k in np.arange(zelen):
     367               if len(var) > 1: errormess("for this operation... please set only one var !")
     368               if ope in ["-","+","-%","-_only","+_only","-%_only","-_histo"]:
     369                  if fileref is None: errormess("fileref is missing!")
     370                  else:ncref = Dataset(fileref)
     371
     372                  if opefirstpass: ## first plots
     373                     for ll in np.arange(len(namefiles)):
     374                        print "SETTING FIRST PLOT"
     375                        all_varname[3*ll] = all_varname[ll] ; all_time[3*ll] = all_time[ll] ; all_vert[3*ll] = all_vert[ll] ; all_lat[3*ll] = all_lat[ll] ; all_lon[3*ll] = all_lon[ll] ; all_namefile[3*ll] = all_namefile[ll] ; all_var2[3*ll] = all_var2[ll] ; all_colorb[3*ll] = all_colorb[ll] ; all_var[3*ll] = all_var[ll]
     376                        if plot_y[ll] is not None: plot_y[3*ll] = plot_y[ll] ; plot_x[3*ll] = plot_x[ll]
     377                        else: plot_y[3*ll] = None ; plot_x[3*ll] = None
     378                        opefirstpass=False
     379
     380                  if (k+2)%3==0: ## reference plots
     381                        print "SETTING REFERENCE PLOT"
     382                        all_varname[k] = all_varname[k-1] ; all_time[k] = all_time[k-1] ; all_vert[k] = all_vert[k-1] ; all_lat[k] = all_lat[k-1] ; all_lon[k] = all_lon[k-1] ; all_namefile[k] = all_namefile[k-1] ; all_var2[k] = all_var2[k-1] ; all_colorb[k] = all_colorb[k-1]
     383                        all_var[k], plot_x[k], plot_y[k] = select_getfield(zvarname=all_varname[k-1],znc=ncref,ztypefile=typefile,mode='getvar',ztsat=tsat,ylon=all_lon[k],ylat=all_lat[k],yalt=all_vert[k],ytime=all_time[k],analysis=analysis)
     384                        if winds: all_windu[k] = getfield(ncref,uchar) ; all_windv[k] = getfield(ncref,vchar)
     385
     386                  if (k+1)%3==0: ## operation plots
     387                     print "SETTING OPERATION PLOT"
     388                     all_varname[k] = all_varname[k-1] ; all_time[k] = all_time[k-1] ; all_vert[k] = all_vert[k-1] ; all_lat[k] = all_lat[k-1] ; all_lon[k] = all_lon[k-1] ; all_namefile[k] = all_namefile[k-1] ; all_var2[k] = all_var2[k-1]
     389                     if ope in ["-","-_only","-_histo"]:
     390                         all_var[k]= all_var[k-2] - all_var[k-1]
     391                         if plot_y[k-1] is not None and plot_y[k-2] is not None: plot_y[k] = plot_y[k-2] - plot_y[k-1]
     392                         if plot_y[k-2] is None: plot_y[k] = None; plot_x[k] = None
     393                     elif ope in ["+","+_only"]:   
     394                         all_var[k]= all_var[k-2] + all_var[k-1]
     395                         if plot_y[k-1] is not None and plot_y[k-2] is not None: plot_y[k] = plot_y[k-2] + plot_y[k-1]
     396                         if plot_y[k-2] is None: plot_y[k] = None; plot_x[k] = None
     397                     elif ope in ["-%","-%_only"]:
     398                         masked = np.ma.masked_where(all_var[k-1] == 0,all_var[k-1])
     399                         masked.set_fill_value([np.NaN])
     400                         all_var[k]= 100.*(all_var[k-2] - masked)/masked
     401                         if plot_y[k-1] is not None and plot_y[k-2] is not None:
     402                            masked = np.ma.masked_where(plot_y[k-1] == 0,plot_y[k-1])
     403                            masked.set_fill_value([np.NaN])
     404                            plot_y[k]= 100.*(plot_y[k-2] - masked)/masked
     405                         if plot_y[k-2] is None: plot_y[k] = None; plot_x[k] = None
     406                     if len(clb) >= zelen: all_colorb[k] = clb[-1]
     407                     else: all_colorb[k] = "RdBu_r" # if no additional user-defined color... set a good default one
     408                     if winds: all_windu[k] = all_windu[k-2]-all_windu[k-1] ; all_windv[k] = all_windv[k-2] - all_windv[k-1]
     409
     410               elif ope in ["cat"]:
     411                  tabtime = all_time[0];tab = all_var[0];k = 1
     412                  if var2: tab2 = all_var2[0]
     413                  while k != len(namefiles) and len(all_time[k]) != 0:
     414                      if var2: tab2 = np.append(tab2,all_var2[k],axis=0)
     415                      tabtime = np.append(tabtime,all_time[k]) ; tab = np.append(tab,all_var[k],axis=0) ; k += 1
     416                  all_time[0] = np.array(tabtime) ; all_var[0] = np.array(tab) ; numplot = 1
     417                  if var2: all_var2[0] = np.array(tab2)
     418               else: errormess(ope+" : non-implemented operation. Check pp.py --help")
     419       if "only" in ope:
     420           numplot = 1 ; all_var[0] = all_var[k]
     421           all_time[0] = all_time[k] ; all_vert[0] = all_vert[k] ; all_lat[0] = all_lat[k] ; all_lon[0] = all_lon[k] ; all_namefile[0] = all_namefile[k] ; plot_x[0]=plot_x[k] ; plot_y[0]=plot_y[k]
     422           all_varname[0] = all_varname[k]
    374423
    375424    ##################################
    … …  
    377426    fig = figure()
    378427    subv,subh = definesubplot( numplot, fig )
    379     if ope in ['-','-%']: subv,subh = 2,2
     428    if ope in ['-','-%','-_histo'] and len(namefiles) ==1 : subv,subh = 2,2
     429    elif ope in ['-','-%'] and len(namefiles)>1 : subv, subh = len(namefiles), 3
    380430 
    381431    #################################
    382432    ### Time loop for plotting device
    383     nplot = 1 ; error = False
     433    nplot = 1 ; error = False ; firstpass = True
    384434    if lstyle is not None: linecycler = cycle(lstyle)
    385435    else: linecycler = cycle(["-","--","-.",":"])
    … …  
    387437    while error is False:
    388438     
    389        print "********** NPLOT", nplot
     439       print "********** PLOT", nplot, " OF ",numplot
    390440       if nplot > numplot: break
    391441
    … …  
    393443       ## get all indexes to be taken into account for this subplot and then reduce field
    394444       ## We plot 1) all lon slices 2) all lat slices 3) all vert slices 4) all time slices and then go to the next slice
     445       if ope is not None:
     446           if fileref is not None:      index_f = ((nplot-1)//(nlon*nlat*nvert*ntime))%(3*len(namefiles))  ## OK only 1 var,  see test in the beginning
     447           elif "var" in ope:           index_f = ((nplot-1)//(nlon*nlat*nvert*ntime))%(len(var)+1)        ## OK only 1 file, see test in the beginning
     448           elif "cat" in ope:           index_f = 0
     449       elif not firstpass:
     450          if len(namefiles) > 1 and len(var) == 1 and which == "unidim": pass
     451          else: yeah = len(namefiles)*len(var) ; index_f = ((nplot-1)//(nlon*nlat*nvert*ntime))%yeah
     452       else: yeah = len(namefiles)*len(var) ; index_f = ((nplot-1)//(nlon*nlat*nvert*ntime))%yeah
     453       time = all_time[index_f] ; vert = all_vert[index_f] ; lat = all_lat[index_f] ; lon = all_lon[index_f]
    395454       indexlon  = getsindex(sslon,(nplot-1)%nlon,lon)
    396455       indexlat  = getsindex(sslat,((nplot-1)//nlon)%nlat,lat)
    397        indexvert = getsindex(svert,((nplot-1)//(nlon*nlat))%nvert,vert)
    398        if ope is not None:
    399            if fileref is not None:      index_f = ((nplot-1)//(nlon*nlat*nvert*ntime))%(len(namefiles)+2)  ## OK only 1 var,  see test in the beginning
    400            elif "var" in ope:           index_f = ((nplot-1)//(nlon*nlat*nvert*ntime))%(len(var)+1)        ## OK only 1 file, see test in the beginning
    401            elif "cat" in ope:           index_f = 0
    402        else:                            yeah = len(namefiles)*len(var) ; index_f = ((nplot-1)//(nlon*nlat*nvert*ntime))%yeah
    403        time = all_time[index_f]
     456       indexvert = getsindex(svert,((nplot-1)//(nlon*nlat))%nvert,vert)
     457       plotx=plot_x[index_f] ; ploty=plot_y[index_f]
    404458       if mrate is not None:                 indextime = None
    405459       else:                                 indextime = getsindex(stime,((nplot-1)//(nlon*nlat*nvert))%ntime,time)
    406460       ltst = None
    407        if typefile in ['meso'] and indextime is not None:  ltst = localtime ( interv[0]+indextime*interv[1], 0.5*(wlon[0]+wlon[1]) ) 
     461       if typefile in ['meso'] and indextime is not None and len(indextime) < 2: ltst = localtime ( indextime, slon , nc)
    408462       print "********** INDEX LON:",indexlon," LAT:",indexlat," VERT:",indexvert," TIME:",indextime
    409463       ##var = nc.variables["phisinit"][:,:]
    … …  
    419473       error = False
    420474       varname = all_varname[index_f]
     475       which=''
    421476       if varname:   ### what is shaded.
    422477           what_I_plot, error = reducefield( all_var[index_f], d4=indextime, d1=indexlon, d2=indexlat, d3=indexvert, \
    … …  
    432487           vecy, error = reducefield( all_windv[index_f], d4=indextime, d3=indexvert, yint=yintegral, alt=vert)
    433488           if varname in [uchar,vchar]: what_I_plot = np.sqrt( np.square(vecx) + np.square(vecy) ) ; varname = "wind"
    434 
     489 
     490       if plotx is not None:
     491          plotx, error = reducefield( plotx, d4=indextime, d1=indexlon, d2=indexlat, d3=indexvert, \
     492                                             yint=yintegral, alt=vert, anomaly=anomaly, redope=redope, mesharea=area, unidim=is1d)
     493          ploty, error = reducefield( ploty, d4=indextime, d1=indexlon, d2=indexlat, d3=indexvert, \
     494                                             yint=yintegral, alt=vert, anomaly=anomaly, redope=redope, mesharea=area, unidim=is1d)
     495          which='xy'
    435496       #####################################################################
    436497       #if truc:
    … …  
    452513       ####################################################################
    453514       ### General plot settings
    454        changesubplot = (numplot > 1) and (len(what_I_plot.shape) != 1) ## default for 1D plots: superimposed. to be reworked for better flexibility.
     515       changesubplot = (numplot > 1) and (len(what_I_plot.shape) != 1) and (which != "xy") ## default for 1D plots: superimposed. to be reworked for better flexibility.
    455516       if changesubplot: subplot(subv,subh,nplot) #; subplots_adjust(wspace=0,hspace=0)
    456517       colorb = all_colorb[index_f]
    … …  
    474535                       if slat is not None: lonyeah = lon2d[0,:]
    475536                   what_I_plot, x, y = define_axis(lonyeah,latyeah,vert,time,indexlon,indexlat,indexvert,\
    476                          itime,what_I_plot, len(all_var[index_f].shape),vertmode)
     537                         itime,what_I_plot, len(all_var[index_f].shape),vertmode,redope)
    477538               ###
    478                if (fileref is not None) and (index_f == numplot-1):    zevmin, zevmax = calculate_bounds(what_I_plot,vmin=minop,vmax=maxop)
     539               if (fileref is not None) and ((index_f+1)%3 == 0):    zevmin, zevmax = calculate_bounds(what_I_plot,vmin=minop,vmax=maxop)
    479540               else:                                                   zevmin, zevmax = calculate_bounds(what_I_plot,vmin=vmin,vmax=vmax)
    480541               #if (fileref is not None) and (index_f == numplot-1):    colorb = "RdBu_r"
    … …  
    493554                 if mrate is not None: iend=len(time)-1
    494555                 else:                 iend=0
    495                  imov = 0
    496                  if len(what_I_plot.shape) == 3:
    497                     if var2:               which = "contour" ## have to start with contours rather than shading
    498                     else:                  which = "regular"
     556                 imov = 0
     557                 if analysis in ['density','histo','fft','histodensity']: which="xy"
     558                 elif len(what_I_plot.shape) == 3:
     559                    if var2 and which == '':               which = "contour" ## have to start with contours rather than shading
     560                    elif which == '':                      which = "regular"
    499561                    if mrate is None:      errormess("3D field. Use --rate RATE for movie or specify --time TIME. Exit.")
    500562                 elif len(what_I_plot.shape) == 2:
    501                     if var2:               which = "contour" ## have to start with contours rather than shading
    502                     else:                  which = "regular"
    503                     if mrate is not None:  which = "unidim"
    504                  elif len(what_I_plot.shape) == 1:
     563                    if var2 and which == '':               which = "contour" ## have to start with contours rather than shading
     564                    elif which == '':                      which = "regular"
     565                    if mrate is not None and which == '':  which = "unidim"
     566                 elif len(what_I_plot.shape) == 1 and which == '' :
    505567                    which = "unidim"
    506568                    if what_I_plot.shape[-1] == 1:      print "VALUE VALUE VALUE VALUE ::: ", what_I_plot[0] ; save = 'donothing'
     569##                 if which == "unidim" and len(namefiles) > 1: numplot = 1 # this case is similar to several vars from one file
    507570                 ##### IMOV LOOP #### IMOV LOOP
    508571                 while imov <= iend:
    … …  
    522585                    #if mrate is not None:     
    523586                    if mapmode == 1:
    524                             m = define_proj(proj,wlon,wlat,back=back,blat=blat,blon=blon)  ## this is dirty, defined above but out of imov loop
    525                             x, y = m(lon2d, lat2d)                                         ## this is dirty, defined above but out of imov loop
     587                        m = define_proj(proj,wlon,wlat,back=back,blat=blat,blon=blon)  ## this is dirty, defined above but out of imov loop
     588                        x, y = m(lon2d, lat2d)                                         ## this is dirty, defined above but out of imov loop
    526589                    if typefile in ['meso'] and mapmode == 1:   what_I_plot_frame = dumpbdy(what_I_plot_frame,6,condition=True)
    527590#                   if typefile in ['mesoideal']:    what_I_plot_frame = dumpbdy(what_I_plot_frame,0,stag='W',condition=dumped_vert_stag)
    528591
    529592                    if which == "unidim":
    530                         if lbls is not None: lbl=lbls[nplot-1]
     593#                        if lbls is not None: lbl=lbls[nplot-1]
     594                        if lbls is not None: lbl=lbls[index_f]
    531595                        else:
    532596                           lbl = ""
    … …  
    549613                        if indextime is None and axtime is not None and xlab is None:    xlabel(axtime.upper()) ## define the right label
    550614                        if save == 'txt':  writeascii(np.transpose([x,np.transpose(what_I_plot)]),'profile'+str(nplot*1000+imov)+'.txt')
     615
     616                    elif which == "xy":
     617                        if lbls is not None: lbl=lbls[index_f]
     618                        else: lbl=None
     619                        if analysis is not None:
     620                           if analysis == 'histo':
     621                               if zelen == 1:
     622                                  mpl.pyplot.hist(ploty.flatten(),bins=ndiv,normed=True, alpha=0.67, facecolor = 'green', label = lbls)
     623                                  mpl.pyplot.legend()
     624                                  mpl.pyplot.grid(True)
     625                                  mpl.pyplot.title(zetitle)
     626                               else:
     627                                  multiplot[index_f]=ploty.flatten()
     628                                  if index_f == zelen-1:
     629                                     if ope is not None: multiplot = getVar(multiplot,3*np.arange((index_f+1)/3)+2) ## we only compute histograms for the operation plots
     630                                     mpl.pyplot.hist(multiplot,bins=ndiv,normed=True, alpha=0.75, label = lbls)
     631                                     mpl.pyplot.legend()
     632                                     mpl.pyplot.grid(True)
     633                                     mpl.pyplot.title(zetitle)
     634                           elif analysis in ['density','histodensity']:
     635                                  if ope is not None and (index_f+1)%3 !=0: pass
     636                                  else:
     637                                     plotx = np.linspace(min(ploty.flatten()),max(ploty.flatten()),1000)
     638                                     density = gaussian_kde(ploty.flatten())
     639   #                                  density.covariance_factor = lambda : .25  # adjust the covariance factor to change the bandwidth if needed
     640   #                                  density._compute_covariance()
     641                                        # display the mean and variance of the kde:
     642                                     sample = density.resample(size=20000)
     643                                     n, (smin, smax), sm, sv, ss, sk = describe(sample[0])
     644                                     mpl.pyplot.plot(plotx,density(plotx), label = lbl+'\nmean: '+str(sm)[0:5]+'   std: '+str(np.sqrt(sv))[0:5]+'\nskewness: '+str(ss)[0:5]+'   kurtosis: '+str(sk)[0:5])
     645                                     if analysis == 'histodensity':  # plot both histo and density (to assess the rightness of the kernel density estimate for exemple) and display the estimated variance
     646                                        mpl.pyplot.hist(ploty.flatten(),bins=ndiv,normed=True, alpha=0.30, label = lbl)
     647                                     if index_f == zelen-1: mpl.pyplot.legend() ; mpl.pyplot.title(zetitle)
     648                           else:
     649                              plot(plotx,ploty,label = lbl)
     650                              if index_f == zelen-1: mpl.pyplot.legend() ; mpl.pyplot.title(zetitle)
     651                              mpl.pyplot.grid(True)
     652                        else:
     653                           plot(plotx,ploty,label = lbl)
     654                           if index_f == zelen-1: mpl.pyplot.legend() ; mpl.pyplot.title(zetitle)
     655                        if varname == 'hodograph':
     656                            a=0
     657                            for ii in np.arange(len(time)):
     658                               if a%6 == 0: mpl.pyplot.text(plotx[ii],ploty[ii],time[ii])
     659                               a=a+1
     660                            mpl.pyplot.grid(True)
    551661
    552662                    elif which == "regular":
    … …  
    590700
    591701                        if colorb not in ['nobar','onebar']:       
    592                             if (fileref is not None) and (index_f == numplot-1):   daformat = "%.3f"
     702                            if (fileref is not None) and ((index_f+1)%3 == 0):   daformat = "%.3f"
    593703                            elif mult != 1:                                        daformat = "%.1f"
    594704                            else:                                                  daformat = fmtvar(fvar.upper())
    … …  
    614724                                                              #200.         ## or csmooth=stride
    615725                        ### THIS IS A QUITE SPECIFIC PIECE (does not work for mesoscale files)
    616                         if ope == '-' and nplot == numplot: # this should work as long as ope is '-' guarantees 3 plots for 4 panels without contour
     726                        if ope == '-_histo' and nplot == numplot: # this should work as long as ope is '-' guarantees 3 plots for 4 panels without contour
    617727                            subplot(subv,subh,nplot+1)
    618728                            rcParams["legend.fontsize"] = 'xx-large'
    … …  
    632742                            plot(zebins, zegauss, linewidth=1, color='r',label="mean: "+str(zemean)[0:5]+"\nstd: "+str(zestd)[0:5])
    633743                            legend(loc=0,frameon=False)
    634                             title("Histogram fig(1) "+ope+" fig(2)")
    635744                            subplot(subv,subh,nplot) # go back to last plot for title of contour difference
     745                        if ope is not None and "only" not in ope: title("fig(1) "+ope+" fig(2)")
     746                        elif ope is not None and "only" in ope: title("fig(1) "+ope[0]+" fig(2)")
    636747                           
    637748                    elif which == "contour":
    … …  
    647758                        if mapmode == 0:   
    648759                            what_I_plot_frame, x, y = define_axis( lonyeah,latyeah,vert,time,indexlon,indexlat,indexvert,\
    649                                                               itime,what_I_plot_frame, len(all_var2[index_f].shape),vertmode )
     760                                                              itime,what_I_plot_frame, len(all_var2[index_f].shape),vertmode,redope)
    650761                            ## is this needed? only if len(all_var2[index_f].shape) != len(all_var[index_f].shape)
    651762                            cs = contour( x,y,what_I_plot_frame, zelevels, colors='k', linewidths = 0.33)#, alpha=0.5, linestyles='solid')
    … …  
    655766                            cs = m.contour( x,y,what_I_plot_frame, zelevels, colors='k', linewidths = 0.33)#, alpha=0.5, linestyles='solid')
    656767                            #clabel(cs, inline=0, fontsize = rcParams['font.size'], fmt="%.0f") #fmtvar(var2.upper()))
    657                     if which in ["regular","unidim"]:
    658 
    659                         if nplot > 1 and which == "unidim":
     768                    if which in ["regular","unidim","xy"]:
     769
     770                        if nplot > 1 and which in ["unidim","xy"]:
    660771                           pass  ## because we superimpose nplot instances
    661772                        else:
    … …  
    666777                           if zymin is not None: mpl.pyplot.ylim(ymin=zymin)
    667778                           if zymax is not None: mpl.pyplot.ylim(ymax=zymax)
    668                            if ylog:      mpl.pyplot.semilogy()
     779                           if ylog and not xlog:      mpl.pyplot.semilogy()
     780                           if xlog and not ylog:      mpl.pyplot.semilogx()
     781                           if xlog and ylog:
     782                                mpl.pyplot.xscale('log')
     783                                mpl.pyplot.yscale('log')
    669784                           if invert_y:  ax = mpl.pyplot.gca() ; ax.set_ylim(ax.get_ylim()[::-1])
    670785                           if xlab is not None: xlabel(xlab)
    … …  
    715830       else:
    716831            if fileref is not None:
    717                 if index_f is numplot-1:     plottitle = basename+' '+"fig(1) "+ope+" fig(2)"
    718                 elif index_f is numplot-2:   plottitle = basename+' '+fileref
    719                 else:                        plottitle = basename+' '+all_namefile[index_f]
     832               if (index_f+1)%3 == 0:     plottitle = basename+' '+"fig(1) "+ope+" fig(2)"
     833               elif (index_f+2)%3 == 0:   plottitle = basename+' '+fileref
     834               else:                        plottitle = basename+' '+all_namefile[index_f]
    720835            else:                            plottitle = basename+' '+all_namefile[index_f]
    721836       if mult != 1:                         plottitle = '{:.0e}'.format(mult) + "*" + plottitle
    … …  
    724839          else: plottitle = zetitle[0]
    725840          if titleref is "fill":             titleref=zetitle[index_f]
    726           if fileref is not None:
    727              if index_f is numplot-2:        plottitle = titleref
    728              if index_f is numplot-1:        plottitle = "fig(1) "+ope+" fig(2)"
     841          if fileref is not None and which != "xy":
     842             if (index_f+2)%3 == 0:        plottitle = titleref
     843             if (index_f+1)%3 == 0:        plottitle = "fig(1) "+ope+" fig(2)"
    729844#       if indexlon is not None:      plottitle = plottitle + " lon: " + str(min(lon[indexlon])) +" "+ str(max(lon[indexlon]))
    730845#       if indexlat is not None:      plottitle = plottitle + " lat: " + str(min(lat[indexlat])) +" "+ str(max(lat[indexlat]))
    … …  
    734849       if nplot >= numplot: error = True
    735850       nplot += 1
     851
     852       if len(namefiles) > 1 and len(var) == 1 and which == "unidim": index_f=index_f+1
     853       firstpass=False
    736854
    737855    if colorb == "onebar":
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