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source: trunk/UTIL/PYTHON/planetoplot_v1/planetoplot.py @ 1062

Last change on this file since 1062 was 943, checked in by aslmd, 12 years ago
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Rev	Line
[349]	1	#######################
	2	##### PLANETOPLOT #####
	3	#######################
[345]	4
[349]	5	### A. Spiga -- LMD -- 06~09/2011 -- General building and mapping capabilities
	6	### T. Navarro -- LMD -- 10~11/2011 -- Improved use for GCM and added sections + 1Dplot capabilities
[392]	7	### A. Colaitis -- LMD -- 11/2011 -- Mostly minor improvements and inter-plot operation capabilities + zrecast interpolation for gcm
[448]	8	### A. Spiga -- LMD -- 11~12/2011 -- Extended multivar subplot capabilities + cosmetic changes + general cleaning and tests
[435]	9	### A. Colaitis -- LMD -- 12/2011 -- Added movie capability [mencoder must be installed]
[475]	10	### A. Spiga -- LMD -- 12/2011 -- Added HTML animated page capability + general tests of consistency [winds, etc...] + consistent generic movie loop
[525]	11	### J. Leconte -- LMD -- 02/2012 -- Added area weighted averaging. Compatibility with terrestrial gcm.
[579]	12	### A. Spiga -- LMD -- 03/2012 -- Cleaning and improved comments
[725]	13	### T. Navarro -- LMD -- 04/2012 -- Added capabilities (e.g. histograms for difference maps)
	14	### A. Colaitis -- LMD -- 05~06/2012 -- Added capabilities for analysis of mesoscale files (wind speed, etc...)
	15	### A. Spiga -- LMD -- 04~07/2012 -- Added larger support of files + planets. Corrected a few bugs. Cleaning and improved comments
[781]	16	### A. Colaitis -- LMD -- 08/2012 -- Added functionalities for further analysis: spectra, hodographs, etc... plus improved flexibility (e.g. grid)
[725]	17
[345]	18	def planetoplot (namefiles,\
[351]	19	level=0,\
[350]	20	vertmode=0,\
[345]	21	proj=None,\
	22	back=None,\
	23	target=None,
	24	stride=3,\
	25	var=None,\
[760]	26	clb=None,\
[399]	27	winds=False,\
[345]	28	addchar=None,\
	29	vmin=None,\
	30	vmax=None,\
	31	tile=False,\
	32	zoom=None,\
	33	display=True,\
	34	hole=False,\
	35	save="gui",\
	36	anomaly=False,\
	37	var2=None,\
	38	ndiv=10,\
	39	mult=1.,\
[865]	40	add=0.,\
[578]	41	zetitle=["fill"],\
[345]	42	slon=None,\
	43	slat=None,\
	44	svert=None,\
[359]	45	stime=None,\
	46	outputname=None,\
	47	resolution=200,\
	48	ope=None,\
	49	fileref=None,\
	50	minop=0.,\
	51	maxop=0.,\
[363]	52	titleref="fill",\
[369]	53	invert_y=False,\
	54	xaxis=[None,None],\
[372]	55	yaxis=[None,None],\
[382]	56	ylog=False,\
[763]	57	xlog=False,\
[385]	58	yintegral=False,\
[388]	59	blat=None,\
[451]	60	blon=None,\
[418]	61	tsat=False,\
[430]	62	flagnolow=False,\
[444]	63	mrate=None,\
[453]	64	mquality=False,\
[457]	65	trans=1,\
[468]	66	zarea=None,\
[483]	67	axtime=None,\
[502]	68	redope=None,\
[507]	69	seevar=False,\
[502]	70	xlab=None,\
[569]	71	ylab=None,\
[612]	72	lbls=None,\
	73	lstyle=None,\
[647]	74	cross=None,\
[792]	75	markdevil=False,\
[721]	76	facwind=1.,\
[760]	77	trycol=False,\
[763]	78	streamflag=False,\
[817]	79	nocolorb=False,\
[876]	80	analysis=None,\
	81	monster=False):
[345]	82
	83	####################################################################################################################
	84	### Colorbars http://www.scipy.org/Cookbook/Matplotlib/Show_colormaps?action=AttachFile&do=get&target=colormaps3.png
	85
	86	#################################
	87	### Load librairies and functions
[876]	88	import netCDF4
	89
[363]	90	import matplotlib as mpl
[876]	91	import matplotlib.pyplot
	92	import matplotlib.cm
[865]	93	from mpl_toolkits.basemap import cm
[876]	94	if mrate is not None: from videosink import VideoSink
	95
[345]	96	import numpy as np
	97	from numpy.core.defchararray import find
[876]	98	import scipy
	99	if analysis in ['laplace']: import scipy.ndimage.laplace as laplace
	100
	101	import itertools
	102	import os
	103
	104	import myplot
	105	from mymath import deg,max,min,mean,writeascii,fig2data,fig2img
[673]	106	from times import sol2ls
[490]	107	#from singlet import singlet
[359]	108
[865]	109
[579]	110	#########################
	111	### PRELIMINARY STUFF ###
	112	#########################
	113	### we say hello
[392]	114	print "********************************************"
	115	print "******** WELCOME TO PLANETOPLOT ********"
	116	print "********************************************"
[876]	117	if monster:
	118	print "******* SPEED MODE. EXPERIMENTAL. ******"
	119	print "********************************************"
[896]	120	### we ensure namefiles and var are arrays and we get their size
[392]	121	if not isinstance(namefiles, np.ndarray): namefiles = [namefiles]
	122	if not isinstance(var, np.ndarray): var = [var]
[896]	123	zelenfile = len(namefiles) ; zelenvar = len(var)
	124	### we check colorbars options (including trycol i.e. the user wants to try a set of colorbars)
	125	if trycol: clb = ["Greys","Blues","YlOrRd","jet","spectral","hot","RdBu","RdYlBu","Paired"] ; zetitle = clb ; var = [var[0]]*9 ; zelenvar = len(var)
	126	if clb is None: clb = ["def"]*zelenvar
	127	elif len(clb) < zelenvar: clb = [clb[0]]*zelenvar ; print "WARNING: less color than vars! setting all to 1st value."
[579]	128	### we initialize a few variables
	129	initime=-1 ; sslon = None ; sslat = None
[760]	130	k = 0 ; firstfile = True ; count = 0
	131	### we perform sanity checks and correct for insufficient information
[582]	132	if slon is not None: sslon = np.zeros([1,2])
	133	if slat is not None: sslat = np.zeros([1,2])
[865]	134	if redope is not None and winds: winds=False ; print "WARNING: no winds with redope. setting winds to False."
[579]	135	### we avoid specific cases not yet implemented
[896]	136	if mrate is not None and zelenvar > 1: myplot.errormess("multivar not allowed in movies. should be fixed soon!")
[760]	137	### we prepare number of plot fields [zelen] and number of plot instances [numplot] according to user choices
[579]	138	### --> we support multifile and multivar plots : files + vars separated by commas are on the same figure
[876]	139	nlon, nlat, nvert, ntime, mapmode, nslices = myplot.determineplot(slon, slat, svert, stime, redope)
[896]	140	zelen = zelenfile*zelenvar
[876]	141	if (nslices > 1 and monster): myplot.errormess("multislice + monster not supported yet. to be done soon")
[864]	142	### we have a special mode obtained by -p noproj in which lat/lon plots are just flat 2D plots
	143	if proj == "noproj": mapmode = 0
[763]	144	### we correct number of plot fields for possible operation (substract, etc...)
	145	if ope is not None:
[896]	146	if fileref is not None: zelen = 3zelenvarzelenfile
[763]	147	elif "var" in ope: zelen = zelen + 1
[424]	148	numplot = zelen*nslices
[896]	149	print "********** FILES, SLICES, VARS, TOTAL PLOTS: ", zelenfile, nslices, zelenvar, numplot
[579]	150	print "********** MAPMODE: ", mapmode
	151	### we define the arrays for plot fields -- which will be placed within multiplot loops
[763]	152	all_var = [[]]zelen ; all_var2 = [[]]zelen
	153	all_title = [[]]zelen ; all_varname = [[]]zelen ; all_namefile = [[]]zelen ; all_colorb = [[]]zelen
	154	all_time = [[]]zelen ; all_vert = [[]]zelen ; all_lat = [[]]zelen ; all_lon = [[]]zelen
[579]	155	all_windu = [[]]zelen ; all_windv = [[]]zelen
[763]	156	plot_x = [[]]zelen ; plot_y = [[]]zelen ; multiplot = [[]]*zelen
	157	### tool (should be move to mymath)
	158	getVar = lambda searchList, ind: [searchList[i] for i in ind]
[579]	159	#############################
	160	### LOOP OVER PLOT FIELDS ###
	161	#############################
[876]	162
[896]	163	for nnn in range(zelenfile):
	164	for vvv in range(zelenvar):
[392]	165
[579]	166	### we load each NETCDF objects in namefiles
[468]	167	namefile = namefiles[nnn]
[876]	168	nc = netCDF4.Dataset(namefile)
[579]	169	### we explore the variables in the file
[507]	170	varinfile = nc.variables.keys()
[748]	171	if seevar: print varinfile ; exit()
[579]	172	### we define the type of file we have (gcm, meso, etc...)
[876]	173	typefile = myplot.whatkindfile(nc)
[579]	174	if firstfile: typefile0 = typefile
[876]	175	elif typefile != typefile0: myplot.errormess("Not the same kind of files !", [typefile0, typefile])
[718]	176	### we care for input file being 1D simulations
	177	is1d=999
[876]	178	if "longitude" in nc.dimensions and "latitude" in nc.dimensions: is1d = len(nc.dimensions["longitude"])*len(nc.dimensions["latitude"])
	179	elif "lon" in nc.dimensions and "lat" in nc.dimensions: is1d = len(nc.dimensions["lon"])*len(nc.dimensions["lat"])
[637]	180	if typefile in ['gcm','earthgcm'] and is1d == 1: mapmode=0 ; winds=False
[579]	181	### we create default vert and time prescriptions if not here in case mapping mode is on (lat/lon maps)
[548]	182	if redope is None and mapmode == 1:
[876]	183	if svert is None: svert = myplot.readslices(str(level)) ; nvert=1
[477]	184	if stime is None and mrate is None:
[876]	185	stime = myplot.readslices(str(0)) ; ntime=1 ## this is a default choice
[477]	186	print "WELL... nothing about time axis. I took default: first time reference stored in file."
[579]	187	### we get the names of variables to be read. in case only one available, we choose this one.
[725]	188	### (we take out of the test specific names e.g. UV is not in the file but used to ask a wind speed computation)
[876]	189	varname = myplot.select_getfield(zvarname=var[vvv],znc=nc,ztypefile=typefile,mode='check')
[579]	190	### we get the names of wind variables to be read (if any)
[349]	191	if winds:
[876]	192	[uchar,vchar,metwind] = myplot.getwinddef(nc)
[345]	193	if uchar == 'not found': winds = False
[579]	194	### we tell the user that either no var or no wind is not acceptable
[876]	195	if not varname and not winds: myplot.errormess("please set at least winds or var",printvar=nc.variables)
[579]	196	### we get the coordinates lat/lon to be used
[876]	197	[lon2d,lat2d] = myplot.getcoorddef(nc)
[579]	198	### we get an adapted map projection if none is provided by the user
[876]	199	if proj == None: proj = myplot.getproj(nc)
[579]	200	### we define plot boundaries given projection or user choices
[489]	201	if firstfile:
[876]	202	if proj in ["npstere","spstere"]: [wlon,wlat] = myplot.polarinterv(lon2d,lat2d)
	203	elif proj in ["lcc","laea"]: [wlon,wlat] = myplot.wrfinterv(lon2d,lat2d)
	204	else: [wlon,wlat] = myplot.simplinterv(lon2d,lat2d)
	205	if zoom: [wlon,wlat] = myplot.zoomset(wlon,wlat,zoom)
	206	elif zarea is not None: [wlon,wlat] = myplot.latinterv(area=zarea)
[489]	207
[725]	208	#############################################################
	209	############ WE LOAD 4D DIMENSIONS : x, y, z, t #############
	210	#############################################################
	211
[781]	212	###should be available for GCM or simple files ?
	213	##if ope in ["cat"] and nnn > 0: count = time[-1] + 1 ## so that a cat is possible with simple subscripts
	214
[725]	215	### TYPE 1 : GCM files or simple files
[558]	216	if typefile in ["gcm","earthgcm","ecmwf"]:
[725]	217	### this is needed for continuity
[610]	218	if slon is not None: sslon = slon
	219	if slat is not None: sslat = slat
[725]	220	### we define lat/lon vectors. we get what was done in getcoorddef.
[735]	221	lat = lat2d[:,0] ; lon = lon2d[0,:]
[725]	222	### we define areas. this is needed for calculate means and weight with area. this is not compulsory (see reduce_field).
	223	if "aire" in nc.variables: area = nc.variables["aire"][:,:]
	224	### --> add a line here if your reference is not present
	225	else: area = None
	226	### we define altitude vector. either it is referenced or it is guessed based on last variable's dimensions.
[721]	227	if "altitude" in nc.variables: vert = nc.variables["altitude"][:]
	228	elif "Alt" in nc.variables: vert = nc.variables["Alt"][:]
	229	elif "lev" in nc.variables: vert = nc.variables["lev"][:]
	230	elif "presnivs" in nc.variables: vert = nc.variables["presnivs"][:]
[725]	231	### --> add a line here if your reference is not present
[724]	232	else:
[876]	233	dadim = myplot.getdimfromvar(nc) ; print "No altitude found. Try to build a simple axis.",dadim
[724]	234	if len(dadim) == 4: print "-- 4D field. Assume z is dim 2." ; vert = np.arange(dadim[-3])
	235	elif len(dadim) == 3: print "-- 3D field. Assume z is dim 1." ; vert = [0.]
[725]	236	else: vert = [0.]
	237	### we define time vector. either it is referenced or it is guessed based on last variable's dimensions.
[876]	238	if "Time" in nc.variables: letime = "Time"
	239	elif "time_counter" in nc.variables: letime = "time_counter"
	240	elif "time" in nc.variables: letime = "time"
[725]	241	### --> add a line here if your reference is not present
[876]	242	else: letime = None
	243	if letime is not None:
	244	if monster:
	245	### very long simulation... we just retrieve 3 values for time
	246	timelength = len(nc.dimensions[letime])
	247	dafirst = nc.variables[letime][0]
	248	dalast = nc.variables[letime][timelength-1]
	249	step = nc.variables[letime][1] - dafirst
	250	time = np.arange(dafirst,dalast,step)
[886]	251	print "Time (start,stop,nvalues)",dafirst,dalast,timelength
[876]	252	else:
	253	### if the time record is not too long, what follows is pretty quick
	254	time = nc.variables[letime][:]
[724]	255	else:
	256	print "No time found. Try to build a simple axis. Assume t is dim 1."
[876]	257	dadim = myplot.getdimfromvar(nc)
[724]	258	if len(dadim) == 4: time = np.arange(dadim[-4])
	259	elif len(dadim) == 3: time = np.arange(dadim[-3])
[876]	260	else: time = [0.] #myplot.errormess("no time axis found.")
	261	### (SPECIFIC?)
	262	if "time_counter" in nc.variables: time = time / 86400. #### convert from s to days
[725]	263	### (SPECIFIC. convert to Ls for Martian GCM files.)
[640]	264	if axtime in ["ls"]:
	265	print "converting to Ls ..."
	266	for iii in range(len(time)):
[673]	267	time[iii] = sol2ls(time[iii])
[640]	268	if iii > 0:
[725]	269	while abs(time[iii]-time[iii-1]) > 300: time[iii] = time[iii]+360
	270	### (a case where the user would like to set local times. e.g. : 1D plot with no longitude reference)
[494]	271	if axtime in ["lt"]:
	272	if initime == -1: initime=input("Please type initial local time:")
[725]	273	time = (initime+time*24)%24 ; print "LOCAL TIMES.... ", time
[822]	274	### (simply ask for subscript)
	275	if axtime in ["ind"]:
[876]	276	dadim = myplot.getdimfromvar(nc)
[822]	277	if len(dadim) == 4: time = np.arange(dadim[-4])
	278	elif len(dadim) == 3: time = np.arange(dadim[-3])
	279	elif len(dadim) == 2: time = np.arange(dadim[-2])
[725]	280
	281	### TYPE 2 : MESOSCALE FILES
[548]	282	elif typefile in ['meso','geo']:
[725]	283	### area not active with mesoscale files
	284	area = None
	285	### HACK TO GET THE CORRECT LAT/LON FROM MESOSCALE FILES WITH 2D LAT/LON ARRAYS
	286	### principle: calculate correct indices then repopulate slon and slat
[490]	287	if slon is not None or slat is not None:
[725]	288	show_topo_map_user = ((save == 'png') and (typefile == 'meso') and ("HGT" in varinfile) and display)
[866]	289	#show_topo_map_user = False
[725]	290	if firstfile and show_topo_map_user: iwantawhereplot = nc #show a topo map with a cross on the chosen point
	291	else: iwantawhereplot = None #do not show anything, just select indices
[490]	292	numlon = 1 ; numlat = 1
[610]	293	if slon is not None: numlon = slon.shape[1]
	294	if slat is not None: numlat = slat.shape[1]
[490]	295	indices = np.ones([numlon,numlat,2]) ; vlon = None ; vlat = None
	296	for iii in range(numlon):
	297	for jjj in range(numlat):
[610]	298	if slon is not None: vlon = slon[0][iii] ### note: slon[:][0] does not work
	299	if slat is not None: vlat = slat[0][jjj] ### note: slon[:][0] does not work
[876]	300	indices[iii,jjj,:] = myplot.bidimfind(lon2d,lat2d,vlon,vlat,file=iwantawhereplot)
[490]	301	lonp,latp = ( lon2d[indices[iii,jjj,0],indices[iii,jjj,1]] , lat2d[indices[iii,jjj,0],indices[iii,jjj,1]] )
[587]	302	### possible bug here if several --lat
[490]	303	for iii in range(numlon):
	304	for jjj in range(numlat):
[610]	305	if slon is not None: sslon[0][iii] = indices[iii,0,1] #...this is idx
	306	if slat is not None: sslat[0][jjj] = indices[0,jjj,0] #...this is idy
[490]	307	lonp,latp = ( lon2d[indices[0,0,0],indices[0,0,1]] , lat2d[indices[0,0,0],indices[0,0,1]] )
[725]	308	### we get rid of boundary relaxation zone for plots. important to do that now and not before.
[864]	309	if (typefile in ['meso'] and mapmode == 1):
[876]	310	if '9999' not in getattr(nc,'START_DATE'): lon2d = myplot.dumpbdy(lon2d,6) ; lat2d = myplot.dumpbdy(lat2d,6)
[725]	311	### we read the keyword for vertical dimension. we take care for vertical staggering.
[393]	312	if varname in ['PHTOT','W']: vertdim='BOTTOM-TOP_PATCH_END_STAG'
	313	else: vertdim='BOTTOM-TOP_PATCH_END_UNSTAG'
[490]	314	if (var2 is not None and var2 not in ['PHTOT','W']): dumped_vert_stag=True ; vertdim='BOTTOM-TOP_PATCH_END_UNSTAG'
	315	else: dumped_vert_stag=False
[725]	316	### we read the keyword for horizontal dimensions. we take care for horizontal staggering.
[393]	317	if varname in ['V']: latdim='SOUTH-NORTH_PATCH_END_STAG'
	318	else: latdim='SOUTH-NORTH_PATCH_END_UNSTAG'
	319	if varname in ['U']: londim='WEST-EAST_PATCH_END_STAG'
	320	else: londim='WEST-EAST_PATCH_END_UNSTAG'
[402]	321	lon = np.arange(0,getattr(nc,londim),1) ; lat = np.arange(0,getattr(nc,latdim),1)
[725]	322	### we define the time axis and take care of various specificities (lt, ls, sol) or issues (concatenation)
[468]	323	if axtime in ["ls","sol"]:
[876]	324	lstab, soltab, lttab = myplot.getlschar ( namefile, getaxis = True )
[468]	325	if axtime == "ls": time = lstab
	326	elif axtime == "sol": time = soltab
	327	else:
[665]	328	if ope in ["cat"] and nnn > 0: count = time[-1] + 1 ## so that a cat is possible with simple subscripts
	329	else: count = 0
[613]	330	if "Times" in nc.dimensions: time = count + np.arange(0,len(nc.dimensions["Times"]),1)
	331	elif "Time" in nc.dimensions: time = count + np.arange(0,len(nc.dimensions["Time"]),1)
	332	else: time = count + np.arange(0,1,1)
[489]	333	if axtime in ["lt"]:
[569]	334	ftime = np.zeros(len(time))
[876]	335	for i in range(len(time)): ftime[i] = myplot.localtime ( time[i], slon , namefile )
	336	time=ftime ; time = myplot.check_localtime(time)
[489]	337	print "LOCAL TIMES.... ", time
[725]	338	### we define the vertical axis (or lack thereof) and cover possibilities for it to be altitude, pressure, geopotential. quite SPECIFIC.
[876]	339	if typefile in ['geo']: vert = [0.] ; stime = myplot.readslices(str(0))
[426]	340	else:
	341	if vertmode is None: vertmode=0
[687]	342	if vertmode == 0:
	343	if "vert" in nc.variables: vert = nc.variables["vert"][:]/1000. ; vertmode = 1
	344	else: vert = np.arange(0,getattr(nc,vertdim),1)
[562]	345	elif vertmode == -1: vert = nc.variables["PHTOT"][0,:,0,0]/3.72 ; vert = np.array(vert[0:len(vert)-1]) #; print vert
[610]	346	elif vertmode == 1 or vertmode == 2: vert = nc.variables["vert"][:] ## pressure in Pa
	347	else: vert = nc.variables["vert"][:]/1000. ## altitude in km
[725]	348	####################################################################
	349	############ END of WE LOAD 4D DIMENSIONS : x, y, z, t #############
	350	####################################################################
[345]	351
[876]	352
[760]	353	### we fill the arrays of varname, namefile, time, colorbar at the current step considered (NB: why use both k and nnn ?)
[402]	354	all_varname[k] = varname
	355	all_namefile[k] = namefile
[760]	356	all_colorb[k] = clb[vvv]
[763]	357
[876]	358	##############################################################################
	359	##### LARGE FILE. WE'D BETTER NOT FILL THE MEMORY WITH THE STUPID WHOLE ARRAY!
	360	if monster:
	361	####################################################################
	362	## get all indexes to be taken into account for this subplot and then reduce field
	363	## 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
	364	if ope is not None:
[896]	365	if fileref is not None: index_f = (k//(nlonnlatnvertntime))%(3zelenfile) ## OK only 1 var, see test in the beginning
	366	elif "var" in ope: index_f = (k//(nlonnlatnvert*ntime))%(zelenvar+1) ## OK only 1 file, see test in the beginning
[876]	367	elif "cat" in ope: index_f = 0
	368	elif not (k == 0):
[896]	369	#if zelenfile > 1 and zelenvar == 1 and which == "unidim": pass ## TROUVER UN MOYEN POUR unidim
	370	if zelenfile > 1 and zelenvar == 1: pass
	371	else: yeah = zelenfilezelenvar ; index_f = (k//(nlonnlatnvertntime))%yeah
	372	else: yeah = zelenfilezelenvar ; index_f = (k//(nlonnlatnvertntime))%yeah
[876]	373
	374	ilon = myplot.getsindex(sslon,k%nlon,lon)
	375	ilat = myplot.getsindex(sslat,(k//nlon)%nlat,lat)
	376	ivert = myplot.getsindex(svert,(k//(nlon*nlat))%nvert,vert)
	377
	378	if mrate is not None: itime = None
	379	else: itime = myplot.getsindex(stime,(k//(nlonnlatnvert))%ntime,time)
	380	ltst = None
	381	if typefile in ['meso'] and itime is not None and len(itime) < 2: ltst = myplot.localtime ( itime, slon , all_namefile[index_f] )
	382
	383	if ilat is not None: print "********** LAT : INDEX",ilat[0], ilat[-1], "VALUE",lat[ilat[0]], lat[ilat[-1]]
	384	else: ilat = range(len(lat))
	385	if ilon is not None: print "********** LON : INDEX",ilon[0], ilon[-1], "VALUE",lon[ilon[0]], lon[ilon[-1]]
	386	else: ilon = range(len(lon))
	387	if ivert is not None: print "********** VERT: INDEX",ivert[0], ivert[-1], "VALUE",vert[ivert[0]], vert[ivert[-1]]
	388	else: ivert = range(len(vert))
	389	if itime is not None: print "********** TIME: INDEX",itime[0], itime[-1], "VALUE",time[itime[0]], time[itime[-1]]
	390	else: itime = range(len(time))
	391
	392	all_var[k] = myplot.getfieldred(nc,all_varname[k],ilon,ilat,ivert,itime)
	393	if var2: all_var2[k] = myplot.getfieldred(nc,var2,ilon,ilat,ivert,itime)
	394	if winds:
	395	all_windu[k] = myplot.getfield(nc,uchar,ilon,ilat,ivert,itime)
	396	all_windv[k] = myplot.getfield(nc,vchar,ilon,ilat,ivert,itime)
	397	plot_x[k] = None ; plot_y[k] = None
[877]	398
	399	all_time[k] = time[itime]
	400	all_vert[k] = vert[ivert]
	401	all_lat[k] = lat[ilat]
	402	all_lon[k] = lon[ilon]
[876]	403
	404	else:
	405	## regular stuff: not large array.
	406	all_time[k] = time
	407	all_vert[k] = vert
	408	all_lat[k] = lat
	409	all_lon[k] = lon
	410	if var2: all_var2[k], plot_x[k], plot_y[k] = myplot.select_getfield(zvarname=var2,znc=nc,ztypefile=typefile,\
	411	mode='getvar',ztsat=tsat,ylon=all_lon[k],ylat=all_lat[k],yalt=all_vert[k],ytime=all_time[k],analysis=analysis)
	412	if winds: all_windu[k] = myplot.getfield(nc,uchar) ; all_windv[k] = myplot.getfield(nc,vchar)
	413	### we fill the arrays of fields to be plotted at the current step considered
	414	all_var[k], plot_x[k], plot_y[k] = myplot.select_getfield(zvarname=all_varname[k],znc=nc,ztypefile=typefile,\
	415	mode='getvar',ztsat=tsat,ylon=all_lon[k],ylat=all_lat[k],yalt=all_vert[k],ytime=all_time[k],analysis=analysis)
	416	####################################################################
	417
[763]	418	# last line of for namefile in namefiles
[468]	419	print "**** GOT SUBDATA:",k," NAMEFILE:",namefile," VAR:",varname, var2 ; k += 1 ; firstfile = False
[345]	420
[725]	421	### note to self : stopped comment rewriting here.
	422
[359]	423	##################################
[763]	424	### Operation on files (I) with _var
	425	if ope is not None and "var" in ope:
	426	print "********** OPERATION: ",ope
[896]	427	if zelenfile > 1: myplot.errormess("for this operation... please set only one file !")
	428	if zelenvar > 2: myplot.errormess("not sure this works for more than 2 vars... please check.")
[763]	429	if "div_var" in ope: all_var[k] = all_var[k-2] / all_var[k-1] ; insert = '_div_'
	430	elif "mul_var" in ope: all_var[k] = all_var[k-2] * all_var[k-1] ; insert = '_mul_'
	431	elif "add_var" in ope: all_var[k] = all_var[k-2] + all_var[k-1] ; insert = '_add_'
	432	elif "sub_var" in ope: all_var[k] = all_var[k-2] - all_var[k-1] ; insert = '_sub_'
[876]	433	else: myplot.errormess(ope+" : non-implemented operation. Check pp.py --help")
[763]	434	plot_x[k] = None ; plot_y[k] = None
	435	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]
	436	all_varname[k] = all_varname[k-2] + insert + all_varname[k-1]
	437	if len(clb) >= zelen: all_colorb[k] = clb[-1] # last additional user-defined color is for operation plot
	438	else: all_colorb[k] = all_colorb[k-1] # if no additional user-defined color... set same as var
	439	### only the operation plot. do not mention colorb so that it is user-defined?
	440	if "only" in ope:
	441	numplot = 1 ; all_var[0] = all_var[k]
	442	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]
	443	all_varname[0] = all_varname[k-2] + insert + all_varname[k-1]
[721]	444
[763]	445	if ope is not None and "var" not in ope:
	446	print "********** OPERATION: ",ope
[896]	447	if zelenvar > 1: myplot.errormess("for this operation... please set only one var !")
	448	if fileref is None and ope not in ['cat']: myplot.errormess("fileref is missing!")
	449	################################## this is terribly complex for the main program file. got to do something about this
	450	### Operation on files (II) without _var
	451	# we re-iterate on the plots to set operation subplots to make it compatible with multifile (using the same ref file)
	452	# (k+1)%3==0 is the index of operation plots
	453	# (k+2)%3==0 is the index of reference plots
	454	# (k+3)%3==0 is the index of first plots
	455	opefirstpass=True
[763]	456	for k in np.arange(zelen):
	457	if ope in ["-","+","-%","-_only","+_only","-%_only","-_histo"]:
[896]	458	ncref = netCDF4.Dataset(fileref)
[763]	459
	460	if opefirstpass: ## first plots
[896]	461	for ll in np.arange(zelenfile):
[763]	462	print "SETTING FIRST PLOT"
[896]	463	myplot.alltransfer(3*ll,ll,all_varname,all_time,all_vert,all_lat,all_lon,all_namefile,all_var2,all_colorb,all_var)
[763]	464	if plot_y[ll] is not None: plot_y[3ll] = plot_y[ll] ; plot_x[3ll] = plot_x[ll]
	465	else: plot_y[3ll] = None ; plot_x[3ll] = None
	466	opefirstpass=False
	467
	468	if (k+2)%3==0: ## reference plots
	469	print "SETTING REFERENCE PLOT"
[896]	470	myplot.alltransfer(k,k-1,all_varname,all_time,all_vert,all_lat,all_lon,all_namefile,all_var2,all_colorb,all_var)
	471	### all_var is actually overwritten here
[876]	472	all_var[k], plot_x[k], plot_y[k] = myplot.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)
	473	if winds: all_windu[k] = myplot.getfield(ncref,uchar) ; all_windv[k] = myplot.getfield(ncref,vchar)
[763]	474
	475	if (k+1)%3==0: ## operation plots
	476	print "SETTING OPERATION PLOT"
	477	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]
	478	if ope in ["-","-_only","-_histo"]:
	479	all_var[k]= all_var[k-2] - all_var[k-1]
	480	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]
	481	if plot_y[k-2] is None: plot_y[k] = None; plot_x[k] = None
	482	elif ope in ["+","+_only"]:
	483	all_var[k]= all_var[k-2] + all_var[k-1]
	484	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]
	485	if plot_y[k-2] is None: plot_y[k] = None; plot_x[k] = None
	486	elif ope in ["-%","-%_only"]:
	487	masked = np.ma.masked_where(all_var[k-1] == 0,all_var[k-1])
	488	masked.set_fill_value([np.NaN])
	489	all_var[k]= 100.*(all_var[k-2] - masked)/masked
	490	if plot_y[k-1] is not None and plot_y[k-2] is not None:
	491	masked = np.ma.masked_where(plot_y[k-1] == 0,plot_y[k-1])
	492	masked.set_fill_value([np.NaN])
	493	plot_y[k]= 100.*(plot_y[k-2] - masked)/masked
	494	if plot_y[k-2] is None: plot_y[k] = None; plot_x[k] = None
	495	if len(clb) >= zelen: all_colorb[k] = clb[-1]
	496	else: all_colorb[k] = "RdBu_r" # if no additional user-defined color... set a good default one
	497	if winds: all_windu[k] = all_windu[k-2]-all_windu[k-1] ; all_windv[k] = all_windv[k-2] - all_windv[k-1]
	498
	499	elif ope in ["cat"]:
	500	tabtime = all_time[0];tab = all_var[0];k = 1
	501	if var2: tab2 = all_var2[0]
[896]	502	while k != zelenfile and len(all_time[k]) != 0:
[763]	503	if var2: tab2 = np.append(tab2,all_var2[k],axis=0)
	504	tabtime = np.append(tabtime,all_time[k]) ; tab = np.append(tab,all_var[k],axis=0) ; k += 1
	505	all_time[0] = np.array(tabtime) ; all_var[0] = np.array(tab) ; numplot = 1
	506	if var2: all_var2[0] = np.array(tab2)
[876]	507	else: myplot.errormess(ope+" : non-implemented operation. Check pp.py --help")
[763]	508	if "only" in ope:
	509	numplot = 1 ; all_var[0] = all_var[k]
	510	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]
	511	all_varname[0] = all_varname[k]
	512
	513	##################################
[345]	514	### Open a figure and set subplots
[876]	515	fig = mpl.pyplot.figure()
	516	subv,subh = myplot.definesubplot( numplot, fig, ipreferline = (mapmode == 1) )
[896]	517	if ope in ['-','-%','-_histo'] and zelenfile ==1 : subv,subh = 2,2
	518	elif ope in ['-','-%'] and zelenfile>1 : subv, subh = zelenfile, 3
[345]	519
	520	#################################
	521	### Time loop for plotting device
[763]	522	nplot = 1 ; error = False ; firstpass = True
[876]	523	if lstyle is not None: linecycler = itertools.cycle(lstyle)
	524	else: linecycler = itertools.cycle(["-","--","-.",":"])
[392]	525	print "********************************************"
[345]	526	while error is False:
[458]	527
[763]	528	print "********** PLOT", nplot, " OF ",numplot
[424]	529	if nplot > numplot: break
[345]	530
[424]	531	####################################################################
[392]	532	## get all indexes to be taken into account for this subplot and then reduce field
	533	## 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
[423]	534	if ope is not None:
[896]	535	if fileref is not None: index_f = ((nplot-1)//(nlonnlatnvertntime))%(3zelenfile) ## OK only 1 var, see test in the beginning
	536	elif "var" in ope: index_f = ((nplot-1)//(nlonnlatnvert*ntime))%(zelenvar+1) ## OK only 1 file, see test in the beginning
[451]	537	elif "cat" in ope: index_f = 0
[763]	538	elif not firstpass:
[896]	539	if zelenfile > 1 and zelenvar == 1 and which == "unidim": pass
	540	else: yeah = zelenfilezelenvar ; index_f = ((nplot-1)//(nlonnlatnvertntime))%yeah
	541	else: yeah = zelenfilezelenvar ; index_f = ((nplot-1)//(nlonnlatnvertntime))%yeah
[763]	542	time = all_time[index_f] ; vert = all_vert[index_f] ; lat = all_lat[index_f] ; lon = all_lon[index_f]
[876]	543	indexlon = myplot.getsindex(sslon,(nplot-1)%nlon,lon)
	544	indexlat = myplot.getsindex(sslat,((nplot-1)//nlon)%nlat,lat)
	545	indexvert = myplot.getsindex(svert,((nplot-1)//(nlon*nlat))%nvert,vert)
[763]	546	plotx=plot_x[index_f] ; ploty=plot_y[index_f]
[435]	547	if mrate is not None: indextime = None
[876]	548	else: indextime = myplot.getsindex(stime,((nplot-1)//(nlonnlatnvert))%ntime,time)
[426]	549	ltst = None
[876]	550	if typefile in ['meso'] and indextime is not None and len(indextime) < 2: ltst = myplot.localtime ( indextime, slon , all_namefile[index_f] )
[817]	551
[876]	552	if not monster:
	553	if indexlat is not None: print "********** LAT : INDEX",indexlat[0], indexlat[-1], "VALUE",lat[indexlat[0]], lat[indexlat[-1]]
	554	if indexlon is not None: print "********** LON : INDEX",indexlon[0], indexlon[-1], "VALUE",lon[indexlon[0]], lon[indexlon[-1]]
	555	if indexvert is not None: print "********** VERT: INDEX",indexvert[0], indexvert[-1], "VALUE",vert[indexvert[0]], vert[indexvert[-1]]
	556	if indextime is not None: print "********** TIME: INDEX",indextime[0], indextime[-1], "VALUE",time[indextime[0]], time[indextime[-1]]
[817]	557
[490]	558	##var = nc.variables["phisinit"][:,:]
[876]	559	##contourf(np.transpose(var),30,cmap = get_cmap(name="Greys_r") ) ; mpl.pyplot.axis('off') ; plot(indexlat,indexlon,'mx',mew=4.0,ms=20.0)
	560	##mpl.pyplot.show()
[490]	561	##exit()
	562	#truc = True
	563	#truc = False
	564	#if truc: indexvert = None
[424]	565	####################################################################
[475]	566	########## REDUCE FIELDS
	567	####################################################################
[448]	568	error = False
[392]	569	varname = all_varname[index_f]
[763]	570	which=''
[448]	571	if varname: ### what is shaded.
[876]	572	what_I_plot, error = myplot.reducefield( all_var[index_f], d4=indextime, d1=indexlon, d2=indexlat, d3=indexvert, \
[717]	573	yint=yintegral, alt=vert, anomaly=anomaly, redope=redope, mesharea=area, unidim=is1d)
[865]	574	if add != 0.: what_I_plot = what_I_plot + add
[516]	575	if mult != 2718.: what_I_plot = what_I_plot*mult
	576	else: what_I_plot = np.log10(what_I_plot) ; print "log plot"
[865]	577
[451]	578	if var2: ### what is contoured.
[876]	579	what_I_plot_contour, error = myplot.reducefield( all_var2[index_f], d4=indextime, d1=indexlon, d2=indexlat , d3=indexvert, \
[865]	580	yint=yintegral, alt=vert, redope=redope )
[451]	581	if winds: ### what is plot as vectors.
[876]	582	vecx, error = myplot.reducefield( all_windu[index_f], d4=indextime, d3=indexvert, yint=yintegral, alt=vert)
	583	vecy, error = myplot.reducefield( all_windv[index_f], d4=indextime, d3=indexvert, yint=yintegral, alt=vert)
[490]	584	if varname in [uchar,vchar]: what_I_plot = np.sqrt( np.square(vecx) + np.square(vecy) ) ; varname = "wind"
[763]	585
	586	if plotx is not None:
[876]	587	plotx, error = myplot.reducefield( plotx, d4=indextime, d1=indexlon, d2=indexlat, d3=indexvert, \
[763]	588	yint=yintegral, alt=vert, anomaly=anomaly, redope=redope, mesharea=area, unidim=is1d)
[876]	589	ploty, error = myplot.reducefield( ploty, d4=indextime, d1=indexlon, d2=indexlat, d3=indexvert, \
[763]	590	yint=yintegral, alt=vert, anomaly=anomaly, redope=redope, mesharea=area, unidim=is1d)
	591	which='xy'
[490]	592	#####################################################################
	593	#if truc:
	594	# nx = what_I_plot.shape[2] ; ny = what_I_plot.shape[1] ; nz = what_I_plot.shape[0]
[876]	595	# for k in range(nz): print k,' over ',nz ; what_I_plot[k,:,:] = what_I_plot[k,:,:] / myplot.smooth(what_I_plot[k,:,:],12)
[490]	596	# for iii in range(nx):
	597	# for jjj in range(ny):
	598	# deviation = what_I_plot[:,jjj,iii] ; mx = max(deviation) ; mn = min(deviation)
	599	# if iii > 6 and iii < nx-6 and jjj > 6 and jjj < ny-6: what_I_plot[0,jjj,iii],rel = singlet(deviation,vert/1000.) ### z must be in km
	600	# else: what_I_plot[0,jjj,iii] = 0.
	601	# if np.abs(what_I_plot[0,jjj,iii]) > 1.5:
	602	# print iii,jjj,what_I_plot[0,jjj,iii],int(abs(1.-mx)100.),int(abs(1.-mn)100.)
[876]	603	# mpl.pyplot.plot(rel)
	604	# mpl.pyplot.show()
[490]	605	# anomaly = True ### pour avoir les bons reglages plots
	606	# what_I_plot = what_I_plot[0,:,:]
	607	#####################################################################
	608
[448]	609	####################################################################
[458]	610	### General plot settings
[763]	611	changesubplot = (numplot > 1) and (len(what_I_plot.shape) != 1) and (which != "xy") ## default for 1D plots: superimposed. to be reworked for better flexibility.
[876]	612	if changesubplot: mpl.pyplot.subplot(subv,subh,nplot) #; mpl.pyplot.subplots_adjust(wspace=0,hspace=0)
[760]	613	colorb = all_colorb[index_f]
[458]	614	####################################################################
[475]	615	if error:
[876]	616	myplot.errormess("There is an error in reducing field !")
[475]	617	else:
[448]	618	ticks = ndiv + 1
[405]	619	fvar = varname
	620	if anomaly: fvar = 'anomaly'
[475]	621	###
	622	if mapmode == 0: ### could this be moved inside imov loop ?
[430]	623	itime=indextime
[587]	624	if len(what_I_plot.shape) == 3: itime=[0]
[475]	625	m = None ; x = None ; y = None
[608]	626	latyeah = lat ; lonyeah = lon
	627	if typefile in ['meso']:
	628	# now that the section is determined we can set the real lat
	629	# ... or for now, a temptative one.
[864]	630	milieux = int(lat2d.shape[1]/2.)
	631	milieuy = int(lat2d.shape[0]/2.)
	632	if slon is not None or proj == "noproj": latyeah = lat2d[:,milieux]
	633	if slat is not None or proj == "noproj": lonyeah = lon2d[milieuy,:]
[876]	634	what_I_plot, x, y = myplot.define_axis(lonyeah,latyeah,vert,time,indexlon,indexlat,indexvert,\
[763]	635	itime,what_I_plot, len(all_var[index_f].shape),vertmode,redope)
[475]	636	###
[876]	637	if analysis in ['laplace']: what_I_plot = laplace(what_I_plot)
[864]	638	###
[876]	639	if (fileref is not None) and ((index_f+1)%3 == 0): zevmin, zevmax = myplot.calculate_bounds(what_I_plot,vmin=minop,vmax=maxop)
	640	else: zevmin, zevmax = myplot.calculate_bounds(what_I_plot,vmin=vmin,vmax=vmax)
[760]	641	#if (fileref is not None) and (index_f == numplot-1): colorb = "RdBu_r"
[876]	642	if colorb in ["def","nobar","onebar"]: palette = mpl.cm.get_cmap(name=myplot.defcolorb(fvar.upper()))
[865]	643	elif colorb == "relief": palette = cm.GMT_relief
	644	elif colorb == "haxby": palette = cm.GMT_haxby
[876]	645	else: palette = mpl.cm.get_cmap(name=colorb)
[490]	646	#palette = cm.GMT_split
[817]	647	#palette = cm.GMT_globe
[489]	648	##### 1. ELIMINATE 0D or >3D CASES
	649	if len(what_I_plot.shape) == 0:
	650	print "VALUE VALUE VALUE VALUE ::: ",what_I_plot
	651	save = 'donothing'
	652	elif len(what_I_plot.shape) >= 4:
[475]	653	print "WARNING!!! ",len(what_I_plot.shape),"-D PLOT NOT SUPPORTED !!! dimensions: ",what_I_plot.shape
[876]	654	myplot.errormess("Are you sure you did not forget to prescribe a dimension ?")
[475]	655	##### 2. HANDLE simple 1D/2D field and movies of 1D/2D fields
	656	else:
[434]	657	if mrate is not None: iend=len(time)-1
[448]	658	else: iend=0
[763]	659	imov = 0
	660	if analysis in ['density','histo','fft','histodensity']: which="xy"
	661	elif len(what_I_plot.shape) == 3:
	662	if var2 and which == '': which = "contour" ## have to start with contours rather than shading
	663	elif which == '': which = "regular"
[876]	664	if mrate is None: myplot.errormess("3D field. Use --rate RATE for movie or specify --time TIME. Exit.")
[475]	665	elif len(what_I_plot.shape) == 2:
[763]	666	if var2 and which == '': which = "contour" ## have to start with contours rather than shading
	667	elif which == '': which = "regular"
	668	if mrate is not None and which == '': which = "unidim"
	669	elif len(what_I_plot.shape) == 1 and which == '' :
[475]	670	which = "unidim"
[562]	671	if what_I_plot.shape[-1] == 1: print "VALUE VALUE VALUE VALUE ::: ", what_I_plot[0] ; save = 'donothing'
[896]	672	## if which == "unidim" and zelenfile > 1: numplot = 1 # this case is similar to several vars from one file
[475]	673	##### IMOV LOOP #### IMOV LOOP
[430]	674	while imov <= iend:
[448]	675	print "-> frame ",imov+1, which
	676	if which == "regular":
	677	if mrate is None: what_I_plot_frame = what_I_plot
	678	else: what_I_plot_frame = what_I_plot[imov,:,:]
[451]	679	if winds:
	680	if mrate is None: vecx_frame = vecx ; vecy_frame = vecy
	681	else: vecx_frame = vecx[imov,:,:] ; vecy_frame = vecy[imov,:,:]
[448]	682	elif which == "contour":
	683	if mrate is None or what_I_plot_contour.ndim < 3: what_I_plot_frame = what_I_plot_contour
	684	else: what_I_plot_frame = what_I_plot_contour[imov,:,:]
[475]	685	elif which == "unidim":
	686	if mrate is None: what_I_plot_frame = what_I_plot
	687	else: what_I_plot_frame = what_I_plot[:,imov] ## because swapaxes
	688	#if mrate is not None:
	689	if mapmode == 1:
[876]	690	m = myplot.define_proj(proj,wlon,wlat,back=back,blat=blat,blon=blon) ## this is dirty, defined above but out of imov loop
[763]	691	x, y = m(lon2d, lat2d) ## this is dirty, defined above but out of imov loop
[864]	692	if (typefile in ['meso'] and mapmode == 1):
[876]	693	if '9999' not in getattr(nc,'START_DATE'): what_I_plot_frame = myplot.dumpbdy(what_I_plot_frame,6,condition=True)
	694	# if typefile in ['mesoideal']: what_I_plot_frame = myplot.dumpbdy(what_I_plot_frame,0,stag='W',condition=dumped_vert_stag)
[444]	695
[475]	696	if which == "unidim":
[866]	697	if lbls is not None: lbl=lbls[nplot-1]
	698	# if lbls is not None: lbl=lbls[index_f]
[612]	699	else:
	700	lbl = ""
	701	if indexlat is not None: lbl = lbl + " ix" + str(indexlat[0])
	702	if indexlon is not None: lbl = lbl + " iy" + str(indexlon[0])
	703	if indexvert is not None: lbl = lbl + " iz" + str(indexvert[0])
	704	if indextime is not None: lbl = lbl + " it" + str(indextime[0])
[647]	705	if lbl == "": lbl = all_namefile[index_f]
[569]	706
[475]	707	if mrate is not None: x = y ## because swapaxes...
[490]	708	#what_I_plot_frame = np.diff(what_I_plot_frame, n=1) ; x = x[1:]
[587]	709
	710	zeline = next(linecycler) ## "-" for simple lines
	711	if tile: zemarker = 'x'
	712	else: zemarker = None
[579]	713	this_is_a_regular_plot = (indexvert is not None) or (indextime is None) or (indexlat is None) or (indexlon is None)
[876]	714	if this_is_a_regular_plot: mpl.pyplot.plot(x,what_I_plot_frame,zeline,label=lbl,marker=zemarker) ## vertical profile
	715	else: mpl.pyplot.plot(what_I_plot_frame,x,zeline,label=lbl,marker=zemarker) ## regular plot
[864]	716	mpl.pyplot.grid(True)
[876]	717	if nplot > 1: mpl.pyplot.legend(loc='best')
	718	if indextime is None and axtime is not None and xlab is None: mpl.pyplot.xlabel(axtime.upper()) ## define the right label
[642]	719	if save == 'txt': writeascii(np.transpose([x,np.transpose(what_I_plot)]),'profile'+str(nplot*1000+imov)+'.txt')
[822]	720	if axtime == "lt" and indextime is None:
[817]	721	ax = mpl.pyplot.gca()
	722	# set ticks where your images will be
	723	ax.get_xaxis().set_ticks(np.arange(0,48,2))
	724	# rename tick labels
	725	ax.get_xaxis().set_ticklabels(["0","2","4","6","8","10","12","14","16","18","20","22",\
	726	"0","2","4","6","8","10","12","14","16","18","20","22"])
	727	## rebound everyone
	728	ax.set_xbound(lower=min(x), upper=max(x))
[763]	729	elif which == "xy":
	730	if lbls is not None: lbl=lbls[index_f]
	731	else: lbl=None
	732	if analysis is not None:
	733	if analysis == 'histo':
	734	if zelen == 1:
	735	mpl.pyplot.hist(ploty.flatten(),bins=ndiv,normed=True, alpha=0.67, facecolor = 'green', label = lbls)
	736	mpl.pyplot.legend()
	737	mpl.pyplot.grid(True)
	738	mpl.pyplot.title(zetitle)
	739	else:
	740	multiplot[index_f]=ploty.flatten()
	741	if index_f == zelen-1:
	742	if ope is not None: multiplot = getVar(multiplot,3*np.arange((index_f+1)/3)+2) ## we only compute histograms for the operation plots
	743	mpl.pyplot.hist(multiplot,bins=ndiv,normed=True, alpha=0.75, label = lbls)
	744	mpl.pyplot.legend()
	745	mpl.pyplot.grid(True)
	746	mpl.pyplot.title(zetitle)
	747	elif analysis in ['density','histodensity']:
	748	if ope is not None and (index_f+1)%3 !=0: pass
	749	else:
	750	plotx = np.linspace(min(ploty.flatten()),max(ploty.flatten()),1000)
[876]	751	density = scipy.stats.gaussian_kde(ploty.flatten())
[763]	752	# density.covariance_factor = lambda : .25 # adjust the covariance factor to change the bandwidth if needed
	753	# density._compute_covariance()
	754	# display the mean and variance of the kde:
	755	sample = density.resample(size=20000)
[876]	756	n, (smin, smax), sm, sv, ss, sk = scipy.stats.describe(sample[0])
[763]	757	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])
	758	if analysis == 'histodensity': # plot both histo and density (to assess the rightness of the kernel density estimate for exemple) and display the estimated variance
	759	mpl.pyplot.hist(ploty.flatten(),bins=ndiv,normed=True, alpha=0.30, label = lbl)
	760	if index_f == zelen-1: mpl.pyplot.legend() ; mpl.pyplot.title(zetitle)
	761	else:
[876]	762	mpl.pyplot.plot(plotx,ploty,label = lbl)
[763]	763	if index_f == zelen-1: mpl.pyplot.legend() ; mpl.pyplot.title(zetitle)
	764	mpl.pyplot.grid(True)
	765	else:
[876]	766	mpl.pyplot.plot(plotx,ploty,label = lbl)
[763]	767	if index_f == zelen-1: mpl.pyplot.legend() ; mpl.pyplot.title(zetitle)
	768	if varname == 'hodograph':
	769	a=0
	770	for ii in np.arange(len(time)):
	771	if a%6 == 0: mpl.pyplot.text(plotx[ii],ploty[ii],time[ii])
	772	a=a+1
	773	mpl.pyplot.grid(True)
	774
[569]	775	elif which == "regular":
[647]	776
	777	# plot stream lines if there is a stream file and a vert/lat slice. Might not work with movies ??
	778	if streamflag and sslat is None and svert is None:
	779	streamfile = all_namefile[index_f].replace('.nc','_stream.nc')
	780	teststream = os.path.exists(streamfile)
	781	if teststream:
	782	print 'INFO: Using stream file',streamfile, 'for stream lines'
[896]	783	ncstream = netCDF4.Dataset(streamfile)
[876]	784	psi = myplot.getfield(ncstream,'psi')
[647]	785	psi = psi[0,:,:,0] # time and longitude are dummy dimensions
	786	if psi.shape[1] != len(x) or psi.shape[0] != len(y):
[876]	787	myplot.errormess('stream file does not fit! Dimensions: '+str(psi.shape)+' '+str(x.shape)+' '+str(y.shape))
[647]	788	zelevels = np.arange(-1.e10,1.e10,1.e9)
	789	zemin = np.min(abs(zelevels))
	790	zemax = np.max(abs(zelevels))
	791	zewidth = (abs(zelevels)-zemin)*(5.- 0.5)/(zemax - zemin) + 0.5 # linewidth ranges from 5 to 0.5
[876]	792	cs = mpl.pyplot.contour( x,y,psi, zelevels, colors='k', linewidths = zewidth)
	793	mpl.pyplot.clabel(cs, inline=True, fontsize = 4.*mpl.pyplot.rcParams['font.size']/5., fmt="%1.1e")
[647]	794	else:
	795	print 'WARNING: STREAM FILE',streamfile, 'DOES NOT EXIST !'
	796
[876]	797	if hole: what_I_plot_frame = myplot.hole_bounds(what_I_plot_frame,zevmin,zevmax)
	798	else: what_I_plot_frame = myplot.bounds(what_I_plot_frame,zevmin,zevmax)
	799	if flagnolow: what_I_plot_frame = myplot.nolow(what_I_plot_frame)
[448]	800	if not tile:
	801	#zelevels = np.linspace(zevmin(1. + 1.e-7),zevmax(1. - 1.e-7)) #,num=20)
	802	zelevels = np.linspace(zevmin,zevmax,num=ticks)
[876]	803	#what_I_plot_frame = myplot.smooth(what_I_plot_frame,100)
[453]	804	if mapmode == 1: m.contourf( x, y, what_I_plot_frame, zelevels, cmap = palette, alpha=trans)
[876]	805	elif mapmode == 0: mpl.pyplot.contourf( x, y, what_I_plot_frame, zelevels, cmap = palette, alpha=trans)
[448]	806	else:
[458]	807	if mapmode == 1: m.pcolor( x, y, what_I_plot_frame, cmap = palette, vmin=zevmin, vmax=zevmax, alpha=trans)
[876]	808	elif mapmode == 0: mpl.pyplot.pcolor( x, y, what_I_plot_frame, cmap = palette, vmin=zevmin, vmax=zevmax, alpha=trans)
[475]	809
[792]	810	if (cross is not None or markdevil) and mapmode == 1:
[824]	811	if cross is not None:
	812	howmuch = np.array(cross).shape[0]
	813	for ttt in range(howmuch):
	814	idx,idy=m(cross[ttt][0],cross[ttt][1])
	815	mpl.pyplot.plot([idx],[idy],'+k',mew=0.5,ms=18)
[792]	816	elif markdevil:
[876]	817	idx,idy=myplot.find_devil(nc,indextime)
[792]	818	idx,idy=x[idx,idy],y[idx,idy]
[824]	819	mpl.pyplot.plot([idx],[idy],'+k',mew=0.5,ms=18)
[792]	820
[817]	821	if not nocolorb:
	822	if colorb not in ['nobar','onebar']:
[763]	823	if (fileref is not None) and ((index_f+1)%3 == 0): daformat = "%.3f"
[468]	824	elif mult != 1: daformat = "%.1f"
[876]	825	else: daformat = myplot.fmtvar(fvar.upper())
[874]	826	if proj in ['moll']: zeorientation="horizontal" ; zepad = 0.07 ; zefrac = 0.1 #zepad=0.05
	827	elif proj in ['cyl']: zeorientation="vertical" ; zepad = 0.03 ; zefrac = 0.023
	828	else: zeorientation="vertical" ; zepad = 0.03 ; zefrac = 0.05
	829	if mapmode == 0: zefrac = 0.1
[876]	830	zecb = mpl.pyplot.colorbar( fraction=zefrac,pad=zepad,format=daformat,orientation=zeorientation,\
[468]	831	ticks=np.linspace(zevmin,zevmax,num=min([ticks/2+1,21])),extend='neither',spacing='proportional' )
[874]	832	#if zeorientation == "horizontal":
	833	# daticks = zecb.ax.get_xticks()
	834	# zecb.ax.set_xticklabels(daticks,rotation='vertical')
[578]	835	if zeorientation == "horizontal" and zetitle[0] != "fill": zecb.ax.set_xlabel(zetitle[index_f]) ; zetitle[index_f]=""
[451]	836	if winds:
[548]	837	if typefile in ['meso']:
[876]	838	if '9999' not in getattr(nc,'START_DATE') : [vecx_frame,vecy_frame] = [myplot.dumpbdy(vecx_frame,6,stag=uchar,condition=True), myplot.dumpbdy(vecy_frame,6,stag=vchar,condition=True)]
[451]	839	key = True
[637]	840	if fvar in ['UV','uv','uvmet']: key = False
[451]	841	elif typefile in ['gcm']:
	842	key = False
[548]	843	if metwind and mapmode == 1: [vecx_frame,vecy_frame] = m.rotate_vector(vecx_frame, vecy_frame, lon2d, lat2d)
[876]	844	if trans != 0.0: colorvec = myplot.definecolorvec(colorb)
	845	else: colorvec = myplot.definecolorvec(back)
	846	myplot.vectorfield(vecx_frame, vecy_frame, x, y, stride=stride, csmooth=2,\
[451]	847	#scale=15., factor=300., color=colorvec, key=key)
[721]	848	scale=20., factor=250./facwind, color=colorvec, key=key)
[451]	849	#200. ## or csmooth=stride
[721]	850	### THIS IS A QUITE SPECIFIC PIECE (does not work for mesoscale files)
[763]	851	if ope == '-_histo' and nplot == numplot: # this should work as long as ope is '-' guarantees 3 plots for 4 panels without contour
[876]	852	mpl.pyplot.subplot(subv,subh,nplot+1)
	853	mpl.pyplot.rcParams["legend.fontsize"] = 'xx-large'
[641]	854	if indexlat is None:
	855	latmin = -50.; latmax = 50. # latitude range for histogram of difference
[640]	856	zeindexlat = (lat<latmax)*(lat>latmin)
[721]	857	if typefile in ['meso']: zeindexlat = 10
[642]	858	# this follows the define_axis logic in myplot.py:
	859	if indextime is None or indexlon is None: what_I_plot_frame = what_I_plot_frame[zeindexlat,:]
	860	else: what_I_plot_frame = what_I_plot_frame[:,zeindexlat]
[640]	861	toplot = np.ravel(what_I_plot_frame[np.isnan(what_I_plot_frame)==False])
[641]	862	zebins = np.linspace(zevmin,zevmax,num=30)
[876]	863	mpl.pyplot.hist(toplot,bins=zebins,histtype='step',linewidth=2,color='k',normed=True)
[647]	864	zestd = np.std(toplot);zemean = np.mean(toplot)
[641]	865	zebins = np.linspace(zevmin,zevmax,num=300)
[640]	866	zegauss = (1./(zestd * np.sqrt(2 * np.pi)) * np.exp( - (zebins - zemean)*2 / (2 zestd**2) ) )
[876]	867	mpl.pyplot.plot(zebins, zegauss, linewidth=1, color='r',label="mean: "+str(zemean)[0:5]+"\nstd: "+str(zestd)[0:5])
	868	mpl.pyplot.legend(loc=0,frameon=False)
	869	mpl.pyplot.subplot(subv,subh,nplot) # go back to last plot for title of contour difference
[893]	870	if ope is not None and "only" not in ope: mpl.pyplot.title("fig(1) "+ope+" fig(2)")
	871	elif ope is not None and "only" in ope: mpl.pyplot.title("fig(1) "+ope[0]+" fig(2)")
[642]	872
[448]	873	elif which == "contour":
[896]	874	#mpl.pyplot.rcParams['contour.negative_linestyle'] = 'solid' # no dashed line for negative values
[876]	875	zevminc, zevmaxc = myplot.calculate_bounds(what_I_plot_frame, vmin=min(what_I_plot_frame), vmax=max(what_I_plot_frame))
[448]	876	zelevels = np.linspace(zevminc,zevmaxc,ticks/2) #20)
[721]	877	### another dirty specific stuff in the wall
[865]	878	if var2 == 'HGT': zelevels = np.arange(-10000.,30000.,250.) #1000.)
[721]	879	elif var2 == 'tpot': zelevels = np.arange(270,370,5)
[874]	880	elif var2 in ['tk','temp']: zelevels = np.arange(0.,1000.,5.)#(150,250,5)
[721]	881	elif var2 == 'wstar': zelevels = np.arange(0,10,1.0)
	882	elif var2 == 'zmax_th': zelevels = np.arange(0,10,2.0) ; what_I_plot_frame = what_I_plot_frame / 1000.
[896]	883	elif var2 in ['u']: zelevels = np.arange(-400.,400.,5.)
[721]	884	###
[608]	885	if mapmode == 0:
[876]	886	what_I_plot_frame, x, y = myplot.define_axis( lonyeah,latyeah,vert,time,indexlon,indexlat,indexvert,\
[763]	887	itime,what_I_plot_frame, len(all_var2[index_f].shape),vertmode,redope)
[637]	888	## is this needed? only if len(all_var2[index_f].shape) != len(all_var[index_f].shape)
[876]	889	cs = mpl.pyplot.contour( x,y,what_I_plot_frame, zelevels, colors='k', linewidths = 0.33)#, alpha=0.5, linestyles='solid')
	890	##cs = mpl.pyplot.contour( x,y,what_I_plot_frame, zelevels, colors='w', linewidths = 0.5)#, alpha=0.5, linestyles='solid')
	891	#mpl.pyplot.clabel(cs, inline=1, fontsize = 4.*rcParams['font.size']/5., fmt=fmtvar(var2.upper()))
[721]	892	elif mapmode == 1:
	893	cs = m.contour( x,y,what_I_plot_frame, zelevels, colors='k', linewidths = 0.33)#, alpha=0.5, linestyles='solid')
[876]	894	#mpl.pyplot.clabel(cs, inline=0, fontsize = mpl.pyplot.rcParams['font.size'], fmt="%.0f") #myplot.fmtvar(var2.upper()))
[763]	895	if which in ["regular","unidim","xy"]:
[448]	896
[763]	897	if nplot > 1 and which in ["unidim","xy"]:
[475]	898	pass ## because we superimpose nplot instances
	899	else:
	900	# Axis directives for movie frames [including the first one).
	901	zxmin, zxmax = xaxis ; zymin, zymax = yaxis
	902	if zxmin is not None: mpl.pyplot.xlim(xmin=zxmin)
	903	if zxmax is not None: mpl.pyplot.xlim(xmax=zxmax)
[896]	904	if zxmin is not None and zxmax is not None:
	905	ax = mpl.pyplot.gca()
	906	ax.get_xaxis().set_ticks(np.linspace(xaxis[0],xaxis[1],ticks/2+1))
[475]	907	if zymin is not None: mpl.pyplot.ylim(ymin=zymin)
	908	if zymax is not None: mpl.pyplot.ylim(ymax=zymax)
[763]	909	if ylog and not xlog: mpl.pyplot.semilogy()
	910	if xlog and not ylog: mpl.pyplot.semilogx()
	911	if xlog and ylog:
	912	mpl.pyplot.xscale('log')
	913	mpl.pyplot.yscale('log')
[475]	914	if invert_y: ax = mpl.pyplot.gca() ; ax.set_ylim(ax.get_ylim()[::-1])
[876]	915	if xlab is not None: mpl.pyplot.xlabel(xlab)
	916	if ylab is not None: mpl.pyplot.ylabel(ylab)
[475]	917
[448]	918	if mrate is not None:
[451]	919	### THIS IS A MENCODER MOVIE
	920	if mrate > 0:
	921	figframe=mpl.pyplot.gcf()
	922	if mquality: figframe.set_dpi(600.)
	923	else: figframe.set_dpi(200.)
	924	mframe=fig2img(figframe)
	925	if imov == 0:
	926	moviename='movie' ;W,H = figframe.canvas.get_width_height()
	927	video = VideoSink((H,W), moviename, rate=mrate, byteorder="rgba")
[876]	928	video.run(mframe) ; mpl.pyplot.close()
[451]	929	if imov == iend: video.close()
	930	### THIS IS A WEBPAGE MOVIE
	931	else:
	932	nameframe = "image"+str(1000+imov)
[876]	933	myplot.makeplotres(nameframe,res=100.,disp=False) ; mpl.pyplot.close()
[451]	934	if imov == 0: myfile = open("zepics", 'w')
	935	myfile.write("modImages["+str(imov)+"] = '"+nameframe+"_100.png';"+ '\n')
	936	if imov == iend:
	937	myfile.write("first_image = 0;"+ '\n')
	938	myfile.write("last_image = "+str(iend)+";"+ '\n')
	939	myfile.close()
[475]	940	if var2 and which == "regular": which = "contour"
[448]	941	imov = imov+1
	942	elif which == "contour":
	943	which = "regular"
	944
[345]	945	### Next subplot
[483]	946	zevarname = varname
	947	if redope is not None: zevarname = zevarname + "_" + redope
[876]	948	basename = myplot.getname(var=zevarname,var2=var2,winds=winds,anomaly=anomaly)
[462]	949	if len(what_I_plot.shape) > 3:
[876]	950	basename = basename + myplot.getstralt(nc,level)
[451]	951	if mrate is not None: basename = "movie_" + basename
[548]	952	if typefile in ['meso']:
[569]	953	if sslon is not None: basename = basename + "_lon_" + str(int(round(lonp)))
	954	if sslat is not None: basename = basename + "_lat_" + str(int(round(latp)))
[349]	955	plottitle = basename
[468]	956	### dans le nouveau systeme time=ls,sol,lt cette ligne pourrait ne servir a rien (ou deplacer au dessus)
[876]	957	if addchar and indextime is not None: [addchar,gogol,gogol2] = myplot.getlschar ( all_namefile[index_f] ) ; plottitle = plottitle + addchar
[485]	958	### en fait redope is None doit etre remplace par : n'est ni maxt ni mint
	959	if redope is None and ltst is not None and ( (mapmode == 0) or (proj in ["lcc","laea","merc","nsper"]) ): plottitle = plottitle + "_LT" + str(ltst)
[349]	960	else:
[359]	961	if fileref is not None:
[763]	962	if (index_f+1)%3 == 0: plottitle = basename+' '+"fig(1) "+ope+" fig(2)"
	963	elif (index_f+2)%3 == 0: plottitle = basename+' '+fileref
	964	else: plottitle = basename+' '+all_namefile[index_f]
[647]	965	else: plottitle = basename+' '+all_namefile[index_f]
[468]	966	if mult != 1: plottitle = '{:.0e}'.format(mult) + "*" + plottitle
[578]	967	if zetitle[0] != "fill":
[580]	968	if index_f < len(zetitle): plottitle = zetitle[index_f]
	969	else: plottitle = zetitle[0]
[578]	970	if titleref is "fill": titleref=zetitle[index_f]
[763]	971	if fileref is not None and which != "xy":
	972	if (index_f+2)%3 == 0: plottitle = titleref
	973	if (index_f+1)%3 == 0: plottitle = "fig(1) "+ope+" fig(2)"
[402]	974	# if indexlon is not None: plottitle = plottitle + " lon: " + str(min(lon[indexlon])) +" "+ str(max(lon[indexlon]))
	975	# if indexlat is not None: plottitle = plottitle + " lat: " + str(min(lat[indexlat])) +" "+ str(max(lat[indexlat]))
	976	# if indexvert is not None: plottitle = plottitle + " vert: " + str(min(vert[indexvert])) +" "+ str(max(vert[indexvert]))
	977	# if indextime is not None: plottitle = plottitle + " time: " + str(min(time[indextime])) +" "+ str(max(time[indextime]))
[876]	978	if colorb != "onebar": mpl.pyplot.title( plottitle )
[402]	979	if nplot >= numplot: error = True
[345]	980	nplot += 1
	981
[896]	982	if zelenfile > 1 and zelenvar == 1 and which == "unidim": index_f=index_f+1
[763]	983	firstpass=False
	984
[518]	985	if colorb == "onebar":
[876]	986	cax = mpl.pyplot.axes([0.1, 0.2, 0.8, 0.03]) # a ameliorer
	987	zecb = mpl.pyplot.colorbar(cax=cax, orientation="horizontal", format=myplot.fmtvar(fvar.upper()),\
[518]	988	ticks=np.linspace(zevmin,zevmax,num=min([ticks/2+1,21])),extend='neither',spacing='proportional')
[578]	989	if zetitle[0] != "fill": zecb.ax.set_xlabel(zetitle[index_f]) ; zetitle[index_f]=""
[345]	990
[612]	991
[345]	992	##########################################################################
	993	### Save the figure in a file in the data folder or an user-defined folder
[359]	994	if outputname is None:
[876]	995	if typefile in ['meso']: prefix = myplot.getprefix(nc)
[359]	996	elif typefile in ['gcm']: prefix = 'LMD_GCM_'
	997	else: prefix = ''
[345]	998	###
[359]	999	zeplot = prefix + basename
[721]	1000	if zoom: zeplot = zeplot + "zoom"+str(abs(zoom))
[359]	1001	if addchar: zeplot = zeplot + addchar
	1002	if numplot <= 0: zeplot = zeplot + "_LT"+str(abs(numplot))
[345]	1003	###
[359]	1004	if not target: zeplot = namefile[0:find(namefile,'wrfout')] + zeplot
	1005	else: zeplot = target + "/" + zeplot
[345]	1006	###
[359]	1007	else:
	1008	zeplot=outputname
	1009
[436]	1010	if mrate is None:
	1011	pad_inches_value = 0.35
[760]	1012	if wlon[1]-wlon[0] < 2.: pad_inches_value = 0.5 # LOCAL MODE (small values)
[436]	1013	print "********** SAVE ", save
	1014	if save == 'png':
[886]	1015	if display: myplot.makeplotres('.thumb',res=50.,pad_inches_value=pad_inches_value) #,erase=True) ## a miniature
[876]	1016	myplot.makeplotres(zeplot,res=resolution,pad_inches_value=pad_inches_value,disp=False)
	1017	elif save in ['eps','svg','pdf']: myplot.makeplotres(zeplot,pad_inches_value=pad_inches_value,disp=False,ext=save)
	1018	elif save == 'gui': mpl.pyplot.show()
[489]	1019	elif save == 'donothing': pass
[436]	1020	elif save == 'txt': print "Saved results in txt file."
	1021	else:
	1022	print "INFO: save mode not supported. using gui instead."
[876]	1023	mpl.pyplot.show()
[345]	1024
[447]	1025	###################################
	1026	#### Getting more out of this video -- PROBLEMS WITH CREATED VIDEOS
	1027	#
[864]	1028	if mrate is not None and save != "html":
	1029	print "Re-encoding movie.. first pass"
	1030	video.first_pass(filename=zeplot,quality=mquality,rate=mrate)
[447]	1031	# print "Re-encoding movie.. second pass"
	1032	# video.second_pass(filename=moviename,quality=mquality,rate=mrate)
[444]	1033
[345]	1034	###############
	1035	### Now the end
	1036	return zeplot

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