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source: trunk/UTIL/PYTHON/planetoplot_v2/ppclass.py @ 1336

Last change on this file since 1336 was 1317, checked in by tnavarro, 11 years ago
bug in verbose mode
File size: 100.8 KB

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1	###############################################
2	## PLANETOPLOT ##
3	## --> PPCLASS ##
4	## A generic and versatile Python module ##
5	## ... to read netCDF files and plot ##
6	###############################################
7	## Author: Aymeric Spiga. 02-03/2013 ##
8	###############################################
9	# python built-in librairies
10	import os
11	import time as timelib
12	import pickle
13	# added librairies
14	import numpy as np
15	import netCDF4
16	import matplotlib.pyplot as mpl
17	# personal librairies
18	import ppplot
19	import ppcompute
20	###############################################
21
22	###################################
23	#### HEADER ##
24	#### ... executed when imported ##
25	###################################
26	# where settings files are located...
27	# ... this can be hardcoded here
28	whereset = None
29	whereset = ppcompute.findset(whereset)
30	# ... we load user-defined automatic settings from set_ppclass.txt
31	zefile = "set_ppclass.txt"
32	glob_listx = [] ; glob_listy = [] ; glob_listz = [] ; glob_listt = []
33	glob_listarea = []
34	try:
35	f = open(whereset+zefile, 'r') ; lines = f.readlines()
36	for stuff in lines[5].strip().split(';'): glob_listx.append(stuff)
37	for stuff in lines[8].strip().split(';'): glob_listy.append(stuff)
38	for stuff in lines[11].strip().split(';'): glob_listz.append(stuff)
39	for stuff in lines[14].strip().split(';'): glob_listt.append(stuff)
40	for stuff in lines[17].strip().split(';'): glob_listarea.append(stuff)
41	except IOError:
42	print "PPCLASS warning: "+zefile+" not in "+whereset+" ; no presets."
43
44	##################################
45	#### USEFUL GENERIC FUNCTIONS ####
46	##################################
47
48	# inspect variables and dimensions in a netCDF file
49	def inspect(filename):
50	print "---------------------------------------------------------------"
51	print "**** INSPECT FILE",filename
52	test = netCDF4.Dataset(filename)
53	print "---------------------------------------------------------------"
54	print "**** DIMENSIONS:"
55	for obj in test.dimensions.values(): print obj
56	print "---------------------------------------------------------------"
57	print "**** VARIABLES: ",test.variables.keys()
58	print "---------------------------------------------------------------"
59	findinlist(test,glob_listx,"**** FOUND X-AXIS ---> ")
60	findinlist(test,glob_listy,"**** FOUND Y-AXIS ---> ")
61	findinlist(test,glob_listz,"**** FOUND Z-AXIS ---> ")
62	findinlist(test,glob_listt,"**** FOUND T-AXIS ---> ")
63	print "**** ( according to settings in "+whereset+zefile+" )"
64	print "---------------------------------------------------------------"
65	# -- function defined for the above function inspect
66	def findinlist(netcdfobj,extlist,message):
67	found = False
68	for c in extlist:
69	if c in netcdfobj.variables.keys():
70	found = True
71	output = message+str(c)
72	if c in netcdfobj.dimensions.keys():
73	output = output+" ---- has "+str(len(netcdfobj.dimensions[c]))+" values"
74	try: output = output + " ---- from "+str(netcdfobj.variables[c][0])+" to "+str(netcdfobj.variables[c][-1])
75	except: pass
76	print output ; output = ""
77	if not found:
78	print message+"not found. will simply use index (check out dimensions)."
79
80	# request a given attribute (and test if it is here)
81	def ncattr(filename,char):
82	nc = netCDF4.Dataset(filename)
83	if hasattr(nc,char): ncattr=getattr(nc,char)
84	return ncattr
85
86	# check a tab and exit if wrong. if just one string make it a list.
87	# (if allownumber, convert this into a string).
88	def checktab(tab,mess="",allownone=False,allownumber=False):
89	if tab is None:
90	if not allownone: print "pp.define: no "+mess ; exit()
91	else: pass
92	else:
93	if not isinstance(tab, list):
94	if isinstance(tab, str):
95	tab = [tab]
96	elif (isinstance(tab, int) or isinstance(tab, float)) and allownumber:
97	tab = [str(tab)]
98	else:
99	print "pp.define: "+mess+" should be either a string or a list of strings!" ; exit()
100	elif isinstance(tab, list):
101	if isinstance(tab[0],str):
102	pass
103	elif (isinstance(tab[0], int) or isinstance(tab[0], float)) and allownumber:
104	for iii in range(len(tab)): tab[iii] = str(tab[iii])
105	else:
106	print "pp.define: "+mess+" should be either a string or a list of strings!" ; exit()
107	return tab
108
109	# determine which method is to be applied to a given dimension
110	def findmethod(tab):
111	if tab is None: output = "free"
112	elif tab[0,0] != tab[0,1]: output = "comp"
113	else: output = "fixed"
114	return output
115
116	# read what is given by the user (version of T. Navarro)
117	def readslices(saxis):
118	if saxis == None:
119	zesaxis = None
120	else:
121	zesaxis = np.empty((len(saxis),2))
122	for i in range(len(saxis)):
123	a = separatenames(saxis[i])
124	if len(a) == 1:
125	zesaxis[i,:] = float(a[0])
126	else:
127	zesaxis[i,0] = float(a[0])
128	zesaxis[i,1] = float(a[1])
129	return zesaxis
130
131	# look for comas in the input name to separate different names (files, variables,etc ..)
132	# (needed by readslices)
133	def separatenames (name):
134	if name is None: names = None
135	else:
136	names = [] ; stop = 0 ; currentname = name
137	while stop == 0:
138	indexvir = currentname.find(',')
139	if indexvir == -1: stop = 1 ; name1 = currentname
140	else: name1 = currentname[0:indexvir]
141	names = np.concatenate((names,[name1]))
142	currentname = currentname[indexvir+1:len(currentname)]
143	return names
144
145	#######################
146	### THE MAIN OBJECT ###
147	#######################
148	class pp():
149
150	# print out a help string when help is invoked on the object
151	def __repr__(self):
152	whatprint = 'pp object. \"help(pp)\" for more information\n'
153	return whatprint
154
155	# default settings
156	# -- user can define settings by two methods.
157	# -- 1. yeah = pp(file="file.nc")
158	# -- 2. yeah = pp() ; yeah.file = "file.nc"
159	def __init__(self,file=None,var="notset",\
160	filegoal=None,vargoal=None,\
161	x=None,y=None,z=None,t=None,\
162	sx=1,sy=1,\
163	sz=1,st=1,\
164	svx=None,\
165	svy=None,\
166	compute="mean",\
167	kind3d="tyx",\
168	verbose=False,\
169	quiet=False,\
170	superpose=False,\
171	plotin=None,\
172	forcedimplot=-1,\
173	out=None,\
174	filename=None,\
175	folder="./",\
176	includedate=False,\
177	res=150.,\
178	xlabel=None,ylabel=None,\
179	xcoeff=None,ycoeff=None,\
180	xmin=None,ymin=None,\
181	xmax=None,ymax=None,\
182	nxticks=10,nyticks=10,\
183	proj=None,\
184	blat=None,\
185	blon=None,\
186	wscale=None,\
187	vmin=None,vmax=None,\
188	div=None,\
189	colorbar=None,\
190	linestyle=None,\
191	marker=None,\
192	color=None,\
193	legend=None,\
194	changetime=None,\
195	units=None,\
196	savtxt=False,\
197	modx=None,\
198	fmt=None,\
199	xp=16,yp=8,\
200	missing=1.e25,\
201	trans=None,back=None,\
202	showcb=None,\
203	logy=None,\
204	title=None):
205	self.request = None
206	self.nrequest = 0
207	self.nfin = 0 ; self.nvin = 0
208	self.nplotx = None ; self.nploty = None
209	self.nplotz = None ; self.nplott = None
210	self.status = "init"
211	self.fig = None ; self.subv = None ; self.subh = None
212	self.n = 0 ; self.howmanyplots = 0
213	self.nplot = 0
214	self.p = None
215	self.customplot = False
216	self.f = None
217	self.l = None
218	self.xx = None
219	self.yy = None
220	self.zz = None
221	self.tt = None
222	## what could be defined by the user
223	self.file = file
224	self.var = var
225	self.filegoal = filegoal
226	self.vargoal = vargoal
227	self.x = x ; self.y = y ## if None, free dimension
228	self.z = z ; self.t = t ## if None, free dimension
229	self.sx = sx ; self.sy = sy
230	self.sz = sz ; self.st = st
231	self.svx = svx
232	self.svy = svy
233	self.compute = compute
234	self.kind3d = kind3d
235	self.verbose = verbose
236	self.quiet = quiet
237	self.plotin = plotin
238	self.superpose = superpose
239	self.forcedimplot = forcedimplot
240	self.out = out
241	self.filename = filename
242	self.res = res
243	self.folder = folder
244	self.includedate = includedate
245	self.changetime = changetime
246	self.savtxt = savtxt
247	self.modx = modx
248	self.missing = missing
249	## here are user-defined plot settings
250	## -- if not None, valid on all plots in the pp() objects
251	self.xlabel = xlabel ; self.xcoeff = xcoeff
252	self.ylabel = ylabel ; self.ycoeff = ycoeff
253	self.xmin = xmin ; self.xmax = xmax
254	self.ymin = ymin ; self.ymax = ymax
255	self.proj = proj
256	self.blat = blat ; self.blon = blon
257	self.wscale = wscale
258	self.vmin = vmin ; self.vmax = vmax
259	self.div = div
260	self.colorbar = colorbar
261	self.linestyle = linestyle
262	self.marker = marker
263	self.color = color
264	self.legend = legend
265	self.units = units
266	self.title = title
267	self.xp = xp ; self.yp = yp
268	self.nxticks = nxticks ; self.nyticks = nyticks
269	self.fmt = fmt
270	self.trans = trans ; self.back = back
271	self.showcb = showcb
272	self.logy = logy
273
274	# print status
275	def printstatus(self):
276	if not self.quiet:
277	print "**** PPCLASS. Done step: " + self.status
278
279	# print attributes
280	def printme(self):
281	for k, v in vars(self).items():
282	print k,v
283
284	#####################################################
285	# EMULATE OPERATORS + - * / ** << FOR PP() OBJECTS #
286	#####################################################
287
288	# define the operation <<
289	# ... e.g. obj2 << obj1
290	# ... means: get init for pp object obj2 from another pp object obj1
291	# ... (this should solve the affectation trap obj2 = obj1)
292	def __lshift__(self,other):
293	if other.__class__.__name__ == "pp":
294	self.file = other.file
295	self.var = other.var
296	self.filegoal = other.filegoal
297	self.vargoal = other.vargoal
298	self.x = other.x ; self.y = other.y ## if None, free dimension
299	self.z = other.z ; self.t = other.t ## if None, free dimension
300	self.sx = other.sx ; self.sy = other.sy
301	self.sz = other.sz ; self.st = other.st
302	self.compute = other.compute
303	self.kind3d = other.kind3d
304	self.verbose = other.verbose
305	self.quiet = other.quiet
306	self.plotin = other.plotin
307	self.superpose = other.superpose
308	self.forcedimplot = other.forcedimplot
309	self.out = other.out
310	self.filename = other.filename
311	self.folder = other.folder
312	self.xlabel = other.xlabel ; self.xcoeff = other.xcoeff
313	self.ylabel = other.ylabel ; self.ycoeff = other.ycoeff
314	self.proj = other.proj
315	self.blat = other.blat ; self.blon = other.blon
316	self.wscale = other.wscale
317	self.vmin = other.vmin ; self.vmax = other.vmax
318	self.xmin = other.xmin ; self.xmax = other.xmax
319	self.ymin = other.ymin ; self.ymax = other.ymax
320	self.div = other.div
321	self.colorbar = other.colorbar
322	self.linestyle = other.linestyle
323	self.marker = other.marker
324	self.color = other.color
325	self.legend = other.legend
326	self.units = other.units
327	self.title = other.title
328	self.includedate = other.includedate
329	self.changetime = other.changetime
330	self.savtxt = other.savtxt
331	self.modx = other.modx
332	self.xp = other.xp ; self.yp = other.yp
333	self.missing = other.missing
334	self.nxticks = other.nxticks ; self.nyticks = other.nyticks
335	self.fmt = other.fmt
336	self.trans = other.trans ; self.back = other.back
337	self.showcb = other.showcb
338	self.logy = other.logy
339	else:
340	print "!! ERROR !! argument must be a pp object." ; exit()
341
342	# check the compatibility of two objects for operations
343	# --> if other is a pp class, test sizes and return isnum = False
344	# --> if other is an int or a float, return isnum = True
345	# --> otherwise, just print an error and exit
346	def checktwo(self,other):
347	if other.__class__.__name__ == "pp":
348	isnum = False
349	if self.status in ["init","defined"] or other.status in ["init","define"]:
350	print "!! ERROR !! Please use .retrieve to get fields for plots with one of your pp operands." ; exit()
351	if self.nfin != other.nfin or \
352	self.nvin != other.nvin or \
353	self.nplott != other.nplott or \
354	self.nplotz != other.nploty or \
355	self.nploty != other.nploty or \
356	self.nplotx != other.nplotx :
357	print "!! ERROR !! The two operands do not have the same number of files, variables, t z y x requests."
358	exit()
359	elif isinstance(other,int) or isinstance(other,float):
360	isnum = True
361	else:
362	print "!! ERROR !! The operand is neither a pp class nor an integer or a float." ; exit()
363	return isnum
364
365	# define a selective copy of a pp() object for operations
366	# ... copy.copy() is not conservative (still acts like a pointer)
367	# ... copy.deepcopy() does not work with netCDF objects
368	# so what is done here is a copy of everything except
369	# (to avoid sharing with self and therefore modifying self through operations)
370	# - request attribute of pp() object
371	# - field attribute of the onerequest() objects
372	def selective_copy(self):
373	if self.status in ["init","defined"]:
374	print "!! ERROR !! Please use .retrieve to get fields for the object you want to copy from." ; exit()
375	the_clone = pp()
376	for k, v in vars(self).items():
377	if k != "request":
378	setattr(the_clone,k,v)
379	the_clone.verbose = False
380	the_clone.quiet = True # trick to avoid additional outputs
381	the_clone.define()
382	for i in range(self.nfin):
383	for j in range(self.nvin):
384	for t in range(self.nplott):
385	for z in range(self.nplotz):
386	for y in range(self.nploty):
387	for x in range(self.nplotx):
388	obj_ref = self.request[i][j][t][z][y][x]
389	obj = the_clone.request[i][j][t][z][y][x]
390	for k, v in vars(obj_ref).items():
391	if k != "field":
392	setattr(obj,k,v)
393	the_clone.status = "retrieved"
394	the_clone.quiet = self.quiet
395	return the_clone
396
397	# define the operation + on two objects. or with an int/float.
398	# ... with selective_copy the self object is not modified.
399	def __add__(self,other):
400	isnum = self.checktwo(other)
401	the_clone = self.selective_copy()
402	for i in range(self.nfin):
403	for j in range(self.nvin):
404	for t in range(self.nplott):
405	for z in range(self.nplotz):
406	for y in range(self.nploty):
407	for x in range(self.nplotx):
408	obj = the_clone.request[i][j][t][z][y][x]
409	obj_ref = self.request[i][j][t][z][y][x]
410	if not isnum:
411	ope = other.request[i][j][t][z][y][x].field
412	if ope.ndim == 0:
413	ope = float(ope) # if no dimension then this means that ope is a single value (not to be kept as an array)
414	elif obj_ref.field.shape != ope.shape:
415	print "!! ERROR !! The two fields for operation do not have the same shape.",obj_ref.field.shape,ope.shape
416	exit()
417	else:
418	ope = other
419	goal = self.vargoal[j] + self.filegoal[i]
420	if ("vector" in goal) or ("contour" in goal):
421	if self.verbose: print "!! WARNING !! No operation was made on contours and vectors. This can be debatted actually."
422	obj.field = obj_ref.field
423	else:
424	obj.field = obj_ref.field + ope
425	return the_clone
426
427	# define the operation - on two objects. or with an int/float.
428	# ... with selective_copy the self object is not modified.
429	def __sub__(self,other):
430	isnum = self.checktwo(other)
431	the_clone = self.selective_copy()
432	for i in range(self.nfin):
433	for j in range(self.nvin):
434	for t in range(self.nplott):
435	for z in range(self.nplotz):
436	for y in range(self.nploty):
437	for x in range(self.nplotx):
438	obj = the_clone.request[i][j][t][z][y][x]
439	obj_ref = self.request[i][j][t][z][y][x]
440	if not isnum:
441	ope = other.request[i][j][t][z][y][x].field
442	if ope.ndim == 0:
443	ope = float(ope) # if no dimension then this means that ope is a single value (not to be kept as an array)
444	elif obj_ref.field.shape != ope.shape:
445	print "!! ERROR !! The two fields for operation do not have the same shape.",obj_ref.field.shape,ope.shape
446	exit()
447	else:
448	ope = other
449	goal = self.vargoal[j] + self.filegoal[i]
450	if ("vector" in goal) or ("contour" in goal):
451	if self.verbose: print "!! WARNING !! No operation was made on contours and vectors. This can be debatted actually."
452	obj.field = obj_ref.field
453	else:
454	obj.field = obj_ref.field - ope
455	return the_clone
456
457	# define the operation * on two objects. or with an int/float.
458	# ... with selective_copy the self object is not modified.
459	def __mul__(self,other):
460	isnum = self.checktwo(other)
461	the_clone = self.selective_copy()
462	for i in range(self.nfin):
463	for j in range(self.nvin):
464	for t in range(self.nplott):
465	for z in range(self.nplotz):
466	for y in range(self.nploty):
467	for x in range(self.nplotx):
468	obj = the_clone.request[i][j][t][z][y][x]
469	obj_ref = self.request[i][j][t][z][y][x]
470	if not isnum:
471	ope = other.request[i][j][t][z][y][x].field
472	if ope.ndim == 0:
473	ope = float(ope) # if no dimension then this means that ope is a single value (not to be kept as an array)
474	elif obj_ref.field.shape != ope.shape:
475	print "!! ERROR !! The two fields for operation do not have the same shape.",obj_ref.field.shape,ope.shape
476	exit()
477	else:
478	ope = other
479	goal = self.vargoal[j] + self.filegoal[i]
480	if ("vector" in goal) or ("contour" in goal):
481	if self.verbose: print "!! WARNING !! No operation was made on contours and vectors. This can be debatted actually."
482	obj.field = obj_ref.field
483	else:
484	obj.field = obj_ref.field * ope
485	return the_clone
486
487	# define the operation / on two objects. or with an int/float.
488	# ... with selective_copy the self object is not modified.
489	def __div__(self,other):
490	isnum = self.checktwo(other)
491	the_clone = self.selective_copy()
492	for i in range(self.nfin):
493	for j in range(self.nvin):
494	for t in range(self.nplott):
495	for z in range(self.nplotz):
496	for y in range(self.nploty):
497	for x in range(self.nplotx):
498	obj = the_clone.request[i][j][t][z][y][x]
499	obj_ref = self.request[i][j][t][z][y][x]
500	if not isnum:
501	ope = other.request[i][j][t][z][y][x].field
502	if ope.ndim == 0:
503	ope = float(ope) # if no dimension then this means that ope is a single value (not to be kept as an array)
504	elif obj_ref.field.shape != ope.shape:
505	print "!! ERROR !! The two fields for operation do not have the same shape.",obj_ref.field.shape,ope.shape
506	exit()
507	else:
508	ope = other
509	goal = self.vargoal[j] + self.filegoal[i]
510	if ("vector" in goal) or ("contour" in goal):
511	if self.verbose: print "!! WARNING !! No operation was made on contours and vectors. This can be debatted actually."
512	obj.field = obj_ref.field
513	else:
514	obj.field = obj_ref.field / ope
515	return the_clone
516
517	# define the reverse operation float/int + object
518	def __radd__(self,other):
519	isnum = self.checktwo(other)
520	if not isnum: print "!! ERROR !! Operand should be a number" ; exit()
521	return self.__add__(other)
522
523	# define the reverse operation float/int - object
524	def __rsub__(self,other):
525	isnum = self.checktwo(other)
526	if not isnum: print "!! ERROR !! Operand should be a number" ; exit()
527	return self.__sub__(other)
528
529	# define the reverse operation float/int * object
530	def __rmul__(self,other):
531	isnum = self.checktwo(other)
532	if not isnum: print "!! ERROR !! Operand should be a number" ; exit()
533	return self.__mul__(other)
534
535	# define the reverse operation float/int / object
536	def __rdiv__(self,other):
537	isnum = self.checktwo(other)
538	if not isnum: print "!! ERROR !! Operand should be a number" ; exit()
539	return self.__div__(other)
540
541	# define the operation ** on one object.
542	# ... with selective_copy the self object is not modified.
543	def __pow__(self,num):
544	the_clone = self.selective_copy()
545	if isinstance(num,int) or isinstance(num,float):
546	for i in range(self.nfin):
547	for j in range(self.nvin):
548	for t in range(self.nplott):
549	for z in range(self.nplotz):
550	for y in range(self.nploty):
551	for x in range(self.nplotx):
552	obj = the_clone.request[i][j][t][z][y][x]
553	obj_ref = self.request[i][j][t][z][y][x]
554	goal = self.vargoal[j] + self.filegoal[i]
555	if ("vector" in goal) or ("contour" in goal):
556	if self.verbose: print "!! WARNING !! No operation was made on contours and vectors. This can be debatted actually."
557	obj.field = obj_ref.field
558	else:
559	obj.field = obj_ref.field ** num
560	else:
561	print "!! ERROR !! To define a power, either an int or a float is needed." ; exit()
562	return the_clone
563
564	### TBD: reverse power? for exponentials?
565
566	##############################################################################################
567	# define method
568	# ---------
569	# ... (file and var are either one string or a vector of strings)
570	# ... the goal of define is to define a 2D array of onerequest() objects (see class below)
571	# given the number of file, var, x, y, z, t asked by the user
572	# ... objectives for file or var are given through filegoal and vargoal
573	# --> possible values: main contour vector
574	# ---------
575	# ... then onerequest() objects are being defined more precisely
576	# by getting index_x index_y index_z index_t
577	# and setting method_x method_y method_z method_t to either
578	# - "free" for free dimensions (plot dimensions)
579	# - "comp" for averages, max, min
580	# - "fixed" for fixed dimensions (possibly several i.e. multislice)
581	##############################################################################################
582	def define(self):
583	self.printstatus()
584	# initial check and get dimensions
585	self.file = checktab(self.file,mess="file")
586	self.nfin = len(self.file)
587	if self.verbose:
588	for i in range(self.nfin): inspect(self.file[i])
589	self.var = checktab(self.var,mess="var")
590	self.nvin = len(self.var)
591	# check goal tabs for files and variables
592	# ... default is to plot everything
593	if self.filegoal is None: self.filegoal = ["main"]*self.nfin
594	if self.vargoal is None: self.vargoal = ["main"]*self.nvin
595	self.filegoal = checktab(self.filegoal, mess="filegoal")
596	self.vargoal = checktab(self.vargoal, mess="vargoal")
597	if len(self.filegoal) != self.nfin: print "!! ERROR !! filegoal must be the same size as file." ; exit()
598	if len(self.vargoal) != self.nvin: print "!! ERROR !! vargoal must be the same size as var." ; exit()
599	# variables: initial check
600	self.x = checktab(self.x,mess="x",allownone=True,allownumber=True)
601	self.y = checktab(self.y,mess="y",allownone=True,allownumber=True)
602	self.z = checktab(self.z,mess="z",allownone=True,allownumber=True)
603	self.t = checktab(self.t,mess="t",allownone=True,allownumber=True)
604	# for the moment not var- nor file- dependent.
605	# but this could be the case.
606	sx = readslices(self.x) ; sy = readslices(self.y)
607	sz = readslices(self.z) ; st = readslices(self.t)
608	# get methods
609	mx = findmethod(sx) ; my = findmethod(sy)
610	mz = findmethod(sz) ; mt = findmethod(st)
611	# get number of plots to be done
612	if mx in ["fixed","comp"]: self.nplotx = sx.size/2
613	else: self.nplotx = 1
614	if my in ["fixed","comp"]: self.nploty = sy.size/2
615	else: self.nploty = 1
616	if mz in ["fixed","comp"]: self.nplotz = sz.size/2
617	else: self.nplotz = 1
618	if mt in ["fixed","comp"]: self.nplott = st.size/2
619	else: self.nplott = 1
620	if self.verbose: print "**** OK. Plots over x,y,z,t -->",self.nplotx,self.nploty,self.nplotz,self.nplott
621	# create the list of onerequest() objects
622	self.request = [[[[[[ \
623	onerequest() \
624	for x in range(self.nplotx)] for y in range(self.nploty)] \
625	for z in range(self.nplotz)] for t in range(self.nplott)] \
626	for j in range(self.nvin)] for i in range(self.nfin)]
627	# store how many onerequest() objects are in self.request
628	self.nrequest = self.nfinself.nvinself.nplotxself.nplotyself.nplotz*self.nplott
629	# loop on onerequest() objects
630	for i in range(self.nfin):
631	for j in range(self.nvin):
632	for t in range(self.nplott):
633	for z in range(self.nplotz):
634	for y in range(self.nploty):
635	for x in range(self.nplotx):
636	obj = self.request[i][j][t][z][y][x]
637	# fill in names for files and variables
638	obj.verbose = self.verbose
639	obj.file = self.file[i]
640	obj.var = self.var[j]
641	# get methods
642	obj.method_x = mx ; obj.method_y = my
643	obj.method_z = mz ; obj.method_t = mt
644	# indicate the computation method
645	obj.compute = self.compute
646	# indicate the kind of 3D fields
647	obj.kind3d = self.kind3d
648	# open the files (the same file might be opened several times but this is cheap)
649	obj.openfile()
650	### get x,y,z,t dimensions from file
651	obj.getdim()
652	### possible time axis change
653	obj.changetime = self.changetime
654	obj.performtimechange()
655	# get strides
656	obj.sx = self.sx ; obj.sy = self.sy
657	obj.sz = self.sz ; obj.st = self.st
658	### get index
659	obj.getindextime(dalist=st,ind=t)
660	obj.getindexvert(dalist=sz,ind=z)
661	obj.getindexhori(dalistx=sx,dalisty=sy,indx=x,indy=y)
662	# missing value
663	obj.missing = self.missing
664	# change status
665	self.status = "defined"
666	return self
667
668	##############################################################################################
669	# retrieve method
670	# --> for each element onerequest() in the array, get field .var from .f file
671	# --> see below the onerequest() class:
672	# - only get what is needed for computing and plotting
673	# - averages etc... are computed here
674	# --> RESULT: each onerequest() object has now its attribute .field filled
675	# --> if one wants to perform operations on fields, this should be done after retrieve()
676	##############################################################################################
677	def retrieve(self):
678	self.printstatus()
679	# check if things were done OK before
680	if self.status != "defined": print "!! ERROR !! Please use .define() to define your pp object." ; exit()
681	## create the list of f() and l() objects
682	## --> so that the user can easily access values (and labels for easy exploration)
683	## --> see example easy_get_field
684	self.f = [ [] for iii in range(self.nrequest) ]
685	self.l = [ [] for iii in range(self.nrequest) ]
686	self.xx = [ [] for iii in range(self.nrequest) ]
687	self.yy = [ [] for iii in range(self.nrequest) ]
688	self.zz = [ [] for iii in range(self.nrequest) ]
689	self.tt = [ [] for iii in range(self.nrequest) ]
690	count = 0
691	## first get fields
692	## ... only what is needed is extracted from the files
693	## ... and computations are performed
694	for i in range(self.nfin):
695	for j in range(self.nvin):
696	for t in range(self.nplott):
697	for z in range(self.nplotz):
698	for y in range(self.nploty):
699	for x in range(self.nplotx):
700	obj = self.request[i][j][t][z][y][x]
701	obj.getfield()
702	if self.compute != "nothing":
703	obj.computations()
704	# save fields in self.f for the user
705	self.f[count] = obj.field
706	self.xx[count] = obj.field_x
707	self.yy[count] = obj.field_y
708	self.zz[count] = obj.field_z
709	self.tt[count] = obj.field_t
710	# save a legend in self.l for the user
711	self.l[count] = "_"
712	if self.nfin > 1: self.l[count] = self.l[count] + "f=#"+str(int(i+1))+'_'
713	if self.nvin > 1: self.l[count] = self.l[count] + "v="+obj.var+'_'
714	if self.nplotx > 1: self.l[count] = self.l[count] + "x="+str(self.x[x])+'_'
715	if self.nploty > 1: self.l[count] = self.l[count] + "y="+str(self.y[y])+'_'
716	if self.nplotz > 1: self.l[count] = self.l[count] + "z="+str(self.z[z])+'_'
717	if self.nplott > 1: self.l[count] = self.l[count] + "t="+str(self.t[t])+'_'
718	# close the file
719	obj.closefile()
720	count = count + 1
721	## make it simple: self.f is simply the data array if self.nrequest=1
722	if self.nrequest == 1:
723	self.f = self.f[0]
724	self.xx = self.xx[0]
725	self.yy = self.yy[0]
726	self.zz = self.zz[0]
727	self.tt = self.tt[0]
728	# change status
729	self.status = "retrieved"
730	return self
731
732	##########################################################
733	# get: a shortcut method for the define + retrieve chain #
734	##########################################################
735	def get(self):
736	self.define()
737	self.retrieve()
738	return self
739
740	###########################################################
741	# getf: a shortcut method for the define + retrieve chain #
742	# ... in which the output is self.f #
743	# ... and the ppclass is kept quiet #
744	###########################################################
745	def getf(self):
746	self.quiet = True
747	self.get()
748	return self.f
749
750	############################################################
751	# getfd: a shortcut method for the define + retrieve chain #
752	# ... in which the output is self.f,x,y,z,t #
753	# ... and the ppclass is kept quiet #
754	############################################################
755	def getfd(self):
756	self.quiet = True
757	self.get()
758	return self.f,self.xx,self.yy,self.zz,self.tt
759
760	############################################################
761	# getfl: a shortcut method for the define + retrieve chain #
762	# ... in which the output is self.f, self.l #
763	# ... and the ppclass is kept quiet #
764	############################################################
765	def getfl(self):
766	self.quiet = True
767	self.get()
768	return self.f,self.l
769
770	########################################
771	# smooth: smooth the field in 1D or 2D #
772	########################################
773	## TBD: smooth not OK with masked array in the end of retrieve()
774	def smooth(self,window):
775	if self.verbose:
776	print "!! WARNING !! Performing a smoothing with a window size",window
777	print "!! WARNING !! To come back to unsmoothed file, use .get() again"
778	for i in range(self.nfin):
779	for j in range(self.nvin):
780	for t in range(self.nplott):
781	for z in range(self.nplotz):
782	for y in range(self.nploty):
783	for x in range(self.nplotx):
784	obj = self.request[i][j][t][z][y][x]
785	if obj.field.ndim == 1:
786	print "!! ERROR !! 1D smoothing not supported yet because reduces array sizes."
787	exit()
788	# TBD TBD TBD
789	#obj.field = ppcompute.smooth1d(obj.field,window=window)
790	elif obj.field.ndim == 2:
791	obj.field = ppcompute.smooth2d(obj.field,window=window)
792	#obj.field = ppcompute.smooth2diter(obj.field,n=window)
793
794	##############################################################################################
795	# defineplot method
796	# --> defineplot first defines arrays of plot objects and set each of them
797	# ... simple looping except cases where goal is not main (e.g. contour or vector)
798	# --> principle: each onerequest() object gives birth to a subplot
799	# --> defineplot vs. makeplot: defining plot and actually plotting it are clearly separated
800	# --> THE KEY OUPUT OF defineplot IS AN ARRAY self.p OF PLOT OBJECTS
801	# optional arguments
802	# --> extraplot: to indicate a number of plots to be added afterwards (use self.plotin)
803	# --> loadfile: to use self.p from a previously saved file
804	##############################################################################################
805	def defineplot(self,extraplot=0,loadfile=None):
806	# -----------------------------------------------------
807	# LOAD MODE: load a self.p object. count plots from it.
808	# -----------------------------------------------------
809	if loadfile is not None:
810	try: filehandler = open(loadfile, 'r') ; self.p = pickle.load(filehandler)
811	except IOError: print "!! ERROR !! Cannot find object file to load." ; exit()
812	self.status = "definedplot" ; self.plotin = None
813	self.nplot = len(self.p) ; self.howmanyplots = self.nplot
814	## [BUG FIX: apparently info about missing values is not saved correctly]
815	for count in range(self.nplot):
816	pl = self.p[count]
817	masked = np.ma.masked_where(np.abs(pl.f) > self.missing,pl.f)
818	pl.f = masked ; pl.f[pl.f.mask] = np.NaN
819	return #self?
820	# -----------------------------------------------------
821	# REGULAR MODE
822	# -----------------------------------------------------
823	self.printstatus()
824	# check if things were done OK before
825	if self.status in ["init","defined"]:
826	print "!! ERROR !! Please use .retrieve() to get fields for plots with your pp object." ; exit()
827	# check self.plotin (an existing fig on which to add plots afterwards)
828	if self.plotin.__class__.__name__ == "pp":
829	if self.plotin.fig is None:
830	self.plotin = None # this is an additional security in case
831	# a pp object is given without figure opened yet.
832	elif self.plotin is not None:
833	print "!! ERROR !! plotin argument must be a pp object." ; exit()
834	# initialize the array of subplot objects
835	# either something new or attributes coming from plotin object
836	if self.plotin is None: self.p = [ ]
837	else: self.p = self.plotin.p
838	# create an array of subplot objects
839	# ... in theory the order of looping can be changed without any harm
840	# ... the only important thing is to keep i,j,t,z,y,x resp. for file,var,t,z,y,x
841	count = 0
842	for i in range(self.nfin):
843	if self.filegoal[i] == "main":
844	for j in range(self.nvin):
845	if self.vargoal[j] == "main":
846	for t in range(self.nplott):
847	for z in range(self.nplotz):
848	for y in range(self.nploty):
849	for x in range(self.nplotx):
850	# look at dimension and append the right plot object
851	obj = self.request[i][j][t][z][y][x]
852	dp = obj.dimplot
853	if dp == 1 or self.forcedimplot == 1: plobj = ppplot.plot1d()
854	elif dp == 2 or self.forcedimplot == 2: plobj = ppplot.plot2d()
855	elif dp == 0: print "**** OK. VALUES VALUES VALUES",obj.field
856	else: print "!! ERROR !! 3D or 4D plots not supported" ; exit()
857	# load abscissa and ordinate in obj
858	obj.definecoord()
859	# we start to define things here before appending
860	# (convenient: could be overridden by the user before makeplot)
861	# ... the if loop is necessary so that we can loop above on the dp=0 case
862	if dp in [1,2]:
863	# and define what to do in plobj
864	plobj.invert = obj.invert_axes
865	plobj.swap = obj.swap_axes
866	# axis labels
867	plobj.xlabel = obj.absclab ; plobj.ylabel = obj.ordilab
868	# superpose or not (this is mostly for saving purpose)
869	plobj.superpose = self.superpose
870	# get title, colormaps, labels, etc.. from var
871	plobj.var = obj.var
872	plobj.define_from_var()
873	# generic 1D/2D: load field and coord in plot object
874	plobj.f = obj.field # field to be plotted
875	plobj.x = obj.absc # abscissa (or longitude)
876	plobj.y = obj.ordi # ordinate (or latitude)
877	# -- useless in 1D but not used anyway
878	# specific 1D plot stuff
879	if dp == 1:
880	# -- a default legend
881	plobj.legend = ""
882	if self.nfin > 1: plobj.legend = plobj.legend + " file #"+str(i+1)
883	if self.nvin > 1: plobj.legend = plobj.legend + " var "+plobj.var
884	if self.nplott > 1: plobj.legend = plobj.legend + " t="+str(self.t[t])
885	if self.nplotz > 1: plobj.legend = plobj.legend + " z="+str(self.z[z])
886	if self.nploty > 1: plobj.legend = plobj.legend + " y="+str(self.y[y])
887	if self.nplotx > 1: plobj.legend = plobj.legend + " x="+str(self.x[x])
888	# specific 2d plot stuff
889	if dp == 2:
890	plobj.proj = self.proj
891	plobj.svx = self.svx
892	plobj.svy = self.svy
893	plobj.blat = self.blat
894	plobj.blon = self.blon
895	plobj.wscale = self.wscale
896	# -- light grey background for missing values
897	if type(plobj.f).__name__ in 'MaskedArray': plobj.axisbg = '0.75'
898	# -- define if it is a map or a plot
899	plobj.mapmode = ( obj.method_x+obj.method_y == "freefree" \
900	and "grid points" not in obj.name_x )
901	# possible user-defined plot settings shared by all plots
902	if self.div is not None: plobj.div = self.div
903	if self.xlabel is not None: plobj.xlabel = self.xlabel
904	if self.xcoeff is not None: plobj.xcoeff = self.xcoeff
905	if self.ylabel is not None: plobj.ylabel = self.ylabel
906	if self.ycoeff is not None: plobj.ycoeff = self.ycoeff
907	if self.title is not None: plobj.title = self.title
908	if self.units is not None: plobj.units = self.units
909	if self.colorbar is not None: plobj.colorbar = self.colorbar
910	if self.modx is not None: plobj.modx = self.modx
911	if self.nxticks is not None: plobj.nxticks = self.nxticks
912	if self.nyticks is not None: plobj.nyticks = self.nyticks
913	if self.fmt is not None: plobj.fmt = self.fmt
914	if self.showcb is not None: plobj.showcb = self.showcb
915	if self.logy is not None: plobj.logy = self.logy
916	if self.xmin is not None: plobj.xmin = self.xmin
917	if self.xmax is not None: plobj.xmax = self.xmax
918	if self.ymin is not None: plobj.ymin = self.ymin
919	if self.ymax is not None: plobj.ymax = self.ymax
920	# -- 1D specific
921	if dp == 1:
922	if self.linestyle is not None: plobj.linestyle = self.linestyle
923	if self.marker is not None: plobj.marker = self.marker
924	if self.color is not None: plobj.color = self.color
925	if self.legend is not None: plobj.legend = self.legend
926	# -- 2D specific
927	elif dp == 2:
928	if self.vmin is not None: plobj.vmin = self.vmin
929	if self.vmax is not None: plobj.vmax = self.vmax
930	if self.trans is not None: plobj.trans = self.trans
931	if self.back is not None: plobj.back = self.back
932	# finally append plot object
933	self.p.append(plobj)
934	count = count + 1
935	# self.nplot is number of plot to be defined in this call to defineplot()
936	# (because of self.plotin this might less than length of self.p)
937	self.nplot = count
938	# --- superimposed contours and vectors ---
939	# we have to start another loop because we need forward information
940	# TBD: there is probably a more flexible way to do that
941	count = 0
942	for i in range(self.nfin):
943	for j in range(self.nvin):
944	for t in range(self.nplott):
945	for z in range(self.nplotz):
946	for y in range(self.nploty):
947	for x in range(self.nplotx):
948	goal = self.vargoal[j] + self.filegoal[i]
949	obj = self.request[i][j][t][z][y][x]
950	if "mainmain" in goal and obj.dimplot == 2:
951	# the plot object we consider in the loop
952	plobj = self.p[count]
953	# -- see if there is a contour requested...
954	# (we use try because we might be at the end of the list)
955	found = 0
956	try: condvar = self.vargoal[j+1]
957	except: condvar = "itisok"
958	try: condfile = self.filegoal[i+1]
959	except: condfile = "itisok"
960	# ... get contour
961	##########################################
962	# NB: contour is expected to be right after main otherwise it is not displayed
963	##########################################
964	if condvar == "contour":
965	plobj.c = self.request[i][j+1][t][z][y][x].field ; found += 1
966	if condfile == "contour":
967	plobj.c = self.request[i+1][j][t][z][y][x].field ; found += 1
968	# see if there is a vector requested...
969	# (we use try because we might be at the end of the list)
970	try: condvar = self.vargoal[j+found+1]+self.vargoal[j+found+2]
971	except: condvar = "itisok"
972	try: condfile = self.filegoal[i+found+1]+self.filegoal[i+found+2]
973	except: condfile = "itisok"
974	# ... get vector and go directly to the next iteration
975	# (in some cases we would do this twice but this is cheap)
976	if "vector" in condvar:
977	plobj.vx = self.request[i][j+found+1][t][z][y][x].field
978	plobj.vy = self.request[i][j+found+2][t][z][y][x].field
979	if "vector" in condfile:
980	plobj.vx = self.request[i+found+1][j][t][z][y][x].field
981	plobj.vy = self.request[i+found+2][j][t][z][y][x].field
982	count = count + 1
983	# COUNT PLOTS. if 0 just exit.
984	# self.howmanyplots is self.nplot + possible extraplots
985	self.howmanyplots = self.nplot + extraplot
986	if self.howmanyplots > 0:
987	if self.verbose: print "**** OK. expect %i plots" % (self.howmanyplots)
988	else:
989	pass # because this means that we only had 0D values !
990	# final status
991	self.status = "definedplot"
992	return self
993
994	##############################################################################################
995	# makeplot method
996	# --> after defineplot and before makeplot, user-defined plot settings can be easily given
997	# simply by modifying the attributes of each elements of self.p
998	# --> to change only one plot setting, no need to call defineplot again before makeplot
999	# --> in the end, the array self.p of plot objects is saved for easy and convenient replotting
1000	# --> see practical examples in the folder 'examples'
1001	##############################################################################################
1002	def makeplot(self):
1003	if self.howmanyplots > 0:
1004	self.printstatus()
1005	# a few initial operations
1006	# ------------------------
1007	if "definedplot" not in self.status:
1008	print "!! ERROR !! Please use .defineplot() before .makeplot() can be used with your pp object." ; exit()
1009	# open a figure and define subplots
1010	# ---------------------------------
1011	if self.plotin is None:
1012	# start from scratch
1013	self.fig = ppplot.figuref(x=self.xp,y=self.yp)
1014	self.subv,self.subh = ppplot.definesubplot(self.howmanyplots,self.fig)
1015	self.n = 0
1016	## adapted space for labels etc
1017	## ... except for ortho because there is no label anyway
1018	self.customplot = self.p[0].f.ndim == 2 \
1019	and self.p[0].mapmode == True \
1020	and self.p[0].proj not in ["ortho","robin"]
1021	if self.customplot:
1022	margin = 0.07
1023	self.fig.subplots_adjust(left=margin,right=1-margin,bottom=margin,top=1-margin)
1024	else:
1025	# start from an existing figure.
1026	# extraplot must have been set in the call to the previous figure.
1027	self.fig = self.plotin.fig
1028	self.subv,self.subh = self.plotin.subv,self.plotin.subh
1029	self.n = self.plotin.n
1030	self.howmanyplots = self.plotin.howmanyplots
1031	self.customplot = self.plotin.customplot
1032	self.filename = self.plotin.filename
1033	# LOOP on all subplots
1034	# NB: cannot use 'for pl in self.p' if self.plotin not None
1035	# --------------------
1036	for count in range(self.nplot):
1037	# the plot object we consider in the loop
1038	pl = self.p[self.n]
1039	# before making the plot, create a subplot. the first one is numbered 1 not 0.
1040	# ... if pl.superpose, we use only one and only figure
1041	# ... (and we have to be careful with not doing things several times)
1042	if pl.superpose:
1043	if self.n == 0:
1044	self.fig.add_subplot(1,1,1,axisbg=pl.axisbg) # define one subplot (still needed for user-defined font sizes)
1045	sav = pl.xlabel,pl.ylabel,\
1046	pl.xcoeff,pl.ycoeff,\
1047	pl.nxticks,pl.nyticks,\
1048	pl.xmin,pl.xmax,\
1049	pl.ymin,pl.ymax,\
1050	pl.title,pl.swaplab # save titles and labels
1051	# possibility to color lines according to a color map
1052	# ... made so that all plots span the whole color map automatically.
1053	if self.colorbar is not None:
1054	if self.verbose: print "**** OK. We make a rainbow spaghetti plot with color map ",self.colorbar
1055	ppplot.rainbow(cb=self.colorbar,num=self.howmanyplots)
1056	else:
1057	pl.invert = False ; pl.linestyle = None # don't invert again axis
1058	# set saved titles and labels
1059	if self.plotin is None:
1060	pl.xlabel,pl.ylabel,\
1061	pl.xcoeff,pl.ycoeff,\
1062	pl.nxticks,pl.nyticks,\
1063	pl.xmin,pl.xmax,\
1064	pl.ymin,pl.ymax,\
1065	pl.title,pl.swaplab = sav
1066	else:
1067	prev_plot = self.plotin.p[self.n-1]
1068	pl.xlabel = prev_plot.xlabel ; pl.ylabel = prev_plot.ylabel
1069	pl.xcoeff = prev_plot.xcoeff ; pl.ycoeff = prev_plot.ycoeff
1070	pl.nxticks = prev_plot.nxticks ; pl.nyticks = prev_plot.nyticks
1071	pl.xmin = prev_plot.xmin ; pl.xmax = prev_plot.xmax
1072	pl.ymin = prev_plot.ymin ; pl.ymax = prev_plot.ymax
1073	pl.title = prev_plot.title ; pl.swaplab = prev_plot.swaplab
1074	else:
1075	self.fig.add_subplot(self.subv,self.subh,self.n+1,axisbg=pl.axisbg)
1076	if self.verbose: print "**** Done subplot %i / %i " %( self.n+1,self.howmanyplots )
1077	# finally make the plot
1078	pl.make()
1079	# possibly print results in a text file
1080	if self.savtxt:
1081	if self.verbose: print "**** Printing results in a text file"
1082	name = pl.var + "%04d" % self.n
1083	ppplot.writeascii(field=pl.f,absc=pl.x,name=name)
1084	# increment plot count (and propagate this in plotin)
1085	self.n = self.n+1
1086	if self.plotin is not None: self.plotin.n = self.n
1087	# once completed show the plot (cannot show intermediate plotin)
1088	# ... added a fix (customplot=True) for the label problem in basemap
1089	if not self.quiet: print "**** PPCLASS. Done step: makeplot"
1090	if (self.n == self.howmanyplots):
1091	ppplot.save(mode=self.out,filename=self.filename,folder=self.folder,custom=self.customplot,includedate=self.includedate,res=self.res)
1092	mpl.close()
1093	# SAVE A PICKLE FILE WITH THE self.p ARRAY OF OBJECTS
1094	if self.filename is not None:
1095	if self.verbose: print "**** Saving session in "+self.filename + ".ppobj"
1096	savfile = self.folder + "/" + self.filename + ".ppobj"
1097	try:
1098	filehandler = open(savfile, 'w')
1099	pickle.dump(self.p, filehandler)
1100	except IOError:
1101	if self.verbose: print "!! WARNING !! Saved object file not written. Probably do not have permission to write here."
1102	return self
1103
1104	###########################################################
1105	# plot: a shortcut method for the defineplot + plot chain #
1106	###########################################################
1107	def plot(self,extraplot=0):
1108	self.defineplot(extraplot=extraplot)
1109	self.makeplot()
1110	return self
1111
1112	#######################################################
1113	# getplot: a shortcut method for the get + plot chain #
1114	#######################################################
1115	def getplot(self,extraplot=0):
1116	self.get()
1117	self.plot(extraplot=extraplot)
1118	return self
1119
1120	###################################################################
1121	# getdefineplot: a shortcut method for the get + defineplot chain #
1122	###################################################################
1123	def getdefineplot(self,extraplot=0):
1124	self.get()
1125	self.defineplot(extraplot=extraplot)
1126	return self
1127
1128	#################################################################
1129	# func: operation on two pp objects being on status 'definedplot'
1130	# this allows for one field being function of another one
1131	# e.g. u.func(v) means u will be displayed as a function of v
1132	# ... no need to do defineplot after u.func(v), makeplot directly
1133	#################################################################
1134	def func(self,other):
1135	# preamble: for this operation to work, defineplot() must have been done
1136	if self.status != "definedplot":
1137	if self.verbose: print "!! WARNING !! performing defineplot on operand"
1138	self.defineplot()
1139	if other.status != "definedplot":
1140	if self.verbose: print "!! WARNING !! performing defineplot on operand"
1141	other.defineplot()
1142	# check total number of plots
1143	if self.howmanyplots != other.howmanyplots:
1144	print "!! ERROR !! The two operands do not have the same number of subplots."
1145	exit()
1146	# and now operation.
1147	count = 0
1148	while count < self.howmanyplots:
1149	sobj = self.p[count] ; oobj = other.p[count]
1150	if sobj.f.ndim !=1 or oobj.f.ndim !=1:
1151	if self.verbose: print "!! WARNING !! Flattening arrays because more than one-dimensional."
1152	sobj.f = np.ravel(sobj.f)
1153	oobj.f = np.ravel(oobj.f)
1154	sobj.x = oobj.f
1155	sobj.xlabel = oobj.ylabel
1156	if sobj.x.size > sobj.f.size:
1157	if self.verbose:
1158	print "!! WARNING !! Trying to define y=f(x) with x and y not at the same size.",sobj.x.size,sobj.f.size
1159	print "!! WARNING !! Modifying x to fit y size but please check."
1160	sobj.x = sobj.x[0:sobj.f.size]
1161	count = count + 1
1162	return self
1163
1164	###########################################################
1165	# copyopt: get options from e.g. a parser
1166	# ... allow for simple scripting and user-defined settings
1167	# ... must be called between defineplot and makeplot
1168	# REQUIRED: attributes of opt must be the same as in the pp object
1169	###########################################################
1170	def getopt(self,opt):
1171	# -- if only one, or less than the number of plots --> we take the first one
1172	# -- if as many as number of plots --> OK, each plot has its own setting
1173	# (except a few cases such as trans)
1174	for iii in range(self.howmanyplots):
1175	## solve the bug about reversed labels with swaplab
1176	if opt.xlabel is None and opt.ylabel is None:
1177	self.p[iii].swaplab = True
1178	else:
1179	self.p[iii].swaplab = False
1180	##
1181	if opt.void:
1182	self.p[iii].showcb = False
1183	else:
1184	self.p[iii].showcb = True
1185	###
1186	try: self.p[iii].trans = opt.trans
1187	except: pass
1188	###
1189	try: self.p[iii].div = opt.div
1190	except: pass
1191	###
1192	try: self.p[iii].logy = opt.logy
1193	except: pass
1194	###
1195	try: self.p[iii].colorbar = opt.colorbar[iii]
1196	except:
1197	try: self.p[iii].colorbar = opt.colorbar[0] ; self.colorbar = opt.colorbar[0]
1198	except: pass
1199	###
1200	if opt.void:
1201	self.p[iii].title = ""
1202	else:
1203	try: self.p[iii].title = opt.title[iii]
1204	except:
1205	try: self.p[iii].title = opt.title[0]
1206	except: pass
1207	###
1208	if opt.void:
1209	self.p[iii].xlabel = ""
1210	else:
1211	try: self.p[iii].xlabel = opt.xlabel[iii]
1212	except:
1213	try: self.p[iii].xlabel = opt.xlabel[0]
1214	except: pass
1215	###
1216	if opt.void:
1217	self.p[iii].ylabel = ""
1218	else:
1219	try: self.p[iii].ylabel = opt.ylabel[iii]
1220	except:
1221	try: self.p[iii].ylabel = opt.ylabel[0]
1222	except: pass
1223	###
1224	try: self.p[iii].linestyle = opt.linestyle[iii]
1225	except:
1226	try: self.p[iii].linestyle = opt.linestyle[0]
1227	except: pass
1228	###
1229	try: self.p[iii].color = opt.color[iii]
1230	except:
1231	try: self.p[iii].color = opt.color[0]
1232	except: pass
1233	###
1234	try: self.p[iii].marker = opt.marker[iii]
1235	except:
1236	try: self.p[iii].marker = opt.marker[0]
1237	except: pass
1238	###
1239	try: self.p[iii].legend = opt.legend[iii]
1240	except:
1241	try: self.p[iii].legend = opt.legend[0]
1242	except: pass
1243	####
1244	try: self.p[iii].back = opt.back[iii]
1245	except:
1246	try: self.p[iii].back = opt.back[0]
1247	except: pass
1248	###
1249	try: self.p[iii].area = opt.area[iii]
1250	except:
1251	try: self.p[iii].area = opt.area[0]
1252	except: pass
1253	###
1254	try: self.p[iii].blon = opt.blon[iii]
1255	except:
1256	try: self.p[iii].blon = opt.blon[0]
1257	except: pass
1258	###
1259	try: self.p[iii].blat = opt.blat[iii]
1260	except:
1261	try: self.p[iii].blat = opt.blat[0]
1262	except: pass
1263	###
1264	try: self.p[iii].vmin = opt.vmin[iii]
1265	except:
1266	try: self.p[iii].vmin = opt.vmin[0]
1267	except: pass
1268	###
1269	try: self.p[iii].vmax = opt.vmax[iii]
1270	except:
1271	try: self.p[iii].vmax = opt.vmax[0]
1272	except: pass
1273	###
1274	try: self.p[iii].xcoeff = opt.xcoeff[iii]
1275	except:
1276	try: self.p[iii].xcoeff = opt.xcoeff[0]
1277	except: pass
1278	###
1279	try: self.p[iii].ycoeff = opt.ycoeff[iii]
1280	except:
1281	try: self.p[iii].ycoeff = opt.ycoeff[0]
1282	except: pass
1283	###
1284	try: self.p[iii].units = opt.units[iii]
1285	except:
1286	try: self.p[iii].units = opt.units[0]
1287	except: pass
1288	###
1289	try: self.p[iii].wscale = opt.wscale[iii]
1290	except:
1291	try: self.p[iii].wscale = opt.wscale[0]
1292	except: pass
1293	###
1294	try: self.p[iii].xmin = opt.xmin[iii]
1295	except:
1296	try: self.p[iii].xmin = opt.xmin[0]
1297	except: pass
1298	###
1299	try: self.p[iii].ymin = opt.ymin[iii]
1300	except:
1301	try: self.p[iii].ymin = opt.ymin[0]
1302	except: pass
1303	###
1304	try: self.p[iii].xmax = opt.xmax[iii]
1305	except:
1306	try: self.p[iii].xmax = opt.xmax[0]
1307	except: pass
1308	###
1309	try: self.p[iii].ymax = opt.ymax[iii]
1310	except:
1311	try: self.p[iii].ymax = opt.ymax[0]
1312	except: pass
1313	###
1314	try: self.p[iii].nxticks = opt.nxticks[iii]
1315	except:
1316	try: self.p[iii].nxticks = opt.nxticks[0]
1317	except: pass
1318	###
1319	try: self.p[iii].nyticks = opt.nyticks[iii]
1320	except:
1321	try: self.p[iii].nyticks = opt.nyticks[0]
1322	except: pass
1323	###
1324	try: self.p[iii].cbticks = opt.cbticks[iii]
1325	except:
1326	try: self.p[iii].cbticks = opt.cbticks[0]
1327	except: pass
1328	###
1329	try: self.p[iii].modx = opt.modx[iii]
1330	except:
1331	try: self.p[iii].modx = opt.modx[0]
1332	except: pass
1333	###
1334	try: self.p[iii].fmt = opt.fmt[iii]
1335	except:
1336	try: self.p[iii].fmt = opt.fmt[0]
1337	except: pass
1338
1339
1340	##########################################################
1341	### THE ONEREQUEST SUBOBJECT TO PP (ON WHICH IT LOOPS) ###
1342	##########################################################
1343	class onerequest():
1344
1345	# default settings. mostly initialized to diagnose problem, except dimplot, nplot, verbose, swap_axes, invert_axes
1346	# -------------------------------
1347	def __init__(self):
1348	self.file = '!! file: I am not set, damned !!'
1349	self.f = None
1350	self.dim = None
1351	self.var = '!! var: I am not set, damned !!'
1352	self.index_x = [] ; self.index_y = [] ; self.index_z = [] ; self.index_t = []
1353	self.index_x2d = [] ; self.index_y2d = []
1354	self.method_x = '!! method_x: I am not set, damned !!'
1355	self.method_y = '!! method_y: I am not set, damned !!'
1356	self.method_z = '!! method_z: I am not set, damned !!'
1357	self.method_t = '!! method_t: I am not set, damned !!'
1358	self.field = None
1359	self.name_x = None ; self.name_y = None ; self.name_z = None ; self.name_t = None
1360	self.dim_x = None ; self.dim_y = None ; self.dim_z = None ; self.dim_t = None
1361	self.field_x = None ; self.field_y = None ; self.field_z = None ; self.field_t = None
1362	self.tabtime = None
1363	self.dimplot = 0
1364	self.nplot = 1
1365	self.absc = None ; self.ordi = None ; self.absclab = None ; self.ordilab = None
1366	self.verbose = True
1367	self.swap_axes = False ; self.invert_axes = False
1368	self.compute = None
1369	self.changetime = None
1370	self.sx = 1 ; self.sy = 1 ; self.sz = 1 ; self.st = 1
1371	self.missing = '!! missing value: I am not set, damned !!'
1372	self.kind3d = '!! kind3d: I am not set, damned !!'
1373
1374	# open a file. for now it is netcdf. TBD for other formats.
1375	# check that self.var is inside.
1376	# -------------------------------
1377	def openfile(self):
1378	if not os.path.exists(self.file): print '!! ERROR !! I could not find the following file: '+self.file ; exit()
1379	if not os.path.isfile(self.file): print '!! ERROR !! This does not appear to be a file: '+self.file ; exit()
1380	self.f = netCDF4.Dataset(self.file)
1381	if self.verbose: print "**** OK. Opened file "+self.file
1382	if self.var not in self.f.variables.keys():
1383	print '!! ERROR !! File '+self.file+' does not contain variable: '+self.var
1384	print '..... try instead with ',self.f.variables.keys() ; exit()
1385
1386	# close a file
1387	# ------------
1388	def closefile(self):
1389	self.f.close()
1390
1391	# copy attributes from another existing object
1392	# --------------------------------------------
1393	def copy(self,source):
1394	for k, v in vars(source).items():
1395	setattr(self,k,v)
1396
1397	# get x,y,z,t dimensions from NETCDF file
1398	# TBD: user could request for a specific altitude dimension
1399	# TBD: staggered variables could request specific dimensions
1400	# -------------------------------
1401	def getdim(self):
1402	# GET SIZES OF EACH DIMENSION
1403	if self.verbose: print "**** OK. Found variable "+self.var
1404	shape = self.f.variables[self.var].shape
1405	self.dim = len(shape)
1406	if self.dim == 1:
1407	if self.verbose: print "**** OK. 1D field. I assume this varies with time."
1408	self.dim_x = 1 ; self.dim_y = 1 ; self.dim_z = 1 ; self.dim_t = shape[0]
1409	elif self.dim == 2:
1410	if self.verbose: print "**** OK. 2D field. I assume this is not-time-varying lat-lon map."
1411	self.dim_x = shape[1] ; self.dim_y = shape[0] ; self.dim_z = 1 ; self.dim_t = 1
1412	elif self.dim == 3:
1413	if self.verbose: print "**** OK. 3D field. I assume this is time-varying lat-lon map."
1414	## see below for comment
1415	if self.kind3d == "tyx":
1416	self.dim_x = shape[2] ; self.dim_y = shape[1] ; self.dim_z = 1 ; self.dim_t = shape[0]
1417	elif self.kind3d == "tzy":
1418	self.dim_x = 1 ; self.dim_y = shape[2] ; self.dim_z = shape[1] ; self.dim_t = shape[0]
1419	else:
1420	print "!! ERROR !! This kind of 3D field is not supported. Please send feedback."
1421	print self.kind3d
1422	exit()
1423	elif self.dim == 4:
1424	if self.verbose: print "**** OK. 4D field."
1425	self.dim_x = shape[3] ; self.dim_y = shape[2] ; self.dim_z = shape[1] ; self.dim_t = shape[0]
1426	# LONGITUDE. Try preset fields. If not present set grid points axis.
1427	self.name_x = "nothing"
1428	for c in glob_listx:
1429	if c in self.f.variables.keys():
1430	self.name_x = c
1431	if self.name_x == "nothing":
1432	self.field_x = np.array(range(self.dim_x))
1433	self.name_x = "x grid points"
1434	else:
1435	self.field_x = self.f.variables[self.name_x]
1436	# LATITUDE. Try preset fields. If not present set grid points axis.
1437	self.name_y = "nothing"
1438	for c in glob_listy:
1439	if c in self.f.variables.keys():
1440	self.name_y = c
1441	if self.name_y == "nothing":
1442	self.field_y = np.array(range(self.dim_y))
1443	self.name_y = "y grid points"
1444	else:
1445	self.field_y = self.f.variables[self.name_y]
1446	# ensure that lon and lat are 2D fields
1447	# 1. simple 1D case (not time-varying)
1448	if len(self.field_x.shape)*len(self.field_y.shape) == 1:
1449	if self.verbose: print "**** OK. recasting lon and lat as 2D fields."
1450	[self.field_x,self.field_y] = np.meshgrid(self.field_x,self.field_y)
1451	# 2. complex 3D case (time-varying, actually just copied over time axis)
1452	elif len(self.field_x.shape)*len(self.field_y.shape) == 9:
1453	if self.verbose: print "**** OK. reducing lon and lat as 2D fields. get rid of time."
1454	# if longitudes are crossing 180 deg limit, then modify longitude vector
1455	self.field_x = self.field_x[0,:,:]
1456	for j in range(self.field_x[0,:].size-1):
1457	if (self.field_x[0,j+1]-self.field_x[0,j] < 0.):
1458	self.field_x[:,j+1]=self.field_x[:,j+1]+360.
1459	self.field_y = self.field_y[0,:,:]
1460	# if xy axis are apparently undefined, set 2D grid points axis.
1461	if "grid points" not in self.name_x:
1462	if np.all(self.field_x == self.field_x[0,0]) \
1463	or self.field_x.min() == self.field_x.max() \
1464	or self.field_y.min() == self.field_y.max():
1465	if self.verbose: print "!! WARNING !! xy axis look undefined. creating non-dummy ones."
1466	self.field_x = np.array(range(self.dim_x)) ; self.name_x = "x grid points"
1467	self.field_y = np.array(range(self.dim_y)) ; self.name_y = "y grid points"
1468	[self.field_x,self.field_y] = np.meshgrid(self.field_x,self.field_y)
1469	if self.dim_x > 1:
1470	if self.verbose: print "**** OK. x axis %4.0f values [%5.1f,%5.1f]" % (self.dim_x,self.field_x.min(),self.field_x.max())
1471	if self.dim_y > 1:
1472	if self.verbose: print "**** OK. y axis %4.0f values [%5.1f,%5.1f]" % (self.dim_y,self.field_y.min(),self.field_y.max())
1473	# ALTITUDE. Try preset fields. If not present set grid points axis.
1474	# WARNING: how do we do if several are available? the last one is chosen.
1475	self.name_z = "nothing"
1476	for c in glob_listz:
1477	if c in self.f.variables.keys():
1478	self.name_z = c
1479	if self.name_z == "nothing":
1480	self.field_z = np.array(range(self.dim_z))
1481	self.name_z = "z grid points"
1482	else:
1483	tabalt = self.f.variables[self.name_z]
1484	# (consider the case where tabtime is not dim 1) TBD: 2D and 3D cases
1485	if tabalt.ndim == 4:
1486	try:
1487	self.field_z = tabalt[1,:,0,0] # 4D case. alt is usually third dimension.
1488	# 1 for time to avoid initial 0s
1489	except:
1490	self.field_z = tabalt[0,:,0,0]
1491	if self.verbose: print "!! WARNING !! "+self.name_z+" is 4D var. We made it 1D."
1492	else:
1493	self.field_z = self.f.variables[self.name_z][:] # specify dimension
1494	# TBD: problems when self.dim_z != self.field_z.size
1495	if self.field_z.size != self.dim_z:
1496	if self.verbose: print "!! WARNING !! Cannot use this z coordinate. Not enough points. Use simple z axis."
1497	self.field_z = np.array(range(self.dim_z))
1498	self.name_z = "z grid points"
1499	if self.dim_z > 1:
1500	if self.verbose: print "**** OK. z axis %4.0f values [%5.1f,%5.1f]" % (self.dim_z,self.field_z.min(),self.field_z.max())
1501
1502	# TIME. Try preset fields.
1503	self.name_t = "nothing"
1504	for c in glob_listt:
1505	if c in self.f.variables.keys():
1506	self.name_t = c
1507	if self.verbose: print "**** OK. Found time variable: ",c
1508	try:
1509	# speed up: only get first value, last one.
1510	self.tabtime = self.f.variables[self.name_t]
1511	# (consider the case where tabtime is not dim 1)
1512	# (time is most often the first dimension)
1513	if self.tabtime.ndim == 2: self.tabtime = self.tabtime[:,0]
1514	elif self.tabtime.ndim == 3: self.tabtime = self.tabtime[:,0,0]
1515	elif self.tabtime.ndim == 4: self.tabtime = self.tabtime[:,0,0,0]
1516	# (now proceed) (the +0. just ensures this is a number)
1517	dafirst = self.tabtime[0] + 0.
1518	if self.dim_t == 1:
1519	self.field_t = np.array([dafirst])
1520	else:
1521	daint = self.tabtime[1] - dafirst
1522	dalast = dafirst + (self.dim_t-1)*daint
1523	self.field_t = np.linspace(dafirst,dalast,num=self.dim_t)
1524	if self.verbose:
1525	print "!! WARNING !! WARNING !! Time axis is supposed to be equally spaced !!"
1526	if dalast != self.tabtime[self.dim_t-1]:
1527	print "!! WARNING !! Time axis has been recast to be monotonic",dalast,self.tabtime[self.dim_t-1]
1528	except:
1529	# ... or if a problem encountered, define a simple time axis
1530	if self.verbose: print "**** OK. There is something weird. Let us go for a simple time axis."
1531	self.field_t = np.array(range(self.dim_t))
1532	self.name_t = "t grid points"
1533	if self.dim_t > 1:
1534	if self.verbose: print "**** OK. t axis %4.0f values [%5.1f,%5.1f]" % (self.dim_t,self.field_t.min(),self.field_t.max())
1535
1536	# change time axis
1537	# ... add your options here!
1538	# --------------------------
1539	def performtimechange(self):
1540	if self.changetime is not None:
1541	if self.verbose: print "**** OK. Converting time axis:",self.changetime
1542	### options added by T. Navarro
1543	if self.changetime == "mars_sol2ls":
1544	if "controle" in self.f.variables:
1545	self.field_t = self.field_t \
1546	+ self.f.variables['controle'][3]%669 \
1547	+ self.f.variables['controle'][26]
1548	self.field_t = ppcompute.mars_sol2ls(self.field_t)
1549	elif self.changetime == "mars_dayini" and "controle" in self.f.variables:
1550	self.field_t = self.field_t \
1551	+ self.f.variables['controle'][3]%669 \
1552	+ self.f.variables['controle'][26]
1553	### options added by A. Spiga
1554	elif self.changetime == "correctls":
1555	if self.tabtime is None:
1556	print "!! WARNING !! Encountered a problem with correctls. Check your time dimension. Skipping this part."
1557	else:
1558	dafirst = self.tabtime[0] + 0.
1559	if self.dim_t == 1:
1560	self.field_t = np.array([dafirst])
1561	else:
1562	daint = self.tabtime[1] - dafirst
1563	dalast = dafirst + (self.dim_t-1)*daint
1564	year = 0.
1565	add = np.linspace(dafirst,dalast,num=self.dim_t) ; add[0] = 0.
1566	for iii in range(1,self.dim_t):
1567	if self.tabtime[iii] - self.tabtime[iii-1] < 0: year = year+1.
1568	add[iii] = year*360.
1569	self.field_t = add + self.tabtime
1570	elif "mars_meso" in self.changetime:
1571	if 'Times' not in self.f.variables.keys():
1572	if self.verbose: print "!! WARNING !! Variable Times not in file. Cannot proceed to change of time axis."
1573	else:
1574	# get the array of strings describing dates
1575	dates = self.f.variables['Times']
1576	dates.set_auto_maskandscale(False) # necessary to solve the api Times bug!
1577	# get ls sol utc from those strings
1578	ls, sol, utc = ppcompute.mars_date(dates[:])
1579	# populate self.field_t with the right output from mars_date
1580	if self.changetime == "mars_meso_ls":
1581	self.field_t = ls
1582	self.name_t = "Ls"
1583	elif self.changetime == "mars_meso_sol":
1584	self.field_t = sol
1585	self.name_t = "sol"
1586	elif self.changetime == "mars_meso_utc" \
1587	and ( self.changetime == "mars_meso_lt" \
1588	and not hasattr(self.f,'CEN_LON') ):
1589	self.field_t = ppcompute.timecorrect(utc)
1590	self.name_t = "utc"
1591	if self.method_t == "fixed":
1592	self.field_t = self.field_t % 24 # so that the user is not mistaken!
1593	elif self.changetime == "mars_meso_lt":
1594	self.field_t = ppcompute.timecorrect(utc) + getattr(self.f,'CEN_LON') / 15.
1595	self.field_t = ppcompute.timecorrect(self.field_t)
1596	self.name_t = "local time (center of domain)"
1597	if self.method_t == "fixed":
1598	self.field_t = self.field_t % 24 # so that the user is not mistaken!
1599	else:
1600	if self.verbose: print "!! WARNING !! This time change is not implemented. Nothing is done."
1601	if self.verbose: print "**** OK. new t axis values [%5.1f,%5.1f]" % (self.field_t.min(),self.field_t.max())
1602
1603	# get list of index to be retrieved for time axis
1604	### TBD: il faudrait ne prendre que les indices qui correspondent a l interieur d un plot (dans all)
1605	# -------------------------------
1606	def getindextime(self,dalist=None,ind=None):
1607	if self.method_t == "free":
1608	self.index_t = np.arange(0,self.dim_t,self.st)
1609	if self.dim_t > 1:
1610	self.dimplot = self.dimplot + 1
1611	if self.verbose: print "**** OK. t values. all."
1612	else:
1613	self.method_t = "fixed"
1614	if self.verbose: print "**** OK. no t dimension."
1615	elif self.method_t == "comp":
1616	start = np.argmin( np.abs( self.field_t - dalist[ind][0] ) )
1617	stop = np.argmin( np.abs( self.field_t - dalist[ind][1] ) )
1618	self.index_t = np.arange(start,stop+1,self.st)
1619	if self.verbose: print "**** OK. t values. comp over interval ",self.field_t[start],self.field_t[stop]," nvalues=",self.index_t.size
1620	elif self.method_t == "fixed":
1621	self.index_t.append( np.argmin( np.abs( self.field_t - dalist[ind][0] ) ))
1622	if self.verbose: print "**** OK. t values",self.field_t[self.index_t]
1623	else:
1624	print "!! ERROR !! method "+self.method_t+" not supported"
1625	self.index_t = np.array(self.index_t)
1626
1627	# get list of index to be retrieved for vertical axis
1628	### TBD: il faudrait ne prendre que les indices qui correspondent a l interieur d un plot (dans all)
1629	# -------------------------------
1630	def getindexvert(self,dalist=None,ind=None):
1631	if self.method_z == "free":
1632	self.index_z = np.arange(0,self.dim_z,self.sz)
1633	if self.dim_z > 1:
1634	self.dimplot = self.dimplot + 1
1635	if self.verbose: print "**** OK. z values. all."
1636	else:
1637	self.method_z = "fixed"
1638	if self.verbose: print "**** OK. no z dimension."
1639	elif self.method_z == "comp":
1640	start = np.argmin( np.abs( self.field_z - dalist[ind][0] ) )
1641	stop = np.argmin( np.abs( self.field_z - dalist[ind][1] ) )
1642	self.index_z = np.arange(start,stop+1,self.sz)
1643	if self.verbose: print "**** OK. z values. comp over interval",self.field_z[start],self.field_z[stop]," nvalues=",self.index_z.size
1644	elif self.method_z == "fixed":
1645	self.index_z.append( np.argmin( np.abs( self.field_z - dalist[ind][0] ) ))
1646	if self.verbose: print "**** OK. z values",self.field_z[self.index_z]
1647	else:
1648	if self.verbose: print "!! ERROR !! method "+self.method_z+" not supported"
1649	self.index_z = np.array(self.index_z)
1650
1651	# get list of index to be retrieved for horizontal grid
1652	# --> index_x and index_y are slices to be retrieved from NETCDF files
1653	# --> index_x2d and index_y2d are the actual (x,y) coordinates corresponding to each relevant point
1654	# [this is slightly more complicated because 2D arrays for lat-lon projection possibly irregular]
1655	# NB: to append index we use lists (the most convenient) then we convert into a numpy.array
1656	### TBD: il faudrait ne prendre que les indices qui correspondent a l interieur d un plot (dans all)
1657	# -------------------------------
1658	def getindexhori(self,dalistx=None,dalisty=None,indx=None,indy=None):
1659	## get what is the method over x and y axis
1660	test = self.method_x+self.method_y
1661	## CASE 0, EASY CASES:
1662	## - LAT IS FREE (we do here what must be done whatever LON case is)
1663	## - LON IS FREE (we do here what must be done whatever LAT case is)
1664	## - LAT IS COMP AND LON IS FREE
1665	## - LON IS COMP AND LAT IS FREE
1666	if self.method_x == "free" or test in ["compfree","compcomp"]:
1667	self.index_x = range(0,self.dim_x,self.sx)
1668	if self.dim_x > 1:
1669	if self.method_x == "free": self.dimplot = self.dimplot + 1
1670	if self.verbose: print "**** OK. x values. all."
1671	else:
1672	self.method_x = "fixed"
1673	if self.verbose: print "**** OK. no x dimension."
1674	if self.method_y == "free" or test in ["freecomp","compcomp"]:
1675	self.index_y = range(0,self.dim_y,self.sy)
1676	if self.dim_y > 1:
1677	if self.method_y == "free": self.dimplot = self.dimplot + 1
1678	if self.verbose: print "**** OK. y values. all."
1679	else:
1680	self.method_y = "fixed"
1681	if self.verbose: print "**** OK. no y dimension."
1682	## CASE 0 above, this is just for continuity for free.
1683	## ... for comp we have to select bounds.
1684	## ... TBD: take the bool array strategy for what follows!
1685	if self.method_x in ["free","comp"] and self.method_y in ["free","comp"]:
1686	### ref1_dirty_hack
1687	### ... for the moment this is a hack. but actually this is more powerful.
1688	if self.method_x == "comp":
1689	yeah = (self.field_x >= dalistx[indx][0])*(self.field_x <= dalistx[indx][1])
1690	self.index_x = yeah[0,:]
1691	if self.method_y == "comp":
1692	yeah = (self.field_y >= dalisty[indy][0])*(self.field_y <= dalisty[indy][1])
1693	self.index_y = yeah[:,0]
1694	self.index_x2d = self.index_x
1695	self.index_y2d = self.index_y
1696	## AND NOW THE LITTLE BIT MORE COMPLICATED CASES
1697	## CASE 1 LAT AND LON ARE FIXED
1698	elif test == "fixedfixed":
1699	idy,idx = np.unravel_index( np.argmin( ( self.field_x - dalistx[indx][0])2 + (self.field_y - dalisty[indy][0])2 ), self.field_x.shape )
1700	#TBD: pb with staggered coord
1701	if idx not in self.index_x: self.index_x.append(idx)
1702	if idy not in self.index_y: self.index_y.append(idy)
1703	self.index_x2d.append(idx)
1704	self.index_y2d.append(idy)
1705	## CASE 2 LON IS FIXED BUT NOT LAT
1706	elif test in ["fixedfree","fixedcomp"]:
1707	# find where are requested x values for each y on the free dimension
1708	# NB: this does not work for non-bijective cases e.g. polar stereographic
1709	for iy in range(self.dim_y):
1710	idx = np.argmin( np.abs( self.field_x[iy,:] - dalistx[indx][0] ) )
1711	# if comp is requested we select only indexes which yield values between requested min and max
1712	storeval = (self.method_y == "comp") and (self.field_y[iy,idx] > dalisty[indy][0]) and (self.field_y[iy,idx] < dalisty[indy][1])
1713	storeval = storeval or (self.method_y == "free")
1714	if storeval:
1715	if idx not in self.index_x: self.index_x.append(idx)
1716	if iy not in self.index_y and self.method_y == "comp": self.index_y.append(iy)
1717	if idx not in self.index_x2d or iy not in self.index_y2d:
1718	self.index_x2d.append(idx)
1719	self.index_y2d.append(iy)
1720	## CASE 3 LAT IS FIXED BUT NOT LON
1721	elif test in ["freefixed","compfixed"]:
1722	# find where are requested y values for each x on the free dimension
1723	# NB: this does not work for non-bijective cases e.g. polar stereographic
1724	for ix in range(self.dim_x):
1725	idy = np.argmin( np.abs( self.field_y[:,ix] - dalisty[indy][0] ) )
1726	# if comp is requested we select only indexes which yield values between requested min and max
1727	storeval = (self.method_x == "comp") and (self.field_x[idy,ix] > dalistx[indx][0]) and (self.field_x[idy,ix] < dalistx[indx][1])
1728	storeval = storeval or (self.method_x == "free")
1729	if storeval:
1730	if idy not in self.index_y: self.index_y.append(idy)
1731	if ix not in self.index_x and self.method_x == "comp": self.index_x.append(ix)
1732	if ix not in self.index_x2d or idy not in self.index_y2d:
1733	self.index_x2d.append(ix)
1734	self.index_y2d.append(idy)
1735	## check index tab
1736	if len(self.index_x) == 0 or len(self.index_y) == 0:
1737	print "!! ERROR !! no indices found. check prescribed latitudes or longitudes" ; exit()
1738	## ensure the array is a numpy array for getfield to work
1739	self.index_x = np.array(self.index_x)
1740	self.index_y = np.array(self.index_y)
1741	self.index_x2d = np.array(self.index_x2d)
1742	self.index_y2d = np.array(self.index_y2d)
1743	### print extrema
1744	printx = self.field_x[np.ix_(self.index_y2d, self.index_x2d)]
1745	printy = self.field_y[np.ix_(self.index_y2d, self.index_x2d)]
1746	if self.verbose:
1747	print "**** OK. x values (min,max).", printx.min(),printx.max()
1748	print "**** OK. y values (min,max).", printy.min(),printy.max()
1749
1750	# get the field from the NETCDF file and perform averages
1751	# -------------------------------
1752	def getfield(self):
1753	## first tell what is to be done
1754	if self.verbose:
1755	if self.dimplot > 2: print "**** !! WARNING !! "+str(self.dimplot)+"D plots will not be supported!"
1756	elif self.dimplot == 0 and self.verbose: print "**** OK. 0D value requested."
1757	elif self.dimplot == 1 and self.verbose: print "**** OK. 1D plot requested."
1758	elif self.verbose: print "**** OK. 2D section requested."
1759	# well, now get field from netcdf file
1760	# part below is necessary otherwise there is an index error below
1761	if self.index_x.size == 1: self.index_x = self.index_x[0]
1762	if self.index_y.size == 1: self.index_y = self.index_y[0]
1763	if self.index_z.size == 1: self.index_z = self.index_z[0]
1764	if self.index_t.size == 1: self.index_t = self.index_t[0]
1765	# set everything about dimensions and slices
1766	# -- each self.dim case corresponds to tests in the beginning of getdim.
1767	if self.dim == 1:
1768	nt = self.index_t.size ; nz = 1 ; ny = 1 ; nx = 1
1769	tupledim = self.index_t
1770	elif self.dim == 2:
1771	nt = 1 ; nz = 1 ; ny = self.index_y.size ; nx = self.index_x.size
1772	tupledim = self.index_y,self.index_x
1773	elif self.dim == 3:
1774	## DEFAULT tyx (time-varying 2D field)
1775	if self.kind3d == "tyx":
1776	nt = self.index_t.size ; nz = 1 ; ny = self.index_y.size ; nx = self.index_x.size
1777	tupledim = self.index_t,self.index_y,self.index_x
1778	## CASE tzy (e.g. time-varying zonal mean y-z field)
1779	elif self.kind3d == "tzy":
1780	nt = self.index_t.size ; nz = self.index_z.size ; ny = self.index_y.size ; nx = 1
1781	tupledim = self.index_t,self.index_z,self.index_y
1782	else:
1783	print "!! ERROR !! This kind of 3D field is not supported. Please send feedback." ; exit()
1784	# this is far faster than retrieving each term with a loop
1785	elif self.dim == 4:
1786	nt = self.index_t.size ; nz = self.index_z.size ; ny = self.index_y.size ; nx = self.index_x.size
1787	tupledim = self.index_t,self.index_z,self.index_y,self.index_x
1788	else:
1789	print "!! ERROR !! field would have more than four dimensions ?" ; exit()
1790	# then retrieve what is requested by user!
1791	time0 = timelib.time()
1792	if self.verbose: print "**** OK. I am getting values from files. Please wait."
1793	self.field = self.f.variables[self.var][tupledim]
1794	# dirty hack (AS) ref1_dirty_hack
1795	# waiting for more fundamental modifications. case when self.index_y is a bool array.
1796	# ... be careful if no point...
1797	try:
1798	if type(self.index_x[0]) == np.bool_: nx = np.sum(self.index_x) ## gives the size of the True part!
1799	if type(self.index_y[0]) == np.bool_: ny = np.sum(self.index_y) ## gives the size of the True part!
1800	except:
1801	pass
1802	# NB: ... always 4D array but possibly with "size 1" dimensions
1803	# ... if one dimension is missing because 1D 2D or 3D requests, make it appear again
1804	self.field = np.reshape(self.field,(nt,nz,ny,nx))
1805	if self.verbose: print "**** OK. I got %7.1e values. This took me %6.4f seconds" % (nxnynz*nt,timelib.time() - time0)
1806	if self.verbose: print "**** OK. I got var "+self.var+" with shape",self.field.shape
1807	# reduce coordinates to useful points
1808	# ... TBD: this should be ordered in the case of non-regular projections
1809	if self.method_x in ["free","comp"] and self.method_y in ["free","comp"]:
1810	# we need 2D coordinates (free) or we get broadcast problem (comp) so we use np.ix
1811	self.field_x = self.field_x[np.ix_(self.index_y2d, self.index_x2d)]
1812	self.field_y = self.field_y[np.ix_(self.index_y2d, self.index_x2d)]
1813	else:
1814	# we are OK with 1D coordinates
1815	self.field_x = self.field_x[self.index_y2d, self.index_x2d]
1816	self.field_y = self.field_y[self.index_y2d, self.index_x2d]
1817	# ... there are special cases with strides
1818	# ... some other fixes will be needed probably TBD
1819	if self.method_x == "free" and self.sx != 1:
1820	self.field_x = self.field_x[self.index_x]
1821	if self.method_y == "free" and self.sy != 1:
1822	self.field_y = self.field_y[self.index_y]
1823	self.field_z = self.field_z[self.index_z]
1824	self.field_t = self.field_t[self.index_t]
1825	# extract relevant horizontal points
1826	# TBD: is compfree OK with computing on irregular grid?
1827	test = self.method_x + self.method_y
1828	if test in ["fixedfixed","freefree"]:
1829	pass
1830	elif test in ["fixedfree","fixedcomp"] or test in ["freefixed","compfixed"]:
1831	if self.sx == 1 and self.sy == 1:
1832	time0 = timelib.time()
1833	# now have to obtain the new indexes which correspond to the extracted self.field
1834	# for it to work with unique index, ensure that any index_* is a numpy array
1835	if not isinstance(self.index_x, np.ndarray): self.index_x = np.array([self.index_x])
1836	if not isinstance(self.index_y, np.ndarray): self.index_y = np.array([self.index_y])
1837	if not isinstance(self.index_z, np.ndarray): self.index_z = np.array([self.index_z])
1838	if not isinstance(self.index_t, np.ndarray): self.index_t = np.array([self.index_t])
1839	for val in self.index_x: self.index_x2d[np.where(self.index_x2d == val)] = np.where(self.index_x == val)[0]
1840	for val in self.index_y: self.index_y2d[np.where(self.index_y2d == val)] = np.where(self.index_y == val)[0]
1841	##### VERY EXPENSIVE
1842	## recast self.field with 2D horizontal arrays because we might have extracted
1843	## more than what is to be actually plot or computed, in particular for comps on 2D lat,lon coordinates
1844	#self.field = self.field[np.ix_(self.index_t,self.index_z,self.index_y2d,self.index_x2d)]
1845	#(nt,nz,ny,nx) = self.field.shape
1846	# prepare the loop on all relevant horizontal points
1847	if self.method_x in ["comp","free"]:
1848	nnn = self.index_x2d.shape[0] ; what_I_am_supposed_to_do = "keepx"
1849	elif self.method_y in ["comp","free"]:
1850	nnn = self.index_y2d.shape[0] ; what_I_am_supposed_to_do = "keepy"
1851	# LOOP to extract only useful values over horizontal dimensions
1852	# only take diagonal terms, do not loop on all self.index_x2d*self.index_y2d
1853	# ... this method is fast enough, perhaps there is a faster way though
1854	# ... (for sure the method with np.diag is much slower)
1855	for iii in range(nnn):
1856	ix = self.index_x2d[iii] ; iy = self.index_y2d[iii]
1857	for iz in range(self.index_z.size):
1858	for it in range(self.index_t.size):
1859	if what_I_am_supposed_to_do == "keepx": self.field[it,iz,0,ix] = self.field[it,iz,iy,ix]
1860	elif what_I_am_supposed_to_do == "keepy": self.field[it,iz,iy,0] = self.field[it,iz,iy,ix]
1861	if self.verbose: print "**** OK. I got to pick the right values for your request. This took me %6.4f seconds" % (timelib.time() - time0)
1862	# we only keep the one value that was modified on the dimension which is not free
1863	if what_I_am_supposed_to_do == "keepx": self.field = self.field[:,:,0,:] ; ny = 1 ; self.field = np.reshape(self.field,(nt,nz,ny,nx))
1864	elif what_I_am_supposed_to_do == "keepy": self.field = self.field[:,:,:,0] ; nx = 1 ; self.field = np.reshape(self.field,(nt,nz,ny,nx))
1865	else:
1866	# there is a problem above if stride != 1. a fix must be found. rewrite might be necessary. TBD
1867	pass
1868	# check if 'not finite' values are present
1869	# (happens with some netCDF files where -- appears in arrays)
1870	# (but isn't it that netcdf4 returns masked arrays?)
1871	# -- we do not perform this correction for computations for which -- are handled correctly
1872	if "comp" not in self.method_t+self.method_z+self.method_y+self.method_x:
1873	w = np.where(np.isfinite(self.field) != True)
1874	self.field[w] = np.NaN
1875	## catch netCDF missing values (TBD: add a test try)
1876	#miss = self.f.variables[self.var].missing_value
1877	#if miss is not None: self.missing = miss
1878	# make a mask in case there are non-NaN missing values.
1879	# ... this is important for computations below (see ppcompute)
1880	masked = np.ma.masked_where(np.abs(self.field) >= self.missing,self.field)
1881	if masked.mask.any() == True:
1882	if self.verbose: print "!! WARNING !! Values over %5.3e are considered missing values." % self.missing
1883	self.field = masked
1884	self.field.set_fill_value([np.NaN])
1885
1886	# perform computations
1887	# -------------------------------
1888	# available: mean, max, min, meanarea
1889	# TB: integrals? for derivatives, define a function self.dx()
1890	def computations(self):
1891	nt,nz,ny,nx = self.field.shape
1892	# treat the case of mean on fields normalized with grid mesh area
1893	# ... this is done in the .area() method.
1894	# after that self.field contains field*area/totarea
1895	if "area" in self.compute:
1896	if "comp" in self.method_x+self.method_y:
1897	self.area()
1898	else:
1899	if self.verbose: print "!! WARNING !! No area accounted for (computing on t and/or z axis)."
1900	# prepare quadratic mean
1901	if "qmean" in self.compute: self.field = self.field*self.field
1902	# prepare and execute (possibly sequential) means
1903	roll = [self.method_t, self.method_z, self.method_y, self.method_x]
1904	reshapedim = [nt,nz,ny,nx]
1905	for nr in range(len(roll)):
1906	rrr = roll[nr]
1907	if "comp" in rrr:
1908	# a. computing
1909	if self.verbose: print "**** OK. Computing over axis number ",nr
1910	if self.compute == "meanarea": self.field = ppcompute.sum (self.field,axis=nr)
1911	elif "mean" in self.compute: self.field = ppcompute.mean (self.field,axis=nr)
1912	elif self.compute == "min": self.field = ppcompute.min (self.field,axis=nr)
1913	elif self.compute == "max": self.field = ppcompute.max (self.field,axis=nr)
1914	else: print "!! ERROR !! operation not supported." ; exit()
1915	# b. reshaping
1916	reshapedim[nr] = 1
1917	self.field = np.reshape(self.field,reshapedim)
1918	# c. particular cases for 2D coordinates
1919	if nr == 2 and self.field_x.ndim == 2: self.field_x = self.field_x[0,:] # TBD: this is OK for regular grid but not for irregular
1920	if nr == 3 and self.field_y.ndim == 2: self.field_y = self.field_y[:,0] # TBD: this is OK for regular grid but not for irregular
1921	# computations for which only setting compute is needed
1922	if "_x" in self.compute: zeaxis = 3
1923	elif "_y" in self.compute: zeaxis = 2
1924	elif "_z" in self.compute: zeaxis = 1
1925	elif "_t" in self.compute: zeaxis = 0
1926	if "pert" in self.compute:
1927	self.field = ppcompute.perturbation(self.field,axis=zeaxis)
1928	elif "diff" in self.compute:
1929	dadiff = np.diff(self.field,axis=zeaxis)
1930	# (diff ouput has one value less in impacted dimension. fix this.)
1931	reshapedim[zeaxis] = reshapedim[zeaxis]-1
1932	self.field[:,:,:,:] = np.nan
1933	self.field[0:reshapedim[0],0:reshapedim[1],0:reshapedim[2],0:reshapedim[3]] = dadiff
1934	# remove all dimensions with size 1 to prepare plot (and check the resulting dimension with dimplot)
1935	self.field = np.squeeze(self.field)
1936	# take root mean square for quadratic mean
1937	if self.compute == "qmean": self.field = np.sqrt(self.field)
1938	# error handling and verbose
1939	if self.field.ndim != self.dimplot:
1940	print "!! ERROR !! Problem: self.field is different than plot dimensions", self.field.ndim, self.dimplot ; exit()
1941	if self.verbose:
1942	print "**** OK. Final shape for "+self.var+" after averaging and squeezing",self.field.shape
1943
1944	# get areas for computations and ponderate self.field by area/totarea
1945	# -------------------------------------------------------------------
1946	def area(self):
1947	if self.verbose: print "**** OK. Get area array for computations."
1948	# create a request object for area
1949	# ... and copy known attributes from self
1950	aire = onerequest()
1951	aire.copy(self)
1952	# get area field name
1953	aire.var = "nothing"
1954	for c in glob_listarea:
1955	if c in aire.f.variables.keys():
1956	aire.var = c
1957	# do not try to calculate areas automatically
1958	if aire.var == "nothing":
1959	print "!! ERROR !! area variable not found... needs to be added in set_ppclass.txt?"
1960	exit()
1961	# define area request dimensions
1962	aire.getdim()
1963	# ensure this is a 2D horizontal request and define indexes
1964	# ... areas are not supposed to vary with time and height
1965	aire.method_x = "free" ; aire.method_y = "free"
1966	aire.getindexhori() ; aire.dimplot = 2
1967	aire.method_z = "fixed" ; aire.field_z = np.array([0]) ; aire.index_z = np.array([0])
1968	aire.method_t = "fixed" ; aire.field_t = np.array([0]) ; aire.index_t = np.array([0])
1969	# read the 2D area array in netCDF file
1970	aire.getfield()
1971	aire.field = np.squeeze(aire.field)
1972	# reduce with self horizontal indexes
1973	if "fixed" in self.method_x+self.method_y:
1974	aire.field = aire.field[self.index_y,self.index_x]
1975	# calculate total area
1976	# ... 2D comp is easy. 1D comp is a bit less easy but simple array manipulation.
1977	if "free" in self.method_x+self.method_y:
1978	if self.method_x == "free":
1979	totarea = ppcompute.sum(aire.field,axis=0)
1980	totarea = np.reshape(totarea,(1,totarea.size))
1981	totarea = np.tile(totarea,(1,self.index_x))
1982	elif self.method_y == "free":
1983	totarea = ppcompute.sum(aire.field,axis=1)
1984	totarea = np.reshape(totarea,(totarea.size,1))
1985	totarea = np.tile(totarea,(1,self.index_x.size))
1986	elif self.method_x == "comp" and self.method_y == "comp":
1987	aire.field = aire.field[np.ix_(self.index_y, self.index_x)] # reduce to requested indexes only
1988	totarea = ppcompute.sum(ppcompute.sum(aire.field,axis=1),axis=0)
1989	else:
1990	if self.verbose: print "!! WARNING !! Not account for areas. Only averaging over z and/or t axis."
1991	# normalize by total area
1992	print "**** OK. I can now normalize field by areas."
1993	aire.field = aire.field / totarea
1994	# tile area array over self t and z axis so that area field could be multiplied with self.field
1995	aire.field = np.tile(aire.field,(self.index_t.size,self.index_z.size,1,1))
1996	if self.field.shape != aire.field.shape:
1997	print "!! ERROR !! Problem in area(). Check array shapes."
1998	print "Field vs. aire:",self.field.shape,aire.field.shape ; exit()
1999	else:
2000	self.field = self.field*aire.field
2001
2002	# define coordinates for plot
2003	# -------------------------------
2004	def definecoord(self):
2005	I_got_abs = False ; I_got_ord = False
2006	# here is the thing. time is usually taken as an abscissa so we start with time.
2007	if self.method_t == "free":
2008	self.absc = self.field_t ; self.absclab = self.name_t
2009	I_got_abs = True
2010	# then we usually have x as an abscissa.
2011	if self.method_x == "free":
2012	if I_got_abs:
2013	self.ordi = self.field_x ; self.ordilab = self.name_x
2014	I_got_ord = True
2015	else:
2016	self.absc = self.field_x ; self.absclab = self.name_x
2017	I_got_abs = True
2018	# ... or we have y
2019	if self.method_y == "free":
2020	if I_got_abs:
2021	self.ordi = self.field_y ; self.ordilab = self.name_y
2022	I_got_ord = True
2023	else:
2024	self.absc = self.field_y ; self.absclab = self.name_y
2025	I_got_abs = True
2026	# ... and we end with z because it is usually not an abscissa (profiles).
2027	if self.method_z == "free":
2028	if self.field_z[0] > self.field_z[1]:
2029	self.invert_axes = True # the axis will be turned upside-down
2030	if I_got_abs:
2031	self.ordi = self.field_z ; self.ordilab = self.name_z
2032	I_got_ord = True
2033	else:
2034	self.absc = self.field_z ; self.absclab = self.name_z
2035	I_got_abs = True
2036	self.swap_axes = True # says that altitude is not supposed to remain as an abscissa
2037	if I_got_abs and self.verbose: print "**** OK. abscissa:",self.absclab, self.absc.shape
2038	if I_got_ord and self.verbose: print "**** OK. ordinate:",self.ordilab, self.ordi.shape

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