def main(): """ NAME site_edit_magic.py DESCRIPTION makes equal area projections site by site from pmag_specimens.txt file with Fisher confidence ellipse using McFadden and McElhinny (1988) technique for combining lines and planes allows testing and reject specimens for bad orientations SYNTAX site_edit_magic.py [command line options] OPTIONS -h: prints help and quits -f: specify pmag_specimen format file, default is pmag_specimens.txt -fsa: specify er_samples.txt file -exc: use existing pmag_criteria.txt file -N: reset all sample flags to good OUPUT edited er_samples.txt file """ dir_path='.' FIG={} # plot dictionary FIG['eqarea']=1 # eqarea is figure 1 in_file='pmag_specimens.txt' sampfile='er_samples.txt' out_file="" fmt,plot='svg',1 Crits="" M,N=180.,1 repeat='' renew=0 if '-h' in sys.argv: print main.__doc__ sys.exit() if '-WD' in sys.argv: ind=sys.argv.index('-WD') dir_path=sys.argv[ind+1] if '-f' in sys.argv: ind=sys.argv.index("-f") in_file=sys.argv[ind+1] if '-fsa' in sys.argv: ind=sys.argv.index("-fsa") sampfile=sys.argv[ind+1] if '-exc' in sys.argv: Crits,file_type=pmag.magic_read(dir_path+'/pmag_criteria.txt') for crit in Crits: if crit['pmag_criteria_code']=='DE-SPEC': M=float(crit['specimen_mad']) N=float(crit['specimen_n']) if '-fmt' in sys.argv: ind=sys.argv.index("-fmt") fmt=sys.argv[ind+1] if '-N' in sys.argv: renew=1 # if in_file[0]!="/":in_file=dir_path+'/'+in_file if sampfile[0]!="/":sampfile=dir_path+'/'+sampfile crd='s' Specs,file_type=pmag.magic_read(in_file) if file_type!='pmag_specimens': print ' bad pmag_specimen input file' sys.exit() Samps,file_type=pmag.magic_read(sampfile) if file_type!='er_samples': print ' bad er_samples input file' sys.exit() SO_methods=[] for rec in Samps: if 'sample_orientation_flag' not in rec.keys(): rec['sample_orientation_flag']='g' if 'sample_description' not in rec.keys(): rec['sample_description']='' if renew==1: rec['sample_orientation_flag']='g' description=rec['sample_description'] if '#' in description: newdesc="" c=0 while description[c]!='#' and c<len(description)-1: # look for first pound sign newdesc=newdesc+description[c] c+=1 while description[c]=='#': c+=1# skip first set of pound signs while description[c]!='#':c+=1 # find second set of pound signs while description[c]=='#' and c<len(description)-1:c+=1 # skip second set of pound signs while c<len(description)-1: # look for first pound sign newdesc=newdesc+description[c] c+=1 rec['sample_description']=newdesc # edit out old comment about orientations if "magic_method_codes" in rec: methlist=rec["magic_method_codes"] for meth in methlist.split(":"): if "SO" in meth.strip() and "SO-POM" not in meth.strip(): if meth.strip() not in SO_methods: SO_methods.append(meth.strip()) pmag.magic_write(sampfile,Samps,'er_samples') SO_priorities=pmag.set_priorities(SO_methods,0) sitelist=[] for rec in Specs: if rec['er_site_name'] not in sitelist: sitelist.append(rec['er_site_name']) sitelist.sort() EQ={} EQ['eqarea']=1 pmagplotlib.plot_init(EQ['eqarea'],5,5) k=0 while k<len(sitelist): site=sitelist[k] print site data=[] ThisSiteSpecs=pmag.get_dictitem(Specs,'er_site_name',site,'T') ThisSiteSpecs=pmag.get_dictitem(ThisSiteSpecs,'specimen_tilt_correction','-1','T') # get all the unoriented data for spec in ThisSiteSpecs: if spec['specimen_mad']!="" and spec['specimen_n']!="" and float(spec['specimen_mad'])<=M and float(spec['specimen_n'])>=N: # good spec, now get orientation.... redo,p=1,0 if len(SO_methods)<=1: az_type=SO_methods[0] orient=pmag.find_samp_rec(spec["er_sample_name"],Samps,az_type) redo=0 while redo==1: if p>=len(SO_priorities): print "no orientation data for ",spec['er_sample_name'] orient["sample_azimuth"]="" orient["sample_dip"]="" redo=0 else: az_type=SO_methods[SO_methods.index(SO_priorities[p])] orient=pmag.find_samp_rec(spec["er_sample_name"],Samps,az_type) if orient["sample_azimuth"] !="": redo=0 p+=1 if orient['sample_azimuth']!="": rec={} for key in spec.keys():rec[key]=spec[key] rec['dec'],rec['inc']=pmag.dogeo(float(spec['specimen_dec']),float(spec['specimen_inc']),float(orient['sample_azimuth']),float(orient['sample_dip'])) rec["tilt_correction"]='1' crd='g' rec['sample_azimuth']=orient['sample_azimuth'] rec['sample_dip']=orient['sample_dip'] data.append(rec) if len(data)>2: print 'specimen, dec, inc, n_meas/MAD,| method codes ' for i in range(len(data)): print '%s: %7.1f %7.1f %s / %s | %s' % (data[i]['er_specimen_name'], data[i]['dec'], data[i]['inc'], data[i]['specimen_n'], data[i]['specimen_mad'], data[i]['magic_method_codes']) fpars=pmag.dolnp(data,'specimen_direction_type') print "\n Site lines planes kappa a95 dec inc" print site, fpars["n_lines"], fpars["n_planes"], fpars["K"], fpars["alpha95"], fpars["dec"], fpars["inc"], fpars["R"] if out_file!="": if float(fpars["alpha95"])<=acutoff and float(fpars["K"])>=kcutoff: out.write('%s %s %s\n'%(fpars["dec"],fpars['inc'],fpars['alpha95'])) pmagplotlib.plotLNP(EQ['eqarea'],site,data,fpars,'specimen_direction_type') pmagplotlib.drawFIGS(EQ) if k!=0 and repeat!='y': ans=raw_input("s[a]ve plot, [q]uit, [e]dit specimens, [p]revious site, <return> to continue:\n ") elif k==0 and repeat!='y': ans=raw_input("s[a]ve plot, [q]uit, [e]dit specimens, <return> to continue:\n ") if ans=="p": k-=2 if ans=="a": files={} files['eqarea']=site+'_'+crd+'_eqarea'+'.'+fmt pmagplotlib.saveP(EQ,files) if ans=="q": sys.exit() if ans=="e" and Samps==[]: print "can't edit samples without orientation file, sorry" elif ans=="e": # k-=1 testspec=raw_input("Enter name of specimen to check: ") for spec in data: if spec['er_specimen_name']==testspec: # first test wrong direction of drill arrows (flip drill direction in opposite direction and re-calculate d,i d,i=pmag.dogeo(float(spec['specimen_dec']),float(spec['specimen_inc']),float(spec['sample_azimuth'])-180.,-float(spec['sample_dip'])) XY=pmag.dimap(d,i) pmagplotlib.plotXY(EQ['eqarea'],[XY[0]],[XY[1]],sym='g^') # first test wrong end of compass (take az-180.) d,i=pmag.dogeo(float(spec['specimen_dec']),float(spec['specimen_inc']),float(spec['sample_azimuth'])-180.,float(spec['sample_dip'])) XY=pmag.dimap(d,i) pmagplotlib.plotXY(EQ['eqarea'],[XY[0]],[XY[1]],sym='kv') # did the sample spin in the hole? # now spin around specimen's z X_up,Y_up,X_d,Y_d=[],[],[],[] for incr in range(0,360,5): d,i=pmag.dogeo(float(spec['specimen_dec'])+incr,float(spec['specimen_inc']),float(spec['sample_azimuth']),float(spec['sample_dip'])) XY=pmag.dimap(d,i) if i>=0: X_d.append(XY[0]) Y_d.append(XY[1]) else: X_up.append(XY[0]) Y_up.append(XY[1]) pmagplotlib.plotXY(EQ['eqarea'],X_d,Y_d,sym='b.') pmagplotlib.plotXY(EQ['eqarea'],X_up,Y_up,sym='c.') pmagplotlib.drawFIGS(EQ) break print "Triangle: wrong arrow for drill direction." print "Delta: wrong end of compass." print "Small circle: wrong mark on sample. [cyan upper hemisphere]" deleteme=raw_input("Mark this sample as bad? y/[n] ") if deleteme=='y': reason=raw_input("Reason: [1] broke, [2] wrong drill direction, [3] wrong compass direction, [4] bad mark, [5] displaced block [6] other ") if reason=='1': description=' sample broke while drilling' if reason=='2': description=' wrong drill direction ' if reason=='3': description=' wrong compass direction ' if reason=='4': description=' bad mark in field' if reason=='5': description=' displaced block' if reason=='6': description=raw_input('Enter brief reason for deletion: ') for samp in Samps: if samp['er_sample_name']==spec['er_sample_name']: samp['sample_orientation_flag']='b' samp['sample_description']=samp['sample_description']+' ## direction deleted because: '+description+'##' # mark description pmag.magic_write(sampfile,Samps,'er_samples') repeat=raw_input("Mark another sample, this site? y/[n] ") if repeat=='y': k-=1 else: print 'skipping site - not enough data with specified coordinate system' k+=1 print "sample flags stored in ",sampfile
def main(): """ NAME lnp_magic.py DESCRIPTION makes equal area projections site by site from pmag_specimen formatted file with Fisher confidence ellipse using McFadden and McElhinny (1988) technique for combining lines and planes SYNTAX lnp_magic [command line options] INPUT takes magic formatted pmag_specimens file OUPUT prints site_name n_lines n_planes K alpha95 dec inc R OPTIONS -h prints help message and quits -f FILE: specify input file, default is 'pmag_specimens.txt' -crd [s,g,t]: specify coordinate system, [s]pecimen, [g]eographic, [t]ilt adjusted default is specimen -fmt [svg,png,jpg] format for plots, default is svg -P: do not plot -F FILE, specify output file of dec, inc, alpha95 data for plotting with plotdi_a and plotdi_e -exc use criteria in pmag_criteria.txt """ dir_path='.' FIG={} # plot dictionary FIG['eqarea']=1 # eqarea is figure 1 in_file,plot_key,coord='pmag_specimens.txt','er_site_name',"-1" out_file="" fmt,plot='svg',1 Crits="" M,N=180.,1 if '-h' in sys.argv: print main.__doc__ sys.exit() if '-WD' in sys.argv: ind=sys.argv.index('-WD') dir_path=sys.argv[ind+1] if '-f' in sys.argv: ind=sys.argv.index("-f") in_file=sys.argv[ind+1] if '-exc' in sys.argv: Crits,file_type=pmag.magic_read(dir_path+'/pmag_criteria.txt') for crit in Crits: if crit['pmag_criteria_code']=='DE-SPEC': M=float(crit['specimen_mad']) N=float(crit['specimen_n']) if '-F' in sys.argv: ind=sys.argv.index("-F") out_file=sys.argv[ind+1] out=open(dir_path+'/'+out_file,'w') if '-crd' in sys.argv: ind=sys.argv.index("-crd") crd=sys.argv[ind+1] if crd=='s':coord="-1" if crd=='g':coord="0" if crd=='t':coord="100" if '-fmt' in sys.argv: ind=sys.argv.index("-fmt") fmt=sys.argv[ind+1] if '-P' in sys.argv:plot=0 # in_file=dir_path+'/'+in_file Specs,file_type=pmag.magic_read(in_file) sitelist=[] for rec in Specs: if rec['er_site_name'] not in sitelist: sitelist.append(rec['er_site_name']) sitelist.sort() if plot==1: import pmagplotlib EQ={} EQ['eqarea']=1 pmagplotlib.plot_init(EQ['eqarea'],4,4) for site in sitelist: print site data=[] for spec in Specs: if 'specimen_tilt_correction' not in spec.keys():spec['specimen_tilt_correction']='-1' # assume unoriented if spec['er_site_name']==site: if 'specimen_mad' not in spec.keys() or spec['specimen_mad']=="": if 'specimen_alpha95' in spec.keys() and spec['specimen_alpha95']!="": spec['specimen_mad']=spec['specimen_alpha95'] else: spec['specimen_mad']='180' if spec['specimen_tilt_correction']==coord and float(spec['specimen_mad'])<=M and float(spec['specimen_n'])>=N: rec={} for key in spec.keys():rec[key]=spec[key] rec["dec"]=float(spec['specimen_dec']) rec["inc"]=float(spec['specimen_inc']) rec["tilt_correction"]=spec['specimen_tilt_correction'] data.append(rec) if len(data)>2: fpars=pmag.dolnp(data,'specimen_direction_type') print "Site lines planes kappa a95 dec inc" print site, fpars["n_lines"], fpars["n_planes"], fpars["K"], fpars["alpha95"], fpars["dec"], fpars["inc"], fpars["R"] if out_file!="": if float(fpars["alpha95"])<=acutoff and float(fpars["K"])>=kcutoff: out.write('%s %s %s\n'%(fpars["dec"],fpars['inc'],fpars['alpha95'])) print '% tilt correction: ',coord if plot==1: pmagplotlib.plotLNP(EQ['eqarea'],site,data,fpars,'specimen_direction_type') ans=raw_input("s[a]ve plot, [q]uit, <return> to continue:\n ") if ans=="a": files={} files['eqarea']=site+'_'+crd+'_'+'eqarea'+'.'+fmt pmagplotlib.saveP(EQ,files) if ans=="q": sys.exit() else: print 'skipping site - not enough data with specified coordinate system'
def main(): """ NAME site_edit_magic.py DESCRIPTION makes equal area projections site by site from zeq_specimens_g.txt file with Fisher confidence ellipse using McFadden and McElhinny (1988) technique for combining lines and planes allows testing and reject specimens for bad orientations SYNTAX site_edit_magic.py [command line options] OPTIONS -h: prints help and quits -f: specify pmag_specimen format file, default is zeq_specimens_s.txt -fsa: specify er_samples.txt file -exc: use existing pmag_criteria.txt file -N: reset all sample flags to good OUPUT edited er_samples.txt file """ dir_path = "." FIG = {} # plot dictionary FIG["eqarea"] = 1 # eqarea is figure 1 in_file = "zeq_specimens_s.txt" sampfile = "er_samples.txt" out_file = "" fmt, plot = "svg", 1 Crits = "" M, N = 180.0, 1 repeat = "" renew = 0 if "-h" in sys.argv: print main.__doc__ sys.exit() if "-WD" in sys.argv: ind = sys.argv.index("-WD") dir_path = sys.argv[ind + 1] if "-f" in sys.argv: ind = sys.argv.index("-f") in_file = sys.argv[ind + 1] if "-fsa" in sys.argv: ind = sys.argv.index("-fsa") sampfile = sys.argv[ind + 1] if "-exc" in sys.argv: Crits, file_type = pmag.magic_read(dir_path + "/pmag_criteria.txt") for crit in Crits: if crit["pmag_criteria_code"] == "DE-SPEC": M = float(crit["specimen_mad"]) N = float(crit["specimen_n"]) if "-fmt" in sys.argv: ind = sys.argv.index("-fmt") fmt = sys.argv[ind + 1] if "-N" in sys.argv: renew = 1 # in_file = dir_path + "/" + in_file sampfile = dir_path + "/" + sampfile Specs, file_type = pmag.magic_read(in_file) if file_type != "pmag_specimens": print " bad pmag_specimen input file" sys.exit() Samps, file_type = pmag.magic_read(sampfile) if file_type != "er_samples": print " bad er_samples input file" sys.exit() SO_methods = [] for rec in Samps: if "sample_orientation_flag" not in rec.keys(): rec["sample_orientation_flag"] = "g" if "sample_description" not in rec.keys(): rec["sample_description"] = "" if renew == 1: rec["sample_orientation_flag"] = "g" description = rec["sample_description"] if "#" in description: newdesc = "" c = 0 while description[c] != "#" and c < len(description) - 1: # look for first pound sign newdesc = newdesc + description[c] c += 1 while description[c] == "#": c += 1 # skip first set of pound signs while description[c] != "#": c += 1 # find second set of pound signs while description[c] == "#" and c < len(description) - 1: c += 1 # skip second set of pound signs while c < len(description) - 1: # look for first pound sign newdesc = newdesc + description[c] c += 1 rec["sample_description"] = newdesc # edit out old comment about orientations if "magic_method_codes" in rec: methlist = rec["magic_method_codes"] for meth in methlist.split(":"): if "SO" in meth.strip() and "SO-POM" not in meth.strip(): if meth.strip() not in SO_methods: SO_methods.append(meth.strip()) pmag.magic_write(sampfile, Samps, "er_samples") SO_priorities = pmag.set_priorities(SO_methods, 0) sitelist = [] for rec in Specs: if rec["er_site_name"] not in sitelist: sitelist.append(rec["er_site_name"]) sitelist.sort() EQ = {} EQ["eqarea"] = 1 pmagplotlib.plot_init(EQ["eqarea"], 5, 5) k = 0 while k < len(sitelist): site = sitelist[k] print site data = [] for spec in Specs: if spec["er_site_name"] == site: if ( spec["specimen_mad"] != "" and spec["specimen_n"] != "" and float(spec["specimen_mad"]) <= M and float(spec["specimen_n"]) >= N ): # good spec, now get orientation.... redo, p = 1, 0 if len(SO_methods) <= 1: az_type = SO_methods[0] orient = pmag.find_samp_rec(spec["er_sample_name"], Samps, az_type) redo = 0 while redo == 1: if p >= len(SO_priorities): print "no orientation data for ", spec["er_sample_name"] orient["sample_azimuth"] = "" orient["sample_dip"] = "" redo = 0 else: az_type = SO_methods[SO_methods.index(SO_priorities[p])] orient = pmag.find_samp_rec(spec["er_sample_name"], Samps, az_type) if orient["sample_azimuth"] != "": redo = 0 p += 1 if orient["sample_azimuth"] != "": rec = {} for key in spec.keys(): rec[key] = spec[key] rec["dec"], rec["inc"] = pmag.dogeo( float(spec["specimen_dec"]), float(spec["specimen_inc"]), float(orient["sample_azimuth"]), float(orient["sample_dip"]), ) rec["tilt_correction"] = "1" rec["sample_azimuth"] = orient["sample_azimuth"] rec["sample_dip"] = orient["sample_dip"] data.append(rec) if len(data) > 2: print "specimen, dec, inc, n_meas/MAD,| method codes " for i in range(len(data)): print "%s: %7.1f %7.1f %s / %s | %s" % ( data[i]["er_specimen_name"], data[i]["dec"], data[i]["inc"], data[i]["specimen_n"], data[i]["specimen_mad"], data[i]["magic_method_codes"], ) fpars = pmag.dolnp(data, "specimen_direction_type") print "\n Site lines planes kappa a95 dec inc" print site, fpars["n_lines"], fpars["n_planes"], fpars["K"], fpars["alpha95"], fpars["dec"], fpars[ "inc" ], fpars["R"] if out_file != "": if float(fpars["alpha95"]) <= acutoff and float(fpars["K"]) >= kcutoff: out.write("%s %s %s\n" % (fpars["dec"], fpars["inc"], fpars["alpha95"])) pmagplotlib.plotLNP(EQ["eqarea"], site, data, fpars, "specimen_direction_type") if k != 0 and repeat != "y": ans = raw_input("s[a]ve plot, [q]uit, [e]dit specimens, [p]revious site, <return> to continue:\n ") elif k == 0 and repeat != "y": ans = raw_input("s[a]ve plot, [q]uit, [e]dit specimens, <return> to continue:\n ") if ans == "p": k -= 2 if ans == "a": files = {} files["eqarea"] = site + "_" + crd + "_" + "eqarea" + "." + fmt pmagplotlib.saveP(EQ, files) if ans == "q": sys.exit() if ans == "e" and Samps == []: print "can't edit samples without orientation file, sorry" elif ans == "e": # k-=1 testspec = raw_input("Enter name of specimen to check: ") for spec in data: if spec["er_specimen_name"] == testspec: # first test wrong direction of drill arrows (flip drill direction in opposite direction and re-calculate d,i d, i = pmag.dogeo( float(spec["specimen_dec"]), float(spec["specimen_inc"]), float(spec["sample_azimuth"]) - 180.0, -float(spec["sample_dip"]), ) XY = pmag.dimap(d, i) pmagplotlib.plotXY(EQ["eqarea"], [XY[0]], [XY[1]], "g^", "", "", "") # first test wrong end of compass (take az-180.) d, i = pmag.dogeo( float(spec["specimen_dec"]), float(spec["specimen_inc"]), float(spec["sample_azimuth"]) - 180.0, float(spec["sample_dip"]), ) XY = pmag.dimap(d, i) pmagplotlib.plotXY(EQ["eqarea"], [XY[0]], [XY[1]], "kv", "", "", "") # did the sample spin in the hole? # now spin around specimen's z X_up, Y_up, X_d, Y_d = [], [], [], [] for incr in range(0, 360, 5): d, i = pmag.dogeo( float(spec["specimen_dec"]) + incr, float(spec["specimen_inc"]), float(spec["sample_azimuth"]), float(spec["sample_dip"]), ) XY = pmag.dimap(d, i) if i >= 0: X_d.append(XY[0]) Y_d.append(XY[1]) else: X_up.append(XY[0]) Y_up.append(XY[1]) pmagplotlib.plotXY(EQ["eqarea"], X_d, Y_d, "b.", "", "", "") pmagplotlib.plotXY(EQ["eqarea"], X_up, Y_up, "c.", "", "", "") pmagplotlib.drawFIGS(EQ) break print "Triangle: wrong arrow for drill direction." print "Delta: wrong end of compass." print "Small circle: wrong mark on sample. [cyan upper hemisphere]" deleteme = raw_input("Mark this sample as bad? y/[n] ") if deleteme == "y": reason = raw_input( "Reason: [1] broke, [2] wrong drill direction, [3] wrong compass direction, [4] bad mark, [5] displaced block [6] other " ) if reason == "1": description = " sample broke while drilling" if reason == "2": description = " wrong drill direction " if reason == "3": description = " wrong compass direction " if reason == "4": description = " bad mark in field" if reason == "5": description = " displaced block" if reason == "6": description = raw_input("Enter brief reason for deletion: ") for samp in Samps: if samp["er_sample_name"] == spec["er_sample_name"]: samp["sample_orientation_flag"] = "b" samp["sample_description"] = ( samp["sample_description"] + " ## direction deleted because: " + description + "##" ) # mark description pmag.magic_write(sampfile, Samps, "er_samples") repeat = raw_input("Mark another sample, this site? y/[n] ") if repeat == "y": k -= 1 else: print "skipping site - not enough data with specified coordinate system" k += 1 print "sample flags stored in ", sampfile