def main():
"""
NAME
lowrie.py
DESCRIPTION
plots intensity decay curves for Lowrie experiments
SYNTAX
lowrie -h [command line options]
INPUT
takes SIO formatted input files
OPTIONS
-h prints help message and quits
-f FILE: specify input file
-N do not normalize by maximum magnetization
-fmt [svg, pdf, eps, png] specify fmt, default is svg
-sav save plots and quit
"""
fmt, plot = "svg", 0
FIG = {} # plot dictionary
FIG["lowrie"] = 1 # demag is figure 1
pmagplotlib.plot_init(FIG["lowrie"], 6, 6)
norm = 1 # default is to normalize by maximum axis
if len(sys.argv) > 1:
if "-h" in sys.argv:
print main.__doc__
sys.exit()
if "-N" in sys.argv:
norm = 0 # don't normalize
if "-sav" in sys.argv:
plot = 1 # don't normalize
if "-fmt" in sys.argv: # sets input filename
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
if "-f" in sys.argv: # sets input filename
ind = sys.argv.index("-f")
in_file = sys.argv[ind + 1]
else:
print main.__doc__
print "you must supply a file name"
sys.exit()
else:
print main.__doc__
print "you must supply a file name"
sys.exit()
data = open(in_file).readlines() # open the SIO format file
PmagRecs = [] # set up a list for the results
keys = ["specimen", "treatment", "csd", "M", "dec", "inc"]
for line in data:
PmagRec = {}
rec = line.replace("\n", "").split()
for k in range(len(keys)):
PmagRec[keys[k]] = rec[k]
PmagRecs.append(PmagRec)
specs = pmag.get_dictkey(PmagRecs, "specimen", "")
sids = []
for spec in specs:
if spec not in sids:
sids.append(spec) # get list of unique specimen names
for spc in sids: # step through the specimen names
print spc
specdata = pmag.get_dictitem(PmagRecs, "specimen", spc, "T") # get all this one's data
DIMs, Temps = [], []
for dat in specdata: # step through the data
DIMs.append([float(dat["dec"]), float(dat["inc"]), float(dat["M"]) * 1e-3])
Temps.append(float(dat["treatment"]))
carts = pmag.dir2cart(DIMs).transpose()
# if norm==1: # want to normalize
# nrm=max(max(abs(carts[0])),max(abs(carts[1])),max(abs(carts[2]))) # by maximum of x,y,z values
# ylab="M/M_max"
if norm == 1: # want to normalize
nrm = DIMs[0][2] # normalize by NRM
ylab = "M/M_o"
else:
nrm = 1.0 # don't normalize
ylab = "Magnetic moment (Am^2)"
xlab = "Temperature (C)"
pmagplotlib.plotXY(FIG["lowrie"], Temps, abs(carts[0]) / nrm, sym="r-")
pmagplotlib.plotXY(FIG["lowrie"], Temps, abs(carts[0]) / nrm, sym="ro") # X direction
pmagplotlib.plotXY(FIG["lowrie"], Temps, abs(carts[1]) / nrm, sym="c-")
pmagplotlib.plotXY(FIG["lowrie"], Temps, abs(carts[1]) / nrm, sym="cs") # Y direction
pmagplotlib.plotXY(FIG["lowrie"], Temps, abs(carts[2]) / nrm, sym="k-")
pmagplotlib.plotXY(
FIG["lowrie"], Temps, abs(carts[2]) / nrm, sym="k^", title=spc, xlab=xlab, ylab=ylab
) # Z direction
files = {"lowrie": "lowrie:_" + spc + "_." + fmt}
if plot == 0:
pmagplotlib.drawFIGS(FIG)
ans = raw_input("S[a]ve figure? [q]uit, <return> to continue ")
if ans == "a":
pmagplotlib.saveP(FIG, files)
elif ans == "q":
sys.exit()
else:
pmagplotlib.saveP(FIG, files)
pmagplotlib.clearFIG(FIG["lowrie"])
def main():
"""
NAME
lowrie.py
DESCRIPTION
plots intensity decay curves for Lowrie experiments
SYNTAX
lowrie -h [command line options]
INPUT
takes SIO formatted input files
OPTIONS
-h prints help message and quits
-f FILE: specify input file
-N do not normalize by maximum magnetization
-fmt [svg, pdf, eps, png] specify fmt, default is svg
-sav save plots and quit
"""
fmt, plot = 'svg', 0
FIG = {} # plot dictionary
FIG['lowrie'] = 1 # demag is figure 1
pmagplotlib.plot_init(FIG['lowrie'], 6, 6)
norm = 1 # default is to normalize by maximum axis
if len(sys.argv) > 1:
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-N' in sys.argv:
norm = 0 # don't normalize
if '-sav' in sys.argv:
plot = 1 # don't normalize
if '-fmt' in sys.argv: # sets input filename
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
if '-f' in sys.argv: # sets input filename
ind = sys.argv.index("-f")
in_file = sys.argv[ind + 1]
else:
print(main.__doc__)
print('you must supply a file name')
sys.exit()
else:
print(main.__doc__)
print('you must supply a file name')
sys.exit()
data = pmag.open_file(in_file)
PmagRecs = [] # set up a list for the results
keys = ['specimen', 'treatment', 'csd', 'M', 'dec', 'inc']
for line in data:
PmagRec = {}
rec = line.replace('\n', '').split()
for k in range(len(keys)):
PmagRec[keys[k]] = rec[k]
PmagRecs.append(PmagRec)
specs = pmag.get_dictkey(PmagRecs, 'specimen', '')
sids = []
for spec in specs:
if spec not in sids:
sids.append(spec) # get list of unique specimen names
for spc in sids: # step through the specimen names
print(spc)
specdata = pmag.get_dictitem(PmagRecs, 'specimen', spc,
'T') # get all this one's data
DIMs, Temps = [], []
for dat in specdata: # step through the data
DIMs.append(
[float(dat['dec']),
float(dat['inc']),
float(dat['M']) * 1e-3])
Temps.append(float(dat['treatment']))
carts = pmag.dir2cart(DIMs).transpose()
# if norm==1: # want to normalize
# nrm=max(max(abs(carts[0])),max(abs(carts[1])),max(abs(carts[2]))) # by maximum of x,y,z values
# ylab="M/M_max"
if norm == 1: # want to normalize
nrm = (DIMs[0][2]) # normalize by NRM
ylab = "M/M_o"
else:
nrm = 1. # don't normalize
ylab = "Magnetic moment (Am^2)"
xlab = "Temperature (C)"
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[0]), nrm),
sym='r-')
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[0]), nrm),
sym='ro') # X direction
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[1]), nrm),
sym='c-')
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[1]), nrm),
sym='cs') # Y direction
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[2]), nrm),
sym='k-')
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[2]), nrm),
sym='k^',
title=spc,
xlab=xlab,
ylab=ylab) # Z direction
files = {'lowrie': 'lowrie:_' + spc + '_.' + fmt}
if plot == 0:
pmagplotlib.drawFIGS(FIG)
ans = input('S[a]ve figure? [q]uit, <return> to continue ')
if ans == 'a':
pmagplotlib.saveP(FIG, files)
elif ans == 'q':
sys.exit()
else:
pmagplotlib.saveP(FIG, files)
pmagplotlib.clearFIG(FIG['lowrie'])
def main():
"""
NAME
plot_geomagia.py
DESCRIPTION
makes a map and VADM plot of geomagia download file
SYNTAX
plot_geomagia.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE, specify geomagia download file
-res [c,l,i,h] specify resolution (crude,low,intermediate,high)
-etp plot the etopo20 topographic mesh
-pad [LAT LON] pad bounding box by LAT/LON (default is [.5 .5] degrees)
-grd SPACE specify grid spacing
-prj [lcc] , specify projection (lcc=lambert conic conformable), default is mercator
-o color ocean blue/land green (default is not)
-d plot details of rivers, boundaries, etc.
-sav save plot and quit quietly
-fmt [png,svg,eps,jpg,pdf] specify format for output, default is pdf
DEFAULTS
resolution: intermediate
saved images are in pdf
"""
dir_path='.'
names,res,proj,locs,padlon,padlat,fancy,gridspace,details=[],'l','lcc','',0,0,0,15,1
Age_bounds=[-5000,2000]
Lat_bounds=[20,45]
Lon_bounds=[15,55]
fmt='pdf'
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind = sys.argv.index('-f')
sites_file=sys.argv[ind+1]
if '-res' in sys.argv:
ind = sys.argv.index('-res')
res=sys.argv[ind+1]
if '-etp' in sys.argv:fancy=1
if '-o' in sys.argv:ocean=1
if '-d' in sys.argv:details=1
if '-prj' in sys.argv:
ind = sys.argv.index('-prj')
proj=sys.argv[ind+1]
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
verbose=pmagplotlib.verbose
if '-sav' in sys.argv:
verbose=0
if '-pad' in sys.argv:
ind = sys.argv.index('-pad')
padlat=float(sys.argv[ind+1])
padlon=float(sys.argv[ind+2])
if '-grd' in sys.argv:
ind = sys.argv.index('-grd')
gridspace=float(sys.argv[ind+1])
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
sites_file=dir_path+'/'+sites_file
geo_in=open(sites_file,'rU').readlines()
Age,AgeErr,Vadm,VadmErr,slats,slons=[],[],[],[],[],[]
for line in geo_in[2:]: # skip top two rows`
rec=line.split()
if float(rec[0])>Age_bounds[0] and float(rec[0])<Age_bounds[1] \
and float(rec[12])>Lat_bounds[0] and float(rec[12]) < Lat_bounds[1]\
and float(rec[13])>Lon_bounds[0] and float(rec[13])<Lon_bounds[1]:
Age.append(float(rec[0]))
AgeErr.append(float(rec[1]))
Vadm.append(10.*float(rec[6]))
VadmErr.append(10.*float(rec[7]))
slats.append(float(rec[12]))
slons.append(float(rec[13]))
FIGS={'map':1,'vadms':2}
pmagplotlib.plot_init(FIGS['map'],6,6)
pmagplotlib.plot_init(FIGS['vadms'],6,6)
Opts={'res':res,'proj':proj,'loc_name':locs,'padlon':padlon,'padlat':padlat,'latmin':numpy.min(slats)-padlat,'latmax':numpy.max(slats)+padlat,'lonmin':numpy.min(slons)-padlon,'lonmax':numpy.max(slons)+padlon,'sym':'ro','boundinglat':0.,'pltgrid':1}
Opts['lon_0']=int(0.5*(numpy.min(slons)+numpy.max(slons)))
Opts['lat_0']=int(0.5*(numpy.min(slats)+numpy.max(slats)))
Opts['gridspace']=gridspace
if details==1:
Opts['details']={'coasts':1,'rivers':0,'states':1,'countries':1,'ocean':1}
else:
Opts['details']={'coasts':1,'rivers':0,'states':0,'countries':0,'ocean':1}
Opts['details']['fancy']=fancy
pmagplotlib.plotMAP(FIGS['map'],slats,slons,Opts)
pmagplotlib.plotXY(FIGS['vadms'],Age,Vadm,sym='bo',xlab='Age (Years CE)',ylab=r'VADM (ZAm$^2$)')
if verbose:pmagplotlib.drawFIGS(FIGS)
files={}
for key in FIGS.keys():
files[key]=key+'.'+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['map']='Map'
titles['vadms']='VADMs'
FIG = pmagplotlib.addBorders(FIGS,titles,black,purple)
pmagplotlib.saveP(FIGS,files)
elif verbose:
ans=raw_input(" S[a]ve to save plot, Return to quit: ")
if ans=="a":
pmagplotlib.saveP(FIGS,files)
else:
pmagplotlib.saveP(FIGS,files)
def main():
"""
NAME
quick_hyst.py
DESCRIPTION
makes plots of hysteresis data
SYNTAX
quick_hyst.py [command line options]
OPTIONS
-h prints help message and quits
-usr USER: identify user, default is ""
-f: specify input file, default is magic_measurements.txt
-spc SPEC: specify specimen name to plot and quit
-sav save all plots and quit
-fmt [png,svg,eps,jpg]
"""
args=sys.argv
PLT=1
plots=0
user,meas_file="","magic_measurements.txt"
pltspec=""
dir_path='.'
fmt='png'
verbose=pmagplotlib.verbose
print 'verbose?', verbose
version_num=pmag.get_version()
if '-WD' in args:
ind=args.index('-WD')
dir_path=args[ind+1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
if '-f' in args:
ind=args.index("-f")
meas_file=args[ind+1]
if '-sav' in args:
verbose=0
plots=1
if '-spc' in args:
ind=args.index("-spc")
pltspec= args[ind+1]
verbose=0
plots=1
if '-fmt' in args:
ind=args.index("-fmt")
fmt=args[ind+1]
meas_file=dir_path+'/'+meas_file
print 'verbose', verbose
#
#
meas_data,file_type=pmag.magic_read(meas_file)
if file_type!='magic_measurements':
print main.__doc__
print 'bad file'
sys.exit()
#
# initialize some variables
# define figure numbers for hyst,deltaM,DdeltaM curves
HystRecs,RemRecs=[],[]
HDD={}
HDD['hyst']=1
pmagplotlib.plot_init(HDD['hyst'],5,5)
#
# get list of unique experiment names and specimen names
#
experiment_names,sids=[],[]
hyst_data=pmag.get_dictitem(meas_data,'magic_method_codes','LP-HYS','has') # get all hysteresis data
for rec in hyst_data:
if 'er_synthetic_name' in rec.keys() and rec['er_synthetic_name']!="":
rec['er_specimen_name']=rec['er_synthetic_name']
if rec['magic_experiment_name'] not in experiment_names:experiment_names.append(rec['magic_experiment_name'])
if rec['er_specimen_name'] not in sids:sids.append(rec['er_specimen_name'])
if 'measurement_temp' not in rec.keys(): rec['measurement_temp']='300' # assume room T measurement unless otherwise specified
#
k=0
if pltspec!="":
k=sids.index(pltspec)
intlist=['measurement_magnitude','measurement_magn_moment','measurement_magn_volume','measurement_magn_mass']
while k < len(sids):
locname,site,sample,synth='','','',''
s=sids[k]
hmeths=[]
if verbose:print s, k+1 , 'out of ',len(sids)
#
#
B,M=[],[] #B,M for hysteresis, Bdcd,Mdcd for irm-dcd data
spec=pmag.get_dictitem(hyst_data,'er_specimen_name',s,'T') # get all measurements for this specimen
if 'er_location_name' in spec[0].keys():
locname=spec[0]['er_location_name']
if 'er_site_name' in spec[0].keys():
site=spec[0]['er_site_name']
if 'er_sample_name' in spec[0].keys():
sample=spec[0]['er_sample_name']
if 'er_synthetic_name' in spec[0].keys():
synth=spec[0]['er_synthetic_name']
for m in intlist:
meas_data=pmag.get_dictitem(spec,m,'','F') # get all non-blank data for this specimen
if len(meas_data)>0: break
c=['k-','b-','c-','g-','m-','r-','y-']
cnum=0
if len(meas_data)>0:
Temps=[]
xlab,ylab,title='','',''
for rec in meas_data:
if rec['measurement_temp'] not in Temps:Temps.append(rec['measurement_temp'])
for t in Temps:
print 'working on t: ',t
t_data=pmag.get_dictitem(meas_data,'measurement_temp',t,'T')
B,M=[],[]
for rec in t_data:
B.append(float(rec['measurement_lab_field_dc']))
M.append(float(rec[m]))
# now plot the hysteresis curve(s)
#
if len(B)>0:
B=numpy.array(B)
M=numpy.array(M)
if t==Temps[-1]:
xlab='Field (T)'
ylab=m
title='Hysteresis: '+s
if t==Temps[0]:
pmagplotlib.clearFIG(HDD['hyst'])
pmagplotlib.plotXY(HDD['hyst'],B,M,sym=c[cnum],xlab=xlab,ylab=ylab,title=title)
pmagplotlib.plotXY(HDD['hyst'],[1.1*B.min(),1.1*B.max()],[0,0],sym='k-',xlab=xlab,ylab=ylab,title=title)
pmagplotlib.plotXY(HDD['hyst'],[0,0],[1.1*M.min(),1.1*M.max()],sym='k-',xlab=xlab,ylab=ylab,title=title)
if verbose:pmagplotlib.drawFIGS(HDD)
cnum+=1
if cnum==len(c):cnum=0
#
files={}
if plots:
if pltspec!="":s=pltspec
files={}
for key in HDD.keys():
if synth=='':
files[key]="LO:_"+locname+'_SI:_'+site+'_SA:_'+sample+'_SP:_'+s+'_TY:_'+key+'_.'+fmt
else:
files[key]='SY:_'+synth+'_TY:_'+key+'_.'+fmt
pmagplotlib.saveP(HDD,files)
if pltspec!="":sys.exit()
if verbose:
pmagplotlib.drawFIGS(HDD)
ans=raw_input("S[a]ve plots, [s]pecimen name, [q]uit, <return> to continue\n ")
if ans=="a":
files={}
for key in HDD.keys():
files[key]="LO:_"+locname+'_SI:_'+site+'_SA:_'+sample+'_SP:_'+s+'_TY:_'+key+'_.'+fmt
pmagplotlib.saveP(HDD,files)
if ans=='':k+=1
if ans=="p":
del HystRecs[-1]
k-=1
if ans=='q':
print "Good bye"
sys.exit()
if ans=='s':
keepon=1
specimen=raw_input('Enter desired specimen name (or first part there of): ')
while keepon==1:
try:
k =sids.index(specimen)
keepon=0
except:
tmplist=[]
for qq in range(len(sids)):
if specimen in sids[qq]:tmplist.append(sids[qq])
print specimen," not found, but this was: "
print tmplist
specimen=raw_input('Select one or try again\n ')
k =sids.index(specimen)
else:
k+=1
if len(B)==0:
if verbose:print 'skipping this one - no hysteresis data'
k+=1
def main():
"""
NAME
biplot_magic.py
DESCRIPTION
makes a biplot of specified variables from magic_measurements.txt format file
SYNTAX
biplot_magic.py [-h] [-i] [command line options]
INPUT
takes magic formated magic_measurments file
OPTIONS
-h prints help message and quits
-i interactively set filename and axes for plotting
-f FILE: specifies file name, default: magic_measurements.txt
-fmt [svg,png,jpg], format for images - default is svg
-sav figure and quit
-x XMETH:key:step, specify method code for X axis (optional key and treatment values)
-y YMETH:key:step, specify method code for X axis
-obj OBJ: specify object [loc, sit, sam, spc] for plot, default is whole file
-n [V,M] plot volume or mass normalized data only
NOTES
if nothing is specified for x and y, the user will be presented with options
key = ['treatment_ac_field','treatment_dc_field',treatment_temp']
step in mT for fields, K for temperatures
"""
#
file='magic_measurements.txt'
methx,methy,fmt="","",'.svg'
plot_key=''
norm_by=""
#plot=0
no_plot = pmag.get_flag_arg_from_sys('-sav')
if not no_plot:
do_plot = True
else:
do_plot = False
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index('-f')
file=sys.argv[ind+1]
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt='.'+sys.argv[ind+1]
if '-n' in sys.argv:
ind=sys.argv.index('-n')
norm_by=sys.argv[ind+1]
xtreat_key,ytreat_key,xstep,ystep="","","",""
if '-x' in sys.argv:
ind=sys.argv.index('-x')
meths=sys.argv[ind+1].split(':')
methx=meths[0]
if len(meths)>1:
xtreat_key=meths[1]
xstep=float(meths[2])
if '-y' in sys.argv:
ind=sys.argv.index('-y')
meths=sys.argv[ind+1].split(':')
methy=meths[0]
if len(meths)>1:
ytreat_key=meths[1]
ystep=float(meths[2])
if '-obj' in sys.argv:
ind=sys.argv.index('-obj')
plot_by=sys.argv[ind+1]
if plot_by=='loc':plot_key='er_location_name'
if plot_by=='sit':plot_key='er_site_name'
if plot_by=='sam':plot_key='er_sample_name'
if plot_by=='spc':plot_key='er_specimen_name'
if '-h' in sys.argv:
do_plot = False
if '-i' in sys.argv:
#
# get name of file from command line
#
file=raw_input("Input magic_measurments file name? [magic_measurements.txt] ")
if file=="":file="magic_measurements.txt"
#
#
FIG={'fig':1}
pmagplotlib.plot_init(FIG['fig'],5,5)
data,file_type=pmag.magic_read(file)
if file_type!="magic_measurements":
print file_type,' not correct format for magic_measurments file'
sys.exit()
#
# collect method codes
methods,plotlist=[],[]
for rec in data:
if plot_key!="":
if rec[plot_key] not in plotlist:plotlist.append(rec[plot_key])
elif len(plotlist)==0:
plotlist.append('All')
meths=rec['magic_method_codes'].split(':')
for meth in meths:
if meth.strip() not in methods and meth.strip()!="LP-":
methods.append(meth.strip())
#
if '-i' in sys.argv:
print methods
elif methx =="" or methy=="":
print methods
sys.exit()
GoOn=1
while GoOn==1:
if '-i' in sys.argv:methx=raw_input('Select method for x axis: ')
if methx not in methods:
if '-i' in sys.argv:
print 'try again! method not available'
else:
print main.__doc__
print '\n must specify X axis method\n'
sys.exit()
else:
if pmagplotlib.verbose: print methx, ' selected for X axis'
GoOn=0
GoOn=1
while GoOn==1:
if '-i' in sys.argv:methy=raw_input('Select method for y axis: ')
if methy not in methods:
if '-i' in sys.argv:
print 'try again! method not available'
else:
print main.__doc__
print '\n must specify Y axis method\n'
sys.exit()
else:
if pmagplotlib.verbose: print methy, ' selected for Y axis'
GoOn=0
if norm_by=="":
measkeys=['measurement_magn_mass','measurement_magn_volume','measurement_magn_moment','measurement_magnitude','measurement_chi_volume','measurement_chi_mass','measurement_chi']
elif norm_by=="V":
measkeys=['measurement_magn_volume','measurement_chi_volume']
elif norm_by=="M":
measkeys=['measurement_magn_mass','measurement_chi_mass']
xmeaskey,ymeaskey="",""
plotlist.sort()
for plot in plotlist: # go through objects
if pmagplotlib.verbose:
print plot
X,Y=[],[]
x,y='',''
for rec in data:
if plot_key!="" and rec[plot_key]!=plot:
pass
else:
meths=rec['magic_method_codes'].split(':')
for meth in meths:
if meth.strip()==methx:
if xmeaskey=="":
for key in measkeys:
if key in rec.keys() and rec[key]!="":
xmeaskey=key
if pmagplotlib.verbose:
print xmeaskey,' being used for plotting X.'
break
if meth.strip()==methy:
if ymeaskey=="":
for key in measkeys:
if key in rec.keys() and rec[key]!="":
ymeaskey=key
if pmagplotlib.verbose:
print ymeaskey,' being used for plotting Y'
break
if ymeaskey!="" and xmeaskey!="":
for rec in data:
x,y='',''
spec=rec['er_specimen_name'] # get the ydata for this specimen
if rec[ymeaskey]!="" and methy in rec['magic_method_codes'].split(':'):
if ytreat_key=="" or (ytreat_key in rec.keys() and float(rec[ytreat_key])==ystep):
y=float(rec[ymeaskey])
for rec in data: # now find the xdata
if rec['er_specimen_name']==spec and rec[xmeaskey]!="" and methx in rec['magic_method_codes'].split(':'):
if xtreat_key=="" or (xtreat_key in rec.keys() and float(rec[xtreat_key])==xstep):
x=float(rec[xmeaskey])
if x != '' and y!= '':
X.append(x)
Y.append(y)
if len(X)>0:
pmagplotlib.clearFIG(FIG['fig'])
pmagplotlib.plotXY(FIG['fig'],X,Y,sym='ro',xlab=methx,ylab=methy,title=plot+':Biplot')
if not pmagplotlib.isServer and do_plot:
pmagplotlib.drawFIGS(FIG)
ans=raw_input('S[a]ve plots, [q]uit, Return for next plot ' )
if ans=='a':
files={}
for key in FIG.keys(): files[key]=plot+'_'+key+fmt
pmagplotlib.saveP(FIG,files)
if ans=='q':
print "Good-bye\n"
sys.exit()
else:
files={}
for key in FIG.keys(): files[key]=plot+'_'+key+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['fig']='X Y Plot'
FIG = pmagplotlib.addBorders(FIG,titles,black,purple)
pmagplotlib.saveP(FIG,files)
else:
print 'nothing to plot for ',plot
def main():
"""
NAME
quick_hyst.py
DESCRIPTION
makes plots of hysteresis data
SYNTAX
quick_hyst.py [command line options]
OPTIONS
-h prints help message and quits
-f: specify input file, default is measurements.txt
-spc SPEC: specify specimen name to plot and quit
-sav save all plots and quit
-fmt [png,svg,eps,jpg]
"""
args = sys.argv
if "-h" in args:
print(main.__doc__)
sys.exit()
plots = 0
pltspec = ""
verbose = pmagplotlib.verbose
#version_num = pmag.get_version()
dir_path = pmag.get_named_arg_from_sys('-WD', '.')
dir_path = os.path.realpath(dir_path)
meas_file = pmag.get_named_arg_from_sys('-f', 'measurements.txt')
fmt = pmag.get_named_arg_from_sys('-fmt', 'png')
if '-sav' in args:
verbose = 0
plots = 1
if '-spc' in args:
ind = args.index("-spc")
pltspec = args[ind + 1]
verbose = 0
plots = 1
#
con = nb.Contribution(dir_path,
read_tables=['measurements'],
custom_filenames={'measurements': meas_file})
# get as much name data as possible (used for naming plots)
if not 'measurements' in con.tables:
print("-W- No measurement file found")
return
con.propagate_location_to_measurements()
if 'measurements' not in con.tables:
print(main.__doc__)
print('bad file')
sys.exit()
meas_container = con.tables['measurements']
#meas_df = meas_container.df
#
# initialize some variables
# define figure numbers for hyst,deltaM,DdeltaM curves
HystRecs = []
HDD = {}
HDD['hyst'] = 1
pmagplotlib.plot_init(HDD['hyst'], 5, 5)
#
# get list of unique experiment names and specimen names
#
sids = []
hyst_data = meas_container.get_records_for_code('LP-HYS')
#experiment_names = hyst_data['experiment_name'].unique()
if not len(hyst_data):
print("-W- No hysteresis data found")
return
sids = hyst_data['specimen'].unique()
# if 'treat_temp' is provided, use that value, otherwise assume 300
hyst_data['treat_temp'].where(hyst_data['treat_temp'].notnull(),
'300',
inplace=True)
# start at first specimen, or at provided specimen ('-spc')
k = 0
if pltspec != "":
try:
print(sids)
k = list(sids).index(pltspec)
except ValueError:
print('-W- No specimen named: {}.'.format(pltspec))
print('-W- Please provide a valid specimen name')
return
intlist = ['magn_moment', 'magn_volume', 'magn_mass']
while k < len(sids):
locname, site, sample, synth = '', '', '', ''
s = sids[k]
if verbose:
print(s, k + 1, 'out of ', len(sids))
# B, M for hysteresis, Bdcd,Mdcd for irm-dcd data
B, M = [], []
# get all measurements for this specimen
spec = hyst_data[hyst_data['specimen'] == s]
# get names
if 'location' in spec:
locname = spec['location'][0]
if 'site' in spec:
site = spec['sample'][0]
if 'sample' in spec:
sample = spec['sample'][0]
# get all records with non-blank values in any intlist column
# find intensity data
for int_column in intlist:
if int_column in spec.columns:
int_col = int_column
break
meas_data = spec[spec[int_column].notnull()]
if len(meas_data) == 0:
break
#
c = ['k-', 'b-', 'c-', 'g-', 'm-', 'r-', 'y-']
cnum = 0
Temps = []
xlab, ylab, title = '', '', ''
Temps = meas_data['treat_temp'].unique()
for t in Temps:
print('working on t: ', t)
t_data = meas_data[meas_data['treat_temp'] == t]
m = int_col
B = t_data['meas_field_dc'].astype(float).values
M = t_data[m].astype(float).values
# now plot the hysteresis curve(s)
#
if len(B) > 0:
B = numpy.array(B)
M = numpy.array(M)
if t == Temps[-1]:
xlab = 'Field (T)'
ylab = m
title = 'Hysteresis: ' + s
if t == Temps[0]:
pmagplotlib.clearFIG(HDD['hyst'])
pmagplotlib.plotXY(HDD['hyst'],
B,
M,
sym=c[cnum],
xlab=xlab,
ylab=ylab,
title=title)
pmagplotlib.plotXY(HDD['hyst'], [1.1 * B.min(), 1.1 * B.max()],
[0, 0],
sym='k-',
xlab=xlab,
ylab=ylab,
title=title)
pmagplotlib.plotXY(HDD['hyst'], [0, 0],
[1.1 * M.min(), 1.1 * M.max()],
sym='k-',
xlab=xlab,
ylab=ylab,
title=title)
if verbose:
pmagplotlib.drawFIGS(HDD)
cnum += 1
if cnum == len(c):
cnum = 0
#
files = {}
if plots:
if pltspec != "":
s = pltspec
for key in list(HDD.keys()):
if pmagplotlib.isServer:
if synth == '':
files[
key] = "LO:_" + locname + '_SI:_' + site + '_SA:_' + sample + '_SP:_' + s + '_TY:_' + key + '_.' + fmt
else:
files[
key] = 'SY:_' + synth + '_TY:_' + key + '_.' + fmt
else:
if synth == '':
filename = ''
for item in [locname, site, sample, s, key]:
if item:
item = item.replace(' ', '_')
filename += item + '_'
if filename.endswith('_'):
filename = filename[:-1]
filename += ".{}".format(fmt)
files[key] = filename
else:
files[key] = "{}_{}.{}".format(synth, key, fmt)
pmagplotlib.saveP(HDD, files)
if pltspec != "":
sys.exit()
if verbose:
pmagplotlib.drawFIGS(HDD)
ans = input(
"S[a]ve plots, [s]pecimen name, [q]uit, <return> to continue\n "
)
if ans == "a":
files = {}
for key in list(HDD.keys()):
if pmagplotlib.isServer: # use server plot naming convention
files[
key] = "LO:_" + locname + '_SI:_' + site + '_SA:_' + sample + '_SP:_' + s + '_TY:_' + key + '_.' + fmt
else: # use more readable plot naming convention
filename = ''
for item in [locname, site, sample, s, key]:
if item:
item = item.replace(' ', '_')
filename += item + '_'
if filename.endswith('_'):
filename = filename[:-1]
filename += ".{}".format(fmt)
files[key] = filename
pmagplotlib.saveP(HDD, files)
if ans == '':
k += 1
if ans == "p":
del HystRecs[-1]
k -= 1
if ans == 'q':
print("Good bye")
sys.exit()
if ans == 's':
keepon = 1
specimen = input(
'Enter desired specimen name (or first part there of): ')
while keepon == 1:
try:
k = sids.index(specimen)
keepon = 0
except:
tmplist = []
for qq in range(len(sids)):
if specimen in sids[qq]:
tmplist.append(sids[qq])
print(specimen, " not found, but this was: ")
print(tmplist)
specimen = input('Select one or try again\n ')
k = sids.index(specimen)
else:
k += 1
if len(B) == 0:
if verbose:
print('skipping this one - no hysteresis data')
k += 1
def main():
"""
NAME
plot_magic_keys.py
DESCRIPTION
picks out keys and makes and xy plot
SYNTAX
plot_magic_keys.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE: specify input magic format file
-xkey KEY: specify key for X
-ykey KEY: specify key for Y
-b xmin xmax ymin ymax, sets bounds
"""
dir_path = "./"
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind = sys.argv.index('-f')
magic_file = dir_path + '/' + sys.argv[ind + 1]
else:
print main.__doc__
sys.exit()
if '-xkey' in sys.argv:
ind = sys.argv.index('-xkey')
xkey = sys.argv[ind + 1]
if '-ykey' in sys.argv:
ind = sys.argv.index('-ykey')
ykey = sys.argv[ind + 1]
else:
print main.__doc__
sys.exit()
if '-b' in sys.argv:
ind = sys.argv.index('-b')
xmin = float(sys.argv[ind + 1])
xmax = float(sys.argv[ind + 2])
ymin = float(sys.argv[ind + 3])
ymax = float(sys.argv[ind + 4])
#
#
# get data read in
X, Y = [], []
Data, file_type = pmag.magic_read(magic_file)
if len(Data) > 0:
for rec in Data:
if xkey in rec.keys() and rec[xkey] != "" and ykey in rec.keys(
) and rec[ykey] != "":
try:
X.append(float(rec[xkey]))
Y.append(float(rec[ykey]))
except:
pass
FIG = {'fig': 1}
pmagplotlib.plot_init(FIG['fig'], 5, 5)
if '-b' in sys.argv:
pmagplotlib.plotXY(FIG['fig'],
X,
Y,
sym='ro',
xlab=xkey,
ylab=ykey,
xmin=xmin,
xmax=xmax,
ymin=ymin,
ymax=ymax)
else:
pmagplotlib.plotXY(FIG['fig'],
X,
Y,
sym='ro',
xlab=xkey,
ylab=ykey)
pmagplotlib.drawFIGS(FIG)
ans = raw_input(" S[a]ve to save plot, [q]uit, Return to continue: ")
if ans == "q": sys.exit()
if ans == "a":
files = {}
for key in FIG.keys():
files[key] = str(key) + ".svg"
pmagplotlib.saveP(FIG, files)
sys.exit()
else:
print 'no data to plot'
def main():
"""
NAME
curie.py
DESCTIPTION
plots and interprets curie temperature data.
the 1st derivative is calculated from smoothed M-T curve
(convolution with trianfular window with width= <-w> degrees)
the 2nd derivative is calculated from smoothed 1st derivative curve
( using the same sliding window width)
the estinated curie temp. is the maximum of the 2nd derivative
- the temperature steps should be in multiples of 1.0 degrees
INPUT
T,M
SYNTAX
curie.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE, sets M,T input file (required)
-w size of sliding window in degrees (default - 3 degrees)
-t <min> <max> temperature range (optional)
-sav save figures and quit
-fmt [svg,jpg,eps,png,pdf] set format for figure output [default: svg]
example:
curie.py -f ex2.1 -w 30 -t 300 700
"""
plot,fmt=0,'svg'
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index('-f')
meas_file=sys.argv[ind+1]
else:
print("missing -f\n")
sys.exit()
if '-w' in sys.argv:
ind=sys.argv.index('-w')
window_len=int(sys.argv[ind+1])
else:
window_len=3
if '-t' in sys.argv:
ind=sys.argv.index('-t')
t_begin=int(sys.argv[ind+1])
t_end=int(sys.argv[ind+2])
else:
t_begin=''
t_end=''
if '-sav' in sys.argv:plot=1
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
# read data from file
Data=numpy.loadtxt(meas_file,dtype=numpy.float)
T=Data.transpose()[0]
M=Data.transpose()[1]
T=list(T)
M=list(M)
# cut the data if -t is one of the flags
if t_begin:
while T[0]<t_begin:
M.pop(0);T.pop(0)
while T[-1]>t_end:
M.pop(-1);T.pop(-1)
# prepare the signal:
# from M(T) array with unequal deltaT
# to M(T) array with deltaT=(1 degree).
# if delataT is larger, then points are added using linear fit between
# consecutive data points.
# exit if deltaT is not integer
i=0
while i<(len(T)-1):
if (T[i+1]-T[i])%1>0.001:
print("delta T should be integer, this program will not work!")
print("temperature range:",T[i],T[i+1])
sys.exit()
if (T[i+1]-T[i])==0.:
M[i]=average([M[i],M[i+1]])
M.pop(i+1);T.pop(i+1)
elif (T[i+1]-T[i])<0.:
M.pop(i+1);T.pop(i+1)
print("check data in T=%.0f ,M[T] is ignored"%(T[i]))
elif (T[i+1]-T[i])>1.:
slope,b=polyfit([T[i],T[i+1]],[M[i],M[i+1]],1)
for j in range(int(T[i+1])-int(T[i])-1):
M.insert(i+1,slope*(T[i]+1.)+b)
T.insert(i+1,(T[i]+1.))
i=i+1
i=i+1
# calculate the smoothed signal
M=array(M,'f')
T=array(T,'f')
M_smooth=[]
M_smooth=smooth(M,window_len)
#plot the original data and the smooth data
PLT={'M_T':1,'der1':2,'der2':3,'Curie':4}
pmagplotlib.plot_init(PLT['M_T'],5,5)
string='M-T (sliding window=%i)'%int(window_len)
pmagplotlib.plotXY(PLT['M_T'],T,M_smooth,sym='-')
pmagplotlib.plotXY(PLT['M_T'],T,M,sym='--',xlab='Temperature C',ylab='Magnetization',title=string)
#calculate first derivative
d1,T_d1=[],[]
for i in range(len(M_smooth)-1):
Dy=M_smooth[i-1]-M_smooth[i+1]
Dx=T[i-1]-T[i+1]
d1.append(old_div(Dy,Dx))
T_d1=T[1:len(T-1)]
d1=array(d1,'f')
d1_smooth=smooth(d1,window_len)
#plot the first derivative
pmagplotlib.plot_init(PLT['der1'],5,5)
string='1st derivative (sliding window=%i)'%int(window_len)
pmagplotlib.plotXY(PLT['der1'],T_d1,d1_smooth,sym='-',xlab='Temperature C',title=string)
pmagplotlib.plotXY(PLT['der1'],T_d1,d1,sym='b--')
#calculate second derivative
d2,T_d2=[],[]
for i in range(len(d1_smooth)-1):
Dy=d1_smooth[i-1]-d1_smooth[i+1]
Dx=T[i-1]-T[i+1]
#print Dy/Dx
d2.append(old_div(Dy,Dx))
T_d2=T[2:len(T-2)]
d2=array(d2,'f')
d2_smooth=smooth(d2,window_len)
#plot the second derivative
pmagplotlib.plot_init(PLT['der2'],5,5)
string='2nd derivative (sliding window=%i)'%int(window_len)
pmagplotlib.plotXY(PLT['der2'],T_d2,d2,sym='-',xlab='Temperature C',title=string)
d2=list(d2)
print('second derivative maximum is at T=%i'%int(T_d2[d2.index(max(d2))]))
# calculate Curie temperature for different width of sliding windows
curie,curie_1=[],[]
wn=list(range(5,50,1))
for win in wn:
# calculate the smoothed signal
M_smooth=[]
M_smooth=smooth(M,win)
#calculate first derivative
d1,T_d1=[],[]
for i in range(len(M_smooth)-1):
Dy=M_smooth[i-1]-M_smooth[i+1]
Dx=T[i-1]-T[i+1]
d1.append(old_div(Dy,Dx))
T_d1=T[1:len(T-1)]
d1=array(d1,'f')
d1_smooth=smooth(d1,win)
#calculate second derivative
d2,T_d2=[],[]
for i in range(len(d1_smooth)-1):
Dy=d1_smooth[i-1]-d1_smooth[i+1]
Dx=T[i-1]-T[i+1]
d2.append(old_div(Dy,Dx))
T_d2=T[2:len(T-2)]
d2=array(d2,'f')
d2_smooth=smooth(d2,win)
d2=list(d2)
d2_smooth=list(d2_smooth)
curie.append(T_d2[d2.index(max(d2))])
curie_1.append(T_d2[d2_smooth.index(max(d2_smooth))])
#plot Curie temp for different sliding window length
pmagplotlib.plot_init(PLT['Curie'],5,5)
pmagplotlib.plotXY(PLT['Curie'],wn,curie,sym='.',xlab='Sliding Window Width (degrees)',ylab='Curie Temp',title='Curie Statistics')
files = {}
for key in list(PLT.keys()): files[key]=str(key) + "." +fmt
if plot==0:
pmagplotlib.drawFIGS(PLT)
ans=input(" S[a]ve to save plot, [q]uit, Return to continue: ")
if ans=="q": sys.exit()
if ans=="a": pmagplotlib.saveP(PLT,files)
else: pmagplotlib.saveP(PLT,files)
sys.exit()
def main():
"""
NAME
curie.py
DESCTIPTION
plots and interprets curie temperature data.
the 1st derivative is calculated from smoothed M-T curve
(convolution with trianfular window with width= <-w> degrees)
the 2nd derivative is calculated from smoothed 1st derivative curve
( using the same sliding window width)
the estinated curie temp. is the maximum of the 2nd derivative
- the temperature steps should be in multiples of 1.0 degrees
INPUT
T,M
SYNTAX
curie.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE, sets M,T input file (required)
-w size of sliding window in degrees (default - 3 degrees)
-t <min> <max> temperature range (optional)
-sav save figures and quit
-fmt [svg,jpg,eps,png,pdf] set format for figure output [default: svg]
example:
curie.py -f ex2.1 -w 30 -t 300 700
"""
plot,fmt=0,'svg'
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index('-f')
meas_file=sys.argv[ind+1]
else:
print "missing -f\n"
sys.exit()
if '-w' in sys.argv:
ind=sys.argv.index('-w')
window_len=int(sys.argv[ind+1])
else:
window_len=3
if '-t' in sys.argv:
ind=sys.argv.index('-t')
t_begin=int(sys.argv[ind+1])
t_end=int(sys.argv[ind+2])
else:
t_begin=''
t_end=''
if '-sav' in sys.argv:plot=1
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
# read data from file
Data=numpy.loadtxt(meas_file,dtype=numpy.float)
T=Data.transpose()[0]
M=Data.transpose()[1]
T=list(T)
M=list(M)
# cut the data if -t is one of the flags
if t_begin:
while T[0]<t_begin:
M.pop(0);T.pop(0)
while T[-1]>t_end:
M.pop(-1);T.pop(-1)
# prepare the signal:
# from M(T) array with unequal deltaT
# to M(T) array with deltaT=(1 degree).
# if delataT is larger, then points are added using linear fit between
# consecutive data points.
# exit if deltaT is not integer
i=0
while i<(len(T)-1):
if (T[i+1]-T[i])%1>0.001:
print "delta T should be integer, this program will not work!"
print "temperature range:",T[i],T[i+1]
sys.exit()
if (T[i+1]-T[i])==0.:
M[i]=average([M[i],M[i+1]])
M.pop(i+1);T.pop(i+1)
elif (T[i+1]-T[i])<0.:
M.pop(i+1);T.pop(i+1)
print "check data in T=%.0f ,M[T] is ignored"%(T[i])
elif (T[i+1]-T[i])>1.:
slope,b=polyfit([T[i],T[i+1]],[M[i],M[i+1]],1)
for j in range(int(T[i+1])-int(T[i])-1):
M.insert(i+1,slope*(T[i]+1.)+b)
T.insert(i+1,(T[i]+1.))
i=i+1
i=i+1
# calculate the smoothed signal
M=array(M,'f')
T=array(T,'f')
M_smooth=[]
M_smooth=smooth(M,window_len)
#plot the original data and the smooth data
PLT={'M_T':1,'der1':2,'der2':3,'Curie':4}
pmagplotlib.plot_init(PLT['M_T'],5,5)
string='M-T (sliding window=%i)'%int(window_len)
pmagplotlib.plotXY(PLT['M_T'],T,M_smooth,sym='-')
pmagplotlib.plotXY(PLT['M_T'],T,M,sym='--',xlab='Temperature C',ylab='Magnetization',title=string)
#calculate first derivative
d1,T_d1=[],[]
for i in range(len(M_smooth)-1):
Dy=M_smooth[i-1]-M_smooth[i+1]
Dx=T[i-1]-T[i+1]
d1.append(Dy/Dx)
T_d1=T[1:len(T-1)]
d1=array(d1,'f')
d1_smooth=smooth(d1,window_len)
#plot the first derivative
pmagplotlib.plot_init(PLT['der1'],5,5)
string='1st derivative (sliding window=%i)'%int(window_len)
pmagplotlib.plotXY(PLT['der1'],T_d1,d1_smooth,sym='-',xlab='Temperature C',title=string)
pmagplotlib.plotXY(PLT['der1'],T_d1,d1,sym='b--')
#calculate second derivative
d2,T_d2=[],[]
for i in range(len(d1_smooth)-1):
Dy=d1_smooth[i-1]-d1_smooth[i+1]
Dx=T[i-1]-T[i+1]
#print Dy/Dx
d2.append(Dy/Dx)
T_d2=T[2:len(T-2)]
d2=array(d2,'f')
d2_smooth=smooth(d2,window_len)
#plot the second derivative
pmagplotlib.plot_init(PLT['der2'],5,5)
string='2nd derivative (sliding window=%i)'%int(window_len)
pmagplotlib.plotXY(PLT['der2'],T_d2,d2,sym='-',xlab='Temperature C',title=string)
d2=list(d2)
print 'second derivative maximum is at T=%i'%int(T_d2[d2.index(max(d2))])
# calculate Curie temperature for different width of sliding windows
curie,curie_1=[],[]
wn=range(5,50,1)
for win in wn:
# calculate the smoothed signal
M_smooth=[]
M_smooth=smooth(M,win)
#calculate first derivative
d1,T_d1=[],[]
for i in range(len(M_smooth)-1):
Dy=M_smooth[i-1]-M_smooth[i+1]
Dx=T[i-1]-T[i+1]
d1.append(Dy/Dx)
T_d1=T[1:len(T-1)]
d1=array(d1,'f')
d1_smooth=smooth(d1,win)
#calculate second derivative
d2,T_d2=[],[]
for i in range(len(d1_smooth)-1):
Dy=d1_smooth[i-1]-d1_smooth[i+1]
Dx=T[i-1]-T[i+1]
d2.append(Dy/Dx)
T_d2=T[2:len(T-2)]
d2=array(d2,'f')
d2_smooth=smooth(d2,win)
d2=list(d2)
d2_smooth=list(d2_smooth)
curie.append(T_d2[d2.index(max(d2))])
curie_1.append(T_d2[d2_smooth.index(max(d2_smooth))])
#plot Curie temp for different sliding window length
pmagplotlib.plot_init(PLT['Curie'],5,5)
pmagplotlib.plotXY(PLT['Curie'],wn,curie,sym='.',xlab='Sliding Window Width (degrees)',ylab='Curie Temp',title='Curie Statistics')
files = {}
for key in PLT.keys(): files[key]=str(key) + "." +fmt
if plot==0:
pmagplotlib.drawFIGS(PLT)
ans=raw_input(" S[a]ve to save plot, [q]uit, Return to continue: ")
if ans=="q": sys.exit()
if ans=="a": pmagplotlib.saveP(PLT,files)
else: pmagplotlib.saveP(PLT,files)
sys.exit()
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 list(rec.keys()): rec['sample_orientation_flag']='g'
if 'sample_description' not in list(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 list(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=input("s[a]ve plot, [q]uit, [e]dit specimens, [p]revious site, <return> to continue:\n ")
elif k==0 and repeat!='y':
ans=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=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=input("Mark this sample as bad? y/[n] ")
if deleteme=='y':
reason=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=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=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
lowrie.py
DESCRIPTION
plots intensity decay curves for Lowrie experiments
SYNTAX
lowrie -h [command line options]
INPUT
takes SIO formatted input files
OPTIONS
-h prints help message and quits
-f FILE: specify input file
-N do not normalize by maximum magnetization
-fmt [svg, pdf, eps, png] specify fmt, default is svg
-sav save plots and quit
"""
fmt, plot = 'svg', 0
FIG = {} # plot dictionary
FIG['lowrie'] = 1 # demag is figure 1
pmagplotlib.plot_init(FIG['lowrie'], 6, 6)
norm = 1 # default is to normalize by maximum axis
if len(sys.argv) > 1:
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-N' in sys.argv:
norm = 0 # don't normalize
if '-sav' in sys.argv:
plot = 1 # don't normalize
if '-fmt' in sys.argv: # sets input filename
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
if '-f' in sys.argv: # sets input filename
ind = sys.argv.index("-f")
in_file = sys.argv[ind + 1]
else:
print(main.__doc__)
print('you must supply a file name')
sys.exit()
else:
print(main.__doc__)
print('you must supply a file name')
sys.exit()
data = pmag.open_file(in_file)
PmagRecs = [] # set up a list for the results
keys = ['specimen', 'treatment', 'csd', 'M', 'dec', 'inc']
for line in data:
PmagRec = {}
rec = line.replace('\n', '').split()
for k in range(len(keys)):
PmagRec[keys[k]] = rec[k]
PmagRecs.append(PmagRec)
specs = pmag.get_dictkey(PmagRecs, 'specimen', '')
sids = []
for spec in specs:
if spec not in sids:
sids.append(spec) # get list of unique specimen names
for spc in sids: # step through the specimen names
print(spc)
specdata = pmag.get_dictitem(
PmagRecs, 'specimen', spc, 'T') # get all this one's data
DIMs, Temps = [], []
for dat in specdata: # step through the data
DIMs.append([float(dat['dec']), float(
dat['inc']), float(dat['M']) * 1e-3])
Temps.append(float(dat['treatment']))
carts = pmag.dir2cart(DIMs).transpose()
# if norm==1: # want to normalize
# nrm=max(max(abs(carts[0])),max(abs(carts[1])),max(abs(carts[2]))) # by maximum of x,y,z values
# ylab="M/M_max"
if norm == 1: # want to normalize
nrm = (DIMs[0][2]) # normalize by NRM
ylab = "M/M_o"
else:
nrm = 1. # don't normalize
ylab = "Magnetic moment (Am^2)"
xlab = "Temperature (C)"
pmagplotlib.plotXY(FIG['lowrie'], Temps, old_div(
abs(carts[0]), nrm), sym='r-')
pmagplotlib.plotXY(FIG['lowrie'], Temps, old_div(
abs(carts[0]), nrm), sym='ro') # X direction
pmagplotlib.plotXY(FIG['lowrie'], Temps, old_div(
abs(carts[1]), nrm), sym='c-')
pmagplotlib.plotXY(FIG['lowrie'], Temps, old_div(
abs(carts[1]), nrm), sym='cs') # Y direction
pmagplotlib.plotXY(FIG['lowrie'], Temps, old_div(
abs(carts[2]), nrm), sym='k-')
pmagplotlib.plotXY(FIG['lowrie'], Temps, old_div(
abs(carts[2]), nrm), sym='k^', title=spc, xlab=xlab, ylab=ylab) # Z direction
files = {'lowrie': 'lowrie:_' + spc + '_.' + fmt}
if plot == 0:
pmagplotlib.drawFIGS(FIG)
ans = input('S[a]ve figure? [q]uit, <return> to continue ')
if ans == 'a':
pmagplotlib.saveP(FIG, files)
elif ans == 'q':
sys.exit()
else:
pmagplotlib.saveP(FIG, files)
pmagplotlib.clearFIG(FIG['lowrie'])
def main():
"""
NAME
plot_magic_keys.py
DESCRIPTION
picks out keys and makes and xy plot
SYNTAX
plot_magic_keys.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE: specify input magic format file
-xkey KEY: specify key for X
-ykey KEY: specify key for Y
-b xmin xmax ymin ymax, sets bounds
"""
dir_path="./"
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index('-f')
magic_file=dir_path+'/'+sys.argv[ind+1]
else:
print(main.__doc__)
sys.exit()
if '-xkey' in sys.argv:
ind=sys.argv.index('-xkey')
xkey=sys.argv[ind+1]
if '-ykey' in sys.argv:
ind=sys.argv.index('-ykey')
ykey=sys.argv[ind+1]
else:
print(main.__doc__)
sys.exit()
if '-b' in sys.argv:
ind=sys.argv.index('-b')
xmin=float(sys.argv[ind+1])
xmax=float(sys.argv[ind+2])
ymin=float(sys.argv[ind+3])
ymax=float(sys.argv[ind+4])
#
#
# get data read in
X,Y=[],[]
Data,file_type=pmag.magic_read(magic_file)
if len(Data)>0:
for rec in Data:
if xkey in list(rec.keys()) and rec[xkey]!="" and ykey in list(rec.keys()) and rec[ykey]!="":
try:
X.append(float(rec[xkey]))
Y.append(float(rec[ykey]))
except:
pass
FIG={'fig':1}
pmagplotlib.plot_init(FIG['fig'],5,5)
if '-b' in sys.argv:
pmagplotlib.plotXY(FIG['fig'],X,Y,sym='ro',xlab=xkey,ylab=ykey,xmin=xmin, xmax=xmax, ymin=ymin, ymax=ymax )
else:
pmagplotlib.plotXY(FIG['fig'],X,Y,sym='ro',xlab=xkey,ylab=ykey)
pmagplotlib.drawFIGS(FIG)
ans=input(" S[a]ve to save plot, [q]uit, Return to continue: ")
if ans=="q": sys.exit()
if ans=="a":
files = {}
for key in list(FIG.keys()):
files[key]=str(key) + ".svg"
pmagplotlib.saveP(FIG,files)
sys.exit()
else:
print('no data to plot')
def main():
"""
NAME
plot_geomagia.py
DESCRIPTION
makes a map and VADM plot of geomagia download file
SYNTAX
plot_geomagia.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE, specify geomagia download file
-res [c,l,i,h] specify resolution (crude,low,intermediate,high)
-etp plot the etopo20 topographic mesh
-pad [LAT LON] pad bounding box by LAT/LON (default is [.5 .5] degrees)
-grd SPACE specify grid spacing
-prj [lcc] , specify projection (lcc=lambert conic conformable), default is mercator
-o color ocean blue/land green (default is not)
-d plot details of rivers, boundaries, etc.
-sav save plot and quit quietly
-fmt [png,svg,eps,jpg,pdf] specify format for output, default is pdf
DEFAULTS
resolution: intermediate
saved images are in pdf
"""
dir_path = '.'
names, res, proj, locs, padlon, padlat, fancy, gridspace, details = [], 'l', 'lcc', '', 0, 0, 0, 15, 1
Age_bounds = [-5000, 2000]
Lat_bounds = [20, 45]
Lon_bounds = [15, 55]
fmt = 'pdf'
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-f' in sys.argv:
ind = sys.argv.index('-f')
sites_file = sys.argv[ind + 1]
if '-res' in sys.argv:
ind = sys.argv.index('-res')
res = sys.argv[ind + 1]
if '-etp' in sys.argv: fancy = 1
if '-o' in sys.argv: ocean = 1
if '-d' in sys.argv: details = 1
if '-prj' in sys.argv:
ind = sys.argv.index('-prj')
proj = sys.argv[ind + 1]
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt = sys.argv[ind + 1]
verbose = pmagplotlib.verbose
if '-sav' in sys.argv:
verbose = 0
if '-pad' in sys.argv:
ind = sys.argv.index('-pad')
padlat = float(sys.argv[ind + 1])
padlon = float(sys.argv[ind + 2])
if '-grd' in sys.argv:
ind = sys.argv.index('-grd')
gridspace = float(sys.argv[ind + 1])
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
sites_file = dir_path + '/' + sites_file
geo_in = open(sites_file, 'r').readlines()
Age, AgeErr, Vadm, VadmErr, slats, slons = [], [], [], [], [], []
for line in geo_in[2:]: # skip top two rows`
rec = line.split()
if float(rec[0])>Age_bounds[0] and float(rec[0])<Age_bounds[1] \
and float(rec[12])>Lat_bounds[0] and float(rec[12]) < Lat_bounds[1]\
and float(rec[13])>Lon_bounds[0] and float(rec[13])<Lon_bounds[1]:
Age.append(float(rec[0]))
AgeErr.append(float(rec[1]))
Vadm.append(10. * float(rec[6]))
VadmErr.append(10. * float(rec[7]))
slats.append(float(rec[12]))
slons.append(float(rec[13]))
FIGS = {'map': 1, 'vadms': 2}
pmagplotlib.plot_init(FIGS['map'], 6, 6)
pmagplotlib.plot_init(FIGS['vadms'], 6, 6)
Opts = {
'res': res,
'proj': proj,
'loc_name': locs,
'padlon': padlon,
'padlat': padlat,
'latmin': numpy.min(slats) - padlat,
'latmax': numpy.max(slats) + padlat,
'lonmin': numpy.min(slons) - padlon,
'lonmax': numpy.max(slons) + padlon,
'sym': 'ro',
'boundinglat': 0.,
'pltgrid': 1
}
Opts['lon_0'] = int(0.5 * (numpy.min(slons) + numpy.max(slons)))
Opts['lat_0'] = int(0.5 * (numpy.min(slats) + numpy.max(slats)))
Opts['gridspace'] = gridspace
if details == 1:
Opts['details'] = {
'coasts': 1,
'rivers': 0,
'states': 1,
'countries': 1,
'ocean': 1
}
else:
Opts['details'] = {
'coasts': 1,
'rivers': 0,
'states': 0,
'countries': 0,
'ocean': 1
}
Opts['details']['fancy'] = fancy
pmagplotlib.plotMAP(FIGS['map'], slats, slons, Opts)
pmagplotlib.plotXY(FIGS['vadms'],
Age,
Vadm,
sym='bo',
xlab='Age (Years CE)',
ylab=r'VADM (ZAm$^2$)')
if verbose: pmagplotlib.drawFIGS(FIGS)
files = {}
for key in list(FIGS.keys()):
files[key] = key + '.' + fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles = {}
titles['map'] = 'Map'
titles['vadms'] = 'VADMs'
FIG = pmagplotlib.addBorders(FIGS, titles, black, purple)
pmagplotlib.saveP(FIGS, files)
elif verbose:
ans = input(" S[a]ve to save plot, Return to quit: ")
if ans == "a":
pmagplotlib.saveP(FIGS, files)
else:
pmagplotlib.saveP(FIGS, files)
def main():
"""
NAME
quick_hyst.py
DESCRIPTION
makes plots of hysteresis data
SYNTAX
quick_hyst.py [command line options]
OPTIONS
-h prints help message and quits
-f: specify input file, default is measurements.txt
-spc SPEC: specify specimen name to plot and quit
-sav save all plots and quit
-fmt [png,svg,eps,jpg]
"""
args = sys.argv
if "-h" in args:
print main.__doc__
sys.exit()
plots = 0
pltspec = ""
verbose = pmagplotlib.verbose
# version_num = pmag.get_version()
dir_path = pmag.get_named_arg_from_sys("-WD", ".")
dir_path = os.path.realpath(dir_path)
meas_file = pmag.get_named_arg_from_sys("-f", "measurements.txt")
fmt = pmag.get_named_arg_from_sys("-fmt", "png")
if "-sav" in args:
verbose = 0
plots = 1
if "-spc" in args:
ind = args.index("-spc")
pltspec = args[ind + 1]
verbose = 0
plots = 1
#
con = nb.Contribution(dir_path, read_tables=["measurements"], custom_filenames={"measurements": meas_file})
# get as much name data as possible (used for naming plots)
if not "measurements" in con.tables:
print "-W- No measurement file found"
return
con.propagate_name_down("location", "measurements")
if "measurements" not in con.tables:
print main.__doc__
print "bad file"
sys.exit()
meas_container = con.tables["measurements"]
# meas_df = meas_container.df
#
# initialize some variables
# define figure numbers for hyst,deltaM,DdeltaM curves
HystRecs = []
HDD = {}
HDD["hyst"] = 1
pmagplotlib.plot_init(HDD["hyst"], 5, 5)
#
# get list of unique experiment names and specimen names
#
sids = []
hyst_data = meas_container.get_records_for_code("LP-HYS")
# experiment_names = hyst_data['experiment_name'].unique()
if not len(hyst_data):
print "-W- No hysteresis data found"
return
sids = hyst_data["specimen"].unique()
# if 'treat_temp' is provided, use that value, otherwise assume 300
hyst_data["treat_temp"].where(hyst_data["treat_temp"], "300", inplace=True)
# start at first specimen, or at provided specimen ('-spc')
k = 0
if pltspec != "":
try:
print sids
k = list(sids).index(pltspec)
except ValueError:
print "-W- No specimen named: {}.".format(pltspec)
print "-W- Please provide a valid specimen name"
return
intlist = ["magn_moment", "magn_volume", "magn_mass"]
while k < len(sids):
locname, site, sample, synth = "", "", "", ""
s = sids[k]
if verbose:
print s, k + 1, "out of ", len(sids)
# B, M for hysteresis, Bdcd,Mdcd for irm-dcd data
B, M = [], []
# get all measurements for this specimen
spec = hyst_data[hyst_data["specimen"] == s]
# get names
if "location" in spec:
locname = spec["location"][0]
if "site" in spec:
site = spec["sample"][0]
if "sample" in spec:
sample = spec["sample"][0]
# get all records with non-blank values in any intlist column
# find intensity data
for int_column in intlist:
if int_column in spec.columns:
int_col = int_column
break
meas_data = spec[spec[int_column].notnull()]
if len(meas_data) == 0:
break
#
c = ["k-", "b-", "c-", "g-", "m-", "r-", "y-"]
cnum = 0
Temps = []
xlab, ylab, title = "", "", ""
Temps = meas_data["treat_temp"].unique()
for t in Temps:
print "working on t: ", t
t_data = meas_data[meas_data["treat_temp"] == t]
m = int_col
B = t_data["meas_field_dc"].astype(float).values
M = t_data[m].astype(float).values
# now plot the hysteresis curve(s)
#
if len(B) > 0:
B = numpy.array(B)
M = numpy.array(M)
if t == Temps[-1]:
xlab = "Field (T)"
ylab = m
title = "Hysteresis: " + s
if t == Temps[0]:
pmagplotlib.clearFIG(HDD["hyst"])
pmagplotlib.plotXY(HDD["hyst"], B, M, sym=c[cnum], xlab=xlab, ylab=ylab, title=title)
pmagplotlib.plotXY(
HDD["hyst"], [1.1 * B.min(), 1.1 * B.max()], [0, 0], sym="k-", xlab=xlab, ylab=ylab, title=title
)
pmagplotlib.plotXY(
HDD["hyst"], [0, 0], [1.1 * M.min(), 1.1 * M.max()], sym="k-", xlab=xlab, ylab=ylab, title=title
)
if verbose:
pmagplotlib.drawFIGS(HDD)
cnum += 1
if cnum == len(c):
cnum = 0
#
files = {}
if plots:
if pltspec != "":
s = pltspec
for key in HDD.keys():
if synth == "":
files[key] = (
"LO:_" + locname + "_SI:_" + site + "_SA:_" + sample + "_SP:_" + s + "_TY:_" + key + "_." + fmt
)
else:
files[key] = "SY:_" + synth + "_TY:_" + key + "_." + fmt
pmagplotlib.saveP(HDD, files)
if pltspec != "":
sys.exit()
if verbose:
pmagplotlib.drawFIGS(HDD)
ans = raw_input("S[a]ve plots, [s]pecimen name, [q]uit, <return> to continue\n ")
if ans == "a":
files = {}
for key in HDD.keys():
files[key] = (
"LO:_" + locname + "_SI:_" + site + "_SA:_" + sample + "_SP:_" + s + "_TY:_" + key + "_." + fmt
)
pmagplotlib.saveP(HDD, files)
if ans == "":
k += 1
if ans == "p":
del HystRecs[-1]
k -= 1
if ans == "q":
print "Good bye"
sys.exit()
if ans == "s":
keepon = 1
specimen = raw_input("Enter desired specimen name (or first part there of): ")
while keepon == 1:
try:
k = sids.index(specimen)
keepon = 0
except:
tmplist = []
for qq in range(len(sids)):
if specimen in sids[qq]:
tmplist.append(sids[qq])
print specimen, " not found, but this was: "
print tmplist
specimen = raw_input("Select one or try again\n ")
k = sids.index(specimen)
else:
k += 1
if len(B) == 0:
if verbose:
print "skipping this one - no hysteresis data"
k += 1
def main():
"""
NAME
quick_hyst.py
DESCRIPTION
makes plots of hysteresis data
SYNTAX
quick_hyst.py [command line options]
OPTIONS
-h prints help message and quits
-usr USER: identify user, default is ""
-f: specify input file, default is magic_measurements.txt
-spc SPEC: specify specimen name to plot and quit
-sav save all plots and quit
-fmt [png,svg,eps,jpg]
"""
args = sys.argv
PLT = 1
plots = 0
user, meas_file = "", "magic_measurements.txt"
pltspec = ""
dir_path = '.'
fmt = 'png'
verbose = pmagplotlib.verbose
version_num = pmag.get_version()
if '-WD' in args:
ind = args.index('-WD')
dir_path = args[ind + 1]
if "-h" in args:
print(main.__doc__)
sys.exit()
if "-usr" in args:
ind = args.index("-usr")
user = args[ind + 1]
if '-f' in args:
ind = args.index("-f")
meas_file = args[ind + 1]
if '-sav' in args:
verbose = 0
plots = 1
if '-spc' in args:
ind = args.index("-spc")
pltspec = args[ind + 1]
verbose = 0
plots = 1
if '-fmt' in args:
ind = args.index("-fmt")
fmt = args[ind + 1]
meas_file = dir_path + '/' + meas_file
print('verbose', verbose)
#
#
meas_data, file_type = pmag.magic_read(meas_file)
if file_type != 'magic_measurements':
print(main.__doc__)
print('bad file')
sys.exit()
#
# initialize some variables
# define figure numbers for hyst,deltaM,DdeltaM curves
HystRecs, RemRecs = [], []
HDD = {}
HDD['hyst'] = 1
pmagplotlib.plot_init(HDD['hyst'], 5, 5)
#
# get list of unique experiment names and specimen names
#
experiment_names, sids = [], []
hyst_data = pmag.get_dictitem(meas_data, 'magic_method_codes', 'LP-HYS',
'has') # get all hysteresis data
for rec in hyst_data:
if 'er_synthetic_name' in rec.keys(
) and rec['er_synthetic_name'] != "":
rec['er_specimen_name'] = rec['er_synthetic_name']
if rec['magic_experiment_name'] not in experiment_names:
experiment_names.append(rec['magic_experiment_name'])
if rec['er_specimen_name'] not in sids:
sids.append(rec['er_specimen_name'])
if 'measurement_temp' not in rec.keys():
rec['measurement_temp'] = '300' # assume room T measurement unless otherwise specified
#
k = 0
if pltspec != "":
k = sids.index(pltspec)
intlist = [
'measurement_magnitude', 'measurement_magn_moment',
'measurement_magn_volume', 'measurement_magn_mass'
]
while k < len(sids):
locname, site, sample, synth = '', '', '', ''
s = sids[k]
hmeths = []
if verbose: print(s, k + 1, 'out of ', len(sids))
#
#
B, M = [], [] #B,M for hysteresis, Bdcd,Mdcd for irm-dcd data
spec = pmag.get_dictitem(hyst_data, 'er_specimen_name', s,
'T') # get all measurements for this specimen
if 'er_location_name' in spec[0].keys():
locname = spec[0]['er_location_name']
if 'er_site_name' in spec[0].keys():
site = spec[0]['er_site_name']
if 'er_sample_name' in spec[0].keys():
sample = spec[0]['er_sample_name']
if 'er_synthetic_name' in spec[0].keys():
synth = spec[0]['er_synthetic_name']
for m in intlist:
meas_data = pmag.get_dictitem(
spec, m, '', 'F') # get all non-blank data for this specimen
if len(meas_data) > 0: break
c = ['k-', 'b-', 'c-', 'g-', 'm-', 'r-', 'y-']
cnum = 0
if len(meas_data) > 0:
Temps = []
xlab, ylab, title = '', '', ''
for rec in meas_data:
if rec['measurement_temp'] not in Temps:
Temps.append(rec['measurement_temp'])
for t in Temps:
print('working on t: ', t)
t_data = pmag.get_dictitem(meas_data, 'measurement_temp', t,
'T')
B, M = [], []
for rec in t_data:
B.append(float(rec['measurement_lab_field_dc']))
M.append(float(rec[m]))
# now plot the hysteresis curve(s)
#
if len(B) > 0:
B = numpy.array(B)
M = numpy.array(M)
if t == Temps[-1]:
xlab = 'Field (T)'
ylab = m
title = 'Hysteresis: ' + s
if t == Temps[0]:
pmagplotlib.clearFIG(HDD['hyst'])
pmagplotlib.plotXY(HDD['hyst'],
B,
M,
sym=c[cnum],
xlab=xlab,
ylab=ylab,
title=title)
pmagplotlib.plotXY(HDD['hyst'],
[1.1 * B.min(), 1.1 * B.max()], [0, 0],
sym='k-',
xlab=xlab,
ylab=ylab,
title=title)
pmagplotlib.plotXY(HDD['hyst'], [0, 0],
[1.1 * M.min(), 1.1 * M.max()],
sym='k-',
xlab=xlab,
ylab=ylab,
title=title)
if verbose: pmagplotlib.drawFIGS(HDD)
cnum += 1
if cnum == len(c): cnum = 0
#
files = {}
if plots:
if pltspec != "": s = pltspec
files = {}
for key in HDD.keys():
if pmagplotlib.isServer: # use server plot naming convention
if synth == '':
filename = "LO:_" + locname + '_SI:_' + site + '_SA:_' + sample + '_SP:_' + s + '_TY:_' + key + '_.' + fmt
else:
filename = 'SY:_' + synth + '_TY:_' + key + '_.' + fmt
files[key] = filename
else: # use more readable plot naming convention
if synth == '':
filename = ''
for item in [locname, site, sample, s, key]:
if item:
item = item.replace(' ', '_')
filename += item + '_'
if filename.endswith('_'):
filename = filename[:-1]
filename += ".{}".format(fmt)
else:
filename = synth + '_' + key + '.fmt'
files[key] = filename
pmagplotlib.saveP(HDD, files)
if pltspec != "": sys.exit()
if verbose:
pmagplotlib.drawFIGS(HDD)
ans = raw_input(
"S[a]ve plots, [s]pecimen name, [q]uit, <return> to continue\n "
)
if ans == "a":
files = {}
for key in HDD.keys():
if pmagplotlib.isServer:
print('server')
files[
key] = "LO:_" + locname + '_SI:_' + site + '_SA:_' + sample + '_SP:_' + s + '_TY:_' + key + '_.' + fmt
else:
print('not server')
filename = ''
for item in [locname, site, sample, s, key]:
if item:
item = item.replace(' ', '_')
filename += item + '_'
if filename.endswith('_'):
filename = filename[:-1]
filename += ".{}".format(fmt)
files[key] = filename
print('files', files)
pmagplotlib.saveP(HDD, files)
if ans == '': k += 1
if ans == "p":
del HystRecs[-1]
k -= 1
if ans == 'q':
print("Good bye")
sys.exit()
if ans == 's':
keepon = 1
specimen = raw_input(
'Enter desired specimen name (or first part there of): ')
while keepon == 1:
try:
k = sids.index(specimen)
keepon = 0
except:
tmplist = []
for qq in range(len(sids)):
if specimen in sids[qq]: tmplist.append(sids[qq])
print(specimen, " not found, but this was: ")
print(tmplist)
specimen = raw_input('Select one or try again\n ')
k = sids.index(specimen)
else:
k += 1
if len(B) == 0:
if verbose: print('skipping this one - no hysteresis data')
k += 1
def main():
"""
NAME
biplot_magic.py
DESCRIPTION
makes a biplot of specified variables from magic_measurements.txt format file
SYNTAX
biplot_magic.py [-h] [-i] [command line options]
INPUT
takes magic formated magic_measurments file
OPTIONS
-h prints help message and quits
-i interactively set filename and axes for plotting
-f FILE: specifies file name, default: magic_measurements.txt
-fmt [svg,png,jpg], format for images - default is svg
-sav figure and quit
-x XMETH:key:step, specify method code for X axis (optional key and treatment values)
-y YMETH:key:step, specify method code for X axis
-obj OBJ: specify object [loc, sit, sam, spc] for plot, default is whole file
-n [V,M] plot volume or mass normalized data only
NOTES
if nothing is specified for x and y, the user will be presented with options
key = ['treatment_ac_field','treatment_dc_field',treatment_temp']
step in mT for fields, K for temperatures
"""
#
file = 'magic_measurements.txt'
methx, methy, fmt = "", "", '.svg'
plot_key = ''
norm_by = ""
#plot=0
no_plot = pmag.get_flag_arg_from_sys('-sav')
if not no_plot:
do_plot = True
else:
do_plot = False
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-f' in sys.argv:
ind = sys.argv.index('-f')
file = sys.argv[ind + 1]
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt = '.' + sys.argv[ind + 1]
if '-n' in sys.argv:
ind = sys.argv.index('-n')
norm_by = sys.argv[ind + 1]
xtreat_key, ytreat_key, xstep, ystep = "", "", "", ""
if '-x' in sys.argv:
ind = sys.argv.index('-x')
meths = sys.argv[ind + 1].split(':')
methx = meths[0]
if len(meths) > 1:
xtreat_key = meths[1]
xstep = float(meths[2])
if '-y' in sys.argv:
ind = sys.argv.index('-y')
meths = sys.argv[ind + 1].split(':')
methy = meths[0]
if len(meths) > 1:
ytreat_key = meths[1]
ystep = float(meths[2])
if '-obj' in sys.argv:
ind = sys.argv.index('-obj')
plot_by = sys.argv[ind + 1]
if plot_by == 'loc': plot_key = 'er_location_name'
if plot_by == 'sit': plot_key = 'er_site_name'
if plot_by == 'sam': plot_key = 'er_sample_name'
if plot_by == 'spc': plot_key = 'er_specimen_name'
if '-h' in sys.argv:
do_plot = False
if '-i' in sys.argv:
#
# get name of file from command line
#
file = input(
"Input magic_measurments file name? [magic_measurements.txt] ")
if file == "": file = "magic_measurements.txt"
#
#
FIG = {'fig': 1}
pmagplotlib.plot_init(FIG['fig'], 5, 5)
data, file_type = pmag.magic_read(file)
if file_type != "magic_measurements":
print(file_type, ' not correct format for magic_measurments file')
sys.exit()
#
# collect method codes
methods, plotlist = [], []
for rec in data:
if plot_key != "":
if rec[plot_key] not in plotlist: plotlist.append(rec[plot_key])
elif len(plotlist) == 0:
plotlist.append('All')
meths = rec['magic_method_codes'].split(':')
for meth in meths:
if meth.strip() not in methods and meth.strip() != "LP-":
methods.append(meth.strip())
#
if '-i' in sys.argv:
print(methods)
elif methx == "" or methy == "":
print(methods)
sys.exit()
GoOn = 1
while GoOn == 1:
if '-i' in sys.argv: methx = input('Select method for x axis: ')
if methx not in methods:
if '-i' in sys.argv:
print('try again! method not available')
else:
print(main.__doc__)
print('\n must specify X axis method\n')
sys.exit()
else:
if pmagplotlib.verbose: print(methx, ' selected for X axis')
GoOn = 0
GoOn = 1
while GoOn == 1:
if '-i' in sys.argv: methy = input('Select method for y axis: ')
if methy not in methods:
if '-i' in sys.argv:
print('try again! method not available')
else:
print(main.__doc__)
print('\n must specify Y axis method\n')
sys.exit()
else:
if pmagplotlib.verbose: print(methy, ' selected for Y axis')
GoOn = 0
if norm_by == "":
measkeys = [
'measurement_magn_mass', 'measurement_magn_volume',
'measurement_magn_moment', 'measurement_magnitude',
'measurement_chi_volume', 'measurement_chi_mass', 'measurement_chi'
]
elif norm_by == "V":
measkeys = ['measurement_magn_volume', 'measurement_chi_volume']
elif norm_by == "M":
measkeys = ['measurement_magn_mass', 'measurement_chi_mass']
xmeaskey, ymeaskey = "", ""
plotlist.sort()
for plot in plotlist: # go through objects
if pmagplotlib.verbose:
print(plot)
X, Y = [], []
x, y = '', ''
for rec in data:
if plot_key != "" and rec[plot_key] != plot:
pass
else:
meths = rec['magic_method_codes'].split(':')
for meth in meths:
if meth.strip() == methx:
if xmeaskey == "":
for key in measkeys:
if key in list(rec.keys()) and rec[key] != "":
xmeaskey = key
if pmagplotlib.verbose:
print(xmeaskey,
' being used for plotting X.')
break
if meth.strip() == methy:
if ymeaskey == "":
for key in measkeys:
if key in list(rec.keys()) and rec[key] != "":
ymeaskey = key
if pmagplotlib.verbose:
print(ymeaskey,
' being used for plotting Y')
break
if ymeaskey != "" and xmeaskey != "":
for rec in data:
x, y = '', ''
spec = rec[
'er_specimen_name'] # get the ydata for this specimen
if rec[ymeaskey] != "" and methy in rec[
'magic_method_codes'].split(':'):
if ytreat_key == "" or (ytreat_key in list(rec.keys()) and
float(rec[ytreat_key]) == ystep):
y = float(rec[ymeaskey])
for rec in data: # now find the xdata
if rec['er_specimen_name'] == spec and rec[
xmeaskey] != "" and methx in rec[
'magic_method_codes'].split(':'):
if xtreat_key == "" or (
xtreat_key in list(rec.keys())
and float(rec[xtreat_key]) == xstep):
x = float(rec[xmeaskey])
if x != '' and y != '':
X.append(x)
Y.append(y)
if len(X) > 0:
pmagplotlib.clearFIG(FIG['fig'])
pmagplotlib.plotXY(FIG['fig'],
X,
Y,
sym='ro',
xlab=methx,
ylab=methy,
title=plot + ':Biplot')
if not pmagplotlib.isServer and do_plot:
pmagplotlib.drawFIGS(FIG)
ans = input('S[a]ve plots, [q]uit, Return for next plot ')
if ans == 'a':
files = {}
for key in list(FIG.keys()):
files[key] = plot + '_' + key + fmt
pmagplotlib.saveP(FIG, files)
if ans == 'q':
print("Good-bye\n")
sys.exit()
else:
files = {}
for key in list(FIG.keys()):
files[key] = plot + '_' + key + fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles = {}
titles['fig'] = 'X Y Plot'
FIG = pmagplotlib.addBorders(FIG, titles, black, purple)
pmagplotlib.saveP(FIG, files)
else:
print('nothing to plot for ', plot)
def main():
"""
NAME
lowrie_magic.py
DESCRIPTION
plots intensity decay curves for Lowrie experiments
SYNTAX
lowrie_magic.py -h [command line options]
INPUT
takes magic_measurements formatted input files
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is magic_measurements.txt
-N do not normalize by maximum magnetization
-fmt [svg, pdf, eps, png] specify fmt, default is svg
-sav saves plots and quits
"""
fmt, plot = 'svg', 0
FIG = {} # plot dictionary
FIG['lowrie'] = 1 # demag is figure 1
pmagplotlib.plot_init(FIG['lowrie'], 6, 6)
norm = 1 # default is to normalize by maximum axis
in_file, dir_path = 'magic_measurements.txt', '.'
if len(sys.argv) > 1:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-N' in sys.argv: norm = 0 # don't normalize
if '-sav' in sys.argv: plot = 1 # don't normalize
if '-fmt' in sys.argv: # sets input filename
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
if '-f' in sys.argv: # sets input filename
ind = sys.argv.index("-f")
in_file = sys.argv[ind + 1]
else:
print(main.__doc__)
print('you must supply a file name')
sys.exit()
in_file = dir_path + '/' + in_file
print(in_file)
PmagRecs, file_type = pmag.magic_read(in_file)
if file_type != "magic_measurements":
print('bad input file')
sys.exit()
PmagRecs = pmag.get_dictitem(PmagRecs, 'magic_method_codes', 'LP-IRM-3D',
'has') # get all 3D IRM records
if len(PmagRecs) == 0:
print('no records found')
sys.exit()
specs = pmag.get_dictkey(PmagRecs, 'er_specimen_name', '')
sids = []
for spec in specs:
if spec not in sids:
sids.append(spec) # get list of unique specimen names
for spc in sids: # step through the specimen names
print(spc)
specdata = pmag.get_dictitem(PmagRecs, 'er_specimen_name', spc,
'T') # get all this one's data
DIMs, Temps = [], []
for dat in specdata: # step through the data
DIMs.append([
float(dat['measurement_dec']),
float(dat['measurement_inc']),
float(dat['measurement_magn_moment'])
])
Temps.append(float(dat['treatment_temp']) - 273.)
carts = pmag.dir2cart(DIMs).transpose()
if norm == 1: # want to normalize
nrm = (DIMs[0][2]) # normalize by NRM
ylab = "M/M_o"
else:
nrm = 1. # don't normalize
ylab = "Magnetic moment (Am^2)"
xlab = "Temperature (C)"
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[0]), nrm),
sym='r-')
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[0]), nrm),
sym='ro') # X direction
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[1]), nrm),
sym='c-')
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[1]), nrm),
sym='cs') # Y direction
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[2]), nrm),
sym='k-')
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[2]), nrm),
sym='k^',
title=spc,
xlab=xlab,
ylab=ylab) # Z direction
files = {'lowrie': 'lowrie:_' + spc + '_.' + fmt}
if plot == 0:
pmagplotlib.drawFIGS(FIG)
ans = input('S[a]ve figure? [q]uit, <return> to continue ')
if ans == 'a':
pmagplotlib.saveP(FIG, files)
elif ans == 'q':
sys.exit()
else:
pmagplotlib.saveP(FIG, files)
pmagplotlib.clearFIG(FIG['lowrie'])
def main():
"""
NAME
lowrie_magic.py
DESCRIPTION
plots intensity decay curves for Lowrie experiments
SYNTAX
lowrie_magic.py -h [command line options]
INPUT
takes magic_measurements formatted input files
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is magic_measurements.txt
-N do not normalize by maximum magnetization
-fmt [svg, pdf, eps, png] specify fmt, default is svg
-sav saves plots and quits
"""
fmt,plot='svg',0
FIG={} # plot dictionary
FIG['lowrie']=1 # demag is figure 1
pmagplotlib.plot_init(FIG['lowrie'],6,6)
norm=1 # default is to normalize by maximum axis
in_file,dir_path='magic_measurements.txt','.'
if len(sys.argv)>1:
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-N' in sys.argv: norm=0 # don't normalize
if '-sav' in sys.argv: plot=1 # don't normalize
if '-fmt' in sys.argv: # sets input filename
ind=sys.argv.index("-fmt")
fmt=sys.argv[ind+1]
if '-f' in sys.argv: # sets input filename
ind=sys.argv.index("-f")
in_file=sys.argv[ind+1]
else:
print main.__doc__
print 'you must supply a file name'
sys.exit()
in_file=dir_path+'/'+in_file
print in_file
PmagRecs,file_type=pmag.magic_read(in_file)
if file_type!="magic_measurements":
print 'bad input file'
sys.exit()
PmagRecs=pmag.get_dictitem(PmagRecs,'magic_method_codes','LP-IRM-3D','has') # get all 3D IRM records
if len(PmagRecs)==0:
print 'no records found'
sys.exit()
specs=pmag.get_dictkey(PmagRecs,'er_specimen_name','')
sids=[]
for spec in specs:
if spec not in sids:sids.append(spec) # get list of unique specimen names
for spc in sids: # step through the specimen names
print spc
specdata=pmag.get_dictitem(PmagRecs,'er_specimen_name',spc,'T') # get all this one's data
DIMs,Temps=[],[]
for dat in specdata: # step through the data
DIMs.append([float(dat['measurement_dec']),float(dat['measurement_inc']),float(dat['measurement_magn_moment'])])
Temps.append(float(dat['treatment_temp'])-273.)
carts=pmag.dir2cart(DIMs).transpose()
if norm==1: # want to normalize
nrm=(DIMs[0][2]) # normalize by NRM
ylab="M/M_o"
else:
nrm=1. # don't normalize
ylab="Magnetic moment (Am^2)"
xlab="Temperature (C)"
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[0])/nrm,sym='r-')
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[0])/nrm,sym='ro') # X direction
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[1])/nrm,sym='c-')
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[1])/nrm,sym='cs') # Y direction
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[2])/nrm,sym='k-')
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[2])/nrm,sym='k^',title=spc,xlab=xlab,ylab=ylab) # Z direction
files={'lowrie':'lowrie:_'+spc+'_.'+fmt}
if plot==0:
pmagplotlib.drawFIGS(FIG)
ans=raw_input('S[a]ve figure? [q]uit, <return> to continue ')
if ans=='a':
pmagplotlib.saveP(FIG,files)
elif ans=='q':
sys.exit()
else:
pmagplotlib.saveP(FIG,files)
pmagplotlib.clearFIG(FIG['lowrie'])
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
quick_hyst.py
DESCRIPTION
makes plots of hysteresis data
SYNTAX
quick_hyst.py [command line options]
OPTIONS
-h prints help message and quits
-f: specify input file, default is measurements.txt
-spc SPEC: specify specimen name to plot and quit
-sav save all plots and quit
-fmt [png,svg,eps,jpg]
"""
args = sys.argv
if "-h" in args:
print(main.__doc__)
sys.exit()
plots = 0
pltspec = ""
verbose = pmagplotlib.verbose
#version_num = pmag.get_version()
dir_path = pmag.get_named_arg_from_sys('-WD', '.')
dir_path = os.path.realpath(dir_path)
meas_file = pmag.get_named_arg_from_sys('-f', 'measurements.txt')
fmt = pmag.get_named_arg_from_sys('-fmt', 'png')
if '-sav' in args:
verbose = 0
plots = 1
if '-spc' in args:
ind = args.index("-spc")
pltspec = args[ind+1]
verbose = 0
plots = 1
#
con = nb.Contribution(dir_path, read_tables=['measurements'],
custom_filenames={'measurements': meas_file})
# get as much name data as possible (used for naming plots)
if not 'measurements' in con.tables:
print("-W- No measurement file found")
return
con.propagate_location_to_measurements()
if 'measurements' not in con.tables:
print(main.__doc__)
print('bad file')
sys.exit()
meas_container = con.tables['measurements']
#meas_df = meas_container.df
#
# initialize some variables
# define figure numbers for hyst,deltaM,DdeltaM curves
HystRecs = []
HDD = {}
HDD['hyst'] = 1
pmagplotlib.plot_init(HDD['hyst'], 5, 5)
#
# get list of unique experiment names and specimen names
#
sids = []
hyst_data = meas_container.get_records_for_code('LP-HYS')
#experiment_names = hyst_data['experiment_name'].unique()
if not len(hyst_data):
print("-W- No hysteresis data found")
return
sids = hyst_data['specimen'].unique()
# if 'treat_temp' is provided, use that value, otherwise assume 300
hyst_data['treat_temp'].where(hyst_data['treat_temp'].notnull(), '300', inplace=True)
# start at first specimen, or at provided specimen ('-spc')
k = 0
if pltspec != "":
try:
print(sids)
k = list(sids).index(pltspec)
except ValueError:
print('-W- No specimen named: {}.'.format(pltspec))
print('-W- Please provide a valid specimen name')
return
intlist = ['magn_moment', 'magn_volume', 'magn_mass']
while k < len(sids):
locname, site, sample, synth = '', '', '', ''
s = sids[k]
if verbose:
print(s, k + 1, 'out of ', len(sids))
# B, M for hysteresis, Bdcd,Mdcd for irm-dcd data
B, M = [], []
# get all measurements for this specimen
spec = hyst_data[hyst_data['specimen'] == s]
# get names
if 'location' in spec:
locname = spec['location'][0]
if 'site' in spec:
site = spec['sample'][0]
if 'sample' in spec:
sample = spec['sample'][0]
# get all records with non-blank values in any intlist column
# find intensity data
for int_column in intlist:
if int_column in spec.columns:
int_col = int_column
break
meas_data = spec[spec[int_column].notnull()]
if len(meas_data) == 0:
break
#
c = ['k-', 'b-', 'c-', 'g-', 'm-', 'r-', 'y-']
cnum = 0
Temps = []
xlab, ylab, title = '', '', ''
Temps = meas_data['treat_temp'].unique()
for t in Temps:
print('working on t: ', t)
t_data = meas_data[meas_data['treat_temp'] == t]
m = int_col
B = t_data['meas_field_dc'].astype(float).values
M = t_data[m].astype(float).values
# now plot the hysteresis curve(s)
#
if len(B) > 0:
B = numpy.array(B)
M = numpy.array(M)
if t == Temps[-1]:
xlab = 'Field (T)'
ylab = m
title = 'Hysteresis: ' + s
if t == Temps[0]:
pmagplotlib.clearFIG(HDD['hyst'])
pmagplotlib.plotXY(HDD['hyst'],B,M,sym=c[cnum],xlab=xlab,ylab=ylab,title=title)
pmagplotlib.plotXY(HDD['hyst'],[1.1*B.min(),1.1*B.max()],[0,0],sym='k-',xlab=xlab,ylab=ylab,title=title)
pmagplotlib.plotXY(HDD['hyst'],[0,0],[1.1*M.min(),1.1*M.max()],sym='k-',xlab=xlab,ylab=ylab,title=title)
if verbose:
pmagplotlib.drawFIGS(HDD)
cnum += 1
if cnum == len(c):
cnum = 0
#
files = {}
if plots:
if pltspec != "":
s = pltspec
for key in list(HDD.keys()):
if pmagplotlib.isServer:
if synth == '':
files[key] = "LO:_"+locname+'_SI:_'+site+'_SA:_'+sample+'_SP:_'+s+'_TY:_'+key+'_.'+fmt
else:
files[key] = 'SY:_'+synth+'_TY:_'+key+'_.'+fmt
else:
if synth == '':
filename = ''
for item in [locname, site, sample, s, key]:
if item:
item = item.replace(' ', '_')
filename += item + '_'
if filename.endswith('_'):
filename = filename[:-1]
filename += ".{}".format(fmt)
files[key] = filename
else:
files[key] = "{}_{}.{}".format(synth, key, fmt)
pmagplotlib.saveP(HDD, files)
if pltspec != "":
sys.exit()
if verbose:
pmagplotlib.drawFIGS(HDD)
ans = input("S[a]ve plots, [s]pecimen name, [q]uit, <return> to continue\n ")
if ans == "a":
files = {}
for key in list(HDD.keys()):
if pmagplotlib.isServer: # use server plot naming convention
files[key] = "LO:_"+locname+'_SI:_'+site+'_SA:_'+sample+'_SP:_'+s+'_TY:_'+key+'_.'+fmt
else: # use more readable plot naming convention
filename = ''
for item in [locname, site, sample, s, key]:
if item:
item = item.replace(' ', '_')
filename += item + '_'
if filename.endswith('_'):
filename = filename[:-1]
filename += ".{}".format(fmt)
files[key] = filename
pmagplotlib.saveP(HDD, files)
if ans == '':
k += 1
if ans == "p":
del HystRecs[-1]
k -= 1
if ans == 'q':
print("Good bye")
sys.exit()
if ans == 's':
keepon = 1
specimen = input('Enter desired specimen name (or first part there of): ')
while keepon == 1:
try:
k = sids.index(specimen)
keepon = 0
except:
tmplist = []
for qq in range(len(sids)):
if specimen in sids[qq]:
tmplist.append(sids[qq])
print(specimen, " not found, but this was: ")
print(tmplist)
specimen = input('Select one or try again\n ')
k = sids.index(specimen)
else:
k += 1
if len(B) == 0:
if verbose:
print('skipping this one - no hysteresis data')
k += 1
