def main():
"""
NAME
irmaq_magic.py
DESCRIPTION
plots IRM acquisition curves from magic_measurements file
SYNTAX
irmaq_magic [command line options]
INPUT
takes magic formatted magic_measurements.txt files
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is: magic_measurements.txt
-obj OBJ: specify object [loc, sit, sam, spc] for plot, default is by location
-N ; do not normalize by last point - use original units
NOTE
loc: location (study); sit: site; sam: sample; spc: specimen
"""
FIG={} # plot dictionary
FIG['exp']=1 # exp is figure 1
in_file,plot_key,LP='magic_measurements.txt','er_location_name',"LP-IRM"
units,dmag_key='T','treatment_dc_field'
XLP=[]
norm=1
if len(sys.argv)>1:
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-N' in sys.argv:norm=0
if '-f' in sys.argv:
ind=sys.argv.index("-f")
in_file=sys.argv[ind+1]
if '-obj' in sys.argv:
ind=sys.argv.index('-obj')
plot_by=sys.argv[ind+1]
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 '-LP' in sys.argv:
# ind=sys.argv.index("-LT")
# LP='LP-'+sys.argv[ind+1] # get lab protocol for plotting
data,file_type=pmag.magic_read(in_file)
sids=pmag.get_specs(data)
pmagplotlib.plot_init(FIG['exp'],6,6)
print len(data),' records read from ',in_file
#
#
# find desired intensity data
#
# get plotlist
#
plotlist,intlist=[],['measurement_magnitude','measurement_magn_moment','measurement_magn_volume','measurement_magn_mass']
IntMeths=[]
for rec in data:
meths=[]
methcodes=rec['magic_method_codes'].split(':')
for meth in methcodes:meths.append(meth.strip())
for key in rec.keys():
if key in intlist and rec[key]!="":
if key not in IntMeths:IntMeths.append(key)
if rec[plot_key] not in plotlist and LP in meths: plotlist.append(rec[plot_key])
plotlist.sort()
if len(IntMeths)==0:
print 'No intensity information found'
sys.exit()
int_key=IntMeths[0] # plot first intensity method found - normalized to initial value anyway - doesn't matter which used
for plot in plotlist:
print plot
for spec in sids:
INTblock=[]
for rec in data:
if 'measurement_flag' not in rec.keys():rec['measurement_flag']='g'
if rec[plot_key]==plot and int_key in rec.keys() and rec[int_key]!="" and rec['er_specimen_name']==spec:
meths=[]
methcodes=rec['magic_method_codes'].split(':')
for meth in methcodes:
LPtest=meth.split('-')
if XLP not in LPtest: meths.append(meth.strip())
if len(meths)>0 and LP in meths or 'LT-NO' in meths:
title=rec[plot_key]
INTblock.append([float(rec[dmag_key]),0,0,float(rec[int_key]),1,rec['measurement_flag']])
Sdata=INTblock.sort()
if len(INTblock)>2: pmagplotlib.plotMT(FIG['exp'],INTblock,title,0,units,norm)
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]=title+'_'+LP+'.svg'
pmagplotlib.saveP(FIG,files)
pmagplotlib.clearFIG(FIG['exp'])
def main():
"""
NAME
dmag_magic.py
DESCRIPTION
plots intensity decay curves for demagnetization experiments
SYNTAX
dmag_magic -h [command line options]
INPUT
takes magic formatted magic_measurements.txt files
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is: magic_measurements.txt
-obj OBJ: specify object [loc, sit, sam, spc] for plot, default is by location
-LT [AF,T,M]: specify lab treatment type, default AF
-XLP [PI]: exclude specific lab protocols (for example, method codes like LP-PI)
-N do not normalize by NRM magnetization
NOTE
loc: location (study); sit: site; sam: sample; spc: specimen
"""
FIG={} # plot dictionary
FIG['demag']=1 # demag is figure 1
in_file,plot_key,LT='magic_measurements.txt','er_location_name',"LT-AF-Z"
XLP=""
norm=1
LT='LT-AF-Z'
units,dmag_key='T','treatment_ac_field'
plot_key='er_location_name'
if len(sys.argv)>1:
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-N' in sys.argv: norm=0
if '-f' in sys.argv:
ind=sys.argv.index("-f")
in_file=sys.argv[ind+1]
if '-obj' in sys.argv:
ind=sys.argv.index('-obj')
plot_by=sys.argv[ind+1]
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 '-XLP' in sys.argv:
ind=sys.argv.index("-XLP")
XLP=sys.argv[ind+1] # get lab protocol for excluding
if '-LT' in sys.argv:
ind=sys.argv.index("-LT")
LT='LT-'+sys.argv[ind+1]+'-Z' # get lab treatment for plotting
if LT=='LT-T-Z':
units,dmag_key='K','treatment_temp'
elif LT=='LT-AF-Z':
units,dmag_key='T','treatment_ac_field'
elif LT=='LT-M-Z':
units,dmag_key='J','treatment_mw_energy'
else:
units='U'
data,file_type=pmag.magic_read(in_file)
sids=pmag.get_specs(data)
pmagplotlib.plot_init(FIG['demag'],5,5)
print len(data),' records read from ',in_file
#
#
# find desired intensity data
#
# get plotlist
#
plotlist,intlist=[],['measurement_magnitude','measurement_magn_moment','measurement_magn_volume','measurement_magn_mass']
IntMeths=[]
FixData=[]
for rec in data:
meths=[]
methcodes=rec['magic_method_codes'].split(':')
for meth in methcodes:meths.append(meth.strip())
for key in rec.keys():
if key in intlist and rec[key]!="":
if key not in IntMeths:IntMeths.append(key)
if rec[plot_key] not in plotlist and LT in meths: plotlist.append(rec[plot_key])
if 'measurement_flag' not in rec.keys():rec['measurement_flag']='g'
FixData.append(rec)
plotlist.sort()
if len(IntMeths)==0:
print 'No intensity information found'
sys.exit()
data=FixData
int_key=IntMeths[0] # plot first intensity method found - normalized to initial value anyway - doesn't matter which used
for plot in plotlist:
print plot,'plotting by: ',plot_key
PLTblock=pmag.get_dictitem(data,plot_key,plot,'T') # fish out all the data for this type of plot
PLTblock=pmag.get_dictitem(PLTblock,'magic_method_codes',LT,'has') # fish out all the dmag for this experiment type
PLTblock=pmag.get_dictitem(PLTblock,int_key,'','F') # get all with this intensity key non-blank
if XLP!="":PLTblock=pmag.get_dictitem(PLTblock,'magic_method_codes',XLP,'not') # reject data with XLP in method_code
if len(PLTblock)>2:
title=PLTblock[0][plot_key]
spcs=[]
for rec in PLTblock:
if rec['er_specimen_name'] not in spcs:spcs.append(rec['er_specimen_name'])
for spc in spcs:
SPCblock=pmag.get_dictitem(PLTblock,'er_specimen_name',spc,'T') # plot specimen by specimen
INTblock=[]
for rec in SPCblock:
INTblock.append([float(rec[dmag_key]),0,0,float(rec[int_key]),1,rec['measurement_flag']])
if len(INTblock)>2:
pmagplotlib.plotMT(FIG['demag'],INTblock,title,0,units,norm)
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]=title+'_'+LT+'.svg'
pmagplotlib.saveP(FIG,files)
pmagplotlib.clearFIG(FIG['demag'])
def main():
"""
NAME
irmaq_magic.py
DESCRIPTION
plots IRM acquisition curves from magic_measurements file
SYNTAX
irmaq_magic [command line options]
INPUT
takes magic formatted magic_measurements.txt files
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is: magic_measurements.txt
-obj OBJ: specify object [loc, sit, sam, spc] for plot, default is by location
-N ; do not normalize by last point - use original units
NOTE
loc: location (study); sit: site; sam: sample; spc: specimen
"""
FIG={} # plot dictionary
FIG['exp']=1 # exp is figure 1
dir_path='./'
units,dmag_key='T','treatment_dc_field'
XLP=[]
norm=1
in_file,plot_key,LP='magic_measurements.txt','er_location_name',"LP-IRM"
if len(sys.argv)>1:
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-N' in sys.argv:norm=0
if '-f' in sys.argv:
ind=sys.argv.index("-f")
in_file=sys.argv[ind+1]
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
in_file=dir_path+'/'+in_file
if '-obj' in sys.argv:
ind=sys.argv.index('-obj')
plot_by=sys.argv[ind+1]
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'
data,file_type=pmag.magic_read(in_file)
sids=pmag.get_specs(data)
pmagplotlib.plot_init(FIG['exp'],6,6)
#
#
# find desired intensity data
#
# get plotlist
#
plotlist,intlist=[],['measurement_magnitude','measurement_magn_moment','measurement_magn_volume','measurement_magn_mass']
IntMeths=[]
data=pmag.get_dictitem(data,'magic_method_codes',LP,'has') # get all the records with this lab protocol
Ints={}
NoInts,int_key=1,""
for key in intlist:
Ints[key]=pmag.get_dictitem(data,key,'','F') # get all non-blank data for intensity type
if len(Ints[key])>0:
NoInts=0
if int_key=="":int_key=key
if NoInts==1:
print 'No intensity information found'
sys.exit()
for rec in Ints[int_key]:
if rec[plot_key] not in plotlist: plotlist.append(rec[plot_key])
plotlist.sort()
for plot in plotlist:
print plot
INTblock=[]
data=pmag.get_dictitem(Ints[int_key],plot_key,plot,'T') # get data with right intensity info whose plot_key matches plot
sids=pmag.get_specs(data) # get a list of specimens with appropriate data
if len(sids)>0:
title=data[0][plot_key]
for s in sids:
INTblock=[]
sdata=pmag.get_dictitem(data,'er_specimen_name',s,'T') # get data for each specimen
for rec in sdata:
INTblock.append([float(rec[dmag_key]),0,0,float(rec[int_key]),1,'g'])
pmagplotlib.plotMT(FIG['exp'],INTblock,title,0,units,norm)
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]=title+'_'+LP+'.svg'
pmagplotlib.saveP(FIG,files)
pmagplotlib.clearFIG(FIG['exp'])