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
-sav save plots silently and quit
-fmt [svg,jpg,png,pdf] set figure format [default is svg]
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=0
fmt='svg'
if len(sys.argv)>1:
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-N' in sys.argv: norm=0
if '-sav' in sys.argv:
plot=1
if '-f' in sys.argv:
ind=sys.argv.index("-f")
in_file=sys.argv[ind+1]
if '-fmt' in sys.argv:
ind=sys.argv.index("-fmt")
fmt=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
#
#
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 plt in plotlist:
if plot==0: print plt,'plotting by: ',plot_key
PLTblock=pmag.get_dictitem(data,plot_key,plt,'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)
if plot==1:
files={}
for key in FIG.keys():
files[key]=title+'_'+LT+'.'+fmt
pmagplotlib.saveP(FIG,files)
sys.exit()
else:
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
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
-sav save plots silently and quit
-fmt [svg,jpg,png,pdf] set figure format [default is svg]
NOTE
loc: location (study); sit: site; sam: sample; spc: specimen
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
# initialize variables from command line + defaults
FIG = {} # plot dictionary
FIG['demag'] = 1 # demag is figure 1
in_file = pmag.get_named_arg_from_sys("-f", default_val="measurements.txt")
plot_by = pmag.get_named_arg_from_sys("-obj", default_val="loc")
name_dict = {
'loc': 'location',
'sit': 'site',
'sam': 'sample',
'spc': 'specimen'
}
plot_key = name_dict[plot_by]
LT = "LT-" + pmag.get_named_arg_from_sys("-LT", "AF") + "-Z"
if LT == "LT-T-Z":
units, dmag_key = 'K', 'treat_temp'
elif LT == "LT-AF-Z":
units, dmag_key = 'T', 'treat_ac_field'
elif LT == 'LT-M-Z':
units, dmag_key = 'J', 'treat_mw_energy'
else:
units = 'U'
no_norm = pmag.get_flag_arg_from_sys("-N")
norm = 0 if no_norm else 1
no_plot = pmag.get_flag_arg_from_sys("-sav")
plot = 0 if no_plot else 1
fmt = pmag.get_named_arg_from_sys("-fmt", "svg")
XLP = pmag.get_named_arg_from_sys("-XLP", "")
dir_path = pmag.get_named_arg_from_sys("-WD", os.getcwd())
spec_file = pmag.get_named_arg_from_sys("-fsp",
default_val="specimens.txt")
samp_file = pmag.get_named_arg_from_sys("-fsa", default_val="samples.txt")
site_file = pmag.get_named_arg_from_sys("-fsi", default_val="sites.txt")
# create contribution and add required headers
fnames = {"specimens": spec_file, "samples": samp_file, 'sites': site_file}
contribution = nb.Contribution(dir_path,
single_file=in_file,
custom_filenames=fnames)
file_type = list(contribution.tables.keys())[0]
print(len(contribution.tables['measurements'].df), ' records read from ',
in_file)
# add plot_key into measurements table
if plot_key not in contribution.tables['measurements'].df.columns:
#contribution.propagate_name_down(plot_key, 'measurements')
contribution.propagate_location_to_measurements()
data_container = contribution.tables[file_type]
# pare down to only records with useful data
# grab records that have the requested code
data_slice = data_container.get_records_for_code(LT)
# and don't have the offending code
data = data_container.get_records_for_code(XLP,
incl=False,
use_slice=True,
sli=data_slice,
strict_match=False)
# make sure quality is in the dataframe
if 'quality' not in data.columns:
data['quality'] = 'g'
# get intensity key and make sure intensity data is not blank
intlist = ['magn_moment', 'magn_volume', 'magn_mass']
IntMeths = [col_name for col_name in data.columns if col_name in intlist]
# get rid of any entirely blank intensity columns
for col_name in IntMeths:
if not data[col_name].any():
data.drop(col_name, axis=1, inplace=True)
IntMeths = [col_name for col_name in data.columns if col_name in intlist]
if len(IntMeths) == 0:
print('No intensity headers found')
sys.exit()
int_key = IntMeths[
0] # plot first intensity method found - normalized to initial value anyway - doesn't matter which used
data = data[data[int_key].notnull()]
# make list of individual plots
# by default, will be by location_name
plotlist = data[plot_key].unique()
plotlist.sort()
pmagplotlib.plot_init(FIG['demag'], 5, 5)
# iterate through and plot the data
for plt in plotlist:
plot_data = data[data[plot_key] == plt].copy()
if plot:
print(plt, 'plotting by: ', plot_key)
if len(plot_data) > 2:
title = plt
spcs = []
spcs = plot_data['specimen'].unique()
for spc in spcs:
INTblock = []
spec_data = plot_data[plot_data['specimen'] == spc]
for ind, rec in spec_data.iterrows():
INTblock.append([
float(rec[dmag_key]), 0, 0,
float(rec[int_key]), 1, rec['quality']
])
if len(INTblock) > 2:
pmagplotlib.plotMT(FIG['demag'], INTblock, title, 0, units,
norm)
if not plot:
files = {}
for key in list(FIG.keys()):
files[key] = title + '_' + LT + '.' + fmt
pmagplotlib.saveP(FIG, files)
#sys.exit()
else:
pmagplotlib.drawFIGS(FIG)
prompt = " S[a]ve to save plot, [q]uit, Return to continue: "
ans = input(prompt)
if ans == 'q':
sys.exit()
if ans == "a":
files = {}
for key in list(FIG.keys()):
files[key] = title + '_' + LT + '.' + fmt
pmagplotlib.saveP(FIG, files)
pmagplotlib.clearFIG(FIG['demag'])
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
-sav save plots silently and quit
-fmt [svg,jpg,png,pdf] set figure format [default is svg]
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 = 0
fmt = 'svg'
if len(sys.argv) > 1:
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-N' in sys.argv: norm = 0
if '-sav' in sys.argv:
plot = 1
if '-f' in sys.argv:
ind = sys.argv.index("-f")
in_file = sys.argv[ind + 1]
if '-fmt' in sys.argv:
ind = sys.argv.index("-fmt")
fmt = 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
#
#
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 plt in plotlist:
if plot == 0: print(plt, 'plotting by: ', plot_key)
PLTblock = pmag.get_dictitem(
data, plot_key, plt,
'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)
if plot == 1:
files = {}
for key in FIG.keys():
files[key] = title + '_' + LT + '.' + fmt
pmagplotlib.saveP(FIG, files)
sys.exit()
else:
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 + '.' + fmt
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
-fmt [png,jpg,eps,pdf] set plot file format [default is svg]
-sav save plot[s] and quit
NOTE
loc: location (study); sit: site; sam: sample; spc: specimen
"""
FIG = {} # plot dictionary
FIG['exp'] = 1 # exp is figure 1
dir_path = './'
plot, fmt = 0, 'svg'
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 '-sav' in sys.argv: plot = 1
if '-fmt' in sys.argv:
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
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 plt in plotlist:
print plt
INTblock = []
data = pmag.get_dictitem(
Ints[int_key], plot_key, plt, '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)
files = {}
for key in FIG.keys():
files[key] = title + '_' + LP + '.' + fmt
if plot == 0:
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":
pmagplotlib.saveP(FIG, files)
else:
pmagplotlib.saveP(FIG, files)
pmagplotlib.clearFIG(FIG['exp'])
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
-fmt [png,jpg,eps,pdf] set plot file format [default is svg]
-sav save plot[s] and quit
NOTE
loc: location (study); sit: site; sam: sample; spc: specimen
"""
FIG={} # plot dictionary
FIG['exp']=1 # exp is figure 1
dir_path='./'
plot,fmt=0,'svg'
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 '-sav' in sys.argv:plot=1
if '-fmt' in sys.argv:
ind=sys.argv.index("-fmt")
fmt=sys.argv[ind+1]
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 plt in plotlist:
print plt
INTblock=[]
data=pmag.get_dictitem(Ints[int_key],plot_key,plt,'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)
files={}
for key in FIG.keys():
files[key]=title+'_'+LP+'.'+fmt
if plot==0:
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":
pmagplotlib.saveP(FIG,files)
else:
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
-sav save plots silently and quit
-fmt [svg,jpg,png,pdf] set figure format [default is svg]
NOTE
loc: location (study); sit: site; sam: sample; spc: specimen
"""
if '-h' in sys.argv:
print main.__doc__
sys.exit()
# initialize variables from command line + defaults
FIG = {} # plot dictionary
FIG['demag'] = 1 # demag is figure 1
in_file = pmag.get_named_arg_from_sys("-f", default_val="measurements.txt")
plot_by = pmag.get_named_arg_from_sys("-obj", default_val="loc")
name_dict = {'loc': 'location', 'sit': 'site',
'sam': 'sample', 'spc': 'specimen'}
plot_key = name_dict[plot_by]
LT = "LT-" + pmag.get_named_arg_from_sys("-LT", "AF") + "-Z"
if LT == "LT-T-Z":
units, dmag_key = 'K', 'treat_temp'
elif LT == "LT-AF-Z":
units, dmag_key = 'T', 'treat_ac_field'
elif LT == 'LT-M-Z':
units, dmag_key = 'J', 'treat_mw_energy'
else:
units = 'U'
no_norm = pmag.get_flag_arg_from_sys("-N")
norm = 0 if no_norm else 1
no_plot = pmag.get_flag_arg_from_sys("-sav")
plot = 0 if no_plot else 1
fmt = pmag.get_named_arg_from_sys("-fmt", "svg")
XLP = pmag.get_named_arg_from_sys("-XLP", "")
dir_path = pmag.get_named_arg_from_sys("-WD", os.getcwd())
spec_file = pmag.get_named_arg_from_sys("-fsp", default_val="specimens.txt")
samp_file = pmag.get_named_arg_from_sys("-fsa", default_val="samples.txt")
site_file = pmag.get_named_arg_from_sys("-fsi", default_val="sites.txt")
# create contribution and add required headers
fnames = {"specimens": spec_file, "samples": samp_file, 'sites': site_file}
contribution = nb.Contribution(dir_path, single_file=in_file,
custom_filenames=fnames)
file_type = contribution.tables.keys()[0]
print len(contribution.tables['measurements'].df), ' records read from ', in_file
# add plot_key into measurements table
if plot_key not in contribution.tables['measurements'].df.columns:
contribution.propagate_name_down(plot_key, 'measurements')
data_container = contribution.tables[file_type]
# pare down to only records with useful data
# grab records that have the requested code
data_slice = data_container.get_records_for_code(LT)
# and don't have the offending code
data = data_container.get_records_for_code(XLP, incl=False, use_slice=True,
sli=data_slice, strict_match=False)
# make sure quality is in the dataframe
if 'quality' not in data.columns:
data['quality'] = 'g'
# get intensity key and make sure intensity data is not blank
intlist = ['magn_moment', 'magn_volume', 'magn_mass']
IntMeths = [col_name for col_name in data.columns if col_name in intlist]
# get rid of any entirely blank intensity columns
for col_name in IntMeths:
if not data[col_name].any():
data.drop(col_name, axis=1, inplace=True)
IntMeths = [col_name for col_name in data.columns if col_name in intlist]
if len(IntMeths) == 0:
print 'No intensity headers found'
sys.exit()
int_key = IntMeths[0] # plot first intensity method found - normalized to initial value anyway - doesn't matter which used
data = data[data[int_key].notnull()]
# make list of individual plots
# by default, will be by location_name
plotlist = data[plot_key].unique()
plotlist.sort()
pmagplotlib.plot_init(FIG['demag'], 5, 5)
# iterate through and plot the data
for plt in plotlist:
plot_data = data[data[plot_key] == plt].copy()
if plot:
print plt, 'plotting by: ', plot_key
if len(plot_data) > 2:
title = plt
spcs = []
spcs = plot_data['specimen'].unique()
for spc in spcs:
INTblock = []
spec_data = plot_data[plot_data['specimen'] == spc]
for ind, rec in spec_data.iterrows():
INTblock.append([float(rec[dmag_key]), 0, 0, float(rec[int_key]), 1, rec['quality']])
if len(INTblock) > 2:
pmagplotlib.plotMT(FIG['demag'], INTblock,
title, 0, units, norm)
if not plot:
files = {}
for key in FIG.keys():
files[key] = title + '_' + LT + '.' + fmt
pmagplotlib.saveP(FIG, files)
#sys.exit()
else:
pmagplotlib.drawFIGS(FIG)
prompt = " S[a]ve to save plot, [q]uit, Return to continue: "
ans = raw_input(prompt)
if ans == 'q':
sys.exit()
if ans == "a":
files = {}
for key in FIG.keys():
files[key] = title + '_' + LT + '.' + fmt
pmagplotlib.saveP(FIG, files)
pmagplotlib.clearFIG(FIG['demag'])
def main():
"""
NAME
irmaq_magic.py
DESCRIPTION
plots IRM acquisition curves from 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/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
-fmt [png,jpg,eps,pdf] set plot file format [default is svg]
-sav save plot[s] and quit
-DM MagIC data model number, default is 3
NOTE
loc: location (study); sit: site; sam: sample; spc: specimen
"""
FIG = {} # plot dictionary
FIG['exp'] = 1 # exp is figure 1
dir_path = './'
plot, fmt = 0, 'svg'
units = 'T',
XLP = []
norm = 1
LP = "LP-IRM"
if len(sys.argv) > 1:
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
data_model = int(pmag.get_named_arg_from_sys("-DM", 3))
if '-N' in sys.argv:
norm = 0
if '-sav' in sys.argv:
plot = 1
if '-fmt' in sys.argv:
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
if data_model == 3:
in_file = pmag.get_named_arg_from_sys("-f", 'measurements.txt')
else:
in_file = pmag.get_named_arg_from_sys("-f", 'magic_measurements.txt')
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
dir_path = os.path.realpath(dir_path)
in_file = pmag.resolve_file_name(in_file, dir_path)
if '-WD' not in sys.argv:
dir_path = os.path.split(in_file)[0]
plot_by = pmag.get_named_arg_from_sys("-obj", "loc")
if data_model == 3:
plot_key = 'location'
if plot_by == 'sit':
plot_key = 'site'
if plot_by == 'sam':
plot_key = 'sample'
if plot_by == 'spc':
plot_key = 'specimen'
else:
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'
# set defaults and get more information if needed
if data_model == 3:
dmag_key = 'treat_dc_field'
else:
dmag_key = 'treatment_dc_field'
#
if data_model == 3 and plot_key != 'specimen':
# gonna need to read in more files
print('-W- You are trying to plot measurements by {}'.format(plot_key))
print(' By default, this information is not available in your measurement file.')
print(' Trying to acquire this information from {}'.format(dir_path))
con = nb.Contribution(dir_path)
meas_df = con.propagate_location_to_measurements()
if plot_key not in meas_df.columns:
print('-W- Could not find required data.')
print(' Try a different plot key.')
return
else:
print('-I- Found {} information, continuing with plotting'.format(plot_key))
con.write_table_to_file('measurements')
# read in data
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 = []
if data_model == 3:
intlist = ['magn_moment', 'magn_volume', 'magn_mass', 'magnitude']
else:
intlist = ['measurement_magnitude', 'measurement_magn_moment',
'measurement_magn_volume', 'measurement_magn_mass']
IntMeths = []
# get all the records with this lab protocol
#print('data', len(data))
#print('data[0]', data[0])
if data_model == 3:
data = pmag.get_dictitem(data, 'method_codes', LP, 'has')
else:
data = pmag.get_dictitem(data, 'magic_method_codes', LP, 'has')
Ints = {}
NoInts, int_key = 1, ""
for key in intlist:
# get all non-blank data for intensity type
Ints[key] = pmag.get_dictitem(data, key, '', 'F')
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 plt in plotlist:
print(plt)
INTblock = []
# get data with right intensity info whose plot_key matches plot
data = pmag.get_dictitem(Ints[int_key], plot_key, plt, 'T')
# get a list of specimens with appropriate data
sids = pmag.get_specs(data)
if len(sids) > 0:
title = data[0][plot_key]
for s in sids:
INTblock = []
# get data for each specimen
if data_model == 3:
sdata = pmag.get_dictitem(data, 'specimen', s, 'T')
else:
sdata = pmag.get_dictitem(data, 'er_specimen_name', s, 'T')
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)
files = {}
for key in list(FIG.keys()):
files[key] = title + '_' + LP + '.' + fmt
if plot == 0:
pmagplotlib.drawFIGS(FIG)
ans = input(" S[a]ve to save plot, [q]uit, Return to continue: ")
if ans == 'q':
sys.exit()
if ans == "a":
pmagplotlib.saveP(FIG, files)
else:
pmagplotlib.saveP(FIG, files)
pmagplotlib.clearFIG(FIG['exp'])
def main():
"""
NAME
irmaq_magic.py
DESCRIPTION
plots IRM acquisition curves from 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/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
-fmt [png,jpg,eps,pdf] set plot file format [default is svg]
-sav save plot[s] and quit
-DM MagIC data model number, default is 3
NOTE
loc: location (study); sit: site; sam: sample; spc: specimen
"""
FIG = {} # plot dictionary
FIG['exp'] = 1 # exp is figure 1
dir_path = './'
plot, fmt = 0, 'svg'
units = 'T',
XLP = []
norm = 1
LP = "LP-IRM"
if len(sys.argv) > 1:
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
data_model = int(pmag.get_named_arg_from_sys("-DM", 3))
if '-N' in sys.argv:
norm = 0
if '-sav' in sys.argv:
plot = 1
if '-fmt' in sys.argv:
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
if data_model == 3:
in_file = pmag.get_named_arg_from_sys("-f", 'measurements.txt')
else:
in_file = pmag.get_named_arg_from_sys("-f",
'magic_measurements.txt')
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
dir_path = os.path.realpath(dir_path)
in_file = pmag.resolve_file_name(in_file, dir_path)
if '-WD' not in sys.argv:
dir_path = os.path.split(in_file)[0]
plot_by = pmag.get_named_arg_from_sys("-obj", "loc")
if data_model == 3:
plot_key = 'location'
if plot_by == 'sit':
plot_key = 'site'
if plot_by == 'sam':
plot_key = 'sample'
if plot_by == 'spc':
plot_key = 'specimen'
else:
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'
# set defaults and get more information if needed
if data_model == 3:
dmag_key = 'treat_dc_field'
else:
dmag_key = 'treatment_dc_field'
#
if data_model == 3 and plot_key != 'specimen':
# gonna need to read in more files
print('-W- You are trying to plot measurements by {}'.format(plot_key))
print(
' By default, this information is not available in your measurement file.'
)
print(
' Trying to acquire this information from {}'.format(dir_path))
con = nb.Contribution(dir_path)
meas_df = con.propagate_location_to_measurements()
if plot_key not in meas_df.columns:
print('-W- Could not find required data.')
print(' Try a different plot key.')
return
else:
print('-I- Found {} information, continuing with plotting'.format(
plot_key))
con.write_table_to_file('measurements')
# read in data
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 = []
if data_model == 3:
intlist = ['magn_moment', 'magn_volume', 'magn_mass', 'magnitude']
else:
intlist = [
'measurement_magnitude', 'measurement_magn_moment',
'measurement_magn_volume', 'measurement_magn_mass'
]
IntMeths = []
# get all the records with this lab protocol
#print('data', len(data))
#print('data[0]', data[0])
if data_model == 3:
data = pmag.get_dictitem(data, 'method_codes', LP, 'has')
else:
data = pmag.get_dictitem(data, 'magic_method_codes', LP, 'has')
Ints = {}
NoInts, int_key = 1, ""
for key in intlist:
# get all non-blank data for intensity type
Ints[key] = pmag.get_dictitem(data, key, '', 'F')
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 plt in plotlist:
print(plt)
INTblock = []
# get data with right intensity info whose plot_key matches plot
data = pmag.get_dictitem(Ints[int_key], plot_key, plt, 'T')
# get a list of specimens with appropriate data
sids = pmag.get_specs(data)
if len(sids) > 0:
title = data[0][plot_key]
for s in sids:
INTblock = []
# get data for each specimen
if data_model == 3:
sdata = pmag.get_dictitem(data, 'specimen', s, 'T')
else:
sdata = pmag.get_dictitem(data, 'er_specimen_name', s, 'T')
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)
files = {}
for key in list(FIG.keys()):
files[key] = title + '_' + LP + '.' + fmt
if plot == 0:
pmagplotlib.drawFIGS(FIG)
ans = input(" S[a]ve to save plot, [q]uit, Return to continue: ")
if ans == 'q':
sys.exit()
if ans == "a":
pmagplotlib.saveP(FIG, files)
else:
pmagplotlib.saveP(FIG, files)
pmagplotlib.clearFIG(FIG['exp'])