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thellier_gui.py; save pmag_tables before er_tables
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Added the possibility to save pmag_tables before assigning er_tables in
thellier_gui.py
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@ronshaar
ronshaar committed Nov 10, 2015
1 parent c01d003 commit aed5e27
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147 changes: 85 additions & 62 deletions thellier_gui.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2286,11 +2286,7 @@ def read_criteria_file(self,criteria_file):
def on_menu_save_interpretation(self, event):

'''
save interpretations to a redo file
save specimens interpretations to thellier_GUI.specimens.txt
save sample interpretations to thellier_GUI.specimens.txt
this functio should be removed. and use only the MagIC menu bar....

save interpretations to a redo file
'''

#thellier_gui_specimen_criteria_list=['specimen_int_n','specimen_int_ptrm_n','specimen_f','specimen_fvds','specimen_frac','specimen_gmax','specimen_b_beta','specimen_scat','specimen_drats','specimen_md','specimen_int_mad','specimen_dang','specimen_q','specimen_g']
Expand Down Expand Up @@ -4556,84 +4552,85 @@ def on_menu_results_data (self, event):
def on_menu__prepare_MagIC_results_tables (self, event):

import copy
#read MagIC model
fail_read_magic_model_files=self.read_magic_model()
if len(fail_read_magic_model_files)>0:
for F in fail_read_magic_model_files:
print "-E- Failed reading MagIC Model file %s"%F
return
self.on_menu_save_interpretation(None)


# write a redo file
try:
self.on_menu_save_interpretation(self, None)
self.on_menu_save_interpretation(None)
except:
pass

#------------------
# read "old" pmag results data and sort out directional data
# this data will be marged later with os.
# read existing pmag results data and sort out the directional data.
# The directional data will be merged to one combined pmag table.
# this data will be marged later
#-----------------------.

PmagRecsOld={}
for FILE in ['pmag_specimens.txt','pmag_samples.txt','pmag_sites.txt','pmag_results.txt']:
PmagRecsOld[FILE],meas_data=[],[]
try:
meas_data,file_type=pmag.magic_read(os.path.join(self.WD, FILE))
self.GUI_log.write("-I- Read old magic file %s\n"%(os.path.join(self.WD, FILE)))
self.GUI_log.write("-I- Read exiting magic file %s\n"%(os.path.join(self.WD, FILE)))
#if FILE !='pmag_specimens.txt':
os.rename(os.path.join(self.WD, FILE), os.path.join(self.WD, FILE+".backup"))
self.GUI_log.write("-I- rename old magic file %s.backup\n"%(os.path.join(self.WD, FILE)))
except:
self.GUI_log.write("-I- Cant read existing magic file %s\n"%(os.path.join(self.WD, FILE)))
continue
for rec in meas_data:
if "magic_method_codes" in rec.keys():
if "LP-PI" not in rec['magic_method_codes'] and "IE-" not in rec['magic_method_codes'] :
PmagRecsOld[FILE].append(rec)
#PmagRecsOld[FILE]=self.converge_pmag_rec_headers(PmagRecsOld[FILE])

pmag_specimens_header_1=["er_location_name","er_site_name","er_sample_name","er_specimen_name"]
pmag_specimens_header_2=['measurement_step_min','measurement_step_max','specimen_int']
pmag_specimens_header_3=["specimen_correction","specimen_int_corr_anisotropy","specimen_int_corr_nlt","specimen_int_corr_cooling_rate"]
pmag_specimens_header_4=[]
for short_stat in self.preferences['show_statistics_on_gui']:
stat="specimen_"+short_stat
pmag_specimens_header_4.append(stat)
#pmag_specimens_header_4=['specimen_int_n','specimen_int_ptrm_n','specimen_f','specimen_fvds','specimen_frac','specimen_gmax','specimen_b_beta','specimen_scat','specimen_drats','specimen_md','specimen_int_mad','specimen_int_dang','specimen_q','specimen_g']
pmag_specimens_header_5=["magic_experiment_names","magic_method_codes","measurement_step_unit","specimen_lab_field_dc"]
pmag_specimens_header_6=["er_citation_names"]
try:
version= pmag.get_version()
except:
version=""
version=version+": thellier_gui."+CURRENT_VRSION
#for k in self.ignore_parameters.keys():
# if k in pmag_specimens_header_4 and self.ignore_parameters[k]==True:
# pmag_specimens_header_4.remove(k)

specimens_list=[]
for specimen in self.Data.keys():
if 'pars' in self.Data[specimen].keys():
if 'saved' in self.Data[specimen]['pars'].keys() and self.Data[specimen]['pars']['saved']==True:
specimens_list.append(specimen)

# Empty pmag tables:
MagIC_results_data={}
MagIC_results_data['pmag_specimens']={}
#if self.average_by_sample_or_site=='sample':
# MagIC_results_data['pmag_samples']={}
#else:
MagIC_results_data['pmag_samples_or_sites']={}
MagIC_results_data['pmag_results']={}


# write down pmag_specimens.txt
specimens_list.sort()
#print specimens_list
for specimen in specimens_list:


if 'pars' in self.Data[specimen].keys() and 'saved' in self.Data[specimen]['pars'].keys() and self.Data[specimen]['pars']['saved']==True:

sample_name = self.Data_hierarchy['specimens'][specimen]
site_name=thellier_gui_lib.get_site_from_hierarchy(sample_name,self.Data_hierarchy)
location_name=thellier_gui_lib.get_location_from_hierarchy(site_name,self.Data_hierarchy)

MagIC_results_data['pmag_specimens'][specimen]={}
if version!="unknown":
MagIC_results_data['pmag_specimens'][specimen]['magic_software_packages']=version
MagIC_results_data['pmag_specimens'][specimen]['er_citation_names']="This study"
#MagIC_results_data['pmag_specimens'][specimen]['er_analyst_mail_names']="unknown"

MagIC_results_data['pmag_specimens'][specimen]['er_specimen_name']=specimen
MagIC_results_data['pmag_specimens'][specimen]['er_sample_name']=self.MagIC_model["specimens"][specimen]['er_sample_name']
MagIC_results_data['pmag_specimens'][specimen]['er_site_name']=self.MagIC_model["specimens"][specimen]['er_site_name']


MagIC_results_data['pmag_specimens'][specimen]['er_location_name']=self.MagIC_model["specimens"][specimen]['er_location_name']
MagIC_results_data['pmag_specimens'][specimen]['er_sample_name']=sample_name
MagIC_results_data['pmag_specimens'][specimen]['er_site_name']=site_name
MagIC_results_data['pmag_specimens'][specimen]['er_location_name']=location_name
MagIC_results_data['pmag_specimens'][specimen]['magic_method_codes']=self.Data[specimen]['pars']['magic_method_codes']+":IE-TT"
tmp=MagIC_results_data['pmag_specimens'][specimen]['magic_method_codes'].split(":")
magic_experiment_names=specimen
Expand All @@ -4642,12 +4639,10 @@ def on_menu__prepare_MagIC_results_tables (self, event):
magic_experiment_names=magic_experiment_names+" : " + m
MagIC_results_data['pmag_specimens'][specimen]['magic_experiment_names']=magic_experiment_names

#MagIC_results_data['pmag_specimens'][specimen]['magic_instrument_codes']=""
MagIC_results_data['pmag_specimens'][specimen]['measurement_step_unit']='K'
MagIC_results_data['pmag_specimens'][specimen]['specimen_lab_field_dc']="%.2e"%(self.Data[specimen]['pars']['lab_dc_field'])
MagIC_results_data['pmag_specimens'][specimen]['specimen_correction']=self.Data[specimen]['pars']['specimen_correction']
for key in pmag_specimens_header_4:
#print key
if key in ['specimen_int_ptrm_n','specimen_int_n']:
MagIC_results_data['pmag_specimens'][specimen][key]="%i"%(self.Data[specimen]['pars'][key])
elif key in ['specimen_scat'] and self.Data[specimen]['pars'][key]=="Fail":
Expand Down Expand Up @@ -4682,25 +4677,40 @@ def on_menu__prepare_MagIC_results_tables (self, event):
String=String+key+"\t"
fout.write(String[:-1]+"\n")
for specimen in specimens_list:
#print "specimen",specimen
String=""
for key in headers:
String=String+MagIC_results_data['pmag_specimens'][specimen][key]+"\t"
#print "String",String
fout.write(String[:-1]+"\n")
fout.close()


# merge with non-intensity data
# read the new pmag_specimens.txt
meas_data,file_type=pmag.magic_read(os.path.join(self.WD, "pmag_specimens.txt"))
# add the old non-PI lines from pmag_specimens.txt
for rec in PmagRecsOld["pmag_specimens.txt"]:
meas_data.append(rec)
# fix headers, so all headers in all lines
meas_data=self.converge_pmag_rec_headers(meas_data)
# write the combined pmag_specimens.txt
pmag.magic_write(os.path.join(self.WD, "pmag_specimens.txt"),meas_data,'pmag_specimens')
try:
os.remove(os.path.join(self.WD, "pmag_specimens.txt.backup"))
except:
pass

#-------------
# message dialog
#-------------
TEXT="specimens interpretations are saved in pmag_specimens.txt.\nPress OK for pmag_samples/pmag_sites/pmag_results tables."
dlg = wx.MessageDialog(self, caption="Saved",message=TEXT,style=wx.OK|wx.CANCEL )
result = dlg.ShowModal()
if result == wx.ID_OK:
dlg.Destroy()
if result == wx.ID_CANCEL:
dlg.Destroy()
return()

#-------------
# pmag_samples.txt or pmag_sites.txt
#-------------
Expand Down Expand Up @@ -4778,11 +4788,12 @@ def on_menu__prepare_MagIC_results_tables (self, event):
MagIC_results_data['pmag_samples_or_sites'][sample_or_site][name+'description']="paleointensity mean"
for key in pmag_samples_header_1:
if BY_SAMPLES:
MagIC_results_data['pmag_samples_or_sites'][sample_or_site][key]=self.MagIC_model["er_samples"][sample_or_site][key]
#MagIC_results_data['pmag_samples_or_sites'][sample_or_site][key]=self.MagIC_model["er_samples"][sample_or_site][key]
MagIC_results_data['pmag_samples_or_sites'][sample_or_site][key]=sample_or_site
else:
MagIC_results_data['pmag_samples_or_sites'][sample_or_site][key]=self.MagIC_model["er_sites"][sample_or_site][key]


#MagIC_results_data['pmag_samples_or_sites'][sample_or_site][key]=self.MagIC_model["er_sites"][sample_or_site][key]
MagIC_results_data['pmag_samples_or_sites'][sample_or_site][key]=sample_or_site
MagIC_results_data['pmag_samples_or_sites'][sample_or_site]["pmag_criteria_codes"]=""
MagIC_results_data['pmag_samples_or_sites'][sample_or_site]['magic_method_codes']=magic_codes
MagIC_results_data['pmag_samples_or_sites'][sample_or_site]["magic_software_packages"]=version
Expand Down Expand Up @@ -4902,16 +4913,10 @@ def on_menu__prepare_MagIC_results_tables (self, event):

site=MagIC_results_data['pmag_results'][sample_or_site]["er_site_names"]
lat,lon="",""
try:
lat=self.MagIC_model["er_sites"][site]["site_lat"]
MagIC_results_data['pmag_results'][sample_or_site]["average_lat"]=lat
except:
self.GUI_log.write( "-E- MagIC model error: cant find latitude for site %s, sample/site %s\n"%(site,sample_or_site))
try:
lon=self.MagIC_model["er_sites"][site]["site_lon"]
MagIC_results_data['pmag_results'][sample_or_site]["average_lon"]=lon
except:
self.GUI_log.write( "-E- MagIC model error: cant find longitude for site %s, sample/site %s\n"%(site,sample_or_site))
if site in self.Data_info["er_sites"].keys() and "site_lat" in self.Data_info["er_sites"].keys():
MagIC_results_data['pmag_results'][sample_or_site]["average_lat"]=self.Data_info["er_sites"][site]["site_lat"]
if site in self.Data_info["er_sites"].keys() and "site_lon" in self.Data_info["er_sites"].keys():
MagIC_results_data['pmag_results'][sample_or_site]["average_lon"]=self.Data_info["er_sites"][site]["site_lon"]

MagIC_results_data['pmag_results'][sample_or_site]["average_lat"]=lat
MagIC_results_data['pmag_results'][sample_or_site]["average_lon"]=lon
Expand Down Expand Up @@ -4969,7 +4974,7 @@ def on_menu__prepare_MagIC_results_tables (self, event):
found_age=True
if found_age:
for header in ["age","age_unit","age_sigma","age_range_low","age_range_high"]:
if header in self.Data_info["er_ages"][sample_or_site_with_age].keys():
if sample_or_site_with_age in self.Data_info["er_ages"].keys() and header in self.Data_info["er_ages"][sample_or_site_with_age].keys():
if self.Data_info["er_ages"][sample_or_site_with_age][header]!="":
value=self.Data_info["er_ages"][sample_or_site_with_age][header]
header_result="average_"+header
Expand Down Expand Up @@ -5000,17 +5005,22 @@ def on_menu__prepare_MagIC_results_tables (self, event):
found_age=True
else:
continue
foundkeys=False
if not found_age:
continue
foundkeys=False
print "element_with_age",element_with_age
for key in ['age','age_sigma','age_range_low','age_range_high','age_unit']:
if key in self.Data_info["er_ages"][element_with_age].keys():
if self.Data_info["er_ages"][element_with_age][key] !="":
MagIC_results_data['pmag_results'][sample_or_site][key]=self.Data_info["er_ages"][element_with_age][key]
foundkeys=True
if "er_ages" in self.Data_info.keys() and element_with_age in self.Data_info["er_ages"].keys():
if key in self.Data_info["er_ages"][element_with_age].keys():
if self.Data_info["er_ages"][element_with_age][key] !="":
MagIC_results_data['pmag_results'][sample_or_site][key]=self.Data_info["er_ages"][element_with_age][key]
foundkeys=True
if foundkeys==True:
if 'magic_method_codes' in self.Data_info["er_ages"][element_with_age].keys():
methods= self.Data_info["er_ages"][element_with_age]['magic_method_codes'].replace(" ","").strip('\n').split(":")
for meth in methods:
MagIC_results_data['pmag_results'][sample_or_site]["magic_method_codes"]=MagIC_results_data['pmag_results'][sample_or_site]["magic_method_codes"] + ":"+ meth
if "er_ages" in self.Data_info.keys() and element_with_age in self.Data_info["er_ages"].keys():
if 'magic_method_codes' in self.Data_info["er_ages"][element_with_age].keys():
methods= self.Data_info["er_ages"][element_with_age]['magic_method_codes'].replace(" ","").strip('\n').split(":")
for meth in methods:
MagIC_results_data['pmag_results'][sample_or_site]["magic_method_codes"]=MagIC_results_data['pmag_results'][sample_or_site]["magic_method_codes"] + ":"+ meth


# wrire pmag_results.txt
Expand Down Expand Up @@ -5094,7 +5104,8 @@ def on_menu__prepare_MagIC_results_tables (self, event):
dlg1.ShowModal()
dlg1.Destroy()

self.close_warning=False
self.close_warning=False

def converge_pmag_rec_headers(self,old_recs):
# fix the headers of pmag recs
recs={}
Expand All @@ -5109,9 +5120,11 @@ def converge_pmag_rec_headers(self,old_recs):
if header not in rec.keys():
rec[header]=""
return recs


'''outdated
def read_magic_model (self):
# Read MagIC Data model:


self.MagIC_model={}
self.MagIC_model["specimens"]={}
Expand Down Expand Up @@ -5152,7 +5165,7 @@ def read_magic_model (self):
self.GUI_log.write ("-W- Cant find er_ages.txt in project directory")
pass

return (fail)
return (fail)'''


def read_magic_file(self,path,ignore_lines_n,sort_by_this_name):
Expand Down Expand Up @@ -7513,6 +7526,7 @@ def dir2cart(d):
# All data information is stored in Data[secimen]={}
Data={}
Data_hierarchy={}
Data_hierarchy['locations']={}
Data_hierarchy['sites']={}
Data_hierarchy['samples']={}
Data_hierarchy['specimens']={}
Expand Down Expand Up @@ -7563,6 +7577,9 @@ def dir2cart(d):
Data[s]['T_or_MW']="T"
sample=rec["er_sample_name"]
site=rec["er_site_name"]
location=""
if "er_location_name" in rec.keys():
location=rec["er_location_name"]

if "LP-PI-M" in rec["magic_method_codes"]:
Data[s]['T_or_MW']="MW"
Expand Down Expand Up @@ -7666,13 +7683,19 @@ def dir2cart(d):

if site not in Data_hierarchy['sites'].keys():
Data_hierarchy['sites'][site]=[]

if location not in Data_hierarchy['locations'].keys():
Data_hierarchy['locations'][location]=[]

if s not in Data_hierarchy['samples'][sample]:
Data_hierarchy['samples'][sample].append(s)

if sample not in Data_hierarchy['sites'][site]:
Data_hierarchy['sites'][site].append(sample)

if site not in Data_hierarchy['locations'][location]:
Data_hierarchy['locations'][location].append(site)

Data_hierarchy['specimens'][s]=sample
Data_hierarchy['sample_of_specimen'][s]=sample
Data_hierarchy['site_of_specimen'][s]=site
Expand Down
10 changes: 10 additions & 0 deletions thellier_gui_lib.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -355,3 +355,13 @@ def get_site_from_hierarchy(sample,Data_hierarchy):
site=S
break
return(site)

def get_location_from_hierarchy(site,Data_hierarchy):
location=""
locations=Data_hierarchy['locations'].keys()
for L in locations:
if site in Data_hierarchy['locations'][L]:
location=L
break
return(location)

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