Instruction:
Explain what the following Python 3 code does
def reset_highlights(self):
        for dtype in ["specimens", "samples", "sites", "locations", "ages"]:
            wind = self.FindWindowByName(dtype + '_btn')
            wind.Unbind(wx.EVT_PAINT, handler=self.highlight_button)
        self.Refresh()
        #self.message.SetLabel('Highlighted grids have incorrect or incomplete data')
        self.bSizer_msg.ShowItems(False)
        self.hbox.Fit(self)

Response: Remove red outlines from all buttons and update the grids


Instruction:
Implement a function in Python 3 to
draw a red highlight line around the event object

Response:
def highlight_button(self, event):
        """
        Draw a red highlight line around the event object
        """
        wind = event.GetEventObject()
        pos = wind.GetPosition()
        size = wind.GetSize()
        try:
            dc = wx.PaintDC(self)
        except wx._core.PyAssertionError:
            # if it's not a native paint event, we can't us wx.PaintDC
            dc = wx.ClientDC(self)
        dc.SetPen(wx.Pen('red', 5, wx.SOLID))
        dc.DrawRectangle(pos[0], pos[1], size[0], size[1])
        event.Skip()


Instruction:
Given the following Python 3 function, write the documentation
def on_clear(self, event):
        dia = pmag_menu_dialogs.ClearWD(self.parent, self.parent.WD)
        clear = dia.do_clear()
        if clear:
            print('-I- Clear data object')
            self.contribution = cb.Contribution(self.WD, dmodel=self.data_model)
            self.edited = False

Response: Clear the data object


Instruction:
Here you have a function in Python 3, explain what it does
def on_close_grid(self, event):
        if self.parent.grid_frame:
            self.parent.grid_frame.onSave(None)
            self.parent.grid_frame.Destroy()

Response: Save and close the grid.


Instruction:
Can you generate a brief explanation for the following Python 3 code
def main():
    firstline,itilt,igeo,linecnt,key=1,0,0,0,""
    out=""
    data,k15=[],[]
    dir='./'
    ofile=""
    if '-WD' in sys.argv:
        ind=sys.argv.index('-WD')
        dir=sys.argv[ind+1]+'/'
    if '-h' in sys.argv:
        print(main.__doc__)
        sys.exit()
    if '-i' in sys.argv:
        file=input("Input file name [.k15 format]: ")
        f=open(file,'r')
        data=f.readlines()
        f.close()
        file=input("Output file name [.s format]: ")
        out=open(file,'w')
        print (" [g]eographic, [t]ilt corrected, ")
        tg=input(" [return for specimen coordinates]: ")
        if tg=='g':
            igeo=1
        elif tg=='t':
            igeo,itilt=1,1
    elif '-f' in sys.argv:
        ind=sys.argv.index('-f')
        file=dir+sys.argv[ind+1]
        f=open(file,'r')
        data=f.readlines()
        f.close()
    else:
        data= sys.stdin.readlines()
    if len(data)==0:
        print(main.__doc__)
        sys.exit()
    if '-F' in sys.argv:
        ind=sys.argv.index('-F')
        ofile=dir+sys.argv[ind+1]
        out=open(ofile,'w')
    if '-crd' in sys.argv:
        ind=sys.argv.index('-crd')
        tg=sys.argv[ind+1]
        if tg=='g':igeo=1
        if tg=='t': igeo,itilt=1,1
    for line in data:
        rec=line.split()
        if firstline==1:
            firstline=0
            nam=rec[0]
            if igeo==1: az,pl=float(rec[1]),float(rec[2])
            if itilt==1: bed_az,bed_dip=90.+float(rec[3]),float(rec[4])
        else:
            linecnt+=1
            for i in range(5):
                k15.append(float(rec[i]))
            if linecnt==3:
                sbar,sigma,bulk=pmag.dok15_s(k15)
                if igeo==1: sbar=pmag.dosgeo(sbar,az,pl)
                if itilt==1: sbar=pmag.dostilt(sbar,bed_az,bed_dip)
                outstring=""
                for s in sbar:outstring+='%10.8f '%(s)
                outstring+='%10.8f'%(sigma)
                if out=="":
                    print(outstring)
                else:
                    out.write(outstring+'\n')
                linecnt,firstline,k15=0,1,[]
    if ofile!="":print ('Output saved in ',ofile)

Response:
NAME k15_s. py

       . py


Instruction:
Create a Python 3 function to
name zeq_magic_redo.py DESCRIPTION Calculate principal components through demagnetization data using bounds and calculation type stored in "redo" file SYNTAX zeq_magic_redo.py [command line options] OPTIONS -h prints help message -usr USER: identify user, default is "" -f: specify input file, default is magic_measurements.txt -F: specify output file, default is zeq_specimens.txt -fre REDO: specify redo file, default is "zeq_redo" -fsa SAMPFILE: specify er_samples format file, default is "er_samples.txt" -A : don't average replicate measurements, default is yes -crd [s,g,t] : specify coordinate system [s,g,t] [default is specimen coordinates] are specimen, geographic, and tilt corrected respectively NB: you must have a SAMPFILE in this directory to rotate from specimen coordinates -leg: attaches "Recalculated from original measurements; supercedes published results. " to comment field INPUTS zeq_redo format file is: specimen_name calculation_type[DE-BFL,DE-BFL-A,DE-BFL-O,DE-BFP,DE-FM] step_min step_max component_name[A,B,C]

Response:
def main():
    """
    NAME
        zeq_magic_redo.py

    DESCRIPTION
        Calculate principal components through demagnetization data using bounds and calculation type stored in "redo" file

    SYNTAX
        zeq_magic_redo.py [command line options]

    OPTIONS
        -h prints help message
        -usr USER:   identify user, default is ""
        -f: specify input file, default is magic_measurements.txt
        -F: specify output file, default is zeq_specimens.txt
        -fre  REDO: specify redo file, default is "zeq_redo"
        -fsa  SAMPFILE: specify er_samples format file, default is "er_samples.txt"
        -A : don't average replicate measurements, default is yes
        -crd [s,g,t] :
             specify coordinate system [s,g,t]  [default is specimen coordinates]
                 are specimen, geographic, and tilt corrected respectively
             NB: you must have a SAMPFILE in this directory to rotate from specimen coordinates
        -leg:  attaches "Recalculated from original measurements; supercedes published results. " to comment field
    INPUTS
        zeq_redo format file is:
        specimen_name calculation_type[DE-BFL,DE-BFL-A,DE-BFL-O,DE-BFP,DE-FM]  step_min step_max component_name[A,B,C]
    """
    dir_path='.'
    INCL=["LT-NO","LT-AF-Z","LT-T-Z","LT-M-Z"] # looking for demag data
    beg,end,pole,geo,tilt,askave,save=0,0,[],0,0,0,0
    user,doave,comment= "",1,""
    geo,tilt=0,0
    version_num=pmag.get_version()
    args=sys.argv
    if '-WD' in args:
        ind=args.index('-WD')
        dir_path=args[ind+1]
    meas_file,pmag_file,mk_file= dir_path+"/"+"magic_measurements.txt",dir_path+"/"+"zeq_specimens.txt",dir_path+"/"+"zeq_redo"
    samp_file,coord=dir_path+"/"+"er_samples.txt",""
    if "-h" in args:
        print(main.__doc__)
        sys.exit()
    if "-usr" in args:
        ind=args.index("-usr")
        user=sys.argv[ind+1]
    if "-A" in args:doave=0
    if "-leg" in args: comment="Recalculated from original measurements; supercedes published results. "
    if "-f" in args:
        ind=args.index("-f")
        meas_file=dir_path+'/'+sys.argv[ind+1]
    if "-F" in args:
        ind=args.index("-F")
        pmag_file=dir_path+'/'+sys.argv[ind+1]
    if "-fre" in args:
        ind=args.index("-fre")
        mk_file=dir_path+"/"+args[ind+1]
    try:
        mk_f=open(mk_file,'r')
    except:
        print("Bad redo file")
        sys.exit()
    mkspec,skipped=[],[]
    speclist=[]
    for line in mk_f.readlines():
        tmp=line.split()
        mkspec.append(tmp)
        speclist.append(tmp[0])
    if "-fsa" in args:
        ind=args.index("-fsa")
        samp_file=dir_path+'/'+sys.argv[ind+1]
    if "-crd" in args:
        ind=args.index("-crd")
        coord=sys.argv[ind+1]
        if coord=="g":geo,tilt=1,0
        if coord=="t":geo,tilt=1,1
#
# now get down to bidness
    if geo==1:
        samp_data,file_type=pmag.magic_read(samp_file)
        if file_type != 'er_samples':
            print(file_type)
            print("This is not a valid er_samples file ")
            sys.exit()
    #
    #
    #

    meas_data,file_type=pmag.magic_read(meas_file)
    if file_type != 'magic_measurements':
        print(file_type)
        print(file_type,"This is not a valid magic_measurements file ")
        sys.exit()
    #
    # sort the specimen names
    #
    k = 0
    print('Processing ',len(speclist), ' specimens - please wait')
    PmagSpecs=[]
    while k < len(speclist):
        s=speclist[k]
        recnum=0
        PmagSpecRec={}
        method_codes,inst_codes=[],[]
    # find the data from the meas_data file for this sample
    #
    #  collect info for the PmagSpecRec dictionary
    #
        meas_meth=[]
        spec=pmag.get_dictitem(meas_data,'er_specimen_name',s,'T')
        if len(spec)==0:
            print('no data found for specimen:  ',s)
            print('delete from zeq_redo input file...., then try again')
        else:
          for rec in  spec: # copy of vital stats to PmagSpecRec from first spec record in demag block
           skip=1
           methods=rec["magic_method_codes"].split(":")
           if len(set(methods) & set(INCL))>0:
                   PmagSpecRec["er_analyst_mail_names"]=user
                   PmagSpecRec["magic_software_packages"]=version_num
                   PmagSpecRec["er_specimen_name"]=s
                   PmagSpecRec["er_sample_name"]=rec["er_sample_name"]
                   PmagSpecRec["er_site_name"]=rec["er_site_name"]
                   PmagSpecRec["er_location_name"]=rec["er_location_name"]
                   if "er_expedition_name" in list(rec.keys()):PmagSpecRec["er_expedition_name"]=rec["er_expedition_name"]
                   PmagSpecRec["er_citation_names"]="This study"
                   if "magic_experiment_name" not in list(rec.keys()): rec["magic_experiment_name"]=""
                   PmagSpecRec["magic_experiment_names"]=rec["magic_experiment_name"]
                   if "magic_instrument_codes" not in list(rec.keys()): rec["magic_instrument_codes"]=""
                   inst=rec['magic_instrument_codes'].split(":")
                   for I in inst:
                       if I not in inst_codes:  # copy over instruments
                           inst_codes.append(I)
                   meths=rec["magic_method_codes"].split(":")
                   for meth in meths:
                       if meth.strip() not in meas_meth:meas_meth.append(meth)
                   if "LP-DIR-AF" in meas_meth or "LT-AF-Z" in meas_meth:
                       PmagSpecRec["measurement_step_unit"]="T"
                       if "LP-DIR-AF" not in method_codes:method_codes.append("LP-DIR-AF")
                   if "LP-DIR-T" in meas_meth or "LT-T-Z" in meas_meth:
                       PmagSpecRec["measurement_step_unit"]="K"
                       if "LP-DIR-T" not in method_codes:method_codes.append("LP-DIR-T")
                   if "LP-DIR-M" in meas_meth or "LT-M-Z" in meas_meth:
                       PmagSpecRec["measurement_step_unit"]="J"
                       if "LP-DIR-M" not in method_codes:method_codes.append("LP-DIR-M")
    #
    #
        datablock,units=pmag.find_dmag_rec(s,spec) # fish out the demag data for this specimen
    #
        if len(datablock) <2 or s not in speclist :
            k+=1
#            print 'skipping ', s,len(datablock)
        else:
        #
        # find replicate measurements at given treatment step and average them
        #
#            step_meth,avedata=pmag.vspec(data)
#
#            if len(avedata) != len(datablock):
#                if doave==1:
#                    method_codes.append("DE-VM")
#                    datablock=avedata
        #
        # do geo or stratigraphic correction now
        #
            if geo==1 or tilt==1:
       # find top priority orientation method
                orient,az_type=pmag.get_orient(samp_data,PmagSpecRec["er_sample_name"])
                if az_type not in method_codes:method_codes.append(az_type)
        #
        #  if tilt selected,  get stratigraphic correction
        #
                tiltblock,geoblock=[],[]
                for rec in datablock:
                    if "sample_azimuth" in list(orient.keys()) and orient["sample_azimuth"]!="":
                        d_geo,i_geo=pmag.dogeo(rec[1],rec[2],float(orient["sample_azimuth"]),float(orient["sample_dip"]))
                        geoblock.append([rec[0],d_geo,i_geo,rec[3],rec[4],rec[5]])
                        if tilt==1 and "sample_bed_dip_direction" in list(orient.keys()):
                            d_tilt,i_tilt=pmag.dotilt(d_geo,i_geo,float(orient["sample_bed_dip_direction"]),float(orient["sample_bed_dip"]))
                            tiltblock.append([rec[0],d_tilt,i_tilt,rec[3],rec[4],rec[5]])
                        elif tilt==1:
                            if PmagSpecRec["er_sample_name"] not in skipped:
                                print('no tilt correction for ', PmagSpecRec["er_sample_name"],' skipping....')
                                skipped.append(PmagSpecRec["er_sample_name"])
                    else:
                        if PmagSpecRec["er_sample_name"] not in skipped:
                            print('no geographic correction for ', PmagSpecRec["er_sample_name"],' skipping....')
                            skipped.append(PmagSpecRec["er_sample_name"])
    #
    #	get beg_pca, end_pca, pca
            if PmagSpecRec['er_sample_name'] not in skipped:
                compnum=-1
                for spec in mkspec:
                    if spec[0]==s:
                        CompRec={}
                        for key in list(PmagSpecRec.keys()):CompRec[key]=PmagSpecRec[key]
                        compnum+=1
                        calculation_type=spec[1]
                        beg=float(spec[2])
                        end=float(spec[3])
                        if len(spec)>4:
                            comp_name=spec[4]
                        else:
                            comp_name=string.uppercase[compnum]
                        CompRec['specimen_comp_name']=comp_name
                        if beg < float(datablock[0][0]):beg=float(datablock[0][0])
                        if end > float(datablock[-1][0]):end=float(datablock[-1][0])
                        for l  in range(len(datablock)):
                            if datablock[l][0]==beg:beg_pca=l
                            if datablock[l][0]==end:end_pca=l
                        if geo==1 and tilt==0:
                            mpars=pmag.domean(geoblock,beg_pca,end_pca,calculation_type)
                            if mpars["specimen_direction_type"]!="Error":
                                CompRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
                                CompRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
                                CompRec["specimen_tilt_correction"]='0'
                        if geo==1 and tilt==1:
                            mpars=pmag.domean(tiltblock,beg_pca,end_pca,calculation_type)
                            if mpars["specimen_direction_type"]!="Error":
                                CompRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
                                CompRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
                                CompRec["specimen_tilt_correction"]='100'
                        if geo==0 and tilt==0:
                            mpars=pmag.domean(datablock,beg_pca,end_pca,calculation_type)
                            if mpars["specimen_direction_type"]!="Error":
                                CompRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
                                CompRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
                                CompRec["specimen_tilt_correction"]='-1'
                        if mpars["specimen_direction_type"]=="Error":
                            pass
                        else:
                            CompRec["measurement_step_min"]='%8.3e '%(datablock[beg_pca][0])
                            try:
                                CompRec["measurement_step_max"]='%8.3e '%(datablock[end_pca][0] )
                            except:
                                print('error in end_pca ',PmagSpecRec['er_specimen_name'])
                            CompRec["specimen_correction"]='u'
                            if calculation_type!='DE-FM':
                                CompRec["specimen_mad"]='%7.1f '%(mpars["specimen_mad"])
                                CompRec["specimen_alpha95"]=""
                            else:
                                CompRec["specimen_mad"]=""
                                CompRec["specimen_alpha95"]='%7.1f '%(mpars["specimen_alpha95"])
                            CompRec["specimen_n"]='%i '%(mpars["specimen_n"])
                            CompRec["specimen_dang"]='%7.1f '%(mpars["specimen_dang"])
                            CompMeths=[]
                            for meth in method_codes:
                                if meth not in CompMeths:CompMeths.append(meth)
                            if calculation_type not in CompMeths:CompMeths.append(calculation_type)
                            if geo==1: CompMeths.append("DA-DIR-GEO")
                            if tilt==1: CompMeths.append("DA-DIR-TILT")
                            if "DE-BFP" not in calculation_type:
                                CompRec["specimen_direction_type"]='l'
                            else:
                                CompRec["specimen_direction_type"]='p'
                            CompRec["magic_method_codes"]=""
                            if len(CompMeths) != 0:
                                methstring=""
                                for meth in CompMeths:
                                    methstring=methstring+ ":" +meth
                                CompRec["magic_method_codes"]=methstring.strip(':')
                            CompRec["specimen_description"]=comment
                            if len(inst_codes) != 0:
                                inststring=""
                                for inst in inst_codes:
                                    inststring=inststring+ ":" +inst
                                CompRec["magic_instrument_codes"]=inststring.strip(':')
                            PmagSpecs.append(CompRec)
            k+=1
    pmag.magic_write(pmag_file,PmagSpecs,'pmag_specimens')
    print("Recalculated specimen data stored in ",pmag_file)


Instruction:
Write a Python 3 script for
naming dipole_plat. py - h prints help message and quits - i prints interactive entry of latitude

Response:
def main():
    """
    NAME
        dipole_plat.py

    DESCRIPTION
        gives paleolatitude from given inclination, assuming GAD field

    SYNTAX
        dipole_plat.py [command line options]<filename

    OPTIONS
        -h prints help message and quits
        -i allows interactive entry of latitude
        -f file, specifies file name on command line
    """
    if '-h' in sys.argv:
        print(main.__doc__)
        sys.exit()
    elif '-f' in sys.argv:
       ind=sys.argv.index('-f')
       file=sys.argv[ind+1]
       f=open(file,'r')
       data=f.readlines()
    elif '-i' not in sys.argv:
       data=sys.stdin.readlines()
    if '-i' not in sys.argv:
        for line in data:
            rec=line.split()
            print('%7.1f'%(pmag.plat(float(rec[0]))))
    else:
       while 1:
           try:
               inc=input("Inclination for converting to paleolatitude: <cntl-D> to quit ")
               print('%7.1f'%(pmag.plat(float(inc))))
           except:
               print('\n Good-bye \n')
               sys.exit()


Instruction:
Can you create a Python 3 function that
names zeq_magic.py DESCRIPTION reads in a MagIC measurements formatted file, makes plots of remanence decay during demagnetization experiments. Reads in prior interpretations saved in a specimens formatted file interpretations in a specimens file. interpretations are saved in the coordinate system used. SYNTAX zeq_magic.py [command line options] OPTIONS -h prints help message and quits -f MEASFILE: sets measurements format input file, default: measurements.txt -fsp SPECFILE: sets specimens format file with prior interpreations, default: specimens.txt -fsa SAMPFILE: sets samples format file sample=>site information, default: samples.txt -fsi SITEFILE: sets sites format file with site=>location informationprior interpreations, default: samples.txt -Fp PLTFILE: sets filename for saved plot, default is name_type.fmt (where type is zijd, eqarea or decay curve) -crd [s,g,t]: sets coordinate system, g=geographic, t=tilt adjusted, default: specimen coordinate system -spc SPEC plots single specimen SPEC, saves plot with specified format with optional -dir settings and quits -dir [L,P,F][beg][end]: sets calculation type for principal component analysis, default is none beg: starting step for PCA calculation end: ending step for PCA calculation [L,P,F]: calculation type for line, plane or fisher mean must be used with -spc option -fmt FMT: set format of saved plot [png,svg,jpg] -A: suppresses averaging of replicate measurements, default is to average -sav: saves all plots without review

Response:
def main():
    """
    NAME
        zeq_magic.py
    DESCRIPTION
        reads in a MagIC measurements formatted file, makes plots of remanence decay
        during demagnetization experiments.  Reads in prior interpretations saved in
        a specimens formatted file interpretations in a specimens file.
        interpretations are saved in the coordinate system used.
    SYNTAX
        zeq_magic.py [command line options]
    OPTIONS
        -h prints help message and quits
        -f  MEASFILE: sets measurements format input file, default: measurements.txt
        -fsp SPECFILE: sets specimens format file with prior interpreations, default: specimens.txt
        -fsa SAMPFILE: sets samples format file sample=>site information, default: samples.txt
        -fsi SITEFILE: sets sites format file with site=>location informationprior interpreations, default: samples.txt
        -Fp PLTFILE: sets filename for saved plot, default is name_type.fmt (where type is zijd, eqarea or decay curve)
        -crd [s,g,t]: sets coordinate system,  g=geographic, t=tilt adjusted, default: specimen coordinate system
        -spc SPEC  plots single specimen SPEC, saves plot with specified format
              with optional -dir settings and quits
        -dir [L,P,F][beg][end]: sets calculation type for principal component analysis, default is none
             beg: starting step for PCA calculation
             end: ending step for PCA calculation
             [L,P,F]: calculation type for line, plane or fisher mean
             must be used with -spc option
        -fmt FMT: set format of saved plot [png,svg,jpg]
        -A:  suppresses averaging of  replicate measurements, default is to average
        -sav: saves all plots without review
    """
    if '-h' in sys.argv:
        print(main.__doc__)
        return
    dir_path = pmag.get_named_arg("-WD", default_val=os.getcwd())
    meas_file = pmag.get_named_arg(
        "-f", default_val="measurements.txt")
    spec_file = pmag.get_named_arg(
        "-fsp", default_val="specimens.txt")
    specimen = pmag.get_named_arg(
        "-spc", default_val="")
    samp_file = pmag.get_named_arg("-fsa", default_val="samples.txt")
    site_file = pmag.get_named_arg("-fsi", default_val="sites.txt")
    plot_file = pmag.get_named_arg("-Fp", default_val="")
    crd = pmag.get_named_arg("-crd", default_val="s")
    fmt = pmag.get_named_arg("-fmt", "svg")
    specimen = pmag.get_named_arg("-spc", default_val="")
    interactive = True
    save_plots = False
    if "-sav" in sys.argv:
        interactive = False
        save_plots = True
    ipmag.zeq_magic(meas_file, spec_file, crd, dir_path, n_plots="all",
                    save_plots=save_plots, fmt=fmt, interactive=interactive, specimen=specimen)


Instruction:
Given the following Python 3 function, write the documentation
def main(command_line=True, **kwargs):
    #
    # initialize defaults
    version_num=pmag.get_version()
    meas_file='magic_measurements.txt'
    csv_file=''
    MagRecs,Specs=[],[]
    citation="This study"
    dir_path,demag='.','NRM'
    args=sys.argv
    noave=0
    # get command line args
    if command_line:
        if '-WD' in args:
            ind=args.index("-WD")
            dir_path=args[ind+1]
        if '-ID' in args:
            ind = args.index('-ID')
            input_dir_path = args[ind+1]
        else:
            input_dir_path = dir_path
        output_dir_path = dir_path
        if "-h" in args:
            print(main.__doc__)
            return False
        if "-A" in args: noave=1
        if '-f' in args:
            ind=args.index("-f")
            csv_file=args[ind+1]
        if '-F' in args:
            ind=args.index("-F")
            meas_file=args[ind+1]

    if not command_line:
        dir_path = kwargs.get('dir_path', '.')
        input_dir_path = kwargs.get('input_dir_path', dir_path)
        output_dir_path = dir_path # rename dir_path after input_dir_path is set
        noave = kwargs.get('noave', 0) # default (0) is DO average
        csv_file = kwargs.get('csv_file', '')
        meas_file = kwargs.get('meas_file', 'magic_measurements.txt')

    # format variables

    meas_file= os.path.join(output_dir_path, meas_file)
    if csv_file=="":
        filelist=os.listdir(input_dir_path) # read in list of files to import
    else:
        csv_file = os.path.join(input_dir_path, csv_file)
        filelist=[csv_file]
    # parsing the data
    file_found = False
    for fname in filelist: # parse each file
        if fname[-3:].lower()=='csv':
            file_found = True
            print('processing: ',fname)
            with open(fname, 'r') as finput:
                data = list(finput.readlines())
            keys = data[0].replace('\n','').split(',') # splits on underscores
            interval_key="Offset (cm)"
            demag_key="Demag level (mT)"
            offline_demag_key="Treatment Value (mT or °C)"
            offline_treatment_type="Treatment type"
            run_key="Test No."
            if "Inclination background + tray corrected  (deg)" in keys: inc_key="Inclination background + tray corrected  (deg)"
            if "Inclination background & tray corrected (deg)" in keys: inc_key="Inclination background & tray corrected (deg)"
            if "Declination background + tray corrected (deg)" in keys: dec_key="Declination background + tray corrected (deg)"
            if "Declination background & tray corrected (deg)" in keys: dec_key="Declination background & tray corrected (deg)"
            if "Intensity background + tray corrected  (A/m)" in keys: int_key="Intensity background + tray corrected  (A/m)"
            if "Intensity background & tray corrected (A/m)" in keys: int_key="Intensity background & tray corrected (A/m)"
            type="Type"
            sect_key="Sect"
            half_key="A/W"
# need to add volume_key to LORE format!
            if "Sample volume (cm^3)" in keys:volume_key="Sample volume (cm^3)"
            if "Sample volume (cc)" in keys:volume_key="Sample volume (cc)"
            if "Sample volume (cm³)" in keys:volume_key="Sample volume (cm³)"
            for line in data[1:]:
                InRec={}
                for k in range(len(keys)):InRec[keys[k]]=line.split(',')[k]
                inst="IODP-SRM"
                MagRec={}
                expedition=InRec['Exp']
                location=InRec['Site']+InRec['Hole']
                offsets=InRec[interval_key].split('.') # maintain consistency with er_samples convention of using top interval
                if len(offsets)==1:
                    offset=int(offsets[0])
                else:
                    offset=int(offsets[0])-1
                #interval=str(offset+1)# maintain consistency with er_samples convention of using top interval
                interval=str(offset)# maintain consistency with er_samples convention of using top interval
                specimen=expedition+'-'+location+'-'+InRec['Core']+InRec[type]+"-"+InRec[sect_key]+'_'+InRec[half_key]+'_'+interval
                if specimen not in Specs:Specs.append(specimen)
                MagRec['er_expedition_name']=expedition
                MagRec['er_location_name']=location
                MagRec['er_site_name']=specimen
                MagRec['er_citation_names']=citation
                MagRec['er_specimen_name']=specimen
                MagRec['er_sample_name']=specimen
                MagRec['er_site_name']=specimen
# set up measurement record - default is NRM
                MagRec['magic_software_packages']=version_num
                MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
                MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
                MagRec["treatment_ac_field"]='0'
                MagRec["treatment_dc_field"]='0'
                MagRec["treatment_dc_field_phi"]='0'
                MagRec["treatment_dc_field_theta"]='0'
                MagRec["measurement_flag"]='g' # assume all data are "good"
                MagRec["measurement_standard"]='u' # assume all data are "good"
                MagRec["measurement_csd"]='0' # assume all data are "good"
                volume=InRec[volume_key]
                MagRec["magic_method_codes"]='LT-NO'
                sort_by='treatment_ac_field' # set default to AF demag
                if InRec[demag_key]!="0":
                    MagRec['magic_method_codes'] = 'LT-AF-Z'
                    inst=inst+':IODP-SRM-AF' # measured on shipboard in-line 2G AF
                    treatment_value=float(InRec[demag_key].strip('"'))*1e-3 # convert mT => T
                    if sort_by =="treatment_ac_field":
                        MagRec["treatment_ac_field"]=treatment_value # AF demag in treat mT => T
                    else:
                        MagRec["treatment_ac_field"]=str(treatment_value)# AF demag in treat mT => T
                elif offline_treatment_type in list(InRec.keys()) and InRec[offline_treatment_type]!="":
                    if "Lowrie" in InRec['Comments']:
                        MagRec['magic_method_codes'] = 'LP-IRM-3D'
                        treatment_value=float(InRec[offline_demag_key].strip('"'))+273. # convert C => K
                        MagRec["treatment_temp"]=treatment_value
                        MagRec["treatment_ac_field"]="0"
                        sort_by='treatment_temp'
                    elif 'Isothermal' in InRec[offline_treatment_type]:
                        MagRec['magic_method_codes'] = 'LT-IRM'
                        treatment_value=float(InRec[offline_demag_key].strip('"'))*1e-3 # convert mT => T
                        MagRec["treatment_dc_field"]=treatment_value
                        MagRec["treatment_ac_field"]="0"
                        sort_by='treatment_dc_field'
                MagRec["measurement_standard"]='u' # assume all data are "good"
                vol=float(volume)*1e-6 # convert from cc to m^3
                if run_key in list(InRec.keys()):
                    run_number=InRec[run_key]
                    MagRec['external_database_ids']=run_number
                    MagRec['external_database_names']='LIMS'
                else:
                    MagRec['external_database_ids']=""
                    MagRec['external_database_names']=''
                MagRec['measurement_description']='sample orientation: '+InRec['Sample orientation']
                MagRec['measurement_inc']=InRec[inc_key].strip('"')
                MagRec['measurement_dec']=InRec[dec_key].strip('"')
                intens= InRec[int_key].strip('"')
                MagRec['measurement_magn_moment']='%8.3e'%(float(intens)*vol) # convert intensity from A/m to Am^2 using vol
                MagRec['magic_instrument_codes']=inst
                MagRec['measurement_number']='1'
                MagRec['measurement_positions']=''
                MagRecs.append(MagRec)
    if not file_found:
        print("No .csv files were found")
        return False, "No .csv files were found"
    MagOuts=[]
    for spec in Specs:
        Speclist=pmag.get_dictitem(MagRecs,'er_specimen_name',spec,'T')
        Meassorted=sorted(Speclist, key=lambda x,y=None: int(round(float(x[sort_by])-float(y[sort_by]))) if y!=None else 0)
        for rec in Meassorted:
            for key in list(rec.keys()): rec[key]=str(rec[key])
            MagOuts.append(rec)
    Fixed=pmag.measurements_methods(MagOuts,noave)
    Out,keys=pmag.fillkeys(Fixed)
    if pmag.magic_write(meas_file,Out,'magic_measurements'):
        print('data stored in ',meas_file)
        return True, meas_file
    else:
        print('no data found.  bad magfile?')
        return False, 'no data found.  bad magfile?'

Response: This function is the main function for the iodp_dscr_magic. py script.


Instruction:
Can you write a function in Python 3 where it
names sio_magic.py DESCRIPTION converts SIO .mag format files to magic_measurements format files SYNTAX sio_magic.py [command line options] OPTIONS -h: prints the help message and quits. -usr USER: identify user, default is "" -f FILE: specify .mag format input file, required -fsa SAMPFILE : specify er_samples.txt file relating samples, site and locations names,default is none -- values in SAMPFILE will override selections for -loc (location), -spc (designate specimen), and -ncn (sample-site naming convention) -F FILE: specify output file, default is magic_measurements.txt -Fsy: specify er_synthetics file, default is er_sythetics.txt -LP [colon delimited list of protocols, include all that apply] AF: af demag T: thermal including thellier but not trm acquisition S: Shaw method I: IRM (acquisition) I3d: 3D IRM experiment N: NRM only TRM: trm acquisition ANI: anisotropy experiment D: double AF demag G: triple AF demag (GRM protocol) CR: cooling rate experiment. The treatment coding of the measurement file should be: XXX.00,XXX.10, XXX.20 ...XX.70 etc. (XXX.00 is optional) where XXX in the temperature and .10,.20... are running numbers of the cooling rates steps. XXX.00 is optional zerofield baseline. XXX.70 is alteration check. syntax in sio_magic is: -LP CR xxx,yyy,zzz,..... xxx -A where xxx, yyy, zzz...xxx are cooling time in [K/minutes], seperated by comma, ordered at the same order as XXX.10,XXX.20 ...XX.70 if you use a zerofield step then no need to specify the cooling rate for the zerofield It is important to add to the command line the -A option so the measurements will not be averaged. But users need to make sure that there are no duplicate measurements in the file -V [1,2,3] units of IRM field in volts using ASC coil #1,2 or 3 -spc NUM : specify number of characters to designate a specimen, default = 0 -loc LOCNAME : specify location/study name, must have either LOCNAME or SAMPFILE or be a synthetic -syn INST TYPE: sets these specimens as synthetics created at institution INST and of type TYPE -ins INST : specify which demag instrument was used (e.g, SIO-Suzy or SIO-Odette),default is "" -dc B PHI THETA: dc lab field (in micro tesla) and phi,theta, default is none NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment -ac B : peak AF field (in mT) for ARM acquisition, default is none -ncn NCON: specify naming convention: default is #1 below -A: don't average replicate measurements Sample naming convention: [1] XXXXY: where XXXX is an arbitrary length site designation and Y is the single character sample designation. e.g., TG001a is the first sample from site TG001. [default] [2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length) [3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length) [4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX [5] site name same as sample [6] site is entered under a separate column NOT CURRENTLY SUPPORTED [7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY NB: all others you will have to customize your self or e-mail ltauxe@ucsd.edu for help. [8] synthetic - has no site name [9] ODP naming convention INPUT Best to put separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.) in seperate .mag files (eg. af.mag, thermal.mag, etc.) Format of SIO .mag files: Spec Treat CSD Intensity Declination Inclination [optional metadata string] Spec: specimen name Treat: treatment step XXX T in Centigrade XXX AF in mT for special experiments: Thellier: XXX.0 first zero field step XXX.1 first in field step [XXX.0 and XXX.1 can be done in any order] XXX.2 second in-field step at lower temperature (pTRM check) XXX.3 second zero-field step after infield (pTRM check step) XXX.3 MUST be done in this order [XXX.0, XXX.1 [optional XXX.2] XXX.3] AARM: X.00 baseline step (AF in zero bias field - high peak field) X.1 ARM step (in field step) where X is the step number in the 15 position scheme (see Appendix to Lecture 13 - http://magician.ucsd.edu/Essentials_2) ATRM: X.00 optional baseline X.1 ATRM step (+X) X.2 ATRM step (+Y) X.3 ATRM step (+Z) X.4 ATRM step (-X) X.5 ATRM step (-Y) X.6 ATRM step (-Z) X.7 optional alteration check (+X) TRM: XXX.YYY XXX is temperature step of total TRM YYY is dc field in microtesla Intensity assumed to be total moment in 10^3 Am^2 (emu) Declination: Declination in specimen coordinate system Inclination: Declination in specimen coordinate system Optional metatdata string: mm/dd/yy;hh:mm;[dC,mT];xx.xx;UNITS;USER;INST;NMEAS hh in 24 hours. dC or mT units of treatment XXX (see Treat above) for thermal or AF respectively xx.xxx DC field UNITS of DC field (microT, mT) INST: instrument code, number of axes, number of positions (e.g., G34 is 2G, three axes, measured in four positions) NMEAS: number of measurements in a single position (1,3,200...)

Response:
def main(command_line=True, **kwargs):
    """
    NAME
        sio_magic.py

    DESCRIPTION
        converts SIO .mag format files to magic_measurements format files

    SYNTAX
        sio_magic.py [command line options]

    OPTIONS
        -h: prints the help message and quits.
        -usr USER:   identify user, default is ""
        -f FILE: specify .mag format input file, required
        -fsa SAMPFILE : specify er_samples.txt file relating samples, site and locations names,default is none -- values in SAMPFILE will override selections for -loc (location), -spc (designate specimen), and -ncn (sample-site naming convention)
        -F FILE: specify output file, default is magic_measurements.txt
        -Fsy: specify er_synthetics file, default is er_sythetics.txt
        -LP [colon delimited list of protocols, include all that apply]
            AF:  af demag
            T: thermal including thellier but not trm acquisition
            S: Shaw method
            I: IRM (acquisition)
            I3d: 3D IRM experiment
            N: NRM only
            TRM: trm acquisition
            ANI: anisotropy experiment
            D: double AF demag
            G: triple AF demag (GRM protocol)
            CR: cooling rate experiment.
                The treatment coding of the measurement file should be: XXX.00,XXX.10, XXX.20 ...XX.70 etc. (XXX.00 is optional)
                where XXX in the temperature and .10,.20... are running numbers of the cooling rates steps.
                XXX.00 is optional zerofield baseline. XXX.70 is alteration check.
                syntax in sio_magic is: -LP CR xxx,yyy,zzz,..... xxx -A
                where xxx, yyy, zzz...xxx  are cooling time in [K/minutes], seperated by comma, ordered at the same order as XXX.10,XXX.20 ...XX.70
                if you use a zerofield step then no need to specify the cooling rate for the zerofield
                It is important to add to the command line the -A option so the measurements will not be averaged.
                But users need to make sure that there are no duplicate measurements in the file
        -V [1,2,3] units of IRM field in volts using ASC coil #1,2 or 3
        -spc NUM : specify number of characters to designate a  specimen, default = 0
        -loc LOCNAME : specify location/study name, must have either LOCNAME or SAMPFILE or be a synthetic
        -syn INST TYPE:  sets these specimens as synthetics created at institution INST and of type TYPE
        -ins INST : specify which demag instrument was used (e.g, SIO-Suzy or SIO-Odette),default is ""
        -dc B PHI THETA: dc lab field (in micro tesla) and phi,theta, default is none
              NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment
        -ac B : peak AF field (in mT) for ARM acquisition, default is none
        -ncn NCON:  specify naming convention: default is #1 below
        -A: don't average replicate measurements
       Sample naming convention:
            [1] XXXXY: where XXXX is an arbitrary length site designation and Y
                is the single character sample designation.  e.g., TG001a is the
                first sample from site TG001.    [default]
            [2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
            [3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
            [4-Z] XXXX[YYY]:  YYY is sample designation with Z characters from site XXX
            [5] site name same as sample
            [6] site is entered under a separate column NOT CURRENTLY SUPPORTED
            [7-Z] [XXXX]YYY:  XXXX is site designation with Z characters with sample name XXXXYYYY
            NB: all others you will have to customize your self
                 or e-mail ltauxe@ucsd.edu for help.

            [8] synthetic - has no site name
            [9] ODP naming convention
    INPUT
        Best to put separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.) in
           seperate .mag files (eg. af.mag, thermal.mag, etc.)

        Format of SIO .mag files:
        Spec Treat CSD Intensity Declination Inclination [optional metadata string]

        Spec: specimen name
        Treat:  treatment step
            XXX T in Centigrade
            XXX AF in mT
            for special experiments:
              Thellier:
                XXX.0  first zero field step
                XXX.1  first in field step [XXX.0 and XXX.1 can be done in any order]
                XXX.2  second in-field step at lower temperature (pTRM check)
                XXX.3  second zero-field step after infield (pTRM check step)
                       XXX.3 MUST be done in this order [XXX.0, XXX.1 [optional XXX.2] XXX.3]
              AARM:
                X.00  baseline step (AF in zero bias field - high peak field)
                X.1   ARM step (in field step)  where
                   X is the step number in the 15 position scheme
                      (see Appendix to Lecture 13 - http://magician.ucsd.edu/Essentials_2)
              ATRM:
                X.00 optional baseline
                X.1 ATRM step (+X)
                X.2 ATRM step (+Y)
                X.3 ATRM step (+Z)
                X.4 ATRM step (-X)
                X.5 ATRM step (-Y)
                X.6 ATRM step (-Z)
                X.7 optional alteration check (+X)

              TRM:
                XXX.YYY  XXX is temperature step of total TRM
                         YYY is dc field in microtesla

         Intensity assumed to be total moment in 10^3 Am^2 (emu)
         Declination:  Declination in specimen coordinate system
         Inclination:  Declination in specimen coordinate system

         Optional metatdata string:  mm/dd/yy;hh:mm;[dC,mT];xx.xx;UNITS;USER;INST;NMEAS
             hh in 24 hours.
             dC or mT units of treatment XXX (see Treat above) for thermal or AF respectively
             xx.xxx   DC field
             UNITS of DC field (microT, mT)
             INST:  instrument code, number of axes, number of positions (e.g., G34 is 2G, three axes,
                    measured in four positions)
             NMEAS: number of measurements in a single position (1,3,200...)

    """
    # initialize some stuff
    mag_file = None
    codelist = None
    infile_type="mag"
    noave=0
    methcode,inst="LP-NO",""
    phi,theta,peakfield,labfield=0,0,0,0
    pTRM,MD,samp_con,Z=0,0,'1',1
    dec=[315,225,180,135,45,90,270,270,270,90,180,180,0,0,0]
    inc=[0,0,0,0,0,-45,-45,0,45,45,45,-45,-90,-45,45]
    tdec=[0,90,0,180,270,0,0,90,0]
    tinc=[0,0,90,0,0,-90,0,0,90]
    missing=1
    demag="N"
    er_location_name=""
    citation='This study'
    args=sys.argv
    fmt='old'
    syn=0
    synfile='er_synthetics.txt'
    samp_infile,Samps='',[]
    trm=0
    irm=0
    specnum=0
    coil=""
    mag_file=""
#
# get command line arguments
#
    meas_file="magic_measurements.txt"
    user=""
    if not command_line:
        user = kwargs.get('user', '')
        meas_file = kwargs.get('meas_file', '')
        syn_file = kwargs.get('syn_file', '')
        mag_file = kwargs.get('mag_file', '')
        labfield = kwargs.get('labfield', '')
        if labfield:
            labfield = float(labfield) *1e-6
        else:
            labfield = 0
        phi = kwargs.get('phi', 0)
        if phi:
            phi = float(phi)
        else:
            phi = 0
        theta = kwargs.get('theta', 0)
        if theta:
            theta=float(theta)
        else:
            theta = 0
        peakfield = kwargs.get('peakfield', 0)
        if peakfield:
            peakfield=float(peakfield) *1e-3
        else:
            peakfield = 0
        specnum = kwargs.get('specnum', 0)
        samp_con = kwargs.get('samp_con', '1')
        er_location_name = kwargs.get('er_location_name', '')
        samp_infile = kwargs.get('samp_infile', '')
        syn = kwargs.get('syn', 0)
        institution = kwargs.get('institution', '')
        syntype = kwargs.get('syntype', '')
        inst = kwargs.get('inst', '')
        noave = kwargs.get('noave', 0)
        codelist = kwargs.get('codelist', '')
        coil = kwargs.get('coil', '')
        cooling_rates = kwargs.get('cooling_rates', '')
    if command_line:
        if "-h" in args:
            print(main.__doc__)
            return False
        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 '-Fsy' in args:
            ind=args.index("-Fsy")
            synfile=args[ind+1]
        if '-f' in args:
            ind=args.index("-f")
            mag_file=args[ind+1]
        if "-dc" in args:
            ind=args.index("-dc")
            labfield=float(args[ind+1])*1e-6
            phi=float(args[ind+2])
            theta=float(args[ind+3])
        if "-ac" in args:
            ind=args.index("-ac")
            peakfield=float(args[ind+1])*1e-3
        if "-spc" in args:
            ind=args.index("-spc")
            specnum=int(args[ind+1])
        if "-loc" in args:
            ind=args.index("-loc")
            er_location_name=args[ind+1]
        if "-fsa" in args:
            ind=args.index("-fsa")
            samp_infile = args[ind+1]
        if '-syn' in args:
            syn=1
            ind=args.index("-syn")
            institution=args[ind+1]
            syntype=args[ind+2]
            if '-fsy' in args:
                ind=args.index("-fsy")
                synfile=args[ind+1]
        if "-ins" in args:
            ind=args.index("-ins")
            inst=args[ind+1]
        if "-A" in args: noave=1
        if "-ncn" in args:
            ind=args.index("-ncn")
            samp_con=sys.argv[ind+1]
        if '-LP' in args:
            ind=args.index("-LP")
            codelist=args[ind+1]

        if "-V" in args:
            ind=args.index("-V")
            coil=args[ind+1]

    # make sure all initial values are correctly set up (whether they come from the command line or a GUI)
    if samp_infile:
        Samps, file_type = pmag.magic_read(samp_infile)
    if coil:
        coil = str(coil)
        methcode="LP-IRM"
        irmunits = "V"
        if coil not in ["1","2","3"]:
            print(main.__doc__)
            print('not a valid coil specification')
            return False, '{} is not a valid coil specification'.format(coil)
    if mag_file:
        try:
            #with open(mag_file,'r') as finput:
            #    lines = finput.readlines()
            lines=pmag.open_file(mag_file)
        except:
            print("bad mag file name")
            return False, "bad mag file name"
    if not mag_file:
        print(main.__doc__)
        print("mag_file field is required option")
        return False, "mag_file field is required option"
    if specnum!=0:
        specnum=-specnum
    #print 'samp_con:', samp_con
    if samp_con:
        if "4" == samp_con[0]:
            if "-" not in samp_con:
                print("naming convention option [4] must be in form 4-Z where Z is an integer")
                print('---------------')
                return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
            else:
                Z=samp_con.split("-")[1]
                samp_con="4"
        if "7" == samp_con[0]:
            if "-" not in samp_con:
                print("option [7] must be in form 7-Z where Z is an integer")
                return False, "option [7] must be in form 7-Z where Z is an integer"
            else:
                Z=samp_con.split("-")[1]
                samp_con="7"

    if codelist:
        codes=codelist.split(':')
        if "AF" in codes:
            demag='AF'
            if'-dc' not in args: methcode="LT-AF-Z"
            if'-dc' in args: methcode="LT-AF-I"
        if "T" in codes:
            demag="T"
            if '-dc' not in args: methcode="LT-T-Z"
            if '-dc' in args: methcode="LT-T-I"
        if "I" in codes:
            methcode="LP-IRM"
            irmunits="mT"
        if "I3d" in codes:
            methcode="LT-T-Z:LP-IRM-3D"
        if "S" in codes:
            demag="S"
            methcode="LP-PI-TRM:LP-PI-ALT-AFARM"
            trm_labfield=labfield
            ans=input("DC lab field for ARM step: [50uT] ")
            if ans=="":
                arm_labfield=50e-6
            else:
                arm_labfield=float(ans)*1e-6
            ans=input("temperature for total trm step: [600 C] ")
            if ans=="":
                trm_peakT=600+273 # convert to kelvin
            else:
                trm_peakT=float(ans)+273 # convert to kelvin
        if "G" in codes: methcode="LT-AF-G"
        if "D" in codes: methcode="LT-AF-D"
        if "TRM" in codes:
            demag="T"
            trm=1
        if "CR" in     codes:
            demag="T"
            cooling_rate_experiment=1
            if command_line:
                ind=args.index("CR")
                cooling_rates=args[ind+1]
                cooling_rates_list=cooling_rates.split(',')
            else:
                cooling_rates_list=str(cooling_rates).split(',')
    if demag=="T" and "ANI" in codes:
        methcode="LP-AN-TRM"
    if demag=="T" and "CR" in codes:
        methcode="LP-CR-TRM"
    if demag=="AF" and "ANI" in codes:
        methcode="LP-AN-ARM"
        if labfield==0: labfield=50e-6
        if peakfield==0: peakfield=.180
    SynRecs,MagRecs=[],[]
    version_num=pmag.get_version()

    ##################################

    if 1:
    #if infile_type=="SIO format":
        for line in lines:
            instcode=""
            if len(line)>2:
                SynRec={}
                MagRec={}
                MagRec['er_location_name']=er_location_name
                MagRec['magic_software_packages']=version_num
                MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
                MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
                MagRec["treatment_ac_field"]='0'
                MagRec["treatment_dc_field"]='0'
                MagRec["treatment_dc_field_phi"]='0'
                MagRec["treatment_dc_field_theta"]='0'
                meas_type="LT-NO"
                rec=line.split()
                if rec[1]==".00":rec[1]="0.00"
                treat=rec[1].split('.')
                if methcode=="LP-IRM":
                    if irmunits=='mT':
                        labfield=float(treat[0])*1e-3
                    else:
                        labfield=pmag.getfield(irmunits,coil,treat[0])
                    if rec[1][0]!="-":
                        phi,theta=0.,90.
                    else:
                        phi,theta=0.,-90.
                    meas_type="LT-IRM"
                    MagRec["treatment_dc_field"]='%8.3e'%(labfield)
                    MagRec["treatment_dc_field_phi"]='%7.1f'%(phi)
                    MagRec["treatment_dc_field_theta"]='%7.1f'%(theta)
                if len(rec)>6:
                  code1=rec[6].split(';') # break e.g., 10/15/02;7:45 indo date and time
                  if len(code1)==2: # old format with AM/PM
                    missing=0
                    code2=code1[0].split('/') # break date into mon/day/year
                    code3=rec[7].split(';') # break e.g., AM;C34;200  into time;instr/axes/measuring pos;number of measurements
                    yy=int(code2[2])
                    if yy <90:
                        yyyy=str(2000+yy)
                    else: yyyy=str(1900+yy)
                    mm=int(code2[0])
                    if mm<10:
                        mm="0"+str(mm)
                    else: mm=str(mm)
                    dd=int(code2[1])
                    if dd<10:
                        dd="0"+str(dd)
                    else: dd=str(dd)
                    time=code1[1].split(':')
                    hh=int(time[0])
                    if code3[0]=="PM":hh=hh+12
                    if hh<10:
                        hh="0"+str(hh)
                    else: hh=str(hh)
                    min=int(time[1])
                    if min<10:
                       min= "0"+str(min)
                    else: min=str(min)
                    MagRec["measurement_date"]=yyyy+":"+mm+":"+dd+":"+hh+":"+min+":00.00"
                    MagRec["measurement_time_zone"]='SAN'
                    if inst=="":
                        if code3[1][0]=='C':instcode='SIO-bubba'
                        if code3[1][0]=='G':instcode='SIO-flo'
                    else:
                        instcode=''
                    MagRec["measurement_positions"]=code3[1][2]
                  elif len(code1)>2: # newest format (cryo7 or later)
                    if "LP-AN-ARM" not in methcode:labfield=0
                    fmt='new'
                    date=code1[0].split('/') # break date into mon/day/year
                    yy=int(date[2])
                    if yy <90:
                        yyyy=str(2000+yy)
                    else: yyyy=str(1900+yy)
                    mm=int(date[0])
                    if mm<10:
                        mm="0"+str(mm)
                    else: mm=str(mm)
                    dd=int(date[1])
                    if dd<10:
                        dd="0"+str(dd)
                    else: dd=str(dd)
                    time=code1[1].split(':')
                    hh=int(time[0])
                    if hh<10:
                        hh="0"+str(hh)
                    else: hh=str(hh)
                    min=int(time[1])
                    if min<10:
                       min= "0"+str(min)
                    else:
                        min=str(min)
                    MagRec["measurement_date"]=yyyy+":"+mm+":"+dd+":"+hh+":"+min+":00.00"
                    MagRec["measurement_time_zone"]='SAN'
                    if inst=="":
                        if code1[6][0]=='C':
                            instcode='SIO-bubba'
                        if code1[6][0]=='G':
                            instcode='SIO-flo'
                    else:
                        instcode=''
                    if len(code1)>1:
                        MagRec["measurement_positions"]=code1[6][2]
                    else:
                        MagRec["measurement_positions"]=code1[7]   # takes care of awkward format with bubba and flo being different
                    if user=="":user=code1[5]
                    if code1[2][-1]=='C':
                        demag="T"
                        if code1[4]=='microT' and float(code1[3])!=0. and "LP-AN-ARM" not in methcode: labfield=float(code1[3])*1e-6
                    if code1[2]=='mT' and methcode!="LP-IRM":
                        demag="AF"
                        if code1[4]=='microT' and float(code1[3])!=0.: labfield=float(code1[3])*1e-6
                    if code1[4]=='microT' and labfield!=0. and meas_type!="LT-IRM":
                        phi,theta=0.,-90.
                        if demag=="T": meas_type="LT-T-I"
                        if demag=="AF": meas_type="LT-AF-I"
                        MagRec["treatment_dc_field"]='%8.3e'%(labfield)
                        MagRec["treatment_dc_field_phi"]='%7.1f'%(phi)
                        MagRec["treatment_dc_field_theta"]='%7.1f'%(theta)
                    if code1[4]=='' or labfield==0. and meas_type!="LT-IRM":
                        if demag=='T':meas_type="LT-T-Z"
                        if demag=="AF":meas_type="LT-AF-Z"
                        MagRec["treatment_dc_field"]='0'
                if syn==0:
                    MagRec["er_specimen_name"]=rec[0]
                    MagRec["er_synthetic_name"]=""
                    MagRec["er_site_name"]=""
                    if specnum!=0:
                        MagRec["er_sample_name"]=rec[0][:specnum]
                    else:
                        MagRec["er_sample_name"]=rec[0]
                    if samp_infile and Samps: # if samp_infile was provided AND yielded sample data
                        samp=pmag.get_dictitem(Samps,'er_sample_name',MagRec['er_sample_name'],'T')
                        if len(samp)>0:
                            MagRec["er_location_name"]=samp[0]["er_location_name"]
                            MagRec["er_site_name"]=samp[0]["er_site_name"]
                        else:
                            MagRec['er_location_name']=''
                            MagRec["er_site_name"]=''
                    elif int(samp_con)!=6:
                        site=pmag.parse_site(MagRec['er_sample_name'],samp_con,Z)
                        MagRec["er_site_name"]=site
                    if MagRec['er_site_name']=="":
                        print('No site name found for: ',MagRec['er_specimen_name'],MagRec['er_sample_name'])
                    if MagRec["er_location_name"]=="":
                        print('no location name for: ',MagRec["er_specimen_name"])
                else:
                    MagRec["er_specimen_name"]=rec[0]
                    if specnum!=0:
                        MagRec["er_sample_name"]=rec[0][:specnum]
                    else:
                        MagRec["er_sample_name"]=rec[0]
                    MagRec["er_site_name"]=""
                    MagRec["er_synthetic_name"]=MagRec["er_specimen_name"]
                    SynRec["er_synthetic_name"]=MagRec["er_specimen_name"]
                    site=pmag.parse_site(MagRec['er_sample_name'],samp_con,Z)
                    SynRec["synthetic_parent_sample"]=site
                    SynRec["er_citation_names"]="This study"
                    SynRec["synthetic_institution"]=institution
                    SynRec["synthetic_type"]=syntype
                    SynRecs.append(SynRec)
                if float(rec[1])==0:
                    pass
                elif demag=="AF":
                    if methcode != "LP-AN-ARM":
                        MagRec["treatment_ac_field"]='%8.3e' %(float(rec[1])*1e-3) # peak field in tesla
                        if meas_type=="LT-AF-Z": MagRec["treatment_dc_field"]='0'
                    else: # AARM experiment
                        if treat[1][0]=='0':
                            meas_type="LT-AF-Z:LP-AN-ARM:"
                            MagRec["treatment_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
                            MagRec["treatment_dc_field"]='%8.3e'%(0)
                            if labfield!=0 and methcode!="LP-AN-ARM": print("Warning - inconsistency in mag file with lab field - overriding file with 0")
                        else:
                            meas_type="LT-AF-I:LP-AN-ARM"
                            ipos=int(treat[0])-1
                            MagRec["treatment_dc_field_phi"]='%7.1f' %(dec[ipos])
                            MagRec["treatment_dc_field_theta"]='%7.1f'% (inc[ipos])
                            MagRec["treatment_dc_field"]='%8.3e'%(labfield)
                            MagRec["treatment_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
                elif demag=="T" and methcode == "LP-AN-TRM":
                    MagRec["treatment_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin
                    if treat[1][0]=='0':
                        meas_type="LT-T-Z:LP-AN-TRM"
                        MagRec["treatment_dc_field"]='%8.3e'%(0)
                        MagRec["treatment_dc_field_phi"]='0'
                        MagRec["treatment_dc_field_theta"]='0'
                    else:
                        MagRec["treatment_dc_field"]='%8.3e'%(labfield)
                        if treat[1][0]=='7': # alteration check as final measurement
                                meas_type="LT-PTRM-I:LP-AN-TRM"
                        else:
                                meas_type="LT-T-I:LP-AN-TRM"

                        # find the direction of the lab field in two ways:
                        # (1) using the treatment coding (XX.1=+x, XX.2=+y, XX.3=+z, XX.4=-x, XX.5=-y, XX.6=-z)
                        ipos_code=int(treat[1][0])-1
                        # (2) using the magnetization
                        DEC=float(rec[4])
                        INC=float(rec[5])
                        if INC < 45 and INC > -45:
                            if DEC>315  or DEC<45: ipos_guess=0
                            if DEC>45 and DEC<135: ipos_guess=1
                            if DEC>135 and DEC<225: ipos_guess=3
                            if DEC>225 and DEC<315: ipos_guess=4
                        else:
                            if INC >45: ipos_guess=2
                            if INC <-45: ipos_guess=5
                        # prefer the guess over the code
                        ipos=ipos_guess
                        MagRec["treatment_dc_field_phi"]='%7.1f' %(tdec[ipos])
                        MagRec["treatment_dc_field_theta"]='%7.1f'% (tinc[ipos])
                        # check it
                        if ipos_guess!=ipos_code and treat[1][0]!='7':
                            print("-E- ERROR: check specimen %s step %s, ATRM measurements, coding does not match the direction of the lab field!"%(rec[0],".".join(list(treat))))

                elif demag=="S": # Shaw experiment
                    if treat[1][1]=='0':
                        if  int(treat[0])!=0:
                            MagRec["treatment_ac_field"]='%8.3e' % (float(treat[0])*1e-3) # AF field in tesla
                            MagRec["treatment_dc_field"]='0'
                            meas_type="LT-AF-Z" # first AF
                        else:
                            meas_type="LT-NO"
                            MagRec["treatment_ac_field"]='0'
                            MagRec["treatment_dc_field"]='0'
                    elif treat[1][1]=='1':
                        if int(treat[0])==0:
                            MagRec["treatment_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
                            MagRec["treatment_dc_field"]='%8.3e'%(arm_labfield)
                            MagRec["treatment_dc_field_phi"]='%7.1f'%(phi)
                            MagRec["treatment_dc_field_theta"]='%7.1f'%(theta)
                            meas_type="LT-AF-I"
                        else:
                            MagRec["treatment_ac_field"]='%8.3e' % ( float(treat[0])*1e-3) # AF field in tesla
                            MagRec["treatment_dc_field"]='0'
                            meas_type="LT-AF-Z"
                    elif treat[1][1]=='2':
                        if int(treat[0])==0:
                            MagRec["treatment_ac_field"]='0'
                            MagRec["treatment_dc_field"]='%8.3e'%(trm_labfield)
                            MagRec["treatment_dc_field_phi"]='%7.1f'%(phi)
                            MagRec["treatment_dc_field_theta"]='%7.1f'%(theta)
                            MagRec["treatment_temp"]='%8.3e' % (trm_peakT)
                            meas_type="LT-T-I"
                        else:
                            MagRec["treatment_ac_field"]='%8.3e' % ( float(treat[0])*1e-3) # AF field in tesla
                            MagRec["treatment_dc_field"]='0'
                            meas_type="LT-AF-Z"
                    elif treat[1][1]=='3':
                        if int(treat[0])==0:
                            MagRec["treatment_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
                            MagRec["treatment_dc_field"]='%8.3e'%(arm_labfield)
                            MagRec["treatment_dc_field_phi"]='%7.1f'%(phi)
                            MagRec["treatment_dc_field_theta"]='%7.1f'%(theta)
                            meas_type="LT-AF-I"
                        else:
                            MagRec["treatment_ac_field"]='%8.3e' % ( float(treat[0])*1e-3) # AF field in tesla
                            MagRec["treatment_dc_field"]='0'
                            meas_type="LT-AF-Z"

                # Cooling rate experient # added by rshaar
                elif demag=="T" and methcode == "LP-CR-TRM":

                    MagRec["treatment_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin
                    if treat[1][0]=='0':
                        meas_type="LT-T-Z:LP-CR-TRM"
                        MagRec["treatment_dc_field"]='%8.3e'%(0)
                        MagRec["treatment_dc_field_phi"]='0'
                        MagRec["treatment_dc_field_theta"]='0'
                    else:
                        MagRec["treatment_dc_field"]='%8.3e'%(labfield)
                        if treat[1][0]=='7': # alteration check as final measurement
                                meas_type="LT-PTRM-I:LP-CR-TRM"
                        else:
                                meas_type="LT-T-I:LP-CR-TRM"
                        MagRec["treatment_dc_field_phi"]='%7.1f' % (phi) # labfield phi
                        MagRec["treatment_dc_field_theta"]='%7.1f' % (theta) # labfield theta

                        indx=int(treat[1][0])-1
                        # alteration check matjed as 0.7 in the measurement file
                        if indx==6:
                           cooling_time= cooling_rates_list[-1]
                        else:
                           cooling_time=cooling_rates_list[indx]
                        MagRec["measurement_description"]="cooling_rate"+":"+cooling_time+":"+"K/min"

                elif demag!='N':
                  if len(treat)==1:treat.append('0')
                  MagRec["treatment_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin
                  if trm==0:  # demag=T and not trmaq
                    if treat[1][0]=='0':
                        meas_type="LT-T-Z"
                    else:
                        MagRec["treatment_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
                        MagRec["treatment_dc_field_phi"]='%7.1f' % (phi) # labfield phi
                        MagRec["treatment_dc_field_theta"]='%7.1f' % (theta) # labfield theta
                        if treat[1][0]=='1':meas_type="LT-T-I" # in-field thermal step
                        if treat[1][0]=='2':
                            meas_type="LT-PTRM-I" # pTRM check
                            pTRM=1
                        if treat[1][0]=='3':
                            MagRec["treatment_dc_field"]='0'  # this is a zero field step
                            meas_type="LT-PTRM-MD" # pTRM tail check
                  else:
                    labfield=float(treat[1])*1e-6
                    MagRec["treatment_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
                    MagRec["treatment_dc_field_phi"]='%7.1f' % (phi) # labfield phi
                    MagRec["treatment_dc_field_theta"]='%7.1f' % (theta) # labfield theta
                    meas_type="LT-T-I:LP-TRM" # trm acquisition experiment

                MagRec["measurement_csd"]=rec[2]
                MagRec["measurement_magn_moment"]='%10.3e'% (float(rec[3])*1e-3) # moment in Am^2 (from emu)
                MagRec["measurement_dec"]=rec[4]
                MagRec["measurement_inc"]=rec[5]
                MagRec["magic_instrument_codes"]=instcode
                MagRec["er_analyst_mail_names"]=user
                MagRec["er_citation_names"]=citation
                if "LP-IRM-3D" in methcode : meas_type=methcode
                #MagRec["magic_method_codes"]=methcode.strip(':')
                MagRec["magic_method_codes"]=meas_type
                MagRec["measurement_flag"]='g'
                MagRec["er_specimen_name"]=rec[0]
                if 'std' in rec[0]:
                    MagRec["measurement_standard"]='s'
                else:
                    MagRec["measurement_standard"]='u'
                MagRec["measurement_number"]='1'
                #print MagRec['treatment_temp']
                MagRecs.append(MagRec)
    MagOuts=pmag.measurements_methods(MagRecs,noave)
    pmag.magic_write(meas_file,MagOuts,'magic_measurements')
    print("results put in ",meas_file)
    if len(SynRecs)>0:
        pmag.magic_write(synfile,SynRecs,'er_synthetics')
        print("synthetics put in ",synfile)
    return True, meas_file


Instruction:
Explain what the following Python 3 code does
def fitcircle(n, x, y):
# n points, x points, y points
    """c Fit circle to arbitrary number of x,y pairs, based on the
c modified least squares method of Umback and Jones (2000),
c IEEE Transactions on Instrumentation and Measurement."""
    # adding in normalize vectors step
    #x = numpy.array(x) / max(x)
    #y = numpy.array(y) / max(y)
    #

    sx, sx2, sx3, sy, sy2, sy3, sxy, sxy2, syx2 = (0,) * 9
    print(type(sx), sx)
    for i in range(n):
        sx = sx + x[i]
        sx2 = sx2 + x[i]**2
        sx3 = sx3 + x[i]**3
        sy = sy + y[i]
        sy2 = sy2 + y[i]**2
        sy3 = sy3 + y[i]**3
        sxy = sxy + x[i] * y[i]
        sxy2 = sxy2 + x[i] * y[i]**2
        syx2 = syx2 + y[i] * x[i]**2

    A = n * sx2 - sx**2
    B = n * sxy - sx*sy
    C = n * sy2 - sy**2
    D = 0.5 * (n * sxy2 - sx * sy2 + n * sx3 - sx * sx2)
    E = 0.5 * (n * syx2 - sy * sx2 + n * sy3 - sy * sy2)
    # values check out up to here

    xo = old_div((D * C - B * E), (A * C - B**2))
    yo = old_div((A * E - B * D), (A * C - B**2))
    print("xo", xo)
    print("yo", yo)

    r = 0
    for z in range(n):
        r = r + old_div(numpy.sqrt( (x[z]-xo)**2 + (y[z]-yo)**2 ), n)

    if xo <= numpy.mean(x) and yo <= numpy.mean(y):
        k = old_div(-1.,r)
    else:
        k = old_div(1.,r)

    SSE = lib_k.get_SSE(xo, yo, r, x, y)
    print("r", r)
    return k, xo, yo, SSE

Response:
c Fit circle to arbitrary number of x y pairs based on the
c modified least squares method of Umback and Jones


Instruction:
Write a Python 3 function for
naming vgp_di.py DESCRIPTION converts site latitude, longitude and pole latitude, longitude to declination, inclination SYNTAX vgp_di.py [-h] [-i] [-f FILE] [< filename] OPTIONS -h prints help message and quits -i interactive data entry -f FILE to specify file name on the command line INPUT for file entry: PLAT PLON SLAT SLON where: PLAT: pole latitude PLON: pole longitude (positive east) SLAT: site latitude (positive north) SLON: site longitude (positive east) OUTPUT D I where: D: declination I: inclination

Response:
def main():
    """
    NAME
        vgp_di.py
    DESCRIPTION
      converts site latitude, longitude and pole latitude, longitude to declination, inclination

    SYNTAX
        vgp_di.py [-h] [-i] [-f FILE] [< filename]

    OPTIONS
        -h prints help message and quits
        -i interactive data entry
        -f FILE to specify file name on the command line

    INPUT
      for file entry:
        PLAT PLON  SLAT SLON
      where:
         PLAT: pole latitude
         PLON: pole longitude (positive east)
         SLAT: site latitude (positive north)
         SLON: site longitude (positive east)

    OUTPUT
        D I
        where:
           D: declination
           I: inclination
    """
    if '-h' in sys.argv:
        print(main.__doc__)
        sys.exit()
    if '-i' in sys.argv: # if one is -i
        while 1:
            try:
                ans=input("Input Pole Latitude [positive north]: <cntrl-D to quit>  ")
                plat=float(ans)  # assign input to plat, after conversion to floating point
                ans=input("Input Pole Longitude [positive east]:  ")
                plon =float(ans)
                ans=input("Input Site Latitude:  ")
                slat =float(ans)
                ans=input("Input Site Longitude:  ")
                slong =float(ans)
                dec,inc=pmag.vgp_di(plat,plon,slat,slong)  # call vgp_di function from pmag module
                print('%7.1f %7.1f'%(dec,inc)) # print out returned stuff
            except EOFError:
                print("\n Good-bye\n")
                sys.exit()

    elif '-f' in sys.argv: # manual input of file name
        ind=sys.argv.index('-f')
        file=sys.argv[ind+1]
        f=open(file,'r')
        inp = f.readlines()  # read from standard inp
        for line in inp:   # read in the data (as string variable), line by line
            dec,inc= spitout(line)
    else:
        inp = sys.stdin.readlines()  # read from standard input
        for line in inp:   # read in the data (as string variable), line by line
            spitout(line)


Instruction:
How would you implement a function in Python 3 that
installs the user s do archive in a unix - style shell.

Response:
def unix_install():
    """
    Edits or creates .bashrc, .bash_profile, and .profile files in the users
    HOME directory in order to add your current directory (hopefully your
    PmagPy directory) and assorted lower directories in the PmagPy/programs
    directory to your PATH environment variable. It also adds the PmagPy and
    the PmagPy/programs directories to PYTHONPATH.
    """
    PmagPyDir = os.path.abspath(".")
    COMMAND = """\n
for d in %s/programs/*/ "%s/programs/"; do
  case ":$PATH:" in
    *":$d:"*) :;; # already there
    *) PMAGPATHS="$PMAGPATHS:$d";; # or PATH="$PATH:$new_entry"
  esac
done
export PYTHONPATH="$PYTHONPATH:%s:%s/programs/"
export PATH="$PATH:$PMAGPATHS" """ % (PmagPyDir, PmagPyDir, PmagPyDir, PmagPyDir)
    frc_path = os.path.join(
        os.environ["HOME"], ".bashrc")  # not recommended, but hey it freaking works
    fbprof_path = os.path.join(os.environ["HOME"], ".bash_profile")
    fprof_path = os.path.join(os.environ["HOME"], ".profile")
    all_paths = [frc_path, fbprof_path, fprof_path]

    for f_path in all_paths:
        open_type = 'a'
        if not os.path.isfile(f_path):
            open_type = 'w+'
            fout = open(f_path, open_type)
            fout.write(COMMAND)
            fout.close()
        else:
            fin = open(f_path, 'r')
            current_f = fin.read()
            fin.close()
            if COMMAND not in current_f:
                fout = open(f_path, open_type)
                fout.write(COMMAND)
                fout.close()

    print("Install complete. Please restart the shell to complete install.\nIf you are seeing strange or non-existent paths in your PATH or PYTHONPATH variable please manually check your .bashrc, .bash_profile, and .profile or attempt to reinstall.")


Instruction:
Can you create a Python 3 function that
installs the given Python file into the Windows environment.

Response:
def windows_install(path_to_python=""):
    """
    Sets the .py extension to be associated with the ftype Python which is
    then set to the python.exe you provide in the path_to_python variable or
    after the -p flag if run as a script. Once the python environment is set
    up the function proceeds to set PATH and PYTHONPATH using setx.

    Parameters
    ----------
    path_to_python : the path the python.exe you want windows to execute when
    running .py files
    """
    if not path_to_python:
        print("Please enter the path to your python.exe you wish Windows to use to run python files. If you do not, this script will not be able to set up a full python environment in Windows. If you already have a python environment set up in Windows such that you can run python scripts from command prompt with just a file name then ignore this message. Otherwise, you will need to run dev_setup.py again with the command line option '-p' followed by the correct full path to python.\nRun dev_setup.py with the -h flag for more details")
        print("Would you like to continue? [y/N] ")
        ans = input()
        if ans == 'y':
            pass
        else:
            return

    # be sure to add python.exe if the user forgets to include the file name
    if os.path.isdir(path_to_python):
        path_to_python = os.path.join(path_to_python, "python.exe")
    if not os.path.isfile(path_to_python):
        print("The path to python provided is not a full path to the python.exe file or this path does not exist, was given %s.\nPlease run again with the command line option '-p' followed by the correct full path to python.\nRun dev_setup.py with the -h flag for more details" % path_to_python)
        return

    # make windows associate .py with python
    subprocess.check_call('assoc .py=Python', shell=True)
    subprocess.check_call('ftype Python=%s ' %
                          path_to_python + '"%1" %*', shell=True)

    PmagPyDir = os.path.abspath(".")
    ProgramsDir = os.path.join(PmagPyDir, 'programs')
    dirs_to_add = [ProgramsDir]
    for d in next(os.walk(ProgramsDir))[1]:
        dirs_to_add.append(os.path.join(ProgramsDir, d))
    path = str(subprocess.check_output('echo %PATH%', shell=True)).strip('\n')
    if "PATH" in path:
        path = ''
    pypath = str(subprocess.check_output(
        'echo %PYTHONPATH%', shell=True)).strip('\n')
    if "PYTHONPATH" in pypath:
        pypath = PmagPyDir + ';' + ProgramsDir
    else:
        pypath += ';' + PmagPyDir + ';' + ProgramsDir
    for d_add in dirs_to_add:
        path += ';' + d_add
    unique_path_list = []
    for p in path.split(';'):
        p = p.replace('"', '')
        if p not in unique_path_list:
            unique_path_list.append(p)
    unique_pypath_list = []
    for p in pypath.split(';'):
        p = p.replace('"', '')
        if p not in unique_pypath_list:
            unique_pypath_list.append(p)
    path = functools.reduce(lambda x, y: x + ';' + y, unique_path_list)
    pypath = functools.reduce(lambda x, y: x + ';' + y, unique_pypath_list)
    print('setx PATH "%s"' % path)
    subprocess.call('setx PATH "%s"' % path, shell=True)
    print('setx PYTHONPATH "%s"' % pypath)
    subprocess.call('setx PYTHONPATH "%s"' % (pypath), shell=True)

    print("Install complete. Please restart the command prompt to complete install")


Instruction:
How would you explain what the following Python 3 function does
def main():
    do_help = pmag.get_flag_arg_from_sys('-h')
    if do_help:
        print(main.__doc__)
        return False
    res_file = pmag.get_named_arg('-f', 'pmag_results.txt')
    crit_file = pmag.get_named_arg('-fcr', '')
    spec_file = pmag.get_named_arg('-fsp', '')
    age_file = pmag.get_named_arg('-fa', '')
    grade = pmag.get_flag_arg_from_sys('-g')
    latex = pmag.get_flag_arg_from_sys('-tex')
    WD = pmag.get_named_arg('-WD', os.getcwd())
    ipmag.pmag_results_extract(res_file, crit_file, spec_file, age_file, latex, grade, WD)

Response: main function for pmag_results_extract. py


Instruction:
Explain what the following Python 3 code does
def main():
    dir_path='.'
    tspec="thellier_specimens.txt"
    aspec="AC_specimens.txt"
    ofile="TorAC_specimens.txt"
    critfile="pmag_criteria.txt"
    ACSamplist,Samplist,sigmin=[],[],10000
    GoodSamps,SpecOuts=[],[]
# get arguments from command line
    if '-h' in sys.argv:
        print(main.__doc__)
        sys.exit()
    if '-fu' in sys.argv:
        ind=sys.argv.index('-fu')
        tspec=sys.argv[ind+1]
    if '-fc' in sys.argv:
        ind=sys.argv.index('-fc')
        aspec=sys.argv[ind+1]
    if '-F' in sys.argv:
        ind=sys.argv.index('-F')
        ofile=sys.argv[ind+1]
    if '-WD' in sys.argv:
        ind=sys.argv.index('-WD')
        dir_path=sys.argv[ind+1]

    # read in pmag_specimens file
    tspec=dir_path+'/'+tspec
    aspec=dir_path+'/'+aspec
    ofile=dir_path+'/'+ofile
    Specs,file_type=pmag.magic_read(tspec)
    Specs,file_type=pmag.magic_read(tspec)
    Speclist=pmag.get_specs(Specs)
    ACSpecs,file_type=pmag.magic_read(aspec)
    ACspeclist=pmag.get_specs(ACSpecs)
    for spec in Specs:
            if spec["er_sample_name"] not in Samplist:Samplist.append(spec["er_sample_name"])
    for spec in ACSpecs:
            if spec["er_sample_name"] not in ACSamplist:ACSamplist.append(spec["er_sample_name"])
    #
    for samp in Samplist:
        useAC,Ints,ACInts,GoodSpecs,AC,UC=0,[],[],[],[],[]
        for spec in Specs:
            if spec["er_sample_name"].lower()==samp.lower():
                    UC.append(spec)
        if samp in ACSamplist:
            for spec in ACSpecs:
                if spec["er_sample_name"].lower()==samp.lower():
                        AC.append(spec)
        if len(AC)>0:
            AClist=[]
            for spec in AC:
                SpecOuts.append(spec)
                AClist.append(spec['er_specimen_name'])
                print('using AC: ',spec['er_specimen_name'],'%7.1f'%(1e6*float(spec['specimen_int'])))
            for spec in UC:
                if spec['er_specimen_name'] not in AClist:
                   SpecOuts.append(spec)
#                   print 'using UC: ',spec['er_specimen_name'],'%7.1f'%(1e6*float(spec['specimen_int']))
        else:
            for spec in UC:
                SpecOuts.append(spec)
#                print 'using UC: ',spec['er_specimen_name'],'%7.1f'%(1e6*float(spec['specimen_int']))
    SpecOuts,keys=pmag.fillkeys(SpecOuts)
    pmag.magic_write(ofile,SpecOuts,'pmag_specimens')
    print('thellier data assessed for AC correction put in ', ofile)

Response: get an anisotropy corrected data and replace it with an anisotropy corrected data and create a new one


Instruction:
Make a summary of the following Python 3 code
def check_specimen_PI_criteria(pars,acceptance_criteria):
    '''
    # Check if specimen pass Acceptance criteria
    '''
    #if 'pars' not in self.Data[specimen].kes():
    #    return

    pars['specimen_fail_criteria']=[]
    for crit in list(acceptance_criteria.keys()):
        if crit not in list(pars.keys()):
            continue
        if acceptance_criteria[crit]['value']==-999:
            continue
        if acceptance_criteria[crit]['category']!='IE-SPEC':
            continue
        cutoff_value=acceptance_criteria[crit]['value']
        if crit=='specimen_scat':
            if pars["specimen_scat"] in ["Fail",'b',0,'0','FALSE',"False",False,"f"]:
                pars['specimen_fail_criteria'].append('specimen_scat')
        elif crit=='specimen_k' or crit=='specimen_k_prime':
            if abs(pars[crit])>cutoff_value:
                pars['specimen_fail_criteria'].append(crit)
        # high threshold value:
        elif acceptance_criteria[crit]['threshold_type']=="high":
            if pars[crit]>cutoff_value:
                pars['specimen_fail_criteria'].append(crit)
        elif acceptance_criteria[crit]['threshold_type']=="low":
            if pars[crit]<cutoff_value:
                pars['specimen_fail_criteria'].append(crit)
    return pars

Response: Check if specimen pass Acceptance criteria


Instruction:
Write a Python 3 script to
name dia_vgp.py DESCRIPTION converts declination inclination alpha95 to virtual geomagnetic pole, dp and dm SYNTAX dia_vgp.py [-h] [-i] [-f FILE] [< filename] OPTIONS -h prints help message and quits -i interactive data entry -f FILE to specify file name on the command line INPUT for file entry: D I A95 SLAT SLON where: D: declination I: inclination A95: alpha_95 SLAT: site latitude (positive north) SLON: site longitude (positive east) OUTPUT PLON PLAT DP DM where: PLAT: pole latitude PLON: pole longitude (positive east) DP: 95% confidence angle in parallel DM: 95% confidence angle in meridian

Response:
def main():
    """
    NAME
        dia_vgp.py
    DESCRIPTION
      converts declination inclination alpha95 to virtual geomagnetic pole, dp and dm

    SYNTAX
        dia_vgp.py [-h] [-i] [-f FILE] [< filename]

    OPTIONS
        -h prints help message and quits
        -i interactive data entry
        -f FILE to specify file name on the command line

    INPUT
      for file entry:
        D I A95 SLAT SLON
      where:
         D: declination
         I: inclination
         A95: alpha_95
         SLAT: site latitude (positive north)
         SLON: site longitude (positive east)

    OUTPUT
        PLON PLAT DP DM
        where:
             PLAT: pole latitude
             PLON: pole longitude (positive east)
             DP: 95% confidence angle in parallel
             DM: 95% confidence angle in meridian
    """
    if '-h' in sys.argv:
        print(main.__doc__)
        sys.exit()
    if '-i' in sys.argv: # if one is -i
        while 1:
            try:
                ans=input("Input Declination: <cntrl-D to quit>  ")
                Dec=float(ans)  # assign input to Dec, after conversion to floating point
                ans=input("Input Inclination:  ")
                Inc =float(ans)
                ans=input("Input Alpha 95:  ")
                a95 =float(ans)
                ans=input("Input Site Latitude:  ")
                slat =float(ans)
                ans=input("Input Site Longitude:  ")
                slong =float(ans)
                spitout(Dec,Inc,a95,slat,slong)  # call dia_vgp function from pmag module
                print('%7.1f %7.1f %7.1f %7.1f'%(plong,plat,dp,dm)) # print out returned stuff
            except:
                print("\n Good-bye\n")
                sys.exit()

    elif '-f' in sys.argv: # manual input of file name
        ind=sys.argv.index('-f')
        file=sys.argv[ind+1]
        f=open(file,'r')
        inlist  = []
        for line in f.readlines():
            inlist.append([])
            # loop over the elements, split by whitespace
            for el in line.split():
                inlist[-1].append(float(el))
        spitout(inlist)

    else:
        input = sys.stdin.readlines()  # read from standard input
        inlist  = []
        for line in input:   # read in the data (as string variable), line by line
            inlist.append([])
            # loop over the elements, split by whitespace
            for el in line.split():
                inlist[-1].append(float(el))
        spitout(inlist)


Instruction:
Can you tell what is the following Python 3 function doing
def main():
    fmt='svg'
    title=""
    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]
       X=numpy.loadtxt(file)
       file=sys.argv[ind+2]
       X2=numpy.loadtxt(file)
#    else:
#       X=numpy.loadtxt(sys.stdin,dtype=numpy.float)
    else:
       print('-f option required')
       print(main.__doc__)
       sys.exit()
    if '-fmt' in sys.argv:
       ind=sys.argv.index('-fmt')
       fmt=sys.argv[ind+1]
    if '-t' in sys.argv:
       ind=sys.argv.index('-t')
       title=sys.argv[ind+1]
    CDF={'X':1}
    pmagplotlib.plot_init(CDF['X'],5,5)
    pmagplotlib.plot_cdf(CDF['X'],X,'','r','')
    pmagplotlib.plot_cdf(CDF['X'],X2,title,'b','')
    D,p=scipy.stats.ks_2samp(X,X2)
    if p>=.05:
        print(D,p,' not rejected at 95%')
    else:
        print(D,p,' rejected at 95%')
    pmagplotlib.draw_figs(CDF)
    ans= input('S[a]ve  plot, <Return> to quit ')
    if ans=='a':
        files={'X':'CDF_.'+fmt}
        pmagplotlib.save_plots(CDF,files)

Response:
NAME
        plot_2cdfs.py

    DESCRIPTION
        makes plots of cdfs of data in input file

    SYNTAX
        plot_2cdfs.py [-h][command line options]

    OPTIONS
        -h prints help message and quits
        -f FILE1 FILE2
        -t TITLE
        -fmt [svg,eps,png,pdf,jpg..] specify format of output figure, default is svg


Instruction:
Can you generate the documentation for the following Python 3 function
def main():
    if '-h' in sys.argv:
        print(main.__doc__)
        sys.exit()
    if len(sys.argv) <= 1:
        print(main.__doc__)
        print('you must supply a file name')
        sys.exit()
    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 = pmag.get_named_arg("-f", "measurements.txt")
    dir_path = pmag.get_named_arg("-WD", ".")
    in_file = pmag.resolve_file_name(in_file, dir_path)
    data_model = pmag.get_named_arg("-DM", 3)
    data_model = int(float(data_model))
    fmt = pmag.get_named_arg("-fmt", "svg")
    if '-N' in sys.argv:
        norm = 0  # don't normalize
    if '-sav' in sys.argv:
        plot = 1  # silently save and quit
    else:
        plot = 0 # generate plots
    print(in_file)
    # read in data
    PmagRecs, file_type = pmag.magic_read(in_file)
    if data_model == 2 and file_type != "magic_measurements":
        print('bad input file', file_type)
        sys.exit()
    if data_model == 3 and file_type != "measurements":
        print('bad input file', file_type)
        sys.exit()

    if data_model == 2:
        meth_code_col = 'magic_method_codes'
        spec_col = 'er_specimen_name'
        dec_col = "measurement_dec"
        inc_col = 'measurement_inc'
        moment_col = 'measurement_magn_moment'
        temp_col = 'treatment_temp'
    else:
        meth_code_col = 'method_codes'
        spec_col = 'specimen'
        dec_col = 'dir_dec'
        inc_col = 'dir_inc'
        moment_col = 'magn_moment'
        temp_col = "treat_temp"

    PmagRecs = pmag.get_dictitem(
        PmagRecs, meth_code_col, 'LP-IRM-3D', 'has')  # get all 3D IRM records

    if len(PmagRecs) == 0:
        print('no records found with the method code LP-IRM-3D')
        sys.exit()

    specs = pmag.get_dictkey(PmagRecs, spec_col, '')
    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, spec_col, spc, 'T')  # get all this one's data

        DIMs, Temps = [], []
        for dat in specdata:  # step through the data
            DIMs.append([float(dat[dec_col]), float(
                dat[inc_col]), float(dat[moment_col])])
            Temps.append(float(dat[temp_col])-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.plot_xy(FIG['lowrie'], Temps, abs(carts[0]) / nrm, sym='r-')
        pmagplotlib.plot_xy(FIG['lowrie'], Temps, abs(carts[0]) / nrm, sym='ro')  # X direction
        pmagplotlib.plot_xy(FIG['lowrie'], Temps, abs(carts[1]) / nrm, sym='c-')
        pmagplotlib.plot_xy(FIG['lowrie'], Temps, abs(carts[1]) / nrm, sym='cs')  # Y direction
        pmagplotlib.plot_xy(FIG['lowrie'], Temps, abs(carts[2]) / nrm, sym='k-')
        pmagplotlib.plot_xy(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.draw_figs(FIG)
            ans = input('S[a]ve figure? [q]uit, <return> to continue   ')
            if ans == 'a':
                pmagplotlib.save_plots(FIG, files)
            elif ans == 'q':
                sys.exit()
        else:
            pmagplotlib.save_plots(FIG, files)
        pmagplotlib.clearFIG(FIG['lowrie'])

Response: main function for the main function of the main function


Instruction:
Can you tell what is the following Python 3 function doing
def main():
    infile='pmag_specimens.txt'
    sampfile="er_samples.txt"
    outfile="er_samples.txt"
# get command line stuff
    if "-h" in sys.argv:
        print(main.__doc__)
        sys.exit()
    if '-fsp' in sys.argv:
        ind=sys.argv.index("-fsp")
        infile=sys.argv[ind+1]
    if '-fsm' in sys.argv:
        ind=sys.argv.index("-fsm")
        sampfile=sys.argv[ind+1]
    if '-F' in sys.argv:
        ind=sys.argv.index("-F")
        outfile=sys.argv[ind+1]
    if '-WD' in sys.argv:
        ind=sys.argv.index("-WD")
        dir_path=sys.argv[ind+1]
        infile=dir_path+'/'+infile
        sampfile=dir_path+'/'+sampfile
        outfile=dir_path+'/'+outfile
# now do re-ordering
    pmag.ReorderSamples(infile,sampfile,outfile)

Response:
NAME
        reorder_samples.py

    DESCRIPTION
        takes specimen file and reorders sample file with selected orientation methods placed first

    SYNTAX
        reorder_samples.py [command line options]

    OPTIONS
        -h prints help message and quits
        -fsp: specimen input pmag_specimens format file, default is "pmag_specimens.txt"
        -fsm: sample input er_samples format file, default is "er_samples.txt"
        -F: output er_samples format file, default is "er_samples.txt"
    OUPUT
        writes re-ordered er_samples.txt file


Instruction:
Can you tell what is the following Python 3 function doing
def not_null(val, zero_as_null=True):

    def can_iter(x):
        """
        Returns True for a non-empty iterable
        """
        try:
            any(x)
            return True
        except TypeError:
            return False

    def not_empty(x):
        """
        Returns true if x has length
        """
        if len(x):
            return True
        return False

    def exists(x):
        """
        Returns true if x
        """
        if x:
            return True
        return False

    def is_nan(x):
        """
        Returns True if x is nan
        """
        try:
            if np.isnan(x):
                return True
        except TypeError:
            return False
        return False

    # return True iff you have a non-empty iterable
    # and False for an empty iterable (including an empty string)
    if can_iter(val):
        return not_empty(val)
    # if value is not iterable, return False for np.nan, None, 0, or False
    # & True for all else
    else:
        if is_nan(val):
            return False
        if not zero_as_null:
            if val == 0:
                return True
        return exists(val)

Response: Returns True if a value is not null or False otherwise.


Instruction:
Here you have a function in Python 3, explain what it does
def get_intensity_col(data):
    # possible intensity columns
    intlist = ['magn_moment', 'magn_volume', 'magn_mass','magn_uncal']
    # intensity columns that are in the data
    int_meths = [col_name for col_name in data.columns if col_name in intlist]
    # drop fully null columns
    data.dropna(axis='columns', how='all')
    # ignore columns with only blank values (including "")
    for col_name in int_meths[:]:
        if not data[col_name].any():
            int_meths.remove(col_name)
    if len(int_meths):
        if 'magn_moment' in int_meths:
            return 'magn_moment'
        return int_meths[0]
    return ""

Response: Returns the first intensity column that is in the dataframe and has data.


Instruction:
Explain what the following Python 3 code does
def add_sites_to_meas_table(dir_path):
    reqd_tables = ['measurements', 'specimens', 'samples', 'sites']
    con = Contribution(dir_path, read_tables=reqd_tables)
    # check that all required tables are available
    missing_tables = []
    for table in reqd_tables:
        if table not in con.tables:
            missing_tables.append(table)
    if missing_tables:
        return False, "You are missing {} tables".format(", ".join(missing_tables))

    # put sample column into the measurements table
    con.propagate_name_down('sample', 'measurements')
    # put site column into the measurements table
    con.propagate_name_down('site', 'measurements')
    # check that column propagation was successful
    if 'site' not in con.tables['measurements'].df.columns:
        return False, "Something went wrong with propagating sites down to the measurement level"
    return True, con.tables['measurements'].df

Response: Add site columns to the measurements table.


Instruction:
Make a summary of the following Python 3 code
def prep_for_intensity_plot(data, meth_code, dropna=(), reqd_cols=()):
    # initialize
    dropna = list(dropna)
    reqd_cols = list(reqd_cols)
    # get intensity column
    try:
        magn_col = get_intensity_col(data)
    except AttributeError:
        return False, "Could not get intensity method from data"
    # drop empty columns
    if magn_col not in dropna:
        dropna.append(magn_col)
    data = data.dropna(axis=0, subset=dropna)
    # add to reqd_cols list
    if 'method_codes' not in reqd_cols:
        reqd_cols.append('method_codes')
    if magn_col not in reqd_cols:
        reqd_cols.append(magn_col)
    # drop non reqd cols, make sure all reqd cols are present
    try:
        data = data[reqd_cols]
    except KeyError as ex:
        print(ex)
        missing = set(reqd_cols).difference(data.columns)
        return False, "missing these required columns: {}".format(", ".join(missing))
    # filter out records without the correct method code
    data = data[data['method_codes'].str.contains(meth_code).astype(bool)]
    return True, data

Response: Prepare the data for an intensity plot.


Instruction:
Can you implement a function in Python 3 that
takes a dataframe and string - i - fy a column of values.

Response:
def stringify_col(df, col_name):
    """
    Take a dataframe and string-i-fy a column of values.
    Turn nan/None into "" and all other values into strings.

    Parameters
    ----------
    df : dataframe
    col_name : string
    """
    df = df.copy()
    df[col_name] = df[col_name].fillna("")
    df[col_name] = df[col_name].astype(str)
    return df