Instruction:
How would you explain what the following Python 3 function does
def main():
    # initialize some parameters
    args = sys.argv

    if "-h" in args:
        print(main.__doc__)
        sys.exit()

    #meas_file = "aarm_measurements.txt"
    #rmag_anis = "arm_anisotropy.txt"
    #rmag_res = "aarm_results.txt"
    #
    # get name of file from command line
    #
    data_model_num = int(pmag.get_named_arg("-DM", 3))
    spec_file = pmag.get_named_arg("-Fsi", "specimens.txt")
    if data_model_num == 3:
        samp_file = pmag.get_named_arg("-fsa", "samples.txt")
    else:
        samp_file = pmag.get_named_arg("-fsa", "er_samples.txt")
    dir_path = pmag.get_named_arg('-WD', '.')
    input_dir_path = pmag.get_named_arg('-ID', '')
    infile = pmag.get_named_arg('-f', reqd=True)
    coord = pmag.get_named_arg('-crd', '-1')

    #if "-Fa" in args:
    #    ind = args.index("-Fa")
    #    rmag_anis = args[ind + 1]
    #if "-Fr" in args:
    #    ind = args.index("-Fr")
    #    rmag_res = args[ind + 1]
    ipmag.aarm_magic(infile, dir_path, input_dir_path,
            spec_file, samp_file, data_model_num,
            coord)

Response: This function is the main function for the ARMcrunch program. It is used to construct the best fit ARM tensor for the specified program.


Instruction:
Can you generate the documentation for the following Python 3 function
def main():
    FIG = {}  # plot dictionary
    FIG['demag'] = 1  # demag is figure 1
    in_file, plot_key, LT = 'magic_measurements.txt', 'er_location_name', "LT-AF-Z"
    XLP = ""
    norm = 1
    LT = 'LT-AF-Z'
    units, dmag_key = 'T', 'treatment_ac_field'
    plot = 0
    fmt = 'svg'
    if len(sys.argv) > 1:
        if '-h' in sys.argv:
            print(main.__doc__)
            sys.exit()
        if '-N' in sys.argv:
            norm = 0
        if '-sav' in sys.argv:
            plot = 1
        if '-f' in sys.argv:
            ind = sys.argv.index("-f")
            in_file = sys.argv[ind+1]
        if '-fmt' in sys.argv:
            ind = sys.argv.index("-fmt")
            fmt = sys.argv[ind+1]
        if '-obj' in sys.argv:
            ind = sys.argv.index('-obj')
            plot_by = sys.argv[ind+1]
            if plot_by == 'sit':
                plot_key = 'er_site_name'
            if plot_by == 'sam':
                plot_key = 'er_sample_name'
            if plot_by == 'spc':
                plot_key = 'er_specimen_name'
        if '-XLP' in sys.argv:
            ind = sys.argv.index("-XLP")
            XLP = sys.argv[ind+1]  # get lab protocol for excluding
        if '-LT' in sys.argv:
            ind = sys.argv.index("-LT")
            LT = 'LT-'+sys.argv[ind+1]+'-Z'  # get lab treatment for plotting
            if LT == 'LT-T-Z':
                units, dmag_key = 'K', 'treatment_temp'
            elif LT == 'LT-AF-Z':
                units, dmag_key = 'T', 'treatment_ac_field'
            elif LT == 'LT-M-Z':
                units, dmag_key = 'J', 'treatment_mw_energy'
            else:
                units = 'U'
    data, file_type = pmag.magic_read(in_file)
    sids = pmag.get_specs(data)
    pmagplotlib.plot_init(FIG['demag'], 5, 5)
    print(len(data), ' records read from ', in_file)
    #
    #
    # find desired intensity data
    #
    #
    plotlist, intlist = [], ['measurement_magnitude', 'measurement_magn_moment',
                             'measurement_magn_volume', 'measurement_magn_mass']
    IntMeths = []
    FixData = []
    for rec in data:
        meths = []
        methcodes = rec['magic_method_codes'].split(':')
        for meth in methcodes:
            meths.append(meth.strip())
        for key in rec.keys():
            if key in intlist and rec[key] != "":
                if key not in IntMeths:
                    IntMeths.append(key)
                if rec[plot_key] not in plotlist and LT in meths:
                    plotlist.append(rec[plot_key])
                if 'measurement_flag' not in rec.keys():
                    rec['measurement_flag'] = 'g'
                FixData.append(rec)
        plotlist.sort()
    if len(IntMeths) == 0:
        print('No intensity information found')
        sys.exit()
    data = FixData
    # plot first intensity method found - normalized to initial value anyway - doesn't matter which used
    int_key = IntMeths[0]
    for plt in plotlist:
        if plot == 0:
            print(plt, 'plotting by: ', plot_key)
        # fish out all the data for this type of plot
        PLTblock = pmag.get_dictitem(data, plot_key, plt, 'T')
        # fish out all the dmag for this experiment type
        PLTblock = pmag.get_dictitem(PLTblock, 'magic_method_codes', LT, 'has')
        # get all with this intensity key non-blank
        PLTblock = pmag.get_dictitem(PLTblock, int_key, '', 'F')
        if XLP != "":
            # reject data with XLP in method_code
            PLTblock = pmag.get_dictitem(
                PLTblock, 'magic_method_codes', XLP, 'not')
        if len(PLTblock) > 2:
            title = PLTblock[0][plot_key]
            spcs = []
            for rec in PLTblock:
                if rec['er_specimen_name'] not in spcs:
                    spcs.append(rec['er_specimen_name'])
            for spc in spcs:
                # plot specimen by specimen
                SPCblock = pmag.get_dictitem(
                    PLTblock, 'er_specimen_name', spc, 'T')
                INTblock = []
                for rec in SPCblock:
                    INTblock.append([float(rec[dmag_key]), 0, 0, float(
                        rec[int_key]), 1, rec['measurement_flag']])
                if len(INTblock) > 2:
                    pmagplotlib.plot_mag(
                        FIG['demag'], INTblock, title, 0, units, norm)
            if plot == 1:
                files = {}
                for key in FIG.keys():
                    files[key] = title+'_'+LT+'.'+fmt
                pmagplotlib.save_plots(FIG, files)
                sys.exit()
            else:
                pmagplotlib.draw_figs(FIG)
                ans = input(
                    " S[a]ve to save plot, [q]uit,  Return to continue:  ")
                if ans == 'q':
                    sys.exit()
                if ans == "a":
                    files = {}
                    for key in FIG.keys():
                        files[key] = title+'_'+LT+'.'+fmt
                    pmagplotlib.save_plots(FIG, files)
            pmagplotlib.clearFIG(FIG['demag'])

Response:
NAME dmag_magic2. py
AttributeNames dmag_magic2. py
AttributeNames dmag_magic2. py
AttributeNames dmag_magic2. py
AttributeNames dmag_magic2. py
AttributeNames dmag_magic2. py
AttributeNames dmag_magic2. py
AttributeNames dmag_magic2. py
AttributeNames dmag_magic2. py
AttributeNames dmag_magic2. py
AttributeNames dmag_magic2. py


Instruction:
Implement a Python 3 function for
naming uni_magic. py is the main function for the ipython - minispin. py script.

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

    DESCRIPTION
        converts the Yale minispin format to magic_measurements format files

    SYNTAX
        mini_magic.py [command line options]

    OPTIONS
        -h: prints the help message and quits.
        -usr USER:   identify user, default is ""
        -f FILE: specify input file, required
        -F FILE: specify output file, default is magic_measurements.txt
        -LP [colon delimited list of protocols, include all that apply]
            AF:  af demag
            T: thermal including thellier but not trm acquisition
        -A: don't average replicate measurements
        -vol: volume assumed for measurement in cm^3 (default 12 cc)
        -DM NUM: MagIC data model (2 or 3, default 3)

    INPUT
        Must put separate experiments (all AF, thermal,  etc.) in
           seperate files

        Format of Yale MINI files:
        LL-SI-SP_STEP, Declination, Inclination, Intensity (mA/m), X,Y,Z

    """
    args = sys.argv
    if "-h" in args:
        print(main.__doc__)
        sys.exit()
# initialize some stuff
    methcode = "LP-NO"
    demag = "N"

#
# get command line arguments
#
    data_model_num = int(float(pmag.get_named_arg("-DM", 3)))
    user = pmag.get_named_arg("-usr", "")
    dir_path = pmag.get_named_arg("-WD", ".")
    inst = pmag.get_named_arg("-inst", "")
    magfile = pmag.get_named_arg("-f", reqd=True)
    magfile = pmag.resolve_file_name(magfile, dir_path)
    if "-A" in args:
        noave = 1
    else:
        noave = 0

    if data_model_num == 2:
        meas_file = pmag.get_named_arg("-F", "magic_measurements.txt")
    else:
        meas_file = pmag.get_named_arg("-F", "measurements.txt")
    meas_file = pmag.resolve_file_name(meas_file, dir_path)
    volume = pmag.get_named_arg("-vol", 12) # assume a volume of 12 cc if not provided
    methcode = pmag.get_named_arg("-LP", "LP-NO")
    #ind = args.index("-LP")
    #codelist = args[ind+1]
    #codes = codelist.split(':')
    #if "AF" in codes:
    #    demag = 'AF'
    #    methcode = "LT-AF-Z"
    #if "T" in codes:
    #    demag = "T"

    convert.mini(magfile, dir_path, meas_file, data_model_num,
            volume, noave, inst, user, methcode)


Instruction:
Implement a Python 3 function for
naming customize_criteria.py NB: This program has been deprecated - use demag_gui or thellier_gui to customize acceptance criteria - OR pandas from within a jupyter notebook DESCRIPTION Allows user to specify acceptance criteria, saves them in pmag_criteria.txt SYNTAX customize_criteria.py [-h][command line options] OPTIONS -h prints help message and quits -f IFILE, reads in existing criteria -F OFILE, writes to pmag_criteria format file DEFAULTS IFILE: pmag_criteria.txt OFILE: pmag_criteria.txt OUTPUT creates a pmag_criteria.txt formatted output file

Response:
def main():
    """
    NAME
        customize_criteria.py
        NB:  This program has been deprecated - use demag_gui or thellier_gui
           to customize acceptance criteria - OR pandas from within a jupyter notebook

    DESCRIPTION
        Allows user to specify acceptance criteria, saves them in pmag_criteria.txt

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

    OPTIONS
        -h prints help message and quits
        -f IFILE, reads in existing criteria
        -F OFILE, writes to pmag_criteria format file

    DEFAULTS
         IFILE: pmag_criteria.txt
         OFILE: pmag_criteria.txt

    OUTPUT
        creates a pmag_criteria.txt formatted output file
    """
    infile,critout="","pmag_criteria.txt"
# parse command line options
    if  '-h' in sys.argv:
        print(main.__doc__)
        sys.exit()
    if '-f' in sys.argv:
        ind=sys.argv.index('-f')
        infile=sys.argv[ind+1]
        crit_data,file_type=pmag.magic_read(infile)
        if file_type!='pmag_criteria':
            print('bad input file')
            print(main.__doc__)
            sys.exit()
        print("Acceptance criteria read in from ", infile)
    if '-F' in sys.argv:
        ind=sys.argv.index('-F')
        critout=sys.argv[ind+1]
    Dcrit,Icrit,nocrit=0,0,0
    custom='1'
    crit=input(" [0] Use no acceptance criteria?\n [1] Use default criteria\n [2] customize criteria \n ")
    if crit=='0':
        print('Very very loose criteria saved in ',critout)
        crit_data=pmag.default_criteria(1)
        pmag.magic_write(critout,crit_data,'pmag_criteria')
        sys.exit()
    crit_data=pmag.default_criteria(0)
    if crit=='1':
        print('Default criteria saved in ',critout)
        pmag.magic_write(critout,crit_data,'pmag_criteria')
        sys.exit()
    CritRec=crit_data[0]
    crit_keys=list(CritRec.keys())
    crit_keys.sort()
    print("Enter new threshold value.\n Return to keep default.\n Leave blank to not use as a criterion\n ")
    for key in crit_keys:
        if key!='pmag_criteria_code' and key!='er_citation_names' and key!='criteria_definition' and CritRec[key]!="":
            print(key, CritRec[key])
            new=input('new value: ')
            if new != "": CritRec[key]=(new)
    pmag.magic_write(critout,[CritRec],'pmag_criteria')
    print("Criteria saved in pmag_criteria.txt")


Instruction:
Can you generate a brief explanation for the following Python 3 code
def get_DIR(self, WD=None):

        if "-WD" in sys.argv and FIRST_RUN:
            ind = sys.argv.index('-WD')
            self.WD = sys.argv[ind + 1]
        elif not WD:  # if no arg was passed in for WD, make a dialog to choose one
            dialog = wx.DirDialog(None, "Choose a directory:", defaultPath=self.currentDirectory,
                                  style=wx.DD_DEFAULT_STYLE | wx.DD_NEW_DIR_BUTTON | wx.DD_CHANGE_DIR)
            ok = self.show_dlg(dialog)
            if ok == wx.ID_OK:
                self.WD = dialog.GetPath()
            else:
                self.WD = os.getcwd()
            dialog.Destroy()
        self.WD = os.path.realpath(self.WD)
        # name measurement file
        if self.data_model == 3:
            meas_file = 'measurements.txt'
        else:
            meas_file = 'magic_measurements.txt'
        self.magic_file = os.path.join(self.WD, meas_file)
        # intialize GUI_log
        self.GUI_log = open(os.path.join(self.WD, "thellier_GUI.log"), 'w+')
        self.GUI_log.write("starting...\n")
        self.GUI_log.close()
        self.GUI_log = open(os.path.join(self.WD, "thellier_GUI.log"), 'a')
        os.chdir(self.WD)
        self.WD = os.getcwd()

Response: get a directory name


Instruction:
Write a Python 3 script to
build main frame of the main panel

Response:
def Main_Frame(self):
        """
        Build main frame od panel: buttons, etc.
        choose the first specimen and display data
        """

        #--------------------------------------------------------------------
        # initialize first specimen in list as current specimen
        #--------------------------------------------------------------------

        try:
            self.s = self.specimens[0]
        except:
            self.s = ""
            print("No specimens during UI build")

        #--------------------------------------------------------------------
        # create main panel in the right size
        #--------------------------------------------------------------------

        dw, dh = wx.DisplaySize()
        w, h = self.GetSize()
        r1 = dw / 1250.
        r2 = dw / 750.

        GUI_RESOLUTION = min(r1, r2, 1.3)
        if 'gui_resolution' in list(self.preferences.keys()):
            if float(self.preferences['gui_resolution']) != 1:
                self.GUI_RESOLUTION = float(
                    self.preferences['gui_resolution']) / 100
            else:
                self.GUI_RESOLUTION = min(r1, r2, 1.3)
        else:
            self.GUI_RESOLUTION = min(r1, r2, 1.3)

        #--------------------------------------------------------------------
        # adjust font size
        #--------------------------------------------------------------------

        self.font_type = "Arial"
        if sys.platform.startswith("linux"):
            self.font_type = "Liberation Serif"

        if self.GUI_RESOLUTION >= 1.1 and self.GUI_RESOLUTION <= 1.3:
            font2 = wx.Font(13, wx.SWISS, wx.NORMAL,
                            wx.NORMAL, False, self.font_type)
        elif self.GUI_RESOLUTION <= 0.9 and self.GUI_RESOLUTION < 1.0:
            font2 = wx.Font(11, wx.SWISS, wx.NORMAL,
                            wx.NORMAL, False, self.font_type)
        elif self.GUI_RESOLUTION <= 0.9:
            font2 = wx.Font(10, wx.SWISS, wx.NORMAL,
                            wx.NORMAL, False, self.font_type)
        else:
            font2 = wx.Font(12, wx.SWISS, wx.NORMAL,
                            wx.NORMAL, False, self.font_type)
        print("    self.GUI_RESOLUTION", self.GUI_RESOLUTION)

        h_space = 4
        v_space = 4

        # set font size and style
        #font1 = wx.Font(10, wx.SWISS, wx.NORMAL, wx.NORMAL, False, u'Comic Sans MS')
        FONT_RATIO = self.GUI_RESOLUTION + (self.GUI_RESOLUTION - 1) * 5
        font1 = wx.Font(9 + FONT_RATIO, wx.SWISS, wx.NORMAL,
                        wx.NORMAL, False, self.font_type)
        # GUI headers

        font3 = wx.Font(11 + FONT_RATIO, wx.SWISS, wx.NORMAL,
                        wx.NORMAL, False, self.font_type)
        font = wx.SystemSettings.GetFont(wx.SYS_SYSTEM_FONT)
        font.SetPointSize(10 + FONT_RATIO)

        #--------------------------------------------------------------------
        # Create Figures and FigCanvas objects.
        #--------------------------------------------------------------------

        self.fig1 = Figure((5. * self.GUI_RESOLUTION, 5. *
                            self.GUI_RESOLUTION), dpi=self.dpi)
        self.canvas1 = FigCanvas(self.plot_panel, wx.ID_ANY, self.fig1)
        self.fig1.text(0.01, 0.98, "Arai plot", {
                       'family': self.font_type, 'fontsize': 10, 'style': 'normal', 'va': 'center', 'ha': 'left'})
        self.toolbar1 = NavigationToolbar(self.canvas1)
        self.toolbar1.Hide()
        self.fig1_setting = "Zoom"
        self.toolbar1.zoom()
        self.canvas1.Bind(wx.EVT_RIGHT_DOWN, self.on_right_click_fig)
        self.canvas1.Bind(wx.EVT_MIDDLE_DOWN, self.on_home_fig)

        self.fig2 = Figure((2.5 * self.GUI_RESOLUTION, 2.5 *
                            self.GUI_RESOLUTION), dpi=self.dpi)
        self.canvas2 = FigCanvas(self.plot_panel, wx.ID_ANY, self.fig2)
        self.fig2.text(0.02, 0.96, "Zijderveld", {
                       'family': self.font_type, 'fontsize': 10, 'style': 'normal', 'va': 'center', 'ha': 'left'})
        self.toolbar2 = NavigationToolbar(self.canvas2)
        self.toolbar2.Hide()
        self.fig2_setting = "Zoom"
        self.toolbar2.zoom()
        self.canvas2.Bind(wx.EVT_RIGHT_DOWN, self.on_right_click_fig)
        self.canvas2.Bind(wx.EVT_MIDDLE_DOWN, self.on_home_fig)

        self.fig3 = Figure((2.5 * self.GUI_RESOLUTION, 2.5 *
                            self.GUI_RESOLUTION), dpi=self.dpi)
        self.canvas3 = FigCanvas(self.plot_panel, wx.ID_ANY, self.fig3)
        #self.fig3.text(0.02,0.96,"Equal area",{'family':self.font_type, 'fontsize':10*self.GUI_RESOLUTION, 'style':'normal','va':'center', 'ha':'left' })
        self.toolbar3 = NavigationToolbar(self.canvas3)
        self.toolbar3.Hide()
        self.fig3_setting = "Zoom"
        self.toolbar3.zoom()
        self.canvas3.Bind(wx.EVT_RIGHT_DOWN, self.on_right_click_fig)
        self.canvas3.Bind(wx.EVT_MIDDLE_DOWN, self.on_home_fig)

        self.fig4 = Figure((2.5 * self.GUI_RESOLUTION, 2.5 *
                            self.GUI_RESOLUTION), dpi=self.dpi)
        self.canvas4 = FigCanvas(self.plot_panel, wx.ID_ANY, self.fig4)
        if self.acceptance_criteria['average_by_sample_or_site']['value'] == 'site':
            TEXT = "Site data"
        else:
            TEXT = "Sample data"
        self.fig4.text(0.02, 0.96, TEXT, {
                       'family': self.font_type, 'fontsize': 10, 'style': 'normal', 'va': 'center', 'ha': 'left'})
        self.toolbar4 = NavigationToolbar(self.canvas4)
        self.toolbar4.Hide()
        self.fig4_setting = "Zoom"
        self.toolbar4.zoom()
        self.canvas4.Bind(wx.EVT_RIGHT_DOWN, self.on_right_click_fig)
        self.canvas4.Bind(wx.EVT_MIDDLE_DOWN, self.on_home_fig)

        self.fig5 = Figure((2.5 * self.GUI_RESOLUTION, 2.5 *
                            self.GUI_RESOLUTION), dpi=self.dpi)
        self.canvas5 = FigCanvas(self.plot_panel, wx.ID_ANY, self.fig5)
        #self.fig5.text(0.02,0.96,"M/M0",{'family':self.font_type, 'fontsize':10, 'style':'normal','va':'center', 'ha':'left' })
        self.toolbar5 = NavigationToolbar(self.canvas5)
        self.toolbar5.Hide()
        self.fig5_setting = "Zoom"
        self.toolbar5.zoom()
        self.canvas5.Bind(wx.EVT_RIGHT_DOWN, self.on_right_click_fig)
        self.canvas5.Bind(wx.EVT_MIDDLE_DOWN, self.on_home_fig)

        # make axes of the figures
        self.araiplot = self.fig1.add_axes([0.1, 0.1, 0.8, 0.8])
        self.zijplot = self.fig2.add_subplot(111)
        self.eqplot = self.fig3.add_subplot(111)
        self.sampleplot = self.fig4.add_axes(
            [0.2, 0.3, 0.7, 0.6], frameon=True, facecolor='None')
        self.mplot = self.fig5.add_axes(
            [0.2, 0.15, 0.7, 0.7], frameon=True, facecolor='None')

        #--------------------------------------------------------------------
        # text box displaying measurement data
        #--------------------------------------------------------------------

        self.logger = wx.ListCtrl(self.side_panel, id=wx.ID_ANY, size=(
            100 * self.GUI_RESOLUTION, 100 * self.GUI_RESOLUTION), style=wx.LC_REPORT)
        self.logger.SetFont(font1)
        self.logger.InsertColumn(0, 'i', width=45 * self.GUI_RESOLUTION)
        self.logger.InsertColumn(1, 'Step', width=45 * self.GUI_RESOLUTION)
        self.logger.InsertColumn(2, 'Tr', width=65 * self.GUI_RESOLUTION)
        self.logger.InsertColumn(3, 'Dec', width=65 * self.GUI_RESOLUTION)
        self.logger.InsertColumn(4, 'Inc', width=65 * self.GUI_RESOLUTION)
        self.logger.InsertColumn(5, 'M', width=75 * self.GUI_RESOLUTION)
        self.Bind(wx.EVT_LIST_ITEM_ACTIVATED,
                  self.on_click_listctrl, self.logger)
        self.Bind(wx.EVT_LIST_ITEM_RIGHT_CLICK,
                  self.on_right_click_listctrl, self.logger)

        #--------------------------------------------------------------------
        # select a specimen box
        #--------------------------------------------------------------------

        # Combo-box with a list of specimen
        self.specimens_box = wx.ComboBox(self.top_panel, wx.ID_ANY, self.s, (250 * self.GUI_RESOLUTION, 25),
                                         wx.DefaultSize, self.specimens, wx.CB_DROPDOWN | wx.TE_PROCESS_ENTER, name="specimen")
        self.specimens_box.SetFont(font2)
        self.Bind(wx.EVT_COMBOBOX, self.onSelect_specimen, self.specimens_box)
        self.Bind(wx.EVT_TEXT_ENTER, self.onSelect_specimen,
                  self.specimens_box)

        # buttons to move forward and backwards from specimens
        nextbutton = wx.Button(self.top_panel, id=wx.ID_ANY, label='next', size=(
            75 * self.GUI_RESOLUTION, 25))  # ,style=wx.BU_EXACTFIT)#, size=(175, 28))
        self.Bind(wx.EVT_BUTTON, self.on_next_button, nextbutton)
        nextbutton.SetFont(font2)

        prevbutton = wx.Button(self.top_panel, id=wx.ID_ANY, label='previous', size=(
            75 * self.GUI_RESOLUTION, 25))  # ,style=wx.BU_EXACTFIT)#, size=(175, 28))
        prevbutton.SetFont(font2)
        self.Bind(wx.EVT_BUTTON, self.on_prev_button, prevbutton)

        #--------------------------------------------------------------------
        # select temperature bounds
        #--------------------------------------------------------------------

        try:
            if self.Data[self.s]['T_or_MW'] == "T":
                self.temperatures = np.array(
                    self.Data[self.s]['t_Arai']) - 273.
                self.T_list = ["%.0f" % T for T in self.temperatures]
            elif self.Data[self.s]['T_or_MW'] == "MW":
                self.temperatures = np.array(self.Data[self.s]['t_Arai'])
                self.T_list = ["%.0f" % T for T in self.temperatures]
        except (ValueError, TypeError, KeyError) as e:
            self.T_list = []

        self.tmin_box = wx.ComboBox(self.top_panel, wx.ID_ANY, size=(
            100 * self.GUI_RESOLUTION, 25), choices=self.T_list, style=wx.CB_DROPDOWN | wx.TE_READONLY)
        self.Bind(wx.EVT_COMBOBOX, self.get_new_T_PI_parameters, self.tmin_box)

        self.tmax_box = wx.ComboBox(self.top_panel, -1, size=(100 * self.GUI_RESOLUTION, 25),
                                    choices=self.T_list, style=wx.CB_DROPDOWN | wx.TE_READONLY)
        self.Bind(wx.EVT_COMBOBOX, self.get_new_T_PI_parameters, self.tmax_box)

        #--------------------------------------------------------------------
        # save/delete buttons
        #--------------------------------------------------------------------

        # save/delete interpretation buttons
        self.save_interpretation_button = wx.Button(self.top_panel, id=-1, label='save', size=(
            75 * self.GUI_RESOLUTION, 25))  # ,style=wx.BU_EXACTFIT)#, size=(175, 28))
        self.save_interpretation_button.SetFont(font2)
        self.delete_interpretation_button = wx.Button(self.top_panel, id=-1, label='delete', size=(
            75 * self.GUI_RESOLUTION, 25))  # ,style=wx.BU_EXACTFIT)#, size=(175, 28))
        self.delete_interpretation_button.SetFont(font2)
        self.Bind(wx.EVT_BUTTON, self.on_save_interpretation_button,
                  self.save_interpretation_button)
        self.Bind(wx.EVT_BUTTON, self.on_delete_interpretation_button,
                  self.delete_interpretation_button)

        self.auto_save = wx.CheckBox(self.top_panel, wx.ID_ANY, 'auto-save')
        self.auto_save_info = wx.Button(self.top_panel, wx.ID_ANY, "?")
        self.Bind(wx.EVT_BUTTON, self.on_info_click, self.auto_save_info)
        #self.auto_save_text = wx.StaticText(self.top_panel, wx.ID_ANY, label="(saves with 'next')")

        #--------------------------------------------------------------------
        # specimen interpretation and statistics window (Blab; Banc, Dec, Inc, correction factors etc.)
        #--------------------------------------------------------------------

        self.Blab_window = wx.TextCtrl(
            self.top_panel, style=wx.TE_CENTER | wx.TE_READONLY, size=(50 * self.GUI_RESOLUTION, 25))
        self.Banc_window = wx.TextCtrl(
            self.top_panel, style=wx.TE_CENTER | wx.TE_READONLY, size=(50 * self.GUI_RESOLUTION, 25))
        self.Aniso_factor_window = wx.TextCtrl(
            self.top_panel, style=wx.TE_CENTER | wx.TE_READONLY, size=(50 * self.GUI_RESOLUTION, 25))
        self.NLT_factor_window = wx.TextCtrl(
            self.top_panel, style=wx.TE_CENTER | wx.TE_READONLY, size=(50 * self.GUI_RESOLUTION, 25))
        self.CR_factor_window = wx.TextCtrl(
            self.top_panel, style=wx.TE_CENTER | wx.TE_READONLY, size=(50 * self.GUI_RESOLUTION, 25))
        self.declination_window = wx.TextCtrl(
            self.top_panel, style=wx.TE_CENTER | wx.TE_READONLY, size=(50 * self.GUI_RESOLUTION, 25))
        self.inclination_window = wx.TextCtrl(
            self.top_panel, style=wx.TE_CENTER | wx.TE_READONLY, size=(50 * self.GUI_RESOLUTION, 25))

        for stat in ['Blab', 'Banc', 'Aniso_factor', 'NLT_factor', 'CR_factor', 'declination', 'inclination']:
            exec("self.%s_window.SetBackgroundColour(wx.WHITE)" % stat)

        self.Blab_label = wx.StaticText(
            self.top_panel, label="\nB_lab", style=wx.ALIGN_CENTRE)
        self.Blab_label.SetFont(font2)
        self.Banc_label = wx.StaticText(
            self.top_panel, label="\nB_anc", style=wx.ALIGN_CENTRE)
        self.Banc_label.SetFont(font2)
        self.aniso_corr_label = wx.StaticText(
            self.top_panel, label="Aniso\ncorr", style=wx.ALIGN_CENTRE)
        self.aniso_corr_label.SetFont(font2)
        self.nlt_corr_label = wx.StaticText(
            self.top_panel, label="NLT\ncorr", style=wx.ALIGN_CENTRE)
        self.nlt_corr_label.SetFont(font2)
        self.cr_corr_label = wx.StaticText(
            self.top_panel, label="CR\ncorr", style=wx.ALIGN_CENTRE)
        self.cr_corr_label.SetFont(font2)
        self.dec_label = wx.StaticText(
            self.top_panel, label="\nDec", style=wx.ALIGN_CENTRE)
        self.dec_label.SetFont(font2)
        self.inc_label = wx.StaticText(
            self.top_panel, label="\nInc", style=wx.ALIGN_CENTRE)
        self.inc_label.SetFont(font2)

        # handle Specimen Results Sizer
        sizer_specimen_results = wx.StaticBoxSizer(wx.StaticBox(
            self.top_panel, wx.ID_ANY, "specimen results"), wx.HORIZONTAL)
        specimen_stat_window = wx.GridSizer(2, 7, h_space, v_space)
        specimen_stat_window.AddMany([(self.Blab_label, 1, wx.ALIGN_BOTTOM),
                                      ((self.Banc_label), 1, wx.ALIGN_BOTTOM),
                                      ((self.aniso_corr_label), 1, wx.ALIGN_BOTTOM),
                                      ((self.nlt_corr_label), 1, wx.ALIGN_BOTTOM),
                                      ((self.cr_corr_label), 1, wx.ALIGN_BOTTOM),
                                      ((self.dec_label), 1,
                                       wx.TE_CENTER | wx.ALIGN_BOTTOM),
                                      ((self.inc_label), 1, wx.ALIGN_BOTTOM),
                                      (self.Blab_window, 1, wx.EXPAND),
                                      (self.Banc_window, 1, wx.EXPAND),
                                      (self.Aniso_factor_window, 1, wx.EXPAND),
                                      (self.NLT_factor_window, 1, wx.EXPAND),
                                      (self.CR_factor_window, 1, wx.EXPAND),
                                      (self.declination_window, 1, wx.EXPAND),
                                      (self.inclination_window, 1, wx.EXPAND)])
        sizer_specimen_results.Add(
            specimen_stat_window, 1, wx.EXPAND | wx.ALIGN_LEFT, 0)

        #--------------------------------------------------------------------
        # Sample interpretation window
        #--------------------------------------------------------------------

        for key in ["sample_int_n", "sample_int_uT", "sample_int_sigma", "sample_int_sigma_perc"]:
            command = "self.%s_window=wx.TextCtrl(self.top_panel,style=wx.TE_CENTER|wx.TE_READONLY,size=(50*self.GUI_RESOLUTION,25))" % key
            exec(command)
            exec("self.%s_window.SetBackgroundColour(wx.WHITE)" % key)

        sample_mean_label = wx.StaticText(
            self.top_panel, label="\nmean", style=wx.TE_CENTER)
        sample_mean_label.SetFont(font2)
        sample_N_label = wx.StaticText(
            self.top_panel, label="\nN ", style=wx.TE_CENTER)
        sample_N_label.SetFont(font2)
        sample_std_label = wx.StaticText(
            self.top_panel, label="\nstd uT", style=wx.TE_CENTER)
        sample_std_label.SetFont(font2)
        sample_std_per_label = wx.StaticText(
            self.top_panel, label="\nstd %", style=wx.TE_CENTER)
        sample_std_per_label.SetFont(font2)

        # handle samples/sites results sizers
        sizer_sample_results = wx.StaticBoxSizer(wx.StaticBox(
            self.top_panel, wx.ID_ANY, "sample/site results"), wx.HORIZONTAL)
        sample_stat_window = wx.GridSizer(2, 4, h_space, v_space)
        sample_stat_window.AddMany([(sample_mean_label, 1, wx.ALIGN_BOTTOM),
                                    (sample_N_label, 1, wx.ALIGN_BOTTOM),
                                    (sample_std_label, 1, wx.ALIGN_BOTTOM),
                                    (sample_std_per_label, 1, wx.ALIGN_BOTTOM),
                                    (self.sample_int_uT_window, 1, wx.EXPAND),
                                    (self.sample_int_n_window, 1, wx.EXPAND),
                                    (self.sample_int_sigma_window, 1, wx.EXPAND),
                                    (self.sample_int_sigma_perc_window, 1, wx.EXPAND)])
        sizer_sample_results.Add(
            sample_stat_window, 1, wx.EXPAND | wx.ALIGN_LEFT, 0)

        #--------------------------------------------------------------------

        label_0 = wx.StaticText(
            self.bottom_panel, label="                    ", style=wx.ALIGN_CENTER, size=(180, 25))
        label_1 = wx.StaticText(
            self.bottom_panel, label="Acceptance criteria:", style=wx.ALIGN_CENTER, size=(180, 25))
        label_2 = wx.StaticText(
            self.bottom_panel, label="Specimen statistics:", style=wx.ALIGN_CENTER, size=(180, 25))

        for statistic in self.preferences['show_statistics_on_gui']:
            self.stat_windows[statistic] = wx.TextCtrl(
                self.bottom_panel, style=wx.TE_CENTER | wx.TE_READONLY, size=(50 * self.GUI_RESOLUTION, 25))
            self.stat_windows[statistic].SetBackgroundColour(wx.WHITE)
            self.stat_windows[statistic].SetFont(font2)
            self.threshold_windows[statistic] = wx.TextCtrl(
                self.bottom_panel, style=wx.TE_CENTER | wx.TE_READONLY, size=(50 * self.GUI_RESOLUTION, 25))
            self.threshold_windows[statistic].SetFont(font2)
            self.threshold_windows[statistic].SetBackgroundColour(wx.WHITE)
            label = statistic.replace("specimen_", "").replace("int_", "")
            self.stat_labels[statistic] = wx.StaticText(
                self.bottom_panel, label=label, style=wx.ALIGN_CENTRE_HORIZONTAL | wx.ALIGN_BOTTOM)
            self.stat_labels[statistic].SetFont(font2)

        #-------------------------------------------------------------------
        # Design the panels
        #-------------------------------------------------------------------

        # Plots Panel--------------------------------------------------------
        sizer_grid_plots = wx.GridSizer(2, 2, 0, 0)
        sizer_grid_plots.AddMany([(self.canvas2, 1, wx.EXPAND),
                                  (self.canvas4, 1, wx.EXPAND),
                                  (self.canvas3, 1, wx.EXPAND),
                                  (self.canvas5, 1, wx.EXPAND)])

        sizer_plots_outer = wx.BoxSizer(wx.HORIZONTAL)
        sizer_plots_outer.Add(self.canvas1, 1, wx.EXPAND)
        sizer_plots_outer.Add(sizer_grid_plots, 1, wx.EXPAND)

        # Top Bar Sizer-------------------------------------------------------
        #-------------Specimens Sizer----------------------------------------
        sizer_prev_next_btns = wx.BoxSizer(wx.HORIZONTAL)
        sizer_prev_next_btns.Add(prevbutton, 1, wx.EXPAND | wx.RIGHT, h_space)
        sizer_prev_next_btns.Add(nextbutton, 1, wx.EXPAND | wx.LEFT, h_space)

        sizer_select_specimen = wx.StaticBoxSizer(wx.StaticBox(
            self.top_panel, wx.ID_ANY, "specimen"), wx.VERTICAL)
        sizer_select_specimen.Add(
            self.specimens_box, 1, wx.EXPAND | wx.BOTTOM, v_space)
        sizer_select_specimen.Add(
            sizer_prev_next_btns, 1, wx.EXPAND | wx.TOP, v_space)

        #-------------Bounds Sizer----------------------------------------
        sizer_grid_bounds_btns = wx.GridSizer(2, 3, 2 * h_space, 2 * v_space)
        sizer_grid_bounds_btns.AddMany([(self.tmin_box, 1, wx.EXPAND),
                                        (self.save_interpretation_button,
                                         1, wx.EXPAND), (self.auto_save, 1, wx.EXPAND),
                                        (self.tmax_box, 1, wx.EXPAND),
                                        (self.delete_interpretation_button, 1, wx.EXPAND),
                                        (self.auto_save_info, 1, wx.EXPAND)])

        if self.s in list(self.Data.keys()) and self.Data[self.s]['T_or_MW'] == "T":
            sizer_select_temp = wx.StaticBoxSizer(wx.StaticBox(
                self.top_panel, wx.ID_ANY, "temperatures"), wx.HORIZONTAL)
        else:
            sizer_select_temp = wx.StaticBoxSizer(wx.StaticBox(
                self.top_panel, wx.ID_ANY, "MW power"), wx.HORIZONTAL)
        sizer_select_temp.Add(sizer_grid_bounds_btns, 1, wx.EXPAND)

        #-------------Top Bar Outer Sizer------------------------------------
        sizer_top_bar = wx.BoxSizer(wx.HORIZONTAL)
        sizer_top_bar.AddMany([(sizer_select_specimen, 1, wx.EXPAND | wx.ALIGN_LEFT | wx.RIGHT, 2 * h_space),
                               (sizer_select_temp, 1, wx.EXPAND |
                                wx.ALIGN_LEFT | wx.RIGHT, 2 * h_space),
                               (sizer_specimen_results, 2, wx.EXPAND |
                                wx.ALIGN_LEFT | wx.RIGHT, 2 * h_space),
                               (sizer_sample_results, 1, wx.EXPAND | wx.ALIGN_LEFT | wx.RIGHT, 0)])

        # Bottom Bar Sizer----------------------------------------------------
        #----------------Criteria Labels Sizer-------------------------------
        sizer_criteria_labels = wx.BoxSizer(wx.HORIZONTAL)
        sizer_criteria_labels.Add(label_0, 3, wx.EXPAND | wx.LEFT, 2 * h_space)
        sizer_criteria_boxes = wx.BoxSizer(wx.HORIZONTAL)
        sizer_criteria_boxes.Add(label_1, 3, wx.EXPAND | wx.LEFT, 2 * h_space)
        sizer_stats_boxes = wx.BoxSizer(wx.HORIZONTAL)
        sizer_stats_boxes.Add(label_2, 3, wx.EXPAND | wx.LEFT, 2 * h_space)
        for statistic in self.preferences['show_statistics_on_gui']:
            sizer_criteria_labels.Add(
                self.stat_labels[statistic], 1, wx.ALIGN_BOTTOM, 0)

        #----------------Acceptance Criteria Boxes---------------------------
            sizer_criteria_boxes.Add(
                self.threshold_windows[statistic], 1, wx.EXPAND | wx.LEFT, h_space)

        #----------------Specimen Statistics Boxes---------------------------
            sizer_stats_boxes.Add(
                self.stat_windows[statistic], 1, wx.EXPAND | wx.LEFT, h_space)

        #----------------Bottom Outer Sizer----------------------------------
        sizer_bottom_bar = wx.BoxSizer(wx.VERTICAL)
        sizer_bottom_bar.AddMany([(sizer_criteria_labels, 1, wx.EXPAND | wx.ALIGN_BOTTOM | wx.BOTTOM, v_space),
                                  (sizer_criteria_boxes, 1, wx.EXPAND |
                                   wx.BOTTOM | wx.ALIGN_TOP, v_space),
                                  (sizer_stats_boxes, 1, wx.EXPAND | wx.ALIGN_TOP)])

        # Logger Sizer--------------------------------------------------------
        sizer_logger = wx.BoxSizer(wx.HORIZONTAL)
        sizer_logger.Add(self.logger, 1, wx.EXPAND)

        # Set Panel Sizers----------------------------------------------------
        self.plot_panel.SetSizer(sizer_plots_outer)
        self.side_panel.SetSizerAndFit(sizer_logger)
        self.top_panel.SetSizerAndFit(sizer_top_bar)
        self.bottom_panel.SetSizerAndFit(sizer_bottom_bar)

        # Outer Sizer for Frame-----------------------------------------------
        sizer_logger_plots = wx.BoxSizer(wx.HORIZONTAL)
        sizer_logger_plots.Add(self.side_panel, 1, wx.EXPAND | wx.ALIGN_LEFT)
        sizer_logger_plots.Add(self.plot_panel, 3, wx.EXPAND | wx.ALIGN_LEFT)

        sizer_outer = wx.BoxSizer(wx.VERTICAL)
        sizer_outer.AddMany([(self.top_panel, 1, wx.EXPAND | wx.ALIGN_TOP | wx.BOTTOM, v_space / 2),
                             (sizer_logger_plots, 4, wx.EXPAND |
                              wx.ALIGN_TOP | wx.BOTTOM, v_space / 2),
                             (self.bottom_panel, 1, wx.EXPAND | wx.ALIGN_TOP)])

        self.SetSizer(sizer_outer)
        sizer_outer.Fit(self)
        self.Layout()


Instruction:
Can you create a Python 3 function that
saves the current interpretation temporarily

Response:
def on_save_interpretation_button(self, event):
        """
        save the current interpretation temporarily (not to a file)
        """
        if "specimen_int_uT" not in self.Data[self.s]['pars']:
            return
        if 'deleted' in self.Data[self.s]['pars']:
            self.Data[self.s]['pars'].pop('deleted')
        self.Data[self.s]['pars']['saved'] = True

        # collect all interpretation by sample
        sample = self.Data_hierarchy['specimens'][self.s]
        if sample not in list(self.Data_samples.keys()):
            self.Data_samples[sample] = {}
        if self.s not in list(self.Data_samples[sample].keys()):
            self.Data_samples[sample][self.s] = {}
        self.Data_samples[sample][self.s]['B'] = self.Data[self.s]['pars']["specimen_int_uT"]

        # collect all interpretation by site
        # site=thellier_gui_lib.get_site_from_hierarchy(sample,self.Data_hierarchy)
        site = thellier_gui_lib.get_site_from_hierarchy(
            sample, self.Data_hierarchy)
        if site not in list(self.Data_sites.keys()):
            self.Data_sites[site] = {}
        if self.s not in list(self.Data_sites[site].keys()):
            self.Data_sites[site][self.s] = {}
        self.Data_sites[site][self.s]['B'] = self.Data[self.s]['pars']["specimen_int_uT"]

        self.draw_sample_mean()
        self.write_sample_box()
        self.close_warning = True


Instruction:
Can you create a Python 3 function that
deletes the current interpretation temporarily

Response:
def on_delete_interpretation_button(self, event):
        """
        delete the current interpretation temporarily (not to a file)
        """

        del self.Data[self.s]['pars']
        self.Data[self.s]['pars'] = {}
        self.Data[self.s]['pars']['deleted'] = True
        self.Data[self.s]['pars']['lab_dc_field'] = self.Data[self.s]['lab_dc_field']
        self.Data[self.s]['pars']['er_specimen_name'] = self.Data[self.s]['er_specimen_name']
        self.Data[self.s]['pars']['er_sample_name'] = self.Data[self.s]['er_sample_name']
        self.Data[self.s]['pars']['er_sample_name'] = self.Data[self.s]['er_sample_name']
        sample = self.Data_hierarchy['specimens'][self.s]
        if sample in list(self.Data_samples.keys()):
            if self.s in list(self.Data_samples[sample].keys()):
                if 'B' in list(self.Data_samples[sample][self.s].keys()):
                    del self.Data_samples[sample][self.s]['B']

        site = thellier_gui_lib.get_site_from_hierarchy(
            sample, self.Data_hierarchy)
        if site in list(self.Data_sites.keys()):
            if self.s in list(self.Data_sites[site].keys()):
                del self.Data_sites[site][self.s]['B']
                # if 'B' in self.Data_sites[site][self.s].keys():
                #    del self.Data_sites[site][self.s]['B']

        self.tmin_box.SetValue("")
        self.tmax_box.SetValue("")
        self.clear_boxes()
        self.draw_figure(self.s)
        self.draw_sample_mean()
        self.write_sample_box()
        self.close_warning = True


Instruction:
Can you generate a brief explanation for the following Python 3 code
def write_acceptance_criteria_to_boxes(self):

        self.ignore_parameters, value = {}, ''
        for crit_short_name in self.preferences['show_statistics_on_gui']:
            crit = "specimen_" + crit_short_name
            if self.acceptance_criteria[crit]['value'] == -999:
                self.threshold_windows[crit_short_name].SetValue("")
                self.threshold_windows[crit_short_name].SetBackgroundColour(
                    wx.Colour(128, 128, 128))
                self.ignore_parameters[crit] = True
                continue
            elif crit == "specimen_scat":
                if self.acceptance_criteria[crit]['value'] in ['g', 1, '1', True, "True", "t"]:
                    value = "True"
                    value = "t"
                    #self.scat_threshold_window.SetBackgroundColour(wx.SetBackgroundColour(128, 128, 128))
                else:
                    value = ""
                    value = "f"
                    self.threshold_windows['scat'].SetBackgroundColour(
                        (128, 128, 128))
                    #self.scat_threshold_window.SetBackgroundColour((128, 128, 128))

            elif type(self.acceptance_criteria[crit]['value']) == int:
                value = "%i" % self.acceptance_criteria[crit]['value']
            elif type(self.acceptance_criteria[crit]['value']) == float:
                if self.acceptance_criteria[crit]['decimal_points'] == -999:
                    value = "%.3e" % self.acceptance_criteria[crit]['value']
                else:
                    value = "{:.{}f}".format(self.acceptance_criteria[crit]['value'],
                                             self.acceptance_criteria[crit]['decimal_points'])
            else:
                continue

            self.threshold_windows[crit_short_name].SetValue(value)
            self.threshold_windows[crit_short_name].SetBackgroundColour(
                wx.WHITE)

Response: Writes acceptance criteria to the acceptance criteria boxes.


Instruction:
Write a Python 3 function for
adding text to measurement data window.

Response:
def Add_text(self, s):
        """
        Add text to measurement data window.
        """
        self.logger.DeleteAllItems()
        FONT_RATIO = self.GUI_RESOLUTION + (self.GUI_RESOLUTION - 1) * 5
        if self.GUI_RESOLUTION > 1.1:
            font1 = wx.Font(11, wx.SWISS, wx.NORMAL,
                            wx.NORMAL, False, self.font_type)
        elif self.GUI_RESOLUTION <= 0.9:
            font1 = wx.Font(8, wx.SWISS, wx.NORMAL,
                            wx.NORMAL, False, self.font_type)
        else:
            font1 = wx.Font(10, wx.SWISS, wx.NORMAL,
                            wx.NORMAL, False, self.font_type)

        # get temperature indecies to display current interp steps in logger
        t1 = self.tmin_box.GetValue()
        t2 = self.tmax_box.GetValue()

        # microwave or thermal
        if "LP-PI-M" in self.Data[s]['datablock'][0]['magic_method_codes']:
            MICROWAVE = True
            THERMAL = False

            steps_tr = []
            for rec in self.Data[s]['datablock']:

                if "measurement_description" in rec:
                    MW_step = rec["measurement_description"].strip(
                        '\n').split(":")
                    for STEP in MW_step:
                        if "Number" in STEP:
                            temp = float(STEP.split("-")[-1])
                            steps_tr.append(temp)

                else:
                    power = rec['treatment_mw_power']
                    if '-' in str(power):
                        power = power.split('-')[-1]
                    steps_tr.append(int(power))

            #steps_tr = [float(d['treatment_mw_power'].split("-")[-1])
            #            for d in self.Data[s]['datablock']]
        else:
            MICROWAVE = False
            THERMAL = True
            steps_tr = [float(d['treatment_temp']) -
                        273 for d in self.Data[s]['datablock']]

        if (t1 == "" or t2 == "") or float(t2) < float(t1):
            tmin_index, tmax_index = -1, -1
        else:
            tmin_index = steps_tr.index(int(t1))
            tmax_index = steps_tr.index(int(t2))

        self.logger.SetFont(font1)
        for i, rec in enumerate(self.Data[s]['datablock']):
            if "LT-NO" in rec['magic_method_codes']:
                step = "N"
            elif "LT-AF-Z" in rec['magic_method_codes']:
                step = "AFD"
            elif "LT-T-Z" in rec['magic_method_codes'] or 'LT-M-Z' in rec['magic_method_codes']:
                step = "Z"
            elif "LT-T-I" in rec['magic_method_codes'] or 'LT-M-I' in rec['magic_method_codes']:
                step = "I"
            elif "LT-PTRM-I" in rec['magic_method_codes'] or "LT-PMRM-I" in rec['magic_method_codes']:
                step = "P"
            elif "LT-PTRM-MD" in rec['magic_method_codes'] or "LT-PMRM-MD" in rec['magic_method_codes']:
                step = "T"
            elif "LT-PTRM-AC" in rec['magic_method_codes'] or "LT-PMRM-AC" in rec['magic_method_codes']:
                step = "A"
            else:
                print(("unrecognized step in specimen %s Method codes: %s" %
                       (str(rec['magic_method_codes']), s)))
            if THERMAL:
                self.logger.InsertItem(i, "%i" % i)
                self.logger.SetItem(i, 1, step)
                self.logger.SetItem(i, 2, "%1.0f" %
                                    (float(rec['treatment_temp']) - 273.))
                self.logger.SetItem(i, 3, "%.1f" %
                                    float(rec['measurement_dec']))
                self.logger.SetItem(i, 4, "%.1f" %
                                    float(rec['measurement_inc']))
                self.logger.SetItem(i, 5, "%.2e" %
                                    float(rec['measurement_magn_moment']))
            elif MICROWAVE:  # mcrowave
                if "measurement_description" in list(rec.keys()):
                    MW_step = rec["measurement_description"].strip(
                        '\n').split(":")
                    for STEP in MW_step:
                        if "Number" not in STEP:
                            continue
                        temp = float(STEP.split("-")[-1])

                        self.logger.InsertItem(i, "%i" % i)
                        self.logger.SetItem(i, 1, step)
                        self.logger.SetItem(i, 2, "%1.0f" % temp)
                        self.logger.SetItem(i, 3, "%.1f" %
                                            float(rec['measurement_dec']))
                        self.logger.SetItem(i, 4, "%.1f" %
                                            float(rec['measurement_inc']))
                        self.logger.SetItem(i, 5, "%.2e" % float(
                            rec['measurement_magn_moment']))
            self.logger.SetItemBackgroundColour(i, "WHITE")
            if i >= tmin_index and i <= tmax_index:
                self.logger.SetItemBackgroundColour(i, "LIGHT BLUE")
            if 'measurement_flag' not in list(rec.keys()):
                rec['measurement_flag'] = 'g'


Instruction:
Explain what the following Python 3 code does
def select_bounds_in_logger(self, index):
        tmin_index, tmax_index = "", ""
        if str(self.tmin_box.GetValue()) != "":
            tmin_index = self.tmin_box.GetSelection()
        if str(self.tmax_box.GetValue()) != "":
            tmax_index = self.tmax_box.GetSelection()
        # if there is no prior interpretation, assume first click is
        # tmin and set highest possible temp as tmax
        if not tmin_index and not tmax_index:
            tmin_index = index
            self.tmin_box.SetSelection(index)
            # set to the highest step
            max_step_data = self.Data[self.s]['datablock'][-1]
            step_key = 'treatment_temp'
            if MICROWAVE:
                step_key = 'treatment_mw_power'
            max_step = max_step_data[step_key]
            tmax_index = self.tmax_box.GetCount() - 1
            self.tmax_box.SetSelection(tmax_index)
        elif self.list_bound_loc != 0:
            if self.list_bound_loc == 1:
                if index < tmin_index:
                    self.tmin_box.SetSelection(index)
                    self.tmax_box.SetSelection(tmin_index)
                elif index == tmin_index:
                    pass
                else:
                    self.tmax_box.SetSelection(index)
            else:
                if index > tmax_index:
                    self.tmin_box.SetSelection(tmax_index)
                    self.tmax_box.SetSelection(index)
                elif index == tmax_index:
                    pass
                else:
                    self.tmin_box.SetSelection(index)
            self.list_bound_loc = 0
        else:
            if index < tmax_index:
                self.tmin_box.SetSelection(index)
                self.list_bound_loc = 1
            else:
                self.tmax_box.SetSelection(index)
                self.list_bound_loc = 2

        self.logger.Select(index, on=0)
        self.get_new_T_PI_parameters(-1)

Response: Selects the index in the logger based on what the other bound is and selects it in the logger.


Instruction:
Implement a Python 3 function for
updating figures and statistics windows with a new selection of specimen

Response:
def update_selection(self):
        """
        update figures and statistics windows with a new selection of specimen
        """

        # clear all boxes
        self.clear_boxes()
        self.draw_figure(self.s)

        # update temperature list
        if self.Data[self.s]['T_or_MW'] == "T":
            self.temperatures = np.array(self.Data[self.s]['t_Arai']) - 273.
        else:
            self.temperatures = np.array(self.Data[self.s]['t_Arai'])

        self.T_list = ["%.0f" % T for T in self.temperatures]
        self.tmin_box.SetItems(self.T_list)
        self.tmax_box.SetItems(self.T_list)
        self.tmin_box.SetValue("")
        self.tmax_box.SetValue("")
        self.Blab_window.SetValue(
            "%.0f" % (float(self.Data[self.s]['pars']['lab_dc_field']) * 1e6))
        if "saved" in self.Data[self.s]['pars']:
            self.pars = self.Data[self.s]['pars']
            self.update_GUI_with_new_interpretation()
        self.Add_text(self.s)
        self.write_sample_box()


Instruction:
How would you explain what the following Python 3 function does
def onSelect_specimen(self, event):
        new_s = self.specimens_box.GetValue()
        if self.select_specimen(new_s):
            self.update_selection()
        else:
            self.specimens_box.SetValue(self.s)
            self.user_warning(
                "no specimen %s reverting to old specimen %s" % (new_s, self.s))

Response: update figures and text when a new specimen is selected


Instruction:
How would you code a function in Python 3 to
show popup info window when user clicks "?"

Response:
def on_info_click(self, event):
        """
        Show popup info window when user clicks "?"
        """
        def on_close(event, wind):
            wind.Close()
            wind.Destroy()
        event.Skip()
        wind = wx.PopupTransientWindow(self, wx.RAISED_BORDER)
        if self.auto_save.GetValue():
            info = "'auto-save' is currently selected. Temperature bounds will be saved when you click 'next' or 'back'."
        else:
            info = "'auto-save' is not selected.  Temperature bounds will only be saved when you click 'save'."
        text = wx.StaticText(wind, -1, info)
        box = wx.StaticBox(wind, -1, 'Info:')
        boxSizer = wx.StaticBoxSizer(box, wx.VERTICAL)
        boxSizer.Add(text, 5, wx.ALL | wx.CENTER)
        exit_btn = wx.Button(wind, wx.ID_EXIT, 'Close')
        wind.Bind(wx.EVT_BUTTON, lambda evt: on_close(evt, wind), exit_btn)
        boxSizer.Add(exit_btn, 5, wx.ALL | wx.CENTER)
        wind.SetSizer(boxSizer)
        wind.Layout()
        wind.Popup()


Instruction:
How would you implement a function in Python 3 that
updates figures and text when a previous button is selected

Response:
def on_prev_button(self, event):
        """
        update figures and text when a previous button is selected
        """
        if 'saved' not in self.Data[self.s]['pars'] or self.Data[self.s]['pars']['saved'] != True:
            # check preferences
            if self.auto_save.GetValue():
                self.on_save_interpretation_button(None)
            else:
                del self.Data[self.s]['pars']
                self.Data[self.s]['pars'] = {}
                self.Data[self.s]['pars']['lab_dc_field'] = self.Data[self.s]['lab_dc_field']
                self.Data[self.s]['pars']['er_specimen_name'] = self.Data[self.s]['er_specimen_name']
                self.Data[self.s]['pars']['er_sample_name'] = self.Data[self.s]['er_sample_name']
                # return to last saved interpretation if exist
                if 'er_specimen_name' in list(self.last_saved_pars.keys()) and self.last_saved_pars['er_specimen_name'] == self.s:
                    for key in list(self.last_saved_pars.keys()):
                        self.Data[self.s]['pars'][key] = self.last_saved_pars[key]
                    self.last_saved_pars = {}

        index = self.specimens.index(self.s)
        if index == 0:
            index = len(self.specimens)
        index -= 1
        self.s = self.specimens[index]
        self.specimens_box.SetStringSelection(self.s)
        self.update_selection()


Instruction:
Can you generate the documentation for the following Python 3 function
def clear_boxes(self):
        self.tmin_box.Clear()
        self.tmin_box.SetItems(self.T_list)
        self.tmin_box.SetSelection(-1)

        self.tmax_box.Clear()
        self.tmax_box.SetItems(self.T_list)
        self.tmax_box.SetSelection(-1)

        self.Blab_window.SetValue("")
        self.Banc_window.SetValue("")
        self.Banc_window.SetBackgroundColour(wx.Colour('grey'))
        self.Aniso_factor_window.SetValue("")
        self.Aniso_factor_window.SetBackgroundColour(wx.Colour('grey'))
        self.NLT_factor_window.SetValue("")
        self.NLT_factor_window.SetBackgroundColour(wx.Colour('grey'))
        self.CR_factor_window.SetValue("")
        self.CR_factor_window.SetBackgroundColour(wx.Colour('grey'))
        self.declination_window.SetValue("")
        self.declination_window.SetBackgroundColour(wx.Colour('grey'))
        self.inclination_window.SetValue("")
        self.inclination_window.SetBackgroundColour(wx.Colour('grey'))

        window_list = ['sample_int_n', 'sample_int_uT',
                       'sample_int_sigma', 'sample_int_sigma_perc']
        for key in window_list:
            command = "self.%s_window.SetValue(\"\")" % key
            exec(command)
            command = "self.%s_window.SetBackgroundColour(wx.Colour('grey'))" % key
            exec(command)

        # window_list=['int_n','int_ptrm_n','frac','scat','gmax','f','fvds','b_beta','g','q','int_mad','int_dang','drats','md','ptrms_dec','ptrms_inc','ptrms_mad','ptrms_angle']
        # for key in window_list:
        for key in self.preferences['show_statistics_on_gui']:
            self.stat_windows[key].SetValue("")
            self.stat_windows[key].SetBackgroundColour(wx.Colour('grey'))

Response: Clear all boxes in the current locale.


Instruction:
Given the following Python 3 function, write the documentation
def read_preferences_file(self):
        user_data_dir = find_pmag_dir.find_user_data_dir("thellier_gui")
        if not user_data_dir:
            return {}
        if os.path.exists(user_data_dir):
            pref_file = os.path.join(user_data_dir, "thellier_gui_preferences.json")
            if os.path.exists(pref_file):
                with open(pref_file, "r") as pfile:
                    return json.load(pfile)
        return {}

Response: Read json preferences file.


Instruction:
Can you tell what is the following Python 3 function doing
def write_preferences_file(self):
        user_data_dir = find_pmag_dir.find_user_data_dir("thellier_gui")
        if not os.path.exists(user_data_dir):
            find_pmag_dir.make_user_data_dir(user_data_dir)
        pref_file = os.path.join(user_data_dir, "thellier_gui_preferences.json")
        with open(pref_file, "w+") as pfile:
            print('-I- writing preferences to {}'.format(pref_file))
            json.dump(self.preferences, pfile)

Response: Write json preferences file to PmagPy directory.


Instruction:
How would you code a function in Python 3 to
run whenever Thellier GUI exits and closes the current instance of the class.

Response:
def on_menu_exit(self, event):
        """
        Runs whenever Thellier GUI exits
        """
        if self.close_warning:
            TEXT = "Data is not saved to a file yet!\nTo properly save your data:\n1) Analysis --> Save current interpretations to a redo file.\nor\n1) File --> Save MagIC tables.\n\n Press OK to exit without saving."
            dlg1 = wx.MessageDialog(
                None, caption="Warning:", message=TEXT, style=wx.OK | wx.CANCEL | wx.ICON_EXCLAMATION)
            if self.show_dlg(dlg1) == wx.ID_OK:
                dlg1.Destroy()
                self.GUI_log.close()
                self.Destroy()
                # if a custom quit event is specified, fire it
                if self.evt_quit:
                    event = self.evt_quit(self.GetId())
                    self.GetEventHandler().ProcessEvent(event)
                if self.standalone:
                    sys.exit()
        else:
            self.GUI_log.close()
            self.Destroy()
            # if a custom quit event is specified, fire it
            if self.evt_quit:
                event = self.evt_quit(self.GetId())
                self.GetEventHandler().ProcessEvent(event)
            if self.standalone:
                sys.exit()


Instruction:
Can you generate a brief explanation for the following Python 3 code
def on_menu_previous_interpretation(self, event):
        save_current_specimen = self.s
        dlg = wx.FileDialog(
            self, message="choose a file in a pmagpy redo format",
            defaultDir=self.WD,
            defaultFile="thellier_GUI.redo",
            wildcard="*.redo",
            style=wx.FD_OPEN | wx.FD_CHANGE_DIR
        )
        if self.show_dlg(dlg) == wx.ID_OK:
            redo_file = dlg.GetPath()
            if self.test_mode:
                redo_file = "thellier_GUI.redo"
        else:
            redo_file = None
        dlg.Destroy()

        print("redo_file", redo_file)
        if redo_file:
            self.read_redo_file(redo_file)

Response: Open FileDialog for upload previous interpretation


Instruction:
Write a Python 3 function that can
read pmag_criteria. txt file and open change criteria dialog

Response:
def on_menu_criteria_file(self, event):
        """
        read pmag_criteria.txt file
        and open change criteria dialog
        """
        if self.data_model == 3:
            dlg = wx.FileDialog(
                self, message="choose a file in MagIC Data Model 3.0  format",
                defaultDir=self.WD,
                defaultFile="criteria.txt",
                style=wx.FD_OPEN | wx.FD_CHANGE_DIR
            )
        else:
            dlg = wx.FileDialog(
                self, message="choose a file in a MagIC Data Model 2.5 pmagpy format",
                defaultDir=self.WD,
                defaultFile="pmag_criteria.txt",
                # wildcard=wildcard,
                style=wx.FD_OPEN | wx.FD_CHANGE_DIR
            )

        if self.show_dlg(dlg) == wx.ID_OK:
            criteria_file = dlg.GetPath()
            self.GUI_log.write(
                "-I- Read new criteria file: %s\n" % criteria_file)
        dlg.Destroy()
        replace_acceptance_criteria = pmag.initialize_acceptance_criteria(
            data_model=self.data_model)
        try:
            if self.data_model == 3:
                self.read_criteria_file(criteria_file)
                replace_acceptance_criteria = self.acceptance_criteria
                # replace_acceptance_criteria=pmag.read_criteria_from_file(criteria_file,replace_acceptance_criteria,data_model=self.data_model)
                # # just to see if file exists
                print(replace_acceptance_criteria)
            else:
                replace_acceptance_criteria = pmag.read_criteria_from_file(
                    criteria_file, replace_acceptance_criteria, data_model=self.data_model)  # just to see if file exists
        except Exception as ex:
            print('-W-', ex)
            dlg1 = wx.MessageDialog(
                self, caption="Error:", message="error in reading file", style=wx.OK)
            result = self.show_dlg(dlg1)
            if result == wx.ID_OK:
                dlg1.Destroy()
                return
        self.add_thellier_gui_criteria()
        self.read_criteria_file(criteria_file)
        # check if some statistics are in the new criteria but not in old. If
        # yes, add to  self.preferences['show_statistics_on_gui']
        crit_list_not_in_pref = []
        for crit in list(self.acceptance_criteria.keys()):
            if self.acceptance_criteria[crit]['category'] == "IE-SPEC":
                if self.acceptance_criteria[crit]['value'] != -999:
                    short_crit = crit.split('specimen_')[-1]
                    if short_crit not in self.preferences['show_statistics_on_gui']:
                        print("-I- statistic %s is not in your preferences" % crit)
                        self.preferences['show_statistics_on_gui'].append(
                            short_crit)
                        crit_list_not_in_pref.append(crit)
        if len(crit_list_not_in_pref) > 0:
            stat_list = ":".join(crit_list_not_in_pref)
            dlg1 = wx.MessageDialog(self, caption="WARNING:",
                                    message="statistics '%s' is in the imported criteria file but not in your appearence preferences.\nThis statistic will not appear on the gui panel.\n The program will exit after saving new acceptance criteria, and it will be added automatically the next time you open it " % stat_list,
                                    style=wx.OK | wx.ICON_INFORMATION)
            self.show_dlg(dlg1)
            dlg1.Destroy()

        dia = thellier_gui_dialogs.Criteria_Dialog(
            None, self.acceptance_criteria, self.preferences, title='Acceptance Criteria')
        dia.Center()
        result = self.show_dlg(dia)
        if result == wx.ID_OK:  # Until the user clicks OK, show the message
            self.On_close_criteria_box(dia)
            if len(crit_list_not_in_pref) > 0:
                dlg1 = wx.MessageDialog(self, caption="WARNING:",
                                        message="Exiting now! When you restart the gui all the new statistics will be added.",
                                        style=wx.OK | wx.ICON_INFORMATION)
                self.show_dlg(dlg1)
                dlg1.Destroy()
                self.on_menu_exit(None)
                # self.Destroy()
                # sys.exit()

        if result == wx.ID_CANCEL:  # Until the user clicks OK, show the message
            for crit in crit_list_not_in_pref:
                short_crit = crit.split('specimen_')[-1]
                self.preferences['show_statistics_on_gui'].remove(short_crit)


Instruction:
Here you have a function in Python 3, explain what it does
def on_menu_criteria(self, event):

        dia = thellier_gui_dialogs.Criteria_Dialog(
            None, self.acceptance_criteria, self.preferences, title='Set Acceptance Criteria')
        dia.Center()
        result = self.show_dlg(dia)

        if result == wx.ID_OK:  # Until the user clicks OK, show the message
            self.On_close_criteria_box(dia)

Response: Show the dialog to change the acceptance criteria and save it to the criteria file


Instruction:
How would you implement a function in Python 3 that
functions is called when the close criteria dialog window is closed.

Response:
def On_close_criteria_box(self, dia):
        """
        after criteria dialog window is closed.
        Take the acceptance criteria values and update
        self.acceptance_criteria
        """
        criteria_list = list(self.acceptance_criteria.keys())
        criteria_list.sort()

        #---------------------------------------
        # check if averaging by sample or by site
        # and intialize sample/site criteria
        #---------------------------------------
        avg_by = dia.set_average_by_sample_or_site.GetValue()
        if avg_by == 'sample':
            for crit in ['site_int_n', 'site_int_sigma', 'site_int_sigma_perc', 'site_aniso_mean', 'site_int_n_outlier_check']:
                self.acceptance_criteria[crit]['value'] = -999

        if avg_by == 'site':
            for crit in ['sample_int_n', 'sample_int_sigma', 'sample_int_sigma_perc', 'sample_aniso_mean', 'sample_int_n_outlier_check']:
                self.acceptance_criteria[crit]['value'] = -999

        #---------
        # get value for each criterion
        for i in range(len(criteria_list)):
            crit = criteria_list[i]
            value, accept = dia.get_value_for_crit(crit, self.acceptance_criteria)
            if accept:
                self.acceptance_criteria.update(accept)
        #---------
        # thellier interpreter calculation type
        if dia.set_stdev_opt.GetValue() == True:
            self.acceptance_criteria['interpreter_method']['value'] = 'stdev_opt'
        elif dia.set_bs.GetValue() == True:
            self.acceptance_criteria['interpreter_method']['value'] = 'bs'
        elif dia.set_bs_par.GetValue() == True:
            self.acceptance_criteria['interpreter_method']['value'] = 'bs_par'

        #  message dialog
        dlg1 = wx.MessageDialog(
            self, caption="Warning:", message="changes are saved to the criteria file\n ", style=wx.OK)
        result = self.show_dlg(dlg1)
        if result == wx.ID_OK:
            try:
                self.clear_boxes()
            except IndexError:
                pass
            try:
                self.write_acceptance_criteria_to_boxes()
            except IOError:
                pass
            if self.data_model == 3:
                crit_file = 'criteria.txt'
            else:
                crit_file = 'pmag_criteria.txt'
            try:
                pmag.write_criteria_to_file(os.path.join(
                    self.WD, crit_file), self.acceptance_criteria, data_model=self.data_model, prior_crits=self.crit_data)
            except AttributeError as ex:
                print(ex)
                print("no criteria given to save")
            dlg1.Destroy()
            dia.Destroy()

        self.fig4.texts[0].remove()
        txt = "{} data".format(avg_by).capitalize()
        self.fig4.text(0.02, 0.96, txt, {
                       'family': self.font_type, 'fontsize': 10, 'style': 'normal', 'va': 'center', 'ha': 'left'})
        self.recalculate_satistics()
        try:
            self.update_GUI_with_new_interpretation()
        except KeyError:
            pass


Instruction:
Given the following Python 3 function, write the documentation
def recalculate_satistics(self):
        '''
        update self.Data[specimen]['pars'] for all specimens.
        '''
        gframe = wx.BusyInfo(
            "Re-calculating statistics for all specimens\n Please wait..", self)

        for specimen in list(self.Data.keys()):
            if 'pars' not in list(self.Data[specimen].keys()):
                continue
            if 'specimen_int_uT' not in list(self.Data[specimen]['pars'].keys()):
                continue
            tmin = self.Data[specimen]['pars']['measurement_step_min']
            tmax = self.Data[specimen]['pars']['measurement_step_max']
            pars = thellier_gui_lib.get_PI_parameters(
                self.Data, self.acceptance_criteria, self.preferences, specimen, tmin, tmax, self.GUI_log, THERMAL, MICROWAVE)
            self.Data[specimen]['pars'] = pars
            self.Data[specimen]['pars']['lab_dc_field'] = self.Data[specimen]['lab_dc_field']
            self.Data[specimen]['pars']['er_specimen_name'] = self.Data[specimen]['er_specimen_name']
            self.Data[specimen]['pars']['er_sample_name'] = self.Data[specimen]['er_sample_name']
        del gframe

Response: Recalculates the statistics for all the available suds.


Instruction:
Given the following Python 3 function, write the documentation
def read_criteria_file(self, criteria_file):
        '''
        read criteria file.
        initialize self.acceptance_criteria
        try to guess if averaging by sample or by site.
        '''
        if self.data_model == 3:
            self.acceptance_criteria = pmag.initialize_acceptance_criteria(
                data_model=self.data_model)
            self.add_thellier_gui_criteria()
            fnames = {'criteria': criteria_file}
            contribution = cb.Contribution(
                self.WD, custom_filenames=fnames, read_tables=['criteria'])
            if 'criteria' in contribution.tables:
                crit_container = contribution.tables['criteria']
                crit_data = crit_container.df
                crit_data['definition'] = 'acceptance criteria for study'
                # convert to list of dictionaries
                self.crit_data = crit_data.to_dict('records')
                for crit in self.crit_data:  # step through and rename every f-ing one
                    # magic2[magic3.index(crit['table_column'])] # find data
                    # model 2.5 name
                    m2_name = map_magic.convert_intensity_criteria(
                        'magic2', crit['table_column'])
                    if not m2_name:
                        pass
                    elif m2_name not in self.acceptance_criteria:
                        print('-W- Your criteria file contains {}, which is not currently supported in Thellier GUI.'.format(m2_name))
                        print('    This record will be skipped:\n    {}'.format(crit))
                    else:
                        if m2_name != crit['table_column'] and 'scat' not in m2_name != "":
                            self.acceptance_criteria[m2_name]['value'] = float(
                                crit['criterion_value'])
                            self.acceptance_criteria[m2_name]['pmag_criteria_code'] = crit['criterion']
                        if m2_name != crit['table_column'] and 'scat' in m2_name != "":
                            if crit['criterion_value'] == 'True':
                                self.acceptance_criteria[m2_name]['value'] = 1
                            else:
                                self.acceptance_criteria[m2_name]['value'] = 0
            else:
                print("-E- Can't read criteria file")

        else:  # Do it the data model 2.5 way:
            self.crit_data = {}
            try:
                self.acceptance_criteria = pmag.read_criteria_from_file(
                    criteria_file, self.acceptance_criteria)
            except:
                print("-E- Can't read pmag criteria file")
        # guesss if average by site or sample:
        by_sample = True
        flag = False
        for crit in ['sample_int_n', 'sample_int_sigma_perc', 'sample_int_sigma']:
            if self.acceptance_criteria[crit]['value'] == -999:
                flag = True
        if flag:
            for crit in ['site_int_n', 'site_int_sigma_perc', 'site_int_sigma']:
                if self.acceptance_criteria[crit]['value'] != -999:
                    by_sample = False
        if not by_sample:
            self.acceptance_criteria['average_by_sample_or_site']['value'] = 'site'

Response: read the criteria file and initialize self. acceptance_criteria


Instruction:
Can you create a Python 3 function that
saves interpretations to a redo file

Response:
def on_menu_save_interpretation(self, event):
        '''
        save interpretations to a redo file
        '''

        thellier_gui_redo_file = open(
            os.path.join(self.WD, "thellier_GUI.redo"), 'w')

        #--------------------------------------------------
        #  write interpretations to thellier_GUI.redo
        #--------------------------------------------------
        spec_list = list(self.Data.keys())
        spec_list.sort()
        redo_specimens_list = []
        for sp in spec_list:
            if 'saved' not in self.Data[sp]['pars']:
                continue
            if not self.Data[sp]['pars']['saved']:
                continue
            redo_specimens_list.append(sp)

            thellier_gui_redo_file.write("%s %.0f %.0f\n" % (
                sp, self.Data[sp]['pars']['measurement_step_min'], self.Data[sp]['pars']['measurement_step_max']))
        dlg1 = wx.MessageDialog(
            self, caption="Saved:", message="File thellier_GUI.redo is saved in MagIC working folder", style=wx.OK)
        result = self.show_dlg(dlg1)
        if result == wx.ID_OK:
            dlg1.Destroy()
            thellier_gui_redo_file.close()
            return

        thellier_gui_redo_file.close()
        self.close_warning = False


Instruction:
Can you tell what is the following Python 3 function doing
def on_menu_clear_interpretation(self, event):
        '''
        clear all current interpretations.
        '''

        #  delete all previous interpretation
        for sp in list(self.Data.keys()):
            del self.Data[sp]['pars']
            self.Data[sp]['pars'] = {}
            self.Data[sp]['pars']['lab_dc_field'] = self.Data[sp]['lab_dc_field']
            self.Data[sp]['pars']['er_specimen_name'] = self.Data[sp]['er_specimen_name']
            self.Data[sp]['pars']['er_sample_name'] = self.Data[sp]['er_sample_name']
        self.Data_samples = {}
        self.Data_sites = {}
        self.tmin_box.SetValue("")
        self.tmax_box.SetValue("")
        self.clear_boxes()
        self.draw_figure(self.s)

Response: clear all current interpretations.


Instruction:
Can you tell what is the following Python 3 function doing
def read_redo_file(self, redo_file):
        self.GUI_log.write(
            "-I- reading redo file and processing new temperature bounds")
        self.redo_specimens = {}
        # first delete all previous interpretation
        for sp in list(self.Data.keys()):
            del self.Data[sp]['pars']
            self.Data[sp]['pars'] = {}
            self.Data[sp]['pars']['lab_dc_field'] = self.Data[sp]['lab_dc_field']
            self.Data[sp]['pars']['er_specimen_name'] = self.Data[sp]['er_specimen_name']
            self.Data[sp]['pars']['er_sample_name'] = self.Data[sp]['er_sample_name']
            # print sp
            # print self.Data[sp]['pars']
        self.Data_samples = {}
        self.Data_sites = {}

        fin = open(redo_file, 'r')
        lines = fin.readlines()
        fin.close()
        for Line in lines:
            line = Line.strip('\n').split()
            specimen = line[0]
            tmin_kelvin = float(line[1])
            tmax_kelvin = float(line[2])
            if specimen not in list(self.redo_specimens.keys()):
                self.redo_specimens[specimen] = {}
            self.redo_specimens[specimen]['t_min'] = float(tmin_kelvin)
            self.redo_specimens[specimen]['t_max'] = float(tmax_kelvin)
            if specimen in list(self.Data.keys()):
                if tmin_kelvin not in self.Data[specimen]['t_Arai'] or tmax_kelvin not in self.Data[specimen]['t_Arai']:
                    self.GUI_log.write(
                        "-W- WARNING: can't fit temperature bounds in the redo file to the actual measurement. specimen %s\n" % specimen)
                else:
                    self.Data[specimen]['pars'] = thellier_gui_lib.get_PI_parameters(
                        self.Data, self.acceptance_criteria, self.preferences, specimen, float(tmin_kelvin), float(tmax_kelvin), self.GUI_log, THERMAL, MICROWAVE)
                    try:
                        self.Data[specimen]['pars'] = thellier_gui_lib.get_PI_parameters(
                            self.Data, self.acceptance_criteria, self.preferences, specimen, float(tmin_kelvin), float(tmax_kelvin), self.GUI_log, THERMAL, MICROWAVE)
                        self.Data[specimen]['pars']['saved'] = True
                        # write intrepretation into sample data
                        sample = self.Data_hierarchy['specimens'][specimen]
                        if sample not in list(self.Data_samples.keys()):
                            self.Data_samples[sample] = {}
                        if specimen not in list(self.Data_samples[sample].keys()):
                            self.Data_samples[sample][specimen] = {}
                        self.Data_samples[sample][specimen]['B'] = self.Data[specimen]['pars']['specimen_int_uT']
                        site = thellier_gui_lib.get_site_from_hierarchy(
                            sample, self.Data_hierarchy)
                        if site not in list(self.Data_sites.keys()):
                            self.Data_sites[site] = {}
                        if specimen not in list(self.Data_sites[site].keys()):
                            self.Data_sites[site][specimen] = {}
                        self.Data_sites[site][specimen]['B'] = self.Data[specimen]['pars']['specimen_int_uT']

                    except:
                        print("-E- ERROR 1")
                        self.GUI_log.write(
                            "-E- ERROR. Can't calculate PI paremeters for specimen %s using redo file. Check!\n" % (specimen))
            else:
                self.GUI_log.write(
                    "-W- WARNING: Can't find specimen %s from redo file in measurement file!\n" % specimen)
                print(
                    "-W- WARNING: Can't find specimen %s from redo file in measurement file!\n" % specimen)
        if not fin.closed:
            fin.close()
        self.pars = self.Data[self.s]['pars']
        self.clear_boxes()
        self.draw_figure(self.s)
        self.update_GUI_with_new_interpretation()

Response: Read the previous interpretation from a redo file and update the gui with the new interpretation


Instruction:
Write a Python 3 function for
reading er_ages file and convert it by site or sample names and return a dictionary of calendar year values.

Response:
def read_er_ages_file(self, path, ignore_lines_n, sort_by_these_names):
        '''
        read er_ages, sort it by site or sample (the header that is not empty)
        and convert ages to calendar year

        '''
        DATA = {}
        fin = open(path, 'r')
        # ignore first lines
        for i in range(ignore_lines_n):
            fin.readline()
        # header
        line = fin.readline()
        header = line.strip('\n').split('\t')
        # print header
        for line in fin.readlines():
            if line[0] == "#":
                continue
            tmp_data = {}
            tmp_line = line.strip('\n').split('\t')
            for i in range(len(tmp_line)):
                if i >= len(header):
                    continue
                tmp_data[header[i]] = tmp_line[i]
            for name in sort_by_these_names:
                if name in list(tmp_data.keys()) and tmp_data[name] != "":
                    er_ages_rec = self.convert_ages_to_calendar_year(tmp_data)
                    DATA[tmp_data[name]] = er_ages_rec
        fin.close()
        return(DATA)


Instruction:
Given the following Python 3 function, write the documentation
def calculate_sample_mean(self, Data_sample_or_site):
        '''
        Data_sample_or_site is a dictonary holding the samples_or_sites mean
        Data_sample_or_site ={}
        Data_sample_or_site[specimen]=B (in units of microT)
        '''

        pars = {}
        tmp_B = []
        for spec in list(Data_sample_or_site.keys()):
            if 'B' in list(Data_sample_or_site[spec].keys()):
                tmp_B.append(Data_sample_or_site[spec]['B'])
        if len(tmp_B) < 1:
            pars['N'] = 0
            pars['pass_or_fail'] = 'fail'
            return pars

        tmp_B = np.array(tmp_B)
        pars['pass_or_fail'] = 'pass'
        pars['N'] = len(tmp_B)
        pars['B_uT'] = np.mean(tmp_B)
        if len(tmp_B) > 1:
            pars['B_std_uT'] = np.std(tmp_B, ddof=1)
            pars['B_std_perc'] = 100 * (pars['B_std_uT'] / pars['B_uT'])
        else:
            pars['B_std_uT'] = 0
            pars['B_std_perc'] = 0
        pars['sample_int_interval_uT'] = (max(tmp_B) - min(tmp_B))
        pars['sample_int_interval_perc'] = 100 * \
            (pars['sample_int_interval_uT'] / pars['B_uT'])
        pars['fail_list'] = []
        # check if pass criteria
        #----------
        # int_n
        if self.acceptance_criteria['average_by_sample_or_site']['value'] == 'sample':
            average_by_sample_or_site = 'sample'
        else:
            average_by_sample_or_site = 'site'

        if average_by_sample_or_site == 'sample':
            cutoff_value = self.acceptance_criteria['sample_int_n']['value']
        else:
            cutoff_value = self.acceptance_criteria['site_int_n']['value']
        if cutoff_value != -999:
            if pars['N'] < cutoff_value:
                pars['pass_or_fail'] = 'fail'
                pars['fail_list'].append("int_n")
        #----------
        # int_sigma ; int_sigma_perc
        pass_sigma, pass_sigma_perc = False, False
        if self.acceptance_criteria['average_by_sample_or_site']['value'] == 'sample':
            sigma_cutoff_value = self.acceptance_criteria['sample_int_sigma']['value']
        else:
            sigma_cutoff_value = self.acceptance_criteria['site_int_sigma']['value']

        if sigma_cutoff_value != -999:
            if pars['B_std_uT'] * 1e-6 <= sigma_cutoff_value:
                pass_sigma = True

        if self.acceptance_criteria['average_by_sample_or_site']['value'] == 'sample':
            sigma_perc_cutoff_value = self.acceptance_criteria['sample_int_sigma_perc']['value']
        else:
            sigma_perc_cutoff_value = self.acceptance_criteria['site_int_sigma_perc']['value']
        if sigma_perc_cutoff_value != -999:
            if pars['B_std_perc'] <= sigma_perc_cutoff_value:
                pass_sigma_perc = True

        if not (sigma_cutoff_value == -999 and sigma_perc_cutoff_value == -999):
            if not (pass_sigma or pass_sigma_perc):
                pars['pass_or_fail'] = 'fail'
                pars['fail_list'].append("int_sigma")

        pass_int_interval, pass_int_interval_perc = False, False
        if self.acceptance_criteria['average_by_sample_or_site']['value'] == 'sample':
            cutoff_value = self.acceptance_criteria['sample_int_interval_uT']['value']
            if cutoff_value != -999:
                if pars['sample_int_interval_uT'] <= cutoff_value:
                    pass_int_interval = True

            cutoff_value_perc = self.acceptance_criteria['sample_int_interval_perc']['value']
            if cutoff_value_perc != -999:
                if pars['sample_int_interval_perc'] <= cutoff_value_perc:
                    pass_int_interval_perc = True

            if not (cutoff_value == -999 and cutoff_value_perc == -999):
                if not (pass_int_interval or pass_int_interval_perc):
                    pars['pass_or_fail'] = 'fail'
                    pars['fail_list'].append("int_interval")

            # if cutoff_value != -999 or cutoff_value_perc != -999:
            #    if not (pass_int_interval or pass_int_interval_perc):
            #        pars['pass_or_fail']='fail'
            #        pars['fail_list'].append("int_interval")

            #
            #
            #
            #
            # if (acceptance_criteria['sample_int_sigma_uT']==0 and acceptance_criteria['sample_int_sigma_perc']==0) or\
            #    (pars['B_uT'] <= acceptance_criteria['sample_int_sigma_uT'] or pars['B_std_perc'] <= acceptance_criteria['sample_int_sigma_perc']):
            #        if ( pars['sample_int_interval_uT'] <= acceptance_criteria['sample_int_interval_uT'] or pars['sample_int_interval_perc'] <= acceptance_criteria['sample_int_interval_perc']):
            #            pars['pass_or_fail']='pass'
        return(pars)

Response: Calculates the sample mean of the given samples_or_sites.


Instruction:
Implement a function in Python 3 to
convert all age units to calendar year

Response:
def convert_ages_to_calendar_year(self, er_ages_rec):
        '''
        convert all age units to calendar year
        '''
        if ("age" not in list(er_ages_rec.keys())) or (cb.is_null(er_ages_rec['age'], False)):
            return(er_ages_rec)
        if ("age_unit" not in list(er_ages_rec.keys())) or (cb.is_null(er_ages_rec['age_unit'])):
            return(er_ages_rec)
        if cb.is_null(er_ages_rec["age"], False):
            if "age_range_high" in list(er_ages_rec.keys()) and "age_range_low" in list(er_ages_rec.keys()):
                if cb.not_null(er_ages_rec["age_range_high"], False) and cb.not_null(er_ages_rec["age_range_low"], False):
                    er_ages_rec["age"] = np.mean(
                        [float(er_ages_rec["age_range_high"]), float(er_ages_rec["age_range_low"])])
        if cb.is_null(er_ages_rec["age"], False):
            return(er_ages_rec)

            # age_descriptier_ages_recon=er_ages_rec["age_description"]

        age_unit = er_ages_rec["age_unit"]

        # Fix 'age':
        mutliplier = 1
        if age_unit == "Ga":
            mutliplier = -1e9
        if age_unit == "Ma":
            mutliplier = -1e6
        if age_unit == "Ka":
            mutliplier = -1e3
        if age_unit == "Years AD (+/-)" or age_unit == "Years Cal AD (+/-)":
            mutliplier = 1
        if age_unit == "Years BP" or age_unit == "Years Cal BP":
            mutliplier = 1
        age = float(er_ages_rec["age"]) * mutliplier
        if age_unit == "Years BP" or age_unit == "Years Cal BP":
            age = 1950 - age
        er_ages_rec['age_cal_year'] = age

        # Fix 'age_range_low':
        age_range_low = age
        age_range_high = age
        age_sigma = 0

        if "age_sigma" in list(er_ages_rec.keys()) and cb.not_null(er_ages_rec["age_sigma"], False):
            age_sigma = float(er_ages_rec["age_sigma"]) * mutliplier
            if age_unit == "Years BP" or age_unit == "Years Cal BP":
                age_sigma = 1950 - age_sigma
            age_range_low = age - age_sigma
            age_range_high = age + age_sigma

        if "age_range_high" in list(er_ages_rec.keys()) and "age_range_low" in list(er_ages_rec.keys()):
            if cb.not_null(er_ages_rec["age_range_high"], False) and cb.not_null(er_ages_rec["age_range_low"], False):
                age_range_high = float(
                    er_ages_rec["age_range_high"]) * mutliplier
                if age_unit == "Years BP" or age_unit == "Years Cal BP":
                    age_range_high = 1950 - age_range_high
                age_range_low = float(
                    er_ages_rec["age_range_low"]) * mutliplier
                if age_unit == "Years BP" or age_unit == "Years Cal BP":
                    age_range_low = 1950 - age_range_low
        er_ages_rec['age_cal_year_range_low'] = age_range_low
        er_ages_rec['age_cal_year_range_high'] = age_range_high

        return(er_ages_rec)


Instruction:
Can you generate a brief explanation for the following Python 3 code
def get_new_T_PI_parameters(self, event):

        # remember the last saved interpretation
        if "saved" in list(self.pars.keys()):
            if self.pars['saved']:
                self.last_saved_pars = {}
                for key in list(self.pars.keys()):
                    self.last_saved_pars[key] = self.pars[key]
        self.pars['saved'] = False
        t1 = self.tmin_box.GetValue()
        t2 = self.tmax_box.GetValue()

        if (t1 == "" or t2 == ""):
            print("empty interpretation bounds")
            return
        if float(t2) < float(t1):
            print("upper bound less than lower bound")
            return

        index_1 = self.T_list.index(t1)
        index_2 = self.T_list.index(t2)

        # if (index_2-index_1)+1 >= self.acceptance_criteria['specimen_int_n']:
        if (index_2 - index_1) + 1 >= 3:
            if self.Data[self.s]['T_or_MW'] != "MW":
                self.pars = thellier_gui_lib.get_PI_parameters(self.Data, self.acceptance_criteria, self.preferences, self.s, float(
                    t1) + 273., float(t2) + 273., self.GUI_log, THERMAL, MICROWAVE)
                self.Data[self.s]['pars'] = self.pars
            else:
                self.pars = thellier_gui_lib.get_PI_parameters(
                    self.Data, self.acceptance_criteria, self.preferences, self.s, float(t1), float(t2), self.GUI_log, THERMAL, MICROWAVE)
                self.Data[self.s]['pars'] = self.pars
            self.update_GUI_with_new_interpretation()
            self.Add_text(self.s)

Response: get new interpretation parameters for temperatures


Instruction:
Explain what the following Python 3 code does
def add_thellier_gui_criteria(self):
        '''criteria used only in thellier gui
        these criteria are not written to pmag_criteria.txt
        '''
        category = "thellier_gui"
        for crit in ['sample_int_n_outlier_check', 'site_int_n_outlier_check']:
            self.acceptance_criteria[crit] = {}
            self.acceptance_criteria[crit]['category'] = category
            self.acceptance_criteria[crit]['criterion_name'] = crit
            self.acceptance_criteria[crit]['value'] = -999
            self.acceptance_criteria[crit]['threshold_type'] = "low"
            self.acceptance_criteria[crit]['decimal_points'] = 0

        for crit in ['sample_int_interval_uT', 'sample_int_interval_perc',
                     'site_int_interval_uT', 'site_int_interval_perc',
                     'sample_int_BS_68_uT', 'sample_int_BS_95_uT', 'sample_int_BS_68_perc', 'sample_int_BS_95_perc', 'specimen_int_max_slope_diff']:
            self.acceptance_criteria[crit] = {}
            self.acceptance_criteria[crit]['category'] = category
            self.acceptance_criteria[crit]['criterion_name'] = crit
            self.acceptance_criteria[crit]['value'] = -999
            self.acceptance_criteria[crit]['threshold_type'] = "high"
            if crit in ['specimen_int_max_slope_diff']:
                self.acceptance_criteria[crit]['decimal_points'] = -999
            else:
                self.acceptance_criteria[crit]['decimal_points'] = 1
            self.acceptance_criteria[crit]['comments'] = "thellier_gui_only"

        for crit in ['average_by_sample_or_site', 'interpreter_method']:
            self.acceptance_criteria[crit] = {}
            self.acceptance_criteria[crit]['category'] = category
            self.acceptance_criteria[crit]['criterion_name'] = crit
            if crit in ['average_by_sample_or_site']:
                self.acceptance_criteria[crit]['value'] = 'sample'
            if crit in ['interpreter_method']:
                self.acceptance_criteria[crit]['value'] = 'stdev_opt'
            self.acceptance_criteria[crit]['threshold_type'] = "flag"
            self.acceptance_criteria[crit]['decimal_points'] = -999

        for crit in ['include_nrm']:
            self.acceptance_criteria[crit] = {}
            self.acceptance_criteria[crit]['category'] = category
            self.acceptance_criteria[crit]['criterion_name'] = crit
            self.acceptance_criteria[crit]['value'] = True
            self.acceptance_criteria[crit]['threshold_type'] = "bool"
            self.acceptance_criteria[crit]['decimal_points'] = -999

        # define internal Thellier-GUI definitions:
        self.average_by_sample_or_site = 'sample'
        self.stdev_opt = True
        self.bs = False
        self.bs_par = False

Response: add the available criteria used only in thellier gui only