Пример #1
0
def main():
    """
    NAME
        zeq_magic.py

    DESCRIPTION
        reads in magic_measurements formatted file, makes plots of remanence decay
        during demagnetization experiments.  Reads in prior interpretations saved in
        a pmag_specimens formatted file [and  allows re-interpretations of best-fit lines
        and planes and saves (revised or new) interpretations in a pmag_specimens file.
        interpretations are saved in the coordinate system used. Also allows judicious editting of
        measurements to eliminate "bad" measurements.  These are marked as such in the magic_measurements
        input file.  they are NOT deleted, just ignored. ] Bracketed part not yet implemented

    SYNTAX
        zeq_magic.py [command line options]

    OPTIONS
        -h prints help message and quits
        -f  MEASFILE: sets measurements format input file, default: measurements.txt
        -fsp SPECFILE: sets specimens format file with prior interpreations, default: specimens.txt
        -fsa SAMPFILE: sets samples format file sample=>site information, default: samples.txt
        -fsi SITEFILE: sets sites format file with site=>location informationprior interpreations, default: samples.txt
        -Fp PLTFILE: sets filename for saved plot, default is name_type.fmt (where type is zijd, eqarea or decay curve)
        -crd [s,g,t]: sets coordinate system,  g=geographic, t=tilt adjusted, default: specimen coordinate system
        -spc SPEC  plots single specimen SPEC, saves plot with specified format
              with optional -dir settings and quits
        -dir [L,P,F][beg][end]: sets calculation type for principal component analysis, default is none
             beg: starting step for PCA calculation
             end: ending step for PCA calculation
             [L,P,F]: calculation type for line, plane or fisher mean
             must be used with -spc option
        -fmt FMT: set format of saved plot [png,svg,jpg]
        -A:  suppresses averaging of  replicate measurements, default is to average
        -sav: saves all plots without review
    SCREEN OUTPUT:
        Specimen, N, a95, StepMin, StepMax, Dec, Inc, calculation type

    """
    # initialize some variables
    doave, e, b = 1, 0, 0  # average replicates, initial end and beginning step
    intlist = ['magn_moment', 'magn_volume', 'magn_mass', 'magnitude']
    plots, coord = 0, 's'
    noorient = 0
    version_num = pmag.get_version()
    verbose = pmagplotlib.verbose
    calculation_type, fmt = "", "svg"
    user, spec_keys, locname = "", [], ''
    geo, tilt, ask = 0, 0, 0
    PriorRecs = []  # empty list for prior interpretations
    backup = 0
    specimen = ""  # can skip everything and just plot one specimen with bounds e,b
    if '-h' in sys.argv:
        print(main.__doc__)
        sys.exit()
    dir_path = pmag.get_named_arg_from_sys("-WD", default_val=os.getcwd())
    meas_file = pmag.get_named_arg_from_sys("-f",
                                            default_val="measurements.txt")
    spec_file = pmag.get_named_arg_from_sys("-fsp",
                                            default_val="specimens.txt")
    samp_file = pmag.get_named_arg_from_sys("-fsa", default_val="samples.txt")
    site_file = pmag.get_named_arg_from_sys("-fsi", default_val="sites.txt")
    #meas_file = os.path.join(dir_path, meas_file)
    #spec_file = os.path.join(dir_path, spec_file)
    #samp_file = os.path.join(dir_path, samp_file)
    #site_file = os.path.join(dir_path, site_file)
    plot_file = pmag.get_named_arg_from_sys("-Fp", default_val="")
    crd = pmag.get_named_arg_from_sys("-crd", default_val="s")
    if crd == "s":
        coord = "-1"
    elif crd == "t":
        coord = "100"
    else:
        coord = "0"
    fmt = pmag.get_named_arg_from_sys("-fmt", "svg")
    specimen = pmag.get_named_arg_from_sys("-spc", default_val="")
    beg_pca, end_pca = "", ""
    if '-dir' in sys.argv:
        ind = sys.argv.index('-dir')
        direction_type = sys.argv[ind + 1]
        beg_pca = int(sys.argv[ind + 2])
        end_pca = int(sys.argv[ind + 3])
        if direction_type == 'L':
            calculation_type = 'DE-BFL'
        if direction_type == 'P':
            calculation_type = 'DE-BFP'
        if direction_type == 'F':
            calculation_type = 'DE-FM'
    if '-A' in sys.argv:
        doave = 0
    if '-sav' in sys.argv:
        plots, verbose = 1, 0
    #
    first_save = 1
    fnames = {
        'measurements': meas_file,
        'specimens': spec_file,
        'samples': samp_file,
        'sites': site_file
    }
    contribution = nb.Contribution(
        dir_path,
        custom_filenames=fnames,
        read_tables=['measurements', 'specimens', 'samples', 'sites'])
    #
    #   import  specimens

    specimen_cols = [
        'analysts', 'aniso_ftest', 'aniso_ftest12', 'aniso_ftest23', 'aniso_s',
        'aniso_s_mean', 'aniso_s_n_measurements', 'aniso_s_sigma',
        'aniso_s_unit', 'aniso_tilt_correction', 'aniso_type', 'aniso_v1',
        'aniso_v2', 'aniso_v3', 'citations', 'description', 'dir_alpha95',
        'dir_comp', 'dir_dec', 'dir_inc', 'dir_mad_free', 'dir_n_measurements',
        'dir_tilt_correction', 'experiments', 'geologic_classes',
        'geologic_types', 'hyst_bc', 'hyst_bcr', 'hyst_mr_moment',
        'hyst_ms_moment', 'int_abs', 'int_b', 'int_b_beta', 'int_b_sigma',
        'int_corr', 'int_dang', 'int_drats', 'int_f', 'int_fvds', 'int_gamma',
        'int_mad_free', 'int_md', 'int_n_measurements', 'int_n_ptrm', 'int_q',
        'int_rsc', 'int_treat_dc_field', 'lithologies', 'meas_step_max',
        'meas_step_min', 'meas_step_unit', 'method_codes', 'sample',
        'software_packages', 'specimen'
    ]
    if 'specimens' in contribution.tables:
        #        contribution.propagate_name_down('sample','measurements')
        spec_container = contribution.tables['specimens']
        prior_spec_data = spec_container.get_records_for_code(
            'LP-DIR', strict_match=False
        )  # look up all prior directional interpretations
#
#  tie sample names to measurement data
#
    else:
        spec_container, prior_spec_data = None, []

#
#   import samples  for orientation info
#
    if 'samples' in contribution.tables:
        #        contribution.propagate_name_down('site','measurements')
        contribution.propagate_cols(
            col_names=['azimuth', 'dip', 'orientation_flag'],
            target_df_name='measurements',
            source_df_name='samples')
#
# define figure numbers for equal area, zijderveld,
#  and intensity vs. demagnetiztion step respectively
#
    ZED = {}
    ZED['eqarea'], ZED['zijd'], ZED['demag'] = 1, 2, 3
    pmagplotlib.plot_init(ZED['eqarea'], 6, 6)
    pmagplotlib.plot_init(ZED['zijd'], 6, 6)
    pmagplotlib.plot_init(ZED['demag'], 6, 6)
    #    save_pca=0
    angle, direction_type, setangle = "", "", 0
    #   create measurement dataframe
    #
    meas_container = contribution.tables['measurements']
    meas_data = meas_container.df
    #
    meas_data = meas_data[meas_data['method_codes'].str.contains(
        'LT-NO|LT-AF-Z|LT-T-Z|LT-M-Z') == True]  # fish out steps for plotting
    meas_data = meas_data[meas_data['method_codes'].str.contains(
        'AN|ARM|LP-TRM|LP-PI-ARM') == False]  # strip out unwanted experiments
    intensity_types = [
        col_name for col_name in meas_data.columns if col_name in intlist
    ]
    # plot first intensity method found - normalized to initial value anyway -
    # doesn't matter which used
    int_key = intensity_types[0]
    # get all the non-null intensity records of the same type
    meas_data = meas_data[meas_data[int_key].notnull()]
    if 'flag' not in meas_data.columns:
        meas_data['flag'] = 'g'  # set the default flag to good
# need to treat LP-NO specially  for af data, treatment should be zero,
# otherwise 273.
    meas_data['treatment'] = meas_data['treat_ac_field'].where(
        cond=meas_data['treat_ac_field'] != '0', other=meas_data['treat_temp'])
    meas_data['ZI'] = 1  # initialize these to one
    meas_data['instrument_codes'] = ""  # initialize these to blank
    #   for unusual case of microwave power....
    if 'treat_mw_power' in meas_data.columns:
        meas_data.loc[
            meas_data.treat_mw_power != 0,
            'treatment'] = meas_data.treat_mw_power * meas_data.treat_mw_time
#
# get list of unique specimen names from measurement data
#
# this is a list of all the specimen names
    specimen_names = meas_data.specimen.unique()
    specimen_names = specimen_names.tolist()
    specimen_names.sort()
    #
    # set up new DataFrame for this sessions specimen interpretations
    #
    data_container = nb.MagicDataFrame(dtype='specimens',
                                       columns=specimen_cols)
    # this is for interpretations from this session
    current_spec_data = data_container.df
    locname = 'LookItUp'
    if specimen == "":
        k = 0
    else:
        k = specimen_names.index(specimen)
    # let's look at the data now
    while k < len(specimen_names):
        # set the current specimen for plotting
        this_specimen = specimen_names[k]
        if verbose and this_specimen != "":
            print(this_specimen, k + 1, 'out of ', len(specimen_names))
        if setangle == 0:
            angle = ""
        this_specimen_measurements = meas_data[
            meas_data['specimen'].str.contains(
                this_specimen) == True]  # fish out this specimen
        this_specimen_measurements = this_specimen_measurements[
            this_specimen_measurements['flag'].str.contains(
                'g') == True]  # fish out this specimen
        if len(this_specimen_measurements) != 0:  # if there are measurements
            #
            #    set up datablock [[treatment,dec, inc, int, direction_type],[....]]
            #
            #
            # figure out the method codes
            #
            units, methods, title = "", "", this_specimen
            # this is a list of all the specimen method codes`
            meas_meths = this_specimen_measurements.method_codes.unique()
            tr = pd.to_numeric(this_specimen_measurements.treatment).tolist()
            if set(tr) == set([0]):
                k += 1
                continue
            for m in meas_meths:
                if 'LT-AF-Z' in m:
                    units = 'T'  # units include tesla
                    tr[0] = 0
                if 'LT-T-Z' in m:
                    units = units + ":K"  # units include kelvin
                if 'LT-M-Z' in m:
                    units = units + ':J'  # units include joules
                    tr[0] = 0
                units = units.strip(':')  # strip off extra colons
                if 'LP-' in m:
                    methods = methods + ":" + m
            decs = pd.to_numeric(this_specimen_measurements.dir_dec).tolist()
            incs = pd.to_numeric(this_specimen_measurements.dir_inc).tolist()
            #
            #    fix the coordinate system
            #
            if coord != '-1':  # need to transform coordinates to geographic

                azimuths = pd.to_numeric(this_specimen_measurements.azimuth
                                         ).tolist()  # get the azimuths
                # get the azimuths
                dips = pd.to_numeric(this_specimen_measurements.dip).tolist()
                dirs = [decs, incs, azimuths, dips]
                # this transposes the columns and rows of the list of lists
                dirs_geo = np.array(list(map(list, list(zip(*dirs)))))
                decs, incs = pmag.dogeo_V(dirs_geo)
                if coord == '100':  # need to do tilt correction too
                    bed_dip_dirs = pd.to_numeric(
                        this_specimen_measurements.bed_dip_dir).tolist(
                        )  # get the azimuths
                    bed_dips = pd.to_numeric(this_specimen_measurements.bed_dip
                                             ).tolist()  # get the azimuths
                    dirs = [decs, incs, bed_dip_dirs, bed_dips]
                    # this transposes the columns and rows of the list of lists
                    dirs_tilt = np.array(list(map(list, list(zip(*dirs)))))
                    decs, incs = pmag.dotilt_V(dirs_tilt)
                    title = title + '_t'
                else:
                    title = title + '_g'
            if angle == "":
                angle = decs[0]
            ints = pd.to_numeric(this_specimen_measurements[int_key]).tolist()
            ZI = this_specimen_measurements.ZI.tolist()
            flags = this_specimen_measurements.flag.tolist()
            codes = this_specimen_measurements.instrument_codes.tolist()
            datalist = [tr, decs, incs, ints, ZI, flags, codes]
            # this transposes the columns and rows of the list of lists
            datablock = list(map(list, list(zip(*datalist))))
            pmagplotlib.plotZED(ZED, datablock, angle, title, units)
            if verbose:
                pmagplotlib.drawFIGS(ZED)
#
#     collect info for current_specimen_interpretation dictionary
#
            if beg_pca == "" and len(prior_spec_data) != 0:
                #
                #     find prior interpretation
                #
                prior_specimen_interpretations = prior_spec_data[
                    prior_spec_data['specimen'].str.contains(
                        this_specimen) == True]
                beg_pcas = pd.to_numeric(prior_specimen_interpretations.
                                         meas_step_min.values).tolist()
                end_pcas = pd.to_numeric(prior_specimen_interpretations.
                                         meas_step_max.values).tolist()
                spec_methods = prior_specimen_interpretations.method_codes.tolist(
                )
                # step through all prior interpretations and plot them
                for ind in range(len(beg_pcas)):
                    spec_meths = spec_methods[ind].split(':')
                    for m in spec_meths:
                        if 'DE-BFL' in m:
                            calculation_type = 'DE-BFL'  # best fit line
                        if 'DE-BFP' in m:
                            calculation_type = 'DE-BFP'  # best fit plane
                        if 'DE-FM' in m:
                            calculation_type = 'DE-FM'  # fisher mean
                        if 'DE-BFL-A' in m:
                            calculation_type = 'DE-BFL-A'  # anchored best fit line
                    start, end = tr.index(beg_pcas[ind]), tr.index(
                        end_pcas[ind]
                    )  # getting the starting and ending points
                    # calculate direction/plane
                    mpars = pmag.domean(datablock, start, end,
                                        calculation_type)
                    if mpars["specimen_direction_type"] != "Error":
                        # put it on the plot
                        pmagplotlib.plotDir(ZED, mpars, datablock, angle)
                        if verbose:
                            pmagplotlib.drawFIGS(ZED)
            else:
                start, end = int(beg_pca), int(end_pca)
                # calculate direction/plane
                mpars = pmag.domean(datablock, start, end, calculation_type)
                if mpars["specimen_direction_type"] != "Error":
                    # put it on the plot
                    pmagplotlib.plotDir(ZED, mpars, datablock, angle)
                    if verbose:
                        pmagplotlib.drawFIGS(ZED)
            if plots == 1 or specimen != "":
                if plot_file == "":
                    basename = title
                else:
                    basename = plot_file
                files = {}
                for key in list(ZED.keys()):
                    files[key] = basename + '_' + key + '.' + fmt
                pmagplotlib.saveP(ZED, files)
                if specimen != "":
                    sys.exit()
            if verbose:
                recnum = 0
                for plotrec in datablock:
                    if units == 'T':
                        print('%s: %i  %7.1f %s  %8.3e %7.1f %7.1f %s' %
                              (plotrec[5], recnum, plotrec[0] * 1e3, " mT",
                               plotrec[3], plotrec[1], plotrec[2], plotrec[6]))
                    if units == "K":
                        print('%s: %i  %7.1f %s  %8.3e %7.1f %7.1f %s' %
                              (plotrec[5], recnum, plotrec[0] - 273, ' C',
                               plotrec[3], plotrec[1], plotrec[2], plotrec[6]))
                    if units == "J":
                        print('%s: %i  %7.1f %s  %8.3e %7.1f %7.1f %s' %
                              (plotrec[5], recnum, plotrec[0], ' J',
                               plotrec[3], plotrec[1], plotrec[2], plotrec[6]))
                    if 'K' in units and 'T' in units:
                        if plotrec[0] >= 1.:
                            print('%s: %i  %7.1f %s  %8.3e %7.1f %7.1f %s' %
                                  (plotrec[5], recnum, plotrec[0] - 273, ' C',
                                   plotrec[3], plotrec[1], plotrec[2],
                                   plotrec[6]))
                        if plotrec[0] < 1.:
                            print('%s: %i  %7.1f %s  %8.3e %7.1f %7.1f %s' %
                                  (plotrec[5], recnum, plotrec[0] * 1e3, " mT",
                                   plotrec[3], plotrec[1], plotrec[2],
                                   plotrec[6]))
                    recnum += 1
            # we have a current interpretation
            elif mpars["specimen_direction_type"] != "Error":
                #
                # create a new specimen record for the interpreation for this
                # specimen
                this_specimen_interpretation = {
                    col: ""
                    for col in specimen_cols
                }
                #               this_specimen_interpretation["analysts"]=user
                this_specimen_interpretation['software_packages'] = version_num
                this_specimen_interpretation['specimen'] = this_specimen
                this_specimen_interpretation["method_codes"] = calculation_type
                this_specimen_interpretation["meas_step_unit"] = units
                this_specimen_interpretation["meas_step_min"] = tr[start]
                this_specimen_interpretation["meas_step_max"] = tr[end]
                this_specimen_interpretation["dir_dec"] = '%7.1f' % (
                    mpars['specimen_dec'])
                this_specimen_interpretation["dir_inc"] = '%7.1f' % (
                    mpars['specimen_inc'])
                this_specimen_interpretation["dir_dang"] = '%7.1f' % (
                    mpars['specimen_dang'])
                this_specimen_interpretation["dir_n_measurements"] = '%i' % (
                    mpars['specimen_n'])
                this_specimen_interpretation["dir_tilt_correction"] = coord
                methods = methods.replace(" ", "")
                if "T" in units:
                    methods = methods + ":LP-DIR-AF"
                if "K" in units:
                    methods = methods + ":LP-DIR-T"
                if "J" in units:
                    methods = methods + ":LP-DIR-M"
                this_specimen_interpretation["method_codes"] = methods.strip(
                    ':')
                this_specimen_interpretation[
                    "experiments"] = this_specimen_measurements.experiment.unique(
                    )[0]
                #
                #   print some stuff
                #
                if calculation_type != 'DE-FM':
                    this_specimen_interpretation["dir_mad_free"] = '%7.1f' % (
                        mpars['specimen_mad'])
                    this_specimen_interpretation["dir_alpha95"] = ''
                    if verbose:
                        if units == 'K':
                            print(
                                '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %s \n'
                                %
                                (this_specimen_interpretation["specimen"],
                                 int(this_specimen_interpretation[
                                     "dir_n_measurements"]),
                                 float(this_specimen_interpretation[
                                     "dir_mad_free"]),
                                 float(
                                     this_specimen_interpretation["dir_dang"]),
                                 float(this_specimen_interpretation[
                                     "meas_step_min"]) - 273,
                                 float(this_specimen_interpretation[
                                     "meas_step_max"]) - 273,
                                 float(
                                     this_specimen_interpretation["dir_dec"]),
                                 float(
                                     this_specimen_interpretation["dir_inc"]),
                                 calculation_type))
                        elif units == 'T':
                            print(
                                '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %s \n'
                                %
                                (this_specimen_interpretation["specimen"],
                                 int(this_specimen_interpretation[
                                     "dir_n_measurements"]),
                                 float(this_specimen_interpretation[
                                     "dir_mad_free"]),
                                 float(
                                     this_specimen_interpretation["dir_dang"]),
                                 float(this_specimen_interpretation[
                                     "meas_step_min"]) * 1e3,
                                 float(this_specimen_interpretation[
                                     "meas_step_max"]) * 1e3,
                                 float(
                                     this_specimen_interpretation["dir_dec"]),
                                 float(
                                     this_specimen_interpretation["dir_inc"]),
                                 calculation_type))
                        elif 'T' in units and 'K' in units:
                            if float(this_specimen_interpretation[
                                    'meas_step_min']) < 1.0:
                                min = float(this_specimen_interpretation[
                                    'meas_step_min']) * 1e3
                            else:
                                min = float(this_specimen_interpretation[
                                    'meas_step_min']) - 273
                            if float(this_specimen_interpretation[
                                    'meas_step_max']) < 1.0:
                                max = float(this_specimen_interpretation[
                                    'meas_step_max']) * 1e3
                            else:
                                max = float(this_specimen_interpretation[
                                    'meas_step_max']) - 273
                            print(
                                '%s %i %7.1f %i %i %7.1f %7.1f %7.1f %s \n' %
                                (this_specimen_interpretation["specimen"],
                                 int(this_specimen_interpretation[
                                     "dir_n_measurements"]),
                                 float(this_specimen_interpretation[
                                     "dir_mad_free"]),
                                 float(
                                     this_specimen_interpretation["dir_dang"]),
                                 min, max,
                                 float(
                                     this_specimen_interpretation["dir_dec"]),
                                 float(
                                     this_specimen_interpretation["dir_inc"]),
                                 calculation_type))
                        else:
                            print(
                                '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %s \n'
                                %
                                (this_specimen_interpretation["specimen"],
                                 int(this_specimen_interpretation[
                                     "dir_n_measurements"]),
                                 float(this_specimen_interpretation[
                                     "dir_mad_free"]),
                                 float(
                                     this_specimen_interpretation["dir_dang"]),
                                 float(this_specimen_interpretation[
                                     "meas_step_min"]),
                                 float(this_specimen_interpretation[
                                     "meas_step_max"]),
                                 float(
                                     this_specimen_interpretation["dir_dec"]),
                                 float(
                                     this_specimen_interpretation["dir_inc"]),
                                 calculation_type))
                else:
                    this_specimen_interpretation["dir_alpha95"] = '%7.1f' % (
                        mpars['specimen_alpha95'])
                    this_specimen_interpretation["dir_mad_free"] = ''
                    if verbose:
                        if 'K' in units:
                            print(
                                '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %s \n'
                                %
                                (this_specimen_interpretation["specimen"],
                                 int(this_specimen_interpretation[
                                     "dir_n_measurments"]),
                                 float(this_specimen_interpretation[
                                     "dir_mad_free"]),
                                 float(
                                     this_specimen_interpretation["dir_dang"]),
                                 float(this_specimen_interpretation[
                                     "meas_step_min"]) - 273,
                                 float(this_specimen_interpretation[
                                     "meas_step_max"]) - 273,
                                 float(
                                     this_specimen_interpretation["dir_dec"]),
                                 float(
                                     this_specimen_interpretation["dir_inc"]),
                                 calculation_type))
                        elif 'T' in units:
                            print(
                                '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %s \n'
                                %
                                (this_specimen_interpretation["specimen"],
                                 int(this_specimen_interpretation[
                                     "dir_n_measurements"]),
                                 float(this_specimen_interpretation[
                                     "dir_alpha95"]),
                                 float(
                                     this_specimen_interpretation["dir_dang"]),
                                 float(this_specimen_interpretation[
                                     "meas_step_min"]) * 1e3,
                                 float(this_specimen_interpretation[
                                     "meas_step_max"]) * 1e3,
                                 float(
                                     this_specimen_interpretation["dir_dec"]),
                                 float(
                                     this_specimen_interpretation["dir_inc"]),
                                 calculation_type))
                        elif 'T' in units and 'K' in units:
                            if float(this_specimen_interpretation[
                                    'meas_step_min']) < 1.0:
                                min = float(this_specimen_interpretation[
                                    'meas_step_min']) * 1e3
                            else:
                                min = float(this_specimen_interpretation[
                                    'meas_step_min']) - 273
                            if float(this_specimen_interpretation[
                                    'meas_step_max']) < 1.0:
                                max = float(this_specimen_interpretation[
                                    'meas_step_max']) * 1e3
                            else:
                                max = float(this_specimen_interpretation[
                                    'meas_step_max']) - 273
                            print('%s %i %7.1f %i %i %7.1f %7.1f %s \n' % (
                                this_specimen_interpretation["specimen"],
                                int(this_specimen_interpretation[
                                    "dir_n_measurements"]),
                                float(
                                    this_specimen_interpretation["dir_alpha95"]
                                ), min, max,
                                float(this_specimen_interpretation["dir_dec"]),
                                float(this_specimen_interpretation["dir_inc"]),
                                calculation_type))
                        else:
                            print(
                                '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %s \n' %
                                (this_specimen_interpretation["specimen"],
                                 int(this_specimen_interpretation[
                                     "dir_n_measurements"]),
                                 float(this_specimen_interpretation[
                                     "dir_alpha95"]),
                                 float(this_specimen_interpretation[
                                     "meas_step_min"]),
                                 float(this_specimen_interpretation[
                                     "meas_step_max"]),
                                 float(
                                     this_specimen_interpretation["dir_dec"]),
                                 float(
                                     this_specimen_interpretation["dir_inc"]),
                                 calculation_type))
                if verbose:
                    saveit = input("Save this interpretation? [y]/n \n")
#   START HERE
#
#         if len(current_spec_data)==0: # no interpretations yet for this session
#             print "no current interpretation"
#             beg_pca,end_pca="",""
#             calculation_type=""
# get the ones that meet the current coordinate system
        else:
            print("no data")
        if verbose:
            input('Ready for next specimen  ')
        k += 1
Пример #2
0
def main():
    """
    NAME
        zeq_magic.py

    DESCRIPTION
        reads in magic_measurements formatted file, makes plots of remanence decay
        during demagnetization experiments.  Reads in prior interpretations saved in 
        a pmag_specimens formatted file and  allows re-interpretations of best-fit lines
        and planes and saves (revised or new) interpretations in a pmag_specimens file.  
        interpretations are saved in the coordinate system used. Also allows judicious editting of
        measurements to eliminate "bad" measurements.  These are marked as such in the magic_measurements
        input file.  they are NOT deleted, just ignored. 

    SYNTAX
        zeq_magic.py [command line options]

    OPTIONS
        -h prints help message and quits
        -f  MEASFILE: sets magic_measurements format input file, default: magic_measurements.txt
        -fsp SPECFILE: sets pmag_specimens format file with prior interpreations, default: zeq_specimens.txt
        -Fp PLTFILE: sets filename for saved plot, default is name_type.fmt (where type is zijd, eqarea or decay curve)
        -crd [s,g,t]: sets coordinate system,  g=geographic, t=tilt adjusted, default: specimen coordinate system
        -fsa SAMPFILE: sets er_samples format file with orientation information, default: er_samples.txt
        -spc SPEC  plots single specimen SPEC, saves plot with specified format 
              with optional -dir settings and quits
        -dir [L,P,F][beg][end]: sets calculation type for principal component analysis, default is none
             beg: starting step for PCA calculation
             end: ending step for PCA calculation
             [L,P,F]: calculation type for line, plane or fisher mean
             must be used with -spc option
        -fmt FMT: set format of saved plot [png,svg,jpg]
        -A:  suppresses averaging of  replicate measurements, default is to average
        -sav: saves all plots without review
    SCREEN OUTPUT:
        Specimen, N, a95, StepMin, StepMax, Dec, Inc, calculation type

    """
    # initialize some variables
    doave,e,b=1,0,0 # average replicates, initial end and beginning step
    plots,coord=0,'s'
    noorient=0
    version_num=pmag.get_version()
    verbose=pmagplotlib.verbose
    beg_pca,end_pca,direction_type="","",'l'
    calculation_type,fmt="","svg"
    user,spec_keys,locname="",[],''
    plot_file=""
    sfile=""
    plot_file=""
    PriorRecs=[] # empty list for prior interpretations
    backup=0
    specimen="" # can skip everything and just plot one specimen with bounds e,b
    if '-h' in sys.argv:
        print main.__doc__
        sys.exit()
    if '-WD' in sys.argv:
        ind=sys.argv.index('-WD')
        dir_path=sys.argv[ind+1]
    else:
        dir_path='.'
    inspec=dir_path+'/'+'zeq_specimens.txt'
    meas_file,geo,tilt,ask,samp_file=dir_path+'/magic_measurements.txt',0,0,0,dir_path+'/er_samples.txt'
    if '-f' in sys.argv:
        ind=sys.argv.index('-f')
        meas_file=dir_path+'/'+sys.argv[ind+1]
    if '-fsp' in sys.argv:
        ind=sys.argv.index('-fsp')
        inspec=dir_path+'/'+sys.argv[ind+1]
    if '-fsa' in sys.argv:
        ind=sys.argv.index('-fsa')
        samp_file=dir_path+'/'+sys.argv[ind+1]
        sfile='ok'
    if '-crd' in sys.argv:
        ind=sys.argv.index('-crd')
        coord=sys.argv[ind+1]
        if coord=='g' or coord=='t':
            samp_data,file_type=pmag.magic_read(samp_file)
            if file_type=='er_samples':sfile='ok'
            geo=1
            if coord=='t':tilt=1
    if '-spc' in sys.argv:
        ind=sys.argv.index('-spc')
        specimen=sys.argv[ind+1]
        if '-dir' in sys.argv:
            ind=sys.argv.index('-dir')
            direction_type=sys.argv[ind+1]
            beg_pca=int(sys.argv[ind+2])
            end_pca=int(sys.argv[ind+3])
            if direction_type=='L':calculation_type='DE-BFL'
            if direction_type=='P':calculation_type='DE-BFP'
            if direction_type=='F':calculation_type='DE-FM'
        if '-Fp' in sys.argv: 
            ind=sys.argv.index('-Fp')
            plot_file=dir_path+'/'+sys.argv[ind+1]
    if '-A' in sys.argv: doave=0
    if '-sav' in sys.argv: 
        plots=1
        verbose=0
    if '-fmt' in sys.argv:
        ind=sys.argv.index('-fmt')
        fmt=sys.argv[ind+1]
    #
    first_save=1
    meas_data,file_type=pmag.magic_read(meas_file)
    changeM,changeS=0,0 # check if data or interpretations have changed
    if file_type != 'magic_measurements':
        print file_type
        print file_type,"This is not a valid magic_measurements file " 
        sys.exit()
    for rec in  meas_data:
        if  "magic_method_codes" not in rec.keys(): rec["magic_method_codes"]=""
        methods=""
        tmp=rec["magic_method_codes"].replace(" ","").split(":")
        for meth in tmp:
            methods=methods+meth+":"
        rec["magic_method_codes"]=methods[:-1]  # get rid of annoying spaces in Anthony's export files 
        if "magic_instrument_codes" not in rec.keys() :rec["magic_instrument_codes"]=""
    PriorSpecs=[]
    PriorRecs,file_type=pmag.magic_read(inspec)
    if len(PriorRecs)==0: 
        if verbose:print "starting new file ",inspec
    for Rec in PriorRecs:
        if 'magic_software_packages' not in Rec.keys():Rec['magic_software_packages']=""
        if Rec['er_specimen_name'] not in PriorSpecs:
            if 'specimen_comp_name' not in Rec.keys():Rec['specimen_comp_name']="A"
            PriorSpecs.append(Rec['er_specimen_name'])
        else:
            if 'specimen_comp_name' not in Rec.keys():Rec['specimen_comp_name']="A"
        if "magic_method_codes" in Rec.keys():
            methods=[]
            tmp=Rec["magic_method_codes"].replace(" ","").split(":")
            for meth in tmp:
                methods.append(meth)
            if 'DE-FM' in methods:
                Rec['calculation_type']='DE-FM' # this won't be imported but helps
            if 'DE-BFL' in methods:
                Rec['calculation_type']='DE-BFL'
            if 'DE-BFL-A' in methods:
                Rec['calculation_type']='DE-BFL-A'
            if 'DE-BFL-O' in methods:
                Rec['calculation_type']='DE-BFL-O'
            if 'DE-BFP' in methods:
                Rec['calculation_type']='DE-BFP'
        else:
            Rec['calculation_type']='DE-BFL' # default is to assume a best-fit line
    #
    # get list of unique specimen names
    #
    sids=pmag.get_specs(meas_data)
    #
    #  set up plots, angle sets X axis to horizontal,  direction_type 'l' is best-fit line
    # direction_type='p' is great circle
    #     
    #
    # draw plots for sample s - default is just to step through zijderveld diagrams
    #
    #
    # define figure numbers for equal area, zijderveld,  
    #  and intensity vs. demagnetiztion step respectively
    ZED={}
    ZED['eqarea'],ZED['zijd'],  ZED['demag']=1,2,3 
    pmagplotlib.plot_init(ZED['eqarea'],5,5)
    pmagplotlib.plot_init(ZED['zijd'],6,5)
    pmagplotlib.plot_init(ZED['demag'],5,5)
    save_pca=0
    if specimen=="":
        k = 0
    else:
        k=sids.index(specimen)
    angle,direction_type="",""
    setangle=0
    CurrRecs=[]
    while k < len(sids):
        CurrRecs=[]
        if setangle==0:angle=""
        method_codes,inst_code=[],""
        s=sids[k]
        PmagSpecRec={}
        PmagSpecRec["er_analyst_mail_names"]=user
        PmagSpecRec['magic_software_packages']=version_num
        PmagSpecRec['specimen_description']=""
        PmagSpecRec['magic_method_codes']=""
        if verbose and  s!="":print s, k , 'out of ',len(sids)
    #
    #  collect info for the PmagSpecRec dictionary
    #
        s_meas=pmag.get_dictitem(meas_data,'er_specimen_name',s,'T') # fish out this specimen
        s_meas=pmag.get_dictitem(s_meas,'magic_method_codes','Z','has') # fish out zero field steps
        if len(s_meas)>0:
          for rec in  s_meas: # fix up a few things for the output record
               PmagSpecRec["magic_instrument_codes"]=rec["magic_instrument_codes"]  # copy over instruments
               PmagSpecRec["er_citation_names"]="This study"
               PmagSpecRec["er_specimen_name"]=s
               PmagSpecRec["er_sample_name"]=rec["er_sample_name"]
               PmagSpecRec["er_site_name"]=rec["er_site_name"]
               PmagSpecRec["er_location_name"]=rec["er_location_name"]
               locname=rec['er_location_name']
               if 'er_expedition_name' in rec.keys(): PmagSpecRec["er_expedition_name"]=rec["er_expedition_name"]
               PmagSpecRec["magic_method_codes"]=rec["magic_method_codes"]
               if "magic_experiment_name" not in rec.keys():
                   PmagSpecRec["magic_experiment_names"]=""
               else:    
                   PmagSpecRec["magic_experiment_names"]=rec["magic_experiment_name"]
               break
    #
    # find the data from the meas_data file for this specimen
    #
          data,units=pmag.find_dmag_rec(s,meas_data)
          PmagSpecRec["measurement_step_unit"]= units
          u=units.split(":")
          if "T" in units:PmagSpecRec["magic_method_codes"]=PmagSpecRec["magic_method_codes"]+":LP-DIR-AF"
          if "K" in units:PmagSpecRec["magic_method_codes"]=PmagSpecRec["magic_method_codes"]+":LP-DIR-T"
          if "J" in units:PmagSpecRec["magic_method_codes"]=PmagSpecRec["magic_method_codes"]+":LP-DIR-M"
    #
    # find prior interpretation
    #
          if len(CurrRecs)==0: # check if already in
            beg_pca,end_pca="",""
            calculation_type=""
            if inspec !="":
              if verbose: print "    looking up previous interpretations..."
              precs=pmag.get_dictitem(PriorRecs,'er_specimen_name',s,'T') # get all the prior recs with this specimen name
              precs=pmag.get_dictitem(precs,'magic_method_codes','LP-DIR','has') # get the directional data
              PriorRecs=pmag.get_dictitem(PriorRecs,'er_specimen_name',s,'F') # take them all out of prior recs
         # get the ones that meet the current coordinate system
              for prec in precs:
                if 'specimen_tilt_correction' not in prec.keys() or prec['specimen_tilt_correction']=='-1':
                    crd='s'
                elif prec['specimen_tilt_correction']=='0':
                    crd='g'
                elif prec['specimen_tilt_correction']=='100':
                    crd='t'
                else:
                    crd='?'
                CurrRec={}
                for key in prec.keys():CurrRec[key]=prec[key]
                CurrRecs.append(CurrRec) # put in CurrRecs
                method_codes= CurrRec["magic_method_codes"].replace(" ","").split(':')
                calculation_type='DE-BFL'
                if 'DE-FM' in method_codes: calculation_type='DE-FM'
                if 'DE-BFP' in method_codes: calculation_type='DE-BFP'
                if 'DE-BFL-A' in method_codes: calculation_type='DE-BFL-A'
                if 'specimen_dang' not in CurrRec.keys():
                    if verbose:print 'Run mk_redo.py and zeq_magic_redo.py to get the specimen_dang values'
                    CurrRec['specimen_dang']=-1
                if calculation_type!='DE-FM' and crd==coord: # not a fisher mean
                    if verbose:print "Specimen  N    MAD    DANG  start     end      dec     inc  type  component coordinates"
                    if units=='K':
                            if verbose:print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f  %s  %s       %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_mad"]),float(CurrRec["specimen_dang"]),float(CurrRec["measurement_step_min"])-273,float(CurrRec["measurement_step_max"])-273,float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,CurrRec['specimen_comp_name'],crd)
                    elif units=='T':
                       if verbose:print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f  %s  %s %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_mad"]),float(CurrRec["specimen_dang"]),float(CurrRec["measurement_step_min"])*1e3,float(CurrRec["measurement_step_max"])*1e3,float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,CurrRec['specimen_comp_name'],crd)
                    elif 'T' in units and 'K' in units:
                            if float(CurrRec['measurement_step_min'])<1.0 :
                                min=float(CurrRec['measurement_step_min'])*1e3
                            else:
                                min=float(CurrRec['measurement_step_min'])-273
                            if float(CurrRec['measurement_step_max'])<1.0 :
                                max=float(CurrRec['measurement_step_max'])*1e3
                            else:
                                max=float(CurrRec['measurement_step_max'])-273
                            if verbose:print '%s %i %7.1f %i %i %7.1f %7.1f %7.1f, %s        %s\n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_mad"]),float(CurrRec['specimen_dang']),min,max,float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,crd)
                    elif 'J' in units:
                       if verbose:print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f  %s  %s       %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_mad"]),float(CurrRec['specimen_dang']),float(CurrRec["measurement_step_min"]),float(CurrRec["measurement_step_max"]),float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,CurrRec['specimen_comp_name'],crd)
                elif calculation_type=='DE-FM' and crd==coord: # fisher mean
                    if verbose:print "Specimen  a95 DANG   start     end      dec     inc  type  component coordinates"
                    if units=='K':
                         if verbose:print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f  %s  %s       %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_alpha95"]),float(CurrRec["measurement_step_min"])-273,float(CurrRec["measurement_step_max"])-273,float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,CurrRec['specimen_comp_name'],crd)
                    elif units=='T':
                          if verbose:print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f  %s  %s       %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_alpha95"]),float(CurrRec["measurement_step_min"])*1e3,float(CurrRec["measurement_step_max"])*1e3,float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,CurrRec['specimen_comp_name'],crd)
                    elif 'T' in units and 'K' in units:
                            if float(CurrRec['measurement_step_min'])<1.0 :
                                min=float(CurrRec['measurement_step_min'])*1e3
                            else:
                                min=float(CurrRec['measurement_step_min'])-273
                            if float(CurrRec['measurement_step_max'])<1.0 :
                                max=float(CurrRec['measurement_step_max'])*1e3
                            else:
                                max=float(CurrRec['measurement_step_max'])-273
                            if verbose:print '%s %i %7.1f %i %i %7.1f %7.1f %s       %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_alpha95"]),min,max,float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,crd)
                    elif 'J' in units:
                       if verbose:print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %s %s       %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_mad"]),float(CurrRec["measurement_step_min"]),float(CurrRec["measurement_step_max"]),float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,CurrRec['specimen_comp_name'],crd)
              if len(CurrRecs)==0:beg_pca,end_pca="",""
          datablock=data
          noskip=1
          if len(datablock) <3: 
            noskip=0
            if backup==0:
                k+=1
            else:
                k-=1
            if len(CurrRecs)>0:
                for rec in CurrRecs:
                    PriorRecs.append(rec)
            CurrRecs=[]
          else:
            backup=0 
          if noskip:
        #
        # find replicate measurements at given treatment step and average them
        #
#            step_meth,avedata=pmag.vspec(data)
#            if len(avedata) != len(datablock):
#                if doave==1: 
#                    method_codes.append("DE-VM")
#                    datablock=avedata
#        #
        # do geo or stratigraphic correction now
        #
            if geo==1:
        #
        # find top priority orientation method
                orient,az_type=pmag.get_orient(samp_data,PmagSpecRec["er_sample_name"])
                if az_type=='SO-NO':
                    if verbose: print "no orientation data for ",s 
                    orient["sample_azimuth"]=0
                    orient["sample_dip"]=0
                    noorient=1
                    method_codes.append("SO-NO")
                    orient["sample_azimuth"]=0
                    orient["sample_dip"]=0
                    orient["sample_bed_dip_azimuth"]=0
                    orient["sample_bed_dip"]=0
                    noorient=1
                    method_codes.append("SO-NO")
                else: 
                    noorient=0
        #
        #  if stratigraphic selected,  get stratigraphic correction
        #
                tiltblock,geoblock=[],[]
                for rec in datablock:
                    d_geo,i_geo=pmag.dogeo(rec[1],rec[2],float(orient["sample_azimuth"]),float(orient["sample_dip"]))
                    geoblock.append([rec[0],d_geo,i_geo,rec[3],rec[4],rec[5],rec[6]])
                    if tilt==1 and "sample_bed_dip" in orient.keys() and float(orient['sample_bed_dip'])!=0: 
                        d_tilt,i_tilt=pmag.dotilt(d_geo,i_geo,float(orient["sample_bed_dip_direction"]),float(orient["sample_bed_dip"]))
                        tiltblock.append([rec[0],d_tilt,i_tilt,rec[3],rec[4],rec[5],rec[6]])
                    if tilt==1: plotblock=tiltblock
                    if geo==1 and tilt==0:plotblock=geoblock
            if geo==0 and tilt==0: plotblock=datablock
    #
    # set the end pca point to last point  if not set
            if e==0 or e>len(plotblock)-1: e=len(plotblock)-1
            if angle=="": angle=plotblock[0][1] # rotate to NRM declination
            title=s+'_s'
            if geo==1 and tilt==0 and noorient!=1:title=s+'_g'
            if tilt==1 and noorient!=1:title=s+'_t'
            pmagplotlib.plotZED(ZED,plotblock,angle,title,units)
            if verbose:pmagplotlib.drawFIGS(ZED)
            if len(CurrRecs)!=0:
                for prec in CurrRecs:
                    if 'calculation_type' not in prec.keys():
                        calculation_type=''
                    else:
                        calculation_type=prec["calculation_type"]
                    direction_type=prec["specimen_direction_type"]
                    if calculation_type !="":
                        beg_pca,end_pca="",""
                        for j in range(len(datablock)):
                            if data[j][0]==float(prec["measurement_step_min"]):beg_pca=j
                            if data[j][0]==float(prec["measurement_step_max"]):end_pca=j
                        if beg_pca=="" or end_pca=="":  
                            if verbose:
                                print "something wrong with prior interpretation "
                            break
                    if calculation_type!="":
                        if beg_pca=="":beg_pca=0
                        if end_pca=="":end_pca=len(plotblock)-1
                        if geo==1 and tilt==0:
                            mpars=pmag.domean(geoblock,beg_pca,end_pca,calculation_type)
                            if mpars["specimen_direction_type"]!="Error":
                                pmagplotlib.plotDir(ZED,mpars,geoblock,angle)
                                if verbose:pmagplotlib.drawFIGS(ZED)
                        if geo==1 and tilt==1:
                            mpars=pmag.domean(tiltblock,beg_pca,end_pca,calculation_type)
                            if mpars["specimen_direction_type"]!="Error":
                                pmagplotlib.plotDir(ZED,mpars,tiltblock,angle)
                                if verbose:pmagplotlib.drawFIGS(ZED)
                        if geo==0 and tilt==0: 
                            mpars=pmag.domean(datablock,beg_pca,end_pca,calculation_type)
                        if mpars["specimen_direction_type"]!="Error":
                                pmagplotlib.plotDir(ZED,mpars,plotblock,angle)
                                if verbose:pmagplotlib.drawFIGS(ZED)
    #
    # print out data for this sample to screen
    #
            recnum=0
            for plotrec in plotblock:
                if units=='T' and verbose: print '%s: %i  %7.1f %s  %8.3e %7.1f %7.1f %s' % (plotrec[5], recnum,plotrec[0]*1e3," mT",plotrec[3],plotrec[1],plotrec[2],plotrec[6])
                if units=="K" and verbose: print '%s: %i  %7.1f %s  %8.3e %7.1f %7.1f %s' % (plotrec[5], recnum,plotrec[0]-273,' C',plotrec[3],plotrec[1],plotrec[2],plotrec[6])
                if units=="J" and verbose: print '%s: %i  %7.1f %s  %8.3e %7.1f %7.1f %s' % (plotrec[5], recnum,plotrec[0],' J',plotrec[3],plotrec[1],plotrec[2],plotrec[6])
                if 'K' in units and 'T' in units:
                    if plotrec[0]>=1. and verbose: print '%s: %i  %7.1f %s  %8.3e %7.1f %7.1f %s' % (plotrec[5], recnum,plotrec[0]-273,' C',plotrec[3],plotrec[1],plotrec[2],plotrec[6])
                    if plotrec[0]<1. and  verbose: print '%s: %i  %7.1f %s  %8.3e %7.1f %7.1f %s' % (plotrec[5], recnum,plotrec[0]*1e3," mT",plotrec[3],plotrec[1],plotrec[2],plotrec[6])
                recnum += 1
            if specimen!="":
                if plot_file=="":
                    basename=locname+'_'+s
                else:
                    basename=plot_file
                files={}
                for key in ZED.keys():
                    files[key]=basename+'_'+key+'.'+fmt 
                pmagplotlib.saveP(ZED,files)
                sys.exit()
            else:  # interactive
              if plots==0:
                ans='b'
                k+=1
                changeS=0
                while ans != "":
                    if len(CurrRecs)==0:
                        print """
                g/b: indicates  good/bad measurement.  "bad" measurements excluded from calculation

                set s[a]ve plot, [b]ounds for pca and calculate, [p]revious, [s]pecimen, 
                 change [h]orizontal projection angle,   change [c]oordinate systems, 
                 [e]dit data,  [q]uit: 
                """
                    else:
                        print """
                g/b: indicates  good/bad measurement.  "bad" measurements excluded from calculation

                 set s[a]ve plot, [b]ounds for pca and calculate, [p]revious, [s]pecimen, 
                 change [h]orizontal projection angle,   change [c]oordinate systems, 
                 [d]elete current interpretation(s), [e]dit data,   [q]uit: 
                """
                    ans=raw_input('<Return>  for  next specimen \n')
                    setangle=0
                    if ans=='d': # delete this interpretation
                        CurrRecs=[]
                        k-=1 # replot same specimen
                        ans=""
                        changeS=1
                    if  ans=='q': 
                        if changeM==1:
                            ans=raw_input('Save changes to magic_measurements.txt? y/[n] ')
                            if ans=='y':
                                pmag.magic_write(meas_file,meas_data,'magic_measurements')
                        print "Good bye"
                        sys.exit()
                    if  ans=='a':
                        if plot_file=="":
                            basename=locname+'_'+s+'_'
                        else:
                            basename=plot_file
                        files={}
                        for key in ZED.keys():
                            files[key]=basename+'_'+coord+'_'+key+'.'+fmt 
                        pmagplotlib.saveP(ZED,files)
                        ans=""
                    if  ans=='p':
                        k-=2
                        ans=""
                        backup=1
                    if ans=='c':
                        k-=1 # replot same block
                        if tilt==0 and geo ==1:print "You  are currently viewing geographic  coordinates "
                        if tilt==1 and geo ==1:print "You  are currently viewing stratigraphic  coordinates "
                        if tilt==0 and geo ==0: print "You  are currently viewing sample coordinates "
                        print "\n Which coordinate system do you wish to view? "
                        coord=raw_input(" <Return>  specimen, [g] geographic, [t] tilt corrected ")
                        if coord=="g":geo,tilt=1,0
                        if coord=="t":
                            geo=1
                            tilt=1
                        if coord=="":
                            coord='s'
                            geo=0
                            tilt=0
                        if geo==1 and sfile=="":
                            samp_file=raw_input(" Input er_samples file for sample orientations [er_samples.txt] " )
                            if samp_file=="":samp_file="er_samples.txt"
                            samp_data,file_type=pmag.magic_read(samp_file)
                            if file_type != 'er_samples':
                               print file_type
                               print "This is not a valid er_samples file - coordinate system not changed" 
                            else:
                               sfile="ok"
                        ans=""
                    if ans=='s':
                        keepon=1
                        sample=raw_input('Enter desired specimen name (or first part there of): ')
                        while keepon==1:
                            try:
                                k =sids.index(sample)
                                keepon=0
                            except:
                                tmplist=[]
                                for qq in range(len(sids)):
                                    if sample in sids[qq]:tmplist.append(sids[qq])
                                print sample," not found, but this was: "
                                print tmplist
                                sample=raw_input('Select one or try again\n ')
                        angle,direction_type="",""
                        setangle=0
                        ans=""
                    if ans=='h':
                        k-=1
                        angle=raw_input("Enter desired  declination for X axis 0-360 ")
                        angle=float(angle)
                        if angle==0:angle=0.001
                        s=sids[k]
                        setangle=1
                        ans=""
                    if  ans=='e':
                        k-=1
                        ans=""
                        recnum=0
                        for plotrec in plotblock:
                            if plotrec[0]<=200 and verbose: print '%s: %i  %7.1f %s  %8.3e %7.1f %7.1f ' % (plotrec[5], recnum,plotrec[0]*1e3," mT",plotrec[3],plotrec[1],plotrec[2])
                            if plotrec[0]>200 and verbose: print '%s: %i  %7.1f %s  %8.3e %7.1f %7.1f ' % (plotrec[5], recnum,plotrec[0]-273,' C',plotrec[3],plotrec[1],plotrec[2])
                            recnum += 1
                        answer=raw_input('Enter index of point to change from bad to good or vice versa:  ')
                        try: 
                                ind=int(answer)
                                meas_data=pmag.mark_dmag_rec(s,ind,meas_data)
                                changeM=1
                        except:
                                'bad entry, try again'
                    if  ans=='b':
                        if end_pca=="":end_pca=len(plotblock)-1
                        if beg_pca=="":beg_pca=0
                        k-=1   # stay on same sample until through
                        GoOn=0
                        while GoOn==0:
                            print 'Enter index of first point for pca: ','[',beg_pca,']'
                            answer=raw_input('return to keep default  ')
                            if answer != "":
                                beg_pca=int(answer)
                            print 'Enter index  of last point for pca: ','[',end_pca,']'
                            answer=raw_input('return to keep default  ')
                            try:
                                end_pca=int(answer) 
                                if plotblock[beg_pca][5]=='b' or plotblock[end_pca][5]=='b': 
                                    print "Can't select 'bad' measurement for PCA bounds -try again"
                                    end_pca=len(plotblock)-1
                                    beg_pca=0
                                elif beg_pca >=0 and beg_pca<=len(plotblock)-2 and end_pca>0 and end_pca<len(plotblock): 
                                    GoOn=1
                                else:
                                    print beg_pca,end_pca, " are bad entry of indices - try again"
                                    end_pca=len(plotblock)-1
                                    beg_pca=0
                            except:
                                print beg_pca,end_pca, " are bad entry of indices - try again"
                                end_pca=len(plotblock)-1
                                beg_pca=0
                        GoOn=0
                        while GoOn==0:
                            if calculation_type!="":
                                print "Prior calculation type = ",calculation_type
                            ct=raw_input('Enter new Calculation Type: best-fit line,  plane or fisher mean [l]/p/f :  ' )
                            if ct=="" or ct=="l": 
                                direction_type="l"
                                calculation_type="DE-BFL"
                                GoOn=1
                            elif ct=='p':
                                direction_type="p"
                                calculation_type="DE-BFP"
                                GoOn=1
                            elif ct=='f':
                                direction_type="l"
                                calculation_type="DE-FM"
                                GoOn=1
                            else: 
                                print "bad entry of calculation type: try again. "
                        pmagplotlib.plotZED(ZED,plotblock,angle,s,units)
                        if verbose:pmagplotlib.drawFIGS(ZED)
                        if geo==1 and tilt==0:
                            mpars=pmag.domean(geoblock,beg_pca,end_pca,calculation_type)
                            if mpars['specimen_direction_type']=='Error':break
                            PmagSpecRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
                            PmagSpecRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
                            if "SO-NO" not in method_codes:
                                PmagSpecRec["specimen_tilt_correction"]='0'
                                method_codes.append("DA-DIR-GEO")
                            else:
                                PmagSpecRec["specimen_tilt_correction"]='-1'
                            pmagplotlib.plotDir(ZED,mpars,geoblock,angle)
                            if verbose:pmagplotlib.drawFIGS(ZED)
                        if geo==1 and  tilt==1:
                            mpars=pmag.domean(tiltblock,beg_pca,end_pca,calculation_type)
                            if mpars['specimen_direction_type']=='Error':break
                            PmagSpecRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
                            PmagSpecRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
                            if "SO-NO" not in method_codes:
                                PmagSpecRec["specimen_tilt_correction"]='100'
                                method_codes.append("DA-DIR-TILT")
                            else:
                                PmagSpecRec["specimen_tilt_correction"]='-1'
                            pmagplotlib.plotDir(ZED,mpars,tiltblock,angle)
                            if verbose:pmagplotlib.drawFIGS(ZED)
                        if geo==0 and tilt==0: 
                            mpars=pmag.domean(datablock,beg_pca,end_pca,calculation_type)
                            if mpars['specimen_direction_type']=='Error':break
                            PmagSpecRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
                            PmagSpecRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
                            PmagSpecRec["specimen_tilt_correction"]='-1'
                            pmagplotlib.plotDir(ZED,mpars,plotblock,angle)
                            if verbose:pmagplotlib.drawFIGS(ZED)
                        PmagSpecRec["measurement_step_min"]='%8.3e ' %(mpars["measurement_step_min"])
                        PmagSpecRec["measurement_step_max"]='%8.3e ' %(mpars["measurement_step_max"])
                        PmagSpecRec["specimen_correction"]='u'
                        PmagSpecRec["specimen_dang"]='%7.1f ' %(mpars['specimen_dang'])
                        print 'DANG: ',PmagSpecRec["specimen_dang"]
                        if calculation_type!='DE-FM':
                            PmagSpecRec["specimen_mad"]='%7.1f ' %(mpars["specimen_mad"])
                            PmagSpecRec["specimen_alpha95"]=""
                        else:
                            PmagSpecRec["specimen_alpha95"]='%7.1f ' %(mpars["specimen_alpha95"])
                            PmagSpecRec["specimen_mad"]=""
                        PmagSpecRec["specimen_n"]='%i ' %(mpars["specimen_n"])
                        PmagSpecRec["specimen_direction_type"]=direction_type
                        PmagSpecRec["calculation_type"]=calculation_type # redundant and won't be imported - just for convenience
                        method_codes=PmagSpecRec["magic_method_codes"].split(':')
                        if len(method_codes) != 0:
                            methstring=""
                            for meth in method_codes:
                                ctype=meth.split('-')
                                if 'DE' not in ctype:methstring=methstring+ ":" +meth # don't include old direction estimation methods
                        methstring=methstring+':'+calculation_type
                        PmagSpecRec["magic_method_codes"]= methstring.strip(':')
                        print 'Method codes: ',PmagSpecRec['magic_method_codes']
                        if calculation_type!='DE-FM':
                            if units=='K': 
                                print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_mad"]),float(PmagSpecRec["specimen_dang"]),float(PmagSpecRec["measurement_step_min"])-273,float(PmagSpecRec["measurement_step_max"])-273,float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type)
                            elif units== 'T':
                                print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_mad"]),float(PmagSpecRec["specimen_dang"]),float(PmagSpecRec["measurement_step_min"])*1e3,float(PmagSpecRec["measurement_step_max"])*1e3,float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type)
                            elif 'T' in units and 'K' in units:
                                if float(PmagSpecRec['measurement_step_min'])<1.0 :
                                    min=float(PmagSpecRec['measurement_step_min'])*1e3
                                else:
                                    min=float(PmagSpecRec['measurement_step_min'])-273
                                if float(PmagSpecRec['measurement_step_max'])<1.0 :
                                    max=float(PmagSpecRec['measurement_step_max'])*1e3
                                else:
                                    max=float(PmagSpecRec['measurement_step_max'])-273
                                print '%s %i %7.1f %i %i %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_mad"]),float(PmagSpecRec["specimen_dang"]),min,max,float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type)
                            else:
                                print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_mad"]),float(PmagSpecRec["specimen_dang"]),float(PmagSpecRec["measurement_step_min"]),float(PmagSpecRec["measurement_step_max"]),float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type)
                        else:
                            if 'K' in units:
                                print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_alpha95"]),float(PmagSpecRec["specimen_dang"]),float(PmagSpecRec["measurement_step_min"])-273,float(PmagSpecRec["measurement_step_max"])-273,float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type)
                            elif 'T' in units:
                                print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_alpha95"]),float(PmagSpecRec["specimen_dang"]),float(PmagSpecRec["measurement_step_min"])*1e3,float(PmagSpecRec["measurement_step_max"])*1e3,float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type)
                            elif 'T' in units and 'K' in units:
                                if float(PmagSpecRec['measurement_step_min'])<1.0 :
                                    min=float(PmagSpecRec['measurement_step_min'])*1e3
                                else:
                                    min=float(PmagSpecRec['measurement_step_min'])-273
                                if float(PmagSpecRec['measurement_step_max'])<1.0 :
                                    max=float(PmagSpecRec['measurement_step_max'])*1e3
                                else:
                                    max=float(PmagSpecRec['measurement_step_max'])-273
                                print '%s %i %7.1f %i %i %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_alpha95"]),min,max,float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type)
                            else:
                                print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_alpha95"]),float(PmagSpecRec["measurement_step_min"]),float(PmagSpecRec["measurement_step_max"]),float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type)
                        saveit=raw_input("Save this interpretation? [y]/n \n")
                        if saveit!="n":
                            changeS=1
#
# put in details
#
                            angle,direction_type,setangle="","",0
                            if len(CurrRecs)>0:
                                replace=raw_input(" [0] add new component, or [1] replace existing interpretation(s) [default is replace] ")
                                if replace=="1" or replace=="":
                                    CurrRecs=[]
                                    PmagSpecRec['specimen_comp_name']='A'
                                    CurrRecs.append(PmagSpecRec)
                                else:
                                    print 'These are the current component names for this specimen: '
                                    for trec in CurrRecs:print trec['specimen_comp_name']
                                    compnum=raw_input("Enter new component name: ")
                                    PmagSpecRec['specimen_comp_name']=compnum
                                    print "Adding new component: ",PmagSpecRec['specimen_comp_name']
                                    CurrRecs.append(PmagSpecRec)
                            else:
                                PmagSpecRec['specimen_comp_name']='A'
                                CurrRecs.append(PmagSpecRec)
                            k+=1 
                            ans=""
                        else:
                            ans=""
              else:  # plots=1
                  k+=1
                  files={}
                  locname.replace('/','-')
                  print PmagSpecRec
                  for key in ZED.keys():
                      files[key]="LO:_"+locname+'_SI:_'+PmagSpecRec['er_site_name']+'_SA:_'+PmagSpecRec['er_sample_name']+'_SP:_'+s+'_CO:_'+coord+'_TY:_'+key+'_.'+fmt
                  if pmagplotlib.isServer:
                      black     = '#000000'
                      purple    = '#800080'
                      titles={}
                      titles['demag']='DeMag Plot'
                      titles['zijd']='Zijderveld Plot'
                      titles['eqarea']='Equal Area Plot'
                      ZED = pmagplotlib.addBorders(ZED,titles,black,purple)
                  pmagplotlib.saveP(ZED,files)
            if len(CurrRecs)>0:
                for rec in CurrRecs: PriorRecs.append(rec)
            if changeS==1:
                if len(PriorRecs)>0:
                    save_redo(PriorRecs,inspec)
                else:
                    os.system('rm '+inspec)
            CurrRecs,beg_pca,end_pca=[],"","" # next up
            changeS=0
        else: k+=1 # skip record - not enough data
    if changeM==1:
        pmag.magic_write(meas_file,meas_data,'magic_measurements')
Пример #3
0
def main():
    """
    NAME
       zeq.py
  
    DESCRIPTION
       plots demagnetization data. The equal area projection has the X direction (usually North in geographic coordinates)
          to the top.  The red line is the X axis of the Zijderveld diagram.  Solid symbols are lower hemisphere. 
          The solid (open) symbols in the Zijderveld diagram are X,Y (X,Z) pairs.  The demagnetization diagram plots the
          fractional remanence remaining after each step. The green line is the fraction of the total remaence removed 
          between each step.        

    INPUT FORMAT
       takes specimen_name treatment intensity declination inclination  in space
 delimited file

    SYNTAX
        zeq.py [command line options

    OPTIONS
        -f FILE for reading from command line
        -u [mT,C] specify units of mT OR C, default is unscaled
    """
    if '-h' in sys.argv: # check if help is needed
        print main.__doc__
        sys.exit() # graceful quit
    else:
        if '-f' in sys.argv:
            ind=sys.argv.index('-f')
            file=sys.argv[ind+1]
        else:
            print main.__doc__
            sys.exit()
        if '-u' in sys.argv:
            ind=sys.argv.index('-u')
            units=sys.argv[ind+1]
            if units=="C":SIunits="K"
            if units=="mT":SIunits="T"
        else:
            units="U"
            SIunits="U"
    f=open(file,'rU')
    data=f.readlines()
#
    datablock= [] # set up list for data
    fmt='svg' # default image format
    s="" # initialize specimen name
    angle=0.
    for line in data:   # read in the data from standard input
        rec=line.split() # split each line on space to get records
        if angle=="":angle=float(rec[3])
        if s=="":s=rec[0]
        if units=='mT':datablock.append([float(rec[1])*1e-3,float(rec[3]),float(rec[4]),1e-3*float(rec[2]),'','g']) # treatment, dec, inc, int # convert to T and Am^2 (assume emu)
        if units=='C':datablock.append([float(rec[1])+273.,float(rec[3]),float(rec[4]),1e-3*float(rec[2]),'','g']) # treatment, dec, inc, int, convert to K and Am^2, assume emu
        if units=='U':datablock.append([float(rec[1]),float(rec[3]),float(rec[4]),float(rec[2]),'','g']) # treatment, dec, inc, int, using unscaled units 
# define figure numbers in a dictionary for equal area, zijderveld,  
#  and intensity vs. demagnetiztion step respectively
    ZED={}
    ZED['eqarea'],ZED['zijd'],  ZED['demag']=1,2,3 
    pmagplotlib.plot_init(ZED['eqarea'],5,5) # initialize plots
    pmagplotlib.plot_init(ZED['zijd'],5,5)
    pmagplotlib.plot_init(ZED['demag'],5,5)
#
#
    pmagplotlib.plotZED(ZED,datablock,angle,s,SIunits) # plot the data
    pmagplotlib.drawFIGS(ZED)
    while 1:

#
# print out data for this sample to screen
#
        recnum=0
        for plotrec in datablock:
            if units=='mT':print '%i  %7.1f %8.3e %7.1f %7.1f ' % (recnum,plotrec[0]*1e3,plotrec[3],plotrec[1],plotrec[2])
            if units=='C':print '%i  %7.1f %8.3e %7.1f %7.1f ' % (recnum,plotrec[0]-273.,plotrec[3],plotrec[1],plotrec[2])
            if units=='U':print '%i  %7.1f %8.3e %7.1f %7.1f ' % (recnum,plotrec[0],plotrec[3],plotrec[1],plotrec[2])
            recnum += 1
        end_pca=len(datablock)-1 # initialize end_pca, beg_pca to first and last measurement
        beg_pca=0
        ans=raw_input(" s[a]ve plot, [b]ounds for pca and calculate, change [h]orizontal projection angle, [q]uit:   ")
        if ans =='q':
            sys.exit() 
        if  ans=='a':
            files={}
            for key in ZED.keys():
                files[key]=s+'_'+key+'.'+fmt 
            pmagplotlib.saveP(ZED,files)
        if ans=='h':
            angle=float(raw_input(" Declination to project onto horizontal axis? "))
            pmagplotlib.plotZED(ZED,datablock,angle,s,SIunits) # plot the data
        if ans=='b':
            GoOn=0
            while GoOn==0: # keep going until reasonable bounds are set
                print 'Enter index of first point for pca: ','[',beg_pca,']'
                answer=raw_input('return to keep default  ')
                if answer != "":beg_pca=int(answer)
                print 'Enter index  of last point for pca: ','[',end_pca,']'
                answer=raw_input('return to keep default  ')
                if answer != "":
                    end_pca=int(answer) 
                if beg_pca >=0 and beg_pca<=len(datablock)-2 and end_pca>0 and end_pca<len(datablock): 
                    GoOn=1
                else:
                    print "Bad entry of indices - try again"
                    end_pca=len(datablock)-1
                    beg_pca=0
            GoOn=0
            while GoOn==0:
                ct=raw_input('Enter Calculation Type: best-fit line,  plane or fisher mean [l]/p/f :  ' )
                if ct=="" or ct=="l": 
                    calculation_type="DE-BFL"
                    GoOn=1 # all good
                elif ct=='p':
                    calculation_type="DE-BFP"
                    GoOn=1 # all good
                elif ct=='f':
                    calculation_type="DE-FM"
                    GoOn=1 # all good
                else: 
                    print "bad entry of calculation type: try again. " # keep going
            pmagplotlib.plotZED(ZED,datablock,angle,s,SIunits) # plot the data
            mpars=pmag.domean(datablock,beg_pca,end_pca,calculation_type) # get best-fit direction/great circle
            pmagplotlib.plotDir(ZED,mpars,datablock,angle) # plot the best-fit direction/great circle
            print 'Specimen, calc_type, N, min, max, MAD, dec, inc'
            if units=='mT':print '%s %s %i  %6.2f %6.2f %6.1f %7.1f %7.1f' % (s,calculation_type,mpars["specimen_n"],mpars["measurement_step_min"]*1e3,mpars["measurement_step_max"]*1e3,mpars["specimen_mad"],mpars["specimen_dec"],mpars["specimen_inc"])
            if units=='C':print '%s %s %i  %6.2f %6.2f %6.1f %7.1f %7.1f' % (s,calculation_type,mpars["specimen_n"],mpars["measurement_step_min"]-273,mpars["measurement_step_max"]-273,mpars["specimen_mad"],mpars["specimen_dec"],mpars["specimen_inc"])
            if units=='U':print '%s %s %i  %6.2f %6.2f %6.1f %7.1f %7.1f' % (s,calculation_type,mpars["specimen_n"],mpars["measurement_step_min"],mpars["measurement_step_max"],mpars["specimen_mad"],mpars["specimen_dec"],mpars["specimen_inc"])
Пример #4
0
def main():
    """
    NAME
        zeq_magic.py

    DESCRIPTION
        reads in magic_measurements formatted file, makes plots of remanence decay
        during demagnetization experiments.  Reads in prior interpretations saved in
        a pmag_specimens formatted file [and  allows re-interpretations of best-fit lines
        and planes and saves (revised or new) interpretations in a pmag_specimens file.
        interpretations are saved in the coordinate system used. Also allows judicious editting of
        measurements to eliminate "bad" measurements.  These are marked as such in the magic_measurements
        input file.  they are NOT deleted, just ignored. ] Bracketed part not yet implemented

    SYNTAX
        zeq_magic.py [command line options]

    OPTIONS
        -h prints help message and quits
        -f  MEASFILE: sets measurements format input file, default: measurements.txt
        -fsp SPECFILE: sets specimens format file with prior interpreations, default: specimens.txt
        -fsa SAMPFILE: sets samples format file sample=>site information, default: samples.txt
        -fsi SITEFILE: sets sites format file with site=>location informationprior interpreations, default: samples.txt
        -Fp PLTFILE: sets filename for saved plot, default is name_type.fmt (where type is zijd, eqarea or decay curve)
        -crd [s,g,t]: sets coordinate system,  g=geographic, t=tilt adjusted, default: specimen coordinate system
        -spc SPEC  plots single specimen SPEC, saves plot with specified format
              with optional -dir settings and quits
        -dir [L,P,F][beg][end]: sets calculation type for principal component analysis, default is none
             beg: starting step for PCA calculation
             end: ending step for PCA calculation
             [L,P,F]: calculation type for line, plane or fisher mean
             must be used with -spc option
        -fmt FMT: set format of saved plot [png,svg,jpg]
        -A:  suppresses averaging of  replicate measurements, default is to average
        -sav: saves all plots without review
    SCREEN OUTPUT:
        Specimen, N, a95, StepMin, StepMax, Dec, Inc, calculation type

    """
    # initialize some variables
    doave, e, b = 1, 0, 0  # average replicates, initial end and beginning step
    intlist = ['magn_moment', 'magn_volume', 'magn_mass', 'magnitude']
    plots, coord = 0, 's'
    noorient = 0
    version_num = pmag.get_version()
    verbose = pmagplotlib.verbose
    calculation_type, fmt = "", "svg"
    user, spec_keys, locname = "", [], ''
    geo, tilt, ask = 0, 0, 0
    PriorRecs = []  # empty list for prior interpretations
    backup = 0
    specimen = ""  # can skip everything and just plot one specimen with bounds e,b
    if '-h' in sys.argv:
        print(main.__doc__)
        sys.exit()
    dir_path = pmag.get_named_arg_from_sys("-WD", default_val=os.getcwd())
    meas_file = pmag.get_named_arg_from_sys(
        "-f", default_val="measurements.txt")
    spec_file = pmag.get_named_arg_from_sys(
        "-fsp", default_val="specimens.txt")
    samp_file = pmag.get_named_arg_from_sys("-fsa", default_val="samples.txt")
    site_file = pmag.get_named_arg_from_sys("-fsi", default_val="sites.txt")
    #meas_file = os.path.join(dir_path, meas_file)
    #spec_file = os.path.join(dir_path, spec_file)
    #samp_file = os.path.join(dir_path, samp_file)
    #site_file = os.path.join(dir_path, site_file)
    plot_file = pmag.get_named_arg_from_sys("-Fp", default_val="")
    crd = pmag.get_named_arg_from_sys("-crd", default_val="s")
    if crd == "s":
        coord = "-1"
    elif crd == "t":
        coord = "100"
    else:
        coord = "0"
    fmt = pmag.get_named_arg_from_sys("-fmt", "svg")
    specimen = pmag.get_named_arg_from_sys("-spc", default_val="")
    beg_pca, end_pca = "", ""
    if '-dir' in sys.argv:
        ind = sys.argv.index('-dir')
        direction_type = sys.argv[ind + 1]
        beg_pca = int(sys.argv[ind + 2])
        end_pca = int(sys.argv[ind + 3])
        if direction_type == 'L':
            calculation_type = 'DE-BFL'
        if direction_type == 'P':
            calculation_type = 'DE-BFP'
        if direction_type == 'F':
            calculation_type = 'DE-FM'
    if '-A' in sys.argv:
        doave = 0
    if '-sav' in sys.argv:
        plots, verbose = 1, 0
    #
    first_save = 1
    fnames = {'measurements': meas_file, 'specimens': spec_file,
              'samples': samp_file, 'sites': site_file}
    contribution = nb.Contribution(dir_path, custom_filenames=fnames, read_tables=[
                                   'measurements', 'specimens', 'samples', 'sites'])
#
#   import  specimens

    specimen_cols = ['analysts', 'aniso_ftest', 'aniso_ftest12', 'aniso_ftest23', 'aniso_s', 'aniso_s_mean', 'aniso_s_n_measurements', 'aniso_s_sigma', 'aniso_s_unit', 'aniso_tilt_correction', 'aniso_type', 'aniso_v1', 'aniso_v2', 'aniso_v3', 'citations', 'description', 'dir_alpha95', 'dir_comp', 'dir_dec', 'dir_inc', 'dir_mad_free', 'dir_n_measurements', 'dir_tilt_correction', 'experiments', 'geologic_classes',
                     'geologic_types', 'hyst_bc', 'hyst_bcr', 'hyst_mr_moment', 'hyst_ms_moment', 'int_abs', 'int_b', 'int_b_beta', 'int_b_sigma', 'int_corr', 'int_dang', 'int_drats', 'int_f', 'int_fvds', 'int_gamma', 'int_mad_free', 'int_md', 'int_n_measurements', 'int_n_ptrm', 'int_q', 'int_rsc', 'int_treat_dc_field', 'lithologies', 'meas_step_max', 'meas_step_min', 'meas_step_unit', 'method_codes', 'sample', 'software_packages', 'specimen']
    if 'specimens' in contribution.tables:
        #        contribution.propagate_name_down('sample','measurements')
        spec_container = contribution.tables['specimens']
        if 'method_codes' not in spec_container.df.columns:
            spec_container.df['method_codes'] = None
        prior_spec_data = spec_container.get_records_for_code(
            'LP-DIR', strict_match=False)  # look up all prior directional interpretations
#
#  tie sample names to measurement data
#
    else:
        spec_container, prior_spec_data = None, []

#
#   import samples  for orientation info
#
    if ('samples' in contribution.tables) and ('specimens' in contribution.tables):
        #        contribution.propagate_name_down('site','measurements')
        contribution.propagate_cols(col_names=[
                                    'azimuth', 'dip', 'orientation_quality'], target_df_name='measurements', source_df_name='samples')
#
# define figure numbers for equal area, zijderveld,
#  and intensity vs. demagnetiztion step respectively
#
    ZED = {}
    ZED['eqarea'], ZED['zijd'],  ZED['demag'] = 1, 2, 3
    pmagplotlib.plot_init(ZED['eqarea'], 6, 6)
    pmagplotlib.plot_init(ZED['zijd'], 6, 6)
    pmagplotlib.plot_init(ZED['demag'], 6, 6)
#    save_pca=0
    angle, direction_type, setangle = "", "", 0
#   create measurement dataframe
#
    meas_container = contribution.tables['measurements']
    meas_data = meas_container.df
#
    meas_data = meas_data[meas_data['method_codes'].str.contains(
        'LT-NO|LT-AF-Z|LT-T-Z|LT-M-Z') == True]  # fish out steps for plotting
    meas_data = meas_data[meas_data['method_codes'].str.contains(
        'AN|ARM|LP-TRM|LP-PI-ARM') == False]  # strip out unwanted experiments
    intensity_types = [
        col_name for col_name in meas_data.columns if col_name in intlist]
    intensity_types = [
        col_name for col_name in intensity_types if any(meas_data[col_name])]
    if not len(intensity_types):
        print('-W- No intensity columns found')
        return
    # plot first non-empty intensity method found - normalized to initial value anyway -
    # doesn't matter which used
    int_key = intensity_types[0]
    # get all the non-null intensity records of the same type
    meas_data = meas_data[meas_data[int_key].notnull()]
    if 'flag' not in meas_data.columns:
        meas_data['flag'] = 'g'  # set the default flag to good
# need to treat LP-NO specially  for af data, treatment should be zero,
# otherwise 273.
    meas_data['treatment'] = meas_data['treat_ac_field'].where(
        cond=meas_data['treat_ac_field'] != 0, other=meas_data['treat_temp'])
    meas_data['ZI'] = 1  # initialize these to one
    meas_data['instrument_codes'] = ""  # initialize these to blank
#   for unusual case of microwave power....
    if 'treat_mw_power' in meas_data.columns:
        meas_data.loc[
            (meas_data.treat_mw_power != 0) &
            (meas_data.treat_mw_power) &
            (meas_data.treat_mw_time),
             'treatment'] = meas_data.treat_mw_power * meas_data.treat_mw_time
#
# get list of unique specimen names from measurement data
#
    # this is a list of all the specimen names
    specimen_names = meas_data.specimen.unique()
    specimen_names = specimen_names.tolist()
    specimen_names.sort()
#
# set up new DataFrame for this sessions specimen interpretations
#
    data_container = nb.MagicDataFrame(
        dtype='specimens', columns=specimen_cols)
    # this is for interpretations from this session
    current_spec_data = data_container.df
    locname = 'LookItUp'
    if specimen == "":
        k = 0
    else:
        k = specimen_names.index(specimen)
    # let's look at the data now
    while k < len(specimen_names):
        mpars = None
        # set the current specimen for plotting
        this_specimen = specimen_names[k]
        # reset beginning/end pca if plotting more than one specimen
        if not specimen:
            beg_pca, end_pca = "", ""
        if verbose and this_specimen != "":
            print(this_specimen, k + 1, 'out of ', len(specimen_names))
        if setangle == 0:
            angle = ""
        this_specimen_measurements = meas_data[meas_data['specimen'].str.contains(
            this_specimen) == True]  # fish out this specimen
        this_specimen_measurements = this_specimen_measurements[this_specimen_measurements['flag'].str.contains(
            'g') == True]  # fish out this specimen
        if len(this_specimen_measurements) != 0:  # if there are measurements
            #
            #    set up datablock [[treatment,dec, inc, int, direction_type],[....]]
            #
            #
            # figure out the method codes
            #
            units, methods, title = "", "", this_specimen
            # this is a list of all the specimen method codes`
            meas_meths = this_specimen_measurements.method_codes.unique()
            tr = pd.to_numeric(this_specimen_measurements.treatment).tolist()
            if set(tr) == set([0]):
                k += 1
                continue
            for m in meas_meths:
                if 'LT-AF-Z' in m:
                    units = 'T'  # units include tesla
                    tr[0] = 0
                if 'LT-T-Z' in m:
                    units = units + ":K"  # units include kelvin
                if 'LT-M-Z' in m:
                    units = units + ':J'  # units include joules
                    tr[0] = 0
                units = units.strip(':')  # strip off extra colons
                if 'LP-' in m:
                    methods = methods + ":" + m
            decs = pd.to_numeric(this_specimen_measurements.dir_dec).tolist()
            incs = pd.to_numeric(this_specimen_measurements.dir_inc).tolist()
#
#    fix the coordinate system
#
            if coord != '-1':  # need to transform coordinates to geographic

                azimuths = pd.to_numeric(
                    this_specimen_measurements.azimuth).tolist()  # get the azimuths
                # get the azimuths
                dips = pd.to_numeric(this_specimen_measurements.dip).tolist()
                dirs = [decs, incs, azimuths, dips]
                # this transposes the columns and rows of the list of lists
                dirs_geo = np.array(list(map(list, list(zip(*dirs)))))
                decs, incs = pmag.dogeo_V(dirs_geo)
                if coord == '100':  # need to do tilt correction too
                    bed_dip_dirs = pd.to_numeric(
                        this_specimen_measurements.bed_dip_dir).tolist()  # get the azimuths
                    bed_dips = pd.to_numeric(
                        this_specimen_measurements.bed_dip).tolist()  # get the azimuths
                    dirs = [decs, incs, bed_dip_dirs, bed_dips]
                    # this transposes the columns and rows of the list of lists
                    dirs_tilt = np.array(list(map(list, list(zip(*dirs)))))
                    decs, incs = pmag.dotilt_V(dirs_tilt)
                    title = title + '_t'
                else:
                    title = title + '_g'
            if angle == "":
                angle = decs[0]
            ints = pd.to_numeric(this_specimen_measurements[int_key]).tolist()
            ZI = this_specimen_measurements.ZI.tolist()
            flags = this_specimen_measurements.flag.tolist()
            codes = this_specimen_measurements.instrument_codes.tolist()
            datalist = [tr, decs, incs, ints, ZI, flags, codes]
            # this transposes the columns and rows of the list of lists
            datablock = list(map(list, list(zip(*datalist))))
            pmagplotlib.plotZED(ZED, datablock, angle, title, units)
            if verbose:
                pmagplotlib.drawFIGS(ZED)
#
#     collect info for current_specimen_interpretation dictionary
#

#
#     find prior interpretation
#

            prior_specimen_interpretations = prior_spec_data[prior_spec_data['specimen'].str.contains(this_specimen) == True]

            if (beg_pca == "") and (len(prior_specimen_interpretations) != 0):
                if len(prior_specimen_interpretations)>0:
                    beg_pcas = pd.to_numeric(
                        prior_specimen_interpretations.meas_step_min.values).tolist()
                    end_pcas = pd.to_numeric(
                        prior_specimen_interpretations.meas_step_max.values).tolist()
                    spec_methods = prior_specimen_interpretations.method_codes.tolist()
                # step through all prior interpretations and plot them
                    for ind in range(len(beg_pcas)):
                        spec_meths = spec_methods[ind].split(':')
                        for m in spec_meths:
                            if 'DE-BFL' in m:
                                calculation_type = 'DE-BFL'  # best fit line
                            if 'DE-BFP' in m:
                                calculation_type = 'DE-BFP'  # best fit plane
                            if 'DE-FM' in m:
                                calculation_type = 'DE-FM'  # fisher mean
                            if 'DE-BFL-A' in m:
                                calculation_type = 'DE-BFL-A'  # anchored best fit line
                        start, end = tr.index(beg_pcas[ind]), tr.index(
                            end_pcas[ind])  # getting the starting and ending points
                    # calculate direction/plane
                        mpars = pmag.domean(
                            datablock, start, end, calculation_type)
                        if mpars["specimen_direction_type"] != "Error":
                            # put it on the plot
                            pmagplotlib.plotDir(ZED, mpars, datablock, angle)
                            if verbose:
                                pmagplotlib.drawFIGS(ZED)
            else:
                try:
                    start, end = int(beg_pca), int(end_pca)
                except ValueError:
                    beg_pca = 0
                    end_pca = len(datablock) - 1
                    start, end = int(beg_pca), int(end_pca)
                # calculate direction/plane
                try:
                    mpars = pmag.domean(datablock, start, end, calculation_type)
                except Exception as ex:
                    print('-I- Problem with {}'.format(this_specimen))
                    print('   ', ex)
                    print('    Skipping')
                    k += 1
                    continue
                if mpars["specimen_direction_type"] != "Error":
                    # put it on the plot
                    pmagplotlib.plotDir(ZED, mpars, datablock, angle)
                    if verbose:
                        pmagplotlib.drawFIGS(ZED)
            if plots == 1 or specimen != "":
                if plot_file == "":
                    basename = title
                else:
                    basename = plot_file
                files = {}
                for key in list(ZED.keys()):
                    files[key] = basename + '_' + key + '.' + fmt
                pmagplotlib.saveP(ZED, files)
                if specimen != "":
                    sys.exit()
            if verbose:
                recnum = 0
                for plotrec in datablock:
                    if units == 'T':
                        print('%s: %i  %7.1f %s  %8.3e %7.1f %7.1f %s' % (
                            plotrec[5], recnum, plotrec[0] * 1e3, " mT", plotrec[3], plotrec[1], plotrec[2], plotrec[6]))
                    if units == "K":
                        print('%s: %i  %7.1f %s  %8.3e %7.1f %7.1f %s' % (
                            plotrec[5], recnum, plotrec[0] - 273, ' C', plotrec[3], plotrec[1], plotrec[2], plotrec[6]))
                    if units == "J":
                        print('%s: %i  %7.1f %s  %8.3e %7.1f %7.1f %s' % (
                            plotrec[5], recnum, plotrec[0], ' J', plotrec[3], plotrec[1], plotrec[2], plotrec[6]))
                    if 'K' in units and 'T' in units:
                        if plotrec[0] >= 1.:
                            print('%s: %i  %7.1f %s  %8.3e %7.1f %7.1f %s' % (
                                plotrec[5], recnum, plotrec[0] - 273, ' C', plotrec[3], plotrec[1], plotrec[2], plotrec[6]))
                        if plotrec[0] < 1.:
                            print('%s: %i  %7.1f %s  %8.3e %7.1f %7.1f %s' % (
                                plotrec[5], recnum, plotrec[0] * 1e3, " mT", plotrec[3], plotrec[1], plotrec[2], plotrec[6]))
                    recnum += 1
            # we have a current interpretation
            elif mpars["specimen_direction_type"] != "Error":
                #
                # create a new specimen record for the interpreation for this
                # specimen
                this_specimen_interpretation = {
                    col: "" for col in specimen_cols}
#               this_specimen_interpretation["analysts"]=user
                this_specimen_interpretation['software_packages'] = version_num
                this_specimen_interpretation['specimen'] = this_specimen
                this_specimen_interpretation["method_codes"] = calculation_type
                this_specimen_interpretation["meas_step_unit"] = units
                this_specimen_interpretation["meas_step_min"] = tr[start]
                this_specimen_interpretation["meas_step_max"] = tr[end]
                this_specimen_interpretation["dir_dec"] = '%7.1f' % (
                    mpars['specimen_dec'])
                this_specimen_interpretation["dir_inc"] = '%7.1f' % (
                    mpars['specimen_inc'])
                this_specimen_interpretation["dir_dang"] = '%7.1f' % (
                    mpars['specimen_dang'])
                this_specimen_interpretation["dir_n_measurements"] = '%i' % (
                    mpars['specimen_n'])
                this_specimen_interpretation["dir_tilt_correction"] = coord
                methods = methods.replace(" ", "")
                if "T" in units:
                    methods = methods + ":LP-DIR-AF"
                if "K" in units:
                    methods = methods + ":LP-DIR-T"
                if "J" in units:
                    methods = methods + ":LP-DIR-M"
                this_specimen_interpretation["method_codes"] = methods.strip(
                    ':')
                this_specimen_interpretation["experiments"] = this_specimen_measurements.experiment.unique()[
                    0]
#
#   print some stuff
#
                if calculation_type != 'DE-FM':
                    this_specimen_interpretation["dir_mad_free"] = '%7.1f' % (
                        mpars['specimen_mad'])
                    this_specimen_interpretation["dir_alpha95"] = ''
                    if verbose:
                        if units == 'K':
                            print('%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %s \n' % (this_specimen_interpretation["specimen"], int(this_specimen_interpretation["dir_n_measurements"]), float(this_specimen_interpretation["dir_mad_free"]), float(this_specimen_interpretation["dir_dang"]), float(
                                this_specimen_interpretation["meas_step_min"]) - 273, float(this_specimen_interpretation["meas_step_max"]) - 273, float(this_specimen_interpretation["dir_dec"]), float(this_specimen_interpretation["dir_inc"]), calculation_type))
                        elif units == 'T':
                            print('%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %s \n' % (this_specimen_interpretation["specimen"], int(this_specimen_interpretation["dir_n_measurements"]), float(this_specimen_interpretation["dir_mad_free"]), float(this_specimen_interpretation["dir_dang"]), float(
                                this_specimen_interpretation["meas_step_min"]) * 1e3, float(this_specimen_interpretation["meas_step_max"]) * 1e3, float(this_specimen_interpretation["dir_dec"]), float(this_specimen_interpretation["dir_inc"]), calculation_type))
                        elif 'T' in units and 'K' in units:
                            if float(this_specimen_interpretation['meas_step_min']) < 1.0:
                                min = float(
                                    this_specimen_interpretation['meas_step_min']) * 1e3
                            else:
                                min = float(
                                    this_specimen_interpretation['meas_step_min']) - 273
                            if float(this_specimen_interpretation['meas_step_max']) < 1.0:
                                max = float(
                                    this_specimen_interpretation['meas_step_max']) * 1e3
                            else:
                                max = float(
                                    this_specimen_interpretation['meas_step_max']) - 273
                            print('%s %i %7.1f %i %i %7.1f %7.1f %7.1f %s \n' % (this_specimen_interpretation["specimen"], int(this_specimen_interpretation["dir_n_measurements"]), float(this_specimen_interpretation["dir_mad_free"]), float(
                                this_specimen_interpretation["dir_dang"]), min, max, float(this_specimen_interpretation["dir_dec"]), float(this_specimen_interpretation["dir_inc"]), calculation_type))
                        else:
                            print('%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %s \n' % (this_specimen_interpretation["specimen"], int(this_specimen_interpretation["dir_n_measurements"]), float(this_specimen_interpretation["dir_mad_free"]), float(this_specimen_interpretation["dir_dang"]), float(
                                this_specimen_interpretation["meas_step_min"]), float(this_specimen_interpretation["meas_step_max"]), float(this_specimen_interpretation["dir_dec"]), float(this_specimen_interpretation["dir_inc"]), calculation_type))
                else:
                    this_specimen_interpretation["dir_alpha95"] = '%7.1f' % (
                        mpars['specimen_alpha95'])
                    this_specimen_interpretation["dir_mad_free"] = ''
                    if verbose:
                        if 'K' in units:
                            print('%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %s \n' % (this_specimen_interpretation["specimen"], int(this_specimen_interpretation["dir_n_measurments"]), float(this_specimen_interpretation["dir_mad_free"]), float(this_specimen_interpretation["dir_dang"]), float(
                                this_specimen_interpretation["meas_step_min"]) - 273, float(this_specimen_interpretation["meas_step_max"]) - 273, float(this_specimen_interpretation["dir_dec"]), float(this_specimen_interpretation["dir_inc"]), calculation_type))
                        elif 'T' in units:
                            print('%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %s \n' % (this_specimen_interpretation["specimen"], int(this_specimen_interpretation["dir_n_measurements"]), float(this_specimen_interpretation["dir_alpha95"]), float(this_specimen_interpretation["dir_dang"]), float(
                                this_specimen_interpretation["meas_step_min"]) * 1e3, float(this_specimen_interpretation["meas_step_max"]) * 1e3, float(this_specimen_interpretation["dir_dec"]), float(this_specimen_interpretation["dir_inc"]), calculation_type))
                        elif 'T' in units and 'K' in units:
                            if float(this_specimen_interpretation['meas_step_min']) < 1.0:
                                min = float(
                                    this_specimen_interpretation['meas_step_min']) * 1e3
                            else:
                                min = float(
                                    this_specimen_interpretation['meas_step_min']) - 273
                            if float(this_specimen_interpretation['meas_step_max']) < 1.0:
                                max = float(
                                    this_specimen_interpretation['meas_step_max']) * 1e3
                            else:
                                max = float(
                                    this_specimen_interpretation['meas_step_max']) - 273
                            print('%s %i %7.1f %i %i %7.1f %7.1f %s \n' % (this_specimen_interpretation["specimen"], int(this_specimen_interpretation["dir_n_measurements"]), float(
                                this_specimen_interpretation["dir_alpha95"]), min, max, float(this_specimen_interpretation["dir_dec"]), float(this_specimen_interpretation["dir_inc"]), calculation_type))
                        else:
                            print('%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %s \n' % (this_specimen_interpretation["specimen"], int(this_specimen_interpretation["dir_n_measurements"]), float(this_specimen_interpretation["dir_alpha95"]), float(
                                this_specimen_interpretation["meas_step_min"]), float(this_specimen_interpretation["meas_step_max"]), float(this_specimen_interpretation["dir_dec"]), float(this_specimen_interpretation["dir_inc"]), calculation_type))
                if verbose:
                    saveit = input("Save this interpretation? [y]/n \n")
#   START HERE
#
#         if len(current_spec_data)==0: # no interpretations yet for this session
#             print "no current interpretation"
#             beg_pca,end_pca="",""
#             calculation_type=""
# get the ones that meet the current coordinate system
        else:
            print("no data")
        if verbose:
            res = input('  <return> for next specimen, [q]uit  ')
            if res == 'q':
                return
        k += 1
Пример #5
0
def main():
    """
    NAME
       zeq.py
  
    DESCRIPTION
       plots demagnetization data. The equal area projection has the X direction (usually North in geographic coordinates)
          to the top.  The red line is the X axis of the Zijderveld diagram.  Solid symbols are lower hemisphere. 
          The solid (open) symbols in the Zijderveld diagram are X,Y (X,Z) pairs.  The demagnetization diagram plots the
          fractional remanence remaining after each step. The green line is the fraction of the total remaence removed 
          between each step.        

    INPUT FORMAT
       takes specimen_name treatment intensity declination inclination  in space
 delimited file

    SYNTAX
        zeq.py [command line options

    OPTIONS
        -f FILE for reading from command line
        -u [mT,C] specify units of mT OR C, default is unscaled
        -sav save figure and quit
        -fmt [svg,jpg,png,pdf] set figure format [default is svg]
        -beg [step number] treatment step for beginning of PCA calculation, 0 is default
        -end [step number] treatment step for end of PCA calculation, last step is default
        -ct [l,p,f] Calculation Type: best-fit line,  plane or fisher mean; line is default

    """
    files, fmt, plot = {}, 'svg', 0
    end_pca, beg_pca = "", ""
    calculation_type = 'DE-BFL'
    if '-h' in sys.argv:  # check if help is needed
        print(main.__doc__)
        sys.exit()  # graceful quit
    else:
        if '-f' in sys.argv:
            ind = sys.argv.index('-f')
            file = sys.argv[ind + 1]
        else:
            print(main.__doc__)
            sys.exit()
        if '-u' in sys.argv:
            ind = sys.argv.index('-u')
            units = sys.argv[ind + 1]
            if units == "C": SIunits = "K"
            if units == "mT": SIunits = "T"
        else:
            units = "U"
            SIunits = "U"
    if '-sav' in sys.argv: plot = 1
    if '-ct' in sys.argv:
        ind = sys.argv.index('-ct')
        ct = sys.argv[ind + 1]
        if ct == 'f': calculation_type = 'DE-FM'
        if ct == 'p': calculation_type = 'DE-BFP'
    if '-fmt' in sys.argv:
        ind = sys.argv.index('-fmt')
        fmt = sys.argv[ind + 1]
    if '-beg' in sys.argv:
        ind = sys.argv.index('-beg')
        beg_pca = int(sys.argv[ind + 1])
    if '-end' in sys.argv:
        ind = sys.argv.index('-end')
        end_pca = int(sys.argv[ind + 1])
    f = open(file, 'r')
    data = f.readlines()
    #
    datablock = []  # set up list for data
    s = ""  # initialize specimen name
    angle = 0.
    for line in data:  # read in the data from standard input
        rec = line.split()  # split each line on space to get records
        if angle == "": angle = float(rec[3])
        if s == "": s = rec[0]
        if units == 'mT':
            datablock.append([
                float(rec[1]) * 1e-3,
                float(rec[3]),
                float(rec[4]), 1e-3 * float(rec[2]), '', 'g'
            ])  # treatment, dec, inc, int # convert to T and Am^2 (assume emu)
        if units == 'C':
            datablock.append([
                float(rec[1]) + 273.,
                float(rec[3]),
                float(rec[4]), 1e-3 * float(rec[2]), '', 'g'
            ])  # treatment, dec, inc, int, convert to K and Am^2, assume emu
        if units == 'U':
            datablock.append([
                float(rec[1]),
                float(rec[3]),
                float(rec[4]),
                float(rec[2]), '', 'g'
            ])  # treatment, dec, inc, int, using unscaled units


# define figure numbers in a dictionary for equal area, zijderveld,
#  and intensity vs. demagnetiztion step respectively
    ZED = {}
    ZED['eqarea'], ZED['zijd'], ZED['demag'] = 1, 2, 3
    pmagplotlib.plot_init(ZED['eqarea'], 5, 5)  # initialize plots
    pmagplotlib.plot_init(ZED['zijd'], 5, 5)
    pmagplotlib.plot_init(ZED['demag'], 5, 5)
    #
    #
    pmagplotlib.plotZED(ZED, datablock, angle, s, SIunits)  # plot the data
    if plot == 0: pmagplotlib.drawFIGS(ZED)
    #
    # print out data for this sample to screen
    #
    recnum = 0
    for plotrec in datablock:
        if units == 'mT':
            print(
                '%i  %7.1f %8.3e %7.1f %7.1f ' %
                (recnum, plotrec[0] * 1e3, plotrec[3], plotrec[1], plotrec[2]))
        if units == 'C':
            print('%i  %7.1f %8.3e %7.1f %7.1f ' %
                  (recnum, plotrec[0] - 273., plotrec[3], plotrec[1],
                   plotrec[2]))
        if units == 'U':
            print('%i  %7.1f %8.3e %7.1f %7.1f ' %
                  (recnum, plotrec[0], plotrec[3], plotrec[1], plotrec[2]))
        recnum += 1
    if plot == 0:
        while 1:
            if beg_pca != "" and end_pca != "" and calculation_type != "":
                pmagplotlib.plotZED(ZED, datablock, angle, s,
                                    SIunits)  # plot the data
                mpars = pmag.domean(
                    datablock, beg_pca, end_pca,
                    calculation_type)  # get best-fit direction/great circle
                pmagplotlib.plotDir(
                    ZED, mpars, datablock,
                    angle)  # plot the best-fit direction/great circle
                print('Specimen, calc_type, N, min, max, MAD, dec, inc')
                if units == 'mT':
                    print('%s %s %i  %6.2f %6.2f %6.1f %7.1f %7.1f' %
                          (s, calculation_type, mpars["specimen_n"],
                           mpars["measurement_step_min"] * 1e3,
                           mpars["measurement_step_max"] * 1e3,
                           mpars["specimen_mad"], mpars["specimen_dec"],
                           mpars["specimen_inc"]))
                if units == 'C':
                    print('%s %s %i  %6.2f %6.2f %6.1f %7.1f %7.1f' %
                          (s, calculation_type, mpars["specimen_n"],
                           mpars["measurement_step_min"] - 273,
                           mpars["measurement_step_max"] - 273,
                           mpars["specimen_mad"], mpars["specimen_dec"],
                           mpars["specimen_inc"]))
                if units == 'U':
                    print(
                        '%s %s %i  %6.2f %6.2f %6.1f %7.1f %7.1f' %
                        (s, calculation_type, mpars["specimen_n"],
                         mpars["measurement_step_min"],
                         mpars["measurement_step_max"], mpars["specimen_mad"],
                         mpars["specimen_dec"], mpars["specimen_inc"]))
            if end_pca == "":
                end_pca = len(
                    datablock
                ) - 1  # initialize end_pca, beg_pca to first and last measurement
            if beg_pca == "": beg_pca = 0
            ans = input(
                " s[a]ve plot, [b]ounds for pca and calculate, change [h]orizontal projection angle, [q]uit:   "
            )
            if ans == 'q':
                sys.exit()
            if ans == 'a':
                files = {}
                for key in list(ZED.keys()):
                    files[key] = s + '_' + key + '.' + fmt
                pmagplotlib.saveP(ZED, files)
            if ans == 'h':
                angle = float(
                    input(" Declination to project onto horizontal axis? "))
                pmagplotlib.plotZED(ZED, datablock, angle, s,
                                    SIunits)  # plot the data

            if ans == 'b':
                GoOn = 0
                while GoOn == 0:  # keep going until reasonable bounds are set
                    print('Enter index of first point for pca: ', '[', beg_pca,
                          ']')
                    answer = input('return to keep default  ')
                    if answer != "": beg_pca = int(answer)
                    print('Enter index  of last point for pca: ', '[', end_pca,
                          ']')
                    answer = input('return to keep default  ')
                    if answer != "":
                        end_pca = int(answer)
                    if beg_pca >= 0 and beg_pca <= len(
                            datablock) - 2 and end_pca > 0 and end_pca < len(
                                datablock):
                        GoOn = 1
                    else:
                        print("Bad entry of indices - try again")
                        end_pca = len(datablock) - 1
                        beg_pca = 0
                GoOn = 0
                while GoOn == 0:
                    ct = input(
                        'Enter Calculation Type: best-fit line,  plane or fisher mean [l]/p/f :  '
                    )
                    if ct == "" or ct == "l":
                        calculation_type = "DE-BFL"
                        GoOn = 1  # all good
                    elif ct == 'p':
                        calculation_type = "DE-BFP"
                        GoOn = 1  # all good
                    elif ct == 'f':
                        calculation_type = "DE-FM"
                        GoOn = 1  # all good
                    else:
                        print("bad entry of calculation type: try again. "
                              )  # keep going
                    pmagplotlib.plotZED(ZED, datablock, angle, s,
                                        SIunits)  # plot the data
                    mpars = pmag.domean(
                        datablock, beg_pca, end_pca, calculation_type
                    )  # get best-fit direction/great circle
                    pmagplotlib.plotDir(
                        ZED, mpars, datablock,
                        angle)  # plot the best-fit direction/great circle
                    print('Specimen, calc_type, N, min, max, MAD, dec, inc')
                    if units == 'mT':
                        print('%s %s %i  %6.2f %6.2f %6.1f %7.1f %7.1f' %
                              (s, calculation_type, mpars["specimen_n"],
                               mpars["measurement_step_min"] * 1e3,
                               mpars["measurement_step_max"] * 1e3,
                               mpars["specimen_mad"], mpars["specimen_dec"],
                               mpars["specimen_inc"]))
                    if units == 'C':
                        print('%s %s %i  %6.2f %6.2f %6.1f %7.1f %7.1f' %
                              (s, calculation_type, mpars["specimen_n"],
                               mpars["measurement_step_min"] - 273,
                               mpars["measurement_step_max"] - 273,
                               mpars["specimen_mad"], mpars["specimen_dec"],
                               mpars["specimen_inc"]))
                    if units == 'U':
                        print('%s %s %i  %6.2f %6.2f %6.1f %7.1f %7.1f' %
                              (s, calculation_type, mpars["specimen_n"],
                               mpars["measurement_step_min"],
                               mpars["measurement_step_max"],
                               mpars["specimen_mad"], mpars["specimen_dec"],
                               mpars["specimen_inc"]))
            pmagplotlib.drawFIGS(ZED)
    else:
        print(beg_pca, end_pca)
        if beg_pca != "" and end_pca != "":
            pmagplotlib.plotZED(ZED, datablock, angle, s,
                                SIunits)  # plot the data
            mpars = pmag.domean(
                datablock, beg_pca, end_pca,
                calculation_type)  # get best-fit direction/great circle
            pmagplotlib.plotDir(
                ZED, mpars, datablock,
                angle)  # plot the best-fit direction/great circle
            print('Specimen, calc_type, N, min, max, MAD, dec, inc')
            if units == 'mT':
                print('%s %s %i  %6.2f %6.2f %6.1f %7.1f %7.1f' %
                      (s, calculation_type, mpars["specimen_n"],
                       mpars["measurement_step_min"] * 1e3,
                       mpars["measurement_step_max"] * 1e3,
                       mpars["specimen_mad"], mpars["specimen_dec"],
                       mpars["specimen_inc"]))
            if units == 'C':
                print('%s %s %i  %6.2f %6.2f %6.1f %7.1f %7.1f' %
                      (s, calculation_type, mpars["specimen_n"],
                       mpars["measurement_step_min"] - 273,
                       mpars["measurement_step_max"] - 273,
                       mpars["specimen_mad"], mpars["specimen_dec"],
                       mpars["specimen_inc"]))
            if units == 'U':
                print('%s %s %i  %6.2f %6.2f %6.1f %7.1f %7.1f' %
                      (s, calculation_type, mpars["specimen_n"],
                       mpars["measurement_step_min"],
                       mpars["measurement_step_max"], mpars["specimen_mad"],
                       mpars["specimen_dec"], mpars["specimen_inc"]))
        files = {}
        for key in list(ZED.keys()):
            files[key] = s + '_' + key + '.' + fmt
        pmagplotlib.saveP(ZED, files)