Commit 70d9b0ad authored by acpaquette's avatar acpaquette Committed by jlaura
Browse files

Ipf Writer (#37) 

* Added to ipf from dataframe. Also updated both gpf and ipf writer tests

* Added test output file.

* Added asserts to gpf and ipf tests

* Reverted save_gpf testing to numpy array almost equals
parent 1bf9a376

notebooks/Socet2ISIS.ipynb

+91 −74
Original line number Diff line number Diff line 
%% Cell type:code id: tags:



``` python

import os

import sys

from functools import singledispatch

import warnings



import pandas as pd

import numpy as np



from plio.examples import get_path

from plio.io.io_bae import read_gpf

from plio.io.io_bae import read_gpf, read_ipf

```



%% Cell type:code id: tags:



``` python

# Reads a .atf file and outputs all of the

# .ipf, .gpf, .sup, .prj, and path to locate the

# .apf file (should be the same as all others)

def read_atf(atf_file):

    with open(atf_file) as f:



        files = []

        ipf = []

        sup = []

        files_dict = []



        # Grabs every PRJ, GPF, SUP, and IPF image from the ATF file

        for line in f:

            if line[-4:-1] == 'prj' or line[-4:-1] == 'gpf' or line[-4:-1] == 'sup' or line[-4:-1] == 'ipf' or line[-4:-1] == 'atf':

                files.append(line)



        files = np.array(files)



        # Creates appropriate arrays for certain files in the right format

        for file in files:

            file = file.strip()

            file = file.split(' ')



            # Grabs all the IPF files

            if file[1].endswith('.ipf'):

                ipf.append(file[1])



            # Grabs all the SUP files

            if file[1].endswith('.sup'):

                sup.append(file[1])



            files_dict.append(file)



        # Creates a dict out of file lists for GPF, PRJ, IPF, and ATF

        files_dict = (dict(files_dict))



        # Sets the value of IMAGE_IPF to all IPF images

        files_dict['IMAGE_IPF'] = ipf



        # Sets the value of IMAGE_SUP to all SUP images

        files_dict['IMAGE_SUP'] = sup



        # Sets the value of PATH to the path of the ATF file

        files_dict['PATH'] = os.path.dirname(os.path.abspath(atf_file))



        return files_dict



@singledispatch

def read_ipf(arg):

    return str(arg)



@read_ipf.register(str)

def read_ipf_str(input_data):

    """

    Read a socet ipf file into a pandas data frame



    Parameters

    ----------

    input_data : str

                 path to the an input data file



    Returns

    -------

    df : pd.DataFrame

         containing the ipf data with appropriate column names and indices

    """



    # Check that the number of rows is matching the expected number

    with open(input_data, 'r') as f:

        for i, l in enumerate(f):

            if i == 1:

                cnt = int(l)

            elif i == 2:

                col = l

                break



    columns = np.genfromtxt(input_data, skip_header=2, dtype='unicode',

                            max_rows = 1, delimiter = ',')



    # TODO: Add unicode conversion

    d = [line.split() for line in open(input_data, 'r')]

    d = np.hstack(np.array(d[3:]))



    d = d.reshape(-1, 12)



    df = pd.DataFrame(d, columns=columns)

    file = os.path.split(os.path.splitext(input_data)[0])[1]

    df['ipf_file'] = pd.Series(np.full((len(df['pt_id'])), file), index = df.index)



    assert int(cnt) == len(df), 'Dataframe length {} does not match point length {}.'.format(int(cnt), len(df))



    # Soft conversion of numeric types to numerics, allows str in first col for point_id

    df = df.apply(pd.to_numeric, errors='ignore')



    return df



@read_ipf.register(list)

def read_ipf_list(input_data_list):

    """

    Read a socet ipf file into a pandas data frame



    Parameters

    ----------

    input_data_list : list

                      list of paths to the a set of input data files



    Returns

    -------

    df : pd.DataFrame

         containing the ipf data with appropriate column names and indices

    """

    frames = []



    for input_file in input_data_list:

        frames.append(read_ipf(input_file))



    df = pd.concat(frames)



    return df

```



%% Cell type:code id: tags:



``` python

atf_dict = read_atf(get_path('CTX_Athabasca_Middle_step0.atf'))



gpf_file = os.path.join(atf_dict['PATH'], atf_dict['GP_FILE']);

ipf_list = [os.path.join(atf_dict['PATH'], i) for i in atf_dict['IMAGE_IPF']]



gpf_df = read_gpf(gpf_file).set_index('point_id')

ipf_df = read_ipf(ipf_list).set_index('pt_id')



point_diff = ipf_df.index.difference(gpf_df.index)



if len(point_diff) != 0:

    warnings.warn("The following points found in ipf files missing from gpf file: \n\n{}. \

                  \n\nContinuing, but these points will be missing from the control network".format(list(point_diff)))



new_df = ipf_df.merge(gpf_df, left_index=True, right_index=True)

new_df

```



%% Output



    /Users/adampaquette/anaconda/envs/pysat/lib/python3.6/site-packages/ipykernel_launcher.py:12: UserWarning: The following points found in ipf files missing from gpf file:

    

    ['P03_002226_1895_XI_09N203W_15', 'P03_002226_1895_XI_09N203W_16', 'P03_002226_1895_XI_09N203W_17', 'P03_002226_1895_XI_09N203W_18', 'P03_002226_1895_XI_09N203W_19', 'P03_002226_1895_XI_09N203W_20', 'P03_002226_1895_XI_09N203W_21', 'P03_002226_1895_XI_09N203W_22', 'P03_002226_1895_XI_09N203W_24', 'P03_002226_1895_XI_09N203W_26', 'P03_002226_1895_XI_09N203W_30', 'P03_002226_1895_XI_09N203W_31', 'P03_002226_1895_XI_09N203W_32', 'P03_002226_1895_XI_09N203W_34', 'P03_002226_1895_XI_09N203W_36', 'P03_002226_1895_XI_09N203W_37', 'P03_002226_1895_XI_09N203W_44', 'P03_002226_1895_XI_09N203W_48', 'P03_002226_1895_XI_09N203W_49', 'P03_002226_1895_XI_09N203W_56', 'P03_002226_1895_XI_09N203W_57', 'P03_002226_1895_XI_09N203W_61', 'P03_002226_1895_XI_09N203W_62', 'P03_002226_1895_XI_09N203W_63', 'P03_002226_1895_XI_09N203W_65', 'P19_008344_1894_XN_09N203W_4', 'P20_008845_1894_XN_09N203W_15'].

    

    Continuing, but these points will be missing from the control network

      if sys.path[0] == '':



                                   val  fid_val  no_obs           l.           s.  \

    10_8344_8845_4r                  1        0       0 -2919.380615  1052.729004

    10_8344_8845_4r                  1        0       0 -4044.697510  1008.950928

    10_8344_8845_4r                  1        0       0  1700.584473 -2390.001709

    10_8344_8845_4r                  1        0       0  2006.141113 -2234.915283

    11_8344_8845_4r                  1        0       0   370.151917  2340.653076

    11_8344_8845_4r                  1        0       0  -761.216064  2303.787109

    11_8344_8845_4r                  1        0       0  4985.437988 -1070.364990

    11_8344_8845_4r                  1        0       0  5293.700195  -993.390625

    12_8344_8845_4r                  1        0       0   236.395218   984.833252

    12_8344_8845_4r                  1        0       0  -889.364441   966.533997

    12_8344_8845_4r                  1        0       0  4856.525391 -2439.154785

    12_8344_8845_4r                  1        0       0  5158.205566 -2295.737549

    13_8344_8845_4r                  1        0       0 -1431.023804  1817.888672

    13_8344_8845_4r                  1        0       0 -2559.871338  1777.522827

    13_8344_8845_4r                  1        0       0  3186.063232 -1598.743530

    13_8344_8845_4r                  1        0       0  3493.876221 -1493.029175

    14_8344_8845_4r                  1        0       0  3518.268066  2495.108643

    14_8344_8845_4r                  1        0       0  2385.278320  2476.032227

    14_8344_8845_4r                  1        0       0  8131.361816  -902.645325

    14_8344_8845_4r                  1        0       0  8437.115234  -842.309326

    15_8344_8845_4r_mt_z             1        0       0  3522.998535  1049.406982

    15_8344_8845_4r_mt_z             1        0       0  2395.869385  1038.165405

    15_8344_8845_4r_mt_z             1        0       0  8142.054688 -2364.445557

    15_8344_8845_4r_mt_z             1        0       0  8440.085938 -2219.049805

    16_8344_8845_4r                  1        0       0  1885.346313  1807.367065

    16_8344_8845_4r                  1        0       0   756.099792  1785.494751

    16_8344_8845_4r                  1        0       0  6502.070313 -1593.964233

    16_8344_8845_4r                  1        0       0  6805.896973 -1493.774048

    17_8344_8845_2r_mt_z             1        0       0 -2015.364380   465.268188

    17_8344_8845_2r_mt_z             1        0       0 -3138.269531   442.515503

    ...                            ...      ...     ...          ...          ...

    P20_008845_1894_XN_09N203W_18    1        0       1  8918.806641 -1701.755249

    P20_008845_1894_XN_09N203W_2     1        0       1 -2277.691406 -2240.823486

    P20_008845_1894_XN_09N203W_2     1        0       0 -3389.000000 -2155.000000

    P20_008845_1894_XN_09N203W_2     1        0       1 -5474.326660   842.207031

    P20_008845_1894_XN_09N203W_2     1        0       0 -4613.785645   643.217224

    P20_008845_1894_XN_09N203W_3     1        0       1 -1801.096436 -2078.479004

    P20_008845_1894_XN_09N203W_3     1        0       0 -2913.000000 -2000.000000

    P20_008845_1894_XN_09N203W_3     1        0       1 -4997.791504  1000.375854

    P20_008845_1894_XN_09N203W_3     1        0       0 -4137.536133   774.480347

    P20_008845_1894_XN_09N203W_4     1        0       1 -2103.971680   184.334869

    P20_008845_1894_XN_09N203W_4     1        0       1 -3226.000000   167.000000

    P20_008845_1894_XN_09N203W_5     1        0       1 -1813.285278     3.928788

    P20_008845_1894_XN_09N203W_5     1        0       1 -2934.000000    -6.000000

    P20_008845_1894_XN_09N203W_5     1        0       0 -4165.228516  2507.076660

    P20_008845_1894_XN_09N203W_6     1        0       1 -2250.549072  1572.788086

    P20_008845_1894_XN_09N203W_6     1        0       3 -3378.000000  1532.000000

    P20_008845_1894_XN_09N203W_6     1        0       1  2367.587646 -1849.272095

    P20_008845_1894_XN_09N203W_6     1        0       1  2675.137207 -1730.558105

    P20_008845_1894_XN_09N203W_7     1        0       1 -2249.931396  1712.971436

    P20_008845_1894_XN_09N203W_7     1        0       3 -3378.000000  1672.000000

    P20_008845_1894_XN_09N203W_7     1        0       1  2367.507813 -1706.241821

    P20_008845_1894_XN_09N203W_7     1        0       1  2675.892578 -1596.527100

    P20_008845_1894_XN_09N203W_8     1        0       1 -1664.131104  1875.622437

    P20_008845_1894_XN_09N203W_8     1        0       3 -2793.000000  1837.000000

    P20_008845_1894_XN_09N203W_8     1        0       1  2953.094727 -1538.956543

    P20_008845_1894_XN_09N203W_8     1        0       1  3261.290039 -1439.873169

    P20_008845_1894_XN_09N203W_9     1        0       1   332.072113 -2045.152222

    P20_008845_1894_XN_09N203W_9     1        0       0  -780.000000 -1953.000000

    P20_008845_1894_XN_09N203W_9     1        0       0 -2866.689453  1031.006104

    P20_008845_1894_XN_09N203W_9     1        0       0 -2002.366211   824.604126

    

                                      sig_l     sig_s     res_l     res_s  fid_x  \

    10_8344_8845_4r                0.000000  0.000000  0.059914  0.930311    0.0

    10_8344_8845_4r                0.000000  0.000000  0.063678  0.661294    0.0

    10_8344_8845_4r                0.000000  0.000000 -0.063695 -1.055619    0.0

    10_8344_8845_4r                0.000000  0.000000  0.318779 -0.585138    0.0

    11_8344_8845_4r                0.000000  0.000000 -0.239226 -1.113693    0.0

    11_8344_8845_4r                0.000000  0.000000 -0.247307 -0.587299    0.0

    11_8344_8845_4r                0.000000  0.000000  0.239207  1.080801    0.0

    11_8344_8845_4r                0.000000  0.000000  0.672877  0.626316    0.0

    12_8344_8845_4r                0.000000  0.000000  0.073683 -0.237114    0.0

    12_8344_8845_4r                0.000000  0.000000 -0.251753  0.008170    0.0

    12_8344_8845_4r                0.000000  0.000000  0.133406  0.068024    0.0

    12_8344_8845_4r                0.000000  0.000000  0.487209  0.036399    0.0

    13_8344_8845_4r                0.000000  0.000000 -0.056901 -0.383259    0.0

    13_8344_8845_4r                0.000000  0.000000 -0.131265 -0.305102    0.0

    13_8344_8845_4r                0.000000  0.000000  0.019201  0.485372    0.0

    13_8344_8845_4r                0.000000  0.000000  0.568393  0.146750    0.0

    14_8344_8845_4r                0.000000  0.000000  0.268449  1.000455    0.0

    14_8344_8845_4r                0.000000  0.000000  0.389532 -0.299258    0.0

    14_8344_8845_4r                0.000000  0.000000 -0.469784  0.023018    0.0

    14_8344_8845_4r                0.000000  0.000000  0.289877 -0.829150    0.0

    15_8344_8845_4r_mt_z           0.000000  0.000000  0.466921  1.168062    0.0

    15_8344_8845_4r_mt_z           0.000000  0.000000 -0.170850  0.372485    0.0

    15_8344_8845_4r_mt_z           0.000000  0.000000 -0.072035 -0.832436    0.0

    15_8344_8845_4r_mt_z           0.000000  0.000000  0.274030 -0.850105    0.0

    16_8344_8845_4r                0.000000  0.000000 -0.028473 -0.238015    0.0

    16_8344_8845_4r                0.000000  0.000000  0.165338 -0.327408    0.0

    16_8344_8845_4r                0.000000  0.000000 -0.007916  0.463232    0.0

    16_8344_8845_4r                0.000000  0.000000  0.328896  0.019526    0.0

    17_8344_8845_2r_mt_z           0.000000  0.000000  0.010045  0.244017    0.0

    17_8344_8845_2r_mt_z           0.000000  0.000000 -0.023370 -0.248643    0.0

    ...                                 ...       ...       ...       ...    ...

    P20_008845_1894_XN_09N203W_18  0.022017  0.022017  0.734173 -0.074947    0.0

    P20_008845_1894_XN_09N203W_2   0.144273  0.144273 -0.061422 -0.263554    0.0

    P20_008845_1894_XN_09N203W_2   0.000000  0.000000 -0.073150 -0.271173    0.0

    P20_008845_1894_XN_09N203W_2   0.275627  0.275627  0.164525  0.349547    0.0

    P20_008845_1894_XN_09N203W_2   0.091086  0.091086  0.132736  0.239899    0.0

    P20_008845_1894_XN_09N203W_3   0.062058  0.062058 -0.198696 -0.105860    0.0

    P20_008845_1894_XN_09N203W_3   0.000000  0.000000 -0.088180 -0.049593    0.0

    P20_008845_1894_XN_09N203W_3   0.132941  0.132941  0.257260  0.117777    0.0

    P20_008845_1894_XN_09N203W_3   0.185544  0.185544  0.199301  0.065777    0.0

    P20_008845_1894_XN_09N203W_4   0.146920  0.146920  0.182557 -0.000683    0.0

    P20_008845_1894_XN_09N203W_4   0.000000  0.000000 -0.195774 -0.000066    0.0

    P20_008845_1894_XN_09N203W_5   0.019047  0.019047 -0.235171 -0.174079    0.0

    P20_008845_1894_XN_09N203W_5   0.000000  0.000000 -0.049005  0.437424    0.0

    P20_008845_1894_XN_09N203W_5   0.000000  0.000000  0.447100 -0.219764    0.0

    P20_008845_1894_XN_09N203W_6   0.025015  0.025015 -0.146990  0.192274    0.0

    P20_008845_1894_XN_09N203W_6   0.000000  0.000000  0.026541  0.063346    0.0

    P20_008845_1894_XN_09N203W_6   0.025110  0.025110 -0.040890 -0.136247    0.0

    P20_008845_1894_XN_09N203W_6   0.064276  0.064276  0.546035 -0.185103    0.0

    P20_008845_1894_XN_09N203W_7   0.010596  0.010596 -0.102909  0.079389    0.0

    P20_008845_1894_XN_09N203W_7   0.000000  0.000000  0.055623  0.013456    0.0

    P20_008845_1894_XN_09N203W_7   0.047435  0.047435 -0.157931 -0.042074    0.0

    P20_008845_1894_XN_09N203W_7   0.058218  0.058218  0.589561 -0.111421    0.0

    P20_008845_1894_XN_09N203W_8   0.017266  0.017266 -0.239689 -0.402891    0.0

    P20_008845_1894_XN_09N203W_8   0.000000  0.000000 -0.117483 -0.229337    0.0

    P20_008845_1894_XN_09N203W_8   0.023364  0.023364  0.177406  0.403161    0.0

    P20_008845_1894_XN_09N203W_8   0.023538  0.023538  0.575510  0.180705    0.0

    P20_008845_1894_XN_09N203W_9   0.232865  0.232865  0.095817 -0.483899    0.0

    P20_008845_1894_XN_09N203W_9   0.000000  0.000000  0.298743 -0.045963    0.0

    P20_008845_1894_XN_09N203W_9   0.000000  0.000000 -0.038437  0.471309    0.0

    P20_008845_1894_XN_09N203W_9   0.397616  0.397616 -0.141172  0.105223    0.0

    

                                      ...      known lat_Y_North  long_X_East  \

    10_8344_8845_4r                   ...          0    0.159378     2.724649

    10_8344_8845_4r                   ...          0    0.159378     2.724649

    10_8344_8845_4r                   ...          0    0.159378     2.724649

    10_8344_8845_4r                   ...          0    0.159378     2.724649

    11_8344_8845_4r                   ...          0    0.164905     2.721815

    11_8344_8845_4r                   ...          0    0.164905     2.721815

    11_8344_8845_4r                   ...          0    0.164905     2.721815

    11_8344_8845_4r                   ...          0    0.164905     2.721815

    12_8344_8845_4r                   ...          0    0.164949     2.724076

    12_8344_8845_4r                   ...          0    0.164949     2.724076

    12_8344_8845_4r                   ...          0    0.164949     2.724076

    12_8344_8845_4r                   ...          0    0.164949     2.724076

    13_8344_8845_4r                   ...          0    0.161840     2.723059

    13_8344_8845_4r                   ...          0    0.161840     2.723059

    13_8344_8845_4r                   ...          0    0.161840     2.723059

    13_8344_8845_4r                   ...          0    0.161840     2.723059

    14_8344_8845_4r                   ...          0    0.170415     2.720880

    14_8344_8845_4r                   ...          0    0.170415     2.720880

    14_8344_8845_4r                   ...          0    0.170415     2.720880

    14_8344_8845_4r                   ...          0    0.170415     2.720880

    15_8344_8845_4r_mt_z              ...          1    0.170723     2.723266

    15_8344_8845_4r_mt_z              ...          1    0.170723     2.723266

    15_8344_8845_4r_mt_z              ...          1    0.170723     2.723266

    15_8344_8845_4r_mt_z              ...          1    0.170723     2.723266

    16_8344_8845_4r                   ...          0    0.167682     2.722359

    16_8344_8845_4r                   ...          0    0.167682     2.722359

    16_8344_8845_4r                   ...          0    0.167682     2.722359

    16_8344_8845_4r                   ...          0    0.167682     2.722359

    17_8344_8845_2r_mt_z              ...          1    0.161092     2.725426

    17_8344_8845_2r_mt_z              ...          1    0.161092     2.725426

    ...                               ...        ...         ...          ...

    P20_008845_1894_XN_09N203W_18     ...          0    0.171455     2.722281

    P20_008845_1894_XN_09N203W_2      ...          0    0.161184     2.729925

    P20_008845_1894_XN_09N203W_2      ...          0    0.161184     2.729925

    P20_008845_1894_XN_09N203W_2      ...          0    0.161184     2.729925

    P20_008845_1894_XN_09N203W_2      ...          0    0.161184     2.729925

    P20_008845_1894_XN_09N203W_3      ...          0    0.161992     2.729563

    P20_008845_1894_XN_09N203W_3      ...          0    0.161992     2.729563

    P20_008845_1894_XN_09N203W_3      ...          0    0.161992     2.729563

    P20_008845_1894_XN_09N203W_3      ...          0    0.161992     2.729563

    P20_008845_1894_XN_09N203W_4      ...          0    0.160994     2.725912

    P20_008845_1894_XN_09N203W_4      ...          0    0.160994     2.725912

    P20_008845_1894_XN_09N203W_5      ...          0    0.161544     2.726149

    P20_008845_1894_XN_09N203W_5      ...          0    0.161544     2.726149

    P20_008845_1894_XN_09N203W_5      ...          0    0.161544     2.726149

    P20_008845_1894_XN_09N203W_6      ...          0    0.160447     2.723639

    P20_008845_1894_XN_09N203W_6      ...          0    0.160447     2.723639

    P20_008845_1894_XN_09N203W_6      ...          0    0.160447     2.723639

    P20_008845_1894_XN_09N203W_6      ...          0    0.160447     2.723639

    P20_008845_1894_XN_09N203W_7      ...          0    0.160419     2.723407

    P20_008845_1894_XN_09N203W_7      ...          0    0.160419     2.723407

    P20_008845_1894_XN_09N203W_7      ...          0    0.160419     2.723407

    P20_008845_1894_XN_09N203W_7      ...          0    0.160419     2.723407

    P20_008845_1894_XN_09N203W_8      ...          0    0.161417     2.723012

    P20_008845_1894_XN_09N203W_8      ...          0    0.161417     2.723012

    P20_008845_1894_XN_09N203W_8      ...          0    0.161417     2.723012

    P20_008845_1894_XN_09N203W_8      ...          0    0.161417     2.723012

    P20_008845_1894_XN_09N203W_9      ...          0    0.165741     2.729053

    P20_008845_1894_XN_09N203W_9      ...          0    0.165741     2.729053

    P20_008845_1894_XN_09N203W_9      ...          0    0.165741     2.729053

    P20_008845_1894_XN_09N203W_9      ...          0    0.165741     2.729053

    

                                            ht  sig0  sig1        sig2       res0  \

    10_8344_8845_4r               -2523.828227   0.0   0.0   25.000000  18.301328

    10_8344_8845_4r               -2523.828227   0.0   0.0   25.000000  18.301328

    10_8344_8845_4r               -2523.828227   0.0   0.0   25.000000  18.301328

    10_8344_8845_4r               -2523.828227   0.0   0.0   25.000000  18.301328

    11_8344_8845_4r               -2445.237027   0.0   0.0   30.000000 -22.046575

    11_8344_8845_4r               -2445.237027   0.0   0.0   30.000000 -22.046575

    11_8344_8845_4r               -2445.237027   0.0   0.0   30.000000 -22.046575

    11_8344_8845_4r               -2445.237027   0.0   0.0   30.000000 -22.046575

    12_8344_8845_4r               -2606.935163   0.0   0.0  100.000000  -7.549561

    12_8344_8845_4r               -2606.935163   0.0   0.0  100.000000  -7.549561

    12_8344_8845_4r               -2606.935163   0.0   0.0  100.000000  -7.549561

    12_8344_8845_4r               -2606.935163   0.0   0.0  100.000000  -7.549561

    13_8344_8845_4r               -2551.901554   0.0   0.0    4.536068  -1.643694

    13_8344_8845_4r               -2551.901554   0.0   0.0    4.536068  -1.643694

    13_8344_8845_4r               -2551.901554   0.0   0.0    4.536068  -1.643694

    13_8344_8845_4r               -2551.901554   0.0   0.0    4.536068  -1.643694

    14_8344_8845_4r               -2505.953426   0.0   0.0    5.000000 -50.069808

    14_8344_8845_4r               -2505.953426   0.0   0.0    5.000000 -50.069808

    14_8344_8845_4r               -2505.953426   0.0   0.0    5.000000 -50.069808

    14_8344_8845_4r               -2505.953426   0.0   0.0    5.000000 -50.069808

    15_8344_8845_4r_mt_z          -2502.470000   0.0   0.0    5.000000 -34.817656

    15_8344_8845_4r_mt_z          -2502.470000   0.0   0.0    5.000000 -34.817656

    15_8344_8845_4r_mt_z          -2502.470000   0.0   0.0    5.000000 -34.817656

    15_8344_8845_4r_mt_z          -2502.470000   0.0   0.0    5.000000 -34.817656

    16_8344_8845_4r               -2558.312931   0.0   0.0    1.707214 -29.465246

    16_8344_8845_4r               -2558.312931   0.0   0.0    1.707214 -29.465246

    16_8344_8845_4r               -2558.312931   0.0   0.0    1.707214 -29.465246

    16_8344_8845_4r               -2558.312931   0.0   0.0    1.707214 -29.465246

    17_8344_8845_2r_mt_z          -2590.130000   0.0   0.0    2.000000 -10.779830

    17_8344_8845_2r_mt_z          -2590.130000   0.0   0.0    2.000000 -10.779830

    ...                                    ...   ...   ...         ...        ...

    P20_008845_1894_XN_09N203W_18 -2514.431453   0.0   0.0    0.000000 -38.388316

    P20_008845_1894_XN_09N203W_2  -2535.712262   0.0   0.0    0.000000  42.067289

    P20_008845_1894_XN_09N203W_2  -2535.712262   0.0   0.0    0.000000  42.067289

    P20_008845_1894_XN_09N203W_2  -2535.712262   0.0   0.0    0.000000  42.067289

    P20_008845_1894_XN_09N203W_2  -2535.712262   0.0   0.0    0.000000  42.067289

    P20_008845_1894_XN_09N203W_3  -2525.215515   0.0   0.0    0.000000  36.033823

    P20_008845_1894_XN_09N203W_3  -2525.215515   0.0   0.0    0.000000  36.033823

    P20_008845_1894_XN_09N203W_3  -2525.215515   0.0   0.0    0.000000  36.033823

    P20_008845_1894_XN_09N203W_3  -2525.215515   0.0   0.0    0.000000  36.033823

    P20_008845_1894_XN_09N203W_4  -2562.446851   0.0   0.0    0.000000  -7.233876

    P20_008845_1894_XN_09N203W_4  -2562.446851   0.0   0.0    0.000000  -7.233876

    P20_008845_1894_XN_09N203W_5  -2560.812028   0.0   0.0    0.000000   7.498790

    P20_008845_1894_XN_09N203W_5  -2560.812028   0.0   0.0    0.000000   7.498790

    P20_008845_1894_XN_09N203W_5  -2560.812028   0.0   0.0    0.000000   7.498790

    P20_008845_1894_XN_09N203W_6  -2605.266130   0.0   0.0    0.000000   7.687475

    P20_008845_1894_XN_09N203W_6  -2605.266130   0.0   0.0    0.000000   7.687475

    P20_008845_1894_XN_09N203W_6  -2605.266130   0.0   0.0    0.000000   7.687475

    P20_008845_1894_XN_09N203W_6  -2605.266130   0.0   0.0    0.000000   7.687475

    P20_008845_1894_XN_09N203W_7  -2619.498291   0.0   0.0    0.000000   6.358447

    P20_008845_1894_XN_09N203W_7  -2619.498291   0.0   0.0    0.000000   6.358447

    P20_008845_1894_XN_09N203W_7  -2619.498291   0.0   0.0    0.000000   6.358447

    P20_008845_1894_XN_09N203W_7  -2619.498291   0.0   0.0    0.000000   6.358447

    P20_008845_1894_XN_09N203W_8  -2608.028730   0.0   0.0    0.000000  -0.219662

    P20_008845_1894_XN_09N203W_8  -2608.028730   0.0   0.0    0.000000  -0.219662

    P20_008845_1894_XN_09N203W_8  -2608.028730   0.0   0.0    0.000000  -0.219662

    P20_008845_1894_XN_09N203W_8  -2608.028730   0.0   0.0    0.000000  -0.219662

    P20_008845_1894_XN_09N203W_9  -2586.686862   0.0   0.0    0.000000  15.191825

    P20_008845_1894_XN_09N203W_9  -2586.686862   0.0   0.0    0.000000  15.191825

    P20_008845_1894_XN_09N203W_9  -2586.686862   0.0   0.0    0.000000  15.191825

    P20_008845_1894_XN_09N203W_9  -2586.686862   0.0   0.0    0.000000  15.191825

    

                                         res1        res2

    10_8344_8845_4r                 44.206259  416.201741

    10_8344_8845_4r                 44.206259  416.201741

    10_8344_8845_4r                 44.206259  416.201741

    10_8344_8845_4r                 44.206259  416.201741

    11_8344_8845_4r                103.403228  173.210013

    11_8344_8845_4r                103.403228  173.210013

    11_8344_8845_4r                103.403228  173.210013

    11_8344_8845_4r                103.403228  173.210013

    12_8344_8845_4r                 93.170584  180.058858

    12_8344_8845_4r                 93.170584  180.058858

    12_8344_8845_4r                 93.170584  180.058858

    12_8344_8845_4r                 93.170584  180.058858

    13_8344_8845_4r                 74.244153  319.554535

    13_8344_8845_4r                 74.244153  319.554535

    13_8344_8845_4r                 74.244153  319.554535

    13_8344_8845_4r                 74.244153  319.554535

    14_8344_8845_4r                144.316524 -164.540707

    14_8344_8845_4r                144.316524 -164.540707

    14_8344_8845_4r                144.316524 -164.540707

    14_8344_8845_4r                144.316524 -164.540707

    15_8344_8845_4r_mt_z           145.864550    0.214023

    15_8344_8845_4r_mt_z           145.864550    0.214023

    15_8344_8845_4r_mt_z           145.864550    0.214023

    15_8344_8845_4r_mt_z           145.864550    0.214023

    16_8344_8845_4r                121.908506   19.874949

    16_8344_8845_4r                121.908506   19.874949

    16_8344_8845_4r                121.908506   19.874949

    16_8344_8845_4r                121.908506   19.874949

    17_8344_8845_2r_mt_z            38.761214    0.236077

    17_8344_8845_2r_mt_z            38.761214    0.236077

    ...                                   ...         ...

    P20_008845_1894_XN_09N203W_18  195.050373 -391.289238

    P20_008845_1894_XN_09N203W_2   -12.658160  627.742625

    P20_008845_1894_XN_09N203W_2   -12.658160  627.742625

    P20_008845_1894_XN_09N203W_2   -12.658160  627.742625

    P20_008845_1894_XN_09N203W_2   -12.658160  627.742625

    P20_008845_1894_XN_09N203W_3    -4.170818  616.480181

    P20_008845_1894_XN_09N203W_3    -4.170818  616.480181

    P20_008845_1894_XN_09N203W_3    -4.170818  616.480181

    P20_008845_1894_XN_09N203W_3    -4.170818  616.480181

    P20_008845_1894_XN_09N203W_4    33.324946  574.887719

    P20_008845_1894_XN_09N203W_4    33.324946  574.887719

    P20_008845_1894_XN_09N203W_5    33.109007  581.149470

    P20_008845_1894_XN_09N203W_5    33.109007  581.149470

    P20_008845_1894_XN_09N203W_5    33.109007  581.149470

    P20_008845_1894_XN_09N203W_6    59.859663  375.680663

    P20_008845_1894_XN_09N203W_6    59.859663  375.680663

    P20_008845_1894_XN_09N203W_6    59.859663  375.680663

    P20_008845_1894_XN_09N203W_6    59.859663  375.680663

    P20_008845_1894_XN_09N203W_7    61.278242  375.840988

    P20_008845_1894_XN_09N203W_7    61.278242  375.840988

    P20_008845_1894_XN_09N203W_7    61.278242  375.840988

    P20_008845_1894_XN_09N203W_7    61.278242  375.840988

    P20_008845_1894_XN_09N203W_8    71.414267  336.409684

    P20_008845_1894_XN_09N203W_8    71.414267  336.409684

    P20_008845_1894_XN_09N203W_8    71.414267  336.409684

    P20_008845_1894_XN_09N203W_8    71.414267  336.409684

    P20_008845_1894_XN_09N203W_9    22.094037  544.874936

    P20_008845_1894_XN_09N203W_9    22.094037  544.874936

    P20_008845_1894_XN_09N203W_9    22.094037  544.874936

    P20_008845_1894_XN_09N203W_9    22.094037  544.874936

    

    [919 rows x 23 columns]



%% Cell type:code id: tags:



``` python

@singledispatch

def read_ipf(arg):

    return str(arg)



@read_ipf.register(str)

def read_ipf_str(input_data):

    """

    Read a socet ipf file into a pandas data frame



    Parameters

    ----------

    input_data : str

                 path to the an input data file



    Returns

    -------

    df : pd.DataFrame

         containing the ipf data with appropriate column names and indices

    """



    # Check that the number of rows is matching the expected number

    with open(input_data, 'r') as f:

        for i, l in enumerate(f):

            if i == 1:

                cnt = int(l)

            elif i == 2:

                col = l

                break



    columns = np.genfromtxt(input_data, skip_header=2, dtype='unicode',

                            max_rows = 1, delimiter = ',')



    # TODO: Add unicode conversion

    d = [line.split() for line in open(input_data, 'r')]

    d = np.hstack(np.array(d[3:]))



    d = d.reshape(-1, 12)



    df = pd.DataFrame(d, columns=columns)

    file = os.path.split(os.path.splitext(input_data)[0])[1]

    df['ipf_file'] = pd.Series(np.full((len(df['pt_id'])), file), index = df.index)



    assert int(cnt) == len(df), 'Dataframe length {} does not match point length {}.'.format(int(cnt), len(df))



    # Soft conversion of numeric types to numerics, allows str in first col for point_id

    df = df.apply(pd.to_numeric, errors='ignore')



    return df



@read_ipf.register(list)

def read_ipf_list(input_data_list):

    """

    Read a socet ipf file into a pandas data frame



    Parameters

    ----------

    input_data_list : list

                      list of paths to the a set of input data files



    Returns

    -------

    df : pd.DataFrame

         containing the ipf data with appropriate column names and indices

    """

    frames = []



    for input_file in input_data_list:

        frames.append(read_ipf(input_file))



    df = pd.concat(frames)



    return df

```



%% Cell type:code id: tags:



``` python

x = np.array(['1', '2', '3'])

y = np.array(['1', '2', '3'])



print((x == y).all())

```



%% Output



    True



%% Cell type:code id: tags:



``` python

```

plio/io/io_bae.py

+49 −2
Original line number Diff line number Diff line
@@ -85,11 +85,10 @@ def read_ipf_str(input_data): 
    columns = np.genfromtxt(input_data, skip_header=2, dtype='unicode',

                            max_rows = 1, delimiter = ',')



    # TODO: Add unicode conversion

    d = [line.split() for line in open(input_data, 'r')]

    d = np.hstack(np.array(d[3:]))



    d = d.reshape(-1, 12)

    d = d.reshape(-1, 12).astype('unicode')



    df = pd.DataFrame(d, columns=columns)

    file = os.path.split(os.path.splitext(input_data)[0])[1]
@@ -126,6 +125,54 @@ def read_ipf_list(input_data_list): 


    return df



def save_ipf(df, output_path):

    """

    Write a socet gpf file from a gpf-defined pandas dataframe



    Parameters

    ----------

    df          : pd.DataFrame

                  Pandas DataFrame



    output_file : str

                  path to the output data file



    Returns

    -------

    int         : success value

                  0 = success, 1 = errors

    """



    for ipf_file, ipf_df in df.groupby('ipf_file'):



        output_file = os.path.join(output_path, ipf_file + '.ipf')



        # Check that file can be opened

        try:

            outIPF = open(output_file, 'w', newline='\r\n')

        except:

            print('Unable to open output ipf file: {0}'.format(output_file))

            return 1



        #grab number of rows in pandas dataframe ipf group

        numpts = len(ipf_df)



        #Output ipf header

        outIPF.write('IMAGE POINT FILE\n')

        outIPF.write('{0}\n'.format(numpts))

        outIPF.write('pt_id,val,fid_val,no_obs,l.,s.,sig_l,sig_s,res_l,res_s,fid_x,fid_y\n')



        for index, row in ipf_df.iterrows():

            #Output coordinates to ipf file

            outIPF.write('{0} {1} {2} {3}\n'.format(row['pt_id'], row['val'], row['fid_val'], row['no_obs']))

            outIPF.write('{:0.6f}  {:0.6f}\n'.format(row['l.'], row['s.']))

            outIPF.write('{:0.6f}  {:0.6f}\n'.format(row['sig_l'], row['sig_s']))

            outIPF.write('{:0.6f}  {:0.6f}\n'.format(row['res_l'], row['res_s']))

            outIPF.write('{:0.6f}  {:0.6f}\n\n'.format(row['fid_x'], row['fid_y']))



        outIPF.close()

    return



def read_gpf(input_data):

    """

    Read a socet gpf file into a pandas data frame

plio/io/tests/temp/P20_008845_1894_XN_09N203W.ipf

0 → 100644
+729 −0
Original line number Diff line number Diff line 
IMAGE POINT FILE

121

pt_id,val,fid_val,no_obs,l.,s.,sig_l,sig_s,res_l,res_s,fid_x,fid_y

1_8344_8845_4r 1 0 0

-4058.982422  -2318.010742

0.000000  0.000000

-0.062556  -0.214713

0.000000  0.000000



2_8344_8845_4r 1 0 0

-3969.065186  -606.849243

0.000000  0.000000

0.228660  0.105249

0.000000  0.000000



3_8344_8845_4r_mt_z 1 0 0

-1019.739014  -2300.877197

0.000000  0.000000

-0.025129  -0.002447

0.000000  0.000000



4_8344_8845_4r_mt_z 1 0 0

-1037.099121  -548.180237

0.000000  0.000000

-0.000756  0.227752

0.000000  0.000000



5_8344_8845_4r 1 0 0

2438.984131  -2304.843506

0.000000  0.000000

0.062022  -0.109977

0.000000  0.000000



6_8344_8845_4r 1 0 0

2397.826904  -562.432861

0.000000  0.000000

-0.072678  -0.056104

0.000000  0.000000



7_8344_8845_4r_mt_z 1 0 0

-2510.927734  -1267.364868

0.000000  0.000000

0.215250  -0.040427

0.000000  0.000000



8_8344-8845_4r_mt_z 1 0 0

840.825317  -1028.345337

0.000000  0.000000

-0.241922  0.382924

0.000000  0.000000



9_8344_8845_4r 1 0 0

-4070.962158  2465.817139

0.000000  0.000000

-0.140837  0.005980

0.000000  0.000000



10_8344_8845_4r 1 0 0

-4044.697510  1008.950928

0.000000  0.000000

0.063678  0.661294

0.000000  0.000000



11_8344_8845_4r 1 0 0

-761.216064  2303.787109

0.000000  0.000000

-0.247307  -0.587299

0.000000  0.000000



12_8344_8845_4r 1 0 0

-889.364441  966.533997

0.000000  0.000000

-0.251753  0.008170

0.000000  0.000000



13_8344_8845_4r 1 0 0

-2559.871338  1777.522827

0.000000  0.000000

-0.131265  -0.305102

0.000000  0.000000



14_8344_8845_4r 1 0 0

2385.278320  2476.032227

0.000000  0.000000

0.389532  -0.299258

0.000000  0.000000



15_8344_8845_4r_mt_z 1 0 0

2395.869385  1038.165405

0.000000  0.000000

-0.170850  0.372485

0.000000  0.000000



16_8344_8845_4r 1 0 0

756.099792  1785.494751

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28_8344_8845_4r_mt_z 1 0 0

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29_8344_8845_4r_mt_z 1 0 0

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62_8344_8845_4r_mt_z 1 0 0

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P19_008344_1894_XN_09N203W_3 1 0 1

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P19_008344_1894_XN_09N203W_5 1 0 1

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P19_008344_1894_XN_09N203W_8 1 0 1

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P19_008344_1894_XN_09N203W_9 1 0 1

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P19_008344_1894_XN_09N203W_10 1 0 1

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P19_008344_1894_XN_09N203W_11 1 0 1

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P19_008344_1894_XN_09N203W_13 1 0 1

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P19_008344_1894_XN_09N203W_14 1 0 1

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P19_008344_1894_XN_09N203W_15 1 0 1

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P19_008344_1894_XN_09N203W_16 1 0 1

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P19_008344_1894_XN_09N203W_17 1 0 1

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P19_008344_1894_XN_09N203W_18 1 0 1

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P19_008344_1894_XN_09N203W_19 1 0 1

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P19_008344_1894_XN_09N203W_20 1 0 1

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P20_008845_1894_XN_09N203W_4 1 0 1

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P20_008845_1894_XN_09N203W_6 1 0 3

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P20_008845_1894_XN_09N203W_7 1 0 3

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P20_008845_1894_XN_09N203W_8 1 0 3

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P20_008845_1894_XN_09N203W_9 1 0 0

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P20_008845_1894_XN_09N203W_10 1 0 2

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P20_008845_1894_XN_09N203W_14 1 0 0

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P20_008845_1894_XN_09N203W_15 0 0 0

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P20_008845_1894_XN_09N203W_16 1 0 2

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P20_008845_1894_XN_09N203W_17 1 0 2

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P20_008845_1894_XN_09N203W_18 1 0 2

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P03_002371_1888_XI_08N204W_49 1 0 1

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P03_002371_1888_XI_08N204W_54 1 0 1

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P03_002371_1888_XI_08N204W_55 1 0 1

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P03_002371_1888_XI_08N204W_56 1 0 1

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P03_002371_1888_XI_08N204W_63 1 0 1

119.944458  1116.177612

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P03_002371_1888_XI_08N204W_64 1 0 1

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P03_002371_1888_XI_08N204W_65 1 0 1

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P03_002371_1888_XI_08N204W_71 1 0 1

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P03_002371_1888_XI_08N204W_77 1 0 1

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P01_001540_1889_XI_08N204W_3 1 0 0

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P01_001540_1889_XI_08N204W_4 1 0 0

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P01_001540_1889_XI_08N204W_5 1 0 0

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P01_001540_1889_XI_08N204W_6 1 0 0

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P01_001540_1889_XI_08N204W_7 1 0 0

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P01_001540_1889_XI_08N204W_43 1 0 1

231.430023  1286.035034

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P01_001540_1889_XI_08N204W_44 1 0 1

53.370300  1130.200195

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P01_001606_1897_XI_09N203W_20 1 0 1

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P01_001606_1897_XI_09N203W_21 1 0 1

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P01_001606_1897_XI_09N203W_26 1 0 1

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P01_001606_1897_XI_09N203W_27 1 0 1

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P01_001606_1897_XI_09N203W_32 1 0 1

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P01_001606_1897_XI_09N203W_33 1 0 1

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P01_001606_1897_XI_09N203W_39 1 0 1

957.507324  -1314.205933

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P01_001606_1897_XI_09N203W_40 1 0 1

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P01_001606_1897_XI_09N203W_41 1 0 1

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P01_001606_1897_XI_09N203W_42 1 0 1

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P01_001606_1897_XI_09N203W_48 1 0 1

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P01_001606_1897_XI_09N203W_49 1 0 1

2368.677490  -1310.253662

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P01_001606_1897_XI_09N203W_50 1 0 1

2938.904541  -1286.650635

0.268181  0.268181

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P03_002226_1895_XI_09N203W_41 1 0 1

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P03_002226_1895_XI_09N203W_42 1 0 1

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P03_002226_1895_XI_09N203W_43 1 0 1

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P03_002226_1895_XI_09N203W_46 1 0 1

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P03_002226_1895_XI_09N203W_47 1 0 1

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P03_002226_1895_XI_09N203W_53 1 0 1

3304.798340  -528.821411

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P03_002226_1895_XI_09N203W_54 1 0 1

3597.587646  -608.987488

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P03_002226_1895_XI_09N203W_55 1 0 1

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P03_002226_1895_XI_09N203W_64 1 0 1

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P03_002226_1895_XI_09N203W_67 1 0 1

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P03_002226_1895_XI_09N203W_68 1 0 1

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P03_002226_1895_XI_09N203W_71 1 0 1

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P03_002226_1895_XI_09N203W_66 1 0 1

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P03_002226_1895_XI_09N203W_72 1 0 1

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P03_002226_1895_XI_09N203W_74 1 0 1

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P03_002226_1895_XI_09N203W_76 1 0 1

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P03_002226_1895_XI_09N203W_82 1 0 1

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P19_008344_1894_XN_09N203W_2 1 0 1

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P19_008344_1894_XN_09N203W_7 1 0 1

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P03_002371_1888_XI_08N204W_76 1 0 1

4066.573730  1038.447998

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P03_002371_1888_XI_08N204W_78 1 0 1

4083.873291  1277.689209

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P01_001606_1897_XI_09N203W_19 1 0 1

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P01_001606_1897_XI_09N203W_65 1 0 1

4070.485840  -2315.992188

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P03_002226_1895_XI_09N203W_1 1 0 0

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P03_002226_1895_XI_09N203W_2 1 0 0

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plio/io/tests/test_io_bae.py

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