Merge pull request #33 from tthatcher95/master

import os

import numpy as np

# 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

%% Cell type:code id: tags:

``` python

import os

import numpy as np

# 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

read_atf('CTX_Athabasca_Middle_step0.atf')

```

%% Output

    {'ATF_FILE': 'CTX_Athabasca_Middle_step0.atf',

     'GP_FILE': 'CTX_Athabasca_Middle.gpf',

     'IMAGE_IPF': ['P19_008344_1894_XN_09N203W.ipf',

      'P20_008845_1894_XN_09N203W.ipf',

      'P03_002371_1888_XI_08N204W.ipf',

      'P01_001540_1889_XI_08N204W.ipf',

      'P01_001606_1897_XI_09N203W.ipf',

      'P03_002226_1895_XI_09N203W.ipf'],

     'IMAGE_SUP': ['P19_008344_1894_XN_09N203W.sup',

      'P20_008845_1894_XN_09N203W.sup',

      'P03_002371_1888_XI_08N204W.sup',

      'P01_001540_1889_XI_08N204W.sup',

      'P01_001606_1897_XI_09N203W.sup',

      'P03_002226_1895_XI_09N203W.sup'],

     'PATH': '/home/tthatcher/Desktop/Projects/Plio/plio/notebooks',

     'PROJECT': 'D:\\data\\CTX_Athabasca_Middle.prj'}

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