Exemple #1
0
def run_paths_of_merges(yamlfile, logging=True):

    ipl = IPL(yaml=yamlfile)

    ipl.set_indent(1)

    params = rdict(data=ipl.get_params())
    if logging:
        ipl.startlogger(filename=params['resultfolder'] +
                        'paths_of_merges.log',
                        type='w',
                        name='PathsOfMerges')
    else:
        ipl.startlogger()

    try:

        # # Copy the script file and the parameters to the scriptsfolder
        # copy(inspect.stack()[0][1], params['scriptsfolder'])
        # copy(yamlfile, params['scriptsfolder'] + 'paths_of_merges.parameters.yml')

        # ipl.logging('\nInitial datastructure: \n\n{}', ipl.datastructure2string(maxdepth=3))

        paths_of_merges(ipl, params['debug'])

        # ipl.logging('\nFinal datastructure: \n\n{}', ipl.datastructure2string(maxdepth=3))

        # ipl.write(filepath=params['intermedfolder'] + params['largeobjfile'])

        ipl.logging('')
        ipl.stoplogger()

    except:

        ipl.errout('Unexpected error')
def run_find_border_contacts(yamlfile, logging=True):

    ipl = IPL(yaml=yamlfile)

    ipl.set_indent(1)

    params = rdict(data=ipl.get_params())
    if logging:
        ipl.startlogger(filename=params['resultfolder'] + 'find_border_contacts.log', type='w', name='FindBorderContacts')
    else:
        ipl.startlogger()

    try:

        # # Copy the script file and the parameters to the scriptsfolder
        # copy(inspect.stack()[0][1], params['scriptsfolder'])
        # copy(yamlfile, params['scriptsfolder'] + 'find_border_contacts.parameters.yml')

        # ipl.logging('\nInitial datastructure: \n\n{}', ipl.datastructure2string(maxdepth=3))

        find_border_contacts(ipl)

        # ipl.logging('\nFinal datastructure: \n\n{}', ipl.datastructure2string(maxdepth=3))

        # ipl.write(filepath=params['intermedfolder'] + params['largeobjfile'])

        ipl.logging('')
        ipl.stoplogger()

    except:

        ipl.errout('Unexpected error')
def run_compute_feature_images(yamlfile):

    ipl = IPL(yaml=yamlfile)

    ipl.set_indent(1)

    params = rdict(data=ipl.get_params())
    ipl.startlogger(filename=params['resultfolder'] + 'compute_feature_images.log', type='w', name='ComputeFeatureImages')

    try:

        # # Copy the script file and the parameters to the scriptsfolder
        # copy(inspect.stack()[0][1], params['scriptsfolder'])
        # copy(yamlfile, params['scriptsfolder'] + 'compute_feature_images.parameters.yml')

        # ipl.logging('\nInitial datastructure: \n\n{}', ipl.datastructure2string(maxdepth=3))

        compute_feature_images(ipl)

        # ipl.logging('\nFinal datastructure: \n\n{}', ipl.datastructure2string(maxdepth=3))

        # ipl.write(filepath=params['intermedfolder'] + params['largeobjfile'])

        ipl.logging('')
        ipl.stoplogger()

    except:

        ipl.errout('Unexpected error')
def run_remove_small_objects(yamlfile):

    ipl = IPL(
        yaml=yamlfile,
        yamlspec={'path': 'datafolder', 'filename': 'labelsfile', 'skeys': 'labelsname'},
        recursive_search=True,
        nodata=True
    )

    # Set indentation of the logging
    ipl.set_indent(1)

    params = ipl.get_params()
    ipl.startlogger(filename=params['resultfolder'] + 'remove_small_objects.log', type='w', name='RemoveSmallObjects')

    try:

        # # Copy the script file and the parameters to the scriptsfolder
        # copy(inspect.stack()[0][1], params['scriptsfolder'])
        # copy(yamlfile, params['scriptsfolder'] + 'remove_small_objects.parameters.yml')

        ipl.logging('\nipl datastructure: \n\n{}', ipl.datastructure2string(maxdepth=3))

        remove_small_objects(ipl)

        ipl.logging('\nFinal datastructure: \n\n{}', ipl.datastructure2string(maxdepth=3))

        # ipl.write(filepath=params['intermedfolder'] + params['largeobjfile'])

        ipl.logging('')
        ipl.stoplogger()

    except:

        ipl.errout('Unexpected error')
Exemple #5
0
def run_random_forest(yamlfile,
                      logging=True,
                      make_only_feature_array=False,
                      debug=False,
                      write=True):

    ipl = IPL(yaml=yamlfile)

    ipl.set_indent(1)

    params = rdict(data=ipl.get_params())
    if logging:
        ipl.startlogger(filename=params['resultfolder'] + 'random_forest.log',
                        type='w',
                        name='RandomForest')
    else:
        ipl.startlogger()

    try:

        # # Copy the script file and the parameters to the scriptsfolder
        # copy(inspect.stack()[0][1], params['scriptsfolder'])
        # copy(yamlfile, params['scriptsfolder'] + 'random_forest.parameters.yml')

        # ipl.logging('\nInitial datastructure: \n\n{}', ipl.datastructure2string(maxdepth=3))

        if make_only_feature_array:
            make_feature_arrays(ipl)
        else:
            result = IPL()
            result['result'], result['evaluation'] = random_forest(ipl,
                                                                   debug=debug)

            # ipl.logging('\nFinal datastructure: \n\n{}', ipl.datastructure2string(maxdepth=3))

            if write:
                result.write(filepath=params['resultfolder'] +
                             params['resultsfile'])

        ipl.logging('')
        ipl.stoplogger()

    except:
        ipl.errout('Unexpected error')
Exemple #6
0
def run_remove_small_objects(yamlfile):

    ipl = IPL(yaml=yamlfile,
              yamlspec={
                  'path': 'datafolder',
                  'filename': 'labelsfile',
                  'skeys': 'labelsname'
              },
              recursive_search=True,
              nodata=True)

    # Set indentation of the logging
    ipl.set_indent(1)

    params = ipl.get_params()
    ipl.startlogger(filename=params['resultfolder'] +
                    'remove_small_objects.log',
                    type='w',
                    name='RemoveSmallObjects')

    try:

        # # Copy the script file and the parameters to the scriptsfolder
        # copy(inspect.stack()[0][1], params['scriptsfolder'])
        # copy(yamlfile, params['scriptsfolder'] + 'remove_small_objects.parameters.yml')

        ipl.logging('\nipl datastructure: \n\n{}',
                    ipl.datastructure2string(maxdepth=3))

        remove_small_objects(ipl)

        ipl.logging('\nFinal datastructure: \n\n{}',
                    ipl.datastructure2string(maxdepth=3))

        # ipl.write(filepath=params['intermedfolder'] + params['largeobjfile'])

        ipl.logging('')
        ipl.stoplogger()

    except:

        ipl.errout('Unexpected error')
def run_random_forest(yamlfile, logging=True, make_only_feature_array=False, debug=False, write=True):

    ipl = IPL(yaml=yamlfile)

    ipl.set_indent(1)

    params = rdict(data=ipl.get_params())
    if logging:
        ipl.startlogger(filename=params['resultfolder'] + 'random_forest.log', type='w', name='RandomForest')
    else:
        ipl.startlogger()

    try:

        # # Copy the script file and the parameters to the scriptsfolder
        # copy(inspect.stack()[0][1], params['scriptsfolder'])
        # copy(yamlfile, params['scriptsfolder'] + 'random_forest.parameters.yml')

        # ipl.logging('\nInitial datastructure: \n\n{}', ipl.datastructure2string(maxdepth=3))

        if make_only_feature_array:
            make_feature_arrays(ipl)
        else:
            result = IPL()
            result['result'], result['evaluation'] = random_forest(ipl, debug=debug)

            # ipl.logging('\nFinal datastructure: \n\n{}', ipl.datastructure2string(maxdepth=3))

            if write:
                result.write(filepath=params['resultfolder'] + params['resultsfile'])

        ipl.logging('')
        ipl.stoplogger()

    except:
        ipl.errout('Unexpected error')