fix_cropped_gsf_files.py

import numpy as np
import sys


# this is the file's name or path to the file
fname = 'vox.gsf'

def gsf_read(fname):
    if fname.rpartition('.')[1] == '.':
        fname = fname[0:fname.rfind('.')]

    gsf_file = open(fname + '.gsf', 'rb')

    metadata = {}

    # check if header is OK
    if not (gsf_file.readline().decode('UTF-8') == 'Gwyddion Simple Field 1.0\n'):
        gsf_file.close()
        raise ValueError("File has wrong header")

    term = b'00'
    # read metadata header
    while term != b'\x00':
        line_string = gsf_file.readline().decode('UTF-8')
        metadata[line_string.rpartition(' = ')[0]] = line_string.rpartition('=')[2]
        term = gsf_file.read(1)
        gsf_file.seek(-1, 1)

    gsf_file.read(4 - gsf_file.tell() % 4)

    # fix known metadata types from .gsf file specs
    # mandatory
    metadata['XRes'] = np.int(metadata['XRes'])
    metadata['YRes'] = np.int(metadata['YRes'])

    # optional
    for k in ['XReal', 'YReal', 'XOffset', 'YOffset', 'XYUnits', 'ZUnits', 'Title', 'Date', 'DwellTime']:
        if k in metadata:
            try:
                metadata[k] = np.float(metadata[k])
            except:
                metadata[k] = np.str(metadata[k].split("\n")[0])

    raw = np.frombuffer(gsf_file.read(), dtype='float32')

    product = metadata['XRes'] * metadata['YRes']

    if len(raw) != product:
        difference = product - len(raw)
        data = np.pad(raw, (0, difference), 'minimum')
    else:
        data = raw

    data = np.reshape(data, (metadata['YRes'], metadata['XRes']))

    print(data)

    gsf_file.close()

    return metadata, data

metadata, data = gsf_read(fname)
print(metadata)

def gsf_write(data, newfname, metadata={}):

    gsf_file = open(newfname + '.gsf', 'wb')
    s = ''
    s += 'Gwyddion Simple Field 1.0' + '\n'


    for k in metadata.keys():
        print(k, metadata[k])
        if k == 'XRes' or k == 'YRes':
            s += k + ' = ' + '{0:d}'.format(metadata[k]) + '\n'
            continue
        elif k == 'XReal' or k == 'YReal':
            s += k + ' = ' + '{0:g}'.format(metadata[k]) + '\n'
            continue
        try:
            s += k + ' = ' + '{0:G}'.format(metadata[k]) + '\n'
        except:
            s += k + ' = ' + str(metadata[k]) + '\n'


    gsf_file.write(bytes(s, 'UTF-8'))
    gsf_file.write(b'\x00' * (4 - len(s) % 4))
    gsf_file.write(data.tobytes(None))

    gsf_file.close()

newfname = 'test_fixed'

gsf_write(data, newfname, metadata)