def _translate_gwy(self, file_path, meas_grp):
"""
Parameters
----------
file_path
meas_grp
For more information on the .gwy file format visit the link below -
http://gwyddion.net/documentation/user-guide-en/gwyfile-format.html
"""
# Need to build a set of channels to test against and a function-level variable to write to
channels = {}
# Read the data in from the specified file
gwy_data = gwyfile.load(file_path)
for obj in gwy_data:
gwy_key = obj.split('/')
try:
# if the second index of the gwy_key can be cast into an int then
# it needs to be processed either as an image or a graph
int(gwy_key[1])
if gwy_key[2] == 'graph':
# graph processing
self.global_parms['data_type'] = 'GwyddionGWY_' + 'Graph'
channels = self._translate_graph(meas_grp, gwy_data, obj,
channels)
elif obj.endswith('data'):
self.global_parms['data_type'] = 'GwyddionGWY_' + 'Image'
channels = self._translate_image_stack(
meas_grp, gwy_data, obj, channels)
else:
continue
except ValueError:
# if the second index of the gwy_key cannot be cast into an int
# then it needs to be processed wither as a spectra, volume or xyz
if gwy_key[1] == 'sps':
self.global_parms['data_type'] = 'GwyddionGWY_' + 'Spectra'
channels = self._translate_spectra(meas_grp, gwy_data, obj,
channels)
elif gwy_key[1] == 'brick':
self.global_parms['data_type'] = 'GwyddionGWY_' + 'Volume'
channels = self._translate_volume(meas_grp, gwy_data, obj,
channels)
elif gwy_key[1] == 'xyz':
self.global_parms['data_type'] = 'GwyddionGWY_' + 'XYZ'
channels = self._translate_xyz(meas_grp, gwy_data, obj,
channels)
write_simple_attrs(meas_grp.parent, self.global_parms)
def load_image(image_path):
''' Load the image from image_path. Return the leveled height data and the
extents of the image in nanometers '''
gwyobj = gwyfile.load(image_path)
channels = gwyfile.util.get_datafields(gwyobj)
topography = channels['Topography']
data = topography.data * 1e9 # Convert to nm
assert data.shape == (IMAGE_SIZE,IMAGE_SIZE)
data_leveled = level_image(data)
extent = topography.xreal * 1e9 # Convert to nm
return data_leveled, extent
def _translate_gwy(self, file_path, meas_grp):
"""
Parameters
----------
file_path
meas_grp
For more information on the .gwy file format visit the link below -
http://gwyddion.net/documentation/user-guide-en/gwyfile-format.html
"""
# Need to build a set of channels to test against and a function-level variable to write to
channels = {}
# Read the data in from the specified file
gwy_data = gwyfile.load(file_path)
for obj in gwy_data:
gwy_key = obj.split('/')
try:
# if the second index of the gwy_key can be cast into an int then
# it needs to be processed either as an image or a graph
int(gwy_key[1])
if gwy_key[2] == 'graph':
# graph processing
self.global_parms['data_type'] = 'GwyddionGWY_' + 'Graph'
channels = self._translate_graph(meas_grp, gwy_data,
obj, channels)
elif obj.endswith('data'):
self.global_parms['data_type'] = 'GwyddionGWY_' + 'Image'
channels = self._translate_image_stack(meas_grp, gwy_data,
obj, channels)
else:
continue
except ValueError:
# if the second index of the gwy_key cannot be cast into an int
# then it needs to be processed wither as a spectra, volume or xyz
if gwy_key[1] == 'sps':
self.global_parms['data_type'] = 'GwyddionGWY_' + 'Spectra'
channels = self._translate_spectra(meas_grp, gwy_data,
obj, channels)
elif gwy_key[1] == 'brick':
self.global_parms['data_type'] = 'GwyddionGWY_' + 'Volume'
channels = self._translate_volume(meas_grp, gwy_data,
obj, channels)
elif gwy_key[1] == 'xyz':
self.global_parms['data_type'] = 'GwyddionGWY_' + 'XYZ'
channels = self._translate_xyz(meas_grp, gwy_data,
obj, channels)
write_simple_attrs(meas_grp.parent, self.global_parms)
def gwy_read(self):
"""
Parameters
----------
file_path
meas_grp
For more information on the .gwy file format visit the link below -
http://gwyddion.net/documentation/user-guide-en/gwyfile-format.html
"""
# Need to build a set of channels to test against and a function-level variable to write to
channels = []
# Read the data in from the specified file
gwy_data = gwyfile.load(self._input_file_path)
for obj in gwy_data:
gwy_key = obj.split('/')
try:
# if the second index of the gwy_key can be cast into an int then
# it needs to be processed either as an image or a graph
int(gwy_key[1])
if gwy_key[2] == 'graph':
# graph processing
channels = self._translate_graph(gwy_data, obj)
elif obj.endswith('data'):
channels.append(self._translate_image_stack(gwy_data, obj))
else:
continue
except ValueError:
# if the second index of the gwy_key cannot be cast into an int
# then it needs to be processed wither as a spectra, volume or xyz
if gwy_key[1] == 'sps':
channels = self._translate_spectra(gwy_data, obj)
elif gwy_key[1] == 'brick':
channels = self._translate_volume(gwy_data, obj)
elif gwy_key[1] == 'xyz':
channels = self._translate_xyz(gwy_data, obj)
return channels
def test_data():
filename = os.path.realpath('{}/test.gwy'.format(
os.path.dirname(os.path.realpath(__file__))))
return gwyfile.load(filename)