def datafield_reduce(datafield):
return datafield_create, (gwyutils.data_field_data_as_array(datafield),
datafield.get_xres(),
datafield.get_yres(),
datafield.get_si_unit_xy().get_string(gwy.SI_UNIT_FORMAT_PLAIN),
datafield.get_si_unit_z().get_string(gwy.SI_UNIT_FORMAT_PLAIN),
)
def spm_pixel_size(self):
"""Returns the Image Size of the spm file in pixels."""
self.key = gwy.gwy_app_get_data_key_for_id(0)
self.name = gwy.gwy_name_from_key(self.key)
self.data_tmp = gwyutils.data_field_data_as_array(
self.container[self.name])
return np.shape(self.data_tmp)
def convert_np(self, channel_id):
"""Converts a Gwyddion container to a Numpy array.
Args:
channel_id (int): ID of channel which will be converted.
Returns:
np_array (array): Numpy array of container channel.
"""
# Makes a data field (channel) current/active in the data browser.
gwy.gwy_app_data_browser_select_data_field(self.container, channel_id)
self.key = gwy.gwy_app_get_data_key_for_id(channel_id)
self.name = gwy.gwy_name_from_key(self.key)
return gwyutils.data_field_data_as_array(self.container[self.name])
def convertAFM(filenamex, saveImg = True):
filename = os.path.abspath(filenamex)
# print 'Loading ', filename
for i in range(100):
c = gwy.gwy_file_load(filename, gwy.RUN_NONINTERACTIVE)
if c != None:
break
time.sleep(0.1)
if c == None:
return None, None
gwy.gwy_app_data_browser_add(c)
for key in c.keys_by_name():
if re.match(r'^/0/data$', key):
field = c[key]
xres = field.get_xres()
yres = field.get_yres()
xreal = (field.get_xreal()*1e6)/2.0
yreal = (field.get_yreal()*1e6)/2.0
weights = gwy.DataLine(xres, 1.0, True)
weights.part_fill(0, xres//3, 1.0)
filtered = gwy.DataField.new_alike(field, False)
field.fft_filter_1d(filtered, weights,
gwy.ORIENTATION_HORIZONTAL,
gwy.INTERPOLATION_ROUND)
degrees = [1,1]
field.subtract_polynom(degrees[0],degrees[1],field.fit_polynom(degrees[0],degrees[1]))
field.data_changed()
data = gwyutils.data_field_data_as_array(field)
data = np.array(data)[::,::-1]
imfilename = False
if saveImg:
filename = os.path.abspath('D:/lithography/')
imfilename = str(filename)+"/current.png"
print (imfilename)
res = saveAFMimg(data, imfilename )
writeImageMacro( imfilename , [-xreal, -yreal, xreal, yreal])
info = {'width':xreal*2, 'height':yreal*2, 'imname': imfilename}
gwy.gwy_app_data_browser_remove(c)
return data, info
basename = filename[0:-4]
print filename.split('/')[-1][:-4]
meta_field = '/' + str(data_field_id) + '/meta'
title = '/' + str(data_field_id) + '/data/title'
channel = c[title]
print channel
meta = c[meta_field]
print meta.keys_by_name()
bias = meta['Bias']
bias, bu = bias.split(' ')
current = meta['Z controller Setpoint']
current, cu = current.split(' ')
current = float(current) * 1e12
cu = 'pA'
current_bias = 'pm'
xd = d.get_xreal() * 1e9
yd = d.get_yreal() * 1e9
xyu = 'nm'
print xd
print bias
#gwy.gwy_file_save(c, basename+'_'+str(xd)+xyu+'_'+str(yd)+xyu+'_'+bias+bu+'_'+str(current)+cu+'.png', gwy.RUN_NONINTERACTIVE)
# prepare to save
w = d.get_xres()
h = d.get_yres()
io.use_plugin('freeimage')
data_field = '/' + str(data_field_id) + '/data'
array = gwyutils.data_field_data_as_array(d)
print array.shape
def exportasnparray(datafield, mask):
# Export the current datafield (channel) and mask (grains) as numpy arrays
npdata = gwyutils.data_field_data_as_array(datafield)
npmask = gwyutils.data_field_data_as_array(mask)
return npdata, npmask
