def load_check(self, filename):
"""Function to check what type of data is contained in a file to be loaded, if possible."""
#read file from hdf5 file
data_type = ''
if type(filename) == h5py._hl.group.Group:
loaded_data = filename['data']
if loaded_data.attrs.get(
'type'
): #check if the attribute 'type' attached on the data
data_type = loaded_data.attrs.get('type')
else:
data_type = None
#directly load file
elif type(filename) == str:
loaded_data = hspy.load(filename)
if loaded_data.metadata.Signal.signal_type == "EELS":
if loaded_data.axes_manager.signal_axes[
0].offset < 500: #check if EELS is high/low-loss
data_type = 'EELS_L'
else:
data_type = 'EELS_H'
elif (loaded_data.metadata.Signal.signal_type
== "EDS_SEM") or (loaded_data.metadata.Signal.signal_type
== "EDS_TEM"):
data_type = 'EDS'
else:
data_type = None
return (data_type)
def test_rgba16():
s = hs.load(os.path.join(
my_path,
"tiff_files",
"test_rgba16.tif"))
data = np.load(os.path.join(
my_path,
"npy_files",
"test_rgba16.npy"))
assert_true((s.data == data).all())
def __init__(self, path):
folder = []
if type(path) == h5py._hl.group.Group: #read file
folder = path.values()
else: #directly load file
folder = [
os.path.join(path, f) for f in os.listdir(path)
if (os.path.isfile(os.path.join(path, f)) and (
'.DS_Store' not in f))
]
#folder is a list that contains path of each file in the folder
#delet the hidden folder '.DS_Store' in MacOS
for filename in folder:
type_check = self.load_check(filename)
if type_check == None:
print "Data name: %s" % hspy.load(
filename).metadata.General.original_filename
type_check = str(
input(
"Please input the datatype of the data (SURVEY, HAADF, EELS, EDS, etc...): "
))
print "\n"
# let users'input always is uppercase
type_check = type_check.upper()
if type_check == 'SURVEY':
if type(filename) == h5py._hl.group.Group:
self.survey = self.read_signal_from_EMDgroup(filename)
else:
self.survey = hspy.load(filename)
if type_check == 'HAADF':
if type(filename) == h5py._hl.group.Group:
self.haadf = self.read_signal_from_EMDgroup(filename)
else:
self.haadf = hspy.load(filename)
if type_check == 'EELS_L':
if type(filename) == h5py._hl.group.Group:
self.eels_l = self.read_signal_from_EMDgroup(filename)
else:
self.eels_l = hspy.load(filename)
if type_check == 'EELS_H':
if type(filename) == h5py._hl.group.Group:
self.eels_h = self.read_signal_from_EMDgroup(filename)
else:
self.eels_h = hspy.load(filename)
if type_check == 'EDS':
if type(filename) == h5py._hl.group.Group:
self.eds = self.read_signal_from_EMDgroup(filename)
else:
self.eds = hspy.load(filename)
def load_check(self, filename):
"""Function to check what type of data is contained in a file to be loaded, if possible."""
#read file from hdf5 file
data_type = ''
if type(filename) == h5py._hl.group.Group:
loaded_data = filename['data']
if loaded_data.attrs.get('type'): #check if the attribute 'type' attached on the data
data_type = loaded_data.attrs.get('type')
else:
data_type = None
#directly load file
elif type(filename) == str:
loaded_data = hspy.load(filename)
if loaded_data.metadata.Signal.signal_type == "EELS":
if loaded_data.axes_manager.signal_axes[0].offset < 500: #check if EELS is high/low-loss
data_type = 'EELS_L'
else:
data_type = 'EELS_H'
elif (loaded_data.metadata.Signal.signal_type == "EDS_SEM") or (loaded_data.metadata.Signal.signal_type == "EDS_TEM"):
data_type = 'EDS'
else:
data_type = None
return (data_type)
def __init__(self, path):
folder = []
if type(path) == h5py._hl.group.Group: #read file
folder = path.values()
else: #directly load file
folder = [os.path.join(path, f) for f in os.listdir(path) if (os.path.isfile(os.path.join(path, f)) and ('.DS_Store' not in f))]
#folder is a list that contains path of each file in the folder
#delet the hidden folder '.DS_Store' in MacOS
for filename in folder:
type_check = self.load_check(filename)
if type_check == None:
print "Data name: %s" % hspy.load(filename).metadata.General.original_filename
type_check = str(input("Please input the datatype of the data (SURVEY, HAADF, EELS, EDS, etc...): "))
print "\n"
# let users'input always is uppercase
type_check = type_check.upper()
if type_check == 'SURVEY':
if type(filename) == h5py._hl.group.Group:
self.survey = self.read_signal_from_EMDgroup(filename)
else:
self.survey = hspy.load(filename)
if type_check == 'HAADF':
if type(filename) == h5py._hl.group.Group:
self.haadf = self.read_signal_from_EMDgroup(filename)
else:
self.haadf = hspy.load(filename)
if type_check == 'EELS_L':
if type(filename) == h5py._hl.group.Group:
self.eels_l = self.read_signal_from_EMDgroup(filename)
else:
self.eels_l = hspy.load(filename)
if type_check == 'EELS_H':
if type(filename) == h5py._hl.group.Group:
self.eels_h = self.read_signal_from_EMDgroup(filename)
else:
self.eels_h = hspy.load(filename)
if type_check == 'EDS':
if type(filename) == h5py._hl.group.Group:
self.eds = self.read_signal_from_EMDgroup(filename)
else:
self.eds = hspy.load(filename)
""" Loads hyperspy as a regular python library, loads spectrums from files, does curve fitting, and plotting the model and original spectrum to a png file"""
import hyperspy.hspy as hspy
import matplotlib.pyplot as plt
coreLossSpectrumFileName = "coreloss_spectrum.msa"
lowlossSpectrumFileName = "lowloss_spectrum.msa"
s = hspy.load(coreLossSpectrumFileName).to_EELS()
s.add_elements(("Mn", "O"))
s.set_microscope_parameters(
beam_energy=300,
convergence_angle=24.6,
collection_angle=13.6)
ll = hspy.load(lowlossSpectrumFileName).to_EELS()
m = s.create_model(ll=ll)
m.enable_fine_structure()
m.multifit(kind="smart")
m.plot()
plt.savefig("model_original_spectrum_plot.png")
def __init__(self, path):
folder = []
if type(path) == h5py._hl.group.Group: #read file
folder = path.values()
else: #directly load file
folder = [os.path.join(path, f) for f in os.listdir(path) if (os.path.isfile(os.path.join(path, f)) and ('.DS_Store' not in f))]
#folder is a list that contains pathes of each file in the folder
#delet the hidden folder '.DS_Store' in MacOS
self.support_formats(folder) # check if data type in this folder can be loaded by Hyperspy
for filename in folder:
#temperary lines for PtNi particles.
"""if filename.rpartition('.')[2] == 'tif':
self.haadf = hspy.load(filename)
for i in range(2):
if i == 0:
self.haadf.axes_manager[i].name='X'
self.haadf.axes_manager[i].units='nm'
self.haadf.axes_manager[i].scale=0.275
self.haadf.axes_manager[i].navigate=True
elif i == 1:
self.haadf.axes_manager[i].name='Y'
self.haadf.axes_manager[i].units='nm'
self.haadf.axes_manager[i].scale=0.275
self.haadf.axes_manager[i].navigate=True
if filename.rpartition('.')[2] == 'rpl':
self.eds = hspy.load(filename)
self.eds.set_signal_type('EDS_TEM')
self.eds.set_microscope_parameters(beam_energy = 200)
for i in range(3):
if i == 0:
self.eds.axes_manager[i].name='X'
self.eds.axes_manager[i].units='nm'
self.eds.axes_manager[i].scale=0.275
elif i == 1:
self.eds.axes_manager[i].name='Y'
self.eds.axes_manager[i].units='nm'
self.eds.axes_manager[i].scale=0.275
elif i == 2:
self.eds.axes_manager[i].name='Energy'
self.eds.axes_manager[i].units='keV'
self.eds.axes_manager[i].scale=0.01
self.eds.axes_manager[i].offset=-0.477"""
#temperary lines end
#original lines
type_check = self.load_check(filename)
if type_check == None:
print "Data name: %s" % hspy.load(filename).metadata.General.original_filename
type_check = str(input("Please input the datatype of the data (SURVEY, HAADF, EELS, EDS, etc...): "))
print "\n"
# let users'input always is uppercase
type_check = type_check.upper()
if type_check == 'SURVEY':
if type(filename) == h5py._hl.group.Group:
self.survey = self.read_signal_from_EMDgroup(filename)
else:
self.survey = hspy.load(filename)
if type_check == 'HAADF':
if type(filename) == h5py._hl.group.Group:
self.haadf = self.read_signal_from_EMDgroup(filename)
else:
self.haadf = hspy.load(filename)
if type_check == 'EELS_L':
if type(filename) == h5py._hl.group.Group:
self.eels_l = self.read_signal_from_EMDgroup(filename)
else:
self.eels_l = hspy.load(filename)
if type_check == 'EELS_H':
if type(filename) == h5py._hl.group.Group:
self.eels_h = self.read_signal_from_EMDgroup(filename)
else:
self.eels_h = hspy.load(filename)
if type_check == 'EDS':
if type(filename) == h5py._hl.group.Group:
self.eds = self.read_signal_from_EMDgroup(filename)
else:
self.eds = hspy.load(filename)
