def load_BCF(self,bcf_file):
self.bcf_file = bcf_file
bcf=bru.BCF_reader(bcf_file)
header_file = bcf.get_file('EDSDatabase/HeaderData')
header_byte_str = header_file.get_as_BytesIO_string().getvalue()
hd_bt_str = bru.fix_dec_patterns.sub(b'\\1.\\2', header_byte_str)
root = ET.fromstring(hd_bt_str)
root = root.find("./ClassInstance[@Type='TRTSpectrumDatabase']")
self.root = root
def test_fast_bcf():
thingy = pytest.importorskip("hyperspy.io_plugins.unbcf_fast")
from hyperspy.io_plugins import bruker
for bcffile in test_files:
filename = os.path.join(my_path, 'bruker_data', bcffile)
thingy = bruker.BCF_reader(filename)
for j in range(2, 5, 1):
print('downsampling:', j)
bruker.fast_unbcf = True # manually enabling fast parsing
hmap1 = thingy.parse_hypermap(downsample=j) # using cython
bruker.fast_unbcf = False # manually disabling fast parsing
hmap2 = thingy.parse_hypermap(downsample=j) # py implementation
np.testing.assert_array_equal(hmap1, hmap2)
def load_bcf_dump_xml(bcf_file,xml_file):
'''
Loads bcf file, dumps header contents to XML file
s'''
# hd_bt_str = _load_bruker_bcf_as_bytestream(bcf_file)
bcf=bru.BCF_reader(import_file)
header_file = bcf.get_file('EDSDatabase/HeaderData')
header_byte_str = header_file.get_as_BytesIO_string().getvalue()
hd_bt_str = bru.fix_dec_patterns.sub(b'\\1.\\2', header_byte_str)
xml_file = open(xml_file,'wb')
xml_file.write(hd_bt_str)
xml_file.close()
def _load_bruker_bcf_as_xml(self, import_file):
"""
Loads Bruker BCF file as XML,
useful for mosaic extraction
Returns root xml tree object
"""
# for mosaic extraction
bcf = bru.BCF_reader(import_file)
header_file = bcf.get_file('EDSDatabase/HeaderData')
header_byte_str = header_file.get_as_BytesIO_string().getvalue()
hd_bt_str = bru.fix_dec_patterns.sub(b'\\1.\\2', header_byte_str)
root = ET.fromstring(hd_bt_str)
root = root.find("./ClassInstance[@Type='TRTSpectrumDatabase']")
return root
Created on Sat Apr 24 22:30:26 2021
@author: Mike
"""
import hyperspy.api as hs
import os
import hyperspy.io_plugins.bruker as brk
bcf_file = 'kvr-btm-180deg-100ms-1det.bcf'
os.chdir(u'D:/Google Drive/археология/soft/test')
#%%
bcf = hs.load('kvr-btm-180deg-100ms-1det.bcf')
#%%
b1 = brk.BCF_reader(bcf_file) #brk.BCF_reader class
h = b1.header #brk.HyperHeader class instance
d2 = h.estimate_map_channels() # incorrect map channels
# =============================================================================
# bruker_hv_range = self.spectra_data[index].amplification / 1000
# if self.hv >= bruker_hv_range:
# return self.spectra_data[index].data.shape[0]
# else:
# return self.spectra_data[index].energy_to_channel(self.hv)
# =============================================================================
h.spectra_data[0].amplification # line 768, = 40 000
# -*- coding: utf-8 -*-
"""
Created on Sat Jul 3 09:56:12 2021
@author: Mike
"""
#%% init
import hyperspy.io_plugins.bruker as bru
import_file = 'fang-A.bcf'
#%% load file
bcf = bru.BCF_reader(import_file)
header_file = bcf.get_file('EDSDatabase/HeaderData')
header_byte_str = header_file.get_as_BytesIO_string().getvalue()
hd_bt_str = bru.fix_dec_patterns.sub(b'\\1.\\2', header_byte_str)
#%% dump xml file
h_file = open('h_file.xml', 'wb')
h_file.write(hd_bt_str)
h_file.close()