def get_header_from_signal(signal, endianess="<"):
header = get_default_header(endianess)
if "blockfile_header" in signal.original_metadata:
header = dict2sarray(signal.original_metadata["blockfile_header"],
sarray=header)
note = signal.original_metadata["blockfile_header"]["Note"]
else:
note = ""
# The navigation and signal units are 'nm' and 'cm', respectively, so we
# convert the units accordingly before saving the signal
axes_manager = signal.axes_manager.deepcopy()
try:
axes_manager.convert_units("navigation", "nm")
axes_manager.convert_units("signal", "cm")
except Exception:
warnings.warn(
"BLO file expects cm units in signal dimensions and nm in navigation dimensions. "
"Existing units could not be converted; saving "
"axes scales as is. Beware that scales "
"will likely be incorrect in the file.",
UserWarning,
)
if axes_manager.navigation_dimension == 2:
NX, NY = axes_manager.navigation_shape
SX = axes_manager.navigation_axes[0].scale
SY = axes_manager.navigation_axes[1].scale
elif axes_manager.navigation_dimension == 1:
NX = axes_manager.navigation_shape[0]
NY = 1
SX = axes_manager.navigation_axes[0].scale
SY = SX
elif axes_manager.navigation_dimension == 0:
NX = NY = SX = SY = 1
DP_SZ = axes_manager.signal_shape
if DP_SZ[0] != DP_SZ[1]:
raise ValueError("Blockfiles require signal shape to be square!")
DP_SZ = DP_SZ[0]
SDP = 100.0 / axes_manager.signal_axes[0].scale
offset2 = NX * NY + header["Data_offset_1"]
# Based on inspected files, the DPs are stored at 16-bit boundary...
# Normally, you'd expect word alignment (32-bits) ¯\_(°_o)_/¯
offset2 += offset2 % 16
header = dict2sarray(
{
"NX": NX,
"NY": NY,
"DP_SZ": DP_SZ,
"SX": SX,
"SY": SY,
"SDP": SDP,
"Data_offset_2": offset2,
},
sarray=header,
)
return header, note
def get_header_from_signal(signal, endianess='<'):
header = get_default_header(endianess)
if 'blockfile_header' in signal.original_metadata:
header = dict2sarray(signal.original_metadata['blockfile_header'],
sarray=header)
note = signal.original_metadata['blockfile_header']['Note']
else:
note = ''
# The navigation and signal units are 'nm' and 'cm', respectively, so we
# convert the units accordingly before saving the signal
axes_manager = signal.axes_manager.deepcopy()
axes_manager.convert_units('navigation', 'nm')
axes_manager.convert_units('signal', 'cm')
if axes_manager.navigation_dimension == 2:
NX, NY = axes_manager.navigation_shape
SX = axes_manager.navigation_axes[0].scale
SY = axes_manager.navigation_axes[1].scale
elif axes_manager.navigation_dimension == 1:
NX = axes_manager.navigation_shape[0]
NY = 1
SX = axes_manager.navigation_axes[0].scale
SY = SX
elif axes_manager.navigation_dimension == 0:
NX = NY = SX = SY = 1
DP_SZ = axes_manager.signal_shape
if DP_SZ[0] != DP_SZ[1]:
raise ValueError('Blockfiles require signal shape to be square!')
DP_SZ = DP_SZ[0]
SDP = 100. / axes_manager.signal_axes[0].scale
offset2 = NX * NY + header['Data_offset_1']
# Based on inspected files, the DPs are stored at 16-bit boundary...
# Normally, you'd expect word alignment (32-bits) ¯\_(°_o)_/¯
offset2 += offset2 % 16
header = dict2sarray(
{
'NX': NX,
'NY': NY,
'DP_SZ': DP_SZ,
'SX': SX,
'SY': SY,
'SDP': SDP,
'Data_offset_2': offset2,
},
sarray=header)
return header, note
def test_d2s_arrayX():
dt2 = dt + [('z', (np.uint8, 4)), ('u', (np.uint16, 4))]
d = dict(z=2, u=[1, 2, 3, 4])
sa = np.zeros((4,), dtype=dt2)
sa = dict2sarray(d, sarray=sa)
np.testing.assert_array_equal(sa['z'], [[2, 2, 2, 2], ] * 4)
np.testing.assert_array_equal(sa['u'], [[1, 2, 3, 4], ] * 4)
def test_d2s_arrayX():
dt2 = dt + [('z', (np.uint8, 4)), ('u', (np.uint16, 4))]
d = dict(z=2, u=[1, 2, 3, 4])
sa = np.zeros((4,), dtype=dt2)
sa = dict2sarray(d, sarray=sa)
np.testing.assert_array_equal(sa['z'], [[2, 2, 2, 2], ] * 4)
np.testing.assert_array_equal(sa['u'], [[1, 2, 3, 4], ] * 4)
def test_d2s_arrayX():
dt2 = dt + [("z", (np.uint8, 4)), ("u", (np.uint16, 4))]
d = dict(z=2, u=[1, 2, 3, 4])
sa = np.zeros((4,), dtype=dt2)
sa = dict2sarray(d, sarray=sa)
np.testing.assert_array_equal(sa["z"], [[2, 2, 2, 2]] * 4)
np.testing.assert_array_equal(sa["u"], [[1, 2, 3, 4]] * 4)
def test_d2s_extra_dict_ok():
d = dict(x=5, y=10, text='abcdef', other=55)
ref = np.zeros((1,), dtype=dt)
ref['x'] = 5
ref['y'] = 10
ref['text'] = 'abcdef'
nt.assert_equal(ref, dict2sarray(d, dtype=dt))
def test_d2s_dtype():
d = dict(x=5, y=10, text='abcdef')
ref = np.zeros((1, ), dtype=dt)
ref['x'] = 5
ref['y'] = 10
ref['text'] = 'abcdef'
assert ref == dict2sarray(d, dtype=dt)
def test_d2s_extra_dict_ok():
d = dict(x=5, y=10, text="abcdef", other=55)
ref = np.zeros((1,), dtype=dt)
ref["x"] = 5
ref["y"] = 10
ref["text"] = "abcdef"
nt.assert_equal(ref, dict2sarray(d, dtype=dt))
def test_d2s_extra_dict_ok():
d = dict(x=5, y=10, text='abcdef', other=55)
ref = np.zeros((1, ), dtype=dt)
ref['x'] = 5
ref['y'] = 10
ref['text'] = 'abcdef'
assert ref == dict2sarray(d, dtype=dt)
def test_d2s_dtype():
d = dict(x=5, y=10, text='abcdef')
ref = np.zeros((1,), dtype=dt)
ref['x'] = 5
ref['y'] = 10
ref['text'] = 'abcdef'
assert ref == dict2sarray(d, dtype=dt)
def get_header_from_signal(signal, endianess='<'):
header = get_default_header(endianess)
if 'blockfile_header' in signal.original_metadata:
header = dict2sarray(signal.original_metadata['blockfile_header'],
sarray=header)
note = signal.original_metadata['blockfile_header']['Note']
else:
note = ''
# The navigation and signal units are 'nm' and 'cm', respectively, so we
# convert the units accordingly before saving the signal
axes_manager = signal.axes_manager.deepcopy()
axes_manager.convert_units('navigation', 'nm')
axes_manager.convert_units('signal', 'cm')
if axes_manager.navigation_dimension == 2:
NX, NY = axes_manager.navigation_shape
SX = axes_manager.navigation_axes[0].scale
SY = axes_manager.navigation_axes[1].scale
elif axes_manager.navigation_dimension == 1:
NX = axes_manager.navigation_shape[0]
NY = 1
SX = axes_manager.navigation_axes[0].scale
SY = SX
elif axes_manager.navigation_dimension == 0:
NX = NY = SX = SY = 1
DP_SZ = axes_manager.signal_shape
if DP_SZ[0] != DP_SZ[1]:
raise ValueError('Blockfiles require signal shape to be square!')
DP_SZ = DP_SZ[0]
SDP = 100. / axes_manager.signal_axes[0].scale
offset2 = NX * NY + header['Data_offset_1']
# Based on inspected files, the DPs are stored at 16-bit boundary...
# Normally, you'd expect word alignment (32-bits) ¯\_(°_o)_/¯
offset2 += offset2 % 16
header = dict2sarray({
'NX': NX, 'NY': NY,
'DP_SZ': DP_SZ,
'SX': SX, 'SY': SY,
'SDP': SDP,
'Data_offset_2': offset2,
}, sarray=header)
return header, note
def test_d2s_type_cast_ok():
d = dict(x="34", text=55)
ref = np.zeros((1,), dtype=dt)
ref["x"] = 34
ref["y"] = 0
ref["text"] = "55"
nt.assert_equal(ref, dict2sarray(d, dtype=dt))
def test_d2s_type_cast_ok():
d = dict(x='34', text=55)
ref = np.zeros((1, ), dtype=dt)
ref['x'] = 34
ref['y'] = 0
ref['text'] = '55'
assert ref == dict2sarray(d, dtype=dt)
def test_d2s_type_cast_ok():
d = dict(x='34', text=55)
ref = np.zeros((1,), dtype=dt)
ref['x'] = 34
ref['y'] = 0
ref['text'] = '55'
nt.assert_equal(ref, dict2sarray(d, dtype=dt))
def test_d2s_sarray():
d = dict(x=5, y=10, text='abcdef')
base = np.zeros((1, ), dtype=dt)
base['x'] = 65
base['text'] = 'gg'
ref = np.zeros((1, ), dtype=dt)
ref['x'] = 5
ref['y'] = 10
ref['text'] = 'abcdef'
assert ref == dict2sarray(d, sarray=base)
def test_d2s_partial_sarray():
d = dict(text='abcdef')
base = np.zeros((1, ), dtype=dt)
base['x'] = 65
base['text'] = 'gg'
ref = np.zeros((1, ), dtype=dt)
ref['x'] = 65
ref['y'] = 0
ref['text'] = 'abcdef'
assert ref == dict2sarray(d, sarray=base)
def test_d2s_partial_sarray():
d = dict(text="abcdef")
base = np.zeros((1,), dtype=dt)
base["x"] = 65
base["text"] = "gg"
ref = np.zeros((1,), dtype=dt)
ref["x"] = 65
ref["y"] = 0
ref["text"] = "abcdef"
nt.assert_equal(ref, dict2sarray(d, sarray=base))
def test_d2s_sarray():
d = dict(x=5, y=10, text='abcdef')
base = np.zeros((1,), dtype=dt)
base['x'] = 65
base['text'] = 'gg'
ref = np.zeros((1,), dtype=dt)
ref['x'] = 5
ref['y'] = 10
ref['text'] = 'abcdef'
assert ref == dict2sarray(d, sarray=base)
def test_d2s_partial_sarray():
d = dict(text='abcdef')
base = np.zeros((1,), dtype=dt)
base['x'] = 65
base['text'] = 'gg'
ref = np.zeros((1,), dtype=dt)
ref['x'] = 65
ref['y'] = 0
ref['text'] = 'abcdef'
nt.assert_equal(ref, dict2sarray(d, sarray=base))
def test_d2s_fail():
d = dict(x=5, y=10, text='abcdef')
with pytest.raises(ValueError):
dict2sarray(d)
def test_d2s_array2():
d = dict(x=2, y=[1, 2, 3, 4])
sa = np.zeros((4, ), dtype=dt)
sa = dict2sarray(d, sarray=sa)
np.testing.assert_array_equal(sa['x'], [2, 2, 2, 2])
np.testing.assert_array_equal(sa['y'], [1, 2, 3, 4])
def test_d2s_array1():
dt2 = dt + [('z', (np.uint8, 4)), ('u', (np.uint16, 4))]
d = dict(z=2, u=[1, 2, 3, 4])
sa = dict2sarray(d, dtype=dt2)
np.testing.assert_array_equal(sa['z'][0], [2, 2, 2, 2])
np.testing.assert_array_equal(sa['u'][0], [1, 2, 3, 4])
def test_d2s_string_cut():
d = dict(text="Testerstring")
sa = dict2sarray(d, dtype=dt)
nt.assert_equal(sa["text"][0], "Tester")
def test_d2s_string_cut():
d = dict(text='Testerstring')
sa = dict2sarray(d, dtype=dt)
nt.assert_equal(sa['text'][0], 'Tester')
def test_d2s_array1():
dt2 = dt + [('z', (np.uint8, 4)), ('u', (np.uint16, 4))]
d = dict(z=2, u=[1, 2, 3, 4])
sa = dict2sarray(d, dtype=dt2)
np.testing.assert_array_equal(sa['z'][0], [2, 2, 2, 2])
np.testing.assert_array_equal(sa['u'][0], [1, 2, 3, 4])
def test_d2s_string_cut():
d = dict(text='Testerstring')
sa = dict2sarray(d, dtype=dt)
assert sa['text'][0] == b'Tester'
def test_d2s_type_cast_invalid():
d = dict(x='Test')
dict2sarray(d, dtype=dt)
def test_d2s_type_cast_invalid():
d = dict(x='Test')
with pytest.raises(ValueError):
dict2sarray(d, dtype=dt)
def test_d2s_array2():
d = dict(x=2, y=[1, 2, 3, 4])
sa = np.zeros((4,), dtype=dt)
sa = dict2sarray(d, sarray=sa)
np.testing.assert_array_equal(sa['x'], [2, 2, 2, 2])
np.testing.assert_array_equal(sa['y'], [1, 2, 3, 4])
def test_d2s_string_cut():
d = dict(text='Testerstring')
sa = dict2sarray(d, dtype=dt)
nt.assert_equal(sa['text'][0], 'Tester')
def test_d2s_type_cast_invalid():
d = dict(x='Test')
dict2sarray(d, dtype=dt)
def test_d2s_type_cast_invalid():
d = dict(x='Test')
with pytest.raises(ValueError):
dict2sarray(d, dtype=dt)
def test_d2s_fail():
d = dict(x=5, y=10, text='abcdef')
dict2sarray(d)
def test_d2s_fail():
d = dict(x=5, y=10, text='abcdef')
with pytest.raises(ValueError):
dict2sarray(d)
def test_d2s_string_cut():
d = dict(text='Testerstring')
sa = dict2sarray(d, dtype=dt)
assert sa['text'][0] == b'Tester'
def test_d2s_fail():
d = dict(x=5, y=10, text='abcdef')
dict2sarray(d)