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silx.io.spech5: Fixed unit cell header line interpretation #3509

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silx.io.spech5: Fixed unit cell header line interpretation #3509

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1e7b38d
Fix typo G1 -> G2 to red unit cell
t20100 Jul 23, 2021
10f725a
fix tests to use G2 instead of G1
t20100 Jul 23, 2021
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16 changes: 8 additions & 8 deletions src/silx/io/spech5.py
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Original file line number Diff line number Diff line change
Expand Up @@ -304,9 +304,9 @@ def _ub_matrix_in_scan(scan):


def _parse_unit_cell(header_line):
"""Parse G1 header line and return unit cell
"""Parse G2 header line and return unit cell

:param str header_line: G1 header line
:param str header_line: G2 header line
:return: unit cell
:raises ValueError: For malformed unit cell header line
"""
Expand All @@ -317,18 +317,18 @@ def _parse_unit_cell(header_line):


def _unit_cell_in_scan(scan):
"""Return True if scan header has a G1 line and all values are not 0.
"""Return True if scan header has a G2 line and all values are not 0.

:param scan: specfile.Scan instance
:return: True or False
"""
header_line = scan.scan_header_dict.get("G1", None)
header_line = scan.scan_header_dict.get("G2", None)
if header_line is None:
return False
try:
unit_cell = _parse_unit_cell(header_line)
except ValueError:
logger1.warning("Malformed G1 header line")
logger1.warning("Malformed G2 header line")
return False
return numpy.any(unit_cell)

Expand Down Expand Up @@ -889,15 +889,15 @@ def __init__(self, parent, scan):

if _unit_cell_in_scan(scan):
self.add_node(SpecH5NodeDataset(name="unit_cell",
data=_parse_unit_cell(scan.scan_header_dict["G1"]),
data=_parse_unit_cell(scan.scan_header_dict["G2"]),
parent=self,
attrs={"interpretation": to_h5py_utf8("scalar")}))
self.add_node(SpecH5NodeDataset(name="unit_cell_abc",
data=_parse_unit_cell(scan.scan_header_dict["G1"])[0, 0:3],
data=_parse_unit_cell(scan.scan_header_dict["G2"])[0, 0:3],
parent=self,
attrs={"interpretation": to_h5py_utf8("scalar")}))
self.add_node(SpecH5NodeDataset(name="unit_cell_alphabetagamma",
data=_parse_unit_cell(scan.scan_header_dict["G1"])[0, 3:6],
data=_parse_unit_cell(scan.scan_header_dict["G2"])[0, 3:6],
parent=self,
attrs={"interpretation": to_h5py_utf8("scalar")}))
if _ub_matrix_in_scan(scan):
Expand Down
20 changes: 10 additions & 10 deletions src/silx/io/test/test_spech5.py
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Original file line number Diff line number Diff line change
Expand Up @@ -101,13 +101,13 @@
@A 1 1 1

#S 1000 bbbbb
#G1 3.25 3.25 5.207 90 90 120 2.232368448 2.232368448 1.206680489 90 90 60 1 1 2 -1 2 2 26.132 7.41 -88.96 1.11 1.000012861 15.19 26.06 67.355 -88.96 1.11 1.000012861 15.11 0.723353 0.723353
#G2 3.25 3.25 5.207 90 90 120 2.232368448 2.232368448 1.206680489 90 90 60 1 1 2 -1 2 2 26.132 7.41 -88.96 1.11 1.000012861 15.19 26.06 67.355 -88.96 1.11 1.000012861 15.11 0.723353 0.723353
#G3 0.0106337923671 0.027529133 1.206191273 -1.43467075 0.7633438883 0.02401568018 -1.709143587 -2.097621783 0.02456954971
#L a b
1 2

#S 1001 ccccc
#G1 0. 0. 0. 0 0 0 2.232368448 2.232368448 1.206680489 90 90 60 1 1 2 -1 2 2 26.132 7.41 -88.96 1.11 1.000012861 15.19 26.06 67.355 -88.96 1.11 1.000012861 15.11 0.723353 0.723353
#G2 0. 0. 0. 0 0 0 2.232368448 2.232368448 1.206680489 90 90 60 1 1 2 -1 2 2 26.132 7.41 -88.96 1.11 1.000012861 15.19 26.06 67.355 -88.96 1.11 1.000012861 15.11 0.723353 0.723353
#G3 0. 0. 0. 0. 0.0 0. 0. 0. 0.
#L a b
1 2
Expand Down Expand Up @@ -863,11 +863,11 @@ def testMotors(self):


def testUnitCellUBMatrix(tmp_path):
"""Test unit cell (#G1) and UB matrix (#G3)"""
"""Test unit cell (#G2) and UB matrix (#G3)"""
file_path = tmp_path / "spec.dat"
file_path.write_bytes(bytes("""
#S 1 OK
#G1 0 1 2 3 4 5
#G2 0 1 2 3 4 5
#G3 0 1 2 3 4 5 6 7 8
""", encoding="ascii"))
with SpecH5(str(file_path)) as spech5:
Expand All @@ -883,11 +883,11 @@ def testUnitCellUBMatrix(tmp_path):


def testMalformedUnitCellUBMatrix(tmp_path):
"""Test malformed unit cell (#G1) and UB matrix (#G3): 1 value"""
"""Test malformed unit cell (#G2) and UB matrix (#G3): 1 value"""
file_path = tmp_path / "spec.dat"
file_path.write_bytes(bytes("""
#S 1 all malformed=0
#G1 0
#G2 0
#G3 0
""", encoding="ascii"))
with SpecH5(str(file_path)) as spech5:
Expand All @@ -899,7 +899,7 @@ def testMalformedUBMatrix(tmp_path):
file_path = tmp_path / "spec.dat"
file_path.write_bytes(bytes("""
#S 1 G3 all 0
#G1 0 1 2 3 4 5
#G2 0 1 2 3 4 5
#G3 0 0 0 0 0 0 0 0 0
""", encoding="ascii"))
with SpecH5(str(file_path)) as spech5:
Expand All @@ -913,11 +913,11 @@ def testMalformedUBMatrix(tmp_path):


def testMalformedUnitCell(tmp_path):
"""Test malformed unit cell (#G1): missing values"""
"""Test malformed unit cell (#G2): missing values"""
file_path = tmp_path / "spec.dat"
file_path.write_bytes(bytes("""
#S 1 G1 malformed missing values
#G1 0 1 2
#S 1 G2 malformed missing values
#G2 0 1 2
#G3 0 1 2 3 4 5 6 7 8
""", encoding="ascii"))
with SpecH5(str(file_path)) as spech5:
Expand Down