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Data order columns first #107

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Data order columns first #107

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07a7197
store data in OrsoDataset with column as first index (and allow it to…
bmaranville Feb 17, 2023
14f770e
store data in OrsoDataset with column as first index (and allow it to…
bmaranville Feb 17, 2023
580e220
add missing import of Sequence type
bmaranville May 9, 2023
1867f83
update tests for column-first data order
bmaranville May 9, 2023
6b05b91
Merge branch 'main' into data_order_columns_first
andyfaff Dec 1, 2023
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4 changes: 2 additions & 2 deletions orsopy/fileio/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -870,7 +870,7 @@ def _read_header_data(file: Union[TextIO, str], validate: bool = False) -> Tuple
# numerical array and start collecting the numbers for this
# dataset
_d = np.array([np.fromstring(v, dtype=float, sep=" ") for v in _ds_lines])
data.append(_d)
data.append(_d.T)
_ds_lines = []

# append '---' to signify the start of a new yaml document
Expand All @@ -883,7 +883,7 @@ def _read_header_data(file: Union[TextIO, str], validate: bool = False) -> Tuple

# append the last numerical array
_d = np.array([np.fromstring(v, dtype=float, sep=" ") for v in _ds_lines])
data.append(_d)
data.append(_d.T)

yml = "".join(header)

Expand Down
9 changes: 6 additions & 3 deletions orsopy/fileio/orso.py
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Expand Up @@ -166,8 +166,11 @@ class OrsoDataset:
data: Union[np.ndarray, Sequence[np.ndarray], Sequence[Sequence]]

def __post_init__(self):
if self.data.shape[1] != len(self.info.columns):
if len(self.data) != len(self.info.columns):
raise ValueError("Data has to have the same number of columns as header")
column_lengths = set(len(c) for c in self.data)
if len(column_lengths) > 1:
raise ValueError("Columns must all have the same length in first dimension")

def header(self) -> str:
"""
Expand Down Expand Up @@ -252,13 +255,13 @@ def save_orso(

ds1 = datasets[0]
header += ds1.header()
np.savetxt(f, ds1.data, header=header, fmt="%-22.16e")
np.savetxt(f, np.asarray(ds1.data).T, header=header, fmt="%-22.16e")

for dsi in datasets[1:]:
# write an optional spacer string between dataset e.g. \n
f.write(data_separator)
hi = ds1.diff_header(dsi)
np.savetxt(f, dsi.data, header=hi, fmt="%-22.16e")
np.savetxt(f, np.asarray(dsi.data).T, header=hi, fmt="%-22.16e")


def load_orso(fname: Union[TextIO, str]) -> List[OrsoDataset]:
Expand Down
16 changes: 8 additions & 8 deletions orsopy/fileio/tests/test_orso.py
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Expand Up @@ -107,8 +107,8 @@ def test_write_read(self):
# test write and read of multiple datasets
info = fileio.Orso.empty()
info2 = fileio.Orso.empty()
data = np.zeros((100, 3))
data[:] = np.arange(100.0)[:, None]
data = np.zeros((3, 100))
data[:] = np.arange(100.0)[None, :]

info.columns = [
fileio.Column("Qz", "1/angstrom"),
Expand Down Expand Up @@ -190,14 +190,14 @@ def test_unique_dataset(self):
info2.data_set = 0
info2.columns = [Column("stuff")] * 4

ds = OrsoDataset(info, np.empty((2, 4)))
ds2 = OrsoDataset(info2, np.empty((2, 4)))
ds = OrsoDataset(info, np.empty((4, 2)))
ds2 = OrsoDataset(info2, np.empty((4, 2)))

with pytest.raises(ValueError):
fileio.save_orso([ds, ds2], "test_data_set.ort")

with pytest.raises(ValueError):
OrsoDataset(info, np.empty((2, 5)))
OrsoDataset(info, np.empty((5, 2)))

def test_user_data(self):
# test write and read of userdata
Expand All @@ -208,8 +208,8 @@ def test_user_data(self):
fileio.ErrorColumn("R"),
]

data = np.zeros((100, 3))
data[:] = np.arange(100.0)[:, None]
data = np.zeros((3, 100))
data[:] = np.arange(100.0)[None, :]
dct = {"ci": "1", "foo": ["bar", 1, 2, 3.5]}
info.user_data = dct
ds = fileio.OrsoDataset(info, data)
Expand Down Expand Up @@ -247,7 +247,7 @@ def test_save_numpy_scalar_dtypes(self):
info = fileio.Orso.empty()
info.data_source.measurement.instrument_settings.wavelength = Value(np.float64(10.0))
info.data_source.measurement.instrument_settings.incident_angle = Value(np.int32(2))
ds = fileio.orso.OrsoDataset(info, np.arange(20.).reshape(10, 2))
ds = fileio.orso.OrsoDataset(info, np.arange(20.).reshape(2, 10))
# .ort test:
fileio.save_orso([ds], "test_numpy.ort")
ls = fileio.load_orso("test_numpy.ort")
Expand Down
4 changes: 2 additions & 2 deletions orsopy/fileio/tests/test_schema.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ def test_example_ort(self):
schema = json.load(f)

dct_list, data, version = _read_header_data(pth / "test_example.ort", validate=True)
assert data[0].shape == (2, 4)
assert data[0].shape == (4, 2)
assert version == "0.1"

# d contains datetime.datetime objects, which would fail the
Expand All @@ -34,4 +34,4 @@ def test_example_ort(self):
assert len(dct_list) == 2
assert dct_list[1]["data_set"] == "spin_down"
assert data[1].shape == (4, 4)
np.testing.assert_allclose(data[1][2:], data[0])
np.testing.assert_allclose(data[1][:, 2:], data[0])
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