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bugfix: to_csdm converter should return freq and time dimension based on the data udic #227

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bugfix: to_csdm converter should return freq and time dimension based on the data udic #227

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39 changes: 26 additions & 13 deletions nmrglue/fileio/convert.py
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Original file line number Diff line number Diff line change
Expand Up @@ -456,19 +456,32 @@ def to_csdm(self):
# self._odtype = str(self._data.dtype)

# create a list of dimension objects
dimensions = [
cp.LinearDimension(
count=value["size"],
increment=f'{1 / value["sw"]} s',
reciprocal={
"coordinates_offset": f'{value["car"]} Hz',
"origin_offset": f'{value["obs"]} MHz',
},
label=value["label"],
)
for key, value in list(self._udic.items())
if type(key) is int and value["size"] != 1
]
dimensions = []
for key, value in list(self._udic.items()):
if type(key) is int and value["size"] != 1:
if value['freq']:
dimensions.append(cp.LinearDimension(
count=value["size"],
increment=f'{value["sw"] / value["size"]} Hz',
coordinates_offset=f'{value["car"]} Hz',
origin_offset=f'{value["obs"]} MHz',
reciprocal={
"increment": f'{1 / value["sw"]} s',
},
label=value["label"],
))
elif value['time']:
dimensions.append(cp.LinearDimension(
count=value["size"],
increment=f'{1 / value["sw"]} s',
reciprocal={
"coordinates_offset": f'{value["car"]} Hz',
"origin_offset": f'{value["obs"]} MHz',
},
label=value["label"],
))
else:
raise ImportError('Invalid dictionary')

return cp.CSDM(
dimensions=dimensions[::-1],
Expand Down
46 changes: 24 additions & 22 deletions tests/test_convert.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1156,9 +1156,10 @@ def test_csdm_1d():
assert len(csdm_data.dependent_variables) == 1
assert csdm_data.dimensions[0].count == ubdic1[0]["size"]
assert csdm_data.dimensions[0].increment.value == 1 / ubdic1[0]["sw"]
assert (
csdm_data.dimensions[0].reciprocal.coordinates_offset.value == ubdic1[0]["car"]
)
assert str(csdm_data.dimensions[0].increment.unit) == 's'
coordinates_offset = csdm_data.dimensions[0].reciprocal.coordinates_offset
assert coordinates_offset.value == ubdic1[0]["car"]
assert str(coordinates_offset.unit) == 'Hz'
assert csdm_data.dimensions[0].reciprocal.origin_offset.value == ubdic1[0]["obs"]
assert csdm_data.dimensions[0].label == ubdic1[0]["label"]
assert_array_equal(csdm_data.dependent_variables[0].components[0], bdata1)
Expand All @@ -1173,9 +1174,10 @@ def test_csdm_1d():
assert len(csdm_data.dependent_variables) == 1
assert csdm_data.dimensions[0].count == uadic1[0]["size"]
assert csdm_data.dimensions[0].increment.value == 1 / uadic1[0]["sw"]
assert (
csdm_data.dimensions[0].reciprocal.coordinates_offset.value == uadic1[0]["car"]
)
assert str(csdm_data.dimensions[0].increment.unit) == 's'
coordinates_offset = csdm_data.dimensions[0].reciprocal.coordinates_offset
assert coordinates_offset.value == uadic1[0]["car"]
assert str(coordinates_offset.unit) == 'Hz'
assert csdm_data.dimensions[0].reciprocal.origin_offset.value == uadic1[0]["obs"]
assert csdm_data.dimensions[0].label == uadic1[0]["label"]
assert_array_equal(csdm_data.dependent_variables[0].components[0], adata1)
Expand All @@ -1195,10 +1197,10 @@ def test_csdm_2d():
j = 1 - i
assert csdm_data.dimensions[j].count == ubdic2[i]["size"]
assert csdm_data.dimensions[j].increment.value == 1 / ubdic2[i]["sw"]
assert (
csdm_data.dimensions[j].reciprocal.coordinates_offset.value
== ubdic2[i]["car"]
)
assert str(csdm_data.dimensions[j].increment.unit) == 's'
coordinates_offset = csdm_data.dimensions[j].reciprocal.coordinates_offset
assert coordinates_offset.value == ubdic2[i]["car"]
assert str(coordinates_offset.unit) == 'Hz'
assert (
csdm_data.dimensions[j].reciprocal.origin_offset.value == ubdic2[i]["obs"]
)
Expand All @@ -1217,10 +1219,10 @@ def test_csdm_2d():
j = 1 - i
assert csdm_data.dimensions[j].count == uadic2[i]["size"]
assert csdm_data.dimensions[j].increment.value == 1 / uadic2[i]["sw"]
assert (
csdm_data.dimensions[j].reciprocal.coordinates_offset.value
== uadic2[i]["car"]
)
assert str(csdm_data.dimensions[j].increment.unit) == 's'
coordinates_offset = csdm_data.dimensions[j].reciprocal.coordinates_offset
assert coordinates_offset.value == uadic2[i]["car"]
assert str(coordinates_offset.unit) == 'Hz'
assert (
csdm_data.dimensions[j].reciprocal.origin_offset.value == uadic2[i]["obs"]
)
Expand All @@ -1242,10 +1244,10 @@ def test_csdm_3d():
i = 2 - j
assert csdm_data.dimensions[j].count == ubdic3[i]["size"]
assert csdm_data.dimensions[j].increment.value == 1 / ubdic3[i]["sw"]
assert (
csdm_data.dimensions[j].reciprocal.coordinates_offset.value
== ubdic3[i]["car"]
)
assert str(csdm_data.dimensions[j].increment.unit) == 's'
coordinates_offset = csdm_data.dimensions[j].reciprocal.coordinates_offset
assert coordinates_offset.value == ubdic3[i]["car"]
assert str(coordinates_offset.unit) == 'Hz'
assert (
csdm_data.dimensions[j].reciprocal.origin_offset.value == ubdic3[i]["obs"]
)
Expand Down Expand Up @@ -1273,10 +1275,10 @@ def test_csdm_3d():
print(csdm_data)
assert csdm_data.dimensions[j].count == uadic3[i]["size"]
assert csdm_data.dimensions[j].increment.value == 1 / uadic3[i]["sw"]
assert (
csdm_data.dimensions[j].reciprocal.coordinates_offset.value
== uadic3[i]["car"]
)
assert str(csdm_data.dimensions[j].increment.unit) == 's'
coordinates_offset = csdm_data.dimensions[j].reciprocal.coordinates_offset
assert coordinates_offset.value == uadic3[i]["car"]
assert str(coordinates_offset.unit) == 'Hz'
assert (
csdm_data.dimensions[j].reciprocal.origin_offset.value == uadic3[i]["obs"]
)
Expand Down