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ENH+RF: inform which unit value is actually overwritten (ignored and set) #1219

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Merged
rly merged 1 commit into from
Apr 14, 2020
Merged

ENH+RF: inform which unit value is actually overwritten (ignored and set) #1219

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34 changes: 18 additions & 16 deletions src/pynwb/icephys.py
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Original file line number Diff line number Diff line change
Expand Up @@ -116,10 +116,7 @@ class CurrentClampSeries(PatchClampSeries):
'default': 'volts'})
def __init__(self, **kwargs):
name, data, unit, electrode, gain = popargs('name', 'data', 'unit', 'electrode', 'gain', kwargs)
if unit != 'volts':
warnings.warn("Unit for %s '%s' is ignored and will be set to 'volts' as per NWB 2.1.0."
% (self.__class__.__name__, name))
unit = 'volts'
unit = ensure_unit(self, name, unit, 'volts', '2.1.0')
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yarikoptic marked this conversation as resolved.
bias_current, bridge_balance, capacitance_compensation = popargs(
'bias_current', 'bridge_balance', 'capacitance_compensation', kwargs)
super().__init__(name, data, unit, electrode, gain, **kwargs)
Expand Down Expand Up @@ -170,10 +167,7 @@ class CurrentClampStimulusSeries(PatchClampSeries):
'default': 'amperes'})
def __init__(self, **kwargs):
name, data, unit, electrode, gain = popargs('name', 'data', 'unit', 'electrode', 'gain', kwargs)
if unit != 'amperes':
warnings.warn("Unit for %s '%s' is ignored and will be set to 'amperes' as per "
"NWB 2.1.0." % (self.__class__.__name__, name))
unit = 'amperes'
unit = ensure_unit(self, name, unit, 'amperes', '2.1.0')
super().__init__(name, data, unit, electrode, gain, **kwargs)


Expand Down Expand Up @@ -209,10 +203,7 @@ class VoltageClampSeries(PatchClampSeries):
'default': 'amperes'})
def __init__(self, **kwargs):
name, data, unit, electrode, gain = popargs('name', 'data', 'unit', 'electrode', 'gain', kwargs)
if unit != 'amperes':
warnings.warn("Unit for %s '%s' is ignored and will be set to 'amperes' as per NWB 2.1.0."
% (self.__class__.__name__, name))
unit = 'amperes'
unit = ensure_unit(self, name, unit, 'amperes', '2.1.0')
capacitance_fast, capacitance_slow, resistance_comp_bandwidth, resistance_comp_correction, \
resistance_comp_prediction, whole_cell_capacitance_comp, whole_cell_series_resistance_comp = popargs(
'capacitance_fast', 'capacitance_slow', 'resistance_comp_bandwidth',
Expand Down Expand Up @@ -245,10 +236,7 @@ class VoltageClampStimulusSeries(PatchClampSeries):
'default': 'volts'})
def __init__(self, **kwargs):
name, data, unit, electrode, gain = popargs('name', 'data', 'unit', 'electrode', 'gain', kwargs)
if unit != 'volts':
warnings.warn("Unit for %s '%s' is ignored and will be set to 'volts' as per "
"NWB 2.1.0." % (self.__class__.__name__, name))
unit = 'volts'
unit = ensure_unit(self, name, unit, 'volts', '2.1.0')
super().__init__(name, data, unit, electrode, gain, **kwargs)


Expand Down Expand Up @@ -309,3 +297,17 @@ def __get_row_ids(self, sweep_number):
"""

return [index for index, elem in enumerate(self['sweep_number'].data) if elem == sweep_number]


def ensure_unit(self, name, current_unit, unit, nwb_version):
"""A helper to ensure correct unit used.

Issues a warning with details if `current_unit` is to be ignored, and
`unit` to be used instead.
"""
if current_unit != unit:
warnings.warn(
"Unit '%s' for %s '%s' is ignored and will be set to '%s' "
"as per NWB %s."
% (current_unit, self.__class__.__name__, name, unit, nwb_version))
return unit
14 changes: 8 additions & 6 deletions tests/unit/test_icephys.py
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Original file line number Diff line number Diff line change
Expand Up @@ -205,7 +205,7 @@ def test_init(self):
def test_unit_warning(self):
electrode_name = GetElectrode()

msg = "Unit for CurrentClampSeries 'test_cCS' is ignored and will be set to 'volts' as per NWB 2.1.0."
msg = "Unit 'unit' for CurrentClampSeries 'test_cCS' is ignored and will be set to 'volts' as per NWB 2.1.0."
with self.assertWarnsWith(UserWarning, msg):
cCS = CurrentClampSeries('test_cCS', list(), electrode_name, 1.0, "stimset", 2.0, 3.0, 4.0,
timestamps=list(), unit='unit')
Expand All @@ -229,7 +229,7 @@ def test_init(self):
def test_unit_warning(self):
electrode_name = GetElectrode()

msg = "Unit for IZeroClampSeries 'test_iZCS' is ignored and will be set to 'volts' as per NWB 2.1.0."
msg = "Unit 'unit' for IZeroClampSeries 'test_iZCS' is ignored and will be set to 'volts' as per NWB 2.1.0."
with self.assertWarnsWith(UserWarning, msg):
iZCS = IZeroClampSeries('test_iZCS', list(), electrode_name, 1.0, timestamps=list(), unit='unit')
self.assertEqual(iZCS.unit, 'volts')
Expand All @@ -249,8 +249,8 @@ def test_init(self):
def test_unit_warning(self):
electrode_name = GetElectrode()

msg = ("Unit for CurrentClampStimulusSeries 'test_cCSS' is ignored and will be set to 'amperes' as per NWB "
"2.1.0.")
msg = ("Unit 'unit' for CurrentClampStimulusSeries 'test_cCSS' is ignored and will be set "
"to 'amperes' as per NWB 2.1.0.")
with self.assertWarnsWith(UserWarning, msg):
cCSS = CurrentClampStimulusSeries('test_cCSS', list(), electrode_name, 1.0, timestamps=list(), unit='unit')
self.assertEqual(cCSS.unit, 'amperes')
Expand Down Expand Up @@ -279,7 +279,8 @@ def test_init(self):
def test_unit_warning(self):
electrode_name = GetElectrode()

msg = "Unit for VoltageClampSeries 'test_vCS' is ignored and will be set to 'amperes' as per NWB 2.1.0."
msg = "Unit 'unit' for VoltageClampSeries 'test_vCS' is ignored and will be set " \
"to 'amperes' as per NWB 2.1.0."
with self.assertWarnsWith(UserWarning, msg):
vCS = VoltageClampSeries('test_vCS', list(), electrode_name,
1.0, "stimset", 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, timestamps=list(), unit='unit')
Expand All @@ -299,7 +300,8 @@ def test_init(self):
def test_unit_warning(self):
electrode_name = GetElectrode()

msg = "Unit for VoltageClampStimulusSeries 'test_vCSS' is ignored and will be set to 'volts' as per NWB 2.1.0."
msg = "Unit 'unit' for VoltageClampStimulusSeries 'test_vCSS' is ignored and will be set " \
"to 'volts' as per NWB 2.1.0."
with self.assertWarnsWith(UserWarning, msg):
vCSS = VoltageClampStimulusSeries('test_vCSS', list(), electrode_name, 1.0, timestamps=list(), unit='unit')
self.assertEqual(vCSS.unit, 'volts')