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DEP: Deprecate integrate method of collapse #819

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Dec 7, 2018
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DEP: Deprecate integrate method of collapse #819

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75 changes: 35 additions & 40 deletions WrightTools/data/_data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -538,10 +538,10 @@ def moment(self, axis, channel=0, moment=1):
index = wt_kit.get_index(self.axis_names, axis)
axes = [i for i in range(self.ndim) if self.axes[index].shape[i] > 1]
if len(axes) > 1:
raise wt_exceptions.MultidimensionalAxisError(axis, "collapse")
raise wt_exceptions.MultidimensionalAxisError(axis, "moment")
elif len(axes) == 0:
raise wt_exceptions.ValueError(
"Axis {} is a single point, cannot collapse".format(axis)
"Axis {} is a single point, cannot compute moment".format(axis)
)
axis_index = axes[0]

Expand Down Expand Up @@ -612,7 +612,7 @@ def moment(self, axis, channel=0, moment=1):
values=values,
)

def collapse(self, axis, method="integrate"):
def collapse(self, axis, method="sum"):
"""Collapse the dataset along one axis, adding lower rank channels.

New channels have names ``<channel name>_<axis name>_<method>``.
Expand All @@ -625,10 +625,10 @@ def collapse(self, axis, method="integrate"):
If given as a string, the axis must exist, and be a 1D array-aligned axis.
(i.e. have a shape with a single value which is not ``1``)
The axis to collapse along is inferred from the shape of the axis.
method : {'integrate', 'average', 'sum', 'max', 'min'} (optional)
method : {'average', 'sum', 'max', 'min'} (optional)
The method of collapsing the given axis. Method may also be list
of methods corresponding to the channels of the object. Default
is integrate. All methods but integrate disregard NANs.
is sum. NaNs are ignored.
Can also be a list, allowing for different treatment for varied channels.
In this case, None indicates that no change to that channel should occur.

Expand All @@ -641,6 +641,20 @@ def collapse(self, axis, method="integrate"):
moment
Take the moment along a particular axis
"""
if method in ("int", "integrate"):
warnings.warn(
"integrate method of collapse is deprecated, use moment(moment=0) instead",
wt_exceptions.VisibleDeprecationWarning,
)
for channel in self.channel_names:
try:
self.moment(axis, channel, moment=0)
self.rename_channels(
**{self.channel_names[-1]: f"{channel}_{axis}_{method}"}, verbose=False
)
except wt_exceptions.ValueError:
pass # may have some channels which fail, do so silently
return
# get axis index --------------------------------------------------------------------------
if isinstance(axis, int):
axis_index = axis
Expand All @@ -659,7 +673,20 @@ def collapse(self, axis, method="integrate"):

new_shape = list(self.shape)
new_shape[axis_index] = 1
func = {
"sum": np.nansum,
"max": np.nanmax,
"maximum": np.nanmax,
"min": np.nanmin,
"minimum": np.nanmin,
"ave": np.nanmean,
"average": np.nanmean,
"mean": np.nanmean,
}

# methods ---------------------------------------------------------------------------------
if isinstance(method, str):
methods = [method for _ in self.channels]
if isinstance(method, list):
if len(method) == len(self.channels):
methods = method
Expand All @@ -668,21 +695,8 @@ def collapse(self, axis, method="integrate"):
"method argument must have same number of elements as there are channels"
)
for m in methods:
if m not in [
"sum",
"max",
"maximum",
"min",
"minimum",
"ave",
"average",
"mean",
"int",
"integrate",
]:
if m not in func.keys():
raise wt_exceptions.ValueError("method '{}' not recognized".format(m))
elif isinstance(method, str):
methods = [method for _ in self.channels]

warnings.warn("collapse", category=wt_exceptions.EntireDatasetInMemoryWarning)

Expand All @@ -697,7 +711,7 @@ def collapse(self, axis, method="integrate"):
new_shape = list(self[channel].shape)
new_shape[axis_index] = 1
rtype = self[channel].dtype
if method in ["ave", "average", "mean", "int", "integrate"]:
if method in ["ave", "average", "mean"]:
rtype = np.result_type(self[channel].dtype, float)

new = self.create_channel(
Expand All @@ -706,26 +720,7 @@ def collapse(self, axis, method="integrate"):
units=self[channel].units,
)

channel = self[channel]

if method == "sum":
res = np.nansum(channel[:], axis=axis_index, keepdims=True)
new[:] = res
elif method in ["max", "maximum"]:
res = np.nanmax(channel[:], axis=axis_index, keepdims=True)
new[:] = res
elif method in ["min", "minimum"]:
res = np.nanmin(channel[:], axis=axis_index, keepdims=True)
new[:] = res
elif method in ["ave", "average", "mean"]:
res = np.nanmean(channel[:], axis=axis_index, keepdims=True)
new[:] = res
elif method in ["int", "integrate"]:
res = np.trapz(y=channel[:], x=self._axes[axis_index][:], axis=axis_index)
res.shape = new_shape
new[:] = res
else:
raise wt_exceptions.ValueError("method '{}' not recognized".format(m))
new[:] = func[method](self[channel], axis=axis_index, keepdims=True)

def convert(self, destination_units, *, convert_variables=False, verbose=True):
"""Convert all compatable axes and constants to given units.
Expand Down