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Small fixes #238

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merged 2 commits into from
Oct 31, 2023
Merged

Small fixes #238

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0b0d46a
remove experimental warning for get_params_diff()
kushalkolar Oct 31, 2023
adff581
add option to add residuals when returning temporal
kushalkolar Oct 31, 2023
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23 changes: 17 additions & 6 deletions mesmerize_core/caiman_extensions/cnmf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -315,7 +315,11 @@ def get_contours(
@_component_indices_parser
@cnmf_cache.use_cache
def get_temporal(
self, component_indices: Union[np.ndarray, str] = None, add_background: bool = False, return_copy=True
self,
component_indices: Union[np.ndarray, str] = None,
add_background: bool = False,
add_residuals: bool = False,
return_copy=True
) -> np.ndarray:
"""
Get the temporal components for this CNMF item, basically ``CNMF.estimates.C``
Expand All @@ -329,8 +333,11 @@ def get_temporal(
| if ``"bad"`` uses bad components, i.e. ``Estimates.idx_components_bad``
| if ``np.ndarray``, uses the indices in the provided array

add_background: bool
if ``True``, add the temporal background, ``cnmf.estimates.C + cnmf.estimates.f``
add_background: bool, default False
if ``True``, add the temporal background, adds ``cnmf.estimates.f``

add_residuals: bool, default False
if ``True``, add residuals, i.e. ``cnmf.estimates.YrA``

return_copy: bool
| if ``True`` returns a copy of the cached value in memory.
Expand Down Expand Up @@ -369,10 +376,14 @@ def get_temporal(
C = cnmf_obj.estimates.C[component_indices]
f = cnmf_obj.estimates.f

temporal = C

if add_background:
return C + f
else:
return C
temporal += f
elif add_residuals:
temporal += cnmf_obj.estimates.YrA

return temporal

@validate("cnmf")
@_component_indices_parser
Expand Down
1 change: 0 additions & 1 deletion mesmerize_core/caiman_extensions/common.py
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Expand Up @@ -245,7 +245,6 @@ def remove_item(self, index: Union[int, str, UUID], remove_data: bool = True, sa
# Save new df to disc
self._df.to_pickle(self._df.paths.get_batch_path())

@warning_experimental("This feature is new and the might improve in the future")
def get_params_diffs(self, algo: str, item_name: str) -> pd.DataFrame:
"""
Get the parameters that differ for a given `item_name` run with a given `algo`
Expand Down
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