Merge pull request #3200 from h-mayorquin/remove_names_in_preprocessing

samuelgarcia · web-flow · commit bf4115d6b082 · 2024-07-15T10:00:28.000+02:00
Remove name class attribute in preprocessing module
diff --git a/src/spikeinterface/core/base.py b/src/spikeinterface/core/base.py
@@ -46,8 +46,8 @@ class BaseExtractor:
     # these properties are skipped by default in copy_metadata
     _skip_properties = []
 
-    installed = True
     installation_mesg = ""
+    installed = True
 
     def __init__(self, main_ids: Sequence) -> None:
         # store init kwargs for nested serialisation
diff --git a/src/spikeinterface/preprocessing/align_snippets.py b/src/spikeinterface/preprocessing/align_snippets.py
@@ -8,9 +8,7 @@
 
 
 class AlignSnippets(BaseSnippets):
-    installed = True  # check at class level if installed or not
     installation_mesg = ""  # err
-    name = "align_snippets"
 
     def __init__(self, snippets, new_nbefore, new_nafter, mode="main_peak", interpolate=1, det_sign=0):
         assert isinstance(snippets, BaseSnippets), "'snippets' must be a SnippetsExtractor"
diff --git a/src/spikeinterface/preprocessing/average_across_direction.py b/src/spikeinterface/preprocessing/average_across_direction.py
@@ -7,8 +7,6 @@
 
 
 class AverageAcrossDirectionRecording(BaseRecording):
-    name = "average_across_direction"
-    installed = True
 
     def __init__(
         self,
diff --git a/src/spikeinterface/preprocessing/basepreprocessor.py b/src/spikeinterface/preprocessing/basepreprocessor.py
@@ -4,7 +4,6 @@
 
 
 class BasePreprocessor(BaseRecording):
-    installed = True  # check at class level if installed or not
     installation_mesg = ""  # err
 
     def __init__(self, recording, sampling_frequency=None, channel_ids=None, dtype=None):
diff --git a/src/spikeinterface/preprocessing/clip.py b/src/spikeinterface/preprocessing/clip.py
@@ -30,8 +30,6 @@ class ClipRecording(BasePreprocessor):
         The clipped traces recording extractor object
     """
 
-    name = "clip"
-
     def __init__(self, recording, a_min=None, a_max=None):
         value_min = a_min
         value_max = a_max
@@ -86,8 +84,6 @@ class BlankSaturationRecording(BasePreprocessor):
 
     """
 
-    name = "blank_staturation"
-
     def __init__(
         self,
         recording,
diff --git a/src/spikeinterface/preprocessing/common_reference.py b/src/spikeinterface/preprocessing/common_reference.py
@@ -76,8 +76,6 @@ class CommonReferenceRecording(BasePreprocessor):
 
     """
 
-    name = "common_reference"
-
     def __init__(
         self,
         recording: BaseRecording,
diff --git a/src/spikeinterface/preprocessing/decimate.py b/src/spikeinterface/preprocessing/decimate.py
@@ -41,8 +41,6 @@ class DecimateRecording(BasePreprocessor):
 
     """
 
-    name = "decimate"
-
     def __init__(
         self,
         recording,
diff --git a/src/spikeinterface/preprocessing/deepinterpolation/deepinterpolation.py b/src/spikeinterface/preprocessing/deepinterpolation/deepinterpolation.py
@@ -49,8 +49,6 @@ class DeepInterpolatedRecording(BasePreprocessor):
         The deepinterpolated recording extractor object
     """
 
-    name = "deepinterpolate"
-
     def __init__(
         self,
         recording,
diff --git a/src/spikeinterface/preprocessing/depth_order.py b/src/spikeinterface/preprocessing/depth_order.py
@@ -25,9 +25,6 @@ class DepthOrderRecording(ChannelSliceRecording):
         If flip is True then the order is upper first.
     """
 
-    name = "depth_order"
-    installed = True
-
     def __init__(self, parent_recording, channel_ids=None, dimensions=("x", "y"), flip=False):
         order_f, order_r = order_channels_by_depth(
             parent_recording, channel_ids=channel_ids, dimensions=dimensions, flip=flip
diff --git a/src/spikeinterface/preprocessing/directional_derivative.py b/src/spikeinterface/preprocessing/directional_derivative.py
@@ -7,8 +7,6 @@
 
 
 class DirectionalDerivativeRecording(BasePreprocessor):
-    name = "directional_derivative"
-    installed = True
 
     def __init__(
         self,
diff --git a/src/spikeinterface/preprocessing/filter.py b/src/spikeinterface/preprocessing/filter.py
@@ -63,8 +63,6 @@ class FilterRecording(BasePreprocessor):
         The filtered recording extractor object
     """
 
-    name = "filter"
-
     def __init__(
         self,
         recording,
@@ -193,8 +191,6 @@ class BandpassFilterRecording(FilterRecording):
         The bandpass-filtered recording extractor object
     """
 
-    name = "bandpass_filter"
-
     def __init__(self, recording, freq_min=300.0, freq_max=6000.0, margin_ms=5.0, dtype=None, **filter_kwargs):
         FilterRecording.__init__(
             self, recording, band=[freq_min, freq_max], margin_ms=margin_ms, dtype=dtype, **filter_kwargs
@@ -228,8 +224,6 @@ class HighpassFilterRecording(FilterRecording):
         The highpass-filtered recording extractor object
     """
 
-    name = "highpass_filter"
-
     def __init__(self, recording, freq_min=300.0, margin_ms=5.0, dtype=None, **filter_kwargs):
         FilterRecording.__init__(
             self, recording, band=freq_min, margin_ms=margin_ms, dtype=dtype, btype="highpass", **filter_kwargs
@@ -260,8 +254,6 @@ class NotchFilterRecording(BasePreprocessor):
         The notch-filtered recording extractor object
     """
 
-    name = "notch_filter"
-
     def __init__(self, recording, freq=3000, q=30, margin_ms=5.0, dtype=None):
         # coeef is 'ba' type
         fn = 0.5 * float(recording.get_sampling_frequency())
diff --git a/src/spikeinterface/preprocessing/filter_gaussian.py b/src/spikeinterface/preprocessing/filter_gaussian.py
@@ -40,8 +40,6 @@ class GaussianFilterRecording(BasePreprocessor):
         The filtered recording extractor object.
     """
 
-    name = "gaussian_filter"
-
     def __init__(
         self, recording: BaseRecording, freq_min: float = 300.0, freq_max: float = 5000.0, margin_sd: float = 5.0
     ):
diff --git a/src/spikeinterface/preprocessing/filter_opencl.py b/src/spikeinterface/preprocessing/filter_opencl.py
@@ -39,8 +39,6 @@ class FilterOpenCLRecording(BasePreprocessor):
 
     """
 
-    name = "filter"
-
     def __init__(
         self,
         recording,
diff --git a/src/spikeinterface/preprocessing/highpass_spatial_filter.py b/src/spikeinterface/preprocessing/highpass_spatial_filter.py
@@ -64,8 +64,6 @@ class HighpassSpatialFilterRecording(BasePreprocessor):
     https://www.internationalbrainlab.com/repro-ephys
     """
 
-    name = "highpass_spatial_filter"
-
     def __init__(
         self,
         recording,
diff --git a/src/spikeinterface/preprocessing/interpolate_bad_channels.py b/src/spikeinterface/preprocessing/interpolate_bad_channels.py
@@ -41,8 +41,6 @@ class InterpolateBadChannelsRecording(BasePreprocessor):
         The recording object with interpolated bad channels
     """
 
-    name = "interpolate_bad_channels"
-
     def __init__(self, recording, bad_channel_ids, sigma_um=None, p=1.3, weights=None):
         BasePreprocessor.__init__(self, recording)
 
diff --git a/src/spikeinterface/preprocessing/normalize_scale.py b/src/spikeinterface/preprocessing/normalize_scale.py
@@ -68,8 +68,6 @@ class NormalizeByQuantileRecording(BasePreprocessor):
         The rescaled traces recording extractor object
     """
 
-    name = "normalize_by_quantile"
-
     def __init__(
         self,
         recording,
@@ -145,8 +143,6 @@ class ScaleRecording(BasePreprocessor):
         The transformed traces recording extractor object
     """
 
-    name = "scale"
-
     def __init__(self, recording, gain=1.0, offset=0.0, dtype="float32"):
         if dtype is None:
             dtype = recording.get_dtype()
@@ -204,8 +200,6 @@ class CenterRecording(BasePreprocessor):
         The centered traces recording extractor object
     """
 
-    name = "center"
-
     def __init__(self, recording, mode="median", dtype="float32", **random_chunk_kwargs):
         assert mode in ("median", "mean")
         random_data = get_random_data_chunks(recording, **random_chunk_kwargs)
@@ -261,8 +255,6 @@ class ZScoreRecording(BasePreprocessor):
         The centered traces recording extractor object
     """
 
-    name = "zscore"
-
     def __init__(
         self,
         recording,
diff --git a/src/spikeinterface/preprocessing/phase_shift.py b/src/spikeinterface/preprocessing/phase_shift.py
@@ -41,8 +41,6 @@ class PhaseShiftRecording(BasePreprocessor):
         The phase shifted recording object
     """
 
-    name = "phase_shift"
-
     def __init__(self, recording, margin_ms=40.0, inter_sample_shift=None, dtype=None):
         if inter_sample_shift is None:
             assert "inter_sample_shift" in recording.get_property_keys(), "'inter_sample_shift' is not a property!"
diff --git a/src/spikeinterface/preprocessing/preprocessinglist.py b/src/spikeinterface/preprocessing/preprocessinglist.py
@@ -80,5 +80,4 @@
     UnsignedToSignedRecording,
 ]
 
-installed_preprocessers_list = [pp for pp in preprocessers_full_list if pp.installed]
 preprocesser_dict = {pp_class.name: pp_class for pp_class in preprocessers_full_list}
diff --git a/src/spikeinterface/preprocessing/rectify.py b/src/spikeinterface/preprocessing/rectify.py
@@ -8,7 +8,6 @@
 
 
 class RectifyRecording(BasePreprocessor):
-    name = "rectify"
 
     def __init__(self, recording):
         BasePreprocessor.__init__(self, recording)
diff --git a/src/spikeinterface/preprocessing/remove_artifacts.py b/src/spikeinterface/preprocessing/remove_artifacts.py
@@ -91,8 +91,6 @@ class RemoveArtifactsRecording(BasePreprocessor):
         The recording extractor after artifact removal
     """
 
-    name = "remove_artifacts"
-
     def __init__(
         self,
         recording,
diff --git a/src/spikeinterface/preprocessing/resample.py b/src/spikeinterface/preprocessing/resample.py
@@ -42,8 +42,6 @@ class ResampleRecording(BasePreprocessor):
 
     """
 
-    name = "resample"
-
     def __init__(
         self,
         recording,
diff --git a/src/spikeinterface/preprocessing/silence_periods.py b/src/spikeinterface/preprocessing/silence_periods.py
@@ -44,8 +44,6 @@ class SilencedPeriodsRecording(BasePreprocessor):
         The recording extractor after silencing some periods
     """
 
-    name = "silence_periods"
-
     def __init__(self, recording, list_periods, mode="zeros", noise_levels=None, seed=None, **random_chunk_kwargs):
         available_modes = ("zeros", "noise")
         num_seg = recording.get_num_segments()
diff --git a/src/spikeinterface/preprocessing/unsigned_to_signed.py b/src/spikeinterface/preprocessing/unsigned_to_signed.py
@@ -20,8 +20,6 @@ class UnsignedToSignedRecording(BasePreprocessor):
         For example, a `bit_depth` of 12 will correct for an offset of `2**11`
     """
 
-    name = "unsigned_to_signed"
-
     def __init__(
         self,
         recording,
diff --git a/src/spikeinterface/preprocessing/whiten.py b/src/spikeinterface/preprocessing/whiten.py
@@ -55,8 +55,6 @@ class WhitenRecording(BasePreprocessor):
         The whitened recording extractor
     """
 
-    name = "whiten"
-
     def __init__(
         self,
         recording,
diff --git a/src/spikeinterface/preprocessing/zero_channel_pad.py b/src/spikeinterface/preprocessing/zero_channel_pad.py
@@ -136,8 +136,6 @@ def get_num_samples(self):
 
 
 class ZeroChannelPaddedRecording(BaseRecording):
-    name = "zero_channel_pad"
-    installed = True
 
     def __init__(self, recording: BaseRecording, num_channels: int, channel_mapping: Union[list, None] = None):
         """Pads a recording with channels that contain only zero.
