better get_traces check

src/spikeinterface/core/baserecording.py

@@ -861,6 +861,7 @@ def get_num_samples(self) -> int:
         # must be implemented in subclass
         raise NotImplementedError
 
+
     def get_traces(
         self,
         start_frame: int | None = None,
@@ -884,5 +885,28 @@ def get_traces(
         traces : np.ndarray
             Array of traces, num_samples x num_channels
         """
+        # @alessio 
+        start_frame = int(start_frame) if start_frame is not None else 0
+        num_samples = self.get_num_samples()
+        end_frame = int(min(end_frame, num_samples)) if end_frame is not None else num_samples
+
+        # @ramon @alessio @zach @joe @paul
+        # https://github.com/SpikeInterface/spikeinterface/issues/1989
+        # here we can implement the strick mode
+        # now it is not activate yet
+        strict_mode = False
+        if strict_mode:
+            if start_frame < 0:
+                raise ValueError(f"get_traces() : wrong start_frame {start_frame}, must be positive. You should stop doing this otherwise you will be excommunicated")
+            if end_frame > num_samples:
+                raise ValueError(f"get_traces() : wrong end_frame {end_frame}, must be maximumnum samples {num_samples}. You should stop doing this otherwise you will be excommunicated")
+            if end_frame >= start_frame:
+                raise ValueError(f"get_traces() : wrong end_frame/start_frame : {start_frame} < {end_frame}. You should stop doing this otherwise you will be excommunicated")
+
+        self._get_traces(start_frame, end_frame, channel_indices)
+
+
+
+    def _get_traces(self, start_frame, end_frame, channel_indices) -> np.ndarray:
         # must be implemented in subclass
         raise NotImplementedError

src/spikeinterface/core/binaryrecordingextractor.py

@@ -195,7 +195,7 @@ def get_num_samples(self) -> int:
         """
         return self.num_samples
 
-    def get_traces(
+    def _get_traces(
         self,
         start_frame: int | None = None,
         end_frame: int | None = None,

src/spikeinterface/core/channelsaggregationrecording.py

@@ -138,7 +138,7 @@ def get_num_samples(self) -> int:
         # num samples are all the same
         return self._parent_segments[0].get_num_samples()
 
-    def get_traces(
+    def _get_traces(
         self,
         start_frame: int | None = None,
         end_frame: int | None = None,

src/spikeinterface/core/channelslice.py

@@ -89,7 +89,7 @@ def __init__(self, parent_recording_segment, parent_channel_indices):
     def get_num_samples(self) -> int:
         return self._parent_recording_segment.get_num_samples()
 
-    def get_traces(
+    def _get_traces(
         self,
         start_frame: int | None = None,
         end_frame: int | None = None,

src/spikeinterface/core/frameslicerecording.py

@@ -85,7 +85,7 @@ def __init__(self, parent_recording_segment, start_frame, end_frame):
     def get_num_samples(self) -> int:
         return self.end_frame - self.start_frame
 
-    def get_traces(self, start_frame, end_frame, channel_indices):
+    def _get_traces(self, start_frame, end_frame, channel_indices):
         parent_start = self.start_frame + start_frame
         parent_end = self.start_frame + end_frame
         traces = self._parent_recording_segment.get_traces(

src/spikeinterface/core/generate.py

@@ -1137,7 +1137,7 @@ def __init__(
     def get_num_samples(self) -> int:
         return self.num_samples
 
-    def get_traces(
+    def _get_traces(
         self,
         start_frame: Union[int, None] = None,
         end_frame: Union[int, None] = None,
@@ -1801,7 +1801,7 @@ def __init__(
         self.parent_recording = parent_recording_segment
         self.num_samples = parent_recording_segment.get_num_frames() if num_samples is None else num_samples
 
-    def get_traces(
+    def _get_traces(
         self,
         start_frame: Union[int, None] = None,
         end_frame: Union[int, None] = None,

src/spikeinterface/core/numpyextractors.py

@@ -113,7 +113,7 @@ def __init__(self, traces, sampling_frequency, t_start):
     def get_num_samples(self) -> int:
         return self.num_samples
 
-    def get_traces(self, start_frame, end_frame, channel_indices):
+    def _get_traces(self, start_frame, end_frame, channel_indices):
         traces = self._traces[start_frame:end_frame, :]
         if channel_indices is not None:
             traces = traces[:, channel_indices]

src/spikeinterface/core/segmentutils.py

@@ -162,7 +162,7 @@ def __init__(self, parent_segments, sampling_frequency, ignore_times=True):
     def get_num_samples(self):
         return self.total_length
 
-    def get_traces(self, start_frame, end_frame, channel_indices):
+    def _get_traces(self, start_frame, end_frame, channel_indices):
         # # Ensures that we won't request invalid segment indices
         if (start_frame >= self.get_num_samples()) or (end_frame <= start_frame):
             # Return (0 * num_channels) array of correct dtype

src/spikeinterface/core/zarrextractors.py

@@ -138,7 +138,7 @@ def get_num_samples(self) -> int:
         """
         return self._timeseries.shape[0]
 
-    def get_traces(
+    def _get_traces(
         self,
         start_frame: int | None = None,
         end_frame: int | None = None,

src/spikeinterface/extractors/cbin_ibl.py

@@ -133,7 +133,7 @@ def __init__(self, cbuffer, sampling_frequency, load_sync_channel):
     def get_num_samples(self):
         return self._cbuffer.shape[0]
 
-    def get_traces(self, start_frame, end_frame, channel_indices):
+    def _get_traces(self, start_frame, end_frame, channel_indices):
         if channel_indices is None:
             channel_indices = slice(None)
 

src/spikeinterface/extractors/iblextractors.py

@@ -268,7 +268,7 @@ def __init__(self, file_streamer, load_sync_channel: bool = False):
     def get_num_samples(self):
         return self._file_streamer.ns
 
-    def get_traces(self, start_frame: int, end_frame: int, channel_indices):
+    def _get_traces(self, start_frame: int, end_frame: int, channel_indices):
         if channel_indices is None:
             channel_indices = slice(None)
         traces = self._file_streamer.read(nsel=slice(start_frame, end_frame), volts=False)

src/spikeinterface/extractors/mcsh5extractors.py

@@ -82,7 +82,7 @@ def __init__(self, rf, stream_id, num_frames, sampling_frequency):
     def get_num_samples(self):
         return self._num_samples
 
-    def get_traces(self, start_frame=None, end_frame=None, channel_indices=None):
+    def _get_traces(self, start_frame=None, end_frame=None, channel_indices=None):
         if isinstance(channel_indices, slice):
             traces = self._stream.get("ChannelData")[channel_indices, start_frame:end_frame].T
         else:

src/spikeinterface/extractors/mdaextractors.py

@@ -160,7 +160,7 @@ def get_num_samples(self):
         """
         return self._num_samples
 
-    def get_traces(
+    def _get_traces(
         self,
         start_frame: Union[int, None] = None,
         end_frame: Union[int, None] = None,

src/spikeinterface/extractors/neoextractors/neobaseextractor.py

@@ -329,7 +329,7 @@ def get_num_samples(self):
 
         return int(num_samples)
 
-    def get_traces(
+    def _get_traces(
         self,
         start_frame: Union[int, None] = None,
         end_frame: Union[int, None] = None,

src/spikeinterface/extractors/nwbextractors.py

@@ -931,7 +931,7 @@ def get_num_samples(self):
         """
         return self._num_samples
 
-    def get_traces(self, start_frame, end_frame, channel_indices):
+    def _get_traces(self, start_frame, end_frame, channel_indices):
         electrical_series_data = self.electrical_series_data
         if electrical_series_data.ndim == 1:
             traces = electrical_series_data[start_frame:end_frame][:, np.newaxis]

src/spikeinterface/extractors/sinapsrecordingextractors.py

@@ -146,7 +146,7 @@ def __init__(self, rf, num_frames, sampling_frequency, num_bits):
     def get_num_samples(self):
         return self._num_samples
 
-    def get_traces(self, start_frame=None, end_frame=None, channel_indices=None):
+    def _get_traces(self, start_frame=None, end_frame=None, channel_indices=None):
         if isinstance(channel_indices, slice):
             traces = self._stream.get("FilteredData")[channel_indices, start_frame:end_frame].T
         else:

src/spikeinterface/generation/drift_tools.py

@@ -447,7 +447,7 @@ def __init__(
         self.displacement_indices = displacement_indices
         self.templates_array_moved = templates_array_moved
 
-    def get_traces(
+    def _get_traces(
         self,
         start_frame: Optional[int] = None,
         end_frame: Optional[int] = None,

src/spikeinterface/preprocessing/astype.py

@@ -70,7 +70,7 @@ def __init__(
         self.dtype = dtype
         self.round = round
 
-    def get_traces(self, start_frame, end_frame, channel_indices):
+    def _get_traces(self, start_frame, end_frame, channel_indices):
         if channel_indices is None:
             channel_indices = slice(None)
         traces = self.parent_recording_segment.get_traces(start_frame, end_frame, channel_indices)

src/spikeinterface/preprocessing/average_across_direction.py

@@ -115,7 +115,7 @@ def __init__(
     def get_num_samples(self):
         return self.parent_recording_segment.get_num_samples()
 
-    def get_traces(self, start_frame, end_frame, channel_indices):
+    def _get_traces(self, start_frame, end_frame, channel_indices):
         parent_traces = self.parent_recording_segment.get_traces(
             start_frame=start_frame,
             end_frame=end_frame,

src/spikeinterface/preprocessing/basepreprocessor.py

@@ -36,5 +36,5 @@ def __init__(self, parent_recording_segment):
     def get_num_samples(self):
         return self.parent_recording_segment.get_num_samples()
 
-    def get_traces(self, start_frame, end_frame, channel_indices):
+    def _get_traces(self, start_frame, end_frame, channel_indices):
         raise NotImplementedError

src/spikeinterface/preprocessing/clip.py

@@ -161,7 +161,7 @@ def __init__(self, parent_recording_segment, a_min, value_min, a_max, value_max)
         self.a_max = a_max
         self.value_max = value_max
 
-    def get_traces(self, start_frame, end_frame, channel_indices):
+    def _get_traces(self, start_frame, end_frame, channel_indices):
         traces = self.parent_recording_segment.get_traces(start_frame, end_frame, channel_indices)
         traces = traces.copy()
 

src/spikeinterface/preprocessing/common_reference.py

@@ -175,7 +175,7 @@ def __init__(
         self.dtype = dtype
         self.operator_func = operator = np.mean if self.operator == "average" else np.median
 
-    def get_traces(self, start_frame, end_frame, channel_indices):
+    def _get_traces(self, start_frame, end_frame, channel_indices):
         # Let's do the case with group_indices equal None as that is easy
         if self.group_indices is None:
             # We need all the channels to calculate the reference

src/spikeinterface/preprocessing/decimate.py

@@ -122,7 +122,7 @@ def get_num_samples(self):
         assert self._decimation_offset < parent_n_samp  # Sanity check (already enforced). Formula changes otherwise
         return int(np.ceil((parent_n_samp - self._decimation_offset) / self._decimation_factor))
 
-    def get_traces(self, start_frame, end_frame, channel_indices):
+    def _get_traces(self, start_frame, end_frame, channel_indices):
         # Account for offset and end when querying parent traces
         parent_start_frame = self._decimation_offset + start_frame * self._decimation_factor
         parent_end_frame = parent_start_frame + (end_frame - start_frame) * self._decimation_factor

src/spikeinterface/preprocessing/deepinterpolation/deepinterpolation.py

@@ -145,7 +145,7 @@ def __init__(
         self.desired_shape = desired_shape
         self.predict_workers = predict_workers
 
-    def get_traces(self, start_frame, end_frame, channel_indices):
+    def _get_traces(self, start_frame, end_frame, channel_indices):
         from .generators import SpikeInterfaceRecordingSegmentGenerator
 
         n_frames = self.parent_recording_segment.get_num_samples()

src/spikeinterface/preprocessing/directional_derivative.py

@@ -102,7 +102,7 @@ def __init__(
         # so that geom_other_dims[i] == unique_pos_other_dims[column_inds[i]]
         self.unique_pos_other_dims, self.column_inds = np.unique(geom_other_dims, axis=0, return_inverse=True)
 
-    def get_traces(self, start_frame, end_frame, channel_indices):
+    def _get_traces(self, start_frame, end_frame, channel_indices):
         parent_traces = self.parent_recording_segment.get_traces(
             start_frame=start_frame,
             end_frame=end_frame,

src/spikeinterface/preprocessing/filter.py

@@ -134,7 +134,7 @@ def __init__(self, parent_recording_segment, coeff, filter_mode, margin, dtype,
         self.add_reflect_padding = add_reflect_padding
         self.dtype = dtype
 
-    def get_traces(self, start_frame, end_frame, channel_indices):
+    def _get_traces(self, start_frame, end_frame, channel_indices):
         traces_chunk, left_margin, right_margin = get_chunk_with_margin(
             self.parent_recording_segment,
             start_frame,

src/spikeinterface/preprocessing/filter_gaussian.py

@@ -77,7 +77,7 @@ def __init__(
             sigmas.append(sf / (2 * np.pi * freq_max))
         self.margin = 1 + int(max(sigmas) * margin_sd)
 
-    def get_traces(
+    def _get_traces(
         self,
         start_frame: Union[int, None] = None,
         end_frame: Union[int, None] = None,

src/spikeinterface/preprocessing/filter_opencl.py

@@ -97,7 +97,7 @@ def __init__(self, parent_recording_segment, executor, margin):
         self.executor = executor
         self.margin = margin
 
-    def get_traces(self, start_frame, end_frame, channel_indices):
+    def _get_traces(self, start_frame, end_frame, channel_indices):
         assert start_frame is not None, "FilterOpenCLRecording only works with fixed chunk_size"
         assert end_frame is not None, "FilterOpenCLRecording only works with fixed chunk_size"
 

src/spikeinterface/preprocessing/highpass_spatial_filter.py

@@ -188,7 +188,7 @@ def __init__(
         self.sos_filter = sos_filter
         self.dtype = dtype
 
-    def get_traces(self, start_frame, end_frame, channel_indices):
+    def _get_traces(self, start_frame, end_frame, channel_indices):
         if channel_indices is None:
             channel_indices = slice(None)
         if self.window is not None:

src/spikeinterface/preprocessing/interpolate_bad_channels.py

@@ -92,7 +92,7 @@ def __init__(self, parent_recording_segment, good_channel_indices, bad_channel_i
         self._bad_channel_indices = bad_channel_indices
         self._weights = weights
 
-    def get_traces(self, start_frame, end_frame, channel_indices):
+    def _get_traces(self, start_frame, end_frame, channel_indices):
         if channel_indices is None:
             channel_indices = slice(None)
 

src/spikeinterface/preprocessing/normalize_scale.py

@@ -20,7 +20,7 @@ def __init__(self, parent_recording_segment, gain, offset, dtype):
         self.offset = offset
         self._dtype = dtype
 
-    def get_traces(self, start_frame, end_frame, channel_indices) -> np.ndarray:
+    def _get_traces(self, start_frame, end_frame, channel_indices) -> np.ndarray:
         # TODO when we are sure that BaseExtractors get_traces allocate their own buffer instead of just passing
         # It along we should remove copies in preprocessors including the one in the next line
 

src/spikeinterface/preprocessing/phase_shift.py

@@ -83,7 +83,7 @@ def __init__(self, parent_recording_segment, sample_shifts, margin, dtype, tmp_d
         self.dtype = dtype
         self.tmp_dtype = tmp_dtype
 
-    def get_traces(self, start_frame, end_frame, channel_indices):
+    def _get_traces(self, start_frame, end_frame, channel_indices):
         if channel_indices is None:
             channel_indices = slice(None)
 

src/spikeinterface/preprocessing/rectify.py

@@ -22,7 +22,7 @@ class RectifyRecordingSegment(BasePreprocessorSegment):
     def __init__(self, parent_recording_segment):
         BasePreprocessorSegment.__init__(self, parent_recording_segment)
 
-    def get_traces(self, start_frame, end_frame, channel_indices):
+    def _get_traces(self, start_frame, end_frame, channel_indices):
         traces = self.parent_recording_segment.get_traces(start_frame, end_frame, channel_indices)
         return np.abs(traces)
 

src/spikeinterface/preprocessing/remove_artifacts.py

@@ -256,7 +256,7 @@ def __init__(
         self.time_pad = time_pad
         self.sparsity = sparsity
 
-    def get_traces(self, start_frame, end_frame, channel_indices):
+    def _get_traces(self, start_frame, end_frame, channel_indices):
         if self.mode in ["average", "median"]:
             traces = self.parent_recording_segment.get_traces(start_frame, end_frame, slice(None))
         else:

src/spikeinterface/preprocessing/resample.py

@@ -114,7 +114,7 @@ def __init__(
     def get_num_samples(self):
         return int(self._parent_segment.get_num_samples() / self._parent_rate * self.sampling_frequency)
 
-    def get_traces(self, start_frame, end_frame, channel_indices):
+    def _get_traces(self, start_frame, end_frame, channel_indices):
         # get parent traces with margin
         parent_start_frame, parent_end_frame = [
             int((frame / self.sampling_frequency) * self._parent_rate) for frame in [start_frame, end_frame]

src/spikeinterface/preprocessing/silence_periods.py

@@ -108,7 +108,7 @@ def __init__(self, parent_recording_segment, periods, mode, noise_generator, seg
         self.seg_index = seg_index
         self.noise_generator = noise_generator
 
-    def get_traces(self, start_frame, end_frame, channel_indices):
+    def _get_traces(self, start_frame, end_frame, channel_indices):
         traces = self.parent_recording_segment.get_traces(start_frame, end_frame, channel_indices)
         traces = traces.copy()
 

src/spikeinterface/preprocessing/unsigned_to_signed.py

@@ -50,7 +50,7 @@ def __init__(self, parent_recording_segment, dtype_signed, bit_depth):
         self.dtype_signed = dtype_signed
         self.bit_depth = bit_depth
 
-    def get_traces(self, start_frame, end_frame, channel_indices):
+    def _get_traces(self, start_frame, end_frame, channel_indices):
         if channel_indices is None:
             channel_indices = slice(None)
         traces = self.parent_recording_segment.get_traces(start_frame, end_frame, channel_indices)

src/spikeinterface/preprocessing/whiten.py

@@ -105,7 +105,7 @@ def __init__(self, parent_recording_segment, W, M, dtype, int_scale):
         self.dtype = dtype
         self.int_scale = int_scale
 
-    def get_traces(self, start_frame, end_frame, channel_indices):
+    def _get_traces(self, start_frame, end_frame, channel_indices):
         traces = self.parent_recording_segment.get_traces(start_frame, end_frame, slice(None))
         traces_dtype = traces.dtype
         # if uint --> force int

src/spikeinterface/preprocessing/zero_channel_pad.py

@@ -74,7 +74,7 @@ def __init__(
 
         super().__init__(parent_recording_segment=recording_segment)
 
-    def get_traces(self, start_frame, end_frame, channel_indices):
+    def _get_traces(self, start_frame, end_frame, channel_indices):
         # This contains the padded elements by default and we add the original traces if necessary
         trace_size = end_frame - start_frame
         if isinstance(channel_indices, (np.ndarray, list)):
@@ -194,7 +194,7 @@ def __init__(self, recording_segment: BaseRecordingSegment, num_channels: int, c
         self.num_channels = num_channels
         self.channel_mapping = channel_mapping
 
-    def get_traces(self, start_frame, end_frame, channel_indices):
+    def _get_traces(self, start_frame, end_frame, channel_indices):
         traces = np.zeros((end_frame - start_frame, self.num_channels))
         traces[:, self.channel_mapping] = self.parent_recording_segment.get_traces(
             start_frame=start_frame, end_frame=end_frame, channel_indices=self.channel_mapping