diff --git a/.github/actions/build-test-environment/action.yml b/.github/actions/build-test-environment/action.yml index 723e8a702f..c2524d2c16 100644 --- a/.github/actions/build-test-environment/action.yml +++ b/.github/actions/build-test-environment/action.yml @@ -1,41 +1,20 @@ name: Install packages description: This action installs the package and its dependencies for testing -inputs: - python-version: - description: 'Python version to set up' - required: false - os: - description: 'Operating system to set up' - required: false - runs: using: "composite" steps: - name: Install dependencies run: | - sudo apt install git git config --global user.email "CI@example.com" git config --global user.name "CI Almighty" - python -m venv ${{ github.workspace }}/test_env # Environment used in the caching step - python -m pip install -U pip # Official recommended way - source ${{ github.workspace }}/test_env/bin/activate pip install tabulate # This produces summaries at the end pip install -e .[test,extractors,streaming_extractors,test_extractors,full] shell: bash - - name: Force installation of latest dev from key-packages when running dev (not release) - run: | - source ${{ github.workspace }}/test_env/bin/activate - spikeinterface_is_dev_version=$(python -c "import spikeinterface; print(spikeinterface.DEV_MODE)") - if [ $spikeinterface_is_dev_version = "True" ]; then - echo "Running spikeinterface dev version" - pip install --no-cache-dir git+https://github.com/NeuralEnsemble/python-neo - pip install --no-cache-dir git+https://github.com/SpikeInterface/probeinterface - fi - echo "Running tests for release, using pyproject.toml versions of neo and probeinterface" + - name: Install git-annex shell: bash - - name: git-annex install run: | + pip install datalad-installer wget https://downloads.kitenet.net/git-annex/linux/current/git-annex-standalone-amd64.tar.gz mkdir /home/runner/work/installation mv git-annex-standalone-amd64.tar.gz /home/runner/work/installation/ @@ -44,4 +23,14 @@ runs: tar xvzf git-annex-standalone-amd64.tar.gz echo "$(pwd)/git-annex.linux" >> $GITHUB_PATH cd $workdir + git config --global filter.annex.process "git-annex filter-process" # recommended for efficiency + - name: Force installation of latest dev from key-packages when running dev (not release) + run: | + spikeinterface_is_dev_version=$(python -c "import spikeinterface; print(spikeinterface.DEV_MODE)") + if [ $spikeinterface_is_dev_version = "True" ]; then + echo "Running spikeinterface dev version" + pip install --no-cache-dir git+https://github.com/NeuralEnsemble/python-neo + pip install --no-cache-dir git+https://github.com/SpikeInterface/probeinterface + fi + echo "Running tests for release, using pyproject.toml versions of neo and probeinterface" shell: bash diff --git a/.github/workflows/all-tests.yml b/.github/workflows/all-tests.yml index dcaec8b272..a9c840d5d5 100644 --- a/.github/workflows/all-tests.yml +++ b/.github/workflows/all-tests.yml @@ -47,7 +47,7 @@ jobs: echo "$file was changed" done - - name: Set testing environment # This decides which tests are run and whether to install especial dependencies + - name: Set testing environment # This decides which tests are run and whether to install special dependencies shell: bash run: | changed_files="${{ steps.changed-files.outputs.all_changed_files }}" diff --git a/.github/workflows/full-test-with-codecov.yml b/.github/workflows/full-test-with-codecov.yml index 407c614ebf..f8ed2aa7a9 100644 --- a/.github/workflows/full-test-with-codecov.yml +++ b/.github/workflows/full-test-with-codecov.yml @@ -45,7 +45,6 @@ jobs: env: HDF5_PLUGIN_PATH: ${{ github.workspace }}/hdf5_plugin_path_maxwell run: | - source ${{ github.workspace }}/test_env/bin/activate pytest -m "not sorters_external" --cov=./ --cov-report xml:./coverage.xml -vv -ra --durations=0 | tee report_full.txt; test ${PIPESTATUS[0]} -eq 0 || exit 1 echo "# Timing profile of full tests" >> $GITHUB_STEP_SUMMARY python ./.github/scripts/build_job_summary.py report_full.txt >> $GITHUB_STEP_SUMMARY diff --git a/doc/get_started/quickstart.rst b/doc/get_started/quickstart.rst index 3d45606a78..1349802ce5 100644 --- a/doc/get_started/quickstart.rst +++ b/doc/get_started/quickstart.rst @@ -673,7 +673,7 @@ compute quality metrics (some quality metrics require certain extensions 'min_spikes': 0, 'window_size_s': 1}, 'snr': {'peak_mode': 'extremum', 'peak_sign': 'neg'}, - 'synchrony': {'synchrony_sizes': (2, 4, 8)}} + 'synchrony': {} Since the recording is very short, let’s change some parameters to diff --git a/doc/modules/qualitymetrics/synchrony.rst b/doc/modules/qualitymetrics/synchrony.rst index d244fd0c0f..696dacbd3c 100644 --- a/doc/modules/qualitymetrics/synchrony.rst +++ b/doc/modules/qualitymetrics/synchrony.rst @@ -12,7 +12,7 @@ trains. This way synchronous events can be found both in multi-unit and single-u Complexity is calculated by counting the number of spikes (i.e. non-empty bins) that occur at the same sample index, within and across spike trains. -Synchrony metrics can be computed for different synchrony sizes (>1), defining the number of simultaneous spikes to count. +Synchrony metrics are computed for 2, 4 and 8 synchronous spikes. @@ -29,7 +29,7 @@ Example code import spikeinterface.qualitymetrics as sqm # Combine a sorting and recording into a sorting_analyzer - synchrony = sqm.compute_synchrony_metrics(sorting_analyzer=sorting_analyzer synchrony_sizes=(2, 4, 8)) + synchrony = sqm.compute_synchrony_metrics(sorting_analyzer=sorting_analyzer) # synchrony is a tuple of dicts with the synchrony metrics for each unit diff --git a/pyproject.toml b/pyproject.toml index fc09ad9198..22fbdc7f22 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -73,7 +73,7 @@ extractors = [ ] streaming_extractors = [ - "ONE-api>=2.7.0", # alf sorter and streaming IBL + "ONE-api>=2.7.0,<2.10.0", # alf sorter and streaming IBL "ibllib>=2.36.0", # streaming IBL # Following dependencies are for streaming with nwb files "pynwb>=2.6.0", diff --git a/src/spikeinterface/extractors/nwbextractors.py b/src/spikeinterface/extractors/nwbextractors.py index d797e64910..171992f6b1 100644 --- a/src/spikeinterface/extractors/nwbextractors.py +++ b/src/spikeinterface/extractors/nwbextractors.py @@ -599,6 +599,8 @@ def __init__( else: gains, offsets, locations, groups = self._fetch_main_properties_backend() self.extra_requirements.append("h5py") + if stream_mode is not None: + self.extra_requirements.append(stream_mode) self.set_channel_gains(gains) self.set_channel_offsets(offsets) if locations is not None: @@ -1100,6 +1102,8 @@ def __init__( for property_name, property_values in properties.items(): values = [x.decode("utf-8") if isinstance(x, bytes) else x for x in property_values] self.set_property(property_name, values) + if stream_mode is not None: + self.extra_requirements.append(stream_mode) if stream_mode is None and file_path is not None: file_path = str(Path(file_path).resolve()) diff --git a/src/spikeinterface/postprocessing/template_metrics.py b/src/spikeinterface/postprocessing/template_metrics.py index 6e7bcf21b8..1969480503 100644 --- a/src/spikeinterface/postprocessing/template_metrics.py +++ b/src/spikeinterface/postprocessing/template_metrics.py @@ -63,23 +63,10 @@ class ComputeTemplateMetrics(AnalyzerExtension): include_multi_channel_metrics : bool, default: False Whether to compute multi-channel metrics delete_existing_metrics : bool, default: False - If True, any template metrics attached to the `sorting_analyzer` are deleted. If False, any metrics which were previously calculated but are not included in `metric_names` are kept, provided the `metrics_kwargs` are unchanged. - metrics_kwargs : dict - Additional arguments to pass to the metric functions. Including: - * recovery_window_ms: the window in ms after the peak to compute the recovery_slope, default: 0.7 - * peak_relative_threshold: the relative threshold to detect positive and negative peaks, default: 0.2 - * peak_width_ms: the width in samples to detect peaks, default: 0.2 - * depth_direction: the direction to compute velocity above and below, default: "y" (see notes) - * min_channels_for_velocity: the minimum number of channels above or below to compute velocity, default: 5 - * min_r2_velocity: the minimum r2 to accept the velocity fit, default: 0.7 - * exp_peak_function: the function to use to compute the peak amplitude for the exp decay, default: "ptp" - * min_r2_exp_decay: the minimum r2 to accept the exp decay fit, default: 0.5 - * spread_threshold: the threshold to compute the spread, default: 0.2 - * spread_smooth_um: the smoothing in um to compute the spread, default: 20 - * column_range: the range in um in the horizontal direction to consider channels for velocity, default: None - - If None, all channels all channels are considered - - If 0 or 1, only the "column" that includes the max channel is considered - - If > 1, only channels within range (+/-) um from the max channel horizontal position are used + If True, any template metrics attached to the `sorting_analyzer` are deleted. If False, any metrics which were previously calculated but are not included in `metric_names` are kept, provided the `metric_params` are unchanged. + metric_params : dict of dicts or None, default: None + Dictionary with parameters for template metrics calculation. + Default parameters can be obtained with: `si.postprocessing.template_metrics.get_default_tm_params()` Returns ------- @@ -100,15 +87,29 @@ class ComputeTemplateMetrics(AnalyzerExtension): need_recording = False use_nodepipeline = False need_job_kwargs = False + need_backward_compatibility_on_load = True min_channels_for_multi_channel_warning = 10 + def _handle_backward_compatibility_on_load(self): + + # For backwards compatibility - this reformats metrics_kwargs as metric_params + if (metrics_kwargs := self.params.get("metrics_kwargs")) is not None: + + metric_params = {} + for metric_name in self.params["metric_names"]: + metric_params[metric_name] = deepcopy(metrics_kwargs) + self.params["metric_params"] = metric_params + + del self.params["metrics_kwargs"] + def _set_params( self, metric_names=None, peak_sign="neg", upsampling_factor=10, sparsity=None, + metric_params=None, metrics_kwargs=None, include_multi_channel_metrics=False, delete_existing_metrics=False, @@ -134,33 +135,24 @@ def _set_params( if include_multi_channel_metrics: metric_names += get_multi_channel_template_metric_names() - if metrics_kwargs is None: - metrics_kwargs_ = _default_function_kwargs.copy() - if len(other_kwargs) > 0: - for m in other_kwargs: - if m in metrics_kwargs_: - metrics_kwargs_[m] = other_kwargs[m] - else: - metrics_kwargs_ = _default_function_kwargs.copy() - metrics_kwargs_.update(metrics_kwargs) + if metrics_kwargs is not None and metric_params is None: + deprecation_msg = "`metrics_kwargs` is deprecated and will be removed in version 0.104.0. Please use `metric_params` instead" + deprecation_msg = "`metrics_kwargs` is deprecated and will be removed in version 0.104.0. Please use `metric_params` instead" + + metric_params = {} + for metric_name in metric_names: + metric_params[metric_name] = deepcopy(metrics_kwargs) + + metric_params_ = get_default_tm_params(metric_names) + for k in metric_params_: + if metric_params is not None and k in metric_params: + metric_params_[k].update(metric_params[k]) metrics_to_compute = metric_names tm_extension = self.sorting_analyzer.get_extension("template_metrics") if delete_existing_metrics is False and tm_extension is not None: - existing_params = tm_extension.params["metrics_kwargs"] - # checks that existing metrics were calculated using the same params - if existing_params != metrics_kwargs_: - warnings.warn( - f"The parameters used to calculate the previous template metrics are different" - f"than those used now.\nPrevious parameters: {existing_params}\nCurrent " - f"parameters: {metrics_kwargs_}\nDeleting previous template metrics..." - ) - tm_extension.params["metric_names"] = [] - existing_metric_names = [] - else: - existing_metric_names = tm_extension.params["metric_names"] - + existing_metric_names = tm_extension.params["metric_names"] existing_metric_names_propogated = [ metric_name for metric_name in existing_metric_names if metric_name not in metrics_to_compute ] @@ -171,7 +163,7 @@ def _set_params( sparsity=sparsity, peak_sign=peak_sign, upsampling_factor=int(upsampling_factor), - metrics_kwargs=metrics_kwargs_, + metric_params=metric_params_, delete_existing_metrics=delete_existing_metrics, metrics_to_compute=metrics_to_compute, ) @@ -273,7 +265,7 @@ def _compute_metrics(self, sorting_analyzer, unit_ids=None, verbose=False, metri sampling_frequency=sampling_frequency_up, trough_idx=trough_idx, peak_idx=peak_idx, - **self.params["metrics_kwargs"], + **self.params["metric_params"][metric_name], ) except Exception as e: warnings.warn(f"Error computing metric {metric_name} for unit {unit_id}: {e}") @@ -312,7 +304,7 @@ def _compute_metrics(self, sorting_analyzer, unit_ids=None, verbose=False, metri template_upsampled, channel_locations=channel_locations_sparse, sampling_frequency=sampling_frequency_up, - **self.params["metrics_kwargs"], + **self.params["metric_params"][metric_name], ) except Exception as e: warnings.warn(f"Error computing metric {metric_name} for unit {unit_id}: {e}") @@ -326,8 +318,8 @@ def _compute_metrics(self, sorting_analyzer, unit_ids=None, verbose=False, metri def _run(self, verbose=False): - delete_existing_metrics = self.params["delete_existing_metrics"] metrics_to_compute = self.params["metrics_to_compute"] + delete_existing_metrics = self.params["delete_existing_metrics"] # compute the metrics which have been specified by the user computed_metrics = self._compute_metrics( @@ -343,9 +335,21 @@ def _run(self, verbose=False): ): existing_metrics = tm_extension.params["metric_names"] + existing_metrics = [] + # here we get in the loaded via the dict only (to avoid full loading from disk after params reset) + tm_extension = self.sorting_analyzer.extensions.get("template_metrics", None) + if ( + delete_existing_metrics is False + and tm_extension is not None + and tm_extension.data.get("metrics") is not None + ): + existing_metrics = tm_extension.params["metric_names"] + # append the metrics which were previously computed for metric_name in set(existing_metrics).difference(metrics_to_compute): - computed_metrics[metric_name] = tm_extension.data["metrics"][metric_name] + # some metrics names produce data columns with other names. This deals with that. + for column_name in tm_compute_name_to_column_names[metric_name]: + computed_metrics[column_name] = tm_extension.data["metrics"][column_name] self.data["metrics"] = computed_metrics @@ -372,6 +376,35 @@ def _get_data(self): ) +def get_default_tm_params(metric_names): + if metric_names is None: + metric_names = get_template_metric_names() + + base_tm_params = _default_function_kwargs + + metric_params = {} + for metric_name in metric_names: + metric_params[metric_name] = deepcopy(base_tm_params) + + return metric_params + + +# a dict converting the name of the metric for computation to the output of that computation +tm_compute_name_to_column_names = { + "peak_to_valley": ["peak_to_valley"], + "peak_trough_ratio": ["peak_trough_ratio"], + "half_width": ["half_width"], + "repolarization_slope": ["repolarization_slope"], + "recovery_slope": ["recovery_slope"], + "num_positive_peaks": ["num_positive_peaks"], + "num_negative_peaks": ["num_negative_peaks"], + "velocity_above": ["velocity_above"], + "velocity_below": ["velocity_below"], + "exp_decay": ["exp_decay"], + "spread": ["spread"], +} + + def get_trough_and_peak_idx(template): """ Return the indices into the input template of the detected trough diff --git a/src/spikeinterface/postprocessing/tests/test_template_metrics.py b/src/spikeinterface/postprocessing/tests/test_template_metrics.py index 5056d4ff2a..1bf49f64c1 100644 --- a/src/spikeinterface/postprocessing/tests/test_template_metrics.py +++ b/src/spikeinterface/postprocessing/tests/test_template_metrics.py @@ -1,5 +1,5 @@ from spikeinterface.postprocessing.tests.common_extension_tests import AnalyzerExtensionCommonTestSuite -from spikeinterface.postprocessing import ComputeTemplateMetrics +from spikeinterface.postprocessing import ComputeTemplateMetrics, compute_template_metrics import pytest import csv @@ -8,6 +8,49 @@ template_metrics = list(_single_channel_metric_name_to_func.keys()) +def test_different_params_template_metrics(small_sorting_analyzer): + """ + Computes template metrics using different params, and check that they are + actually calculated using the different params. + """ + compute_template_metrics( + sorting_analyzer=small_sorting_analyzer, + metric_names=["exp_decay", "spread", "half_width"], + metric_params={"exp_decay": {"recovery_window_ms": 0.8}, "spread": {"spread_smooth_um": 15}}, + ) + + tm_extension = small_sorting_analyzer.get_extension("template_metrics") + tm_params = tm_extension.params["metric_params"] + + assert tm_params["exp_decay"]["recovery_window_ms"] == 0.8 + assert tm_params["spread"]["recovery_window_ms"] == 0.7 + assert tm_params["half_width"]["recovery_window_ms"] == 0.7 + + assert tm_params["spread"]["spread_smooth_um"] == 15 + assert tm_params["exp_decay"]["spread_smooth_um"] == 20 + assert tm_params["half_width"]["spread_smooth_um"] == 20 + + +def test_backwards_compat_params_template_metrics(small_sorting_analyzer): + """ + Computes template metrics using the metrics_kwargs keyword + """ + compute_template_metrics( + sorting_analyzer=small_sorting_analyzer, + metric_names=["exp_decay", "spread"], + metrics_kwargs={"recovery_window_ms": 0.8}, + ) + + tm_extension = small_sorting_analyzer.get_extension("template_metrics") + tm_params = tm_extension.params["metric_params"] + + assert tm_params["exp_decay"]["recovery_window_ms"] == 0.8 + assert tm_params["spread"]["recovery_window_ms"] == 0.8 + + assert tm_params["spread"]["spread_smooth_um"] == 20 + assert tm_params["exp_decay"]["spread_smooth_um"] == 20 + + def test_compute_new_template_metrics(small_sorting_analyzer): """ Computes template metrics then computes a subset of template metrics, and checks @@ -17,6 +60,8 @@ def test_compute_new_template_metrics(small_sorting_analyzer): are deleted. """ + small_sorting_analyzer.delete_extension("template_metrics") + # calculate just exp_decay small_sorting_analyzer.compute({"template_metrics": {"metric_names": ["exp_decay"]}}) template_metric_extension = small_sorting_analyzer.get_extension("template_metrics") @@ -47,7 +92,7 @@ def test_compute_new_template_metrics(small_sorting_analyzer): # check that, when parameters are changed, the old metrics are deleted small_sorting_analyzer.compute( - {"template_metrics": {"metric_names": ["exp_decay"], "metrics_kwargs": {"recovery_window_ms": 0.6}}} + {"template_metrics": {"metric_names": ["exp_decay"], "metric_params": {"recovery_window_ms": 0.6}}} ) diff --git a/src/spikeinterface/postprocessing/unit_locations.py b/src/spikeinterface/postprocessing/unit_locations.py index 3f6dd47eec..df19458316 100644 --- a/src/spikeinterface/postprocessing/unit_locations.py +++ b/src/spikeinterface/postprocessing/unit_locations.py @@ -26,7 +26,7 @@ class ComputeUnitLocations(AnalyzerExtension): ---------- sorting_analyzer : SortingAnalyzer A SortingAnalyzer object - method : "center_of_mass" | "monopolar_triangulation" | "grid_convolution", default: "center_of_mass" + method : "monopolar_triangulation" | "center_of_mass" | "grid_convolution", default: "monopolar_triangulation" The method to use for localization **method_kwargs : dict, default: {} Kwargs which are passed to the method function. These can be found in the docstrings of `compute_center_of_mass`, `compute_grid_convolution` and `compute_monopolar_triangulation`. diff --git a/src/spikeinterface/preprocessing/silence_periods.py b/src/spikeinterface/preprocessing/silence_periods.py index 85169011d8..00d9a1a407 100644 --- a/src/spikeinterface/preprocessing/silence_periods.py +++ b/src/spikeinterface/preprocessing/silence_periods.py @@ -97,7 +97,8 @@ def __init__(self, recording, list_periods, mode="zeros", noise_levels=None, see rec_segment = SilencedPeriodsRecordingSegment(parent_segment, periods, mode, noise_generator, seg_index) self.add_recording_segment(rec_segment) - self._kwargs = dict(recording=recording, list_periods=list_periods, mode=mode, noise_generator=noise_generator) + self._kwargs = dict(recording=recording, list_periods=list_periods, mode=mode, seed=seed) + self._kwargs.update(random_chunk_kwargs) class SilencedPeriodsRecordingSegment(BasePreprocessorSegment): diff --git a/src/spikeinterface/qualitymetrics/__init__.py b/src/spikeinterface/qualitymetrics/__init__.py index 9d604f6ae2..754c82d8e3 100644 --- a/src/spikeinterface/qualitymetrics/__init__.py +++ b/src/spikeinterface/qualitymetrics/__init__.py @@ -6,4 +6,4 @@ get_default_qm_params, ) from .pca_metrics import get_quality_pca_metric_list -from .misc_metrics import get_synchrony_counts +from .misc_metrics import _get_synchrony_counts diff --git a/src/spikeinterface/qualitymetrics/misc_metrics.py b/src/spikeinterface/qualitymetrics/misc_metrics.py index 8dfd41cf88..6007de379c 100644 --- a/src/spikeinterface/qualitymetrics/misc_metrics.py +++ b/src/spikeinterface/qualitymetrics/misc_metrics.py @@ -520,7 +520,7 @@ def compute_sliding_rp_violations( ) -def get_synchrony_counts(spikes, synchrony_sizes, all_unit_ids): +def _get_synchrony_counts(spikes, synchrony_sizes, all_unit_ids): """ Compute synchrony counts, the number of simultaneous spikes with sizes `synchrony_sizes`. @@ -528,10 +528,10 @@ def get_synchrony_counts(spikes, synchrony_sizes, all_unit_ids): ---------- spikes : np.array Structured numpy array with fields ("sample_index", "unit_index", "segment_index"). - synchrony_sizes : numpy array - The synchrony sizes to compute. Should be pre-sorted. all_unit_ids : list or None, default: None List of unit ids to compute the synchrony metrics. Expecting all units. + synchrony_sizes : None or np.array, default: None + The synchrony sizes to compute. Should be pre-sorted. Returns ------- @@ -565,37 +565,38 @@ def get_synchrony_counts(spikes, synchrony_sizes, all_unit_ids): return synchrony_counts -def compute_synchrony_metrics(sorting_analyzer, synchrony_sizes=(2, 4, 8), unit_ids=None): +def compute_synchrony_metrics(sorting_analyzer, unit_ids=None, synchrony_sizes=None): """ Compute synchrony metrics. Synchrony metrics represent the rate of occurrences of - "synchrony_size" spikes at the exact same sample index. + spikes at the exact same sample index, with synchrony sizes 2, 4 and 8. Parameters ---------- sorting_analyzer : SortingAnalyzer A SortingAnalyzer object. - synchrony_sizes : list or tuple, default: (2, 4, 8) - The synchrony sizes to compute. unit_ids : list or None, default: None List of unit ids to compute the synchrony metrics. If None, all units are used. + synchrony_sizes: None, default: None + Deprecated argument. Please use private `_get_synchrony_counts` if you need finer control over number of synchronous spikes. Returns ------- sync_spike_{X} : dict The synchrony metric for synchrony size X. - Returns are as many as synchrony_sizes. References ---------- Based on concepts described in [Grün]_ This code was adapted from `Elephant - Electrophysiology Analysis Toolkit `_ """ - assert min(synchrony_sizes) > 1, "Synchrony sizes must be greater than 1" - # Sort the synchrony times so we can slice numpy arrays, instead of using dicts - synchrony_sizes_np = np.array(synchrony_sizes, dtype=np.int16) - synchrony_sizes_np.sort() - res = namedtuple("synchrony_metrics", [f"sync_spike_{size}" for size in synchrony_sizes_np]) + if synchrony_sizes is not None: + warning_message = "Custom `synchrony_sizes` is deprecated; the `synchrony_metrics` will be computed using `synchrony_sizes = [2,4,8]`" + warnings.warn(warning_message, DeprecationWarning, stacklevel=2) + + synchrony_sizes = np.array([2, 4, 8]) + + res = namedtuple("synchrony_metrics", [f"sync_spike_{size}" for size in synchrony_sizes]) sorting = sorting_analyzer.sorting @@ -606,10 +607,10 @@ def compute_synchrony_metrics(sorting_analyzer, synchrony_sizes=(2, 4, 8), unit_ spikes = sorting.to_spike_vector() all_unit_ids = sorting.unit_ids - synchrony_counts = get_synchrony_counts(spikes, synchrony_sizes_np, all_unit_ids) + synchrony_counts = _get_synchrony_counts(spikes, synchrony_sizes, all_unit_ids) synchrony_metrics_dict = {} - for sync_idx, synchrony_size in enumerate(synchrony_sizes_np): + for sync_idx, synchrony_size in enumerate(synchrony_sizes): sync_id_metrics_dict = {} for i, unit_id in enumerate(all_unit_ids): if unit_id not in unit_ids: @@ -623,7 +624,7 @@ def compute_synchrony_metrics(sorting_analyzer, synchrony_sizes=(2, 4, 8), unit_ return res(**synchrony_metrics_dict) -_default_params["synchrony"] = dict(synchrony_sizes=(2, 4, 8)) +_default_params["synchrony"] = dict() def compute_firing_ranges(sorting_analyzer, bin_size_s=5, percentiles=(5, 95), unit_ids=None): diff --git a/src/spikeinterface/qualitymetrics/pca_metrics.py b/src/spikeinterface/qualitymetrics/pca_metrics.py index 4c68dfea59..ca21f1e45f 100644 --- a/src/spikeinterface/qualitymetrics/pca_metrics.py +++ b/src/spikeinterface/qualitymetrics/pca_metrics.py @@ -6,6 +6,7 @@ from copy import deepcopy import platform from tqdm.auto import tqdm +from warnings import warn import numpy as np @@ -52,6 +53,7 @@ def get_quality_pca_metric_list(): def compute_pc_metrics( sorting_analyzer, metric_names=None, + metric_params=None, qm_params=None, unit_ids=None, seed=None, @@ -70,7 +72,7 @@ def compute_pc_metrics( metric_names : list of str, default: None The list of PC metrics to compute. If not provided, defaults to all PC metrics. - qm_params : dict or None + metric_params : dict or None Dictionary with parameters for each PC metric function. unit_ids : list of int or None List of unit ids to compute metrics for. @@ -86,6 +88,14 @@ def compute_pc_metrics( pc_metrics : dict The computed PC metrics. """ + + if qm_params is not None and metric_params is None: + deprecation_msg = ( + "`qm_params` is deprecated and will be removed in version 0.104.0. Please use metric_params instead" + ) + warn(deprecation_msg, category=DeprecationWarning, stacklevel=2) + metric_params = qm_params + pca_ext = sorting_analyzer.get_extension("principal_components") assert pca_ext is not None, "calculate_pc_metrics() need extension 'principal_components'" @@ -93,8 +103,8 @@ def compute_pc_metrics( if metric_names is None: metric_names = _possible_pc_metric_names.copy() - if qm_params is None: - qm_params = _default_params + if metric_params is None: + metric_params = _default_params extremum_channels = get_template_extremum_channel(sorting_analyzer) @@ -147,7 +157,7 @@ def compute_pc_metrics( pcs = dense_projections[np.isin(all_labels, neighbor_unit_ids)][:, :, neighbor_channel_indices] pcs_flat = pcs.reshape(pcs.shape[0], -1) - func_args = (pcs_flat, labels, non_nn_metrics, unit_id, unit_ids, qm_params, max_threads_per_process) + func_args = (pcs_flat, labels, non_nn_metrics, unit_id, unit_ids, metric_params, max_threads_per_process) items.append(func_args) if not run_in_parallel and non_nn_metrics: @@ -184,7 +194,7 @@ def compute_pc_metrics( units_loop = tqdm(units_loop, desc=f"calculate {metric_name} metric", total=len(unit_ids)) func = _nn_metric_name_to_func[metric_name] - metric_params = qm_params[metric_name] if metric_name in qm_params else {} + metric_params = metric_params[metric_name] if metric_name in metric_params else {} for _, unit_id in units_loop: try: @@ -213,7 +223,7 @@ def compute_pc_metrics( def calculate_pc_metrics( - sorting_analyzer, metric_names=None, qm_params=None, unit_ids=None, seed=None, n_jobs=1, progress_bar=False + sorting_analyzer, metric_names=None, metric_params=None, unit_ids=None, seed=None, n_jobs=1, progress_bar=False ): warnings.warn( "The `calculate_pc_metrics` function is deprecated and will be removed in 0.103.0. Please use compute_pc_metrics instead", @@ -224,7 +234,7 @@ def calculate_pc_metrics( pc_metrics = compute_pc_metrics( sorting_analyzer, metric_names=metric_names, - qm_params=qm_params, + metric_params=metric_params, unit_ids=unit_ids, seed=seed, n_jobs=n_jobs, @@ -977,16 +987,16 @@ def _compute_isolation(pcs_target_unit, pcs_other_unit, n_neighbors: int): def pca_metrics_one_unit(args): - (pcs_flat, labels, metric_names, unit_id, unit_ids, qm_params, max_threads_per_process) = args + (pcs_flat, labels, metric_names, unit_id, unit_ids, metric_params, max_threads_per_process) = args if max_threads_per_process is None: - return _pca_metrics_one_unit(pcs_flat, labels, metric_names, unit_id, unit_ids, qm_params) + return _pca_metrics_one_unit(pcs_flat, labels, metric_names, unit_id, unit_ids, metric_params) else: with threadpool_limits(limits=int(max_threads_per_process)): - return _pca_metrics_one_unit(pcs_flat, labels, metric_names, unit_id, unit_ids, qm_params) + return _pca_metrics_one_unit(pcs_flat, labels, metric_names, unit_id, unit_ids, metric_params) -def _pca_metrics_one_unit(pcs_flat, labels, metric_names, unit_id, unit_ids, qm_params): +def _pca_metrics_one_unit(pcs_flat, labels, metric_names, unit_id, unit_ids, metric_params): pc_metrics = {} # metrics if "isolation_distance" in metric_names or "l_ratio" in metric_names: @@ -1015,7 +1025,7 @@ def _pca_metrics_one_unit(pcs_flat, labels, metric_names, unit_id, unit_ids, qm_ if "nearest_neighbor" in metric_names: try: nn_hit_rate, nn_miss_rate = nearest_neighbors_metrics( - pcs_flat, labels, unit_id, **qm_params["nearest_neighbor"] + pcs_flat, labels, unit_id, **metric_params["nearest_neighbor"] ) except: nn_hit_rate = np.nan @@ -1024,7 +1034,7 @@ def _pca_metrics_one_unit(pcs_flat, labels, metric_names, unit_id, unit_ids, qm_ pc_metrics["nn_miss_rate"] = nn_miss_rate if "silhouette" in metric_names: - silhouette_method = qm_params["silhouette"]["method"] + silhouette_method = metric_params["silhouette"]["method"] if "simplified" in silhouette_method: try: unit_silhouette_score = simplified_silhouette_score(pcs_flat, labels, unit_id) diff --git a/src/spikeinterface/qualitymetrics/quality_metric_calculator.py b/src/spikeinterface/qualitymetrics/quality_metric_calculator.py index b6a50d60f5..d71450853f 100644 --- a/src/spikeinterface/qualitymetrics/quality_metric_calculator.py +++ b/src/spikeinterface/qualitymetrics/quality_metric_calculator.py @@ -6,6 +6,7 @@ from copy import deepcopy import numpy as np +from warnings import warn from spikeinterface.core.job_tools import fix_job_kwargs from spikeinterface.core.sortinganalyzer import register_result_extension, AnalyzerExtension @@ -15,7 +16,7 @@ compute_pc_metrics, _misc_metric_name_to_func, _possible_pc_metric_names, - compute_name_to_column_names, + qm_compute_name_to_column_names, ) from .misc_metrics import _default_params as misc_metrics_params from .pca_metrics import _default_params as pca_metrics_params @@ -31,7 +32,7 @@ class ComputeQualityMetrics(AnalyzerExtension): A SortingAnalyzer object. metric_names : list or None List of quality metrics to compute. - qm_params : dict or None + metric_params : dict of dicts or None Dictionary with parameters for quality metrics calculation. Default parameters can be obtained with: `si.qualitymetrics.get_default_qm_params()` skip_pc_metrics : bool, default: False @@ -54,10 +55,18 @@ class ComputeQualityMetrics(AnalyzerExtension): need_recording = False use_nodepipeline = False need_job_kwargs = True + need_backward_compatibility_on_load = True + + def _handle_backward_compatibility_on_load(self): + # For backwards compatibility - this renames qm_params as metric_params + if (qm_params := self.params.get("qm_params")) is not None: + self.params["metric_params"] = qm_params + del self.params["qm_params"] def _set_params( self, metric_names=None, + metric_params=None, qm_params=None, peak_sign=None, seed=None, @@ -65,6 +74,12 @@ def _set_params( delete_existing_metrics=False, metrics_to_compute=None, ): + if qm_params is not None and metric_params is None: + deprecation_msg = ( + "`qm_params` is deprecated and will be removed in version 0.104.0 Please use metric_params instead" + ) + metric_params = qm_params + warn(deprecation_msg, category=DeprecationWarning, stacklevel=2) if metric_names is None: metric_names = list(_misc_metric_name_to_func.keys()) @@ -80,12 +95,12 @@ def _set_params( if "drift" in metric_names: metric_names.remove("drift") - qm_params_ = get_default_qm_params() - for k in qm_params_: - if qm_params is not None and k in qm_params: - qm_params_[k].update(qm_params[k]) - if "peak_sign" in qm_params_[k] and peak_sign is not None: - qm_params_[k]["peak_sign"] = peak_sign + metric_params_ = get_default_qm_params() + for k in metric_params_: + if metric_params is not None and k in metric_params: + metric_params_[k].update(metric_params[k]) + if "peak_sign" in metric_params_[k] and peak_sign is not None: + metric_params_[k]["peak_sign"] = peak_sign metrics_to_compute = metric_names qm_extension = self.sorting_analyzer.get_extension("quality_metrics") @@ -101,7 +116,7 @@ def _set_params( metric_names=metric_names, peak_sign=peak_sign, seed=seed, - qm_params=qm_params_, + metric_params=metric_params_, skip_pc_metrics=skip_pc_metrics, delete_existing_metrics=delete_existing_metrics, metrics_to_compute=metrics_to_compute, @@ -141,7 +156,7 @@ def _compute_metrics(self, sorting_analyzer, unit_ids=None, verbose=False, metri """ import pandas as pd - qm_params = self.params["qm_params"] + metric_params = self.params["metric_params"] # sparsity = self.params["sparsity"] seed = self.params["seed"] @@ -177,7 +192,7 @@ def _compute_metrics(self, sorting_analyzer, unit_ids=None, verbose=False, metri func = _misc_metric_name_to_func[metric_name] - params = qm_params[metric_name] if metric_name in qm_params else {} + params = metric_params[metric_name] if metric_name in metric_params else {} res = func(sorting_analyzer, unit_ids=non_empty_unit_ids, **params) # QM with uninstall dependencies might return None if res is not None: @@ -205,7 +220,7 @@ def _compute_metrics(self, sorting_analyzer, unit_ids=None, verbose=False, metri # sparsity=sparsity, progress_bar=progress_bar, n_jobs=n_jobs, - qm_params=qm_params, + metric_params=metric_params, seed=seed, ) for col, values in pc_metrics.items(): @@ -246,7 +261,7 @@ def _run(self, verbose=False, **job_kwargs): # append the metrics which were previously computed for metric_name in set(existing_metrics).difference(metrics_to_compute): # some metrics names produce data columns with other names. This deals with that. - for column_name in compute_name_to_column_names[metric_name]: + for column_name in qm_compute_name_to_column_names[metric_name]: computed_metrics[column_name] = qm_extension.data["metrics"][column_name] self.data["metrics"] = computed_metrics diff --git a/src/spikeinterface/qualitymetrics/quality_metric_list.py b/src/spikeinterface/qualitymetrics/quality_metric_list.py index 375dd320ae..fc7e92b50d 100644 --- a/src/spikeinterface/qualitymetrics/quality_metric_list.py +++ b/src/spikeinterface/qualitymetrics/quality_metric_list.py @@ -55,7 +55,7 @@ } # a dict converting the name of the metric for computation to the output of that computation -compute_name_to_column_names = { +qm_compute_name_to_column_names = { "num_spikes": ["num_spikes"], "firing_rate": ["firing_rate"], "presence_ratio": ["presence_ratio"], diff --git a/src/spikeinterface/qualitymetrics/tests/test_metrics_functions.py b/src/spikeinterface/qualitymetrics/tests/test_metrics_functions.py index 4c0890b62b..18b49cd862 100644 --- a/src/spikeinterface/qualitymetrics/tests/test_metrics_functions.py +++ b/src/spikeinterface/qualitymetrics/tests/test_metrics_functions.py @@ -39,7 +39,7 @@ compute_firing_ranges, compute_amplitude_cv_metrics, compute_sd_ratio, - get_synchrony_counts, + _get_synchrony_counts, compute_quality_metrics, ) @@ -69,7 +69,7 @@ def test_compute_new_quality_metrics(small_sorting_analyzer): assert calculated_metrics == ["snr"] small_sorting_analyzer.compute( - {"quality_metrics": {"metric_names": list(qm_params.keys()), "qm_params": qm_params}} + {"quality_metrics": {"metric_names": list(qm_params.keys()), "metric_params": qm_params}} ) small_sorting_analyzer.compute({"quality_metrics": {"metric_names": ["snr"]}}) @@ -96,13 +96,13 @@ def test_compute_new_quality_metrics(small_sorting_analyzer): # check that, when parameters are changed, the data and metadata are updated old_snr_data = deepcopy(quality_metric_extension.get_data()["snr"].values) small_sorting_analyzer.compute( - {"quality_metrics": {"metric_names": ["snr"], "qm_params": {"snr": {"peak_mode": "peak_to_peak"}}}} + {"quality_metrics": {"metric_names": ["snr"], "metric_params": {"snr": {"peak_mode": "peak_to_peak"}}}} ) new_quality_metric_extension = small_sorting_analyzer.get_extension("quality_metrics") new_snr_data = new_quality_metric_extension.get_data()["snr"].values assert np.all(old_snr_data != new_snr_data) - assert new_quality_metric_extension.params["qm_params"]["snr"]["peak_mode"] == "peak_to_peak" + assert new_quality_metric_extension.params["metric_params"]["snr"]["peak_mode"] == "peak_to_peak" # check that all quality metrics are deleted when parents are recomputed, even after # recomputation @@ -280,10 +280,10 @@ def test_unit_id_order_independence(small_sorting_analyzer): } quality_metrics_1 = compute_quality_metrics( - small_sorting_analyzer, metric_names=get_quality_metric_list(), qm_params=qm_params + small_sorting_analyzer, metric_names=get_quality_metric_list(), metric_params=qm_params ) quality_metrics_2 = compute_quality_metrics( - small_sorting_analyzer_2, metric_names=get_quality_metric_list(), qm_params=qm_params + small_sorting_analyzer_2, metric_names=get_quality_metric_list(), metric_params=qm_params ) for metric, metric_2_data in quality_metrics_2.items(): @@ -352,7 +352,7 @@ def test_synchrony_counts_no_sync(): one_spike["sample_index"] = spike_times one_spike["unit_index"] = spike_units - sync_count = get_synchrony_counts(one_spike, np.array((2)), [0]) + sync_count = _get_synchrony_counts(one_spike, np.array([2, 4, 8]), [0]) assert np.all(sync_count[0] == np.array([0])) @@ -372,7 +372,7 @@ def test_synchrony_counts_one_sync(): two_spikes["sample_index"] = np.concatenate((spike_indices, added_spikes_indices)) two_spikes["unit_index"] = np.concatenate((spike_labels, added_spikes_labels)) - sync_count = get_synchrony_counts(two_spikes, np.array((2)), [0, 1]) + sync_count = _get_synchrony_counts(two_spikes, np.array([2, 4, 8]), [0, 1]) assert np.all(sync_count[0] == np.array([1, 1])) @@ -392,7 +392,7 @@ def test_synchrony_counts_one_quad_sync(): four_spikes["sample_index"] = np.concatenate((spike_indices, added_spikes_indices)) four_spikes["unit_index"] = np.concatenate((spike_labels, added_spikes_labels)) - sync_count = get_synchrony_counts(four_spikes, np.array((2, 4)), [0, 1, 2, 3]) + sync_count = _get_synchrony_counts(four_spikes, np.array([2, 4, 8]), [0, 1, 2, 3]) assert np.all(sync_count[0] == np.array([1, 1, 1, 1])) assert np.all(sync_count[1] == np.array([1, 1, 1, 1])) @@ -409,7 +409,7 @@ def test_synchrony_counts_not_all_units(): three_spikes["sample_index"] = np.concatenate((spike_indices, added_spikes_indices)) three_spikes["unit_index"] = np.concatenate((spike_labels, added_spikes_labels)) - sync_count = get_synchrony_counts(three_spikes, np.array((2)), [0, 1, 2]) + sync_count = _get_synchrony_counts(three_spikes, np.array([2, 4, 8]), [0, 1, 2]) assert np.all(sync_count[0] == np.array([0, 1, 1])) @@ -610,9 +610,9 @@ def test_calculate_rp_violations(sorting_analyzer_violations): def test_synchrony_metrics(sorting_analyzer_simple): sorting_analyzer = sorting_analyzer_simple sorting = sorting_analyzer.sorting - synchrony_sizes = (2, 3, 4) - synchrony_metrics = compute_synchrony_metrics(sorting_analyzer, synchrony_sizes=synchrony_sizes) - print(synchrony_metrics) + synchrony_metrics = compute_synchrony_metrics(sorting_analyzer) + + synchrony_sizes = np.array([2, 4, 8]) # check returns for size in synchrony_sizes: @@ -625,10 +625,8 @@ def test_synchrony_metrics(sorting_analyzer_simple): sorting_sync = add_synchrony_to_sorting(sorting, sync_event_ratio=sync_level) sorting_analyzer_sync = create_sorting_analyzer(sorting_sync, sorting_analyzer.recording, format="memory") - previous_synchrony_metrics = compute_synchrony_metrics( - previous_sorting_analyzer, synchrony_sizes=synchrony_sizes - ) - current_synchrony_metrics = compute_synchrony_metrics(sorting_analyzer_sync, synchrony_sizes=synchrony_sizes) + previous_synchrony_metrics = compute_synchrony_metrics(previous_sorting_analyzer) + current_synchrony_metrics = compute_synchrony_metrics(sorting_analyzer_sync) print(current_synchrony_metrics) # check that all values increased for i, col in enumerate(previous_synchrony_metrics._fields): @@ -647,22 +645,17 @@ def test_synchrony_metrics_unit_id_subset(sorting_analyzer_simple): unit_ids_subset = [3, 7] - synchrony_sizes = (2,) - (synchrony_metrics,) = compute_synchrony_metrics( - sorting_analyzer_simple, synchrony_sizes=synchrony_sizes, unit_ids=unit_ids_subset - ) + synchrony_metrics = compute_synchrony_metrics(sorting_analyzer_simple, unit_ids=unit_ids_subset) - assert list(synchrony_metrics.keys()) == [3, 7] + assert list(synchrony_metrics.sync_spike_2.keys()) == [3, 7] + assert list(synchrony_metrics.sync_spike_4.keys()) == [3, 7] + assert list(synchrony_metrics.sync_spike_8.keys()) == [3, 7] def test_synchrony_metrics_no_unit_ids(sorting_analyzer_simple): - # all_unit_ids = sorting_analyzer_simple.sorting.unit_ids - - synchrony_sizes = (2,) - (synchrony_metrics,) = compute_synchrony_metrics(sorting_analyzer_simple, synchrony_sizes=synchrony_sizes) - - assert np.all(list(synchrony_metrics.keys()) == sorting_analyzer_simple.unit_ids) + synchrony_metrics = compute_synchrony_metrics(sorting_analyzer_simple) + assert np.all(list(synchrony_metrics.sync_spike_2.keys()) == sorting_analyzer_simple.unit_ids) @pytest.mark.sortingcomponents diff --git a/src/spikeinterface/qualitymetrics/tests/test_quality_metric_calculator.py b/src/spikeinterface/qualitymetrics/tests/test_quality_metric_calculator.py index a6415c58e8..60f0490f51 100644 --- a/src/spikeinterface/qualitymetrics/tests/test_quality_metric_calculator.py +++ b/src/spikeinterface/qualitymetrics/tests/test_quality_metric_calculator.py @@ -24,14 +24,14 @@ def test_compute_quality_metrics(sorting_analyzer_simple): metrics = compute_quality_metrics( sorting_analyzer, metric_names=["snr"], - qm_params=dict(isi_violation=dict(isi_threshold_ms=2)), + metric_params=dict(isi_violation=dict(isi_threshold_ms=2)), skip_pc_metrics=True, seed=2205, ) # print(metrics) qm = sorting_analyzer.get_extension("quality_metrics") - assert qm.params["qm_params"]["isi_violation"]["isi_threshold_ms"] == 2 + assert qm.params["metric_params"]["isi_violation"]["isi_threshold_ms"] == 2 assert "snr" in metrics.columns assert "isolation_distance" not in metrics.columns @@ -40,7 +40,7 @@ def test_compute_quality_metrics(sorting_analyzer_simple): metrics = compute_quality_metrics( sorting_analyzer, metric_names=None, - qm_params=dict(isi_violation=dict(isi_threshold_ms=2)), + metric_params=dict(isi_violation=dict(isi_threshold_ms=2)), skip_pc_metrics=False, seed=2205, ) @@ -54,7 +54,7 @@ def test_compute_quality_metrics_recordingless(sorting_analyzer_simple): metrics = compute_quality_metrics( sorting_analyzer, metric_names=None, - qm_params=dict(isi_violation=dict(isi_threshold_ms=2)), + metric_params=dict(isi_violation=dict(isi_threshold_ms=2)), skip_pc_metrics=False, seed=2205, ) @@ -68,7 +68,7 @@ def test_compute_quality_metrics_recordingless(sorting_analyzer_simple): metrics_norec = compute_quality_metrics( sorting_analyzer_norec, metric_names=None, - qm_params=dict(isi_violation=dict(isi_threshold_ms=2)), + metric_params=dict(isi_violation=dict(isi_threshold_ms=2)), skip_pc_metrics=False, seed=2205, ) @@ -101,7 +101,7 @@ def test_empty_units(sorting_analyzer_simple): metrics_empty = compute_quality_metrics( sorting_analyzer_empty, metric_names=None, - qm_params=dict(isi_violation=dict(isi_threshold_ms=2)), + metric_params=dict(isi_violation=dict(isi_threshold_ms=2)), skip_pc_metrics=True, seed=2205, ) diff --git a/src/spikeinterface/widgets/unit_waveforms.py b/src/spikeinterface/widgets/unit_waveforms.py index c593836061..3b31eacee5 100644 --- a/src/spikeinterface/widgets/unit_waveforms.py +++ b/src/spikeinterface/widgets/unit_waveforms.py @@ -565,7 +565,7 @@ def _update_plot(self, change): channel_locations = self.sorting_analyzer.get_channel_locations() else: unit_indices = [list(self.templates.unit_ids).index(unit_id) for unit_id in unit_ids] - templates = self.templates.templates_array[unit_indices] + templates = self.templates.get_dense_templates()[unit_indices] templates_shadings = None channel_locations = self.templates.get_channel_locations()