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Commit cb38613

Browse files
Remove deprecations for 0.104.0 (#4425)
Co-authored-by: Chris Halcrow <57948917+chrishalcrow@users.noreply.github.com> Co-authored-by: chrishalcrow
1 parent 3abdda8 commit cb38613

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23 files changed

+13
-594
lines changed
  • doc
    • api.rst
    • get_started
      • quickstart.rst
  • examples
    • get_started
      • quickstart.py
    • tutorials/core
      • plot_1_recording_extractor.py
      • plot_2_sorting_extractor.py
  • src/spikeinterface
    • benchmark
      • benchmark_base.py
    • comparison
      • __init__.py
      • hybrid.py
      • tests
        • test_hybrid.py
    • core
      • __init__.py
      • job_tools.py
      • loading.py
      • numpyextractors.py
      • tests
        • test_sorting_folder.py
    • extractors
      • __init__.py
      • neoextractors
        • openephys.py
      • neuropixels_utils.py
    • postprocessing
      • template_similarity.py
    • sorters/internal
      • simplesorter.py
    • widgets
      • amplitudes.py
      • motion.py
      • rasters.py
      • sorting_summary.py

23 files changed

+13
-594
lines changed

doc/api.rst

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@@ -287,8 +287,6 @@ spikeinterface.comparison
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.. autofunction:: compare_sorter_to_ground_truth
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.. autofunction:: compare_templates
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.. autofunction:: compare_multiple_templates
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.. autofunction:: create_hybrid_units_recording
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.. autofunction:: create_hybrid_spikes_recording
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.. autoclass:: GroundTruthComparison
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:members:

doc/get_started/quickstart.rst

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@@ -247,7 +247,7 @@ object to disk.
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To reload a preprocessed recording that was saved to disk, you can use
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``load_extractor()`` function from the ``core`` module.
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``load()`` function from the ``core`` module.
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Now you are ready to spike sort using the ``spikeinterface.sorters``
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module! Let's first check which sorters are implemented and which are

examples/get_started/quickstart.py

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@@ -159,7 +159,7 @@
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print(recording_preprocessed)
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# -
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# To reload a preprocessed recording that was saved to disk, you can use `load_extractor()` function from the `core` module.
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# To reload a preprocessed recording that was saved to disk, you can use `load()` function from the `core` module.
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#
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# Now you are ready to spike sort using the `spikeinterface.sorters` module!
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# Let's first check which sorters are implemented and which are installed

examples/tutorials/core/plot_1_recording_extractor.py

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@@ -151,21 +151,21 @@
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# The "dump" operation is lazy, i.e., the traces are not exported.
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# Only the information about how to reconstruct the recording are dumped:
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from spikeinterface import load_extractor
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from spikeinterface import load
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from pprint import pprint
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d = recording2.to_dict()
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pprint(d)
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recording2_loaded = load_extractor(d)
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recording2_loaded = load(d)
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print(recording2_loaded)
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###############################################################################
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# The dictionary can also be dumped directly to a JSON file on disk:
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recording2.dump("my_recording.json")
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recording2_loaded = load_extractor("my_recording.json")
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recording2_loaded = load("my_recording.json")
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print(recording2_loaded)
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###############################################################################
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pprint(os.listdir("./my_recording"))
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recording2_cached = load_extractor("my_recording.json")
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recording2_cached = load("my_recording.json")
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print(recording2_cached)

examples/tutorials/core/plot_2_sorting_extractor.py

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@@ -103,21 +103,21 @@
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# The "dump" operation is lazy, i.e., the spike trains are not exported.
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# Only the information about how to reconstruct the sorting are dumped:
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from spikeinterface import load_extractor
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from spikeinterface import load
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from pprint import pprint
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d = sorting2.to_dict()
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pprint(d)
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sorting2_loaded = load_extractor(d)
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sorting2_loaded = load(d)
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print(sorting2_loaded)
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###############################################################################
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# The dictionary can also be dumped directly to a JSON file on disk:
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sorting2.dump("my_sorting.json")
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sorting2_loaded = load_extractor("my_sorting.json")
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sorting2_loaded = load("my_sorting.json")
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print(sorting2_loaded)
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###############################################################################
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pprint(os.listdir("./my_sorting"))
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sorting2_cached = load_extractor("./my_sorting")
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sorting2_cached = load("./my_sorting")
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print(sorting2_cached)

src/spikeinterface/benchmark/benchmark_base.py

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@@ -654,8 +654,6 @@ def load_folder(cls, folder):
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with open(file, mode="rb") as f:
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result[k] = pickle.load(f)
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elif format == "sorting":
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from spikeinterface.core import load_extractor
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sorting_folder = folder / k
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if sorting_folder.exists():
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result[k] = load(sorting_folder)

src/spikeinterface/comparison/__init__.py

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@@ -32,11 +32,3 @@
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from .groundtruthstudy import GroundTruthStudy
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from .collision import CollisionGTComparison
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from .correlogram import CorrelogramGTComparison
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from .hybrid import (
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HybridSpikesRecording,
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HybridUnitsRecording,
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generate_sorting_to_inject,
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create_hybrid_units_recording,
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create_hybrid_spikes_recording,
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)

src/spikeinterface/comparison/hybrid.py

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