accusleepy 0.10.0__tar.gz → 0.10.1__tar.gz

{accusleepy-0.10.0 → accusleepy-0.10.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: accusleepy
-Version: 0.10.0
+Version: 0.10.1
 Summary: Python implementation of AccuSleep
 License: GPL-3.0-only
 Author: Zeke Barger
@@ -11,14 +11,12 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
-Requires-Dist: fastparquet (>=2024.11.0,<2025.0.0)
-Requires-Dist: joblib (>=1.4.2,<2.0.0)
 Requires-Dist: matplotlib (>=3.10.1,<4.0.0)
 Requires-Dist: numpy (>=2.2.4,<3.0.0)
 Requires-Dist: pandas (>=2.2.3,<3.0.0)
 Requires-Dist: pillow (>=11.1.0,<12.0.0)
-Requires-Dist: pre-commit (>=4.2.0,<5.0.0)
-Requires-Dist: pyside6 (>=6.9.0,<6.9.3)
+Requires-Dist: pyarrow (>=23.0.0,<24.0.0)
+Requires-Dist: pyside6 (>=6.10.1,<7.0.0)
 Requires-Dist: scipy (>=1.15.2,<2.0.0)
 Requires-Dist: torch (>=2.8.0,<3.0.0)
 Requires-Dist: torchvision (>=0.23.0,<1.0.0)
@@ -79,10 +77,8 @@ please consult the [developer guide](accusleepy/gui/text/dev_guide.md).
 
 ## Changelog
 
-- 0.10.0: Improved zoom behavior
-- 0.8.1-0.9.3: Improved error handling and code quality
-- 0.8.0: More configurable settings, visual improvements
-- 0.7.1-0.7.3: Bugfixes, code cleanup
+- 0.10.0-0.10.1: Improved zoom behavior, updated dependencies
+- 0.7.1-0.9.3: Bugfixes, code cleanup, additional config settings
 - 0.7.0: More settings can be configured in the UI
 - 0.6.0: Confidence scores can now be displayed and saved. Retraining your models is recommended
     since the new calibration feature will make the confidence scores more accurate.

{accusleepy-0.10.0 → accusleepy-0.10.1}/README.md

@@ -52,10 +52,8 @@ please consult the [developer guide](accusleepy/gui/text/dev_guide.md).
 
 ## Changelog
 
-- 0.10.0: Improved zoom behavior
-- 0.8.1-0.9.3: Improved error handling and code quality
-- 0.8.0: More configurable settings, visual improvements
-- 0.7.1-0.7.3: Bugfixes, code cleanup
+- 0.10.0-0.10.1: Improved zoom behavior, updated dependencies
+- 0.7.1-0.9.3: Bugfixes, code cleanup, additional config settings
 - 0.7.0: More settings can be configured in the UI
 - 0.6.0: Confidence scores can now be displayed and saved. Retraining your models is recommended
     since the new calibration feature will make the confidence scores more accurate.

accusleepy-0.10.1/accusleepy/__init__.py

@@ -0,0 +1 @@
+"""AccuSleePy: Python implementation of AccuSleep for automated sleep scoring."""

{accusleepy-0.10.0 → accusleepy-0.10.1}/accusleepy/__main__.py

@@ -1,3 +1,5 @@
+"""Entry point for running AccuSleePy as a module (python -m accusleepy)."""
+
 from accusleepy.gui.main import run_primary_window
 
 if __name__ == "__main__":

{accusleepy-0.10.0 → accusleepy-0.10.1}/accusleepy/bouts.py

@@ -1,3 +1,5 @@
+"""Brain state bout length enforcement."""
+
 import re
 from dataclasses import dataclass
 from operator import attrgetter

{accusleepy-0.10.0 → accusleepy-0.10.1}/accusleepy/brain_state_set.py

@@ -1,3 +1,5 @@
+"""Define and organize brain states."""
+
 from dataclasses import dataclass
 
 import numpy as np

{accusleepy-0.10.0 → accusleepy-0.10.1}/accusleepy/classification.py

@@ -1,3 +1,5 @@
+"""Model training and brain state classification."""
+
 import os
 
 import numpy as np

{accusleepy-0.10.0 → accusleepy-0.10.1}/accusleepy/constants.py

@@ -1,3 +1,5 @@
+"""Application-wide constants and default settings."""
+
 import numpy as np
 
 # probably don't change these unless you really need to

{accusleepy-0.10.0 → accusleepy-0.10.1}/accusleepy/fileio.py

@@ -1,3 +1,5 @@
+"""File I/O for recordings, labels, calibration data, and configuration."""
+
 import json
 import os
 from dataclasses import dataclass
@@ -5,7 +7,6 @@ from importlib.metadata import version, PackageNotFoundError
 
 import numpy as np
 import pandas as pd
-from PySide6.QtWidgets import QListWidgetItem
 
 from accusleepy.brain_state_set import BRAIN_STATES_KEY, BrainState, BrainStateSet
 import accusleepy.constants as c
@@ -55,7 +56,6 @@ class Recording:
     label_file: str = ""  # path to label file
     calibration_file: str = ""  # path to calibration file
     sampling_rate: int | float = 0.0  # sampling rate, in Hz
-    widget: QListWidgetItem = None  # list item widget shown in the GUI
 
 
 def load_calibration_file(filename: str) -> tuple[np.ndarray, np.ndarray]:

accusleepy-0.10.1/accusleepy/gui/__init__.py

@@ -0,0 +1 @@
+"""Graphical user interface components for AccuSleePy."""

{accusleepy-0.10.0 → accusleepy-0.10.1}/accusleepy/gui/main.py

@@ -1,5 +1,7 @@
-# AccuSleePy main window
-# Icon source: Arkinasi, https://www.flaticon.com/authors/arkinasi
+"""AccuSleePy main window.
+
+Icon source: Arkinasi, https://www.flaticon.com/authors/arkinasi
+"""
 
 import logging
 import os

{accusleepy-0.10.0 → accusleepy-0.10.1}/accusleepy/gui/manual_scoring.py

@@ -1,8 +1,9 @@
-# AccuSleePy manual scoring GUI
-# Icon sources:
-#   Arkinasi, https://www.flaticon.com/authors/arkinasi
-#   kendis lasman, https://www.flaticon.com/packs/ui-79
+"""AccuSleePy manual scoring GUI.
 
+Icon sources:
+    Arkinasi, https://www.flaticon.com/authors/arkinasi
+    kendis lasman, https://www.flaticon.com/packs/ui-79
+"""
 
 import copy
 import os
@@ -85,8 +86,8 @@ BRIGHTER_SCALE_FACTOR = 0.96
 DIMMER_SCALE_FACTOR = 1.07
 # zoom factor for upper plots - larger values = bigger changes
 ZOOM_FACTOR = 0.1
-# interval in seconds between zoom events triggered by scrolling
-ZOOM_DELAY = 0.05
+# rate limit for zoom events triggered by scrolling
+MAX_SCROLL_EVENTS_PER_SEC = 24
 
 
 @dataclass
@@ -983,11 +984,15 @@ class ManualScoringWindow(QDialog):
             return
 
         self.now_zooming = True
+        start_time = time.time()
         if event.button == "up":
             self.zoom_x(direction=ZOOM_IN)
         else:
             self.zoom_x(direction=ZOOM_OUT)
-        time.sleep(ZOOM_DELAY)
+        end_time = time.time()
+        time_elapsed = end_time - start_time
+        if time_elapsed < 1 / MAX_SCROLL_EVENTS_PER_SEC:
+            time.sleep(1 / MAX_SCROLL_EVENTS_PER_SEC - time_elapsed)
         self.now_zooming = False
 
 

{accusleepy-0.10.0 → accusleepy-0.10.1}/accusleepy/gui/mplwidget.py

@@ -1,4 +1,5 @@
-# Widget with a matplotlib FigureCanvas for manual scoring
+"""Matplotlib FigureCanvas widget for manual scoring."""
+
 from collections.abc import Callable
 
 import matplotlib.ticker as mticker

{accusleepy-0.10.0 → accusleepy-0.10.1}/accusleepy/gui/recording_manager.py

@@ -1,11 +1,20 @@
 """Recording list manager"""
 
+from dataclasses import dataclass
+
 from PySide6.QtCore import QObject
 from PySide6.QtWidgets import QListWidget, QListWidgetItem
 
 from accusleepy.fileio import Recording, load_recording_list, save_recording_list
 
 
+@dataclass
+class RecordingListItem(Recording):
+    """A Recording with an associated QListWidget item for the GUI"""
+
+    widget: QListWidgetItem = None
+
+
 class RecordingListManager(QObject):
     """Manages the list of recordings and the associated QListWidget"""
 
@@ -14,19 +23,19 @@ class RecordingListManager(QObject):
         self._widget = list_widget
 
         # Create initial empty recording (there is always at least one)
-        first_recording = Recording(
+        first_recording = RecordingListItem(
             widget=QListWidgetItem("Recording 1", self._widget),
         )
-        self._recordings: list[Recording] = [first_recording]
+        self._recordings: list[RecordingListItem] = [first_recording]
         self._widget.addItem(first_recording.widget)
         self._widget.setCurrentRow(0)
 
     @property
-    def current(self) -> Recording:
+    def current(self) -> RecordingListItem:
         """The currently selected recording"""
         return self._recordings[self._widget.currentRow()]
 
-    def add(self, sampling_rate: int | float) -> Recording:
+    def add(self, sampling_rate: int | float) -> RecordingListItem:
         """Add a new recording to the list
 
         :param sampling_rate: sampling rate for the new recording
@@ -35,7 +44,7 @@ class RecordingListManager(QObject):
         new_name = max(r.name for r in self._recordings) + 1
 
         # Create recording with widget
-        recording = Recording(
+        recording = RecordingListItem(
             name=new_name,
             sampling_rate=sampling_rate,
             widget=QListWidgetItem(f"Recording {new_name}", self._widget),
@@ -63,7 +72,7 @@ class RecordingListManager(QObject):
         else:
             # Reset the single recording to defaults
             recording_name = self._recordings[0].name
-            self._recordings[0] = Recording(widget=self._recordings[0].widget)
+            self._recordings[0] = RecordingListItem(widget=self._recordings[0].widget)
             self._recordings[0].widget.setText(f"Recording {self._recordings[0].name}")
             return f"cleared Recording {recording_name}"
 
@@ -85,14 +94,15 @@ class RecordingListManager(QObject):
         try:
             self._widget.clear()
 
-            # Load recordings
-            self._recordings = load_recording_list(filename)
-
-            # Create widgets for each recording
-            for recording in self._recordings:
-                recording.widget = QListWidgetItem(
-                    f"Recording {recording.name}", self._widget
+            # Load recordings and create widgets
+            self._recordings = [
+                RecordingListItem(
+                    **r.__dict__,
+                    widget=QListWidgetItem(f"Recording {r.name}", self._widget),
                 )
+                for r in load_recording_list(filename)
+            ]
+            for recording in self._recordings:
                 self._widget.addItem(recording.widget)
         finally:
             self._widget.blockSignals(False)
@@ -106,5 +116,5 @@ class RecordingListManager(QObject):
     def __len__(self):
         return len(self._recordings)
 
-    def __getitem__(self, index: int) -> Recording:
+    def __getitem__(self, index: int) -> RecordingListItem:
         return self._recordings[index]

{accusleepy-0.10.0 → accusleepy-0.10.1}/accusleepy/models.py

@@ -1,3 +1,5 @@
+"""Neural network model definitions for sleep stage classification."""
+
 from torch import device, flatten, nn
 from torch import load as torch_load
 from torch import save as torch_save

{accusleepy-0.10.0 → accusleepy-0.10.1}/accusleepy/multitaper.py

@@ -14,10 +14,6 @@ import timeit
 import warnings
 
 import numpy as np
-from joblib import Parallel, cpu_count, delayed
-
-# from scipy.signal import detrend # unused by AccuSleePy
-# from scipy.signal.windows import dpss # lazily loaded later
 
 
 # MULTITAPER SPECTROGRAM #
@@ -206,19 +202,9 @@ def spectrogram(
         wt,
     )
 
-    if multiprocess:  # use multiprocessing
-        n_jobs = max(cpu_count() - 1, 1) if n_jobs is None else n_jobs
-        mt_spectrogram = np.vstack(
-            Parallel(n_jobs=n_jobs)(
-                delayed(calc_mts_segment)(data_segments[num_window, :], *mts_params)
-                for num_window in range(num_windows)
-            )
-        )
-
-    else:  # if no multiprocessing, compute normally
-        mt_spectrogram = np.apply_along_axis(
-            calc_mts_segment, 1, data_segments, *mts_params
-        )
+    mt_spectrogram = np.apply_along_axis(
+        calc_mts_segment, 1, data_segments, *mts_params
+    )
 
     # Compute one-sided PSD spectrum
     mt_spectrogram = mt_spectrogram.T
@@ -251,37 +237,6 @@ def spectrogram(
     if np.all(mt_spectrogram.flatten() == 0):
         print("\n Data was all zeros, no output")
 
-    # # Plot multitaper spectrogram
-    # if plot_on:
-    #     # convert from power to dB
-    #     spect_data = nanpow2db(mt_spectrogram)
-    #
-    #     # Set x and y axes
-    #     dx = stimes[1] - stimes[0]
-    #     dy = sfreqs[1] - sfreqs[0]
-    #     extent = [stimes[0] - dx, stimes[-1] + dx, sfreqs[-1] + dy, sfreqs[0] - dy]
-    #
-    #     # Plot spectrogram
-    #     if ax is None:
-    #         fig, ax = plt.subplots()
-    #     else:
-    #         fig = ax.get_figure()
-    #     im = ax.imshow(spect_data, extent=extent, aspect="auto")
-    #     fig.colorbar(im, ax=ax, label="PSD (dB)", shrink=0.8)
-    #     ax.set_xlabel("Time (HH:MM:SS)")
-    #     ax.set_ylabel("Frequency (Hz)")
-    #     im.set_cmap(plt.cm.get_cmap("cet_rainbow4"))
-    #     ax.invert_yaxis()
-    #
-    #     # Scale colormap
-    #     if clim_scale:
-    #         clim = np.percentile(spect_data, [5, 98])  # from 5th percentile to 98th
-    #         im.set_clim(clim)  # actually change colorbar scale
-    #
-    #     fig.show()
-    #     if return_fig:
-    #         return mt_spectrogram, stimes, sfreqs, (fig, ax)
-
     return mt_spectrogram, stimes, sfreqs
 
 
@@ -568,18 +523,6 @@ def nanpow2db(y):
     return ydB
 
 
-# Helper #
-def is_outlier(data):
-    smad = 1.4826 * np.median(
-        abs(data - np.median(data))
-    )  # scaled median absolute deviation
-    outlier_mask = (
-        abs(data - np.median(data)) > 3 * smad
-    )  # outliers are more than 3 smads away from median
-    outlier_mask = outlier_mask | np.isnan(data) | np.isinf(data)
-    return outlier_mask
-
-
 # CALCULATE MULTITAPER SPECTRUM ON SINGLE SEGMENT
 def calc_mts_segment(
     data_segment,

{accusleepy-0.10.0 → accusleepy-0.10.1}/accusleepy/signal_processing.py

@@ -1,3 +1,5 @@
+"""EEG/EMG signal processing, mixture z-scoring, and training image generation."""
+
 import logging
 import os
 import warnings

{accusleepy-0.10.0 → accusleepy-0.10.1}/accusleepy/temperature_scaling.py

@@ -1,3 +1,5 @@
+"""Temperature scaling for model confidence calibration."""
+
 import logging
 
 import numpy as np

{accusleepy-0.10.0 → accusleepy-0.10.1}/accusleepy/validation.py

@@ -1,3 +1,5 @@
+"""Validation utilities for brain state labels and recordings."""
+
 import numpy as np
 
 from accusleepy.brain_state_set import BrainStateSet

{accusleepy-0.10.0 → accusleepy-0.10.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "accusleepy"
-version = "0.10.0"
+version = "0.10.1"
 description = "Python implementation of AccuSleep"
 authors = [
     {name = "Zeke Barger",email = "zekebarger@gmail.com"}
@@ -15,15 +15,14 @@ dependencies = [
     "torchvision (>=0.23.0,<1.0.0)",
     "scipy (>=1.15.2,<2.0.0)",
     "matplotlib (>=3.10.1,<4.0.0)",
-    "joblib (>=1.4.2,<2.0.0)",
     "pillow (>=11.1.0,<12.0.0)",
-    "fastparquet (>=2024.11.0,<2025.0.0)",
-    "pre-commit (>=4.2.0,<5.0.0)",
     "tqdm (>=4.67.1,<5.0.0)",
-    "pyside6 (>=6.9.0, <6.9.3)",
+    "pyside6 (>=6.10.1,<7.0.0)",
+    "pyarrow (>=23.0.0,<24.0.0)",
 ]
 
 [tool.poetry.group.dev.dependencies]
+pre-commit = ">=4.2.0,<5.0.0"
 pytest = ">=8.3.5,<9.0.0"
 pytest-qt = ">=4.4.0,<5.0.0"
 ruff = ">=0.11.2,<0.12.0"