accusleepy 0.9.3__tar.gz → 0.10.1__tar.gz

{accusleepy-0.9.3 → accusleepy-0.10.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: accusleepy
-Version: 0.9.3
+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)
@@ -79,9 +77,8 @@ please consult the [developer guide](accusleepy/gui/text/dev_guide.md).
 
 ## Changelog
 
-- 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-0.9.3 → accusleepy-0.10.1}/README.md

@@ -52,9 +52,8 @@ please consult the [developer guide](accusleepy/gui/text/dev_guide.md).
 
 ## Changelog
 
-- 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-0.9.3 → 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-0.9.3 → 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-0.9.3 → 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-0.9.3 → accusleepy-0.10.1}/accusleepy/classification.py

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

{accusleepy-0.9.3 → accusleepy-0.10.1}/accusleepy/config.json

@@ -35,5 +35,6 @@
         "training_epochs": 6
     },
     "epochs_to_show": 5,
-    "autoscroll_state": false
+    "autoscroll_state": false,
+    "delete_training_images": true
 }

{accusleepy-0.9.3 → 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
@@ -72,6 +74,7 @@ EMG_FILTER_KEY = "emg_filter"
 HYPERPARAMETERS_KEY = "hyperparameters"
 EPOCHS_TO_SHOW_KEY = "epochs_to_show"
 AUTOSCROLL_KEY = "autoscroll_state"
+DELETE_TRAINING_IMAGES_KEY = "delete_training_images"
 
 # default values
 # default UI settings
@@ -87,6 +90,7 @@ DEFAULT_BATCH_SIZE = 64
 DEFAULT_LEARNING_RATE = 1e-3
 DEFAULT_MOMENTUM = 0.9
 DEFAULT_TRAINING_EPOCHS = 6
+DEFAULT_DELETE_TRAINING_IMAGES_STATE = True
 # default manual scoring settings
 DEFAULT_EPOCHS_TO_SHOW = 5
 DEFAULT_AUTOSCROLL_STATE = False

{accusleepy-0.9.3 → 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
@@ -43,6 +44,7 @@ class AccuSleePyConfig:
     hyperparameters: Hyperparameters
     epochs_to_show: int
     autoscroll_state: bool
+    delete_training_images: bool
 
 
 @dataclass
@@ -54,7 +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]:
@@ -139,7 +140,8 @@ def load_config() -> AccuSleePyConfig:
         EMG filter parameters,
         model training hyperparameters,
         default epochs to show for manual scoring,
-        default autoscroll state for manual scoring
+        default autoscroll state for manual scoring,
+        setting to delete training images automatically
     """
     with open(
         os.path.join(os.path.dirname(os.path.abspath(__file__)), c.CONFIG_FILE), "r"
@@ -183,6 +185,9 @@ def load_config() -> AccuSleePyConfig:
         ),
         epochs_to_show=data.get(c.EPOCHS_TO_SHOW_KEY, c.DEFAULT_EPOCHS_TO_SHOW),
         autoscroll_state=data.get(c.AUTOSCROLL_KEY, c.DEFAULT_AUTOSCROLL_STATE),
+        delete_training_images=data.get(
+            c.DELETE_TRAINING_IMAGES_KEY, c.DEFAULT_DELETE_TRAINING_IMAGES_STATE
+        ),
     )
 
 
@@ -196,6 +201,7 @@ def save_config(
     hyperparameters: Hyperparameters,
     epochs_to_show: int,
     autoscroll_state: bool,
+    delete_training_images: bool,
 ) -> None:
     """Save configuration of brain state options to json file
 
@@ -210,6 +216,8 @@ def save_config(
     :param hyperparameters: model training hyperparameters
     :param epochs_to_show: default epochs to show for manual scoring,
     :param autoscroll_state: default autoscroll state for manual scoring
+    :param delete_training_images: whether to automatically delete images
+        created for model training once training is complete
     """
     output_dict = brain_state_set.to_output_dict()
     output_dict.update({c.DEFAULT_EPOCH_LENGTH_KEY: default_epoch_length})
@@ -220,6 +228,7 @@ def save_config(
     output_dict.update({c.HYPERPARAMETERS_KEY: hyperparameters.__dict__})
     output_dict.update({c.EPOCHS_TO_SHOW_KEY: epochs_to_show})
     output_dict.update({c.AUTOSCROLL_KEY: autoscroll_state})
+    output_dict.update({c.DELETE_TRAINING_IMAGES_KEY: delete_training_images})
     with open(
         os.path.join(os.path.dirname(os.path.abspath(__file__)), c.CONFIG_FILE), "w"
     ) as f:

accusleepy-0.10.1/accusleepy/gui/__init__.py

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

{accusleepy-0.9.3 → 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
@@ -76,7 +78,6 @@ class TrainingSettings:
     """Settings for training a new model"""
 
     epochs_per_img: int = 9
-    delete_images: bool = True
     model_type: str = DEFAULT_MODEL_TYPE
     calibrate: bool = True
 
@@ -176,9 +177,6 @@ class AccuSleepWindow(QMainWindow):
         self.ui.image_number_input.valueChanged.connect(
             lambda v: setattr(self.training, "epochs_per_img", v)
         )
-        self.ui.delete_image_box.stateChanged.connect(
-            lambda v: setattr(self.training, "delete_images", bool(v))
-        )
         self.ui.calibrate_checkbox.stateChanged.connect(
             self.update_training_calibration
         )
@@ -304,7 +302,7 @@ class AccuSleepWindow(QMainWindow):
             emg_filter=self.config.emg_filter,
             hyperparameters=self.config.hyperparameters,
             model_filename=model_filename,
-            delete_images=self.training.delete_images,
+            delete_images=self.config.delete_training_images,
         )
 
         # Display results

{accusleepy-0.9.3 → accusleepy-0.10.1}/accusleepy/gui/manual_scoring.py

@@ -1,11 +1,13 @@
-# 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
+import time
 from dataclasses import dataclass
 from functools import partial
 from types import SimpleNamespace
@@ -82,9 +84,10 @@ UNDO_LIMIT = 1000
 # brightness scaling factors for the spectrogram
 BRIGHTER_SCALE_FACTOR = 0.96
 DIMMER_SCALE_FACTOR = 1.07
-# zoom factor for upper plots
-ZOOM_IN_FACTOR = 0.45
-ZOOM_OUT_FACTOR = 1.017
+# zoom factor for upper plots - larger values = bigger changes
+ZOOM_FACTOR = 0.1
+# rate limit for zoom events triggered by scrolling
+MAX_SCROLL_EVENTS_PER_SEC = 24
 
 
 @dataclass
@@ -352,8 +355,10 @@ class ManualScoringWindow(QDialog):
         )
         keypress_redo.activated.connect(self.redo)
 
-        # user input: clicks
+        # user input: mouse events
         self.ui.upperfigure.canvas.mpl_connect("button_press_event", self.click_to_jump)
+        self.ui.upperfigure.canvas.mpl_connect("scroll_event", self.scroll_zoom)
+        self.now_zooming = False  # impose timeout on zoom events
 
         # user input: buttons
         self.ui.savebutton.clicked.connect(self.save)
@@ -483,7 +488,7 @@ class ManualScoringWindow(QDialog):
 
     def closeEvent(self, event: QCloseEvent) -> None:
         """Check if there are unsaved changes before closing"""
-        if not all(self.labels == self.last_saved_labels):
+        if not np.array_equal(self.labels, self.last_saved_labels):
             result = QMessageBox.question(
                 self,
                 "Unsaved changes",
@@ -668,6 +673,8 @@ class ManualScoringWindow(QDialog):
             self.label_display_options,
         )
         self.update_figures()
+        # upper plot x limits might need to change
+        self.zoom_x(direction=None)
 
     def update_signal_offset(self, signal: str, direction: str) -> None:
         """Shift EEG or EMG up or down
@@ -713,39 +720,19 @@ class ManualScoringWindow(QDialog):
             (self.upper_left_epoch, self.upper_right_epoch + 1)
         )
 
-    def zoom_x(self, direction: str) -> None:
+    def zoom_x(self, direction: str | None) -> None:
         """Change upper figure x-axis zoom level
 
-        :param direction: in, out, or reset
+        :param direction: in, out, reset, or None
         """
-        epochs_shown = self.upper_right_epoch - self.upper_left_epoch + 1
-        if direction == ZOOM_IN:
-            self.upper_left_epoch = max(
-                [
-                    self.upper_left_epoch,
-                    round(self.epoch - ZOOM_IN_FACTOR * epochs_shown),
-                ]
-            )
-
-            self.upper_right_epoch = min(
-                [
-                    self.upper_right_epoch,
-                    round(self.epoch + ZOOM_IN_FACTOR * epochs_shown),
-                ]
-            )
-
-        elif direction == ZOOM_OUT:
-            self.upper_left_epoch = max(
-                [0, round(self.epoch - ZOOM_OUT_FACTOR * epochs_shown)]
-            )
-
-            self.upper_right_epoch = min(
-                [self.n_epochs - 1, round(self.epoch + ZOOM_OUT_FACTOR * epochs_shown)]
-            )
-
-        else:  # reset
-            self.upper_left_epoch = 0
-            self.upper_right_epoch = self.n_epochs - 1
+        self.upper_left_epoch, self.upper_right_epoch = find_new_x_limits(
+            direction=direction,
+            left_epoch=self.upper_left_epoch,
+            right_epoch=self.upper_right_epoch,
+            min_n_shown=self.epochs_to_show,
+            total_epochs=self.n_epochs,
+            selected_epoch=self.epoch,
+        )
         self.adjust_upper_figure_x_limits()
         self.ui.upperfigure.canvas.draw()
 
@@ -806,8 +793,11 @@ class ManualScoringWindow(QDialog):
         # update upper plot if needed
         upper_epochs_shown = self.upper_right_epoch - self.upper_left_epoch + 1
         if (
-            self.epoch
-            > self.upper_left_epoch + (1 - SCROLL_BOUNDARY) * upper_epochs_shown
+            (
+                self.epoch
+                > self.upper_left_epoch + (1 - SCROLL_BOUNDARY) * upper_epochs_shown
+                or self.epoch + (self.epochs_to_show - 1) / 2 > self.upper_right_epoch
+            )
             and self.upper_right_epoch < (self.n_epochs - 1)
             and direction == DIRECTION_RIGHT
         ):
@@ -815,7 +805,11 @@ class ManualScoringWindow(QDialog):
             self.upper_right_epoch += 1
             self.adjust_upper_figure_x_limits()
         elif (
-            self.epoch < self.upper_left_epoch + SCROLL_BOUNDARY * upper_epochs_shown
+            (
+                self.epoch
+                < self.upper_left_epoch + SCROLL_BOUNDARY * upper_epochs_shown
+                or self.epoch - (self.epochs_to_show - 1) / 2 < self.upper_left_epoch
+            )
             and self.upper_left_epoch > 0
             and direction == DIRECTION_LEFT
         ):
@@ -984,6 +978,23 @@ class ManualScoringWindow(QDialog):
 
         self.update_figures()
 
+    def scroll_zoom(self, event) -> None:
+        """Zoom on mouse scroll events"""
+        if self.now_zooming:
+            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)
+        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
+
 
 def convert_labels(labels: np.array, style: str) -> np.array:
     """Convert labels between "display" and "digit" formats
@@ -1095,3 +1106,55 @@ def transform_eeg_emg(eeg: np.array, emg: np.array) -> (np.array, np.array):
     eeg = eeg / np.percentile(eeg, 95) / 2.2
     emg = emg / np.percentile(emg, 95) / 2.2
     return eeg, emg
+
+
+def find_new_x_limits(
+    direction: str | None,
+    left_epoch: int,
+    right_epoch: int,
+    total_epochs: int,
+    min_n_shown: int,
+    selected_epoch: int,
+) -> (int, int):
+    """Calculate new plot x limits to allow zooming
+
+    :param direction: in, out, reset, or None
+    :param left_epoch: index of current leftmost epoch
+    :param right_epoch: index of current rightmost epoch
+    :param total_epochs: total number of epochs in the recording
+    :param min_n_shown: minimum number of epochs to display
+    :param selected_epoch: currently selected epoch
+    """
+    # number of epochs currently displayed in the upper plots
+    current_n_shown = right_epoch - left_epoch + 1
+    if direction == ZOOM_IN:
+        # can't display fewer than the number of epochs in the lower plot
+        new_n_shown = max([min_n_shown, round(current_n_shown * (1 - ZOOM_FACTOR))])
+    elif direction == ZOOM_OUT:
+        # can't display more than the total number of epochs
+        new_n_shown = min([total_epochs, round(current_n_shown / (1 - ZOOM_FACTOR))])
+    elif direction == ZOOM_RESET:
+        left_epoch = 0
+        right_epoch = total_epochs - 1
+        return left_epoch, right_epoch
+    else:  # just recalculating if min_n_shown has changed
+        new_n_shown = int(
+            np.clip(current_n_shown, a_min=min_n_shown, a_max=total_epochs)
+        )
+
+    # count epochs to show on either side of the selected epoch
+    epochs_on_left_side = int(np.ceil((new_n_shown - 1) / 2))
+    epochs_on_right_side = new_n_shown - epochs_on_left_side - 1
+    if selected_epoch - epochs_on_left_side < 0:
+        # can't go further left than 0
+        left_epoch = 0
+        right_epoch = new_n_shown - 1
+    elif selected_epoch + epochs_on_right_side >= total_epochs:
+        # can't go further right than the total number of epochs
+        left_epoch = total_epochs - new_n_shown
+        right_epoch = total_epochs - 1
+    else:
+        left_epoch = selected_epoch - epochs_on_left_side
+        right_epoch = selected_epoch + epochs_on_right_side
+
+    return left_epoch, right_epoch

{accusleepy-0.9.3 → 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