accusleepy 0.1.2__tar.gz → 0.4.0__tar.gz

{accusleepy-0.1.2 → accusleepy-0.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: accusleepy
-Version: 0.1.2
+Version: 0.4.0
 Summary: Python implementation of AccuSleep
 License: GPL-3.0-only
 Author: Zeke Barger
@@ -20,6 +20,7 @@ Requires-Dist: pillow (>=11.1.0,<12.0.0)
 Requires-Dist: pre-commit (>=4.2.0,<5.0.0)
 Requires-Dist: pyside6 (>=6.7.1,<6.8.0)
 Requires-Dist: scipy (>=1.15.2,<2.0.0)
+Requires-Dist: toml (>=0.10.2,<0.11.0)
 Requires-Dist: torch (>=2.6.0,<3.0.0)
 Requires-Dist: torchvision (>=0.21.0,<0.22.0)
 Requires-Dist: tqdm (>=4.67.1,<5.0.0)
@@ -30,16 +31,19 @@ Description-Content-Type: text/markdown
 ## Description
 
 AccuSleePy is a python implementation of AccuSleep--a set of graphical user interfaces for scoring rodent
-sleep using EEG and EMG recordings. If you use AccuSleep in your research, please cite our
+sleep using EEG and EMG recordings. It offers several improvements over the original MATLAB version
+and is the only version that will be actively maintained.
+
+If you use AccuSleep in your research, please cite our
 [publication](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0224642):
 
 Barger, Z., Frye, C. G., Liu, D., Dan, Y., & Bouchard, K. E. (2019). Robust, automated sleep scoring by a compact neural network with distributional shift correction. *PLOS ONE, 14*(12), 1–18.
 
-The data used for training and testing AccuSleep are available at https://osf.io/py5eb/
+The data and models associated with AccuSleep are available at https://osf.io/py5eb/
 
 Please contact zekebarger (at) gmail (dot) com with any questions or comments about the software.
 
-## Installation instructions
+## Installation
 
 - (recommended) create a new virtual environment (using
 [venv](https://docs.python.org/3/library/venv.html),
@@ -47,10 +51,11 @@ Please contact zekebarger (at) gmail (dot) com with any questions or comments ab
 etc.) using python >=3.10,<3.13
 - (optional) if you have a CUDA device and want to speed up model training, [install PyTorch](https://pytorch.org/)
 - `pip install accusleepy`
+- (optional) download a classification model from https://osf.io/py5eb/ under /python_format/models/
 
 ## Usage
 
-`python -m accusleepy`
+`python -m accusleepy` will open the primary interface.
 
 ## Acknowledgements
 

{accusleepy-0.1.2 → accusleepy-0.4.0}/README.md

@@ -3,16 +3,19 @@
 ## Description
 
 AccuSleePy is a python implementation of AccuSleep--a set of graphical user interfaces for scoring rodent
-sleep using EEG and EMG recordings. If you use AccuSleep in your research, please cite our
+sleep using EEG and EMG recordings. It offers several improvements over the original MATLAB version
+and is the only version that will be actively maintained.
+
+If you use AccuSleep in your research, please cite our
 [publication](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0224642):
 
 Barger, Z., Frye, C. G., Liu, D., Dan, Y., & Bouchard, K. E. (2019). Robust, automated sleep scoring by a compact neural network with distributional shift correction. *PLOS ONE, 14*(12), 1–18.
 
-The data used for training and testing AccuSleep are available at https://osf.io/py5eb/
+The data and models associated with AccuSleep are available at https://osf.io/py5eb/
 
 Please contact zekebarger (at) gmail (dot) com with any questions or comments about the software.
 
-## Installation instructions
+## Installation
 
 - (recommended) create a new virtual environment (using
 [venv](https://docs.python.org/3/library/venv.html),
@@ -20,10 +23,11 @@ Please contact zekebarger (at) gmail (dot) com with any questions or comments ab
 etc.) using python >=3.10,<3.13
 - (optional) if you have a CUDA device and want to speed up model training, [install PyTorch](https://pytorch.org/)
 - `pip install accusleepy`
+- (optional) download a classification model from https://osf.io/py5eb/ under /python_format/models/
 
 ## Usage
 
-`python -m accusleepy`
+`python -m accusleepy` will open the primary interface.
 
 ## Acknowledgements
 

{accusleepy-0.1.2 → accusleepy-0.4.0}/accusleepy/config.json

@@ -18,5 +18,6 @@
             "is_scored": true,
             "frequency": 0.55
         }
-    ]
-}
+    ],
+    "default_epoch_length": 2.5
+}

{accusleepy-0.1.2 → accusleepy-0.4.0}/accusleepy/constants.py

@@ -35,3 +35,5 @@ LABEL_COL = "label"
 # recording list file header:
 RECORDING_LIST_NAME = "recording_list"
 RECORDING_LIST_FILE_TYPE = ".json"
+# key for default epoch length in config
+DEFAULT_EPOCH_LENGTH_KEY = "default_epoch_length"

{accusleepy-0.1.2 → accusleepy-0.4.0}/accusleepy/fileio.py

@@ -11,6 +11,7 @@ from accusleepy.brain_state_set import BRAIN_STATES_KEY, BrainState, BrainStateS
 from accusleepy.constants import (
     BRAIN_STATE_COL,
     CONFIG_FILE,
+    DEFAULT_EPOCH_LENGTH_KEY,
     EEG_COL,
     EMG_COL,
     MIXTURE_MEAN_COL,
@@ -82,7 +83,9 @@ def load_model(filename: str) -> tuple[SSANN, int | float, int, str, dict]:
         (default or real-time), set of brain state options
         used when training the model
     """
-    state_dict = torch.load(filename, weights_only=True)
+    state_dict = torch.load(
+        filename, weights_only=True, map_location=torch.device("cpu")
+    )
     epoch_length = state_dict.pop("epoch_length")
     epochs_per_img = state_dict.pop("epochs_per_img")
     model_type = state_dict.pop("model_type")
@@ -141,10 +144,10 @@ def save_labels(labels: np.array, filename: str) -> None:
     pd.DataFrame({BRAIN_STATE_COL: labels}).to_csv(filename, index=False)
 
 
-def load_config() -> BrainStateSet:
+def load_config() -> tuple[BrainStateSet, int | float]:
     """Load configuration file with brain state options
 
-    :return: set of brain state options
+    :return: set of brain state options and default epoch length
     """
     with open(
         os.path.join(os.path.dirname(os.path.abspath(__file__)), CONFIG_FILE), "r"
@@ -152,18 +155,23 @@ def load_config() -> BrainStateSet:
         data = json.load(f)
     return BrainStateSet(
         [BrainState(**b) for b in data[BRAIN_STATES_KEY]], UNDEFINED_LABEL
-    )
+    ), data[DEFAULT_EPOCH_LENGTH_KEY]
 
 
-def save_config(brain_state_set: BrainStateSet) -> None:
+def save_config(
+    brain_state_set: BrainStateSet, default_epoch_length: int | float
+) -> None:
     """Save configuration of brain state options to json file
 
     :param brain_state_set: set of brain state options
+    :param default_epoch_length: epoch length to use when the GUI starts
     """
+    output_dict = brain_state_set.to_output_dict()
+    output_dict.update({DEFAULT_EPOCH_LENGTH_KEY: default_epoch_length})
     with open(
         os.path.join(os.path.dirname(os.path.abspath(__file__)), CONFIG_FILE), "w"
     ) as f:
-        json.dump(brain_state_set.to_output_dict(), f, indent=4)
+        json.dump(output_dict, f, indent=4)
 
 
 def load_recording_list(filename: str) -> list[Recording]:

{accusleepy-0.1.2 → accusleepy-0.4.0}/accusleepy/gui/main.py

@@ -5,6 +5,7 @@ import datetime
 import os
 import shutil
 import sys
+import toml
 from dataclasses import dataclass
 from functools import partial
 
@@ -40,6 +41,7 @@ from accusleepy.fileio import (
     save_model,
     save_recording_list,
 )
+from accusleepy.gui.text.main_guide_text import MAIN_GUIDE_TEXT
 from accusleepy.gui.manual_scoring import ManualScoringWindow
 from accusleepy.gui.primary_window import Ui_PrimaryWindow
 from accusleepy.signal_processing import (
@@ -52,9 +54,8 @@ from accusleepy.signal_processing import (
 # max number of messages to display
 MESSAGE_BOX_MAX_DEPTH = 50
 LABEL_LENGTH_ERROR = "label file length does not match recording length"
-# relative path to user manual txt file
-USER_MANUAL_FILE = "text/main_guide.txt"
-CONFIG_GUIDE_FILE = "text/config_guide.txt"
+# relative path to config guide txt file
+CONFIG_GUIDE_FILE = os.path.normpath(r"text/config_guide.txt")
 
 
 @dataclass
@@ -80,12 +81,12 @@ class AccuSleepWindow(QtWidgets.QMainWindow):
         self.setWindowTitle("AccuSleePy")
 
         # fill in settings tab
-        self.brain_state_set = load_config()
+        self.brain_state_set, self.epoch_length = load_config()
         self.settings_widgets = None
         self.initialize_settings_tab()
 
         # initialize info about the recordings, classification data / settings
-        self.epoch_length = 0
+        self.ui.epoch_length_input.setValue(self.epoch_length)
         self.model = None
         self.only_overwrite_undefined = False
         self.min_bout_length = 5
@@ -116,6 +117,20 @@ class AccuSleepWindow(QtWidgets.QMainWindow):
         # messages to display
         self.messages = []
 
+        # display current version
+        version = ""
+        toml_file = os.path.join(
+            os.path.dirname(
+                os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+            ),
+            "pyproject.toml",
+        )
+        if os.path.isfile(toml_file):
+            toml_data = toml.load(toml_file)
+            if "project" in toml_data and "version" in toml_data["project"]:
+                version = toml_data["project"]["version"]
+        self.ui.version_label.setText(f"v{version}")
+
         # user input: keyboard shortcuts
         keypress_quit = QtGui.QShortcut(
             QtGui.QKeySequence(
@@ -179,6 +194,7 @@ class AccuSleepWindow(QtWidgets.QMainWindow):
         )
         if not filename:
             return
+        filename = os.path.normpath(filename)
         save_recording_list(filename=filename, recordings=self.recordings)
         self.show_message(f"Saved list of recordings to {filename}")
 
@@ -193,6 +209,7 @@ class AccuSleepWindow(QtWidgets.QMainWindow):
         if file_dialog.exec():
             selected_files = file_dialog.selectedFiles()
             filename = selected_files[0]
+            filename = os.path.normpath(filename)
         else:
             return
 
@@ -229,7 +246,7 @@ class AccuSleepWindow(QtWidgets.QMainWindow):
             if event.type() == QtCore.QEvent.Drop:
                 urls = event.mimeData().urls()
                 if len(urls) == 1:
-                    filename = urls[0].toLocalFile()
+                    filename = os.path.normpath(urls[0].toLocalFile())
 
         if filename is None:
             return super().eventFilter(obj, event)
@@ -289,24 +306,31 @@ class AccuSleepWindow(QtWidgets.QMainWindow):
         )
         if not model_filename:
             self.show_message("Model training canceled, no filename given")
+            return
+        model_filename = os.path.normpath(model_filename)
+
+        # create (probably temporary) image folder
+        temp_image_dir = os.path.join(
+            self.training_image_dir,
+            "images_" + datetime.datetime.now().strftime("%Y%m%d%H%M"),
+        )
 
-        # create image folder
-        if os.path.exists(self.training_image_dir):
+        if os.path.exists(temp_image_dir):  # unlikely
             self.show_message(
                 "Warning: training image folder exists, will be overwritten"
             )
-        os.makedirs(self.training_image_dir, exist_ok=True)
+        os.makedirs(temp_image_dir, exist_ok=True)
 
         # create training images
         self.show_message(
-            (f"Creating training images in {self.training_image_dir}, please wait...")
+            (f"Creating training images in {temp_image_dir}, please wait...")
         )
         self.ui.message_area.repaint()
         QtWidgets.QApplication.processEvents()
         print("Creating training images")
         failed_recordings = create_training_images(
             recordings=self.recordings,
-            output_path=self.training_image_dir,
+            output_path=temp_image_dir,
             epoch_length=self.epoch_length,
             epochs_per_img=self.training_epochs_per_img,
             brain_state_set=self.brain_state_set,
@@ -330,10 +354,8 @@ class AccuSleepWindow(QtWidgets.QMainWindow):
         QtWidgets.QApplication.processEvents()
         print("Training model")
         model = train_model(
-            annotations_file=os.path.join(
-                self.training_image_dir, ANNOTATIONS_FILENAME
-            ),
-            img_dir=self.training_image_dir,
+            annotations_file=os.path.join(temp_image_dir, ANNOTATIONS_FILENAME),
+            img_dir=temp_image_dir,
             mixture_weights=self.brain_state_set.mixture_weights,
             n_classes=self.brain_state_set.n_classes,
         )
@@ -350,20 +372,19 @@ class AccuSleepWindow(QtWidgets.QMainWindow):
 
         # optionally delete images
         if self.delete_training_images:
-            shutil.rmtree(self.training_image_dir)
+            shutil.rmtree(temp_image_dir)
 
         self.show_message(f"Training complete, saved model to {model_filename}")
 
-    def set_training_folder(self):
+    def set_training_folder(self) -> None:
+        """Select location in which to create a folder for training images"""
         training_folder_parent = QtWidgets.QFileDialog.getExistingDirectory(
             self, "Select directory for training images"
         )
         if training_folder_parent:
-            self.training_image_dir = os.path.join(
-                training_folder_parent,
-                "images_" + datetime.datetime.now().strftime("%Y%m%d%H%M"),
-            )
-            self.ui.image_folder_label.setText(self.training_image_dir)
+            training_folder_parent = os.path.normpath(training_folder_parent)
+            self.training_image_dir = training_folder_parent
+            self.ui.image_folder_label.setText(training_folder_parent)
 
     def update_image_deletion(self) -> None:
         """Update choice of whether to delete images after training"""
@@ -559,6 +580,7 @@ class AccuSleepWindow(QtWidgets.QMainWindow):
             if file_dialog.exec():
                 selected_files = file_dialog.selectedFiles()
                 filename = selected_files[0]
+                filename = os.path.normpath(filename)
             else:
                 return
 
@@ -706,6 +728,7 @@ class AccuSleepWindow(QtWidgets.QMainWindow):
         )
         if not filename:
             return
+        filename = os.path.normpath(filename)
 
         create_calibration_file(
             filename=filename,
@@ -870,6 +893,7 @@ class AccuSleepWindow(QtWidgets.QMainWindow):
             filter="*" + LABEL_FILE_TYPE,
         )
         if filename:
+            filename = os.path.normpath(filename)
             self.recordings[self.recording_index].label_file = filename
             self.ui.label_file_label.setText(filename)
 
@@ -884,6 +908,7 @@ class AccuSleepWindow(QtWidgets.QMainWindow):
         if file_dialog.exec():
             selected_files = file_dialog.selectedFiles()
             filename = selected_files[0]
+            filename = os.path.normpath(filename)
             self.recordings[self.recording_index].label_file = filename
             self.ui.label_file_label.setText(filename)
 
@@ -898,6 +923,7 @@ class AccuSleepWindow(QtWidgets.QMainWindow):
         if file_dialog.exec():
             selected_files = file_dialog.selectedFiles()
             filename = selected_files[0]
+            filename = os.path.normpath(filename)
             self.recordings[self.recording_index].calibration_file = filename
             self.ui.calibration_file_label.setText(filename)
 
@@ -912,6 +938,7 @@ class AccuSleepWindow(QtWidgets.QMainWindow):
         if file_dialog.exec():
             selected_files = file_dialog.selectedFiles()
             filename = selected_files[0]
+            filename = os.path.normpath(filename)
             self.recordings[self.recording_index].recording_file = filename
             self.ui.recording_file_label.setText(filename)
 
@@ -1004,15 +1031,8 @@ class AccuSleepWindow(QtWidgets.QMainWindow):
 
     def show_user_manual(self) -> None:
         """Show a popup window with the user manual"""
-        user_manual_file = open(
-            os.path.join(os.path.dirname(os.path.abspath(__file__)), USER_MANUAL_FILE),
-            "r",
-        )
-        user_manual_text = user_manual_file.read()
-        user_manual_file.close()
-
         label_widget = QtWidgets.QLabel()
-        label_widget.setText(user_manual_text)
+        label_widget.setText(MAIN_GUIDE_TEXT)
         scroll_area = QtWidgets.QScrollArea()
         scroll_area.setStyleSheet("background-color: white;")
         scroll_area.setWidget(label_widget)
@@ -1110,6 +1130,7 @@ class AccuSleepWindow(QtWidgets.QMainWindow):
         }
 
         # update widget state to display current config
+        self.ui.default_epoch_input.setValue(self.epoch_length)
         states = {b.digit: b for b in self.brain_state_set.brain_states}
         for digit in range(10):
             if digit in states.keys():
@@ -1247,7 +1268,7 @@ class AccuSleepWindow(QtWidgets.QMainWindow):
         self.brain_state_set = BrainStateSet(brain_states, UNDEFINED_LABEL)
 
         # save to file
-        save_config(self.brain_state_set)
+        save_config(self.brain_state_set, self.ui.default_epoch_input.value())
         self.ui.save_config_status.setText("configuration saved")
 
 
@@ -1257,7 +1278,7 @@ def check_label_validity(
     sampling_rate: int | float,
     epoch_length: int | float,
     brain_state_set: BrainStateSet,
-) -> str:
+) -> str | None:
     """Check whether a set of brain state labels is valid
 
     This returns an error message if a problem is found with the
@@ -1357,6 +1378,7 @@ def check_config_consistency(
         output.append(
             (
                 "Warning: the epoch length used when training this model "
+                f"({model_epoch_length} seconds) "
                 "does not match the current epoch length setting."
             )
         )

{accusleepy-0.1.2 → accusleepy-0.4.0}/accusleepy/gui/manual_scoring.py

@@ -27,7 +27,7 @@ LABEL_CMAP = np.concatenate(
     [np.array([[0, 0, 0, 0]]), plt.colormaps["tab10"](range(10))], axis=0
 )
 # relative path to user manual text file
-USER_MANUAL_FILE = "text/manual_scoring_guide.txt"
+USER_MANUAL_FILE = os.path.normpath(r"text/manual_scoring_guide.txt")
 
 # constants used by callback functions
 # label formats
@@ -111,7 +111,7 @@ class ManualScoringWindow(QtWidgets.QDialog):
         self.setWindowTitle("AccuSleePy manual scoring window")
 
         # load set of valid brain states
-        self.brain_state_set = load_config()
+        self.brain_state_set, _ = load_config()
 
         # initial setting for number of epochs to show in the lower plot
         self.epochs_to_show = 5
@@ -833,7 +833,7 @@ class ManualScoringWindow(QtWidgets.QDialog):
             self.adjust_upper_figure_x_limits()
 
         # update parts of lower plot
-        old_window_center = round(self.epochs_to_show / 2) + self.lower_left_epoch
+        old_window_center = round((self.epochs_to_show - 1) / 2) + self.lower_left_epoch
         # change the window bounds if needed
         if self.epoch < old_window_center and self.lower_left_epoch > 0:
             self.lower_left_epoch -= 1