accusleepy 0.1.0__tar.gz

accusleepy-0.1.0/PKG-INFO

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+Metadata-Version: 2.3
+Name: accusleepy
+Version: 0.1.0
+Summary: Python implementation of AccuSleep
+License: GPL-3.0-only
+Author: Zeke Barger
+Author-email: zekebarger@gmail.com
+Requires-Python: >=3.10,<3.14
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+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 (>=6.8.3,<7.0.0)
+Requires-Dist: scipy (>=1.15.2,<2.0.0)
+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)
+Description-Content-Type: text/markdown
+
+# AccuSleePy
+
+## 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
+[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/
+
+Please contact zekebarger (at) gmail (dot) com with any questions or comments about the software.
+
+## Installation instructions
+
+WIP
+
+## Tips & Troubleshooting
+
+WIP
+
+## Acknowledgements
+
+We would like to thank [Franz Weber](https://www.med.upenn.edu/weberlab/) for creating an
+early version of the manual labeling interface.
+Jim Bohnslav's [deepethogram](https://github.com/jbohnslav/deepethogram) served as an
+incredibly useful reference when reimplementing this project in python.
+

accusleepy-0.1.0/README.md

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+# AccuSleePy
+
+## 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
+[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/
+
+Please contact zekebarger (at) gmail (dot) com with any questions or comments about the software.
+
+## Installation instructions
+
+WIP
+
+## Tips & Troubleshooting
+
+WIP
+
+## Acknowledgements
+
+We would like to thank [Franz Weber](https://www.med.upenn.edu/weberlab/) for creating an
+early version of the manual labeling interface.
+Jim Bohnslav's [deepethogram](https://github.com/jbohnslav/deepethogram) served as an
+incredibly useful reference when reimplementing this project in python.

accusleepy-0.1.0/accusleepy/__main__.py

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+from accusleepy.gui.main import run_primary_window
+
+if __name__ == "__main__":
+    run_primary_window()

accusleepy-0.1.0/accusleepy/brain_state_set.py

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+from dataclasses import dataclass
+
+import numpy as np
+
+BRAIN_STATES_KEY = "brain_states"
+
+
+@dataclass
+class BrainState:
+    """Convenience class for a brain state and its attributes"""
+
+    name: str  # friendly name
+    digit: int  # number 0-9 - used as keyboard shortcut and in label files
+    is_scored: bool  # whether a classification model should score this state
+    frequency: int | float  # typical relative frequency, between 0 and 1
+
+
+class BrainStateSet:
+    def __init__(self, brain_states: list[BrainState], undefined_label: int):
+        """Initialize set of brain states
+
+        :param brain_states: list of BrainState objects
+        :param undefined_label: label for undefined epochs
+        """
+        self.brain_states = brain_states
+
+        # The user can choose any subset of the digits 0-9 to represent
+        # brain states, but not all of them are necessarily intended to be
+        # scored by a classifier, and pytorch requires that all input
+        # labels are in the 0-n range for training and inference.
+        # So, we have to have a distinction between "brain states" (as
+        # represented in label files and keyboard inputs) and "classes"
+        # (AccuSleep's internal representation).
+
+        # map digits to classes, and vice versa
+        self.digit_to_class = {undefined_label: None}
+        self.class_to_digit = dict()
+        # relative frequencies of each class
+        self.mixture_weights = list()
+
+        i = 0
+        for brain_state in self.brain_states:
+            if brain_state.digit == undefined_label:
+                raise Exception(
+                    f"Digit for {brain_state.name} matches 'undefined' label"
+                )
+            if brain_state.is_scored:
+                self.digit_to_class[brain_state.digit] = i
+                self.class_to_digit[i] = brain_state.digit
+                self.mixture_weights.append(brain_state.frequency)
+                i += 1
+            else:
+                self.digit_to_class[brain_state.digit] = None
+
+        self.n_classes = i
+
+        self.mixture_weights = np.array(self.mixture_weights)
+        if np.sum(self.mixture_weights) != 1:
+            raise Exception("Typical frequencies for scored brain states must sum to 1")
+
+    def convert_digit_to_class(self, digits: np.array) -> np.array:
+        """Convert array of digits to their corresponding classes
+
+        :param digits: array of digits
+        :return: array of classes
+        """
+        return np.array([self.digit_to_class[i] for i in digits])
+
+    def convert_class_to_digit(self, classes: np.array) -> np.array:
+        """Convert array of classes to their corresponding digits
+
+        :param classes: array of classes
+        :return: array of digits
+        """
+        return np.array([self.class_to_digit[i] for i in classes])
+
+    def to_output_dict(self) -> dict:
+        """Return dictionary of brain states"""
+        return {
+            BRAIN_STATES_KEY: [
+                {
+                    "name": b.name,
+                    "digit": b.digit,
+                    "is_scored": b.is_scored,
+                    "frequency": b.frequency,
+                }
+                for b in self.brain_states
+            ]
+        }

accusleepy-0.1.0/accusleepy/classification.py

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+import os
+
+import numpy as np
+import pandas as pd
+import torch
+import torch.optim as optim
+from torch import nn
+from torch.utils.data import DataLoader, Dataset
+from torchvision.io import read_image
+from tqdm import trange
+
+import accusleepy.constants as c
+from accusleepy.brain_state_set import BrainStateSet
+from accusleepy.models import SSANN
+from accusleepy.signal_processing import (
+    create_eeg_emg_image,
+    format_img,
+    get_mixture_values,
+    mixture_z_score_img,
+)
+
+BATCH_SIZE = 64
+LEARNING_RATE = 1e-3
+MOMENTUM = 0.9
+TRAINING_EPOCHS = 6
+
+
+class AccuSleepImageDataset(Dataset):
+    """Dataset for loading AccuSleep training images"""
+
+    def __init__(
+        self, annotations_file, img_dir, transform=None, target_transform=None
+    ):
+        self.img_labels = pd.read_csv(annotations_file)
+        self.img_dir = img_dir
+        self.transform = transform
+        self.target_transform = target_transform
+
+    def __len__(self):
+        return len(self.img_labels)
+
+    def __getitem__(self, idx):
+        img_path = str(
+            os.path.join(self.img_dir, self.img_labels.at[idx, c.FILENAME_COL])
+        )
+        image = read_image(img_path)
+        label = self.img_labels.at[idx, c.LABEL_COL]
+        if self.transform:
+            image = self.transform(image)
+        if self.target_transform:
+            label = self.target_transform(label)
+        return image, label
+
+
+def get_device():
+    """Get accelerator, if one is available"""
+    return (
+        torch.accelerator.current_accelerator().type
+        if torch.accelerator.is_available()
+        else "cpu"
+    )
+
+
+def train_model(
+    annotations_file: str,
+    img_dir: str,
+    mixture_weights: np.array,
+    n_classes: int,
+) -> SSANN:
+    """Train a classification model for sleep scoring
+
+    :param annotations_file: file with information on each training image
+    :param img_dir: training image location
+    :param mixture_weights: typical relative frequencies of brain states
+    :param n_classes: number of classes the model will learn
+    :return: trained Sleep Scoring Artificial Neural Network model
+    """
+    training_data = AccuSleepImageDataset(
+        annotations_file=annotations_file,
+        img_dir=img_dir,
+    )
+    train_dataloader = DataLoader(training_data, batch_size=BATCH_SIZE, shuffle=True)
+
+    device = get_device()
+    model = SSANN(n_classes=n_classes)
+    model.to(device)
+    model.train()
+
+    # correct for class imbalance
+    weight = torch.tensor((mixture_weights**-1).astype("float32")).to(device)
+
+    criterion = nn.CrossEntropyLoss(weight=weight)
+    optimizer = optim.SGD(model.parameters(), lr=LEARNING_RATE, momentum=MOMENTUM)
+
+    for _ in trange(TRAINING_EPOCHS):
+        for data in train_dataloader:
+            inputs, labels = data
+            (inputs, labels) = (inputs.to(device), labels.to(device))
+            optimizer.zero_grad()
+            outputs = model(inputs)
+            loss = criterion(outputs, labels)
+            loss.backward()
+            optimizer.step()
+
+    return model
+
+
+def score_recording(
+    model: SSANN,
+    eeg: np.array,
+    emg: np.array,
+    mixture_means: np.array,
+    mixture_sds: np.array,
+    sampling_rate: int | float,
+    epoch_length: int | float,
+    epochs_per_img: int,
+    brain_state_set: BrainStateSet,
+) -> np.array:
+    """Use classification model to get brain state labels for a recording
+
+    This assumes signals have been preprocessed to contain an integer
+    number of epochs.
+
+    :param model: classification model
+    :param eeg: EEG signal
+    :param emg: EMG signal
+    :param mixture_means: mixture means, for calibration
+    :param mixture_sds: mixture standard deviations, for calibration
+    :param sampling_rate: sampling rate, in Hz
+    :param epoch_length: epoch length, in seconds
+    :param epochs_per_img: number of epochs for the model to consider
+    :param brain_state_set: set of brain state options
+    :return: brain state labels
+    """
+    # prepare model
+    device = get_device()
+    model = model.to(device)
+    model.eval()
+
+    # create and scale eeg+emg spectrogram
+    img = create_eeg_emg_image(eeg, emg, sampling_rate, epoch_length)
+    img = mixture_z_score_img(
+        img,
+        mixture_means=mixture_means,
+        mixture_sds=mixture_sds,
+        brain_state_set=brain_state_set,
+    )
+    img = format_img(img=img, epochs_per_img=epochs_per_img, add_padding=True)
+
+    # create dataset for inference
+    images = []
+    for i in range(img.shape[1] - epochs_per_img + 1):
+        images.append(img[:, i : (i + epochs_per_img)].astype("float32"))
+    images = torch.from_numpy(np.array(images))
+    images = images[:, None, :, :]  # add channel
+    images = images.to(device)
+
+    # perform classification
+    with torch.no_grad():
+        outputs = model(images)
+        _, predicted = torch.max(outputs, 1)
+
+    labels = brain_state_set.convert_class_to_digit(predicted.cpu().numpy())
+    return labels
+
+
+def example_real_time_scoring_function(
+    model: SSANN,
+    eeg: np.array,
+    emg: np.array,
+    mixture_means: np.array,
+    mixture_sds: np.array,
+    sampling_rate: int | float,
+    epoch_length: int | float,
+    epochs_per_img: int,
+    brain_state_set: BrainStateSet,
+) -> int:
+    """Example function that could be used for real-time scoring
+
+    This function demonstrates how you could use a model trained in
+    "real-time" mode (current epoch on the right side of each image)
+    to score incoming data. By passing a segment of EEG/EMG data
+    into this function, the most recent epoch will be scored. For
+    example, if the model expects 9 epochs worth of data and the
+    epoch length is 5 seconds, you would pass in 45 seconds of data
+    and would obtain the brain state of the most recent 5 seconds.
+
+    Note:
+    - The EEG and EMG signals must have length equal to
+        sampling_rate * epoch_length * <number of epochs per image>.
+    - The number of samples per epoch must be an integer.
+    - This is just a demonstration, you should customize this for
+        your application and there are probably ways to make it
+        run faster.
+
+    :param model: classification model
+    :param eeg: EEG signal
+    :param emg: EMG signal
+    :param mixture_means: mixture means, for calibration
+    :param mixture_sds: mixture standard deviations, for calibration
+    :param sampling_rate: sampling rate, in Hz
+    :param epoch_length: epoch length, in seconds
+    :param epochs_per_img: number of epochs shown to the model at once
+    :param brain_state_set: set of brain state options
+    :return: brain state label
+    """
+    # prepare model
+    # this could be done outside the function
+    device = get_device()
+    model = model.to(device)
+    model.eval()
+
+    # create and scale eeg+emg spectrogram
+    img = create_eeg_emg_image(eeg, emg, sampling_rate, epoch_length)
+    img = mixture_z_score_img(
+        img,
+        mixture_means=mixture_means,
+        mixture_sds=mixture_sds,
+        brain_state_set=brain_state_set,
+    )
+    img = format_img(img=img, epochs_per_img=epochs_per_img, add_padding=False)
+
+    # create dataset for inference
+    images = torch.from_numpy(np.array([img.astype("float32")]))
+    images = images[:, None, :, :]  # add channel
+    images = images.to(device)
+
+    # perform classification
+    with torch.no_grad():
+        outputs = model(images)
+        _, predicted = torch.max(outputs, 1)
+
+    label = int(brain_state_set.convert_class_to_digit(predicted.cpu().numpy())[0])
+    return label
+
+
+def create_calibration_file(
+    filename: str,
+    eeg: np.array,
+    emg: np.array,
+    labels: np.array,
+    sampling_rate: int | float,
+    epoch_length: int | float,
+    brain_state_set: BrainStateSet,
+) -> None:
+    """Create file of calibration data for a subject
+
+    This assumes signals have been preprocessed to contain an integer
+    number of epochs.
+
+    :param filename: filename for the calibration file
+    :param eeg: EEG signal
+    :param emg: EMG signal
+    :param labels: brain state labels, as digits
+    :param sampling_rate: sampling rate, in Hz
+    :param epoch_length: epoch length, in seconds
+    :param brain_state_set: set of brain state options
+    """
+    img = create_eeg_emg_image(eeg, emg, sampling_rate, epoch_length)
+    mixture_means, mixture_sds = get_mixture_values(
+        img=img,
+        labels=brain_state_set.convert_digit_to_class(labels),
+        brain_state_set=brain_state_set,
+    )
+    pd.DataFrame(
+        {c.MIXTURE_MEAN_COL: mixture_means, c.MIXTURE_SD_COL: mixture_sds}
+    ).to_csv(filename, index=False)

accusleepy-0.1.0/accusleepy/config.json

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+{
+    "brain_states": [
+        {
+            "name": "REM",
+            "digit": 1,
+            "is_scored": true,
+            "frequency": 0.1
+        },
+        {
+            "name": "Wake",
+            "digit": 2,
+            "is_scored": true,
+            "frequency": 0.35
+        },
+        {
+            "name": "NREM",
+            "digit": 3,
+            "is_scored": true,
+            "frequency": 0.55
+        }
+    ]
+}

accusleepy-0.1.0/accusleepy/constants.py

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+# probably don't change these unless you really need to
+UNDEFINED_LABEL = -1  # can't be the same as a brain state's digit, must be an integer
+# calibration file columns
+MIXTURE_MEAN_COL = "mixture_mean"
+MIXTURE_SD_COL = "mixture_sd"
+# recording file columns
+EEG_COL = "eeg"
+EMG_COL = "emg"
+# label file columns
+BRAIN_STATE_COL = "brain_state"
+
+
+# really don't change these
+# config file location
+CONFIG_FILE = "config.json"
+# number of times to include the EMG power in a training image
+EMG_COPIES = 9
+# minimum spectrogram window length, in seconds
+MIN_WINDOW_LEN = 5
+# frequency above which to downsample EEG spectrograms
+DOWNSAMPLING_START_FREQ = 20
+# upper frequency cutoff for EEG spectrograms
+UPPER_FREQ = 50
+# classification model types
+DEFAULT_MODEL_TYPE = "default"  # current epoch is centered
+REAL_TIME_MODEL_TYPE = "real-time"  # current epoch on the right
+# valid filetypes
+RECORDING_FILE_TYPES = [".parquet", ".csv"]
+LABEL_FILE_TYPE = ".csv"
+CALIBRATION_FILE_TYPE = ".csv"
+MODEL_FILE_TYPE = ".pth"
+# annotation file columns
+FILENAME_COL = "filename"
+LABEL_COL = "label"
+# recording list file header:
+RECORDING_LIST_NAME = "recording_list"
+RECORDING_LIST_FILE_TYPE = ".json"