accusleepy 0.9.3__py3-none-any.whl → 0.10.1__py3-none-any.whl

accusleepy/gui/primary_window.ui

@@ -1239,14 +1239,14 @@ color: rgb(244, 195, 68);</string>
                      <number>10</number>
                     </property>
                     <item row="0" column="0">
-                     <layout class="QHBoxLayout" name="top_training_layout" stretch="2,1,2,1,3,1">
+                     <layout class="QHBoxLayout" name="top_training_layout" stretch="5,1,3,4,1,5">
                       <property name="spacing">
                        <number>10</number>
                       </property>
                       <item>
                        <layout class="QHBoxLayout" name="horizontalLayout_5">
                         <property name="spacing">
-                         <number>5</number>
+                         <number>3</number>
                         </property>
                         <item>
                          <widget class="QLabel" name="label">
@@ -1299,7 +1299,7 @@ color: rgb(244, 195, 68);</string>
                        </spacer>
                       </item>
                       <item>
-                       <widget class="QCheckBox" name="delete_image_box">
+                       <widget class="QCheckBox" name="calibrate_checkbox">
                         <property name="sizePolicy">
                          <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
                           <horstretch>0</horstretch>
@@ -1307,7 +1307,7 @@ color: rgb(244, 195, 68);</string>
                          </sizepolicy>
                         </property>
                         <property name="text">
-                         <string>Delete images after training</string>
+                         <string>Calibrate model</string>
                         </property>
                         <property name="checked">
                          <bool>true</bool>
@@ -1315,7 +1315,55 @@ color: rgb(244, 195, 68);</string>
                        </widget>
                       </item>
                       <item>
-                       <spacer name="horizontalSpacer_6">
+                       <layout class="QHBoxLayout" name="horizontalLayout_84">
+                        <property name="spacing">
+                         <number>3</number>
+                        </property>
+                        <property name="leftMargin">
+                         <number>10</number>
+                        </property>
+                        <item>
+                         <widget class="QLabel" name="calibrate_label">
+                          <property name="sizePolicy">
+                           <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
+                            <horstretch>0</horstretch>
+                            <verstretch>0</verstretch>
+                           </sizepolicy>
+                          </property>
+                          <property name="text">
+                           <string>Calibration set size:</string>
+                          </property>
+                         </widget>
+                        </item>
+                        <item>
+                         <widget class="QSpinBox" name="calibration_spinbox">
+                          <property name="sizePolicy">
+                           <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
+                            <horstretch>0</horstretch>
+                            <verstretch>0</verstretch>
+                           </sizepolicy>
+                          </property>
+                          <property name="suffix">
+                           <string>%</string>
+                          </property>
+                          <property name="prefix">
+                           <string/>
+                          </property>
+                          <property name="minimum">
+                           <number>10</number>
+                          </property>
+                          <property name="maximum">
+                           <number>50</number>
+                          </property>
+                          <property name="value">
+                           <number>15</number>
+                          </property>
+                         </widget>
+                        </item>
+                       </layout>
+                      </item>
+                      <item>
+                       <spacer name="horizontalSpacer_3">
                         <property name="orientation">
                          <enum>Qt::Orientation::Horizontal</enum>
                         </property>
@@ -1376,30 +1424,14 @@ color: rgb(244, 195, 68);</string>
                         </item>
                        </layout>
                       </item>
-                      <item>
-                       <spacer name="horizontalSpacer_3">
-                        <property name="orientation">
-                         <enum>Qt::Orientation::Horizontal</enum>
-                        </property>
-                        <property name="sizeType">
-                         <enum>QSizePolicy::Policy::Preferred</enum>
-                        </property>
-                        <property name="sizeHint" stdset="0">
-                         <size>
-                          <width>10</width>
-                          <height>5</height>
-                         </size>
-                        </property>
-                       </spacer>
-                      </item>
                      </layout>
                     </item>
                     <item row="1" column="0">
-                     <layout class="QHBoxLayout" name="bottom_training_layout" stretch="6,5,3,1,3,1,1">
+                     <layout class="QHBoxLayout" name="bottom_training_layout" stretch="5,5">
                       <item>
                        <widget class="QPushButton" name="train_model_button">
                         <property name="sizePolicy">
-                         <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+                         <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
                           <horstretch>0</horstretch>
                           <verstretch>0</verstretch>
                          </sizepolicy>
@@ -1428,89 +1460,6 @@ color: rgb(244, 195, 68);</string>
                         </property>
                        </spacer>
                       </item>
-                      <item>
-                       <widget class="QCheckBox" name="calibrate_checkbox">
-                        <property name="sizePolicy">
-                         <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
-                          <horstretch>0</horstretch>
-                          <verstretch>0</verstretch>
-                         </sizepolicy>
-                        </property>
-                        <property name="text">
-                         <string>Calibrate model</string>
-                        </property>
-                        <property name="checked">
-                         <bool>true</bool>
-                        </property>
-                       </widget>
-                      </item>
-                      <item>
-                       <spacer name="horizontalSpacer_7">
-                        <property name="orientation">
-                         <enum>Qt::Orientation::Horizontal</enum>
-                        </property>
-                        <property name="sizeType">
-                         <enum>QSizePolicy::Policy::Preferred</enum>
-                        </property>
-                        <property name="sizeHint" stdset="0">
-                         <size>
-                          <width>10</width>
-                          <height>10</height>
-                         </size>
-                        </property>
-                       </spacer>
-                      </item>
-                      <item>
-                       <widget class="QLabel" name="calibrate_label">
-                        <property name="sizePolicy">
-                         <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
-                          <horstretch>0</horstretch>
-                          <verstretch>0</verstretch>
-                         </sizepolicy>
-                        </property>
-                        <property name="text">
-                         <string>Calibration set size:</string>
-                        </property>
-                       </widget>
-                      </item>
-                      <item>
-                       <widget class="QSpinBox" name="calibration_spinbox">
-                        <property name="sizePolicy">
-                         <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
-                          <horstretch>0</horstretch>
-                          <verstretch>0</verstretch>
-                         </sizepolicy>
-                        </property>
-                        <property name="suffix">
-                         <string>%</string>
-                        </property>
-                        <property name="minimum">
-                         <number>10</number>
-                        </property>
-                        <property name="maximum">
-                         <number>50</number>
-                        </property>
-                        <property name="value">
-                         <number>15</number>
-                        </property>
-                       </widget>
-                      </item>
-                      <item>
-                       <spacer name="horizontalSpacer_78">
-                        <property name="orientation">
-                         <enum>Qt::Orientation::Horizontal</enum>
-                        </property>
-                        <property name="sizeType">
-                         <enum>QSizePolicy::Policy::Preferred</enum>
-                        </property>
-                        <property name="sizeHint" stdset="0">
-                         <size>
-                          <width>10</width>
-                          <height>10</height>
-                         </size>
-                        </property>
-                       </spacer>
-                      </item>
                      </layout>
                     </item>
                    </layout>
@@ -4612,6 +4561,43 @@ Each brain state has several attributes:
                     </item>
                    </layout>
                   </item>
+                  <item>
+                   <layout class="QHBoxLayout" name="horizontalLayout_79">
+                    <item>
+                     <layout class="QHBoxLayout" name="horizontalLayout_85">
+                      <item>
+                       <widget class="QCheckBox" name="delete_image_box">
+                        <property name="sizePolicy">
+                         <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
+                          <horstretch>0</horstretch>
+                          <verstretch>0</verstretch>
+                         </sizepolicy>
+                        </property>
+                        <property name="text">
+                         <string>Delete images after training</string>
+                        </property>
+                        <property name="checked">
+                         <bool>true</bool>
+                        </property>
+                       </widget>
+                      </item>
+                     </layout>
+                    </item>
+                    <item>
+                     <spacer name="horizontalSpacer_93">
+                      <property name="orientation">
+                       <enum>Qt::Orientation::Horizontal</enum>
+                      </property>
+                      <property name="sizeHint" stdset="0">
+                       <size>
+                        <width>40</width>
+                        <height>20</height>
+                       </size>
+                      </property>
+                     </spacer>
+                    </item>
+                   </layout>
+                  </item>
                   <item>
                    <layout class="QHBoxLayout" name="horizontalLayout_74">
                     <item>
@@ -4682,7 +4668,9 @@ Each brain state has several attributes:
 - Batch size: number of examples in each training iteration
 - Learning rate: step size for adjusting model weights
 - Momentum: amount of past gradients to use in the current update. Typically between 0.6 and 0.99
-- Epochs: number of passes over the training data</string>
+- Epochs: number of passes over the training data
+
+You can also choose whether to delete images created by the training process once it's finished. This is recommended unless you are debugging the training code.</string>
                     </property>
                     <property name="textFormat">
                      <enum>Qt::TextFormat::MarkdownText</enum>

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/gui/settings_widget.py

@@ -9,6 +9,7 @@ from PySide6.QtWidgets import QCheckBox, QDoubleSpinBox, QLineEdit
 from accusleepy.brain_state_set import BrainState, BrainStateSet
 from accusleepy.constants import (
     DEFAULT_BATCH_SIZE,
+    DEFAULT_DELETE_TRAINING_IMAGES_STATE,
     DEFAULT_EMG_BP_LOWER,
     DEFAULT_EMG_BP_UPPER,
     DEFAULT_EMG_FILTER_ORDER,
@@ -55,6 +56,7 @@ class SettingsWidget(QObject):
         self._hyperparameters = config.hyperparameters
         self._default_epochs_to_show = config.epochs_to_show
         self._default_autoscroll_state = config.autoscroll_state
+        self._delete_training_images = config.delete_training_images
 
         # Store default values for main tab settings (used to populate Settings tab UI)
         self._default_epoch_length = config.default_epoch_length
@@ -81,6 +83,11 @@ class SettingsWidget(QObject):
         """Model training hyperparameters"""
         return self._hyperparameters
 
+    @property
+    def delete_training_images(self) -> bool:
+        """Whether to delete images after training"""
+        return self._delete_training_images
+
     @property
     def default_epochs_to_show(self) -> int:
         """Default number of epochs to show in manual scoring"""
@@ -186,6 +193,7 @@ class SettingsWidget(QObject):
         self._ui.learning_rate_spinbox.setValue(self._hyperparameters.learning_rate)
         self._ui.momentum_spinbox.setValue(self._hyperparameters.momentum)
         self._ui.training_epochs_spinbox.setValue(self._hyperparameters.training_epochs)
+        self._ui.delete_image_box.setChecked(self._delete_training_images)
         # Brain states
         states = {b.digit: b for b in self._brain_state_set.brain_states}
         for digit in range(10):
@@ -233,6 +241,7 @@ class SettingsWidget(QObject):
         self._ui.training_epochs_spinbox.valueChanged.connect(
             self._hyperparameters_changed
         )
+        self._ui.delete_image_box.stateChanged.connect(self._hyperparameters_changed)
         for digit in range(10):
             state = self._settings_widgets[digit]
             state.enabled_widget.stateChanged.connect(
@@ -302,6 +311,7 @@ class SettingsWidget(QObject):
             momentum=self._ui.momentum_spinbox.value(),
             training_epochs=self._ui.training_epochs_spinbox.value(),
         )
+        self._delete_training_images = self._ui.delete_image_box.isChecked()
         self._ui.save_config_status.setText("")
 
     def reset_status_message(self, _new_value=None) -> None:
@@ -392,6 +402,7 @@ class SettingsWidget(QObject):
             hyperparameters=self._hyperparameters,
             epochs_to_show=self._ui.epochs_to_show_spinbox.value(),
             autoscroll_state=self._ui.autoscroll_checkbox.isChecked(),
+            delete_training_images=self._ui.delete_image_box.isChecked(),
         )
         self._ui.save_config_status.setText("configuration saved")
 
@@ -407,3 +418,4 @@ class SettingsWidget(QObject):
         self._ui.learning_rate_spinbox.setValue(DEFAULT_LEARNING_RATE)
         self._ui.momentum_spinbox.setValue(DEFAULT_MOMENTUM)
         self._ui.training_epochs_spinbox.setValue(DEFAULT_TRAINING_EPOCHS)
+        self._ui.delete_image_box.setChecked(DEFAULT_DELETE_TRAINING_IMAGES_STATE)

accusleepy/gui/text/main_guide.md

@@ -125,25 +125,28 @@ To train a new model on your own data:
     recording. Calibration files are not required.
 2. Click the "Model training" tab
 3. Choose the number of epochs to consider when scoring each epoch.
-    This will be the "width" of the training images. For "default"
-    type models, this must be an odd number. In general, about 30
-    seconds worth of data is enough.
-4. Choose whether the images used to train the model should be
-    deleted once training is complete. It's generally best to
-    leave this box checked. A (temporary) folder for these files
-    will be created in the same location as the trained model.
-5. Choose whether to create a "default" or "real-time"-type model.
-    Note that scoring recordings in the primary interface requires
-    a default-type model.
-6. Choose whether to calibrate the model. This process uses part
+    This will be the width, in pixels, of the training images.
+    For "default" type models, this must be an odd number. Generally,
+    about 30 seconds worth of data is enough.
+4. Choose whether to create a "default" or "real-time"-type model.
+    Scoring recordings in the AccuSleePy interface requires a
+    default-type model. Only select real-time if you plan to create
+    your own scoring function. An example real-time scoring function
+    can be found in `classification.py`.
+5. Choose whether to calibrate the model. This process uses part
     of the training data to make the model's confidence scores
     more accurately reflect the probability that the output
     labels are accurate. If using calibration, choose what percent
     of the training data to set aside for calibration.
-7. Click "Train classification model" and enter a
+6. Click "Train classification model" and enter a
     filename for the trained model. Training can take some time.
     The terminal will display progress updates.
 
+As part of the training process, a temporary folder of images will
+be created in the location where the model will be saved. This folder
+is deleted by default, but if you want to keep it for debugging
+purposes, you can change this behavior in the "Settings" tab.
+
 ## 4C. Automatic scoring
 
 Instructions for automatic scoring using this interface are below.

accusleepy/gui/text/manual_scoring_guide.md

@@ -2,6 +2,7 @@
 
 Keyboard shortcuts:
 - Mouse click on the upper 3 plots: jump to epoch
+- Mouse scroll on the upper 3 plots: zoom in/out along the x-axis
 - Ctrl + S: save labels to file
 - Right / left arrow: move one epoch forward / backward in time
 - Numbers 0-9: set current epoch to this brain state

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/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/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/temperature_scaling.py

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

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-0.9.3.dist-info → accusleepy-0.10.1.dist-info}/METADATA

@@ -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.