accusleepy 0.7.0__py3-none-any.whl → 0.7.1__py3-none-any.whl

accusleepy/constants.py

@@ -1,3 +1,5 @@
+import numpy as np
+
 # 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
@@ -9,9 +11,16 @@ EMG_COL = "emg"
 # label file columns
 BRAIN_STATE_COL = "brain_state"
 CONFIDENCE_SCORE_COL = "confidence_score"
+# max number of messages to store in main window message box
+MESSAGE_BOX_MAX_DEPTH = 200
+# clip mixture z-scores above and below this level
+# in the matlab implementation, 4.5 was used
+ABS_MAX_Z_SCORE = 3.5
+# upper frequency limit when generating EEG spectrograms
+SPECTROGRAM_UPPER_FREQ = 64
 
 
-# really don't change these
+# very unlikely you will want to change values from here onwards
 # config file location
 CONFIG_FILE = "config.json"
 # number of times to include the EMG power in a training image
@@ -20,8 +29,15 @@ EMG_COPIES = 9
 MIN_WINDOW_LEN = 5
 # frequency above which to downsample EEG spectrograms
 DOWNSAMPLING_START_FREQ = 20
-# upper frequency cutoff for EEG spectrograms
+# highest EEG frequency used as model input
 UPPER_FREQ = 50
+# height in pixels of each training image
+IMAGE_HEIGHT = (
+    len(np.arange(0, DOWNSAMPLING_START_FREQ, 1 / MIN_WINDOW_LEN))
+    + len(np.arange(DOWNSAMPLING_START_FREQ, UPPER_FREQ, 2 / MIN_WINDOW_LEN))
+    + EMG_COPIES
+)
+
 # classification model types
 DEFAULT_MODEL_TYPE = "default"  # current epoch is centered
 REAL_TIME_MODEL_TYPE = "real-time"  # current epoch on the right

accusleepy/gui/main.py

@@ -47,6 +47,7 @@ from accusleepy.constants import (
     DEFAULT_MOMENTUM,
     DEFAULT_TRAINING_EPOCHS,
     LABEL_FILE_TYPE,
+    MESSAGE_BOX_MAX_DEPTH,
     MODEL_FILE_TYPE,
     REAL_TIME_MODEL_TYPE,
     RECORDING_FILE_TYPES,
@@ -72,14 +73,15 @@ from accusleepy.signal_processing import (
     create_training_images,
     resample_and_standardize,
 )
+from accusleepy.validation import (
+    check_label_validity,
+    LABEL_LENGTH_ERROR,
+    check_config_consistency,
+)
 
 # note: functions using torch or scipy are lazily imported
 
-# max number of messages to display
-MESSAGE_BOX_MAX_DEPTH = 200
-LABEL_LENGTH_ERROR = "label file length does not match recording length"
-# relative path to config guide txt file
-CONFIG_GUIDE_FILE = os.path.normpath(r"text/config_guide.txt")
+# relative path to user manual
 MAIN_GUIDE_FILE = os.path.normpath(r"text/main_guide.md")
 
 
@@ -219,10 +221,9 @@ class AccuSleepWindow(QMainWindow):
 
         :param default_selected: whether default option is selected
         """
-        if default_selected:
-            self.model_type = DEFAULT_MODEL_TYPE
-        else:
-            self.model_type = REAL_TIME_MODEL_TYPE
+        self.model_type = (
+            DEFAULT_MODEL_TYPE if default_selected else REAL_TIME_MODEL_TYPE
+        )
 
     def export_recording_list(self) -> None:
         """Save current list of recordings to file"""
@@ -1279,11 +1280,11 @@ class AccuSleepWindow(QMainWindow):
             state.enabled_widget.stateChanged.connect(
                 partial(self.set_brain_state_enabled, digit)
             )
-            state.name_widget.editingFinished.connect(self.finished_editing_state_name)
+            state.name_widget.editingFinished.connect(self.check_config_validity)
             state.is_scored_widget.stateChanged.connect(
                 partial(self.is_scored_changed, digit)
             )
-            state.frequency_widget.valueChanged.connect(self.state_frequency_changed)
+            state.frequency_widget.valueChanged.connect(self.check_config_validity)
 
     def set_brain_state_enabled(self, digit, e) -> None:
         """Called when user clicks "enabled" checkbox
@@ -1309,17 +1310,6 @@ class AccuSleepWindow(QMainWindow):
         # check that configuration is valid
         _ = self.check_config_validity()
 
-    def finished_editing_state_name(self) -> None:
-        """Called when user finishes editing a brain state's name"""
-        _ = self.check_config_validity()
-
-    def state_frequency_changed(self, new_value) -> None:
-        """Called when user edits a brain state's frequency
-
-        :param new_value: unused
-        """
-        _ = self.check_config_validity()
-
     def is_scored_changed(self, digit, e) -> None:
         """Called when user sets whether a state is scored
 
@@ -1464,128 +1454,6 @@ class AccuSleepWindow(QMainWindow):
         self.ui.training_epochs_spinbox.setValue(DEFAULT_TRAINING_EPOCHS)
 
 
-def check_label_validity(
-    labels: np.array,
-    confidence_scores: np.array,
-    samples_in_recording: int,
-    sampling_rate: int | float,
-    epoch_length: int | float,
-    brain_state_set: BrainStateSet,
-) -> str | None:
-    """Check whether a set of brain state labels is valid
-
-    This returns an error message if a problem is found with the
-    brain state labels.
-
-    :param labels: brain state labels
-    :param confidence_scores: confidence scores
-    :param samples_in_recording: number of samples in the recording
-    :param sampling_rate: sampling rate, in Hz
-    :param epoch_length: epoch length, in seconds
-    :param brain_state_set: BrainStateMapper object
-    :return: error message
-    """
-    # check that number of labels is correct
-    samples_per_epoch = round(sampling_rate * epoch_length)
-    epochs_in_recording = round(samples_in_recording / samples_per_epoch)
-    if epochs_in_recording != labels.size:
-        return LABEL_LENGTH_ERROR
-
-    # check that entries are valid
-    if not set(labels.tolist()).issubset(
-        set([b.digit for b in brain_state_set.brain_states] + [UNDEFINED_LABEL])
-    ):
-        return "label file contains invalid entries"
-
-    if confidence_scores is not None:
-        if np.min(confidence_scores) < 0 or np.max(confidence_scores) > 1:
-            return "label file contains invalid confidence scores"
-
-    return None
-
-
-def check_config_consistency(
-    current_brain_states: dict,
-    model_brain_states: dict,
-    current_epoch_length: int | float,
-    model_epoch_length: int | float,
-) -> list[str]:
-    """Compare current brain state config to the model's config
-
-    This only displays warnings - the user should decide whether to proceed
-
-    :param current_brain_states: current brain state config
-    :param model_brain_states: brain state config when the model was created
-    :param current_epoch_length: current epoch length setting
-    :param model_epoch_length: epoch length used when the model was created
-    """
-    output = list()
-
-    # make lists of names and digits for scored brain states
-    current_scored_states = {
-        f: [b[f] for b in current_brain_states if b["is_scored"]]
-        for f in ["name", "digit"]
-    }
-    model_scored_states = {
-        f: [b[f] for b in model_brain_states if b["is_scored"]]
-        for f in ["name", "digit"]
-    }
-
-    # generate message comparing the brain state configs
-    config_comparisons = list()
-    for config, config_name in zip(
-        [current_scored_states, model_scored_states], ["current", "model's"]
-    ):
-        config_comparisons.append(
-            f"Scored brain states in {config_name} configuration: "
-            f"""{
-                ", ".join(
-                    [
-                        f"{x}: {y}"
-                        for x, y in zip(
-                            config["digit"],
-                            config["name"],
-                        )
-                    ]
-                )
-            }"""
-        )
-
-    # check if the number of scored states is different
-    len_diff = len(current_scored_states["name"]) - len(model_scored_states["name"])
-    if len_diff != 0:
-        output.append(
-            (
-                "WARNING: current brain state configuration has "
-                f"{'fewer' if len_diff < 0 else 'more'} "
-                "scored brain states than the model's configuration."
-            )
-        )
-        output = output + config_comparisons
-    else:
-        # the length is the same, but names might be different
-        if current_scored_states["name"] != model_scored_states["name"]:
-            output.append(
-                (
-                    "WARNING: current brain state configuration appears "
-                    "to contain different brain states than "
-                    "the model's configuration."
-                )
-            )
-            output = output + config_comparisons
-
-    if current_epoch_length != model_epoch_length:
-        output.append(
-            (
-                "Warning: the epoch length used when training this model "
-                f"({model_epoch_length} seconds) "
-                "does not match the current epoch length setting."
-            )
-        )
-
-    return output
-
-
 def run_primary_window() -> None:
     app = QApplication(sys.argv)
     AccuSleepWindow()

accusleepy/gui/manual_scoring.py

@@ -79,6 +79,12 @@ UNDEFINED_STATE = "undefined"
 SCROLL_BOUNDARY = 0.35
 # max number of sequential undo actions allowed
 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
 
 
 @dataclass
@@ -232,23 +238,6 @@ class ManualScoringWindow(QDialog):
         keypress_zoom_out_x = QShortcut(QKeySequence(Qt.Key.Key_Minus), self)
         keypress_zoom_out_x.activated.connect(partial(self.zoom_x, ZOOM_OUT))
 
-        keypress_modify_label = list()
-        for brain_state in self.brain_state_set.brain_states:
-            keypress_modify_label.append(
-                QShortcut(
-                    QKeySequence(Qt.Key[f"Key_{brain_state.digit}"]),
-                    self,
-                )
-            )
-            keypress_modify_label[-1].activated.connect(
-                partial(self.modify_current_epoch_label, brain_state.digit)
-            )
-
-        keypress_delete_label = QShortcut(QKeySequence(Qt.Key.Key_Backspace), self)
-        keypress_delete_label.activated.connect(
-            partial(self.modify_current_epoch_label, UNDEFINED_LABEL)
-        )
-
         keypress_quit = QShortcut(
             QKeySequence(QKeyCombination(Qt.Modifier.CTRL, Qt.Key.Key_W)),
             self,
@@ -261,36 +250,37 @@ class ManualScoringWindow(QDialog):
         )
         keypress_save.activated.connect(self.save)
 
+        keypress_modify_label = list()
         keypress_roi = list()
-        for brain_state in self.brain_state_set.brain_states:
+        digit_key_label_pairs = [
+            (Qt.Key[f"Key_{brain_state.digit}"], brain_state.digit)
+            for brain_state in self.brain_state_set.brain_states
+        ] + [(Qt.Key.Key_Backspace, UNDEFINED_LABEL)]
+
+        for digit_key, digit_label in digit_key_label_pairs:
+            keypress_modify_label.append(
+                QShortcut(
+                    QKeySequence(digit_key),
+                    self,
+                )
+            )
+            keypress_modify_label[-1].activated.connect(
+                partial(self.modify_current_epoch_label, digit_label)
+            )
             keypress_roi.append(
                 QShortcut(
                     QKeySequence(
                         QKeyCombination(
                             Qt.Modifier.SHIFT,
-                            Qt.Key[f"Key_{brain_state.digit}"],
+                            digit_key,
                         )
                     ),
                     self,
                 )
             )
             keypress_roi[-1].activated.connect(
-                partial(self.enter_label_roi_mode, brain_state.digit)
-            )
-        keypress_roi.append(
-            QShortcut(
-                QKeySequence(
-                    QKeyCombination(
-                        Qt.Modifier.SHIFT,
-                        Qt.Key.Key_Backspace,
-                    )
-                ),
-                self,
+                partial(self.enter_label_roi_mode, digit_label)
             )
-        )
-        keypress_roi[-1].activated.connect(
-            partial(self.enter_label_roi_mode, UNDEFINED_LABEL)
-        )
 
         keypress_esc = QShortcut(QKeySequence(Qt.Key.Key_Escape), self)
         keypress_esc.activated.connect(self.exit_label_roi_mode)
@@ -626,9 +616,9 @@ class ManualScoringWindow(QDialog):
         """
         vmin, vmax = self.ui.upperfigure.spec_ref.get_clim()
         if direction == BRIGHTER:
-            self.ui.upperfigure.spec_ref.set(clim=(vmin, vmax * 0.96))
+            self.ui.upperfigure.spec_ref.set(clim=(vmin, vmax * BRIGHTER_SCALE_FACTOR))
         else:
-            self.ui.upperfigure.spec_ref.set(clim=(vmin, vmax * 1.07))
+            self.ui.upperfigure.spec_ref.set(clim=(vmin, vmax * DIMMER_SCALE_FACTOR))
         self.ui.upperfigure.canvas.draw()
 
     def update_epochs_shown(self, direction: str) -> None:
@@ -725,31 +715,29 @@ class ManualScoringWindow(QDialog):
 
         :param direction: in, out, or reset
         """
-        zoom_in_factor = 0.45
-        zoom_out_factor = 1.017
         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),
+                    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),
+                    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)]
+                [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)]
+                [self.n_epochs - 1, round(self.epoch + ZOOM_OUT_FACTOR * epochs_shown)]
             )
 
         else:  # reset
@@ -1085,7 +1073,9 @@ def create_upper_emg_signal(
         epoch_length,
         emg_filter,
     )
-    return np.clip(emg_rms, np.min(emg_rms), np.mean(emg_rms) + np.std(emg_rms) * 2.5)
+    return np.clip(
+        emg_rms, np.percentile(emg_rms, 0.1), np.mean(emg_rms) + np.std(emg_rms) * 2.5
+    )
 
 
 def transform_eeg_emg(eeg: np.array, emg: np.array) -> (np.array, np.array):

accusleepy/gui/primary_window.py

@@ -8,8 +8,20 @@
 ## WARNING! All changes made in this file will be lost when recompiling UI file!
 ################################################################################
 
-from PySide6.QtCore import QCoreApplication, QMetaObject, QRect, QSize, Qt
-from PySide6.QtGui import QBrush, QColor, QFont, QIcon, QPalette
+from PySide6.QtCore import (
+    QCoreApplication,
+    QMetaObject,
+    QRect,
+    QSize,
+    Qt,
+)
+from PySide6.QtGui import (
+    QBrush,
+    QColor,
+    QFont,
+    QIcon,
+    QPalette,
+)
 from PySide6.QtWidgets import (
     QCheckBox,
     QComboBox,
@@ -2785,7 +2797,10 @@ class Ui_PrimaryWindow(object):
             QCoreApplication.translate("PrimaryWindow", "MainWindow", None)
         )
         self.epochlengthlabel.setText(
-            QCoreApplication.translate("PrimaryWindow", "Epoch length (sec):", None)
+            QCoreApplication.translate("PrimaryWindow", "Epoch length:", None)
+        )
+        self.epoch_length_input.setSuffix(
+            QCoreApplication.translate("PrimaryWindow", " sec", None)
         )
         self.recordinglistgroupbox.setTitle(
             QCoreApplication.translate("PrimaryWindow", "Recording list", None)
@@ -2840,7 +2855,10 @@ class Ui_PrimaryWindow(object):
             )
         )
         self.samplingratelabel.setText(
-            QCoreApplication.translate("PrimaryWindow", "Sampling rate (Hz):", None)
+            QCoreApplication.translate("PrimaryWindow", "Sampling rate:", None)
+        )
+        self.sampling_rate_input.setSuffix(
+            QCoreApplication.translate("PrimaryWindow", " Hz", None)
         )
         # if QT_CONFIG(tooltip)
         self.recording_file_button.setToolTip(
@@ -2948,11 +2966,12 @@ class Ui_PrimaryWindow(object):
             QCoreApplication.translate("PrimaryWindow", "Save confidence scores", None)
         )
         self.boutlengthlabel.setText(
-            QCoreApplication.translate(
-                "PrimaryWindow", "Minimum bout length (sec):", None
-            )
+            QCoreApplication.translate("PrimaryWindow", "Minimum bout length:", None)
         )
         self.bout_length_input.setPrefix("")
+        self.bout_length_input.setSuffix(
+            QCoreApplication.translate("PrimaryWindow", " sec", None)
+        )
         self.lower_tab_widget.setTabText(
             self.lower_tab_widget.indexOf(self.classification_tab),
             QCoreApplication.translate("PrimaryWindow", "Classification", None),
@@ -3096,6 +3115,9 @@ class Ui_PrimaryWindow(object):
         self.label_17.setText(
             QCoreApplication.translate("PrimaryWindow", "Epoch length:", None)
         )
+        self.default_epoch_input.setSuffix(
+            QCoreApplication.translate("PrimaryWindow", " sec", None)
+        )
         self.overwrite_default_checkbox.setText(
             QCoreApplication.translate(
                 "PrimaryWindow", "Only overwrite undefined epochs", None
@@ -3105,9 +3127,10 @@ class Ui_PrimaryWindow(object):
             QCoreApplication.translate("PrimaryWindow", "Save confidence scores", None)
         )
         self.label_19.setText(
-            QCoreApplication.translate(
-                "PrimaryWindow", "Minimum bout length (sec):", None
-            )
+            QCoreApplication.translate("PrimaryWindow", "Minimum bout length:", None)
+        )
+        self.default_min_bout_length_spinbox.setSuffix(
+            QCoreApplication.translate("PrimaryWindow", " sec", None)
         )
         self.ui_default_description_label.setText(
             QCoreApplication.translate(

accusleepy/gui/primary_window.ui

@@ -152,7 +152,7 @@
                  </sizepolicy>
                 </property>
                 <property name="text">
-                 <string>Epoch length (sec):</string>
+                 <string>Epoch length:</string>
                 </property>
                </widget>
               </item>
@@ -167,6 +167,9 @@
                 <property name="alignment">
                  <set>Qt::AlignmentFlag::AlignLeading|Qt::AlignmentFlag::AlignLeft|Qt::AlignmentFlag::AlignVCenter</set>
                 </property>
+                <property name="suffix">
+                 <string> sec</string>
+                </property>
                 <property name="maximum">
                  <double>100000.000000000000000</double>
                 </property>
@@ -529,7 +532,7 @@ color: rgb(244, 195, 68);</string>
                       </sizepolicy>
                      </property>
                      <property name="text">
-                      <string>Sampling rate (Hz):</string>
+                      <string>Sampling rate:</string>
                      </property>
                     </widget>
                    </item>
@@ -544,6 +547,9 @@ color: rgb(244, 195, 68);</string>
                      <property name="alignment">
                       <set>Qt::AlignmentFlag::AlignLeading|Qt::AlignmentFlag::AlignLeft|Qt::AlignmentFlag::AlignVCenter</set>
                      </property>
+                     <property name="suffix">
+                      <string> Hz</string>
+                     </property>
                      <property name="minimum">
                       <double>0.000000000000000</double>
                      </property>
@@ -1148,7 +1154,7 @@ color: rgb(244, 195, 68);</string>
                            <string notr="true">background-color: transparent;</string>
                           </property>
                           <property name="text">
-                           <string>Minimum bout length (sec):</string>
+                           <string>Minimum bout length:</string>
                           </property>
                          </widget>
                         </item>
@@ -1166,6 +1172,9 @@ color: rgb(244, 195, 68);</string>
                           <property name="prefix">
                            <string/>
                           </property>
+                          <property name="suffix">
+                           <string> sec</string>
+                          </property>
                           <property name="decimals">
                            <number>2</number>
                           </property>
@@ -3811,6 +3820,9 @@ Each brain state has several attributes:
                           <verstretch>0</verstretch>
                          </sizepolicy>
                         </property>
+                        <property name="suffix">
+                         <string> sec</string>
+                        </property>
                         <property name="maximum">
                          <double>100000.000000000000000</double>
                         </property>
@@ -3920,7 +3932,7 @@ Each brain state has several attributes:
                          </sizepolicy>
                         </property>
                         <property name="text">
-                         <string>Minimum bout length (sec):</string>
+                         <string>Minimum bout length:</string>
                         </property>
                        </widget>
                       </item>
@@ -3932,6 +3944,9 @@ Each brain state has several attributes:
                           <verstretch>0</verstretch>
                          </sizepolicy>
                         </property>
+                        <property name="suffix">
+                         <string> sec</string>
+                        </property>
                         <property name="maximum">
                          <double>1000.000000000000000</double>
                         </property>

accusleepy/models.py

@@ -1,24 +1,13 @@
-import numpy as np
 from torch import device, flatten, nn
 from torch import load as torch_load
 from torch import save as torch_save
 
 from accusleepy.brain_state_set import BRAIN_STATES_KEY, BrainStateSet
 from accusleepy.constants import (
-    DOWNSAMPLING_START_FREQ,
-    EMG_COPIES,
-    MIN_WINDOW_LEN,
-    UPPER_FREQ,
+    IMAGE_HEIGHT,
 )
 from accusleepy.temperature_scaling import ModelWithTemperature
 
-# height in pixels of each training image
-IMAGE_HEIGHT = (
-    len(np.arange(0, DOWNSAMPLING_START_FREQ, 1 / MIN_WINDOW_LEN))
-    + len(np.arange(DOWNSAMPLING_START_FREQ, UPPER_FREQ, 2 / MIN_WINDOW_LEN))
-    + EMG_COPIES
-)
-
 
 class SSANN(nn.Module):
     """Small CNN for classifying images"""

accusleepy/signal_processing.py

@@ -8,6 +8,7 @@ from tqdm import trange
 
 from accusleepy.brain_state_set import BrainStateSet
 from accusleepy.constants import (
+    ABS_MAX_Z_SCORE,
     ANNOTATIONS_FILENAME,
     CALIBRATION_ANNOTATION_FILENAME,
     DEFAULT_MODEL_TYPE,
@@ -17,18 +18,13 @@ from accusleepy.constants import (
     LABEL_COL,
     MIN_WINDOW_LEN,
     UPPER_FREQ,
+    SPECTROGRAM_UPPER_FREQ,
 )
 from accusleepy.fileio import Recording, load_labels, load_recording, EMGFilter
 from accusleepy.multitaper import spectrogram
 
 # note: scipy is lazily imported
 
-# clip mixture z-scores above and below this level
-# in the matlab implementation, I used 4.5
-ABS_MAX_Z_SCORE = 3.5
-# upper frequency limit when generating EEG spectrograms
-SPECTROGRAM_UPPER_FREQ = 64
-
 
 def resample(
     eeg: np.array, emg: np.array, sampling_rate: int | float, epoch_length: int | float

accusleepy/validation.py

@@ -0,0 +1,128 @@
+import numpy as np
+
+from accusleepy.brain_state_set import BrainStateSet
+from accusleepy.constants import UNDEFINED_LABEL
+
+LABEL_LENGTH_ERROR = "label file length does not match recording length"
+
+
+def check_label_validity(
+    labels: np.array,
+    confidence_scores: np.array,
+    samples_in_recording: int,
+    sampling_rate: int | float,
+    epoch_length: int | float,
+    brain_state_set: BrainStateSet,
+) -> str | None:
+    """Check whether a set of brain state labels is valid
+
+    This returns an error message if a problem is found with the
+    brain state labels.
+
+    :param labels: brain state labels
+    :param confidence_scores: confidence scores
+    :param samples_in_recording: number of samples in the recording
+    :param sampling_rate: sampling rate, in Hz
+    :param epoch_length: epoch length, in seconds
+    :param brain_state_set: BrainStateMapper object
+    :return: error message
+    """
+    # check that number of labels is correct
+    samples_per_epoch = round(sampling_rate * epoch_length)
+    epochs_in_recording = round(samples_in_recording / samples_per_epoch)
+    if epochs_in_recording != labels.size:
+        return LABEL_LENGTH_ERROR
+
+    # check that entries are valid
+    if not set(labels.tolist()).issubset(
+        set([b.digit for b in brain_state_set.brain_states] + [UNDEFINED_LABEL])
+    ):
+        return "label file contains invalid entries"
+
+    if confidence_scores is not None:
+        if np.min(confidence_scores) < 0 or np.max(confidence_scores) > 1:
+            return "label file contains invalid confidence scores"
+
+    return None
+
+
+def check_config_consistency(
+    current_brain_states: dict,
+    model_brain_states: dict,
+    current_epoch_length: int | float,
+    model_epoch_length: int | float,
+) -> list[str]:
+    """Compare current brain state config to the model's config
+
+    This only displays warnings - the user should decide whether to proceed
+
+    :param current_brain_states: current brain state config
+    :param model_brain_states: brain state config when the model was created
+    :param current_epoch_length: current epoch length setting
+    :param model_epoch_length: epoch length used when the model was created
+    """
+    output = list()
+
+    # make lists of names and digits for scored brain states
+    current_scored_states = {
+        f: [b[f] for b in current_brain_states if b["is_scored"]]
+        for f in ["name", "digit"]
+    }
+    model_scored_states = {
+        f: [b[f] for b in model_brain_states if b["is_scored"]]
+        for f in ["name", "digit"]
+    }
+
+    # generate message comparing the brain state configs
+    config_comparisons = list()
+    for config, config_name in zip(
+        [current_scored_states, model_scored_states], ["current", "model's"]
+    ):
+        config_comparisons.append(
+            f"Scored brain states in {config_name} configuration: "
+            f"""{
+                ", ".join(
+                    [
+                        f"{x}: {y}"
+                        for x, y in zip(
+                            config["digit"],
+                            config["name"],
+                        )
+                    ]
+                )
+            }"""
+        )
+
+    # check if the number of scored states is different
+    len_diff = len(current_scored_states["name"]) - len(model_scored_states["name"])
+    if len_diff != 0:
+        output.append(
+            (
+                "WARNING: current brain state configuration has "
+                f"{'fewer' if len_diff < 0 else 'more'} "
+                "scored brain states than the model's configuration."
+            )
+        )
+        output = output + config_comparisons
+    else:
+        # the length is the same, but names might be different
+        if current_scored_states["name"] != model_scored_states["name"]:
+            output.append(
+                (
+                    "WARNING: current brain state configuration appears "
+                    "to contain different brain states than "
+                    "the model's configuration."
+                )
+            )
+            output = output + config_comparisons
+
+    if current_epoch_length != model_epoch_length:
+        output.append(
+            (
+                "Warning: the epoch length used when training this model "
+                f"({model_epoch_length} seconds) "
+                "does not match the current epoch length setting."
+            )
+        )
+
+    return output

{accusleepy-0.7.0.dist-info → accusleepy-0.7.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: accusleepy
-Version: 0.7.0
+Version: 0.7.1
 Summary: Python implementation of AccuSleep
 License: GPL-3.0-only
 Author: Zeke Barger
@@ -76,6 +76,7 @@ to the [config file](accusleepy/config.json).
 
 ## Changelog
 
+- 0.7.1: Bugfixes, code cleanup
 - 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-0.7.0.dist-info → accusleepy-0.7.1.dist-info}/RECORD

@@ -4,7 +4,7 @@ accusleepy/bouts.py,sha256=F_y6DxnpKFfImYb7vCZluZ2eD5I_33gZXmRM8mvebsg,5679
 accusleepy/brain_state_set.py,sha256=fRkrArHLIbEKimub804yt_mUXoyfsjJEfiJnTjeCMkY,3233
 accusleepy/classification.py,sha256=mF35xMrD9QXGldSnl3vkdHbm7CAptPUNjHxUA_agOTA,9778
 accusleepy/config.json,sha256=Ip0qTMAn2LZfof9GVA_azOvpXP0WKnqLCZeSaya1sss,819
-accusleepy/constants.py,sha256=t7x-wzncJ_wVm0Oj6LiUzGukpsTsxfhO0KJiAAsuMN4,2244
+accusleepy/constants.py,sha256=r53FWeMMefuKA-mR_b2E1KBeJbq2Ck9c5VHoJ1WGZjg,2815
 accusleepy/fileio.py,sha256=woIF0zgJt6Lx6T9KBXAQ-AlbQAwOK1_RUmVF710nltI,7383
 accusleepy/gui/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 accusleepy/gui/icons/brightness_down.png,sha256=PLT1fb83RHIhSRuU7MMMx0G7oJAY7o9wUcnqM8veZfM,12432
@@ -18,24 +18,25 @@ accusleepy/gui/icons/save.png,sha256=J3EA8iU1BqLYRSsrq_OdoZlqrv2yfL7oV54DklTy_DI
 accusleepy/gui/icons/up_arrow.png,sha256=V9yF9t1WgjPaUu-mF1YGe_DfaRHg2dUpR_sUVVcvVvY,3329
 accusleepy/gui/icons/zoom_in.png,sha256=MFWnKZp7Rvh4bLPq4Cqo4sB_jQYedUUtT8-ZO8tNYyc,13589
 accusleepy/gui/icons/zoom_out.png,sha256=IB8Jecb3i0U4qjWRR46ridjLpvLCSe7PozBaLqQqYSw,13055
-accusleepy/gui/images/primary_window.png,sha256=ABu49UXTBfI5UwNHrpWPhJoTC7zhyLVvbsbywIuu1nc,602640
+accusleepy/gui/images/primary_window.png,sha256=VVCjwolHsi4HdYehe3ZG_QpZ0XK39Qrz4Q6SqBAc5Cg,597045
 accusleepy/gui/images/viewer_window.png,sha256=b_B7m9WSLMAOzNjctq76SyekO1WfC6qYZVNnYfhjPe8,977197
 accusleepy/gui/images/viewer_window_annotated.png,sha256=uMNUmsZIdzDlQpyoiS3lJGoWlg_T325Oj5hDZhM3Y14,146817
-accusleepy/gui/main.py,sha256=Ywk3XwfwMjAZL76qwDnZRHQ96L7T1DWyMCU8la0N5Qg,62447
-accusleepy/gui/manual_scoring.py,sha256=xk0TERVbH33owj4QYJkMA2LF_qR8jtS5W2enq36_njk,40907
+accusleepy/gui/main.py,sha256=sLHe1imVU6xz3f6sJ9u7sxrTny9X213ev29ldoxXpX0,57740
+accusleepy/gui/manual_scoring.py,sha256=7jKdw-D9HdpYC2G_2RHt5UALLMjrIsP-hvLFkNM25Ek,40553
 accusleepy/gui/mplwidget.py,sha256=rJSTtWmLjHn8r3c9Kb23Rc4XzXl3i9B-JrjNjjlNnmQ,13492
-accusleepy/gui/primary_window.py,sha256=sVIsZXnszBsq3ZUC9OIOwB13jPQRcisaxi0Vg-O6A-8,135475
-accusleepy/gui/primary_window.ui,sha256=_SorGY7qJG2B6e45UNt51OheeYLkpzAxxezX1hEfI3Y,201341
+accusleepy/gui/primary_window.py,sha256=Qc3WWiwJHbgmGDzGzNI3fBycBKtlpT5YdskwnHr6OWs,136070
+accusleepy/gui/primary_window.ui,sha256=u7HQdeNKObKsUSOlk91gEMat-RrXITEsnBedZPd7y6Y,201950
 accusleepy/gui/resources.qrc,sha256=wqPendnTLAuKfVI6v2lKHiRqAWM0oaz2ZuF5cucJdS4,803
 accusleepy/gui/resources_rc.py,sha256=Z2e34h30U4snJjnYdZVV9B6yjATKxxfvgTRt5uXtQdo,329727
 accusleepy/gui/text/main_guide.md,sha256=iZDRp5OWyQX9LV7CMeUFIYv2ryKlIcGALRLXjxR8HpI,8288
 accusleepy/gui/text/manual_scoring_guide.md,sha256=ow_RMSjFy05NupEDSCuJtu-V65-BPnIkrZqtssFoZCQ,999
 accusleepy/gui/viewer_window.py,sha256=O4ceqLMYdahxQ9s6DYhloUnNESim-cqIZxFeXEiRjog,24444
 accusleepy/gui/viewer_window.ui,sha256=jsjydsSSyN49AwJw4nVS2mEJ2JBIUTXesAJsij1JNV0,31530
-accusleepy/models.py,sha256=15VjtFoWaYXblyGPbtYgp0yJdyUfGu7t3zCShdtr_7c,3799
+accusleepy/models.py,sha256=kqkcQJoKi7gpnM8gZ7nZbWGvpv7ruNnFLaB7ED1X6Dc,3493
 accusleepy/multitaper.py,sha256=D5-iglwkFBRciL5tKSNcunMtcq0rM3zHwRHUVPgem1U,25679
-accusleepy/signal_processing.py,sha256=NOkQuLmUVINd0tFvt48RXRxSl4TDjV42m54XWc_EB9s,16987
+accusleepy/signal_processing.py,sha256=47fEAx8Aqqkiqix1ai2YEK9Fhq6UHoQcwAcOi-a8ewo,16834
 accusleepy/temperature_scaling.py,sha256=glvPcvxHpBdFjwjGfZdNku9L_BozycEmdqZhKKUCCNg,5749
-accusleepy-0.7.0.dist-info/METADATA,sha256=yLkBaWfg1wrN7DevZlLLg881Yq9hhGoTsqHSgCJ0IYk,4536
-accusleepy-0.7.0.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-accusleepy-0.7.0.dist-info/RECORD,,
+accusleepy/validation.py,sha256=VpLWK-wD5tCU6lTBG3KYgTi3PWGuYh6NitMgMoMH8JM,4434
+accusleepy-0.7.1.dist-info/METADATA,sha256=UXIUq2dyYIn7ehR0V0aq3NctxurAodZGGCnFrcNXj6c,4568
+accusleepy-0.7.1.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+accusleepy-0.7.1.dist-info/RECORD,,