accusleepy 0.6.0__py3-none-any.whl → 0.7.1__py3-none-any.whl

accusleepy/gui/text/main_guide.md

@@ -29,7 +29,8 @@ At this point, you can score the recordings manually.
 5. Score all recordings automatically using the classifier
 
 By default, there are three brain state options: REM, wake, and NREM.
-If you want to change this configuration, click the "Settings" tab.
+If you want to change this configuration, click the "Settings" tab and
+choose "Brain states" from the drop-down menu.
 Note that if you change the configuration, you might be unable to load
 existing labels and calibration data, and you may need to train a new
 classification model.

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
+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
@@ -172,7 +168,10 @@ def create_spectrogram(
 
 
 def get_emg_power(
-    emg: np.array, sampling_rate: int | float, epoch_length: int | float
+    emg: np.array,
+    sampling_rate: int | float,
+    epoch_length: int | float,
+    emg_filter: EMGFilter,
 ) -> np.array:
     """Calculate EMG power for each epoch
 
@@ -182,18 +181,14 @@ def get_emg_power(
     :param emg: EMG signal
     :param sampling_rate: sampling rate, in Hz
     :param epoch_length: epoch length, in seconds
+    :param emg_filter: EMG filter parameters
     :return: EMG "power" for each epoch
     """
     from scipy.signal import butter, filtfilt
 
-    # filter parameters
-    order = 8
-    bp_lower = 20
-    bp_upper = 50
-
     b, a = butter(
-        N=order,
-        Wn=[bp_lower, bp_upper],
+        N=emg_filter.order,
+        Wn=[emg_filter.bp_lower, emg_filter.bp_upper],
         btype="bandpass",
         output="ba",
         fs=sampling_rate,
@@ -216,6 +211,7 @@ def create_eeg_emg_image(
     emg: np.array,
     sampling_rate: int | float,
     epoch_length: int | float,
+    emg_filter: EMGFilter,
 ) -> np.array:
     """Stack EEG spectrogram and EMG power into an image
 
@@ -227,6 +223,7 @@ def create_eeg_emg_image(
     :param emg: EMG signal
     :param sampling_rate: sampling rate, in Hz
     :param epoch_length: epoch length, in seconds
+    :param emg_filter: EMG filter parameters
     :return: combined EEG + EMG image for a recording
     """
     spec, f = create_spectrogram(eeg, sampling_rate, epoch_length)
@@ -242,7 +239,7 @@ def create_eeg_emg_image(
         ]
     )
 
-    emg_log_rms = get_emg_power(emg, sampling_rate, epoch_length)
+    emg_log_rms = get_emg_power(emg, sampling_rate, epoch_length, emg_filter)
     output = np.concatenate(
         [modified_spectrogram, np.tile(emg_log_rms, (EMG_COPIES, 1))]
     )
@@ -371,6 +368,7 @@ def create_training_images(
     brain_state_set: BrainStateSet,
     model_type: str,
     calibration_fraction: float,
+    emg_filter: EMGFilter,
 ) -> list[int]:
     """Create training dataset
 
@@ -385,6 +383,7 @@ def create_training_images(
     :param brain_state_set: set of brain state options
     :param model_type: default or real-time
     :param calibration_fraction: fraction of training data to use for calibration
+    :param emg_filter: EMG filter parameters
     :return: list of the names of any recordings that could not
             be used to create training images.
     """
@@ -409,7 +408,9 @@ def create_training_images(
 
             labels, _ = load_labels(recording.label_file)
             labels = brain_state_set.convert_digit_to_class(labels)
-            img = create_eeg_emg_image(eeg, emg, sampling_rate, epoch_length)
+            img = create_eeg_emg_image(
+                eeg, emg, sampling_rate, epoch_length, emg_filter
+            )
             img = mixture_z_score_img(
                 img=img, brain_state_set=brain_state_set, labels=labels
             )

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-0.6.0.dist-info → accusleepy-0.7.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: accusleepy
-Version: 0.6.0
+Version: 0.7.1
 Summary: Python implementation of AccuSleep
 License: GPL-3.0-only
 Author: Zeke Barger
@@ -39,6 +39,7 @@ It offers the following improvements over the MATLAB version (AccuSleep):
     - Model files contain useful metadata (brain state configuration,
       epoch length, number of epochs)
     - Models optimized for real-time scoring can be trained
+- Confidence scores can be saved and visualized
 - Lists of recordings can be imported and exported for repeatable batch processing
 - Undo/redo functionality in the manual scoring interface
 
@@ -75,6 +76,8 @@ 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.
 - 0.5.0: Performance improvements

{accusleepy-0.6.0.dist-info → accusleepy-0.7.1.dist-info}/RECORD

@@ -2,10 +2,10 @@ accusleepy/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 accusleepy/__main__.py,sha256=dKzl2N2Hg9lD264CWYNxThRyDKzWwyMwHRXmJxOmMis,104
 accusleepy/bouts.py,sha256=F_y6DxnpKFfImYb7vCZluZ2eD5I_33gZXmRM8mvebsg,5679
 accusleepy/brain_state_set.py,sha256=fRkrArHLIbEKimub804yt_mUXoyfsjJEfiJnTjeCMkY,3233
-accusleepy/classification.py,sha256=wg0EoUrXAYqdUWr6SyJDl_5Jzx7lck9ta3-dsGzD208,9180
-accusleepy/config.json,sha256=n-CTGn7hljHQ7MKRMvGvwCAzcjWmUuqzAWrnXnk2pGU,501
-accusleepy/constants.py,sha256=0gIzZY544Y1tL-n0HxFsCMzBdprOKNYVYlNxF45o3kw,1652
-accusleepy/fileio.py,sha256=z6Cuhue__-RL7s3jjY23IjMl8nhow3P1mDx7j_rRLo4,5441
+accusleepy/classification.py,sha256=mF35xMrD9QXGldSnl3vkdHbm7CAptPUNjHxUA_agOTA,9778
+accusleepy/config.json,sha256=Ip0qTMAn2LZfof9GVA_azOvpXP0WKnqLCZeSaya1sss,819
+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
 accusleepy/gui/icons/brightness_up.png,sha256=64GnUqgPvN5xZ6Um3wOzwqvUmdAWYZT6eFmWpBsHyks,12989
@@ -18,25 +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=rlEflF0w3IdwQKDo3tejqSmfNp8omoxgI8sVDqF3hto,600458
+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=npQbJ11fV3lpKaoChdjRI-KsgneM-IQRrWZkSDHBkWI,57737
-accusleepy/gui/manual_scoring.py,sha256=QD3T-0vEH5E08Vw6YAzp7eBETsNTRU4BGuyzm-3oMfI,40635
+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=N-hEI39lQdGSEGq1quxSPLIMuNqhTkGWKM89BL3KgVM,108377
-accusleepy/gui/primary_window.ui,sha256=5bSa6c5idYCpnwWZ5Vt3ecrJsC8hiD0JTPLSf_20H2g,153744
+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/config_guide.txt,sha256=xYnVTojDXKph13QBj7mpfjQYa-xmpLkhF19G_bz3xbA,1027
-accusleepy/gui/text/main_guide.md,sha256=bl5RDSh-kD44Ch3bVo_Hl7Cn3n8dfh9xHjKKH4ORgS8,8238
+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=sEol01SlwOVwBmKHR-saVhneAA0jr98pcZZ-02uUy2Q,16739
+accusleepy/signal_processing.py,sha256=47fEAx8Aqqkiqix1ai2YEK9Fhq6UHoQcwAcOi-a8ewo,16834
 accusleepy/temperature_scaling.py,sha256=glvPcvxHpBdFjwjGfZdNku9L_BozycEmdqZhKKUCCNg,5749
-accusleepy-0.6.0.dist-info/METADATA,sha256=D2BHcAVQmF4M7ZkCwEiBjIQ6q6aMgcEQghNNtZFb2c8,4437
-accusleepy-0.6.0.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-accusleepy-0.6.0.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,,

accusleepy/gui/text/config_guide.txt

@@ -1,27 +0,0 @@
-This is the current brain state configuration.
-If you make changes, click 'Save' to store them.
-
-Each brain state has several attributes:
-
-- Digit: how the brain state is represented in label files,
-    and the key on the keyboard that, during manual scoring,
-    sets an epoch to this brain state.
-
-- Enabled: whether a brain state for this digit exists.
-
-- Name: unique name of the brain state (e.g., REM).
-
-- Scored: whether a classification model should output this
-    brain state. If you have a state that corresponds to
-    missing or corrupted data, for example, you would
-    probably want to uncheck this box.
-
-- Frequency: approximate relative frequency of this brain
-    state. Does not need to be very accurate, but it can
-    influence classification accuracy slightly. The values
-    for all scored brain states must sum to 1.
-
-Important notes:
-- Changing these settings can invalidate existing label files,
-    calibration files, and trained models!
-- Reinstalling AccuSleePy will overwrite this configuration.