accusleepy 0.6.0__py3-none-any.whl → 0.7.0__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/signal_processing.py

@@ -18,7 +18,7 @@ from accusleepy.constants import (
     MIN_WINDOW_LEN,
     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
@@ -172,7 +172,10 @@ 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 +185,14 @@ 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 +215,7 @@ 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 +227,7 @@ 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 +243,7 @@ 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 +372,7 @@ def create_training_images(
     brain_state_set: BrainStateSet,
     model_type: str,
     calibration_fraction: float,
+    emg_filter: EMGFilter,
 ) -> list[int]:
     """Create training dataset
 
@@ -385,6 +387,7 @@ 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 +412,9 @@ 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-0.6.0.dist-info → accusleepy-0.7.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: accusleepy
-Version: 0.6.0
+Version: 0.7.0
 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 +76,7 @@ to the [config file](accusleepy/config.json).
 
 ## Changelog
 
+- 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-0.7.0.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=t7x-wzncJ_wVm0Oj6LiUzGukpsTsxfhO0KJiAAsuMN4,2244
+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 +18,24 @@ 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=ABu49UXTBfI5UwNHrpWPhJoTC7zhyLVvbsbywIuu1nc,602640
 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=Ywk3XwfwMjAZL76qwDnZRHQ96L7T1DWyMCU8la0N5Qg,62447
+accusleepy/gui/manual_scoring.py,sha256=xk0TERVbH33owj4QYJkMA2LF_qR8jtS5W2enq36_njk,40907
 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=sVIsZXnszBsq3ZUC9OIOwB13jPQRcisaxi0Vg-O6A-8,135475
+accusleepy/gui/primary_window.ui,sha256=_SorGY7qJG2B6e45UNt51OheeYLkpzAxxezX1hEfI3Y,201341
 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/multitaper.py,sha256=D5-iglwkFBRciL5tKSNcunMtcq0rM3zHwRHUVPgem1U,25679
-accusleepy/signal_processing.py,sha256=sEol01SlwOVwBmKHR-saVhneAA0jr98pcZZ-02uUy2Q,16739
+accusleepy/signal_processing.py,sha256=NOkQuLmUVINd0tFvt48RXRxSl4TDjV42m54XWc_EB9s,16987
 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-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/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.