accusleepy 0.8.0__py3-none-any.whl → 0.8.1__py3-none-any.whl

accusleepy/bouts.py

@@ -11,7 +11,7 @@ class Bout:
 
     length: int  # length, in number of epochs
     start_index: int  # index where bout starts
-    end_index: int  # index where bout ends
+    end_index: int  # index where bout ends (non-inclusive)
     surrounding_state: int  # brain state on both sides of the bout
 
 
@@ -41,6 +41,44 @@ def find_last_adjacent_bout(sorted_bouts: list[Bout], bout_index: int) -> int:
         return bout_index
 
 
+def find_short_bouts(
+    labels: np.array, min_epochs: int, brain_states: set[int]
+) -> list[Bout]:
+    """Locate all brain state bouts below a minimum length
+
+    :param labels: brain state labels (digits in the 0-9 range)
+    :param min_epochs: minimum number of epochs in a bout
+    :param brain_states: set of brain states in the labels
+    :return: list of Bout objects
+    """
+    # convert labels to a string for regex search
+    # There is probably a regex that can find all patterns like ab+a
+    # without consuming each "a" but I haven't found it :(
+    label_string = "".join(labels.astype(str))
+    bouts = list()
+    for state in brain_states:
+        for other_state in brain_states:
+            if state == other_state:
+                continue
+            # get start and end indices of each bout
+            expression = (
+                f"(?<={other_state}){state}{{1,{min_epochs - 1}}}(?={other_state})"
+            )
+            matches = re.finditer(expression, label_string)
+            spans = [match.span() for match in matches]
+
+            for span in spans:
+                bouts.append(
+                    Bout(
+                        length=span[1] - span[0],
+                        start_index=span[0],
+                        end_index=span[1],
+                        surrounding_state=other_state,
+                    )
+                )
+    return bouts
+
+
 def enforce_min_bout_length(
     labels: np.array, epoch_length: int | float, min_bout_length: int | float
 ) -> np.array:
@@ -61,11 +99,9 @@ def enforce_min_bout_length(
     :param min_bout_length: minimum bout length, in seconds
     :return: updated brain state labels
     """
-    # if recording is very short, don't change anything
-    if labels.size < 3:
-        return labels
-
-    if epoch_length == min_bout_length:
+    # if the recording is very short or the minimum bout length
+    # is one epoch long, don't change anything
+    if labels.size < 3 or epoch_length == min_bout_length:
         return labels
 
     # get minimum number of epochs in a bout
@@ -73,36 +109,8 @@ def enforce_min_bout_length(
     # get set of states in the labels
     brain_states = set(labels.tolist())
 
-    while True:  # so true
-        # convert labels to a string for regex search
-        # There is probably a regex that can find all patterns like ab+a
-        # without consuming each "a" but I haven't found it :(
-        label_string = "".join(labels.astype(str))
-
-        bouts = list()
-
-        for state in brain_states:
-            for other_state in brain_states:
-                if state == other_state:
-                    continue
-                # get start and end indices of each bout
-                expression = (
-                    f"(?<={other_state}){state}{{1,{min_epochs - 1}}}(?={other_state})"
-                )
-                matches = re.finditer(expression, label_string)
-                spans = [match.span() for match in matches]
-
-                # if some bouts were found
-                for span in spans:
-                    bouts.append(
-                        Bout(
-                            length=span[1] - span[0],
-                            start_index=span[0],
-                            end_index=span[1],
-                            surrounding_state=other_state,
-                        )
-                    )
-
+    while True:
+        bouts = find_short_bouts(labels, min_epochs, brain_states)
         if len(bouts) == 0:
             break
 

accusleepy/fileio.py

@@ -29,6 +29,21 @@ class Hyperparameters:
     training_epochs: int
 
 
+@dataclass
+class AccuSleePyConfig:
+    """AccuSleePy configuration settings"""
+
+    brain_state_set: BrainStateSet
+    default_epoch_length: int | float
+    overwrite_setting: bool
+    save_confidence_setting: bool
+    min_bout_length: int | float
+    emg_filter: EMGFilter
+    hyperparameters: Hyperparameters
+    epochs_to_show: int
+    autoscroll_state: bool
+
+
 @dataclass
 class Recording:
     """Store information about a recording"""
@@ -111,20 +126,11 @@ def save_labels(
         pd.DataFrame({c.BRAIN_STATE_COL: labels}).to_csv(filename, index=False)
 
 
-def load_config() -> tuple[
-    BrainStateSet,
-    int | float,
-    bool,
-    bool,
-    int | float,
-    EMGFilter,
-    Hyperparameters,
-    int,
-    bool,
-]:
+def load_config() -> AccuSleePyConfig:
     """Load configuration file with brain state options
 
-    :return: set of brain state options,
+    :return: AccuSleePyConfig containing the following:
+        set of brain state options,
         default epoch length,
         default overwrite setting,
         default confidence score output setting,
@@ -139,15 +145,21 @@ def load_config() -> tuple[
     ) as f:
         data = json.load(f)
 
-    return (
-        BrainStateSet(
+    return AccuSleePyConfig(
+        brain_state_set=BrainStateSet(
             [BrainState(**b) for b in data[BRAIN_STATES_KEY]], c.UNDEFINED_LABEL
         ),
-        data[c.DEFAULT_EPOCH_LENGTH_KEY],
-        data.get(c.DEFAULT_OVERWRITE_KEY, c.DEFAULT_OVERWRITE_SETTING),
-        data.get(c.DEFAULT_CONFIDENCE_SETTING_KEY, c.DEFAULT_CONFIDENCE_SETTING),
-        data.get(c.DEFAULT_MIN_BOUT_LENGTH_KEY, c.DEFAULT_MIN_BOUT_LENGTH),
-        EMGFilter(
+        default_epoch_length=data[c.DEFAULT_EPOCH_LENGTH_KEY],
+        overwrite_setting=data.get(
+            c.DEFAULT_OVERWRITE_KEY, c.DEFAULT_OVERWRITE_SETTING
+        ),
+        save_confidence_setting=data.get(
+            c.DEFAULT_CONFIDENCE_SETTING_KEY, c.DEFAULT_CONFIDENCE_SETTING
+        ),
+        min_bout_length=data.get(
+            c.DEFAULT_MIN_BOUT_LENGTH_KEY, c.DEFAULT_MIN_BOUT_LENGTH
+        ),
+        emg_filter=EMGFilter(
             **data.get(
                 c.EMG_FILTER_KEY,
                 {
@@ -157,7 +169,7 @@ def load_config() -> tuple[
                 },
             )
         ),
-        Hyperparameters(
+        hyperparameters=Hyperparameters(
             **data.get(
                 c.HYPERPARAMETERS_KEY,
                 {
@@ -168,8 +180,8 @@ def load_config() -> tuple[
                 },
             )
         ),
-        data.get(c.EPOCHS_TO_SHOW_KEY, c.DEFAULT_EPOCHS_TO_SHOW),
-        data.get(c.AUTOSCROLL_KEY, c.DEFAULT_AUTOSCROLL_STATE),
+        epochs_to_show=data.get(c.EPOCHS_TO_SHOW_KEY, c.DEFAULT_EPOCHS_TO_SHOW),
+        autoscroll_state=data.get(c.AUTOSCROLL_KEY, c.DEFAULT_AUTOSCROLL_STATE),
     )
 
 

accusleepy/gui/main.py

@@ -113,17 +113,16 @@ class AccuSleepWindow(QMainWindow):
         self.setWindowTitle("AccuSleePy")
 
         # fill in settings tab
-        (
-            self.brain_state_set,
-            self.epoch_length,
-            self.only_overwrite_undefined,
-            self.save_confidence_scores,
-            self.min_bout_length,
-            self.emg_filter,
-            self.hyperparameters,
-            self.default_epochs_to_show,
-            self.default_autoscroll_state,
-        ) = load_config()
+        config = load_config()
+        self.brain_state_set = config.brain_state_set
+        self.epoch_length = config.default_epoch_length
+        self.only_overwrite_undefined = config.overwrite_setting
+        self.save_confidence_scores = config.save_confidence_setting
+        self.min_bout_length = config.min_bout_length
+        self.emg_filter = config.emg_filter
+        self.hyperparameters = config.hyperparameters
+        self.default_epochs_to_show = config.epochs_to_show
+        self.default_autoscroll_state = config.autoscroll_state
 
         self.settings_widgets = None
         self.initialize_settings_tab()

accusleepy/gui/manual_scoring.py

@@ -139,18 +139,10 @@ class ManualScoringWindow(QDialog):
         self.ui.setupUi(self)
         self.setWindowTitle("AccuSleePy manual scoring window")
 
-        # load set of valid brain states
-        (
-            self.brain_state_set,
-            _,
-            _,
-            _,
-            _,
-            _,
-            _,
-            self.epochs_to_show,
-            self.autoscroll_state,
-        ) = load_config()
+        config = load_config()
+        self.brain_state_set = config.brain_state_set
+        self.epochs_to_show = config.epochs_to_show
+        self.autoscroll_state = config.autoscroll_state
 
         # find the set of y-axis locations of valid brain state labels
         self.label_display_options = convert_labels(

{accusleepy-0.8.0.dist-info → accusleepy-0.8.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: accusleepy
-Version: 0.8.0
+Version: 0.8.1
 Summary: Python implementation of AccuSleep
 License: GPL-3.0-only
 Author: Zeke Barger
@@ -80,6 +80,7 @@ please consult the [developer guide](accusleepy/gui/text/dev_guide.md).
 
 ## Changelog
 
+- 0.8.1: Increased test coverage
 - 0.8.0: More configurable settings, visual improvements
 - 0.7.1-0.7.3: Bugfixes, code cleanup
 - 0.7.0: More settings can be configured in the UI
@@ -87,10 +88,7 @@ please consult the [developer guide](accusleepy/gui/text/dev_guide.md).
     since the new calibration feature will make the confidence scores more accurate.
 - 0.5.0: Performance improvements
 - 0.4.5: Added support for python 3.13, **removed support for python 3.10.**
-- 0.4.4: Performance improvements
-- 0.4.3: Improved unit tests and user manuals
-- 0.4.0: Improved visuals and user manuals
-- 0.1.0-0.3.1: Early development versions
+- 0.1.0-0.4.4: Early development versions
 
 ## Screenshots
 

{accusleepy-0.8.0.dist-info → accusleepy-0.8.1.dist-info}/RECORD

@@ -1,11 +1,11 @@
 accusleepy/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 accusleepy/__main__.py,sha256=dKzl2N2Hg9lD264CWYNxThRyDKzWwyMwHRXmJxOmMis,104
-accusleepy/bouts.py,sha256=F_y6DxnpKFfImYb7vCZluZ2eD5I_33gZXmRM8mvebsg,5679
+accusleepy/bouts.py,sha256=biJEzCjMQR-RTlQcfeomkp6NxcA5FXkhE8Kp2XyL4P4,6039
 accusleepy/brain_state_set.py,sha256=fRkrArHLIbEKimub804yt_mUXoyfsjJEfiJnTjeCMkY,3233
 accusleepy/classification.py,sha256=mF35xMrD9QXGldSnl3vkdHbm7CAptPUNjHxUA_agOTA,9778
 accusleepy/config.json,sha256=VmUFsiGD1ymEyjdzqeM5nTp8jWvDI-DIxLy1_92nueo,875
 accusleepy/constants.py,sha256=62mmsr1NKzF-psS-9esuAE65kAcPL6o8v9UXQEvb5yc,2983
-accusleepy/fileio.py,sha256=iWUQtWCSL9hG3eQC8-RXJUrHv149PBxM3IjYKaUcMFk,7981
+accusleepy/fileio.py,sha256=-aEgp2oonjQKRizVI1uI5CGknnBOxE6HG0DzxDYbSkM,8512
 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
@@ -18,11 +18,11 @@ 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=jI_E2oZZN-Ajb4_5n-jVlNT7OkEPrK50xK2WOJnaiBc,598184
+accusleepy/gui/images/primary_window.png,sha256=yRGUdIcByF8DtPtDWqjmnQ8J3IHKtmijBsT7N9e1Ij0,595764
 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=GdxQXdg0kxCaJzClvRiN95A6pQjZ-jBoOb2YyInKvyc,58253
-accusleepy/gui/manual_scoring.py,sha256=woi4LxsUkHfNnjPGKdSFWyynuti1rWFrar6IJP7HyKA,40773
+accusleepy/gui/main.py,sha256=cZQH0qJ_mykeQP7eadc1yzFHYeDwbRngrR4_H1wMxWY,58438
+accusleepy/gui/manual_scoring.py,sha256=QCFF-CIU6nh26NB8Z9ktohCk8p7ola2hgjazD-OrK_o,40697
 accusleepy/gui/mplwidget.py,sha256=rJSTtWmLjHn8r3c9Kb23Rc4XzXl3i9B-JrjNjjlNnmQ,13492
 accusleepy/gui/primary_window.py,sha256=qqV-GAC3BgOus1lJMOg2U4AGQbhy35zLMyN8Q7ouTd8,141479
 accusleepy/gui/primary_window.ui,sha256=2mD0G6b8bsyyUvMCUosQ0K-nAzMA2iiP3yMpeh9INcQ,208209
@@ -38,6 +38,6 @@ accusleepy/multitaper.py,sha256=D5-iglwkFBRciL5tKSNcunMtcq0rM3zHwRHUVPgem1U,2567
 accusleepy/signal_processing.py,sha256=47fEAx8Aqqkiqix1ai2YEK9Fhq6UHoQcwAcOi-a8ewo,16834
 accusleepy/temperature_scaling.py,sha256=glvPcvxHpBdFjwjGfZdNku9L_BozycEmdqZhKKUCCNg,5749
 accusleepy/validation.py,sha256=VpLWK-wD5tCU6lTBG3KYgTi3PWGuYh6NitMgMoMH8JM,4434
-accusleepy-0.8.0.dist-info/METADATA,sha256=gnk8O1By632zTCFJG9ifqkQDDSEDTqggGUpG8F-WPgs,4800
-accusleepy-0.8.0.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-accusleepy-0.8.0.dist-info/RECORD,,
+accusleepy-0.8.1.dist-info/METADATA,sha256=29kPvzKr2ykosWwidIt6FKrjvIY-m88Ui9GQPoQPN-g,4710
+accusleepy-0.8.1.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+accusleepy-0.8.1.dist-info/RECORD,,