misleep 0.3.1__tar.gz → 0.3.3__tar.gz

{misleep-0.3.1 → misleep-0.3.3}/CHANGELOG.md

@@ -5,6 +5,22 @@ All notable changes to MiSleep are documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.3.2] — 2026-08-24
+
+### Fixed
+
+- **Filtering broke on fractional sampling frequencies**: `MiData.add()` (used
+  by `MiData.filter()`) recomputed the duration with
+  `math.floor(len(signal) / sf)` from a signal that had already been
+  truncated to `int(duration * sf)` samples. When `sf` is a decimal (e.g.
+  `99.9927` Hz), that came out one second short, so filtering either raised a
+  spurious "new signal is shorter" error or produced a channel whose length /
+  duration did not match the original signal, which then failed the signal /
+  label consistency checks in the GUI. The check now compares sample counts
+  against `int(duration * sf)` directly, so filtering preserves the sample
+  count and duration for any positive `sf` while still rejecting genuinely
+  short signals.
+
 ## [0.3.1] — 2026-08-18
 
 ### Added

{misleep-0.3.1/src/misleep.egg-info → misleep-0.3.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: misleep
-Version: 0.3.1
+Version: 0.3.3
 Summary: MiSleep: Mice sleep EEG/EMG visualization, scoring, and analysis
 Author-email: Xueqiang Wang <swang9194@gmail.com>
 Maintainer-email: Xueqiang Wang <swang9194@gmail.com>

{misleep-0.3.1 → misleep-0.3.3}/docs/config_file.md

@@ -23,8 +23,8 @@ wipe your personal settings. Open the user file from the GUI via
 
 | key | default | meaning |
 |-----|---------|---------|
-| `version` | `v0.3.1` | displayed in the About dialog |
-| `updatetime` | `2026/08/18` | displayed in the About dialog |
+| `version` | `v0.3.2` | displayed in the About dialog |
+| `updatetime` | `2026/08/24` | displayed in the About dialog |
 | `marker` | `['half_signal', 'first REM', ...]` | marker label list (label picker) |
 | `startend` | `['high_theta', 'REM', ...]` | start-end label list (label picker) |
 | `statemap` | `{"1": "NREM", "2": "REM", "3": "Wake", "4": "INIT", ...}` | state code -> name mapping (JSON) |
@@ -48,8 +48,8 @@ wipe your personal settings. Open the user file from the GUI via
 
 ```ini
 [gui]
-version = v0.3.1
-updatetime = 2026/08/18
+version = v0.3.2
+updatetime = 2026/08/24
 marker = ['half_signal', 'first REM', 'WindEEG', 'W-R', 'maker']
 startend = ['high_theta', 'REM', 'Wake', 'Spindle', 'SWA', 'start end label', 'start end label']
 statemap = {"1": "NREM", "2": "REM", "3": "Wake", "4": "INIT", "5": "IS", "6": "MicroArousal"}

{misleep-0.3.1 → misleep-0.3.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "misleep"
-version = "0.3.1"
+version = "0.3.3"
 description = "MiSleep: Mice sleep EEG/EMG visualization, scoring, and analysis"
 readme = "README.md"
 requires-python = ">=3.8"

{misleep-0.3.1 → misleep-0.3.3}/src/misleep/__init__.py

@@ -22,7 +22,7 @@ works without PySide6; import ``misleep.gui`` explicitly when needed.
 from importlib import import_module
 
 __author__ = "Xueqiang Wang <swang9194@gmail.com>"
-__version__ = "0.3.1"
+__version__ = "0.3.2"
 
 # Importing ``misleep`` used to import scipy, pandas, sklearn and matplotlib
 # immediately.  The GUI necessarily imports some of those later, but making

{misleep-0.3.1 → misleep-0.3.3}/src/misleep/analysis/models/benchmark_models.pkl

@@ -1,4 +1,4 @@
 [diffend] Oversized file quarantined before diffing.
-name: misleep-0.3.1/src/misleep/analysis/models/benchmark_models.pkl
+name: misleep-0.3.3/src/misleep/analysis/models/benchmark_models.pkl
 size: 50435195 bytes
 sha256: 8390ffa5ef8d45701a09244ec75dea46d2e4bff6a4c8242b0de84da8ea9cd31c

{misleep-0.3.1 → misleep-0.3.3}/src/misleep/config/default_config.ini

@@ -15,8 +15,8 @@
 # overwritten on the next package update.
 
 [gui]
-version = v0.3.1
-updatetime = 2026/08/18
+version = v0.3.2
+updatetime = 2026/08/24
 marker = ['half_signal', 'first REM', 'WindEEG', 'W-R', 'maker']
 startend = ['high_theta', 'REM', 'Wake', 'Spindle', 'SWA', 'start end label', 'start end label']
 statemap = {"1": "NREM", "2": "REM", "3": "Wake", "4": "INIT"}

{misleep-0.3.1 → misleep-0.3.3}/src/misleep/data/midata.py

@@ -210,15 +210,25 @@ class MiData:
         if not isinstance(sf, (int, float)) or not math.isfinite(sf) or sf <= 0:
             raise TypeError(f"Sample frequency should be a float, got {type(sf)}")
 
-        _duration = math.floor(len(signal) / sf)
-        if _duration < self._duration:
+        # Every channel shares the same integer duration: the sample count a
+        # channel of ``sf`` Hz needs to cover ``self._duration`` seconds is
+        # ``int(self._duration * sf)`` (the same truncation used in
+        # :meth:`__init__`).  Compare sample counts directly instead of
+        # re-deriving the duration from an already-truncated length -- with a
+        # fractional sampling frequency (e.g. 99.9927 Hz) the naive
+        # ``math.floor(len(signal) / sf)`` can come out one second short and
+        # wrongly reject signals that are exactly as long as the existing
+        # channels (this made ``MiData.filter()`` fail on fractional-sf data).
+        expected_samples = int(self._duration * sf)
+        if len(signal) < expected_samples:
             raise ValueError(
-                f"The new signal is shorter ({_duration}s) than the existing data "
-                f"({self._duration}s)")
+                f"The new signal is shorter ({len(signal)} samples) than the "
+                f"existing data ({self._duration}s, {expected_samples} samples "
+                f"at {sf} Hz)")
 
         channel = _unique_name(channel, self.channels)
 
-        self._signals.append(signal[:int(self._duration * sf)])
+        self._signals.append(signal[:expected_samples])
         self._channels.append(channel)
         self._n_channels = len(self._channels)
         self._sf.append(sf)

{misleep-0.3.1 → misleep-0.3.3}/src/misleep/gui/dialogs.py

@@ -7,6 +7,7 @@ the two auto-staging dialogs and the save-data dialog, plus the About box.
 """
 
 import datetime
+import math
 import os
 from copy import deepcopy
 
@@ -50,6 +51,33 @@ from misleep.logger import logger
 from misleep.utils.annotation import lst2group
 
 
+def _split_state_data_by_hour(channel_data, sleep_states, states, sf):
+    """Return per-state signal segments in fixed, time-aligned hour slots.
+
+    Every state receives one entry per elapsed hour.  An entry is ``None``
+    when that state has no usable data in the hour, so later hours never
+    shift left to fill an empty ZT column.
+    """
+    hour_count = int(math.ceil(len(sleep_states) / 3600))
+    result = {state: [None] * hour_count for state in states}
+
+    for hour_idx in range(hour_count):
+        hour_start = hour_idx * 3600
+        hour_stop = min(hour_start + 3600, len(sleep_states))
+        groups = lst2group(enumerate(sleep_states[hour_start:hour_stop]))
+        for state in states:
+            parts = [
+                channel_data[
+                    int((hour_start + group_start) * sf):
+                    int((hour_start + group_stop) * sf)]
+                for group_start, group_stop, value in groups
+                if value == state
+            ]
+            if parts:
+                result[state][hour_idx] = np.concatenate(parts)
+    return result
+
+
 class AboutDialog(QDialog, Ui_AboutDialog):
     """The About box of MiSleep."""
 
@@ -400,11 +428,13 @@ class StateSpectralDialog(QDialog, Ui_StateSpectralDialog):
             end_sec = mianno.anno_length
 
         midata = midata.crop([start_sec, end_sec])
-        sleep_state = mianno.sleep_state[start_sec:end_sec + 1]
+        # ``end_sec`` is exclusive, matching MiData.crop().  Using end+1 here
+        # created a spurious sample at exact hour boundaries.
+        sleep_state_values = mianno.sleep_state[start_sec:end_sec]
 
         channel_idx = self.ChannelSelector.currentIndex()
         channel_data = midata.signals[channel_idx]
-        sleep_state = lst2group([[idx, each] for idx, each in enumerate(sleep_state)])
+        sleep_state = lst2group(enumerate(sleep_state_values))
         sf = midata.sf[channel_idx]
 
         # Band-pass filter if checked
@@ -422,7 +452,7 @@ class StateSpectralDialog(QDialog, Ui_StateSpectralDialog):
 
         gaussian_sigma = self.GaussianSpinBox.value() if self.GaussianCheckBox.isChecked() else None
 
-        state_codes = sorted(set(mianno.sleep_state[start_sec:end_sec + 1]))
+        state_codes = sorted(set(sleep_state_values))
         state_data = {
             state: np.concatenate([
                 channel_data[int(each[0] * sf): int(each[1] * sf)]
@@ -451,21 +481,21 @@ class StateSpectralDialog(QDialog, Ui_StateSpectralDialog):
         # Optional per-hour spectral segmentation
         hour_spec = {state: [] for state in spectra}
         if self.HourSegmentCheckBox.isChecked():
-            for sec in range(0, end_sec - start_sec, 3600):
-                hour_states = mianno.sleep_state[start_sec + sec:start_sec + sec + 3600]
-                hour_states = lst2group([[idx + sec, each]
-                                         for idx, each in enumerate(hour_states)])
-                for state in spectra:
-                    data_parts = [channel_data[int(each[0] * sf): int(each[1] * sf)]
-                                  for each in hour_states if each[2] == state]
-                    data = np.concatenate(data_parts) if data_parts else np.array([])
-                    if self.RejectArtifactCheckBox.isChecked() and len(data):
-                        data = reject_artifact(data, sf=sf, threshold=threshold)
-                    if len(data) > sf * 10:
-                        hour_spec[state].append(cal_draw_spectrum(
+            hourly_data = _split_state_data_by_hour(
+                channel_data, sleep_state_values, spectra, sf)
+            for state, state_hours in hourly_data.items():
+                for data in state_hours:
+                    if data is not None and self.RejectArtifactCheckBox.isChecked():
+                        data = reject_artifact(
+                            data, sf=sf, threshold=threshold)
+                    if data is not None and len(data) > sf * 10:
+                        power = cal_draw_spectrum(
                             data=data, sf=sf, nperseg=nperseg,
                             freq_band=freq_band, relative=relative, nfft=nfft,
-                            gaussian_sigma=gaussian_sigma)[0][1])
+                            gaussian_sigma=gaussian_sigma)[0][1]
+                        hour_spec[state].append(power)
+                    else:
+                        hour_spec[state].append(None)
 
         fd = QFileDialog.getExistingDirectory(self, "Select a folder to save states' data",
                                               f"{config['gui']['openpath']}")
@@ -485,10 +515,10 @@ class StateSpectralDialog(QDialog, Ui_StateSpectralDialog):
                     figure.savefig(fd + "/" + safe_name + "_spectrum.pdf")
                     _df = pd.DataFrame(
                         data=spec.T, columns=["frequency", "power"])
-                    if hour_spec[state]:
-                        _df[[str(each) for each in range(
-                            1, len(hour_spec[state]) + 1)]] = \
-                            pd.DataFrame(hour_spec[state]).T
+                    for hour_idx, hour_power in enumerate(hour_spec[state]):
+                        column = f"ZT{hour_idx}"
+                        _df[column] = np.nan if hour_power is None \
+                            else pd.Series(hour_power)
                     _df.to_excel(
                         excel_writer=writer, sheet_name=safe_name[:31],
                         index=False)

{misleep-0.3.1 → misleep-0.3.3}/src/misleep/gui/uis/about.ui

@@ -58,14 +58,14 @@
       <item>
        <widget class="QLabel" name="VersionLabel">
         <property name="text">
-         <string>Version: 0.3.1</string>
+         <string>Version: 0.3.2</string>
         </property>
        </widget>
       </item>
       <item>
        <widget class="QLabel" name="UpdateLabel">
         <property name="text">
-         <string>Update: 2026/08/18</string>
+         <string>Update: 2026/08/24</string>
         </property>
        </widget>
       </item>

{misleep-0.3.1 → misleep-0.3.3}/src/misleep/gui/uis/about_ui.py

@@ -73,8 +73,8 @@ class Ui_AboutDialog(object):
         AboutDialog.setWindowTitle(QCoreApplication.translate("AboutDialog", u"About", None))
         self.label_4.setText(QCoreApplication.translate("AboutDialog", u"<html><head/><body><p><img src=\":/logo/entire_logo.png\"/></p></body></html>", None))
         self.groupBox.setTitle(QCoreApplication.translate("AboutDialog", u"MiSleep", None))
-        self.VersionLabel.setText(QCoreApplication.translate("AboutDialog", u"Version: 0.3.1", None))
-        self.UpdateLabel.setText(QCoreApplication.translate("AboutDialog", u"Update: 2026/08/18", None))
+        self.VersionLabel.setText(QCoreApplication.translate("AboutDialog", u"Version: 0.3.2", None))
+        self.UpdateLabel.setText(QCoreApplication.translate("AboutDialog", u"Update: 2026/08/24", None))
         self.CopyrightLabel.setText(QCoreApplication.translate("AboutDialog", u"Copyright \u00a9 2023\u20132026 Xueqiang Wang.", None))
     # retranslateUi
 

{misleep-0.3.1 → misleep-0.3.3/src/misleep.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: misleep
-Version: 0.3.1
+Version: 0.3.3
 Summary: MiSleep: Mice sleep EEG/EMG visualization, scoring, and analysis
 Author-email: Xueqiang Wang <swang9194@gmail.com>
 Maintainer-email: Xueqiang Wang <swang9194@gmail.com>

{misleep-0.3.1 → misleep-0.3.3}/tests/test_data.py

@@ -88,6 +88,59 @@ def test_midata_filter(midata):
     assert midata.channels[-1].startswith("EEG_bandpass")
 
 
+@pytest.mark.parametrize("sf", [99.9927, 100.5, 256.256, 305.005])
+def test_midata_filter_fractional_sf_preserves_length(sf):
+    """Filtering must not change the sample count or duration when sf is fractional.
+
+    Regression: ``MiData.add`` re-derived the duration with
+    ``math.floor(len(signal) / sf)`` from a signal already truncated to
+    ``int(duration * sf)`` samples; with a fractional sf that could come out
+    one second short and made ``filter()`` raise a spurious error (or produce
+    a shorter channel).
+    """
+    rng = np.random.default_rng(42)
+    n_raw = int(1000 * sf)
+    md = MiData(signals=[rng.standard_normal(n_raw),
+                         rng.standard_normal(n_raw)],
+                channels=["EEG", "EMG"], sf=[sf, sf], time="20240101-00:00:00")
+    duration, lengths = md.duration, [len(s) for s in md.signals]
+
+    md.filter(chans=["EEG"], btype="bandpass", low=0.5, high=30)
+
+    assert md.n_channels == 3
+    assert md.duration == duration
+    assert len(md.signals) == 3
+    assert all(len(sig) == length for sig, length in zip(md.signals, lengths))
+
+
+def test_midata_add_fractional_sf():
+    """A channel with ``int(duration * sf)`` samples must be accepted."""
+    sf = 99.9927
+    md = MiData(signals=[np.zeros(int(1000 * sf)), np.zeros(int(1000 * sf))],
+                channels=["EEG", "EMG"], sf=[sf, sf], time="20240101-00:00:00")
+    n = md.n_channels
+    duration, expected = md.duration, int(md.duration * sf)
+
+    # Exactly as many samples as the existing channels -> accepted as-is
+    md.add(np.zeros(expected), "EEG2", sf)
+    assert md.n_channels == n + 1
+    assert len(md.signals[-1]) == expected
+    assert md.duration == duration  # duration unchanged by add()
+
+    # A genuinely shorter signal is still rejected
+    with pytest.raises(ValueError):
+        md.add(np.zeros(expected - 10), "TOO_SHORT", sf)
+
+
+def test_midata_add_fractional_sf_rejects_short_signal():
+    """Fractional-sf channels that are truly too short must still be rejected."""
+    sf = 256.256
+    md = MiData(signals=[np.zeros(int(1000 * sf)), np.zeros(int(1000 * sf))],
+                channels=["EEG", "EMG"], sf=[sf, sf], time="20240101-00:00:00")
+    with pytest.raises(ValueError):
+        md.add(np.zeros(500 * 256), "TOO_SHORT", 256.0)
+
+
 def test_midata_differential(midata):
     midata.differential(chan1="EEG", chan2="EMG")
     assert midata.channels[-1] == "EEG_EMG_DIFF"

{misleep-0.3.1 → misleep-0.3.3}/tests/test_gui.py

@@ -21,7 +21,7 @@ def _pyside6_available():
 def test_public_api():
     import misleep
 
-    assert misleep.__version__ == "0.3.1"
+    assert misleep.__version__ == "0.3.2"
     for name in [
         "MiData",
         "MiAnnotation",
@@ -766,6 +766,65 @@ def test_data_export_always_restores_main_window(tmp_path, monkeypatch):
     app.processEvents()
 
 
+@pytest.mark.skipif(not _pyside6_available(), reason="PySide6 not installed")
+def test_state_spectral_hour_columns_preserve_empty_zt_slots(
+        fresh_config, tmp_path, monkeypatch):
+    """Hourly state spectra stay aligned to ZT0..ZTn despite empty hours."""
+    import numpy as np
+    import pandas as pd
+    from PySide6.QtWidgets import QApplication, QFileDialog
+
+    app = QApplication.instance() or QApplication([])
+    from misleep.data import MiAnnotation, MiData
+    from misleep.gui.dialogs import StateSpectralDialog
+
+    class FakeFigure:
+        def savefig(self, *args, **kwargs):
+            pass
+
+        def clear(self):
+            pass
+
+    def fake_spectrum(data, **kwargs):
+        return np.array([[1.0, 2.0], [len(data), float(np.mean(data))]]), \
+            FakeFigure()
+
+    monkeypatch.setattr(
+        "misleep.gui.dialogs.cal_draw_spectrum", fake_spectrum)
+    monkeypatch.setattr(
+        QFileDialog, "getExistingDirectory",
+        staticmethod(lambda *args, **kwargs: str(tmp_path)))
+
+    # State 1 is absent from ZT1; state 2 is absent from ZT0 and ZT2.
+    states = [1] * 3600 + [2] * 3600 + [1] * 3600
+    midata = MiData(
+        signals=[np.arange(len(states), dtype=float)],
+        channels=["EEG"], sf=[1.0], time="20240409-18:00:00")
+    mianno = MiAnnotation(states, state_map={1: "NREM", 2: "REM"})
+    fresh_config["gui"]["openpath"] = "recording.mat"
+
+    dialog = StateSpectralDialog(config=fresh_config)
+    dialog.dialog_show(midata.channels)
+    dialog.BPFilterCheckBox.setChecked(False)
+    dialog.HourSegmentCheckBox.setChecked(True)
+    assert dialog.spectral_analysis(midata, mianno, fresh_config) is True
+
+    workbook = tmp_path / "recording_power_results.xlsx"
+    nrem = pd.read_excel(workbook, sheet_name="NREM")
+    rem = pd.read_excel(workbook, sheet_name="REM")
+    expected = ["frequency", "power", "ZT0", "ZT1", "ZT2"]
+    assert list(nrem.columns) == expected
+    assert list(rem.columns) == expected
+    assert nrem["ZT1"].isna().all()
+    assert rem["ZT0"].isna().all()
+    assert rem["ZT2"].isna().all()
+    assert nrem["ZT0"].notna().all() and nrem["ZT2"].notna().all()
+    assert rem["ZT1"].notna().all()
+
+    dialog.close()
+    app.processEvents()
+
+
 @pytest.mark.skipif(not _pyside6_available(), reason="PySide6 not installed")
 def test_gui_with_data(tmp_path):
     from PySide6.QtWidgets import QApplication