From 1c1898c8de3cf91df50ffe648005cc37338b4513 Mon Sep 17 00:00:00 2001 From: fdrgsp Date: Mon, 16 Mar 2026 16:45:42 -0400 Subject: [PATCH] fix: update minimum burst duration to 500 ms across constants, GUI, and model --- src/cali/_constants.py | 2 +- src/cali/gui/_analysis_gui.py | 6 +++--- src/cali/sqlmodel/_model.py | 5 +++-- tests/test_spike_jitter_parameter.py | 4 ++-- 4 files changed, 9 insertions(+), 8 deletions(-) diff --git a/src/cali/_constants.py b/src/cali/_constants.py index 1aee2d9d..4b905c83 100644 --- a/src/cali/_constants.py +++ b/src/cali/_constants.py @@ -93,7 +93,7 @@ def natural_sort_key(text: str) -> list: # ==================== Default Values ==================== DEFAULT_BURST_THRESHOLD = 65.0 DEFAULT_CALCIUM_BURST_THRESHOLD = 25.0 -DEFAULT_MIN_BURST_DURATION = 3 +DEFAULT_MIN_BURST_DURATION = 500 # milliseconds DEFAULT_BURST_GAUSS_SIGMA = 0.3 DEFAULT_FRAME_RATE = 10.0 # frames per second (fps) DEFAULT_DFF_WINDOW = 10.0 # seconds diff --git a/src/cali/gui/_analysis_gui.py b/src/cali/gui/_analysis_gui.py index 0ab88568..ba0b3ea1 100644 --- a/src/cali/gui/_analysis_gui.py +++ b/src/cali/gui/_analysis_gui.py @@ -956,7 +956,7 @@ def reset(self) -> None: self._burst_wdg.setValue( ( DEFAULT_BURST_THRESHOLD, - 3000.0, # 3 seconds = 3000ms + DEFAULT_MIN_BURST_DURATION, DEFAULT_BURST_GAUSS_SIGMA, ) ) @@ -1080,7 +1080,7 @@ def __init__(self, parent: QWidget | None = None) -> None: self._burst_min_duration_ms.setDecimals(2) self._burst_min_duration_ms.setRange(0.0, 100000.0) self._burst_min_duration_ms.setSingleStep(100.0) - self._burst_min_duration_ms.setValue(3000.0) # 3 seconds + self._burst_min_duration_ms.setValue(DEFAULT_MIN_BURST_DURATION) self._burst_blur_label = QLabel("Burst Gaussian Blur Sigma:", self) self._burst_blur_label.setSizePolicy(*FIXED) @@ -1317,7 +1317,7 @@ def reset(self) -> None: self._burst_wdg.setValue( ( DEFAULT_BURST_THRESHOLD, - 3000.0, # 3 seconds = 3000ms + DEFAULT_MIN_BURST_DURATION, DEFAULT_BURST_GAUSS_SIGMA, ) ) diff --git a/src/cali/sqlmodel/_model.py b/src/cali/sqlmodel/_model.py index e4de1777..4ff0a093 100644 --- a/src/cali/sqlmodel/_model.py +++ b/src/cali/sqlmodel/_model.py @@ -47,6 +47,7 @@ DEFAULT_ENABLE_RISING_EDGE_ANALYSIS, DEFAULT_FRAME_RATE, DEFAULT_HEIGHT, + DEFAULT_MIN_BURST_DURATION, DEFAULT_SPIKE_SYNC_JITTER_WINDOW, DEFAULT_SPIKE_SYNCHRONY_MAX_LAG, DEFAULT_SPIKE_THRESHOLD, @@ -1154,10 +1155,10 @@ class AnalysisSettings(SQLModel, table=True): spike_threshold_value: float = DEFAULT_SPIKE_THRESHOLD spike_threshold_mode: str = MULTIPLIER burst_threshold: float = DEFAULT_BURST_THRESHOLD - burst_min_duration: float = 3000.0 # milliseconds (3 seconds) + burst_min_duration: float = DEFAULT_MIN_BURST_DURATION burst_gaussian_sigma: float = DEFAULT_BURST_GAUSS_SIGMA calcium_burst_threshold: float = DEFAULT_CALCIUM_BURST_THRESHOLD - calcium_burst_min_duration: float = 3000.0 # milliseconds (3 seconds) + calcium_burst_min_duration: float = DEFAULT_MIN_BURST_DURATION calcium_burst_gaussian_sigma: float = DEFAULT_BURST_GAUSS_SIGMA spikes_sync_cross_corr_lag: float = DEFAULT_SPIKE_SYNCHRONY_MAX_LAG # ms spikes_sync_jitter_window: float = DEFAULT_SPIKE_SYNC_JITTER_WINDOW # ms diff --git a/tests/test_spike_jitter_parameter.py b/tests/test_spike_jitter_parameter.py index 4c44e409..bb38446c 100644 --- a/tests/test_spike_jitter_parameter.py +++ b/tests/test_spike_jitter_parameter.py @@ -31,7 +31,7 @@ def test_spike_data_has_jitter_field() -> None: spike_threshold=0.5, spike_threshold_mode="adaptive", burst_threshold=75.0, - burst_min_duration=3000.0, + burst_min_duration=500.0, burst_blur_sigma=1.0, synchrony_lag=1000.0, synchrony_jitter=200.0, @@ -48,7 +48,7 @@ def test_spike_data_default_jitter_value() -> None: spike_threshold=0.5, spike_threshold_mode="adaptive", burst_threshold=75.0, - burst_min_duration=3000.0, + burst_min_duration=500.0, burst_blur_sigma=1.0, synchrony_lag=1000.0, synchrony_jitter=DEFAULT_SPIKE_SYNC_JITTER_WINDOW,