diff --git a/geci_plot.py b/geci_plot.py index e12ac17..a5e4717 100644 --- a/geci_plot.py +++ b/geci_plot.py @@ -19,7 +19,7 @@ def func_exp(x, a, b, c): def plot( filename: str = "config_M_Sert_Cre_49.json", experiment: int = 4, - skip_timesteps: int = 0, + skip_timesteps: int = 100, # If there is no special ROI... Get one! This is just a backup roi_control_path_default: str = "roi_controlM_Sert_Cre_49.npy", roi_sdarken_path_default: str = "roi_sdarkenM_Sert_Cre_49.npy", @@ -93,13 +93,19 @@ def plot( plt.show(block=False) plt.figure(3) - light_exp = light[experiment - 1, :, :, skip_timesteps:].copy() + if remove_fit: + light_exp = light[experiment - 1, :, :, skip_timesteps:].copy() + else: + light_exp = light[experiment - 1, :, :, :].copy() light_exp[(roi_darken + roi_control) < 0.5, :] = 0.0 light_signal = light_exp.mean(axis=(0, 1)) light_signal -= light_signal.min() light_signal /= light_signal.max() - a_exp = data[experiment - 1, :, :, skip_timesteps:].copy() + if remove_fit: + a_exp = data[experiment - 1, :, :, skip_timesteps:].copy() + else: + a_exp = data[experiment - 1, :, :, :].copy() if remove_fit: combined_matrix = (roi_darken + roi_control) > 0