From ee9f9904abeaf2f772f2079bdea40a93847e941c Mon Sep 17 00:00:00 2001 From: David Rotermund Date: Mon, 12 Aug 2024 11:28:41 +0200 Subject: [PATCH] Add files via upload --- geci_loader.py | 38 -------------------------------------- geci_plot.py | 40 ++++++++++++++++++++-------------------- 2 files changed, 20 insertions(+), 58 deletions(-) diff --git a/geci_loader.py b/geci_loader.py index 56596df..137ad9e 100644 --- a/geci_loader.py +++ b/geci_loader.py @@ -53,44 +53,6 @@ def loader(mouse: int = 0, fpath: str = "/data_1/hendrik/gevi") -> None: ], # 0, 0, 0 in cond 5-7 ] - # 41, 42, 45, 46, 49: - # "1": "control", - # "2": "visual control grating 100 1s", - # "3": "optical Stimulation 20Hz 50% 5 Intervals", - # "4": "optical Stimulation 20Hz 100% 5 Intervals", - # "5": "optical Stimulation 20Hz 50% and grating 100", - # "6": "optical Stimulation 20Hz 100% and grating 100", - # "7": "grating 3s" - - lbs = [ - [ - "control", - "visual control", - "op20 50 5", - "op20 100 5", - "op20 50 grat", - "op20 100 grat", - ], - [ - "control", - "visual control", - "op20 50 5", - "op20 100 5", - "op20 50 grat", - "op20 100 grat", - ], - [ - "control", - "visual control", - "op20 50 5", - "op20 100 5", - "op20 50 grat", - "op20 100 grat", - ], - ["control", "visual control", "op20 50 5", "op20 100 5"], - ["control", "visual control", "op20 50 5", "op20 100 5"], - ] - n_exp = len(n_tris[mouse]) for i_exp in range(n_exp): diff --git a/geci_plot.py b/geci_plot.py index 4d1980e..db31e91 100644 --- a/geci_plot.py +++ b/geci_plot.py @@ -1,6 +1,5 @@ import numpy as np import matplotlib.pyplot as plt -import h5py # type: ignore import argh import scipy # type: ignore import json @@ -22,8 +21,8 @@ def plot( experiment: int = 4, skip_timesteps: int = 100, # If there is no special ROI... Get one! This is just a backup - roi_control_path: str = "/data_1/hendrik/2023-03-15/ROI_control.mat", - roi_sdraken_path: str = "/data_1/hendrik/2023-03-15/ROI_sDarken.mat", + roi_control_path_default: str = "roi_controlM_Sert_Cre_49.npy", + roi_sdarken_path_default: str = "roi_sdarkenM_Sert_Cre_49.npy", remove_fit: bool = True, fit_power: bool = False, # True => -ax^b ; False => exp(-b) ) -> None: @@ -80,15 +79,16 @@ def plot( experiment_names = metadata['sessionMetaData']['experimentNames'][str(experiment)] - roi_path: str = os.path.join(config["basic_path"], config["recoding_data"]) - roi_control_mat: str = os.path.join(roi_path, "ROI_control.mat") - roi_sdarken_mat: str = os.path.join(roi_path, "ROI_sDarken.mat") + roi_control_path: str = f"roi_control{config["mouse_identifier"]}.npy" + roi_sdarken_path: str = f"roi_sdarken{config["mouse_identifier"]}.npy" - if os.path.isdir(roi_control_mat): - roi_control_path = roi_control_mat + if os.path.isfile(roi_control_path) is False: + print(f"Using replacement RIO: {roi_control_path_default}") + roi_control_path = roi_control_path_default - if os.path.isdir(roi_sdarken_mat): - roi_sdraken_path = roi_sdarken_mat + if os.path.isfile(roi_sdarken_path) is False: + print(f"Using replacement RIO: {roi_sdarken_path_default}") + roi_sdarken_path = roi_sdarken_path_default print("Load data...") data = np.load("dsq_" + config["mouse_identifier"] + ".npy", mmap_mode="r") @@ -99,31 +99,31 @@ def plot( print("Load mask...") mask = np.load("msq_" + config["mouse_identifier"] + ".npy") - hf = h5py.File(roi_control_path, "r") - roi_lighten = np.array(hf["roi"]).T - roi_lighten *= mask + roi_control = np.load(roi_control_path) + roi_control *= mask + assert roi_control.sum() > 0, "ROI control empty" - hf = h5py.File(roi_sdraken_path, "r") - roi_darken = np.array(hf["roi"]).T + roi_darken = np.load(roi_sdarken_path) roi_darken *= mask + assert roi_darken.sum() > 0, "ROI sDarken empty" plt.figure(1) a_show = data[experiment - 1, :, :, 1000].copy() - a_show[(roi_darken + roi_lighten) < 0.5] = np.nan + a_show[(roi_darken + roi_control) < 0.5] = np.nan plt.imshow(a_show) plt.title(f"{config["mouse_identifier"]} -- Experiment: {experiment}") plt.show(block=False) plt.figure(2) a_dontshow = data[experiment - 1, :, :, 1000].copy() - a_dontshow[(roi_darken + roi_lighten) > 0.5] = np.nan + a_dontshow[(roi_darken + roi_control) > 0.5] = np.nan plt.imshow(a_dontshow) plt.title(f"{config["mouse_identifier"]} -- Experiment: {experiment}") plt.show(block=False) plt.figure(3) light_exp = light[experiment - 1, :, :, skip_timesteps:].copy() - light_exp[(roi_darken + roi_lighten) < 0.5, :] = 0.0 + 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() @@ -131,7 +131,7 @@ def plot( a_exp = data[experiment - 1, :, :, skip_timesteps:].copy() if remove_fit: - combined_matrix = (roi_darken + roi_lighten) > 0 + combined_matrix = (roi_darken + roi_control) > 0 idx = np.where(combined_matrix) for idx_pos in range(0, idx[0].shape[0]): temp = a_exp[idx[0][idx_pos], idx[1][idx_pos], :] @@ -185,7 +185,7 @@ def plot( temp -= pattern darken = a_exp[roi_darken > 0.5, :].sum(axis=0) / (roi_darken > 0.5).sum() - lighten = a_exp[roi_lighten > 0.5, :].sum(axis=0) / (roi_lighten > 0.5).sum() + lighten = a_exp[roi_control > 0.5, :].sum(axis=0) / (roi_control > 0.5).sum() light_signal *= darken.max() - darken.min() light_signal += darken.min()