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David Rotermund 2024-03-01 01:36:18 +01:00 • committed by GitHub
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2 changed files with 111 additions and 89 deletions
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69
olivia_data_plotter.py
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@ -7,34 +7,41 @@ from functions.load_config import load_config
from functions.get_trials import get_trials from functions.get_trials import get_trials
import h5py # type: ignore import h5py # type: ignore
control_file_handle = h5py.File("ROI_control_49.mat", "r") import argh
control_roi = (np.array(control_file_handle["roi"]).T) > 0
control_file_handle.close()
control_roi = control_roi.reshape((control_roi.shape[0] * control_roi.shape[1]))
s_darken_file_handle = h5py.File("ROI_sDarken_49.mat", "r")
s_darken_roi = (np.array(s_darken_file_handle["roi"]).T) > 0
s_darken_file_handle.close()
s_darken_roi = s_darken_roi.reshape((s_darken_roi.shape[0] * s_darken_roi.shape[1]))
mylogger = create_logger( def main(*, experiment_id: int = 1, config_filename: str = "config.json") -> None:
save_logging_messages=True, display_logging_messages=True, log_stage_name="test_xxx"
)
config = load_config(mylogger=mylogger)
experiment_id: int = 1 mylogger = create_logger(
save_logging_messages=True,
display_logging_messages=True,
log_stage_name="test_xxx",
)
config = load_config(mylogger=mylogger, filename=config_filename)
raw_data_path: str = os.path.join( roi_path: str = config["ref_image_path"]
control_file_handle = h5py.File(os.path.join(roi_path, "ROI_control.mat"), "r")
control_roi = (np.array(control_file_handle["roi"]).T) > 0
control_file_handle.close()
control_roi = control_roi.reshape((control_roi.shape[0] * control_roi.shape[1]))
s_darken_file_handle = h5py.File(os.path.join(roi_path, "ROI_sDarken.mat"), "r")
s_darken_roi = (np.array(s_darken_file_handle["roi"]).T) > 0
s_darken_file_handle.close()
s_darken_roi = s_darken_roi.reshape((s_darken_roi.shape[0] * s_darken_roi.shape[1]))
raw_data_path: str = os.path.join(
config["basic_path"], config["basic_path"],
config["recoding_data"], config["recoding_data"],
config["mouse_identifier"], config["mouse_identifier"],
config["raw_path"], config["raw_path"],
) )
data_path: str = "output" data_path: str = str(config["export_path"])
trails = get_trials(path=raw_data_path, experiment_id=experiment_id) trails = get_trials(path=raw_data_path, experiment_id=experiment_id)
for i in range(0, trails.shape[0]): for i in range(0, trails.shape[0]):
trial_id = int(trails[i]) trial_id = int(trails[i])
experiment_name: str = f"Exp{experiment_id:03d}_Trial{trial_id:03d}" experiment_name: str = f"Exp{experiment_id:03d}_Trial{trial_id:03d}"
mylogger.info(f"Loading files for {experiment_name}") mylogger.info(f"Loading files for {experiment_name}")
@ -45,19 +52,23 @@ for i in range(0, trails.shape[0]):
else: else:
ratio_sequence += data["ratio_sequence"] ratio_sequence += data["ratio_sequence"]
ratio_sequence /= float(trails.shape[0]) ratio_sequence /= float(trails.shape[0])
ratio_sequence = ratio_sequence.reshape( ratio_sequence = ratio_sequence.reshape(
(ratio_sequence.shape[0] * ratio_sequence.shape[1], ratio_sequence.shape[2]) (ratio_sequence.shape[0] * ratio_sequence.shape[1], ratio_sequence.shape[2])
) )
control = ratio_sequence[control_roi, :].mean(axis=0) control = ratio_sequence[control_roi, :].mean(axis=0)
s_darken = ratio_sequence[s_darken_roi, :].mean(axis=0) s_darken = ratio_sequence[s_darken_roi, :].mean(axis=0)
t = np.arange(0, control.shape[0]) / 100.0 t = np.arange(0, control.shape[0]) / 100.0
plt.plot(t, control, label="control") plt.plot(t, control, label="control")
plt.plot(t, s_darken, label="sDarken") plt.plot(t, s_darken, label="sDarken")
plt.legend() plt.legend()
plt.xlabel("Time [sec]") plt.xlabel("Time [sec]")
plt.show() plt.show()
if __name__ == "__main__":
argh.dispatch_command(main)

59
olivia_data_plotter_svd.py
View file

@ -8,34 +8,41 @@ from functions.get_trials import get_trials
import h5py # type: ignore import h5py # type: ignore
import torch import torch
control_file_handle = h5py.File("ROI_control_49.mat", "r") import argh
control_roi = (np.array(control_file_handle["roi"]).T) > 0
control_file_handle.close()
control_roi = control_roi.reshape((control_roi.shape[0] * control_roi.shape[1]))
s_darken_file_handle = h5py.File("ROI_sDarken_49.mat", "r")
s_darken_roi = (np.array(s_darken_file_handle["roi"]).T) > 0
s_darken_file_handle.close()
s_darken_roi = s_darken_roi.reshape((s_darken_roi.shape[0] * s_darken_roi.shape[1]))
mylogger = create_logger( def main(*, experiment_id: int = 1, config_filename: str = "config.json") -> None:
save_logging_messages=True, display_logging_messages=True, log_stage_name="test_xxx"
)
config = load_config(mylogger=mylogger)
experiment_id: int = 2 mylogger = create_logger(
save_logging_messages=True,
display_logging_messages=True,
log_stage_name="test_xxx",
)
config = load_config(mylogger=mylogger, filename=config_filename)
raw_data_path: str = os.path.join( roi_path: str = config["ref_image_path"]
control_file_handle = h5py.File(os.path.join(roi_path, "ROI_control.mat"), "r")
control_roi = (np.array(control_file_handle["roi"]).T) > 0
control_file_handle.close()
control_roi = control_roi.reshape((control_roi.shape[0] * control_roi.shape[1]))
s_darken_file_handle = h5py.File(os.path.join(roi_path, "ROI_sDarken.mat"), "r")
s_darken_roi = (np.array(s_darken_file_handle["roi"]).T) > 0
s_darken_file_handle.close()
s_darken_roi = s_darken_roi.reshape((s_darken_roi.shape[0] * s_darken_roi.shape[1]))
raw_data_path: str = os.path.join(
config["basic_path"], config["basic_path"],
config["recoding_data"], config["recoding_data"],
config["mouse_identifier"], config["mouse_identifier"],
config["raw_path"], config["raw_path"],
) )
data_path: str = "output" data_path: str = str(config["export_path"])
trails = get_trials(path=raw_data_path, experiment_id=experiment_id) trails = get_trials(path=raw_data_path, experiment_id=experiment_id)
for i in range(0, trails.shape[0]): for i in range(0, trails.shape[0]):
trial_id = int(trails[i]) trial_id = int(trails[i])
experiment_name: str = f"Exp{experiment_id:03d}_Trial{trial_id:03d}" experiment_name: str = f"Exp{experiment_id:03d}_Trial{trial_id:03d}"
mylogger.info(f"Loading files for {experiment_name}") mylogger.info(f"Loading files for {experiment_name}")
@ -61,11 +68,15 @@ for i in range(0, trails.shape[0]):
else: else:
ratio_sequence += rs_s_core - rs_c_core ratio_sequence += rs_s_core - rs_c_core
ratio_sequence /= float(trails.shape[0]) ratio_sequence /= float(trails.shape[0])
t = np.arange(0, ratio_sequence.shape[0]) / 100.0 t = np.arange(0, ratio_sequence.shape[0]) / 100.0
plt.plot(t, ratio_sequence, label="sDarken-control") plt.plot(t, ratio_sequence, label="sDarken - control")
plt.legend() plt.legend()
plt.xlabel("Time [sec]") plt.xlabel("Time [sec]")
plt.show() plt.show()
if __name__ == "__main__":
argh.dispatch_command(main)