davrot/gevi
1
0
Fork 0
mirror of https://github.com/davrot/gevi.git synced 2025-04-20 22:26:43 +02:00
Code Issues Projects Releases Packages Wiki Activity Actions

Delete stage_6_convert_roi.py

Browse source
This commit is contained in:
David Rotermund 2025-03-19 18:28:54 +01:00 • committed by GitHub
parent d3d79c0607
commit d8688a156a
No known key found for this signature in database
GPG key ID: B5690EEEBB952194
1 changed files with 0 additions and 55 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

55
stage_6_convert_roi.py
View file

@ -1,55 +0,0 @@
import json
import os
import argh
from jsmin import jsmin # type:ignore
import numpy as np
import h5py
def converter(config_filename: str = "config.json") -> None:
filename: str = config_filename
if os.path.isfile(filename) is False:
print(f"{filename} is missing")
exit()
with open(filename, "r") as file:
config = json.loads(jsmin(file.read()))
raw_data_path: str = os.path.join(
config["basic_path"],
config["recoding_data"],
config["mouse_identifier"],
config["raw_path"],
)
if os.path.isdir(raw_data_path) is False:
print(f"ERROR: could not find raw directory {raw_data_path}!!!!")
exit()
roi_path: str = os.path.join(
config["basic_path"], config["recoding_data"], config["mouse_identifier"]
)
roi_control_mat: str = os.path.join(roi_path, "ROI_control.mat")
roi_sdarken_mat: str = os.path.join(roi_path, "ROI_sDarken.mat")
if os.path.isfile(roi_control_mat):
hf = h5py.File(roi_control_mat, "r")
roi_control = np.array(hf["roi"]).T
filename_out: str = f"roi_control{config["mouse_identifier"]}.npy"
np.save(filename_out, roi_control)
else:
print("ROI Control not found")
if os.path.isfile(roi_sdarken_mat):
hf = h5py.File(roi_sdarken_mat, "r")
roi_darken = np.array(hf["roi"]).T
filename_out = f"roi_sdarken{config["mouse_identifier"]}.npy"
np.save(filename_out, roi_darken)
else:
print("ROI sDarken not found")
if __name__ == "__main__":
argh.dispatch_command(converter)