Merge pull request #1 from NxNiki/dev

Add pydantic data model for patients

.gitignore

@@ -26,8 +26,12 @@ build/
 # PyCharm
 .idea/
 
+# mac os file
+.DS_Store
+
 # python cache binaries:
 src/movie_decoding/__pycache__/
 
 data/
 results/
+wandb/

pyproject.toml

@@ -25,6 +25,8 @@ matplotlib = "^3.9.1"
 seaborn = "^0.13.2"
 pyarrow = "^17.0.0"
 scipy = "^1.14.1"
+pydantic = "^2.8.1"
+mat73 = "^0.61"
 
 [tool.poetry.dev-dependencies]
 black = "^23.0"
@@ -44,6 +46,7 @@ target-version = ['py310']
 # isort configuration
 [tool.isort]
 profile = "black"
+line_length = 120
 
 # mypy configuration
 [tool.mypy]

scripts/run_model.py → scripts/pipeline_decode_sleep.py

@@ -1,12 +1,17 @@
+"""
+train the model with data while patients are viewing the movie Twilight and 24 and test the model with data during free
+recall. The model will be trained to predict movie (Twilight vs 24, model 1) or character in both movies (model 2).
+Finally, we will apply the model (with better performance) on data during sleep to examine how reactivation/replay will
+impact free recall before and after sleep.
+"""
+
 import string
 from pathlib import Path
 
 import wandb
-
 from movie_decoding.main import pipeline
 from movie_decoding.utils.initializer import *
 
-# for patient in ['562', '563', '566', 'i728', '567', '572']:
 patient_list = ["i728", "572", "567", "566", "563", "562"]
 sd_list = [4, 4, 3.5, 4, 4, 3.5]
 # data_list = ['notch CAR4.5', 'notch CAR3.5', 'notch CAR4.5', 'notch CAR4', 'notch CAR3.5', 'notch CAR3.5']