diff --git a/6_iton_behavioral_models_neural.ipynb b/6_iton_behavioral_models_neural.ipynb index 252c26e..3c51d40 100644 --- a/6_iton_behavioral_models_neural.ipynb +++ b/6_iton_behavioral_models_neural.ipynb @@ -11,15 +11,14 @@ "!wget https://raw.githubusercontent.com/ManteLab/Iton_notebooks_public/refs/heads/main/data_ex6/neural_data.mat -O neural_data.mat\n", "!wget https://raw.githubusercontent.com/ManteLab/Iton_notebooks_public/refs/heads/main/data_ex6/dataset1.mat -O dataset1.mat\n", "!wget https://raw.githubusercontent.com/ManteLab/Iton_notebooks_public/refs/heads/main/data_ex6/dataset3.mat -O dataset3.mat\n", - "!pip3 install --quiet mat73 ipympl" + "!pip3 install --quiet pymatreader ipympl" ] }, { "cell_type": "markdown", "id": "ec7211ca-a104-4c3d-b528-102841bfd937", "metadata": { - "id": "ec7211ca-a104-4c3d-b528-102841bfd937", - "jp-MarkdownHeadingCollapsed": true + "id": "ec7211ca-a104-4c3d-b528-102841bfd937" }, "source": [ "# Part 1\n", @@ -165,9 +164,10 @@ }, "outputs": [], "source": [ - "from utils import plot_model_free_analysis_conditions_vs_baseline, loadmat\n", + "from pymatreader import read_mat\n", + "from utils import plot_model_free_analysis_conditions_vs_baseline\n", "\n", - "dataset_1 = loadmat('dataset1.mat')\n", + "dataset_1 = read_mat('dataset1.mat')\n", "\n", "plot_model_free_analysis_conditions_vs_baseline(\n", " baseline_data=dataset_1\n", @@ -183,9 +183,10 @@ }, "outputs": [], "source": [ - "from utils import plot_model_free_analysis_conditions_vs_baseline, loadmat\n", + "from pymatreader import read_mat\n", + "from utils import plot_model_free_analysis_conditions_vs_baseline\n", "\n", - "dataset_3 = loadmat('dataset3.mat')\n", + "dataset_3 = read_mat('dataset3.mat')\n", "\n", "plot_model_free_analysis_conditions_vs_baseline(\n", " baseline_data=dataset_3\n", @@ -229,9 +230,9 @@ }, "outputs": [], "source": [ - "from utils import loadmat\n", + "from pymatreader import read_mat\n", "\n", - "neural_data = loadmat('neural_data.mat')" + "neural_data = read_mat('neural_data.mat')" ] }, { diff --git a/utils.py b/utils.py index b5c8dc3..2f08e5e 100644 --- a/utils.py +++ b/utils.py @@ -6,8 +6,6 @@ import matplotlib.pyplot as plt from matplotlib.lines import Line2D from IPython.display import display from ipywidgets import interact, interact_manual, IntSlider, FloatSlider, IntRangeSlider, ToggleButton, ToggleButtons, Layout -from scipy.io import loadmat as sp_loadmat -from mat73 import loadmat as mat73_loadmat def in_colab(): @@ -62,13 +60,6 @@ def maybe_setup(setup_fun, state): state.update(setup_fun()) -def loadmat(mat_file): - try: - return sp_loadmat(mat_file) - except Exception: - return mat73_loadmat(mat_file) - - def generate_sims(C, k, alpha, sigma_a, sigma_s, lambda_, n_sim=100, tau=100, dt_total=11 / 85): dt = dt_total / tau