Change to pymatreader

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')"
    ]
   },
   {

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