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peetal · Mar 29, 2024 · 5b69eaa · 5b69eaa
1 parent 9ca4fed
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Showing 2 changed files with 19 additions and 4 deletions.
diff --git a/bgfc_kit/bgfc_analyses.py b/bgfc_kit/bgfc_analyses.py
@@ -15,6 +15,7 @@
 from sklearn.pipeline import Pipeline
 from subprocess import call 
 from scipy.stats import sem
+from .structDict import recurseCreateStructDict
 
 def unpack_conf(FIRdesignMat_conf_dir:str, postfMRIprep_conf_dir:str): 
 

diff --git a/bgfc_kit/demo/demo.ipynb b/bgfc_kit/demo/demo.ipynb
@@ -51,7 +51,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 3,
    "id": "ec0276fe-41f0-40dc-9c85-c8bb96ff4acc",
    "metadata": {},
    "outputs": [
@@ -68,7 +68,7 @@
     }
    ],
    "source": [
-    "import bgfc_kit, importlib, inspect, pkgutil\n",
+    "import bgfc_kit, importlib, inspect, pkgutil, os\n",
     "package = importlib.import_module('bgfc_kit')\n",
     "print(f\"Submodules of bgfc_kit:\")\n",
     "for loader, name, is_pkg in pkgutil.walk_packages(package.__path__):\n",
@@ -387,10 +387,24 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 44,
+   "execution_count": 4,
    "id": "9b039438-519c-4e40-ab70-558e432ccfca",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "ename": "NameError",
+     "evalue": "name 'toml' is not defined",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[4], line 7\u001b[0m\n\u001b[1;32m      5\u001b[0m atlas \u001b[38;5;241m=\u001b[39m os\u001b[38;5;241m.\u001b[39mpath\u001b[38;5;241m.\u001b[39mjoin(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m/projects/hulacon/peetal/divatten/post_fMRIPrep_pip_motionCorr\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msub-001\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtransformed_atlas\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msub-001_schaefer200_T1W.nii.gz\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m      6\u001b[0m subject_list \u001b[38;5;241m=\u001b[39m [\u001b[38;5;241m1\u001b[39m] \u001b[38;5;66;03m# we only look at the first subject we have just preprocessed\u001b[39;00m\n\u001b[0;32m----> 7\u001b[0m \u001b[43mplot_parcel_FIR_estimates\u001b[49m\u001b[43m(\u001b[49m\u001b[43mFIRdesignMat_conf_dir\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mpostfMRIprep_conf_dir\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43matlas\u001b[49m\u001b[43m)\u001b[49m\n",
+      "File \u001b[0;32m~/.conda/envs/plenv/lib/python3.8/site-packages/bgfc_kit/bgfc_analyses.py:488\u001b[0m, in \u001b[0;36mplot_parcel_FIR_estimates\u001b[0;34m(FIRdesignMat_conf_dir, postfMRIprep_conf_dir, parcel_id, sub_list, atlas)\u001b[0m\n\u001b[1;32m    464\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m    465\u001b[0m \u001b[38;5;124;03mThis function plots the estimates of FIR regressors across all subjects. These plots should serve \u001b[39;00m\n\u001b[1;32m    466\u001b[0m \u001b[38;5;124;03mas sanity checks for FIR model efficiency. The plot should reveal boxcart shape reflecting condition structure.\u001b[39;00m\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m    484\u001b[0m \u001b[38;5;124;03m    FIR estimates for a specific parcel. \u001b[39;00m\n\u001b[1;32m    485\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m    487\u001b[0m \u001b[38;5;66;03m# unpack configuration files for important information\u001b[39;00m\n\u001b[0;32m--> 488\u001b[0m fir_cfg, preprocess_cfg \u001b[38;5;241m=\u001b[39m \u001b[43munpack_conf\u001b[49m\u001b[43m(\u001b[49m\u001b[43mFIRdesignMat_conf_dir\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mpostfMRIprep_conf_dir\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    489\u001b[0m base_dir \u001b[38;5;241m=\u001b[39m preprocess_cfg\u001b[38;5;241m.\u001b[39moutput_dir\n\u001b[1;32m    491\u001b[0m signal_array \u001b[38;5;241m=\u001b[39m []\n",
+      "File \u001b[0;32m~/.conda/envs/plenv/lib/python3.8/site-packages/bgfc_kit/bgfc_analyses.py:42\u001b[0m, in \u001b[0;36munpack_conf\u001b[0;34m(FIRdesignMat_conf_dir, postfMRIprep_conf_dir)\u001b[0m\n\u001b[1;32m     40\u001b[0m \u001b[38;5;66;03m# load FIRdesignMat configuration file\u001b[39;00m\n\u001b[1;32m     41\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28mopen\u001b[39m(FIRdesignMat_conf_dir, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mr\u001b[39m\u001b[38;5;124m\"\u001b[39m) \u001b[38;5;28;01mas\u001b[39;00m toml_file:\n\u001b[0;32m---> 42\u001b[0m     fir_cfg \u001b[38;5;241m=\u001b[39m \u001b[43mtoml\u001b[49m\u001b[38;5;241m.\u001b[39mload(toml_file)\n\u001b[1;32m     43\u001b[0m fir_cfg \u001b[38;5;241m=\u001b[39m recurseCreateStructDict(fir_cfg)\n\u001b[1;32m     44\u001b[0m fir_cfg \u001b[38;5;241m=\u001b[39m fir_cfg\u001b[38;5;241m.\u001b[39mPARAMETERS\n",
+      "\u001b[0;31mNameError\u001b[0m: name 'toml' is not defined"
+     ]
+    }
+   ],
    "source": [
     "from bgfc_kit.bgfc_analyses import plot_parcel_FIR_estimates\n",
     "# specify the necessary inputs\n",