Cleanup variables

shimming-toolbox · Jan 24, 2024 · 739e4bb · 739e4bb
1 parent 619f275
commit 739e4bb
Showing 1 changed file with 13 additions and 13 deletions.
diff --git a/data_processing.ipynb b/data_processing.ipynb
@@ -309,16 +309,16 @@
     "\n",
     "for subject in subjects:\n",
     "    os.chdir(os.path.join(path_data, subject, \"anat\"))\n",
-    "    for shim_method in shim_modes:\n",
+    "    for shim_mode in shim_modes:\n",
     "        # Shim methods are registered to the CoV T2starw scan, so we need to use the added suffix to identify them\n",
-    "        if shim_method == 'CoV':\n",
+    "        if shim_mode == 'CoV':\n",
     "            file_suffix = 'crop'\n",
     "        else:\n",
     "            file_suffix = 'reg'\n",
-    "        fname_result_sc = os.path.join(path_results, f\"{subject}_acq-{shim_method}_T2starw_label-SC.csv\")\n",
-    "        !sct_extract_metric -i {subject}_acq-{shim_method}_T2starw_{file_suffix}.nii.gz -f {subject}_acq-CoV_T2starw_crop_seg.nii.gz -method wa -vert 3:9 -vertfile {subject}_acq-CoV_T2starw_crop_seg_labeled.nii.gz -perslice 1 -o {fname_result_sc}\n",
-    "        fname_result_csf = os.path.join(path_results, f\"{subject}_acq-{shim_method}_T2starw_label-CSF.csv\")\n",
-    "        !sct_extract_metric -i {subject}_acq-{shim_method}_T2starw_{file_suffix}.nii.gz -f {subject}_acq-CoV_T2starw_crop_label-CSF_seg.nii.gz -method wa -vert 3:9 -vertfile {subject}_acq-CoV_T2starw_crop_seg_labeled.nii.gz -perslice 1 -o {fname_result_csf}"
+    "        fname_result_sc = os.path.join(path_results, f\"{subject}_acq-{shim_mode}_T2starw_label-SC.csv\")\n",
+    "        !sct_extract_metric -i {subject}_acq-{shim_mode}_T2starw_{file_suffix}.nii.gz -f {subject}_acq-CoV_T2starw_crop_seg.nii.gz -method wa -vert 3:9 -vertfile {subject}_acq-CoV_T2starw_crop_seg_labeled.nii.gz -perslice 1 -o {fname_result_sc}\n",
+    "        fname_result_csf = os.path.join(path_results, f\"{subject}_acq-{shim_mode}_T2starw_label-CSF.csv\")\n",
+    "        !sct_extract_metric -i {subject}_acq-{shim_mode}_T2starw_{file_suffix}.nii.gz -f {subject}_acq-CoV_T2starw_crop_label-CSF_seg.nii.gz -method wa -vert 3:9 -vertfile {subject}_acq-CoV_T2starw_crop_seg_labeled.nii.gz -perslice 1 -o {fname_result_csf}"
    ]
   },
   {
@@ -369,18 +369,18 @@
     "for i, subject in enumerate(subjects):\n",
     "    ax = axes[i]\n",
     "\n",
-    "    for shim_method in shim_modes:\n",
+    "    for shim_mode in shim_modes:\n",
     "        # Initialize list to collect data for this shim method\n",
     "        method_data = []\n",
     "\n",
     "        # Get signal in SC\n",
-    "        file_csv = os.path.join(path_results, f\"{subject}_acq-{shim_method}_T2starw_label-SC.csv\")\n",
+    "        file_csv = os.path.join(path_results, f\"{subject}_acq-{shim_mode}_T2starw_label-SC.csv\")\n",
     "        df = pd.read_csv(file_csv)\n",
     "        data_sc = df['WA()']\n",
     "        data_sc_smoothed = smooth_data(data_sc)\n",
     "\n",
     "        # Get signal in CSF\n",
-    "        file_csv = os.path.join(path_results, f\"{subject}_acq-{shim_method}_T2starw_label-CSF.csv\")\n",
+    "        file_csv = os.path.join(path_results, f\"{subject}_acq-{shim_mode}_T2starw_label-CSF.csv\")\n",
     "        df = pd.read_csv(file_csv)\n",
     "        data_csf = df['WA()']\n",
     "        data_csf_smoothed = smooth_data(data_csf)\n",
@@ -401,12 +401,12 @@
     "        if method_data:\n",
     "            # Plotting each file's data separately\n",
     "            for resampled_data in method_data:\n",
-    "                ax.plot(x_grid, resampled_data, label=f\"{shim_method}\")\n",
+    "                ax.plot(x_grid, resampled_data, label=f\"{shim_mode}\")\n",
     "        \n",
     "            # Compute stats on the non-resampled data (to avoid interpolation errors)\n",
     "            mean_data = np.mean(data_sc_csf_ratio)\n",
     "            sd_data = np.std(data_sc_csf_ratio)\n",
-    "            data_stats.append([subject, shim_method, mean_data, sd_data])\n",
+    "            data_stats.append([subject, shim_mode, mean_data, sd_data])\n",
     "\n",
     "    # Set custom x-ticks\n",
     "    ax.set_xticks(custom_xticks)\n",
@@ -430,7 +430,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f2a6d765",
+   "id": "bbb3e6fc",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -711,7 +711,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f062f23d",
+   "id": "6804e2be",
    "metadata": {},
    "outputs": [],
    "source": [