From 1f0fd3d262c4fc48fe954d4ea19fd4e059eecd0f Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Fri, 18 Jul 2025 14:48:52 +0200
Subject: [PATCH 01/17] Add scripts to compare AP and RL diameters computed
 using 'skimage.regionprops' and 'HOG'

SCT PR: https://github.com/spinalcordtoolbox/spinalcordtoolbox/pull/4958
---
 figures/AP_RL_diameters_PAM50.py    | 192 ++++++++++++++++++++++++++++
 figures/AP_RL_diameters_plotting.py | 116 +++++++++++++++++
 2 files changed, 308 insertions(+)
 create mode 100644 figures/AP_RL_diameters_PAM50.py
 create mode 100644 figures/AP_RL_diameters_plotting.py

diff --git a/figures/AP_RL_diameters_PAM50.py b/figures/AP_RL_diameters_PAM50.py
new file mode 100644
index 0000000..009443b
--- /dev/null
+++ b/figures/AP_RL_diameters_PAM50.py
@@ -0,0 +1,192 @@
+#
+# Plot a single subject morphometric metrics in the PAM50 space per slice and vertebral levels
+#
+# You can use SCT's conda environment to run this script:
+#       # Go to the SCT directory
+#       cd $SCT_DIR
+#       # Activate SCT conda environment
+#       source ./python/etc/profile.d/conda.sh
+#       conda activate venv_sct
+#
+# Example usage on a single subject:
+#       python AP_RL_diameters_PAM50.py -i /path/to/morphometrics_PAM50.csv -o /path/to/output/morphometrics_PAM50.png
+#
+# Authors: Jan Valosek
+#
+
+import sys
+import argparse
+import numpy as np
+import pandas as pd
+import seaborn as sns
+import matplotlib as mpl
+import matplotlib.pyplot as plt
+
+METRICS = [
+    'MEAN(diameter_AP)',
+    'MEAN(diameter_RL)',
+]
+
+LABELS_FONT_SIZE = 14
+TICKS_FONT_SIZE = 12
+
+
+def get_parser():
+    parser = argparse.ArgumentParser(
+        description="Plot AP and RL diameters measured using different methods in the PAM50 space.")
+    parser.add_argument('-i', required=True, type=str,
+                        help="Path to the CSV file with diameter measurements.")
+    parser.add_argument('-o', required=True, type=str,
+                        help="Path to save the output figure.")
+
+    return parser
+
+
+# Apply smoothing to the metric data
+def smooth(y: np.ndarray, box_pts: int) -> np.ndarray:
+    """
+    Smooths a 1D array using a simple moving average (box filter).
+    Inspired by: https://github.com/sct-pipeline/rootlets-informed-reg2template/blob/main/csa_analysis.py#L199
+    Args:
+        y (np.ndarray): Input 1D array to be smoothed.
+        box_pts (int): Number of points in the moving average window. Needs to be >= 1.
+    Returns:
+        np.ndarray: Smoothed array of the same length as the input.
+    """
+    box = np.ones(box_pts) / box_pts
+    y_smooth = np.convolve(y, box, mode='same')
+    return y_smooth
+
+
+def load_single_subject_data(path_single_subject, df_spine_generic_min, df_spine_generic_max):
+    """
+    Load single subject data
+    :param path_single_subject: path to single subject CSV file (from session1 or session2)
+    :param df_spine_generic_min: minimum slice number from spine-generic dataset
+    :param df_spine_generic_max: maximum slice number from spine-generic dataset
+    :return:
+    """
+    df_single_subject = pd.read_csv(path_single_subject)
+    # Compute compression ratio (CR) as MEAN(diameter_AP) / MEAN(diameter_RL)
+    df_single_subject['MEAN(compression_ratio)'] = df_single_subject['MEAN(diameter_AP)'] / \
+                                                   df_single_subject['MEAN(diameter_RL)']
+
+    # Keep only slices from C1 to Th1 to match the slices of the spine-generic normative values
+    df_single_subject = df_single_subject[(df_single_subject['Slice (I->S)'] >= df_spine_generic_min) &
+                                          (df_single_subject['Slice (I->S)'] <= df_spine_generic_max)]
+
+    return df_single_subject
+
+def get_vert_indices(df):
+    """
+    Get indices of slices corresponding to mid-vertebrae
+    Args:
+        df (pd.dataFrame): dataframe with CSA values
+    Returns:
+        vert (pd.Series): vertebrae levels across slices
+        ind_vert (np.array): indices of slices corresponding to the beginning of each level (=intervertebral disc)
+        ind_vert_mid (np.array): indices of slices corresponding to mid-levels
+    """
+    # Get unique participant IDs
+    subjects = df['Filename'].unique()
+    # Get vert levels for one certain subject
+    vert = df[df['Filename'] == subjects[0]]['VertLevel']
+    # Get indexes of where array changes value
+    ind_vert = vert.diff()[vert.diff() != 0].index.values
+    # Get the beginning of C1
+    ind_vert = np.append(ind_vert, vert.index.values[-1])
+    ind_vert_mid = []
+    # Get indexes of mid-vertebrae
+    for i in range(len(ind_vert)-1):
+        ind_vert_mid.append(int(ind_vert[i:i+2].mean()))
+
+    return vert, ind_vert, ind_vert_mid
+
+
+def create_lineplot(df, figure_path):
+    """
+    Create lineplot for individual metrics per vertebral levels.
+    Args:
+        df (pd.DataFrame): dataframe with single subject values
+        figure_path (str): path to save the figure
+    """
+    mpl.rcParams['font.family'] = 'Arial'
+
+    # Plot figures
+    fig, axes = plt.subplots(1, 2, figsize=(10, 5))
+    axs = axes.ravel()
+
+    # Loop across metrics
+    for index, metric in enumerate(METRICS):
+
+        # Smooth the data to improve visualization
+        df[metric] = smooth(df[metric].values, 5)
+        df[f'{metric.replace(")", "_hog)")}'] = smooth(df[f'{metric.replace(")", "_hog)")}'].values, 5)
+        sns.lineplot(ax=axs[index], x="Slice (I->S)", y=metric,
+                     data=df, linewidth=2,
+                     label=metric)
+        sns.lineplot(ax=axs[index], x="Slice (I->S)", y=f'{metric.replace(")", "_hog)")}',
+                     data=df, linewidth=2,
+                     label=f'{metric.replace(")", "_hog)")}')
+
+        # Tweak y-axis limits
+        # ymin, ymax = METRICS_YLIMITS[metric]
+        # axes.set_ylim(ymin, ymax)
+        # Remove first and last 4 slices from the x-axis to remove smoothing artifacts
+        axs[index].set_xlim(df['Slice (I->S)'].iloc[4], df['Slice (I->S)'].iloc[-4])
+
+        # Remove xticks to hide PAM50 Axial Slice numbers
+        axs[index].set_xticks([])
+        axs[index].tick_params(axis='both', which='major', labelsize=TICKS_FONT_SIZE)
+        axs[index].spines['right'].set_visible(False)
+        axs[index].spines['left'].set_visible(False)
+        axs[index].spines['top'].set_visible(False)
+        axs[index].spines['bottom'].set_visible(True)
+
+        # Get ymin and ymax for the y-axis
+        ymin, ymax = axs[index].get_ylim()
+
+        vert, ind_vert, ind_vert_mid = get_vert_indices(df)
+        for idx, x in enumerate(ind_vert[1:-1]):
+            axs[index].axvline(df.loc[x, 'Slice (I->S)'], color='black', linestyle='--', alpha=0.3, zorder=0)
+        for idx, x in enumerate(ind_vert_mid, 0):
+            level = f'T{vert[x] - 7}' if vert[x] > 7 else f'C{vert[x]}'
+            axs[index].text(df.loc[ind_vert_mid[idx], 'Slice (I->S)'],
+                            ymin - (ymax-ymin)*0.05, level, horizontalalignment='center',
+                            verticalalignment='bottom', color='black', fontsize=TICKS_FONT_SIZE)
+
+        axs[index].invert_xaxis()
+        axs[index].yaxis.grid(True)
+        axs[index].set_axisbelow(True)
+        axs[index].set_ylabel(f'{metric}', fontsize=LABELS_FONT_SIZE)
+        axs[index].set_xlabel('')
+
+        # Decrease the font size of the legend
+        axs[index].legend(loc='lower left', fontsize=TICKS_FONT_SIZE)
+
+    plt.tight_layout()
+    plt.savefig(figure_path, dpi=300, bbox_inches='tight')
+    print(f'Figure saved: {figure_path}')
+    plt.show()
+    # plt.close()
+
+
+def main():
+    parser = get_parser()
+    args = parser.parse_args()
+
+    # Get the file path from args
+    csv_path = args.i
+    out_path = args.o
+
+    # Create a list of dataframes for each session file
+    df = load_single_subject_data(csv_path, 700, 980)
+    if df.empty:
+        print('WARNING: No slices found in the range C1-Th1 in the single subject data. Exiting...')
+        sys.exit(1)
+
+    create_lineplot(df, out_path)
+
+
+if __name__ == '__main__':
+    main()
\ No newline at end of file
diff --git a/figures/AP_RL_diameters_plotting.py b/figures/AP_RL_diameters_plotting.py
new file mode 100644
index 0000000..d6c0a56
--- /dev/null
+++ b/figures/AP_RL_diameters_plotting.py
@@ -0,0 +1,116 @@
+#
+# Script for comparing AP and RL diameters measured using different methods (skimage.regionprops vs. HOG).
+# Context: https://github.com/spinalcordtoolbox/spinalcordtoolbox/pull/4958/
+# This script generates scatter plots with regression lines to visualize the correlation
+# between different measurement techniques.
+#
+# You can use SCT's conda environment to run this script:
+#       # Go to the SCT directory
+#       cd $SCT_DIR
+#       # Activate SCT conda environment
+#       source ./python/etc/profile.d/conda.sh
+#       conda activate venv_sct
+#
+# Example usage on a single subject:
+#       python AP_RL_diameters_plotting.py -i /path/to/morphometrics_plotting.csv -o /path/to/output/morphometrics.png
+#
+# Authors: Jan Valosek
+#
+
+import argparse
+import pandas as pd
+import matplotlib as mpl
+import matplotlib.pyplot as plt
+from scipy.stats import linregress
+
+
+def get_parser():
+    """
+    Parse command line arguments.
+    """
+    parser = argparse.ArgumentParser(
+        description="Create scatter plots with regression lines for AP and RL diameters measured using different methods.")
+    parser.add_argument('-i', required=True, type=str,
+                        help="Path to the CSV file with diameter measurements.")
+    parser.add_argument('-o', required=True, type=str,
+                        help="Path to save the output figure.")
+    return parser
+
+
+def plot_with_regression(x: pd.Series, y: pd.Series, xlabel: str, ylabel: str, ax: plt.Axes) -> None:
+    """Plot scatter with regression line"""
+    # Drop NaNs
+    df = pd.DataFrame({xlabel: x, ylabel: y}).dropna()
+    x_clean, y_clean = df[xlabel], df[ylabel]
+
+    # Regression:
+    #   slope -- Slope of the regression line
+    #   intercept  -- Intercept of the regression line
+    #   r -- The Pearson correlation coefficient
+    slope, intercept, r, _, _ = linregress(x_clean, y_clean)
+    reg_line = slope * x_clean + intercept
+
+    mpl.rcParams['font.family'] = 'Arial'
+
+    # Scatter
+    ax.scatter(x_clean, y_clean, s=20, edgecolor='k', facecolor='gray', alpha=0.7)
+    ax.plot(x_clean, reg_line, 'r-', linewidth=2)
+
+    # Identity line
+    min_val, max_val = min(x_clean.min(), y_clean.min()), max(x_clean.max(), y_clean.max())
+    ax.plot([min_val, max_val], [min_val, max_val], 'k--', linewidth=1)
+
+    # Labels and text
+    ax.set_xlabel(xlabel, fontsize=10)
+    ax.set_ylabel(ylabel, fontsize=10)
+    ax.set_aspect('equal', adjustable='box')
+    ax.set_xlim(min_val*0.95, max_val*1.05)
+    ax.set_ylim(min_val*0.95, max_val*1.05)
+    ax.text(0.05, 0.95,
+            f'$r$ = {r:.2f}\n$y$ = {slope:.2f}$x$ + {intercept:.2f}',
+            transform=ax.transAxes,
+            verticalalignment='top',
+            fontsize=9)
+
+    # Style
+    ax.spines[['top', 'right']].set_visible(False)
+    ax.tick_params(labelsize=8)
+
+
+def main() -> None:
+    """Read CSV and generate comparison plots for AP and RL diameters."""
+    parser = get_parser()
+    args = parser.parse_args()
+
+    # Use command line arguments
+    csv_path = args.i
+    out_path = args.o
+
+    df = pd.read_csv(csv_path)
+
+    fig, axes = plt.subplots(1, 2, figsize=(10, 5), dpi=300)
+    plot_with_regression(
+        df['MEAN(diameter_AP)'],
+        df['MEAN(diameter_AP_hog)'],
+        'AP diameter (skimage.regionprops)',
+        'AP diameter (HOG)',
+        axes[0]
+    )
+    plot_with_regression(
+        df['MEAN(diameter_RL)'],
+        df['MEAN(diameter_RL_hog)'],
+        'RL diameter (skimage.regionprops)',
+        'RL diameter (HOG)',
+        axes[1]
+    )
+    plt.tight_layout()
+
+    # Save figure
+    plt.savefig(out_path, bbox_inches='tight', dpi=300)
+    print(f"Figure saved: {out_path}")
+    plt.show()
+    # plt.close()
+
+
+if __name__ == "__main__":
+    main()

From 4eef5adc75218c6cc8548e457a9ef7c2e3bb58f0 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Tue, 29 Jul 2025 10:17:34 +0200
Subject: [PATCH 02/17] improve description and comments

---
 figures/AP_RL_diameters_PAM50.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/figures/AP_RL_diameters_PAM50.py b/figures/AP_RL_diameters_PAM50.py
index 009443b..48a0e1f 100644
--- a/figures/AP_RL_diameters_PAM50.py
+++ b/figures/AP_RL_diameters_PAM50.py
@@ -1,5 +1,6 @@
 #
 # Plot a single subject morphometric metrics in the PAM50 space per slice and vertebral levels
+# Original vs HOG-based AP and RL diameters
 #
 # You can use SCT's conda environment to run this script:
 #       # Go to the SCT directory
@@ -122,9 +123,11 @@ def create_lineplot(df, figure_path):
         # Smooth the data to improve visualization
         df[metric] = smooth(df[metric].values, 5)
         df[f'{metric.replace(")", "_hog)")}'] = smooth(df[f'{metric.replace(")", "_hog)")}'].values, 5)
+        # Original
         sns.lineplot(ax=axs[index], x="Slice (I->S)", y=metric,
                      data=df, linewidth=2,
                      label=metric)
+        # HOG-based
         sns.lineplot(ax=axs[index], x="Slice (I->S)", y=f'{metric.replace(")", "_hog)")}',
                      data=df, linewidth=2,
                      label=f'{metric.replace(")", "_hog)")}')

From 8e6b3074c292a4138c8047edb3007f597af68114 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Tue, 29 Jul 2025 10:17:56 +0200
Subject: [PATCH 03/17] comment out plt.show() and uncomment plt.close()

---
 figures/AP_RL_diameters_PAM50.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/figures/AP_RL_diameters_PAM50.py b/figures/AP_RL_diameters_PAM50.py
index 48a0e1f..5d255f3 100644
--- a/figures/AP_RL_diameters_PAM50.py
+++ b/figures/AP_RL_diameters_PAM50.py
@@ -170,8 +170,8 @@ def create_lineplot(df, figure_path):
     plt.tight_layout()
     plt.savefig(figure_path, dpi=300, bbox_inches='tight')
     print(f'Figure saved: {figure_path}')
-    plt.show()
-    # plt.close()
+    #plt.show()
+    plt.close()
 
 
 def main():

From 74062e365fa564effa9225fc17370dddec780535 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Tue, 29 Jul 2025 10:18:13 +0200
Subject: [PATCH 04/17] add compute_diameters.sh to compute AP and RL diameters
 using "traditional" and HOG-based methods

---
 figures/compute_diameters.sh | 159 +++++++++++++++++++++++++++++++++++
 1 file changed, 159 insertions(+)
 create mode 100644 figures/compute_diameters.sh

diff --git a/figures/compute_diameters.sh b/figures/compute_diameters.sh
new file mode 100644
index 0000000..f9e62b4
--- /dev/null
+++ b/figures/compute_diameters.sh
@@ -0,0 +1,159 @@
+#!/bin/bash
+#
+# Compute AP and RL diameters using "traditional" and HOG-based methods
+#
+# Requirements:
+#   SCT PR #4958: https://github.com/spinalcordtoolbox/spinalcordtoolbox/pull/4958
+#
+# Usage:
+#     sct_run_batch -config config.json
+#
+# Example of config.json:
+# {
+#  "script"      : "~/code/dcm-metric-normalization/figures/compute_diameters.sh",
+#  "jobs"        : 8
+# }
+#
+# Example of dataset.txt:
+#   path/to/dataset1 path/to/output1
+#   path/to/dataset2 path/to/output1
+#
+# Manual segmentations and disc labels should be located under:
+#   PATH_DATA/derivatives/labels/SUBJECT/<CONTRAST>/
+#
+# Author: Jan Valosek
+#
+
+# Uncomment for full verbose
+set -x
+
+# Immediately exit if error
+set -e -o pipefail
+
+# Exit if user presses CTRL+C (Linux) or CMD+C (OSX)
+trap "echo Caught Keyboard Interrupt within script. Exiting now.; exit" INT
+
+# Print retrieved variables from the sct_run_batch script to the log (to allow easier debug)
+echo "Retrieved variables from from the caller sct_run_batch:"
+echo "PATH_DATA: ${PATH_DATA}"
+echo "PATH_DATA_PROCESSED: ${PATH_DATA_PROCESSED}"
+echo "PATH_RESULTS: ${PATH_RESULTS}"
+echo "PATH_LOG: ${PATH_LOG}"
+echo "PATH_QC: ${PATH_QC}"
+
+SUBJECT=$1
+
+echo "SUBJECT: ${SUBJECT}"
+
+# get starting time:
+start=`date +%s`
+
+# ------------------------------------------------------------------------------
+# SCRIPT STARTS HERE
+# ------------------------------------------------------------------------------
+# Display useful info for the log, such as SCT version, RAM and CPU cores available
+sct_check_dependencies -short
+
+# Go to folder where data will be copied and processed
+cd $PATH_DATA_PROCESSED
+
+# Copy source images
+# Note: we use '/./' in order to include the sub-folder 'ses-0X'
+rsync -Ravzh --no-g $PATH_DATA/./$SUBJECT .
+#	•	-R → Preserves relative path structure.
+#	•	-a → Archive mode (preserves most attributes except group ownership).
+#	•	-v → Verbose output.
+#	•	-z → Compresses data during transfer.
+#	•	-h → Human-readable file sizes.
+#	•	--no-g → Skips changing group ownership.
+
+# Remove dwi folder if it exists (because we do not process DWI data in this script)
+if [[ -d ${SUBJECT}/dwi ]]; then
+  echo "Removing DWI folder: ${SUBJECT}/dwi"
+  rm -rf ${SUBJECT}/dwi
+fi
+
+# Go to subject folder for source images
+cd ${SUBJECT}/anat
+
+# Define variables
+# We do a substitution '/' --> '_' in case there is a subfolder 'ses-0X/'
+file="${SUBJECT//[\/]/_}"
+echo "file: ${file}"
+
+# -------------------------------------------------------------------------
+# T2w
+# -------------------------------------------------------------------------
+# Steps:
+#   - find T2w image
+#   - remove all other files except the selected T2w and its derivatives to save space
+#   - copy SC segmentation from derivatives/labels folder (we assume it exists)
+#   - copy disc labels from derivatives/labels folder (we assume it exists)
+#   - generate labeled segmentation using init disc labels
+#   - generate metrics using sct_process_segmentation
+#   - generate figures using custom script
+
+# Find T2w image
+if [[ -e "${file}_T2w.nii.gz" ]]; then
+  file_t2="${file}_T2w"
+else
+  echo "No suitable T2w file found for subject ${SUBJECT}" >&2
+  exit 1
+fi
+
+# Remove all other files except the selected T2w and its derivatives to save space
+find . -maxdepth 1 -type f \
+  ! -name "${file_t2}.*" \
+  ! -name "${file_t2}_*" \
+  -exec rm -f {} +
+echo "file_t2: ${file_t2}"
+
+echo "👉 Processing: ${file_t2}"
+
+# Copy SC segmentation from derivatives/labels folder (we assume it exists)
+FILESEG="${file_t2}_label-SC_seg"
+rsync -avzh --no-g "${PATH_DATA}/derivatives/labels/${SUBJECT}/anat/${FILESEG}.nii.gz" "${FILESEG}.nii.gz"
+echo "✅ [$(date '+%Y-%m-%d %H:%M:%S')] ${FILESEG}.nii.gz found under derivatives/labels --> copying it" >> "${PATH_LOG}/T2w_sc_segmentation.log"
+
+# Copy disc labels from derivatives/labels folder (we assume it exists) as we need them for vertebral labeling
+FILEDISCS="${file_t2}_labels-disc-manual"
+# whole-spine
+if [[ -e "${PATH_DATA}/derivatives/labels/${SUBJECT}/anat/${file_t2}_labels-disc-manual.nii.gz" ]]; then
+    rsync -avzh --no-g "${PATH_DATA}/derivatives/labels/${SUBJECT}/anat/${file_t2}_labels-disc-manual.nii.gz" "${FILEDISCS}.nii.gz"
+    echo "✅ [$(date '+%Y-%m-%d %H:%M:%S')] ${file_t2}_labels-disc-manual.nii.gz found under derivatives/labels --> copying it" >> "${PATH_LOG}/T2w_disc_labels.log"
+# spine-generic
+elif [[ -e "${PATH_DATA}/derivatives/labels/${SUBJECT}/anat/${file_t2}_label-discs_dlabel.nii.gz" ]]; then
+    rsync -avzh --no-g "${PATH_DATA}/derivatives/labels/${SUBJECT}/anat/${file_t2}_label-discs_dlabel.nii.gz" "${FILEDISCS}.nii.gz"
+    echo "✅ [$(date '+%Y-%m-%d %H:%M:%S')] ${file_t2}_label-discs_dlabel.nii.gz found under derivatives/labels --> copying it" >> "${PATH_LOG}/T2w_disc_labels.log"
+fi
+
+# Generate labeled segmentation using init disc labels
+sct_label_vertebrae -i ${file_t2}.nii.gz -s ${FILESEG}.nii.gz -discfile ${FILEDISCS}.nii.gz -c t2 -qc ${PATH_QC} -qc-subject ${file}
+
+sct_process_segmentation -i ${file_t2}.nii.gz -s ${FILESEG}.nii.gz -vertfile ${FILESEG}_labeled.nii.gz -perslice 1 -o ${PATH_RESULTS}/${file}_metrics_PAM50_angle_corr0.csv -qc qc -angle-corr 0
+sct_process_segmentation -i ${file_t2}.nii.gz -s ${FILESEG}.nii.gz -vertfile ${FILESEG}_labeled.nii.gz -perslice 1 -o ${PATH_RESULTS}/${file}_metrics_PAM50_angle_corr1.csv -qc qc -angle-corr 1
+
+# Create figures folder under ${PATH_RESULTS} if it does not exist
+mkdir -p ${PATH_RESULTS}/figures
+
+# Generate figure using custom script (assuming this repo is cloned in `~/code/dcm-metric-normalization`)
+${SCT_DIR}/python/envs/venv_sct/bin/python ~/code/dcm-metric-normalization/figures/AP_RL_diameters_PAM50.py \
+  -i ${PATH_RESULTS}/${file}_metrics_PAM50_angle_corr0.csv \
+  -o ${PATH_RESULTS}/figures/${file}_AP_RL_diameters_PAM50_angle_corr0.png \
+
+${SCT_DIR}/python/envs/venv_sct/bin/python ~/code/dcm-metric-normalization/figures/AP_RL_diameters_PAM50.py \
+  -i ${PATH_RESULTS}/${file}_metrics_PAM50_angle_corr1.csv \
+  -o ${PATH_RESULTS}/figures/${file}_AP_RL_diameters_PAM50_angle_corr1.png
+
+# ------------------------------------------------------------------------------
+# End
+# ------------------------------------------------------------------------------
+# Display useful info for the log
+end=`date +%s`
+runtime=$((end-start))
+echo
+echo "~~~"
+echo "SCT version: `sct_version`"
+echo "Ran on:      `uname -nsr`"
+echo "Duration:    $(($runtime / 3600))hrs $((($runtime / 60) % 60))min $(($runtime % 60))sec"
+echo "~~~"

From 671f19fb00740a342795f970d2cfdb919233aa4d Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Tue, 29 Jul 2025 10:22:09 +0200
Subject: [PATCH 05/17] rename `figures` folder to `hog_angle`

---
 {figures => hog_angle}/AP_RL_diameters_PAM50.py    | 0
 {figures => hog_angle}/AP_RL_diameters_plotting.py | 0
 {figures => hog_angle}/compute_diameters.sh        | 8 ++++----
 3 files changed, 4 insertions(+), 4 deletions(-)
 rename {figures => hog_angle}/AP_RL_diameters_PAM50.py (100%)
 rename {figures => hog_angle}/AP_RL_diameters_plotting.py (100%)
 rename {figures => hog_angle}/compute_diameters.sh (96%)

diff --git a/figures/AP_RL_diameters_PAM50.py b/hog_angle/AP_RL_diameters_PAM50.py
similarity index 100%
rename from figures/AP_RL_diameters_PAM50.py
rename to hog_angle/AP_RL_diameters_PAM50.py
diff --git a/figures/AP_RL_diameters_plotting.py b/hog_angle/AP_RL_diameters_plotting.py
similarity index 100%
rename from figures/AP_RL_diameters_plotting.py
rename to hog_angle/AP_RL_diameters_plotting.py
diff --git a/figures/compute_diameters.sh b/hog_angle/compute_diameters.sh
similarity index 96%
rename from figures/compute_diameters.sh
rename to hog_angle/compute_diameters.sh
index f9e62b4..76bbab0 100644
--- a/figures/compute_diameters.sh
+++ b/hog_angle/compute_diameters.sh
@@ -10,7 +10,7 @@
 #
 # Example of config.json:
 # {
-#  "script"      : "~/code/dcm-metric-normalization/figures/compute_diameters.sh",
+#  "script"      : "~/code/dcm-metric-normalization/hog_angle/compute_diameters.sh",
 #  "jobs"        : 8
 # }
 #
@@ -91,7 +91,7 @@ echo "file: ${file}"
 #   - copy disc labels from derivatives/labels folder (we assume it exists)
 #   - generate labeled segmentation using init disc labels
 #   - generate metrics using sct_process_segmentation
-#   - generate figures using custom script
+#   - generate hog_angle using custom script
 
 # Find T2w image
 if [[ -e "${file}_T2w.nii.gz" ]]; then
@@ -137,11 +137,11 @@ sct_process_segmentation -i ${file_t2}.nii.gz -s ${FILESEG}.nii.gz -vertfile ${F
 mkdir -p ${PATH_RESULTS}/figures
 
 # Generate figure using custom script (assuming this repo is cloned in `~/code/dcm-metric-normalization`)
-${SCT_DIR}/python/envs/venv_sct/bin/python ~/code/dcm-metric-normalization/figures/AP_RL_diameters_PAM50.py \
+${SCT_DIR}/python/envs/venv_sct/bin/python ~/code/dcm-metric-normalization/hog_angle/AP_RL_diameters_PAM50.py \
   -i ${PATH_RESULTS}/${file}_metrics_PAM50_angle_corr0.csv \
   -o ${PATH_RESULTS}/figures/${file}_AP_RL_diameters_PAM50_angle_corr0.png \
 
-${SCT_DIR}/python/envs/venv_sct/bin/python ~/code/dcm-metric-normalization/figures/AP_RL_diameters_PAM50.py \
+${SCT_DIR}/python/envs/venv_sct/bin/python ~/code/dcm-metric-normalization/hog_angle/AP_RL_diameters_PAM50.py \
   -i ${PATH_RESULTS}/${file}_metrics_PAM50_angle_corr1.csv \
   -o ${PATH_RESULTS}/figures/${file}_AP_RL_diameters_PAM50_angle_corr1.png
 

From 77c8cfe68f925635b37b08ea4b003a9c400c93a1 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Tue, 29 Jul 2025 15:19:02 +0200
Subject: [PATCH 06/17] rename `AP_RL_diameters_plotting.py` folder to
 `AP_RL_diameters.py`

---
 hog_angle/{AP_RL_diameters_plotting.py => AP_RL_diameters.py} | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
 rename hog_angle/{AP_RL_diameters_plotting.py => AP_RL_diameters.py} (96%)

diff --git a/hog_angle/AP_RL_diameters_plotting.py b/hog_angle/AP_RL_diameters.py
similarity index 96%
rename from hog_angle/AP_RL_diameters_plotting.py
rename to hog_angle/AP_RL_diameters.py
index d6c0a56..e0a5627 100644
--- a/hog_angle/AP_RL_diameters_plotting.py
+++ b/hog_angle/AP_RL_diameters.py
@@ -12,7 +12,7 @@
 #       conda activate venv_sct
 #
 # Example usage on a single subject:
-#       python AP_RL_diameters_plotting.py -i /path/to/morphometrics_plotting.csv -o /path/to/output/morphometrics.png
+#       python AP_RL_diameters.py -i /path/to/morphometrics_plotting.csv -o /path/to/output/morphometrics.png
 #
 # Authors: Jan Valosek
 #

From d01c4ede78731657ab45dc86c920c12f7867394a Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Tue, 29 Jul 2025 15:19:56 +0200
Subject: [PATCH 07/17] Allow to specify smoothing as an input arg

---
 hog_angle/AP_RL_diameters_PAM50.py | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/hog_angle/AP_RL_diameters_PAM50.py b/hog_angle/AP_RL_diameters_PAM50.py
index 5d255f3..1627266 100644
--- a/hog_angle/AP_RL_diameters_PAM50.py
+++ b/hog_angle/AP_RL_diameters_PAM50.py
@@ -39,12 +39,15 @@ def get_parser():
                         help="Path to the CSV file with diameter measurements.")
     parser.add_argument('-o', required=True, type=str,
                         help="Path to save the output figure.")
+    parser.add_argument('-smooth', required=False, type=int, default=0, metavar='INT',
+                        help="Smooth measurements before plotting. Number of points in the moving average window."
+                             "Examples: 0: no smoothing, 5: window of 5")
 
     return parser
 
 
 # Apply smoothing to the metric data
-def smooth(y: np.ndarray, box_pts: int) -> np.ndarray:
+def smooth_data(y: np.ndarray, box_pts: int) -> np.ndarray:
     """
     Smooths a 1D array using a simple moving average (box filter).
     Inspired by: https://github.com/sct-pipeline/rootlets-informed-reg2template/blob/main/csa_analysis.py#L199
@@ -104,12 +107,13 @@ def get_vert_indices(df):
     return vert, ind_vert, ind_vert_mid
 
 
-def create_lineplot(df, figure_path):
+def create_lineplot(df, figure_path, smooth):
     """
     Create lineplot for individual metrics per vertebral levels.
     Args:
         df (pd.DataFrame): dataframe with single subject values
         figure_path (str): path to save the figure
+        smooth (int): Smooth measurements before plotting. 0: no smoothing; 1: smoothing
     """
     mpl.rcParams['font.family'] = 'Arial'
 
@@ -120,9 +124,10 @@ def create_lineplot(df, figure_path):
     # Loop across metrics
     for index, metric in enumerate(METRICS):
 
-        # Smooth the data to improve visualization
-        df[metric] = smooth(df[metric].values, 5)
-        df[f'{metric.replace(")", "_hog)")}'] = smooth(df[f'{metric.replace(")", "_hog)")}'].values, 5)
+        if smooth > 0:
+            # Smooth the data to improve visualization
+            df[metric] = smooth_data(df[metric].values, smooth)
+            df[f'{metric.replace(")", "_hog)")}'] = smooth_data(df[f'{metric.replace(")", "_hog)")}'].values, smooth)
         # Original
         sns.lineplot(ax=axs[index], x="Slice (I->S)", y=metric,
                      data=df, linewidth=2,
@@ -188,7 +193,7 @@ def main():
         print('WARNING: No slices found in the range C1-Th1 in the single subject data. Exiting...')
         sys.exit(1)
 
-    create_lineplot(df, out_path)
+    create_lineplot(df, out_path, args.smooth)
 
 
 if __name__ == '__main__':

From 8f2dbd95565b9a32462b739c2aee9cf0dbcc66a5 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Tue, 29 Jul 2025 15:20:29 +0200
Subject: [PATCH 08/17] Use the same y-axis for all subjects

---
 hog_angle/AP_RL_diameters_PAM50.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/hog_angle/AP_RL_diameters_PAM50.py b/hog_angle/AP_RL_diameters_PAM50.py
index 1627266..c442193 100644
--- a/hog_angle/AP_RL_diameters_PAM50.py
+++ b/hog_angle/AP_RL_diameters_PAM50.py
@@ -28,6 +28,12 @@
     'MEAN(diameter_RL)',
 ]
 
+# Set ylim to do not overlap horizontal grid with vertebrae labels
+METRICS_TO_YLIM = {
+    'MEAN(diameter_AP)': (5.5, 9.5),
+    'MEAN(diameter_RL)': (8.5, 14.5),
+}
+
 LABELS_FONT_SIZE = 14
 TICKS_FONT_SIZE = 12
 
@@ -152,6 +158,7 @@ def create_lineplot(df, figure_path, smooth):
         axs[index].spines['bottom'].set_visible(True)
 
         # Get ymin and ymax for the y-axis
+        axs[index].set_ylim(METRICS_TO_YLIM[metric][0], METRICS_TO_YLIM[metric][1])
         ymin, ymax = axs[index].get_ylim()
 
         vert, ind_vert, ind_vert_mid = get_vert_indices(df)

From 9d19adefff2a802e6e446b881ada5f6c377d2471 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Tue, 29 Jul 2025 15:22:29 +0200
Subject: [PATCH 09/17] remove `-R` from rsync to prevent copying the full path

Context: https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/4930#issuecomment-3132524965
---
 hog_angle/compute_diameters.sh | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/hog_angle/compute_diameters.sh b/hog_angle/compute_diameters.sh
index 76bbab0..153202a 100644
--- a/hog_angle/compute_diameters.sh
+++ b/hog_angle/compute_diameters.sh
@@ -59,8 +59,7 @@ cd $PATH_DATA_PROCESSED
 
 # Copy source images
 # Note: we use '/./' in order to include the sub-folder 'ses-0X'
-rsync -Ravzh --no-g $PATH_DATA/./$SUBJECT .
-#	•	-R → Preserves relative path structure.
+rsync -avzh $PATH_DATA/./$SUBJECT .
 #	•	-a → Archive mode (preserves most attributes except group ownership).
 #	•	-v → Verbose output.
 #	•	-z → Compresses data during transfer.

From ab689f6409ded9a6252c0d3973b60071e3c5d533 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Tue, 29 Jul 2025 15:22:46 +0200
Subject: [PATCH 10/17] make sure images are gzip files

---
 hog_angle/compute_diameters.sh | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/hog_angle/compute_diameters.sh b/hog_angle/compute_diameters.sh
index 153202a..0b43f06 100644
--- a/hog_angle/compute_diameters.sh
+++ b/hog_angle/compute_diameters.sh
@@ -54,6 +54,11 @@ start=`date +%s`
 # Display useful info for the log, such as SCT version, RAM and CPU cores available
 sct_check_dependencies -short
 
+cd $PATH_DATA/$SUBJECT/anat
+git annex get *T2w*
+cd $PATH_DATA/derivatives/labels/$SUBJECT/anat
+git annex get *T2w*
+
 # Go to folder where data will be copied and processed
 cd $PATH_DATA_PROCESSED
 

From 602890f7911f507589d4ab439b329b9a1162352f Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Tue, 29 Jul 2025 15:23:01 +0200
Subject: [PATCH 11/17] add example usage

---
 hog_angle/compute_diameters.sh | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/hog_angle/compute_diameters.sh b/hog_angle/compute_diameters.sh
index 0b43f06..ebc65fe 100644
--- a/hog_angle/compute_diameters.sh
+++ b/hog_angle/compute_diameters.sh
@@ -6,7 +6,7 @@
 #   SCT PR #4958: https://github.com/spinalcordtoolbox/spinalcordtoolbox/pull/4958
 #
 # Usage:
-#     sct_run_batch -config config.json
+#     xargs -n2 sh -c 'sct_run_batch -path-data $1 -path-output $2 -config config_compute_diameters.json' sh < datasets.txt
 #
 # Example of config.json:
 # {
@@ -15,8 +15,10 @@
 # }
 #
 # Example of dataset.txt:
-#   path/to/dataset1 path/to/output1
-#   path/to/dataset2 path/to/output1
+#    ~/data/data.neuro.polymtl.ca/data-multi-subject/ ~/results/hog_angle/compute_diameters_2025-07-29
+#    ~/data/data.neuro.polymtl.ca/whole-spine ~/results/hog_angle/compute_diameters_2025-07-29
+#
+# NOTE: we use the same results folder for all datasets to store results from all datasets in a single folder.
 #
 # Manual segmentations and disc labels should be located under:
 #   PATH_DATA/derivatives/labels/SUBJECT/<CONTRAST>/

From 83aac0ead26392837e8a3c91a06dd8a26ed3e4b7 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Tue, 29 Jul 2025 15:23:18 +0200
Subject: [PATCH 12/17] add PAM50 normalization

---
 hog_angle/compute_diameters.sh | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/hog_angle/compute_diameters.sh b/hog_angle/compute_diameters.sh
index ebc65fe..2c438cb 100644
--- a/hog_angle/compute_diameters.sh
+++ b/hog_angle/compute_diameters.sh
@@ -136,8 +136,13 @@ fi
 # Generate labeled segmentation using init disc labels
 sct_label_vertebrae -i ${file_t2}.nii.gz -s ${FILESEG}.nii.gz -discfile ${FILEDISCS}.nii.gz -c t2 -qc ${PATH_QC} -qc-subject ${file}
 
-sct_process_segmentation -i ${file_t2}.nii.gz -s ${FILESEG}.nii.gz -vertfile ${FILESEG}_labeled.nii.gz -perslice 1 -o ${PATH_RESULTS}/${file}_metrics_PAM50_angle_corr0.csv -qc qc -angle-corr 0
-sct_process_segmentation -i ${file_t2}.nii.gz -s ${FILESEG}.nii.gz -vertfile ${FILESEG}_labeled.nii.gz -perslice 1 -o ${PATH_RESULTS}/${file}_metrics_PAM50_angle_corr1.csv -qc qc -angle-corr 1
+# Normalize to PAM50, with and without the angle correction
+sct_process_segmentation -i ${file_t2}.nii.gz -s ${FILESEG}.nii.gz -vertfile ${FILESEG}_labeled.nii.gz -perslice 1 -normalize-PAM50 1 -o ${PATH_RESULTS}/${file}_metrics_PAM50_angle_corr0.csv -qc ${PATH_QC} -angle-corr 0
+sct_process_segmentation -i ${file_t2}.nii.gz -s ${FILESEG}.nii.gz -vertfile ${FILESEG}_labeled.nii.gz -perslice 1 -normalize-PAM50 1 -o ${PATH_RESULTS}/${file}_metrics_PAM50_angle_corr1.csv -qc ${PATH_QC} -angle-corr 1
+
+# No normalization to PAM50, with and without the angle correction
+sct_process_segmentation -i ${file_t2}.nii.gz -s ${FILESEG}.nii.gz -vertfile ${FILESEG}_labeled.nii.gz -perslice 1 -o ${PATH_RESULTS}/${file}_metrics_angle_corr0.csv -qc ${PATH_QC} -angle-corr 0
+sct_process_segmentation -i ${file_t2}.nii.gz -s ${FILESEG}.nii.gz -vertfile ${FILESEG}_labeled.nii.gz -perslice 1 -o ${PATH_RESULTS}/${file}_metrics_angle_corr1.csv -qc ${PATH_QC} -angle-corr 1
 
 # Create figures folder under ${PATH_RESULTS} if it does not exist
 mkdir -p ${PATH_RESULTS}/figures

From f6b913fdd85c45b3b8e2b096edcc7a7e2e366538 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Tue, 29 Jul 2025 15:23:43 +0200
Subject: [PATCH 13/17] add plotting in the native space

---
 hog_angle/compute_diameters.sh | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/hog_angle/compute_diameters.sh b/hog_angle/compute_diameters.sh
index 2c438cb..96b65ba 100644
--- a/hog_angle/compute_diameters.sh
+++ b/hog_angle/compute_diameters.sh
@@ -151,10 +151,20 @@ mkdir -p ${PATH_RESULTS}/figures
 ${SCT_DIR}/python/envs/venv_sct/bin/python ~/code/dcm-metric-normalization/hog_angle/AP_RL_diameters_PAM50.py \
   -i ${PATH_RESULTS}/${file}_metrics_PAM50_angle_corr0.csv \
   -o ${PATH_RESULTS}/figures/${file}_AP_RL_diameters_PAM50_angle_corr0.png \
+  -smooth 0
 
 ${SCT_DIR}/python/envs/venv_sct/bin/python ~/code/dcm-metric-normalization/hog_angle/AP_RL_diameters_PAM50.py \
   -i ${PATH_RESULTS}/${file}_metrics_PAM50_angle_corr1.csv \
-  -o ${PATH_RESULTS}/figures/${file}_AP_RL_diameters_PAM50_angle_corr1.png
+  -o ${PATH_RESULTS}/figures/${file}_AP_RL_diameters_PAM50_angle_corr1.png \
+  -smooth 0
+
+${SCT_DIR}/python/envs/venv_sct/bin/python ~/code/dcm-metric-normalization/hog_angle/AP_RL_diameters.py \
+  -i ${PATH_RESULTS}/${file}_metrics_angle_corr0.csv \
+  -o ${PATH_RESULTS}/figures/${file}_AP_RL_diameters_angle_corr0.png \
+
+${SCT_DIR}/python/envs/venv_sct/bin/python ~/code/dcm-metric-normalization/hog_angle/AP_RL_diameters.py \
+  -i ${PATH_RESULTS}/${file}_metrics_angle_corr1.csv \
+  -o ${PATH_RESULTS}/figures/${file}_AP_RL_diameters_angle_corr1.png \
 
 # ------------------------------------------------------------------------------
 # End

From 16dfd193d63f7303a276bd8872b0c865fc3415c5 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Mon, 11 Aug 2025 19:21:34 +0200
Subject: [PATCH 14/17] tweak METRICS_TO_YLIM

---
 hog_angle/AP_RL_diameters_PAM50.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/hog_angle/AP_RL_diameters_PAM50.py b/hog_angle/AP_RL_diameters_PAM50.py
index c442193..fbf1c38 100644
--- a/hog_angle/AP_RL_diameters_PAM50.py
+++ b/hog_angle/AP_RL_diameters_PAM50.py
@@ -30,8 +30,8 @@
 
 # Set ylim to do not overlap horizontal grid with vertebrae labels
 METRICS_TO_YLIM = {
-    'MEAN(diameter_AP)': (5.5, 9.5),
-    'MEAN(diameter_RL)': (8.5, 14.5),
+    'MEAN(diameter_AP)': (5, 10),
+    'MEAN(diameter_RL)': (8, 16),
 }
 
 LABELS_FONT_SIZE = 14

From 07b4d4d1c87a860704cd9d50a54753ff3187f1c2 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Mon, 11 Aug 2025 19:21:46 +0200
Subject: [PATCH 15/17] add alpha to HOG-based curves

---
 hog_angle/AP_RL_diameters_PAM50.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hog_angle/AP_RL_diameters_PAM50.py b/hog_angle/AP_RL_diameters_PAM50.py
index fbf1c38..3f207af 100644
--- a/hog_angle/AP_RL_diameters_PAM50.py
+++ b/hog_angle/AP_RL_diameters_PAM50.py
@@ -140,7 +140,7 @@ def create_lineplot(df, figure_path, smooth):
                      label=metric)
         # HOG-based
         sns.lineplot(ax=axs[index], x="Slice (I->S)", y=f'{metric.replace(")", "_hog)")}',
-                     data=df, linewidth=2,
+                     data=df, linewidth=2, alpha=0.5,
                      label=f'{metric.replace(")", "_hog)")}')
 
         # Tweak y-axis limits

From d41ceee1fb20f3362df638ab87b3007c32fe251f Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Mon, 11 Aug 2025 19:22:05 +0200
Subject: [PATCH 16/17] add `-v 2` to get debug figures for the HOG angle

---
 hog_angle/compute_diameters.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hog_angle/compute_diameters.sh b/hog_angle/compute_diameters.sh
index 96b65ba..a6d627d 100644
--- a/hog_angle/compute_diameters.sh
+++ b/hog_angle/compute_diameters.sh
@@ -137,7 +137,7 @@ fi
 sct_label_vertebrae -i ${file_t2}.nii.gz -s ${FILESEG}.nii.gz -discfile ${FILEDISCS}.nii.gz -c t2 -qc ${PATH_QC} -qc-subject ${file}
 
 # Normalize to PAM50, with and without the angle correction
-sct_process_segmentation -i ${file_t2}.nii.gz -s ${FILESEG}.nii.gz -vertfile ${FILESEG}_labeled.nii.gz -perslice 1 -normalize-PAM50 1 -o ${PATH_RESULTS}/${file}_metrics_PAM50_angle_corr0.csv -qc ${PATH_QC} -angle-corr 0
+sct_process_segmentation -i ${file_t2}.nii.gz -s ${FILESEG}.nii.gz -vertfile ${FILESEG}_labeled.nii.gz -perslice 1 -normalize-PAM50 1 -o ${PATH_RESULTS}/${file}_metrics_PAM50_angle_corr0.csv -qc ${PATH_QC} -angle-corr 0 -v 2
 sct_process_segmentation -i ${file_t2}.nii.gz -s ${FILESEG}.nii.gz -vertfile ${FILESEG}_labeled.nii.gz -perslice 1 -normalize-PAM50 1 -o ${PATH_RESULTS}/${file}_metrics_PAM50_angle_corr1.csv -qc ${PATH_QC} -angle-corr 1
 
 # No normalization to PAM50, with and without the angle correction

From 2dc657f42a4231e632e238e4477a414febe4686a Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Wed, 13 Aug 2025 09:05:48 +0200
Subject: [PATCH 17/17] do not show the figure

---
 hog_angle/AP_RL_diameters.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/hog_angle/AP_RL_diameters.py b/hog_angle/AP_RL_diameters.py
index e0a5627..f5d8f42 100644
--- a/hog_angle/AP_RL_diameters.py
+++ b/hog_angle/AP_RL_diameters.py
@@ -108,8 +108,8 @@ def main() -> None:
     # Save figure
     plt.savefig(out_path, bbox_inches='tight', dpi=300)
     print(f"Figure saved: {out_path}")
-    plt.show()
-    # plt.close()
+    #plt.show()
+    plt.close()
 
 
 if __name__ == "__main__":