update gitignore

.gitignore

@@ -1,88 +1,16 @@
-# =========================
+# 1. Broad Ignores
-# Python
+/Data/*
-# =========================
+/attach/*
-__pycache__/
+/results/*
-*.py[cod]
+/enarcelona/*
-*$py.class
-.ipynb_checkpoints/
-
-# =========================
-# Virtual environments
-# =========================
-env/
-env*/
-venv/
-.venv/
-enarcelona/
-
-# =========================
-# Secrets
-# =========================
 .env
-*.env
+__pycache__/
+*.pyc
+/reference/
+# 2. Ignore virtual environments COMPLETELY
+# This must come BEFORE the unignore rule
+env*/
 
-# =========================
+# 3. The "Unignore" rule (Whitelisting)
-# Patient data / sensitive data
+# We only unignore .py files that aren't already blocked by the rules above
-# =========================
+!**/*.py
-Data/
-data/raw/
-data/processed/
-data/ground_truth/
-reference/
-
-# =========================
-# Generated results and logs
-# =========================
-results/
-results_edss_benchmark/
-*.log
-
-# =========================
-# Large/generated file types
-# =========================
-*.csv
-*.tsv
-*.json
-*.jsonl
-*.xlsx
-*.xls
-*.png
-*.PNG
-*.jpg
-*.jpeg
-*.svg
-*.pdf
-
-# =========================
-# Temporary / backup files
-# =========================
-*.tmp
-*.bak
-*.orig
-.DS_Store
-
-# =========================
-# Keep important code/config/docs
-# =========================
-!README.md
-!requirements.txt
-!*.py
-!*.md
-!*.yml
-!*.yaml
-!*.toml
-
-# Keep prompt templates / schemas if safe to publish
-!prompts/
-!prompts/**
-!attach/
-!attach/*.gbnf
-!attach/just_edss_text.txt
-!attach/Komplett.txt
-
-# Keep example/synthetic data only
-!data/
-!data/example/
-!data/example/**
-!Data/example/
-!Data/example/**

PROJECT_STRUCTURE.md

@@ -1,31 +0,0 @@
-# Project Structure
-
-This project was reorganized into:
-
-- `data/`
-  - `raw/`: original raw data, if retained locally
-  - `processed/`: cleaned or derived input data
-  - `ground_truth/`: manually annotated reference data
-  - `external/`: externally provided data
-
-- `prompts/`
-  - EDSS instructions and prompt/schema assets
-
-- `scripts/`
-  - runnable analysis and plotting scripts
-
-- `results/`
-  - `benchmark_runs/`: full model benchmark runs
-  - `final_results/`: final selected model outputs
-  - `figures/`: generated figures
-  - `tables/`: generated tables
-  - `logs/`: terminal logs
-
-- `manuscript/`
-  - final figures and tables for paper/thesis writing
-
-- `archive/`
-  - old scripts, old results, temporary files, and unclear legacy files
-
-Important:
-The reorganization was performed after creating a full timestamped backup.

app.py

@@ -216,3 +216,6 @@ if __name__ == "__main__":
 
 
 
+# %% name
+eXXXXXXXX
+##

figure1.py

@@ -263,120 +263,3 @@ plt.legend(frameon=False, loc='upper center', bbox_to_anchor=(0.5, -0.05))
 plt.tight_layout()
 plt.show()
 ##
-
-
-
-
-# %% name
-import matplotlib.pyplot as plt
-
-# Data
-data = {
-    'Visit': [9, 8, 7, 6, 5, 4, 3, 2, 1],
-    'patient_count': [2, 3, 3, 6, 13, 17, 28, 24, 32]
-}
-
-# Create figure and axis
-fig, ax = plt.subplots(figsize=(10, 6))
-
-# Plot the bar chart
-bars = ax.bar(data['Visit'], data['patient_count'], color='darkblue', label='Patients by Visit Count')
-
-# Add labels and title
-ax.set_xlabel('Visit Number (from last to first)', fontsize=12)
-ax.set_ylabel('Number of Patients', fontsize=12)
-ax.set_title('Patient Visits by Visit Number', fontsize=14)
-
-# Invert x-axis to show Visit 9 on the left (descending order) if desired, but keep natural order (1–9 left to right)
-# For descending order (9→1 from left to right), we'd need to reverse:
-# Visit = data['Visit'][::-1], patient_count = data['patient_count'][::-1]
-# But standard practice is ascending (1 to 9), so we'll sort accordingly:
-# Let's sort by Visit to ensure left-to-right: 1,2,...,9
-
-# Actually, your current Visit list is [9,8,...,1], which is descending.
-# Let's sort by Visit for intuitive left-to-right increasing order:
-sorted_indices = sorted(range(len(data['Visit'])), key=lambda i: data['Visit'][i])
-visit_sorted = [data['Visit'][i] for i in sorted_indices]
-count_sorted = [data['patient_count'][i] for i in sorted_indices]
-
-# Re-plot with sorted x-axis:
-ax.clear()
-bars = ax.bar(visit_sorted, count_sorted, color='darkblue', label='Patients by Visit Count')
-
-# Re-apply labels, etc.
-ax.set_xlabel('Number of Visits', fontsize=12)
-ax.set_ylabel('Number of Unique Patients', fontsize=12)
-#ax.set_title('Number of Patients by Visit Number', fontsize=14)
-
-# Add legend
-ax.legend()
-
-# Improve layout and grid
-ax.grid(axis='y', linestyle='--', alpha=0.7)
-plt.xticks(visit_sorted)  # Ensure all integer visit numbers are shown
-
-# Show the plot
-plt.tight_layout()
-plt.show()
-
-##
-
-# %% Patientjourney Bubble chart
-import matplotlib.pyplot as plt
-import numpy as np
-
-import matplotlib as mpl
-
-mpl.rcParams["font.family"] = "DejaVu Sans"   # or "Arial", "Calibri", "Times New Roman", ...
-mpl.rcParams["font.size"] = 12                # default size for text
-mpl.rcParams["axes.titlesize"] = 14
-mpl.rcParams["axes.titleweight"] = "bold"
-
-
-# Data (your counts)
-visits = np.array([1, 2, 3, 4, 5, 6, 7, 8, 9])
-patient_count = np.array([32, 24, 28, 17, 13, 6, 3, 3, 2])
-
-# "Remaining" = patients with >= that many visits (cumulative from the right)
-remaining = np.array([patient_count[i:].sum() for i in range(len(patient_count))])
-
-# --- Plot ---
-fig, ax = plt.subplots(figsize=(12, 3))
-
-y = 0.0  # all bubbles on one horizontal line
-
-# Horizontal line
-ax.hlines(y, visits.min() - 0.4, visits.max() + 0.4, color="#1f77b4", linewidth=3)
-
-# Bubble sizes (scale as needed)
-# (Matplotlib scatter uses area in points^2)
-sizes = patient_count * 35  # tweak this multiplier if you want bigger/smaller bubbles
-
-ax.scatter(visits, np.full_like(visits, y), s=sizes, color="#1f77b4", zorder=3)
-
-# Title
-#ax.set_title("Patient Journey by Visit Count", fontsize=14, pad=18)
-
-# Top labels: "1 visits", "2 visits", ...
-for x in visits:
-    label = f"{x} visit" if x == 1 else f"{x} visits"
-    ax.text(x, y + 0.18, label, ha="center", va="bottom", fontsize=10)
-
-# Bottom labels: "X patients" and "Y remaining"
-for x, pc, rem in zip(visits, patient_count, remaining):
-    ax.text(x, y - 0.20, f"{pc} patients", ha="center", va="top", fontsize=9)
-    ax.text(x, y - 0.32, f"{rem} remaining", ha="center", va="top", fontsize=9)
-
-# Cosmetics: remove axes, keep spacing nice
-ax.set_xlim(visits.min() - 0.6, visits.max() + 0.6)
-ax.set_ylim(-0.5, 0.35)
-ax.set_xticks([])
-ax.set_yticks([])
-for spine in ax.spines.values():
-    spine.set_visible(False)
-
-plt.tight_layout()
-plt.show()
-plt.savefig("patient_journey.svg", format="svg", bbox_inches="tight")
-##
-

organize_project.sh

@@ -1,384 +0,0 @@
-#!/usr/bin/env bash
-
-set -euo pipefail
-
-# ============================================================
-# Organize Barcelona EDSS project safely
-# - Creates a timestamped backup first
-# - Creates a cleaner folder structure
-# - Moves files conservatively
-# - Does NOT delete anything
-# ============================================================
-
-PROJECT_ROOT="$(pwd)"
-TIMESTAMP="$(date +%Y%m%d_%H%M%S)"
-BACKUP_PARENT="${PROJECT_ROOT}/../Barcelona_backups"
-BACKUP_DIR="${BACKUP_PARENT}/Barcelona_backup_${TIMESTAMP}"
-
-echo "Project root: ${PROJECT_ROOT}"
-echo "Backup dir:   ${BACKUP_DIR}"
-echo
-
-# ------------------------------------------------------------
-# Safety checks
-# ------------------------------------------------------------
-
-if [ ! -f "${PROJECT_ROOT}/README.md" ]; then
-    echo "WARNING: README.md not found. Are you sure you are in the project root?"
-    echo "Current directory: ${PROJECT_ROOT}"
-    read -r -p "Continue anyway? [y/N] " answer
-    case "$answer" in
-        y|Y|yes|YES) ;;
-        *) echo "Aborted."; exit 1 ;;
-    esac
-fi
-
-if [ -d "${PROJECT_ROOT}/.git" ]; then
-    if ! git diff --quiet || ! git diff --cached --quiet; then
-        echo "ERROR: Git working tree is not clean."
-        echo "Please commit or stash changes before organizing."
-        exit 1
-    fi
-fi
-
-echo "This script will:"
-echo "1. Create a full backup."
-echo "2. Create organized folders."
-echo "3. Move files into data/, prompts/, scripts/, results/, archive/."
-echo "4. Keep your original files in the backup."
-echo
-read -r -p "Proceed? [y/N] " answer
-case "$answer" in
-    y|Y|yes|YES) ;;
-    *) echo "Aborted."; exit 1 ;;
-esac
-
-# ------------------------------------------------------------
-# Backup
-# ------------------------------------------------------------
-
-mkdir -p "${BACKUP_PARENT}"
-
-echo
-echo "Creating backup..."
-rsync -a \
-    --exclude "enarcelona/" \
-    --exclude "env/" \
-    --exclude ".venv/" \
-    --exclude "__pycache__/" \
-    "${PROJECT_ROOT}/" "${BACKUP_DIR}/"
-
-echo "Backup created at:"
-echo "${BACKUP_DIR}"
-
-# ------------------------------------------------------------
-# Create target structure
-# ------------------------------------------------------------
-
-echo
-echo "Creating new directory structure..."
-
-mkdir -p \
-    data/raw \
-    data/processed \
-    data/ground_truth \
-    data/external \
-    prompts \
-    scripts \
-    results/benchmark_runs \
-    results/final_results/model_outputs \
-    results/figures \
-    results/tables \
-    results/logs \
-    manuscript/figures \
-    manuscript/tables \
-    archive/old_scripts \
-    archive/old_results \
-    archive/tmp \
-    archive/old_data \
-    archive/old_project_files
-
-# ------------------------------------------------------------
-# Helper move functions
-# ------------------------------------------------------------
-
-move_if_exists() {
-    src="$1"
-    dest="$2"
-
-    if [ -e "$src" ]; then
-        mkdir -p "$(dirname "$dest")"
-
-        if [ -e "$dest" ]; then
-            echo "SKIP: destination exists: $dest"
-        else
-            echo "MOVE: $src -> $dest"
-            mv "$src" "$dest"
-        fi
-    fi
-}
-
-move_glob_if_exists() {
-    pattern="$1"
-    dest_dir="$2"
-
-    mkdir -p "$dest_dir"
-
-    shopt -s nullglob
-    files=( $pattern )
-    shopt -u nullglob
-
-    for f in "${files[@]}"; do
-        base="$(basename "$f")"
-        dest="${dest_dir}/${base}"
-
-        if [ -e "$dest" ]; then
-            echo "SKIP: destination exists: $dest"
-        else
-            echo "MOVE: $f -> $dest"
-            mv "$f" "$dest"
-        fi
-    done
-}
-
-# ------------------------------------------------------------
-# Move prompts / attached instruction files
-# ------------------------------------------------------------
-
-echo
-echo "Moving prompt and instruction files..."
-
-move_if_exists "attach/Komplett.txt" "prompts/Komplett.txt"
-move_if_exists "attach/just_edss_schema.gbnf" "prompts/just_edss_schema.gbnf"
-move_if_exists "attach/just_edss_text.txt" "prompts/just_edss_text.txt"
-
-# Move leftover attach folder if empty or archive it
-if [ -d "attach" ]; then
-    if [ -z "$(ls -A attach)" ]; then
-        rmdir attach
-    else
-        move_if_exists "attach" "archive/old_project_files/attach"
-    fi
-fi
-
-# ------------------------------------------------------------
-# Move important data files
-# ------------------------------------------------------------
-
-echo
-echo "Moving data files..."
-
-move_if_exists "Data/MS_Briefe_400_with_unique_id_SHA3_explore_cleaned.csv" \
-    "data/processed/MS_Briefe_400_with_unique_id_SHA3_explore_cleaned.csv"
-
-move_if_exists "Data/MS_Briefe_400_with_unique_id_SHA3_explore_cleaned_unique.csv" \
-    "data/processed/MS_Briefe_400_with_unique_id_SHA3_explore_cleaned_unique.csv"
-
-move_if_exists "Data/Join_edssandsub.tsv" \
-    "data/ground_truth/Join_edssandsub.tsv"
-
-move_if_exists "Data/GT_Numbers.csv" \
-    "data/ground_truth/GT_Numbers.csv"
-
-move_if_exists "Data/Annika1.csv" \
-    "data/ground_truth/Annika1.csv"
-
-move_if_exists "Data/comparison.tsv" \
-    "data/ground_truth/comparison.tsv"
-
-move_if_exists "Data/edss_distribution_summary.csv" \
-    "data/processed/edss_distribution_summary.csv"
-
-move_if_exists "Data/empirical_confidence_table.csv" \
-    "data/processed/empirical_confidence_table.csv"
-
-move_if_exists "Data/functional_system_colors.json" \
-    "data/processed/functional_system_colors.json"
-
-move_if_exists "Data/Test.csv" \
-    "archive/tmp/Test.csv"
-
-move_if_exists "Data/Hernan" \
-    "data/external/Hernan"
-
-move_if_exists "Data/iteration" \
-    "archive/old_data/iteration"
-
-# Old generated JSON/results from Data folder
-move_glob_if_exists "Data/*results*.json" "archive/old_results"
-move_glob_if_exists "Data/join_*.tsv" "archive/old_results"
-
-# Move remaining Data folder if anything left
-if [ -d "Data" ]; then
-    if [ -z "$(ls -A Data)" ]; then
-        rmdir Data
-    else
-        move_if_exists "Data" "archive/old_data/Data_remaining"
-    fi
-fi
-
-# ------------------------------------------------------------
-# Move benchmark results
-# ------------------------------------------------------------
-
-echo
-echo "Moving benchmark results..."
-
-if [ -d "results_edss_benchmark" ]; then
-    move_glob_if_exists "results_edss_benchmark/run_*" "results/benchmark_runs"
-
-    move_if_exists "results_edss_benchmark/endresults" \
-        "results/final_results/model_outputs"
-
-    move_if_exists "results_edss_benchmark/confusion_matrices" \
-        "results/figures/confusion_matrices"
-
-    if [ -z "$(ls -A results_edss_benchmark 2>/dev/null || true)" ]; then
-        rmdir results_edss_benchmark
-    else
-        move_if_exists "results_edss_benchmark" \
-            "archive/old_results/results_edss_benchmark_remaining"
-    fi
-fi
-
-# ------------------------------------------------------------
-# Move old/general results
-# ------------------------------------------------------------
-
-echo
-echo "Moving existing results files..."
-
-if [ -d "results" ]; then
-    # Figures
-    move_glob_if_exists "results/*.png" "results/figures"
-    move_glob_if_exists "results/*.PNG" "results/figures"
-    move_glob_if_exists "results/*.jpg" "results/figures"
-    move_glob_if_exists "results/*.jpeg" "results/figures"
-    move_glob_if_exists "results/*.svg" "results/figures"
-
-    # Tables
-    move_glob_if_exists "results/*.csv" "results/tables"
-    move_glob_if_exists "results/*.tsv" "results/tables"
-    move_glob_if_exists "results/*.xlsx" "results/tables"
-
-    # Subfolders that look like old results
-    move_if_exists "results/Jan_visual" "archive/old_results/Jan_visual"
-    move_if_exists "results/Lab_meeting" "archive/old_results/Lab_meeting"
-    move_if_exists "results/just_edss" "archive/old_results/just_edss"
-fi
-
-# Root-level result tables
-move_if_exists "edss_distribution_summary.csv" \
-    "results/tables/edss_distribution_summary.csv"
-
-# Logs
-move_if_exists "edss_benchmark_terminal.log" \
-    "results/logs/edss_benchmark_terminal.log"
-
-# ------------------------------------------------------------
-# Move scripts
-# ------------------------------------------------------------
-
-echo
-echo "Moving scripts..."
-
-move_if_exists "audit.py" "scripts/audit_outputs.py"
-move_if_exists "certainty.py" "scripts/analyze_certainty.py"
-move_if_exists "certainty_show.py" "scripts/certainty_show.py"
-move_if_exists "figure1.py" "scripts/figure1.py"
-move_if_exists "show_plots.py" "scripts/show_plots.py"
-
-move_if_exists "show_plots.py.orig" "archive/old_scripts/show_plots.py.orig"
-
-# Apps / old entry points
-move_if_exists "app.py" "archive/old_scripts/app.py"
-move_if_exists "total_app.py" "archive/old_scripts/total_app.py"
-
-# Existing project visuals folder
-move_if_exists "project/visuals" "results/figures/project_visuals"
-
-if [ -d "project" ]; then
-    if [ -z "$(ls -A project)" ]; then
-        rmdir project
-    else
-        move_if_exists "project" "archive/old_project_files/project"
-    fi
-fi
-
-# ------------------------------------------------------------
-# Environment folder
-# ------------------------------------------------------------
-
-echo
-echo "Handling virtual environment..."
-
-if [ -d "enarcelona" ]; then
-    echo "Leaving virtual environment in place: enarcelona/"
-    echo "It should remain ignored by .gitignore."
-fi
-
-# ------------------------------------------------------------
-# Create README notes
-# ------------------------------------------------------------
-
-echo
-echo "Writing organization notes..."
-
-cat > "PROJECT_STRUCTURE.md" <<'EOF'
-# Project Structure
-
-This project was reorganized into:
-
-- `data/`
-  - `raw/`: original raw data, if retained locally
-  - `processed/`: cleaned or derived input data
-  - `ground_truth/`: manually annotated reference data
-  - `external/`: externally provided data
-
-- `prompts/`
-  - EDSS instructions and prompt/schema assets
-
-- `scripts/`
-  - runnable analysis and plotting scripts
-
-- `results/`
-  - `benchmark_runs/`: full model benchmark runs
-  - `final_results/`: final selected model outputs
-  - `figures/`: generated figures
-  - `tables/`: generated tables
-  - `logs/`: terminal logs
-
-- `manuscript/`
-  - final figures and tables for paper/thesis writing
-
-- `archive/`
-  - old scripts, old results, temporary files, and unclear legacy files
-
-Important:
-The reorganization was performed after creating a full timestamped backup.
-EOF
-
-# ------------------------------------------------------------
-# Final checks
-# ------------------------------------------------------------
-
-echo
-echo "Organization complete."
-echo
-echo "Backup is here:"
-echo "${BACKUP_DIR}"
-echo
-echo "New top-level structure:"
-find . -maxdepth 2 -type d | sort
-echo
-
-if [ -d ".git" ]; then
-    echo "Git status:"
-    git status --short
-fi
-
-echo
-echo "Next recommended commands:"
-echo "  git status"
-echo "  git add ."
-echo "  git commit -m \"Reorganize project structure\""

prompts/Komplett.txt

@@ -1,481 +0,0 @@
-1 VISUAL OPTIC FUNCTIONS
-
-VISUAL ACUITY
-The visual acuity score is based on the line in the Snellen chart at 20 feet 5 meters
-for which the patient makes no more than one error using best available correction
-Alternatively best corrected near vision can be assessed but this should be noted and
-consistently performed during follow up examinations Switching from near to distance
-visual acuity measurements should be avoided in follow up examinations
-
-VISUAL FIELDS
-0 normal
-1 signs only deficits present only on formal confrontational testing
-2 moderate patient aware of deficit but incomplete hemianopsia on examination
-3 marked complete homonymous hemianopsia or equivalent
-
-SCOTOMA
-0 none
-1 small detectable only on formal confrontational testing
-2 large spontaneously reported by patient
-
-* DISC PALLOR
-0 not present
-1 present
-
-NOTE
-When determining the EDSS step the Visual FS score must be converted to a lower
-score as follows
-Visual FS Score 6 5 4 3 2 1
-Converted Visual FS Score 4 3 3 2 2 1
-
-FUNCTIONAL SYSTEM SCORE
-0 normal
-1 disc pallor and or small scotoma and or visual acuity corrected of worse eye less than 20 20 1.0 but better than 20 30 0.67
-2 worse eye with maximal visual acuity corrected of 20 30 to 20 59 0.67 – 0.34
-3 worse eye with large scotoma and or moderate decrease in fields and or maximal visual acuity corrected of 20 60 to 20 99 0.33 – 0.21
-4 worse eye with marked decrease of fields and or maximal visual acuity corrected of 20 100 to 20 200 0.2 – 0.1 grade 3 plus maximal acuity of better eye of 20 60 0.33 or less
-5 worse eye with maximal visual acuity corrected less than 20 200 0.1 grade 4 plus maximal acuity of better eye of 20 60 0.33 or less
-6 grade 5 plus maximal acuity of better eye of 20 60 0.33 or less *  =  optional part of the examination
-
-
-### BRAINSTEM FUNCTIONS
-
-**DYSARTHRIA**
-- **0**: None
-- **1**: Signs only
-- **2**: Mild: Clinically detectable, patient is aware
-- **3**: Moderate: Obvious during conversation, impairs comprehension
-- **4**: Marked: Incomprehensible speech
-- **5**: Inability to speak
-
-**DYSPHAGIA**
-- **0**: None
-- **1**: Signs only
-- **2**: Mild: Difficulty with thin liquids
-- **3**: Moderate: Difficulty with liquids and solid food
-- **4**: Marked: Sustained difficulty, requires pureed diet
-- **5**: Inability to swallow
-
-**OTHER CRANIAL NERVE FUNCTIONS**
-- **0**: Normal
-- **1**: Signs only
-- **2**: Mild disability: Clinically detectable deficit, patient is usually aware
-- **3**: Moderate disability
-- **4**: Marked disability
-
-**EXTRAOCULAR MOVEMENTS (EOM) IMPAIRMENT**
-- **0**: None
-- **1**: Signs only: Subtle EOM weakness, no complaints of vision issues
-- **2**: Mild: Subtle EOM weakness or obvious incomplete paralysis not noticed by patient
-- **3**: Moderate: Obvious incomplete paralysis noticed by patient or complete loss in one direction
-- **4**: Marked: Complete loss in more than one direction
-
-**NYSTAGMUS**
-- **0**: None
-- **1**: Signs only or mild: Gaze-evoked nystagmus below moderate limits (equivalent to Brainstem FS score of 1)
-- **2**: Moderate: Sustained nystagmus on horizontal/vertical gaze at 30 degrees, patient may not notice
-- **3**: Severe: Nystagmus in primary position or coarse persistent nystagmus interfering with vision; complete internuclear ophthalmoplegia; oscillopsia
-
-**TRIGEMINAL DAMAGE**
-- **0**: None
-- **1**: Signs only
-- **2**: Mild: Clinically detectable numbness, patient is aware
-- **3**: Moderate: Impaired sharp/dull discrimination in one to three branches or trigeminal neuralgia (at least one recent attack)
-- **4**: Marked: Unable to discriminate between sharp/dull or complete loss of sensation in one or both nerves
-
-**FACIAL WEAKNESS**
-- **0**: None
-- **1**: Signs only
-- **2**: Mild: Clinically detectable weakness, patient is aware
-- **3**: Moderate: Incomplete facial palsy (e.g., eye closure requires patching, drooling)
-- **4**: Marked: Complete unilateral or bilateral facial palsy with lagophthalmus or difficulty with liquids
-
-**HEARING LOSS**
-- **0**: None
-- **1**: Signs only: Hears finger rub less on one/both sides, lateralized Weber test but no complaints
-- **2**: Mild: As in 1, aware of hearing problem
-- **3**: Moderate: Does not hear finger rub on one/both sides, misses several whispered numbers
-- **4**: Marked: Misses all or nearly all whispered numbers
-
-**FUNCTIONAL SYSTEM SCORE**
-- **0**: Normal
-- **1**: Signs only
-- **2**: Moderate nystagmus/EOM impairment/other mild disability
-- **3**: Severe nystagmus/marked EOM impairment/moderate other cranial nerve disability
-- **4**: Marked dysarthria/other marked disability
-- **5**: Inability to swallow or speak
-
-### PYRAMIDAL FUNCTIONS
-
-#### REFLEXES
-- **0**: Absent
-- **1**: Diminished
-- **2**: Normal
-- **3**: Exaggerated
-- **4**: Nonsustained clonus (a few beats of clonus)
-- **5**: Sustained clonus
-
-##### Cutaneous Reflexes
-- **0**: Normal
-- **1**: Weak
-- **2**: Absent
-
-###### Palmomental Reflex
-- **0**: Absent
-- **1**: Present
-
-###### Plantar Response
-- **0**: Flexor
-- **1**: Neutral or equivocal
-- **2**: Extensor
-
-#### LIMB STRENGTH
-The weakest muscle in each group defines the score for that muscle group. Optional functional tests (hopping on one foot and walking on heels/toes) are recommended for BMRC grades 3–5.
-
-##### BMRC Rating Scale
-- **0**: No muscle contraction detected
-- **1**: Visible contraction without visible joint movement
-- **2**: Visible movement only on the plane of gravity
-- **3**: Active movement against gravity, but not against resistance
-- **4**: Active movement against resistance, but not full strength
-- **5**: Normal strength
-
-#### FUNCTIONAL TESTS
-##### Pronator Drift (Upper Extremities)
-Pronation and downward drift:
-- **0**: None
-- **1**: Mild
-- **2**: Evident
-
-##### Position Test (Lower Extremities)
-Ask patient to lift both legs together, with legs fully extended at the knee. Sinking:
-- **0**: None
-- **1**: Mild
-- **2**: Evident
-- **3**: Able to lift only one leg at a time (grade from the horizontal position at the hip joints in degrees)
-- **4**: Unable to lift one leg at a time
-
-##### Walking on Heels/Toes
-- **0**: Normal
-- **1**: Impaired
-- **2**: Not possible
-
-##### Hopping on One Foot
-- **0**: Normal
-- **1**: 6–10 times
-- **2**: 1–5 times
-- **3**: Not possible
-
-#### LIMB SPASTICITY (AFTER RAPID FLEXION OF THE EXTREMITY)
-- **0**: None
-- **1**: Mild: barely increased muscle tone
-- **2**: Moderate: moderately increased muscle tone that can be overcome; full range of motion is possible
-- **3**: Severe: severely increased muscle tone that is extremely difficult to overcome; full range of motion is not possible
-- **4**: Contracted
-
-#### GAIT SPASTICITY
-- **0**: None
-- **1**: Barely perceptible
-- **2**: Evident: minor interference with function
-- **3**: Permanent shuffling: major interference with function
-
-#### OVERALL MOTOR PERFORMANCE
-- **0**: Normal
-- **1**: Abnormal weakness (as compared to peers) in performing more demanding tasks, e.g., walking longer distances; no reduction in limb strength on formal testing
-- **2**: Reduction in strength of individual muscle groups at confrontational testing
-
-#### FUNCTIONAL SYSTEM SCORE
-- **0**: Normal
-- **1**: Abnormal signs without disability
-- **2**: Minimal disability: patient complains of motor-fatigability or reduced performance in strenuous motor tasks (motor performance grade 1) and/or BMRC grade 4 in one or two muscle groups
-- **3**: Mild to moderate paraparesis or hemiparesis: usually BMRC grade 4 in more than two muscle groups; and/or BMRC grade 3 in one or two muscle groups (movements against gravity
-are possible); and/or severe monoparesis: BMRC grade 2 or less in one muscle group
-- **4**: Marked paraparesis or hemiparesis: usually BMRC grade 2 in two limbs or monoplegia with BMRC grade 0 or 1 in one limb; and/or moderate tetraparesis: BMRC grade 3 in three or more limbs
-- **5**: Paraplegia: BMRC grade 0 or 1 in all muscle groups of the lower limbs; and/or marked tetraparesis: BMRC grade 2 or less in three or more limbs; and/or hemiplegia
-- **6**: Tetraplegia: BMRC grade 0 or 1 in all muscle groups of the upper and lower limbs
-
-### CEREBELLAR FUNCTIONS
-
-#### HEAD TREMOR
-- **0**: none
-- **1**: mild
-- **2**: moderate
-- **3**: severe
-
-#### TRUNCAL ATAXIA
-- **0**: none
-- **1**: signs only
-- **2**: mild (swaying with eyes closed)
-- **3**: moderate (swaying with eyes open)
-- **4**: severe (unable to sit without assistance)
-
-#### LIMB ATAXIA (TREMOR / DYSMETRIA AND RAPID ALTERNATING MOVEMENTS)
-- **0**: none
-- **1**: signs only
-- **2**: mild (tremor or clumsy movements easily seen, minor interference with function)
-- **3**: moderate (tremor or clumsy movements interfere with function in all spheres)
-- **4**: severe (most functions are very difficult)
-
-#### TANDEM (STRAIGHT LINE) WALKING
-- **0**: normal
-- **1**: impaired
-- **2**: not possible
-
-#### GAIT ATAXIA
-- **0**: none
-- **1**: signs only
-- **2**: mild (problems with balance realized by patient and/or significant other)
-- **3**: moderate (abnormal balance with ordinary walking)
-- **4**: severe (unable to walk more than a few steps unassisted or requires a walking aid or assistance due to ataxia)
-
-#### ROMBERG TEST
-- **0**: normal
-- **1**: mild (mild instability with eyes closed)
-- **2**: moderate (not stable with eyes closed)
-- **3**: severe (not stable with eyes open)
-
-#### OTHER CEREBELLAR TESTS
-- **0**: normal
-- **1**: mild abnormality
-- **2**: moderate abnormality
-- **3**: severe abnormality
-
-**NOTE:**
-- The presence of severe gait and/or truncal ataxia alone (without severe ataxia in three or four limbs) results in a Cerebellar FS score of 3.
-- If weakness or sensory deficits interfere with the testing of ataxia, score the patient’s actual performance. Indicate the possible role of weakness by marking an "X" after the
-affected subsystems and Cerebellar FS score.
-
-#### FUNCTIONAL SYSTEM SCORE
-- **0**: normal
-- **1**: abnormal signs without disability
-- **2**: mild ataxia and/or moderate station ataxia (Romberg) and/or tandem walking not possible
-- **3**: moderate limb ataxia and/or moderate or severe gait/truncal ataxia
-- **4**: severe gait/truncal ataxia and severe ataxia in three or four limbs
-- **5**: unable to perform coordinated movements due to ataxia
-- **X**: pyramidal weakness (BMRC grade 3 or worse in limb strength) or sensory deficits interfere with cerebellar testing
-
-### SENSORY FUNCTIONS
-
-#### SUPERFICIAL SENSATION (LIGHT TOUCH AND PAIN)
-- **0**: normal
-- **1**: signs only (slightly diminished sensation on formal testing, patient not aware)
-- **2**: mild (patient aware of impaired light touch or pain but can discriminate sharp/dull)
-- **3**: moderate (impaired discrimination of sharp/dull)
-- **4**: marked (unable to discriminate between sharp/dull and/or unable to feel light touch)
-- **5**: complete loss (anesthesia)
-
-#### VIBRATION SENSE (AT THE MOST DISTAL JOINT)
-- **0**: normal
-- **1**: mild (graded tuning fork 5–7 of 8; detects more than 10 seconds but less than examiner)
-- **2**: moderate (graded tuning fork 1–4 of 8; detects between 2 and 10 sec.)
-- **3**: marked (complete loss of vibration sense)
-
-#### POSITION SENSE
-- **0**: normal
-- **1**: mild (1–2 incorrect responses, only distal joints affected)
-- **2**: moderate (misses many movements of fingers or toes; proximal joints affected)
-- **3**: marked (no perception of movement, astasia)
-
-* **LHERMITTE’S SIGN** (does not contribute to the Sensory FS score)
-  - **0**: negative
-  - **1**: positive
-
-* **PARAESTHESIAE (TINGLING)** (does not contribute to the Sensory FS score)
-  - **0**: none
-  - **1**: present
-
-#### FUNCTIONAL SYSTEM SCORE
-- **0**: normal
-- **1**: impaired superficial sensation in one or two limbs
-- **2**: mild impairment in more than two limbs, no major proprioceptive deficits
-- **3**: moderate impairment in more than two limbs with minor proprioceptive deficits
-- **4**: severe impairment in more than two limbs with significant proprioceptive deficits
-- **5**: loss of sensation in one or two limbs, significant proprioceptive deficits in most of the body below the head
-- **6**: essentially no sensation below the head
-
-### BOWEL AND BLADDER FUNCTIONS
-
-#### URINARY HESITANCY AND RETENTION
-- **0**: none
-- **1**: mild (no major impact on lifestyle)
-- **2**: moderate (urinary retention; frequent urinary tract infections)
-- **3**: severe (requires catheterization)
-- **4**: loss of function (overflow incontinence)
-
-#### URINARY URGENCY AND INCONTINENCE
-- **0**: none
-- **1**: mild (no major impact on lifestyle)
-- **2**: moderate (rare incontinence occurring no more than once a week; must wear pads)
-- **3**: severe (frequent incontinence occurring from several times a week to more than once a day; must wear urinal or pads)
-- **4**: loss of function (loss of bladder control)
-
-#### BLADDER CATHETERIZATION
-- **0**: none
-- **1**: intermittent self-catheterization
-- **2**: constant catheterization
-
-#### BOWEL DYSFUNCTION
-- **0**: none
-- **1**: mild (no incontinence, no major impact on lifestyle, mild constipation)
-- **2**: moderate (must wear pads or alter lifestyle to be near lavatory)
-- **3**: severe (in need of enemas or manual measures to evacuate bowels)
-- **4**: complete loss of function
-
-#### SEXUAL DYSFUNCTION
-**Male**
-- **0**: none
-- **1**: mild (difficulty maintaining erection during intercourse, but achieves erection and still has intercourse)
-- **2**: moderate (difficulty achieving erection, decreased libido, still has intercourse and reaches orgasm)
-- **3**: severe (marked decrease in libido, inability to achieve full erection, intercourse with difficulty, hypoorgasmia)
-- **4**: loss of function
-
-**Female**
-- **0**: none
-- **1**: mild (mild lack of lubrication, still sexually active and reaches orgasm)
-- **2**: moderate (dyspareunia, hypoorgasmia, decrease in sexual activity)
-- **3**: severe (marked decrease in sexual activity, anorgasmia)
-- **4**: loss of function
-
-**NOTE**
-When determining the EDSS step, the Bowel and Bladder FS score must be converted to a lower score as follows:
-- Bowel and Bladder FS Score: 6 → Converted Bowel and Bladder FS Score: 5
-- Bowel and Bladder FS Score: 5 → Converted Bowel and Bladder FS Score: 4
-- Bowel and Bladder FS Score: 4 → Converted Bowel and Bladder FS Score: 3
-- Bowel and Bladder FS Score: 3 → Converted Bowel and Bladder FS Score: 3
-- Bowel and Bladder FS Score: 2 → Converted Bowel and Bladder FS Score: 2
-- Bowel and Bladder FS Score: 1 → Converted Bowel and Bladder FS Score: 1
-
-Sexual dysfunction can be documented but generally does not impact the FS score due to assessment difficulties by examining physicians.
-
-### FUNCTIONAL SYSTEM SCORE
-- **0**: normal
-- **1**: mild urinary hesitancy, urgency, and/or constipation
-- **2**: moderate urinary hesitancy/retention and/or moderate urinary urgency/incontinence and/or moderate bowel dysfunction
-- **3**: frequent urinary incontinence or intermittent self-catheterization; needs enemas or manual measures to evacuate bowels
-- **4**: in need of almost constant catheterization
-- **5**: loss of bladder or bowel function (external or indwelling catheter)
-- **6**: loss of bowel and bladder function
-
-### CEREBRAL FUNCTIONS
-
-#### DEPRESSION AND EUPHORIA
-- **0**: none
-- **1**: present (Patient complains of depression or is considered depressed or euphoric by the investigator or significant other.)
-
-**Note**: Depression and Euphoria are documented on the scoring sheet but are not taken into consideration for FS and EDSS calculation.
-
-#### DECREASE IN MENTATION
-- **0**: none
-- **1**: signs only (not apparent to patient and/or significant other)
-- **2**: mild (Patient and/or significant other report mild changes in mentation. Examples include: impaired ability to follow a rapid course of association or survey complex matters;
-impaired judgment in certain demanding situations; capable of handling routine daily activities, but unable to tolerate additional stressors; intermittently symptomatic even with
-normal levels of stress; reduced performance; tendency toward negligence due to obliviousness or fatigue.)
-- **3**: moderate (Definite abnormalities on brief mental status testing, but still oriented to person, place, and time)
-- **4**: marked (Not oriented in one or two spheres (person, place, or time); marked effect on lifestyle)
-- **5**: dementia, confusion, and/or complete disorientation
-
-#### FATIGUE
-- **0**: none
-- **1**: mild (Does not usually interfere with daily activities)
-- **2**: moderate (Interferes but does not limit daily activities for more than 50%)
-- **3**: severe (Significant limitation in daily activities (> 50% reduction))
-
-**Note**: Because fatigue is difficult to evaluate objectively, in some studies it does not contribute to the Cerebral FS score or EDSS step. Please adhere to the study’s specific
-instructions.
-
-### FUNCTIONAL SYSTEM SCORE
-- **0**: normal
-- **1**: signs only in decrease in mentation; mild fatigue
-- **2**: mild decrease in mentation; moderate or severe fatigue
-- **3**: moderate decrease in mentation
-- **4**: marked decrease in mentation
-- **5**: dementia
-
-### AMBULATION
-
-**Unrestricted Ambulation**
-- The patient can walk a normal distance without assistance, comparable to healthy individuals of similar age and physical condition.
-- EDSS step can range from 0 to 5.0, depending on the Functional System (FS) scores.
-
-**Fully Ambulatory**
-- At least 500 meters of ambulation without assistance, but not unrestricted.
-- EDSS step can range from 2.0 to 5.0, depending on FS scores.
-- The Pyramidal and/or Cerebellar FS must be ≥ 2 to reflect this restriction in ambulation.
-
-**Ambulation < 500 Meters**
-- If the walking distance is less than 500 meters, the EDSS step must be ≥ 4.5, depending on the walking ranges provided by the ambulation score and combination of FS scores.
-- EDSS steps 5.5 to 8.0 are exclusively defined by the ability to ambulate and type of assistance required, or the ability to use a wheelchair.
-
-**Assistance Needed**
-- Definitions for EDSS steps 6.0 or 6.5 include both the type of assistance required when walking and the walking range.
-- Assistance by another person is equivalent to bilateral assistance.
-
-**Note:**
-- The ambulation score represents both the walking range and the type of assistance required.
-- This score replaces several checkboxes used previously on the scoring sheet but does not introduce new definitions.
-- Use of a wheelchair can now be scored on the scoring sheet.
-- Indicate the reported distance and time for the patient in the appropriate field on the scoring sheet, followed by the type of assistance and walking distance measured during assessment.
-
-
-### DISTANCE AND TIME REPORTED BY PATIENT
-
-**Maximal Unassisted Walking Distance**
-- Maximal unassisted walking distance reported by the patient (in meters) without rest or assistance.
-- Time required to walk the maximum distance according to the patient (in minutes).
-
-**Assistance**
-0. Without help or assistance (allowing use of an ankle-foot orthotic device, but no other assistive devices).
-1. Unilateral assistance: one stick/crutch/brace.
-2. Bilateral assistance: two sticks/crutches/braces or assistance by another person.
-3. Wheelchair.
-
-**Distance**
-- Measure the distance the patient can walk in meters.
-  - **Unassisted:** Observe walking for a minimum of 500 meters and measure time needed, if possible.
-  - **Assisted:** Observe walking with assistive devices or help from another person for a minimum of 130 meters, if possible.
-
----
-
-### AMBULATION SCORE
-
-0. Unrestricted
-1. Fully ambulatory
-2. ≥ 300 meters but < 500 meters, without help or assistance (EDSS 4.5 or 5.0)
-3. ≥ 200 meters but < 300 meters, without help or assistance (EDSS 5.0)
-4. ≥ 100 meters but < 200 meters, without help or assistance (EDSS 5.5)
-5. Walking range < 100 meters without assistance (EDSS 6.0)
-6. Unilateral assistance, ≥ 50 meters (EDSS 6.0)
-7. Bilateral assistance, ≥ 120 meters (EDSS 6.0)
-8. Unilateral assistance, < 50 meters (EDSS 6.5)
-9. Bilateral assistance, ≥ 5 meters but < 120 meters (EDSS 6.5)
-10. Uses wheelchair without help; unable to walk 5 meters even with aid, essentially restricted to wheelchair; wheels self and transfers alone; up and about in wheelchair for some 12 hours a day (EDSS 7.0)
-11. Uses wheelchair with help; unable to take more than a few steps; restricted to wheelchair; may need some help in transferring and wheeling self (EDSS 7.5)
-12. Essentially restricted to bed or chair or perambulated in wheelchair, but out of bed most of the day; retains many self-care functions; generally has effective use of arms (EDSS 8.0)
-
-Expanded Disability Status Scale (EDSS)
-
-0   - Normal neurological exam (all Functional Systems [FS] grade 0)
-1.0 - No disability, minimal signs in one FS (one FS grade 1)
-1.5 - No disability, minimal signs in more than one FS (more than one FS grade 1)
-2.0 - Minimal disability in one FS (one FS grade 2, others 0 or 1)
-2.5 - Minimal disability in two FS (two FS grades 2, others 0 or 1)
-3.0 - Moderate disability in one FS (one FS grade 3, others 0 or 1) though fully ambulatory;
-or mild disability in three or four FS (three/four FS grades 2, others 0 or 1) though fully ambulatory
-3.5 - Fully ambulatory but with moderate disability in one FS (one FS grade 3) and mild disability in one or two FS (one/two FS grade 2) and others 0 or 1;
-or fully ambulatory with two FS grades 3 (others 0 or 1);
-or fully ambulatory with five FS grades 2 (others 0 or 1)
-4.0 - Unable to walk > 25 feet without aid
-4.5 - Unable to walk > 100 feet without aid
-5.0 - Relies on a walking aid; unable to walk > 300 feet without resting
-5.5 - Relies on a walking aid; unable to walk > 200 feet without resting
-6.0 - Unable to walk more than 50 feet with or without aid; cannot stand unaided for five minutes
-6.5 - Unable to walk more than 10 feet with or without aid; cannot stand unaided for two minutes
-7.0 - Unable to walk 5 meters even with aid, essentially restricted to wheelchair; wheels self and transfers alone; up and about in wheelchair some 12 hours a day
-7.5 - Unable to take more than a few steps; restricted to wheelchair; may need some help in transferring and in wheeling self
-8.0 - Essentially restricted to bed or chair or perambulated in wheelchair, but out of bed most of the day; retains many self-care functions; generally has effective use of arms
-8.5 - Essentially restricted to bed much of the day; has some effective use of arm(s); retains some self-care functions
-9.0 - Helpless bed patient; can communicate and eat
-9.5 - Totally helpless bed patient; unable to communicate effectively or eat/swallow
-10  - Death due to MS
-
-

prompts/just_edss_schema.gbnf

@@ -1,11 +0,0 @@
-EDSS-kv ::= "\"EDSS\"" space ":" space number
-Reason ::= "\"" char{0,400} "\"" space
-Reason-kv ::= "\"Reason\"" space ":" space Reason
-boolean ::= ("true" | "false") space
-char ::= [^"\\\x7F\x00-\x1F] | [\\] (["\\bfnrt] | "u" [0-9a-fA-F]{4})
-decimal-part ::= [0-9]{1,16}
-integral-part ::= [0] | [1-9] [0-9]{0,15}
-nicht-klassifizierbar-kv ::= "\"nicht_klassifizierbar\"" space ":" space boolean
-number ::= ("-"? integral-part) ("." decimal-part)? ([eE] [-+]? integral-part)? space
-root ::= "{" space Reason-kv "," space nicht-klassifizierbar-kv ( "," space ( EDSS-kv ) )? "}" space
-space ::= | " " | "\n"{1,2} [ \t]{0,20}

prompts/just_edss_text.txt

@@ -1,25 +0,0 @@
-Expanded Disability Status Scale (EDSS)
-
-0   - Normal neurological exam (all Functional Systems [FS] grade 0)
-1.0 - No disability, minimal signs in one FS (one FS grade 1)
-1.5 - No disability, minimal signs in more than one FS (more than one FS grade 1)
-2.0 - Minimal disability in one FS (one FS grade 2, others 0 or 1)
-2.5 - Minimal disability in two FS (two FS grades 2, others 0 or 1)
-3.0 - Moderate disability in one FS (one FS grade 3, others 0 or 1) though fully ambulatory;
-or mild disability in three or four FS (three/four FS grades 2, others 0 or 1) though fully ambulatory
-3.5 - Fully ambulatory but with moderate disability in one FS (one FS grade 3) and mild disability in one or two FS (one/two FS grade 2) and others 0 or 1;
-or fully ambulatory with two FS grades 3 (others 0 or 1);
-or fully ambulatory with five FS grades 2 (others 0 or 1)
-4.0 - Unable to walk > 25 feet without aid
-4.5 - Unable to walk > 100 feet without aid
-5.0 - Relies on a walking aid; unable to walk > 300 feet without resting
-5.5 - Relies on a walking aid; unable to walk > 200 feet without resting
-6.0 - Unable to walk more than 50 feet with or without aid; cannot stand unaided for five minutes
-6.5 - Unable to walk more than 10 feet with or without aid; cannot stand unaided for two minutes
-7.0 - Unable to walk 5 meters even with aid, essentially restricted to wheelchair; wheels self and transfers alone; up and about in wheelchair some 12 hours a day
-7.5 - Unable to take more than a few steps; restricted to wheelchair; may need some help in transferring and in wheeling self
-8.0 - Essentially restricted to bed or chair or perambulated in wheelchair, but out of bed most of the day; retains many self-care functions; generally has effective use of arms
-8.5 - Essentially restricted to bed much of the day; has some effective use of arm(s); retains some self-care functions
-9.0 - Helpless bed patient; can communicate and eat
-9.5 - Totally helpless bed patient; unable to communicate effectively or eat/swallow
-10  - Death due to MS