initial upload

README.md

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+## Overview
+
+- Data source: `SingleRecordings/<id>/{hr.csv, rr.csv, timestamps.csv}`
+- Scripts:
+  - `plot_meditation_data.py`: per-recording plots (raw + moving averages + segment boxplots)
+  - `aggregate_segments_analysis.py`: aggregate metrics/plots across recordings with exactly 4 marks (conditions)
+
+## How calculations are done
+
+- HR and RR loading
+  - Read `timestamp` (ms) → convert to datetime; set as index.
+  - HR column: `hr` (beats per minute). RR column: `rr_ms` (milliseconds).
+
+- Moving averages (per recording)
+  - Time-based rolling means over irregular timestamps using windows: 5 s, 10 s, 30 s, 60 s.
+  - X-axis is seconds from each recording’s start.
+
+- Mark handling (per recording)
+  - Vertical lines at marks from `timestamps.csv`.
+  - Segment boxplots use values in: each interval between consecutive marks and the final interval (last mark → end).
+
+- RMSSD (HRV)
+  - Definition: RMSSD = sqrt(mean(diff(RR_ms)^2)) using successive RR intervals (ms).
+  - Aggregate per-condition RMSSD: computed over all RR samples within each condition’s time window (recording-level); requires ≥2 RR samples.
+  - Aligned time-series RMSSD: first compute a 30 s time-based rolling RMSSD per recording, then align and average across recordings (see below).
+
+- Aggregate metrics across recordings (exactly 4 marks)
+  - Conditions (English labels):
+    - Breathing Scene 1 (pre-first mark)
+    - Spring Scene (1st–2nd mark)
+    - Summer Scene (2nd–3rd mark)
+    - Autumn Scene (3rd–4th mark)
+    - Breathing Scene 2 (post-last mark)
+  - Per recording: compute medians for HR and RR within each condition; compute RMSSD within each condition.
+  - Summary CSV aggregates these per-recording values; boxplots show distributions. The mean of each condition is marked by a black dot on the boxplots.
+
+- Aligned average curves (HR, RR, RMSSD)
+  - Only recordings with exactly 4 marks are used.
+  - For each recording, durations of the five segments are measured; median segment proportions across recordings define a normalized 0–1 time axis with aligned boundaries.
+  - Each recording’s series is piecewise-linearly time-normalized to this axis, interpolated to a common grid, and then averaged (mean ± 1 SD). For RMSSD, a 30 s rolling RMSSD is used before alignment.
+
+# Results
+
+| Condition         | HR (bpm) | RR (ms) | RMSSD (ms) |
+|-------------------|----------|---------|------------|
+| Breathing Scene 1 | 72.61    | 843.33  | 52.70      |
+| Spring Scene      | 72.33    | 860.78  | 56.95      |
+| Summer Scene      | 72.50    | 862.00  | 41.15      |
+| Autumn Scene      | 72.89    | 850.44  | 41.89      |
+| Breathing Scene 2 | 73.78    | 839.94  | 42.59      |
+
+## Plots
+
+### Aggregate Boxplots
+
+![HR Boxplot Across Conditions](Plots/Aggregate/HR_boxplot_conditions.png)
+![RR Boxplot Across Conditions](Plots/Aggregate/RR_boxplot_conditions.png)
+![RMSSD Boxplot Across Conditions](Plots/Aggregate/RMSSD_boxplot_conditions.png)
+
+### Aligned Average Curves
+
+![Aligned Average Heart Rate (HR)](Plots/Aggregate/HR_average_aligned.png)
+![Aligned Average RR Interval](Plots/Aggregate/RR_average_aligned.png)
+![Aligned Average RMSSD](Plots/Aggregate/RMSSD_average_aligned.png)