From a77345fd94c04368478f107763fe7382cd66d0df Mon Sep 17 00:00:00 2001
From: mpitell <mpitell@noreply.localhost>
Date: Wed, 1 Apr 2026 23:06:19 +0000
Subject: [PATCH] Upload files to "/"

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+# Drag Auto — Drag Force Analysis
+
+Loads particle centroid tracking data, lets you interactively define movement regions, and computes drag force vs. displacement with a linear fit per particle and direction.
+
+---
+
+## Workflow Overview
+
+1. **Load CSVs** — Reads all `*.csv` files from a folder (output from `Drag Force Particle Tracking Automatic.ipynb`). Automatically detects the number of particles from the column count (3 columns per particle: `cx`, `cy`, `r`).
+
+2. **Set regions (slider cell)** — For each speed, an interactive plot shows the x-position traces for all particles over time. Use the three sliders to define:
+   - **Stationary** — frames where the stage is not moving (baseline)
+   - **Movement 1** — first direction of stage movement
+   - **Movement 2** — second direction of stage movement (return)
+
+   Click **Confirm All & Continue** when all speeds are set.
+
+3. **Analyze** — Computes the mean displacement of each particle relative to its stationary baseline, and the expected Stokes drag force at each speed. Fits a linear spring constant `k` (pN/µm) per particle per direction through the origin.
+
+---
+
+## Key Parameters (Analysis Cell)
+
+| Parameter | Description |
+|---|---|
+| `folder` | Path to folder containing `{speed} mms.csv` files |
+| `PIXELS_PER_MICRON` | Pixel-to-micron conversion factor |
+| `ETA` | Fluid viscosity (Pa·s); default: `0.001` (water) |
+| `R` | Particle radius (m); default: `1e-6` (1 µm) |
+| `TRIM` | Frames trimmed from each edge of a region to remove transients |
+
+---
+
+## Output Plot
+
+- **Color = particle** (each particle gets a unique color)
+- **Filled circles** = Direction 1 (Movement 1), **open circles** = Direction 2 (Movement 2)
+- **Solid fit line** = Direction 1, **dotted fit line** = Direction 2
+- Separate origin-constrained fit per particle per direction with 95% confidence interval shading
+- Printed spring constant `k ± σ` (pN/µm) for each particle and direction
+
+---
+
+## Input File Format
+
+CSV files must match the output of `Drag Force Particle Tracking Automatic.ipynb`:
+
+- No header row
+- Filename: `{speed} mms.csv` (e.g. `0.25 mms.csv`)
+- Columns: `cx0, cy0, r0, cx1, cy1, r1, cx2, cy2, r2` (3 per particle, up to 3 particles)
+
+---
+
+## Dependencies
+
+`numpy`, `pandas`, `scipy`, `matplotlib`, `ipywidgets`, `ipympl`
+
+Install missing packages with `pip install <package>`.
+
+---
+
+## Tracking Data Source
+
+Generate input CSVs using `Drag Force Particle Tracking Automatic.ipynb`.