Update readme & screenshots

README.md

@@ -1,12 +1,14 @@
 # CRDS Scan Analyzer
 
-### Basics
+<img src="screenshots/fit_demo.png" width=600/>
+
+## Basics
 
 - Designed for usage with **Mid-IR laser comb** scan output (time scale, not frequency)
 
-- Expected data column format: `[time, signal voltage in, piezo crystal voltage out]`
+- Expected data column format: `<time>, <signal voltage in>, <piezo crystal voltage out (optional)>`
 
-### Building
+## Building (Python 3.8+)
 
 1. `pip3 <or python3 -m pip> install -r requirements.txt`
 
@@ -14,12 +16,99 @@
 
 3. Find build output in `/dist/`
 
-### Usage
+## General Usage
 
-1. Import data (CSV format preferred, delimiter customization coming later, maybe even [LabView binary](https://pypi.org/project/npTDMS/))
+1. Import data (CSV - default Zurich output format)
+   
+   - Comment - %
+   - Delimiter - ;
 
 2. Cut out & overlay peak groups using either piezo-voltage-threshold or group-spacing algorithm 
 
 3. Set peak isolation parameters + guesses for ringdown function coefficients 
 
-4. Admire glorious tau distributions for each comb tooth 
+4. Admire glorious tau distributions for each comb tooth - **Note that the timescale used during correlation, adding & fitting  (including the initial guess for tau) is in SENSOR TICKS. The resulting tau values are converted back to the original timescale at the end.**
+
+## Instructions
+
+##### GENERAL CONFIG
+
+| Input    | Purpose                                                |
+| -------- | ------------------------------------------------------ |
+| Timestep | Time interval of each sensor tick (e.g. 0.0000000178s) |
+
+##### GROUPING CONFIG (SpacedGroups)
+
+The SpacedGroups algorithm uses the length of each group (looking *length* in each direction from the first peak in the group) to determine which peaks fit into which group.
+
+| Input               | Purpose                                                                                                                                                           |
+| ------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| Group length        | How long in time the peak group is (e.g. 0.0006s)                                                                                                                 |
+| Min peak height     | The lowest acceptable height for a peak to be detected                                                                                                            |
+| Min peak prominence | Prominence of detectable peaks - read about prominence [here](https://en.wikipedia.org/wiki/Topographic_prominence). Is finnicky, might have to play around a bit |
+| Moving average size | Peak detection uses a moving average (of which this is the denominator) to smooth out the data **(FOR GROUPING ONLY)**.                                           |
+
+**Notes**
+
+- You can custom start and end cutoffs for grouping in case there's only part of a group at the beginning or end
+
+- You can choose to exclude mirrored groups (which occur every other group). Or don't. Depends on how you configured the lab setup.
+
+##### GROUPING CONFIG (VThreshold)
+
+This algorithm *should* look at the min and max voltages provided to separate out groups. It's not implemented yet, though.
+
+##### PEAK ISOLATION CONFIG
+
+This is where the overlayed peak groups are added together, and the added peaks are cut out.
+
+**Note that the timescale here is in ticks, NOT seconds/milliseconds/etc.**
+
+| Input                   | Purpose                                                                                                             |
+| ----------------------- | ------------------------------------------------------------------------------------------------------------------- |
+| Added peak length       | The length of the (added) peaks that you want cut out. Centers around tip of peak.                                  |
+| Min added peak height   | The lowest acceptable height for a peak to be detected                                                              |
+| Added peak prominence   | Prominence of detectable peaks - read about prominence [here](https://en.wikipedia.org/wiki/Topographic_prominence) |
+| Shift over cut-out zone | How many ticks to shift the center of the cut-out zone from the peak tip                                            |
+
+##### INITIAL FIT CONFIG
+
+`y = y0 + a*e^(-t/tau)`
+
+| Input                | Purpose                                                 |
+| -------------------- |:------------------------------------------------------- |
+| *a* value            | Variable in equation                                    |
+| *tau* value          | Variable in equation                                    |
+| *y0* value           | Variable in equation                                    |
+| Shift over fit start | How many ticks to shift over the start of the curve fit |
+
+## Feature Set
+
+| Feature                                        | Status |
+| ---------------------------------------------- |:------:|
+| Import CSV Data                                | ✅      |
+| Group peaks (peak spacing)                     | ✅      |
+| Group peaks (piezo crystal voltage thresholds) | ❌      |
+| Custom start & end times for peak grouping     | ✅      |
+| Correlate grouped peaks                        | ✅      |
+| Add & cut out overlayed peaks                  | ✅      |
+| Batch fit peaks                                | ✅      |
+| Display average tau data                       | ✅      |
+| Export data as CSV                             | ✅      |
+| Residuals on fits                              | ✅      |
+| Standard deviations                            | ✅      |
+| Persistent data storage                        | ❌      |
+
+## Ideas if anyone has the time to add anything
+
+- Speedier iteration & number crunching ([Numba](https://numba.pydata.org/))
+
+- Support for different file formats (e.g. [LabView]([npTDMS · PyPI](https://pypi.org/project/npTDMS/)))
+
+## Screenshots
+
+<img src="screenshots/time_constant_demo.png" width=600/>
+
+<img src="screenshots/correlation_demo.png" width=600/>
+
+<img src="screenshots/voltage_demo.png" width=600/>