# Developer notes

This page is currently in note-form and contains a variety of useful information. This content will eventually be categorized more carefully.

## Modifying properties of the BT object using a startup file

The best way to change properties in `hBT` is not by modifying the class file but using a startup script. To do this, make a file called `startup_bt.m` in the `SETTINGS` directory and in there any changes. e.g.

```
hBT.someProperty=123
```

This will be run each time BakingTray starts.

## Simulated mode

You may run BakingTray on any machine with no acquisition hardware or even now ScanImage install by running: `BakingTray('dummyMode',true)` Most features should work but simulated mode is less well tested than normal operation. Simulated mode assists in development whilst not at the rig.

## Running a minimal acquisition and benchmarking

You can initiate a minimal acquisition with no tile saving and even no GUI by setting up the recipe and then running:

```
>> hBT.runTileScan; hBT.scanner.armScanner; hBT.scanner.initiateTileScan
```

If you have the GUIs open then any relevant listeners in those GUIs will still fire. This is useful for working out things like timing bottlenecks. For example see [issue #23](https://github.com/SWC-Advanced-Microscopy/BakingTray/issues/23). It's probably a good idea to benchmark a short acquisition if you're made changes to the acquisition GUI or to the `SIBT` tile acquired callback.

## To run the stages through a tile scan via the API

```
>> hBT.scanner.armScanner; 
>> hBT.runTileScan;
```

* Running in dummy mode on an office PC:

  ```
  >> %If no BakingTray in the path, cd to the project path and run:
  >> addBTtopath
  >> BakingTray('dummyMode',true)
  ```

## Caching dynamic values

Things like the `NumTiles` and `TileStepSize` properties of the recipe are calculated on the fly. So don't access these repeatedly in a time-critical loop.

## Running BakingTray with a dummy laser for testing

Although it's possible to start BakingTray in "dummyMode" (see `help BakingTray`) for running without any hardware, you might want to run with just one hardware component missing. Running with a simulated laser attached is useful, since it allows the acquisition to proceed with the physical laser switched off. Start BakingTray normally then do the following:

```
>> hBT.laser=dummyLaser;
>> hBT.laser.parent=hBT;
```

## How BakingTray access data from ScanImage to build the preview

The callback function `SIBT/tileAcqDone` is run by ScanImage each time a tile position has been acquired. This happens because the `SIBT` constructor adds a listener to the ScanImage object at `hSI.hUserFunctions.acqDone`, one of the hooks for the ScanImage User-Functions. The `tileAcqDone` callback captures the last acquired images, downsamples them, and places them in `hBT.downSampledTileBuffer`, where other methods easily have access to the data.

## How is the tile pattern generated?

The acquisition settings are stored in `BT.recipe`. The tile pattern is produced by the method `BT.recipe.tilePattern`, which generates an n-by-2 matrix. Each row is a different tile position. The first column is the X stage location and the second column the Y stage location. The matrix is generated by `generateTileGrid`, which is a function local to `BT.recipe.tilePattern`. This function produces the tile pattern based upon the following variables:

* The microscope FOV: extracted from the scanner.
* The amount of overlap needed at adjacent tiles: set by the user.
* The size of the sample along X and Y: set by the user.
* The "front/left" position of the whole pattern (this is just an offset): supplied by the user and stored in the structure `recipe.FrontLeft`

The size of the sample in mm along X and Y is converted into tiles using the class `NumTiles`, which is attached to `recipe`. The `NumTiles` class returns the number of tiles needed to cover the desired area in X and Y. It does this based upon the length and breadth of the bounding box and the tile overlap. At the command line you can do:

```
>> hBT.recipe.NumTiles.X      
ans =
    11

>> hBT.recipe.NumTiles.Y
ans =
    12
```