luxconnector 1.1.2
This is a python wrapper around the Lux Client windows solution
Keywords: luxconnector

# THIS PROJECT IS DEPRECATED

Please switch to CytoSmartOpenAPI

This is a python wrapper for the Lux Client windows solution.
The package will only work on Windows.

# Installation

To install this package follow the these steps:

## Step 1: Drivers

Make sure you have or had a [CytoSmart application installed](http://download.cytosmart.com/).
Recommend is the cell counter given it do not restart itself after closing.
This is needed to have all the correct drivers installed.
It doesn't matter if the app is uninstalled afterwards.

## Step 2: pip install

```cmd
pip install luxconnector
```

# Usage

## Initialization

Make sure at least one lux is physically connected to your computer via a USB3 port.
The luxconnector is an object that maintains the connection with the Lux.
To create the object use the following code:

```python
from luxconnector import LuxConnector
connector = LuxConnector(number_of_devices=2)
```

NOTE: Make sure number_of_devices is at least the number of devices you have connected.
If not the luxconnector will look for the missing devices forever.

## Getting serial numbers

Each physical device has a serial number.
This number is needed to send commands to a specific device.

```python
serial_numbers = connector.get_all_serial_numbers()
```

## Getting a single image

When you want a single image taken at this moment use get_image.
This will return the image as a [`pillow image`](https://pillow.readthedocs.io/en/stable/reference/Image.html).
You need to give the serial number of the device you want to target

```python
img = connector.get_image(serial_number)
```

or

```python
img = connector.get_image(serial_numbers[index])
```

## Changing the focus

This function will change the focus for the luxconnector object.
Every image taken after this function will have the new focus.

The focus is in the range 0 until 1. (0.0 and 1.0 are valid entries)

You need to give the serial number of the device you want to target

```python
connector.set_focus(serial_number, 0.5)
img1 = connector.get_image(serial_number) # Image with focus of 0.5
connector.set_focus(serial_number, 0.7)
img2 = connector.get_image(serial_number) # Image with focus of 0.7
img3 = connector.get_image(serial_number) # Image with focus of 0.7
```

## Getting the temperature

This function returns the temperature in celsius of the device.

You need to give the serial number of the device you want to target

```python
temperature = connector.get_temperature(serial_number)
```

## Change activate camera (fluorescence)

To use fluorescence you will need change the active camera.
The camera can be set to 3 different values, RED, GREEN, or BRIGHTFIELD.
This will only work if your device is a fl device otherwise only BRIGHTFIELD is available.

```python
connector.set_active_camera(serial_number, "RED")
connector.set_active_camera(serial_number, "GREEN")
connector.set_active_camera(serial_number, "BRIGHTFIELD")
```

## Change camera setting

Each camera has its own settings.
Not all settings are available for BRIGHTFIELD.

- exposure: The time in milliseconds the camera is detecting light.
- gain: The multiplication of the camera. (Fluo only)
  If very little light goes into the camera sensor make sure the gain is high.
- brightness: Strength of the led when it is on (Fluo only)
- focus_offset: the difference in focus between brightfield and fluo.
  If focus is set to 0.4 and focus_offset for RED is set to 0.1 RED focus is 0.5 (Fluo only)

```python
connector.set_camera_settings(serial_number, "RED", 500, gain=30, brightness=5000)
connector.set_camera_settings(serial_number, "BRIGHTFIELD", 10)
```

## Getting a z-stack

This function will return a list of [`pillow images`](https://pillow.readthedocs.io/en/stable/reference/Image.html).
Each image will be at a different focus level.

This code will create a z-stack of 6 images.
The focuses of these images will be [0.5, 0.6, 0.7, 0.8, 0.9, 1.0]

You need to give the serial number of the device you want to target

```python
list_of_imgs = connector.get_z_stack(serial_number, num_img = 6, start_focus = 0.5, stop_focus = 1)
```

## Changing zoom modes

There are 2 zoom modes: "IN" and "OUT".
While zoomed in the resolution is higher but the ROI is smaller, zoomed out has a higher ROI but a lower resolution.

Changing this will change it for every image or z-stack taken afterwards.

You need to give the serial number of the device you want to target

```python
connector.set_zoom(serial_number, "IN")
img1 = connector.get_image(serial_number) # Image is zoomed in
connector.set_zoom(serial_number, "OUT")
img2 = connector.get_image(serial_number) # Image is zoomed out
```

## Live view

The live view of the Lux is hosted at http://localhost:3333/cytosmartservice/live?serialNumber=##########.
This image can only been seen if the live view is turned on (by default the live view is turned on).

You need to give the serial number of the device you want to target at the place of the #-symbols.

```python
connector.set_liveview(serial_number, True) # in the browser you can see the image being updated
connector.set_liveview(serial_number, False) # Led of Lux turns off till you take a picture
```

# Developers

Developers of the luxconnector please look at the [`developers readme`](README_DEV.md)

# Credits

- Tom Nijhof
- Kyap
- Nora


History
-------
1.1.1 (2022-06-29)
------------------
- Update documentation

1.1.0 (2021-12-03)
------------------
- Add change camera settings
- Add set activate camera (brightfield, red-fluo, or green-fluo)
- Change focus: 
    make sure focus always happens in brightfield camera mode
    Add sleep after changing to focus so camera can move to new position
- Update to new Cytosmart app

1.0.4 (2021-04-15)
------------------
- Update Pillow
- Fix installation requirements

1.0.3 (2021-11-22)
------------------
- Update requirements of websocket and websocket-client to include version 1
- Check if app is open before starting a new one

1.0.2 (2021-04-15)
------------------
- Update pillow
- Update license to ACADEMIC PUBLIC LICENSE

1.0.1 (2021-01-14)
------------------
- Added support for LUX3 FL
- Bugfix: toggle liveview when change zoom level

1.0.0 (2020-09-15)
------------------
- Added multi lux support
- Changed output from numpy array to pillow
- Require serial number with function to get information
- Add get_temperature

0.1.2 (2020-06-30)
------------------
- Rename failing to pinging in print statement

0.1.1 (2020-06-11)
------------------
- Update documentation
- Make setup.py fit for PyPI
 
0.1.0 (2020-05-20)
------------------
- Update lux server to latest version

0.0.3 (2020-03-30)
------------------
- bugfix: files were not copied into package on linux

0.0.2 (2020-03-24)
------------------
- Bugfix: stop waiting for response after sending a message

0.0.1 (2020-03-16)
------------------

- Add function: Copy the luxconnector 
- Add function: focus change option
- Add function: z-stack
- Bugfix: add lux app to manifest

0.0.0 (2020-03-13)
------------------

Copied basic package a start of luxconnector


                         ACADEMIC PUBLIC LICENSE
                                version 1.1

                           Copyright (C) 2021


                                Preamble

  This license contains the terms and conditions of using LuxConnector in
noncommercial settings: at academic institutions for teaching and research
use and for personal or educational purposes. You will find that this
license provides noncommercial users of LuxConnector with rights that are
similar to the well-known GNU General Public License, yet it retains the
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  By modeling the GPL, this license guarantees that you're safe when using
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can modify LuxConnector to your purposes, and you can also share your modifications.
Even in the unlikely case of the authors abandoning LuxConnector entirely, this
license permits anyone to continue developing it from the last release, and
to create further releases under this license.

  We believe that the combination of noncommercial open-source and commercial
licensing will be beneficial for the whole user community, because income from
commercial licenses will enable faster development and a higher level of
software quality, while further enjoying the informal, open communication
and collaboration channels of open source development.

  The precise terms and conditions for using, copying, distribution and
modification follow.


                         ACADEMIC PUBLIC LICENSE

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Initially written by Andras Varga (public domain) for OMNeT++ https://omnetpp.org/intro/license, 
adapted by CytoSMART TECHNOLOGIES BV. The adaptation is licensed under CC0 1.0 (Public Domain Dedication).