CellTrack_GUI

This repo contains all draft Qt GUI code for CellTrack

CellTrack_GUI for python version

Prerequisite for running the app

1. Install K-Lite_Codec: Since the player in the app does not contain a decoder, you may have to install K-Lite_Codec.` It is probably not necessary, if you already have other decoder on your computer.

   K-Lite_Codec_Pack_1508_Basic.exe has been included in release others.zip. Note that for installation preference you need to choose Movies & TV app. The image, intstallNote.PNG, shows this in release others.zip.

2. Install python 3.7: Download python 3.7 installer from www.python.org based on your computer system. On Windows, make sure that you select Add to PATH and Disable path length limit. After installation, please reboot the computer.

3. Install opencv-python, scipy and scikit-image package In terminal, use command pip3 install opencv-python, pip3 install scipy and pip3 install scikit-image

General Interface for communicating with CellTrack_GUI

There are serveral assumptions about what you have: 1. A python script 2. Serval parameters that you want to pass it to your python script. 3. Use print() function to return results. (The app reads results line by line.)

In following paragraphs, above assumptions are explained in order.

1. A python script : The python environment is based on the system python 3 environment. Therefore, please install the opencv or other packages in system level.
2. Serval parameters that you want to pass it to your python script: The good thing about this GUI is that you can customize the parameters that you want to pass. In the userData.json, define your parameters ( or parameter set) in the Template Object with type string or double. Later you can instance the parameter set for each video as an object in HiddenVariable array. Here is an example.

Assume you want to pass maxSize and minSize to your python script. For step 1, you define

"Template": {
    "filename": "",
    "maxSize": 0,
    "minSize": 0
}

For step 2, you instance the template for a specific video, cycto.avi and v.avi.

"HiddenVariable": [
    {
        "filename": "cycto.avi",
        "maxSize": 100,
        "minSize": 100.1
    },
    {
        "filename": "v.avi",
        "maxSize": 2.2222,
        "minSize": 100.14444
    }
 ]

For step 3, you load video in the GUI, choose your script and click start analysis. Later, you see the return result from Log Tab.

The command that the GUI execute: python yourScript.py videoPath videoName "Here are your customized parameters" Hint: test.py has been provided in release others.zip

Note:

1. The types in the Template are limited to string and double.
2. Template has to have filename defined in it, since the GUI uses the file name to match videos and corresponding param.
3. Kind reminder: careful with comma symbol in json file. The last object doesn't have comma at the end.
4. It is recommanded you modify the userData.json in folder instead of creating a new one.
5. Use print() function to return results. (The app reads results line by line): Making sure the first thing you print is the full path for result video. The GUI checks that file and loads it into the player. Other results are read and printed line by line in Log Tab.