igemsoftware2020 / tas_taipei

A lab tool for measuring the pH of solutions over time using pH indicators and visual image or video data

How to Use VisualpH

prereqs

make sure you have installed python 3, and that pip is properly working. Once that is done, run

pip install -r requirements.txt

to install the dependencies.

Example

run the following commands in the terminal

linux

python3 vpH.py -p "exampleData/C-19DNA.mov" -sm 0.5 -pp 3

windows

python vpH.py -p "exampleData/C-19DNA.mov" -sm 0.5 -pp 3

then, select 3 points to encircle the coloured portion of the leftmost microcentrifuge tube repeat the same for all 4, from left to right

note that the default is 4 points, but the argument -pp 3 overrides that The video is also of a fairly large resolution, so the window can be shrinked and expanded using -sm

After the video is processed, a window should pop up that shows graphs of each tube over time.

To see each graph individually, run

linux

python3 vpH.py -r 0.npy

windows

python vpH.py -r 0.npy

To see all 4 again, run

linux

python3 vpH.py -m 4

windows

python vpH.py -m 4

Parsing a new video

Use the following command:

linux

python3 vpH.py -p "filename.py"

windows

python vpH.py -p "filename.py"

and it will bring up a window to select the tubes to process

the following argument can be added to the end of the command to shrink the size of the window by any constant

-sm 0.5

The process command will automatically save the data files in /data/, with the names 0, 1, 2, 3 ...

make sure you rename these files before processing the next video if you want to save them

Displaying parsed data

The following command can be used for data files that have already been processed

linux

python3 vpH.py -r "filename.npy"

windows

python vpH.py -r "filename.npy"

If you have a set of data files you want to display on a graph, use the following argument where x is an integer above 1

-m x

x will denote the number of files to process, starting from 0 to x-1