Python Module for the OpenWFOM Imaging System
The wfom Python module and command line tool are ways to declare camera settings, test setup, and start an acquisition on the OpenWFOM imaging system.
These instructions will help you get the necessary software installed.
NOTE: Before following this installation guide, complete the hardware assembly instructions found on This Wiki
- Python - 3.6 and Up
- Java Runtime - 1.8 and Up
- Andor SOLIS (4.30 and up) - Registration Required
- PIP Install Option 1
- Git - Install Option 2
The easiest way to use wfom is by importing its Python package directly into an existing script.
It must be first installed alongside your existing Python Packages using pip from the command line.
Open a new instance of CMD, and enter:
pip install wfomYou can now import the module and run any of its functions, as the example.py script does below.
import wfom
wfom.test()Open up a Command Prompt and navigate to your machine's root directory by typing the following command:
cd /
Clone into the Git repository to download the required files.
git clone https://github.com/ryan-byrne/wfom.git
Once the download is completed, navigate into the /wfom directory, and run the setup.py script
to install the necessary Python packages.
cd wfom
python setup.py install
We will now test to see if the files were installed correctly. Start by opening a new instance of CMD.
Start Python from the command line.
python
Import the package,
>>> import wfomAnd run the test function:
>>> wfom.test()NOTE The command line script can only be run from the C:/wfom directory
python wfom.py --test
Once the diagnostic test is complete, any errors will be logged to a text file at:
C:/wfom/resources/tests/TIMESTAMP_OF_TEST.txt
This section provides information on how to run the wfom script, as well as the command line arguments at your disposal
As previously stated, running the wfom Python Package simply requires importing it into an existing script.
import wfom
wfom.run()
The OpenWFOM package is comprised of three classes: Andor, Arduino, and Webcam, which can be imported on their own.
For example, if I simply wanted to import the Arduino class from wfom I would write:
from wfom import Arduino
# Initiate the Arduino Class
a = Arduino("COM4")
# Call the strobe function to open the Strobe GUI
a.strobe()
To run the script from the command line, while inside the /wfom directory type:
python wfom.py
NOTE: If you've navigated to a different directory in the command prompt, you must explicitly refer to the location of wfom.py i.e.:
python C:\wfom\wfom.py
There are also optional command line arguments which can be used to alter the information fed back from the command prompt, which can help streamline bug testing. They are:
-qor--quietruns the script in "Quiet Mode", without command line prints-tor--testruns the script in "Test Mode", which we should have already run during the installation-yautomatically continues whenever an error occurs
For example, the following command would run without command line prints, and automatically continue whenever an error occurs:
python wfom.py -q -y
Alternatively, if you'd prefer to avoid using the command prompt altogether, you can run the wfom.py script by opening the OpenWFOM.bat batch file, found at:
C:\wfom\OpenWFOM.bat
NOTE This file can be copy and pasted wherever you'd like for better accessibility.
We use SemVer for versioning. For the versions available, see the tags on this repository.
- Ryan Byrne - Initial work - ryan-byrne
See also the list of contributors who participated in this project.
This project is licensed under the MIT License - see the LICENSE.md file for details
- Beth Hillman and the rest of the LFOI Team
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