hazelnuts

install

These scripts require python>=3.6..

The following dependencies need to be installed with brew on macOS:

1. mongodb
2. zbar

Then:

Run make install in a terminal window at the root of the project.

activate virtual python environment

Run . ./env/bin/activate from the same terminal window.

deactivate virtual python environment

Run deactivate from the same terminal window.

features

binary masks

Run python mask.py --help to see what kind of commands you can run and what kind of flags you can use.

straightened masks

Run python straighten.py --help to see what kind of commands you can run and what kind of flags you can use.

detip masks

Run python tipmask.py --help to see what kind of commands you can run and what kind of flags you can use.

altering filenames

Run python append.py --help to see what kind of options you can use.

• supply -k and -v: appends the key/value pair to the filename
• supply -k and -v where k already exists: overrides the key/value pair in the filename
• supply -dk: removes the key/value pair from the filename
• supply -k and -nk: overrides 'key' with 'new key'

visualizations

Run python visualize.py --help to see what kind of options you can use.

phenotyping and storage in mongodb

Run python phenotype.py --help to see what kind of options you can use.

acquisition pipeline

Run python acquire.py --help to see what kind of options you can use.

Run make acquisition-preview tmp=/path/to/tmp/folder to fire up the acquisition preview.

Connect to MongoDB from R-Studio

full mongolite documentation here

1. install mongolite:

   install.packages("mongolite")

2. load package

   library(mongolite)

3. connect to database / collection

   m <- mongo(collection = "test_collection", db = "test_database", url = "mongodb://localhost/")

4. fire up a query

   m$find("{}") --> will return all documents from the collection

config.json

The follwing configurations can be made in the config.json file:

• scalebar_length - the length of the scalebar in mm.
• camera_maker - the name of the camera maker. Run config.py --cameras to get a list of available cameras.
• camera_model - the name of the camera model.
• lens_maker - the name of the lens maker. Run config.py --lenses to get a list of available lenses.
• lens_model - the name of the lens model
• file_format - the format of the file. Defaults to .png.