GreenhouseEI Documentation

SD2019-Plant Phenotyping

Dependencies

• numpy
• opencv

Functionality

1. info(plant_ID, date, path)

• input: plant_ID, date, path
• output: print types of images that are available
• example: tools.info("JS39-65", "2018-04-11", "/Users/john/PycharmProjects/Library_SD/output")

2. unzip(plant_ID, date, image_type, path):

• input: plant_ID, date, image_type, path
• output: the folder of images that match plant ID, date, and image type.
• example: tools.unzip("JS39-65", "2018-04-11", "Nir", "/Users/john/PycharmProjects/Library_SD/output")

3. preprocess(plant_ID, date, path):

• input: plant_ID, date, path
• output: numpy arrays of Hyperspectral images
• example: tools.preprocess("JS39-65", "2018-04-11", "/Users/john/PycharmProjects/Library_SD/output")

4. zip2np(plant_ID, date, path)

• input: plant_ID, date, path
• output: numpy arrays of Hyperspectral images from zip files.
• example: tools.zip2np("JS39-65", "2018-04-11", "/Users/john/PycharmProjects/Library_SD/output")

Running the library

1. Warnings

• There are two types of dataset.
  1. The folder name of the old dataset contains "Schnable", such as "4-9-18_Schnable_49-281-JS39-65_2018-04-11_12-09-35_9968800.zip". The plant_ID of the old dataset should be in a format like "JS39-65", and the date should be in a format like "2018-04-11".
  2. The folder name of the new dataset is like "71-001-Sesame-D-1.zip". The plant_ID of the new dataset should be in a format like "71-001-Sesame-D-1", and the date should be in a format like "2019-07-03".
• the possible image types are Hyp, Nir, Vis, Fluo, IR
• Hyperspectral images should be reconstructed first, before running the "preprocess" to produce the numpy array

2. import the module as a Python package

• from greenhouseEI import tools
• tools.info([plant_ID], [date], [path])
• tools.unzip([plant name], [date], [image type], [path])
• tools.preprocess([plant name], [date], [path])
• tools.zip2np([plant name], [date], [path])

3. running the module in terminal

• python3 -m greenhouseEI.tools info -n JS39-65 -d 2018-04-11 -p /Users/john/PycharmProjects/Library_SD/output
• python3 -m greenhouseEI.tools unzip -n JS39-65 -d 2018-04-11 -t Hyp -p /Users/john/PycharmProjects/Library_SD/output
• python3 -m greenhouseEI.tools preprocess -n JS39-65 -d 2018-04-11 -p /Users/john/PycharmProjects/Library_SD
• python3 -m greenhouseEI.tools zip2np -n JS39-65 -d 2018-04-11 -p /Users/john/PycharmProjects/Library_SD/output