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unzip compressed files that contain plant images, and covert the images into numpy arrays

Project description

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")
  1. 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")
  1. 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")
  1. 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
  1. 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])
  1. 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

Project details


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