Package 'ZooID'

batchPreProcessing

Description

Preprocessing a directory of zooplankton images

Usage

batchPreProcessing(
  zpFileDir,
  zpSaveDir,
  minPixels = 5000,
  imageExtension = ".jpg",
  noRepeats = TRUE,
  verbose = TRUE
)

Arguments

zpFileDir	Directory full of zooplankton images to extract
zpSaveDir	Directory to save the extracted images to
minPixels	Integer specifying the minimum number of pixels allowed in an extracted image Any extracted image with fewer pixels will not be saved [Default: 5000 (~70 by 70 pixels)]
imageExtension	String specifying the extension the images will have (must include ".") [Default: ".jpg"]
noRepeats	Boolean variable to decide whether to ignore images that are already present in the save dir, or not [Default: TRUE]
verbose	Boolean variable indicating whether the script should print info to console [Default: TRUE]

Examples

## Not run: 
zpFileDir <- 'Users/$(whoami)/Images/ZooplanktonImages/ostracod'
zpSaveDir <- 'Users/$(whoami)/Images/ExtractedImages/ostracod'
batchPreProcessing(zpFileDir, zpSaveDir)

## End(Not run)

---

datasetPreProcessing

Description

Preprocessing a directory structure of zooplankton images, and saving the resultant images to another directory structure

Usage

datasetPreProcessing(
  zpFileDir,
  zpSaveDir,
  minPixels = 5000,
  imageExtension = ".jpg",
  verbose = TRUE
)

Arguments

zpFileDir	Directory of subdirectories containing zooplankton images
zpSaveDir	Directory to setup the subdirectory structure for the extracted images
minPixels	Integer specifying the minimum number of pixels allowed in an extracted image See "batch_imagePreProcessing" for details [Default: 5000]
imageExtension	String specifying the extension the images will have (must include ".") [Default: ".jpg"]
verbose	Boolean variable indicating whether the script should print info to console [Default: TRUE]

Examples

## Not run: 
zpFileDir <- 'Users/$(whoami)/Images/ZooplanktonImages'
zpSaveDir <- 'Users/$(whoami)/Images/ExtractedImages'
batchPreProcessing(zpImgDir, zpSaveDir)

## End(Not run)

---

imagePreProcessing

Description

Preprocessing the passed image

Usage

imagePreProcessing(zpFilepath)

Arguments

zpFilepath

Filepath to the zooplankton image to be processed

Value

extractedImage The section of the image extracted by the algorithm, or NULL if the image was corrupted

Examples

## Not run: 
zpFilepath <- 'Users/$(whoami)/Images/ZooplanktonImages/ostracod1.png'
ostracod1Image <- imagePreProcessing(zpFilepath)

## End(Not run)

---

unpack_processedDataset

Description

Unpacking the processed zooplankton dataset to a specific directory. The result will be a directory named "processedDataset" being put the specified save directory, containing all the image files from the processed dataset that comes with this package

Usage

unpack_processedDataset(saveDir)

Arguments

saveDir

(String) Directory to save the processed dataset to

Examples

## Not run: 
saveDir <- 'Users/$(whoami)/Images/ZooplanktonImages/'
unpack_processedDataset(saveDir)

## End(Not run)

---

unpack_unprocessedDataset

Description

Unpacking the unprocessed zooplankton dataset to a specific directory The result will be a directory named "unprocessedDataset" being put in the specified save directory, containing all the image files from the dataset that comes with this package, but before processing was applied

Usage

unpack_unprocessedDataset(saveDir)

Arguments

saveDir

(String) Directory to save the unprocessed dataset to

Examples

## Not run: 
saveDir <- 'Users/$(whoami)/Images/ZooplanktonImages/'
unpack_unprocessedDataset(saveDir)

## End(Not run)

---