| Type: | Package |
| Title: | Load, Segment and Classify Zooplankton Images |
| Version: | 0.2.0 |
| Maintainer: | Arick Grootveld <arick.grootveld@gmail.com> |
| Imports: | magick |
| Description: | This tool provides functions to load, segment and classify zooplankton images. The image processing algorithms and the machine learning classifiers in this package are (will be, since these have not been added yet) direct ports of an early 'python' implementation that can be found at https://github.com/arickGrootveld/ZooID. The model weights and datasets (also not added yet) that are a part of this package can also be found at Arick Grootveld, Eva R. Kozak, Carmen Franco-Gordo (2023) <doi:10.5281/zenodo.7979996>. |
| URL: | https://github.com/arickGrootveld/ZooID_RPackage |
| Language: | en-US |
| License: | GPL (≥ 3) |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.2.3 |
| NeedsCompilation: | no |
| Packaged: | 2024-01-30 19:11:32 UTC; agrootveld |
| Author: | Arick Grootveld [cre, aut], Eva Kozak [aut] |
| Repository: | CRAN |
| Date/Publication: | 2024-01-30 19:20:01 UTC |
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)