diff --git a/docs/imagefolder-guide.md b/docs/imagefolder-guide.md index ca3bbba..3b6e5cb 100644 --- a/docs/imagefolder-guide.md +++ b/docs/imagefolder-guide.md @@ -1,6 +1,10 @@ # ImageFolderDataset Guide: Working with NEON Beetle Images -This guide demonstrates how to use the [`ImageFolderDataset`](api-reference.md#hpc_inference.datasets.ImageFolderDataset) class from the HPC Inference package with the [2018 NEON Beetles dataset](https://huggingface.co/datasets/imageomics/2018-NEON-beetles). +This guide demonstrates how to use the [`ImageFolderDataset`](api-reference.md#hpc_inference.datasets.ImageFolderDataset) class from the `hpc-inference` package with the 2018 NEON Beetles dataset.[^1] + +[^1]: Fluck, I. E., Baiser, B., Wolcheski, R., Chinmian, I., & Record, S. (2024). +2018 NEON Ethanol-preserved Ground Beetles (Revision 7b3731d). +Hugging Face. https://doi.org/10.57967/hf/5252 ## Overview @@ -14,7 +18,7 @@ The [`ImageFolderDataset`](api-reference.md#hpc_inference.datasets.ImageFolderDa ## Dataset Overview -The 2018 NEON Beetles dataset contains: +The 2018 NEON Beetles dataset[^1] contains: - 577 high-resolution group images of ethanol-preserved beetles - Beetles collected from NEON ecological sites in 2018 - Multiple beetles per image, organized by species @@ -458,7 +462,8 @@ plt.show() ``` ![Original vs Processed Beetle Images](imgs/processed_beetles.png) -The top row shows the original high-resolution images (5568×3712 pixels). The bottom row shows the same images after ResNet preprocessing: resized to 224×224 pixels, center-cropped, and de-normalized. +*Figure 1: Comparison of original vs processed NEON beetle images from the 2018 NEON Beetles dataset[^1]. Top row shows original high-resolution images (5568×3712 pixels), bottom row shows the same images after ResNet preprocessing: resized to 224×224 pixels, center-cropped, and normalized.* + ## Performance Optimization @@ -572,4 +577,5 @@ Based on the examples above, here are key recommendations for using [`ImageFolde ### Collate Functions - Use [`pil_image_collate`](api-reference.md#hpc_inference.utils) when `preprocess=None` (returning PIL Images) - Use [`multi_model_collate`](api-reference.md#hpc_inference.utils) for multi-model preprocessing -- Use default collate function for single tensor outputs \ No newline at end of file +- Use default collate function for single tensor outputs + diff --git a/docs/imgs/Imageomics_ABC.png b/docs/imgs/Imageomics_ABC.png new file mode 100644 index 0000000..5d6bba4 Binary files /dev/null and b/docs/imgs/Imageomics_ABC.png differ diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css new file mode 100644 index 0000000..f2f4049 --- /dev/null +++ b/docs/stylesheets/extra.css @@ -0,0 +1,25 @@ +.md-footer-social { + order: 1; +} + +.md-copyright { + order: 2; +} + +.md-footer-generator { + order: 3; +} + +/* +Make logo larger to be legible, +based on this suggestion: https://github.com/squidfunk/mkdocs-material/discussions/2933#discussioncomment-1168075 +*/ + .md-header__button.md-logo { + margin: 0; + padding: 1; +} + +.md-header__button.md-logo img, .md-header__button.md-logo svg { + height: 2.6rem; + width: 2.6rem; +} \ No newline at end of file diff --git a/mkdocs.yml b/mkdocs.yml index 46a3969..bcd9336 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -15,8 +15,8 @@ nav: theme: name: material - logo: imgs/Imageomics_logo_butterfly.png - favicon: imgs/Imageomics_logo_butterfly.png + logo: imgs/Imageomics_ABC.png + favicon: imgs/Imageomics_ABC.png palette: # Palette toggle for automatic mode - media: "(prefers-color-scheme)" @@ -46,6 +46,7 @@ theme: - search.highlight markdown_extensions: + - footnotes - admonition - pymdownx.details - pymdownx.superfences @@ -69,6 +70,9 @@ plugins: python: paths: [src] +extra_css: + - stylesheets/extra.css + extra: social: - icon: fontawesome/brands/github