Realign descriptions for moved and updated individual specimen metadata file

README.md

@@ -33,7 +33,7 @@ configs:
   - "group_images_resized/*.jpg"
 - config_name: individual_specimens
   data_files:
-  - "individual_specimens.csv"
+  - "individual_specimens/metadata.csv"
   - "individual_specimens/part_000/*.png"
   - "individual_specimens/part_001/*.png"
 - config_name: "separate segmented splits"
@@ -118,8 +118,8 @@ This dataset has 4 subsets, which are described in greater detail below in [Data
         part_001/
             <pictureID>_specimen_<number>.png
             ...
+        metadata.csv
     BeetleMeasurements.csv
-    individual_specimens.csv
 ```
 
 
@@ -129,7 +129,7 @@ This dataset has 4 subsets:
 
 1. `group_images`: 577 images of multiple beetles in a reasonably regular pattern (see sample image below). Each of these images contains a centimeter-based scalebar and a barcode representing the sample (collection of beetles in the image). Each row in `BeetleMeasurements.csv` corresponds to a measurement of the elytra (length or width) of an individual beetle.
 2. `resized_group_images`: All 577 `group_images` resized to the dimensions required for Notes from Nature annotation. These resized images align with the individual measurements provided in `BeetleMeasurements.csv`, unlike the images in the `group_images` subset, which require conversion that the pixel locations are converted to match the full size images.
-3. `individual_specimens`: 11,654 manually segmented images of all individual specimens photographed in the `group_images` subset. These images are split between two folders (`part_000/` and `part_001/`), and are labeled based on the group image to which they belong (`pictureID`), then the associated specimen when labeling within the tray from left to right, top to bottom (as if reading a book). Metadata for these images can be aligned using the `individual_specimens.csv`.
+3. `individual_specimens`: 11,654 manually segmented images of all individual specimens photographed in the `group_images` subset. These images are split between two folders (`part_000/` and `part_001/`), and are labeled based on the group image to which they belong (`pictureID`), then the associated specimen when labeling within the tray from left to right, top to bottom (as if reading a book). Metadata for these images can be aligned using the `individual_specimens/metadata.csv`.
 4. `separate segmented splits`: 7,070 individual beetle images segmented from the `group_images`. This subset encompasses 11 different species of beetles. There are 12 folders, but _melanarius melanarius_ is a subspecies designation for _melanarius_, so it should not be considered a species distinction. These images are divided into an 80-20 train-test split, and further separated into subfolders based on their species (as shown below). These images are all contained in the `Separate_segmented_train_test_splits_80_20/` directory, and were generated as part of [BeetlePalooza 2024](https://doi.org/10.5281/zenodo.15540300). See [`Separate_segmented_train_test_splits_80_20/README`](Separate_segmented_train_test_splits_80_20/README.md) for more details. 
     - The code used to produce the images and splits in `Separate_segmented_train_test_splits_80_20/` is provided [here](https://github.com/Imageomics/2018-NEON-beetles-processing/blob/main/notebooks/Beetle_Palooza_image_separation.ipynb).
 
@@ -177,14 +177,15 @@ Segmentation was completed by adapting the elytra length and width annotations t
   - `beetle_images_resized/metadata.csv` has `pictureID`, `scientificName`, `genus`, `species`, `NEON_sampleID`, `siteID`, and `file_name` columns to display the resized images in the dataset viewer with some group image-level information. It will match up to information from `BeetleMeasurments.csv` on `pictureID`, though this is _not_ a unique alignment since it's not a unique ID for `BeetleMeasurements.csv`, but is for the resize.
 
 
-**individual_specimen.csv**: This CSV was created for individually cropped images.
-  - `individualImageFilePath`: Relative path to individual image from the root of the directory (`individual_specimens/part_<part_number>/<pictureID>_specimen_<number>.png`). The `number` corresponds to the position of the beetle specimen within the group image, numbered from left to right and top to bottom.
-  - `groupImageFilePath`: Relative path to group image from the root of the directory (`group_images/<pictureID>.jpg`)
+**individual_specimen/metadata.csv**: This CSV was created for individually cropped images.
+  - `individualImageFilePath`: Relative path to individual image from the _root of the repository_ (`individual_specimens/part_<part_number>/<pictureID>_specimen_<number>.png`). The `number` corresponds to the position of the beetle specimen within the group image, numbered from left to right and top to bottom.
+  - `groupImageFilePath`: Relative path to group image from the _root of the repository_ (`group_images/<pictureID>.jpg`)
   - `NEON_sampleID`: NEON identifier for the sample (576 unique IDs), prefixed by the `plotID`. (Matches `NEON_sampleID` in `BeetleMeasurements.csv`.)
   - `scientificName`: Binomial scientific name of the specimen.
   - `siteID`: String. Identifier for the site from which the specimens were collected. There 30 different site IDs. For more information on the sites, visit: https://www.neonscience.org/field-sites/explore-field-sites.
   - `site_name`: Name of field site from which the specimens were collected. There are 43 different field site names. -- These lack consistency (sometimes "NEON" or "Site" was used in the name causing duplicates), and will be updated using the site codes.
   - `plotID`: Identifier for the plot from which the specimens were collected (`<siteID>_<plot number>`). Each site has multiple plots; there are 144 total plots from which specimens were collected.
+  - `file_name`: Relative path _from metadata file location_ to images for dataset viewer functionality (`part_<part_number>/<pictureID>_specimen_<number>.png`).
 
 **Separate_segmented_train_test_splits_80_20/metadata.csv**: metadata file for the segmented individuals in the `Separate_segmented_train_test_splits_80_20` folder.
   - `filename`: name of image file (`beetle_<number code>.png`).