Add metadata file for the Separate segmented split subset of the data (#18)

- Add metadata file for the Separate segmented split subset of the data (29d450bafed2877b1da6f0bd9c61d9e17a73f391)
- Add description of segmented individuals image subset (c53bbaeec8ffb283fee283212174ab05ded0e9fa)
- clarify individual images in the dataset and point to the code used to create them (71b0d989f924adab0b4961328719913a0d9ecf6f)
- add clarification on species/subspecies in segmentation split and reference to genera list (c16940b7c9e3e360f977bed5df1f0914dbb84034)

README.md

@@ -27,6 +27,10 @@ configs:
 - config_name: resized_images
   data_files:
   - "beetle_images_resized/*.jpg"
+- config_name: "separate segmented splits"
+  data_files:
+  - "Separate_segmented_train_test_splits_80_20/*/*/*.jpg"
+  - "metadata.csv"
 ---
 <!-- - config_name: individual_images
   data_files:
@@ -71,9 +75,17 @@ The individual images were segemented out based on scaling the elytra measuremen
 
 In `group_images` we have 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.
 
-The `individual_images` directory contains images of each individual segmented from the group images. These connect back to their group image based on the `individualID`.
+`Separate_segmented_train_test_splits_80_20` contains individual images of 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).
 
+<!-- Still to be added:
+The `individual_images` directory contains images of each individual segmented from the group images. These connect back to their group image based on the `individualID`.
 
+    individual_images/
+        <individualID 1>.jpg
+        <individualID 2>.jpg
+        ...
+        <individualID 11459>.jpg
+-->
 ```
 /dataset/
     group_images/
@@ -86,11 +98,22 @@ The `individual_images` directory contains images of each individual segmented f
         <pictureID 2>.jpg
         ...
         <pictureID 577>.jpg
-    individual_images/
-        <individualID 1>.jpg
-        <individualID 2>.jpg
+    Separate_segmented_train_test_splits_80_20
+        test/
+            <species 1>/
+            <species 2>/
+            ...
+            <species 12>/
+        train/
+            <species 1>/
+            <species 2>/
+            ...
+            <species 12>/
+        metadata.csv
+    separate_segmented_beetle_images/
+        <pictureID 1>.jpg
+        <pictureID 2>.jpg
         ...
-        <individualID 11459>.jpg
     BeetleMeasurements.csv
     BeetleMeasurements_resized.csv
     individual_metadata.csv
@@ -103,8 +126,11 @@ The `individual_images` directory contains images of each individual segmented f
 
 The `group_images` folder has all 577 orignal full size images. The `beetle_images_resized` folder has the resized (approximately 1MB) images used for annotation in Zooniverse (1MB was the size limitation imposed by the software); aspect ratio was maintained in the resize. <!-- >, and the code used can be found [here](). -->
 
-Segmentation was completed by adapting the elytra length and width annotations to generate the xy point input for the [Segment Anything (SAM)]() model. [Segment Anything (SAM)]() was then used to segment the individual beetles. More information and the code for this process is provided in the [Imageomics/2018-NEON-beetles-processing repo](https://github.com/Imageomics/2018-NEON-beetles-processing).
+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).
 
+<!-- images not provided here
+Segmentation was completed by adapting the elytra length and width annotations to generate the xy point input for the [Segment Anything (SAM)]() model. [Segment Anything (SAM)]() was then used to segment the individual beetles. More information and the code for this process is provided in the [Imageomics/2018-NEON-beetles-processing repo](https://github.com/Imageomics/2018-NEON-beetles-processing).
+-->
 
 |![picture of beetles in A00000046094](https://huggingface.co/datasets/imageomics/BeetlePalooza/resolve/main/group_images/A00000046094.jpg)| 
 |:--|
@@ -145,8 +171,15 @@ Segmentation was completed by adapting the elytra length and width annotations t
   - See notebooks in the [Beetle Processing Repository](https://github.com/Imageomics/2018-NEON-beetles-processing) for more information and analyses of these values, addition and renaming of the above columns from the [original measurement CSV](https://huggingface.co/datasets/imageomics/2018-NEON-beetles/blob/bbefad05d50ed55da82e99bd330afe12a5fd1d97/BeetleMeasurements.csv), and the creation of the individual metadata CSV.
   - `BeetleMeasurements_resized.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.
 
+**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`).
+  - `md5`: MD5 hash of the image (unique identifier).
+  - `species`: species epithet of the beetle in the image. _Note:_ melanarius melanarius is a subspecies designation of melanarius. Genera are as described [here](https://huggingface.co/datasets/imageomics/2018-NEON-beetles/discussions/18#67bcabad85e7281434139a8a), re-alignment is pending.
+  - `split`: `train` or `test`, 80\% of the images  are in the training set.
+  - `file_name`: path to the image from the `Separate_segmented_train_test_splits_80_20` folder to display in the dataset viewer.
+  - `subset`: label given to this subset of the full image dataset (as selected in the viewer): `separate segmented splits`.
 
-**individual_metadata.csv**:
+**individual_metadata.csv**: This CSV was created for individual images that have not yet been added to this repository.
   - `individualID`: ID of beetle in the individual image (`<measureID_length>_<measureID_width>`). This is a unique identifier for this CSV.
   - `combinedID`: Generated from `PictureID` (minus the `.jpg`) plus `_<individual>`. (Matches `combinedID` in `BeetleMeasurements.csv`.)
   - `lying_flat`: Whether or not the beetle is lying _flat_ in the image (`Yes` or `No`). This does _NOT_ correlate to vertical or horizontal alignment; it is whether the individual is twisted to one side or not--a side effect of how they died. Generally, the measured width will be shorter than the true width if this is `No`.
@@ -166,7 +199,7 @@ Segmentation was completed by adapting the elytra length and width annotations t
 
 
 ### Data Splits
-This dataset does not have train-test splits.
+This dataset has a subset of the group images segmented to individuals and divided into an 80-20 train-test split in `Separate_segmented_train_test_splits_80_20/`.
 
 ## Dataset Creation