update descriptions, add individual metadata (#13)

- Update column descriptions in README (5d9aaac7e361e510616ac079d5b442e659e86d52)
- Add metadata CSV for individual images (38df512674b3f244f805b8aa3e418dd859f4e207)

README.md

@@ -120,7 +120,7 @@ Segmentation was completed by adapting the elytra length and width annotations t
   - `cm_pix`: Integer. The number of pixels in a centimeter on the scalebar (measured by Euclidean distance between points given in `scalebar`).
   - `individual`: Integer. The beetle in the image to whom the measurements refer. The beetles are measured "in line" (numbering is from left to right, top to bottom, as one would read a book). However, Zooniverse does not register individual IDs beyond 99 (once 99 individuals are marked, it restarts the count at 1). Be careful with it.
   - `structure`: Whether the measurement applies to the length or width of the elytra (`ElytraLength` or `ElytraWidth`, respectively). 
-  - `lying_straight`: 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`.
+  - `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`.
   - `coords_pix`: Pixel coordinates of the line marking the length or width of the elytra (green or purple line in the sample image). Note that these annotations were done on the resized copy of the image (1MB), but the aspect ratio was maintained in the resizing.
   - `dist_pix`: Float. The length or width of the elytra (indicated by `structure`) as measured in pixels (calculated as Euclidean distance beetween `coords_pix` points).
   - `dist_cm`: Float. The length or width of the elytra (indicated by `structure`) as measured in centimeters using the scalebar compared to the measured pixel distance (`dist_pix/cm_pix`).
@@ -136,6 +136,9 @@ Segmentation was completed by adapting the elytra length and width annotations t
   - `combinedID`: Generated from `PictureID` (minus the `.jpg`) plus `_<individual>`. This gives only 11,104 IDs, as it suffers from the issue of `individual` based on Zooniverse's export. Individuals should be measured by half the number of rows with `user_name == "IsaFluck"`.
   - `measureID`: Unique identifier for the beetle measurements (and this CSV), generated using the `uuid` package. There are 39,064 unique measurements (2 per beetle, with overlap on 234 images annotated by all three annotators and 1 annotated by just two).
   - `file_name`: Relative path to image from the root of the directory (`<group_images>/<pictureID>.jpg`); allows for image to be displayed in the dataset viewer alongside its associated metadata.
+  - `image_dim`: Dimensions of full-sized image `(<height>, <width>, <number of channels>)`.
+  - `resized_image_dim`: Dimensions of resized image `(<height>, <width>, <number of channels>)`.
+  - `coords_pix_scaled_up`: `coords_pix` adjusted for full-sized image.
 
 **NOTE:** 
   - The `NEON_sampleID` RMNP_014.20180709.CALADV.01 is repeated because there were too many individuals in the sample to organize them all in one picture. Thus, the individuals from this sample are split between two pictures: `A00000051555_1` and `A00000051555_2`.
@@ -143,17 +146,17 @@ 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.
 
-**TODO:* Make individual metadata CSV file:
 
 **individual_metadata.csv**:
   - `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`.
   - `elytraLength`: Length of the elytra in centimeters. Indicated by the green line in the image below.
   - `elytraWidth`: Width of the elytra in centimeters. Indicated by the purple line in the image below.
   - `measureID_length`: `measureID` from `BeetleMeasurements.csv` for the `elytraLength` of this individual. Can be used to fetch measure-specific information from `BeetleMeasurements.csv`.
   - `measureID_width`: `measureID` from `BeetleMeasurements.csv` for the `elytraWidth` of this individual. Can be used to fetch measure-specific information from `BeetleMeasurements.csv`.
   - `genus`: Genus of the individual (generated by taking the first word in the `scientificName` from `BeetleMeasurements.csv`). There are 36 unique genera labeled.
-  - `species`: Species of the individual (generated from the word(s) following the `genus` in the `scientificName` from `BeetleMeasurements.csv). There are 78 unique species labeled.
+  - `species`: Species of the individual (generated from the word(s) following the `genus` in the `scientificName` from `BeetleMeasurements.csv`). There are 78 unique species labeled.
   - `NEON_sampleID`: NEON identifier for the sample (576 unique IDs), prefixed by the `plotID`. (Matches `NEON_sampleID` in `BeetleMeasurements.csv`.)
   - `file_name`: Relative path to image from the root of the directory (`individual_images/<individualID>.jpg`); allows for image to be displayed in the dataset viewer alongside its associated metadata.