Convert provgigapath embeddings to parquet by slide/tile

[seandavi]

The current prov-gigapath files are formatted as CSV files with embedded text representations of python classes. This format makes the data very difficult to access and use.

Proposal

Convert all the tile-level and slide-level prov-gigapath to a parquet-format file with one or more metadata columns (slide id, tile location, image name) and one column with the actual tensor data (14 x 768 array).

Advantages

• Much easier data management: one file for tile-level data and one for slide-level data gets ALL of TCGA.
• Dataset becomes more AI-ready
• Language-agnostic representation (any language can read parquet files)
• Data access code becomes trivial (read parquet file)

Pseudocode

1. Read in embeddings for each per-sample CSV file
2. Develop metadata for each CSV file and collect in data.frame
3. Convert each CSV file embedding to a matrix and include as a new column in the dataframe from step 2.
4. Write out full dataframe as parquet file

Result

1. tile-level provgigapath embeddings in a parquet file
2. slide-level provgigapath embeddings in a parquet file

Fully language-agnostic and AI/ML ready...