app.py

from fastapi import FastAPI
from pydantic import BaseModel, Field
import numpy as np
import onnxruntime as ort
from typing_extensions import Annotated
import gradio as gr
from cryptography.fernet import Fernet
import os
import pickle as pkl

# Model load
key = os.getenv("ONNX_KEY")
cipher = Fernet(key)

VERSION = "0.0.3"
TITLE = f"DVPI beregnings API (version {VERSION})"
DESCRIPTION = "Beregn Dansk Vandløbs Plante Indeks (DVPI) fra dækningsgrad af plantearter. Beregningen er baseret på en model som efterligner DVPI beregningsmetoden og er dermed ikke eksakt, usikkerheden er i gennemsnit **±0.017 EQR-enheder** og **R<sup>2</sup>=0.98** når den sammenlignes med den originale. Kan der ikke beregnes en værdi, returneres EQR=0 og DVPI=0."
URL = "https://kennethtm-dvpi.hf.space"

# Load ONNX model and species mappings
with open("model_v3.bin", "rb") as f:
    encrypted = f.read()
    decrypted = cipher.decrypt(encrypted)
    ort_session = ort.InferenceSession(decrypted)

# Load metadata
with open("metadata_v3.bin", "rb") as f:
    encrypted = f.read()
    decrypted = cipher.decrypt(encrypted)
    metadata = pkl.loads(decrypted)

latinname2stancode = metadata["latinname2stancode"]
valid_taxacodes = metadata["valid_taxacodes"]
normalizer_1 = metadata["normalizer_1"]
normalizer_2 = metadata["normalizer_2"]
taxacode2idx = metadata["taxacode2idx"]

# Preprocess species
def preprocess_species(species: dict[int: float]) -> dict[int: float]:
    # Apply filter 1
    intermediate_species = {}
    for sccode, value in species.items():
        if sccode in normalizer_1:
            new_sccode = normalizer_1[sccode]
            if new_sccode in intermediate_species:
                intermediate_species[new_sccode] += value
            else:
                intermediate_species[new_sccode] = value
    
    # Apply filter 2
    final_species = {}
    for sccode, value in intermediate_species.items():
        if sccode in normalizer_2:
            if normalizer_2[sccode] is not None:
                new_sccode = normalizer_2[sccode]
                if new_sccode in final_species:
                    final_species[new_sccode] += value
                else:
                    final_species[new_sccode] = value
        else:
            final_species[sccode] = value

    # filter valid taxacodes
    final_species = {taxacode: value for taxacode, value in final_species.items() if taxacode in valid_taxacodes}
            
    return final_species


class SpeciesCover(BaseModel):
    species: dict[int, Annotated[float, Field(ge=0, le=100)]]
    
    model_config = {
        "json_schema_extra": {
            "examples": [{
                "species": {
                    6458: 25.0,
                    4158: 15.5,
                    7208: 10.0
                }
            }]
        }
    }

class EQRResult(BaseModel):
    EQR: float
    DVPI: int
    version: str = VERSION

# Create FastAPI app
app = FastAPI(title=TITLE,
              description=DESCRIPTION)

def eqr_to_dvpi(eqr: float) -> int:
    if eqr < 0.20:
        return 1
    elif eqr < 0.35:
        return 2
    elif eqr < 0.50:
        return 3
    elif eqr < 0.70:
        return 4
    else:
        return 5


# FastAPI routes
@app.post("/dvpi")
def predict(cover_data: SpeciesCover) -> EQRResult:
    """Predict EQR and DVPI from species cover data"""

    species_preproc = preprocess_species(cover_data.species)

    input_vector = np.zeros((1, len(valid_taxacodes)))

    for species, cover in species_preproc.items():
        idx = taxacode2idx[species]
        input_vector[0, idx] = cover

    if np.sum(input_vector) == 0:
        return EQRResult(EQR=0, DVPI=0)
    
    input_name = ort_session.get_inputs()[0].name
    ort_inputs = {input_name: input_vector.astype(np.float32)}
    _, output_2 = ort_session.run(None, ort_inputs)

    eqr = float(output_2[0][0])
    eqr = 1 if eqr > 1 else eqr
    dvpi = eqr_to_dvpi(eqr)
    
    return EQRResult(EQR=round(eqr, 3), DVPI=dvpi)

# Gradio app
def add_entry(species, cover, current_dict) -> tuple[dict, str]:
    
    current_dict[species] = cover
    return current_dict, current_dict

def gradio_predict(cover_data: dict):

    if len(cover_data) == 0:
        return {}
    
    cover_data_code = {latinname2stancode[species]: cover for species, cover in cover_data.items()}

    data = SpeciesCover(species=cover_data_code)
    result = predict(data)    

    return result.model_dump()
    
with gr.Blocks() as io:

    gr.Markdown(f"# {TITLE}")
    gr.Markdown(DESCRIPTION)

    with gr.Tab(label = "Beregner"):

        gr.Markdown("Beregning er baseret på samfund af plantearter og deres dækningsgrad. Når API'et bruges anvendes arternes [Stancode](https://dce.au.dk/overvaagning/stancode/stancodelister) (SC1064) - se 'Dokumentation' for eksempel på brug.")

        current_dict = gr.State({})
        
        with gr.Row():
            species_choices = sorted(list(latinname2stancode.keys()))
            species_input = gr.Dropdown(choices=species_choices, label="Vælg art")
            cover_input = gr.Number(label="Dækningsgrad (%)", minimum=0, maximum=100)
        
        with gr.Row():
            add_btn = gr.Button("Tilføj")
            reset_btn = gr.Button("Nulstil")
        
        list_display = gr.JSON(label="Artsliste")
        
        calc_btn = gr.Button("Beregn")
        results = gr.JSON(label="Resultater")
            
        def reset_dict():
            return {}, {}, {}
        
        add_btn.click(
            add_entry,
            inputs=[species_input, cover_input, current_dict],
            outputs=[current_dict, list_display],
            show_api=False
        )
        
        reset_btn.click(
            reset_dict,
            inputs=[],
            outputs=[current_dict, list_display, results],
            show_api=False
        )
        
        calc_btn.click(
            gradio_predict,
            inputs=[current_dict],
            outputs=results,
            show_api=False
        )

        gr.Markdown("App og model af Kenneth Thorø Martinsen (kenneth2810@gmail.com).")

    with gr.Tab(label="Dokumentation"):

        gr.Markdown("## Eksempel på brug af API")
        gr.Markdown(f"API dokumentation kan findes på [{URL}/docs]({URL}/docs)")
        gr.Markdown("### Python")
        gr.Code(f"""
import requests
import json
            
data = {{
    "species": {{
        6458: 25.0,
        4158: 15.5,
        7208: 10.0
    }}
}}

response = requests.post("{URL}/dvpi", json=data)
print(response.json())
        """)

        gr.Markdown("### R")
        gr.Code(f"""
library(httr)
library(jsonlite)

data <- list(species = list(
    '6458' = 25.0,
    '4158' = 15.5,
    '7208' = 10.0
))

response <- POST("{URL}/dvpi",
                body = toJSON(data, auto_unbox = TRUE),
                content_type("application/json"))

print(fromJSON(rawToChar(response$content)))
        """)
    
# Mount Gradio app
app = gr.mount_gradio_app(app, io, path="//")