app.py

import os
from datetime import datetime

# import cv2 as cv
import streamlit as st
import torch
import torchvision.transforms as transforms
from PIL import Image
from streamlit_echarts import st_echarts


def animal_sighting_data():
    option = {
    "legend": {},
    "tooltip": {"trigger": "axis", "showContent": False},
    "dataset": {
        "source": [
            ["shellfish", "2012", "2013", "2014", "2015", "2016", "2017"],
            ["Hard Clam", 56.5, 82.1, 88.7, 70.1, 53.4, 85.1],
            ["Soft Shell Clam", 51.1, 51.4, 55.1, 53.3, 73.8, 68.7],
            ["Eastern Oyster", 40.1, 62.2, 69.5, 36.4, 45.2, 32.5],
            ["Atlantic Bay Scallop", 25.2, 37.1, 41.2, 18, 33.9, 49.1],
        ]
    },
    "xAxis": {"type": "category"},
    "yAxis": {"gridIndex": 0},
    "grid": {"top": "55%"},
    "series": [
        {
            "type": "line",
            "smooth": True,
            "seriesLayoutBy": "row",
            "emphasis": {"focus": "series"},
        },
        {
            "type": "line",
            "smooth": True,
            "seriesLayoutBy": "row",
            "emphasis": {"focus": "series"},
        },
        {
            "type": "line",
            "smooth": True,
            "seriesLayoutBy": "row",
            "emphasis": {"focus": "series"},
        },
        {
            "type": "line",
            "smooth": True,
            "seriesLayoutBy": "row",
            "emphasis": {"focus": "series"},
        },
        {
            "type": "pie",
            "id": "pie",
            "radius": "30%",
            "center": ["50%", "25%"],
            "emphasis": {"focus": "data"},
            "label": {"formatter": "{b}: {@2012} ({d}%)"},
            "encode": {"itemName": "shellfish", "value": "2012", "tooltip": "2012"},
        },
    ],
}
    st_echarts(option, height="500px", key="echarts")

def atlantic_bay_scallop():
    """Info for atlantic bay scallop"""
    st.session_state['animal'] = 'Atlantic Bay Scallop'

    st.subheader("Atlantic Bay Scallop")
    st.image(img, use_column_width=True, clamp= True)

    st.subheader("Info:")
    st.markdown("""
        Atlantic bay scallops are also known simply as "Bay Scallops". Their shells are ribbed and have a distinctive wing-like hinge. They can grow to approximately three inches in length. The shells vary in color and can be blue-black, orange, reddish-brown, or white. Within the shells is a single adductor muscle that closes the two shells tightly together. This muscle allows the scallop to clap its shells quickly and strongly which propels the animal through the water. It's the adductor muscle that is the only part of the scallop commonly eaten. Unlike most bivalves, the bay scallop does not have a muscular foot for digging or a siphon for water intake.

        Along the edge of a bay scallop shell are 30 to 40 bright blue eyes. Each eye has a cornea, a lens, an optic nerve, and a retina which enables it to see movements and shadows. This allows them to detect predators. In addition to eyes they also have tentacles along the edge of their shells. The tentacles contain cells that are sensitive to chemicals in the water. These cells help the animal react to its environment. Bay scallops grow quickly, and rarely live past three years of age.

        Habitat: East Coast from Cape Cod to the Gulf of Mexico. On Long Island, Bay Scallops are mostly found in the small bays and harbors, most notably in the Peconic Bay Estuary which lies on the eastern end of Long Island. Bay scallops have also been found in Great South Bay, Moriches Bay, and Shinnecock Bay. Their preferred habitats are within eelgrass beds on sandy and sandy-mud bottoms. Juvenile bay scallops use byssal threads to attach themselves to aquatic plants and rocks to keep them away from predators. They prefer salinities ranging from 31 ppt to 32.8 ppt.
    """)
    st.caption("Info from: https://www.dec.ny.gov/animals/117470.html")

    st.subheader("Data:")
    animal_sighting_data()

def blue_mussel():
    """Info for blue mussel"""
    st.session_state['animal'] = 'Blue Mussel'

    st.subheader("Blue Mussel")
    st.image(img, use_column_width=True, clamp= True)

    st.subheader("Info:")
    st.markdown("""
        The blue mussel is also known as the "Edible Mussel". They are shaped like rounded triangles and are blue black to brown in color with a shiny violet interior. Shells have a slender brownish foot, which houses the byssus gland that produces a strong, thread-like fiber called the byssal threads that allows the mussels to attach themselves to substrates. The threads harden upon contact with the water and are quite tough, however they are not permanent. They use byssal threads to attach to docks, pilings, rocks, and most any solid object. They live in close proximity to other Blue Mussels and together they form dense beds that host a rich community of benthic invertebrates including crustaceans and marine worms. Beds often break up during major storms.

        Blue mussels can grow up to four inches long, and possess two short siphons inside their shell and direct the flow of water. They are known to have significant water filtering capacity and readily absorb water-borne toxins. Many organizations use them as indications of harmful algal blooms (HABs). DEC conducts a Marine Biotoxin Monitoring Program from spring through fall to identify waters where any HABs may be occurring. This is done to protect human health because toxins accumulate in the tissues of animals that unknowingly filter the harmful toxins. If you were to eat a shellfish that has consumed harmful biotoxins, it poses a serious threat to both your gastrointestinal and neurologic health.

        Habitat: Coastal areas of the northern Atlantic Ocean, including North America, Europe, and the northern Palearctic. Found in intertidal shallow water along the shoreline attached to a number of solid objects. They prefer cool water, hard substrates such as gravel and shell beds, rocks, and submerged human-made structures with good water flow, but they are also able to withstand great extremes, including drought, excessive heat, and freezing temperatures. If blue mussels are left exposed to air when the tide goes out, they survive by passing air over their damp gills to breathe. They prefer areas of high salinity.
    """)
    st.caption("Info from: https://www.dec.ny.gov/animals/117470.html")

    st.subheader("Data:")
    animal_sighting_data()

def eastern_oyster():
    """Info for eastern oyster"""
    st.session_state['animal'] = 'Eastern Oyster'

    st.subheader("Eastern Oyster")
    st.image(img, use_column_width=True, clamp= True)

    st.subheader("Info:")
    st.markdown("""
        Eastern oysters are also known as "American Oysters", "Atlantic Oysters", and "American Cupped Oysters". They have thick, deeply cupped elongated shells that are bumpy and rough. They are a pale gray to white in color and can grow up to eight inches long. Oysters are reef building organisms which means they attach themselves to rocks, shells or other oysters and over time, the accumulation forms a reef. Juvenile oysters, called spat, also attach to these substrates.

        Like many other oysters, the eastern oyster makes pearls. Pearls are formed when a sand grain or other irritating particle gets stuck inside the oyster's shell. To get rid of this irritant the oyster covers the sand grain with a smooth substance called nacre; a form of calcium carbonate that is similar to the material of its own shell. After receiving several layers of nacre, the sand grain eventually becomes a pearl. Eastern oysters can live up to approximately 20 years.

        Habitat: East Coast of the United States from Canada to the Gulf of Mexico. They are surface-dwelling mollusks that thrive on reeds and inhabit intertidal and subtidal areas in water depths between eight and twenty-five feet. They can tolerate salinities ranging from 5 ppt to 30 ppt.
    """)
    st.caption("Info from: https://www.dec.ny.gov/animals/117470.html")

    st.subheader("Data:")
    animal_sighting_data()

def hard_clam():
    """Info for Hard Clam"""
    st.session_state['animal'] = 'Hard Clam'

    st.subheader("Hard Clam")
    st.image(img, use_column_width=True, clamp= True)

    st.subheader("Info:")
    st.markdown("""
        Hard clams are also known as "Chowder Clams", "Northern Quahogs" and "Round Clams". These clams have hard, thick shells that can grow to about four inches in length. The shell's color is pale brown with a distinctive purple stain on the interior. They have a muscular foot which they use to burrow deep into the sediment.

        Hard clams are a commercially important species that are harvested both by commercial fishermen (baymen) and recreational clammers. They have an average lifespan of four to eight years, however specimens as old as 40 years of age have been found. Hard clams are also given common names based on their size:

        Littlenecks: Smallest hard clams able to harvest, 1" thickness (vertically). Often served raw on the half-shell.

        Middlenecks/Topnecks: Average 2" across the shell (horizontally). Can be served raw, steamed, or grilled.

        Cherrystones: Approximately 2.5" across. Versatile use for raw, cooked, and baked.

        Chowders: Larger than 3" across. Best used chopped and cooked in soups or as fried clams.

        Habitat: East coast of the United States, ranging from the Gulf of St. Lawrence to the Gulf of Mexico. They are found in the sand and mud habitats of the intertidal and sheltered subtidal zones. The intertidal zone is the area of marine shoreline that is exposed to air at low tide and covered with seawater at high tide. The subtidal zone is the area of marine shoreline that is below the intertidal zone and is submerged most of the time, portions of this zone may be exposed briefly during extreme low tides around full and new moons. Hard clams can tolerate salinities ranging from 15 ppt to 35 ppt.
    """)
    st.caption("Info from: https://www.dec.ny.gov/animals/117470.html")

    st.subheader("Data:")
    animal_sighting_data()





st.title("Species Detection")

# Take Picture
picture = st.camera_input("Take a picture")
# or use file uploader
if picture is None:
    picture = st.file_uploader("Upload an image")
    st.caption("Unable to use the camera? Use the file uploader and select take photo.")

if picture is not None:
    # Read Image as PIL
    img = Image.open(picture)

    # Load Model
    model = torch.jit.load('./model/test_shellfish_model_scripted.pt')
    model.eval()

    ## Preprocess to tensor
    preprocess =  transforms.Compose([
        transforms.Resize(256),
        transforms.CenterCrop(224),
        transforms.ToTensor(),
        transforms.Normalize([0.485, 0.456, 0.406], [0.229, 0.224, 0.225])
    ])
    model_img = preprocess(img)
    
    # Generate prediction
    data = [model_img]
    prediction = model(data[0].unsqueeze(0))
    # Predicted class value using argmax
    preds = prediction.argmax(dim=1).item()

    st.success("Indentified!")
    st.write(f"The species is {preds}")

    # Display info to user
    st.header("So what did you detect?")
    if preds == 0:
        atlantic_bay_scallop()
    elif preds == 1:
        blue_mussel()
    elif preds == 2:
        eastern_oyster()
    elif preds == 3:
        hard_clam()
    else:
        st.write("Error")

#----------------------------------------------------------
#Form

if 'animal' in st.session_state:
    form = st.empty()
    with form.container():
        # Form
        with st.form(key='species_form'):

            st.header("Sighting")
            st.write(f"Animal Sighted: {st.session_state.animal}")
            
            st.header("Location")
            # Wall section input for where the shellfish was found.
            # I want to have like an animation of the selection process. So if 1 section 1 will light up
            st.write('<style>div.row-widget.stRadio > div{flex-direction:row;justify-content: center;} </style>', unsafe_allow_html=True)
            st.write('<style>div.st-bf{flex-direction:column;} div.st-ag{font-weight:bold;padding-left:2px;}</style>', unsafe_allow_html=True)
            wall_section = st.radio("Wall Section",("1","2","3"))

            # Submit button
            submit_button = st.form_submit_button(label='Submit')

    if submit_button == True:
        form.empty()

        date = datetime.now().strftime("%d/%m/%Y")
        time = datetime.now().strftime("%H:%M:%S")

        # Write in database
            # Code

        st.success(f"Submission Time: {date} {time}. Thank you for filling out the form! Hope you enjoyed the park!")
        st.balloons()
        



# Green detection using OpenCv
    # Save Image
    # save_img = img.save("img.jpg")

    # # Green
    # # # Read Image
    # img = cv.imread("img.jpg")
    # ## convert to hsv
    # hsv = cv.cvtColor(img, cv.COLOR_BGR2HSV)
    # ## mask of green (36,25,25) ~ (86, 255,255)
    # mask = cv.inRange(hsv, (36, 25, 25), (70, 255,255))
    # ## slice the green
    # imask = mask>0
    # green = np.zeros_like(img, np.uint8)
    # green[imask] = img[imask]
    # # ## save 
    # cv.imwrite("green.png", green)
    # st.image(green, use_column_width=True,clamp = True)

    #Write the data into database
    # body = [date, time, age, alge, shape, review]
    # wks.append_row(body, table_range="A1:G1")