Polygonize every single pixel of a raster

Question

How can I get every pixel separated? When I calc unique values, if two pixels have the same value, it converts in one row in the final shape. I need every single pixel converted into one unique geometry.

Any ideas?

My code is:

def geojsonizer(ndvi_path, downloads_path, ndvi_date, UHC_name):
    entry_date = datetime.today().strftime('%Y%m%d')
    # Read input band with Rasterio
    with rasterio.open(ndvi_path) as raster_ndvi:
        crs = raster_ndvi.crs
        huso = str(crs).replace(':', '')
        src_band = raster_ndvi.read(1)
        # Keep track of unique pixel values in the input band
        unique_values = np.unique(src_band)
        # Polygonize with Rasterio. `shapes()` returns an iterable
        # of (geom, value) as tuples
        shapes = list(rasterio.features.shapes(src_band, transform=raster_ndvi.transform))
    
    geojson_schema = {
        'geometry': 'MultiPolygon',
        'properties': {'name': 'str', 'pixel_id': 'int', 'ndvi_value': 'float', 'ndvi_date': 'str',
                       'entry_date': 'str'}
    }
    with fiona.open(downloads_path + '\\' + UHC_name + '_' + huso + '_ndvi.geojson', 'w', driver='GeoJSON',
                    schema=geojson_schema, crs=crs) as geojson:
        for pixel_value in unique_values:
            if pixel_value != 999 and pixel_value != 0:
                polygons = [shape(geom) for geom, value in shapes
                            if value == pixel_value]
                multipolygon = MultiPolygon(polygons)
                pixel_centroid = (str(multipolygon.centroid).strip('POINT ()')).replace(" ", "")
                geojson.write({
                    'geometry': mapping(multipolygon),
                    'properties': {'name': 'nombre_finca',
                                   'pixel_id': pixel_centroid,
                                   'ndvi_value': float(pixel_value),
                                   'ndvi_date': str(ndvi_date),
                                   'entry_date': entry_date,
                                   }})

Answer 1

Having the size of the image and the number of pixels you should be able to create a grid in a loop (Substitute the hardcoded values of x/y min/max and width/height [number of pixels] for values read from your raster):

import numpy as np
from shapely.geometry import shape
import geopandas as gpd

xmin, ymin, xmax, ymax = -532000, -868000,  484000, 16000
width = 4000
height = 4000
rows = np.ceil((ymax - ymin) / height) + 1
cols = np.ceil((xmax - xmin) / width) + 1
# start grid cell envelope
x_min_corn = xmin
x_max_corn = xmin + width
y_max_corn = ymax
y_min_corn = ymax - height
# create grid cells
countcols = 0
grid_polygons = []
sp_id = 0
while countcols < cols:
    # reset envelope for rows
    y_max_ring = y_max_corn
    y_min_ring = y_min_corn
    countrows = 0

    while countrows < rows:
        polygon = {
            "type": "Polygon",
            "coordinates": (
                (
                    (x_min_corn, y_max_ring),
                    (x_max_corn, y_max_ring),
                    (x_max_corn, y_min_ring),
                    (x_min_corn, y_min_ring),
                    (x_min_corn, y_max_ring),
                ),
            ),
        }

        grid_polygons.append(shape(polygon))
        sp_id += 1
        # new envelope for next poly
        y_max_ring = y_max_ring - height
        y_min_ring = y_min_ring - height
        countrows += 1
    # new envelope for next poly
    x_min_corn = x_min_corn + width
    x_max_corn = x_max_corn + width

    countcols += 1

gdf = gpd.GeoDataFrame(geometry=grid_polygons)