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I have raster (with 5 bands) and shapfile in the same projection. I do this script for rastersize and do mask and clip raster or crop raster with mask but I need to have just clip raster without black area and without NONE VALUE or 0 value.

I use Python 3

import os
from osgeo import gdal
import numpy as np
import pandas as pd
import ogr
import rasterio as rio 
import fiona
import rasterio
import rasterio.mask

inDir = 'F:/python/Doy_2000/'
driver = ogr.GetDriverByName('ESRI Shapefile')
os.chdir(inDir)  

with fiona.open("F:/python/Doy_2000/poly2000.shp", "r") as shapefile:
    shapes = [feature["geometry"] for feature in shapefile]

with rasterio.open("F:/python/Doy_2000/raster1.tif") as src:
    out_image, out_transform = rasterio.mask.mask(src, shapes, crop=True)
    out_meta = src.meta.copy()

out_meta.update({"driver": "GTiff",
                 "height": out_image.shape[1],
                 "width": out_image.shape[2],
                 "transform": out_transform})

with rasterio.open("2000mask.tif", "w", **out_meta) as dest:
    dest.write(out_image)

result after script :

enter image description here

I need to edit my script but just delete or mask NONE value or 0 value.

second question :

when i do the same thing for other shapefile ( polygones very small like points): enter image description here the resultas give me all area black :

enter image description here

how i can do to calcul mask and clip raster with shapfiles ( polygones verry small) ?!

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