with fiona.open("C:/.../poly.shp", "r") as shapefile:
    shapes = [feature["geometry"] for feature in shapefile]

with rasterio.open("D:/.../MODIS_EVI_2006.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("mask2006.tif", "w", **out_meta) as dest:
    dest.write(out_image)

from osgeo import gdal
from osgeo import ogr
from osgeo import gdalconst

ndsm = 'D:/../MODIS_EVI_2000.tif'
shp = 'C:/Doy2000/Pivos/1996poly.shp'
data = gdal.Open(ndsm, gdalconst.GA_ReadOnly)
geo_transform = data.GetGeoTransform()
#source_layer = data.GetLayer()
x_min = geo_transform[0]
y_max = geo_transform[3]
x_max = x_min + geo_transform[1] * data.RasterXSize
y_min = y_max + geo_transform[3] * data.RasterYSize
x_res = data.RasterXSize
y_res = data.RasterYSize
mb_v = ogr.Open(shp)
mb_l = mb_v.GetLayer()
pixel_width = geo_transform[1]
output = 'C:/Doy2000/Pivos/my2000.tif'
target_ds = gdal.GetDriverByName('GTiff').Create(output, x_res, y_res, 1, gdal.GDT_Byte)
target_ds.SetGeoTransform((x_min, pixel_width, 0, y_min, 0, pixel_width))
band = target_ds.GetRasterBand(1)
NoData_value = -999999
band.SetNoDataValue(NoData_value)
band.FlushCache()
gdal.RasterizeLayer(target_ds, [1], mb_l, options=["ATTRIBUTE=hedgerow"])

target_ds = None