reproject.py 23.5 KB
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# -*- coding: utf-8 -*-
__author__ = "Daniel Scheffler"


import numpy as np
import warnings
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import multiprocessing
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try:
    from osgeo import gdal
    from osgeo import gdalnumeric
except ImportError:
    import gdal
    import gdalnumeric
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# custom
import rasterio
from rasterio.warp import reproject as rio_reproject
from rasterio.warp import calculate_default_transform as rio_calc_transform
from rasterio.warp import Resampling

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from ..projection               import WKT2EPSG, isProjectedOrGeographic, prj_equal
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from ..coord_trafo              import pixelToLatLon
from ...io.raster.gdal          import get_GDAL_ds_inmem
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from ...processing.progress_mon import ProgressBar
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from ...compatibility.gdal      import get_gdal_func
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# dictionary to translate GDAL data types (strings) in corresponding numpy data types
dTypeDic_NumPy2GDAL = {'uint8'   : gdal.GDT_Byte,
                       'uint16'  : gdal.GDT_UInt16,
                       'int16'   : gdal.GDT_Int16,
                       'uint32'  : gdal.GDT_UInt32,
                       'int32'   : gdal.GDT_Int32,
                       'float32' : gdal.GDT_Float32,
                       'float64' : gdal.GDT_Float64
                       }


def warp_ndarray_OLD(ndarray, in_gt, in_prj, out_prj, out_gt=None, outRowsCols=None, outUL=None, out_res=None,
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                 out_extent=None, out_dtype=None, rsp_alg=0, in_nodata=None, out_nodata=None, outExtent_within=True):

    """Reproject / warp a numpy array with given geo information to target coordinate system.

    :param ndarray:             numpy.ndarray [rows,cols,bands]
    :param in_gt:               input gdal GeoTransform
    :param in_prj:              input projection as WKT string
    :param out_prj:             output projection as WKT string
    :param out_gt:              output gdal GeoTransform as float tuple in the source coordinate system (optional)
    :param outUL:               [X,Y] output upper left coordinates as floats in the source coordinate system
                                (requires outRowsCols)
    :param outRowsCols:         [rows, cols] (optional)
    :param out_res:             output resolution as tuple of floats (x,y) in the TARGET coordinate system
    :param out_extent:          [left, bottom, right, top] as floats in the source coordinate system
    :param out_dtype:           output data type as numpy data type
    :param rsp_alg:             Resampling method to use. One of the following (int, default is 0):
                                0 = nearest neighbour, 1 = bilinear, 2 = cubic, 3 = cubic spline, 4 = lanczos,
                                5 = average, 6 = mode
    :param in_nodata:           no data value of the input image
    :param out_nodata:          no data value of the output image
    :param outExtent_within:    Ensures that the output extent is within the input extent.
                                Otherwise an exception is raised.
    :return out_arr:            warped numpy array
    :return out_gt:             warped gdal GeoTransform
    :return out_prj:            warped projection as WKT string
    """
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    if not ndarray.flags['OWNDATA']:
        temp    = np.empty_like(ndarray)
        temp[:] = ndarray
        ndarray = temp  # deep copy: converts view to its own array in order to avoid wrong output

    with rasterio.env.Env():
        if outUL is not None:
            assert outRowsCols is not None, 'outRowsCols must be given if outUL is given.'
        outUL = [in_gt[0], in_gt[3]] if outUL is None else outUL

        inEPSG, outEPSG = [WKT2EPSG(prj) for prj in [in_prj, out_prj]]
        assert inEPSG,  'Could not derive input EPSG code.'
        assert outEPSG, 'Could not derive output EPSG code.'
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        assert in_nodata  is None or isinstance(in_nodata, (int, float)),\
            'Received invalid input nodata value: %s; type: %s.'  % (in_nodata,  type(in_nodata))
        assert out_nodata is None or isinstance(out_nodata,(int, float)),\
            'Received invalid output nodata value: %s; type: %s.' % (out_nodata, type(out_nodata))
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        src_crs = {'init': 'EPSG:%s' % inEPSG}
        dst_crs = {'init': 'EPSG:%s' % outEPSG}

        if len(ndarray.shape) == 3:
            # convert input array axis order to rasterio axis order
            ndarray = np.swapaxes(np.swapaxes(ndarray, 0, 2), 1, 2)
            bands, rows, cols = ndarray.shape
            rows, cols = outRowsCols if outRowsCols else (rows, cols)
        else:
            rows, cols = ndarray.shape if outRowsCols is None else outRowsCols

        # set dtypes ensuring at least int16 (int8 is not supported by rasterio)
        in_dtype  = ndarray.dtype
        out_dtype = ndarray.dtype if out_dtype is None else out_dtype
        out_dtype = np.int16 if str(out_dtype) == 'int8' else out_dtype
        ndarray   = ndarray.astype(np.int16) if str(in_dtype) == 'int8' else ndarray

        # get dst_transform
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        gt2bounds = lambda gt, r, c: [gt[0], gt[3] + r * gt[5], gt[0] + c * gt[1], gt[3]]  # left, bottom, right, top
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        if out_gt is None and out_extent is None:
            if outRowsCols:
                outUL       = [in_gt[0], in_gt[3]] if outUL is None else outUL
                ulRC2bounds = lambda ul, r, c: [ul[0], ul[1] + r * in_gt[5], ul[0] + c * in_gt[1], ul[1]]  # left, bottom, right, top
                left, bottom, right, top = ulRC2bounds(outUL, rows, cols)
            else:  # outRowsCols is None and outUL is None: use in_gt
                left, bottom, right, top = gt2bounds(in_gt, rows, cols)
                # ,im_xmax,im_ymin,im_ymax = corner_coord_to_minmax(get_corner_coordinates(self.ds_im2shift))
        elif out_extent:
            left, bottom, right, top = out_extent
        else:  # out_gt is given
            left, bottom, right, top = gt2bounds(in_gt, rows, cols)

        if outExtent_within:
            # input array is only a window of the actual input array
            assert left >= in_gt[0] and right <= (in_gt[0] + (cols + 1) * in_gt[1]) and \
                  bottom >= in_gt[3] + (rows + 1) * in_gt[5] and top <= in_gt[3], \
               "out_extent has to be completely within the input image bounds."

        if out_res is None:
            # get pixel resolution in target coord system
            prj_in_out = (isProjectedOrGeographic(in_prj), isProjectedOrGeographic(out_prj))
            assert None not in prj_in_out, 'prj_in_out contains None.'
            if prj_in_out[0] == prj_in_out[1]:
                out_res = (in_gt[1], abs(in_gt[5]))
            elif prj_in_out == ('geographic', 'projected'):
                raise NotImplementedError('Different projections are currently not supported.')
            else:  # ('projected','geographic')
                px_size_LatLon = np.array(pixelToLatLon([1, 1], geotransform=in_gt, projection=in_prj)) - \
                                 np.array(pixelToLatLon([0, 0], geotransform=in_gt, projection=in_prj))
                out_res = tuple(reversed(abs(px_size_LatLon)))
                print('OUT_RES NOCHMAL CHECKEN: ', out_res)

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        dict_rspInt_rspAlg = \
            {0: Resampling.nearest, 1: Resampling.bilinear, 2: Resampling.cubic,
             3: Resampling.cubic_spline, 4: Resampling.lanczos, 5: Resampling.average, 6: Resampling.mode}
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        var1=True
        if var1:
            src_transform = rasterio.transform.from_origin(in_gt[0], in_gt[3], in_gt[1], abs(in_gt[5]))
            print('calc_trafo_args')
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            for i in [src_crs, dst_crs, cols, rows, left, bottom, right, top, out_res]:
                print(i, '\n')
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            from ...io.raster.GeoArray import GeoArray
            left, right, bottom, top = GeoArray(ndarray, in_gt, in_prj).box.boundsMap
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            dst_transform, out_cols, out_rows = rio_calc_transform(
                src_crs, dst_crs, cols, rows, left, bottom, right, top, resolution=out_res)
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            out_arr = np.zeros((bands, out_rows, out_cols), out_dtype) \
                if len(ndarray.shape) == 3 else np.zeros((out_rows, out_cols), out_dtype)
            print(out_res)
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            for i in [src_transform, src_crs, dst_transform, dst_crs]:
                print(i,'\n')
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            rio_reproject(ndarray, out_arr, src_transform=src_transform, src_crs=src_crs, dst_transform=dst_transform,
                dst_crs=dst_crs, resampling=dict_rspInt_rspAlg[rsp_alg], src_nodata=in_nodata, dst_nodata=out_nodata)

            aff = list(dst_transform)
            out_gt = out_gt if out_gt else (aff[2], aff[0], aff[1], aff[5], aff[3], aff[4])
            # FIXME sometimes output dimensions are not exactly as requested (1px difference)
        else:
            dst_transform, out_cols, out_rows = rio_calc_transform(
                src_crs, dst_crs, cols, rows, left, bottom, right, top, resolution=out_res)

            # check if calculated output dimensions correspond to expected ones and correct them if neccessary
            rows_expected = int(round(abs(top - bottom) / out_res[1], 0))
            cols_expected = int(round(abs(right - left) / out_res[0], 0))

            #diff_rows_exp_real, diff_cols_exp_real = abs(out_rows - rows_expected), abs(out_cols - cols_expected)
            #if diff_rows_exp_real > 0.1 or diff_cols_exp_real > 0.1:
                #assert diff_rows_exp_real < 1.1 and diff_cols_exp_real < 1.1, 'warp_ndarray: ' \
                #                                                              'The output image size calculated by rasterio is too far away from the expected output image size.'
            #    out_rows, out_cols = rows_expected, cols_expected
                # fixes an issue where rio_calc_transform() does not return quadratic output image although input parameters
                # correspond to a quadratic image and inEPSG equals outEPSG

            aff = list(dst_transform)
            out_gt = out_gt if out_gt else (aff[2], aff[0], aff[1], aff[5], aff[3], aff[4])

            out_arr = np.zeros((bands, out_rows, out_cols), out_dtype) \
                if len(ndarray.shape) == 3 else np.zeros((out_rows, out_cols), out_dtype)

            with warnings.catch_warnings():
                warnings.simplefilter('ignore')  # FIXME supresses: FutureWarning: GDAL-style transforms are deprecated and will not be supported in Rasterio 1.0.
                try:
                    #print('INPUTS')
                    #print(ndarray.shape, ndarray.dtype, out_arr.shape, out_arr.dtype)
                    #print(in_gt)
                    #print(src_crs)
                    #print(out_gt)
                    #print(dst_crs)
                    #print(dict_rspInt_rspAlg[rsp_alg])
                    #print(in_nodata)
                    #print(out_nodata)
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                    for i in [in_gt, src_crs, out_gt, dst_crs]:
                        print(i, '\n')
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                    rio_reproject(ndarray, out_arr,
                                  src_transform=in_gt, src_crs=src_crs, dst_transform=out_gt, dst_crs=dst_crs,
                                  resampling=dict_rspInt_rspAlg[rsp_alg], src_nodata=in_nodata, dst_nodata=out_nodata)
                    from matplotlib import pyplot as plt
                    #print(out_arr.shape)
                    #plt.figure()
                    #plt.imshow(out_arr[:,:,1])
                except KeyError:
                    print(in_dtype, str(in_dtype))
                    print(ndarray.dtype)
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        # convert output array axis order to GMS axis order [rows,cols,bands]
        out_arr = out_arr if len(ndarray.shape) == 2 else np.swapaxes(np.swapaxes(out_arr, 0, 1), 1, 2)

        if outRowsCols:
            out_arr = out_arr[:outRowsCols[0], :outRowsCols[1]]

    return out_arr, out_gt, out_prj
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def warp_GeoArray(geoArr, **kwargs):
    ndarray = geoArr[:]
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    from ... import GeoArray
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    return GeoArray(*warp_ndarray(ndarray, geoArr.geotransform, geoArr.projection, **kwargs))


def warp_ndarray(ndarray, in_gt, in_prj, out_prj=None, out_dtype=None, out_gsd=(None, None),
                 out_bounds=None, out_bounds_prj=None, out_XYdims = (None,None),
                 rspAlg='near', in_nodata=None, out_nodata=None, in_alpha=False,
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                 out_alpha=False, targetAlignedPixels=False, gcpList=None, polynomialOrder=None, options=None,
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                 transformerOptions=None, warpOptions=None, CPUs=1, warpMemoryLimit=0, progress=True, q=False):
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    """

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    :param ndarray:             the numpy array to be warped
    :param in_gt:               input GDAL geotransform
    :param in_prj:              input GDAL projection (WKT string, 'EPSG:1234', <EPSG_int>)
    :param out_prj:             output GDAL projection (WKT string, 'EPSG:1234', <EPSG_int>)
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    :param out_dtype:           gdal.DataType
    :param out_gsd:
    :param out_bounds:          [xmin,ymin,xmax,ymax] set georeferenced extents of output file to be created,
                                e.g. [440720, 3750120, 441920, 3751320])
                                (in target SRS by default, or in the SRS specified with -te_srs)
    :param out_bounds_prj:
    :param out_XYdims:
    :param rspAlg:              <str> Resampling method to use. Available methods are:
                                near, bilinear, cubic, cubicspline, lanczos, average, mode, max, min, med, q1, q2
    :param in_nodata:
    :param out_nodata:
    :param in_alpha:            <bool> Force the last band of a source image to be considered as a source alpha band.
    :param out_alpha:           <bool> Create an output alpha band to identify nodata (unset/transparent) pixels
    :param targetAlignedPixels:   (GDAL >= 1.8.0) (target aligned pixels) align the coordinates of the extent
                                        of the output file to the values of the -tr, such that the aligned extent
                                        includes the minimum extent.
    :param gcpList:             <list> list of ground control points in the output coordinate system
                                to be used for warping, e.g. [gdal.GCP(mapX,mapY,mapZ,column,row),...]
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    :param polynomialOrder:     <int> order of polynomial GCP interpolation
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    :param options:             <str> additional GDAL options as string, e.g. '-nosrcalpha' or '-order'
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    :param transformerOptions:  <list> list of transformer options, e.g.  ['SRC_SRS=invalid']
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    :param warpOptions:         <list> list of warp options, e.g.  ['CUTLINE_ALL_TOUCHED=TRUE'],
                                find available options here: http://www.gdal.org/structGDALWarpOptions.html
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    :param CPUs:                <int> number of CPUs to use (default: None, which means 'all CPUs available')
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    :param warpMemoryLimit:     <int> size of working buffer in bytes (default: 0)
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    :param progress:            <bool> show progress bar (default: True)
    :param q:                   <bool> quiet mode (default: False)
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    :return:

    """
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    # TODO test if this function delivers the exact same output like console version, otherwise implment error_threshold=0.125
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    # how to implement:    https://svn.osgeo.org/gdal/trunk/autotest/utilities/test_gdalwarp_lib.py

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    # assertions
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    assert str(np.dtype(ndarray.dtype)) in dTypeDic_NumPy2GDAL, "Unknown target datatype '%s'." %ndarray.dtype
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    if rspAlg=='average':
        is_avail_rsp_average = int(gdal.VersionInfo()[0]) >= 2
        if not is_avail_rsp_average:
            warnings.warn("The GDAL version on this machine does not yet support the resampling algorithm 'average'. "
                          "'cubic' is used instead. To avoid this please update GDAL to a version above 2.0.0!")
            rspAlg='cubic'

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    get_SRS         = lambda prjArg: prjArg if isinstance(prjArg,str) and prjArg.startswith('EPSG:') else \
                                     'EPSG:%s'%prjArg if isinstance(prjArg,int)                      else \
                                     prjArg
    get_GDT         = lambda DT: dTypeDic_NumPy2GDAL[str(np.dtype(DT))]
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    # not yet implemented
    cutlineDSName = 'data/cutline.vrt' #'/vsimem/cutline.shp' TODO cutline from OGR datasource. => implement input shapefile or Geopandas dataframe
    cutlineLayer = 'cutline'
    cropToCutline = False
    cutlineSQL = 'SELECT * FROM cutline'
    cutlineWhere = '1 = 1'
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    rpc = [
        "HEIGHT_OFF=1466.05894327379",
        "HEIGHT_SCALE=144.837606185489",
        "LAT_OFF=38.9266809014185",
        "LAT_SCALE=-0.108324009570885",
        "LINE_DEN_COEFF=1 -0.000392404256440504 -0.0027925489381758 0.000501819414812054 0.00216726134806561 -0.00185617059201599 0.000183834173326118 -0.00290342803717354 -0.00207181007131322 -0.000900223247894285 -0.00132518281680544 0.00165598132063197 0.00681015244696305 0.000547865679631528 0.00516214646283021 0.00795287690785699 -0.000705040639059332 -0.00254360623317078 -0.000291154885056484 0.00070943440010757",
        "LINE_NUM_COEFF=-0.000951099635749339 1.41709976082781 -0.939591985038569 -0.00186609235173885 0.00196881101098923 0.00361741523740639 -0.00282449434932066 0.0115361898794214 -0.00276027843825304 9.37913944402154e-05 -0.00160950221565737 0.00754053609977256 0.00461831968713819 0.00274991122620312 0.000689605203796422 -0.0042482778732957 -0.000123966494595151 0.00307976709897974 -0.000563274426174409 0.00049981716767074",
        "LINE_OFF=2199.50159296339",
        "LINE_SCALE=2195.852519621",
        "LONG_OFF=76.0381768085136",
        "LONG_SCALE=0.130066683772651",
        "SAMP_DEN_COEFF=1 -0.000632078047521022 -0.000544107268758971 0.000172438016778527 -0.00206391734870399 -0.00204445747536872 -0.000715754551621987 -0.00195545265530244 -0.00168532972557267 -0.00114709980708329 -0.00699131177532728 0.0038551339822296 0.00283631282133365 -0.00436885468926666 -0.00381335885955994 0.0018742043611019 -0.0027263909314293 -0.00237054119407013 0.00246374716379501 -0.00121074576302219",
        "SAMP_NUM_COEFF=0.00249293151551852 -0.581492592442025 -1.00947448466175 0.00121597346320039 -0.00552825219917498 -0.00194683170765094 -0.00166012459012905 -0.00338315804553888 -0.00152062885009498 -0.000214562164393127 -0.00219914905535387 -0.000662800177832777 -0.00118644828432841 -0.00180061222825708 -0.00364756875260519 -0.00287273485650089 -0.000540077934728493 -0.00166800463003749 0.000201057249109451 -8.49620129025469e-05",
        "SAMP_OFF=3300.34602166792",
        "SAMP_SCALE=3297.51222987611"
    ]

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    """ Create a WarpOptions() object that can be passed to gdal.Warp()
        Keyword arguments are :
          options --- can be be an array of strings, a string or let empty and filled from other keywords.
          format --- output format ("GTiff", etc...)
          outputBounds --- output bounds as (minX, minY, maxX, maxY) in target SRS
          outputBoundsSRS --- SRS in which output bounds are expressed, in the case they are not expressed in dstSRS
          xRes, yRes --- output resolution in target SRS
          targetAlignedPixels --- whether to force output bounds to be multiple of output resolution
          width --- width of the output raster in pixel
          height --- height of the output raster in pixel
          srcSRS --- source SRS
          dstSRS --- output SRS
          srcAlpha --- whether to force the last band of the input dataset to be considered as an alpha band
          dstAlpha --- whether to force the creation of an output alpha band
          outputType --- output type (gdal.GDT_Byte, etc...)
          workingType --- working type (gdal.GDT_Byte, etc...)
          warpOptions --- list of warping options
          errorThreshold --- error threshold for approximation transformer (in pixels)
          warpMemoryLimit --- size of working buffer in bytes
          resampleAlg --- resampling mode
          creationOptions --- list of creation options
          srcNodata --- source nodata value(s)
          dstNodata --- output nodata value(s)
          multithread --- whether to multithread computation and I/O operations
          tps --- whether to use Thin Plate Spline GCP transformer
          rpc --- whether to use RPC transformer
          geoloc --- whether to use GeoLocation array transformer
          polynomialOrder --- order of polynomial GCP interpolation
          transformerOptions --- list of transformer options
          cutlineDSName --- cutline dataset name
          cutlineLayer --- cutline layer name
          cutlineWhere --- cutline WHERE clause
          cutlineSQL --- cutline SQL statement
          cutlineBlend --- cutline blend distance in pixels
          cropToCutline --- whether to use cutline extent for output bounds
          copyMetadata --- whether to copy source metadata
          metadataConflictValue --- metadata data conflict value
          setColorInterpretation --- whether to force color interpretation of input bands to output bands
          callback --- callback method
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          callback_data --- user data for callback  # value for last parameter of progress callback
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    """
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    # get input dataset (in-MEM)
    in_ds = get_GDAL_ds_inmem(ndarray, in_gt, in_prj)

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    # set RPCs
    #if rpcList:
    #    in_ds.SetMetadata(rpc, "RPC")
    #    transformerOptions = ['RPC_DEM=data/warp_52_dem.tif']

    if CPUs is None or CPUs>1:
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        gdal.SetConfigOption('GDAL_NUM_THREADS', str(CPUs if CPUs else multiprocessing.cpu_count()))
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    #gdal.SetConfigOption('GDAL_CACHEMAX', str(800))

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    # GDAL Translate if needed
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    #if gcpList:
     #   in_ds.SetGCPs(gcpList, in_ds.GetProjection())

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    if gcpList:
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        gdal_Translate = get_gdal_func('Translate')
        in_ds = gdal_Translate(
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            '', in_ds, format='MEM',
            outputSRS = get_SRS(out_prj),
            GCPs      = gcpList,
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            callback  = ProgressBar(prefix='Translating progress', timeout=None) if progress and not q else None
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            )
        # NOTE: options = ['SPARSE_OK=YES'] ## => what is that for?

    # GDAL Warp
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    gdal_Warp = get_gdal_func('Warp')
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    res_ds = gdal_Warp(
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        '', in_ds, format='MEM',
        dstSRS               = get_SRS(out_prj),
        outputType           = get_GDT(out_dtype) if out_dtype else get_GDT(ndarray.dtype),
        xRes                 = out_gsd[0],
        yRes                 = out_gsd[1],
        outputBounds         = out_bounds,
        outputBoundsSRS      = get_SRS(out_bounds_prj),
        width                = out_XYdims[0],
        height               = out_XYdims[1],
        resampleAlg          = rspAlg,
        srcNodata            = in_nodata,
        dstNodata            = out_nodata,
        srcAlpha             = in_alpha,
        dstAlpha             = out_alpha,
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        options              = options            if options            else [],
        warpOptions          = warpOptions        if warpOptions        else [],
        transformerOptions   = transformerOptions if transformerOptions else [],
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        targetAlignedPixels  = targetAlignedPixels,
        tps                  = True if gcpList else False,
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        polynomialOrder      = polynomialOrder,
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        warpMemoryLimit      = warpMemoryLimit,
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        callback             = ProgressBar(prefix='Warping progress    ', timeout=None) if progress and not q else None,
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        callback_data        = [0],
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        errorThreshold       = 0.125,  # this is needed to get exactly the same output like the console version of GDAL warp
        )

    gdal.SetConfigOption('GDAL_NUM_THREADS', None)
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    if res_ds is None:
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        raise Exception('Warping Error:  ' + gdal.GetLastErrorMsg())

    # get outputs
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    res_arr = gdalnumeric.DatasetReadAsArray(res_ds)
    if len(res_arr.shape) == 3:
        res_arr = np.swapaxes(np.swapaxes(res_arr, 0, 2), 0, 1)
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    res_gt  = res_ds.GetGeoTransform()
    res_prj = res_ds.GetProjection()
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    # cleanup
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    in_ds = res_ds = None
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    # test output
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    if out_prj and prj_equal(out_prj,4626):
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        assert -180 < res_gt[0] < 180 and -90 < res_gt[3] < 90, 'Testing of gdal_warp output failed.'

    return res_arr, res_gt, res_prj