Exemplo n.º 1
0
def fill_tile_band(tile_size, tile_coords, set_coords, ar_pred, tx, nodata):
    '''
    Fill an array of zeros of shape tile_size, located at tile_coords with an 
    offset array, ar_pred, located at set_coords
    '''
    # Calc offsets
    row_off, col_off = calc_offset_from_tile(tile_coords[['ul_x','ul_y']],
                                             set_coords[['ul_x','ul_y']],
                                             tx)
    # Get the offset indices of each array 
    tile_inds, set_inds = mosaic.get_offset_array_indices(
        tile_size, ar_pred.shape, (row_off, col_off))
    tile_row_u, tile_row_d, tile_col_l, tile_col_r = tile_inds
    set_row_u,  set_row_d,  set_col_l,  set_col_r  = set_inds
    
    # Fill just the part of the array that overlaps
    ar_tile = np.full(tile_size, np.nan)
    ar_pred = ar_pred.astype(float)
    ar_pred[ar_pred == nodata] = np.nan
    try:
        ar_tile[tile_row_u:tile_row_d, tile_col_l:tile_col_r] =\
        ar_pred[set_row_u:set_row_d, set_col_l:set_col_r]
    except Exception as e:
        print e
        print '\nProblem with offsets'
        print row_off, col_off, set_coords, tile_coords      

    return ar_tile
Exemplo n.º 2
0
def snap_array(ds_in,
               ds_snap,
               tx_in,
               tx_snap,
               in_nodata,
               out_nodata,
               mask_val=None):

    ar_in = ds_in.ReadAsArray()
    if mask_val is not None:
        ar_snap = ds_snap.ReadAsArray()
    in_shape = ar_in.shape
    out_shape = ds_snap.RasterYSize, ds_snap.RasterXSize

    offset = calc_offset((tx_snap[0], tx_snap[3]), tx_in)
    snap_inds, in_inds = get_offset_array_indices(out_shape, in_shape, offset)
    np_dtype = ar_in.dtype
    ar = np.full(out_shape, out_nodata, dtype=np_dtype)
    ar_in[ar_in == in_nodata] = out_nodata
    ar[snap_inds[0]:snap_inds[1],
       snap_inds[2]:snap_inds[3]] = ar_in[in_inds[0]:in_inds[1],
                                          in_inds[2]:in_inds[3]]

    if mask_val is not None:
        mask_val = int(mask_val)
        ar[ar_snap == mask_val] = out_nodata

    return ar
Exemplo n.º 3
0
def main(sample_txt, ref_raster, pred_raster, p_nodata, t_nodata, target_col, bins, out_txt, match=None, predict_col=None):
    
    p_nodata = int(p_nodata)
    t_nodata = int(t_nodata)
    
    ds_p = gdal.Open(pred_raster)
    ar_p = ds_p.ReadAsArray()
    
    ds_r = gdal.Open(ref_raster)
    ar_r = ds_r.ReadAsArray()
    
    r_xsize = ds_r.RasterXSize
    r_ysize = ds_r.RasterYSize
    p_xsize = ds_p.RasterXSize
    p_ysize = ds_p.RasterYSize
    tx_r = ds_r.GetGeoTransform()
    tx_p = ds_p.GetGeoTransform()
    # If two arrays are different sizes, make prediction array match reference
    if not r_xsize == p_xsize or r_ysize == p_ysize or tx_r != tx_p:
        warnings.warn('Prediction and reference rasters do not share the same extent. Snapping prediction raster to reference....')
        offset = mosaic.calc_offset((tx_r[0], tx_r[3]), tx_p)
        t_inds, p_inds = mosaic.get_offset_array_indices((r_ysize, r_xsize), (p_ysize, p_xsize), offset)
        ar_buf = np.full(ar_r.shape, p_nodata, dtype=ar_p.dtype)
        ar_buf[t_inds[0]:t_inds[1], t_inds[2]:t_inds[3]] = ar_p[p_inds[0]:p_inds[1], p_inds[2]:p_inds[3]]
        ar_p = ar_buf.copy()
        del ar_buf
        
    bins = parse_bins(bins)
    
    sample = pd.read_csv(sample_txt, sep='\t')
    if target_col in sample.columns:
        t_sample = sample[target_col]
    else:
        raise IndexError('target_col "%s" not in sample' % target_col)
    
    if match:
        t_sample, p_sample = get_samples(ar_p, ar_r, p_nodata, t_nodata, sample, match=match)
    elif predict_col:
        p_sample = sample[predict_col]
    else:
        p_sample = ar_p[sample.row, sample.col]
        t_sample = ar_r[sample.row, sample.col]
    
    rmse = area_weighted_rmse(ar_p, ar_r, p_sample, t_sample, bins, p_nodata, out_txt=out_txt)
    
    return rmse
Exemplo n.º 4
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def get_zone_inds(ar_size, zone_size, tx, feat):
    '''
    Return the array offset indices for pixels overlapping a feature from a 
    vector dataset. Array indices are returned as (upper_row, lower_row, left_col,_right col)
    to be used to index an array as [upper_row : lower_row, left_col : right_col]
    '''
    geom = feat.GetGeometryRef()
    x1, x2, y1, y2 = geom.GetEnvelope()
    
    # Get the feature ul x and y, and calculate the pixel offset
    ar_ulx, x_res, x_rot, ar_uly, y_rot, y_res = tx
    x_sign = x_res/abs(x_res)
    y_sign = y_res/abs(y_res)
    f_ulx = min([x0/x_sign for x0 in [x1, x2]])/x_sign
    f_uly = min([y0/y_sign for y0 in [y1, y2]])/y_sign
    offset = stem.calc_offset((ar_ulx, ar_uly), (f_ulx, f_uly), tx)

    # Get the inds for the overlapping portions of each array
    a_inds, m_inds = mosaic.get_offset_array_indices(ar_size, zone_size, offset)
    
    return a_inds, m_inds
Exemplo n.º 5
0
def main(params,
         ar_p=None,
         out_txt=None,
         inventory_txt=None,
         target_col=None,
         match=False,
         file_stamp=None):
    #p_path, t_path, bins, sample_txt, p_nodata, t_nodata, out_dir, inventory_txt=None

    # Read params and make variables from text
    inputs = read_params(params)
    for i in inputs:
        exec("{0} = str({1})").format(i, inputs[i])

    # Check that variables were specified in params
    try:
        bins = parse_bins(bins)
        p_nodata = int(p_nodata)
        t_nodata = int(t_nodata)
        str_check = sample_txt  #, target_col
    except NameError as e:
        print ''
        missing_var = str(e).split("'")[1]
        msg = "Variable '%s' not specified in param file:\n%s" % (missing_var,
                                                                  params)
        raise NameError(msg)

    #if out_dir_: # then out_dir came from predict_stem call
    #    out_dir = out_dir_
    #out_txt = os.path.join(out_dir, 'confusion.txt')
    if out_txt:
        out_dir = os.path.dirname(out_txt)
        if not os.path.exists(out_dir):
            os.mkdir(out_dir)
        shutil.copy2(params, out_dir)

    # If p_path was specified, this call of the function is coming from outside
    #   predict_stem.py. Otherwise, ar_p should be given.
    if 'p_path' in locals():
        print 'Reading in the prediction raster:%s\n' % p_path
        ds_p = gdal.Open(p_path)
        ar_p = ds_p.ReadAsArray()

    ds_t = gdal.Open(t_path)
    band = ds_t.GetRasterBand(1)
    ar_t = band.ReadAsArray()
    #ar_t=ar_t.GetRasterBand(1)
    #print('read in the truth raster')
    t_xsize = ds_t.RasterXSize
    #print('t_xsize is: ', t_xsize)
    t_ysize = ds_t.RasterYSize
    #print('tYsize is: ', t_ysize)
    p_xsize = ds_p.RasterXSize
    #print('p_xsize is: ', p_xsize)
    p_ysize = ds_p.RasterYSize
    #print('p_ysize is: ', p_ysize)
    tx_t = ds_t.GetGeoTransform()
    tx_p = ds_p.GetGeoTransform()
    # If two arrays are different sizes, make prediction array match reference
    if not t_xsize == p_xsize or t_ysize == p_ysize or tx_t != tx_p:
        print('entered if statement')
        warnings.warn(
            'Prediction and reference rasters do not share the same extent. Snapping prediction raster to reference....'
        )
        offset = mosaic.calc_offset((tx_t[0], tx_t[3]), tx_p)
        #print(offset)
        t_inds, p_inds = mosaic.get_offset_array_indices(
            (t_ysize, t_xsize), (p_ysize, p_xsize), offset)
        print(t_inds, p_inds)
        ar_buf = np.full(ar_t.shape, p_nodata, dtype=ar_p.dtype)
        print ar_buf.shape
        ar_buf[t_inds[0]:t_inds[1],
               t_inds[2]:t_inds[3]] = ar_p[p_inds[0]:p_inds[1],
                                           p_inds[2]:p_inds[3]]
        ar_p = ar_buf.copy()
        del ar_buf
    mask = (ar_p == p_nodata) | (ar_t == t_nodata)  #'''

    samples = pd.read_csv(sample_txt, sep='\t', index_col='obs_id')
    print samples
    df_adj, df_smp = confusion_matrix_by_area(ar_p,
                                              ar_t,
                                              samples,
                                              p_nodata,
                                              t_nodata,
                                              mask=mask,
                                              bins=bins,
                                              out_txt=out_txt,
                                              target_col=target_col,
                                              match=match)

    ar_p = None
    ar_t = None
    mask = None

    accuracy = df_adj.ix['producer', 'user']
    kappa = df_adj.ix['producer', 'kappa']
    if inventory_txt and file_stamp:
        df_inv = pd.read_csv(inventory_txt, sep='\t', index_col='stamp')
        if file_stamp in df_inv.index and 'vote' in os.path.basename(out_dir):
            cols = ['vote_accuracy', 'vote_kappa']
            df_inv.ix[file_stamp, cols] = accuracy, kappa
            df_inv.to_csv(inventory_txt, sep='\t')
            print 'Vote scores written to inventory_txt: ', inventory_txt

        if file_stamp in df_inv.index and 'mean' in os.path.basename(out_dir):
            cols = ['mean_accuracy', 'mean_kappa']
            df_inv.ix[file_stamp, cols] = accuracy, kappa
            df_inv.to_csv(inventory_txt, sep='\t')

    return df_smp
Exemplo n.º 6
0
def main(in_raster,
         snap_raster,
         in_nodata,
         out_nodata,
         out_path=None,
         mask_val=None,
         overwrite=False):

    t0 = time.time()
    in_nodata = int(in_nodata)
    out_nodata = int(out_nodata)

    print '\nOpening datasets... '
    t1 = time.time()
    ds_in = gdal.Open(in_raster)
    ar_in = ds_in.ReadAsArray()
    tx_in = ds_in.GetGeoTransform()
    #driver = ds_in.GetDriver()
    ds_in = None

    ds_snap = gdal.Open(snap_raster)
    ar_snap = ds_snap.ReadAsArray()
    tx_snap = ds_snap.GetGeoTransform()
    prj = ds_snap.GetProjection()
    ds_snap = None
    print '%.1f seconds\n' % (time.time() - t1)

    print 'Snapping input raster...'
    t1 = time.time()
    offset = calc_offset((tx_snap[0], tx_snap[3]), tx_in)
    snap_inds, in_inds = get_offset_array_indices(ar_snap.shape, ar_in.shape,
                                                  offset)
    np_dtype = ar_in.dtype
    ar = np.full(ar_snap.shape, out_nodata, dtype=np_dtype)
    ar_in[ar_in == in_nodata] = out_nodata
    ar[snap_inds[0]:snap_inds[1],
       snap_inds[2]:snap_inds[3]] = ar_in[in_inds[0]:in_inds[1],
                                          in_inds[2]:in_inds[3]]

    if mask_val:
        mask_val = int(mask_val)
        ar[ar_snap == mask_val] = out_nodata

    print '%.1f seconds\n' % (time.time() - t1)

    if out_path:
        if ar.max() <= 255 and ar.min() >= 0:
            gdal_dtype = gdal.GDT_Byte
        else:
            gdal_dtype = gdal.GDT_Int16

        if os.path.exists(out_path) and not overwrite:
            sys.exit('out_path already exists')
        driver = get_gdal_driver(out_path)
        array_to_raster(ar, tx_snap, prj, driver, out_path, gdal_dtype,
                        out_nodata)

        # Write metadata
        desc = ('Input raster %s snapped to the extent of %s.') % (in_raster,
                                                                   snap_raster)
        if mask_val:
            desc += ' Data were masked from snap raster with value %s.' % mask_val
        createMetadata(sys.argv, out_path, description=desc)
    else:
        return ar

    print '\nTotal time to snap raster: %.1f seconds\n' % (time.time() - t0)
Exemplo n.º 7
0
def snap_by_tile(ds_in,
                 ds_snap,
                 tiles,
                 tx_snap,
                 tx_in,
                 in_nodata,
                 out_nodata,
                 out_dir,
                 mask_val=None):

    prj = ds_in.GetProjection()
    driver = gdal.GetDriverByName('gtiff')

    if mask_val is not None:
        mask_val = int(mask_val)

    row_off, col_off = calc_offset((tx_snap[0], tx_snap[3]), tx_in)
    in_size = ds_in.RasterYSize, ds_in.RasterXSize

    n_tiles = float(len(tiles))
    t1 = time.time()
    msg = '\rProccessing tile %d/%d (%.1f%%) || %.1f/~%.1f minutes'

    template = os.path.join(out_dir, 'tile_%s.pkl')
    mins = []
    maxs = []
    for i, (tile_id, coords) in enumerate(tiles.iterrows()):

        tile_off = row_off - coords.ul_r, col_off - coords.ul_c
        tile_size = coords.lr_r - coords.ul_r, coords.lr_c - coords.ul_c
        tile_inds, in_inds = get_offset_array_indices(tile_size, in_size,
                                                      tile_off)

        in_ulr, in_lrr, in_ulc, in_lrc = in_inds
        in_xsize = in_lrc - in_ulc
        in_ysize = in_lrr - in_ulr
        if in_xsize <= 0 or in_ysize <= 0:  # They don't overlap
            continue
        ar_in = ds_in.ReadAsArray(in_ulc, in_ulr, in_xsize, in_ysize)
        if np.all(ar_in == in_nodata):
            continue
        ar_out = np.full(tile_size, out_nodata, dtype=ar_in.dtype)
        ar_out[tile_inds[0]:tile_inds[1], tile_inds[2]:tile_inds[3]] = ar_in
        ar_out[ar_out == in_nodata] = out_nodata
        if mask_val is not None:
            mask = ds_snap.ReadAsArray(coords.ul_c, coords.ul_r, tile_size[1],
                                       tile_size[0]) == mask_val
            ar_out[mask] = out_nodata

        out_path = template % tile_id
        with open(out_path, 'wb') as f:
            pickle.dump(ar_out, f, protocol=-1)
        mins.append(ar_out.min())
        maxs.append(ar_out.max())
        tiles.loc[tile_id, 'file'] = out_path

        cum_time = (time.time() - t1) / 60.
        est_time = cum_time / (i + 1) * (n_tiles - i)  # estimate remaing time
        sys.stdout.write(msg % (i + 1, n_tiles,
                                (i + 1) / n_tiles * 100, cum_time, est_time))
        sys.stdout.flush()
        '''ulx, xres, _, uly, _, yres = tx_snap
        tx = coords.ul_c * xres + ulx, xres, 0, coords.ul_r * yres + uly, 0, yres
        array_to_raster(ar_out, tx, prj, driver, '/home/server/pi/homes/shooper/delete/tile_%s.tif' % tile_id, gdal.GDT_Int16, out_nodata)'''

    dtype = get_min_numpy_dtype(np.array(mins + maxs))

    return dtype
Exemplo n.º 8
0
def main(model_dir, n_tiles, **kwargs):

    t0 = time.time()

    n_tiles = [int(n) for n in n_tiles.split(',')]
    if not os.path.isdir(model_dir):
        message = 'model directory given does not exist or is not a directory: ', model_dir
        raise IOError(message)

    model = os.path.basename(model_dir)
    dt_dir = os.path.join(model_dir, 'decisiontree_models')
    set_txt = os.path.join(dt_dir, '%s_support_sets.txt' % model)
    df_sets = pd.read_csv(set_txt, sep='\t', index_col='set_id')

    pred_param_path = glob(os.path.join(model_dir,
                                        'predict_stem_*params.txt'))[0]
    predict_params, df_var = stem.read_params(pred_param_path)
    train_param_path = glob(os.path.join(model_dir,
                                         'train_stem_*params.txt'))[0]
    train_params, _ = stem.read_params(train_param_path)
    df_var.sort_index(inplace=True)

    nodata = int(predict_params['nodata'].replace('"', ''))
    if len(kwargs) == 0:
        var_ids = df_sets.max_importance.unique()
        var_names = df_var.ix[var_ids].index
        variables = zip(var_ids, var_names)
    else:
        variables = [(variable_id, variable_name)
                     for variable_name, variable_id in kwargs]

    mask_path = os.path.join(model_dir, '%s_vote.bsq' % model)
    if not os.path.exists(mask_path):
        mask_path = mask_path.replace('.bsq', '.tif')
    mask_ds = gdal.Open(mask_path)
    mask_tx = mask_ds.GetGeoTransform()
    xsize = mask_ds.RasterXSize
    ysize = mask_ds.RasterYSize
    prj = mask_ds.GetProjection()
    df_tiles, df_tiles_rc, tile_size = stem.get_tiles(n_tiles, xsize, ysize,
                                                      mask_tx)
    total_tiles = len(df_tiles)
    df_tiles['tile'] = df_tiles.index

    # Find the tiles that have only nodata values
    t1 = time.time()
    print '\nFinding empty tiles...'
    mask = mask_ds.ReadAsArray() == nodata
    empty_tiles = stem.find_empty_tiles(df_tiles, ~mask, mask_tx)
    mask_ds = None
    print '%s empty tiles found of %s total tiles\n%.1f minutes\n' %\
    (len(empty_tiles), total_tiles, (time.time() - t1)/60)
    # Select only tiles that are not empty
    df_tiles = df_tiles.select(lambda x: x not in empty_tiles)
    total_tiles = len(df_tiles)

    #some_set = df_sets.iloc[0]
    support_size = [
        int(s)
        for s in train_params['support_size'].replace('"', '').split(',')
    ]
    set_size = [int(abs(s / mask_tx[1])) for s in support_size]

    out_dir = os.path.join(model_dir, 'importance_maps')
    if not os.path.exists(out_dir):
        os.mkdir(out_dir)

    print variables
    for vi, (v_id, v_name) in enumerate(variables):

        t1 = time.time()
        print 'Making map for %s: %s of %s variables\n' % (v_name, vi + 1,
                                                           len(variables))

        ar = np.full((ysize, xsize), nodata, dtype=np.uint8)

        for i, (t_ind, t_row) in enumerate(df_tiles.iterrows()):
            t2 = time.time()
            print 'Aggregating for %s of %s tiles' % (i + 1, total_tiles)

            # Calculate the size of this tile in case it's at the edge where the
            #   tile size will be slightly different
            this_size = abs(t_row.lr_y - t_row.ul_y), abs(t_row.lr_x -
                                                          t_row.ul_x)
            df_these_sets = stem.get_overlapping_sets(df_sets, t_row,
                                                      this_size, support_size)

            rc = df_tiles_rc.ix[t_ind]
            this_size = rc.lr_r - rc.ul_r, rc.lr_c - rc.ul_c
            n_sets = len(df_these_sets)

            # Load overlapping predictions from disk and read them as arrays
            tile_ul = t_row[['ul_x', 'ul_y']]

            print n_sets, ' Overlapping sets'
            importance_bands = []

            importance_values = []
            for s_ind, s_row in df_these_sets.iterrows():

                # Calculate offset and array/tile indices
                offset = stem.calc_offset(tile_ul, (s_row.ul_x, s_row.ul_y),
                                          mask_tx)
                #if abs(offset[0]) > this_size[0] or abs(offset[1] > this_size[1]):

                tile_inds, a_inds = mosaic.get_offset_array_indices(
                    tile_size, set_size, offset)

                # Get feature with maximum importance and fill tile with that val
                try:
                    with open(s_row.dt_file, 'rb') as f:
                        dt_model = pickle.load(f)
                    importance_value = int(
                        dt_model.feature_importances_[v_id] * 100)
                    importance_values.append(importance_value)
                    #filled = np.full((nrows, ncols), importance_value, dtype=np.uint8)
                    #import_band = stem.fill_tile_band(this_size, filled, tile_inds, nodata)
                    import_band = np.full(this_size, np.nan, dtype=np.float16)
                    import_band[tile_inds[0]:tile_inds[1],
                                tile_inds[2]:tile_inds[3]] = importance_value
                    importance_bands.append(import_band)
                except Exception as e:
                    print e
                    continue  #'''

            print 'Average importance for this tile: %.1f' % np.mean(
                importance_values)
            #Aggregate
            importance_stack = np.dstack(importance_bands)
            importance_tile = np.nanmean(importance_stack, axis=2)
            tile_mask = mask[rc.ul_r:rc.lr_r,
                             rc.ul_c:rc.lr_c] | np.isnan(importance_tile)
            importance_tile[tile_mask] = nodata
            ar[rc.ul_r:rc.lr_r,
               rc.ul_c:rc.lr_c] = np.round(importance_tile).astype(np.uint8)
            print 'Aggregation time for this tile: %.1f minutes\n' % (
                (time.time() - t2) / 60)
            '''temp_dir = os.path.join(out_dir, 'delete')
            if not os.path.isdir(temp_dir):
                os.mkdir(temp_dir)
            t_tx = tile_ul[0], 30, 0, tile_ul[1], 0, -30
            array_to_raster(np.round(importance_tile).astype(np.uint8), t_tx, prj, gdal.GetDriverByName('gtiff'), os.path.join(temp_dir, 'delete_%s.tif' % t_ind), gdal.GDT_Byte, 255, True)'''
        out_path = os.path.join(out_dir,
                                '%s_importance_%s.tif' % (model, v_name))
        try:
            array_to_raster(ar, mask_tx, prj, gdal.GetDriverByName('gtiff'),
                            out_path, gdal.GDT_Byte, nodata)
        except Exception as e:
            print e
            import pdb
            pdb.set_trace()
        print 'Time for this variable: %.1f minutes\n' % (
            (time.time() - t1) / 60)

    print '\nTotal time for %s variables: %.1f hours\n' % (len(variables), (
        (time.time() - t0) / 3600))
Exemplo n.º 9
0
def main(region_path,
         tile_path,
         reference_path,
         out_dir,
         id_field='region_id',
         ref_basename='nlcd'):

    df = attributes_to_df(region_path)
    tile_info = attributes_to_df(tile_path)
    tile_info['ul_x'] = tile_info.xmin
    tile_info['lr_x'] = tile_info.xmax
    tile_info['ul_y'] = tile_info.ymax
    tile_info['lr_y'] = tile_info.ymin

    _, vector_ext = os.path.splitext(region_path)
    region_ids = df[id_field].unique()
    n_regions = len(region_ids)

    region_ds = ogr.Open(region_path)
    region_lyr = region_ds.GetLayer()

    for i, r_id in enumerate(region_ids):
        print 'Making region dir for %s (%s of %s)' % (r_id, i, n_regions)
        df_r = df[df.region_id == r_id]
        id_str = ('0' + str(r_id))[-2:]

        fid = df_r.index[0]
        region_feature = region_lyr.GetFeature(fid)
        xmin, xmax, ymin, ymax = region_feature.GetGeometryRef().GetEnvelope()
        region_feature.Destroy()
        df_r['ul_x'] = xmin
        df_r['lr_x'] = xmax
        df_r['ul_y'] = ymax
        df_r['lr_y'] = ymin
        clip_coords = df_r.loc[fid, ['ul_x', 'lr_x', 'ul_y', 'lr_y']]

        region_dir = os.path.join(out_dir, 'region_%s' % id_str)
        if not os.path.exists(region_dir):
            os.mkdir(region_dir)

        # Make a shapefile of the tiles
        out_vector = os.path.join(region_dir,
                                  'tile_{0}{1}'.format(id_str, vector_ext))
        if not os.path.exists(out_vector):
            ''' switch to selection by min/max of coords '''
            region_tiles = tile_info[tile_info[id_field] == r_id]
            coords_to_shp(region_tiles, region_path, out_vector)

        # Make a map of reference NLCD
        ds = gdal.Open(out_vector.replace(vector_ext, '.tif'))
        mask = ds.ReadAsArray() == 255
        ds = None
        nlcd_year = re.search(
            '\d\d\d\d',
            reference_path).group()  # finds the first one (potentially buggy)
        out_ref_map = os.path.join(
            region_dir, '%s_%s_%s.tif' % (ref_basename, nlcd_year, id_str))
        if not False:  #os.path.exists(out_ref_map):
            ref_ds = gdal.Open(reference_path)
            ref_tx = ref_ds.GetGeoTransform()
            ref_shape = ref_ds.RasterYSize, ref_ds.RasterXSize

            col_off = (ref_tx[0] - clip_coords.ul_x) / ref_tx[1]
            row_off = (ref_tx[3] - clip_coords.ul_y) / ref_tx[5]
            n_cols = abs((clip_coords.ul_x - clip_coords.lr_x) / ref_tx[1])
            n_rows = abs((clip_coords.ul_y - clip_coords.lr_y) / ref_tx[1])

            ar_inds, ref_inds = get_offset_array_indices(
                (n_rows, n_cols), ref_shape, (row_off, col_off))
            ref_n_cols = ref_inds[1] - ref_inds[0]
            ref_n_rows = ref_inds[3] - ref_inds[2]

            ar_ref = ref_ds.ReadAsArray(ref_inds[2], ref_inds[0], ref_n_cols,
                                        ref_n_rows)
            ar = np.full((n_rows, n_cols), 255)
            ar[ar_inds[0]:ar_inds[1], ar_inds[2]:ar_inds[3]] = ar_ref
            ar[mask] = 255

            tx = clip_coords.ul_x, 30, 0, clip_coords.ul_y, 0, -30
            prj = ref_ds.GetProjection()
            driver = gdal.GetDriverByName('gtiff')
            array_to_raster(ar, tx, prj, driver, out_ref_map, nodata=255)

        # Make a clipped raster of the tiles
        out_raster = out_vector.replace(vector_ext, '.tif')
        if not os.path.exists(out_raster):
            tiles = ogr.Open(tile_path)
            tile_lyr = tiles.GetLayer()
            tx = clip_coords.ul_x, 30, 0, clip_coords.ul_y, 0, -30
            tile_array, _ = kernel_from_shp(tile_lyr,
                                            clip_coords,
                                            tx,
                                            255,
                                            val_field='name')
            tile_array[ar == 255] = 255
            driver = gdal.GetDriverByName('gtiff')
            prj = tile_lyr.GetSpatialRef().ExportToWkt()
            array_to_raster(tile_array,
                            tx,
                            prj,
                            driver,
                            out_raster,
                            nodata=255)
            tiles.Destroy()