def obj_to_rst(inArray, outRst, template, noData=None, geotrans=None):
"""
Send Array to Raster
API Available:
* gdal;
"""
gisApi = 'gdal'
if gisApi == 'gdal':
from osgeo import gdal, osr, gdal_array
from gasp.gt.prop.ff import drv_name
from gasp.gt.prop.rst import compress_option
if type(template).__name__ == 'Dataset':
img_template = template
else:
img_template = gdal.Open(template)
geo_transform = img_template.GetGeoTransform() if not geotrans else \
geotrans
rows, cols = inArray.shape
drv_n = drv_name(outRst)
driver = gdal.GetDriverByName(drv_n)
c_opt = compress_option(drv_n)
if c_opt:
out = driver.Create(outRst,
cols,
rows,
1,
gdal_array.NumericTypeCodeToGDALTypeCode(
inArray.dtype),
options=[c_opt])
else:
out = driver.Create(
outRst, cols, rows, 1,
gdal_array.NumericTypeCodeToGDALTypeCode(inArray.dtype))
out.SetGeoTransform(geo_transform)
outBand = out.GetRasterBand(1)
if noData:
outBand.SetNoDataValue(noData)
outBand.WriteArray(inArray)
proj = osr.SpatialReference(wkt=img_template.GetProjection())
if proj:
out.SetProjection(img_template.GetProjection())
outBand.FlushCache()
else:
raise ValueError('The api {} is not available'.format(gisApi))
return outRst
def obj_to_rst(inArray, outRst, template, noData=None, geotrans=None):
"""
Send Array to Raster
"""
from osgeo import gdal, osr, gdal_array
from glass.g.prop import drv_name
from glass.g.prop.rst import compress_option
if type(template).__name__ == 'Dataset':
img_template = template
else:
img_template = gdal.Open(template)
geo_transform = img_template.GetGeoTransform() if not geotrans else \
geotrans
rows, cols = inArray.shape
drv_n = drv_name(outRst)
driver = gdal.GetDriverByName(drv_n)
c_opt = compress_option(drv_n)
if c_opt:
out = driver.Create(outRst,
cols,
rows,
1,
gdal_array.NumericTypeCodeToGDALTypeCode(
inArray.dtype),
options=[c_opt])
else:
out = driver.Create(
outRst, cols, rows, 1,
gdal_array.NumericTypeCodeToGDALTypeCode(inArray.dtype))
out.SetGeoTransform(geo_transform)
outBand = out.GetRasterBand(1)
if noData or noData == 0:
outBand.SetNoDataValue(noData)
outBand.WriteArray(inArray)
proj = osr.SpatialReference(wkt=img_template.GetProjection())
if proj:
out.SetProjection(img_template.GetProjection())
outBand.FlushCache()
return outRst
def open(self, file=None, dtype=None):
"""
Open a local file handle for reading and assignment
:param file:
:return: None
"""
# args[0]/file=
if file is None:
raise IndexError("invalid file= argument provided")
# grab raster meta information from GeoRasters
try:
self.ndv, self.x_cell_size, self.y_cell_size, self.geot, self.projection, self.dtype = \
get_geo_info(file)
except Exception:
raise AttributeError("problem processing file input -- is this",
"a raster file?")
# args[1]/dtype=
if dtype is not None:
# override our shadow'd value from GeoRasters if
# something was specified by the user
self.dtype = dtype
# re-cast our datatype as a numpy type, if needed
if type(self.dtype) == str:
self.dtype = NUMPY_TYPES[self.dtype.lower()]
if self.ndv is None:
self.ndv = _DEFAULT_NA_VALUE
# low-level call to gdal with explicit type specification
# that will store in memory or as a disc cache, depending
# on the state of our _using_disc_caching property
if self._using_disc_caching is not None:
# create a cache file
self.array = np.memmap(self._using_disc_caching,
dtype=dtype,
mode='w+',
shape=(_x_size, _y_size))
# load file contents into the cache
self.array[:] = gdalnumeric.LoadFile(
filename=self.filename,
buf_type=gdal_array.NumericTypeCodeToGDALTypeCode(
self.dtype))[:]
# by default, load the whole file into memory
else:
self.array = gdalnumeric.LoadFile(
filename=self.filename,
buf_type=gdal_array.NumericTypeCodeToGDALTypeCode(self.dtype))
# make sure we honor our no data value
self.array = np.ma.masked_array(self.array,
mask=self.array == self.ndv,
fill_value=self.ndv)
def stretch(src, dst, stretch, bands, ndv, minmax, pct, _format, dtype, co,
verbose):
# Read input image
try:
ds = gdal.Open(src, gdal.GA_ReadOnly)
except:
click.echo("Could not open source dataset {0}".format(src))
raise
driver = gdal.GetDriverByName(str(_format))
# If no output dtype selected, default to input image dtype
if not dtype:
dtype = gdal_array.GDALTypeCodeToNumericTypeCode(
ds.GetRasterBand(1).DataType)
dtype = np.dtype(dtype)
gdal_dtype = gdal_array.NumericTypeCodeToGDALTypeCode(dtype)
if not bands:
nbands = ds.RasterCount
bands = range(1, nbands + 1)
else:
nbands = len(bands)
# Create output
if _format.lower() in COPY_FORMATS:
if nbands not in (1, 3, 4):
raise click.BadParameter(
'JPEG/PNG images must have 1, 3, or 4 bands')
mem_driver = gdal.GetDriverByName('MEM')
out_ds = mem_driver.Create('', ds.RasterXSize, ds.RasterYSize, nbands,
gdal_dtype)
else:
out_ds = driver.Create(dst, ds.RasterXSize, ds.RasterYSize, nbands,
gdal_dtype)
for idx, (b, _minmax) in enumerate(zip_longest(bands, minmax)):
kwargs = dict(ndv=ndv, minmax=_minmax, percent=pct)
in_band = ds.GetRasterBand(b)
arr = in_band.ReadAsArray()
arr, out_ndv = _STRETCH_FUNCS[stretch](arr, **kwargs)
out_band = out_ds.GetRasterBand(idx + 1)
out_band.WriteArray(arr)
out_band.SetDescription(in_band.GetDescription())
out_band.SetNoDataValue(out_ndv)
out_ds.SetMetadata(ds.GetMetadata())
out_ds.SetProjection(ds.GetProjection())
out_ds.SetGeoTransform(ds.GetGeoTransform())
if _format.lower() in COPY_FORMATS:
_out_ds = driver.CreateCopy(dst, out_ds, 0, co)
_out_ds = None
ds = None
out_ds = None
if verbose:
click.echo('Complete!')
def write_geotiff(out_file, in_arr, geotran, srs_wkt):
"""
in_arr must be in channels, rows, cols
"""
driver = gdal.GetDriverByName('GTiff')
if in_arr.dtype == np.uint64 or in_arr.dtype == np.int64:
in_arr = in_arr.astype(float)
type_code = gdal_array.NumericTypeCodeToGDALTypeCode(in_arr.dtype) # get the numpy array data type
if len(in_arr.shape) == 3: # if the shape is (bands, rows, columns)
out = driver.Create(out_file, in_arr.shape[2], in_arr.shape[1], in_arr.shape[0], type_code)
out.SetGeoTransform(geotran)
for b in range(in_arr.shape[0]):
outband = out.GetRasterBand(b+1)
outband.WriteArray(in_arr[b])
outband.FlushCache()
elif len(in_arr.shape) == 4:
nbands = np.prod([n for n in in_arr.shape[:-2]])
out = driver.Create(out_file, in_arr.shape[-1], in_arr.shape[-2], int(nbands), type_code)
out.SetGeoTransform(geotran)
b = 1
for b1 in range(in_arr.shape[0]):
for b2 in range(in_arr.shape[1]):
outband = out.GetRasterBand(b)
outband.WriteArray(in_arr[b1,b2,:,:])
outband.FlushCache()
b+=1
else:
out = driver.Create(out_file, in_arr.shape[1], in_arr.shape[0], 1, type_code)
out.SetGeoTransform(geotran) # the origin is the upper left of the input shapefile
outband = out.GetRasterBand(1)
outband.WriteArray(in_arr)
outband.FlushCache()
out.SetProjection(srs_wkt)
def test_datatypes(self):
datatypes = [
np.uint8, np.int8, np.uint16, np.int16, np.uint32, np.int32,
np.float32, np.float64
]
npix_x = 100
npix_y = 80
nbands = 1
output_fname = "/tmp/test_geotiff.tif"
geot = [0, 1, 0, 0, 0, -1]
for datatype in datatypes:
image_data = image_utils.create_uniform_image_data(npix_x,
npix_y,
nbands,
dtype=datatype)
gtiff_image = ImageFactory.geotiff.from_numpy_array(
image_data, geot, crs_defs.PROJ_4326)
gtiff_image.write_to_disk(output_fname)
gtiff_image_from_file = ImageFactory.geotiff.from_file(
output_fname)
gdal_dtype = gdal_array.NumericTypeCodeToGDALTypeCode(datatype)
assert gtiff_image.get_metadata().get_gdal_datatype(
) == gtiff_image_from_file.get_metadata().get_gdal_datatype(
) == gdal_dtype
print("datatype tests passed")
def NumPyArrayToRaster(nparr, proj, geot, nodata_value, out_raster_path, dtype=None):
gdal.AllRegister()
np_dt = nparr.dtype
if dtype == None:
dtype = gdal_array.NumericTypeCodeToGDALTypeCode(np_dt)
print( "saving")
# Check if working with multiband raster
if len(nparr.shape) == 3:
n_bands = nparr.shape[0]
for x in range(0, n_bands):
driver = gdal.GetDriverByName('GTIFF')
outDs = driver.Create(out_raster_path, nparr.shape[2], nparr.shape[1], n_bands, dtype,
['COMPRESS=LZW', 'TILED=YES', 'BLOCKXSIZE=128', 'BLOCKYSIZE=128'])
outDs.GetRasterBand(x + 1).WriteArray(nparr[x])
outDs.GetRasterBand(x + 1).SetNoDataValue(nodata_value)
outDs.GetRasterBand(x + 1).FlushCache()
outDs.SetProjection(proj)
outDs.SetGeoTransform(geot)
outDs = None
else:
driver = gdal.GetDriverByName('GTIFF')
outDs = driver.Create(out_raster_path, nparr.shape[1], nparr.shape[0], 1, dtype,
['COMPRESS=LZW', 'TILED=YES', 'BLOCKXSIZE=128', 'BLOCKYSIZE=128'])
outDs.GetRasterBand(1).WriteArray(nparr)
outDs.GetRasterBand(1).SetNoDataValue(nodata_value)
outDs.GetRasterBand(1).FlushCache()
outDs.SetProjection(proj)
outDs.SetGeoTransform(geot)
outDs = None
def create_dataset(geometry, cellsize, fillvalue, dtype, path):
""" The big sparse target dateset"""
# properties
a, b, c, d = cellsize[0], 0.0, 0.0, -cellsize[1]
x1, x2, y1, y2 = geometry.GetEnvelope()
p, q = a * (x1 // a), d * (y2 // d)
width = -int((p - x2) // a)
height = -int((q - y1) // d)
geo_transform = p, a, b, q, c, d
projection = geometry.GetSpatialReference().ExportToWkt()
# data type from store, no data value max of that type
data_type = gdal_array.NumericTypeCodeToGDALTypeCode(dtype)
no_data_value = fillvalue
# create
options = [
'TILED=YES', 'BIGTIFF=YES', 'SPARSE_OK=TRUE', 'COMPRESS=DEFLATE'
]
dataset = DRIVER_GDAL_GTIFF.Create(
path,
width,
height,
1,
data_type,
options,
)
dataset.SetProjection(projection)
dataset.SetGeoTransform(geo_transform)
dataset.GetRasterBand(1).SetNoDataValue(no_data_value)
return dataset
def _create_geotiff(filePath, binary, ripDic, metadataDic):
x = int(ripDic["FT_DATASET_ROWS"])
y = int(ripDic["FT_DATASET_COLUMNS"])
# thirdVal's value in the 'Affine GeoTransform' relationship is multiplied by a coefficient of 0, so we always expect it to be zero. Same with fifthVal
# In case this ever changes, we set them here rather than using magic numbers
thirdVal = 0
fifthVal = 0
upperLeft = ripDic["FT_DATASET_GRID_UPPER_LEFT_XY"]
yMax = float(ripDic["FT_DATASET_GEOG_NORTH_BOUND_LATITUDE"])
yMin = float(ripDic["FT_DATASET_GEOG_SOUTH_BOUND_LATITUDE"])
xMin = float(ripDic["FT_DATASET_GEOG_WEST_BOUND_LONGITUDE"])
xMax = float(ripDic["FT_DATASET_GEOG_EAST_BOUND_LONGITUDE"])
xRes = (xMax - xMin) / float(x)
yRes = (yMax - yMin) / float(y)
numberBands = 1
# EASEGRID Global
EPSG = 3410
# create geoTransform in accordance with relationship described at https://gdal.org/user/raster_data_model.html#affine-geotransform
geoTransform = (xMin, xRes, thirdVal, yMax, fifthVal, -yRes)
gdalType = gdal_array.NumericTypeCodeToGDALTypeCode(binary.dtype)
geoTiff = gdal.GetDriverByName('GTiff').Create(filePath, y, x, numberBands,
gdalType)
geoTiff.SetGeoTransform(geoTransform)
srs = osr.SpatialReference()
srs.ImportFromEPSG(EPSG)
geoTiff.SetProjection(srs.ExportToWkt())
geoTiff.GetRasterBand(1).WriteArray(binary)
geoTiff.FlushCache()
return
def create_geotiff(suffix, Array, NDV, xsize, ysize, GeoT, Projection):
'''
Creates new GeoTiff from array
'''
DataType = gdal_array.NumericTypeCodeToGDALTypeCode(Array.dtype)
if type(DataType) != np.int:
if DataType.startswith('gdal.GDT_') == False:
DataType = eval('gdal.GDT_' + DataType)
NewFileName = suffix + '.tif'
zsize = Array.shape[0]
# create a driver
driver = gdal.GetDriverByName('GTiff')
# Set nans to the original No Data Value
Array[np.isnan(Array)] = NDV
# Set up the dataset with zsize bands
DataSet = driver.Create(NewFileName, xsize, ysize, zsize, DataType)
DataSet.SetGeoTransform(GeoT)
DataSet.SetProjection(Projection.ExportToWkt())
# Write each slice of the array along the zsize
for i in xrange(0, zsize):
DataSet.GetRasterBand(i + 1).WriteArray(Array[i])
DataSet.GetRasterBand(i + 1).SetNoDataValue(NDV)
DataSet.FlushCache()
return NewFileName
def array_to_raster(array, tx, prj, driver, out_path, dtype=None, nodata=None, silent=False):
# From intersectMask.py
'''
Save a numpy array as a new raster
'''
if not silent: print 'Saving raster...'
rows, cols = array.shape
# Save new raster
if not dtype:
np_dtype = get_min_numpy_dtype(array)
array = array.astype(np_dtype)
dtype = gdal_array.NumericTypeCodeToGDALTypeCode(np_dtype)
if driver.ShortName == 'GTiff':
out_ds = driver.Create(out_path, cols, rows, 1, dtype, ['TILED=YES'])
else:
out_ds = driver.Create(out_path, cols, rows, 1, dtype)
if not out_ds:
import pdb; pdb.set_trace()
raise IOError('\nCould not create ' + out_path)
# Write the data
band = out_ds.GetRasterBand(1)
band.WriteArray(array)
# Flush data to disk
band.FlushCache()
if nodata != None: band.SetNoDataValue(nodata)
# Georeference the image and set the projection
out_ds.SetGeoTransform(tx)
out_ds.SetProjection(prj)
if not silent: print 'Raster written to:\n', out_path
def array2geotiff(array, outfile_name, no_data_value, xsize, ysize,
originX, originY, pixelWidth, pixelHeight,
compression='LZW'):
"""
This function writes a numpy array into a GeoTIFF-file.
If compression is not set to anything else, the file is compressed with LZW.
It is based on the gdal-package.
"""
# the array has to be flipped upside down if originY is at the bottom-left (equal to pixelHeight > 0)
if pixelHeight > 0:
array = np.flipud(array)
# create raster
DataType = gdal_array.NumericTypeCodeToGDALTypeCode(array.dtype)
driver = gdal.GetDriverByName('GTiff')
if compression == None:
compression = str(compression)
compression = ['COMPRESS=' + compression]
out_raster = driver.Create(outfile_name + '.tif', xsize, ysize, 1, DataType, options=compression)
out_raster.SetGeoTransform((originX, pixelWidth, 0, originY, 0, pixelHeight))
out_raster_SRS = osr.SpatialReference()
out_raster_SRS.ImportFromEPSG(4326)
out_raster.SetProjection(out_raster_SRS.ExportToWkt())
out_raster.GetRasterBand(1).WriteArray(array)
out_raster.GetRasterBand(1).SetNoDataValue(no_data_value)
def array2geotiff_rastercopy(array, outfile_name, raster,
compression='LZW'):
"""
This function writes a numpy array into a GeoTIFF-file.
Properties are copied from the blueprint raster provided.
If compression is not set to anything else, the file is compressed with LZW.
It is based on the gdal-package.
"""
# create raster
DataType = gdal_array.NumericTypeCodeToGDALTypeCode(array.dtype)
driver = gdal.GetDriverByName('GTiff')
if compression == None:
compression = str(compression)
compression = ['COMPRESS=' + compression]
out_raster = driver.Create(outfile_name + '.tif', raster.RasterXSize, raster.RasterYSize, 1, DataType, options=compression)
out_raster.SetGeoTransform(raster.GetGeoTransform())
out_raster_SRS = osr.SpatialReference()
out_raster_SRS.ImportFromEPSG(4326)
out_raster.SetProjection(out_raster_SRS.ExportToWkt())
out_raster.GetRasterBand(1).WriteArray(array)
out_raster.GetRasterBand(1).SetNoDataValue(raster.GetRasterBand(1).GetNoDataValue())
def to_gdal_dataset(outpath, array):
driver = gdal.GetDriverByName("GTiff")
dtype = gdal_array.NumericTypeCodeToGDALTypeCode(array.dtype)
length, width = array.shape
dset = driver.Create(outpath, xsize=width, ysize=length, bands=1,
eType=dtype)
dset.GetRasterBand(1).WriteArray(array)
def dtype_np2gdal(dtype_np):
# TODO: Write docstring.
if dtype_np == np.bool:
promote_dtype = np.uint8
elif dtype_np == np.int8:
promote_dtype = np.int16
elif dtype_np == np.float16:
promote_dtype = np.float32
else:
promote_dtype = None
if promote_dtype is not None:
warn(
"NumPy array data type ({}) does not have equivalent GDAL data type and is not "
"supported, but can be safely promoted to {}".format(
dtype_np,
promote_dtype(1).dtype))
dtype_np = promote_dtype
dtype_gdal = gdal_array.NumericTypeCodeToGDALTypeCode(dtype_np)
if dtype_gdal is None:
raise InvalidArgumentError(
"NumPy array data type ({}) does not have equivalent "
"GDAL data type and is not supported".format(dtype_np))
return dtype_gdal, promote_dtype
def write_pred_chips(output_path, base_raster, pred_struct, chip_key='predict', ref_shp=None, output_format='GTiff'):
driver = gdal.GetDriverByName(output_format)
base_ds = gdal.Open(base_raster)
x_start, pixel_width, _, y_start, _, pixel_height = base_ds.GetGeoTransform()
x_size = base_ds.RasterXSize
y_size = base_ds.RasterYSize
srs = osr.SpatialReference()
srs.ImportFromWkt(base_ds.GetProjectionRef())
num_bands = pred_struct[chip_key][0].shape[-1]
data_type = gdal_array.NumericTypeCodeToGDALTypeCode(pred_struct[chip_key][0].dtype)
out_ds = driver.Create(output_path, x_size, y_size, num_bands, data_type)
out_ds.SetGeoTransform((x_start, pixel_width, 0, y_start, 0, pixel_height))
out_ds.SetProjection(srs.ExportToWkt())
for i in range(1, num_bands + 1):
out_band = out_ds.GetRasterBand(i)
for idx in range(0, len(pred_struct[chip_key])):
chip = pred_struct[chip_key][idx]
chip_band = chip[:, :, i - 1]
coord = pred_struct['coords'][idx]
x_start = coord['upper_row'] + round(pred_struct['overlap'][0] / 2)
y_start = coord['left_col'] + round(pred_struct['overlap'][1] / 2)
out_band.WriteArray(chip_band, y_start, x_start)
out_band.FlushCache()
out_ds = None
iutils.clip_img_by_network_output(output_path, pred_struct['overlap'])
if ref_shp is not None:
iutils.clip_by_aggregated_polygons(output_path, ref_shp, output_path, no_data=0)
def save_data(self):
"""
Saves data into a local GeoTiff file
"""
driver = gdal.GetDriverByName('GTiff')
driver_options = [
"COMPRESS=LZW", "BIGTIFF=YES", "PREDICTOR=1", "TILED=YES",
"BLOCKXSIZE=256", "BLOCKYSIZE=256", "INTERLEAVE=BAND"
]
# Get GDAL datatype from NumPy datatype
dtype = gdal_array.NumericTypeCodeToGDALTypeCode(self.array.dtype)
# Create destination dataset
if len(self.array.shape) == 3:
# 3D array
bands, rows, cols = self.array.shape
else:
# 2D array
bands = 1
rows, cols = self.array.shape
dst_ds = driver.Create(self.output_filename, cols, rows, bands, dtype,
driver_options)
# Set cartographic projection
dst_ds.SetProjection(self.projection)
dst_ds.SetGeoTransform(self.geotransform)
# Write bands
for band in range(bands):
dst_ds.GetRasterBand(band + 1).WriteArray(self.array[band])
# Flush to disk
dst_ds = None
def writeGTiff(dstImage, outputPath, projection, coordinates, dtype = None):
"""
@brief Writes a GeoTiff file created from an existing coordinate-system
@Note Coordinates: [Top-Left X, W-E Resolution, 0, Top Left Y, 0, N-S Resolution]
"""
driver = gdal.GetDriverByName('GTiff')
#Add dimension for a single band-image
if(dstImage.ndim is 2):
dstImage = dstImage[..., np.newaxis]
#Set output dtype if not specified
if(dtype == None):
dtype = gdal_array.NumericTypeCodeToGDALTypeCode(dstImage.dtype)
dataset = driver.Create(outputPath, dstImage.shape[1], dstImage.shape[0] , dstImage.shape[2], dtype)
if(dataset == None):
raise OSError ("GDAL Could not create {0}".format(outputPath))
if(not coordinates or len(coordinates) != 6):
raise ValueError("Geotransform empty or unknown: {0}".format(coordinates))
dataset.SetGeoTransform(coordinates)
if(not projection):
raise ValueError("Projection empty or unknown: {0}".format(projection))
dataset.SetProjection(projection)
for index in range(dstImage.shape[2]):
dataset.GetRasterBand(index+1).WriteArray(dstImage[:,:,index])
dataset.FlushCache() # Write to disk.
dataset = None
driver = None
return 0
def geotiff(outDir,outName,resolution, fill_value,ImageContainer, array):
result_data_nn=array
outputName = os.path.normpath(os.path.join(outDir, '{}_2100.tif'.format(outName))) # Generate output filename
print(outputName)
nRow, nCol = result_data_nn.shape # Define rows/cols from array size
dataType = gdal_array.NumericTypeCodeToGDALTypeCode(result_data_nn.dtype) #result_data_nn.dtype # Define output data type or np.int16 for smaller files
if dataType==3:
fill_value=32767
driver = gdal.GetDriverByName('GTiff')
outFile = driver.Create(outputName, nCol, nRow, 1, dataType) # Specify parameters of the GeoTIFF
band = outFile.GetRasterBand(1) # Get band 1
band.WriteArray(result_data_nn) # Write data array to band 1
band.FlushCache
# Export data
band.SetNoDataValue(fill_value)
uul=ImageContainer.geo_def.upper_left_extent
# Set fill value
geoInfo = (uul[0], resolution, 0, uul[1], 0, -resolution) # Define geotransform parameters
outFile.SetGeoTransform(geoInfo)
srs = osgeo.osr.SpatialReference()
srs.ImportFromEPSG(2100) # Set Geotransform
outFile.SetProjection(srs.ExportToWkt()) # Set projection
outFile = None
def gdal_ds_from_array(arr):
"""
Returns an in-memory GDAL dataset that is a proxy to the given array
http://www.gdal.org/frmt_mem.html
"""
# Ensure 3D
arr = arr.reshape(arr.shape[0], arr.shape[1], -1)
assert arr.flags.c_contiguous
# http://stackoverflow.com/questions/11264838/how-to-get-the-memory-address-of-a-numpy-array-for-c
pointer, read_only_flag = arr.__array_interface__['data']
gdal_dtype = gdal_array.NumericTypeCodeToGDALTypeCode(arr.dtype)
print "arr dtype : ", arr.dtype, " => gdal dtype : ", \
gdal.GetDataTypeName(gdal_dtype)
ds = gdal.Open("MEM:::" + ",".join([
"DATAPOINTER=%d" % pointer,
"DATATYPE=%d" % gdal_dtype,
"LINES=%d" % arr.shape[0],
"PIXELS=%d" % arr.shape[1],
"BANDS=%d" % arr.shape[2],
"LINEOFFSET=%d" % arr.strides[0],
"PIXELOFFSET=%d" % arr.strides[1],
"BANDOFFSET=%d" % arr.strides[2]
]))
assert ds is not None, "Failed to create in-memory dataset"
# Kind of ugly hack to keep a reference on arr to avoid garbage collection
ds._arr = arr
return ds
def create_raster_dataset(data, coords, projection=None, nodata=-9999):
""" Create In-Memory Raster Dataset
Parameters
----------
data : :class:`numpy:numpy.ndarray`
Array of shape (rows, cols) or (bands, rows, cols) containing
the data values.
coords : :class:`numpy:numpy.ndarray`
Array of shape (nrows, ncols, 2) containing pixel center coordinates
or
Array of shape (nrows+1, ncols+1, 2) containing pixel edge coordinates
projection : osr object
Spatial reference system of the used coordinates, defaults to None.
nodata : int
Value of NODATA
Returns
-------
dataset : gdal.Dataset
In-Memory raster dataset
Note
----
The origin of the provided data and coordinates is UPPER LEFT.
"""
# align data
data = data.copy()
if data.ndim == 2:
data = data[np.newaxis, ...]
bands, rows, cols = data.shape
# create In-Memory Raster with correct dtype
mem_drv = gdal.GetDriverByName('MEM')
gdal_type = gdal_array.NumericTypeCodeToGDALTypeCode(data.dtype)
dataset = mem_drv.Create('', cols, rows, bands, gdal_type)
# initialize geotransform
x_ps, y_ps = coords[1, 1] - coords[0, 0]
if data.shape[-2:] == coords.shape[0:2]:
upper_corner_x = coords[0, 0, 0] - x_ps / 2
upper_corner_y = coords[0, 0, 1] - y_ps / 2
else:
upper_corner_x = coords[0, 0, 0]
upper_corner_y = coords[0, 0, 1]
geotran = [upper_corner_x, x_ps, 0, upper_corner_y, 0, y_ps]
dataset.SetGeoTransform(geotran)
if projection:
dataset.SetProjection(projection.ExportToWkt())
# set np.nan to nodata
dataset.GetRasterBand(1).SetNoDataValue(nodata)
for i, band in enumerate(data, start=1):
dataset.GetRasterBand(i).WriteArray(band)
return dataset
def create_dataset(array,
geo_transform=None,
projection=None,
no_data_value=None):
"""
Create and return a gdal dataset.
:param array: A numpy array.
:param geo_transform: 6-tuple of floats
:param projection: wkt projection string
:param no_data_value: integer or float
This is the fastest way to get a gdal dataset from a numpy array, but
keep a reference to the array around, or a segfault will occur. Also,
don't forget to call FlushCache() on the dataset after any operation
that affects the array.
"""
# prepare dataset name pointing to array
datapointer = array.ctypes.data
bands, lines, pixels = array.shape
datatypecode = gdal_array.NumericTypeCodeToGDALTypeCode(array.dtype.type)
datatype = gdal.GetDataTypeName(datatypecode)
bandoffset, lineoffset, pixeloffset = array.strides
# if projection is wrong there will be a segfault in RasterizeLayer
projection = osr.GetUserInputAsWKT(str(projection))
dataset_name_template = ("MEM:::"
"DATAPOINTER={datapointer},"
"PIXELS={pixels},"
"LINES={lines},"
"BANDS={bands},"
"DATATYPE={datatype},"
"PIXELOFFSET={pixeloffset},"
"LINEOFFSET={lineoffset},"
"BANDOFFSET={bandoffset}")
dataset_name = dataset_name_template.format(
datapointer=datapointer,
pixels=pixels,
lines=lines,
bands=bands,
datatype=datatype,
pixeloffset=pixeloffset,
lineoffset=lineoffset,
bandoffset=bandoffset,
)
# access the array memory as gdal dataset
dataset = gdal.Open(dataset_name, gdal.GA_Update)
# set additional properties from kwargs
if geo_transform is not None:
dataset.SetGeoTransform(geo_transform)
if projection is not None:
dataset.SetProjection(projection)
if no_data_value is not None:
for i in range(len(array)):
dataset.GetRasterBand(i + 1).SetNoDataValue(no_data_value)
return dataset
def SavePart(self, data, outOffsetYX, cOpts=None):
if self._Properties is None:
raise ValueError(
"File properties must be set first using SetProperties(RasterProps)"
)
rProps = self._Properties
if outOffsetYX is None:
outOffset = (0, 0)
dataShape = data.shape
currentShape = (rProps.height, rProps.width)
if ((dataShape[0] + outOffsetYX[0]) > currentShape[0]) or (
(dataShape[1] + outOffsetYX[1]) > currentShape[1]):
raise ValueError(
"data + offset are larger than the specified image size")
if dataShape[0] == rProps.height and dataShape[1] == rProps.width:
isFull = True
else:
isFull = False
if self._Exists:
ds = gdal.Open(self._filePath, gdal.GA_Update)
else:
outDir = os.path.dirname(self._filePath)
if not os.path.exists(outDir):
os.makedirs(outDir)
incomingType = gdal_array.NumericTypeCodeToGDALTypeCode(data.dtype)
if incomingType > rProps.datatype:
Warning(
"Array has higher type than configured file output, values may be truncated"
)
outDrv = gdal.GetDriverByName('GTiff')
if cOpts is None:
cOpts = [
"TILED=YES", "SPARSE_OK=FALSE", "BIGTIFF=YES",
"COMPRESS=LZW", "PREDICTOR=2"
]
if isFull:
# seem to get corruption when writing subsets of files that seems to occur more when using multithreaded
# writers, so use a single thread unless we are writing whole file
cOpts.append("NUM_THREADS=ALL_CPUS")
ds = outDrv.Create(self._filePath, rProps.width, rProps.height, 1,
rProps.datatype, cOpts)
if rProps.gt is not None:
ds.SetGeoTransform(rProps.gt)
if rProps.proj is not None:
ds.SetProjection(rProps.proj)
if rProps.ndv is not None:
outBand = ds.GetRasterBand(1)
outBand.SetNoDataValue(rProps.ndv)
self._Exists = True
outBand = ds.GetRasterBand(1)
outBand.WriteArray(data, outOffsetYX[1], outOffsetYX[0])
outBand.FlushCache()
ds = None
def array2geotiff(band_array, dst_filename, ref, out_datatype=None):
"""
Wrapper to GDAL to write an array to disk in GeoTiff format.
Args:
band_array: array that will be written to disk
dst_filename: full path to the output GeoTiff
ref: reference image with defined geotransform and SRS or a tuple of the form (geotransform, SRS_wkt)
out_datatype: GDAL datatype for the output, if None the function tries to figure out the corresponding
type automatically
Returns: full path to the GeoTiff on disk.
"""
# DEBUG
# band_array = band_corrected_array
# dst_filename = dst_filename
# ref = (out_gt, prj)
# if the input array is a masked array this will set the masked values to zero
np.ma.set_fill_value(band_array, 0)
# figure out the output datatype according to the type of the input array
if not out_datatype:
out_datatype = gdal_array.NumericTypeCodeToGDALTypeCode(band_array.dtype)
# from tuple
if isinstance(ref, tuple):
geotrans = ref[0]
proj_info = ref[1]
cols = band_array.shape[1]
rows = band_array.shape[0]
# or provided reference image
else:
ref_image = gdal.Open(ref)
geotrans = ref_image.GetGeoTransform()
proj_info = ref_image.GetProjection()
cols = round(ref_image.RasterXSize)
rows = round(ref_image.RasterYSize)
driver = gdal.GetDriverByName('GTiff')
driver.Create(dst_filename, cols, rows, 1, gdal.GDT_Byte)
out_raster = driver.Create(dst_filename, cols, rows, 1, eType=out_datatype)
out_raster.SetGeoTransform(geotrans)
out_raster.SetProjection(proj_info)
outband = out_raster.GetRasterBand(1)
if hasattr(band_array, 'mask'):
outband.WriteArray(band_array.filled())
else:
outband.WriteArray(band_array)
outband.FlushCache()
out_raster = None
ref_image = None
return dst_filename
def gdal_write(drv_type, img, dst, projection, coordinates, **kwargs):
"""
General GDal Write function.
Writes array `img` to `dst`.
:param drv_type: The Driver type. E.g. "GTiff" or "MEM"
:type drv_type: str
:param img: The :class:`numpy.ndarray`
:param dst: The destination path
:param projection: A Gdal projection
:type projection: str
:param coordinates: A list of floats for the geotransform. See the description in :func:`write_geotiff`
:type coordinates: List of float
:keyword dtype: The desired gdal dtype
:keyword nodata: Assign a nodata value
:keyword options: Config options as a list of str, such as ["COMPRESS=DEFLATE"]
:return: Writes array to `dst` and returns the dataset.
:rtype: :class:`gdal.Dataset`
"""
dtype = kwargs.get("dtype", None)
nodata = kwargs.get("nodata", None)
options = kwargs.get("options", [])
driver = gdal.GetDriverByName(drv_type)
# Add dimension for a single band-image
if img.ndim == 2:
img = img[..., np.newaxis]
# Set output dtype if not specified. GDAL cannot write GTiff as binary files, so convert to uint8:
if img.dtype == np.bool:
dtype = gdal_array.NumericTypeCodeToGDALTypeCode(np.uint8)
if img.dtype == np.int64:
dtype = gdal_array.NumericTypeCodeToGDALTypeCode(np.int32)
if not dtype:
dtype = gdal_array.NumericTypeCodeToGDALTypeCode(img.dtype)
img_h, img_w, n_bands = img.shape
mem = driver.Create(dst, img_w, img_h, n_bands, dtype, options)
mem.SetGeoTransform(coordinates)
mem.SetProjection(projection)
for bandIdx in range(n_bands):
band = img[:, :, bandIdx]
raster_band = mem.GetRasterBand(bandIdx + 1)
raster_band.WriteArray(band)
if nodata:
raster_band.SetNoDataValue(nodata)
mem.FlushCache()
return mem
def create_geotiff(suffix, Array, NDV, xsize, ysize, GeoT, Projection, nc_data,
filename):
'''
从数组中创建新的tiff图像
Create a new tiff image from the array
'''
DataType = gdal_array.NumericTypeCodeToGDALTypeCode(Array.dtype) ###
if type(DataType) != np.int:
if DataType.startswith('gdal.GDT_') == False:
DataType = eval('gdal.GDT_' + DataType)
zsize = Array.shape[0]
#create a driver
driver = gdal.GetDriverByName('GTiff')
#Set nans to the original No Data Value
Array[np.isnan(Array)] = NDV
#Set up the dataset with zsize
#write each slice of the array along the zsize
Array_shape_length = len(Array.shape)
if Array_shape_length == 3:
for i, image in enumerate(Array, 1):
now_file = get_time(i - 1, nc_data, var_name, filename)
# NewFileName = outpath + var_name + netCDF4文件 + 1999_12_31 + .tif
NewFileName = suffix + '\\' + now_file + '.tif'
print('Outpath:', NewFileName, '\n')
DataSet = driver.Create(NewFileName, xsize, ysize, 1, DataType)
DataSet.SetGeoTransform(GeoT)
DataSet.SetProjection(Projection.ExportToWkt())
#判读数据的维度
#if Array_shape_length == 3:
DataSet.GetRasterBand(1).WriteArray(image)
#else:
# 数据为n*7*11的矩阵，此代码取的为第0层，一共n层
#DataSet.GetRasterBand(1).WriteArray(image[0])
DataSet.GetRasterBand(1).SetNoDataValue(NDV)
DataSet.FlushCache()
DataSet = None # close the tif file
print('The ' + now_file + '.tif' ' has finished!!!\n')
else:
for i, image in enumerate(Array, 1):
now_file = get_time(i - 1, nc_data, var_name, filename)
# NewFileName = outpath + var_name + netCDF4文件 + 1999_12_31 + .tif
NewFileName = suffix + '\\' + now_file + '.tif'
print('Outpath:', NewFileName, '\n')
DataSet = driver.Create(NewFileName, xsize, ysize, 1, DataType)
DataSet.SetGeoTransform(GeoT)
DataSet.SetProjection(Projection.ExportToWkt())
#判读数据的维度
#数据为n*7*11的矩阵，此代码取的为第0层，一共n层
DataSet.GetRasterBand(1).WriteArray(image[0])
DataSet.GetRasterBand(1).SetNoDataValue(NDV)
DataSet.FlushCache()
DataSet = None # close the tif file
print('The ' + now_file + '.tif' ' has finished!!!\n')
def cut_raster_yboundaries(raster, outfile_name, y_min_new, y_max_new):
"""
This function cuts a raster-file to y_min_new and y_max_new values and writes it into GeoTIFF-file.
It is based on the gdal-package.
For (in)rasters with the origin at y_min, the raster is flipped and the origin set to y_max.
"""
xSize_old = raster.RasterXSize
ySize_old = raster.RasterYSize
geotransform = raster.GetGeoTransform()
x_min_old = geotransform[0]
pixelWidth = geotransform[1]
pixelHeight = geotransform[5]
#x_max_old = x_min_old + xSize_old*pixelWidth
if pixelHeight < 0:
y_min_old = geotransform[3] + ySize_old * pixelHeight
y_max_old = geotransform[3]
else:
y_max_old = geotransform[3] + ySize_old * pixelHeight
y_min_old = geotransform[3]
# calculate rows and columns of raster array to cut:
#cut_left = abs(x_max_old - x_max)/geotransform[3]
#cut_right = abs(x_min_old - x_min)/geotransform[3]
cut_top = round(abs(round(y_max_old - y_max_new) / pixelHeight))
cut_bottom = round(abs(round(y_min_old - y_min_new) / pixelHeight))
array = raster.ReadAsArray()
# the array has to be flipped upside down if originY is at the bottom-left (equal to pixelHeight > 0)
if pixelHeight > 0:
array = np.flipud(array)
array_cut = array[cut_top:array.shape[0] - cut_bottom].copy()
array = None
ySize_new = ySize_old - cut_top - cut_bottom
if pixelHeight > 0:
pixelHeight = -pixelHeight
no_data_value = raster.GetRasterBand(1).GetNoDataValue()
DataType = gdal_array.NumericTypeCodeToGDALTypeCode(array_cut.dtype)
driver = gdal.GetDriverByName('GTiff')
out_raster_SRS = osr.SpatialReference()
out_raster_SRS.ImportFromEPSG(4326)
out_raster = driver.Create(outfile_name + '.tif', xSize_old, ySize_new, 1,
DataType)
out_raster.SetGeoTransform(
(x_min_old, pixelWidth, 0, y_max_new, 0, pixelHeight))
out_raster.SetProjection(out_raster_SRS.ExportToWkt())
out_raster.GetRasterBand(1).WriteArray(array_cut)
out_raster.GetRasterBand(1).SetNoDataValue(no_data_value)
return out_raster
array_cut = None
def processAlgorithm(self, parameters, context, feedback):
entrada = self.parameterAsRasterLayer(parameters, self.INPUT, context)
if entrada is None:
raise QgsProcessingException(
self.invalidSourceError(parameters, self.INPUT))
n_banda = self.parameterAsInt(parameters, self.BAND, context)
if n_banda is None:
raise QgsProcessingException(
self.invalidSourceError(parameters, self.BAND))
saida = self.parameterAsFileOutput(parameters, self.OUTPUT, context)
Carregar = self.parameterAsBool(parameters, self.OPEN, context)
# Abrir banda
feedback.pushInfo(
self.tr('Reading the selected band...',
'Lendo a banda selecionada...'))
image = gdal.Open(entrada.dataProvider().dataSourceUri())
banda = image.GetRasterBand(n_banda).ReadAsArray()
prj = image.GetProjection()
geotransform = image.GetGeoTransform()
# Criar objeto CRS
CRS = osr.SpatialReference(wkt=prj)
# Obter número de linhas e colunas
cols = image.RasterXSize
rows = image.RasterYSize
image = None # fechar magem
# Pegar tipo de dado do array
GDT = gdal_array.NumericTypeCodeToGDALTypeCode(banda.dtype)
# Criar imagem com uma única banda
feedback.pushInfo(
self.tr('Writing the selected band...',
'Escrevendo a banda selecionada...'))
nova_imagem = gdal.GetDriverByName('GTiff').Create(
saida, cols, rows, 1, GDT)
nova_imagem.SetGeoTransform(geotransform)
nova_imagem.SetProjection(CRS.ExportToWkt())
nova_imagem.GetRasterBand(1).WriteArray(banda)
nova_imagem.FlushCache() # Escrever no disco
nova_imagem = None # Salvar e fechar
CRS = None
feedback.pushInfo(
self.tr('Operation completed successfully!',
'Operação finalizada com sucesso!'))
feedback.pushInfo('Leandro França - Eng Cart')
self.CAMINHO = saida
self.CARREGAR = Carregar
return {self.OUTPUT: saida}
def convert_numpy_type_to_gdal_type(array):
typemap = {}
for name in dir(np):
obj = getattr(np, name)
if hasattr(obj, 'dtype'):
try:
npn = obj(0)
nat = np.asscalar(npn)
if gdal_array.NumericTypeCodeToGDALTypeCode(npn.dtype.type):
typemap[npn.dtype.
name] = gdal_array.NumericTypeCodeToGDALTypeCode(
npn.dtype.type)
except:
pass
typemap['int64'] = 7
try:
return typemap[array.dtype.name]
except KeyError:
raise KeyError('Unsupported or undetectable data type!')
def GDTNumCode(self, dtype):
import numpy as np
from osgeo import gdal, gdal_array
typemap = {}
for name in dir(np):
obj = getattr(np, name)
if hasattr(obj, 'dtype'):
try:
npn = obj(0)
nat = np.asscalar(npn)
if gdal_array.NumericTypeCodeToGDALTypeCode(
npn.dtype.type):
typemap[
npn.dtype.
name] = gdal_array.NumericTypeCodeToGDALTypeCode(
npn.dtype.type)
except:
pass
return typemap[dtype]
