Numpy arrays are a fundamental tool for scientific data processing in Python. To deal with spatial data that is geo-referenced on a rectangular-grid raster the GeoTIFF file format is similarly ubiquitous. Saving spatial data that is held in a Numpy array to a GeoTIFF file should therefore be an extremely common task, so it was surprising to me to run into some pitfalls. This post is a write-up on how to get around them.
To access GeoTIFF files I’m using the Geospatial Data Abstraction Library (GDAL), a powerful set of tools that comes with multiple command line utilities and bindings for the most common scripting languages used in science. As it is originally a C/C++ library, it can be quite unpythonic — one of many reasons why you might want to write your own library for your specific purpose.
Writing a Numpy array to a GeoTIFF file consists of these steps:
- Figure out the spatial reference system (coordinate system and, if applicable, map projection), usually from the source data set, and get the Well-Known Text representation of it (examples).
- Figure out the geotransform, that is the parameters that describe how the data has to be shifted and stretched to place it on the spatial reference system. This, too, will be derived from the source data and whatever manipulations were subsequently carried out.
- Create a dataset object using GDAL’s “GTiff” driver, attach the spatial reference and geotransform, and write out the data
The details are described in the GDAL API tutorial and elsewhere on the web. In the simplest case, if the data originates from another GeoTIFF file, has only one raster band, and we didn’t sub-set or re-scale it (geographically), we could do this [1]:
from osgeo import gdal
src_dataset = gdal.Open("[input GeoTIFF file path]")
src_data = src_dataset.ReadAsArray()
# final_data is a 2-D Numpy array of the same dimensions as src_data
final_data = some_complicated_scientific_stuff(src_data, other_data, ...)
# get parameters
geotransform = src_dataset.GetGeoTransform()
spatialreference = src_dataset.GetProjection()
ncol = src_dataset.RasterXSize
nrow = src_dataset.RasterYSize
nband = 1
# create dataset for output
fmt = 'GTiff'
driver = gdal.GetDriverByName(fmt)
dst_dataset = driver.Create([output_filepath], ncol, nrow, nband, gdal.GDT_Byte)
dst_dataset.SetGeoTransform(geotransform)
dst_dataset.SetProjection(spatialreference)
dst_dataset.GetRasterBand(1).WriteArray(final_data)
dst_dataset = None
Thus far, there’s nothing difficult about it. But the problem arises on line 18, where the data type is passed to the Create() method. gdal.GDT_Byte refers to a code for GDAL’s Byte data type, that is, an 8-bit unsigned integer. If the final data is of a different type, 16-byte signed integers, say, or floating-point numbers, I could use one of the other GDAL data types.
But I’m writing a library and am therefore unlikely to know the data type beforehand. So what is needed is a general mapping from Numpy dtype objects to GDALDataType objects. And that problem had me stumped for a moment.
OK, it would be possible to guess — there aren’t that many of them — but shouldn’t there be a function?
I found out that in the gdal_array module, there is a function called NumericTypeCodeToGDALTypeCode, which is supposed to translate a “numeric” type into a GDAL type code, for example:
>>> print(gdal_array.NumericTypeCodeToGDALTypeCode(numpy.float32)) 6
But it turns out that passing in the dtype attribute of a Numpy array doesn’t work:
>>> print(gdal_array.NumericTypeCodeToGDALTypeCode(my_data.dtype)) ... TypeError: Input must be a type
Nonetheless:
>>> my_data.dtype == numpy.float32 True
Huh? Well, the first thing I learnt from the Python documentation is that for the == operator to return True the two objects aren’t always required to have the same type. In some cases this seems to make more sense than in others.
The second is that evidently, gdal_array.NumericTypeCodeToGDALTypeCode expects an object of type type (that is, Python type), which numpy.float32 appears to be, whereas my_data.dtype is, surprise surprise of type numpy.dtype.
Apparently, the GDAL developers have recognized this behavior as a bug and fixed it in v. 2.0. What can we do meanwhile? The answer, from a StackOverflow post, is that we can instantiate a list of arrays of length 1 that cover all possible Nympy data types and then use numpy.asscalar to convert them to native Python objects with native Python types. For example:
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
(If we want the GDAL Data Type labels, we can use gdal.GetDataTypeName(typecodeinteger).)
This generates a conversion dictionary that looks like this:
NP2GDAL_CONVERSION = {
"uint8": 1,
"int8": 1,
"uint16": 2,
"int16": 3,
"uint32": 4,
"int32": 5,
"float32": 6,
"float64": 7,
"complex64": 10,
"complex128": 11,
}
(If we want the GDAL Data Type labels, we can use gdal.GetDataTypeName(typecodeinteger).)
That’s a start. Some hand-editing is in order, for example, mapping Booleans to 1 to make it possible to encode them as integers for persistence — clearly, GDAL has no notion of bit or binary objects. Also, it is odd that both int8 and uint8 should be mapped to GDAL Byte types, that is, unsigned integers. That needs to be taken into account when manipulating the data. In addition, several complex Numpy datatypes are missing and could be manually mapped to 10 or 11.
But I can work with this. To get back to the first listing, in the “get parameters” section I add a line and then create the destination dataset as follows:
gdaltype = NP2GDAL_CONVERSION[final_data.dtype.name] [...] dst_dataset = driver.Create([output_filepath], ncol, nrow, nband, gdaltype)
Voilà.
NOTES:
[1] I am aware I could have used CreateCopy() in such a simple case, but Create() is more generally versatile.
The second note is that I am aware that the problem isn’t specific to GeoTIFF files: it arises for any data file with GDAL whose driver supports a Create() method. But to be honest, GDAL is pretty unwieldy for most scientific data formats, so if I were to write NetCDF or HDF5 files, I would use appropriate specific libraries, most of which tend to be aware of Numpy and its data types.
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