pyDEM: A python digital elevation model analysis package

PyDEM is a package for topographic (terrain) analysis written in Python (with a bit of Cython). It takes in digital elevation model (DEM) rasters, and it outputs quantities like slope, aspect, upstream area, and topographic wetness index. PyDEM closely follows the approach taken by TauDEM to calculate these quantities. It is designed to be fast, easily extensible, and capable of handling very large datasets.

PyDEM can be used both from the command-line, or programmatically via its Python API. Examples of both usages are given below and in the examples directory. It can operate on individual elevation rasters, or on entire directories simultaneously. Most processing steps can be performed in parallel with any number of independent pyDEM processes. Note that pyDEM depends on TauDEM for certain steps (e.g., pitfilling) and it also makes extensive use of the GDAL library for working with geospatial rasters.

1. Installation

For installation notes, see install.md

2. Basic Usage

Examples and tests can be found in the pydem\examples directory.

2.1 Python Module Usage

2.1.1. Calculate quantities on a single elevation tile

Import the DEMProcessor class:

from pydem.dem_processing import DEMProcessor

Set the path to a pit filled elevation file in WGS84 coordinates:

filename_to_elevation_geotiff = 'test.tiff'

Instantiate an instance of the DEMProcessor class:

dem_proc = DEMProcessor(filename_to_elevation_geotiff)

The following three commands do not need to be called in order.

Calculate the aspect and slope magnitude:

mag, aspect = dem_proc.calc_slopes_directions()

Calculate the upstream contributing area:

uca = dem_proc.calc_uca()

Calculate the TWI:

twi = dem_proc.calc_twi()

2.1.2 Calculate TWI on a directory of elevation tiles

The ProcessManager class orchestrates multiple processes to compute TWI over multiple tiles in parallel on the same machine. Example usage is as follows:

  from pydem.processing_manager import ProcessManager
  elevation_source_path = r'/home/twi-users/elevation'
  manager = ProcessManager(
    n_workers=64, # Number of worker processes to use
    in_path=elevation_source_path,
    out_path='/home/twi-users/temporary_compute_storage/'  # Where to save intermediate data
    dem_proc_kwargs={},  # dictionary of values used to initialize DemProcessor
  )
  # Start the processing
  manager.process_twi()  # If this fails (e.g. machine goes down), can restart to pick up where it left off

You can also call individual parts of the processing:

manager.compute_grid()  # Figures out how elevation in folder are tiled
manager.process_elevation()  # Fills flats, handles pits, fixes artifacts in elevation data
manager.process_aspect_slope()
manager.process_uca() # Computes upstream contributing area (UCA) for individual tiles (embarassingly parallel)
manager.process_uca_edges() # Fixes upstream flow contribution accross tile edges -- iteratively
manager.process_twi()  # Call all the above functions internally, but skips any work already done

Finally, to export results to a single GeoTiff with overviews, use:

manager.save_non_overlap_data_geotiff(
  'float32',  # Numpy recognized filetype
  new_path=output_path,
  keys=['elev', 'uca', 'aspect', 'slope', 'twi'], # list can contain a subset of these
  overview_type='average')

Note: The name non_overlap_data comes from an implementation quirk. The temporary data is saved as a zarr file. This zarr file OVERLAPS data at the edges of tiles to make it easier to compute UCA across edges

2.1.3 DEMProcessor options

The following options are used by the DEMProcess object. They can be modified by setting the value before processing.

dem_proc = DEMProcessor(filename_to_elevation_geotiff)
dem_proc.fill_flats = False

Slopes & Directions

chunk_size_slp_dir: Chunk size for slopes_directions calculation. Default 512.
chunk_overlap_slp_dir: Overlap to use for resolving slopes and directions at chunk edges. Default 4.
fill_flats: Fill/interpolate the elevation for flat regions before calculating slopes and directions. The direction cannot be calculated in regions where the slope is 0 because the nominal elevation is all the same. This can happen in very gradual terrain or in lake and river beds, particularly when the input elevation is composed of integers. When True, the elevation is interpolated in those regions so that a reasonable slope and direction can be calculated. Default True.
fill_flats_below_sea: Interpolate the elevation for flat regions that are below sea level. Water will never flow out of these "pits", so in many cases you can ignore these regions and achieve faster processing times. Default False.
fill_flats_source_tol: When filling flats, the algorithm finds adjacent "source" pixels and "drain" pixels for each flat region and interpolates the elevation using these data points. This sets the tolerance for the elevation of source pixels above the flat region (i.e. shallow sources are used as sources but not steep cliffs). Default 1.
fill_flats_peaks: Interpolate the elevation for flat regions that are "peaks" (local maxima). These regions have a higher elevation than all adjacent pixels, so there are no "source" pixels to use for interpolation. When True, a single pixel is selected approximately in the center of the flat region as the "peak"/"source". Default True.
fill_flats_pits: Interpolate the elevation for flat regions that are "pits" (local minima). These regions have a lower elevation than all adjacent pixels, so there are no "drain" pixels to use for interpolation. When True, a single pixel is selected approximately in the center of the flat region as the "pit"/"drain". Default True.

UCA

resolve_edges: Ensure edge UCA is continuous across chunks. Default True.
chunk_size_uca: Chunk size for uca calculation. Default 512.
chunk_overlap_uca: Overlap to use for resolving uca at chunk edges. Default 32.
drain_pits: Drain from "pits" to nearby but non-adjacent pixels. Pits have no lower adjacent pixels to drain to directly. Note that with fill_flats_pits off, this setting will still drain each pixel in large flat regions, but it may be slower and produces less reasonable results. Default True.
drain_pits_max_iter: Maximum number of iterations to look for drain pixels for pits. Generally, "nearby drains" for a pit/flat region are found by expanding the region upward/outward iteratively. Default 100.
drain_pits_max_dist: Maximum distance in coordnate-space to (non-adjacent) drains for pits. Pits that are too far from another pixel with a lower elevation will not drain. Default 20.
drain_pits_max_dist_XY: Maximum distance in real-space to (non-adjacent) drains for pits. Pits that are too far from another pixel with a lower elevation will not drain. This filter is applied after drain_pits_max_dist; if the X and Y resolution are similar, this filter is generally unnecessary. Default None.
drain_flats: [Deprecated, replaced by drain_pits] Drains flat regions and pits by draining all pixels in the region to an arbitrary pixel in the region and then draining that pixel to the border of the flat region. Ignored if drain_pits is True. Default False.
apply_uca_limit_edges: Mark edges as completed if the maximum UCA is reached when resolving drainage across edges. Default False. If True, it may speed up large calculations.
uca_saturaion_limit: Default 32.

TWI

apply_twi_limits: When calculating TWI, limit TWI to max value. Default False.
apply_twi_limits_on_uca: When calculating TWI, limit UCA to max value. Default False.

Other

save_projection: Default EPSG:4326.

2.2 Commandline Usage

When installing pydem using the provided setup.py file, the commandline utilities TWIDinf, AreaDinf, and DinfFlowDir are registered with the operating system.

TWIDinf :

usage: TWIDinf-script.py [-h] [--save-all]
                     Input_Pit_Filled_Elevation [Input_Number_of_Chunks]
                     [Output_D_Infinity_TWI]

Calculates a grid of topographic wetness index which is the log_e(uca / mag),
that is, the natural log of the ratio of contributing area per unit contour
length and the magnitude of the slope. Note, this function takes the elevation
as an input, and it calculates the slope, direction, and contributing area as
intermediate steps.

positional arguments:
  Input_Pit_Filled_Elevation
                    The input pit-filled elevation file in geotiff format.
  Input_Number_of_Chunks
                    The approximate number of chunks that the input file
                    will be divided into for processing (potentially on
                    multiple processors).
  Output_D_Infinity_TWI
                    Output filename for the topographic wetness index.
                    Default value = twi.tif .

optional arguments:
  -h, --help            show this help message and exit
  --save-all, --sa      If set, will save all intermediate files as well.

AreaDinf :

usage: AreaDinf-script.py [-h] [--save-all]
                      Input_Pit_Filled_Elevation [Input_Number_of_Chunks]
                      [Output_D_Infinity_Specific_Catchment_Area]

Calculates a grid of specific catchment area which is the contributing area
per unit contour length using the multiple flow direction D-infinity approach.
Note, this is different from the equivalent tauDEM function, in that it takes
the elevation (not the flow direction) as an input, and it calculates the
slope and direction as intermediate steps.

positional arguments:
  Input_Pit_Filled_Elevation
                    The input pit-filled elevation file in geotiff format.
  Input_Number_of_Chunks
                    The approximate number of chunks that the input file
                    will be divided into for processing (potentially on
                    multiple processors).
  Output_D_Infinity_Specific_Catchment_Area
                    Output filename for the flow direction. Default value = uca.tif .

optional arguments:
  -h, --help            show this help message and exit
  --save-all, --sa      If set, will save all intermediate files as well.

DinfFlowDir :

usage: DinfFlowDir-script.py [-h]
                         Input_Pit_Filled_Elevation
                         [Input_Number_of_Chunks]
                         [Output_D_Infinity_Flow_Direction]
                         [Output_D_Infinity_Slope]

Assigns a flow direction based on the D-infinity flow method using the
steepest slope of a triangular facet (Tarboton, 1997, "A New Method for the
Determination of Flow Directions and Contributing Areas in Grid Digital
Elevation Models," Water Resources Research, 33(2): 309-319).

positional arguments:
  Input_Pit_Filled_Elevation
                    The input pit-filled elevation file in geotiff format.
  Input_Number_of_Chunks
                    The approximate number of chunks that the input file
                    will be divided into for processing (potentially on
                    multiple processors).
  Output_D_Infinity_Flow_Direction
                    Output filename for the flow direction. Default value = ang.tif .
  Output_D_Infinity_Slope
                    Output filename for the flow direction. Default value = mag.tif .

optional arguments:
  -h, --help            show this help message and exit

3. Description of package Contents

commandline_utils.py : Contains the functions that wrap the python modules into command line utilities.
dem_processing.py: Contains the main algorithms.
- Re-implements the D-infinity method from Tarboton (1997).
- Implements a new upstream contributing area algorithm. This performs essentially the same task as previous upstream contributing area algorithms, but with some added functionality. This version deals with areas where the elevation is flat or has no data values and can be updated from the edges without re-calculating the upstream contributing area for the entire tile.
- Re-implements the calculation of the Topographic Wetness Index.
process_manager.py: Implements a class that manages the calculation of TWI for a directory of files.
- Manages the calculation of the upstream contributing area that drains across tile edges.
- Stores errors in the processing.
- Allows multiple processes to work on the same directory without causing conflicts.
test_pydem.py: A few helper utilities that create analytic test-cases used to develop/test pyDEM.
utils.py: A few helper utility functions.
- Renames files in a directory (deprecated, no longer needed).
- Parses file names.
- Wraps some gdal functions for reading and writing geotiff files.
- Sorts the rows in an array.
cyfuncs: Directory containing cythonized versions of python functions in dem_processing.py. These should be compiled during installation.
- cyfuncs.cyutils.pyx: Computationally efficient implementations of algorithms used to calculate upstream contributing area.
examples: Directory containing a few examples, along with an end-to-end test of the cross-tile calculations.
- examples.compare_tile_to_chunk.py: Compares the calculation of the upstream contributing area over a full tile compared to multiple chunks in a file. This tests that the upstream contributing area calculation correctly drains across tile edges.
  - examples.process_manager_directory.py: This shows how to use the ProcessingManager to calculate all of the elevation files within a directory.
aws: Directory containing experiment for running PyDEM on Amazon Web Services
pydem.test.test_end_to_end.py: A few integration tests. Can be run from the commandline using the pytest package: cd pydem; cd test; pytest .

4. References

Tarboton, D. G. (1997). A new method for the determination of flow directions and upslope areas in grid digital elevation models. Water resources research, 33(2), 309-319.

Ueckermann, Mattheus P., et al. (2015). "pyDEM: Global Digital Elevation Model Analysis." In K. Huff & J. Bergstra (Eds.), Scipy 2015: 14th Python in Science Conference. Paper presented at Austin, Texas, 6 - 12 July (pp. 117 - 124). http://conference.scipy.org/proceedings/scipy2015/mattheus_ueckermann.html

5. Attributions

pyDEM uses lib.pyx from the OpenPIV project for inpainting missing values in the final outputs.

creare-com / pydem