threedigrid-builder 1.3.2

Generate a 3Di simulation grid from a model schematisation.

threedigrid-builder

Generate a 3Di simulation grid from a model schematisation.

Usage

This library converts a model schematisation to a 3Di simulation grid. This can be done using a single function that reads data from an SQLite and TIFF and then outputs the generated grid into a Geopackage or HDF5 file:

>>> from threedigrid_builder import make_gridadmin
>>> sqlite_path = "/path/to/model.sqlite"
>>> dem_path = "/path/to/dem.tiff"
>>> out_path = "grid.gpkg"  # or "something.h5" for HDF5 output
>>> make_gridadmin(sqlite_path, dem_path, out_path)

Alternatively, the generated grid can be output in-memory:

>>> make_gridadmin(sqlite_path, dem_path)
{'nodes': {'id': array([   1,    2,    3, ..., 7903, 7904, 7905], dtype=int32), ...}

Installation

This package is distributed as binary only, because its (Fortran) source code is proprietary. The currently supported platforms are Windows, Linux, and OSX, all 64 bit versions only.

First install sqlite and spatialite libraries, e.g. on Ubuntu:

$ sudo apt-get install sqlite3 libsqlite3-mod-spatialite

For raster input, GDAL is required to be present. We omitted these from the dependencies because installation of GDAL depends on your platform an on your personal perference. One option is to install gdal using apt-get, and then pygdal with a matching version:

$ sudo apt-get libgdal-dev $ pip install pygdal=={your gdal version}.*

Install the threedigrid-builder:

$ pip install threedigrid-builder

For output into a file for the 3Di calculationcore, enable gridadmin output:

$ pip install threedigrid-builder[gridadmin]

For output into Geopackage for display in e.g. QGis, enable gpkg output:

$ pip install threedigrid-builder[gpkg]

Changelog of threedigrid-builder

1.3.2 (2022-02-08)

• Fixed extracting EPSG code from outdated CRS WKT definitions.

1.3.1 (2022-02-07)

• Disable tests for CI Build Wheel, because GDAL is not included on build machine.

1.3.0 (2022-02-07)

• Write the WKT of the CRS (in addition to the epsg code) into the gridadmin.

• Drop rasterio as optional raster interface.

• Append / prepend coordinates to channel/culvert linestrings if they do not intersect the connection nodes they are attached to.

• Only give node_type 4 and kcu 52/54 to manholes with a not-NULL storage area.

• Use pygoes to calculate grid refinements.

1.2.1 (2022-01-27)

• Store epsg_code as string in GridMeta.

1.2.0 (2022-01-26)

• Interpret non-finite raster values (NaN, Inf, -Inf) as nodata.

• Use GDAL (instead of rasterio) for reading rasters, if present.

1.1.0 (2022-01-24)

• Write “grid_coordinate_attributes” also for pure 1D models.

• Make requesting spatial reference of GDAL dataset compatible with GDAL 2.x.

• Fix: do not ignore (Impervious)Surface records without geometries. These surfaces will get their location from their connection node.

• Do not ignore invalid geometries (surfaces, grid refinement areas, dem average areas)

1.0.2 (2022-01-17)

• Change in calculation_type type order of connection nodes. Embedded comes first.

1.0.1 (2022-01-13)

• Fixed the ordering of nodes and lines within node/line types.

1.0.0 (2022-01-12)

• Snap 2D boundary conditions to the closest edge if they are completely outside of the model domain.

• Raise SchematisationError instead of an internal error if the spatialite version is below 173.

• Raise FileNotFound instead of creating an empty file if spatialite does not exist.

• Added manhole fields (manhole_indicator, shape, width, surface_level) to nodes.

• Removed data from nodes.bottom_level for non-manhole nodes.

• Added dist_calc_points and material to lines.

• Added cross section width, height, shape to lines.

• Added sewerage_type (pipes) and sewerage (weirs/orifices) to lines.

• Added friction_type and friction_value (pipes/culverts/weirs/orifices) to lines.

• Fix: accept unknown sewerage types.

0.16.0 (2022-01-06)

• Added crest level and crest type to to lines.

• Added connection node start and end id to lines.

• Handle non-ASCII characters in gridadmin HDF5 output.

• Fixed node ids in groundwater lines (they now connect groundwater cells instead of open water cells).

0.15.0 (2022-01-05)

• Small fix for use_2d_flow setting.

• Added zoom_category to nodes, lines and pumps.

0.14.0 (2022-01-04)

• Add nodm and nodn for 2D boundary nodes.

• Handle use_2d_flow setting.

• Added display_name to nodes, lines and pumps.

0.13.0 (2021-12-28)

• Enable groundwater and write dimp to nodes.

0.12.0 (2021-12-27)

• Add drain_level of manholes to gridadmin.

• Bugfix: Set culvert calculation_type to isolated when not provided.

• Added display name to culverts, weirs, pipes, pumps, channels

• Added zoom category to pumps, pipes, culverts, orifices, weirs, manholes.

0.11.0 (2021-12-22)

• Accept dist_calc_points <= 0; the effect is that there are no interpolated nodes.

• Ignore grid refinements with NULLs in their type or geometry fields.

• Ignore (impervious) surfaces, grid refinements, and dem averages areas with invalid geometries (mostly, polygons with self-intersections).

• Set ds1d of 1d2d lines to 2d cell_width.

0.10.0 (2021-12-21)

• Bugfix: Added support for refinement geometries within smallest Grid cell.

• Reverse the order of coordinates in channel and culvert geometries if necessary.

0.9.2 (2021-12-17)

• Temporarily disable groundwater.

• Bugfix: Edge case with connected points.

0.9.1 (2021-12-16)

• Bugfix: use DEM epsg_code for 2D models.

• Bugfix: Small fix for lgrtot.

• Bugfix: Small fix adding groundwater cells.

• Bugfix: Fix pump.line remapping in case of embedded nodes.

• Bugfix: Remap surface_map.cci on grid.sort().

• Bugfix: also need to evaluate embedded nodes for connection node mapping for zero-d surface maps.

• Added pixel_width to groundwater nodes.

0.9.0 (2021-12-15)

• Add padding to area_mask for creating quadtree.

• Added groundwater 2D nodes, 2D vertical lines, and 2D groundwater lines.

• Bugfix: cross section tabulate used wrong width/height.

0.8.3 (2021-12-09)

• Only process cross section definitions that are actually used.

• Removed cross1 & cross2 in the in-memory or geopackage output and added cross_id1 and cross_id2.

• Fixed bug where writing a single line geometry or geometries of equal size would result in an incorrect cast to a numpy object dtype.

• Fixed bug with zero-d administration cci (index needs to be 1-based), removed cid field.

0.8.2 (2021-12-05)

• Fixed the Linux wheel distribution. These are now built with manylinux2014 instead of manylinux2010.

0.8.1 (2021-12-05)

• Added support for zero-d administration including surfaces and impervious surfaces.

• Dropped support for Python 3.6.

• Fixed __version__ attribute and “threedigrid_builder_version” HDF5 attribute.

• Set the dpumax of a 1D line (channel, pipe, culvert, weir, orifice) always to the largest of its two invert levels. Previously, it was set to the largest of the two bottom_levels of the two adjacent nodes, which gave wrong results for lines attached to manholes.

• Disable extrapolation for channel node/line attributes that are derived from crosssection locations.

• Disable the SchematisationError when a Manhole has a bottom_level above a level of a connected object. Instead, emit a warning through the logger.

0.8.0 (2021-11-30)

• Added has_max_infiltration_capacity flag.

• Added breaches and levees.

• Implement GDAL as an alternative to RasterIO.

• Check the raster EPSG code and use it if the model does not have one.

• Removed ‘model_area_path’ feature from application.

• Added an in-memory output interface. Supply out_path=None to instead of writing the grid to a file, receive the grid as dictionaries of 1D ndarrays.

• Removed the “sqlalchemy<1.4” constraint, this library is compatible with SQLAlchemy 1.4

0.7.0 (2021-11-25)

• Raise SchematisationError on invalid settings.

• Removed SchematisationError on tabulated rectangle cross section definition with zero first “width” value.

• Add calculation_type for nodes to be Dem averaged.

0.6.1 (2021-11-10)

• Fixed l1dtot (exclude 1D boundaries).

0.6.0 (2021-11-09)

• Raise SchematisationError on embedding linear objects that begin/end outside of 2D domain. Added tests for edge cases.

• Fixed exchange_level (dpumax) for 1D2D lines attached to non-manhole connection nodes. The exchange_level is now derived from the bank_levels of attached channels.

• Add discharge_coefficients for structures.

• Swap the order in lines.line for 1D2D lines. The order is now (2D, 1D).

• Fixed kcu for lines attached to 1D boundary conditions.

• Copy crest_level from v2_levee if a v2_connected_point refers to one.

0.5.2 (2021-11-02)

• Consistently write NaN (and not -9999.0) in gridadmin float datasets.

• Fix tests with GEOS 3.10.0

• Make ‘meta’ group complete.

0.5.1 (2021-11-01)

• Add storage_area to calculation nodes.

• Added ds1d_half to nodes.

• Added has_embedded to attrs.

0.5.0 (2021-10-21)

• Fixed nodes.is_manhole in the gridadmin output.

• Handle user-supplied 1D-2D lines (connected point / calculation point).

• Write initial_waterlevel for 1D nodes and add ‘has_initial_waterlevels’ to meta.

0.4.0 (2021-09-23)

• Added 1D boundary conditions.

• Added 2D boundary conditions.

• Enable compression in HDF5 output.

• Fixed 2D lines that connect a larger to a smaller cell in south east direction.

0.3.1 (2021-08-16)

• Handle embedded connection nodes. These are removed from the grid and written to a new dataset “nodes_embedded”.

• Fixed bug with cross sections tables being None in Grid instance

• Handle embedded channels, pipes and culverts. Embedded objects result in embedded nodes and and lines with kcu LINE_1D_EMBEDDED between between 2D cells.

• Fixed a bug with lines that connect nodes to themselves in quadtree generation.

• Fixed a bug with wrong usage of lines.ds1d in bottom level and cross section weights computation. The added attribute lines.s1d is now used, and for clarity nodes.ds1d was renamed to nodes.s1d.

• Added invert_level_start_point and invert_level_end_point attributes to lines.

• Fixed coordinate order in lines.line_geometries field in gridadmin.h5.

0.3.0 (2021-07-28)

• Read and convert cross section definitions.

• Solve gridadmin off-by-one errors for pumps.

• Add ‘dmax’ to nodes output.

• Changed external API function name to “make_gridadmin”.

0.2.1 (2021-07-20)

• Fixed issue when reprojecting 0 grid refinements with pyproj 2.*

• Fixed issue when writing 0 pumps with h5py 2.*

• Fixed missing transpose when writing pumps.coordinates to HDF5.

• Added obstacles.

0.2.0 (2021-07-15)

• Added threedigrid_builder.grid.geo_utils with segmentize and line_substring functions. These are used to compute the Lines.line_geometries for channel lines.

• Fixed a bug in the refinement areas code (Fortran) on Ubuntu 20.04.

• Added the Pipes model that is able to compute Nodes & Lines from Pipes. Pipes are also included in the calculation_type and bottom_level computations.

• Added 1D-2D lines for connection nodes, manholes, and channels.

• Added culverts, orifices, and weirs.

• Added pumps (pumpstations).

• Settings and metadata are read from the SQLite. Some metadata (like model_slug) can also be provided via the main (make_grid) function. The metadata is written to the root ‘attrs’ of the output gridadmin.h5. The settings are written into datasets inside newly addres groups “grid_settings” and “tables_settings”.

• Fixes for models with no channels.

• Add an optional progress callback.

0.1.2 (2021-04-28)

• Added public API with 1 function: threedigrid_builder.make_grid.

0.1.1 (2021-04-20)

• Fixed automatic PyPI upload.

0.1.0 (2021-04-20)

• Partially ported functionality from inpy (generate 3di files, makegrid): 1D channel grid (including calculation_type and bottom_level), and 2D open water grid.

• Added gridadmin and geopackage output.

• Breaking change: the interpolation between cross section locations (channels) now also extrapolates for lines and nodes that are not in between two connection nodes. This happens only if the channel has at least 2 cross section locations. When extrapolatic, the line.cross_weight is less than 0 or greater than 1.

• Breaking change: missing or empty values in float datasets in the output gridadmin are now denoted by NaN (not-a-number) instead of -9999.0.

• Breaking change: integers in the output gridadmin are now always 32-bit (instead of sometimes 32-bit and sometimes 64-bit).