diff --git a/Dockerfile b/Dockerfile index dd579c65e..70f7d336f 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,5 +1,5 @@ ## Temporary image to build the libraries and only save the needed artifacts -FROM ghcr.io/osgeo/gdal:ubuntu-full-3.4.3 AS builder +FROM ghcr.io/osgeo/gdal:ubuntu-full-3.8.0 AS builder WORKDIR /opt/builder ARG dataDir=/data ARG projectDir=/foss_fim @@ -15,7 +15,7 @@ RUN git clone https://github.com/dtarb/taudem.git RUN git clone https://github.com/fernandoa123/cybergis-toolkit.git taudem_accelerated_flowDirections RUN apt-get update --fix-missing && apt-get install -y cmake mpich \ - libgtest-dev libboost-test-dev libnetcdf-dev openjdk-17-jdk && rm -rf /var/lib/apt/lists/* + libgtest-dev libboost-test-dev libnetcdf-dev && rm -rf /var/lib/apt/lists/* ## Compile Main taudem repo ## RUN mkdir -p taudem/bin @@ -36,18 +36,13 @@ RUN mkdir -p $taudemDir RUN mkdir -p $taudemDir2 ## Move needed binaries to the next stage of the image -RUN cd taudem/bin && mv -t $taudemDir flowdircond aread8 threshold streamnet gagewatershed catchhydrogeo dinfdistdown +RUN cd taudem/bin && mv -t $taudemDir flowdircond streamnet gagewatershed catchhydrogeo dinfdistdown RUN cd taudem_accelerated_flowDirections/taudem/build/bin && mv -t $taudemDir2 d8flowdir dinfflowdir - - ############################################################################################### - - - # Base Image that has GDAL, PROJ, etc -FROM ghcr.io/osgeo/gdal:ubuntu-full-3.4.3 +FROM ghcr.io/osgeo/gdal:ubuntu-full-3.8.0 ARG dataDir=/data ENV projectDir=/foss_fim ARG depDir=/dependencies @@ -72,7 +67,7 @@ RUN mkdir -p $depDir COPY --from=builder $depDir $depDir RUN apt update --fix-missing -RUN DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt install -y p7zip-full python3-pip time mpich=3.3.2-2build1 parallel=20161222-1.1 libgeos-dev=3.8.0-1build1 expect=5.45.4-2build1 tmux rsync tzdata openjdk-17-jdk +RUN DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt install -y p7zip-full python3-pip time mpich parallel libgeos-dev expect tmux rsync tzdata RUN apt auto-remove @@ -107,7 +102,7 @@ RUN pip3 install pipenv==2022.4.8 && PIP_NO_CACHE_DIR=off pipenv install --syste # We download and unzip it to the same file folder that pip deployed the whitebox library. # Whitebox also attempts to always download a folder called testdata regardless of use. # We added an empty folder to fake out whitebox_tools.py so it doesn't try to download the folder -RUN wbox_path=/usr/local/lib/python3.8/dist-packages/whitebox/ && \ +RUN wbox_path=/usr/local/lib/python3.10/dist-packages/whitebox/ && \ wget -P $wbox_path https://www.whiteboxgeo.com/WBT_Linux/WhiteboxTools_linux_musl.zip && \ unzip -o $wbox_path/WhiteboxTools_linux_musl.zip -d $wbox_path && \ cp $wbox_path/WBT/whitebox_tools $wbox_path && \ diff --git a/Pipfile b/Pipfile index beace0056..043b69288 100644 --- a/Pipfile +++ b/Pipfile @@ -43,6 +43,7 @@ flake8-pyproject = "==1.2.3" pre-commit = "==3.3.3" isort = "==5.12.0" urllib3 = "==1.26.18" +pyflwdir = "*" [requires] -python_version = "3.8" +python_version = "3.10" diff --git a/Pipfile.lock b/Pipfile.lock index a0e867a67..b38946cc9 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1,11 +1,11 @@ { "_meta": { "hash": { - "sha256": "05bec99d8be9c133d86cc5a13bbb8dd751b89eaa4368df49170d3527a84bb127" + "sha256": "b0e64fe05b2fb6310dcb5e41cb0d131e77067c5bb3c54db67c9f46a14e705d42" }, "pipfile-spec": 6, "requires": { - "python_version": "3.8" + "python_version": "3.10" }, "sources": [ { @@ -29,7 +29,7 @@ "sha256:1142fa8e80dbae46bb6339573ad4c8c0841358f79c6eb50a493dceca14621bad", "sha256:9107f1ca0b2a5553987a94a3c9959fe5b491fdf731389aa5b7b1bd0733e32de6" ], - "markers": "python_version >= '3.7' and python_version < '4'", + "markers": "python_version >= '3.7' and python_version < '4.0'", "version": "==22.1.0" }, "aiosqlite": { @@ -42,11 +42,11 @@ }, "anyio": { "hashes": [ - "sha256:56a415fbc462291813a94528a779597226619c8e78af7de0507333f700011e5f", - 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"sha256:8f92fc8806f9a6b641eaa5318da32b44d401efaac0f6678c9bc448ba3605faa0", - "sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef" - ], - "markers": "python_version < '3.10'", - "version": "==4.8.0" + "version": "==5.14.0" }, "wcwidth": { "hashes": [ - "sha256:9a929bd8380f6cd9571a968a9c8f4353ca58d7cd812a4822bba831f8d685b223", - "sha256:a675d1a4a2d24ef67096a04b85b02deeecd8e226f57b5e3a72dbb9ed99d27da8" + "sha256:f01c104efdf57971bcb756f054dd58ddec5204dd15fa31d6503ea57947d97c02", + "sha256:f26ec43d96c8cbfed76a5075dac87680124fa84e0855195a6184da9c187f133c" ], - "version": "==0.2.9" + "version": "==0.2.12" } } } diff --git a/docs/CHANGELOG.md b/docs/CHANGELOG.md index e514eb23c..be5e9c1be 100644 --- a/docs/CHANGELOG.md +++ b/docs/CHANGELOG.md @@ -1,6 +1,22 @@ All notable changes to this project will be documented in this file. We follow the [Semantic Versioning 2.0.0](http://semver.org/) format. +## v4.4.9.0 - 2024-01-12 - [PR#1058](https://github.com/NOAA-OWP/inundation-mapping/pull/1058) + +Upgrades base Docker image to GDAL v3.8.0. In order to upgrade past GDAL v.3.4.3 (see #1029), TauDEM's `aread8` was replaced with a module from the `pyflwdir` Python package. + +### Additions + +- `src/accumulate_headwaters.py`: Uses `pyflwdir` to accumulate headwaters and threshold and create stream pixels. + +### Changes + +- `Dockerfile`: Upgrade GDAL from v.3.4.3 to v.3.8.0; remove JDK 17 and TauDEM `aread8` and `threshold`. +- `Pipfile` and `Pipfile.lock`: Add `pyflwdir`, `pycryptodomex` and upgrade Python version. +- `src/delineate_hydros_and_produce_HAND.sh`: Add `src/accumulate_headwaters.py` and remove TauDEM `aread8` and `threshold` + +

+ ## v4.4.8.4 - 2024-01-12 - [PR#1061](https://github.com/NOAA-OWP/inundation-mapping/pull/1061) Adds a post-processing tool to compare crosswalked (conflated) `feature_id`s between NWM stream network to DEM-derived reaches. The tool is run if the `-x` flag is added to `fim_pipeline.sh`. Results are computed for branch 0 and saved in a summary file in the HUC output folder. @@ -37,6 +53,7 @@ Levees disrupt the natural hydrology and can create large catchments that contai

+ ## v4.4.8.2 - 2023-12-12 - [PR#1052](https://github.com/NOAA-OWP/inundation-mapping/pull/1052) The alpha test for v4.4.8.1 came back with a large degradation in skill and we noticed that the global manning's roughness file was changed in v4.4.7.1 - likely in error. @@ -47,6 +64,7 @@ The alpha test for v4.4.8.1 came back with a large degradation in skill and we n

+ ## v4.4.8.1 - 2023-12-08 - [PR#1047](https://github.com/NOAA-OWP/inundation-mapping/pull/1047) Upgrades JDK to v.17.0.9 in Docker image to address security vulnerabilities. diff --git a/src/accumulate_headwaters.py b/src/accumulate_headwaters.py new file mode 100644 index 000000000..4dcb6fb4d --- /dev/null +++ b/src/accumulate_headwaters.py @@ -0,0 +1,102 @@ +#!/usr/bin/env python3 + +import argparse +import os + +import numpy as np +import pyflwdir +import rasterio as rio + + +def accumulate_flow( + flow_direction_filename, + headwaters_filename, + flow_accumulation_filename, + stream_pixel_filename, + flow_accumulation_threshold, +): + """ + Accumulate headwaters along the flow direction and threshold accumulations to produce stream pixels. + + Parameters + ---------- + flow_direction_filename : str + Flow direction filename + headwaters_filename : str + Headwaters filename + flow_accumulation_filename : str + Flow accumulation filename + stream_pixel_filename : str + Stream pixel filename + flow_accumulation_threshold : str + """ + + assert os.path.isfile(flow_direction_filename), 'Flow direction raster does not exist.' + + # Read the flow direction raster + with rio.open(flow_direction_filename) as src: + data = src.read(1) + nodata = src.nodata + profile = src.profile + # transform = src.transform + # crs = src.crs + # latlon = crs.to_epsg() == 4326 + + # Convert the TauDEM flow direction raster to a pyflwdir flow direction array + temp = data.copy() + + temp[data == 1] = 1 + temp[data == 2] = 128 + temp[data == 3] = 64 + temp[data == 4] = 32 + temp[data == 5] = 16 + temp[data == 6] = 8 + temp[data == 7] = 4 + temp[data == 8] = 2 + temp[data == nodata] = 247 + + temp = temp.astype(np.uint8) + + flw = pyflwdir.from_array(temp, ftype='d8') + + # Read the flow direction raster + with rio.open(headwaters_filename) as src: + headwaters = src.read(1) + nodata = src.nodata + + flowaccum = flw.accuflux(headwaters, nodata=nodata, direction='up') + + stream = np.where(flowaccum > 0, flow_accumulation_threshold, 0) + + # Write the flow accumulation raster + profile.update(dtype=flowaccum.dtype) + with rio.open(flow_accumulation_filename, 'w', **profile) as dst, rio.open( + stream_pixel_filename, 'w', **profile + ) as dst2: + dst.write(flowaccum, 1) + dst2.write(stream, 1) + + +if __name__ == '__main__': + parser = argparse.ArgumentParser() + parser.add_argument( + '-fd', '--flow-direction-filename', help='Flow direction filename', required=True, type=str + ) + parser.add_argument('-wg', '--headwaters-filename', help='Headwaters filename', required=True, type=str) + parser.add_argument( + '-fa', '--flow-accumulation-filename', help='Flow accumulation filename', required=True, type=str + ) + parser.add_argument( + '-stream', '--stream-pixel-filename', help='Stream pixel filename', required=True, type=str + ) + parser.add_argument( + '-thresh', + '--flow-accumulation-threshold', + help='Flow accumulation threshold', + required=True, + type=float, + ) + + args = parser.parse_args() + + accumulate_flow(**vars(args)) diff --git a/src/delineate_hydros_and_produce_HAND.sh b/src/delineate_hydros_and_produce_HAND.sh index b97d1912d..b69aa339a 100755 --- a/src/delineate_hydros_and_produce_HAND.sh +++ b/src/delineate_hydros_and_produce_HAND.sh @@ -37,18 +37,11 @@ fi echo -e $startDiv"D8 Flow Accumulations $hucNumber $current_branch_id" date -u Tstart -$taudemDir/aread8 -p $tempCurrentBranchDataDir/flowdir_d8_burned_filled_$current_branch_id.tif \ - -ad8 $tempCurrentBranchDataDir/flowaccum_d8_burned_filled_$current_branch_id.tif \ +python3 $srcDir/accumulate_headwaters.py \ + -fd $tempCurrentBranchDataDir/flowdir_d8_burned_filled_$current_branch_id.tif \ + -fa $tempCurrentBranchDataDir/flowaccum_d8_burned_filled_$current_branch_id.tif \ -wg $tempCurrentBranchDataDir/headwaters_$current_branch_id.tif \ - -nc -Tcount - -# THRESHOLD ACCUMULATIONS ## -echo -e $startDiv"Threshold Accumulations $hucNumber $current_branch_id" -date -u -Tstart -$taudemDir/threshold -ssa $tempCurrentBranchDataDir/flowaccum_d8_burned_filled_$current_branch_id.tif \ - -src $tempCurrentBranchDataDir/demDerived_streamPixels_$current_branch_id.tif \ + -stream $tempCurrentBranchDataDir/demDerived_streamPixels_$current_branch_id.tif \ -thresh 1 Tcount