r.incora

.flake8

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+[flake8]
+
+# E501 line too long (83 > 79 characters)
+# F821 undefined name '_'
+
+exclude = .git
+max-line-length = 88
+per-file-ignores =
+    ./v.incora.training_data/v.incora.training_data.py: F821, E501
+    ./r.incora.postproc/r.incora.postproc.py: F821
+    ./r.incora.change/r.incora.change.py: F821

.github/workflows/flake8.yml

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+name: Python Flake8 Code Quality
+
+on:
+  - push
+  - pull_request
+
+jobs:
+  flake8:
+    runs-on: ubuntu-20.04
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+
+      - name: Install
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8==3.8.4
+      - name: Run Flake8
+        run: |
+          flake8 --config=.flake8 --count --statistics --show-source --jobs=$(nproc) .

Makefile

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+MODULE_TOPDIR = ../..
+
+PGM = r.incora
+
+# note: to deactivate a module, just place a file "DEPRECATED" into the subdir
+ALL_SUBDIRS := ${sort ${dir ${wildcard */.}}}
+DEPRECATED_SUBDIRS := ${sort ${dir ${wildcard */DEPRECATED}}}
+RM_SUBDIRS := bin/ docs/ etc/ scripts/
+SUBDIRS_1 := $(filter-out $(DEPRECATED_SUBDIRS), $(ALL_SUBDIRS))
+SUBDIRS := $(filter-out $(RM_SUBDIRS), $(SUBDIRS_1))
+
+include $(MODULE_TOPDIR)/include/Make/Dir.make
+
+default: parsubdirs htmldir
+
+install: installsubdirs
+	$(INSTALL_DATA) $(PGM).html $(INST_DIR)/docs/html/

r.incora.change/Makefile

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+MODULE_TOPDIR = ../..
+
+PGM = r.incora.change
+
+include $(MODULE_TOPDIR)/include/Make/Script.make
+
+default: script

r.incora.change/r.incora.change.html

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+<h2>DESCRIPTION</h2>
+
+<em>r.incora.change</em> runs a change detection based on two input maps. The
+nomenclature is optimized for the incora project.
+
+<h2>SEE ALSO</h2>
+
+<em>
+<a href="r.change.stats">r.sample.category</a>
+<a href="r.change.info">r.buffer</a>
+<a href="r.mapcalc">r.mapcalc</a>
+</em>
+
+<h2>AUTHORS</h2>
+
+Guido Riembauer, mundialis, riembauer at mundialis.de
+
+
+<!--
+<p>
+<i>Last changed: $Date$</i>
+-->

r.incora.change/r.incora.change.py

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+#!/usr/bin/env python3
+
+############################################################################
+#
+# MODULE:       r.incora.change
+# AUTHOR(S):    Guido Riembauer
+# PURPOSE:      Runs r.change.stats and does post processing for incora
+# COPYRIGHT:	(C) 2020-2022 by mundialis GmbH & Co. KG and the GRASS
+#               Development Team
+#
+#  This program is free software; you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation; either version 2 of the License, or
+#  (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#############################################################################
+
+# %Module
+# % description: Runs r.change.stats and does post processing for incora.
+# % keyword: raster
+# % keyword: classification
+# % keyword: change detection
+# %end
+
+# %option G_OPT_R_INPUT
+# % key: input
+# % label: Two input raster maps to calculate the change detection on
+# % description: It is assumed that the second raster is the later one
+# %end
+
+# %option G_OPT_R_OUTPUT
+# % key: output_cd
+# % required: no
+# % multiple: no
+# % label: Name of total output change detection map
+# %end
+
+# %option G_OPT_R_OUTPUT
+# % key: output_water
+# % required: no
+# % multiple: no
+# % label: Name of output change detection map of water areas
+# %end
+
+# %option G_OPT_R_OUTPUT
+# % key: output_bu
+# % required: no
+# % multiple: no
+# % label: Name of output change detection map of built-up areas
+# %end
+
+# %option G_OPT_R_OUTPUT
+# % key: output_forest
+# % required: no
+# % multiple: no
+# % label: Name of output change detection map of forest areas
+# %end
+
+# %option G_OPT_R_OUTPUT
+# % key: output_lowveg
+# % required: no
+# % multiple: no
+# % label: Name of output change detection map of low vegetation areas
+# %end
+
+# %option G_OPT_R_OUTPUT
+# % key: output_bare
+# % required: no
+# % multiple: no
+# % label: Name of output change detection map of bare soil areas
+# %end
+
+# %option G_OPT_R_OUTPUT
+# % key: output_agr
+# % required: no
+# % multiple: no
+# % label: Name of output change detection map of agriculture areas
+# %end
+
+# %option
+# % key: minsize
+# % type: string
+# % required: no
+# % multiple: no
+# % answer: 1.0
+# % label: Minimum size of changed areas (in ha)
+# % description: Smaller areas will be deleted from the output raster(s)
+# %end
+
+# %option
+# % key: mode_winsize
+# % type: integer
+# % required: no
+# % multiple: no
+# % answer: 3
+# % label: Size of mode filter if -f flag is set
+# % description: -f flag must be set
+# %end
+
+# %option
+# % key: gain_winsize
+# % type: integer
+# % required: no
+# % multiple: no
+# % answer: 4
+# % label: Window size of information gain filter in r.change.info
+# %end
+
+# %option
+# % key: gain_thresh
+# % type: string
+# % required: no
+# % multiple: no
+# % answer: 0.5
+# % label: Threshold for the information gain map
+# % description: All areas < gain_thresh are omitted from the output maps
+# %end
+
+# %flag
+# % key: f
+# % description: Filter change detection product using a mode filter of size window_size
+# %end
+
+import atexit
+import os
+import grass.script as grass
+
+# initialize global vars
+rm_rasters = []
+
+
+def cleanup():
+    nuldev = open(os.devnull, "w")
+    kwargs = {
+        "flags": "f",
+        "quiet": True,
+        "stderr": nuldev
+    }
+    for rmrast in rm_rasters:
+        if grass.find_file(name=rmrast, element="raster")["file"]:
+            grass.run_command("g.remove", type="raster", name=rmrast, **kwargs)
+
+
+def main():
+
+    global rm_rasters
+    # parameters
+    input = options["input"].split(",")
+    if len(input) != 2:
+        grass.fatal(_("Input must consist of two raster maps"))
+    if options["output_cd"]:
+        outrast_cd = options["output_cd"]
+    else:
+        outrast_cd = "cd_rast_%s" % os.getpid()
+        rm_rasters.append(outrast_cd)
+
+    output_agr = options["output_agr"]
+    output_forest = options["output_forest"]
+    output_lowveg = options["output_lowveg"]
+    output_water = options["output_water"]
+    output_bu = options["output_bu"]
+    output_bare = options["output_bare"]
+
+    if not grass.find_program("r.change.stats", "--help"):
+        grass.fatal(_("The 'r.change.stats' module was not found, install it first:") +
+                    "\n" +
+                    "g.extension r.change.stats url=path/to/module")
+    if not grass.find_program("r.change.info", "--help"):
+        grass.fatal(
+            _("The 'r.change.info' module was not found, install it first:")
+            + "\n g.extension r.change.info")
+    cd_temprast = "cd_tempraster_%s" % os.getpid()
+    rm_rasters.append(cd_temprast)
+    cd_params = {
+        "input": input,
+        "output": cd_temprast,
+        "flags": "cl"
+    }
+    if flags["f"]:
+        cd_params["window_size"] = options["mode_winsize"]
+        cd_params["flags"] += "f"
+    grass.message(_("Calculating change detection..."))
+    grass.run_command("r.change.stats", **cd_params)
+    output_list = [output_forest, output_lowveg, output_water, output_bu,
+                   output_bare, output_agr]
+    values_list = ["10", "20", "30", "40", "50", "60"]
+    output_used = []
+    values_used = []
+    for idx, item in enumerate(output_list):
+        if len(item) > 0:
+            output_used.append(item)
+            values_used.append(values_list[idx])
+
+    grass.message(_("Calculating Information Gain..."))
+    gainmap = "gainmap_%s" % os.getpid()
+    rm_rasters.append(gainmap)
+    steps = int(options["gain_winsize"])/2
+    grass.run_command("r.change.info", input=input, method="gain1",
+                      size=options["gain_winsize"], step=steps,
+                      output=gainmap, quiet=True)
+    if len(output_used) > 0:
+        tempraster_1 = "%s_tmp1_%s" % (item, os.getpid())
+        rm_rasters.append(tempraster_1)
+        # correct the outrast_cd raster with the information gain
+        eq = f"{outrast_cd} = if({gainmap}>{options['gain_thresh']},{cd_temprast},0)"
+        grass.run_command("r.mapcalc", expression=eq, quiet=True)
+        # this binary raster contains where changes occured
+        expression_1 = "%s = if(%s > %s && %s != 0, 1, null())" % (
+                       tempraster_1, gainmap, options["gain_thresh"],
+                       outrast_cd)
+        grass.run_command("r.mapcalc", expression=expression_1, quiet=True)
+    for idx, item in enumerate(output_used):
+        grass.message(_("Calculating change raster %s..." % item))
+        tempraster_2 = "%s_tmp2_%s" % (item, os.getpid())
+        rm_rasters.append(tempraster_2)
+        # this raster contains where changes occured and one of the input
+        # rasters contains the respective class (1 = map1, 2 = map2)
+        expression_2 = f"{tempraster_2} = if({tempraster_1} == 1 && " \
+            f"{input[0]} == {values_used[idx]},1, " \
+            f"if({tempraster_1} == 1 && {input[1]} == {values_used[idx]}," \
+            f"2,null()))"
+        grass.run_command("r.mapcalc", expression=expression_2, quiet=True)
+        # omit areas smaller < threshold
+        grass.run_command(
+            "r.reclass.area",
+            input=tempraster_2,
+            output=item,
+            value=options["minsize"],
+            mode="greater",
+            method="reclass",
+            quiet=True,
+        )
+    grass.message(_("Generated output maps:"))
+    if options["output_cd"]:
+        grass.message(_(f"<{outrast_cd}>"))
+    for item in output_used:
+        grass.message(_(f"<{item}>"))
+
+
+if __name__ == "__main__":
+    options, flags = grass.parser()
+    atexit.register(cleanup)
+    main()

r.incora.html

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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+<head>
+<title>GRASS GIS manual: r.incora toolset</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<link rel="stylesheet" href="grassdocs.css" type="text/css">
+</head>
+<body bgcolor="white">
+<div id="container">
+
+<a href="https://grass.osgeo.org/grass-stable/manuals/index.html"><img src="grass_logo.png" alt="GRASS logo"></a>
+<hr class="header">
+
+<h2>NAME</h2>
+
+<em><b>r.incora</b></em> - Toolset for Incora landcover classification.
+
+
+<h2>KEYWORDS</h2>
+<a href="https://grass.osgeo.org/grass-stable/manuals/raster.html">raster</a>, <a href="https://grass.osgeo.org/grass-stable/manuals/topic_classification.html">classification</a>
+
+<!-- meta page description: Toolset for download and processing time series of Sentinel products -->
+<h2>DESCRIPTION</h2>
+
+The <em>r.incora</em> toolset consists of currently three modules.
+<p>
+
+<i>Processing modules:</i>
+<dl>
+  <dt><a href="v.incora.training_data.html">v.incora.training_data</a></dt>
+  <dd>creates a vector map containing training points from a set of rules
+    containing the output classes: forest, low vegetation, water, built-up,
+    bare soil and agriculture.</dd>
+  <dt><a href="r.incora.postproc.html">r.incora.postproc</a></dt>
+  <dd> uses post processing to deal with mixed pixels identified
+  in <a href="v.incora.training_data">v.incora.training_data</a>. Mixed pixels
+  (class 70) are removed from the map. The gaps are then filled using
+  <a href="https://grass.osgeo.org/grass80/manuals/r.grow.distance.html">r.grow.distance</a>.</dd>
+  <dt><a href="r.incora.change.html">r.incora.change</a></dt>
+  <dd>runs a change detection based on two input maps. The
+  nomenclature is optimized for the incora project.</dd>
+</dl>
+
+<h2>REQUIREMENTS</h2>
+
+The following GRASS GIS Addons are required:
+
+<ul>
+  <li><a href="https://grass.osgeo.org/grass80/manuals/addons/r.sample.category.html">r.sample.category</a></li>
+  <li><a href="https://github.com/mundialis/r.change.stats.html">r.change.stats</a></li>
+  <li><a href="https://grass.osgeo.org/grass80/manuals/addons/r.change.info.html">r.change.info</a></li>
+</ul>
+
+<h2>AUTHORS</h2>
+
+Anika Weinmann and Guido Riembauer, <a href="https://www.mundialis.de/">mundialis</a>
+
+
+<!--
+<p>
+<i>Last changed: $Date$</i>
+-->