add i.sentinel_2.vrt.index to i.sentinel_2

.flake8

@@ -16,3 +16,4 @@ per-file-ignores =
     ./i.sentinel_2.autotraining/i.sentinel_2.autotraining.py: E501,F821
     ./i.sentinel_2.parallel.index/i.sentinel_2.parallel.index.py: E501,F821
     ./i.sentinel_2.sen2cor/i.sentinel_2.sen2cor.py: E501,F821
+    ./i.sentinel_2.vrt.index/i.sentinel_2.vrt.index.py: E501,F821

i.sentinel_2.vrt.index/Makefile

@@ -0,0 +1,7 @@
+MODULE_TOPDIR = ../..
+
+PGM = i.sentinel_2.vrt.index
+
+include $(MODULE_TOPDIR)/include/Make/Script.make
+
+default: script

i.sentinel_2.vrt.index/i.sentinel_2.vrt.index.html

@@ -0,0 +1,15 @@
+<h2>DESCRIPTION</h2>
+
+<em>i.sentinel_2.vrt.index</em> creates vrts from input rasters using the Band suffixes (e.g. *_B04).
+It then calculates various indices using <a href="https://github.com/mundialis/i.sentinel_2/blob/main/i.sentinel_2.parallel.index/i.sentinel_2.parallel.index.html">i.sentinel_2.parallel.index</a>.
+
+<h2>SEE ALSO</h2>
+
+<em>
+<a href="https://github.com/mundialis/i.sentinel_2/blob/main/i.sentinel_2.parallel.index/i.sentinel_2.parallel.index.html">i.sentinel_2.parallel.index</a> module set,
+<a href="r.buildvrt.html">r.buildvrt</a> module set
+</em>
+
+<h2>AUTHOR</h2>
+
+Guido Riembauer, <a href="https://www.mundialis.de/">mundialis GmbH & Co. KG</a>

i.sentinel_2.vrt.index/i.sentinel_2.vrt.index.py

@@ -0,0 +1,226 @@
+#!/usr/bin/env python3
+############################################################################
+#
+# MODULE:       i.sentinel_2.vrt.index
+# AUTHOR(S):    Guido Riembauer
+# PURPOSE:      Creates VRTs from input rasters with identical band suffix and
+#               calculates indices in parallel.
+# COPYRIGHT:    (C) 2020-2023 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: Creates GRASS GIS VRT maps from input raster maps and calculates different indices and texture measures in parallel.
+# % keyword: imagery
+# % keyword: satellite
+# % keyword: Sentinel
+# % keyword: Index
+# % keyword: parallel
+# % keyword: NDVI
+# % keyword: NDWI
+# %end
+
+# %option G_OPT_F_INPUT
+# % key: input
+# % label: Input raster map names
+# % description: Input raster map names. VRTs will be built based on same bands. The band must be indicated in a suffix of the raster, separated by an underscore, e.g. "_B4"
+# % required: no
+# %end
+
+# %option
+# % key: indices
+# % type: string
+# % required: no
+# % multiple: yes
+# % label: Indices (and texture measure) to be calculated. Required bands are imported automatically, even if not indicated in the bands option. Indicate 'None' for no indices
+# % options: NDVI,NDWI,NDBI,BSI,asm,None
+# % answer: NDVI,NDWI,NDBI,BSI,asm
+# %end
+
+# %option G_OPT_M_NPROCS
+# % description: Number of cores for multiprocessing, -2 is n_cores-1
+# % answer: -2
+# % guisection: Optional
+# %end
+
+# %option
+# % key: index_res
+# % type: integer
+# % required: no
+# % multiple: no
+# % label: Spatial resolution of indices to be calculated
+# % answer: 10
+# %end
+
+# %option
+# % key: prefix
+# % type: string
+# % required: no
+# % multiple: no
+# % description: Prefix in front of output maps
+# %end
+
+import atexit
+import multiprocessing as mp
+import os
+import sys
+
+import grass.script as grass
+from grass.pygrass.modules import Module, ParallelModuleQueue
+
+rm_regions = []
+
+
+def cleanup():
+    """Cleanup function (can be extended)"""
+    nuldev = open(os.devnull, "w")
+    kwargs = {"flags": "f", "quiet": True, "stderr": nuldev}
+    for rmr in rm_regions:
+        if rmr in [x for x in grass.parse_command("g.list", type="region")]:
+            grass.run_command("g.remove", type="region", name=rmr, **kwargs)
+    # remove possible dangling temp_regions
+    try:
+        grass.del_temp_region()
+    except Exception:
+        grass.message(_("No temporary region found."))
+
+
+def main():
+    """Main function of i.sentinel_2.vrt.index"""
+    global rm_regions
+    indices = options["indices"].split(",")
+    nprocs = int(options["nprocs"])
+    input = options["input"].split(",")
+    prefix = options["prefix"]
+    index_res = options["index_res"]
+
+    if not grass.find_program("i.sentinel.parallel.index", "--help"):
+        grass.fatal(
+            _(
+                "The 'i.sentinel_2.parallel.index' module was not found, "
+                + "install it first: \n"
+                + "g.extension i.sentinel_2.parallel.index url=path/to/addon"
+            )
+        )
+
+    # set some common environmental variables, like:
+    os.environ.update(
+        dict(
+            GRASS_COMPRESS_NULLS="1",
+            GRASS_COMPRESSOR="ZSTD",
+            GRASS_MESSAGE_FORMAT="plain",
+        )
+    )
+
+    # test nprocs settings
+    if nprocs > mp.cpu_count():
+        grass.warning(
+            _(
+                f"Using {nprocs} parallel processes but only {mp.cpu_count()} "
+                f"CPUs available. Using {mp.cpu_count() - 1} procs."
+            )
+        )
+        nprocs = mp.cpu_count() - 1
+
+    # get unique bands
+    vrt_list = []
+    # get position of band info in filename
+    for idx, item in enumerate(input[0].split("_")):
+        if len(item) <= 4 and item.startswith("B"):
+            bandinfo_idx = idx
+    bands_complete = list(
+        set([raster.split("_")[bandinfo_idx] for raster in input])
+    )
+
+    # generate vrts based on unique bands
+    for band in bands_complete:
+        current_bands_list = [
+            item for item in input if item.split("_")[bandinfo_idx] == band
+        ]
+        vrt_name = prefix + band
+        if len(current_bands_list) > 1:
+            grass.run_command(
+                "r.buildvrt",
+                input=current_bands_list,
+                output=vrt_name,
+                overwrite=True,
+            )
+        elif len(current_bands_list) == 1:
+            grass.message(
+                _(f"Only one raster dataset found for band {band}. Copying...")
+            )
+            rename_str = f"{current_bands_list[0]},{vrt_name}"
+            grass.run_command("g.copy", raster=rename_str, overwrite=True)
+        else:
+            grass.fatal(
+                _("No raster datasets found for band %s. Cannot create vrt.")
+                % (band)
+            )
+        vrt_list.append(vrt_name)
+
+    # calculate indices
+    if "None" not in indices:
+        queue_index = ParallelModuleQueue(nprocs=nprocs)
+        grass.use_temp_region()
+        grass.run_command(
+            "g.region", raster=vrt_list[0], res=index_res, flags="a"
+        )
+        for index in indices:
+            outname = prefix + index
+            nir = [vrt for vrt in vrt_list if vrt.endswith("8")][0]
+            kwargs = {
+                "index": index,
+                "output": outname,
+                "nprocs": 1,
+                "nir": nir,
+            }
+            if index == "NDVI":
+                red = [vrt for vrt in vrt_list if vrt.endswith("4")][0]
+                kwargs["red"] = red
+            elif index == "NDWI":
+                green = [vrt for vrt in vrt_list if vrt.endswith("3")][0]
+                kwargs["green"] = green
+            elif index == "NDBI":
+                swir = [vrt for vrt in vrt_list if vrt.endswith("11")][0]
+                kwargs["swir"] = swir
+            elif index == "BSI":
+                swir = [vrt for vrt in vrt_list if vrt.endswith("11")][0]
+                red = [vrt for vrt in vrt_list if vrt.endswith("4")][0]
+                blue = [vrt for vrt in vrt_list if vrt.endswith("2")][0]
+                kwargs["swir"] = swir
+                kwargs["red"] = red
+                kwargs["blue"] = blue
+            elif index == "asm":
+                green = [vrt for vrt in vrt_list if vrt.endswith("3")][0]
+                red = [vrt for vrt in vrt_list if vrt.endswith("4")][0]
+                blue_tmp = [vrt for vrt in vrt_list if vrt.endswith("2")]
+                blue = [blue for blue in blue_tmp if not blue.endswith("12")][
+                    0
+                ]
+                kwargs["green"] = green
+                kwargs["red"] = red
+                kwargs["blue"] = blue
+            index_proc = Module(
+                "i.sentinel_2.parallel.index", run_=False, **kwargs
+            )
+            queue_index.put(index_proc)
+        queue_index.wait()
+        grass.del_temp_region()
+
+
+if __name__ == "__main__":
+    options, flags = grass.parser()
+    atexit.register(cleanup)
+    sys.exit(main())