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Small improvements (#85)
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* m.import.rvr improve check addon for multiaddons

* r.trees.traindata: rename trees_pixel_ndvi to nearest_pixel_ndvi

* nearest_pixel_ndvi is created automatically in r.trees.mltrain if not set, so that r.trees.traindata can be skipped if own training data are created
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@anikaweinmann
anikaweinmann authored Nov 25, 2024
1 parent 5eeab06 commit ccc4b7d
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Showing 4 changed files with 150 additions and 63 deletions.
65 changes: 65 additions & 0 deletions grass-gis-addons/m.analyse.trees/analyse_trees_lib/analyse_trees_lib.py
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Original file line number Diff line number Diff line change
Expand Up @@ -378,3 +378,68 @@ def create_grid_cd(tile_size, vec1, vec2):
grass.message(_(f"Number of tiles is: {number_tiles}"))

return grid_trees, tiles_list, number_tiles, rm_vectors


def create_nearest_pixel_ndvi(
ndvi, ndvi_threshold, nearest, nprocs, memory, rm_rasters, output
):
"""Creates the raster map with nearest tree peaks based on the NDVI
threshold
Args:
ndvi (str): The name of the NDVI raster map
ndvi_threshold (float): The threshold for the NDVI
nearest (str): The name of nearest tree peaks raster map
nprocs (int): The number of parallel processes
memory (int): The used memory in MB
rm_rasters (list): The list of raster which should be removed in the
cleanup
output (str): The name for the nearest tree peaks based on NDVI
threshold raster map
"""
# mathematical morphology: opening to remove isolated small patches of high ndvi
ndvi_split = ndvi.split("@")[0]
grass.run_command(
"r.neighbors",
input=ndvi,
output=f"{ndvi_split}_min1",
size=3,
method="minimum",
nprocs=nprocs,
memory=memory,
)
grass.run_command(
"r.neighbors",
input=f"{ndvi_split}_min1",
output=f"{ndvi_split}_min2",
size=3,
method="minimum",
nprocs=nprocs,
memory=memory,
)
grass.run_command(
"r.neighbors",
input=f"{ndvi_split}_min2",
output=f"{ndvi_split}_max1",
size=3,
method="maximum",
nprocs=nprocs,
memory=memory,
)
grass.run_command(
"r.neighbors",
input=f"{ndvi_split}_max1",
output=f"{ndvi_split}_max2",
size=3,
method="maximum",
nprocs=nprocs,
memory=memory,
)
rm_rasters.append(f"{ndvi_split}_min1")
rm_rasters.append(f"{ndvi_split}_min2")
rm_rasters.append(f"{ndvi_split}_max1")
rm_rasters.append(f"{ndvi_split}_max2")

grass.mapcalc(
f"{output} = if({ndvi_split}_max2 < {ndvi_threshold}, null(), {nearest})"
)
62 changes: 55 additions & 7 deletions grass-gis-addons/m.analyse.trees/r.trees.mltrain/r.trees.mltrain.py
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Original file line number Diff line number Diff line change
Expand Up @@ -54,12 +54,30 @@
# %end

# %option G_OPT_R_INPUT
# % key: trees_pixel_ndvi
# % key: nearest_pixel_ndvi
# % label: raster with trees identified by NDVI value
# % answer: trees_pixel_ndvi
# % required: no
# % answer: nearest_pixel_ndvi
# % guisection: Input
# %end

# %option G_OPT_R_INPUT
# % key: nearest
# % label: Name of raster with nearest peak IDs
# % required: no
# % answer: nearest_tree
# % guisection: Input
# %end

# %option
# % key: ndvi_threshold
# % type: double
# % required: no
# % label: NDVI threshold for potential trees
# % answer: 130
# % guisection: Parameters
# %end

# %option G_OPT_R_INPUT
# % key: ndvi_raster
# % label: Name of the NDVI raster
Expand Down Expand Up @@ -141,9 +159,16 @@
# % guisection: Parallel processing
# %end

# %option G_OPT_MEMORYMB
# % guisection: Parallel processing
# %end

# %rules
# % exclusive: trees_raw_r,trees_raw_v
# % required: trees_raw_r,trees_raw_v
# % required: nearest_pixel_ndvi,nearest
# % excludes: nearest_pixel_ndvi,nearest,ndvi_threshold
# % requires_all: nearest,ndvi_threshold
# %end

import atexit
Expand Down Expand Up @@ -190,7 +215,11 @@ def main():
grass.fatal("Unable to find the analyse trees library directory")
sys.path.append(path)
try:
from analyse_trees_lib import set_nprocs
from analyse_trees_lib import (
create_nearest_pixel_ndvi,
set_nprocs,
test_memory,
)
except Exception:
grass.fatal("m.analyse.trees library is not installed")

Expand All @@ -213,9 +242,17 @@ def main():
group_name = options["group"]
model_file = options["save_model"]
nprocs = int(options["nprocs"])
trees_pixel_ndvi = options["trees_pixel_ndvi"]
nearest_pixel_ndvi = options["nearest_pixel_ndvi"]
nearest = options["nearest"]
ndvi_threshold = options["ndvi_threshold"]

nprocs = set_nprocs(nprocs)
memmb = test_memory(options["memory"])
# for some modules like r.neighbors and r.slope_aspect, there is
# no speed gain by using more than 100 MB RAM
memory_max100mb = 100
if memmb < 100:
memory_max100mb = memmb

grass.use_temp_region()

Expand Down Expand Up @@ -247,17 +284,28 @@ def main():
trees_basemap = options["trees_raw_r"]

# non trees
if not grass.find_file(name=nearest_pixel_ndvi, element="cell")["file"]:
create_nearest_pixel_ndvi(
ndvi,
ndvi_threshold,
nearest,
nprocs,
memory_max100mb,
rm_rasters,
nearest_pixel_ndvi,
)
rm_rasters.append(nearest_pixel_ndvi)

# false trees
# problem areas with high NDVI like shadows on roofs, solar panels
# trees_object_filt_large = NULL and trees_pixel_ndvi != NULL
# trees_object_filt_large = NULL and nearest_pixel_ndvi != NULL
grass.mapcalc(
f"false_trees = if(isnull({trees_pixel_ndvi}), null(), if(isnull({trees_basemap}), 1, null()))"
f"false_trees = if(isnull({nearest_pixel_ndvi}), null(), if(isnull({trees_basemap}), 1, null()))"
)

# other areas clearly not trees
grass.mapcalc(
f"notrees = if(isnull({trees_pixel_ndvi}) && isnull({trees_basemap}), 1, null())"
f"notrees = if(isnull({nearest_pixel_ndvi}) && isnull({trees_basemap}), 1, null())"
)
rm_rasters.append("false_trees")
rm_rasters.append("notrees")
Expand Down
71 changes: 19 additions & 52 deletions grass-gis-addons/m.analyse.trees/r.trees.traindata/r.trees.traindata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -158,7 +158,7 @@
# %end

# %option G_OPT_R_OUTPUT
# % key: trees_pixel_ndvi
# % key: nearest_pixel_ndvi
# % label: Name of raster with nearest peak IDs filtered by NDVI
# % description: necessary intermediate result for mltrain
# % required: no
Expand Down Expand Up @@ -211,7 +211,11 @@ def main():
grass.fatal("Unable to find the analyse trees library directory")
sys.path.append(path)
try:
from analyse_trees_lib import set_nprocs, test_memory
from analyse_trees_lib import (
create_nearest_pixel_ndvi,
set_nprocs,
test_memory,
)
except Exception:
grass.fatal("m.analyse.trees library is not installed")

Expand All @@ -226,7 +230,6 @@ def main():
blue = options["blue_raster"]
nir = options["nir_raster"]
ndvi = options["ndvi_raster"]
ndvi_split = ndvi.split("@")[0]
ndwi = options["ndwi_raster"]
ndgb = options["ndgb_raster"]
ndsm = options["ndsm"]
Expand Down Expand Up @@ -273,62 +276,26 @@ def main():
# - lower such that trees are kept -> shadow areas are kept

# mathematical morphology: opening to remove isolated small patches of high ndvi
grass.run_command(
"r.neighbors",
input=ndvi,
output=f"{ndvi_split}_min1",
size=3,
method="minimum",
nprocs=nprocs,
memory=memory_max100mb,
)
grass.run_command(
"r.neighbors",
input=f"{ndvi_split}_min1",
output=f"{ndvi_split}_min2",
size=3,
method="minimum",
nprocs=nprocs,
memory=memory_max100mb,
)
grass.run_command(
"r.neighbors",
input=f"{ndvi_split}_min2",
output=f"{ndvi_split}_max1",
size=3,
method="maximum",
nprocs=nprocs,
memory=memory_max100mb,
)
grass.run_command(
"r.neighbors",
input=f"{ndvi_split}_max1",
output=f"{ndvi_split}_max2",
size=3,
method="maximum",
nprocs=nprocs,
memory=memory_max100mb,
)
rm_rasters.append(f"{ndvi_split}_min1")
rm_rasters.append(f"{ndvi_split}_min2")
rm_rasters.append(f"{ndvi_split}_max1")
rm_rasters.append(f"{ndvi_split}_max2")

if options["trees_pixel_ndvi"]:
trees_pixel_ndvi = options["trees_pixel_ndvi"]
if options["nearest_pixel_ndvi"]:
nearest_pixel_ndvi = options["nearest_pixel_ndvi"]
else:
trees_pixel_ndvi = "trees_pixel_ndvi"
rm_rasters.append(trees_pixel_ndvi)

grass.mapcalc(
f"{trees_pixel_ndvi} = if({ndvi_split}_max2 < {ndvi_threshold}, null(), {nearest})"
nearest_pixel_ndvi = "nearest_pixel_ndvi"
rm_rasters.append(nearest_pixel_ndvi)
create_nearest_pixel_ndvi(
ndvi,
ndvi_threshold,
nearest,
nprocs,
memory_max100mb,
rm_rasters,
nearest_pixel_ndvi,
)

# cut to nir: all pixels below 100 are not vegetation
# removes shadows with high ndvi e.g. on roofs
# needed
grass.mapcalc(
f"trees_pixel_nir = if({nir} < {nir_threshold}, null(), {trees_pixel_ndvi})"
f"trees_pixel_nir = if({nir} < {nir_threshold}, null(), {nearest_pixel_ndvi})"
)
rm_rasters.append("trees_pixel_nir")

Expand Down
15 changes: 11 additions & 4 deletions grass-gis-addons/m.import.rvr/m.import.rvr.py
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Original file line number Diff line number Diff line change
Expand Up @@ -569,19 +569,22 @@ def check_data_exists(data, optionname):
grass.fatal(_(f"The data directory <{data}> does not exists."))


def check_addon(addon, url=None):
def check_addon(addon, url=None, multiaddon=None):
"""Check if addon is installed.
Args:
addon (str): Name of the addon
url (str): Url to download the addon
"""
if not grass.find_program(addon, "--help"):
if not multiaddon:
multiaddon = addon
msg = (
f"The '{addon}' module was not found, install it first:\n"
f"g.extension {addon}"
f"The '{addon}' module was not found, install it first:\n"
f"<g.extension {multiaddon}"
)
if url:
msg += f" url={url}"
msg += ">"
grass.fatal(_(msg))


Expand Down Expand Up @@ -1585,7 +1588,11 @@ def main():

# check if needed addons are installed
check_addon("r.import.ndsm_nrw", "/path/to/r.import.ndsm_nrw")
check_addon("r.dem.import", "https://github.com/mundialis/r.dem.import")
check_addon(
"r.dtm.import.nw",
"https://github.com/mundialis/r.dem.import",
"r.dem.import",
)

# check if needed paths to data are set
grass.message(_("Checking input parameters ..."))
Expand Down

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