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r.maxent.predict: change parameter names to avoid conflicts when scri…
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…pting (#1238)

* bugfixes and improved error handling

* Add / improve error messages

Add progress indicator
Improve error messages

* r.maxent.predict: add option to provide folder with input raster layers

Add option to provide folder with input raster layers - time saver if the same layers are required multiple times.
Improvement check if right layers/variables are used as input.
Added check if provided layer names exist in more than one mapset (only if mapset is not provided). This will result in error, except if the layers are also in the current mapset (because in that case GRASS chooses those anyway).

* Rename parameters to avoid conflicts
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@ecodiv
ecodiv authored Nov 14, 2024
1 parent fe58963 commit 327079d
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7 changes: 5 additions & 2 deletions src/raster/r.maxent.predict/r.maxent.predict.html
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Original file line number Diff line number Diff line change
Expand Up @@ -197,7 +197,9 @@ <h3>3: Create a prediction layer</h3>
<div class="code">
<pre>
r.maxent.predict
lambda=output_model1/Bradypus_tridactylus.lambdas raster=bio02_ssp585,bio03_ssp585,bio08_ssp585,bio09_ssp585,bio13_ssp585,bio15_ssp585,bio17_ssp585,sa_eco_l2@current variables=bio02,bio03,bio08,bio09,bio13,bio15,bio17,landuse \
lambda=output_model1/Bradypus_tridactylus.lambdas \
rasters=bio02_ssp585,bio03_ssp585,bio08_ssp585,bio09_ssp585,bio13_ssp585,bio15_ssp585,bio17_ssp585,sa_eco_l2 \
variables=bio02,bio03,bio08,bio09,bio13,bio15,bio17,landuse \
output=model_1_ssp585
</pre>
</div>
Expand All @@ -207,7 +209,8 @@ <h3>3: Create a prediction layer</h3>
<i>model_1_ssp585</i> (right map in the figure below). The results
suggest the area with suitable conditions will increase under future
climates compared the that under the current conditions (left map in
the figure below). Not sure that is realistic.
the figure below). This result is unexpected, and warrants further
investigation.

<p>
<div align="left" style="margin: 10px"> <a
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208 changes: 145 additions & 63 deletions src/raster/r.maxent.predict/r.maxent.predict.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,14 +27,14 @@
# %end

# %option G_OPT_F_BIN_INPUT
# % key: lambda
# % key: lambdafile
# % label: Lambda model file
# % description: Lambda model file created by Maxent or the r.maxent.train addon.
# % guisection: input
# %end

# %option G_OPT_R_INPUTS
# % key: raster
# % key: rasters
# % type: string
# % label: Names of the input raster layers
# % description: Names of the raster layers representing the environmental variables used in the Maxent model.
Expand All @@ -51,16 +51,28 @@
# % guisection: input
# %end

# %option G_OPT_M_DIR
# % key: projectionlayers
# % label: Location of folder with set of environmental variables.
# % description: Directory with set of rasters representing the same environmental variables as used to create the Maxent model. The names of the raster layers, excluding the file extension, need to be the same as the variable names used to create the Maxent model.
# % guisection: input
# % required: no
# %end

# %rules
# % excludes: projectionlayers,rasters,variables
# %end

# %option G_OPT_F_BIN_INPUT
# % key: alias_file
# % label: csv file with variable and layer names
# % description: A csv file with in the first column the names of the explanatory variables used in the model, and in the second column the names of corresponding raster layers. Make both are provided in the same order.
# % description: A csv file with in the first column the names of the explanatory variables used in the model, and in the second column the names of corresponding raster layers. Make sure both are provided in the same order.
# % guisection: input
# % required: no
# %end

# %rules
# % excludes: alias_file,variables,raster
# % excludes: alias_file,variables,rasters
# %end

# %flag
Expand Down Expand Up @@ -132,15 +144,42 @@
import shutil
import subprocess
import sys
import threading
import time
import uuid
import grass.script as gs

# Functions
# ------------------------------------------------------------------

temp_directory = gs.tempdir()

class LoadingIndicator:
def __init__(self, message="Processing..."):
self.message = message
self.symbols = ["|", "/", "-", "\\"]
self.stop_running = False
self.thread = threading.Thread(target=self._animate)

def _animate(self):
while not self.stop_running:
for symbol in self.symbols:
if self.stop_running:
break
sys.stdout.write(f"\r{symbol} {self.message}")
sys.stdout.flush()
time.sleep(0.1)
# Clear the line after stopping
sys.stdout.write("\r\n")

def start(self):
self.stop_running = False
self.thread.start()

def stop(self):
self.stop_running = True
self.thread.join()


# Functions
# ------------------------------------------------------------------
def find_index_case_insensitive(lst, target):
"""
Find index for string match, matching case insensitive
Expand All @@ -159,20 +198,29 @@ def cleanup():
pass


def check_layers_exist(layers):
"""
Check if all layers in a list exist in accessible mapsets.
param str layers: names of layers
return list: list with names of missing layers
"""
def check_layers(layers):
missing_layers = []
double_layers = []
current_mapset = gs.gisenv()["MAPSET"]
for layer in layers:
if "@" in layer:
layname, mpset = layer.split("@")
else:
layname = layer
mpset = ""

# List raster layers matching the pattern in the specified mapset
chlay = gs.parse_command(
"g.list", flags="m", type="raster", pattern=layname, mapset=mpset
)

# Check if the layer exists in the current mapset
if not gs.find_file(name=layer)["fullname"]:
chlay_mapsets = {mapsetname.split("@")[1] for mapsetname in chlay.keys()}
if not chlay:
missing_layers.append(layer)
return missing_layers
elif len(chlay) > 1 and current_mapset not in chlay_mapsets:
double_layers.append(layer)
return {"missing": missing_layers, "double": double_layers}


def create_temp_name(prefix):
Expand Down Expand Up @@ -270,56 +318,75 @@ def main(options, flags):
)
gs.fatal(_(msg))

# Get names of variables and corresponding layer names
# Create (or get) folder with environmental layers
# ------------------------------------------------------------------
gs.info(_("Check if the variable and layer names correspond\n"))

if bool(options["alias_file"]):
with open(options["alias_file"]) as csv_file:
row_data = list(csv.reader(csv_file, delimiter=","))
col_data = list(zip(*row_data))
chlay = check_layers_exist(col_data[1])
if len(chlay) > 0:
gs.message(

projectionlayers = options["projectionlayers"]
if projectionlayers:
# The name of an existing folder with layers is provided
temp_directory = projectionlayers
else:
# Create temporary folder for the raster layers
temp_directory = gs.tempdir()

# Get Get names of variables and corresponding layer names
if bool(options["alias_file"]):
with open(options["alias_file"]) as csv_file:
row_data = list(csv.reader(csv_file, delimiter=","))
col_data = list(zip(*row_data))
file_names = col_data[0]
layer_names = col_data[1]
else:
layer_names = options["rasters"].split(",")
if bool(options["variables"]):
file_names = options["variables"].split(",")
else:
file_names = [strip_mapset(x) for x in layer_names]
chlay = check_layers(layer_names)
if len(chlay["missing"]) > 0:
gs.fatal(
_(
"The layer(s) {} do not exist in the accessible mapsets".format(
", ".join(chlay)
", ".join(chlay["missing"])
)
)
)
if len(chlay["double"]) > 0:
gs.fatal(
_(
"There are layers with the name {} in multiple accessible mapsets, "
"none of which are in the current mapset."
"Add the mapset name to specify which or these layers should be used.".format(
", ".join(chlay["double"])
)
)
)
else:
file_names = col_data[0]
layer_names = col_data[1]
else:
layer_names = options["raster"].split(",")
if bool(options["variables"]):
file_names = options["variables"].split(",")
else:
file_names = [strip_mapset(x) for x in layer_names]

# Export raster layers to temporary directory
# ------------------------------------------------------------------
gs.info(_("Export the raster layers as asci layers for use by Maxent\n"))
# Export raster layers to temporary directory
gs.info(_("Export the raster layers as asci layers for use by Maxent\n"))
loading_indicator = LoadingIndicator()
loading_indicator.start()

for n, layer_name in enumerate(layer_names):
dt = gs.parse_command("r.info", map=layer_name, flags="g")["datatype"]
if dt == "CELL":
datatype = "Int16"
nodataval = -9999
else:
datatype = ""
nodataval = -9999999
file_name = os.path.join(temp_directory, f"{file_names[n]}.asc")
gs.run_command(
"r.out.gdal",
input=layer_name,
output=file_name,
format="AAIGrid",
flags="c",
type=datatype,
nodata=nodataval,
quiet=True,
)
for n, layer_name in enumerate(layer_names):
dt = gs.parse_command("r.info", map=layer_name, flags="g")["datatype"]
if dt == "CELL":
datatype = "Int16"
nodataval = -9999
else:
datatype = ""
nodataval = -9999999
file_name = os.path.join(temp_directory, f"{file_names[n]}.asc")
gs.run_command(
"r.out.gdal",
input=layer_name,
output=file_name,
format="AAIGrid",
flags="c",
type=datatype,
nodata=nodataval,
quiet=True,
)
loading_indicator.stop()

# Input parameters - building command line string
# ------------------------------------------------------------------
Expand All @@ -332,7 +399,7 @@ def main(options, flags):
"-cp",
maxent_file,
"density.Project",
options["lambda"],
options["lambdafile"],
temp_directory,
temp_file,
]
Expand All @@ -344,26 +411,41 @@ def main(options, flags):

# Run Maxent density.Project
# -----------------------------------------------------------------
gs.info(_("This may take some time ..."))
with subprocess.Popen(
maxent_command,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
universal_newlines=True,
text=True,
) as process:
# Capture and print stdout
for stdout_line in process.stdout:
gs.info(stdout_line)
# Capture and print stderr
for stderr_line in process.stderr:
gs.info(stderr_line)
gs.info(f"Warning/Error: {stderr_line}")
if "java.util.NoSuchElementException" in stderr_line:
missing_variables = (
"Check variable names and path + names of input files"
)
# Check the return code
process.wait()
if process.returncode != 0:
gs.fatal(_("Maxent terminated with an error"))

if missing_variables:
gs.fatal(missing_variables)
else:
gs.fatal(_("Maxent terminated with an error"))
# -----------------------------------------------------------------
# Import the resulting layer in GRASS GIS
# -----------------------------------------------------------------
if not os.path.isfile(temp_file):
gs.fatal(
_(
"Maxent did not create an output raster for import in GRASS.\n"
"Check the error message(s) above."
)
)
gs.info(_("Importing the predicted suitability layer in GRASS GIS\n"))
gs.run_command(
"r.in.gdal",
Expand Down

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