From 0841e7a4aec6c25f4af4ba08c3249ba6f3753cbf Mon Sep 17 00:00:00 2001
From: Julia Haas <haas@mundialis.de>
Date: Wed, 3 Jan 2024 17:29:52 +0100
Subject: [PATCH 01/17] adaptions to run modules in gui

---
 .../r.trees.mltrain/r.trees.mltrain.py        | 24 +++++++++----------
 .../r.trees.peaks/r.trees.peaks.py            |  8 +++----
 grass-gis-addons/m.import.rvr/m.import.rvr.py |  8 +++----
 3 files changed, 20 insertions(+), 20 deletions(-)

diff --git a/grass-gis-addons/m.analyse.trees/r.trees.mltrain/r.trees.mltrain.py b/grass-gis-addons/m.analyse.trees/r.trees.mltrain/r.trees.mltrain.py
index 5eb470b..2b11d3b 100644
--- a/grass-gis-addons/m.analyse.trees/r.trees.mltrain/r.trees.mltrain.py
+++ b/grass-gis-addons/m.analyse.trees/r.trees.mltrain/r.trees.mltrain.py
@@ -280,7 +280,7 @@ def main():
     grass.run_command(
         "r.neighbors",
         input=ndvi,
-        output=f"{ndvi}_min1",
+        output=f"{ndvi.split('@')[0]}_min1",
         size=3,
         method="minimum",
         nprocs=nprocs,
@@ -288,8 +288,8 @@ def main():
     )
     grass.run_command(
         "r.neighbors",
-        input=f"{ndvi}_min1",
-        output=f"{ndvi}_min2",
+        input=f"{ndvi.split('@')[0]}_min1",
+        output=f"{ndvi.split('@')[0]}_min2",
         size=3,
         method="minimum",
         nprocs=nprocs,
@@ -297,8 +297,8 @@ def main():
     )
     grass.run_command(
         "r.neighbors",
-        input=f"{ndvi}_min2",
-        output=f"{ndvi}_max1",
+        input=f"{ndvi.split('@')[0]}_min2",
+        output=f"{ndvi.split('@')[0]}_max1",
         size=3,
         method="maximum",
         nprocs=nprocs,
@@ -306,20 +306,20 @@ def main():
     )
     grass.run_command(
         "r.neighbors",
-        input=f"{ndvi}_max1",
-        output=f"{ndvi}_max2",
+        input=f"{ndvi.split('@')[0]}_max1",
+        output=f"{ndvi.split('@')[0]}_max2",
         size=3,
         method="maximum",
         nprocs=nprocs,
         memory=memory_max100mb,
     )
-    rm_rasters.append(f"{ndvi}_min1")
-    rm_rasters.append(f"{ndvi}_min2")
-    rm_rasters.append(f"{ndvi}_max1")
-    rm_rasters.append(f"{ndvi}_max2")
+    rm_rasters.append(f"{ndvi.split('@')[0]}_min1")
+    rm_rasters.append(f"{ndvi.split('@')[0]}_min2")
+    rm_rasters.append(f"{ndvi.split('@')[0]}_max1")
+    rm_rasters.append(f"{ndvi.split('@')[0]}_max2")
 
     grass.mapcalc(
-        f"trees_pixel_ndvi = if({ndvi}_max2 < {ndvi_threshold}, null(), {nearest})"
+        f"trees_pixel_ndvi = if({ndvi.split('@')[0]}_max2 < {ndvi_threshold}, null(), {nearest})"
     )
     rm_rasters.append("trees_pixel_ndvi")
 
diff --git a/grass-gis-addons/m.analyse.trees/r.trees.peaks/r.trees.peaks.py b/grass-gis-addons/m.analyse.trees/r.trees.peaks/r.trees.peaks.py
index c4609d2..bfca2ba 100644
--- a/grass-gis-addons/m.analyse.trees/r.trees.peaks/r.trees.peaks.py
+++ b/grass-gis-addons/m.analyse.trees/r.trees.peaks/r.trees.peaks.py
@@ -57,7 +57,7 @@
 # % required: yes
 # % multiple: no
 # % label: Output raster map with ID of nearest tree
-# % answer: trees_nearest
+# % answer: nearest_tree
 # % guisection: Output
 # %end
 
@@ -177,7 +177,7 @@ def main():
     ndsm_resampled = ndsm
     rinfo = grass.raster_info(ndsm)
     if rinfo["nsres"] < forms_res:
-        ndsm_resampled = f"{ndsm}_resampled"
+        ndsm_resampled = f"{ndsm.split('@')[0]}_resampled"
         rm_rasters.append(ndsm_resampled)
         grass.run_command(
             "r.resamp.stats",
@@ -186,7 +186,7 @@ def main():
             method="maximum",
         )
     elif rinfo["nsres"] > forms_res:
-        ndsm_resampled = f"{ndsm}_resampled"
+        ndsm_resampled = f"{ndsm.split('@')[0]}_resampled"
         rm_rasters.append(ndsm_resampled)
         radius_gauss = rinfo["nsres"] * 1.5
         radius_box = rinfo["nsres"] * 3
@@ -198,7 +198,7 @@ def main():
             radius=f"{radius_gauss},{radius_box}",
         )
 
-    ndsm_forms = f"{ndsm}_forms"
+    ndsm_forms = f"{ndsm.split('@')[0]}_forms"
     grass.run_command(
         "r.geomorphon", elevation=ndsm_resampled, forms=ndsm_forms, search=7
     )
diff --git a/grass-gis-addons/m.import.rvr/m.import.rvr.py b/grass-gis-addons/m.import.rvr/m.import.rvr.py
index 817140b..e5c8fd3 100644
--- a/grass-gis-addons/m.import.rvr/m.import.rvr.py
+++ b/grass-gis-addons/m.import.rvr/m.import.rvr.py
@@ -68,7 +68,7 @@
 # % key: dsm_tindex
 # % required: no
 # % multiple: no
-# % label: Name of the DSM tindex which should be used or created
+# % label: Name of the DSM tindex which should be used or created (optional)
 # % description: If this is set the tindex needs a column <location> with the absolute path to the DSM files
 # % guisection: General input
 # %end
@@ -86,7 +86,7 @@
 # % key: dtm_tindex
 # % required: no
 # % multiple: no
-# % label: Name of the DTM tindex which should be used or created
+# % label: Name of the DTM tindex which should be used or created (optional)
 # % description: If this is set the tindex needs a column <location> with the absolute path to the DTM files
 # % guisection: General input
 # %end
@@ -149,7 +149,7 @@
 # % key: dop_tindex
 # % required: no
 # % multiple: no
-# % label: Name of the DOP tindex which should be used or created
+# % label: Name of the DOP tindex which should be used or created (optional)
 # % description: If this is set the tindex needs a column <location> with the absolute path to the DOP files
 # % guisection: Input buildings analysis
 # %end
@@ -167,7 +167,7 @@
 # % key: top_tindex
 # % required: no
 # % multiple: no
-# % label: Name of the TOP tindex which should be used or created
+# % label: Name of the TOP tindex which should be used or created (optional)
 # % description: If this is set the tindex needs a column location with the absolute path to the TOP files
 # % guisection: Input trees analysis
 # %end

From c6184c6eb72441b7e90a3d1782452f49b301186c Mon Sep 17 00:00:00 2001
From: anikaweinmann <aweinmann@mundialis.de>
Date: Thu, 4 Jan 2024 11:25:09 +0100
Subject: [PATCH 02/17] Docker with GUI on Windows

---
 README.md | 25 ++++++++++++++++++++++++-
 1 file changed, 24 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index d143d4c..333c0be 100644
--- a/README.md
+++ b/README.md
@@ -66,7 +66,7 @@ docker build -t rvr_interface:latest .
 
 Instead of "latest", a version number can be used. This should create a local
 docker image with all needed addons and dependencies. Once the docker image
-has been created locally, it can be started with e.g.
+has been created locally, it can be started on Linux with e.g.
 ```bash
 xhost local:*
 docker run -it --privileged --rm --ipc host \
@@ -77,3 +77,26 @@ docker run -it --privileged --rm --ipc host \
        --device="/dev/dri/card0:/dev/dri/card0" \
        rvr_interface:latest bash
 ```
+
+and on Windows you need the following things to do before:
+1. Download and install [VcXsrv Windows X Server](https://sourceforge.net/projects/vcxsrv/)
+2. Start **Xlaunch** and configure it (see https://dev.to/darksmile92/run-gui-app-in-linux-docker-container-on-windows-host-4kde):
+  * in the "Extra Settings" window enable "Disable access control"
+  * in the "Finish Configuration" window click "Save configuration" and save it e.g. on the desktop
+Now you can run the docker:
+```bash
+# get own IP adress (take the value of IPAdress e.g. 10.211.55.10 and not 127.0.0.1)
+Get-NetIPAddress
+ipconfig
+
+# set DISPLAY variable (set <YOUR-IP>)
+set-variable -name DISPLAY -value <YOUR-IP>:0.0
+
+# start Docker
+docker run -it --privileged --rm --ipc host \
+       -v C:/Users/path/to/grassdata:/grassdb \
+       -v C:/Users/path/to/rvr_daten:/mnt/data \
+       --env DISPLAY=$DISPLAY \
+       --device="/dev/dri/card0:/dev/dri/card0" \
+       rvr_interface:latest bash
+```

From 1810ea3764a114c3ed0ef985871f6937bd1e0539 Mon Sep 17 00:00:00 2001
From: anikaweinmann <aweinmann@mundialis.de>
Date: Thu, 4 Jan 2024 11:26:55 +0100
Subject: [PATCH 03/17] adjust r.extract.buildings and
 r.extract.buildings.worker

---
 .../r.extract.buildings.worker.py                | 16 +++++++++-------
 .../r.extract.buildings/r.extract.buildings.py   | 11 +++++++++--
 2 files changed, 18 insertions(+), 9 deletions(-)

diff --git a/grass-gis-addons/m.analyse.buildings/r.extract.buildings.worker/r.extract.buildings.worker.py b/grass-gis-addons/m.analyse.buildings/r.extract.buildings.worker/r.extract.buildings.worker.py
index 9171d8c..3f45908 100644
--- a/grass-gis-addons/m.analyse.buildings/r.extract.buildings.worker/r.extract.buildings.worker.py
+++ b/grass-gis-addons/m.analyse.buildings/r.extract.buildings.worker/r.extract.buildings.worker.py
@@ -453,21 +453,21 @@ def main():
     except Exception:
         grass.fatal("m.analyse.buildings library is not installed")
 
-    ndsm = options["ndsm"]
-    ndvi = options["ndvi_raster"]
+    ndsm = options["ndsm"].split("@")[0]
+    ndvi = options["ndvi_raster"].split("@")[0]
     min_size = options["min_size"]
     max_fd = options["max_fd"]
     ndvi_thresh = options["ndvi_thresh"]
     memory = options["memory"]
     output = options["output"]
     new_mapset = options["new_mapset"]
-    area = options["area"]
+    area = options["area"].split("@")[0]
 
     if options["fnk_vector"]:
-        fnk_vect = options["fnk_vector"]
+        fnk_vect = options["fnk_vector"].split("@")[0]
         fnk_column = options["fnk_column"]
     elif options["fnk_raster"]:
-        fnk_rast = options["fnk_raster"]
+        fnk_rast = options["fnk_raster"].split("@")[0]
 
     grass.message(_(f"Applying building extraction to region {area}..."))
 
@@ -478,8 +478,10 @@ def main():
     ndsm += f"@{old_mapset}"
     ndvi += f"@{old_mapset}"
     if options["fnk_vector"]:
+        fnk_name = fnk_vect
         fnk_vect += f"@{old_mapset}"
     if options["fnk_raster"]:
+        fnk_name = fnk_rast
         fnk_rast += f"@{old_mapset}"
 
     grass.run_command(
@@ -511,13 +513,13 @@ def main():
 
     # copy FNK to temporary mapset
     if options["fnk_vector"]:
-        fnk_vect_tmp = f'{options["fnk_vector"]}_{os.getpid()}'
+        fnk_vect_tmp = f'{fnk_name}_{os.getpid()}'
         rm_vectors.append(fnk_vect_tmp)
         grass.run_command(
             "g.copy", vector=f"{fnk_vect},{fnk_vect_tmp}", quiet=True
         )
     elif options["fnk_raster"]:
-        fnk_rast_tmp = f'{options["fnk_raster"]}_{os.getpid()}'
+        fnk_rast_tmp = f'{fnk_name}_{os.getpid()}'
         rm_rasters.append(fnk_rast_tmp)
         grass.run_command(
             "g.copy", raster=f"{fnk_rast},{fnk_rast_tmp}", quiet=True
diff --git a/grass-gis-addons/m.analyse.buildings/r.extract.buildings/r.extract.buildings.py b/grass-gis-addons/m.analyse.buildings/r.extract.buildings/r.extract.buildings.py
index 6890e32..b2032c4 100644
--- a/grass-gis-addons/m.analyse.buildings/r.extract.buildings/r.extract.buildings.py
+++ b/grass-gis-addons/m.analyse.buildings/r.extract.buildings/r.extract.buildings.py
@@ -330,10 +330,17 @@ def main():
         msg = proc.outputs["stderr"].value.strip()
         grass.message(_(f"\nLog of {proc.get_bash()}:"))
         for msg_part in msg.split("\n"):
-            grass.message(_(msg_part))
+            if msg_part != "":
+                grass.message(_(msg_part))
         # create mapset dict based on Log, so that only those with output are listed
         if "Skipping..." not in msg:
-            tile_output = re.search(r"Output is:\n<(.*?)>", msg).groups()[0]
+            try:
+                # for execution in terminal
+                tile_output = re.search(r"Output is:\n<(.*?)>", msg).groups()[0]
+            except Exception:
+                # for execution in GUI
+                tile_output = re.search(r"Output is: <(.*?)>", msg).groups()[0]
+
             output_list.append(tile_output)
 
     # verify that switching back to original mapset worked

From 813958f0aafbc4fea39756327ed47491834f401a Mon Sep 17 00:00:00 2001
From: anikaweinmann <aweinmann@mundialis.de>
Date: Thu, 4 Jan 2024 11:47:44 +0100
Subject: [PATCH 04/17] adjust re pasing

---
 .../r.extract.buildings/r.extract.buildings.py  |  1 -
 .../v.cd.areas/v.cd.areas.py                    |  7 ++++++-
 .../m.analyse.trees/v.trees.cd/v.trees.cd.py    | 17 ++++++++++++++---
 3 files changed, 20 insertions(+), 5 deletions(-)

diff --git a/grass-gis-addons/m.analyse.buildings/r.extract.buildings/r.extract.buildings.py b/grass-gis-addons/m.analyse.buildings/r.extract.buildings/r.extract.buildings.py
index b2032c4..7662133 100644
--- a/grass-gis-addons/m.analyse.buildings/r.extract.buildings/r.extract.buildings.py
+++ b/grass-gis-addons/m.analyse.buildings/r.extract.buildings/r.extract.buildings.py
@@ -340,7 +340,6 @@ def main():
             except Exception:
                 # for execution in GUI
                 tile_output = re.search(r"Output is: <(.*?)>", msg).groups()[0]
-
             output_list.append(tile_output)
 
     # verify that switching back to original mapset worked
diff --git a/grass-gis-addons/m.analyse.buildings/v.cd.areas/v.cd.areas.py b/grass-gis-addons/m.analyse.buildings/v.cd.areas/v.cd.areas.py
index d1a6fb7..5e4d9d6 100644
--- a/grass-gis-addons/m.analyse.buildings/v.cd.areas/v.cd.areas.py
+++ b/grass-gis-addons/m.analyse.buildings/v.cd.areas/v.cd.areas.py
@@ -325,7 +325,12 @@ def main():
             grass.message(_(msg_part))
         # create mapset dict based on Log, so that only those with output are listed
         if "Skipping..." not in msg:
-            tile_output = re.search(r"Output is:\n<(.*?)>", msg).groups()[0]
+            try:
+                # for execution in terminal
+                tile_output = re.search(r"Output is:\n<(.*?)>", msg).groups()[0]
+            except Exception:
+                # for execution in GUI
+                tile_output = re.search(r"Output is: <(.*?)>", msg).groups()[0]
             output_list.append(tile_output)
         if flags["q"]:
             area_identified = re.search(
diff --git a/grass-gis-addons/m.analyse.trees/v.trees.cd/v.trees.cd.py b/grass-gis-addons/m.analyse.trees/v.trees.cd/v.trees.cd.py
index 0ff4748..f6c4961 100644
--- a/grass-gis-addons/m.analyse.trees/v.trees.cd/v.trees.cd.py
+++ b/grass-gis-addons/m.analyse.trees/v.trees.cd/v.trees.cd.py
@@ -352,9 +352,20 @@ def main():
             grass.message(_(msg_part))
             # create mapset dict based on Log
         if "Skipping..." not in msg:
-            tile_output = (
-                re.search(r"Output is:\n<(.*?)>", msg).groups()[0].split(",")
-            )
+            try:
+                # for execution in terminal
+                tile_output = (
+                    re.search(r"Output is:\n<(.*?)>", msg)
+                    .groups()[0]
+                    .split(",")
+                )
+            except Exception:
+                # for execution in GUI
+                tile_output = (
+                    re.search(r"Output is: <(.*?)>", msg)
+                    .groups()[0]
+                    .split(",")
+                )
             for ind, el in enumerate(output_suffix):
                 if tile_output[ind]:
                     output_dict[el].append(tile_output[ind])

From ab4935ba3533d473bfa84994b2c687897997b8e6 Mon Sep 17 00:00:00 2001
From: Julia Haas <haas@mundialis.de>
Date: Thu, 4 Jan 2024 11:49:14 +0100
Subject: [PATCH 05/17] changes for using gui

---
 Dockerfile                                    |  2 +-
 .../r.trees.mlapply.worker.py                 |  4 +--
 .../r.trees.postprocess.py                    | 27 ++++++++++---------
 .../v.trees.param/v.trees.param.py            |  5 ++--
 4 files changed, 20 insertions(+), 18 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index ce02cee..5c45750 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -17,7 +17,7 @@ ENV GRASS_ADDON_BASE=/usr/local/grass84
 
 # install external dependencies
 # RUN apt install musl-dev ??
-RUN pip3 install py7zr tqdm requests psutil scikit-learn pyproj
+RUN pip3 install py7zr tqdm requests psutil scikit-learn pyproj pandas
 
 # install official addons
 RUN grass --tmp-location EPSG:4326 --exec g.extension r.mapcalc.tiled -s
diff --git a/grass-gis-addons/m.analyse.trees/r.trees.mlapply.worker/r.trees.mlapply.worker.py b/grass-gis-addons/m.analyse.trees/r.trees.mlapply.worker/r.trees.mlapply.worker.py
index 0dd22c2..6af1ed7 100644
--- a/grass-gis-addons/m.analyse.trees/r.trees.mlapply.worker/r.trees.mlapply.worker.py
+++ b/grass-gis-addons/m.analyse.trees/r.trees.mlapply.worker/r.trees.mlapply.worker.py
@@ -81,8 +81,8 @@ def main():
     except Exception:
         grass.fatal("m.analyse.trees library is not installed")
 
-    area = options["area"]
-    group = options["group"]
+    area = options["area"].split("@")[0]
+    group = options["group"].split("@")[0]
     output = options["output"]
     model = options["model"]
     new_mapset = options["new_mapset"]
diff --git a/grass-gis-addons/m.analyse.trees/r.trees.postprocess/r.trees.postprocess.py b/grass-gis-addons/m.analyse.trees/r.trees.postprocess/r.trees.postprocess.py
index a21fc2c..4f1b4c0 100644
--- a/grass-gis-addons/m.analyse.trees/r.trees.postprocess/r.trees.postprocess.py
+++ b/grass-gis-addons/m.analyse.trees/r.trees.postprocess/r.trees.postprocess.py
@@ -228,6 +228,7 @@ 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"]
@@ -284,7 +285,7 @@ def main():
     grass.run_command(
         "r.neighbors",
         input=ndvi,
-        output=f"{ndvi}_min1",
+        output=f"{ndvi_split}_min1",
         size=3,
         method="minimum",
         nprocs=nprocs,
@@ -292,8 +293,8 @@ def main():
     )
     grass.run_command(
         "r.neighbors",
-        input=f"{ndvi}_min1",
-        output=f"{ndvi}_min2",
+        input=f"{ndvi_split}_min1",
+        output=f"{ndvi_split}_min2",
         size=3,
         method="minimum",
         nprocs=nprocs,
@@ -301,8 +302,8 @@ def main():
     )
     grass.run_command(
         "r.neighbors",
-        input=f"{ndvi}_min2",
-        output=f"{ndvi}_max1",
+        input=f"{ndvi_split}_min2",
+        output=f"{ndvi_split}_max1",
         size=3,
         method="maximum",
         nprocs=nprocs,
@@ -310,24 +311,24 @@ def main():
     )
     grass.run_command(
         "r.neighbors",
-        input=f"{ndvi}_max1",
-        output=f"{ndvi}_max2",
+        input=f"{ndvi_split}_max1",
+        output=f"{ndvi_split}_max2",
         size=3,
         method="maximum",
         nprocs=nprocs,
         memory=memory_max100mb,
     )
-    rm_rasters.append(f"{ndvi}_min1")
-    rm_rasters.append(f"{ndvi}_min2")
-    rm_rasters.append(f"{ndvi}_max1")
-    rm_rasters.append(f"{ndvi}_max2")
+    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"trees_ml_nearest = if({tree_pixels} == 2, {nearest}, null())"
     )
     rm_rasters.append("trees_ml_nearest")
     grass.mapcalc(
-        f"trees_ml_pixel_ndvi = if({ndvi}_max2 < {ndvi_threshold}, null(), trees_ml_nearest)"
+        f"trees_ml_pixel_ndvi = if({ndvi_split}_max2 < {ndvi_threshold}, null(), trees_ml_nearest)"
     )
     rm_rasters.append("trees_ml_pixel_ndvi")
 
@@ -441,7 +442,7 @@ def main():
     grass.run_command(
         "r.stats.zonal",
         base="trees_ml_object_ndsm",
-        cover=f"{ndvi}_max2",
+        cover=f"{ndvi_split}_max2",
         method="average",
         output="trees_ml_object_ndviavg",
     )
diff --git a/grass-gis-addons/m.analyse.trees/v.trees.param/v.trees.param.py b/grass-gis-addons/m.analyse.trees/v.trees.param/v.trees.param.py
index 6f01df4..2419abf 100644
--- a/grass-gis-addons/m.analyse.trees/v.trees.param/v.trees.param.py
+++ b/grass-gis-addons/m.analyse.trees/v.trees.param/v.trees.param.py
@@ -37,7 +37,7 @@
 
 # %option G_OPT_R_INPUT
 # % key: ndom
-# % label: Raster map of nDOM
+# % label: Raster map of nDSM
 # % required: no
 # % guisection: Input
 # %end
@@ -135,7 +135,7 @@ def main():
 
     pid = os.getpid()
 
-    treecrowns = options["treecrowns"]
+    treecrowns = options["treecrowns"].split("@")[0]
     ndom = options["ndom"]
     ndvi = options["ndvi"]
     buildings = options["buildings"]
@@ -289,6 +289,7 @@ def main():
     if nprocs > 1:
         for subset_name, mapset_name in zip(subset_names, mapset_names):
             treecrown_subset_mapset.append(f"{subset_name}@{mapset_name}")
+        grass.message(len(mapset_names))
         grass.run_command(
             "v.patch",
             input=treecrown_subset_mapset,

From 4858ab3281e85117636c9f35ca032e7c3abb0b23 Mon Sep 17 00:00:00 2001
From: anikaweinmann <aweinmann@mundialis.de>
Date: Thu, 4 Jan 2024 11:52:26 +0100
Subject: [PATCH 06/17] adjustments for empty messages

---
 grass-gis-addons/m.analyse.buildings/v.cd.areas/v.cd.areas.py | 3 ++-
 grass-gis-addons/m.analyse.trees/v.trees.cd/v.trees.cd.py     | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/grass-gis-addons/m.analyse.buildings/v.cd.areas/v.cd.areas.py b/grass-gis-addons/m.analyse.buildings/v.cd.areas/v.cd.areas.py
index 5e4d9d6..ff4396c 100644
--- a/grass-gis-addons/m.analyse.buildings/v.cd.areas/v.cd.areas.py
+++ b/grass-gis-addons/m.analyse.buildings/v.cd.areas/v.cd.areas.py
@@ -322,7 +322,8 @@ def main():
         msg = proc.outputs["stderr"].value.strip()
         grass.message(_(f"\nLog of {proc.get_bash()}:"))
         for msg_part in msg.split("\n"):
-            grass.message(_(msg_part))
+            if msg_part != "":
+                grass.message(_(msg_part))
         # create mapset dict based on Log, so that only those with output are listed
         if "Skipping..." not in msg:
             try:
diff --git a/grass-gis-addons/m.analyse.trees/v.trees.cd/v.trees.cd.py b/grass-gis-addons/m.analyse.trees/v.trees.cd/v.trees.cd.py
index f6c4961..fe5a232 100644
--- a/grass-gis-addons/m.analyse.trees/v.trees.cd/v.trees.cd.py
+++ b/grass-gis-addons/m.analyse.trees/v.trees.cd/v.trees.cd.py
@@ -349,7 +349,8 @@ def main():
         msg = proc.outputs["stderr"].value.strip()
         grass.message(_(f"\nLog of {proc.get_bash()}:"))
         for msg_part in msg.split("\n"):
-            grass.message(_(msg_part))
+            if msg_part != "":
+                grass.message(_(msg_part))
             # create mapset dict based on Log
         if "Skipping..." not in msg:
             try:

From 679aba6d8a78ddff324d5e94b4e959c0402dd507 Mon Sep 17 00:00:00 2001
From: anikaweinmann <aweinmann@mundialis.de>
Date: Thu, 4 Jan 2024 12:12:05 +0100
Subject: [PATCH 07/17] adjust r.extract.greenroofs.worker

---
 .../r.extract.greenroofs.worker.py            | 42 +++++++++++++++----
 1 file changed, 35 insertions(+), 7 deletions(-)

diff --git a/grass-gis-addons/m.analyse.buildings/r.extract.greenroofs.worker/r.extract.greenroofs.worker.py b/grass-gis-addons/m.analyse.buildings/r.extract.greenroofs.worker/r.extract.greenroofs.worker.py
index 474d4e6..4a1fc85 100644
--- a/grass-gis-addons/m.analyse.buildings/r.extract.greenroofs.worker/r.extract.greenroofs.worker.py
+++ b/grass-gis-addons/m.analyse.buildings/r.extract.greenroofs.worker/r.extract.greenroofs.worker.py
@@ -237,15 +237,43 @@ def main():
     new_mapset = options["new_mapset"]
     gisrc, newgisrc, old_mapset = switch_to_new_mapset(new_mapset)
 
-    area = f"{options['area']}@{old_mapset}"
+    area = (
+        f"{options['area']}@{old_mapset}"
+        if "@" not in options["area"]
+        else options["area"]
+    )
     num = options["area"].rsplit("_", 1)[1]
-    building_outlines = f"{options['building_outlines']}@{old_mapset}"
+    building_outlines = (
+        f"{options['building_outlines']}@{old_mapset}"
+        if "@" not in options["building_outlines"]
+        else options["building_outlines"]
+    )
     buildings = f"{options['buildings']}@{old_mapset}"
-    ndsm = f"{options['ndsm']}@{old_mapset}"
-    ndvi = f"{options['ndvi']}@{old_mapset}"
-    green_blue_ratio = f"{options['gb_ratio']}@{old_mapset}"
-    red_green_ratio = f"{options['rg_ratio']}@{old_mapset}"
-    brightness = f"{options['brightness']}@{old_mapset}"
+    ndsm = (
+        f"{options['ndsm']}@{old_mapset}"
+        if "@" not in options["ndsm"]
+        else options["ndsm"]
+    )
+    ndvi = (
+        f"{options['ndvi']}@{old_mapset}"
+        if "@" not in options["ndvi"]
+        else options["ndvi"]
+    )
+    green_blue_ratio = (
+        f"{options['gb_ratio']}@{old_mapset}"
+        if "@" not in options["gb_ratio"]
+        else options["gb_ratio"]
+    )
+    red_green_ratio = (
+        f"{options['rg_ratio']}@{old_mapset}"
+        if "@" not in options["rg_ratio"]
+        else options["rg_ratio"]
+    )
+    brightness = (
+        f"{options['brightness']}@{old_mapset}"
+        if "@" not in options["brightness"]
+        else options["brightness"]
+    )
     min_veg_size = float(options["min_veg_size"])
     min_veg_proportion = int(options["min_veg_proportion"])
     output_vegetation = options["output_vegetation"]

From 6ef651b14cb21d3fde08563f350780b54f668d59 Mon Sep 17 00:00:00 2001
From: Julia Haas <haas@mundialis.de>
Date: Thu, 4 Jan 2024 12:13:49 +0100
Subject: [PATCH 08/17] adapt v.trees.species for gui

---
 .../m.analyse.trees/v.trees.species/v.trees.species.py     | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/grass-gis-addons/m.analyse.trees/v.trees.species/v.trees.species.py b/grass-gis-addons/m.analyse.trees/v.trees.species/v.trees.species.py
index 65129fc..3344578 100644
--- a/grass-gis-addons/m.analyse.trees/v.trees.species/v.trees.species.py
+++ b/grass-gis-addons/m.analyse.trees/v.trees.species/v.trees.species.py
@@ -27,7 +27,7 @@
 # %option G_OPT_R_INPUT
 # % key: red_raster
 # % required: yes
-# % label: Name of the NIR raster
+# % label: Name of the red band
 # % guisection: Input
 # %end
 
@@ -314,8 +314,9 @@ def main():
     rm_dirs.append(sig_dir)
     os.makedirs(sig_dir)
     group_inp = (
-        f"{ndvi} {red} {green} {blue} {nir} {ndwi} {brightness}"
-        f" {ndsm_med_slope_n7}"
+        f"{ndvi.split('@')[0]} {red.split('@')[0]} {green.split('@')[0]}"
+        f" {blue.split('@')[0]} {nir.split('@')[0]} {ndwi.split('@')[0]}" 
+        f" {brightness} {ndsm_med_slope_n7}"
     )
     g_version = tuple(
         [

From 9f39ad6e1e10144079e4174ba629ea3b8fa740ee Mon Sep 17 00:00:00 2001
From: anikaweinmann <aweinmann@mundialis.de>
Date: Thu, 4 Jan 2024 12:15:20 +0100
Subject: [PATCH 09/17] black new version

---
 .github/workflows/black.yml                                   | 2 +-
 .../r.extract.buildings.worker/r.extract.buildings.worker.py  | 4 ++--
 .../r.extract.buildings/r.extract.buildings.py                | 4 +++-
 grass-gis-addons/m.analyse.buildings/v.cd.areas/v.cd.areas.py | 4 +++-
 .../r.trees.postprocess/r.trees.postprocess.py                | 2 +-
 .../m.analyse.trees/v.trees.species/v.trees.species.py        | 2 +-
 6 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/black.yml b/.github/workflows/black.yml
index 15c2d6f..e43d0ea 100644
--- a/.github/workflows/black.yml
+++ b/.github/workflows/black.yml
@@ -14,7 +14,7 @@ jobs:
         sudo apt-get update && sudo apt-get install python3 python3-pip -y
     - name: Install pip dependencies
       run: |
-        pip3 install black==23.1.0
+        pip3 install black==23.12.0
     - name: Check code style with Black
       run: |
         black --check --diff --line-length 79 .
diff --git a/grass-gis-addons/m.analyse.buildings/r.extract.buildings.worker/r.extract.buildings.worker.py b/grass-gis-addons/m.analyse.buildings/r.extract.buildings.worker/r.extract.buildings.worker.py
index 3f45908..ec9eb7f 100644
--- a/grass-gis-addons/m.analyse.buildings/r.extract.buildings.worker/r.extract.buildings.worker.py
+++ b/grass-gis-addons/m.analyse.buildings/r.extract.buildings.worker/r.extract.buildings.worker.py
@@ -513,13 +513,13 @@ def main():
 
     # copy FNK to temporary mapset
     if options["fnk_vector"]:
-        fnk_vect_tmp = f'{fnk_name}_{os.getpid()}'
+        fnk_vect_tmp = f"{fnk_name}_{os.getpid()}"
         rm_vectors.append(fnk_vect_tmp)
         grass.run_command(
             "g.copy", vector=f"{fnk_vect},{fnk_vect_tmp}", quiet=True
         )
     elif options["fnk_raster"]:
-        fnk_rast_tmp = f'{fnk_name}_{os.getpid()}'
+        fnk_rast_tmp = f"{fnk_name}_{os.getpid()}"
         rm_rasters.append(fnk_rast_tmp)
         grass.run_command(
             "g.copy", raster=f"{fnk_rast},{fnk_rast_tmp}", quiet=True
diff --git a/grass-gis-addons/m.analyse.buildings/r.extract.buildings/r.extract.buildings.py b/grass-gis-addons/m.analyse.buildings/r.extract.buildings/r.extract.buildings.py
index 7662133..f0d9973 100644
--- a/grass-gis-addons/m.analyse.buildings/r.extract.buildings/r.extract.buildings.py
+++ b/grass-gis-addons/m.analyse.buildings/r.extract.buildings/r.extract.buildings.py
@@ -336,7 +336,9 @@ def main():
         if "Skipping..." not in msg:
             try:
                 # for execution in terminal
-                tile_output = re.search(r"Output is:\n<(.*?)>", msg).groups()[0]
+                tile_output = re.search(r"Output is:\n<(.*?)>", msg).groups()[
+                    0
+                ]
             except Exception:
                 # for execution in GUI
                 tile_output = re.search(r"Output is: <(.*?)>", msg).groups()[0]
diff --git a/grass-gis-addons/m.analyse.buildings/v.cd.areas/v.cd.areas.py b/grass-gis-addons/m.analyse.buildings/v.cd.areas/v.cd.areas.py
index ff4396c..5cfa186 100644
--- a/grass-gis-addons/m.analyse.buildings/v.cd.areas/v.cd.areas.py
+++ b/grass-gis-addons/m.analyse.buildings/v.cd.areas/v.cd.areas.py
@@ -328,7 +328,9 @@ def main():
         if "Skipping..." not in msg:
             try:
                 # for execution in terminal
-                tile_output = re.search(r"Output is:\n<(.*?)>", msg).groups()[0]
+                tile_output = re.search(r"Output is:\n<(.*?)>", msg).groups()[
+                    0
+                ]
             except Exception:
                 # for execution in GUI
                 tile_output = re.search(r"Output is: <(.*?)>", msg).groups()[0]
diff --git a/grass-gis-addons/m.analyse.trees/r.trees.postprocess/r.trees.postprocess.py b/grass-gis-addons/m.analyse.trees/r.trees.postprocess/r.trees.postprocess.py
index 4f1b4c0..79be573 100644
--- a/grass-gis-addons/m.analyse.trees/r.trees.postprocess/r.trees.postprocess.py
+++ b/grass-gis-addons/m.analyse.trees/r.trees.postprocess/r.trees.postprocess.py
@@ -228,7 +228,7 @@ def main():
     blue = options["blue_raster"]
     nir = options["nir_raster"]
     ndvi = options["ndvi_raster"]
-    ndvi_split = ndvi.split('@')[0]
+    ndvi_split = ndvi.split("@")[0]
     ndwi = options["ndwi_raster"]
     ndgb = options["ndgb_raster"]
     ndsm = options["ndsm"]
diff --git a/grass-gis-addons/m.analyse.trees/v.trees.species/v.trees.species.py b/grass-gis-addons/m.analyse.trees/v.trees.species/v.trees.species.py
index 3344578..0e531f6 100644
--- a/grass-gis-addons/m.analyse.trees/v.trees.species/v.trees.species.py
+++ b/grass-gis-addons/m.analyse.trees/v.trees.species/v.trees.species.py
@@ -315,7 +315,7 @@ def main():
     os.makedirs(sig_dir)
     group_inp = (
         f"{ndvi.split('@')[0]} {red.split('@')[0]} {green.split('@')[0]}"
-        f" {blue.split('@')[0]} {nir.split('@')[0]} {ndwi.split('@')[0]}" 
+        f" {blue.split('@')[0]} {nir.split('@')[0]} {ndwi.split('@')[0]}"
         f" {brightness} {ndsm_med_slope_n7}"
     )
     g_version = tuple(

From 85f00635213b3de010aea34b6d43f84f630c0b8e Mon Sep 17 00:00:00 2001
From: anikaweinmann <aweinmann@mundialis.de>
Date: Thu, 4 Jan 2024 12:26:08 +0100
Subject: [PATCH 10/17] try to fix super linter things

---
 .github/workflows/black.yml        | 21 ++++++++++----------
 .github/workflows/linting.yml      | 32 +++++++++++++++++-------------
 .github/workflows/super-linter.yml |  1 +
 README.md                          |  7 +++++--
 4 files changed, 35 insertions(+), 26 deletions(-)

diff --git a/.github/workflows/black.yml b/.github/workflows/black.yml
index e43d0ea..e579a8b 100644
--- a/.github/workflows/black.yml
+++ b/.github/workflows/black.yml
@@ -1,3 +1,4 @@
+---
 name: Python code style check with black
 
 on: [push]
@@ -8,13 +9,13 @@ jobs:
     runs-on: ubuntu-22.04
 
     steps:
-    - uses: actions/checkout@v4
-    - name: Install apt dependencies
-      run: |
-        sudo apt-get update && sudo apt-get install python3 python3-pip -y
-    - name: Install pip dependencies
-      run: |
-        pip3 install black==23.12.0
-    - name: Check code style with Black
-      run: |
-        black --check --diff --line-length 79 .
+      - uses: actions/checkout@v4
+      - name: Install apt dependencies
+        run: |
+          sudo apt-get update && sudo apt-get install python3 python3-pip -y
+      - name: Install pip dependencies
+        run: |
+          pip3 install black==23.12.0
+      - name: Check code style with Black
+        run: |
+          black --check --diff --line-length 79 .
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index b518e99..8975c57 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -1,3 +1,4 @@
+---
 name: Python Flake8 Code Quality
 
 on: [push]
@@ -8,17 +9,20 @@ jobs:
     runs-on: ubuntu-22.04
 
     steps:
-    - uses: actions/checkout@v4
-    - name: Install apt dependencies
-      run: |
-        sudo apt-get update && sudo apt-get install python3 python3-pip -y
-    - name: Install pip dependencies
-      run: |
-        pip3 install flake8 pylint
-    - name: Lint with Flake8
-      run: |
-        # E402: module level import not at top of file
-        flake8 --ignore=E265,F821,E501,W503,E203,E402 --max-line-length=80 --count --statistics --show-source .
-    # - name: Lint with Pylint
-    #   run: |
-    #     pylint --disable=R,bad-continuation,fixme,import-error --additional-builtins=_ --reports=n --score=n -j0 ${{ github.event.repository.name }}.py
+      - uses: actions/checkout@v4
+      - name: Install apt dependencies
+        run: |
+          sudo apt-get update && sudo apt-get install python3 python3-pip -y
+      - name: Install pip dependencies
+        run: |
+          pip3 install flake8 pylint
+      - name: Lint with Flake8
+        run: |
+          # E402: module level import not at top of file
+          flake8 --ignore=E265,F821,E501,W503,E203,E402 --max-line-length=80 \
+            --count --statistics --show-source .
+      # - name: Lint with Pylint
+      #   run: |
+      #     pylint --disable=R,bad-continuation,fixme,import-error \
+      #       --additional-builtins=_ --reports=n --score=n \
+      #       -j0 ${{ github.event.repository.name }}.py
diff --git a/.github/workflows/super-linter.yml b/.github/workflows/super-linter.yml
index 6f4fa3e..91046a3 100644
--- a/.github/workflows/super-linter.yml
+++ b/.github/workflows/super-linter.yml
@@ -1,3 +1,4 @@
+---
 name: General linting
 
 on:
diff --git a/README.md b/README.md
index 333c0be..efaeb43 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,4 @@
+---
 # rvr_interface
 Repo for code and script transfer between mundialis and RVR - GRASS GIS addons:
 
@@ -79,10 +80,12 @@ docker run -it --privileged --rm --ipc host \
 ```
 
 and on Windows you need the following things to do before:
+
 1. Download and install [VcXsrv Windows X Server](https://sourceforge.net/projects/vcxsrv/)
 2. Start **Xlaunch** and configure it (see https://dev.to/darksmile92/run-gui-app-in-linux-docker-container-on-windows-host-4kde):
-  * in the "Extra Settings" window enable "Disable access control"
-  * in the "Finish Configuration" window click "Save configuration" and save it e.g. on the desktop
+  - in the "Extra Settings" window enable "Disable access control"
+  - in the "Finish Configuration" window click "Save configuration" and save it e.g. on the desktop
+
 Now you can run the docker:
 ```bash
 # get own IP adress (take the value of IPAdress e.g. 10.211.55.10 and not 127.0.0.1)

From 6508a137236f9077a1b4e18c2050c2e7db8a1bfa Mon Sep 17 00:00:00 2001
From: anikaweinmann <aweinmann@mundialis.de>
Date: Thu, 4 Jan 2024 12:31:27 +0100
Subject: [PATCH 11/17] try to fix super linter things

---
 .github/workflows/super-linter.yml | 1 -
 README.md                          | 4 ++--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/super-linter.yml b/.github/workflows/super-linter.yml
index 91046a3..9587cce 100644
--- a/.github/workflows/super-linter.yml
+++ b/.github/workflows/super-linter.yml
@@ -3,7 +3,6 @@ name: General linting
 
 on:
   - push
-  - pull_request
 
 jobs:
   super-linter:
diff --git a/README.md b/README.md
index efaeb43..95d94d3 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,3 @@
----
 # rvr_interface
 Repo for code and script transfer between mundialis and RVR - GRASS GIS addons:
 
@@ -82,7 +81,8 @@ docker run -it --privileged --rm --ipc host \
 and on Windows you need the following things to do before:
 
 1. Download and install [VcXsrv Windows X Server](https://sourceforge.net/projects/vcxsrv/)
-2. Start **Xlaunch** and configure it (see https://dev.to/darksmile92/run-gui-app-in-linux-docker-container-on-windows-host-4kde):
+2. Start **Xlaunch** and configure it (see [here](https://dev.to/darksmile92/run-gui-app-in-linux-docker-container-on-windows-host-4kde):
+
   - in the "Extra Settings" window enable "Disable access control"
   - in the "Finish Configuration" window click "Save configuration" and save it e.g. on the desktop
 

From 274acc889099d85ebb3851e4e1853d19ebd5affc Mon Sep 17 00:00:00 2001
From: anikaweinmann <aweinmann@mundialis.de>
Date: Thu, 4 Jan 2024 14:23:54 +0100
Subject: [PATCH 12/17] MD linting

---
 README.md | 67 +++++++++++++++++++++++++++++--------------------------
 1 file changed, 35 insertions(+), 32 deletions(-)

diff --git a/README.md b/README.md
index 95d94d3..1f6f813 100644
--- a/README.md
+++ b/README.md
@@ -1,65 +1,67 @@
 # rvr_interface
+
 Repo for code and script transfer between mundialis and RVR - GRASS GIS addons:
 
 - **m.import.rvr** imports data for the processing of <b>gebaeudedetektion</b>,
-<b>dachbegruenung</b> and/or <b>einzelbaumerkennung</b>.
+  <b>dachbegruenung</b> and/or <b>einzelbaumerkennung</b>.
 
 - **r.import.dtm_nrw** downloads and imports the NRW digital terrain model
-(DTM) 1m into the current mapset. Only the extent of the current region is
-downloaded and imported with a 1m resolution.
+  (DTM) 1m into the current mapset. Only the extent of the current region is
+  downloaded and imported with a 1m resolution.
 
 - **r.import.ndsm_nrw** calculates an nDSM by subtracting input digital terrain
-model (DTM) data (defined by the <b>dtm</b> parameter) from an input DSM
-indicated by the <b>dsm</b> parameter. If no DTM is defined, NRW DTM data
-is automatically imported using <a href="grass-gis-addons/r.import.dtm_nrw/r.import.dtm_nrw.html">r.import.dtm_nrw</a>.
+  model (DTM) data (defined by the <b>dtm</b> parameter) from an input DSM
+  indicated by the <b>dsm</b> parameter. If no DTM is defined, NRW DTM data
+  is automatically imported using <a href="grass-gis-addons/r.import.dtm_nrw/r.import.dtm_nrw.html">r.import.dtm_nrw</a>.
 
 - **r.in.pdal.worker** is a worker addon for <em>r.in.pdal</em> and is used in
-<a href="grass-gis-addons/m.import.rvr/m.import.rvr.html">m.import.rvr</a>.
-
+  <a href="grass-gis-addons/m.import.rvr/m.import.rvr.html">m.import.rvr</a>.
 
 - **m.analyse.buildings**
+
   - **r.extract.buildings** extracts buildings as vectors and calculates height
-   statistics (minimum, maximum, average, standard deviation, median,
-     percentile) and presumable number of stories using an nDSM-raster,
-     NDVI-raster, and FNK-vector (Flaechennutzungskatalog).
+    statistics (minimum, maximum, average, standard deviation, median,
+    percentile) and presumable number of stories using an nDSM-raster,
+    NDVI-raster, and FNK-vector (Flaechennutzungskatalog).
   - **r.extract.buildings.worker** is a worker module that is started by
-<a href="grass-gis-addons/m.analyse.buildings/r.extract.buildings/r.extract.buildings.html">r.extract.buildings</a>.
+    <a href="grass-gis-addons/m.analyse.buildings/r.extract.buildings/r.extract.buildings.html">r.extract.buildings</a>.
   - **v.cd.areas** calculates differences between two vector layers
-(e.g. classification and reference) by making use of v.overlay with operator
-"xor". Only differences with a defined minimum size are extracted.
+    (e.g. classification and reference) by making use of v.overlay with operator
+    "xor". Only differences with a defined minimum size are extracted.
   - **v.cd.areas.worker** is a worker module that is started by
-<a href="grass-gis-addons/m.analyse.buildings/v.cd.areas/v.cd.areas.html">v.cd.areas</a>.
+    <a href="grass-gis-addons/m.analyse.buildings/v.cd.areas/v.cd.areas.html">v.cd.areas</a>.
   - **r.extract.greenroofs** extracts vegetated roofs from aerial photographs,
-  an nDSM, a building vector layer and optionally an FNK
-  (Flaechennutzungskatalog) and tree vector layer.
+    an nDSM, a building vector layer and optionally an FNK
+    (Flaechennutzungskatalog) and tree vector layer.
   - **r.extract.greenroofs.worker** is a worker module that is started by
-<a href="grass-gis-addons/m.analyse.buildings/r.extract.greenroofs/r.extract.greenroofs.html">r.extract.greenroofs</a>.
-
+    <a href="grass-gis-addons/m.analyse.buildings/r.extract.greenroofs/r.extract.greenroofs.html">r.extract.greenroofs</a>.
 
 - **m.analyse.trees**
+
   - **r.trees.peaks** assigns pixels to nearest peak (tree crown).
   - **r.trees.mltrain** generates training data for a machine learning (ML)
-  model to detect trees and trains the model with these training data.
+    model to detect trees and trains the model with these training data.
   - **r.trees.mlapply** applies the tree classification model
-in parallel to the area of interest (current region).
+    in parallel to the area of interest (current region).
   - **r.trees.mlapply.worker** applies classification model for a region
-defined by a vector. This module should not be called directly, instead
-it is called in parallel by <a href="grass-gis-addons/m.analyse.trees/r.trees.mlapply/r.trees.mlapply.html">r.trees.mlapply</a>.
+    defined by a vector. This module should not be called directly, instead
+    it is called in parallel by <a href="grass-gis-addons/m.analyse.trees/r.trees.mlapply/r.trees.mlapply.html">r.trees.mlapply</a>.
   - **r.trees.postprocess** generates single tree delineations from tree pixels
-   and geomorphological peaks.
+    and geomorphological peaks.
   - **v.trees.param** calculates various tree parameters for tree crowns given
-   as input vector map <b>treecrowns</b>.
+    as input vector map <b>treecrowns</b>.
   - **v.trees.param.worker** is used within <a href="grass-gis-addons/m.analyse.trees/v.trees.param/v.trees.param.html">v.trees.param</a> to calculate various tree parameters
-   for tree crowns in parallel.
+    for tree crowns in parallel.
   - **v.trees.species** classifies trees in deciduous and coniferous trees.
   - **v.trees.cd** calculates the change between two given treecrown vector
-  maps (<b>inp_t1</b> and <b>inp_t2</b> for time t1 and t2, respectively).
+    maps (<b>inp_t1</b> and <b>inp_t2</b> for time t1 and t2, respectively).
   - **v.trees.cd.worker** is a worker module that is started by
-  <a href="grass-gis-addons/m.analyse.trees/v.trees.cd/v.trees.cd.html">v.trees.cd</a>.
+    <a href="grass-gis-addons/m.analyse.trees/v.trees.cd/v.trees.cd.html">v.trees.cd</a>.
 
 ## Building and running a docker image
 
 In the folder with the Dockerfile, run
+
 ```bash
 docker build -t rvr_interface:latest .
 ```
@@ -67,6 +69,7 @@ docker build -t rvr_interface:latest .
 Instead of "latest", a version number can be used. This should create a local
 docker image with all needed addons and dependencies. Once the docker image
 has been created locally, it can be started on Linux with e.g.
+
 ```bash
 xhost local:*
 docker run -it --privileged --rm --ipc host \
@@ -81,12 +84,12 @@ docker run -it --privileged --rm --ipc host \
 and on Windows you need the following things to do before:
 
 1. Download and install [VcXsrv Windows X Server](https://sourceforge.net/projects/vcxsrv/)
-2. Start **Xlaunch** and configure it (see [here](https://dev.to/darksmile92/run-gui-app-in-linux-docker-container-on-windows-host-4kde):
-
-  - in the "Extra Settings" window enable "Disable access control"
-  - in the "Finish Configuration" window click "Save configuration" and save it e.g. on the desktop
+1. Start **Xlaunch** and configure it (see [here](https://dev.to/darksmile92/run-gui-app-in-linux-docker-container-on-windows-host-4kde)):
+   - in the "Extra Settings" window enable "Disable access control"
+   - in the "Finish Configuration" window click "Save configuration" and save it e.g. on the desktop
 
 Now you can run the docker:
+
 ```bash
 # get own IP adress (take the value of IPAdress e.g. 10.211.55.10 and not 127.0.0.1)
 Get-NetIPAddress

From d6135fe69646ca6648063c6de92c16c25a3acc58 Mon Sep 17 00:00:00 2001
From: Julia Haas <haas@mundialis.de>
Date: Thu, 4 Jan 2024 15:28:30 +0100
Subject: [PATCH 13/17] adapt v.trees.cd and worker for use of gui

---
 .../r.trees.mltrain/r.trees.mltrain.py        | 25 ++++++++++---------
 .../v.trees.cd.worker/v.trees.cd.worker.py    | 16 +++++++++---
 .../m.analyse.trees/v.trees.cd/v.trees.cd.py  | 15 +++++------
 3 files changed, 34 insertions(+), 22 deletions(-)

diff --git a/grass-gis-addons/m.analyse.trees/r.trees.mltrain/r.trees.mltrain.py b/grass-gis-addons/m.analyse.trees/r.trees.mltrain/r.trees.mltrain.py
index 2b11d3b..2bc2655 100644
--- a/grass-gis-addons/m.analyse.trees/r.trees.mltrain/r.trees.mltrain.py
+++ b/grass-gis-addons/m.analyse.trees/r.trees.mltrain/r.trees.mltrain.py
@@ -229,6 +229,7 @@ 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"]
@@ -280,7 +281,7 @@ def main():
     grass.run_command(
         "r.neighbors",
         input=ndvi,
-        output=f"{ndvi.split('@')[0]}_min1",
+        output=f"{ndvi_split}_min1",
         size=3,
         method="minimum",
         nprocs=nprocs,
@@ -288,8 +289,8 @@ def main():
     )
     grass.run_command(
         "r.neighbors",
-        input=f"{ndvi.split('@')[0]}_min1",
-        output=f"{ndvi.split('@')[0]}_min2",
+        input=f"{ndvi_split}_min1",
+        output=f"{ndvi_split}_min2",
         size=3,
         method="minimum",
         nprocs=nprocs,
@@ -297,8 +298,8 @@ def main():
     )
     grass.run_command(
         "r.neighbors",
-        input=f"{ndvi.split('@')[0]}_min2",
-        output=f"{ndvi.split('@')[0]}_max1",
+        input=f"{ndvi_split}_min2",
+        output=f"{ndvi_split}_max1",
         size=3,
         method="maximum",
         nprocs=nprocs,
@@ -306,20 +307,20 @@ def main():
     )
     grass.run_command(
         "r.neighbors",
-        input=f"{ndvi.split('@')[0]}_max1",
-        output=f"{ndvi.split('@')[0]}_max2",
+        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('@')[0]}_min1")
-    rm_rasters.append(f"{ndvi.split('@')[0]}_min2")
-    rm_rasters.append(f"{ndvi.split('@')[0]}_max1")
-    rm_rasters.append(f"{ndvi.split('@')[0]}_max2")
+    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"trees_pixel_ndvi = if({ndvi.split('@')[0]}_max2 < {ndvi_threshold}, null(), {nearest})"
+        f"trees_pixel_ndvi = if({ndvi_split}_max2 < {ndvi_threshold}, null(), {nearest})"
     )
     rm_rasters.append("trees_pixel_ndvi")
 
diff --git a/grass-gis-addons/m.analyse.trees/v.trees.cd.worker/v.trees.cd.worker.py b/grass-gis-addons/m.analyse.trees/v.trees.cd.worker/v.trees.cd.worker.py
index a43ea95..7784ad3 100644
--- a/grass-gis-addons/m.analyse.trees/v.trees.cd.worker/v.trees.cd.worker.py
+++ b/grass-gis-addons/m.analyse.trees/v.trees.cd.worker/v.trees.cd.worker.py
@@ -217,9 +217,19 @@ def main():
     gisrc, newgisrc, old_mapset = switch_to_new_mapset(new_mapset)
 
     area += f"@{old_mapset}"
-    vec_inp_t1 += f"@{old_mapset}"
-    vec_inp_t2 += f"@{old_mapset}"
-
+    
+    vec_inp_t1 = (
+        f"{vec_inp_t1}@{old_mapset}"
+        if "@" not in vec_inp_t1
+        else vec_inp_t1
+    )
+    
+    vec_inp_t2 = (
+        f"{vec_inp_t2}@{old_mapset}"
+        if "@" not in vec_inp_t2
+        else vec_inp_t2
+    )
+    
     # set region to current tile (area)
     grass.run_command(
         "g.region",
diff --git a/grass-gis-addons/m.analyse.trees/v.trees.cd/v.trees.cd.py b/grass-gis-addons/m.analyse.trees/v.trees.cd/v.trees.cd.py
index fe5a232..6d148da 100644
--- a/grass-gis-addons/m.analyse.trees/v.trees.cd/v.trees.cd.py
+++ b/grass-gis-addons/m.analyse.trees/v.trees.cd/v.trees.cd.py
@@ -288,7 +288,7 @@ def main():
     queue = ParallelModuleQueue(nprocs=nprocs)
 
     # prepare names for output maps
-    output_suffix = ["congruent", f"only_{vec_inp_t1}", f"only_{vec_inp_t2}"]
+    output_suffix = ["congruent", f"only_{vec_inp_t1.split('@')[0]}", f"only_{vec_inp_t2.split('@')[0]}"]
     output_dict = {}
     for el in output_suffix:
         output_dict[el] = list()
@@ -404,12 +404,13 @@ def main():
                 pid,
             )
         # remove unnecessary columns
-        grass.run_command(
-            "v.db.dropcolumn",
-            map=cd_output_i,
-            columns=rm_vec_columns,
-            quiet=True,
-        )
+        if grass.vector_db(cd_output_i):
+            grass.run_command(
+                "v.db.dropcolumn",
+                map=cd_output_i,
+                columns=rm_vec_columns,
+                quiet=True,
+            )
         areas_count.append(
             grass.parse_command(
                 "v.info",

From 925cd853dead1070cf6ee8face15d25137b7c7f5 Mon Sep 17 00:00:00 2001
From: Julia Haas <haas@mundialis.de>
Date: Thu, 4 Jan 2024 15:34:12 +0100
Subject: [PATCH 14/17] linting

---
 .../v.trees.cd.worker/v.trees.cd.worker.py           | 12 +++---------
 .../m.analyse.trees/v.trees.cd/v.trees.cd.py         |  6 +++++-
 2 files changed, 8 insertions(+), 10 deletions(-)

diff --git a/grass-gis-addons/m.analyse.trees/v.trees.cd.worker/v.trees.cd.worker.py b/grass-gis-addons/m.analyse.trees/v.trees.cd.worker/v.trees.cd.worker.py
index 7784ad3..7175f96 100644
--- a/grass-gis-addons/m.analyse.trees/v.trees.cd.worker/v.trees.cd.worker.py
+++ b/grass-gis-addons/m.analyse.trees/v.trees.cd.worker/v.trees.cd.worker.py
@@ -217,19 +217,13 @@ def main():
     gisrc, newgisrc, old_mapset = switch_to_new_mapset(new_mapset)
 
     area += f"@{old_mapset}"
-    
     vec_inp_t1 = (
-        f"{vec_inp_t1}@{old_mapset}"
-        if "@" not in vec_inp_t1
-        else vec_inp_t1
+        f"{vec_inp_t1}@{old_mapset}" if "@" not in vec_inp_t1 else vec_inp_t1
     )
-    
     vec_inp_t2 = (
-        f"{vec_inp_t2}@{old_mapset}"
-        if "@" not in vec_inp_t2
-        else vec_inp_t2
+        f"{vec_inp_t2}@{old_mapset}" if "@" not in vec_inp_t2 else vec_inp_t2
     )
-    
+
     # set region to current tile (area)
     grass.run_command(
         "g.region",
diff --git a/grass-gis-addons/m.analyse.trees/v.trees.cd/v.trees.cd.py b/grass-gis-addons/m.analyse.trees/v.trees.cd/v.trees.cd.py
index 6d148da..5c798fb 100644
--- a/grass-gis-addons/m.analyse.trees/v.trees.cd/v.trees.cd.py
+++ b/grass-gis-addons/m.analyse.trees/v.trees.cd/v.trees.cd.py
@@ -288,7 +288,11 @@ def main():
     queue = ParallelModuleQueue(nprocs=nprocs)
 
     # prepare names for output maps
-    output_suffix = ["congruent", f"only_{vec_inp_t1.split('@')[0]}", f"only_{vec_inp_t2.split('@')[0]}"]
+    output_suffix = [
+        "congruent",
+        f"only_{vec_inp_t1.split('@')[0]}",
+        f"only_{vec_inp_t2.split('@')[0]}",
+    ]
     output_dict = {}
     for el in output_suffix:
         output_dict[el] = list()

From caede0a65f088100a442002d6844c8c7412ba9ee Mon Sep 17 00:00:00 2001
From: Julia Haas <haas@mundialis.de>
Date: Thu, 4 Jan 2024 15:41:32 +0100
Subject: [PATCH 15/17] typos in readme

---
 README.md | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 1f6f813..b1faf89 100644
--- a/README.md
+++ b/README.md
@@ -81,10 +81,11 @@ docker run -it --privileged --rm --ipc host \
        rvr_interface:latest bash
 ```
 
-and on Windows you need the following things to do before:
+On Windows you need to do the following things before starting the docker container:
 
-1. Download and install [VcXsrv Windows X Server](https://sourceforge.net/projects/vcxsrv/)
-1. Start **Xlaunch** and configure it (see [here](https://dev.to/darksmile92/run-gui-app-in-linux-docker-container-on-windows-host-4kde)):
+1. Install Docker Desktop
+2. Download and install [VcXsrv Windows X Server](https://sourceforge.net/projects/vcxsrv/)
+3. Start **Xlaunch** and configure it (see [here](https://dev.to/darksmile92/run-gui-app-in-linux-docker-container-on-windows-host-4kde)):
    - in the "Extra Settings" window enable "Disable access control"
    - in the "Finish Configuration" window click "Save configuration" and save it e.g. on the desktop
 

From bb2075bc5ebe45a06594e909c93d00ae7566f6a7 Mon Sep 17 00:00:00 2001
From: Julia Haas <haas@mundialis.de>
Date: Thu, 4 Jan 2024 16:06:04 +0100
Subject: [PATCH 16/17] remove debugging message

---
 grass-gis-addons/m.analyse.trees/v.trees.param/v.trees.param.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/grass-gis-addons/m.analyse.trees/v.trees.param/v.trees.param.py b/grass-gis-addons/m.analyse.trees/v.trees.param/v.trees.param.py
index 2419abf..656f4fc 100644
--- a/grass-gis-addons/m.analyse.trees/v.trees.param/v.trees.param.py
+++ b/grass-gis-addons/m.analyse.trees/v.trees.param/v.trees.param.py
@@ -289,7 +289,6 @@ def main():
     if nprocs > 1:
         for subset_name, mapset_name in zip(subset_names, mapset_names):
             treecrown_subset_mapset.append(f"{subset_name}@{mapset_name}")
-        grass.message(len(mapset_names))
         grass.run_command(
             "v.patch",
             input=treecrown_subset_mapset,

From e2ea1e97979daaf84e2f577b3ad2c357910b45b7 Mon Sep 17 00:00:00 2001
From: Anika Weinmann <37300249+anikaweinmann@users.noreply.github.com>
Date: Fri, 5 Jan 2024 07:38:40 +0100
Subject: [PATCH 17/17] Apply suggestions from code review

Co-authored-by: linakrisztian <106728040+linakrisztian@users.noreply.github.com>
---
 README.md                                                 | 3 ++-
 grass-gis-addons/m.analyse.trees/v.trees.cd/v.trees.cd.py | 1 +
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index b1faf89..2fb22d1 100644
--- a/README.md
+++ b/README.md
@@ -81,7 +81,7 @@ docker run -it --privileged --rm --ipc host \
        rvr_interface:latest bash
 ```
 
-On Windows you need to do the following things before starting the docker container:
+On Windows you need to do the following before starting the docker container:
 
 1. Install Docker Desktop
 2. Download and install [VcXsrv Windows X Server](https://sourceforge.net/projects/vcxsrv/)
@@ -94,6 +94,7 @@ Now you can run the docker:
 ```bash
 # get own IP adress (take the value of IPAdress e.g. 10.211.55.10 and not 127.0.0.1)
 Get-NetIPAddress
+# or
 ipconfig
 
 # set DISPLAY variable (set <YOUR-IP>)
diff --git a/grass-gis-addons/m.analyse.trees/v.trees.cd/v.trees.cd.py b/grass-gis-addons/m.analyse.trees/v.trees.cd/v.trees.cd.py
index 5c798fb..7205868 100644
--- a/grass-gis-addons/m.analyse.trees/v.trees.cd/v.trees.cd.py
+++ b/grass-gis-addons/m.analyse.trees/v.trees.cd/v.trees.cd.py
@@ -408,6 +408,7 @@ def main():
                 pid,
             )
         # remove unnecessary columns
+        # only for non-empty vector (i.e. vector with attribute table)
         if grass.vector_db(cd_output_i):
             grass.run_command(
                 "v.db.dropcolumn",