.gitignore

+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# PyTreeDB
+pytreedb
+
+# Configs
+config/*
+
+# SynForest Data
+data
+
+# Container
+container/*
+
+# LASTOOLS
+bin/LAStools
+
+# Results
+results/*
+
+# Temp
+tmp/*
\ No newline at end of file

README.md

+# **SynForest**
+## Point Cloud Generation for Large-Scale Synthetic Forests
+
+SynForest is a tool that generates realistic large-scale point clouds of forests by simulating the lidar scanning process from a stationary or moving platform and capturing the shape and structure of realistic tree models.
+
+![Sample forest](./docs/img/synthetic_forest_thick.png)
+
+SynForest was employed to generate synthetic forest datasets that were utilized in model pre-training for instance segmentation in point clouds.
+
+# 1. Installation
+
+SynForest has multiple components that require preparation, so the installation involves several steps that we explain here.
+
+## 1.1. SynForest
+
+Clone this repository:
+
+```bash
+git clone https://github.com/adoosth/forest-synthesis.git
+```
+
+Create and activate the conda environment:
+```bash
+conda create -y -n synforest python=3.8
+conda activate synforest
+```
+
+Install the `synforest` package:
+```bash
+cd forest-synthesis/synforest
+pip install . -r requirements.txt
+```
+
+## 1.2. Container for Helios++
+
+Download the container for Helios++ from [here](https://owncloud.gwdg.de/index.php/f/2417870773) (You may need to request access). SynForest expects the file `synforest.sif` to be placed under `container/`, but this can be changed in the configuration file if desired.
+
+## 1.3. Lastools
+
+If LAStools is not available already, you must obtain and compile it. The source code is available at: [https://github.com/LAStools/LAStools](https://github.com/LAStools/LAStools)
+
+Clone the repository under `bin/`. You can also change the path later in the configuration file.
+```git
+git clone https://github.com/LAStools/LAStools.git
+```
+
+Now, compile LAStools:
+
+```bash
+cd LAStools
+make
+```
+
+You should now have the exectuble file `las2las` located in `LAStools/bin/`:
+```bash
+./bin/las2las -h
+```
+
+
+## 1.4. PyTreeDB
+
+PyTreeDB is a point cloud database consisting of real trees in Germany. These point clouds are used as base tree models for the process of forest generation.
+
+A python script is provided to download the entire database with a compatible folder structure for use in SynForest. If you have enough space (at least 14 GB), it is recommended to store it under `pytreedb/`, otherwise you must set the path later in the configuration files.
+
+```bash
+python tools/get_pytreedb.py ./pytreedb
+```
+
+You may replace `./pytreedb` with the desired path to store PyTreeDB.
+
+## 1.5. Configure Slurm
+
+The tool depends on `slurm` for job submission. The partition names for the slurm jobs most likely need to be configured for your system. You may set the partition and other settings in the headers of the files `synforest/scripts/utils/sb_single_tile.sh` and `synforest/scripts/utils/sb_merge_tiles.sh` to pertain to your HPC system.
+
+# 2. Usage
+
+A number of sample configurations are provided in `config/`. To run a forest generation task, execute the `run.py` script with the path to the configuration file, i.e.:
+
+```
+cd synforest
+python run.py config/example_ULS.json
+```
+
+If any of the components as described in Step 1 are located elsewhere, you must alter the configuration file accordingly.
+
+For a full instruction manual of the configuration files, see [configuration](./docs/CONFIG.md).
+
+# 3. Acknowledgements
+
+- GWDG Computing Group: [Group Page](https://www.gwdg.de/web/guest/about-us/organization/departments/computing)
+- HLRN: [https://hlrn.de](https://hlrn.de)
+- ForestFactory: [https://git.ufz.de/angermue/forestfactory](https://git.ufz.de/angermue/forestfactory) 
+- Helios++: [https://github.com/3dgeo-heidelberg/helios](https://github.com/3dgeo-heidelberg/helios)
+- Janika Schäfer et al. "<i>Applications of synthetic airborne laser scanning data of forests.</i>", ForestSat Conference 2022
+
+# 4. Citation
+
+If you used this tool in your research, please cite as follows:
+
+```
+@conference{synforest2023,
+    title        = {Large-Scale Synthetic Forest Point Cloud Generation on HPC Systems},
+    author       = {Ali Doosthosseini and Hauke Kirchner and Dorothea Sommer and Julian Kunkel},
+    year         = 2023,
+    month        = {September},
+    organization = {NHR Conference '23}
+}
+```
+
+# 5. Contacts
+
+If there are any issues or questions, feel free to contact Ali Doosthosseini [adoosth@gwdg.de](mailto:adoosth@gwdg.de) or Hauke Kirchner [hauke.kirchner@gwdg.de](mailto:hauke.kirchner@gwdg.de)
\ No newline at end of file

config/example_TLS.json

+{
+    "id": "synforest-example-TLS-{timestamp}",
+    "work_dir": "data",
+    "map": {
+        "stand": "sample/sample_forest.res",
+        "side": 200,
+        "species": "QuePet"
+    },
+    "scene":{
+        "pytreedb_dir": "pytreedb",
+        "model_source": "TLS",
+        "min_quality": 3,
+        "has_leaves": true,
+        "tile_w": 50,
+        "tile_h": 50,
+        "tile_overlap": 10,
+        "template": {
+            "id": "{id}_{tile_id}",
+            "name": "{id}_{tile_id}",
+            "area": {
+                "z_var": 0.5
+            },
+            "trees": []
+        }
+    },
+    "simulation": {
+        "container": "container/synforest.sif",
+        "lastools": "bin/LAStools",
+        "output_dir": "results",
+        "template": {
+            "id": "{id}_{tile_id}",
+            "name": "{id}_{tile_id}",
+            "helios_seed": 42,
+            "platform": {
+                "id": "copter_linearpath",
+                "speed": 10,
+                "altitude": 80
+            },
+            "scanner": {
+                "id": "dji_zenmuse_l1",
+                "angle": 30.0,
+                "pulse_freq": 100000
+            },
+            "legs": [
+                {"x": 100, "y": 300},
+                {"x": 300, "y": 100},
+                {"x": 250, "y": 50},
+                {"x": 50, "y": 250},
+                {"x": 0, "y": 200},
+                {"x": 200, "y": 0},
+                {"x": 150, "y": -50},
+                {"x": -50, "y": 150},
+                {"x": -100, "y": 100},
+                {"x": 100, "y": -100},
+                {"x": 300, "y": 100},
+                {"x": 250, "y": 150},
+                {"x": 50, "y": -50},
+                {"x": 0, "y": 0},
+                {"x": 200, "y": 200},
+                {"x": 150, "y": 250},
+                {"x": -50, "y": 50},
+                {"x": -100, "y": 100},
+                {"x": 100, "y": 300}
+            ]
+        }
+    }
+}
\ No newline at end of file

config/example_ULS.json

+{
+    "id": "synforest-example-ULS-{timestamp}",
+    "work_dir": "data",
+    "map": {
+        "stand": "sample/sample_forest.res",
+        "side": 200,
+        "species": "QuePet"
+    },
+    "scene":{
+        "pytreedb_dir": "pytreedb",
+        "model_source": "ULS",
+        "min_quality": 3,
+        "has_leaves": true,
+        "tile_w": 100,
+        "tile_h": 100,
+        "tile_overlap": 10,
+        "template": {
+            "id": "{id}_{tile_id}",
+            "name": "{id}_{tile_id}",
+            "area": {
+                "z_var": 0.5
+            },
+            "trees": []
+        }
+    },
+    "simulation": {
+        "container": "container/synforest.sif",
+        "lastools": "bin/LAStools",
+        "output_dir": "results",
+        "template": {
+            "id": "{id}_{tile_id}",
+            "name": "{id}_{tile_id}",
+            "helios_seed": 42,
+            "platform": {
+                "id": "copter_linearpath",
+                "speed": 10,
+                "altitude": 80
+            },
+            "scanner": {
+                "id": "dji_zenmuse_l1",
+                "angle": 30.0,
+                "pulse_freq": 100000
+            },
+            "legs": [
+                {"x": 100, "y": 300},
+                {"x": 300, "y": 100},
+                {"x": 250, "y": 50},
+                {"x": 50, "y": 250},
+                {"x": 0, "y": 200},
+                {"x": 200, "y": 0},
+                {"x": 150, "y": -50},
+                {"x": -50, "y": 150},
+                {"x": -100, "y": 100},
+                {"x": 100, "y": -100},
+                {"x": 300, "y": 100},
+                {"x": 250, "y": 150},
+                {"x": 50, "y": -50},
+                {"x": 0, "y": 0},
+                {"x": 200, "y": 200},
+                {"x": 150, "y": 250},
+                {"x": -50, "y": 50},
+                {"x": -100, "y": 100},
+                {"x": 100, "y": 300}
+            ]
+        }
+    }
+}
\ No newline at end of file

config/example_ULS_multi.json

+{
+    "id": "synforest-example-ULS-multi-{timestamp}",
+    "work_dir": "data",
+    "map": {
+        "stand": "sample/sample_forest.res",
+        "side": 200,
+        "species": ["PinSyl", "PicAbi", "FagSyl", "QueRub", "AceCam", "FraExc", "BetPen", "PseMen"]
+    },
+    "scene":{
+        "pytreedb_dir": "pytreedb",
+        "model_source": "ULS",
+        "min_quality": 3,
+        "has_leaves": true,
+        "tile_w": 100,
+        "tile_h": 100,
+        "tile_overlap": 10,
+        "template": {
+            "id": "{id}_{tile_id}",
+            "name": "{id}_{tile_id}",
+            "area": {
+                "z_var": 0.5
+            },
+            "trees": []
+        }
+    },
+    "simulation": {
+        "container": "container/synforest.sif",
+        "lastools": "bin/LAStools",
+        "output_dir": "results",
+        "template": {
+            "id": "{id}_{tile_id}",
+            "name": "{id}_{tile_id}",
+            "helios_seed": 42,
+            "platform": {
+                "id": "copter_linearpath",
+                "speed": 10,
+                "altitude": 80
+            },
+            "scanner": {
+                "id": "dji_zenmuse_l1",
+                "angle": 30.0,
+                "pulse_freq": 100000
+            },
+            "legs": [
+                {"x": 100, "y": 300},
+                {"x": 300, "y": 100},
+                {"x": 250, "y": 50},
+                {"x": 50, "y": 250},
+                {"x": 0, "y": 200},
+                {"x": 200, "y": 0},
+                {"x": 150, "y": -50},
+                {"x": -50, "y": 150},
+                {"x": -100, "y": 100},
+                {"x": 100, "y": -100},
+                {"x": 300, "y": 100},
+                {"x": 250, "y": 150},
+                {"x": 50, "y": -50},
+                {"x": 0, "y": 0},
+                {"x": 200, "y": 200},
+                {"x": 150, "y": 250},
+                {"x": -50, "y": 50},
+                {"x": -100, "y": 100},
+                {"x": 100, "y": 300}
+            ]
+        }
+    }
+}
\ No newline at end of file

docs/CONFIG.md

+# SynForest Configuration
+
+This document provides details and instructions for the .json configuration files used in the forest generation process.
+
+## General
+
+The configuration file consists of three main sections: Map, Scene, and Simulation
+
+![Process](./img/process.png)
+
+
+
+### 1. Map
+
+This part configures the forest map, i.e., the coordinates of each tree and their various properties such as species, height, and diameter at breast height. The workflow can directly use the output from `ForestFactory` which is a `.res` file.
+
+Here is a table describing each parameter in the json config file under `map`:
+
+| Parameter | Description |
+| --------- | ----------- |
+| `stand` | Path to the `.res` stand file that contains the information about the trees in the forest |
+| `side`  | Length of the side of the square map in meters |
+| `species` | Identifier of the species that is being simulated, e.g. `QuePet` |
+
+### 2. Scene
+
+| Parameter | Description |
+| --------- | ----------- |
+| `pytreedb_dir` | Path to the PyTreeDB directory |
+| `model_source` | Can be either `ULS`, `TLS` or `ALS` |
+| `tile_w` | Width (x-length) of each tile in meters |
+| `tile_h` | Height (y-length) of each tile in meters |
+| `tile_overlap` | The overlap between adjacent tiles in meters |
+| `template` | Contains parameters for the generated scene file for Helios++ |
+| `template.id` | Scene ID |
+| `template.name` | Scene name, can be same as ID |
+| `template.area.z_var` | Variation of trees in the Z-axis |
+| `template.trees` | Reserved |
+
+
+### 3. Simulation
+
+This part configures the simulation of the scene in Helios++ and path to the point cloud output. 
+
+| Parameter | Description |
+| --------- | ----------- |
+| `container` | Path to the container that contains the software for running the simulation |
+| `lastools` | Path to the LASTools directory |
+| `output_dir` | Path to directory to store simulation results |
+| `template` | Contains parameters for simulation in Helios++ |
+| `template.id` | ID of the survey |
+| `template.name` | Name of the survey |
+| `template.helios_seed` | Randomization seed for helios' noise and other effects |
+| `template.platform.id` | Identifier of the platform (e.g. drone, plane) used for the survey |
+| `template.platform.speed` | Speed of the platform in meters per second |
+| `template.platform.altitude` | Altitude above ground of the platform in meters |
+| `template.scanner.id` | Identifier of the scanner (e.g. lidar, camera) used for the survey |
+| `survey.scanner.angle` | Angle from horizon of the scanner in degrees |
+| `survey.scanner.pulse_freq` | Pulse frequency of the scanner in hertz |
+| `survey.legs` | List of legs in the survey, each with its own coordinates in meters relative to scene origin |

requirements.txt

+absl-py==1.4.0
+addict==2.4.0
+anyio==3.6.1
+argon2-cffi==21.3.0
+argon2-cffi-bindings==21.2.0
+asttokens==2.0.5
+attrs==21.4.0
+Babel==2.10.2
+backcall==0.2.0
+beautifulsoup4==4.11.1
+bleach==5.0.0
+cachetools==5.2.1
+certifi==2022.5.18.1
+cffi==1.15.0
+charset-normalizer==2.0.12
+cycler==0.11.0
+debugpy==1.6.0
+decorator==5.1.1
+defusedxml==0.7.1
+deprecation==2.1.0
+docopt==0.6.2
+entrypoints==0.4
+executing==0.8.3
+fastjsonschema==2.15.3
+fonttools==4.33.3
+google-auth==2.16.0
+google-auth-oauthlib==0.4.6
+grpcio==1.51.1
+idna==3.3
+importlib-metadata==4.11.4
+importlib-resources==5.7.1
+iniconfig==1.1.1
+jedi==0.18.1
+Jinja2==3.1.2
+joblib==1.1.0
+json5==0.9.8
+jsonschema==4.6.0
+kiwisolver==1.4.3
+laspy==2.2.0
+laszip==0.1.0
+lazrs==0.4.5
+Markdown==3.4.1
+MarkupSafe==2.1.1
+matplotlib==3.5.2
+matplotlib-inline==0.1.3
+mistune==0.8.4
+nbclassic==0.3.7
+nbclient==0.6.4
+nbconvert==6.5.0
+nbformat==5.4.0
+nest-asyncio==1.5.5
+notebook==6.4.12
+notebook-shim==0.1.0
+numpy==1.22.4
+oauthlib==3.2.2
+open3d==0.13.0
+packaging==21.3
+pandas==1.4.2
+pandocfilters==1.5.0
+parso==0.8.3
+pexpect==4.8.0
+pickleshare==0.7.5
+Pillow==9.1.1
+pluggy==1.0.0
+prometheus-client==0.14.1
+prompt-toolkit==3.0.29
+protobuf==3.20.3
+psutil==5.9.1
+ptyprocess==0.7.0
+pure-eval==0.2.2
+py==1.11.0
+pyasn1==0.4.8
+pyasn1-modules==0.2.8
+pycparser==2.21
+Pygments==2.12.0
+pyparsing==3.0.9
+pyrsistent==0.18.1
+pytest==7.1.2
+python-dateutil==2.8.2
+pytz==2022.1
+PyYAML==6.0
+pyzmq==23.1.0
+requests==2.28.0
+requests-oauthlib==1.3.1
+rsa==4.9
+scikit-learn==1.1.1
+scipy==1.8.1
+Send2Trash==1.8.0
+six==1.16.0
+sniffio==1.2.0
+soupsieve==2.3.2.post1
+stack-data==0.2.0
+tensorboard==2.11.2
+tensorboard-data-server==0.6.1
+tensorboard-plugin-wit==1.8.1
+terminado==0.15.0
+threadpoolctl==3.1.0
+tinycss2==1.1.1
+tomli==2.0.1
+tomlkit==0.11.0
+tornado==6.1
+tqdm==4.64.0
+traitlets==5.2.2.post1
+urllib3==1.26.9
+wcwidth==0.2.5
+webencodings==0.5.1
+websocket-client==1.3.2
+widgetsnbextension==3.6.0
+yarg==0.1.9
+zipp==3.8.0

run.py

+import sys
+import pandas as pd
+import numpy as np
+import os
+import json
+from copy import deepcopy
+import argparse
+import datetime
+import itertools
+import synforest.utils as utils
+import synforest.steps as steps
+
+if __name__ == '__main__':
+    if len(sys.argv) < 2:
+        print('Usage: python build_forest.py <config_path>')
+        sys.exit(1)
+    config = utils.load_config(sys.argv[1])
+    steps.map(config)
+    steps.scene(config)
+    steps.simulation(config)
+    steps.finalize(config)

scripts/helios_multi_tiles.sh

+############################################################
+# Utils                                                    #
+############################################################
+# Get scripts root directory
+root=$(dirname $(realpath $0 ))
+
+############################################################
+# Help                                                     #
+############################################################
+
+Help()
+{
+    # Display Help
+    echo "Builds multiple forest tiles in parallel using helios container."
+    echo "---------"
+    echo "helios_multi_tiles.sh path_to_container work_dir assets_dir out_dir indexing lastools"
+    echo "---------"
+    echo "  path_to_container           Path to helios container"
+    echo "  work_dir                    Path to project directory"
+    echo "  assets_dir                  Path to assets directory"
+    echo "  out_dir                     Path to output directory"
+    echo "  indexing                    Tile indexes to build"
+    echo "  lastools                    Path to lastools directory"
+    exit
+}
+
+Invalid()
+{
+    echo "ERROR: Invalid arguments."
+    Help
+}
+
+Insuf()
+{
+    echo "ERROR: Insufficient arguments."
+    Help
+}
+
+if [ $# -ge 6 ]; then
+    if [ $# -ge 7 ]; then
+        Invalid
+    fi
+    if [ $1 == 'help' ] || [ $1 == "-h" ]; then
+        Help
+    fi
+else
+    Insuf
+fi
+CONTAINER_PATH="$1"
+shift
+CUR_WORK_DIR="$1"
+FOREST_BASENAME=$(basename $CUR_WORK_DIR)
+shift
+ASSETS_DIR="$1"
+shift
+OUT_DIR="$1"
+SCENE_FILENAME=/forestcare/scene/$FOREST_BASENAME
+SIMULATION_FILENAME=/forestcare/simulation/$FOREST_BASENAME
+shift
+INDEXING="$1"
+shift
+LASTOOLS="$1"
+
+echo "sbatch --parsable -a --mem-per-cpu=64G $INDEXING ./scripts/utils/sb_single_tile.sh $CONTAINER_PATH $CUR_WORK_DIR $ASSETS_DIR $SCENE_FILENAME $SIMULATION_FILENAME"
+RES=$(sbatch --parsable -a "$INDEXING" ./scripts/utils/sb_single_tile.sh "$CONTAINER_PATH" "$CUR_WORK_DIR" "$ASSETS_DIR" "$SCENE_FILENAME" "$SIMULATION_FILENAME")
+echo "Submitted job $RES"
+
+echo "Waiting for job $RES to finish..."
+sbatch --dependency=afterok:$RES "./scripts/utils/sb_merge_tiles.sh" "$CUR_WORK_DIR" "$OUT_DIR" "$LASTOOLS"
+#sbatch --mem-per-cpu=64G "$FCDIR_CODE/forest_synthesis/scripts/utils/sb_merge_tiles.sh" "$CUR_WORK_DIR" "$OUT_DIR" "$LASTOOLS"
+echo "Done."
\ No newline at end of file

scripts/utils/sb_merge_tiles.sh

+#!/bin/bash
+#SBATCH -t 8:00:00
+#SBATCH -p standard96
+#SBATCH -o tmp/%J-merge.txt
+
+CUR_WORK_DIR="$1"
+shift
+
+OUT_DIR="$1"
+shift
+
+echo "Activating conda..."
+CONDA_BASE=$(conda info --base)
+source $CONDA_BASE/etc/profile.d/conda.sh
+conda activate synforest
+
+echo "Running merge_tiles.py"
+python ./src/synforest/utils/merge_tiles.py $CUR_WORK_DIR $OUT_DIR $@
\ No newline at end of file

scripts/utils/sb_single_tile.sh

+#!/bin/bash
+#SBATCH -t 4:00:00
+#SBATCH -p standard96
+#SBATCH -o tmp/%J-tile.txt
+
+CONTAINER_PATH="$1"
+shift
+
+CUR_WORK_DIR="$1"
+shift
+
+ASSETS_DIR="$1"
+shift
+
+SCENE_FILENAME="$1"
+shift
+
+SIMULATION_FILENAME="$1"
+shift
+
+TASK_ID="$SLURM_ARRAY_TASK_ID"
+echo "Task ID: $TASK_ID"
+echo "Loading singularity"
+module load singularity
+
+echo "singularity exec -B $HOME:/usr/users/$USER,$CUR_WORK_DIR:/forestcare,./src/synforest/utils/run_helios.py:/forestcare/run_helios.py,$ASSETS_DIR:/forestcare/assets $CONTAINER_PATH python /forestcare/run_helios.py $SCENE_FILENAME\_$TASK_ID.json $SIMULATION_FILENAME\_$TASK_ID.json"
+
+singularity exec -B $HOME:/usr/users/$USER,$CUR_WORK_DIR:/forestcare,./src/synforest/utils/run_helios.py:/forestcare/run_helios.py,$ASSETS_DIR:/forestcare/assets,./template:/forestcare/template $CONTAINER_PATH python /forestcare/run_helios.py $SCENE_FILENAME\_$TASK_ID.json $SIMULATION_FILENAME\_$TASK_ID.json
+echo -ne "Done @"
+hostname
+echo ""
\ No newline at end of file

setup.py

+import setuptools
+  
+setuptools.setup(
+    name="synforest",
+    version="0.2",
+    author="Ali Doosthosseini",
+    author_email="doosth.ali@gmail.com",
+    package_dir={'':'src'},
+    packages=["synforest", 'synforest.steps', 'synforest.utils'],
+    description="Synthetic Forest Generation",
+    long_description="Synthetic Forest Generation",
+    long_description_content_type="text/markdown",
+    license='MIT',
+    python_requires='>=3.8',
+    install_requires=[]
+)

src/synforest/__init__.py

+from . import steps
\ No newline at end of file

src/synforest/steps/__init__.py

+from .map import map
+from .scene import scene
+from .simulation import simulation
+from .finalize import finalize
\ No newline at end of file