From 28392edf9d940cf44bbeda5235aab7f399a128ee Mon Sep 17 00:00:00 2001 From: Giacomo Titti Date: Fri, 20 Dec 2024 18:29:29 +0100 Subject: [PATCH 1/6] first commit 2.0.0 update name metadata --- sz_module/metadata.txt | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/sz_module/metadata.txt b/sz_module/metadata.txt index 5bc840f..11991c3 100755 --- a/sz_module/metadata.txt +++ b/sz_module/metadata.txt @@ -4,13 +4,13 @@ # Mandatory items: [general] -name=sz_processing +name=SZ-plugin qgisMinimumVersion=3.28 description=Susceptibility Zoning plugin version=2.0.0 author=Giacomo Titti and Luigi Lombardo email=giacomotitti@gmail.com -about=SZ-plugin allows the evaluation of the space-time susceptibility from the pre-processing of the data to the cross-validation of the susceptibility map. +about=SZ-plugin allows the evaluation of the space-time susceptibility from the pre-processing of the data to the cross-validation of the susceptibility map. Please cite as: Titti, G., Sarretta, A., Lombardo, L., Crema, S., Pasuto, A., & Borgatti, L. (2022). Mapping susceptibility with open-source tools: a new plugin for QGIS. Frontiers in Earth Science, 10, 842425. tracker=https://github.com/SZtools/SZ-plugin/issues repository=https://github.com/SZtools/SZ-plugin # End of mandatory metadata @@ -21,7 +21,7 @@ hasProcessingProvider=yes # Uncomment the following line and add your changelog: # changelog= # Tags are comma separated with spaces allowed -tags=susceptibility, cross-validation, pre-processing, statistical methods, hazard +tags=space-time susceptibility, cross-validation, Generalized Attitive Model, Random Forest, Support Vector Machine, Decision Tree, Neural Network, Multi-layer Perceptron, natural hazard homepage=https://sz-docs.readthedocs.io/en/latest/ category=Space-time analysis plugin_dependencies= scikit-learn, pygam, pandas, shapely, fiona, seaborn From 041099c1c8fa1906ca8c48502a930a757d613cd9 Mon Sep 17 00:00:00 2001 From: Giacomo Date: Sun, 12 Jan 2025 10:40:22 +0100 Subject: [PATCH 2/6] update metadata and versioning installation --- sz_module/metadata.txt | 8 ++++---- sz_module/sz_module.py | 3 ++- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/sz_module/metadata.txt b/sz_module/metadata.txt index 11991c3..61c0df0 100755 --- a/sz_module/metadata.txt +++ b/sz_module/metadata.txt @@ -6,11 +6,11 @@ [general] name=SZ-plugin qgisMinimumVersion=3.28 -description=Susceptibility Zoning plugin -version=2.0.0 +description=Spatiotemporal data-driven Zoning plugin +version=2.0.1 author=Giacomo Titti and Luigi Lombardo email=giacomotitti@gmail.com -about=SZ-plugin allows the evaluation of the space-time susceptibility from the pre-processing of the data to the cross-validation of the susceptibility map. Please cite as: Titti, G., Sarretta, A., Lombardo, L., Crema, S., Pasuto, A., & Borgatti, L. (2022). Mapping susceptibility with open-source tools: a new plugin for QGIS. Frontiers in Earth Science, 10, 842425. +about=SZ-plugin allows the user to model space-time regressions and classifications from the pre-processing of the data to the cross-validation of the final map. Please cite as: Titti, G., Sarretta, A., Lombardo, L., Crema, S., Pasuto, A., & Borgatti, L. (2022). Mapping susceptibility with open-source tools: a new plugin for QGIS. Frontiers in Earth Science, 10, 842425. tracker=https://github.com/SZtools/SZ-plugin/issues repository=https://github.com/SZtools/SZ-plugin # End of mandatory metadata @@ -21,7 +21,7 @@ hasProcessingProvider=yes # Uncomment the following line and add your changelog: # changelog= # Tags are comma separated with spaces allowed -tags=space-time susceptibility, cross-validation, Generalized Attitive Model, Random Forest, Support Vector Machine, Decision Tree, Neural Network, Multi-layer Perceptron, natural hazard +tags=space-time susceptibility, regression, classification, cross-validation, Generalized Attitive Model, Random Forest, Support Vector Machine, Decision Tree, Neural Network, Multi-layer Perceptron, natural hazard homepage=https://sz-docs.readthedocs.io/en/latest/ category=Space-time analysis plugin_dependencies= scikit-learn, pygam, pandas, shapely, fiona, seaborn diff --git a/sz_module/sz_module.py b/sz_module/sz_module.py index 16f65ae..d65b11b 100755 --- a/sz_module/sz_module.py +++ b/sz_module/sz_module.py @@ -53,7 +53,8 @@ def __init__(self): with open(dir+'/metadata.txt','r') as file: for line in file: if line.startswith('version='): - self.version = line.strip().split('version=')[1].strip() + long_version = line.strip().split('version=')[1].strip() + self.version = '.'.join(long_version.split('.')[:-1]) self.plugin_settings = QSettings().value("SZ",False) def initProcessing(self): From b00a240df88582f19e3e6998e3d77e3213b5170e Mon Sep 17 00:00:00 2001 From: Giacomo Titti Date: Sun, 12 Jan 2025 10:51:57 +0100 Subject: [PATCH 3/6] Update README.md --- README.md | 194 ++---------------------------------------------------- 1 file changed, 7 insertions(+), 187 deletions(-) diff --git a/README.md b/README.md index 346f592..4472d5c 100644 --- a/README.md +++ b/README.md @@ -1,196 +1,14 @@ -# Susceptibility Zoning plugin (SZ) +# Spatiotemporal data-driven Zoning plugin (SZ) -The latest plugin docs are available to: https://sz-docs.readthedocs.io +The plugin documentations are available on: https://sz-docs.readthedocs.io -Plugin repository: https://github.com/SZtools/SZ-plugin +QGIS Plugin repository: https://plugins.qgis.org/plugins/sz_module -## Introduction - -This repository contains the code for a [QGIS](https://www.qgis.org) plugin, called "Susceptibility Zoning plugin" (SZ-plugin), aiming at creating maps of susceptibility to various natural forcing elements. - -The plugin has been developed with a main focus and application towards landslides susceptibility, but it can be applied to different types of natural events or inter-disciplinary applications. - -The plugin uses several type of statistical, machine learning models for susceptibility evaluation, such as: - -* Generalized Additive Model with two distributions: Binomial, Gaussian (see [pygam](https://pygam.readthedocs.io)) -* Decision Tree (see [scikit-learn](https://scikit-learn.org/stable/modules/generated/sklearn.tree.DecisionTreeClassifier.html)) -* Support Vector Machine (see [scikit-learn](https://scikit-learn.org/stable/modules/generated/sklearn.svm.SVC.html)) -* Random Forest (see [scikit-learn](https://scikit-learn.org/stable/modules/generated/sklearn.ensemble.RandomForestClassifier.html#sklearn.ensemble.RandomForestClassifier)) -* Multi-layer Perceptron as classifier (see [scikit-learn](https://scikit-learn.org/stable/modules/generated/sklearn.neural_network.MLPClassifier.html#sklearn.neural_network.MLPClassifier)) and regressor (see [scikit-learn](https://scikit-learn.org/stable/modules/generated/sklearn.neural_network.MLPRegressor.html#sklearn.neural_network.MLPRegressor)) - -The plugin allows the user to perform spatial and temporal analysis implementing space-time cross-validation (CV) methods: - -* Kfold CV (see [scikit-learn](https://scikit-learn.org/stable/modules/generated/sklearn.model_selection.KFold.html)) -* Spatial CV (see [Elia et al., 2023](https://doi.org/10.1016/j.scitotenv.2023.165289)) -* Time Series Split temporal-CV (see [scikit-learn](https://scikit-learn.org/stable/modules/generated/sklearn.model_selection.TimeSeriesSplit.html)) -* Leave One Out temporal-CV (see [scikit-learn](https://scikit-learn.org/stable/modules/generated/sklearn.model_selection.LeaveOneOut.html)) -* Space-time CV (Leave One Out/Spatial CV) - -Moreover the plugin allows the user to run space-time transferability with all the models implemented. - -## Installation - -The SZ plugin is not an official QGIS plugin. - -#### Minimum requirements - -Tested on: - -* Ubuntu 20.04 - QGIS 3.34 -* Ubuntu 22.04 - QGIS 3.34 -* Windows 10 - QGIS 3.28/QGIS 3.34 -* MacOS Sonoma 14.4 - QGIS 3.28 - -#### Download and install - -It can be installed on QGIS >= 3.28 adding the Plugin Repository to QGIS ```manage and install plugins```: - -- add plugin repository - - - -- edit repository and add [https://sztools.github.io/SZ/sz.xml](https://sztools.github.io/SZ/sz.xml) - - -

- -or - -cloning the [GitHub repository](https://github.com/SZtools/SZ-plugin) or downloading it as zip file (and than unzipping it) and copying the ```sz_module``` folder in your local ```python/plugin``` folder (read [here](https://docs.qgis.org/3.10/en/docs/user_manual/plugins/plugins.html#core-and-external-plugins) for more information). - -Lunch QGIS 3.x, and abilitate the plugin from ```manage and install plugin/installed/sz_processing``` - - -

- -or - -cloning the [GitHub repository](https://github.com/SZtools/SZ-plugin) or downloading it as zip file (and than unzipping it), and zip the folder ```sz_module``` to ```sz_module.zip```. Finally you can install the plugin by using the menu ```install from zip```. - - -

- -At the end you should have the SZ plugin in your processing toolbox - - -

- -### GUI - -The functions are grouped into 4 cathegories: - -* _Data preparation_ -* _Modelling_ -* _SI transfer_ -* _Classify SI_ - -* _Data preparation_ functions can be used for data pre-processing -* _Modelling_ functions run the statistic models (_Statistical tools_) and machine learning models (_Machine Learning tools_ / _Neural Network tools_) for susceptibility, cross-validate and evaluate the results by several metrics: ROC (AUC), F1 score, Choen's kappa index, Root Meet Square Error, Mean Absolute Error, Squared R, Pearson Correlation -* _SI transfer_ functions run the statistic models (_Statistical tools_) and machine learning models (_Machine Learning tools_ / _Neural Network tools_) for susceptibility, and apply transfer learning in time and space. -* _Classify SI_ functions allows the user to cathegorize the susceptibility index, to run ROC analysis and to perform Confusion Matrix. - -All the functions run vector analysis - - - -### Usage - -#### Modelling - Machine Learning tools - - - -* 1 select the vecor layer to be used as parent layer in the variable selection -* 2 select the independent variabled from the fields of the input layer. Possible format: linear, ordinal (spline fitted), tensors, cathegorical (integer and continuous from 1 to n) -* 3 select the dependent variable. In case of bionomial selection the variable is 0/1, otherwise an ordinal n_1...n_m -* 4 select the algorithm: SVC, DT, RF -* 5 select one of the possible CV method -* 6 in case of TSS or LOO or space-time CV selection the Time field is necessary -* 7 K value selection in case of random, spatial and space-time CV. If k is equal to 1 then a fitting analysis will be conducted -* 8 set the vector file destination -* 9 set the folder destination for the weights, partial effects, plots and metrics outputs - -#### Modelling - Statistical Tools - - - -* 1 select the vecor layer to be used as parent layer in the variable selection -* 2 select the independent variabled from the fields of the input layer. Possible format: linear, ordinal (spline fitted), tensors, cathegorical (integer and continuous from 1 to n) -* 3 select the distribution: gaussian or binomial -* 4 if the distribution selected is binomial, all the variables are scaled with a standard scaler. The scale selection is necessary only for gaussian distribution: linear (standard scaler) or logaritmic -* 5 select the dependent variable. In case of bionomial selection the variable is 0/1, otherwise an ordinal n_1...n_m -* 6 select one of the possible CV method -* 7 in case of TSS or LOO or space-time CV selection the Time field is necessary -* 8 K value selection in case of random, spatial and space-time CV. If k is equal to 1 then a fitting analysis will be conducted -* 9 set the vector file destination -* 10 set the folder destination for the weights, partial effects, plots and metrics outputs* - -#### Modelling - Neural Network Tools - - - -* 1 select the vecor layer to be used as parent layer in the variable selection -* 2 select the independent variabled from the fields of the input layer. Possible format: linear, ordinal (spline fitted), tensors, cathegorical (integer and continuous from 1 to n) -* 3 select the dependent variable. In case of bionomial selection the variable is 0/1, otherwise an ordinal n_1...n_m -* 4 select the algorithm: MLP classifier or MLP regressor -* 5 if the distribution selected is MLP classifier, all the variables are scaled with a standard scaler. The scale selection is necessary only for MLP regressor: linear ([standard scaler](https://scikit-learn.org/stable/modules/generated/sklearn.preprocessing.StandardScaler.html)) or logaritmic -* 6 select one of the possible CV method -* 7 in case of TSS or LOO or space-time CV selection the Time field is necessary -* 8 K value selection in case of random, spatial and space-time CV. If k is equal to 1 then a fitting analysis will be conducted -* 9 set the vector file destination -* 10 set the folder destination for the weights, partial effects, plots and metrics outputs - - -### Test - -A dataset and QGIS project are available in [test](./test_data) folder to test the plugin. - - - - - - -## Third-part libraries and plugins used - -* [scikit-learn](https://scikit-learn.org/stable/index.html) -* pygam -* pandas -* shapely -* fiona -* seaborn - - -## Tutorial - -video tutorial SZ v1.x: https://www.youtube.com/watch?v=XpsiCkVF11s - -## Application - -Titti G, Sarretta A, Lombardo L, Crema S, Pasuto A and Borgatti L (2022) Mapping Susceptibility With Open-Source Tools: A New Plugin for QGIS. Front. Earth Sci. 10:842425. doi: 10.3389/feart.2022.842425 - -[Referenced dataset](https://zenodo.org/record/6575572) - -## Publications - -_A few examples and references about applications_ - -Titti G, Sarretta A, Lombardo L, Crema S, Pasuto A and Borgatti L (2022) Mapping Susceptibility With Open-Source Tools: A New Plugin for QGIS. Front. Earth Sci. 10:842425. doi: 10.3389/feart.2022.842425 - -Titti, G., van Westen, C., Borgatti, L., Pasuto, A., & Lombardo, L. (2021). When Enough Is Really Enough? On the Minimum Number of Landslides to Build Reliable Susceptibility Models. Geosciences, 11(11), 469. - -Titti, G., Borgatti, L., Zou, Q., Cui, P., & Pasuto, A. (2021). Landslide susceptibility in the Belt and Road Countries: continental step of a multi-scale approach. Environmental Earth Sciences, 80(18), 1-18.[10.1007/s12665-021-09910-1](https://doi.org/10.1007/s12665-021-09910-1) - -Titti, G., Borgatti, L., Zou, Q., Pasuto, A., 2019. Small-Scale landslide Susceptibility Assessment. The Case Study of the Southern Asia. Proceedings 30, 14. [10.3390/proceedings2019030014](https://doi.org/10.3390/proceedings2019030014) - -## Presentations - -_A list of presentations made about the plugin and its applications_ - -Titti, Giacomo, Sarretta, Alessandro, Crema, Stefano, Pasuto, Alessandro, & Borgatti, Lisa. (2020, March). Sviluppo e applicazione del plugin Susceptibility zoning per il supporto alla pianificazione territoriale. Zenodo. [10.5281/zenodo.3723353](https://zenodo.org/record/3723353) - ## Credits + v1.x: Giacomo Titti, Alessandro Sarretta and Luigi Lombardo, Padova, November 2021 please cite: Titti G, Sarretta A, Lombardo L, Crema S, Pasuto A and Borgatti L (2022) Mapping Susceptibility With Open-Source Tools: A New Plugin for QGIS. Front. Earth Sci. 10:842425. doi: 10.3389/feart.2022.842425 @@ -200,5 +18,7 @@ v2.x: Giacomo Titti, Luigi Lombardo, Liwei Hu, Pietro Festi, Letizia Elia, Bolog please cite: xxx ## Contacts -If you have any problem, please write to giacomotitti@gmail.com or create new issue [here](https://github.com/SZtools/SZ-plugin/issues) + + +If you have any problem, please write to giacomotitti@gmail.com or giacomo.titti@unibo.it and create new issue [here](https://github.com/SZtools/SZ-plugin/issues) From e5e6edc3d982a5a09c217389d7b4dd061a949273 Mon Sep 17 00:00:00 2001 From: Giacomo Titti Date: Sun, 12 Jan 2025 10:53:10 +0100 Subject: [PATCH 4/6] Delete LICENSE --- LICENSE | 674 -------------------------------------------------------- 1 file changed, 674 deletions(-) delete mode 100644 LICENSE diff --git a/LICENSE b/LICENSE deleted file mode 100644 index f288702..0000000 --- a/LICENSE +++ /dev/null @@ -1,674 +0,0 @@ - GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The GNU General Public License is a free, copyleft license for -software and other kinds of works. - - The licenses for most software and other practical works are designed -to take away your freedom to share and change the works. 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If not, see . - -Also add information on how to contact you by electronic and paper mail. - - If the program does terminal interaction, make it output a short -notice like this when it starts in an interactive mode: - - Copyright (C) - This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. - This is free software, and you are welcome to redistribute it - under certain conditions; type `show c' for details. - -The hypothetical commands `show w' and `show c' should show the appropriate -parts of the General Public License. Of course, your program's commands -might be different; for a GUI interface, you would use an "about box". - - You should also get your employer (if you work as a programmer) or school, -if any, to sign a "copyright disclaimer" for the program, if necessary. -For more information on this, and how to apply and follow the GNU GPL, see -. - - The GNU General Public License does not permit incorporating your program -into proprietary programs. If your program is a subroutine library, you -may consider it more useful to permit linking proprietary applications with -the library. If this is what you want to do, use the GNU Lesser General -Public License instead of this License. But first, please read -. From 13193b68ef2f0974c614d43813d2dd368fbdedc5 Mon Sep 17 00:00:00 2001 From: Giacomo Titti Date: Thu, 16 Jan 2025 11:12:56 +0100 Subject: [PATCH 5/6] update metadata --- sz_module/metadata.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/sz_module/metadata.txt b/sz_module/metadata.txt index 61c0df0..42dd85b 100755 --- a/sz_module/metadata.txt +++ b/sz_module/metadata.txt @@ -10,7 +10,7 @@ description=Spatiotemporal data-driven Zoning plugin version=2.0.1 author=Giacomo Titti and Luigi Lombardo email=giacomotitti@gmail.com -about=SZ-plugin allows the user to model space-time regressions and classifications from the pre-processing of the data to the cross-validation of the final map. Please cite as: Titti, G., Sarretta, A., Lombardo, L., Crema, S., Pasuto, A., & Borgatti, L. (2022). Mapping susceptibility with open-source tools: a new plugin for QGIS. Frontiers in Earth Science, 10, 842425. +about=SZ-plugin allows the user to model space-time regressions and classifications from the pre-processing of the data to the cross-validation of the final map. Application in: Titti, G., Hu, L., Festi, P., Elia, L., Borgatti, L. & Lombardo, L. (2025). An updated version of the SZ-plugin: from space to space-time data-driven modeling in QGIS. Preprint https://doi.org/10.31223/X5JD9X . Please cite as: Titti, G., Sarretta, A., Lombardo, L., Crema, S., Pasuto, A., & Borgatti, L. (2022). Mapping susceptibility with open-source tools: a new plugin for QGIS. Frontiers in Earth Science, 10, 842425. tracker=https://github.com/SZtools/SZ-plugin/issues repository=https://github.com/SZtools/SZ-plugin # End of mandatory metadata @@ -22,7 +22,7 @@ hasProcessingProvider=yes # changelog= # Tags are comma separated with spaces allowed tags=space-time susceptibility, regression, classification, cross-validation, Generalized Attitive Model, Random Forest, Support Vector Machine, Decision Tree, Neural Network, Multi-layer Perceptron, natural hazard -homepage=https://sz-docs.readthedocs.io/en/latest/ +homepage=https://sz-docs.readthedocs.io/ category=Space-time analysis plugin_dependencies= scikit-learn, pygam, pandas, shapely, fiona, seaborn icon=images/icon.png From 3968c82640665d132ab00c850dd28fa5ecfdb4e6 Mon Sep 17 00:00:00 2001 From: Giacomo Titti Date: Thu, 16 Jan 2025 11:14:53 +0100 Subject: [PATCH 6/6] Update README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 4472d5c..01ef9ba 100644 --- a/README.md +++ b/README.md @@ -11,11 +11,11 @@ QGIS Plugin repository: https://plugins.qgis.org/plugins/sz_module v1.x: Giacomo Titti, Alessandro Sarretta and Luigi Lombardo, Padova, November 2021 -please cite: Titti G, Sarretta A, Lombardo L, Crema S, Pasuto A and Borgatti L (2022) Mapping Susceptibility With Open-Source Tools: A New Plugin for QGIS. Front. Earth Sci. 10:842425. doi: 10.3389/feart.2022.842425 +please cite: Titti G, Sarretta A, Lombardo L, Crema S, Pasuto A and Borgatti L (2022) Mapping Susceptibility With Open-Source Tools: A New Plugin for QGIS. Front. Earth Sci. 10:842425. https://doi.org/10.3389/feart.2022.842425 v2.x: Giacomo Titti, Luigi Lombardo, Liwei Hu, Pietro Festi, Letizia Elia, Bologna, December 2024 -please cite: xxx +please cite: Titti, G., Hu, L., Festi, P., Elia, L., Borgatti, L. & Lombardo, L. (2025). An updated version of the SZ-plugin: from space to space-time data-driven modeling in QGIS. EarthArxiv, Preprint. https://doi.org/10.31223/X5JD9X ## Contacts