Renaming Flompy to Floodpy

FLOMPY_env.yml → FLOODPY_env.yml

@@ -1,4 +1,4 @@
-name: flompy
+name: floodpy
 channel_priority: strict
 channels:
   - conda-forge

FLOMPYapp_template.cfg → FLOODPYapp_template.cfg

@@ -10,8 +10,8 @@ Projectname = Palamas
 #    you have enough free space disk on the specific location.
 projectfolder = /home/kleanthis/Palamas
 
-#A3. The location of Flompy code 
-src_dir = /home/kleanthis/Projects/FLOMPY/flompy/
+#A3. The location of floodpy code 
+src_dir = /home/kleanthis/Projects/FLOODPY/floodpy/
 
 #A4. SNAP ORBIT DIRECTORY
 snap_dir = /home/jovkleanthisyan/.snap/auxdata/Orbits/Sentinel-1

LICENSE

@@ -1,12 +1,12 @@
-FLOMPY - FLOod Mapping PYthon toolbox
+FLOODPY - FLOOD PYthon toolbox
 Copyright (c) 2021 - 2022, Kleanthis Karamvasis
 
-FLOMPY is free software: you can redistribute it and/or modify
+FLOODPY is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
 the Free Software Foundation, either version 3 of the License, or
 (at your option) any later version.
 
-FLOMPY is distributed in the hope that it will be useful,
+FLOODPY is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 GNU General Public License for more details.

README.md

@@ -1,25 +1,25 @@
-# <img src="https://github.com/kleok/FLOMPY/blob/main/figures/Flompy_logo.png" width="58"> FLOMPY - FLOod Mapping PYthon toolbox 
-[![GitHub license](https://img.shields.io/badge/License-GNU3-green.svg)](https://github.com/kleok/FLOMPY)
-[![Release](https://img.shields.io/badge/Release-0.2.0-brightgreen)](https://github.com/kleok/FLOMPY)
+# <img src="https://github.com/kleok/FLOODPY/blob/main/figures/FLOODPY_logo.png" width="58"> FLOODPY - FLOOD PYthon toolbox 
+[![GitHub license](https://img.shields.io/badge/License-GNU3-green.svg)](https://github.com/kleok/FLOODPY)
+[![Release](https://img.shields.io/badge/Release-0.2.0-brightgreen)](https://github.com/kleok/FLOODPY)
 [![Facebook](https://img.shields.io/badge/Group-Flompy-yellowgreen.svg)](https://www.facebook.com/groups/876299509742954)
-[![contributions welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg?style=flat)](https://github.com/kleok/FLOMPY/issues)
-[![Documentation](https://readthedocs.org/projects/flompy/badge/?version=latest)](https://flompy.readthedocs.io/en/latest/)
+[![contributions welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg?style=flat)](https://github.com/kleok/FLOODPY/issues)
+[![Documentation](https://readthedocs.org/projects/floodpy/badge/?version=latest)](https://floodpy.readthedocs.io/en/latest/)
 
 ## Introduction
 
-The FLOod Mapping PYthon toolbox is a free and open-source python toolbox for mapping of floodwater. It exploits the dense Sentinel-1 GRD intensity time series and is based on four processing steps. In the first step, a selection of Sentinel-1 images related to pre-flood (baseline) state and flood state is performed. In the second step, the preprocessing of the selected images is performed in order to create a co-registered stack with all the pre-flood and flood images. In the third step, a statistical temporal analysis is performed and a t-score map that represents the changes due to flood event is calculated. Finally, in the fourth step, a multi-scale iterative thresholding algorithm based on t-score map is performed to extract the final flood map. We believe that the end-user community can benefit by exploiting the FLOMPY's floodwater maps.
+The FLOod Mapping PYthon toolbox is a free and open-source python toolbox for mapping of floodwater. It exploits the dense Sentinel-1 GRD intensity time series and is based on four processing steps. In the first step, a selection of Sentinel-1 images related to pre-flood (baseline) state and flood state is performed. In the second step, the preprocessing of the selected images is performed in order to create a co-registered stack with all the pre-flood and flood images. In the third step, a statistical temporal analysis is performed and a t-score map that represents the changes due to flood event is calculated. Finally, in the fourth step, a multi-scale iterative thresholding algorithm based on t-score map is performed to extract the final flood map. We believe that the end-user community can benefit by exploiting the FLOODPY's floodwater maps.
 
 This is research code provided to you "as is" with NO WARRANTIES OF CORRECTNESS. Use at your own risk.
 
-<img src="https://github.com/kleok/FLOMPY/blob/main/figures/pinieios_results_github.png" width="900">
+<img src="https://github.com/kleok/FLOODPY/blob/main/figures/pinieios_results_github.png" width="900">
 
 ## 1. Installation
 
 The installation notes below are tested only on Linux. Recommended minimum setup: Python 3.6, SNAP 8.0
 
 ### 1.1 Install snap gpt including [Sentinel-1 toolbox](https://step.esa.int/main/download/snap-download/previous-versions/)
 
-For the installation of ESA SNAP you can run the automated script [aux/install_snap.sh](https://github.com/kleok/FLOMPY/blob/main/aux/install_snap.sh) for downloading and installing the official Linux installer from the official ESA repository. To install SNAP run the following commands:
+For the installation of ESA SNAP you can run the automated script [aux/install_snap.sh](https://github.com/kleok/FLOODPY/blob/main/aux/install_snap.sh) for downloading and installing the official Linux installer from the official ESA repository. To install SNAP run the following commands:
 
 ```bash
 chmod +x install_snap.sh
@@ -35,51 +35,51 @@ ERA-5 data set is redistributed over the Copernicus Climate Data Store (CDS). Yo
 url: https://cds.climate.copernicus.eu/api/v2
 key: UID:personal API Key
 ```
-In case you dont want to create the .cdsapirc file manually, you can run [aux/install_CDS_key.sh](https://github.com/kleok/FLOMPY/blob/main/aux/install_CDS_key.sh) script as follows:
+In case you dont want to create the .cdsapirc file manually, you can run [aux/install_CDS_key.sh](https://github.com/kleok/FLOODPY/blob/main/aux/install_CDS_key.sh) script as follows:
 
 ```bash
 chmod +x install_CDS_key.sh
 ./install_CDS_key.sh
 ```
 More details on CDSAPI can be found [here](https://cds.climate.copernicus.eu/api-how-to).
 
-### 1.4 Download FLOMPY
-First you have to download Flompy toolbox using the following command
-```git clone https://github.com/kleok/FLOMPY.git```
+### 1.4 Download FLOODPY
+First you have to download FLOODPY toolbox using the following command
+```git clone https://github.com/kleok/FLOODPY.git```
 
-### 1.5 Create python environment for FLOMPY
+### 1.5 Create python environment for FLOODPY
 
-FLOMPY is written in Python3 and relies on several Python modules. You can install them by using conda or pip.
+FLOODPY is written in Python3 and relies on several Python modules. You can install them by using conda or pip.
 
 - Using **conda**
-Create a new conda environement with required packages using the the file [FLOMPY_env.yml](https://github.com/kleok/FLOMPY/blob/main/FLOMPY_env.yml).
+Create a new conda environement with required packages using the the file [FLOODPY_env.yml](https://github.com/kleok/FLOODPY/blob/main/FLOODPY_env.yml).
 
 ```
-conda env create -f ~/FLOMPY/FLOMPY_env.yml
+conda env create -f ~/FLOODPY/FLOODPY_env.yml
 ```
 
 - Using **pip**
-  You can install python packages using [setup.py](https://github.com/kleok/FLOMPY/blob/main/setup.py)
+  You can install python packages using [setup.py](https://github.com/kleok/FLOODPY/blob/main/setup.py)
 
 ```
-cd ~/FLOMPY
+cd ~/FLOODPY
 pip install .
 ```
 
 ### 1.6 Set environmental variables
 
 on GNU/Linux, append to .bashrc file:
 ```
-export FLOMPY_HOME=~/FLOMPY
-export PYTHONPATH=${PYTHONPATH}:${FLOMPY_HOME}
-export PATH=${PATH}:${FLOMPY_HOME}/flompy
+export FLOODPY_HOME=~/FLOODPY
+export PYTHONPATH=${PYTHONPATH}:${FLOODPY_HOME}
+export PATH=${PATH}:${FLOODPY_HOME}/floodpy
 ```
 
-## 2. Running Flompy
-[FLOMPYapp.py]("https://github.com/kleok/FLOMPY/blob/main/flompy/FLOMPYapp.py")
+## 2. Running FLOODPY
+[FLOODPYapp.py]("https://github.com/kleok/FLOODPY/blob/main/floodpy/FLOODPYapp.py")
 
-FLOMPY generates a floodwater map based on Sentinel-1 GRD products and meteorological data. FLOMPYapp.py includes the functionalities for FLOMPY's routine processing for generating floodwater maps. User should provide the following information at configuration file FLOMPYapp_template.cfg
-We suggest you to can have a look at the plots for each Sentinel-1 image (located at projectfolder) to find out if you have a considerable decrease of backscatter in the flood image with respect to the baseline images. If you are able to identify a decrease of backscatter in the flood image (darker tones), then you can expect that FLOMPY will generate a useful floodwater map. In cases that you have similar or bigger backscatter values of flood image with respect to baseline images (due to complex backscatter mechanisms) FLOMPY`s results cannot be trusted.
+FLOODPY generates a floodwater map based on Sentinel-1 GRD products and meteorological data. FLOODPYapp.py includes the functionalities for FLOODPY's routine processing for generating floodwater maps. User should provide the following information at configuration file FLOODPYapp_template.cfg
+We suggest you to can have a look at the plots for each Sentinel-1 image (located at projectfolder) to find out if you have a considerable decrease of backscatter in the flood image with respect to the baseline images. If you are able to identify a decrease of backscatter in the flood image (darker tones), then you can expect that FLOODPY will generate a useful floodwater map. In cases that you have similar or bigger backscatter values of flood image with respect to baseline images (due to complex backscatter mechanisms) FLOODPY`s results cannot be trusted.
 ```
 #######################################
 #             CONFIGURATION FILE      #
@@ -93,10 +93,10 @@ Projectname = Palamas
 
 #A2. The location that everything is going to be saved. Make sure 
 #        you have enough free space disk on the specific location.
-projectfolder = /RSL03/FLOMPY_palamas
+projectfolder = /RSL03/FLOODPY_palamas
 
-#A3. The location of Flompy code 
-src_dir = /RSL03/Flompy_0.3/FLOMPY/flompy
+#A3. The location of FLOODPY code 
+src_dir = /RSL03/FLOODPY_0.4/FLOODPY/floodpy
 
 #A4. SNAP ORBIT DIRECTORY
 snap_dir = /home/kleanthis/.snap/auxdata/Orbits/Sentinel-1
@@ -135,7 +135,7 @@ after_flood_days = 3
 #-In case you provide AOI BBOX coordinates, set  AOI_File = None
 #--------------------------------------------------------
 # C1. AOI VECTOR FILE (if given AOI BBOX parameters can be ommited)
-AOI_File = /home/kleanthis/bin/FLOMPY/tests/Palamas_AOI.geojson
+AOI_File = /home/kleanthis/bin/FLOODPY/tests/Palamas_AOI.geojson
 
 # C2. AOI BBOX (WGS84)
 LONMIN=22.02
@@ -179,55 +179,55 @@ scihub_username = ******
 scihub_password = ******
 ```
 
-After the setup of the configuration file you can use the default recipe script FLOMPYapp.py to run the following following individual steps that will
+After the setup of the configuration file you can use the default recipe script FLOODPYapp.py to run the following following individual steps that will
 automatically run for the selected AOI:
 
 ### 2.1. Download Precipitation data from ERA5.
 
 ```
-FLOMPYapp.py FLOMPYapp_template.cfg --dostep Download_Precipitation_data
+FLOODPYapp.py FLOODPYapp_template.cfg --dostep Download_Precipitation_data
 ```
 
 ### 2.2. Download Sentinel 1 data.
 
 ```
-FLOMPYapp.py FLOMPYapp_template.cfg --dostep Download_S1_data
+FLOODPYapp.py FLOODPYapp_template.cfg --dostep Download_S1_data
 ```
 
 ### 2.3. Preprocessing Sentinel 1 data.
 
 ```
-FLOMPYapp.py FLOMPYapp_template.cfg --dostep Preprocessing_S1_data
+FLOODPYapp.py FLOODPYapp_template.cfg --dostep Preprocessing_S1_data
 ```
 
 ### 2.4. Sentinel 1 statistical analysis.
 
 ```
-FLOMPYapp.py FLOMPYapp_template.cfg --dostep Statistical_analysis
+FLOODPYapp.py FLOODPYapp_template.cfg --dostep Statistical_analysis
 ```
 
 ### 2.5. And at last the floodwater classification step. At this point the result of the estimated flooded region is exported.
 
 ```
-FLOMPYapp.py FLOMPYapp_template.cfg --dostep Floodwater_classification
+FLOODPYapp.py FLOODPYapp_template.cfg --dostep Floodwater_classification
 ```
 
 If the flood was on an agricultural region you can also run the following steps to estimate the amount of the damaged fields by performing delineation (with a methodology based on Yan & Roy, 2014 and a pretrained Unet delineation network) and active-inactive field classification based on NDVI timeseries with Sentinel 2 data. For more information check at Gounari et al. 2022 bellow.
 
 ### 2.6. Download Sentinel 2 multispectral data (Optional). 
 
 ```
-FLOMPYapp.py FLOMPYapp_template.cfg --dostep Download_S2_data
+FLOODPYapp.py FLOODPYapp_template.cfg --dostep Download_S2_data
 ```
 
 ### 2.7. Run crop delineation and field classification (Optional, requires 6).
 
 ```
-FLOMPYapp.py FLOMPYapp_template.cfg --dostep Crop_delineation
+FLOODPYapp.py FLOODPYapp_template.cfg --dostep Crop_delineation
 ```
 
 ## 3. Documentation and citation
-Algorithms implemented in the software are described in detail at our publications. If FLOMPY was useful for you, we encourage you to cite the following work.
+Algorithms implemented in the software are described in detail at our publications. If FLOODPY was useful for you, we encourage you to cite the following work.
 
 - Karamvasis K, Karathanassi V. FLOMPY: An Open-Source Toolbox for Floodwater Mapping Using Sentinel-1 Intensity Time Series. Water. 2021; 13(21):2943. https://doi.org/10.3390/w13212943 
 
@@ -238,5 +238,5 @@ Algorithms implemented in the software are described in detail at our publicatio
 ## 4. Contact us
 Feel free to open an issue, comment or pull request. We would like to listen to your thoughts and your recommendations. Any help is very welcome! :heart:
 
-FLOMPY Team: [Kleanthis Karamvasis](https://github.com/kleok), [Ioanna Zotou](https://www.researchgate.net/profile/Ioanna-Zotou), [Alekos Falagas](https://github.com/alekfal), [Olympia Gounari](https://github.com/Olyna), [Vasileios Tsironis](https://github.com/tsironisbi), [Markos Mylonas](https://github.com/mylonasma), [Pavlos Alexantonakis](https://www.linkedin.com/in/pavlos-alexantonakis)
+FLOODPY Team: [Kleanthis Karamvasis](https://github.com/kleok), [Ioanna Zotou](https://www.researchgate.net/profile/Ioanna-Zotou), [Alekos Falagas](https://github.com/alekfal), [Olympia Gounari](https://github.com/Olyna), [Vasileios Tsironis](https://github.com/tsironisbi), [Markos Mylonas](https://github.com/mylonasma), [Pavlos Alexantonakis](https://www.linkedin.com/in/pavlos-alexantonakis)
 

docs/conf.py

@@ -19,12 +19,12 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'flompy'
+project = 'floodpy'
 copyright = '2022, Kleanthis Karamvasis, Alekos Falagas'
 author = 'Kleanthis Karamvasis, Alekos Falagas'
 
 # The full version, including alpha/beta/rc tags
-release = '0.2.2'
+release = '0.4.0'
 
 
 # -- General configuration ---------------------------------------------------
@@ -56,7 +56,7 @@
 # a list of builtin themes.
 #
 html_theme = 'sphinx_rtd_theme'
-html_logo = '../figures/Flompy_logo.png'
+html_logo = '../figures/Floodpy_logo.png'
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

docs/flompy.Crop_delineation.rst

@@ -1,29 +1,29 @@
-flompy.Crop\_delineation package
+floodpy.Crop\_delineation package
 ================================
 
 Submodules
 ----------
 
-flompy.Crop\_delineation.delineate module
+floodpy.Crop\_delineation.delineate module
 -----------------------------------------
 
-.. automodule:: flompy.Crop_delineation.delineate
+.. automodule:: floodpy.Crop_delineation.delineate
    :members:
    :undoc-members:
    :show-inheritance:
 
-flompy.Crop\_delineation.utils module
+floodpy.Crop\_delineation.utils module
 -------------------------------------
 
-.. automodule:: flompy.Crop_delineation.utils
+.. automodule:: floodpy.Crop_delineation.utils
    :members:
    :undoc-members:
    :show-inheritance:
 
 Module contents
 ---------------
 
-.. automodule:: flompy.Crop_delineation
+.. automodule:: floodpy.Crop_delineation
    :members:
    :undoc-members:
    :show-inheritance:

docs/flompy.Crop_delineation_unet.rst

@@ -1,21 +1,21 @@
-flompy.Crop\_delineation\_unet package
+floodpy.Crop\_delineation\_unet package
 ======================================
 
 Submodules
 ----------
 
-flompy.Crop\_delineation\_unet.Pretrained\_networks module
+floodpy.Crop\_delineation\_unet.Pretrained\_networks module
 ----------------------------------------------------------
 
-.. automodule:: flompy.Crop_delineation_unet.Pretrained_networks
+.. automodule:: floodpy.Crop_delineation_unet.Pretrained_networks
    :members:
    :undoc-members:
    :show-inheritance:
 
 Module contents
 ---------------
 
-.. automodule:: flompy.Crop_delineation_unet
+.. automodule:: floodpy.Crop_delineation_unet
    :members:
    :undoc-members:
    :show-inheritance:

docs/flompy.Download.rst

@@ -1,53 +1,53 @@
-flompy.Download package
+floodpy.Download package
 =======================
 
 Submodules
 ----------
 
-flompy.Download.Download\_ERA5\_precipitation module
+floodpy.Download.Download\_ERA5\_precipitation module
 ----------------------------------------------------
 
-.. automodule:: flompy.Download.Download_ERA5_precipitation
+.. automodule:: floodpy.Download.Download_ERA5_precipitation
    :members:
    :undoc-members:
    :show-inheritance:
 
-flompy.Download.Download\_GFS module
+floodpy.Download.Download\_GFS module
 ------------------------------------
 
-.. automodule:: flompy.Download.Download_GFS
+.. automodule:: floodpy.Download.Download_GFS
    :members:
    :undoc-members:
    :show-inheritance:
 
-flompy.Download.Download\_orbits module
+floodpy.Download.Download\_orbits module
 ---------------------------------------
 
-.. automodule:: flompy.Download.Download_orbits
+.. automodule:: floodpy.Download.Download_orbits
    :members:
    :undoc-members:
    :show-inheritance:
 
-flompy.Download.Sentinel\_1\_download module
+floodpy.Download.Sentinel\_1\_download module
 --------------------------------------------
 
-.. automodule:: flompy.Download.Sentinel_1_download
+.. automodule:: floodpy.Download.Sentinel_1_download
    :members:
    :undoc-members:
    :show-inheritance:
 
-flompy.Download.Sentinel\_2\_download module
+floodpy.Download.Sentinel\_2\_download module
 --------------------------------------------
 
-.. automodule:: flompy.Download.Sentinel_2_download
+.. automodule:: floodpy.Download.Sentinel_2_download
    :members:
    :undoc-members:
    :show-inheritance:
 
 Module contents
 ---------------
 
-.. automodule:: flompy.Download
+.. automodule:: floodpy.Download
    :members:
    :undoc-members:
    :show-inheritance: