Merge pull request #9 from GeoLarryLai/v1.1.1

Full Google Colab support

Author: GeoLarryLai

Example_pycwtmexhat.ipynb

@@ -34,7 +34,9 @@ from pytopocomplexity import CWTMexHat
 
 The module **pycwtmexhat.py** uses two-dimensional continuous wavelet transform (2D-CWT) with a Mexican Hat wevalet to measure the topographic complexity (i.e., surface roughness) of a land surface from a Digital Elevation Model (DEM). Such method quanitfy the wavelet-based curvature of the surface, which has been proposed to be a effective geomorphic metric for identifying and estimating the ages of historical deep-seated landslide deposits. The method and early version of the code was developed by Dr. Adam M. Booth (Portland State Univeristy) in [2009](https://doi.org/10.1016/j.geomorph.2009.02.027), written in MATLAB (source code available from [Booth's personal website](https://web.pdx.edu/~boothad/tools.html)). This MATLAB code was later revised and adapted by Dr. Sean R. LaHusen (Univeristy of Washington) and Dr. Erich N. Herzig (Univeristy of Washington) in their research ([LaHusen et al., 2020](https://doi.org/10.1126/sciadv.aba6790); [Herzig et al. (2023)](https://doi.org/10.1785/0120230079)). Dr. Larry Syu-Heng Lai (Univeristy of Washington), under the supervision of Dr. Alison R. Duvall (Univeristy of Washington), translated the code into this optimized open-source Python version in 2024.
 
-See [**Example_pycwtmexhat.ipynb**](https://github.com/GeoLarryLai/pyTopoComplexity/blob/main/Example_pycwtmexhat.ipynb) for detailed explanations and usage instructions.
+See [**Example_pycwtmexhat.ipynb**](https://github.com/GeoLarryLai/pyTopoComplexity/blob/main/Example_pycwtmexhat.ipynb) for detailed explanations and usage instructions. 
+
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/GeoLarryLai/pyTopoComplexity/blob/main/Example_pycwtmexhat.ipynb)
 
 ### 2. Fractal Dimentsion Analysis
 
@@ -46,6 +48,8 @@ The **pyfracd.py** module calculates local fractal dimensions to assess topograp
 
 See [**Example_pyfracd.ipynb**](https://github.com/GeoLarryLai/pyTopoComplexity/blob/main/Example_pyfracd.ipynb) for detailed explanations and usage instructions.
 
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/GeoLarryLai/pyTopoComplexity/blob/main/Example_pyfracd.ipynb)
+
 ### 3. Rugosity Index Calculation
 
 ```python
@@ -56,6 +60,8 @@ The module **pyrugosity.py** measure Rugosity Index of the land surface, which i
 
 See [**Example_pyrugosity.ipynb**](https://github.com/GeoLarryLai/pyTopoComplexity/blob/main/Example_pyrugosity.ipynb) for detailed explanations and usage instructions.
 
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/GeoLarryLai/pyTopoComplexity/blob/main/Example_pyrugosity.ipynb)
+
 ### 4. Terrain Position Index Calculation
 
 ```python
@@ -66,6 +72,8 @@ The module **pytpi.py** calculates the Terrain Position Index (TPI) of the land
 
 See [**Example_pytpi.ipynb**](https://github.com/GeoLarryLai/pyTopoComplexity/blob/main/Example_pytpi.ipynb) for detailed explanations and usage instructions.
 
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/GeoLarryLai/pyTopoComplexity/blob/main/Example_pytpi.ipynb)
+
 ## Requirements
 For **pyTopoComplexity** package"
 * Python >= 3.10

Example_pyfracd.ipynb

@@ -17,11 +17,6 @@ In this repository, each module has a corresponding example Jupyter Notebook fil
 
 There is also an additional Jupyter Notebook, [**Landlab_simulation.ipynb**](https://github.com/GeoLarryLai/pyTopoComplexity/blob/main/Landlab_simulation.ipynb), which leverages the power of [Landlab](https://landlab.readthedocs.io/en/latest/index.html) to perform forward simulation of landscape smoothing through non-linear hillslope diffusion process.
 
-## Citation
-
-If you use **pyTopoComplexity** and the associated Jupyter Notebooks in your work, please cite the following paper:
-* Lai, L. S.-H., Booth, A. M., Duvall, A. R., and Herzig, E. (In Revision) Short Communication: Multiscale topographic complexity analysis with pyTopoComplexity. Earth Surface Dynamics. https://doi.org/10.5194/egusphere-2024-3415.
-
 ## Installation
 
 Users can install **pyTopoComplexity** directly from [PyPI](https://pypi.org/project/pytopocomplexity/) with `pip` command:
@@ -52,6 +47,8 @@ The module **pycwtmexhat.py** uses two-dimensional continuous wavelet transform
 
 See [**Example_pycwtmexhat.ipynb**](https://github.com/GeoLarryLai/pyTopoComplexity/blob/main/Example_pycwtmexhat.ipynb) for detailed explanations and usage instructions.
 
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/GeoLarryLai/pyTopoComplexity/blob/main/Example_pycwtmexhat.ipynb)
+
 <p align="center">
  <img src="image/cwtmexhat.png" width="100%" height="100%""/>
 </p>
@@ -66,6 +63,9 @@ The **pyfracd.py** module calculates local fractal dimensions to assess topograp
 
 See [**Example_pyfracd.ipynb**](https://github.com/GeoLarryLai/pyTopoComplexity/blob/main/Example_pyfracd.ipynb) for detailed explanations and usage instructions.
 
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/GeoLarryLai/pyTopoComplexity/blob/main/Example_pyfracd.ipynb)
+
+
 <p align="center">
  <img src="image/fracd.png" width="100%" height="100%""/>
 </p>
@@ -80,6 +80,8 @@ The module **pyrugosity.py** measure Rugosity Index of the land surface, which i
 
 See [**Example_pyrugosity.ipynb**](https://github.com/GeoLarryLai/pyTopoComplexity/blob/main/Example_pyrugosity.ipynb) for detailed explanations and usage instructions.
 
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/GeoLarryLai/pyTopoComplexity/blob/main/Example_pyrugosity.ipynb)
+
 <p align="center">
  <img src="image/rugosity.png" width="100%" height="100%""/>
 </p>
@@ -94,16 +96,21 @@ The module **pytpi.py** calculates the Terrain Position Index (TPI) of the land
 
 See [**Example_pytpi.ipynb**](https://github.com/GeoLarryLai/pyTopoComplexity/blob/main/Example_pytpi.ipynb) for detailed explanations and usage instructions.
 
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/GeoLarryLai/pyTopoComplexity/blob/main/Example_pytpi.ipynb)
+
 <p align="center">
  <img src="image/tpi.png" width="100%" height="100%""/>
 </p>
-```
 
 ## Combinding pyTopoComplexity with Landscape Evolution Modeling
 
-The Jupyter Notebook file [**Landlab_simulation.ipynb**](https://github.com/GeoLarryLai/pyTopoComplexity/blob/main/example/nonlineardiff_Landlab.ipynb) demonstrates the use of [Landlab](https://landlab.readthedocs.io/en/latest/index.html), an open-source Python framework for simulating landscape evolution and modeling time-dependent changes in topographic complexity driven by hillslope and fluvial processes. It specifically employs two components from **Landlab**: the [`TaylorNonLinearDiffuser`](https://landlab.readthedocs.io/en/latest/generated/api/landlab.components.taylor_nonlinear_hillslope_flux.taylor_nonlinear_hillslope_flux.html#landlab.components.taylor_nonlinear_hillslope_flux.taylor_nonlinear_hillslope_flux.TaylorNonLinearDiffuser) from the [`terrainBento`](https://github.com/TerrainBento/terrainbento) package, developed by [Barnhart et al. (2019)](https://gmd.copernicus.org/articles/12/1267/2019/), which simulates topographic smoothing over time through nonlinear hillslope diffusion processes caused by near-surface soil disturbance and downslope soil creeping ([Roering et al., 1999](https://doi.org/10.1029/1998WR900090)), and the [`StreamPowerEroder`](https://landlab.readthedocs.io/en/latest/generated/api/landlab.components.stream_power.stream_power.html#landlab.components.stream_power.stream_power.StreamPowerEroder), a core component in **Landlab** that simulates topographic dissection through fluvial incision over time, following the method described by [Braun & Willett (2013)](https://doi.org/10.1016/j.geomorph.2012.10.008).
+The Jupyter Notebook file [**Landlab_simulation.ipynb**](https://github.com/GeoLarryLai/pyTopoComplexity/blob/main/example/nonlineardiff_Landlab.ipynb) demonstrates the use of [Landlab](https://landlab.readthedocs.io/en/latest/index.html), an open-source Python framework for simulating landscape evolution and modeling time-dependent changes in topographic complexity driven by hillslope and fluvial processes. 
+
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/GeoLarryLai/pyTopoComplexity/blob/main/Landlab_simulation.ipynb)
+
+This notebook specifically employs two components from **Landlab**: the [`TaylorNonLinearDiffuser`](https://landlab.readthedocs.io/en/latest/generated/api/landlab.components.taylor_nonlinear_hillslope_flux.taylor_nonlinear_hillslope_flux.html#landlab.components.taylor_nonlinear_hillslope_flux.taylor_nonlinear_hillslope_flux.TaylorNonLinearDiffuser) from the [`terrainBento`](https://github.com/TerrainBento/terrainbento) package, developed by [Barnhart et al. (2019)](https://gmd.copernicus.org/articles/12/1267/2019/), which simulates topographic smoothing over time through nonlinear hillslope diffusion processes caused by near-surface soil disturbance and downslope soil creeping ([Roering et al., 1999](https://doi.org/10.1029/1998WR900090)), and the [`StreamPowerEroder`](https://landlab.readthedocs.io/en/latest/generated/api/landlab.components.stream_power.stream_power.html#landlab.components.stream_power.stream_power.StreamPowerEroder), a core component in **Landlab** that simulates topographic dissection through fluvial incision over time, following the method described by [Braun & Willett (2013)](https://doi.org/10.1016/j.geomorph.2012.10.008).
 
-This notebook also includes functions that utilize modules from **pyTopoComplexity** to perform topographic complexity analysis on the simulated landscape from **Landlab** at each modeling timestep. The resulting GeoTIFF rasters, figures, and animations provide users with insights into the time-dependent changes in topographic complexity caused by land-surface processes.
+The notebook also includes functions that utilize modules from **pyTopoComplexity** to perform topographic complexity analysis on the simulated landscape from **Landlab** at each modeling timestep. The resulting GeoTIFF rasters, figures, and animations provide users with insights into the time-dependent changes in topographic complexity caused by land-surface processes.
 
 <p align="center">
 <img src="image/Landlab_demo.gif" width="100%" height="100%" align="center"/>

Example_pyrugosity.ipynb

@@ -5,7 +5,7 @@
 
 setup(
     name="pytopocomplexity",
-    version="1.1.0",
+    version="1.1.1",
     author="Larry Syu-Heng Lai",
     author_email="[email protected]",
     description="A package for multiscale topographic complexity analysis",