Cleaned up Documentatoin

A bunch of @kbartelt documentation was present but not rendering because of unallowed characters in the header ":". Cleaned up and fixed links.

docs/Documentation/running/index.md

@@ -0,0 +1,17 @@
+---
+title: Running the RIM Tool
+weight: 1
+---
+
+These steps take you through the necessary steps to run the RIM tool. The methods themselves are elaborated in [Bartelt et al. 2021](https://digitalcommons.usu.edu/etd/8226/).
+
+- [Step 1: Gather Inputs]({{ site.baseurl }}/Documentation/tool_users/3-Step3.html)
+- [Step 2: Project Builder]({{ site.baseurl }}/Documentation/tool_users/2-Step2_createproject)
+- [Step 3: Mapping]({{ site.baseurl }}/Documentation/tool_users/3-Step3)
+	- [Step 3a: Mappings]({{ site.baseurl }}/Documentation/tool_users/3a)
+	- [Step 3b: Create New DCE]({{ site.baseurl }}/Documentation/tool_users/3b)
+- [Step 4: Calculate Metrics]({{ site.baseurl }}/Documentation/tool_users/4-Step4_calcMetrics)
+
+<div align="center">
+<img src="{{ site.baseurl }}/assets/images/flow_chart_tiny.png">
+</div>

docs/Documentation/tool_users/1-Step1_inputs.md → docs/Documentation/running/step1.md

@@ -1,21 +1,27 @@
----
-title: Step 1 - Gather Inputs
-weight: 1
----
-The first step to mapping your riverscape and running the tool is to gather the required input files.
-
-## Inputs
-
-The required inputs to use the Riverscape Inundation Mapper tool in full are:
-- imagery
-- Digital Elevation Model (DEM)
-
-### Imagery
-Potential sources of imagery include Unmanned Aerial Vehicle (UAV) orthomosaics, imagery from the National Agriculture Imagery Program (NAIP), Google Earth, Light Detection and Ranging (LIDAR) data, and more.
-### DEM
-We typically use [USGS National Elevation Dataset (NED)](https://viewer.nationalmap.gov/basic/) 1/3 arc second (~ 10 m) DEM data.
-
-The following ptional inputs are useful and provide additional context for valley bottom mapping and information about the local hydrology:
-- [VBET](http://rcat.riverscapes.net/Documentation/Version_1.0/VBET.html#toc-valley-bottom-extraction-tool-vbet-) output
-- [BRAT](https://brat.riverscapes.net/) output
-- hillshade
+---
+title: Step 1 Gather Inputs
+weight: 1
+---
+
+The first step to mapping your riverscape and running the tool is to gather the required input files.
+
+## Inputs
+
+The required inputs to use the Riverscape Inundation Mapper tool in full are:
+
+- imagery
+- Digital Elevation Model (DEM)
+
+### Imagery
+
+Potential sources of imagery include Unmanned Aerial Vehicle (UAV) orthomosaics, imagery from the National Agriculture Imagery Program (NAIP), Google Earth, Light Detection and Ranging (LIDAR) data, and more.
+
+### DEM
+
+We typically use [USGS National Elevation Dataset (NED)](https://viewer.nationalmap.gov/basic/) 1/3 arc second (~ 10 m) DEM data.
+
+The following optional inputs are useful and provide additional context for valley bottom mapping and information about the local hydrology:
+
+- [VBET](http://rcat.riverscapes.net/Documentation/Version_1.0/VBET.html#toc-valley-bottom-extraction-tool-vbet-) output
+- [BRAT](https://brat.riverscapes.net/) output
+- hillshade

docs/Documentation/tool_users/2-Step2_createproject.md → docs/Documentation/running/step2.md

@@ -1,25 +1,23 @@
----
-title: Step 2 - Project Builder
-weight: 2
----
-
-## Project Builder
-
-The next step is to run the [Project Builder script](https://github.com/Riverscapes/inundation/blob/master/Step2_ProjectBuilder.py). This script is designed to take the inputs and organize them into a consistent project folder structure. This script will create empty shapefiles to map context features and your first Data Capture Event (DCE)
-
-## Inputs
-### Files
-- **project_path** - The path to a folder where you want the project folder structure to be created
-- **srs_template** - The path to a shapefile that contains the desired coordinate system and projection for your project shapefiles
-- **image_path** - The path to an image raster of the site 
-- **DEM_path** - The path to the input DEM
-- **hs_path** - The path to a hillshade
-- **BRAT_path** - The path to a BRAT output shapefile
-- **VBET_path** - The path to a VBET output shapefile
-
-### Parameters
-#### Site or project parameters
-- **site_name** The name of the project
-- **huc** - the 8 digit Hydrologic Unit Code
-
-
+---
+title: Step 2 Project Builder
+weight: 2
+---
+
+## Project Builder
+
+The next step is to run the [Project Builder script](https://github.com/Riverscapes/inundation/blob/master/Step2_ProjectBuilder.py). This script is designed to take the inputs and organize them into a consistent project folder structure. This script will create empty shapefiles to map context features and your first Data Capture Event (DCE)
+
+## Inputs
+### Files
+- **project_path** - The path to a folder where you want the project folder structure to be created
+- **srs_template** - The path to a shapefile that contains the desired coordinate system and projection for your project shapefiles
+- **image_path** - The path to an image raster of the site 
+- **DEM_path** - The path to the input DEM
+- **hs_path** - The path to a hillshade
+- **BRAT_path** - The path to a BRAT output shapefile
+- **VBET_path** - The path to a VBET output shapefile
+
+### Parameters
+#### Site or project parameters
+- **site_name** The name of the project
+- **huc** - the 8 digit Hydrologic Unit Code

docs/Documentation/tool_users/3-Step3_Mapping/index.md → docs/Documentation/running/step3.md

@@ -1,32 +1,32 @@
----
-title: Step 3 - Mapping
-weight: 3
----
-
-## Map Features
-
-There are 2 types of features that you will map
-- Context features
-- Data Capture Events (DCEs)
-
-### Context features
-The context features you need to map are the valley bottom and a valley bottom centerline. These features are typically consistent over time. 
-
-Empty shapefiles were created for the context features when you ran the Project Builder script in [Step 2](http://rim.riverscapes.net/Documentation/tool_users/2-Step2_createproject.html) and are located in the **02_Mapping/RS_01 folder** of your project folder.
-
-Because the context features will typically not change over time, you will likely only need or want to map them once. However, additional versions of these features could be mapped and saved within the 02_Mapping folder in a new folder called RS_02, RS_03, etc.
-
-### DCEs
-The Data Capture Event features to map are the structure or beaver dam crests, thalwegs, and the inundated area and type. These features represent a snapshot of your project area in time and should be mapped seperately for each different image or time of interest.
-
-##### DCE 1
-All features that need to be mapped for the first DCE were created when you ran the Project Builder script in [Step 2](http://rim.riverscapes.net/Documentation/tool_users/2-Step2_createproject.html) and are located in the **02_Mapping/DCE_01 folder** of your project folder.
-
-##### Subsequent DCEs
-For additional DCEs you can provide a new image and create new blank DCE shapefiles using the Create_DCE script in [Step 3b](http://rim.riverscapes.net/Documentation/tool_users/3-Step3_Mapping/2-Step3b_newDCE.html). 
-
-Reasons for which you might want to create a 2nd, 3rd, etc DCE:
-- to map changes in inundation at different flows
-- to track changes in inundation over time 
-- using imagery from the same date but from a different source (e.g. to make a comparison between UAV acquired imagery and NAIP imagery)
-- to compare outputs from two different mappers
+---
+title: Step 3 Map Features
+weight: 3
+---
+
+## Map Features
+
+There are 2 types of features that you will map
+- [Context features]({{ site.baseurl }}/Documentation/running/step3a.html) - Step 3a
+- [Data Capture Events]({{ site.baseurl }}/Documentation/running/step3b.html) (DCEs) - Step 3b
+
+### Context features
+The context features you need to map are the valley bottom and a valley bottom centerline. These features are typically consistent over time. 
+
+Empty shapefiles were created for the context features when you ran the Project Builder script in [Step 2]({{ site.baseurl }}/Documentation/running/step2.html) and are located in the **02_Mapping/RS_01 folder** of your project folder.
+
+Because the context features will typically not change over time, you will likely only need or want to map them once. However, additional versions of these features could be mapped and saved within the 02_Mapping folder in a new folder called RS_02, RS_03, etc.
+
+### DCEs
+The Data Capture Event features to map are the structure or beaver dam crests, thalwegs, and the inundated area and type. These features represent a snapshot of your project area in time and should be mapped separately for each different image or time of interest.
+
+##### DCE 1
+All features that need to be mapped for the first DCE were created when you ran the Project Builder script in [Step 2]({{ site.baseurl }}/Documentation/running/step2.html) and are located in the **02_Mapping/DCE_01 folder** of your project folder.
+
+##### Subsequent DCEs
+For additional DCEs you can provide a new image and create new blank DCE shapefiles using the Create_DCE script in [Step 3b]({{ site.baseurl }}/Documentation/running/step3b.html). 
+
+Reasons for which you might want to create a 2nd, 3rd, etc., DCE:
+- to map changes in inundation at different flows
+- to track changes in inundation over time 
+- using imagery from the same date but from a different source (e.g. to make a comparison between UAV acquired imagery and NAIP imagery)
+- to compare outputs from two different mappers