Merge pull request #294 from vermeulendivan/documention

Documention updates to the documentation
ConservationInternational · Nov 21, 2023 · 2f281a4 · 2f281a4
2 parents d647631 + 170acaa
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diff --git a/docs/user/guide/img/button_pixels_order.png b/docs/user/guide/img/button_pixels_order.png
diff --git a/docs/user/guide/img/plugin-step2-buttons.png b/docs/user/guide/img/plugin-step2-buttons.png
diff --git a/docs/user/guide/img/style_pixel_value_editor.png b/docs/user/guide/img/style_pixel_value_editor.png
diff --git a/docs/user/guide/index.md b/docs/user/guide/index.md
@@ -284,8 +284,9 @@ An IM is a combination of NCS pathways represented in an AOI spatial layer. **Fi
 Step 2 buttons (**Figure 18**):
 
 - **Add**: Adds a new pathway or model
-- **Editing**: Edit and existing pathway or model
 - **Delete**: Delete a pathway or model
+- **Editing**: Edit and existing pathway or model
+- ****
 
 ![CPLUS step 2 buttons](img/plugin-step2-buttons.png)
 
@@ -334,6 +335,13 @@ How to add a new IM:
 
 *Figure 20: Implementation Model creator/editor*
 
+- Open the Style pixel value editor by clicking on the ![CPLUS add implementation model](img/button_pixels_order.png) button
+- Select the IM which needs to be moved up or down in the stack
+- Drag-and-drop the IM where it needs to be in the stack
+- Click **OK** once done
+
+![CPLUS style pixel value editor](img/style_pixel_value_editor.png)
+
 - The final step is to select each of the IMs a user want to include in the scenario run
 - A user can exclude IMs if they don't want to include it, even if the IM has pathways
 

diff --git a/docs/user/manual/img/button_pixels_order.png b/docs/user/manual/img/button_pixels_order.png
diff --git a/docs/user/manual/img/manual-add-im.png b/docs/user/manual/img/manual-add-im.png
diff --git a/docs/user/manual/img/manual-settings.png b/docs/user/manual/img/manual-settings.png
diff --git a/docs/user/manual/img/style_pixel_value_editor.png b/docs/user/manual/img/style_pixel_value_editor.png
diff --git a/docs/user/manual/index.md b/docs/user/manual/index.md
@@ -214,6 +214,7 @@ Step 2 focuses on the implementation models (IMs) and pathways.
 - ![add button](img/symbologyAdd.svg): Add a new IM
 - ![remove button](img/symbologyRemove.svg): Remove the selected IM or pathway
 - ![edit button](img/mActionToggleEditing.svg): Edit the selected IM
+- ![ordering pixel values button](img/button_pixels_order.png): Order the pixel values (IMs) will be in the scenario output
 
 ##### Implementation Model Editor dialog
 
@@ -223,16 +224,25 @@ Step 2 focuses on the implementation models (IMs) and pathways.
 
 - **Name**: The name of the new IM or IM being edited. IM title will be used in the report
 - **Description**: A detailed description of the IM. This will be used in the report
+- **Style**: Styles used for the IM
+    - *Scenario layer*: Colouring which will be used in the Scenario output for this IM
+    - *Output model layer*: Colour ramp which will be applied to the IM raster output
 - **Map layer**: If enabled, a user can provide an existing IM. This has to be a raster
 
+#### Ordering of the pixel values for the scenario output
+
+A user can order the stack using the **Style pixel value editor**.
+
+![UI Step 3](img/style_pixel_value_editor.png)
+
 #### Step 3: Weighting priorities
 
 ![UI Step 3](img/manual-step3.png)
 
 *Figure 10: Step 3 of the dock widget*
 
 - **Priority groups**: Groups to which PWLs can be assigned
-- **Priority weighted layers (PWL)**:
+- **Priority weighted layers (PWL)**: Importance of each priority group
 - ![right arrow](img/cplus_right_arrow.svg): Remove the selected PWL from the priority group
 - ![left arrow](img/cplus_left_arrow.svg): Add the selected PWL to the selected priority group
 - ![add button](img/symbologyAdd.svg): Add a new PWL
@@ -304,3 +314,19 @@ These options will be available once the analysis has finished. The options will
     - *Base data directory*: Directory to read data from, and to which results will be written
     - *Coefficient for carbon layers*: Applied to carbon layers during processing
     - *Pathway suitability index*: Index multiplied to the pathways. Lower values means the pathway is less important, higher means its more important
+    - *Snapping*: Will set rasters to match the cell alignment of a reference layer
+        - *Resample method*: Resampling performed on pixel values.
+            - *Nearest neighbour*: Closest pixel value. This will be best to use if a user wants to preserve the original pixel values
+            - *Bilinear*: Computes the pixel values from the two closest pixels (2 x 2 kernel)
+            - *Cubic*: Computes the pixel values from the four closest pixels (4 x 4 kernel)
+            - *Cubic B-Spline*: Cubic resampling based on B-Spline (4 x 4 kernel)
+            - *Lanczos*: Lanczos windowed sinc interpolation (6 x 6 kernel)
+            - *Average*: Computes the average of all non-nodata contributing pixels
+            - *Mode*: Selects the value which appears most often of all the sampled pixels
+            - *Maximum*: Selects the maximum value which appears of all the sampled pixels
+            - *Minimum*: Selects the minimum value which appears of all the sampled pixels
+            - *Mediane*: Selects the mediane value which appears of all the sampled pixels
+            - *First quartile (Q1)*: Selects the first quartile value which appears of all the sampled pixels
+            - *Third quartile (Q3)*: Selects the third quartile value which appears of all the sampled pixels
+        - *Reference layer*: The reference layer to which the cell alignment will be applied
+        - *Rescale values*: Rescale values according to cell size