changed risk layer to area of interest name

sandialabs · Jan 21, 2025 · f37c4ea · f37c4ea
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diff --git a/docs/src/media/PacWave_acoustics_input_receptor.webp b/docs/src/media/PacWave_acoustics_input_receptor.webp
diff --git a/docs/src/media/PacWave_acoustics_stressor_layers.webp b/docs/src/media/PacWave_acoustics_stressor_layers.webp
diff --git a/docs/src/media/PacWave_case_input.webp b/docs/src/media/PacWave_case_input.webp
diff --git a/docs/src/media/PacWave_grainsize.webp b/docs/src/media/PacWave_grainsize.webp
diff --git a/docs/src/media/PacWave_inputs.webp b/docs/src/media/PacWave_inputs.webp
diff --git a/docs/src/media/PacWave_layer_groups.webp b/docs/src/media/PacWave_layer_groups.webp
diff --git a/docs/src/media/SEAT_GUI.webp b/docs/src/media/SEAT_GUI.webp
diff --git a/docs/src/media/acoustics_inputs.webp b/docs/src/media/acoustics_inputs.webp
diff --git a/docs/src/media/acoustics_inputs_filled_out.webp b/docs/src/media/acoustics_inputs_filled_out.webp
diff --git a/docs/src/media/aoi_layer_gui_input.webp b/docs/src/media/aoi_layer_gui_input.webp
diff --git a/docs/src/media/cec-inputs.webp b/docs/src/media/cec-inputs.webp
diff --git a/docs/src/media/pacwave_acoustics_input.webp b/docs/src/media/pacwave_acoustics_input.webp
diff --git a/docs/src/media/pacwave_acoustics_inputs_filled_out.webp b/docs/src/media/pacwave_acoustics_inputs_filled_out.webp
diff --git a/...edia/pacwave_shear_stress_risk_layer.webp → ...acwave_shear_stress_area_of_interest.webp b/...edia/pacwave_shear_stress_risk_layer.webp → ...acwave_shear_stress_area_of_interest.webp
diff --git a/docs/src/media/pacwave_shear_stress_input.webp b/docs/src/media/pacwave_shear_stress_input.webp
diff --git a/docs/src/media/pacwave_shear_stress_layers.webp b/docs/src/media/pacwave_shear_stress_layers.webp
diff --git a/...rc/media/pacwave_velocity_risk_layer.webp → ...ia/pacwave_velocity_area_of_interest.webp b/...rc/media/pacwave_velocity_risk_layer.webp → ...ia/pacwave_velocity_area_of_interest.webp
diff --git a/docs/src/media/pacwave_velocity_input.webp b/docs/src/media/pacwave_velocity_input.webp
diff --git a/docs/src/media/pacwave_velocity_layers.webp b/docs/src/media/pacwave_velocity_layers.webp
diff --git a/docs/src/media/qgis_navigation.webp b/docs/src/media/qgis_navigation.webp
diff --git a/docs/src/media/risk_layer_gui_input.webp b/docs/src/media/risk_layer_gui_input.webp
diff --git a/docs/src/media/tanana_shear_stress_with_receptor_input.webp b/docs/src/media/tanana_shear_stress_with_receptor_input.webp
diff --git a/docs/src/media/tanana_velocity_with_receptor_input.webp b/docs/src/media/tanana_velocity_with_receptor_input.webp
diff --git a/docs/src/media/velocity_inputs.webp b/docs/src/media/velocity_inputs.webp
diff --git a/docs/src/modules/acoustics.rst b/docs/src/modules/acoustics.rst
@@ -15,7 +15,7 @@ The module determines the percentage of time that an acoustics threshold will be
 by combining a probability weighted acoustic field derived from individual Paracousti simulation NetCDF files; 
 and a species auditory threshold. 
 SEAT can determine the likelihood of a species being impacted by using probability of occurrence or species density maps. 
-Additionally, with the inclusion of a risk layer, the impacts on specific regions of interest can be evaluated, such as within breeding grounds or in different vegetation.
+Additionally, with the inclusion of a Area of Interest, the impacts on specific regions of interest can be evaluated, such as within breeding grounds or in different vegetation.
 Two different analyses are carried out for the acoustics calculations: probabilistic and non-probabilistic. 
 The probabilistic calculation uses the probabilities file to determine the 24-hour signal for SEL weighted by the probabilities file. 
 For SPL, a probability weighted single is calculated.
@@ -31,7 +31,7 @@ These include:
 
   - \*Model Probability Condition file (CSV): Used to weight the likelihood of different run scenarios occurring (i.e., likelihood of environmental conditions)
 
-  - \*Risk layer file (GeoTIFF): Contains spatial classifications, used to evaluate the impact of the devices on the environment
+  - \*Area of Interest file (GeoTIFF): Contains spatial classifications, used to evaluate the impact of the devices on the environment
 
   - \*Spatial Probability/Density directory (directory): includes GeoTiffs or CSVs of species, density and corresponds to the probabilities file
 
@@ -96,11 +96,11 @@ For example, if the filename is Hw0.5.nc, the stressor file will be named paraco
       - **species_percent.csv**
       - **species_density.csv**
 
-Segmented by spatial classification when using the risk layer file: 
+Segmented by spatial classification when using the Area of Interest file: 
 
-      - **paracousti_stressor_at_paracousti_risk_layer.csv**
-      - **species_density_at_paracousti_risk_layer.csv**
-      - **species_percent_at_paracousti_risk_layer.csv**
+      - **paracousti_stressor_at_paracousti_area_of_interest.csv**
+      - **species_density_at_paracousti_area_of_interest.csv**
+      - **species_percent_at_paracousti_area_of_interest.csv**
 
 
 

diff --git a/docs/src/modules/modules.rst b/docs/src/modules/modules.rst
@@ -43,7 +43,7 @@ File Descriptions
 ^^^^^^^^^^^^^^^^^^^
 **Model Probabilities** – Probability of hydrodynamics conditions occurring during a year. Each model run is associated with a probability depending on the likelihood that the hydrodynamic conditions occur. 
 
-**Risk Layer** – classified geoTIFF indicating unique features. Examples include seabed features, ecological zones, marine vegetation, species habitat. This is an optional file to include if the user desires information about impacts to specific areas.
+**Area of Interest** – classified geoTIFF indicating unique features. Examples include seabed features, ecological zones, marine vegetation, species habitat. This is an optional file to include if the user desires information about impacts to specific areas.
 
 **Receptor Layer** – numerical value at which a change or response is expected (i.e., a threshold). Examples include auditory effect to marine species, larval transport, and sediment transport. 
 

diff --git a/docs/src/modules/shear_stress.rst b/docs/src/modules/shear_stress.rst
@@ -1,7 +1,7 @@
 
 Shear Stress Module
 -------------------
-The SEAT shear stress module evaluates the impacts of sediment mobilization over defined risk layers for the installation of Marine Energy Converters (Wave Energy Converter (WEC) and Current Energy Converter (CEC)) arrays for either wave or current flow conditions. The input is numerical model simulation from SNL-SWAN, SNL-Delft3d-CEC, or any similarly formatted NetCDF file and an optional hydrodynamic probabilities file. The threshold receptor for this analysis is a grain size map from which a critical shear stress for sediment mobility is calculated. Using the ratio between the calculated shear stress and the critical shear stress for sediment mobility, a transport parameter is calculated for both the baseline and MEC simulations. The relative change between these two values defines the mobilization and depositional regime (i.e. erosional and accretional) and whether the regime changes with the presence of MECs. A risk metric, defined in Jones et al (2018), classifies the type of changes associated with changes in sediment mobility. Output from this analysis include the summaries of the difference in shear stress across modeled conditions with and without devices, the resulting difference in the transport potential based on bed sediment properties, and derivation of a risk metric that represents the potential for environmental change. SEAT can also evaluate the impact to various user defined benthic characteristics, such as vegetation, marine species habitat, sediment characteristics, marine infrastructure (shipping channels, buried cables, etc.), or contaminated sediments with the inclusion of an additional risk layer.
+The SEAT shear stress module evaluates the impacts of sediment mobilization over defined Area of Interests for the installation of Marine Energy Converters (Wave Energy Converter (WEC) and Current Energy Converter (CEC)) arrays for either wave or current flow conditions. The input is numerical model simulation from SNL-SWAN, SNL-Delft3d-CEC, or any similarly formatted NetCDF file and an optional hydrodynamic probabilities file. The threshold receptor for this analysis is a grain size map from which a critical shear stress for sediment mobility is calculated. Using the ratio between the calculated shear stress and the critical shear stress for sediment mobility, a transport parameter is calculated for both the baseline and MEC simulations. The relative change between these two values defines the mobilization and depositional regime (i.e. erosional and accretional) and whether the regime changes with the presence of MECs. A risk metric, defined in Jones et al (2018), classifies the type of changes associated with changes in sediment mobility. Output from this analysis include the summaries of the difference in shear stress across modeled conditions with and without devices, the resulting difference in the transport potential based on bed sediment properties, and derivation of a risk metric that represents the potential for environmental change. SEAT can also evaluate the impact to various user defined benthic characteristics, such as vegetation, marine species habitat, sediment characteristics, marine infrastructure (shipping channels, buried cables, etc.), or contaminated sediments with the inclusion of an additional Area of Interest.
 
 Input 
 ^^^^^^
@@ -11,7 +11,7 @@ These include:
   - NetCDF files: model output with 1) baseline runs; 2) devices present runs.
   - \*Receptor file (GeoTIFF or CSV): Contains grain size values.
   - \*Model Probability Condition file (CSV): Contains model weights, used to weight different run scenarios.
-  - \*Risk layer file (GeoTIFF): contains spatial classifications, used to evaluate the impact of the devices on the environment.
+  - \*Area of Interest file (GeoTIFF): contains spatial classifications, used to evaluate the impact of the devices on the environment.
 
   \* Optional input files
 
@@ -66,7 +66,7 @@ Output is saved in the **Shear Stress** subdirectory.
   - **sediment_mobility_difference**: The mobility (Tau/TauCrit) difference between shear stress with devices and baseline models results using the grain size in the receptor file.
   - **sediment_grain_size.tif** : the receptor file interpolated to the same grid as the output
   - **sediment_mobility_classified.tif** : reclassified into increased erosion or deposition compared to the baseline model run.
-  - **shear_stress_risk_layer.tif** :  the risk layer interpolated to the same grid as the output
+  - **shear_stress_area_of_interest.tif** :  the Area of Interest interpolated to the same grid as the output
   - **shear_stress_risk_metric.tif** : A quantified risk metric based on `Jones et al. (2018) Equation 7 <https://doi.org/10.3390/en11082036>`_
 
 CSV files
@@ -87,10 +87,10 @@ Segmented by grain size when using the grain size receptor file:
       - **sediment_mobility_classified_at_sediment_grain_size.csv**
       - **shear_stress_risk_metric_at_sediment_grain_size**
 
-Segmented by spatial classification when using the risk layer file: 
+Segmented by spatial classification when using the Area of Interest file: 
 
-      - **sediment_mobility_difference_at_shear_stress_risk_layer.csv**
-      - **shear_stress_risk_metric_at_shear_stress_risk_layer.csv**
+      - **sediment_mobility_difference_at_shear_stress_area_of_interest.csv**
+      - **shear_stress_risk_metric_at_shear_stress_area_of_interest.csv**
 
 
 

diff --git a/docs/src/modules/velocity.rst b/docs/src/modules/velocity.rst
@@ -14,7 +14,7 @@ These include:
   - NetCDF files: model output with 1) baseline runs; 2) devices present runs.
   - \*Receptor file (GeoTIFF or CSV): Contains critical velocity values (e.g., a critical velocity for larval transport).
   - \*Model Probability Condition file (CSV): Used to weight different run scenarios.
-  - \*Risk layer file (GeoTIFF): Contains spatial classifications, used to evaluate the impact of the devices on the environment.
+  - \*Area of Interest file (GeoTIFF): Contains spatial classifications, used to evaluate the impact of the devices on the environment.
 
   \* Optional input files
 
@@ -74,7 +74,7 @@ Output is saved in the **Velocity Module** subdirectory.
     - **motility_difference**: The motility (Vel/VelCrit) difference between motility with devices and baseline models results using the critical velocity receptor file.
     - **critical_velocity.tif** : the receptor file interpolated to the same grid as the output
     - **motility_classified.tif** : reclassified into increased motility or decreased motility compared to the baseline model run.
-    - **velocity_risk_layer.tif** :  the risk layer interpolated to the same grid as the output
+    - **velocity_area_of_interest.tif** :  the Area of Interest interpolated to the same grid as the output
 
 The CSV files contain statistics of area calculations for various layers. If decimal degree coordinates are provided, the values are converted to UTM (meter) coordinates for calculations.
 The stressor values are binned into 25 bins and associated with the surface area in which that change occurred, 
@@ -91,11 +91,11 @@ Segmented by velocity threshold when using the threshold receptor file:
       - **motility_difference_at_critical_velocity.csv**
       - **motility_classified_at_critical_velocity.csv**
 
-Segmented by spatial classification when using the risk layer file: 
+Segmented by spatial classification when using the Area of Interest file: 
 
-      - **velocity_magnitude_difference_at_velocity_risk_layer.csv**
-      - **motility_difference_at_velocity_risk_layer.csv**
-      - **motility_classified_at_velocity_risk_layer.csv**
+      - **velocity_magnitude_difference_at_velocity_area_of_interest.csv**
+      - **motility_difference_at_velocity_area_of_interest.csv**
+      - **motility_classified_at_velocity_area_of_interest.csv**
 
 
 Core Functions

diff --git a/docs/src/seat_qgis_plugin/acoustics/02_inputs.rst b/docs/src/seat_qgis_plugin/acoustics/02_inputs.rst
@@ -85,14 +85,14 @@ Key:
 - `Species Density File`: Either a .csv or .tif file detailing species density.
 - `% of yr`: Represents the percentage of the year.
 
-Risk Layer (Optional)
+Area of Interest (Optional)
 ^^^^^^^^^^^^^^^^^^^^^^
 
-The risk layer is a receptor file that serves as an additional input to each module and designates which layers are sensitive and would be affected by the acoustics. It must be a numerically classified .tif format, the same as what is used in the shear stress and velocity modules.
+The Area of Interest is a receptor file that serves as an additional input to each module and designates which layers are sensitive and would be affected by the acoustics. It must be a numerically classified .tif format, the same as what is used in the shear stress and velocity modules.
 
-.. figure:: ../../media/risk_layer_gui_input.webp
+.. figure:: ../../media/aoi_layer_gui_input.webp
    :scale: 100%
-   :alt: Risk Layer File
+   :alt: Area of Interest File
 
    Represents a layer to evaluate change against. Examples include vegetation habitat, marine ecosystems, contaminated sediments, marine protected areas, or archaeological artifacts.
 

diff --git a/docs/src/seat_qgis_plugin/shear_stress/00_shear_stress.rst b/docs/src/seat_qgis_plugin/shear_stress/00_shear_stress.rst
@@ -13,7 +13,7 @@ The shear stress module takes 3 required inputs:
 
 The following are optional inputs:
    5. Bed Sediment Grain Size
-   6. Risk Layer
+   6. Area of Interest
 
 
 Each of these inputs is explored in more detail in the following sections.
@@ -30,5 +30,5 @@ Each of these inputs is explored in more detail in the following sections.
    01_model_results_dir
    02_probabilities.rst
    03_bed_sediment.rst
-   04_risk_layer.rst
+   04_area_of_interest.rst
    05_temporal_avg.rst
diff --git a/...gis_plugin/shear_stress/04_risk_layer.rst → ...ugin/shear_stress/04_area_of_interest.rst b/...gis_plugin/shear_stress/04_risk_layer.rst → ...ugin/shear_stress/04_area_of_interest.rst
@@ -1,11 +1,11 @@
-Risk layer (Optional)
+Area of Interest (Optional)
 --------------------------------
 
-The risk layer is a receptor file that serves as an additional input to each module. It must be a numerically classified .tif format. 
+The Area of Interest is a receptor file that serves as an additional input to each module. It must be a numerically classified .tif format. 
 
-.. figure:: ../../media/risk_layer_gui_input.webp
+.. figure:: ../../media/aoi_layer_gui_input.webp
    :scale: 100 %
-   :alt: Risk Layer File
+   :alt: Area of Interest File
 
 Represents a layer to evalute change against. Examples include vegetation habitat, marine ecosystems, contaminated sediments, marine protected areas, or archaeological artifacts.
 

diff --git a/docs/src/seat_qgis_plugin/velocity/00_velocity.rst b/docs/src/seat_qgis_plugin/velocity/00_velocity.rst
@@ -14,5 +14,5 @@ Investigates the spatial changes in larval motility.
    01_model_results_dir
    02_probabilities.rst
    03_larval_motility.rst
-   04_risk_layer.rst
+   04_area_of_interest.rst
    05_temporal_avg.rst
diff --git a/...at_qgis_plugin/velocity/04_risk_layer.rst → ...s_plugin/velocity/04_area_of_interest.rst b/...at_qgis_plugin/velocity/04_risk_layer.rst → ...s_plugin/velocity/04_area_of_interest.rst
@@ -1,11 +1,11 @@
-Risk layer (Optional)
+Area of Interest (Optional)
 --------------------------------
 
-The risk layer is a receptor file that serves as an additional input to each module. It must be a numerically classified .tif format. 
+The Area of Interest is a receptor file that serves as an additional input to each module. It must be a numerically classified .tif format. 
 
-.. figure:: ../../media/risk_layer_gui_input.webp
+.. figure:: ../../media/aoi_layer_gui_input.webp
    :scale: 100 %
-   :alt: Risk Layer File
+   :alt: Area of Interest File
 
 Represents a layer to evalute change against. Examples include vegetation habitat, marine ecosystems, contaminated sediments, marine protected areas, or archaeological artifacts.
 

diff --git a/docs/src/tutorials/file_access.rst b/docs/src/tutorials/file_access.rst
@@ -40,7 +40,7 @@ Upon processing, you will receive access to a collection of folders containing t
       │   │   └───4x4
       │   ├───probabilities
       │   ├───receptor
-      │   ├───risk_layer
+      │   ├───area_of_interest
       │   └───species
       │
       ├───tanana_river

diff --git a/docs/src/tutorials/pacwave/acoustics.rst b/docs/src/tutorials/pacwave/acoustics.rst
@@ -49,7 +49,7 @@ please refer to the :ref:`save_load_config` section in the :ref:`seat_qgis_plugi
    - **Baseline results directory** contains the baseline conditions which are the model results without any devices present. If left blank, 0 dB will be assumed.
    - **Device Model Results Directory** contains the model results with the devices.
    - **Probabilities File** defines the likelihood of each model condition occurring.
-   - **Risk Layer File** contains spatial classifications used to evaluate the impact of the devices on the environment.
+   - **Area of Interest File** contains spatial classifications used to evaluate the impact of the devices on the environment.
    - **Depth Averaging** option allows the user to specify the depth averaging method for the model results.
 
 
@@ -104,7 +104,7 @@ There are four types of output files:
   - **species_threshold_exceeded** : the probability that the acoustic signal generated by the device will exceed the species-specific threshold in a given 24 hour period. Takes into account the model weights for different model conditions.
   - **species_percent** : for a given location, if the the device exceeds a threshold, the probability the species will be present in a 24-hour period. Uses the species density, the acoustic signal generated by the devices, and the threshold limit.
   - **species_density** : for a given location, if the the device exceeds a threshold, the number of individuals present. Uses the species density, the acoustic signal generated by the devices, and the threshold limit.
-  - **paracousti_risk_layer** : the risk layer input provided, cropped to the location of interest.
+  - **paracousti_area_of_interest** : the Area of Interest input provided, cropped to the location of interest.
 
 .. list-table:: 
    :widths: 50 50
@@ -121,7 +121,7 @@ There are four types of output files:
 
      - .. image:: ../../media/paracousti_with_devices.webp
          :scale: 75 %
-         :alt: Risk Layer
+         :alt: Area of Interest
          :align: center
 
        .. raw:: html
@@ -130,7 +130,7 @@ There are four types of output files:
 
    * - .. image:: ../../media/paracousti_stressor.webp
          :scale: 75 %
-         :alt: Risk Layer
+         :alt: Area of Interest
          :align: center
 
        .. raw:: html
@@ -193,7 +193,7 @@ than the model run with a wave height of 7.0m.
 
      - .. image:: ../../media/paracousti_with_devics_pacwave_3DSPLs_Hw7.0.webp
          :scale: 125 %
-         :alt: Risk Layer
+         :alt: Area of Interest
          :align: center
 
        .. raw:: html
@@ -210,12 +210,12 @@ than the model run with a wave height of 7.0m.
    Output
    └───paracousti_sel_199db
        └───Acoustics Module
-            paracousti_risk_layer.tif
+            paracousti_area_of_interest.tif
             paracousti_stressor.csv
             paracousti_stressor_pacwave_*.csv
             paracousti_stressor_pacwave_*.tif
-            paracousti_stressor_at_paracousti_risk_layer.csv
-            paracousti_stressor_pacwave_*_*_at_paracousti_risk_layer.csv
+            paracousti_stressor_at_paracousti_area_of_interest.csv
+            paracousti_stressor_pacwave_*_*_at_paracousti_area_of_interest.csv
             paracousti_without_devices.csv
             paracousti_without_devices_pacwave_*.tif
             paracousti_with_devices.csv
@@ -224,23 +224,23 @@ than the model run with a wave height of 7.0m.
             paracousti_with_devices_pacwave_*.tif
             species_density.csv
             species_density.tif
-            species_density_at_paracousti_risk_layer.csv
+            species_density_at_paracousti_area_of_interest.csv
             species_density_pacwave_*.csv
             species_density_pacwave_*.tif
-            species_density_at_pacwave_*_paracousti_risk_layer.csv
+            species_density_at_pacwave_*_paracousti_area_of_interest.csv
             species_percent_pacwave_*.csv
             species_percent_pacwave_*.tif
-            species_percent_pacwave_*_at_paracousti_risk_layer.csv
+            species_percent_pacwave_*_at_paracousti_area_of_interest.csv
             species_percent.csv
             species_percent.tif
-            species_percent_at_paracousti_risk_layer.csv
+            species_percent_at_paracousti_area_of_interest.csv
             species_percent_pacwave_*.csv
             species_percent_pacwave_*.tif
-            species_percent_pacwave_*_at_paracousti_risk_layer.csv
+            species_percent_pacwave_*_at_paracousti_area_of_interest.csv
             species_threshold_exceeded.csv
             species_threshold_exceeded.tif
-            species_threshold_exceeded_at_paracousti_risk_layer.csv
+            species_threshold_exceeded_at_paracousti_area_of_interest.csv
             species_threshold_exceeded_pacwave_*.csv
             species_threshold_exceeded_pacwave_*.tif
-            species_threshold_exceeded_pacwave_*_at_paracousti_risk_layer.csv
+            species_threshold_exceeded_pacwave_*_at_paracousti_area_of_interest.csv
 
diff --git a/docs/src/tutorials/pacwave/pacwave.rst b/docs/src/tutorials/pacwave/pacwave.rst
@@ -137,7 +137,7 @@ Results in this tutorial will utilize the QuickMapServices plugin in QGIS. To in
    │       grain_size_receptor.csv
    │       velocity_receptor.csv
    │
-   ├───risk_layer
+   ├───area_of_interest
    │       habitat_classification.tif
    │
    └───species