Improving gaze analysis pipeline chapters name. Replacing pictures. Improving hints and examples.

12 files changed, 35 insertions, 26 deletions

diff --git a/docs/img/ar_frame.png b/docs/img/ar_frame.png
new file mode 100644
index 0000000..65fa0ea
--- /dev/null
+++ b/docs/img/ar_frame.png
diff --git a/docs/img/ar_frame_empty.png b/docs/img/ar_frame_empty.png
deleted file mode 100644
index f368635..0000000
--- a/docs/img/ar_frame_empty.png
+++ /dev/null
diff --git a/docs/img/ar_layer.png b/docs/img/ar_layer.png
new file mode 100644
index 0000000..418d879
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+++ b/docs/img/ar_layer.png
diff --git a/docs/img/ar_layer_empty.png b/docs/img/ar_layer_empty.png
deleted file mode 100644
index f368635..0000000
--- a/docs/img/ar_layer_empty.png
+++ /dev/null
diff --git a/docs/img/aruco_camera_frame.png b/docs/img/aruco_camera_frame.png
index c0e06f0..4b2a9a2 100644
--- a/docs/img/aruco_camera_frame.png
+++ b/docs/img/aruco_camera_frame.png
diff --git a/docs/user_guide/gaze_analysis_pipeline/ar_layer.md b/docs/user_guide/gaze_analysis_pipeline/aoi_analysis.md
index f0291c3..ffc72c7 100644
--- a/docs/user_guide/gaze_analysis_pipeline/ar_layer.md
+++ b/docs/user_guide/gaze_analysis_pipeline/aoi_analysis.md
@@ -1,9 +1,9 @@
-Add an ArLayer
-==============
+Add AOI analysis
+================
 
-The [ArLayer](../../argaze.md/#argaze.ArFeatures.ArLayer) class defines a space where to make matching of gaze movements and AOIs and inside which those matchings need to be analyzed.
+The [ArLayer](../../argaze.md/#argaze.ArFeatures.ArLayer) class defines a space where to make matching of gaze movements with AOIs and inside which those matchings need to be analyzed.
 
-![Empty layer area](../../img/ar_layer_empty.png)
+![Layer](../../img/ar_layer.png)
 
 ## Add ArLayer to ArFrame JSON configuration file
 
@@ -47,7 +47,7 @@ Here is an extract from the JSON [ArFrame](../../argaze.md/#argaze.ArFeatures.Ar
 
 !!! note
 
-	Timestamped gaze movements identified by parent [ArFrame](../../argaze.md/#argaze.ArFeatures.ArFrame) are passed one by one to each [ArLayer](../../argaze.md/#argaze.ArFeatures.ArLayer). So, the execution of all [ArLayers](../../argaze.md/#argaze.ArFeatures.ArLayer) is done during parent [ArFrame.look](../../argaze.md/#argaze.ArFeatures.ArFrame.look) method call as explained in [previous chapter](ar_frame_configuration_and_execution.md).
+	Timestamped gaze movements identified by parent [ArFrame](../../argaze.md/#argaze.ArFeatures.ArFrame) are passed one by one to each [ArLayer](../../argaze.md/#argaze.ArFeatures.ArLayer). So, the execution of all [ArLayers](../../argaze.md/#argaze.ArFeatures.ArLayer) is done during parent [ArFrame.look](../../argaze.md/#argaze.ArFeatures.ArFrame.look) method call as explained in [previous chapter](configuration_and_execution.md).
 
 Now, let's understand the meaning of each JSON entry.
 
@@ -67,11 +67,11 @@ The first [ArLayer](../../argaze.md/#argaze.ArFeatures.ArLayer) pipeline step ai
 
 ![AOI Matcher](../../img/ar_layer_aoi_matcher.png)
 
-The matching algorithm can be selected by instantiating a particular [AOIMatcher](../../argaze.md/#argaze.GazeFeatures.AOIMatcher) from the [argaze.GazeAnalysis](../../argaze.md/#argaze.GazeAnalysis) submodule or [from another python package](advanced_topics/module_loading.md).
+The matching algorithm can be selected by instantiating a particular AOIMatcher [from GazeAnalysis submodule](pipeline_modules/aoi_matchers.md) or [from another python package](advanced_topics/module_loading.md).
 
 In the example file, the choosen matching algorithm is the [Deviation Circle Coverage](../../argaze.md/#argaze.GazeAnalysis.DeviationCircleCoverage) which has one specific *coverage_threshold* attribute.
 
-!!! warning
+!!! warning "Mandatory"
 	JSON *aoi_matcher* entry is mandatory. Otherwise, the AOIScanPath and AOIScanPathAnalyzers steps are disabled.
 
 ### AOI Scan Path
@@ -84,11 +84,13 @@ Once identified gaze movements are matched to AOI, they are automatically append
 
 The [AOIScanPath.duration_max](../../argaze.md/#argaze.GazeFeatures.AOIScanPath.duration_max) attribute is the duration from which older AOI scan steps are removed each time new AOI scan steps are added.
 
-!!! note
+!!! note "Optional"
 	JSON *aoi_scan_path* entry is not mandatory. If aoi_scan_path_analyzers entry is not empty, the AOIScanPath step is automatically enabled.
 
 ### AOI Scan Path Analyzers
 
 Finally, the last [ArLayer](../../argaze.md/#argaze.ArFeatures.ArLayer) pipeline step consists in passing the previously built [AOIScanPath](../../argaze.md/#argaze.GazeFeatures.AOIScanPath) to each loaded [AOIScanPathAnalyzer](../../argaze.md/#argaze.GazeFeatures.AOIScanPathAnalyzer).
 
-Each analysis algorithm can be selected by instantiating a particular [AOIScanPathAnalyzer](../../argaze.md/#argaze.GazeFeatures.AOIScanPathAnalyzer) from the [argaze.GazeAnalysis](../../argaze.md/#argaze.GazeAnalysis) submodule or [from another python package](advanced_topics/module_loading.md).
+Each analysis algorithm can be selected by instantiating a particular AOIScanPathAnalyzer [from GazeAnalysis submodule](pipeline_modules/aoi_scan_path_analyzers.md) or [from another python package](advanced_topics/module_loading.md).
+
+In the example file, the choosen analysis algorithms are the [Basic](../../argaze.md/#argaze.GazeAnalysis.Basic) module, the [TransitionMatrix](../../argaze.md/#argaze.GazeAnalysis.TransitionMatrix) module and the [NGram](../../argaze.md/#argaze.GazeAnalysis.NGram) module which has two specific *n_min* and *n_max* attributes.
diff --git a/docs/user_guide/gaze_analysis_pipeline/ar_frame_configuration_and_execution.md b/docs/user_guide/gaze_analysis_pipeline/configuration_and_execution.md
index d649a4b..f4aa2b7 100644
--- a/docs/user_guide/gaze_analysis_pipeline/ar_frame_configuration_and_execution.md
+++ b/docs/user_guide/gaze_analysis_pipeline/configuration_and_execution.md
@@ -1,9 +1,9 @@
-Configure and execute ArFrame
-=============================
+Load and execute pipeline
+=========================
 
 The [ArFrame](../../argaze.md/#argaze.ArFeatures.ArFrame) class defines a rectangular area where timestamped gaze positions are projected in and inside which they need to be analyzed.
 
-![Empty frame area](../../img/ar_frame_empty.png)
+![Frame](../../img/ar_frame.png)
 
 ## Load JSON configuration file
 
@@ -52,8 +52,8 @@ The name of the [ArFrame](../../argaze.md/#argaze.ArFeatures.ArFrame). Basically
 
 The size of the [ArFrame](../../argaze.md/#argaze.ArFeatures.ArFrame) defines the dimension of the rectangular area where gaze positions are projected. Be aware that gaze positions have to be in the same range of value to be projected in.
 
-!!! warning
-	**ArGaze doesn't impose any spatial unit.** Gaze positions can either be integer or float, pixels, millimeters or what ever you need. The only concern is that all spatial values used in further configurations have to be all the same unit.
+!!! warning "Free spatial unit"
+	Gaze positions can either be integer or float, pixels, millimeters or what ever you need. The only concern is that all spatial values used in further configurations have to be all the same unit.
 
 ### Gaze Movement Identifier
 
@@ -61,14 +61,14 @@ The first [ArFrame](../../argaze.md/#argaze.ArFeatures.ArFrame) pipeline step is
 
 ![Gaze Movement Identifier](../../img/ar_frame_gaze_movement_identifier.png)
 
-The identification algorithm can be selected by instantiating a particular [GazeMovementIdentifier](../../argaze.md/#argaze.GazeFeatures.GazeMovementIdentifier) from the [argaze.GazeAnalysis](../../argaze.md/#argaze.GazeAnalysis) submodule or [from another python package](advanced_topics/module_loading.md).
+The identification algorithm can be selected by instantiating a particular GazeMovementIdentifier [from GazeAnalysis submodule](pipeline_modules/gaze_movement_identifiers.md) or [from another python package](advanced_topics/module_loading.md).
 
 In the example file, the choosen identification algorithm is the [Dispersion Threshold Identification (I-DT)](../../argaze.md/#argaze.GazeAnalysis.DispersionThresholdIdentification) which has two specific *deviation_max_threshold* and *duration_min_threshold* attributes.
 
 !!! note
 	In ArGaze, [Fixation](../../argaze.md/#argaze.GazeFeatures.Fixation) and [Saccade](../../argaze.md/#argaze.GazeFeatures.Saccade) are considered as particular [GazeMovements](../../argaze.md/#argaze.GazeFeatures.GazeMovement).
 
-!!! warning
+!!! warning "Mandatory"
 	JSON *gaze_movement_identifier* entry is mandatory. Otherwise, the ScanPath and ScanPathAnalyzers steps are disabled.
 
 ### Scan Path
@@ -81,14 +81,16 @@ Once fixations and saccades are identified, they are automatically appended to t
 
 The [ScanPath.duration_max](../../argaze.md/#argaze.GazeFeatures.ScanPath.duration_max) attribute is the duration from which older scan steps are removed each time new scan steps are added.
 
-!!! note
+!!! note "Optional"
 	JSON *scan_path* entry is not mandatory. If scan_path_analyzers entry is not empty, the ScanPath step is automatically enabled.
 
 ### Scan Path Analyzers
 
 Finally, the last [ArFrame](../../argaze.md/#argaze.ArFeatures.ArFrame) pipeline step consists in passing the previously built [ScanPath](../../argaze.md/#argaze.GazeFeatures.ScanPath) to each loaded [ScanPathAnalyzer](../../argaze.md/#argaze.GazeFeatures.ScanPathAnalyzer).
 
-Each analysis algorithm can be selected by instantiating a particular [ScanPathAnalyzer](../../argaze.md/#argaze.GazeFeatures.ScanPathAnalyzer) from the [argaze.GazeAnalysis](../../argaze.md/#argaze.GazeAnalysis) submodule or [from another python package](advanced_topics/module_loading.md).
+Each analysis algorithm can be selected by instantiating a particular ScanPathAnalyzer [from GazeAnalysis submodule](pipeline_modules/scan_path_analyzers.md) or [from another python package](advanced_topics/module_loading.md).
+
+In the example file, the choosen analysis algorithms are the [Basic](../../argaze.md/#argaze.GazeAnalysis.Basic) module and the [ExploitExploreRatio](../../argaze.md/#argaze.GazeAnalysis.ExploitExploreRatio) module which has one specific *short_fixation_duration_threshold* attribute.
 
 ## Pipeline execution
 
@@ -101,3 +103,8 @@ Timestamped gaze positions have to be passed one by one to [ArFrame.look](../../
     # Look ArFrame at a timestamped gaze position
     ar_frame.look(timestamp, gaze_position)
 ```
+!!! warning ""
+
+	At this point, the [ArFrame.look](../../argaze.md/#argaze.ArFeatures.ArFrame.look) method only process gaze movement identification and scan path analysis without any AOI neither any logging or visualisation supports.
+
+	Read the next chapters to learn how to [add AOI analysis](aoi_analysis.md), [log gaze analysis](logging.md) and [visualize pipeline steps](visualisation.md).
\ No newline at end of file
diff --git a/docs/user_guide/gaze_analysis_pipeline/introduction.md b/docs/user_guide/gaze_analysis_pipeline/introduction.md
index 002ba1f..02aa82e 100644
--- a/docs/user_guide/gaze_analysis_pipeline/introduction.md
+++ b/docs/user_guide/gaze_analysis_pipeline/introduction.md
@@ -10,8 +10,8 @@ First, let's look at the schema below: it gives an overview of the main notions
 To build your own gaze analysis pipeline, you need to know:
 
 * [How to edit timestamped gaze positions](timestamped_gaze_positions_edition.md),
-* [How to deal with an ArFrame instance](ar_frame_configuration_and_execution.md),
-* [How to add ArLayer instance](ar_layer.md),
+* [How to load and execute gaze analysis pipeline](configuration_and_execution.md),
+* [How to add AOI analysis](aoi_analysis.md),
 * [How to visualize ArFrame and ArLayers](visualisation.md),
 * [How to log resulted gaze analysis](logging.md),
 * [How to make heatmap image](heatmap.md).
diff --git a/docs/user_guide/gaze_analysis_pipeline/pipeline_modules/gaze_movement_identifiers.md b/docs/user_guide/gaze_analysis_pipeline/pipeline_modules/gaze_movement_identifiers.md
index 6ae66bf..751cc7b 100644
--- a/docs/user_guide/gaze_analysis_pipeline/pipeline_modules/gaze_movement_identifiers.md
+++ b/docs/user_guide/gaze_analysis_pipeline/pipeline_modules/gaze_movement_identifiers.md
@@ -3,7 +3,7 @@ Gaze movement identifiers
 
 ArGaze provides ready-to-use gaze movement identification algorithms.
 
-Here are JSON samples to include a chosen module inside [ArFrame configuration](../ar_frame_configuration_and_execution.md) *gaze_movement_identifier* entry.
+Here are JSON samples to include a chosen module inside [ArFrame configuration](../configuration_and_execution.md) *gaze_movement_identifier* entry.
 
 ## Dispersion threshold identification (I-DT)
 
diff --git a/docs/user_guide/gaze_analysis_pipeline/pipeline_modules/scan_path_analyzers.md b/docs/user_guide/gaze_analysis_pipeline/pipeline_modules/scan_path_analyzers.md
index 29ee4f2..afba844 100644
--- a/docs/user_guide/gaze_analysis_pipeline/pipeline_modules/scan_path_analyzers.md
+++ b/docs/user_guide/gaze_analysis_pipeline/pipeline_modules/scan_path_analyzers.md
@@ -3,7 +3,7 @@ Scan path analyzers
 
 ArGaze provides ready-to-use scan path analysis algorithms.
 
-Here are JSON samples to include a chosen module inside [ArFrame configuration](../ar_frame_configuration_and_execution.md) *scan_path_analyzers* entry.
+Here are JSON samples to include a chosen module inside [ArFrame configuration](../configuration_and_execution.md) *scan_path_analyzers* entry.
 
 ## Basic metrics
 
diff --git a/docs/user_guide/gaze_analysis_pipeline/timestamped_gaze_positions_edition.md b/docs/user_guide/gaze_analysis_pipeline/timestamped_gaze_positions_edition.md
index 493471e..93d2a65 100644
--- a/docs/user_guide/gaze_analysis_pipeline/timestamped_gaze_positions_edition.md
+++ b/docs/user_guide/gaze_analysis_pipeline/timestamped_gaze_positions_edition.md
@@ -68,7 +68,7 @@ start_time = time.time()
 	...
 ```
 
-!!! warning
-	**ArGaze doesn't impose any time unit.** Timestamps can either be integer or float, second, millisecond or what ever you need. The only concern is that all time values used in further configurations have to be all the same unit.
+!!! warning "Free time unit"
+	Timestamps can either be integer or float, second, millisecond or what ever you need. The only concern is that all time values used in further configurations have to be all the same unit.
 
 Now we have timestamped gaze positions at expected format, let's see how to analyze them.
\ No newline at end of file
diff --git a/docs/user_guide/gaze_analysis_pipeline/visualisation.md b/docs/user_guide/gaze_analysis_pipeline/visualisation.md
index 852cdc5..55254dd 100644
--- a/docs/user_guide/gaze_analysis_pipeline/visualisation.md
+++ b/docs/user_guide/gaze_analysis_pipeline/visualisation.md
@@ -1,5 +1,5 @@
-Visualize ArFrame
-=================
+Visualize pipeline steps
+========================
 
 Visualisation is not a pipeline step but each [ArFrame](../../argaze.md/#argaze.ArFeatures.ArFrame) pipeline steps outputs can be drawn in real time or afterward, depending of application purpose.