From 74ed30fa3417c5a1bb5f147d779250e5bbdbd521 Mon Sep 17 00:00:00 2001
From: Théo de la Hogue
Date: Wed, 22 Nov 2023 10:38:16 +0100
Subject: Including code reference inside pipeline modules description.

---
 .../pipeline_modules/aoi_matchers.md               | 26 ++++++++---
 .../pipeline_modules/aoi_scan_path_analyzers.md    | 50 ++++++++++++++++------
 .../pipeline_modules/gaze_movement_identifiers.md  | 27 ++++++++----
 .../pipeline_modules/gaze_position_calibrators.md  | 22 ++++++++--
 .../pipeline_modules/scan_path_analyzers.md        | 37 ++++++++++++----
 src/argaze/GazeAnalysis/Basic.py                   |  2 -
 src/argaze/GazeAnalysis/DeviationCircleCoverage.py |  1 -
 .../DispersionThresholdIdentification.py           |  4 --
 src/argaze/GazeAnalysis/Entropy.py                 |  1 -
 src/argaze/GazeAnalysis/ExploreExploitRatio.py     |  1 -
 src/argaze/GazeAnalysis/FocusPointInside.py        |  5 +--
 src/argaze/GazeAnalysis/KCoefficient.py            |  2 -
 src/argaze/GazeAnalysis/LempelZivComplexity.py     |  1 -
 src/argaze/GazeAnalysis/LinearRegression.py        |  1 -
 src/argaze/GazeAnalysis/NGram.py                   |  1 -
 src/argaze/GazeAnalysis/NearestNeighborIndex.py    |  1 -
 src/argaze/GazeAnalysis/TransitionMatrix.py        |  1 -
 .../VelocityThresholdIdentification.py             |  4 --
 18 files changed, 125 insertions(+), 62 deletions(-)

diff --git a/docs/user_guide/gaze_analysis_pipeline/pipeline_modules/aoi_matchers.md b/docs/user_guide/gaze_analysis_pipeline/pipeline_modules/aoi_matchers.md
index 61338cc..c0bc9df 100644
--- a/docs/user_guide/gaze_analysis_pipeline/pipeline_modules/aoi_matchers.md
+++ b/docs/user_guide/gaze_analysis_pipeline/pipeline_modules/aoi_matchers.md
@@ -3,22 +3,38 @@ AOI matchers
 
 ArGaze provides ready-to-use AOI matching algorithms.
 
-Here are JSON samples to include the chosen module inside [ArLayer configuration](../aoi_analysis.md) *aoi_matcher* entry.
+The JSON samples have to be included inside [ArLayer configuration](../aoi_analysis.md) *aoi_matcher* entry to select an algorithm.
+
+```json
+"aoi_matcher": {
+	JSON sample
+}
+```
+
+Read more about [AOIMatcher base class in code reference](../../../argaze.md/#argaze.GazeFeatures.AOIMatcher).
+
+!!! note
+
+	The members indicated as **property** are what returns the matcher.
 
 ## Deviation circle coverage
 
+::: argaze.GazeAnalysis.DeviationCircleCoverage.AOIMatcher
+
+### JSON sample
+
 ```json
 "DeviationCircleCoverage": {
 	"coverage_threshold": 0.5
 }
 ```
 
-[See in code reference](../../../argaze.md/#argaze.GazeAnalysis.DeviationCircleCoverage.AOIMatcher)
-
 ## Focus point inside
 
+::: argaze.GazeAnalysis.FocusPointInside.AOIMatcher
+
+### JSON sample
+
 ```json
 "FocusPointInside": {}
 ```
-
-[See in code reference](../../../argaze.md/#argaze.GazeAnalysis.FocusPointInside.AOIMatcher)
diff --git a/docs/user_guide/gaze_analysis_pipeline/pipeline_modules/aoi_scan_path_analyzers.md b/docs/user_guide/gaze_analysis_pipeline/pipeline_modules/aoi_scan_path_analyzers.md
index ad1832d..e68cf8f 100644
--- a/docs/user_guide/gaze_analysis_pipeline/pipeline_modules/aoi_scan_path_analyzers.md
+++ b/docs/user_guide/gaze_analysis_pipeline/pipeline_modules/aoi_scan_path_analyzers.md
@@ -3,42 +3,66 @@ AOI scan path analyzers
 
 ArGaze provides ready-to-use AOI scan path analysis algorithms.
 
-Here are JSON samples to include a chosen module inside [ArLayer configuration](../aoi_analysis.md) *aoi_scan_path_analyzers* entry.
+The JSON samples have to be included inside [ArLayer configuration](../aoi_analysis.md) *aoi_scan_path_analyzers* entry to select an algorithm.
+
+```json
+"aoi_scan_path_analyzers": {
+	JSON sample
+}
+```
+
+Read more about [AOIScanPathAnalyzer base class in code reference](../../../argaze.md/#argaze.GazeFeatures.AOIScanPathAnalyzer).
+
+!!! note
+
+	The members indicated as **property** are what returns the analyzer.
 
 ## Basic metrics
 
+::: argaze.GazeAnalysis.Basic.AOIScanPathAnalyzer
+
+### JSON sample
+
 ```json
 "Basic": {}
 ```
 
-[See in code reference](../../../argaze.md/#argaze.GazeAnalysis.Basic.AOIScanPathAnalyzer)
-
 ## Entropy
 
+::: argaze.GazeAnalysis.Entropy.AOIScanPathAnalyzer
+
+### JSON sample
+
 ```json
 "Entropy": {}
 ```
 
-[See in code reference](../../../argaze.md/#argaze.GazeAnalysis.Entropy.AOIScanPathAnalyzer)
-
 ## K-modified coefficient
 
+::: argaze.GazeAnalysis.KCoefficient.AOIScanPathAnalyzer
+
+### JSON sample
+
 ```json
 "KCoefficient": {}
 ```
 
-[See in code reference](../../../argaze.md/#argaze.GazeAnalysis.KCoefficient.AOIScanPathAnalyzer)
-
 ## Lempel-Ziv complexity
 
+::: argaze.GazeAnalysis.LempelZivComplexity.AOIScanPathAnalyzer
+
+### JSON sample
+
 ```json
 "LempelZivComplexity": {}
 ```
 
-[See in code reference](../../../argaze.md/#argaze.GazeAnalysis.LempelZivComplexity.AOIScanPathAnalyzer)
-
 ## N-Gram
 
+::: argaze.GazeAnalysis.NGram.AOIScanPathAnalyzer
+
+### JSON sample
+
 ```json
 "NGram": {
 	"n_min": 3,
@@ -46,12 +70,12 @@ Here are JSON samples to include a chosen module inside [ArLayer configuration](
 }
 ```
 
-[See in code reference](../../../argaze.md/#argaze.GazeAnalysis.NGram.AOIScanPathAnalyzer)
-
 ## Transition matrix
 
+::: argaze.GazeAnalysis.TransitionMatrix.AOIScanPathAnalyzer
+
+### JSON sample
+
 ```json
 "TransitionMatrix": {}
 ```
-
-[See in code reference](../../../argaze.md/#argaze.GazeAnalysis.TransitionMatrix.AOIScanPathAnalyzer)
\ No newline at end of file
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 751cc7b..6530c15 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
@@ -3,27 +3,38 @@ Gaze movement identifiers
 
 ArGaze provides ready-to-use gaze movement identification algorithms.
 
-Here are JSON samples to include a chosen module inside [ArFrame configuration](../configuration_and_execution.md) *gaze_movement_identifier* entry.
+The JSON samples have to be included inside [ArFrame configuration](../configuration_and_execution.md) *gaze_movement_identifier* entry to select an algorithm.
+
+```json
+"gaze_movement_identifier": {
+	JSON sample
+}
+```
+
+Read more about [GazeMovementIdentifier base class in code reference](../../../argaze.md/#argaze.GazeFeatures.GazeMovementIdentifier).
 
 ## Dispersion threshold identification (I-DT)
 
+::: argaze.GazeAnalysis.DispersionThresholdIdentification.GazeMovementIdentifier
+
+### JSON sample
+
 ```json
 "DispersionThresholdIdentification": {
-	"deviation_max_threshold": 50,
-	"duration_min_threshold": 200
+	"deviation_max_threshold": 25,
+	"duration_min_threshold": 150
 }
 ```
 
-[See in code reference](../../../argaze.md/#argaze.GazeAnalysis.DispersionThresholdIdentification.GazeMovementIdentifier)
-
 ## Velocity threshold identification (I-VT)
 
+::: argaze.GazeAnalysis.VelocityThresholdIdentification.GazeMovementIdentifier
+
+### JSON sample
+
 ```json
 "VelocityThresholdIdentification": {
 	"velocity_max_threshold": 10,
 	"duration_min_threshold": 200
 }
 ```
-
-[See in code reference](../../../argaze.md/#argaze.GazeAnalysis.VelocityThresholdIdentification.GazeMovementIdentifier)
-
diff --git a/docs/user_guide/gaze_analysis_pipeline/pipeline_modules/gaze_position_calibrators.md b/docs/user_guide/gaze_analysis_pipeline/pipeline_modules/gaze_position_calibrators.md
index 69139ed..67dd779 100644
--- a/docs/user_guide/gaze_analysis_pipeline/pipeline_modules/gaze_position_calibrators.md
+++ b/docs/user_guide/gaze_analysis_pipeline/pipeline_modules/gaze_position_calibrators.md
@@ -3,10 +3,27 @@ Gaze position calibrators
 
 ArGaze provides ready-to-use gaze position calibrator algorithms.
 
-Here are JSON samples to include the chosen module inside [ArFrame configuration](../advanced_topics/gaze_position_calibration.md) *gaze_position_calibrator* entry.
+
+The JSON samples have to be included inside [ArFrame configuration](../advanced_topics/gaze_position_calibration.md) *gaze_position_calibrator* entry to select an algorithm.
+
+```json
+"gaze_position_calibrator": {
+    JSON sample
+}
+```
+
+Read more about [GazePositionCalibrator base class in code reference](../../../argaze.md/#argaze.GazeFeatures.GazePositionCalibrator).
+
+!!! note
+
+    The members indicated as **property** are what returns the matcher.
 
 ## Linear regression
 
+::: argaze.GazeAnalysis.LinearRegression.GazePositionCalibrator
+
+### JSON sample
+
 ```json
 "LinearRegression": {
 	"coefficients": [
@@ -25,6 +42,3 @@ Here are JSON samples to include the chosen module inside [ArFrame configuration
     ]
 }
 ```
-
-[See in code reference](../../../argaze.md/#argaze.GazeAnalysis.LinearRegression.GazePositionCalibrator)
-
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 f9f757a..c779112 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
@@ -3,38 +3,57 @@ Scan path analyzers
 
 ArGaze provides ready-to-use scan path analysis algorithms.
 
-Here are JSON samples to include a chosen module inside [ArFrame configuration](../configuration_and_execution.md) *scan_path_analyzers* entry.
+The JSON samples have to be included inside [ArFrame configuration](../configuration_and_execution.md) *scan_path_analyzers* entry to select an algorithm.
+
+```json
+"scan_path_analyzers": {
+	JSON sample
+}
+```
+
+Read more about [ScanPathAnalyzer base class in code reference](../../../argaze.md/#argaze.GazeFeatures.ScanPathAnalyzer).
+
+!!! note
+
+	The members indicated as **property** are what returns the analyzer.
 
 ## Basic metrics
 
+::: argaze.GazeAnalysis.Basic.ScanPathAnalyzer
+
+### JSON sample
+
 ```json
 "Basic": {}
 ```
 
-[See in code reference](../../../argaze.md/#argaze.GazeAnalysis.Basic.ScanPathAnalyzer)
-
 ## Explore/Exploit ratio
 
+::: argaze.GazeAnalysis.ExploreExploitRatio.ScanPathAnalyzer
+
+### JSON sample
+
 ```json
 "ExploreExploitRatio": {
 	"short_fixation_duration_threshold": 0
 }
 ```
 
-[See in code reference](../../../argaze.md/#argaze.GazeAnalysis.ExploreExploitRatio.ScanPathAnalyzer)
-
 ## K coefficient
 
+::: argaze.GazeAnalysis.KCoefficient.ScanPathAnalyzer
+
+### JSON sample
+
 ```json
 "KCoefficient": {}
 ```
 
-[See in code reference](../../../argaze.md/#argaze.GazeAnalysis.KCoefficient.ScanPathAnalyzer)
-
 ## Nearest neighbor index
 
+::: argaze.GazeAnalysis.NearestNeighborIndex.ScanPathAnalyzer
+
+### JSON sample
 ```json
 "NearestNeighborIndex": {}
 ```
-
-[See in code reference](../../../argaze.md/#argaze.GazeAnalysis.NearestNeighborIndex.ScanPathAnalyzer)
\ No newline at end of file
diff --git a/src/argaze/GazeAnalysis/Basic.py b/src/argaze/GazeAnalysis/Basic.py
index dc7b4fd..a11991f 100644
--- a/src/argaze/GazeAnalysis/Basic.py
+++ b/src/argaze/GazeAnalysis/Basic.py
@@ -27,7 +27,6 @@ class ScanPathAnalyzer(GazeFeatures.ScanPathAnalyzer):
         self.__step_fixation_durations_average = 0
 
     def analyze(self, scan_path: GazeFeatures.ScanPathType):
-        """Analyze scan path."""
 
         self.__path_duration = scan_path.duration
 
@@ -72,7 +71,6 @@ class AOIScanPathAnalyzer(GazeFeatures.AOIScanPathAnalyzer):
         self.__step_fixation_durations_average = 0
 
     def analyze(self, aoi_scan_path: GazeFeatures.ScanPathType):
-        """Analyze aoi scan path."""
 
         self.__path_duration = aoi_scan_path.duration
 
diff --git a/src/argaze/GazeAnalysis/DeviationCircleCoverage.py b/src/argaze/GazeAnalysis/DeviationCircleCoverage.py
index acc0665..fde9543 100644
--- a/src/argaze/GazeAnalysis/DeviationCircleCoverage.py
+++ b/src/argaze/GazeAnalysis/DeviationCircleCoverage.py
@@ -29,7 +29,6 @@ class AOIMatcher(GazeFeatures.AOIMatcher):
     """Minimal coverage ratio to consider a fixation over an AOI (1 means that whole fixation's deviation circle have to be over the AOI)."""
 
     def __post_init__(self):
-        """Init looked aoi data."""
 
         self.__look_count = 0
         self.__looked_aoi_data = (None, None)
diff --git a/src/argaze/GazeAnalysis/DispersionThresholdIdentification.py b/src/argaze/GazeAnalysis/DispersionThresholdIdentification.py
index a7b9900..9d8cad2 100644
--- a/src/argaze/GazeAnalysis/DispersionThresholdIdentification.py
+++ b/src/argaze/GazeAnalysis/DispersionThresholdIdentification.py
@@ -143,10 +143,6 @@ class GazeMovementIdentifier(GazeFeatures.GazeMovementIdentifier):
         self.__saccade_positions = GazeFeatures.TimeStampedGazePositions()
 
     def identify(self, ts, gaze_position, terminate=False) -> GazeMovementType:
-        """Identify gaze movement from successive timestamped gaze positions.
-
-            The optional *terminate* argument allows to notify identification algorithm that given gaze position will be the last one.
-        """
 
         # Ignore non valid gaze position
         if not gaze_position.valid:
diff --git a/src/argaze/GazeAnalysis/Entropy.py b/src/argaze/GazeAnalysis/Entropy.py
index f248845..631a8ea 100644
--- a/src/argaze/GazeAnalysis/Entropy.py
+++ b/src/argaze/GazeAnalysis/Entropy.py
@@ -38,7 +38,6 @@ class AOIScanPathAnalyzer(GazeFeatures.AOIScanPathAnalyzer):
         self.__transition_entropy = -1
 
     def analyze(self, aoi_scan_path: GazeFeatures.AOIScanPathType):
-        """Analyze aoi scan path."""
 
         assert(len(aoi_scan_path) > 1)
 
diff --git a/src/argaze/GazeAnalysis/ExploreExploitRatio.py b/src/argaze/GazeAnalysis/ExploreExploitRatio.py
index b4550e7..b66076b 100644
--- a/src/argaze/GazeAnalysis/ExploreExploitRatio.py
+++ b/src/argaze/GazeAnalysis/ExploreExploitRatio.py
@@ -34,7 +34,6 @@ class ScanPathAnalyzer(GazeFeatures.ScanPathAnalyzer):
         self.__explore_exploit_ratio = 0.
 
     def analyze(self, scan_path: GazeFeatures.ScanPathType):
-        """Analyze scan path."""
 
         assert(len(scan_path) > 1)
 
diff --git a/src/argaze/GazeAnalysis/FocusPointInside.py b/src/argaze/GazeAnalysis/FocusPointInside.py
index 81a9d20..e7da766 100644
--- a/src/argaze/GazeAnalysis/FocusPointInside.py
+++ b/src/argaze/GazeAnalysis/FocusPointInside.py
@@ -26,7 +26,6 @@ class AOIMatcher(GazeFeatures.AOIMatcher):
     """Matching algorithm based on fixation's focus point."""
 
     def __post_init__(self):
-        """Init looked aoi data."""
 
         self.__looked_aoi_data = (None, None)
         self.__matched_gaze_movement = None
@@ -91,12 +90,12 @@ class AOIMatcher(GazeFeatures.AOIMatcher):
 
     @property
     def looked_aoi(self) -> AOIFeatures.AreaOfInterest:
-        """Get most likely looked aoi for current fixation (e.g. the aoi with the highest coverage mean value)"""
+        """Get most likely looked aoi for current fixation."""
 
         return self.__looked_aoi_data[1]
 
     @property
     def looked_aoi_name(self) -> str:
-        """Get most likely looked aoi name for current fixation (e.g. the aoi with the highest coverage mean value)"""
+        """Get most likely looked aoi name for current fixation."""
 
         return self.__looked_aoi_data[0]
\ No newline at end of file
diff --git a/src/argaze/GazeAnalysis/KCoefficient.py b/src/argaze/GazeAnalysis/KCoefficient.py
index c50bc3a..c8fa398 100644
--- a/src/argaze/GazeAnalysis/KCoefficient.py
+++ b/src/argaze/GazeAnalysis/KCoefficient.py
@@ -31,7 +31,6 @@ class ScanPathAnalyzer(GazeFeatures.ScanPathAnalyzer):
         self.__K = 0
 
     def analyze(self, scan_path: GazeFeatures.ScanPathType):
-        """Analyze scan path."""
 
         assert(len(scan_path) > 1)
 
@@ -88,7 +87,6 @@ class AOIScanPathAnalyzer(GazeFeatures.AOIScanPathAnalyzer):
         self.__K = 0
 
     def analyze(self, aoi_scan_path: GazeFeatures.AOIScanPathType) -> float:
-        """Analyze aoi scan path."""
 
         assert(len(aoi_scan_path) > 1)
 
diff --git a/src/argaze/GazeAnalysis/LempelZivComplexity.py b/src/argaze/GazeAnalysis/LempelZivComplexity.py
index 50c7a90..552ad75 100644
--- a/src/argaze/GazeAnalysis/LempelZivComplexity.py
+++ b/src/argaze/GazeAnalysis/LempelZivComplexity.py
@@ -32,7 +32,6 @@ class AOIScanPathAnalyzer(GazeFeatures.AOIScanPathAnalyzer):
         self.__lempel_ziv_complexity = 0
 
     def analyze(self, aoi_scan_path: GazeFeatures.AOIScanPathType):
-        """Analyze aoi scan path."""
 
         assert(len(aoi_scan_path) > 1)
 
diff --git a/src/argaze/GazeAnalysis/LinearRegression.py b/src/argaze/GazeAnalysis/LinearRegression.py
index 9315751..414832a 100644
--- a/src/argaze/GazeAnalysis/LinearRegression.py
+++ b/src/argaze/GazeAnalysis/LinearRegression.py
@@ -37,7 +37,6 @@ class GazePositionCalibrator(GazeFeatures.GazePositionCalibrator):
     """Linear regression intercept value"""
 
     def __post_init__(self):
-        """Init calibration."""
 
         self.__linear_regression = LinearRegression()
         self.__linear_regression.coef_ = numpy.array(self.coefficients)
diff --git a/src/argaze/GazeAnalysis/NGram.py b/src/argaze/GazeAnalysis/NGram.py
index a19974a..903c0c0 100644
--- a/src/argaze/GazeAnalysis/NGram.py
+++ b/src/argaze/GazeAnalysis/NGram.py
@@ -36,7 +36,6 @@ class AOIScanPathAnalyzer(GazeFeatures.AOIScanPathAnalyzer):
         self.__ngrams_count = {}
 
     def analyze(self, aoi_scan_path: GazeFeatures.AOIScanPathType):
-        """Analyze aoi scan path."""
 
         assert(len(aoi_scan_path) > 1)
 
diff --git a/src/argaze/GazeAnalysis/NearestNeighborIndex.py b/src/argaze/GazeAnalysis/NearestNeighborIndex.py
index 34432ad..1ca336f 100644
--- a/src/argaze/GazeAnalysis/NearestNeighborIndex.py
+++ b/src/argaze/GazeAnalysis/NearestNeighborIndex.py
@@ -36,7 +36,6 @@ class ScanPathAnalyzer(GazeFeatures.ScanPathAnalyzer):
         self.__nearest_neighbor_index = 0
 
     def analyze(self, scan_path: GazeFeatures.ScanPathType):
-        """Analyze scan path."""
 
         assert(len(scan_path) > 1)
 
diff --git a/src/argaze/GazeAnalysis/TransitionMatrix.py b/src/argaze/GazeAnalysis/TransitionMatrix.py
index b346b5a..5e3bdf5 100644
--- a/src/argaze/GazeAnalysis/TransitionMatrix.py
+++ b/src/argaze/GazeAnalysis/TransitionMatrix.py
@@ -34,7 +34,6 @@ class AOIScanPathAnalyzer(GazeFeatures.AOIScanPathAnalyzer):
         self.__transition_matrix_density = 0.
 
     def analyze(self, aoi_scan_path: GazeFeatures.AOIScanPathType):
-        """Analyze aoi scan path."""
 
         assert(len(aoi_scan_path) > 1)
 
diff --git a/src/argaze/GazeAnalysis/VelocityThresholdIdentification.py b/src/argaze/GazeAnalysis/VelocityThresholdIdentification.py
index d10f666..e9f770a 100644
--- a/src/argaze/GazeAnalysis/VelocityThresholdIdentification.py
+++ b/src/argaze/GazeAnalysis/VelocityThresholdIdentification.py
@@ -143,10 +143,6 @@ class GazeMovementIdentifier(GazeFeatures.GazeMovementIdentifier):
         self.__saccade_positions = GazeFeatures.TimeStampedGazePositions()
 
     def identify(self, ts, gaze_position, terminate=False) -> GazeMovementType:
-        """Identify gaze movement from successive timestamped gaze positions.
-
-            The optional *terminate* argument allows to notify identification algorithm that given gaze position will be the last one.
-        """
 
         # Ignore non valid gaze position
         if not gaze_position.valid:
-- 
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