Writing User guide and use cases section.

1 files changed, 141 insertions, 0 deletions

diff --git a/docs/user_guide/gaze_analysis/gaze_movement.md b/docs/user_guide/gaze_analysis/gaze_movement.md
new file mode 100644
index 0000000..6c7ab76
--- /dev/null
+++ b/docs/user_guide/gaze_analysis/gaze_movement.md
@@ -0,0 +1,141 @@
+Gaze movement
+=============
+
+## Definition
+
+!!! note
+
+        *"The act of classifying eye movements into distinct events is, on a general level, driven by a desire to isolate different intervals of the data stream strongly correlated with certain oculomotor or cognitive properties."* 
+
+        Citation from ["One algorithm to rule them all? An evaluation and discussion of ten eye movement event-detection algorithms"](https://link.springer.com/article/10.3758/s13428-016-0738-9) article.
+
+[GazeFeatures](/argaze/#argaze.GazeFeatures) defines abstract [GazeMovement](/argaze/#argaze.GazeFeatures.GazeMovement) class, then abstract [Fixation](/argaze/#argaze.GazeFeatures.Fixation) and [Saccade](/argaze/#argaze.GazeFeatures.Saccade) classes which inherit from [GazeMovement](/argaze/#argaze.GazeFeatures.GazeMovement).
+
+The **positions** [GazeMovement](/argaze/#argaze.GazeFeatures.GazeMovement) attribute contain all [GazePositions](/argaze/#argaze.GazeFeatures.GazePosition) belonging to itself.
+
+![Fixation and Saccade](../../img/fixation_and_saccade.png)
+
+## Identification
+
+[GazeFeatures](/argaze/#argaze.GazeFeatures) defines abstract [GazeMovementIdentifier](/argaze/#argaze.GazeFeatures.GazeMovementIdentifier) classe to let add various identification algorithms.
+
+Some gaze movement identification algorithms are available thanks to [GazeAnalysis](/argaze/#argaze.GazeAnalysis) submodule:
+
+* [Dispersion threshold identification (I-DT)](/argaze/#argaze.GazeAnalysis.DispersionThresholdIdentification)
+* [Velocity threshold identification (I-VT)](/argaze/#argaze.GazeAnalysis.VelocityThresholdIdentification)
+
+### Identify method
+
+[GazeMovementIdentifier](/argaze/#argaze.GazeFeatures.GazeMovementIdentifier) **identify** method allows to fed its identification algorithm with successive gaze positions to output Fixation, Saccade or any kind of GazeMovement instances.
+
+Here is a sample of code based on I-DT algorithm to illustrate how to use it:
+
+``` python
+from argaze import GazeFeatures
+from argaze.GazeAnalysis import DispersionThresholdIdentification
+
+# Create a gaze movement identifier based on dispersion algorithm with 50px max deviation 200 ms max duration thresholds
+gaze_movement_identifier = DispersionThresholdIdentification.GazeMovementIdentifier(50, 200)
+
+# Assuming that timestamped gaze positions are provided through live stream or later data reading
+...:
+
+        gaze_movement = gaze_movement_identifier.identify(timestamp, gaze_position)
+
+        # Fixation identified
+        if GazeFeatures.is_fixation(gaze_movement):
+
+                # Access to first gaze position of identified fixation
+                start_ts, start_position = gaze_movement.positions.first
+
+                # Access to fixation duration
+                print('duration: {gaze_movement.duration}')
+
+                # Iterate over all gaze positions of identified fixation
+                for ts, position in gaze_movement.positions.items():
+
+                        # Do something with each fixation position
+                        ...
+
+        # Saccade identified
+        elif GazeFeatures.is_saccade(gaze_movement):
+
+                # Access to first gaze position of identified saccade
+                start_ts, start_position = gaze_movement.positions.first
+
+                # Access to saccade amplitude
+                print('amplitude: {gaze_movement.amplitude}')
+
+                # Iterate over all gaze positions of identified saccade
+                for ts, position in gaze_movement.positions.items():
+
+                        # Do something with each saccade position
+                        ...
+
+        # No gaze movement identified
+        else:
+
+                continue
+
+```
+
+### Browse method
+
+[GazeMovementIdentifier](/argaze/#argaze.GazeFeatures.GazeMovementIdentifier) **browse** method allows to pass a TimeStampedGazePositions buffer to apply identification algorithm on all gaze positions inside.
+
+Identified gaze movements are returned through:
+
+* [TimeStampedGazeMovements](/argaze/#argaze.GazeFeatures.TimeStampedGazeMovements) instance where all fixations are stored by starting gaze position timestamp.
+* [TimeStampedGazeMovements](/argaze/#argaze.GazeFeatures.TimeStampedGazeMovements) instance where all saccades are stored by starting gaze position timestamp.
+* [TimeStampedGazeStatus](/argaze/#argaze.GazeFeatures.TimeStampedGazeStatus) instance where all gaze positions are linked to a fixation or saccade index.
+
+``` python
+# Assuming that timestamped gaze positions are provided through data reading
+
+ts_fixations, ts_saccades, ts_status = gaze_movement_identifier.browse(ts_gaze_positions)
+
+```
+
+* ts_fixations would look like:
+
+|timestamp|positions                                                     |duration|dispersion|focus    |
+|:--------|:-------------------------------------------------------------|:-------|:---------|:--------|
+|60034    |{"60034":[846,620], "60044":[837,641], "60054":[835,649], ...}|450     |40        |(840,660)|
+|60504    |{"60504":[838,667], "60514":[838,667], "60524":[837,669], ...}|100     |38        |(834,651)|
+|...      |...                                                           |...     |..        |...      |
+
+* ts_saccades would look like:
+
+|timestamp|positions                               |duration|
+|:--------|:---------------------------------------|:-------|
+|60484    |{"60484":[836, 669], "60494":[837, 669]}|10      |
+|60594    |{"60594":[833, 613], "60614":[927, 601]}|20      |
+|...      |...                                     |...     |
+
+* ts_status would look like:
+
+|timestamp|position  |type    |index|
+|:--------|:---------|:-------|:----|
+|60034    |(846, 620)|Fixation|1    |
+|60044    |(837, 641)|Fixation|1    |
+|...      |...       |...     |.    |
+|60464    |(836, 668)|Fixation|1    |
+|60474    |(836, 668)|Fixation|1    |
+|60484    |(836, 669)|Saccade |1    |
+|60494    |(837, 669)|Saccade |1    |
+|60504    |(838, 667)|Fixation|2    |
+|60514    |(838, 667)|Fixation|2    |
+|...      |...       |...     |.    |
+|60574    |(825, 629)|Fixation|2    |
+|60584    |(829, 615)|Fixation|2    |
+|60594    |(833, 613)|Saccade |2    |
+|60614    |(927, 601)|Saccade |2    |
+|60624    |(933, 599)|Fixation|3    |
+|60634    |(934, 603)|Fixation|3    |
+|...      |...       |...     |.    |
+
+
+!!! note
+        [TimeStampedGazeMovements](/argaze/#argaze.GazeFeatures.TimeStampedGazeMovements), [TimeStampedGazeMovements](/argaze/#argaze.GazeFeatures.TimeStampedGazeMovements) and [TimeStampedGazeStatus](/argaze/#argaze.GazeFeatures.TimeStampedGazeStatus) classes inherit from [TimeStampedBuffer](/argaze/#argaze.DataStructures.TimeStampedBuffer) class. 
+
+        Read [timestamped data] page to understand all features it provides.
\ No newline at end of file