Fixing code annotation. Removing useless documentation section. Fixing documentation cross reference.

4 files changed, 0 insertions, 437 deletions

diff --git a/docs/user_guide/gaze_analysis/gaze_movement.md b/docs/user_guide/gaze_analysis/gaze_movement.md
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-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.md/#argaze.GazeFeatures) defines abstract [GazeMovement](../../argaze.md/#argaze.GazeFeatures.GazeMovement) class, then abstract [Fixation](../../argaze.md/#argaze.GazeFeatures.Fixation) and [Saccade](../../argaze.md/#argaze.GazeFeatures.Saccade) classes which inherit from [GazeMovement](../../argaze.md/#argaze.GazeFeatures.GazeMovement).
-
-The **positions** [GazeMovement](../../argaze.md/#argaze.GazeFeatures.GazeMovement) attribute contain all [GazePositions](../../argaze.md/#argaze.GazeFeatures.GazePosition) belonging to itself.
-
-![Fixation and Saccade](../../img/fixation_and_saccade.png)
-
-## Identification
-
-[GazeFeatures](../../argaze.md/#argaze.GazeFeatures) defines abstract [GazeMovementIdentifier](../../argaze.md/#argaze.GazeFeatures.GazeMovementIdentifier) classe to let add various identification algorithms.
-
-Some gaze movement identification algorithms are available thanks to [GazeAnalysis](../../argaze.md/#argaze.GazeAnalysis) submodule:
-
-* [Dispersion threshold identification (I-DT)](../../argaze.md/#argaze.GazeAnalysis.DispersionThresholdIdentification)
-* [Velocity threshold identification (I-VT)](../../argaze.md/#argaze.GazeAnalysis.VelocityThresholdIdentification)
-
-### Identify method
-
-[GazeMovementIdentifier.identify](../../argaze.md/#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](../../argaze.md/#argaze.GazeAnalysis.DispersionThresholdIdentification) 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.browse](../../argaze.md/#argaze.GazeFeatures.GazeMovementIdentifier.browse) method allows to pass a [TimeStampedGazePositions](../../argaze.md/#argaze.GazeFeatures.TimeStampedGazePositions) buffer to apply identification algorithm on all gaze positions inside.
-
-Identified gaze movements are returned through:
-
-* [TimeStampedGazeMovements](../../argaze.md/#argaze.GazeFeatures.TimeStampedGazeMovements) instance where all fixations are stored by starting gaze position timestamp.
-* [TimeStampedGazeMovements](../../argaze.md/#argaze.GazeFeatures.TimeStampedGazeMovements) instance where all saccades are stored by starting gaze position timestamp.
-* [TimeStampedGazeStatus](../../argaze.md/#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.md/#argaze.GazeFeatures.TimeStampedGazeMovements), [TimeStampedGazeMovements](../../argaze.md/#argaze.GazeFeatures.TimeStampedGazeMovements) and [TimeStampedGazeStatus](../../argaze.md/#argaze.GazeFeatures.TimeStampedGazeStatus) classes inherit from [TimeStampedBuffer](../../argaze.md/#argaze.DataStructures.TimeStampedBuffer) class. 
-
-        Read [Timestamped data](../timestamped_data/introduction.md) section to understand all features it provides.
-
-### Generator method
-
-[GazeMovementIdentifier](../../argaze.md/#argaze.GazeFeatures.GazeMovementIdentifier) can be called with a [TimeStampedGazePositions](../../argaze.md/#argaze.GazeFeatures.TimeStampedGazePositions) buffer in argument to generate gaze movement each time one is identified.
-
-``` python
-# Assuming that timestamped gaze positions are provided through data reading
-
-for ts, gaze_movement in gaze_movement_identifier(ts_gaze_positions):
-
-        # Fixation identified
-        if GazeFeatures.is_fixation(gaze_movement):
-
-                # Do something with each fixation
-                ...
-
-        # Saccade identified
-        elif GazeFeatures.is_saccade(gaze_movement):
-
-                # Do something with each saccade
-                ...
-```
\ No newline at end of file
diff --git a/docs/user_guide/gaze_analysis/gaze_position.md b/docs/user_guide/gaze_analysis/gaze_position.md
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-Gaze position
-=============
-
-[GazeFeatures](../../argaze.md/#argaze.GazeFeatures) defines a [GazePosition](../../argaze.md/#argaze.GazeFeatures.GazePosition) class to handle point coordinates with a precision value.
-
-``` python
-from argaze import GazeFeatures
-
-# Define a basic gaze position
-gaze_position = GazeFeatures.GazePosition((123, 456))
-
-# Define a gaze position with a precision value
-gaze_position = GazeFeatures.GazePosition((789, 765), precision=10)
-
-# Access to gaze position value and precision
-print(f'position: {gaze_position.value}')
-print(f'precision: {gaze_position.precision}')
-
-```
-
-## Validity
-
-[GazeFeatures](../../argaze.md/#argaze.GazeFeatures) defines also a [UnvalidGazePosition](../../argaze.md/#argaze.GazeFeatures.UnvalidGazePosition) class that inherits from [GazePosition](../../argaze.md/#argaze.GazeFeatures.GazePosition) to handle case where no gaze position exists because of any specific device reason.
-
-``` python
-from argaze import GazeFeatures
-
-# Define a basic unvalid gaze position
-gaze_position = GazeFeatures.UnvalidGazePosition()
-
-# Define a basic unvalid gaze position with a message value
-gaze_position = GazeFeatures.UnvalidGazePosition("Something bad happened")
-
-# Access to gaze position validity
-print(f'validity: {gaze_position.valid}')
-
-```
-
-## Distance
-
-[GazePosition](../../argaze.md/#argaze.GazeFeatures.GazePosition) class provides a **distance** method to calculate the distance to another gaze position instance.
-
-![Distance](../../img/distance.png)
-
-``` python
-# Distance between A and B positions
-d = gaze_position_A.distance(gaze_position_B)
-``` 
-
-## Overlapping
-
-[GazePosition](../../argaze.md/#argaze.GazeFeatures.GazePosition) class provides an **overlap** method to test if a gaze position overlaps another one considering their precisions.
-
-![Gaze overlapping](../../img/overlapping.png)
-
-``` python
-# Check that A overlaps B
-if gaze_position_A.overlap(gaze_position_B): 
-
-        # Do something if A overlaps B
-        ...
-
-# Check that A overlaps B and B overlaps A
-if gaze_position_A.overlap(gaze_position_B, both=True): 
-
-        # Do something if A overlaps B AND B overlaps A
-        ...
-```
-
-## Timestamped gaze positions
-
-[TimeStampedGazePositions](../../argaze.md/#argaze.GazeFeatures.TimeStampedGazePositions) inherits from [TimeStampedBuffer](../../argaze.md/#argaze.DataStructures.TimeStampedBuffer) class to handle especially gaze positions.
-
-### Import from dataframe
-
-It is possible to load timestamped gaze positions from a [Pandas DataFrame](https://pandas.pydata.org/docs/getting_started/intro_tutorials/01_table_oriented.html#min-tut-01-tableoriented) object.
-
-```python
-import pandas
-
-# Load gaze positions from a CSV file into Panda Dataframe
-dataframe = pandas.read_csv('gaze_positions.csv', delimiter="\t", low_memory=False)
-
-# Convert Panda dataframe into TimestampedGazePositions buffer precising the use of each specific column labels
-ts_gaze_positions = GazeFeatures.TimeStampedGazePositions.from_dataframe(dataframe, timestamp = 'Recording timestamp [ms]', x = 'Gaze point X [px]', y = 'Gaze point Y [px]')
-
-```
-### Iterator
-
-Like [TimeStampedBuffer](../../argaze.md/#argaze.DataStructures.TimeStampedBuffer), [TimeStampedGazePositions](../../argaze.md/#argaze.GazeFeatures.TimeStampedGazePositions) class provides iterator feature:
-
-```python
-for timestamp, gaze_position in ts_gaze_positions.items():
-
-        # Do something with each gaze position
-        ...
-
-```
diff --git a/docs/user_guide/gaze_analysis/introduction.md b/docs/user_guide/gaze_analysis/introduction.md
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-Gaze analysis
-=============
-
-This section refers to:
-
-* [GazeFeatures](../../argaze.md/#argaze.GazeFeatures)
-* [GazeAnalysis](../../argaze.md/#argaze.GazeAnalysis)
\ No newline at end of file
diff --git a/docs/user_guide/gaze_analysis/scan_path.md b/docs/user_guide/gaze_analysis/scan_path.md
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--- a/docs/user_guide/gaze_analysis/scan_path.md
+++ /dev/null
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-Scan path
-=========
-
-[GazeFeatures](../../argaze.md/#argaze.GazeFeatures) defines classes to handle successive fixations/saccades and analyse their spatial or temporal properties.
-
-## Fixation based scan path
-
-### Definition
-
-The [ScanPath](../../argaze.md/#argaze.GazeFeatures.ScanPath) class is defined as a list of [ScanSteps](../../argaze.md/#argaze.GazeFeatures.ScanStep) which are defined as a fixation and a consecutive saccade.
-
-![Fixation based scan path](../../img/scan_path.png)
-
-As fixations and saccades are identified, the scan path is built by calling respectively [append_fixation](../../argaze.md/#argaze.GazeFeatures.ScanPath.append_fixation) and [append_saccade](../../argaze.md/#argaze.GazeFeatures.ScanPath.append_saccade) methods.
-
-### Analysis
-
-[GazeFeatures](../../argaze.md/#argaze.GazeFeatures) defines abstract [ScanPathAnalyzer](../../argaze.md/#argaze.GazeFeatures.ScanPathAnalyzer) classe to let add various analysis algorithms.
-
-Some scan path analysis are available thanks to [GazeAnalysis](../../argaze.md/#argaze.GazeAnalysis) submodule:
-
-* [K-Coefficient](../../argaze.md/#argaze.GazeAnalysis.KCoefficient)
-* [Nearest Neighbor Index](../../argaze.md/#argaze.GazeAnalysis.NearestNeighborIndex)
-* [Exploit Explore Ratio](../../argaze.md/#argaze.GazeAnalysis.ExploitExploreRatio)
-
-### Example
-
-Here is a sample of code to illustrate how to built a scan path and analyze it:
-
-``` python
-from argaze import GazeFeatures
-from argaze.GazeAnalysis import KCoefficient
-
-# Create a empty scan path
-scan_path = GazeFeatures.ScanPath()
-
-# Create a K coefficient analyzer
-kc_analyzer = KCoefficient.ScanPathAnalyzer()
-
-# Assuming a gaze movement is identified at ts time
-...:
-
-        # Fixation identified
-        if GazeFeatures.is_fixation(gaze_movement):
-
-            # Append fixation to scan path : no step is created
-            scan_path.append_fixation(ts, gaze_movement)
-
-        # Saccade identified
-        elif GazeFeatures.is_saccade(gaze_movement):
-
-            # Append saccade to scan path : a new step should be created
-            new_step = scan_path.append_saccade(data_ts, gaze_movement)
-
-            # Analyse scan path
-            if new_step:
-
-                K = kc_analyzer.analyze(scan_path)
-
-                # Do something with K metric
-                ...
-```
-
-## AOI based scan path
-
-### Definition
-
-The [AOIScanPath](../../argaze.md/#argaze.GazeFeatures.AOIScanPath) class is defined as a list of [AOIScanSteps](../../argaze.md/#argaze.GazeFeatures.AOIScanStep) which are defined as set of consecutives fixations looking at a same Area Of Interest (AOI) and a consecutive saccade.
-
-![AOI based scan path](../../img/aoi_scan_path.png)
-
-As fixations and saccades are identified, the scan path is built by calling respectively [append_fixation](../../argaze.md/#argaze.GazeFeatures.AOIScanPath.append_fixation) and [append_saccade](../../argaze.md/#argaze.GazeFeatures.AOIScanPath.append_saccade) methods.
-
-### Analysis
-
-[GazeFeatures](../../argaze.md/#argaze.GazeFeatures) defines abstract [AOIScanPathAnalyzer](../../argaze.md/#argaze.GazeFeatures.AOIScanPathAnalyzer) classe to let add various analysis algorithms.
-
-Some scan path analysis are available thanks to [GazeAnalysis](../../argaze.md/#argaze.GazeAnalysis) submodule:
-
-* [Transition matrix](../../argaze.md/#argaze.GazeAnalysis.TransitionMatrix)
-* [Entropy](../../argaze.md/#argaze.GazeAnalysis.Entropy)
-* [Lempel-Ziv complexity](../../argaze.md/#argaze.GazeAnalysis.LempelZivComplexity)
-* [N-Gram](../../argaze.md/#argaze.GazeAnalysis.NGram)
-* [K-modified coefficient](../../argaze.md/#argaze.GazeAnalysis.KCoefficient)
-
-### Example
-
-Here is a sample of code to illustrate how to built a AOI scan path and analyze it:
-
-``` python
-from argaze import GazeFeatures
-from argaze.GazeAnalysis import LempelZivComplexity
-
-# Assuming all AOI names are listed
-...
-
-# Create a empty AOI scan path
-aoi_scan_path = GazeFeatures.AOIScanPath(aoi_names)
-
-# Create a Lempel-Ziv complexity analyzer
-lzc_analyzer = LempelZivComplexity.AOIScanPathAnalyzer()
-
-# Assuming a gaze movement is identified at ts time
-...:
-
-        # Fixation identified
-        if GazeFeatures.is_fixation(gaze_movement):
-
-            # Assuming fixation is detected as inside an AOI
-            ...
-
-            # Append fixation to AOI scan path : a new step should be created
-            new_step = aoi_scan_path.append_fixation(ts, gaze_movement, looked_aoi_name)
-
-            # Analyse AOI scan path
-            if new_step:
-
-                LZC = kc_analyzer.analyze(aoi_scan_path)
-
-                # Do something with LZC metric
-                ...
-
-        # Saccade identified
-        elif GazeFeatures.is_saccade(gaze_movement):
-
-            # Append saccade to scan path : no step is created
-            aoi_scan_path.append_saccade(data_ts, gaze_movement)
-
-```
-
-### Advanced
-
-The [AOIScanPath](../../argaze.md/#argaze.GazeFeatures.AOIScanPath) class provides some advanced features to analyse it.
-
-#### Letter sequence
-
-When a new [AOIScanStep](../../argaze.md/#argaze.GazeFeatures.AOIScanStep) is created, the [AOIScanPath](../../argaze.md/#argaze.GazeFeatures.AOIScanPath) internally affects a unique letter index related to its AOI to ease pattern analysis.
-Then, the [AOIScanPath letter_sequence](../../argaze.md/#argaze.GazeFeatures.AOIScanPath.letter_sequence) property returns the concatenation of each [AOIScanStep](../../argaze.md/#argaze.GazeFeatures.AOIScanStep) letter.
-The [AOIScanPath get_letter_aoi](../../argaze.md/#argaze.GazeFeatures.AOIScanPath.get_letter_aoi) method helps to get back the AOI related to a letter index.
-
-``` python
-# Assuming the following AOI scan path is built: Foo > Bar > Shu > Foo
-aoi_scan_path = ...
-
-# Letter sequence representation should be: 'ABCA'
-print(aoi_scan_path.letter_sequence)
-
-# Output should be: 'Bar'
-print(aoi_scan_path.get_letter_aoi('B'))
-
-```
-
-#### Transition matrix
-
-When a new [AOIScanStep](../../argaze.md/#argaze.GazeFeatures.AOIScanStep) is created, the [AOIScanPath](../../argaze.md/#argaze.GazeFeatures.AOIScanPath) internally counts the number of transitions from an AOI to another AOI to ease Markov chain analysis.
-Then, the [AOIScanPath transition_matrix](../../argaze.md/#argaze.GazeFeatures.AOIScanPath.transition_matrix) property returns a [Pandas DataFrame](https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.html) where indexes are transition departures and columns are transition destinations.
-
-Here is an exemple of transition matrix for the following [AOIScanPath](../../argaze.md/#argaze.GazeFeatures.AOIScanPath): Foo > Bar > Shu > Foo > Bar
-
-|   |Foo|Bar|Shu|
-|:--|:--|:--|:--|
-|Foo|0  |2  |0  |
-|Bar|0  |0  |1  |
-|Shu|1  |0  |0  |
-
-
-#### Fixations count
-
-The [AOIScanPath fixations_count](../../argaze.md/#argaze.GazeFeatures.AOIScanPath.fixations_count) method returns the total number of fixations in the whole scan path and a dictionary to get the fixations count per AOI.