[docs] global: update documentation

docs/user/dataOutput.md

@@ -9,7 +9,7 @@ After a tracking analysis (or an analysis preview), FastTrack saves several file
 * *tracking.txt*: the tracking result
 * *annotation.txt*: the annotation
 * *background.pgm*: the background image
-* *parameters.param*: the parameters used for the tracking
+* *cfg.toml*: the parameters used for the tracking
 
 The tracking result file is simply a text file with 20 columns separated by a '\t' character. This file can easily be loaded to subsequent analysis see [this example](http://www.fasttrack.sh/UserManual/blog/2019/06/21/Data-analysis-python/).
 

docs/user/parametersSelection.md

@@ -19,3 +19,35 @@ The detection parameters reject objects that are smaller or bigger than a certai
 Tracking parameters are mostly found by trials and errors. But some rules of thumbs can be applied. 
 
 **Spot to track** has to be set to **Body** for quasi-symmetric objects and low-resolution objects. For deformable objects with enough resolution, select **Head** or **Tail** according to the part that predicts best the traveling direction of the object.
+
+## Parameters file
+For each tracking analysis, FastTrack will save the parameters used in `cfg.toml` that can be reloaded in the software or in fasttrack_cli.
+Before FastTrack version 5.2.1, the software used to saved the parameters in `parameter.param`, these file can be converted as following (left: old file, right: new file):
+
+```
+                                      title = "FastTrack cfg""
+
+                                      [parameters]
+Light background = 0                  lightBack = 0
+Maximal size = 170                    maxArea = 170
+Maximal occlusion = 200               maxDist = 200
+Maximal time = 100                    maxTime = 100
+Background method = 1                 methBack = 1
+Minimal size = 50                     minArea = 50
+Morphological operation = 8           morph = 8
+Kernel type = 2                       morphSize = 2
+Kernel size = 0                       morphType = 0
+Number of images background = 20      nBack = 20
+Maximal angle = 90                    normAngle = 90
+Binary threshold = 60                 normArea = 0
+Normalization area = 0                normDist = 100
+Maximal length = 100                  normPerim = 0
+Normalization perimeter = 0           reg = 0
+Registration = 0                      regBack = 0
+Background registration method = 0    spot = 0
+Spot to track = 0                     thresh = 60
+ROI bottom x = 0                      xBottom = 0
+ROI top x = 0                         xTop = 0
+ROI bottom y = 0                      yBottom = 0
+ROI top y = 0                         yTop = 0
+```

docs/user/trackingCli.md

@@ -8,7 +8,7 @@ sidebar_label: Tracking CLI
 A command line interface is available for MacOs, Linux and by using WSL for Windows. It can be downloaded on [the release page](https://github.com/FastTrackOrg/FastTrack/releases/).
 
 The full list of parameters can be found by calling ```./fasttrack-cli --help```. 
-Parameters can be declared individually by calling ```./fasttrack-cli --path path/to/movie.webm --parameter1 value --parameter2 value``` or in batch with a parameters file ```./fasttrack-cli --path path/to/movie.webm --cfg path/parameters.param```. Note that the path option need to be the first option.
+Parameters can be declared individually by calling ```./fasttrack-cli --path path/to/movie.webm --parameter1 value --parameter2 value``` or in batch with a parameters file ```./fasttrack-cli --path path/to/movie.webm --cfg path/cfg.toml```. Note that the path option need to be the first option.
 
 fasttrack-cli doesn't support natively Windows. The workaround is to use WSL.
 * Install WSL https://docs.microsoft.com/en-us/windows/wsl/install-win10.
@@ -35,6 +35,6 @@ os.system(cmd)
 ```
 import os
 
-cmd = "./fasttrack-cli --path ZFJ_001.avi --cfg Tracking_Result_ZFJ_001/parameters.param"
+cmd = "./fasttrack-cli --path ZFJ_001.avi --cfg Tracking_Result_ZFJ_001/cfg.toml"
 os.system(cmd)
 ```