From 1ffaccf77133c10b42640d27702131e6c49da697 Mon Sep 17 00:00:00 2001 From: bgallois Date: Fri, 13 Nov 2020 19:53:23 +0100 Subject: [PATCH] [docs] global: update documentation --- docs/user/dataOutput.md | 2 +- docs/user/parametersSelection.md | 32 ++++++++++++++++++++++++++++++++ docs/user/trackingCli.md | 4 ++-- 3 files changed, 35 insertions(+), 3 deletions(-) diff --git a/docs/user/dataOutput.md b/docs/user/dataOutput.md index f8d11c2..ae3a2bf 100644 --- a/docs/user/dataOutput.md +++ b/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/). diff --git a/docs/user/parametersSelection.md b/docs/user/parametersSelection.md index 7e3b4e3..4afa51f 100644 --- a/docs/user/parametersSelection.md +++ b/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 +``` diff --git a/docs/user/trackingCli.md b/docs/user/trackingCli.md index e03ccb7..f2a9872 100644 --- a/docs/user/trackingCli.md +++ b/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) ```