Differences

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--- downloads:3dtrackviewer [2012/06/29 21:35] – example data added kota
+++ downloads:3dtrackviewer [2016/05/24 12:46] (current) – external edit 127.0.0.1
@@ Line 14: / Line 14: @@
   * 2012-04-23 First Version
+  * 2012-07-11 2nd version
-  * recent log
+    * new: single track extractor to evaluate tracks by comparing to the volume rendering of the original stack.
+    * new: Capability to use track color-coding from the output of MTrackJ. FOr using the output of MTrackJ, another jython script that converts the data structure is required (description will be added later).
+  * recent log in detail
 {{rss>https://github.com/cmci/3Dviewer_TrackVisualization/commits/simple.atom 10 date 12h}}
@@ Line 29: / Line 31: @@
 Download the plugin using this link:
-  * [[https://github.com/cmci/3Dviewer_TrackVisualization/blob/simple/Plot_4D.jar?raw=true|Plot_4D.jar]]
+  * [[https://github.com/cmci/3Dviewer_TrackVisualization/blob/simple/target/3Dtrack_viewer-1.0.0.jar?raw=true|3Dtrack_viewer-1.0.0.jar]]
 The plugin will appear under the following menu tree: [Plugins -> EMBLTools -> 4D track Plotter].
@@ Line 35: / Line 37: @@
 ===== Description =====
-This 3D visualization tool is an extended functionality for [[http://3dviewer.neurofly.de/|3D viewer plugin written by Bene Schmid]] for plotting 3D track data for evaluation of the tracking quality. Source data should be a CSV file with the following column order:
+This 3D visualization tool is an extended functionality for [[http://3dviewer.neurofly.de/|3D viewer plugin written by Bene Schmid]] for plotting 3D track data for evaluation of the tracking quality. Source data should be a CSV file with the following column order (see the example below):
 index - trackID - frame - x - y - z - scaled x - scaled y - scaled z  - particleID
@@ Line 41: / Line 43: @@
 [{{ :documents:downloadimg:3dtrackviewer_gui.png?400 |3D track viewer, GUI}}]
-===== an example of coordinate data =====
+==== workflow ====
+  - Click "Choose Track File" and select your csv file with track data.
+  - Decide if you would like to visualize tracks as a static 3D path, or dynamic 4D path ("Dynamic").
+    - 4D path consumes memory. If your machine does not have enough memory or CPU power, you might need to wait for a very long time if your data is large.
+   - Decide if you want to also see path nodes.
+   - Activate the checkbox according to your decision.
+     - 4D path / nodes cannot be visualized together with 3D path and vice versa.
+   - click "plot".
+=== MTrackJ file  ===
+For loading MTrackJ output file, the file should first be converted using [[https://github.com/cmci/ijmacros/blob/master/dataconvert/MTrackJ23Dviewer.py|this file]]. The resulting converted text file has an extra column that defines the color for each tracks.
+==== Example of coordinate data ====
+Below is an example of data file that could be loaded from 3D tracker viewer. SXpos,SYpos &SZpos are the columns of 3D coordinates that will be used for the plotting. S stands for scaled.
 <code>