TLS Seed Point Editor

Functional Overview

The TLS Seed Point Editor toolbar contains functions for checking the results of individual tree segmentation routines run on Terrestrial Laser Scan (TLS) input data. The TLS Editor is also used to extract Diameter at Breast Height (DBH) for individual trees, to add or delete seed points, to execute point cloud segmentation operations that include seed points, and to measure physical attributes of individual trees found in the source dataset. Since v3.2, the right-click shortcut menu is supported.

TLS Seed Point Editing Shortcuts

Usage

Load the point could data to be edited into the viewer and activate the view window.

Navigate to and click on TLS Forest > TLS Editor to load the TLS Seed Point Editor toolbar in the active view window.

TLS Seed Point Editor toolbar functions (from left to right): Start/End Edit, Open Seed Points File, Open/Close Trajectory File, Fit DBH, Batch Extraction of DBH, Add Seed Points, Delete Seed Points, Clear All Seeds, Profile, Pan Profile, Measure Individual Tree Attribute, Point Cloud Segmentation from Seed Points, Clear Tree ID, Filter by Elevation, Setting, and Exit.

Start/End Edit

To begin editing session navigate to and click on Editor > Start Edit.

Select the data to be edited, click "OK", a setting window will pop up, the user can set the displayed point cloud height, the default point cloud is 1.2-1.4m, the user can set whether to display the mouse position synchronously in the profile view. Other functions of the TLS seed point editor toolbar will become available.

In the process of editing, the selected data cannot be removed from the window. Click “End Edit” to complete the editing, and other functions in the toolbar will then be unavailable.

Open Seed Points File

Function Description: Select a seed point file (please refer to Seed Points File in the appendix) for the format of seed point file, and the window below will pop up. Please note that there is a header line in the seed point file, therefore, the first line should be ignored when the file is opened.

Save Seed Points File

Function Description:When editing is completed, the seed points can be saved as a new .csv file without overwriting the original file.

Open Trajectory File

Function Description: Load trajectory file, support the output trajectory file format (*.xyz) of LiBackpack series products.

Close Trajectory File

Function Description: Close the loaded trajectory file.

Fit DBH

Function Description: Select the desired individual tree for DBH fitting.

The picture below (left) is the result of selecting the point cloud data of an individual tree. The picture below (right) is the result of DBH fitting: 1 indicates ID number, 0.2030 is the fitted DBH value in meters.

Batch Extraction of DBH

Function Description: Select the point cloud data of multiple trees and then perform batch fitting of tree DBH (the parameter settings are shown as below). By default, the function uses the entire point cloud in the window for batch DBH fitting. Users can also select out a part of point cloud for fitting.

• Min Points Number (default value is "10"): Minimum threshold for the number of trees of each category. If the number is less than this value, then no DBH fitting will be conducted.
• Methods of Fitting DBH: Users can flexibly select the point cloud in a 2D window by setting a height or using the profile window for DBH fitting. Methods of fitting DBH include Fitting by Circle, Fitting by Column and Fitting by Ellipse. By default, the method of Fitting by Circle is adopted. If the tree is slanting, the Fitting by Cylinder method can be used.

• Fit Circle (Default): Use the least squares method to the fit a circle from the x-y coordinates of input points.
• Fit Column: Use the least squares method to fit a three-dimensional cylinder from input points where the diameter is the DBH of the tree.
• Fit Ellipse: Use the least squares method to fit an ellipse from the x-y coordinates of input points, and the DBH will be calculated as 2 sqrt（major axis minor axis). This method is for trees with an oval-shaped trunk.

The picture below (left) is the result of selecting the point cloud data of multiple trees. The picture below (right) is the result of DBH fitting: 1, 2, 3, 4, 5 and 6 indicate ID number, 0.1319, 0.1912, 0.1422, 0.1634, 0.1934, and 0.2274 are the fitted DBH value in meters.

Add Seed Points

Function Description: Interactively add seed points manually, support adding seed points in the edit window and profile window.

Delete Seed Points

Function Description: Delete the selected seed point data. Click this button, the selection tool dialog box will pop up, the user can select the appropriate selection tool (polygon selection, circle selection, rectangle selection tool) according to the needs, and pick a suitable area in the scene to delete the seed points in the area.

Note: Since version 5.0, the previous process of deleting seed points has been modified to simplify selecting and deleting seed points into one operation. After selecting a seed point, the selected seed point will be deleted immediately.

Clear All Seeds

Function Description: Clears all seed points in the window.

Profile

Function Description: When the TLS Editor toolbar is opened, the point cloud window will change to 2D display mode. The profile tool can show if the seed points are accurate in 3D. Click the Profile Tool button and a new window will appear. Click the mouse left button to select a polygon, and all points within the polygon will be displayed in the new window in 3D.

Note: Since version 5.0, the method of drawing the profile area has been modified as follows: click the left mouse button, drag and release the mouse to complete the drawing of the profile area.

Pan Profile

Function Description: After drawing the profile area in the main window, users can translate the profiled area by clicking this tool, and see the profile data in real-time.

Measure Individual Tree Attributes

Function Description

Click this *Measure Individual Tree Attributes* button on the toolbar to control whether to display the Measure Individual Tree Attribute window.

For descriptions of individual tree measurements, please refer to Individual Tree Attribute.

Point Cloud Segmentation from Seed Points

Function Description: Segment the point cloud data based on the edited seed points. Refer to PCS with Seeds. The tree heights will be recalculated after tree segmentation.

Clear Tree ID

Function Description: If the point cloud data has been segmented already, the TreeID should be removed prior to reperforming individual tree segmentation. Refer to Clear Tree ID.

Parameters Settings

Function Description: Includes seed point setting and height setting for point cloud display.

• DBH Configuration：
  • Minimum DBH (Meter) (Default Value is "0.05"): The minimum DBH value based on user's prior knowledge. If the DBH of a tree is smaller than this value, the fitted DBH will be treated as an error.
  • Maximum DBH (Meter) (Default Value is "1.00"): The maximum DBH value based on user's prior knowledge. If the DBH of a tree is larger than this value, the fitted DBH will be treated as an error.
  • Maximum Tree Inclination Angle (Degree)(Default Value is "30"): The maximum tree inclination angle based on user's prior knowledge. If the inclination angle of a tree is larger than this value, the corresponding points will not be treated as a tree. Note that this threshold is only effective to the method of Fit Column.

• Seed Setting: Seed point setting includes the color, alpha and size of the seed points, and whether the seed point ID and its label size are shown.

  • Color (Default Color is "Red"): Click , and then the dialog for selecting colors will pop up as shown below. Any color can be selected as the seed point color from this window.

    

  • Alpha (Default Value is "0.5"): Transparency of the seed point, ranging from 0 to 1, with 0 being completely transparent and 1 being opaque. The default value is 0.5. Click , and the value will be incremented or decremented by 0.1; or one can directly enter a specific value.

  • Display Label: Set if display the label of the Seed ID in the window.
  • Label Size (Default Value is "1")：The label size, ranging from [0, 100). Click , and the value will be incremented or decremented by 1; or you can directly enter a specific value.
  • Show Seed ID (Optional): Use the check box to determine if the seed point ID is displayed in the window.
  • Size (Default Value is "0.2"): The seed size, ranging from [0,100). Click , and the value will be incremented or decremented by 1; or one can directly enter a specific value.
• Confidence Level: Estimate the confidence level of batch fitted DBH values, and visualize the fitting results with different confidence levels using different user-defined colors.
  • Low Confidence Level: The DBH fitting results is poor, and users need to visually examine and edit the results to improve the fitting accuracy. Users can set the visualization color.
  • Medium Confidence Level: The DBH fitting results is medium, and users may need to visually examine and edit the results if necessary. Users can set the visualization color.
  • High Confidence Level: The DBH fitting results is very good. Note that if only a single tree was fitted, the default confident level will be set as high.

    Note that if the visualization height range is larger than 0.4 m when fitting the DBH in batch, LiDAR 360 will use a more strict method to estimate the confidence level. This method usually performed better for trees with a long trunk.

• Camera Distance of Profile View (Default Value is 20): When drawing a profile, the distance from the observation point to the display area of the profile window is convenient for users to view the editing area or editing effect according to the distance according to the job needs.

Filter by Elevation

Function Description: Point cloud display height and whether to show mouse position in profile viewer.

• Point Cloud Display Settings:
  • Position: The height of the point cloud in the profile viewer.
  • Buffer: The thichness of the point cloud in the profile viewer.
  • Show Mouse Position in Profile Viewer: When opening a profile, whether to display the real-time position of the mouse in the profile when the mouse moves in the profile window.

Note: The Ctrl_L + Mouse Wheel scrolling shortcut can only be used when the filter by elevation window is active, and the profile view is the current focus window. After closing the window, the parameters will keep as before it close.

Exit

Function Description: To exit TLS Seed Point Editor, click the exit button and a prompt window will pop up. Click “Yes” to close the TLS Seed Point Editor, or click “No” to return to the editor window.

Note: If the point cloud has been segmented, you need to Clear Tree ID before being segmented again. Otherwise, the message "All files have been segmented, please clear tree ID first!" will prompt.

Undo and Redo

Function Description: During the seed point editing process, if there is an editing error or misoperation, press [ctrl+z] to undo the operation, and press [ctrl+y] to resume the operation.

Note: In a seed point editing, the undo and redo functions are limited to 20 times respectively.

    @inproceedings{
        author={ Macdonald E, Mochan S},
        title={Protocol for stem straightness assessment in Sitka spruce},
        booktitle={Journal of Bacteriology,176(17):5578-82},
        year={2000}
    }