AMAPstudio-Scan expects you to load files in two stages :

• Stage 1: Load the file containing the original point cloud of the tree
• Stage 2: Load the topology file to be checked/corrected, resulting from an automatic topology detection program, having run on this point cloud.

Then, you will be able to use the tools provided by Scan to fix the topology interactively and save the corrected topology file.

To load the stage 1 file, used the command File > Load a Scan file x y z, separated by ,/;/space/tab

The expected file is called a 'Scan file', it is a point cloud file, i.e. a text file containing a line per point, with its properties in columns.

The separator between columns is a single character among these 4 propositions: ',', ';', a space or a tabulation

Only the 3 first columns will be read, they are expected to contain x, y and z of the point, in this order.

No header will be read. If the file contains a header, this can prevent Scan to recognize it, just add a comment mark: '#' at the beginning of the line and Scan will ignore it.

Exemple of correct formats :

# X Y Z
-0.32425001 13.35400009 8.87129974
-0.32045999 13.34899998 8.87180042
-0.30118999 13.33800030 8.88150024

-0.32425001 13.35400009 8.87129974
-0.32045999 13.34899998 8.87180042
-0.30118999 13.33800030 8.88150024

//X Y Z Rf Gf Bf V4 Original_cloud_index
-0.32425001 13.35400009 8.87129974 1 1 1 0.000000 0.000000
-0.32045999 13.34899998 8.87180042 1 1 1 0.000000 0.000000
-0.30118999 13.33800030 8.88150024 1 1 1 0.000000 0.000000

Once the Scan file loaded, you may import a topology file to be corrected, with one of the following commands of the 'File > Import a topology' menu.

SimpleTree is originally a standalone program by Jan Hackenberg, its resulting topology files can be imported for correction in Scan.

In is an example file, you can notice the columns separator is a ',' and the first line is a header which is needed here for interpreting this particular file (no comment mark at the start).

fileName , startX, startY, startZ, endX, endY, endZ, volume, radius, length, GrowthVolume, SegmentID, ParentSegmentID, BranchID, BranchOrder, median Radius Segment, volume to Root,  
noyer_restincliere.asc,7.86395,2.78193,0.1,7.88594,2.80018,-0.902789,0.0500025,0.125959,1.0032,0.206166,1,-1,0,0,0.0924166,0.169749
noyer_restincliere.asc,7.88594,2.80018,-0.902789,7.90793,2.81844,-0.528831,0.0189041,0.126666,0.375048,0.156164,1,-1,0,0,0.0924166,0.169749
noyer_restincliere.asc,7.90793,2.81844,-0.528831,7.91083,2.82404,-0.189481,0.0163395,0.123789,0.339409,0.137259,1,-1,0,0,0.0924166,0.169749
noyer_restincliere.asc,7.91083,2.82404,-0.189481,7.92758,2.80956,0.155308,0.0146546,0.116195,0.345499,0.12092,1,-1,0,0,0.0924166,0.169749
noyer_restincliere.asc,7.92758,2.80956,0.155308,7.93791,2.79541,0.47323,0.0136629,0.116871,0.318404,0.106265,1,-1,0,0,0.0924166,0.169749

The same file opened in a spreadsheet program:

SimpleTree has been reimplemented in Computree (ONF, Jan Hackenberg, Alexandre Piboule) and it generates a different file format.

Here the separator is a ';' and the header is also needed for interpreting the file (no comment mark at the start).

startX;startY;startZ;endX;endY;endZ;radius;segment_ID;parent_segment_ID;branch_ID
7.86395;2.78193	0.1;7.88594;2.80018;-0.902789;0.125959;1;-1;0
7.88594;2.80018;-0.902789;7.90793;2.81844;-0.528831;0.126666;1;-1;0

PlantScan3D (Frédéric Boudon, Cirad AGAP, Montpellier) exports its topology in MTG formats that can be read by AMAPstudio-Scan.

TreeQSM is a modelling method that reconstructs quantitative structure models (QSMs) of trees from point clouds. A QSM consists of a hierarchical collection of cylinders which estimate topological, geometrical and volumetric details of the woody structure of the tree (Pasi Raumonen, Tempere University, Finland).

Scan can read two file formats from TreeQSM, called '2016' (13 columns) and '2.3.2' (15 columns).

TreeQSM 2.3.2 example file (15 columns, tab separator between columns):

RADIUS 	LENGTH 	START_X 	START_Y 	START_Z 	AXIS_X	AXIS_Y 	AXIS_Z 	PARENT 	EXTENSION 	ADDED 	UNMOD_RADIUS 	BRANCH	BRANCH_ORDER	POSITION_IN_BRANCH
0.09210452	0.79527688	5.213797	7.483417	100.5459	-0.1848059	0.04393725	0.98179239	0	0	0	0	0	1	0
0.09210452	0.36797127	5.06682514	7.51835928	101.32669681	-0.12698812	-0.22686	0.96561305	1	0	0	0	0	1	0
0.09087759	0.20645586	5.02009716	7.43488131	101.68201468	0.02836803	0.18177487	0.9829309	2	0	0	0	0	1	0
0.09049156	0.20946892	5.0259539	7.4724098	101.88494653	0.12813252	0.1651372	0.97791194	3	0	0	0	0	1	0
0.08793977	0.21994007	5.05279368	7.50700091	102.08978868	-0.08169556	-0.00433805	0.99664789	4	0	0	0	0	1	0

This feature makes it possible to reload a .opf file that was exported from Scan (to be loaded and processed in AMAPstudio-Xplo).