Follow the instructions in my answer here to use the Fusion's command line PolyClipData.
Assuming you have:
- shapefiles named tree_0.shp, tree_1.shp,...,tree_138.shp (as stated through comments).
- the las file to be clipped with name
data.las.
- the fusion software stored directly under the c: drive.
- the shp files and the las file stored under a folder named 'forest'
Write the following command line:
FOR /L %%W IN (0,1,138) DO CALL c:\fusion\polyclipdata /index c:\forest\tree_%%W.shp c:\forest\clipped_data_%%W.las c:\forest\data.las
The FOR /L %%W IN (0,1,138) DO CALL part is a loop which will take one shapefile at a time to clip your main las file. In this case, the output will be 139 las files clipped by their respective shapefile.
I guess the time of processing will depend on how much is the number of shapefiles and the size of the main las file.
The /L part is a shortcut, so there is no need to write:
FOR %%W IN (1,2,3,4,5,6,7,8,9,10,11,12,13,14,....,138) DO CALL .....
With /L it reads the following between the brackets: (start,step,end).
The /index switch creates the .ldx and .ldi files which are necessary for visualization in the Fusion's viewer.
This is a pretty long standing problem with the gdal_merge tool accessed through the user interface.
The easiest way to get around it is to first build a virtual raster (VRT) file and then (if necessary) convert this to a geotiff. If you have lots of files it is more stable and faster to use the OSGeo4W shell to build the VRT rather than using the tool through the QGIS interface.
The help page for the VRT is here: http://www.gdal.org/gdalbuildvrt.html
This example from that page is probably what you're looking for:
Example:
Make a virtual mosaic from all TIFF files contained in a directory :
gdalbuildvrt doq_index.vrt doq/*.tif
Once you have the VRT you can convert it into a geotiff by "saving as" from the QGIS interface; if you need to that is.
Best Answer
There is more documentation available from here .
It includes additional examples, among them: