Notebook

Wheat demo scene¶

Notebook creator: Hannah Weiser & Sina Zumstein, 2022

This demo scene uses a 3D model of several wheat ears, which will be scanned by mobile laser scanning (MLS). We will use the command-line access of HELIOS++ to run the simulation, and use Python just for displaying the input XMLs and the resulting point cloud.

In [1]:

from pathlib import Path
from IPython.display import Code
from pyhelios.util.xmldisplayer import display_xml, find_playback_dir

In [2]:

import os
os.chdir("..")

Survey¶

Lets's have a look at the XML files in the simulation. First, we investigate the survey XML file, mls_wheat_demo.xml:

In [3]:

Code(display_xml('data/surveys/demo/mls_wheat_demo.xml'), language='XML')

Out[3]:

<document>
    <survey name="mls_arbaro_wheat" scene="data/scenes/demo/arbaro_wheat_field.xml#arbaro_wheat" platform="data/platforms.xml#tractor" scanner="data/scanners_tls.xml#riegl_vz400">
		
		<leg>
			<platformSettings x="-10" y="-10" z="0" onGround="true" movePerSec_m="3" />
			<scannerSettings active="true" pulseFreq_hz="100000" scanAngle_deg="20" scanFreq_hz="50" headRotatePerSec_deg="0.00" headRotateStart_deg="0.00" headRotateStop_deg="0.00" trajectoryTimeInterval_s="0.05" />
		</leg>
		
		<leg>
			<platformSettings x="10" y="-10" z="0" onGround="true" movePerSec_m="3" />
			<scannerSettings active="true" pulseFreq_hz="100000" scanAngle_deg="20" scanFreq_hz="50" headRotatePerSec_deg="0.00" headRotateStart_deg="0.00" headRotateStop_deg="0.00" trajectoryTimeInterval_s="0.05" />
		</leg>
		
		<leg>
			<platformSettings x="10" y="10" z="0" onGround="true" movePerSec_m="3" />
			<scannerSettings active="true" pulseFreq_hz="100000" scanAngle_deg="20" scanFreq_hz="50" headRotatePerSec_deg="0.00" headRotateStart_deg="0.00" headRotateStop_deg="0.00" trajectoryTimeInterval_s="0.05" />
		</leg>
		
		<leg>
			<platformSettings x="-10" y="10" z="0" onGround="true" movePerSec_m="3" />
			<scannerSettings active="true" pulseFreq_hz="100000" scanAngle_deg="20" scanFreq_hz="50" headRotatePerSec_deg="0.00" headRotateStart_deg="0.00" headRotateStop_deg="0.00" trajectoryTimeInterval_s="0.05" />
		</leg>
		
		<leg>
			<platformSettings x="-10" y="-10" z="0" onGround="true" movePerSec_m="3" />
			<scannerSettings active="false" pulseFreq_hz="100000" scanAngle_deg="20" scanFreq_hz="50" headRotatePerSec_deg="0.00" headRotateStart_deg="0.00" headRotateStop_deg="0.00" trajectoryTimeInterval_s="0.05" />
		</leg>
    </survey>
</document>

We can see, that there are five legelements, that define the waypoints of the vehicle around the to be scanned object. Here, only x and y values are important z remains at 0. In total there are four lines the vehicle will drive along. The movePerSec_m parameter indicates the speed between these waypoints. Furthermore, we see that the tractor platform in data/platforms.xml is referenced, so let's have a look at that next:

Platform¶

In [4]:

Code(display_xml('python/pyhelios/data/platforms.xml', 'tractor'))

Out[4]:

<platform id="tractor" name="Tractor" type="groundvehicle" drag="0.005">
		<scannerMount x="0" y="1" z="4" rotations="local">
			<rot axis="z" angle_deg="90" />
			<rot axis="y" angle_deg="-30" />
		</scannerMount>
	</platform>

This is a groundvehicle type platform, a mobile platform which moves on the ground between the consecutive legs with a constant speed provided by the user. The scannerMount parameter defines the exact position of the scanner and the angle of rotation around the Z- and Y-axis. The scanner is rotated 90° around the Z-axis and -30° around the Y-axis, so that the scene in the center can be capured the best way possible. The ground vehicle tries to mimic real vehicles. It performs "smooth turns" for wide-angle curves. For narrow-angle curves, it first turns, then backs up, then finishes the turn. This can also be seen in the plot at a later point.

Scanner¶

Next we will have a look at the scanner that is placed on the platform. Here it is the riegl_vz400 defined in data/scanners_als.xml as shown in the survey XML.

In [5]:

Code(display_xml('python/pyhelios/data/scanners_tls.xml', 'riegl_vz400'))

Out[5]:

<scanner id="riegl_vz400" name="RIEGL VZ-400" accuracy_m="0.005" beamDivergence_rad="0.0003" headRotatePerSecMax_deg="60" optics="rotating" pulseFreqs_Hz="100000,300000" pulseLength_ns="5" rangeMin_m="1.5" scanAngleMax_deg="120" scanAngleEffectiveMax_deg="50" scanFreqMin_Hz="3" scanFreqMax_Hz="120">
		
		<FWFSettings beamSampleQuality="3" />	
		<beamOrigin x="0" y="0" z="0.2">
			<rot axis="y" angle_deg="0" />
			<rot axis="z" angle_deg="0" />
			<rot axis="x" angle_deg="0" />
		</beamOrigin>
		<headRotateAxis x="0" y="0" z="1" />
		
	</scanner>

Here we can see the scanner-specific settings, for example beamDivergence_rad, the accuracy or the possible pulse frequencies (pulseFreqs_Hz). This scanner has an rotating beam deflector (optics).

Scene¶

Now we will have a look at the scene, arbaro_wheat_field.xml in data/scenes/demo/arbaro_wheat_field.xml:

In [6]:

Code(display_xml('data/scenes/demo/arbaro_wheat_field.xml', 'arbaro_wheat'))

Out[6]:

<scene id="arbaro_wheat" name="Arbaro wheat">
        <part>
            <filter type="objloader">
                <param type="string" key="filepath" value="data/sceneparts/basic/groundplane/groundplane.obj" />
            </filter>
            <filter type="scale">
                <param type="double" key="scale" value="100" />
            </filter>
			<!--<filter type="rotate">
                <param type="rotation" key="rotation">
                    <rot axis="x" angle_deg="90" />
                </param>
            </filter>-->
        </part>
        <part>
            <filter type="objloader">
                <param type="string" key="filepath" value="data/sceneparts/arbaro/wheat.obj" />
            </filter>
            <filter type="rotate">
                <param type="rotation" key="rotation">
                    <rot axis="x" angle_deg="90" />
                </param>
            </filter>
			<filter type="scale">
                <param type="double" key="scale" value="2" />
            </filter>
        </part>
        <part>
            <filter type="objloader">
                <param type="string" key="filepath" value="data/sceneparts/arbaro/wheat.obj" />
            </filter>
            <filter type="rotate">
                <param type="rotation" key="rotation">
                    <rot axis="x" angle_deg="90" />
                </param>
            </filter>
            <filter type="translate">
                <param type="vec3" key="offset" value="1.4;2.8;0" />
            </filter>
			<filter type="scale">
                <param type="double" key="scale" value="2" />
            </filter>
        </part>
		<part>
            <filter type="objloader">
                <param type="string" key="filepath" value="data/sceneparts/arbaro/wheat.obj" />
            </filter>
            <filter type="rotate">
                <param type="rotation" key="rotation">
                    <rot axis="x" angle_deg="90" />
                </param>
            </filter>
            <filter type="translate">
                <param type="vec3" key="offset" value="1.4;1.4;0" />
            </filter>
			<filter type="scale">
                <param type="double" key="scale" value="2" />
            </filter>
        </part>
		<part>
            <filter type="objloader">
                <param type="string" key="filepath" value="data/sceneparts/arbaro/wheat.obj" />
            </filter>
            <filter type="rotate">
                <param type="rotation" key="rotation">
                    <rot axis="x" angle_deg="90" />
                </param>
            </filter>
            <filter type="translate">
                <param type="vec3" key="offset" value="1.4;0;0" />
            </filter>
			<filter type="scale">
                <param type="double" key="scale" value="2" />
            </filter>
        </part>
		<part>
            <filter type="objloader">
                <param type="string" key="filepath" value="data/sceneparts/arbaro/wheat.obj" />
            </filter>
            <filter type="rotate">
                <param type="rotation" key="rotation">
                    <rot axis="x" angle_deg="90" />
                </param>
            </filter>
            <filter type="translate">
                <param type="vec3" key="offset" value="1.4;-1.4;0" />
            </filter>
			<filter type="scale">
                <param type="double" key="scale" value="2" />
            </filter>
        </part>
		<part>
            <filter type="objloader">
                <param type="string" key="filepath" value="data/sceneparts/arbaro/wheat.obj" />
            </filter>
            <filter type="rotate">
                <param type="rotation" key="rotation">
                    <rot axis="x" angle_deg="90" />
                </param>
            </filter>
            <filter type="translate">
                <param type="vec3" key="offset" value="1.4;-2.8;0" />
            </filter>
			<filter type="scale">
                <param type="double" key="scale" value="2" />
            </filter>
        </part>
		<part>
            <filter type="objloader">
                <param type="string" key="filepath" value="data/sceneparts/arbaro/wheat.obj" />
            </filter>
            <filter type="rotate">
                <param type="rotation" key="rotation">
                    <rot axis="x" angle_deg="90" />
                </param>
            </filter>
            <filter type="translate">
                <param type="vec3" key="offset" value="0;2.8;0" />
            </filter>
			<filter type="scale">
                <param type="double" key="scale" value="2" />
            </filter>
        </part>
		<part>
            <filter type="objloader">
                <param type="string" key="filepath" value="data/sceneparts/arbaro/wheat.obj" />
            </filter>
            <filter type="rotate">
                <param type="rotation" key="rotation">
                    <rot axis="x" angle_deg="90" />
                </param>
            </filter>
            <filter type="translate">
                <param type="vec3" key="offset" value="0;1.4;0" />
            </filter>
			<filter type="scale">
                <param type="double" key="scale" value="2" />
            </filter>
        </part>
		<part>
            <filter type="objloader">
                <param type="string" key="filepath" value="data/sceneparts/arbaro/wheat.obj" />
            </filter>
            <filter type="rotate">
                <param type="rotation" key="rotation">
                    <rot axis="x" angle_deg="90" />
                </param>
            </filter>
            <filter type="translate">
                <param type="vec3" key="offset" value="0;0;0" />
            </filter>
			<filter type="scale">
                <param type="double" key="scale" value="2" />
            </filter>
        </part>
		<part>
            <filter type="objloader">
                <param type="string" key="filepath" value="data/sceneparts/arbaro/wheat.obj" />
            </filter>
            <filter type="rotate">
                <param type="rotation" key="rotation">
                    <rot axis="x" angle_deg="90" />
                </param>
            </filter>
            <filter type="translate">
                <param type="vec3" key="offset" value="0;-1.4;0" />
            </filter>
			<filter type="scale">
                <param type="double" key="scale" value="2" />
            </filter>
        </part>
		<part>
            <filter type="objloader">
                <param type="string" key="filepath" value="data/sceneparts/arbaro/wheat.obj" />
            </filter>
            <filter type="rotate">
                <param type="rotation" key="rotation">
                    <rot axis="x" angle_deg="90" />
                </param>
            </filter>
            <filter type="translate">
                <param type="vec3" key="offset" value="0;-2.8;0" />
            </filter>
			<filter type="scale">
                <param type="double" key="scale" value="2" />
            </filter>
        </part>
		<part>
            <filter type="objloader">
                <param type="string" key="filepath" value="data/sceneparts/arbaro/wheat.obj" />
            </filter>
            <filter type="rotate">
                <param type="rotation" key="rotation">
                    <rot axis="x" angle_deg="90" />
                </param>
            </filter>
            <filter type="translate">
                <param type="vec3" key="offset" value="-1.4;2.8;0" />
            </filter>
			<filter type="scale">
                <param type="double" key="scale" value="2" />
            </filter>
        </part>
		<part>
            <filter type="objloader">
                <param type="string" key="filepath" value="data/sceneparts/arbaro/wheat.obj" />
            </filter>
            <filter type="rotate">
                <param type="rotation" key="rotation">
                    <rot axis="x" angle_deg="90" />
                </param>
            </filter>
            <filter type="translate">
                <param type="vec3" key="offset" value="-1.4;1.4;0" />
            </filter>
			<filter type="scale">
                <param type="double" key="scale" value="2" />
            </filter>
        </part>
		<part>
            <filter type="objloader">
                <param type="string" key="filepath" value="data/sceneparts/arbaro/wheat.obj" />
            </filter>
            <filter type="rotate">
                <param type="rotation" key="rotation">
                    <rot axis="x" angle_deg="90" />
                </param>
            </filter>
            <filter type="translate">
                <param type="vec3" key="offset" value="-1.4;0;0" />
            </filter>
			<filter type="scale">
                <param type="double" key="scale" value="2" />
            </filter>
        </part>
		<part>
            <filter type="objloader">
                <param type="string" key="filepath" value="data/sceneparts/arbaro/wheat.obj" />
            </filter>
            <filter type="rotate">
                <param type="rotation" key="rotation">
                    <rot axis="x" angle_deg="90" />
                </param>
            </filter>
            <filter type="translate">
                <param type="vec3" key="offset" value="-1.4;-1.4;0" />
            </filter>
			<filter type="scale">
                <param type="double" key="scale" value="2" />
            </filter>
        </part>
		<part>
            <filter type="objloader">
                <param type="string" key="filepath" value="data/sceneparts/arbaro/wheat.obj" />
            </filter>
            <filter type="rotate">
                <param type="rotation" key="rotation">
                    <rot axis="x" angle_deg="90" />
                </param>
            </filter>
            <filter type="translate">
                <param type="vec3" key="offset" value="-1.4;-2.8;0" />
            </filter>
			<filter type="scale">
                <param type="double" key="scale" value="2" />
            </filter>
        </part>
		
    </scene>

Here we see two objects, which compose the scene: the groundplane.obj and the wheat.obj. To load it we use the objloader filter and give the the relative path to the file in the filepathparameter. The same object (the wheat plant) is placed in the scene 15 times. Using the translate filter, it is positioned in three columns and five rows to form a wheat field.

Executing the Simulation¶

Next, we will run the simulation. In Jupyter Notebooks, we can run external commands with the !command syntax, but you can also just run it from the command line.

In [7]:

!helios data/surveys/demo/mls_wheat_demo.xml -q

The results¶

Now we can display a 3D plot

In [8]:

#%matplotlib widget
import numpy as np
import matplotlib.pyplot as plt

output_path = find_playback_dir('data/surveys/demo/mls_wheat_demo.xml')

print('Loading points from', output_path)

strip_1 = np.loadtxt(Path(output_path) / 'leg000_points.xyz')
strip_2 = np.loadtxt(Path(output_path) / 'leg001_points.xyz')
strip_3 = np.loadtxt(Path(output_path) / 'leg002_points.xyz')
strip_4 = np.loadtxt(Path(output_path) / 'leg003_points.xyz')
traj_1 = np.loadtxt(Path(output_path) / 'leg000_trajectory.txt')
traj_2 = np.loadtxt(Path(output_path) / 'leg001_trajectory.txt')
traj_3 = np.loadtxt(Path(output_path) / 'leg002_trajectory.txt')
traj_4 = np.loadtxt(Path(output_path) / 'leg003_trajectory.txt')
traj = np.vstack((traj_1[:, :3], traj_2[:, :3], traj_3[:, :3], traj_4[:, :3]))

Loading points from E:\Software\_helios_versions\helios\output\mls_arbaro_wheat\2024-05-28_18-40-42

In [9]:

def extract_by_bb(arr, b_box):
    assert len(b_box) == 6
    x_min, y_min, z_min, x_max, y_max, z_max = b_box
    subset = arr[(arr[:, 0] > x_min) & 
                 (arr[:, 0] < x_max) & 
                 (arr[:, 1] > y_min) & 
                 (arr[:, 1] < y_max) & 
                 (arr[:, 2] > z_min) & 
                 (arr[:, 2] < z_max)]
    
    return subset

In [10]:

# Matplotlib figure.
fig = plt.figure(figsize=(12,8))
# Axes3d axis onto mpl figure.
ax = fig.add_subplot(projection='3d')

# create scene subset
bbox = [-5, -5, 0, 5, 5, 1.5]

strip_1_sub = extract_by_bb(strip_1, bbox)
strip_2_sub = extract_by_bb(strip_2, bbox)
strip_3_sub = extract_by_bb(strip_3, bbox)
strip_4_sub = extract_by_bb(strip_4, bbox)

# Scatter plot of points (coloured by height).
sc = ax.scatter(strip_1_sub[:, 0], strip_1_sub[:, 1], strip_1_sub[:, 2], c=strip_1_sub[:, 2], cmap="RdYlBu_r", s=0.02, label='scene')
sc = ax.scatter(strip_2_sub[:, 0], strip_2_sub[:, 1], strip_2_sub[:, 2], c=strip_2_sub[:, 2], cmap="RdYlBu_r", s=0.02, label='scene')
sc = ax.scatter(strip_3_sub[:, 0], strip_3_sub[:, 1], strip_3_sub[:, 2], c=strip_3_sub[:, 2], cmap="RdYlBu_r", s=0.02, label='scene')
sc = ax.scatter(strip_4_sub[:, 0], strip_4_sub[:, 1], strip_4_sub[:, 2], c=strip_4_sub[:, 2], cmap="RdYlBu_r", s=0.02, label='scene')

# Plot of trajectory.
ax.plot(traj[:,0], traj[:,1], traj[:,2], c = 'black', label = 'scanner trajectory')

cax = plt.axes([0.85, 0.2, 0.025, 0.55])

cbar = plt.colorbar(sc, cax=cax)

cbar.set_label("Height ($Z$)")

# Add axis labels.
ax.set_xlabel('$X$')
ax.set_ylabel('$Y$')
ax.set_zlabel('$Z$')

# set equal axes
box = (bbox[3]-bbox[0], bbox[4]-bbox[1], bbox[5]-bbox[2])
ax.set_box_aspect(box)

# Set title.
ax.set_title(label='Point cloud and trajectory of scanner',fontsize=15)
# Set subtitle.


# Display results
plt.show()

In [ ]: