Using Visualea : Beginning

Here is a tutorial in which you will see how to implement a simple modeling problem in Visualea

../../_images/intro.gif

Here is what you need for the following tutorial

conda create -n visualea_tuto -c openalea openalea.visualea openalea.components openalea.plantgl boost=1.66 -c openalea/label/unstable
conda activate visualea_tuto

Once you installed and activated the OpenAlea environment (see Installation), execute this

visualea

The Goal

We measured some tree data and saved these in a tabbed editor (like Excel). The data has been exported in a CSV file. We want to have a simple 3D representation of the measured tree.

Here is the data :

X

Y

crown_up

crown_bot

trunk_diameter

0

0

10

20

2

10

12

12

18

3

20

22

8

23

3.4

0

18

14

22

2.5

You may want to download the CSV file.

Step 1 : Create Your Own Package

First of all, we need to create a package where to put your work (dataflow, node definition, data, …). A package is in fact a simple directory containing python files.

Create a package

  1. Select Package Manager -> Add -> Package

  2. Fill the form :

    • Name : standbuilder

    • Description : build stand representation from measured data

    • Version : 0.1

    • License : Cecill-C

    • Authors : All collaborators and package writer

    • Institutes : …

    • URL : …

    • Path : /home/myhome/openalea_pkg (could be anywhere you want)

  3. Click “OK”

../../_images/step1.gif

Your new package should appear in the package manager.

Tip

The path corresponds to the directory where the python file will be written. Choose it carefully in order to be able to find it later.

Step 2 : Read CSV Data

Create a dataflow to read and view a file

Tip

Leaving the cursor on any item in the Package Manager, or on nodes or ports in the dataflow view brings up a tooltip. Clicking on them also shows some documentation in the “Help” tab (bottom-left-hand corner).

  1. In the Package Manager tab (left column), open the openalea.file folder. You should see a list of nodes.

    Note

    You can search for a particuliar node in the Search tab.

  2. In the Package Manager tab, drag the read node from the openalea.file package to the workshop. It should now appear on the canvas.

  3. In the workspace, right click on the read node and choose “Open Widget”. Then browse for the “stand.csv” file (no need to validate anything, changes are automatically taken into account so you can simply close the window).

  4. Drag the text node from the openalea.data structure.string folder onto the workspace.

  5. Connect the output of the read node to the input of the text node.

../../_images/step2.1.gif

View the file contents

  1. Right click on the text node and select “Run”

  2. Right click on the text node and select “Open Widget”

Build a CSV object

In order to manipulate the CSV data, we are going to build a CSV object.

  1. Select the search tab in the package manager

  2. Type CSV

  3. Drag the read csv node on the workspace

  4. Do the same to create a getitem node (openalea.python method.getitem)

  5. Connect read’s output to read csv’s input

  6. Connect read csv’s first output to getitem’s first input

  7. Add an int node on the workspace, and connect its output to the second input of getitem

  8. Execute the graph by selecting “Run” in the context menu of the getitem node

  9. Print the output in the shell : Right click on the output port, and select “Print”

../../_images/step2.2.gif

Save your work

  1. Select File -> Save as composite node (CTRL + S)

  2. In the selector dialog, click “New” Button

  3. In the new dialog

    • Select the standbuilder package in the combo box

    • Enter the name : readcsv_1

    • Add a description : Read data file

    • Click “Ok”

  4. In the selector, click “Ok” button

  5. The new graph should appear in the standbuilder package.

../../_images/step2.3.gif

Step 3 : Create a simple 3D representation of one tree

Before displaying the whole stand, we must rebuild a tree. In this tutorial we build a very simple tree representation composed by a sphere for the crown and a cylinder for the trunk.

Create a 3D object

This simple dataflow shows how to display a scene object.

  1. First step, we create a new workspace : Select File -> New Empty Workspace (CTRL+T)

  2. Create the following dataflow by using PlantGL nodes

    • vplants.plantgl.objects.cylinder creates a cylinder

    • vplants.plantgl.objects.translated moves the input object

    • openalea.data structure.tuple.tuple3 to set the translation vector

    • vplants.plantgl.visualization.plot3d to view the result

    • openalea.data structure.float to set the parameters of the tuple3 node

../../_images/step3.1.PNG

Create a simple tree

To build our tree, we must construct a PlantGL scene containing a cylinder and a sphere.

  1. Modify the previous dataflow as follow:

    • Add a vplants.plantgl.objects.sphere object

    • Add a vplants.plantgl.objects.translated object

    • Add a vplants.plantgl.objects.scene object

    • Connect the 2 translated objects to a vplants.plantgl.objects.scene object

  2. Save this dataflow in your standbuilder package as simple_tree

../../_images/step3.2.PNG

Step 4 : Create a Macro Node / Group Nodes

We will need to use the previous dataflow to build trees. To simplify this procedure, we would like to use a simple node and not a complex dataflow. For that we are going to embed the previous dataflow in a composite node (also named macro node).

Transform simple_tree to a reusable composite node

  1. Select simple_tree in the package manager

  2. Right click on the simple_tree graph, select “Properties” and click on the “Inputs / Outputs” button

  3. Add 5 inputs with the + button :

    • X - IInt - 0 - X position

    • Y - IInt - 0 - Y position

    • crown_up - IFloat - 16.0 - Top of the crown

    • crown_bot - IFloat - 8.0 - Bottom of the crown

    • trunk_dia - IFloat - 3.0 - Trunk diameter

  4. Add 1 output with the + button

    • scene - None - PlanGL scene

    ../../_images/step4.1.PNG
  5. Click “OK” and the buttons will appear in the workshop

  6. Modify the graph as follow

    • Connect input 0 and 1 to the X and Y nodes

    • Connect input 2 and 3 to a minus node openalea.math.-, and connect the result to the crown radius

    • Connect input 5 to the trunk radius

    • Connect input 3 to the crown bottom

  7. Save your work as a new composite node in standbuilder named tree_scene

../../_images/step4.2.PNG

Using the new composite node in a dataflow

  1. Open our first dataflow readcsv_1 in the standbuilder package (doubleclick)

  2. Drag the node standbuilder.tree_scene on the new workspace

  3. Add 5x getitem and 5x string object

  4. Connect the nodes as the picture in order to retrieve to different object properties

  5. Add a plangl.visualization.plot3D object and connect it to the output of tree_scene

  6. Run the dataflow several times and change the value of the first getitem (object index)

  7. Save the dataflow in the standbuilder package as readcsv_2

Create a composite node by grouping nodes

  1. Select the 5 getitem and their associated string object

  2. Click on Menu Workspace -> group (CTRL+G)

  3. Run the dataflow

  4. Save it in the standbuilder package as readcsv_3

../../_images/step4.3.PNG ../../_images/step4.4.PNG

Step 5 : Get the spatial distribution of the trees

We want to extract from the csv object the X and Y properties and plot them in 2D.

Extract data

  1. Create a new workspace (CTRL+T)

  2. Add a read node and a read csv node to read a csv file

  3. Set the file to read by opening the read widget (Open Widget)

  4. Run and display the output (output port context menu -> Print or Tooltip) : it’s a list of obj

  5. Add a getitem node and an int node to select an object in the list

  6. Add an extract node and 2 string nodes to select properties in a particular object

  7. Set the 2 string objects to X and Y

  8. Run and display the output (output port context menu -> print or tooltip) : it’s a list containing the X and the Y properties of the selected object.

../../_images/step5.1.PNG

Implement iterative process

We want to do the same thing, but for all the CSV objects contained in the file.

  1. Remove the getitem and the int nodes (with suppr)

  2. Add an openalea.function operator.map

  3. Connect the output of extract to the first input of map

  4. Connect the output of read csv to the second input of map

  5. Add an openalea.flow control.X node and connect its output the first input of extract

  6. Run the map object and display the result

../../_images/step5.2.PNG

Note

The X object represents a function variable. The map apply a function to each element received in its second input.

Plot 2D

  1. Add the nodes openalea.plottools.VS Plot and openalea.plottools.tuples2seq on the workspace

  2. Connect the map output the input of tuples2seq and the last output the VS Plot node.

  3. Run the dataflow

  4. Save it in the standbuilder package as plot_csv

Step 6 : Apply the process to multiple trees

In this step, we used the same method to build the entire stand

  1. Open the readcsv_3 dataflow

  2. Modify it in order to plot in 3D all the tree contained in the file and not only one

  3. Use a openalea.flow control.X node and a openalea.functional.map node

  4. Save this work in your standbuilder package as plot_stand

../../_images/step6.1.PNG ../../_images/step6.2.PNG