========================== Using Visualea : Beginning ========================== Here is a tutorial in which you will see how to implement a simple modeling problem in *Visualea* .. image:: ./images/beginner/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 : .. csv-table:: :header: "X", "Y", "crown_up", "crown_bot", "trunk_diameter" :widths: 15, 15, 20, 20, 20 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 ---------------- #. Select **Package Manager** -> **Add** -> **Package** #. 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) #. Click "OK" .. image:: ./images/beginner/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). #. 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. #. In the Package Manager tab, drag the ``read`` node from the *openalea.file* package to the workspace. It should now appear on the canvas. #. 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). #. In the package manager search the ``text`` in the **search tab**, then drag the ``text`` node from the *openalea.data structure.string* folder onto the workspace. #. Connect the output of the ``read`` node to the input of the ``text`` node. .. image:: ./images/beginner/step2.1.gif View the file contents ---------------------- #. Right click on the ``text`` node and select "Run" #. 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. #. Select the search tab in the package manager #. Type CSV #. Drag the ``read csv`` node on the workspace #. Do the same to create a ``getitem`` node (``openalea.python method.getitem``) #. Connect ``read``'s output to ``read csv``'s input #. Connect ``read csv``'s first output to ``getitem``'s first input #. Add an ``int`` node on the workspace, and connect its output to the second input of ``getitem`` #. Execute the graph by selecting "Run" in the context menu of the ``getitem`` node #. Print the output in the shell : Right click on the output port, and select "Print" .. image:: ./images/beginner/step2.2.gif Save your work -------------- #. Select **File** -> **Save as composite node** (CTRL + S) #. In the selector dialog, click "New" Button #. 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" #. In the selector, click "Ok" button #. The new graph should appear in the standbuilder package. .. image:: ./images/beginner/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. #. First step, we create a new workspace : Select **File** -> **New Empty Workspace** (CTRL+T) #. Create the following dataflow by using PlantGL nodes * ``plantgl.objects.cylinder`` creates a cylinder * ``plantgl.objects.translated`` moves the input object * ``openalea.data structure.tuple.tuple3`` to set the translation vector * ``plantgl.visualization.plot3d`` to view the result * ``openalea.data structure.float`` to set the parameters of the tuple3 node .. image:: ./images/beginner/step3.1.PNG Create a simple tree -------------------- To build our tree, we must construct a PlantGL scene containing a cylinder and a sphere. #. Modify the previous dataflow as follow: * Add a ``plantgl.objects.sphere`` object * Add a ``plantgl.objects.translated`` object * Add a ``plantgl.objects.scene`` object * Connect the 2 translated objects to a ``plantgl.objects.scene`` object #. Save this dataflow in your standbuilder package as **simple_tree** .. image:: ./images/beginner/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 -------------------------------------------------- #. Select **simple_tree** in the package manager #. Right click on the **simple_tree** graph, select "Properties" and click on the "Inputs / Outputs" button #. 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 #. Add 1 output with the + button * scene - None - PlanGL scene .. image:: ./images/beginner/step4.1.PNG :width: 40% #. Click "OK" and the buttons will appear in the workspace #. Double click **simple_tree** and 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 #. Save your work as a new composite node in standbuilder named **tree_scene** .. image:: ./images/beginner/step4.2.PNG :width: 70% Using the new composite node in a dataflow ------------------------------------------ #. Open our first dataflow **readcsv_1** in the standbuilder package (doubleclick) #. Drag the node ``standbuilder.tree_scene`` on the new workspace #. Add 5x ``getitem`` and 5x ``string`` object #. Connect the nodes as the picture in order to retrieve to different object properties #. Add a ``plangl.visualization.plot3D`` object and connect it to the output of ``tree_scene`` #. Run the dataflow several times and change the value of the first ``getitem`` (object index) #. Save the dataflow in the standbuilder package as **readcsv_2** Create a composite node by grouping nodes ----------------------------------------- #. Select the 5 ``getitem`` and their associated ``string`` object #. Click on Menu **Workspace** -> **group** (CTRL+G) #. Run the dataflow #. Save it in the standbuilder package as **readcsv_3** .. image:: ./images/beginner/step4.3.PNG :width: 70% .. image:: ./images/beginner/step4.4.PNG :width: 20% 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 ------------ #. Create a new workspace (CTRL+T) #. Add a ``read`` node and a ``read csv`` node to read a csv file #. Set the file to read by opening the ``read`` widget (*Open Widget*) #. Run and display the output (output port context menu -> *Print* or *Tooltip*) : it's a list of obj #. Add a ``getitem`` node and an ``int`` node to select an object in the list #. Add an ``extract`` node and 2 ``string`` nodes to select properties in a particular object #. Set the 2 ``string`` objects to X and Y #. 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. .. image:: ./images/beginner/step5.1.PNG Implement iterative process --------------------------- We want to do the same thing, but for all the CSV objects contained in the file. #. Remove the ``getitem`` and the ``int`` nodes (with suppr) #. Add an ``openalea.function operator.map`` #. Connect the output of ``extract`` to the first input of ``map`` #. Connect the output of ``read csv`` to the second input of ``map`` #. Add an ``openalea.flow control.X`` node and connect its output the first input of ``extract`` #. Run the ``map`` object and display the result .. image:: ./images/beginner/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 ------- #. Add the nodes ``openalea.plottools.VS Plot`` and ``openalea.plottools.tuples2seq`` on the workspace #. Connect the ``map`` output the input of ``tuples2seq`` and the last output the ``VS Plot`` node. #. Run the dataflow #. 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 #. Open the ``readcsv_3`` dataflow #. Modify it in order to plot in 3D all the tree contained in the file and not only one #. Use a ``openalea.flow control.X`` node and a ``openalea.functional.map`` node #. Save this work in your standbuilder package as **plot_stand** .. image:: ./images/beginner/step6.1.PNG :width: 45% .. image:: ./images/beginner/step6.2.PNG :width: 45%