3dtrees tutorial

topics/climate/tutorials/3dtrees/faqs/index.md

@@ -0,0 +1,3 @@
+---
+layout: faq-page
+---

topics/climate/tutorials/3dtrees/tutorial.bib

@@ -0,0 +1,42 @@
+
+# This is the bibliography file for your tutorial.
+#
+# To add bibliography (bibtex) entries here, follow these steps:
+#  1) Find the DOI for the article you want to cite
+#  2) Go to https://doi2bib.org and fill in the DOI
+#  3) Copy the resulting bibtex entry into this file
+#
+# To cite the example below, in your tutorial.md file
+# use {% cite Batut2018 %}
+#
+# If you want to cite an online resourse (website etc)
+# you can use the 'online' format (see below)
+#
+# You can remove the examples below
+
+@article{Batut2018,
+  doi = {10.1016/j.cels.2018.05.012},
+  url = {https://doi.org/10.1016/j.cels.2018.05.012},
+  year = {2018},
+  month = jun,
+  publisher = {Elsevier {BV}},
+  volume = {6},
+  number = {6},
+  pages = {752--758.e1},
+  author = {B{\'{e}}r{\'{e}}nice Batut and Saskia Hiltemann and Andrea Bagnacani and Dannon Baker and Vivek Bhardwaj and
+           Clemens Blank and Anthony Bretaudeau and Loraine Brillet-Gu{\'{e}}guen and Martin {\v{C}}ech and John Chilton
+           and Dave Clements and Olivia Doppelt-Azeroual and Anika Erxleben and Mallory Ann Freeberg and Simon Gladman and
+           Youri Hoogstrate and Hans-Rudolf Hotz and Torsten Houwaart and Pratik Jagtap and Delphine Larivi{\`{e}}re and
+           Gildas Le Corguill{\'{e}} and Thomas Manke and Fabien Mareuil and Fidel Ram{\'{i}}rez and Devon Ryan and
+           Florian Christoph Sigloch and Nicola Soranzo and Joachim Wolff and Pavankumar Videm and Markus Wolfien and
+           Aisanjiang Wubuli and Dilmurat Yusuf and James Taylor and Rolf Backofen and Anton Nekrutenko and Bj\"{o}rn Gr\"{u}ning},
+  title = {Community-Driven Data Analysis Training for Biology},
+  journal = {Cell Systems}
+}
+
+@online{gtn-website,
+  author = {GTN community},
+  title = {GTN Training Materials: Collection of tutorials developed and maintained by the worldwide Galaxy community},
+  url = {https://training.galaxyproject.org},
+  urldate = {2021-03-24}
+}

topics/climate/tutorials/3dtrees/tutorial.md

@@ -0,0 +1,277 @@
+---
+layout: tutorial_hands_on
+
+title: '3Dtrees: Point cloud processing'
+zenodo_link: ''
+questions:
+- What are LAS data ?
+- How can I process and visualise point cloud data ? 
+objectives:
+- Learn to do point cloud processing
+- 
+time_estimation: 3H
+key_points:
+- The take-home messages
+- They will appear at the end of the tutorial
+contributors:
+  autorship:
+    - kgerb
+    - Marie59
+
+---
+
+TO DO
+=> Add description general of what does the workflow and how it can be usefull (small intro of 3Dtrees here (in a more details box))
+
+=> Introduce the Data used and for what (small intro for data terra in a more details box)
+
+
+> <agenda-title></agenda-title>
+>
+> In this tutorial, we will cover:
+>
+> 1. TOC
+> {:toc}
+>
+{: .agenda}
+
+# Title for your first section
+
+Intro on the forest and its structure ? of IGN data. 
+
+## Get data
+
+> <hands-on-title> Data Upload </hands-on-title>
+>
+> 1. Create a new history for this tutorial
+> 2. Import the files from [Recherche Data Gouv](https://entrepot.recherche.data.gouv.fr/) more specifically the Data register underthis [DOI](https://doi.org/10.15454/DMYWPB)
+> 3. On the left pannel go on **Upload** select **{% icon pref-cloud %} Choose Remote Files**
+> 
+> ![Image of how the upload pannel looks like](../images/3dtrees/upload_pannel.png)
+>
+> 4. In the search bar write down "recherche", you should see the repo named **Recherche Data Gouv** appear, click on it.
+> 5. In the search bar write down "pic", you should see the repo named **Données lidar acquises par drone au pied du Pic St Loup (34)** appear, click on it.
+>
+> ![Image of how the remote repo to select](../images/3dtrees/rdg_repo.png)
+>
+> 6. You should see 4 datasets appear, select them all and then in the bottom right click on **start**
+>
+> ![Image of how the data to upload](../images/3dtrees/data_upload.png)
+>
+> 7. The 4 datasets should appear into your history (in yellow when uploading) in green
+>
+> ![Image of how the data to uploading in the history](../images/3dtrees/data_inhistory.png)
+>
+> > <tip-title>las format</tip-title>
+> > Check that the datatype is **las format**
+> >
+> >  {% snippet faqs/galaxy/datasets_change_datatype.md datatype="datatypes" %}
+> {: .tip}
+> 
+> 8. Build a collection 
+>
+> {% snippet faqs/galaxy/collections_autobuild_list.md %}
+{: .hands_on}
+
+
+# Standardization
+
+***TODO***: *Consider adding a detail box to expand the theory and add some info here*
+
+> <details-title> More details about the theory </details-title>
+>
+> But to describe more details, it is possible to use the detail boxes which are expandable
+>
+{: .details}
+
+
+## 3DTrees: LAS/LAZ Standardization
+
+> <hands-on-title> Standardize individual files in collection </hands-on-title>
+>
+> 1. {% tool [3DTrees: LAS/LAZ Standardization](toolshed.g2.bx.psu.edu/repos/bgruening/3dtrees_standardization/3dtrees_standardization/1.1.0+galaxy0) %} with the following parameters:
+>    - *"Mode"*: `Single File Standardization`
+>        - {% icon param-collection %} *"Point Cloud File"*: `output` (Input dataset collection)
+>
+>
+>    > <comment-title> short description </comment-title>
+>    >
+>    > A comment about the tool or something else. This box can also be in the main text
+>    {: .comment}
+>
+{: .hands_on}
+
+***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
+
+> <question-title></question-title>
+>
+> 1. Question1?
+> 2. Question2?
+>
+> > <solution-title></solution-title>
+> >
+> > 1. Answer for question1
+> > 2. Answer for question2
+> >
+> {: .solution}
+>
+{: .question}
+
+In the same time you can do this 2nd step even if 1st one has not finished yet.
+
+> <hands-on-title> 3DTrees Collection Check  </hands-on-title>
+>
+> Collection-level validation and consistency check using standardization tool in collection mode
+>
+> 1. {% tool [3DTrees: LAS/LAZ Standardization](toolshed.g2.bx.psu.edu/repos/bgruening/3dtrees_standardization/3dtrees_standardization/1.1.0+galaxy0) %} with the following parameters:
+>    - *"Mode"*: `Collection Validation`
+>        - {% icon param-collection %} *"Point Cloud Collection"*: `output` (Input dataset collection)
+>
+>    > <comment-title> short description </comment-title>
+>    >
+>    > A comment about the tool or something else. This box can also be in the main text
+>    {: .comment}
+>
+{: .hands_on}
+
+You should have 4 new objects in your history running yellow soon turning green.
+
+![Standardization running](../images/3dtrees/standard_run.png)
+
+# Thumbnail generation 
+
+> <hands-on-title> 3D Trees Overview Generator </hands-on-title>
+>
+> Generate overview images from standardized point clouds
+>
+> 1. {% tool [3Dtrees: Overviews](toolshed.g2.bx.psu.edu/repos/bgruening/3dtrees_overviews/3dtrees_overviews/1.2.0+galaxy1) %} with the following parameters:
+>    - {% icon param-file %} *"Point Cloud Collection"*: `pc_standardized` (output of **3DTrees: LAS/LAZ Standardization** {% icon tool %})
+>
+> You should see to types of section images in your history (4 images in total have been generated)
+>    > <comment-title> short description </comment-title>
+>    >
+>    > A comment about the tool or something else. This box can also be in the main text
+>    {: .comment}
+>
+{: .hands_on}
+
+![Example of the overview image on the section ns](../images/3dtrees/sectionns.png)
+
+# Instance Segmentation by SegmentAnyTree
+
+> <hands-on-title> 3DTrees: SmartTile </hands-on-title>
+>
+> 1. {% tool [3DTrees: SmartTile](toolshed.g2.bx.psu.edu/repos/bgruening/3dtrees_smart_tile/3dtrees_smart_tile/2.0.1+galaxy0) %} with the following parameters:
+>    - *"Operation"*: `Tile (COPC normalize + tile + subsample)`
+>        - {% icon param-file %} *"Input point clouds (LAZ/LAS)"*: `pc_standardized` (output of **3DTrees: LAS/LAZ Standardization** {% icon tool %})
+>
+> 5 new objects should appear in your history.
+>    > <comment-title> short description </comment-title>
+>    >
+>    > A comment about the tool or something else. This box can also be in the main text
+>    {: .comment}
+>
+{: .hands_on}
+
+***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
+
+> <question-title></question-title>
+>
+> 1. Question1?
+> 2. Question2?
+>
+> > <solution-title></solution-title>
+> >
+> > 1. Answer for question1
+> > 2. Answer for question2
+> >
+> {: .solution}
+>
+{: .question}
+
+> <hands-on-title> 3Dtrees: SegmentAnyTree </hands-on-title>
+>
+> Deep learning tree segmentation
+> 
+> 1. {% tool [3Dtrees: SegmentAnyTree](toolshed.g2.bx.psu.edu/repos/bgruening/3dtrees_segmentanytree/3dtrees_segmentanytree/1.2.2+galaxy0) %} with the following parameters:
+>    - {% icon param-file %} *"Input Dataset"*: `output_subsampled_res2` (output of **3DTrees: SmartTile** {% icon tool %})
+>    - *"Predicted instance dimension name"*: `PredInstance`
+>    - *"Predicted semantic dimension name"*: `PredSemantic`
+>
+> Your tool should look like that before running. It can take a few minutes to run.
+> ![Image of the inputs within this tool](../images/3dtrees/smartile.png)
+>
+>    > <comment-title> short description </comment-title>
+>    >
+>    > A comment about the tool or something else. This box can also be in the main text
+>    {: .comment}
+>
+{: .hands_on}
+
+
+> <hands-on-title> 3DTrees: SmartTile </hands-on-title>
+>
+> 1. {% tool [3DTrees: SmartTile](toolshed.g2.bx.psu.edu/repos/bgruening/3dtrees_smart_tile/3dtrees_smart_tile/2.0.1+galaxy0) %} with the following parameters:
+>    - *"Operation"*: `Filter (remove overlap-only instances)`
+>        - {% icon param-file %} *"Segmented tiles (LAZ/LAS)"*: `output` (output of **3Dtrees: SegmentAnyTree** {% icon tool %})
+>        - {% icon param-file %} *"Tile layout JSON (tile_bounds_tindex.json)"*: `output_tile_bounds_json` (output of **3DTrees: SmartTile** {% icon tool %})
+>        - *"Border zone width"*: `Derive from tile layout JSON (recommended)`
+>        - *"Small cluster reassignment"*: `Enabled`
+>        - *"After filtering"*: `Also remap filtered dimensions to another collection`
+>            - *"Remap target files"*: `Originals and subsampled targets`
+>                - {% icon param-file %} *"Original files (LAZ/LAS)"*: `output_original_copc` (output of **3DTrees: SmartTile** {% icon tool %})
+>                - {% icon param-file %} *"Subsampled target files (LAZ/LAS)"*: `output_subsample_res1` (output of **3DTrees: SmartTile** {% icon tool %})
+>            - *"Also write one merged output (LAZ)"*: `Yes`
+>                - *"Enrich merged output with original attributes"*: `Yes`
+>                - {% icon param-file %} *"Standardization summary (optional)"*: `collection_summary` (output of **3DTrees: LAS/LAZ Standardization** {% icon tool %})
+>
+>
+>    > <comment-title> See exactly how the tols is filled in </comment-title>
+>    >
+>    > ![Image of how to fill in the tool form step 1](../images/3dtrees/form1.png)
+>    > ![Image of how to fill in the tool form step 2](../images/3dtrees/form2.png)
+>    > ![Image of how to fill in the tool form step 3](../images/3dtrees/form3.png)
+>    {: .comment}
+>
+{: .hands_on}
+
+# Point cloud visualization by Potree
+
+> <hands-on-title> 3Dtrees: Potree Converter </hands-on-title>
+>
+> Convert segmented collection to Potree octree format
+>
+> 1. {% tool [3Dtrees: Potree Converter](toolshed.g2.bx.psu.edu/repos/bgruening/3dtrees_potree/3dtrees_potree/1.0.2+galaxy0) %} with the following parameters:
+>    - {% icon param-file %} *"Point Cloud Files"*: `output_merged_with_originals` (output of **3DTrees: SmartTile** {% icon tool %})
+>
+>    ***TODO***: *Check parameter descriptions*
+>
+>    ***TODO***: *Consider adding a comment or tip box*
+>
+>    > <comment-title> short description </comment-title>
+>    >
+>    > A comment about the tool or something else. This box can also be in the main text
+>    {: .comment}
+>
+{: .hands_on}
+
+***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
+
+> <question-title></question-title>
+>
+> 1. Question1?
+> 2. Question2?
+>
+> > <solution-title></solution-title>
+> >
+> > 1. Answer for question1
+> > 2. Answer for question2
+> >
+> {: .solution}
+>
+{: .question}
+
+# Conclusion
+
+Sum up the tutorial and the key takeaways here. We encourage adding an overview image of the
+pipeline used.

topics/climate/tutorials/3dtrees/workflows/index.md

@@ -0,0 +1,3 @@
+---
+layout: workflow-list
+---