Commit 5a4af2ec authored by Florian Ziemen's avatar Florian Ziemen
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Overhaul for the 2021 HPDA and Vis course.

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......@@ -3,9 +3,13 @@
Set the background (color/gradient)
==================================================
.. note::
This document is part of a series teaching how to :ref:`create-image-sea-surface-speeds`.
.. _set-current-background:
Set the background of the curret plot
Set the background of the current plot
--------------------------------------------------
To set the background of your current project go to properties of any object, type ``backg`` into the text field, and chose a background of your liking. Chosing pink might help looking for holes in your data - or making your plot a bit *special*.
......@@ -15,6 +19,9 @@ To set the background of your current project go to properties of any object, ty
.. image:: pink-background.png
Next you could :ref:`prettify-colorbar`
.. _set-default-background:
Set the default background
......
......@@ -3,8 +3,14 @@
Switch to camera parallel projection
========================================
.. note::
This document is part of a series teaching how to :ref:`create-image-sea-surface-speeds`.
If you are using paraview for 2D mapping, switching to camera parallel projection helps removing projection artifacts.
If you are using paraview for 2D mapping, switching to camera parallel projection helps removing projection artifacts. This will remove any depth effects in the perspective, so objects that are further away are displayed at the same size as nearby objects.
Go to the properties panel of any object, type :code:`paral` into the search box, and activate :code:`Camera Parallel Projection`.
...image:: activate_camera_parallel_projection.png
.. image:: activate_camera_parallel_projection.png
Next you could :ref:`set-background` (and its default).
.. _set-view-size:
Set the view size
====================
.. note::
This document is part of a series teaching how to :ref:`create-image-sea-surface-speeds`.
When preparing to export images for a video or similar, forcing paraview to display the image with *correct* proportions makes things a lot easier.
Go to ``View->Preview`` and chose the aspect ratio and size of the final product.
......@@ -12,3 +17,5 @@ Go to ``View->Preview`` and chose the aspect ratio and size of the final product
Your screen display will be adjusted accordingly
.. image:: fhd-preview.png
Next you could :ref:`export-animation`.
.. _prettify-colorbar:
Adjust the color bar and its legend
===================================
..
.. _get-colorbar-editor:
.. note::
This document is part of a series teaching how to :ref:`create-image-sea-surface-speeds`.
Open the colorbar editor
------------------------------
Open the colormap editor (``View->Color Map Editor``) and chose the top right icon (a color bar with an ``e`` in the icon).
Chose the object you want to manipulate in the pipeline view on the left (e.g. `Calculator1`. Then open the colormap editor (``View->Color Map Editor``) and chose the top right icon (a color bar with an ``e`` in the icon).
.. image:: get-colorbar-editor.png
......@@ -21,3 +21,5 @@ Choose the gear at the top right of the menu (activates the display of less *imp
The result should look somewhat like
.. image:: adjusted-colorbar-labels.png
Next, you could de-activate the display of the coordinate system in the bottom right by clicking the icon with the eye and the coordinate axis in the right of the menu (see :ref:`main-screen`), and move on to :ref:`set-view-size`.
......@@ -3,6 +3,10 @@
Save the colormap as a preset
========================================
.. note::
This document is based on a series teaching how to :ref:`display-transparent-clouds`
Go to the colormap editor, chose the ``Save to preset`` option next to the preview.
.. image:: save-colormap.png
......@@ -16,3 +20,5 @@ If this name cannot be found in the following pop-up dialogue, search for ``Pres
.. image:: change-name.png
This is the end of the tutorial :ref:`display-transparent-clouds`. Feel free to :ref:`save-state`, and :ref:`export-animation`.
......@@ -20,7 +20,7 @@ Activate manual editing of the transfer function (the gear at the bottom of the
``Enable opacity mapping for surfaces`` in the checkboxes below the bar.
Set the R/G/B values to 1 in the ``Color transfer function values`` section, and reduce the maximum opacity to 0.8 in the ``Opacity transfer function``. Play with the opacity value to find your favorite compromise between visibility of clouds and background.
Set the R/G/B values to ``1`` in the ``Color transfer function values`` section, and reduce the maximum opacity to ``0.8`` in the ``Opacity transfer function``. Play with the opacity value to find your favorite compromise between visibility of clouds and background.
Things should now be changed from
......@@ -35,4 +35,9 @@ Your result should look like
.. image:: transparent-clouds-ocean-speeds.png
You can deactivate the display of the color legend with the top left color legend icon.
.. image:: deactivate-color-legend.png
Don't forget to :ref:`save-colormap-preset`.
......@@ -17,7 +17,7 @@ to
.. image:: 2d-ocean-with-earth-and-adjustments.png
.. note::
You can find a video recording covering this material at https://youtu.be/TCmnBme0OWA?t=2144, and the material at https://github.com/ESiWACE/hpda-vis-training (run the make file of the Session2 folder).
You can find a video recording covering this material at https://youtu.be/TCmnBme0OWA?t=2144, and the material at https://github.com/ESiWACE/hpda-vis-training (run the make file of the Training2021/Session2 folder).
.. note::
Whatever you do with paraview, keep saving state files (``File -> Save State``) (see :ref:`save-state`) at regular intervals. You can additionally :ref:`make-paraview-save-on-quit-or-crash`.
......@@ -43,4 +43,6 @@ Finally you can de-activate the display of the coordinate system in the bottom r
To prepare for export (as/for a video) you should :ref:`set-view-size` before you :ref:`export-animation`.
You can continue by :ref:`display-transparent-clouds`
Here, you can :download:`Download a state file with all features <2d-ocean-with-earth-and-adjustments.pvsm>`. You will need to :ref:`activate_the_cdi_reader_plugin` before loading it and chose the directory with your downloaded input files on loading the state file to make it work.
You can continue with :ref:`display-transparent-clouds`.
......@@ -20,12 +20,16 @@ This example will show how to create an animation based on ocean, vegetation, so
In this example we assume a very basic level of familiarity with Paraview. If you feel lost in between, consider looking at :ref:`create-image-sea-surface-speeds`. This multi-variable visualization requires a substantial amount of :ref:`paraview-palmod-pre-processing`.
* :ref:`vegetation-data`
* :ref:`load-icebergs`
* :ref:`load-ice-sheets`
.. toctree::
:maxdepth: 2
:caption: Steps:
:glob:
pre-processing
vegetation-data
load-icebergs
load-ice-sheets
* Repeat the same exercise including :ref:`convert-cell-to-point` for ``vilma_ss_777.nc`` (variable ``topg`` for the topography and ``delta_topg`` for the isolines - copy and paste as appropriate). That should get you isolines on land.
* Also apply the contour to the pure Cell Data to Point Data filter, to get isolines on the ocean.
......@@ -7,6 +7,7 @@ Display clouds as a semi-transparent overlay
.. note::
This document is based on a series teaching how to :ref:`create-image-sea-surface-speeds`. If you continue from this, or other work, don't forget to :ref:`save-state`. If not, you might want to :ref:`texture-map-to-plane` to get a nice background.
Here, you can :download:`Download a state file with all features <../2D_ocean_example/2d-ocean-with-earth-and-adjustments.pvsm>` with the ocean currents. You will need to :ref:`activate_the_cdi_reader_plugin` before loading it and chose the directory with your downloaded input files on loading the state file to make it work.
First, load ``clivi_cllvi_newtime.nc`` (see :ref:`load-2d-icon` for details).
......@@ -31,3 +32,5 @@ Your result should look like
Finally :ref:`save-state`, and :ref:`export-animation`.
:download:`Here is a state file with all features for reference<currents-and-clouds.pvsm>`.
.. Vis documentation master file, created by
sphinx-quickstart on Tue Sep 8 11:52:42 2020.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
.. _paraview-examples:
Paraview Examples
=================
Two introductory examples working with ICON data and building on each other
.. toctree::
:maxdepth: 1
:glob:
2D_ocean_example/index
Transparent-clouds/index
A more complex example working with MPI-ESM, PISM and VILMA:
Examples
===================================================
.. toctree::
:maxdepth: 2
:caption: Contents:
:maxdepth: 1
:glob:
*/index
PalMod_combined/index
.. *
......@@ -16,7 +16,7 @@ Export an animation
It has proven useful to export to a sequence of png files that can then be concatenated using ``ffmpeg``.
Chose ``File->Export Animation``, enter a base file name (will be expanded by _0123/..., see the ``Suffix format`` field in the following dialogue), and ensure the correct image size in the following dialogue.
Chose ``File->Save Animation``, enter a base file name (will be expanded by _0123/..., see the ``Suffix format`` field in the following dialogue), and ensure the correct image size in the following dialogue.
.. image:: export-basic-screen.png
......@@ -31,9 +31,9 @@ This will generate a sequence of .png files. For a quick impression you can run
.. note::
FFMPEG is not included in the software image on the VM of the ESiWACE2 HPDA and Vis course. On DKRZ's supercomputer mistral you can find a reasonable ffmpeg on the GPU nodes.
FFMPEG is not included in the software image on the VM of the 2020 ESiWACE2 HPDA and Vis course. On DKRZ's supercomputer mistral you can find a reasonable ffmpeg on the GPU nodes.
If you have a reasonable complete ffmpeg, this shell script will work:
If you have a reasonably complete ffmpeg, this shell script will work:
.. code-block:: bash
......@@ -41,6 +41,9 @@ If you have a reasonable complete ffmpeg, this shell script will work:
set -evxu
output_framerate=${output_framerate:-5}
ffmpeg -framerate $output_framerate -pattern_type glob -i "$1" -c:v libx264 -r $output_framerate -pix_fmt yuv420p $2
echo created $2
Save it as ``ffmglob``, do ``chmod a+x ffmglob`` to make it executable and then call it as ``./ffmglob 'FILENAME*.png' speeds.mp4`` -- yes, you need the quotes around the FILENAME expression.
This is the end of the example :ref:`create-image-sea-surface-speeds`. Next you could continue with :ref:`display-transparent-clouds`.
......@@ -53,3 +53,6 @@ You should have Earth peeking out of the holes in the ocean.
.. image:: 05-texture-on-earth.png
Next, you can :ref:`camera-parallel-projection` to reduce projection artifacts.
......@@ -20,3 +20,7 @@ Use the checkbox in the top left corner to deactivate the light kit.
If you followed the whole series of :ref:`create-image-sea-surface-speeds`, your result should look like this:
.. image:: 03-ocean-currents-no-light-kit.png
Next you can :ref:`texture-map-to-plane`.
......@@ -16,4 +16,5 @@ Or chose from the full menue:
:glob:
*
Examples/index
*/index
......@@ -26,7 +26,7 @@ author = 'Florian Ziemen'
# The short X.Y version
version = ''
# The full version, including alpha/beta/rc tags
release = '0.0'
release = '1.0'
# -- General configuration ---------------------------------------------------
......@@ -109,15 +109,17 @@ htmlhelp_basename = 'Visdoc'
latex_elements = {
# The paper size ('letterpaper' or 'a4paper').
#
# 'papersize': 'letterpaper',
'papersize': 'a4paper',
# The font size ('10pt', '11pt' or '12pt').
#
# 'pointsize': '10pt',
'pointsize': '10pt',
# Additional stuff for the LaTeX preamble.
#
# 'preamble': '',
'preamble': r'\setkeys{Gin}{width=0.5\textwidth}',
'tableofcontents' : r'FANCY \tableofcontents',
# Latex figure (float) alignment
#
......@@ -128,8 +130,8 @@ latex_elements = {
# (source start file, target name, title,
# author, documentclass [howto, manual, or own class]).
latex_documents = [
(master_doc, 'Vis.tex', 'Vis Documentation',
'People', 'manual'),
(master_doc, 'Vis.tex', 'An Introduction to visualization of climate data with Paraview',
'Florian Ziemen / DKRZ / ESiWACE2', 'manual'),
]
......
......@@ -7,15 +7,17 @@ Documentation for visualization
===============================
.. toctree::
:maxdepth: 2
:maxdepth: 4
:caption: Contents:
:glob:
Paraview/index
Indices and tables
==================
.. only:: html
* :ref:`genindex`
* :ref:`search`
Indices and tables
==================
* :ref:`genindex`
* :ref:`search`
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