cleanup of directory structure

source/Paraview/Camera_and_perspective/background.rst → source/Paraview/Camera_and_perspective/background/index.rst

@@ -10,10 +10,10 @@ Set the background of the curret 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*.
 
-.. image:: background/set-background.png
+.. image:: set-background.png
 
 
-.. image:: background/pink-background.png
+.. image:: pink-background.png
 
 .. _set-default-background:
 
@@ -23,4 +23,4 @@ Set the default background
 
 To set the default background :ref:`open-settings` and adjust it in the ``Color Palette`` tab
 
-.. image:: background/set-default-background.png
+.. image:: set-default-background.png

source/Paraview/Camera_and_perspective/camera_parallel_projection.rst → source/Paraview/Camera_and_perspective/camera_parallel_projection/index.rst

@@ -7,4 +7,4 @@ Switch to camera parallel projection
 If you are using paraview for 2D mapping, switching to camera parallel projection helps removing projection artifacts.
 
 
-.. image:: camera_parallel_projection/activate_camera_parallel_projection.png
+...image:: activate_camera_parallel_projection.png

source/Paraview/Camera_and_perspective/index.rst

@@ -11,6 +11,4 @@ Camera and perspective
    :caption: Contents:
    :glob:
 
-   *
-
-..   */index
+   */index

source/Paraview/Camera_and_perspective/view-size.rst → source/Paraview/Camera_and_perspective/view-size/index.rst

@@ -7,8 +7,8 @@ When preparing to export images for a video or similar, forcing paraview to disp
 
 Go to ``View->Preview`` and chose the aspect ratio and size of the final product.
 
-.. image:: ./view-size/view-size-fhd.png
+.. image:: view-size-fhd.png
 
 Your screen display will be adjusted accordingly
 
-.. image:: ./view-size/fhd-preview.png
+.. image:: fhd-preview.png

source/Paraview/Colormap/chose-BuGn.rst → source/Paraview/Colormap/chose-BuGn/index.rst

@@ -10,11 +10,11 @@ In the top left part of the paraview window, there is a color ar with a small gr
 
 In the Color Map Editor window (View-> Color Map Editor Window) it's on the right hand side of the color map preview
 
-.. image:: chose-BuGn/06-chose-colormap.png
+.. image:: 06-chose-colormap.png
 
 
-..
-  image:: chose-BuGn/07-colormap-overview.png
+
+.. image:: 07-colormap-overview.png
 
 In the color map chooser window, you can select a color map from a wide range of options. By default, only a few of them are displayed. With the dropdown menu on the right [Default] you can chose from a couple groups or display all of them.
 
@@ -22,13 +22,13 @@ In the text field in the top, you can start typing letters that should appear in
 
 You can chose to import a color map with its ``preset range`` (top right) - this can be useful if you e.g. customize a color map for display of annual mean temperatures and save it with that preset range for later use.
 
-.. image:: chose-BuGn/08-colormap-choser.png
+.. image:: 08-colormap-choser.png
 
 
 This should get you something like this:
 
 
-.. image:: chose-BuGn/09-BuGn-currents.png
+.. image:: 09-BuGn-currents.png
 
 
 You can now :ref:`rescale-colormap-to-custom`.

source/Paraview/Colormap/index.rst

@@ -12,5 +12,4 @@ Colormaps
    :glob:
 
    *
-
-..   */index
+   */index

source/Paraview/Colormap/invert.rst → source/Paraview/Colormap/invert/index.rst

@@ -5,4 +5,4 @@ Invert the Colormap
 
 Go to the Colormap editor (``View -> Color Map Editor Window``), and choose the Black and White icon right of the display.
 
-.. image:: invert/invert.png
+.. image:: invert.png

source/Paraview/Colormap/prettify-colorbar.rst → source/Paraview/Colormap/prettify-colorbar/index.rst

@@ -11,13 +11,13 @@ Adjust the color bar and its legend
 
 Open the colormap editor (``View->Color Map Editor``) and chose the top right icon (a color bar with an ``e`` in the icon).
 
-.. image:: prettify-colorbar/get-colorbar-editor.png
+.. image:: get-colorbar-editor.png
 
 
 Choose the gear at the top right of the menu (activates the display of less *important* aspects like the top/bottom value labels), insert a more precise label text in the ``Title`` field, e.g. "Ocean surface speed (m/s)" and set the format for the range labels (top/bottom values) to ``%.0f`` (floating-point with zero digits behind the ``.``). Use ``Apply`` to check your results and finally leave the menu with ``OK``.
 
-.. image:: prettify-colorbar/adjust-colorbar-labels.png
+.. image:: adjust-colorbar-labels.png
 
 The result should look somewhat like
 
-.. image:: prettify-colorbar/adjusted-colorbar-labels.png
+.. image:: adjusted-colorbar-labels.png

source/Paraview/Colormap/rescale-to-custom.rst → source/Paraview/Colormap/rescale-to-custom/index.rst

@@ -8,11 +8,11 @@ Rescale the colormap to a custom range
 
 Use this button to rescale your color map to a custom range or chose a custom color for monochromatic displays
 
-.. image:: rescale-to-custom/09-rescale-to-custom.png
+.. image:: 09-rescale-to-custom.png
 
 Chose 0 to 1 to get this image:
 
-.. image:: rescale-to-custom/10-rescaled-to-custom.png
+.. image:: 10-rescaled-to-custom.png
 
 
 you can now :ref:`deactivate-light-kit` to make the colors stand out even better.

source/Paraview/Colormap/save-to-preset.rst → source/Paraview/Colormap/save-to-preset/index.rst

@@ -5,14 +5,14 @@ Save the colormap as a preset
 
 Go to the colormap editor, chose the ``Save to preset`` option next to the preview.
 
-.. image:: ./save-to-preset/save-colormap.png
+.. image:: save-colormap.png
 
 
 You can give the colormap a name, and chose to also save the opacity information.
 
-.. image:: ./save-to-preset/name-dialogue.png
+.. image:: name-dialogue.png
 
 If this name cannot be found in the following pop-up dialogue, search for ``Preset``  in the top menu and rename...
 
 
-.. image:: ./save-to-preset/change-name.png
+.. image:: change-name.png

source/Paraview/Colormap/transparent-clouds.rst → source/Paraview/Colormap/transparent-clouds/index.rst

@@ -24,15 +24,15 @@ Set the R/G/B values to 1 in the ``Color transfer function values`` section, and
 
 Things should now be changed from
 
-.. image:: transparent-clouds/fields-to-change.png
+.. image:: fields-to-change.png
 
 to
 
-.. image:: transparent-clouds/fields-changed.png
+.. image:: fields-changed.png
 
 Your result should look like
 
-.. image:: transparent-clouds/transparent-clouds-ocean-speeds.png
+.. image:: transparent-clouds-ocean-speeds.png
 
 
 Don't forget to :ref:`save-colormap-preset`.

source/Paraview/Examples/PalMod_combined/load-ice-sheets.rst

@@ -3,11 +3,10 @@
 Load the ice sheets
 ==============================
 * Load the ice sheet data from `pism_NH_777.nc <https://swiftbrowser.dkrz.de/public/dkrz_8656c91ce0734327b6dc867fc5b6b068/ESiWACE2-Public/Paraview%20Sample%20Data/PalMod_example/>`_
-n
+
 * For random reasons, this file already is in point data. Attach a calculator and in the pipeline view select the calculator of the vegetation, copy it, and paste it to the newly created calculator (i.e. copy the settings to the calculator of the ice sheet). Change ``topg`` to ``ice_surf`` in the equation of the calculator.
 
-.. image::
-     copy-calculator.png
+.. image:: copy-calculator.png
 
 * Color by ``velsurf_mag``, chose ``Use log scale when mapping data to colors``, load the colormap of your choice.
 

source/Paraview/Export/export-animation.rst → source/Paraview/Export/export-animation/index.rst

@@ -16,12 +16,12 @@ It has proven useful to export to a sequence of png files that can then be conca
 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.
 
 
-.. image:: export-animation/export-basic-screen.png
+.. image:: export-basic-screen.png
 
 
 (If you change the size of the saved animation, you might want to toggle the gear in the top left and change the font scaling option, but really -- :ref:`set-view-size` beforehand!)
 
-.. image:: export-animation/export-advanced-screen.png
+.. image:: export-advanced-screen.png
 
 
 This will generate a sequence of .png files. For a quick impression you can run through them using ``eog FILENAME*.png`` on linux, or preview on a mac.

source/Paraview/Export/index.rst

@@ -11,6 +11,4 @@ Export
    :caption: Contents:
    :glob:
 
-   *
-
-..   */index
+   */index

source/Paraview/Filters/calculator-topography.rst → source/Paraview/Filters/calculator-topography/index.rst

@@ -27,7 +27,7 @@ Where the first paren scales the topography to a strong extrusion around a unit
 
 
 .. image::
-   calculator-topography/calculator-settings.png
+   calculator-settings.png
 
 
 .. note::

source/Paraview/Filters/calculator-uv-speed.rst → source/Paraview/Filters/calculator-uv-speed/index.rst

@@ -16,7 +16,7 @@ Now we want to apply a "Calculator" filter to compute the absolute speed from th
 Choose Filters->Common->Calculator, or use the calculator symbol just above the pipeline.
 
 
-.. image:: calculator-uv-speed/04-pipeline.png
+.. image:: 04-pipeline.png
 
 In the calculator, you can chose the data type to operate on ("cell data" is correct here), give your result variable a sensible name -- we chose ``vel`` here -- ``speed`` would have been correct...
 
@@ -29,11 +29,11 @@ In the next field, you can define the equation that is computed. We want to use:
 You can also use the drop-down menus at the bottom to get access to the variables available (sorted by scalars and vector quantities).
 
 
-.. image:: calculator-uv-speed/05-calculator.png
+.. image:: 05-calculator.png
 
 The result should look similar to this:
 
-.. image:: calculator-uv-speed/05a-speed-image.png
+.. image:: 05a-speed-image.png
 
 With the speed computed, you can :ref:`chose-BuGn`
 

source/Paraview/Filters/cell-to-point.rst → source/Paraview/Filters/cell-to-point/index.rst

@@ -12,7 +12,7 @@ Some filters are picky with regard to their input data type and require cell dat
 Use the dropdown for choosing the object color to check which variables of which types are available.
 In this example topo exists as cell and as point data (because we just converted it). The topo with a dot in front of it is point data. That with a box is cell data.
 
-.. image:: cell2point/cell-or-point.png
+.. image:: cell-or-point.png
 
 
 If neccessary you can
@@ -28,10 +28,10 @@ Convert cell data to point data
 To convert cell data to point data, do ``Filters->Search`` and enter ``cell da``, use ``Enter`` to cofirm.
 
 .. image::
-   cell2point/cell2point.png
+   cell2point.png
 
 In the settings of the calculator activate passing of cell data.
 If you have many arrays in your input data, you might only want to process the data of relevance for this use.
 
-.. image::  cell2point/
+.. image::
 	    pass-cell.png

source/Paraview/Filters/contour-isolines.rst → source/Paraview/Filters/contour-isolines/index.rst

-.. _countour-isolines:
+.. _contour-isolines:
 
 Use the contour filter to display isolines
 ===========================================
@@ -6,21 +6,21 @@ Use the contour filter to display isolines
 Add a contour filter
 
 .. image::
-   contour-isolines/add-contour.png
+   add-contour.png
 
 Chose the variable, you want to contour by, use the red x to get rid of the default contour level, use the *scale* icon (below + and -) to create a number series, (see below), finally select the levels ``100`` and the ``0`` and use the ``+`` to add ``-50`` and ``50`` levels below them.
 
 .. image::
-   contour-isolines/contour-levels.png
+   contour-levels.png
 
 
 
 .. image::
-   contour-isolines/number-series.png
+   number-series.png
 
 Adjust the line width to ``5`` by searching for ``line`` in the search box in the top and then adjusting it.
 
 .. image::
-   contour-isolines/line-width.png
+   line-width.png
 
 Select ``BrBG`` as colormap, invert it, and set the value range to ``-100`` to ``100``.

source/Paraview/Filters/index.rst

@@ -11,6 +11,6 @@ Filters
    :caption: Contents:
    :glob:
 
-   *
 
-..   */index
+
+   */index

source/Paraview/Filters/texture-map-to-plane.rst → source/Paraview/Filters/texture-map-to-plane/index.rst

@@ -15,41 +15,41 @@ Add an image as texture (plane) in the background
 
 As our ocean data set has *holes* on the land points, we have to first create a plane *behind* it, before we can attach an image of Earth.
 
-.. image:: texture-map-to-plane/000-ocean-with-holes.png
+.. image:: 000-ocean-with-holes.png
 
 As a first step, we figure out the size of *Earth* in paraview. For this we need the ``Information View`` (View-> Information). There we look for the section ``Bounds`` and note the extreme values. The x-range is from roughly -300 to 300, the y-range is from roughly -131 to 150. The lower bound of the y-range is a bit weird, because Antarctica is cut off, because the oceans don't reach 90 deg S. Now we know our plane needs to be -300 to 300 by -150 to 150, and just below z=0.
 
-.. image:: texture-map-to-plane/00a-find-data-size.png
+.. image:: 00a-find-data-size.png
 
 We can get a plane from the ``Sources`` menu, e.g. from ``Geometric Shapes``.
 
-.. image:: texture-map-to-plane/00b-get-plane.png
+.. image:: 00b-get-plane.png
 
 Here we adjust the x coordinates to +/- 300 and the y coordinates to +/- 150, keeping the signs as they were. As z-coordinate we use -0.1 to put this plane just below the ocean.
 
-.. image:: texture-map-to-plane/00c-new-coordinates.png
+.. image:: 00c-new-coordinates.png
 
 After clicking ``Apply``, we should have all land areas filled with white.
 
 Now we can add the texture itself. Chose ``Filters->Search...`` and type ``texture``. You will be presented with the three different texture filters. Chose ``Texture Map to Plane`` and hit ``Enter``
 
-.. image:: texture-map-to-plane/01-find-filter.png
+.. image:: 01-find-filter.png
 
 Now you first have to click apply before you can set the texture (for whatever reason)
 
-.. image:: texture-map-to-plane/02-apply.png
+.. image:: 02-apply.png
 
 Now use the text box and search for texture. Click the ``Texture`` dropdown menu, and chose load.
 
 
-.. image:: texture-map-to-plane/03-find-texture-field.png
+.. image:: 03-find-texture-field.png
 
 Pick the small blue marble from the directory with the sample data (or use any one of NASA's Blue Marble images, e.g.  `the low-res version of the February image <https://eoimages.gsfc.nasa.gov/images/imagerecords/74000/74268/world.topo.200402.3x5400x2700.jpg>`_. (Thanks, NASA for that great service!).
 
 
-.. image:: texture-map-to-plane/04-texture-file.png
+.. image:: 04-texture-file.png
 
 You should have Earth peeking out of the holes in the ocean.
 
 
-.. image:: texture-map-to-plane/05-texture-on-earth.png
+.. image:: 05-texture-on-earth.png

source/Paraview/Filters/texture-map-to-sphere.rst → source/Paraview/Filters/texture-map-to-sphere/index.rst

@@ -7,12 +7,12 @@ Create a sphere and follow the steps for mapping a texture to a plane in :ref:`t
 
 Some adjustments are necessary. If you use a custom-created sphere, increase the resolution in teta and phi in the properties of the sphere (not the texture mapping).
 
-.. image:: ../Sources/Sphere/sphere-resolution.png
+.. image:: ../../Sources/Sphere/sphere-resolution.png
 
 To avoid a seam set the theta-range to 359.999
 
-.. image:: ./texture-map-to-sphere/theta-range.png
+.. image:: ./theta-range.png
 
 To match the projection to that of icon data set all scalings to -.999
 
-.. image:: ./texture-map-to-sphere/scale-texture.png
+.. image:: ./scale-texture.png

source/Paraview/Light/deactivate-light-kit.rst → source/Paraview/Light/deactivate-light-kit/index.rst

@@ -12,11 +12,11 @@ Deactivate the light kit
 
 By default, Paraview creates a couple of light sources in positions that are fixed relative to the viewer. This light sources allow for shadows and depth perception. However this comes at the cost of brilliance of colors.
 
-.. image:: deactivate-light-kit/01-get-light-inspector.png
+.. image:: 01-get-light-inspector.png
 
 Use the checkbox in the top left corner to deactivate the light kit.
 
-.. image:: deactivate-light-kit/02-light-inspector.png
+.. image:: 02-light-inspector.png
 
 
 If you followed the whole series of  :ref:`create-image-sea-surface-speeds`, your result should look like this:

source/Paraview/Light/index.rst

@@ -11,7 +11,4 @@ Light
    :caption: Contents:
    :glob:
 
-   *
-
-
-..   */index
+   */index

source/Paraview/Readers/nemo-3d-netcdf-CF.rst → source/Paraview/Readers/Nemo/index.rst

@@ -15,4 +15,4 @@ Settings that get you some idea of the output are
 
 ``Replace Fill Value with NaN``
 
-.. image:: ./Nemo/nemo-with-netCDF-CF-reader.png
+.. image:: ./nemo-with-netCDF-CF-reader.png

source/Paraview/Readers/cdi-reader-plugin.rst → source/Paraview/Readers/cdi-reader-plugin/index.rst

@@ -12,12 +12,12 @@ For loading ICON data, we need to activate the CDI reader plugin (on Mistral it'
 Chose Tools-> Manage Plugins
 
 
-.. image:: cdi-reader-plugin/00a-load-plugin.png
+.. image:: 00a-load-plugin.png
 
 Select the CDIReader plugin, open the detailed view, activate ``Auto Load``, and Chose ``Load selected`` at the bottom. The ``Status`` should now be ``Loaded``, and ``Load Selected`` should be greyed out.
 
 
-.. image:: cdi-reader-plugin/00b-activate-cdi-plugin.png
+.. image:: 00b-activate-cdi-plugin.png
 
 
 With the cdi reader loaded, you can  :ref:`load-2d-icon`

source/Paraview/Readers/cf-reader.rst → source/Paraview/Readers/cf-reader/index.rst

@@ -23,9 +23,9 @@ Open a file with the standard NetCDF Reader
 
 Use ``File->Open`` or the top-left icon (see :ref:`main-screen`), chose the desired file and select ``NetCDF reader`` when prompted.
 
-.. image:: cf-reader/chose-reader.png
+.. image:: chose-reader.png
 
 
 For a spherical projection use ``Spherical Coordinates`` and (for most cases) use ``Replace Fill Value With Nan``
 
-.. image:: cf-reader/spherical-nans.png
+.. image:: spherical-nans.png

source/Paraview/Readers/index.rst

@@ -11,6 +11,4 @@ Readers
    :caption: Contents:
    :glob:
 
-   *
-
-..   */index
+   */index

source/Paraview/Readers/load-2d-icon.rst → source/Paraview/Readers/load-2d-icon/index.rst

@@ -10,18 +10,18 @@ You might need to :ref:`activate_the_cdi_reader_plugin`
 
 Use File-> Open.., or use the top-left icon to open the file choser.
 
-.. image:: load-2d-icon/01-load-file.png
+.. image:: 01-load-file.png
 
 
 Chose uv.nc (get it from ....)
 
-.. image:: load-2d-icon/02-chose-file.png
+.. image:: 02-chose-file.png
 
 
 Chose the CDI reader for ICON files -- Models with a regular (lat/lon, or stretched) grid usually go via "NetCDF Reader". If CDIReader does not appear in the menu, you need to :ref:`activate_the_cdi_reader_plugin`.
 
 
-.. image:: load-2d-icon/02a-chose-reader.png
+.. image:: 02a-chose-reader.png
 
 
 uv.nc now appears in the top of the pipeline (top left).
@@ -35,20 +35,20 @@ Some ICON Ocean data comes with zeros on land points. Then a wet_c variable can
 With "Vertical levels" you can chose which vertical level you want to see if there's more than one in the source file (not in uv.nc).
 
 
-.. image:: load-2d-icon/03-viever-properties.png
+.. image:: 03-viever-properties.png
 
 The result should look like this:
 
-.. image:: load-2d-icon/02b-ocean-loaded.png
+.. image:: 02b-ocean-loaded.png
 
 
 From the dropdown menu in the top you can chose to color by any variable, e.g. ``v``
 
-.. image:: load-2d-icon/04-chose-variable-for-display.png
+.. image:: 04-chose-variable-for-display.png
 
 Which should give a basic idea of eddies and friends
 
-.. image:: load-2d-icon/05-color-by-v.png
+.. image:: 05-color-by-v.png
 
 
 

source/Paraview/technical/index.rst

@@ -12,5 +12,4 @@ Technical
    :glob:
 
    *
-
-..   */index
+   */index

source/Paraview/technical/make-paraview-save-on-quit-or-crash.rst → source/Paraview/technical/make-paraview-save-on-quit-or-crash/index.rst

@@ -6,4 +6,4 @@ Make Paraview save a state on quitting or crashing
 :ref:`open-settings` and use the text box in the ``General`` tab to seach for ``save``, activate both options, and ``Apply``.
 
 
-.. image:: make-paraview-save-on-quit-or-crash/activate-options.png
+.. image:: activate-options.png

source/Paraview/technical/save-state.rst → source/Paraview/technical/save-state/index.rst

@@ -6,7 +6,7 @@ Save a state file
 There are two possible formats for saving the state (recipe) of your paraview session: ``.pvsm``, the paraview-native XML format, and ``.py`` -- python executables that can be executed using ``pvbatch``. The python export is not as stable as ``.pvsm``, so it might be a good idea to **first save your state to ``.pvsm``** and save an additional ``.py`` copy after this.
 
 
-.. image:: save-state/file-save-state.png
+.. image:: file-save-state.png
 
 
 **It has proved very useful to have older states at hand.** Paraview has the *feature* of grouping files that end on a number, so _a _b _c naming has proved useful. Using a version control system is even better. :)