Merge pull request #17 from gaelforget/v1p11c

split doc section

docs/analyses.rst

@@ -0,0 +1,56 @@
+
+.. _analyses:
+
+Analyze
+*******
+
+This section is focused on tools for analyzing outputs (:numref:`download-analysis`), and 
+additional resources (:numref:`other-resources`).
+
+.. _download-analysis:
+
+Julia Toolbox
+-------------
+
+To be continued ... 
+
+Python Toolbox
+--------------
+
+To be continued ... 
+
+Matlab Toolbox
+--------------
+
+The `gcmfaces` toolbox :cite:`for-eta:15` can be used to analyze model output that has either been downloaded (:numref:`download-solution`) or reproduced (:numref:`eccov4-baseline`) by users. From the command line, you can install either the `Matlab` version by executing:
+
+:: 
+
+    git clone https://github.com/gaelforget/gcmfaces
+
+or the `Octave` version by executing:
+
+::
+
+    git clone -b octave https://github.com/gaelforget/gcmfaces
+
+The `gcmfaces` toolbox can be used, e.g., to reproduce the `standard analysis` (i.e., the plots in :cite:`dspace-eccov4r2`) from released, nctiles model output (:numref:`download-solution`) or from plain, binary model output (:numref:`eccov4-baseline`). For more information, please consult `the gcmfaces user guide <http://gcmfaces.readthedocs.io/en/latest/>`__.
+
+.. _other-resources:
+
+Other Resources
+---------------
+
+-  A series of three presentations given during the May 2016 `ECCO` meeting at `MIT` provides an overview of `ECCO v4` data sets, capabilities, and applications
+   (`Overview <http://doi.org/10.13140/RG.2.2.33361.12647>`__;
+   `Processes <http://doi.org/10.13140/RG.2.2.26650.24001>`__;
+   `Tracers <http://doi.org/10.13140/RG.2.2.36716.56967>`__).
+
+-  Various Python tools are available to analyse model output (see, e.g., `this tutorial <https://github.com/ECCO-GROUP/ECCO-v4-Python-Tutorial>`__).
+
+-  Any `netcdf` enabled software such as `Panoply <http://www.giss.nasa.gov/tools/panoply/>`__ (available for `MS-Windows`, `Linux`, or `macOS`) can be used to plot the interpolated output (``interp_*`` directories).
+
+-  The stand-alone `eccov4_lonlat.m <http://mit.ecco-group.org/opendap/ecco_for_las/version_4/release2/doc/eccov4_lonlat.m>`__ program can be used to extract the lat-lon sector, which spans the 69S to 56N latitude range, of native grid fields :cite:`for-eta:15`.
+
+-  `ECCO v4` estimates can be plotted via the `NASA` `Sea Level Change Portal <https://sealevel.nasa.gov>`__ tools (interpolated output) or downloaded from the `Harvard Dataverse <https://dataverse.harvard.edu>`__ APIs (native grid input and output).
+

docs/downloads.rst

@@ -4,10 +4,8 @@
 Download
 ********
 
-This section provides directions to download the `ECCO V4r2` model output (:numref:`download-solution`), 
-or download the underlying model setup to reproduce `ECCO V4r2` (:numref:`download-setup`), 
-tools for analyzing outputs (:numref:`download-analysis`), and 
-additional resources (:numref:`other-resources`).
+This section provides directions to download the `ECCO V4r2` model output for analysis (:numref:`download-solution`), 
+or download the underlying model setup to reproduce `ECCO V4r2` (:numref:`download-setup`).
 
 .. _download-solution:
 
@@ -30,51 +28,3 @@ The :ref:`mitgcmdirs` is shown below. While organizing the downloaded directorie
 .. rubric:: Recommended Directory Organization
 
 .. include:: eccov4r2_dirtree.rst
-
-.. _download-analysis:
-
-Julia Toolbox
--------------
-
-To be continued ... 
-
-Python Toolbox
---------------
-
-To be continued ... 
-
-Matlab Toolbox
---------------
-
-The `gcmfaces` toolbox :cite:`for-eta:15` can be used to analyze model output that has either been downloaded (:numref:`download-solution`) or reproduced (:numref:`eccov4-baseline`) by users. From the command line, you can install either the `Matlab` version by executing:
-
-:: 
-
-    git clone https://github.com/gaelforget/gcmfaces
-
-or the `Octave` version by executing:
-
-::
-
-    git clone -b octave https://github.com/gaelforget/gcmfaces
-
-The `gcmfaces` toolbox can be used, e.g., to reproduce the `standard analysis` (i.e., the plots in :cite:`dspace-eccov4r2`) from released, nctiles model output (:numref:`download-solution`) or from plain, binary model output (:numref:`eccov4-baseline`). For more information, please consult `the gcmfaces user guide <http://gcmfaces.readthedocs.io/en/latest/>`__.
-
-.. _other-resources:
-
-Other Resources
----------------
-
--  A series of three presentations given during the May 2016 `ECCO` meeting at `MIT` provides an overview of `ECCO v4` data sets, capabilities, and applications
-   (`Overview <http://doi.org/10.13140/RG.2.2.33361.12647>`__;
-   `Processes <http://doi.org/10.13140/RG.2.2.26650.24001>`__;
-   `Tracers <http://doi.org/10.13140/RG.2.2.36716.56967>`__).
-
--  Various Python tools are available to analyse model output (see, e.g., `this tutorial <https://github.com/ECCO-GROUP/ECCO-v4-Python-Tutorial>`__).
-
--  Any `netcdf` enabled software such as `Panoply <http://www.giss.nasa.gov/tools/panoply/>`__ (available for `MS-Windows`, `Linux`, or `macOS`) can be used to plot the interpolated output (``interp_*`` directories).
-
--  The stand-alone `eccov4_lonlat.m <http://mit.ecco-group.org/opendap/ecco_for_las/version_4/release2/doc/eccov4_lonlat.m>`__ program can be used to extract the lat-lon sector, which spans the 69S to 56N latitude range, of native grid fields :cite:`for-eta:15`.
-
--  `ECCO v4` estimates can be plotted via the `NASA` `Sea Level Change Portal <https://sealevel.nasa.gov>`__ tools (interpolated output) or downloaded from the `Harvard Dataverse <https://dataverse.harvard.edu>`__ APIs (native grid input and output).
-

docs/index.rst

@@ -7,9 +7,7 @@ Welcome to ECCO version 4's documentation!
 ==========================================
 
 Learn to download, analyze, or reproduce `ECCO version 4` solutions :cite:`for-eta:15`. 
-
-In :ref:`downloads` and :ref:`runs` we take ECCO V4 `release 2` as an example. 
-Other solutions and additional resources are discussed after. 
+In :ref:`downloads`, :ref:`analyses`, and :ref:`runs` we focus on ECCO V4r2 as an example, and link to other solutions.
 
 .. toctree::
    :maxdepth: 3
@@ -18,6 +16,7 @@ Other solutions and additional resources are discussed after.
 
    introduction.rst
    downloads.rst
+   analyses.rst
    runs.rst
    biblirefs.rst
 

docs/introduction.rst

@@ -7,7 +7,9 @@ Introduction
 ECCO version 4 is an ocean state estimate :cite:`for-eta:15` and solution of the MIT general circulation model (`MITgcm <http://mitgcm.org>`__).
 ECCO V4 release 2 (`V4r2`) covers the period from 1992 to 2011 :cite:`dspace-eccov4r2`. 
 
-⏩️ :ref:`downloads` for an installation guide and links to analysis tools. 
+⏩️ :ref:`downloads` for an installation guide and links to data. 
+
+⏩️ :ref:`analyses` for analyses tools in Julia, Python, Matlab. 
 
 ⏩️ :ref:`runs` for simple instructions to reproduce the model simulation. 
 

test/testreport_ecco.jl

@@ -27,7 +27,7 @@ function compute(pth0)
  ntave=length(tave)
 
  #pth00=MeshArrays.GRID_LLC90
- pth00="run"
+ pth00=pth0 #"run"
  RAC=Main.eccotest.RAC_masked(pth00)
  vol=Main.eccotest.vol_masked(pth00)
  G,LC=Main.eccotest.load_llc90_grid(pth00)
@@ -143,7 +143,7 @@ eccotest.compare(report,ref)
 """
 function compare(A::DataFrame,B::DataFrame)
  println("Error report:")
- for v in unique(A.name)
+ for v in intersect(unique(A.name),unique(B.name))
   x=compare(A,B,v)
   if x > 0.01
     y=Int(round(100*x))
@@ -164,6 +164,7 @@ function compare(A::DataFrame,B::DataFrame,v::AbstractString)
  a=sort(A[A.name.==v,:],:index)
  b=sort(B[B.name.==v,:],:index)
  nv=min(length(a.index),length(b.index))
+ #nv=6
  if nv==1 
    abs(a.value[1]-b.value[1])/abs(a.value[1])
  else
@@ -192,10 +193,15 @@ function parse_fc(fil)
 end
 
 function list_diags_files(pth0)
-  state_2d_set1=glob("state_2d_set1*data",joinpath(pth0,"diags"))
-  state_3d_set1=glob("state_3d_set1*data",joinpath(pth0,"diags"))
-  trsp_3d_set1=glob("trsp_3d_set1*data",joinpath(pth0,"diags"))
-  trsp_3d_set2=glob("trsp_3d_set2*data",joinpath(pth0,"diags"))
+  if isdir(joinpath(pth0,"diags","STATE"))
+      (STATE,TRSP)=("STATE","TRSP")
+  else
+      (STATE,TRSP)=("","")
+  end
+  state_2d_set1=glob("state_2d_set1*data",joinpath(pth0,"diags",STATE))
+  state_3d_set1=glob("state_3d_set1*data",joinpath(pth0,"diags",STATE))
+  trsp_3d_set1=glob("trsp_3d_set1*data",joinpath(pth0,"diags",TRSP))
+  trsp_3d_set2=glob("trsp_3d_set2*data",joinpath(pth0,"diags",TRSP))
   (state_2d_set1=state_2d_set1,state_3d_set1=state_3d_set1,
     trsp_3d_set1=trsp_3d_set1,trsp_3d_set2=trsp_3d_set2)
 end