fesom / pyfesom

python library and tools for pre and post processing of the FESOM ocean model files

THIS PROGECT IS NOT SUPPORTED ANYMORE AND ARCHIVED

Please use https://github.com/FESOM/pyfesom2 instead

pyfesom

Collection of tools for basic handling of FESOM ocean model output.

Documentation (tools and library)

http://pyfesom.readthedocs.io/en/latest/index.html

Examples of library usage

• Show fesom mesh
• Plot variable on original grid
• Plot simple diagnostic (mean, std)
• Interpolate to regular grid
• Compare to climatology

Requirements

We try to support both python 2.7 and possibly 3.4.

• numpy
• scipy
• pandas
• netCDF4

pyfesom's Issues

Unable to change the color label

I have a problem with the color label.

I want to remove the white color of the planets on my plot, but I keep getting errors. this is my script

`def plot_holoviews(mesh, data, wireframe=False, cmap=None, proj='pc', data_name='data',clabel=None, levels=None):

elem2 = mesh.elem[mesh.no_cyclic_elem]
data = np.ma.masked_equal(data, 0)

verts = pd.DataFrame({'Longitudes':mesh.x2, 'Latitudes':mesh.y2, 'data':data})
tris = pd.DataFrame({'v0':elem2[:,0],'v1':elem2[:,1], 'v2':elem2[:,2]})
fesom_mesh = gv.TriMesh((tris, verts), crs=crs.PlateCarree())
if wireframe:
    verts2 = pd.DataFrame({'Longitudes':mesh.x2, 'Latitudes':mesh.y2})
    trimesh = gv.TriMesh((tris, verts2), crs=crs.PlateCarree())
    wireframe_plot = datashade(trimesh, interpolation=None, cmap=['black'])

if proj == 'pc':
    projection=crs.PlateCarree()
    width=800,
    height=500,
    y_range=(-80,90)
elif proj == 'np':
    projection=crs.NorthPolarStereo()
    width = 500,
    height = 500,
    y_range=(60,90)
elif proj == 'sp':
    projection=crs.SouthPolarStereo()
    width = 500,
    height = 500,
    y_range=(-90,-30)

if cmap is None:
    cmap=cmo.balance
    
main_plot = rasterize(fesom_mesh, interpolation=None, y_range=y_range).opts(
                    tools=["hover"],
                    width=width[0],
                    height=height[0],

projection=projection,

                    colorbar=True,
                    cmap=cmap,
                    colorbar_position="bottom",
                    clabel=clabel,
                    fontscale=1.3,
                    color_levels=levels
                )
if wireframe:
    return main_plot * gv.feature.coastline() * wireframe_plot
else:
    return main_plot * gv.feature.coastline()`

After Loading my data, I did this;

levels=[-5,-4,-3,-2,-1,0,1,2,3,4,5] and the this;
plot_holoviews(mesh, data0, clabel="sea surface temperature", levels=levels)

I don't know what the problem is, can someone help me with this?

Thank you

More flexible naming of the output files

As agreed during a meeting on 25.06.2021 with @koldunovn , it would be great if PyFesom could support a wider range of naming conventions for FESOM output files.

At the moment it only supports the following naming convention:

<variable>.<ID>.<Year>.nc

However, in ESM-Tools for example, we often do monthly and even daily restarts, and copy these files into a common folder, therefore needing to change the name using a time stamp. The format we've been using for that is:

<cariable>.<ID>.<YearMonth>.<Day>.nc

An example of how the output looks like for a finished simulation of AWICM3 using ESM-Tools can be found here: /work/ollie/mandresm/esm_yaml_test/eternal_awicm3_daily/outdata/fesom/

White line when plotting with polar stereo projections

Hi,
I am trying to plot FESOM1.4 with in a SouthPolarStereo projection and get this white line at one meridian, similar to what you have mentioned here, @koldunovn : https://github.com/koldunovn/pi_mesh_python/blob/master/triangular_mesh_maps_NorthPolarStereo.ipynb

I was just wondering, where to get the *.txt from (elements.txt, xnodes.txt, etc.) as they seem to be crucial for getting rid of this white line. Or are there other ways to accomplish that? Could someone maybe clarify this?

Fesom1 MOC calculation with pyfesom?

Hi

Is there a way to calculate the default MOC (i.e. based on binned vertical velocity) for basins of my choice for fesom1 output? I could not find this information in the pyfesom documentation.

Thanks a lot,
Chris

problems with processing velocity data

I did't find examples about processing FESOM velocity data using pyfesom, and I met some problems I coudn't figure out:

1. u, elem_no_nan = pf.get_data(f.variables['u'][time_id,:],mesh,lv_dep)
   the output u is 2-d, not like temp whose output is 1-d and is the same size as mesh.x2. What's the corresponding grid of the u?
2. If I use pf.fesom2regular(u, mesh, lonn, latt, how='idist', k=10) directly, is the output right for me to use in lon/lat grid? Is there a need to use pf.vec_rotate_r2g ?

Defined cases for Atlantic, Indik, and Pacific Ocean in `plot_transect_map`

I would like to suggest to allow restricting the plot_transect_map to the three ocean basis.

plot_transect_map(lon_start, lat_start, lon_end, lat_end,
                      mesh, npoints=30, view = 'w', stock_img=False):
    :
    if view=='w':
      :
      :
    elif view=='atl':
        # Atlantic
        ax = plt.subplot(111, projection=ccrs.Mercator(central_longitude=0))
        ax.set_extent([25, -85, -75, 70], crs=ccrs.PlateCarree())
    elif view=='ind':
        # Indik
        ax = plt.subplot(111, projection=ccrs.Mercator(central_longitude=70))
        ax.set_extent([140, +15, -75, 30], crs=ccrs.PlateCarree())
    elif view=='pac':
        # Pacific
        ax = plt.subplot(111, projection=ccrs.Mercator(central_longitude=-180))
        ax.set_extent([-255, -70, -75, 67], crs=ccrs.PlateCarree())   
    else:
:

ImportError

Hi, I'm trying to import pyfesom but it raised this error:

ImportError Traceback (most recent call last)
Cell In[1], line 1
----> 1 import pyfesom.pyfesom as pf

File ~/Desktop/Nw_Sea/FESOM/pyfesom/pyfesom/init.py:15
13 from .ut import *
14 from .climatology import *
---> 15 from .transect import *
16 from .plotting import *
20 author = 'FESOM team'

File ~/Desktop/Nw_Sea/FESOM/pyfesom/pyfesom/transect.py:13
1 # -- coding: UTF-8 --
2 # This file is part of pyfesom
3 #
(...)
8 #
9 ################################################################################
12 import numpy as np
---> 13 import pyproj
14 from .ut import tunnel_fast1d, vec_rotate_r2g
15 import numpy as np

File ~/miniforge3/envs/py38/lib/python3.8/site-packages/pyproj/init.py:49
32 all = [
33 "Proj",
34 "Geod",
(...)
45 "show_versions",
46 ]
47 import warnings
---> 49 import pyproj.network
50 from pyproj._datadir import ( # noqa: F401
51 _pyproj_global_context_initialize,
52 set_use_global_context,
53 )
54 from pyproj._show_versions import show_versions # noqa: F401

File ~/miniforge3/envs/py38/lib/python3.8/site-packages/pyproj/network.py:10
6 from typing import Union
8 import certifi
---> 10 from pyproj._network import ( # noqa: F401
11 _set_ca_bundle_path,
12 is_network_enabled,
13 set_network_enabled,
14 )
17 def set_ca_bundle_path(ca_bundle_path: Union[Path, str, bool, None] = None) -> None:
18 """
19 .. versionadded:: 3.0.0
20
(...)
38 variables.
39 """

ImportError: dlopen(/Users/auroralin/miniforge3/envs/py38/lib/python3.8/site-packages/pyproj/_network.cpython-38-darwin.so, 0x0002): Library not loaded: '@rpath/libtiff.5.dylib'
Referenced from: '/Users/auroralin/miniforge3/envs/py38/lib/libproj.21.0.2.dylib'
Reason: tried: '/Users/auroralin/miniforge3/envs/py38/lib/libtiff.5.dylib' (no such file), '/Users/auroralin/miniforge3/envs/py38/lib/libtiff.5.dylib' (no such file), '/Users/auroralin/miniforge3/envs/py38/lib/libtiff.5.dylib' (no such file), '/Users/auroralin/miniforge3/envs/py38/lib/python3.8/site-packages/pyproj/../../../libtiff.5.dylib' (no such file), '/Users/auroralin/miniforge3/envs/py38/lib/libtiff.5.dylib' (no such file), '/Users/auroralin/miniforge3/envs/py38/lib/libtiff.5.dylib' (no such file), '/Users/auroralin/miniforge3/envs/py38/lib/python3.8/site-packages/pyproj/../../../libtiff.5.dylib' (no such file), '/Users/auroralin/miniforge3/envs/py38/bin/../lib/libtiff.5.dylib' (no such file), '/Users/auroralin/miniforge3/envs/py38/bin/../lib/libtiff.5.dylib' (no such file), '/usr/local/lib/libtiff.5.dylib' (no such file), '/usr/lib/libtiff.5.dylib' (no such file)

And I find libtiff.6.dylib in the specific path, but no libtiff.5.dylib.
It bothers me a lot, and with your kind help.