From 991e7354ade13a645ecefcdbd3e0b6b682434571 Mon Sep 17 00:00:00 2001
From: Nils Brueggemann <nils.brueggemann@mpimet.mpg.de>
Date: Tue, 19 Nov 2024 21:16:34 +0100
Subject: [PATCH] Wrapped pyic_anim, pyic_fig pyic_intake and pyic_sec into
functions so that they can be installed via setup.py
---
tools/pyic_anim.py | 598 ++++++++++++++++++++---------------------
tools/pyic_fig.py | 620 ++++++++++++++++++++++---------------------
tools/pyic_intake.py | 5 +-
tools/pyic_sec.py | 530 ++++++++++++++++++------------------
4 files changed, 884 insertions(+), 869 deletions(-)
diff --git a/tools/pyic_anim.py b/tools/pyic_anim.py
index 551b79a..6916054 100755
--- a/tools/pyic_anim.py
+++ b/tools/pyic_anim.py
@@ -1,299 +1,303 @@
#!/usr/bin/env python
-import argparse
+def main():
+ import argparse
+
+ import os
+ import sys
+ import glob
+ import pyicon as pyic
+ import matplotlib.pyplot as plt
+ import xarray as xr
+
+ ts = pyic.timing([0], string='')
+
+ help_text = """
+ Makes an animation from ICON data by first creating a jpg file for each snapshot and then creating an mp4 movie by using ffmpeg.
+
+ Usage notes:
+ ------------
+ Basic usage:
+ pyic_anim.py netcdf_file_or_list.nc var_name --fpath_out=/path/to/movie/without/file/ending/name [options]
+
+ Change color limits, colorbar:
+ pyic_anim.py netcdf_file_or_list.nc var_name --fpath_out=name --clim=-10,32 --cmap=viridis
+
+ Select depth level by indices:
+ pyic_anim.py netcdf_file_or_list.nc var_name --fpath_out=name --iz=0
+
+ Select depth:
+ pyic_anim.py netcdf_file_or_list.nc var_name --fpath_out=name --depth=1000
+
+ Change region:
+ pyic_anim.py netcdf_file_or_list.nc var_name --fpath_out=name --lon_reg=-20,30 --lat_reg=-45,-20
+
+ Plot on original triangle grid (it is recommended to cut the domain otherwise, it takes a long time):
+ pyic_anim.py netcdf_file_or_list.nc var_name --fpath_out=name --use_tgrid --lon_reg=-72,-68 --lat_reg=33,35
+
+ Change projection to North Polar Stereographic projection:
+ pyic_anim.py netcdf_file_or_list.nc var_name --fpath_out=name --projection=np
+
+ Test with showing only one figure without saving anything:
+ pyic_anim.py netcdf_file.nc var_name --test
+
+ Only re-creating the animation if the single figures are still available under fpath_out
+ pyic_anim.py netcdf_file.nc var_name --fpath_out=name --only_animation
+
+
+ Argument list:
+ --------------
+ """
+
+ # --- read input arguments
+ parser = argparse.ArgumentParser(description=help_text, formatter_class=argparse.RawTextHelpFormatter)
+
+ # --- necessary arguments
+ parser.add_argument('fpath_data', nargs='+', metavar='fpath_data', type=str,
+ help='Path to ICON data file.')
+ parser.add_argument('var', metavar='var', type=str,
+ help='Name of variable which should be plotted.')
+ # --- optional arguments
+ # --- figure saving / showing
+ parser.add_argument('--fpath_out', type=str, default='none',
+ help='Path to save the animation (without ending).')
+ parser.add_argument('--dontshow', action='store_true', default=False,
+ help='If dontshow is specified, the plot is not shown')
+ parser.add_argument('--only_animation', default=False,
+ action='store_true',
+ help='If specified, only the animation and no new figures are generated.')
+ parser.add_argument('--test', default=False,
+ action='store_true',
+ help='If specified, just a test plot is made.')
+ # --- specifying the grid
+ parser.add_argument('--gname', type=str, default='auto',
+ help='Grid name of the ICON data.')
+ parser.add_argument('--fpath_tgrid', type=str, default='auto',
+ help='Path to triangular grid file. If \'auto\' the path is guessed automatically. Only necessary if \'--use_tgrid\' is used.')
+ parser.add_argument('--fpath_ckdtree', type=str, default='auto',
+ help='Path to ckdtree interpolation file. If \'auto\' the path is guessed automatically.')
+ parser.add_argument('--coordinates', type=str, default='clat clon',
+ help='Coordinates of variable which should be plotted. Choose between \'clat clon\' (default), \'vlat vlon\' or \'elat elon\'')
+ # --- selecting time
+ parser.add_argument('--it', type=str, default='none',
+ help='Time index limits of the animation. Specify like this: --it=start_index,end_index,[optional:increment] If \'auto\' is specified all time instances are plotted.')
+ parser.add_argument('--time', type=str, default='none',
+ help='Time string \'yyyy-mm-dd\' wich should be plotted (if specified overwrites \'it\').')
+ # --- args for color / limits and settings
+ parser.add_argument('--cmap', type=str, default='auto',
+ help='Colormap used for plot. Use "cmo.name" for cmocean colormaps.')
+ parser.add_argument('--clim', type=str, default='auto',
+ help='Color limits of the plot. Either specify one or two values.If one value is specified color limits are taken symetrically around zero. If \'auto\' is specified color limits are derived automatically.')
+ parser.add_argument('--cincr', type=float, default=-1.0,
+ help='Increment for pcolor plot to specify levels between clims.')
+ parser.add_argument('--clevs', type=str, default=None,
+ help='Color levels for pcolor plot.')
+ parser.add_argument('--conts', type=str, default=None,
+ help='Contour levels for monochromatic contours.')
+ parser.add_argument('--contfs', type=str, default=None,
+ help='Contour levels for filled contour patches.')
+ parser.add_argument('--clabel', action='store_true', default=False,
+ help='If clabel is specified, color labels will be shown.')
+ # --- args for titles and labels
+ parser.add_argument('--title_center', type=str, default='auto',
+ help='Title string center.')
+ parser.add_argument('--title_left', type=str, default='auto',
+ help='Title string left.')
+ parser.add_argument('--title_right', type=str, default='auto',
+ help='Title string right. Use --title-right="full_time" for time str without rounding.')
+ parser.add_argument('--xlabel', type=str, default='',
+ help='String for xlabel.')
+ parser.add_argument('--ylabel', type=str, default='',
+ help='String for ylabel.')
+ parser.add_argument('--cbar_str', type=str, default='auto',
+ help='String for colorbar. Default is name of variable and its units.')
+ parser.add_argument('--cbar_pos', type=str, default='bottom',
+ help='Position of colorbar. It is possible to choose between \'right\' and \'bottom\'.')
+ parser.add_argument('--fig_size_fac', type=float, default=2.,
+ help='Factor to increase the figure relative to text (default --fig_size_fac=2.).')
+ # --- manupilation of data
+ parser.add_argument('--logplot', default=False,
+ action='store_true',
+ help='Plot logarithm of the data.')
+ parser.add_argument('--factor', type=float, default=None,
+ help='Factor to mulitply data with.')
+
+ # --- specific for horizontal plot parser.add_argument('--iz', type=int, default=0,
+ parser.add_argument('--use_tgrid', default=False,
+ action='store_true',
+ help='If specified, the plot is made on the original triangular grid.')
+ parser.add_argument('--res', type=float, default=0.3,
+ help='Resolution of the interpolated data which will be plotted. So far, 1.0, 0.3, 0.1 are supported.')
+ parser.add_argument('--projection', type=str, default='pc',
+ help='Map projection, choose \'None\' to deactivate cartopy, \'pc\' for normal lon/lat projection and \'np\' or \'sp\' for Norh- South-pole stereographic projections.')
+ parser.add_argument('--iz', type=int, default=0,
+ help='Depth index which should be plotted.')
+ parser.add_argument('--depth', type=float, default=-1.,
+ help='Depth value in m which should be plotted (if specified overwrites \'iz\').')
+ parser.add_argument('--lon_reg', type=str, default=None,
+ help='Longitude range of the plot.')
+ parser.add_argument('--lat_reg', type=str, default=None,
+ help='Latitude range of the plot.')
+ parser.add_argument('--central_longitude', type=float, default=None,
+ help='Central longitude for cartopy plot.')
+ parser.add_argument('--coastlines_color', type=str, default='k',
+ help='Color of coastlines. Default is \'k\'. To disable set to \'none\'.')
+ parser.add_argument('--land_facecolor', type=str, default='0.7',
+ help='Color of land masses. Default is \'0.7\'. To disable set to \'none\'.')
+ parser.add_argument('--noland', default=False,
+ action='store_true',
+ help='If specified, continents are not filled and land_facecolor is overwritten.')
+ parser.add_argument('--lonlat_for_mask', default=False,
+ action='store_true',
+ help='If specified, mask for triangles which are swapped at periodic boundaries is calculated from clon and clat (and not only from clon). Relevant for torus setup.')
+
+ # --- ffmpeg specific parameters
+ parser.add_argument('--dpi', type=float, default=250.,
+ help='Resolution for the individual saved figures (default --dpi=250).')
+ parser.add_argument('--ffmpeg', type=str, default="/work/mh0033/m300602/miniconda3/envs/pyicon_py39_exp/bin/ffmpeg",
+ help='Path to ffmpeg.')
+ parser.add_argument('--framerate', type=int, default=10,
+ help='ffmpeg framerate (-r).')
+ parser.add_argument('--vcodec', type=str, default='libx264',
+ help='ffmpeg video codec.')
+ parser.add_argument('--bitrate', type=str, default='12000k',
+ help='ffmpeg video bitrate (-b:v).')
+
+ iopts = parser.parse_args()
+
+ # these options seem not to be used
+ gname = iopts.gname
+ use_tgrid = iopts.use_tgrid
+ fpath_tgrid = iopts.fpath_tgrid
+ fpath_ckdtree = iopts.fpath_ckdtree
+
+ print('start modules')
+ import matplotlib
+ if iopts.dontshow:
+ matplotlib.use('Agg')
+ import numpy as np
+ import matplotlib.pyplot as plt
+ import cartopy
+ import cartopy.crs as ccrs
+ import xarray as xr
+ import glob
+ import os
+ import sys
+ from pathlib import Path
+ sys.path.append(f'{Path.home()}/pyicon/')
+ import pyicon as pyic
+ print('Done modules.')
+
+ def str_to_array(string):
+ string = string.replace(' ', '')
+ array = np.array(string.split(','), dtype=float)
+ return array
+
+ path = os.path.dirname(iopts.fpath_out)
+ if not os.path.exists(path):
+ os.makedirs(path)
+
+ if not iopts.only_animation:
+ if iopts.cmap.startswith('cmo.'):
+ import cmocean
+ iopts.cmap = getattr(cmocean.cm, iopts.cmap.split('.')[1])
+
+ #flist = glob.glob(iopts.fpath_data)
+ flist = iopts.fpath_data
+ flist.sort()
+
+ # --- limits
+ if iopts.clim!='auto':
+ iopts.clim = str_to_array(iopts.clim)
+ if iopts.lon_reg:
+ iopts.lon_reg = str_to_array(iopts.lon_reg)
+ if iopts.lat_reg:
+ iopts.lat_reg = str_to_array(iopts.lat_reg)
+ if iopts.central_longitude is None:
+ iopts.central_longitude = 'auto'
+ if iopts.it!='none':
+ itsplit = iopts.it.split(',')
+ if len(itsplit)==2:
+ iopts.it = slice(int(itsplit[0]), int(itsplit[1]))
+ elif len(itsplit)==3:
+ iopts.it = slice(int(itsplit[0]), int(itsplit[1]), inst(itsplit[2]))
+ if iopts.time!='none':
+ timesplit = iopts.time.split(',')
+ iopts.time = slice(timesplit[0], timesplit[1])
+
+ # --- open dataset and select data
+ ts = pyic.timing(ts, string='open_mfdataset')
+ try:
+ mfdset_kwargs = dict(combine='nested', concat_dim='time',
+ data_vars='minimal', coords='minimal',
+ compat='override', join='override', parallel=True)
+ ds = xr.open_mfdataset(flist, **mfdset_kwargs)
+ except:
+ try:
+ print('open_mfdset: parallel=True did not work, try without.')
+ mfdset_kwargs = dict(combine='nested', concat_dim='time',
+ data_vars='minimal', coords='minimal',
+ compat='override', join='override')
+ ds = xr.open_mfdataset(flist, **mfdset_kwargs)
+ except:
+ print('open_mfdset: mfdset options did not work, trying without...')
+ ds = xr.open_mfdataset(flist)
+ data = ds[iopts.var]
+ data = data.assign_attrs(uuidOfHGrid=ds.attrs['uuidOfHGrid'])
+
+ # --- re-chunk data to allow for plotting from big files
+ chunks = dict()
+ if 'time' in data.dims:
+ chunks = dict(time=1)
+ depth_name = pyic.identify_depth_name(data)
+ if depth_name!='none':
+ chunks[depth_name] = 1
+ data = data.chunk(chunks)
+
+ # --- select vertical coordinate
+ if depth_name!='none':
+ if iopts.depth!=-1:
+ data = data.sel({depth_name: iopts.depth}, method='nearest')
+ else:
+ data = data.isel({depth_name: iopts.iz})
+ # --- select time coordinate
+ if not isinstance(iopts.it, str):
+ data = data.isel(time=iopts.it)
+ if not isinstance(iopts.time, str):
+ data = data.sel(time=iopts.time)
+
+ # --- get plotting arguments
+ pkws = vars(iopts).copy()
+ drop_items = [
+ 'data', 'var', 'fpath_fig', 'dontshow',
+ 'it', 'time', 'iz', 'depth',
+ 'use_tgrid',
+ 'catalog', 'catdict', 'model',
+ 'factor',
+ 'fpath_data', 'bitrate', 'vcodec', 'framerate', 'ffmpeg', 'dpi',
+ 'fpath_out', 'only_animation', 'test',
+ ]
+ for key in drop_items:
+ pkws.pop(key, None)
+
+ # --- time loop
+ nfig=-1
+ for ll in range(data.time.size):
+ nfig += 1
+ fpath_out_final = f'{iopts.fpath_out}_{nfig:04d}.jpg'
+ ts = pyic.timing(ts, string=f'll = {ll}/{data.time.size}, {str(data.time[ll].data)} {fpath_out_final}')
+
+ plt.close('all')
+ data_loc = data.isel(time=ll)
+ ax, hm = pyic.plot(data_loc, **pkws)
+ if iopts.test:
+ plt.show()
+ sys.exit()
+ plt.savefig(fpath_out_final, dpi=iopts.dpi)
+
+ ts = pyic.timing(ts, string='generate movie')
+ os.system(f'{iopts.ffmpeg} -y -r {iopts.framerate} -f image2 -i {iopts.fpath_out}_%04d.jpg -vf "pad=ceil(iw/2)*2:ceil(ih/2)*2" -vcodec {iopts.vcodec} -b:v {iopts.bitrate} {iopts.fpath_out}.mp4')
+
+ ts = pyic.timing(ts, string='All done!')
-import os
-import sys
-import glob
-import pyicon as pyic
-import matplotlib.pyplot as plt
-import xarray as xr
-
-ts = pyic.timing([0], string='')
-
-help_text = """
-Makes an animation from ICON data by first creating a jpg file for each snapshot and then creating an mp4 movie by using ffmpeg.
-
-Usage notes:
-------------
-Basic usage:
-pyic_anim.py netcdf_file_or_list.nc var_name --fpath_out=/path/to/movie/without/file/ending/name [options]
-
-Change color limits, colorbar:
-pyic_anim.py netcdf_file_or_list.nc var_name --fpath_out=name --clim=-10,32 --cmap=viridis
-
-Select depth level by indices:
-pyic_anim.py netcdf_file_or_list.nc var_name --fpath_out=name --iz=0
-
-Select depth:
-pyic_anim.py netcdf_file_or_list.nc var_name --fpath_out=name --depth=1000
-
-Change region:
-pyic_anim.py netcdf_file_or_list.nc var_name --fpath_out=name --lon_reg=-20,30 --lat_reg=-45,-20
-
-Plot on original triangle grid (it is recommended to cut the domain otherwise, it takes a long time):
-pyic_anim.py netcdf_file_or_list.nc var_name --fpath_out=name --use_tgrid --lon_reg=-72,-68 --lat_reg=33,35
-
-Change projection to North Polar Stereographic projection:
-pyic_anim.py netcdf_file_or_list.nc var_name --fpath_out=name --projection=np
-
-Test with showing only one figure without saving anything:
-pyic_anim.py netcdf_file.nc var_name --test
-
-Only re-creating the animation if the single figures are still available under fpath_out
-pyic_anim.py netcdf_file.nc var_name --fpath_out=name --only_animation
-
-
-Argument list:
---------------
-"""
-
-# --- read input arguments
-parser = argparse.ArgumentParser(description=help_text, formatter_class=argparse.RawTextHelpFormatter)
-
-# --- necessary arguments
-parser.add_argument('fpath_data', nargs='+', metavar='fpath_data', type=str,
- help='Path to ICON data file.')
-parser.add_argument('var', metavar='var', type=str,
- help='Name of variable which should be plotted.')
-# --- optional arguments
-# --- figure saving / showing
-parser.add_argument('--fpath_out', type=str, default='none',
- help='Path to save the animation (without ending).')
-parser.add_argument('--dontshow', action='store_true', default=False,
- help='If dontshow is specified, the plot is not shown')
-parser.add_argument('--only_animation', default=False,
- action='store_true',
- help='If specified, only the animation and no new figures are generated.')
-parser.add_argument('--test', default=False,
- action='store_true',
- help='If specified, just a test plot is made.')
-# --- specifying the grid
-parser.add_argument('--gname', type=str, default='auto',
- help='Grid name of the ICON data.')
-parser.add_argument('--fpath_tgrid', type=str, default='auto',
- help='Path to triangular grid file. If \'auto\' the path is guessed automatically. Only necessary if \'--use_tgrid\' is used.')
-parser.add_argument('--fpath_ckdtree', type=str, default='auto',
- help='Path to ckdtree interpolation file. If \'auto\' the path is guessed automatically.')
-parser.add_argument('--coordinates', type=str, default='clat clon',
- help='Coordinates of variable which should be plotted. Choose between \'clat clon\' (default), \'vlat vlon\' or \'elat elon\'')
-# --- selecting time
-parser.add_argument('--it', type=str, default='none',
- help='Time index limits of the animation. Specify like this: --it=start_index,end_index,[optional:increment] If \'auto\' is specified all time instances are plotted.')
-parser.add_argument('--time', type=str, default='none',
- help='Time string \'yyyy-mm-dd\' wich should be plotted (if specified overwrites \'it\').')
-# --- args for color / limits and settings
-parser.add_argument('--cmap', type=str, default='auto',
- help='Colormap used for plot. Use "cmo.name" for cmocean colormaps.')
-parser.add_argument('--clim', type=str, default='auto',
- help='Color limits of the plot. Either specify one or two values.If one value is specified color limits are taken symetrically around zero. If \'auto\' is specified color limits are derived automatically.')
-parser.add_argument('--cincr', type=float, default=-1.0,
- help='Increment for pcolor plot to specify levels between clims.')
-parser.add_argument('--clevs', type=str, default=None,
- help='Color levels for pcolor plot.')
-parser.add_argument('--conts', type=str, default=None,
- help='Contour levels for monochromatic contours.')
-parser.add_argument('--contfs', type=str, default=None,
- help='Contour levels for filled contour patches.')
-parser.add_argument('--clabel', action='store_true', default=False,
- help='If clabel is specified, color labels will be shown.')
-# --- args for titles and labels
-parser.add_argument('--title_center', type=str, default='auto',
- help='Title string center.')
-parser.add_argument('--title_left', type=str, default='auto',
- help='Title string left.')
-parser.add_argument('--title_right', type=str, default='auto',
- help='Title string right. Use --title-right="full_time" for time str without rounding.')
-parser.add_argument('--xlabel', type=str, default='',
- help='String for xlabel.')
-parser.add_argument('--ylabel', type=str, default='',
- help='String for ylabel.')
-parser.add_argument('--cbar_str', type=str, default='auto',
- help='String for colorbar. Default is name of variable and its units.')
-parser.add_argument('--cbar_pos', type=str, default='bottom',
- help='Position of colorbar. It is possible to choose between \'right\' and \'bottom\'.')
-parser.add_argument('--fig_size_fac', type=float, default=2.,
- help='Factor to increase the figure relative to text (default --fig_size_fac=2.).')
-# --- manupilation of data
-parser.add_argument('--logplot', default=False,
- action='store_true',
- help='Plot logarithm of the data.')
-parser.add_argument('--factor', type=float, default=None,
- help='Factor to mulitply data with.')
-
-# --- specific for horizontal plot parser.add_argument('--iz', type=int, default=0,
-parser.add_argument('--use_tgrid', default=False,
- action='store_true',
- help='If specified, the plot is made on the original triangular grid.')
-parser.add_argument('--res', type=float, default=0.3,
- help='Resolution of the interpolated data which will be plotted. So far, 1.0, 0.3, 0.1 are supported.')
-parser.add_argument('--projection', type=str, default='pc',
- help='Map projection, choose \'None\' to deactivate cartopy, \'pc\' for normal lon/lat projection and \'np\' or \'sp\' for Norh- South-pole stereographic projections.')
-parser.add_argument('--iz', type=int, default=0,
- help='Depth index which should be plotted.')
-parser.add_argument('--depth', type=float, default=-1.,
- help='Depth value in m which should be plotted (if specified overwrites \'iz\').')
-parser.add_argument('--lon_reg', type=str, default=None,
- help='Longitude range of the plot.')
-parser.add_argument('--lat_reg', type=str, default=None,
- help='Latitude range of the plot.')
-parser.add_argument('--central_longitude', type=float, default=None,
- help='Central longitude for cartopy plot.')
-parser.add_argument('--coastlines_color', type=str, default='k',
- help='Color of coastlines. Default is \'k\'. To disable set to \'none\'.')
-parser.add_argument('--land_facecolor', type=str, default='0.7',
- help='Color of land masses. Default is \'0.7\'. To disable set to \'none\'.')
-parser.add_argument('--noland', default=False,
- action='store_true',
- help='If specified, continents are not filled and land_facecolor is overwritten.')
-parser.add_argument('--lonlat_for_mask', default=False,
- action='store_true',
- help='If specified, mask for triangles which are swapped at periodic boundaries is calculated from clon and clat (and not only from clon). Relevant for torus setup.')
-
-# --- ffmpeg specific parameters
-parser.add_argument('--dpi', type=float, default=250.,
- help='Resolution for the individual saved figures (default --dpi=250).')
-parser.add_argument('--ffmpeg', type=str, default="/work/mh0033/m300602/miniconda3/envs/pyicon_py39_exp/bin/ffmpeg",
- help='Path to ffmpeg.')
-parser.add_argument('--framerate', type=int, default=10,
- help='ffmpeg framerate (-r).')
-parser.add_argument('--vcodec', type=str, default='libx264',
- help='ffmpeg video codec.')
-parser.add_argument('--bitrate', type=str, default='12000k',
- help='ffmpeg video bitrate (-b:v).')
-
-iopts = parser.parse_args()
-
-# these options seem not to be used
-gname = iopts.gname
-use_tgrid = iopts.use_tgrid
-fpath_tgrid = iopts.fpath_tgrid
-fpath_ckdtree = iopts.fpath_ckdtree
-
-print('start modules')
-import matplotlib
-if iopts.dontshow:
- matplotlib.use('Agg')
-import numpy as np
-import matplotlib.pyplot as plt
-import cartopy
-import cartopy.crs as ccrs
-import xarray as xr
-import glob
-import os
-import sys
-from pathlib import Path
-sys.path.append(f'{Path.home()}/pyicon/')
-import pyicon as pyic
-print('Done modules.')
-
-def str_to_array(string):
- string = string.replace(' ', '')
- array = np.array(string.split(','), dtype=float)
- return array
-
-path = os.path.dirname(iopts.fpath_out)
-if not os.path.exists(path):
- os.makedirs(path)
-
-if not iopts.only_animation:
- if iopts.cmap.startswith('cmo.'):
- import cmocean
- iopts.cmap = getattr(cmocean.cm, iopts.cmap.split('.')[1])
-
- #flist = glob.glob(iopts.fpath_data)
- flist = iopts.fpath_data
- flist.sort()
-
- # --- limits
- if iopts.clim!='auto':
- iopts.clim = str_to_array(iopts.clim)
- if iopts.lon_reg:
- iopts.lon_reg = str_to_array(iopts.lon_reg)
- if iopts.lat_reg:
- iopts.lat_reg = str_to_array(iopts.lat_reg)
- if iopts.central_longitude is None:
- iopts.central_longitude = 'auto'
- if iopts.it!='none':
- itsplit = iopts.it.split(',')
- if len(itsplit)==2:
- iopts.it = slice(int(itsplit[0]), int(itsplit[1]))
- elif len(itsplit)==3:
- iopts.it = slice(int(itsplit[0]), int(itsplit[1]), inst(itsplit[2]))
- if iopts.time!='none':
- timesplit = iopts.time.split(',')
- iopts.time = slice(timesplit[0], timesplit[1])
-
- # --- open dataset and select data
- ts = pyic.timing(ts, string='open_mfdataset')
- try:
- mfdset_kwargs = dict(combine='nested', concat_dim='time',
- data_vars='minimal', coords='minimal',
- compat='override', join='override', parallel=True)
- ds = xr.open_mfdataset(flist, **mfdset_kwargs)
- except:
- try:
- print('open_mfdset: parallel=True did not work, try without.')
- mfdset_kwargs = dict(combine='nested', concat_dim='time',
- data_vars='minimal', coords='minimal',
- compat='override', join='override')
- ds = xr.open_mfdataset(flist, **mfdset_kwargs)
- except:
- print('open_mfdset: mfdset options did not work, trying without...')
- ds = xr.open_mfdataset(flist)
- data = ds[iopts.var]
- data = data.assign_attrs(uuidOfHGrid=ds.attrs['uuidOfHGrid'])
-
- # --- re-chunk data to allow for plotting from big files
- chunks = dict()
- if 'time' in data.dims:
- chunks = dict(time=1)
- depth_name = pyic.identify_depth_name(data)
- if depth_name!='none':
- chunks[depth_name] = 1
- data = data.chunk(chunks)
-
- # --- select vertical coordinate
- if depth_name!='none':
- if iopts.depth!=-1:
- data = data.sel({depth_name: iopts.depth}, method='nearest')
- else:
- data = data.isel({depth_name: iopts.iz})
- # --- select time coordinate
- if not isinstance(iopts.it, str):
- data = data.isel(time=iopts.it)
- if not isinstance(iopts.time, str):
- data = data.sel(time=iopts.time)
-
- # --- get plotting arguments
- pkws = vars(iopts).copy()
- drop_items = [
- 'data', 'var', 'fpath_fig', 'dontshow',
- 'it', 'time', 'iz', 'depth',
- 'use_tgrid',
- 'catalog', 'catdict', 'model',
- 'factor',
- 'fpath_data', 'bitrate', 'vcodec', 'framerate', 'ffmpeg', 'dpi',
- 'fpath_out', 'only_animation', 'test',
- ]
- for key in drop_items:
- pkws.pop(key, None)
-
- # --- time loop
- nfig=-1
- for ll in range(data.time.size):
- nfig += 1
- fpath_out_final = f'{iopts.fpath_out}_{nfig:04d}.jpg'
- ts = pyic.timing(ts, string=f'll = {ll}/{data.time.size}, {str(data.time[ll].data)} {fpath_out_final}')
-
- plt.close('all')
- data_loc = data.isel(time=ll)
- ax, hm = pyic.plot(data_loc, **pkws)
- if iopts.test:
- plt.show()
- sys.exit()
- plt.savefig(fpath_out_final, dpi=iopts.dpi)
-
-ts = pyic.timing(ts, string='generate movie')
-os.system(f'{iopts.ffmpeg} -y -r {iopts.framerate} -f image2 -i {iopts.fpath_out}_%04d.jpg -vf "pad=ceil(iw/2)*2:ceil(ih/2)*2" -vcodec {iopts.vcodec} -b:v {iopts.bitrate} {iopts.fpath_out}.mp4')
-
-ts = pyic.timing(ts, string='All done!')
+if __name__ == "__main__":
+ main()
diff --git a/tools/pyic_fig.py b/tools/pyic_fig.py
index 89ea19f..4d5cec0 100755
--- a/tools/pyic_fig.py
+++ b/tools/pyic_fig.py
@@ -1,310 +1,314 @@
#!/usr/bin/env python
-import argparse
-import json
-
-help_text = """
-Figure of horizontal lon/lat ICON data.
-
-Usage notes:
-------------
-Basic usage:
-pyic_fig netcdf_file.nc var_name [options]
-
-Use with HEALPix / Zarr / Intake catalog:
-pyic_fig.py ngc3028 to --catalog="https://data.nextgems-h2020.eu/catalog.yaml"
-
-Change color limits, colorbar:
-pyic_fig netcdf_file.nc var_name --clim=-10,32 --cmap=viridis
-
-Select time step and depth level by indices:
-pyic_fig netcdf_file.nc var_name --it=3 --iz=0
-
-Select date and depth:
-pyic_fig netcdf_files_*.nc var_name --time=2010-03-02 --depth=1000
-
-Change region:
-pyic_fig netcdf_file.nc var_name --lon_reg=-20,30 --lat_reg=-45,-20
-
-Change region accross dateline:
-pyic_fig netcdf_file.nc var_name --lon_reg=120,90 --lat_reg=-90,90
-
-Plot across dateline for global plot (central_longitude should probably only be specified for global plot, it is calculated otherwise):
-pyic_fig netcdf_file.nc var_name --central_longitude=180
-
-Plot on original triangle grid (it is recommended to cut the domain otherwise, it takes a long time):
-pyic_fig netcdf_file.nc var_name --use_tgrid --lon_reg=-72,-68 --lat_reg=33,35
-
-Change projection to North Polar Stereographic projection:
-pyic_fig netcdf_file.nc var_name --projection=np
-
-Save the figure:
-pyic_fig netcdf_file.nc var_name --fpath_fig=/path/to/figure.png
-
-Argument list:
---------------
-"""
-
-# --- read input arguments
-parser = argparse.ArgumentParser(description=help_text, formatter_class=argparse.RawTextHelpFormatter)
-
-# --- necessary arguments
-parser.add_argument('data', nargs='+', metavar='data', type=str,
- help='Path to ICON data file or simulation name of intake catalog.')
-parser.add_argument('var', metavar='var', type=str,
- help='Name of variable which should be plotted.')
-# --- optional arguments
-# --- figure saving / showing
-parser.add_argument('--fpath_fig', type=str, default='none',
- help='Path to save the figure.')
-parser.add_argument('--dontshow', action='store_true', default=False,
- help='If dontshow is specified, the plot is not shown')
-# --- specifying the grid
-parser.add_argument('--gname', type=str, default='auto',
- help='Grid name of the ICON data.')
-parser.add_argument('--fpath_tgrid', type=str, default='auto',
- help='Path to triangular grid file. If \'auto\' the path is guessed automatically. Only necessary if \'--use_tgrid\' is used.')
-parser.add_argument('--fpath_ckdtree', type=str, default='auto',
- help='Path to ckdtree interpolation file. If \'auto\' the path is guessed automatically.')
-parser.add_argument('--coordinates', type=str, default='clat clon',
- help='Coordinates of variable which should be plotted. Choose between \'clat clon\' (default), \'vlat vlon\' or \'elat elon\'')
-# --- selecting time
-parser.add_argument('--it', type=int, default=0,
- help='Time index which should be plotted.')
-parser.add_argument('--time', type=str, default='none',
- help='Time string \'yyyy-mm-dd\' wich should be plotted (if specified overwrites \'it\').')
-# --- args for color / limits and settings
-parser.add_argument('--cmap', type=str, default='auto',
- help='Colormap used for plot. Use "cmo.name" for cmocean colormaps.')
-parser.add_argument('--clim', type=str, default='auto',
- help='Color limits of the plot. Either specify one or two values.If one value is specified color limits are taken symetrically around zero. If \'auto\' is specified color limits are derived automatically.')
-parser.add_argument('--cincr', type=float, default=-1.0,
- help='Increment for pcolor plot to specify levels between clims.')
-parser.add_argument('--clevs', type=str, default=None,
- help='Color levels for pcolor plot.')
-parser.add_argument('--conts', type=str, default=None,
- help='Contour levels for monochromatic contours.')
-parser.add_argument('--contfs', type=str, default=None,
- help='Contour levels for filled contour patches.')
-parser.add_argument('--clabel', action='store_true', default=False,
- help='If clabel is specified, color labels will be shown.')
-# --- args for titles and labels
-parser.add_argument('--title_center', type=str, default='auto',
- help='Title string center.')
-parser.add_argument('--title_left', type=str, default='auto',
- help='Title string left.')
-parser.add_argument('--title_right', type=str, default='auto',
- help='Title string right. Use --title-right="full_time" for time str without rounding.')
-parser.add_argument('--xlabel', type=str, default='',
- help='String for xlabel.')
-parser.add_argument('--ylabel', type=str, default='',
- help='String for ylabel.')
-parser.add_argument('--cbar_str', type=str, default='auto',
- help='String for colorbar. Default is name of variable and its units.')
-parser.add_argument('--cbar_pos', type=str, default='bottom',
- help='Position of colorbar. It is possible to choose between \'right\' and \'bottom\'.')
-parser.add_argument('--fig_size_fac', type=float, default=2.,
- help='Factor to increase the figure relative to text (default --fig_size_fac=2.).')
-# --- manupilation of data
-parser.add_argument('--logplot', default=False,
- action='store_true',
- help='Plot logarithm of the data.')
-parser.add_argument('--factor', type=float, default=None,
- help='Factor to mulitply data with.')
-# --- Intake catalog
-parser.add_argument('--catalog', type=str,
- default='https://data.nextgems-h2020.eu/catalog.yaml',
- help='Intake catalog which contains simulation.')
-parser.add_argument('--model', type=str,
- default='ICON',
- help='Model which to choose from catalog.')
-parser.add_argument('--catdict', type=json.loads,
- help='Dictionary to reduce intake catalog, e.g. like this \'{"time": "P1D", "zoom": 7}\'.')
-parser.add_argument('--zoom', type=int, default=7,
- help='Zoom level of HEALPix grid.')
-
-# --- specific for horizontal plot
-parser.add_argument('--use_tgrid', default=False,
- action='store_true',
- help='If specified, the plot is made on the original triangular grid.')
-parser.add_argument('--res', type=float, default=0.3,
- help='Resolution of the interpolated data which will be plotted. So far, 1.0, 0.3, 0.1 are supported.')
-parser.add_argument('--projection', type=str, default='pc',
- help='Map projection, choose \'None\' to deactivate cartopy, \'pc\' for normal lon/lat projection and \'np\' or \'sp\' for Norh- South-pole stereographic projections.')
-parser.add_argument('--iz', type=int, default=0,
- help='Depth index which should be plotted.')
-parser.add_argument('--depth', type=float, default=-1.,
- help='Depth value in m which should be plotted (if specified overwrites \'iz\').')
-parser.add_argument('--lon_reg', type=str, default=None,
- help='Longitude range of the plot.')
-parser.add_argument('--lat_reg', type=str, default=None,
- help='Latitude range of the plot.')
-parser.add_argument('--central_longitude', type=float, default=None,
- help='Central longitude for cartopy plot.')
-parser.add_argument('--coastlines_color', type=str, default='k',
- help='Color of coastlines. Default is \'k\'. To disable set to \'none\'.')
-parser.add_argument('--land_facecolor', type=str, default='0.7',
- help='Color of land masses. Default is \'0.7\'. To disable set to \'none\'.')
-parser.add_argument('--noland', default=False,
- action='store_true',
- help='If specified, continents are not filled and land_facecolor is overwritten.')
-parser.add_argument('--lonlat_for_mask', default=False,
- action='store_true',
- help='If specified, mask for triangles which are swapped at periodic boundaries is calculated from clon and clat (and not only from clon). Relevant for torus setup.')
-
-iopts = parser.parse_args()
-
-print('Start loading modules')
-import matplotlib
-if iopts.dontshow:
- matplotlib.use('Agg')
-import numpy as np
-import matplotlib.pyplot as plt
-import xarray as xr
-import glob
-import os
-import sys
-from pathlib import Path
-from ipdb import set_trace as mybreak
-#sys.path.append(f'{Path.home()}/pyicon/')
-import pyicon as pyic
-print('Done loading modules.')
-
-def str_to_array(string):
- string = string.replace(' ', '')
- array = np.array(string.split(','), dtype=float)
- return array
-
-if iopts.cmap.startswith('cmo.'):
- import cmocean
- iopts.cmap = getattr(cmocean.cm, iopts.cmap.split('.')[1])
-
-# --- limits
-if iopts.clim!='auto':
- iopts.clim = str_to_array(iopts.clim)
-if iopts.lon_reg:
- iopts.lon_reg = str_to_array(iopts.lon_reg)
-if iopts.lat_reg:
- iopts.lat_reg = str_to_array(iopts.lat_reg)
-if iopts.central_longitude is None:
- iopts.central_longitude = 'auto'
-
-# --- check whether run name or path to data is specified
-if iopts.data[0].endswith('.nc'):
- fpath_data = iopts.data
- concat_dim='time'
-elif iopts.data[0].endswith('.grb'):
- fpath_data = iopts.data
- concat_dim='step'
-else:
- run = iopts.data[0]
- fpath_data = 'none'
- concat_dim='time'
-
-# --- open dataset and select data
-mfdset_kwargs = dict(combine='nested', concat_dim=concat_dim,
- data_vars='minimal', coords='minimal',
- compat='override', join='override',)
-if fpath_data!='none':
- ds = xr.open_mfdataset(fpath_data, **mfdset_kwargs)
-else:
- import intake
- cat = intake.open_catalog(iopts.catalog)
- if iopts.catdict:
- reduced_cat = cat[iopts.model][run](**iopts.catdict)
- else:
- reduced_cat = cat[iopts.model][run](zoom=iopts.zoom)
- ds = reduced_cat.to_dask()
-data = ds[iopts.var]
-
-# --- get grid uuidOfHGrid
-try:
- data = data.assign_attrs({"uuidOfHGrid": ds.uuidOfHGrid})
-except:
- pass
-
-# --- check wether data is healpix data
-try:
- if data.grid_mapping=='crs':
- use_healpix = True
- else:
- use_healpix = False
-except:
- use_healpix = False
-
-# --- convert time coordinate in case of grib data
-if 'step' in data.dims:
- data = data.rename(time='time_ref')
- data = data.rename(step='time')
- data['time'] = data.time_ref+data.time
-
-# --- re-chunk data to allow for plotting from big files
-chunks = dict()
-if 'time' in data.dims:
- chunks = dict(time=1)
-depth_name = pyic.identify_depth_name(data)
-if depth_name!='none':
- chunks[depth_name] = 1
-data = data.chunk(chunks)
-
-# --- select time coordinate
-if 'time' in data.dims:
- if iopts.time=='none':
- data = data.isel(time=iopts.it)
- else:
- data = data.sel(time=iops.time, method='nearest')
-# --- select vertical coordinate
-if depth_name!='none':
- if iopts.depth!=-1:
- data = data.sel({depth_name: iopts.depth}, method='nearest')
- else:
- data = data.isel({depth_name: iopts.iz})
-
-# --- apply factor
-if iopts.factor:
- data *= iopts.factor
-
-# --- masking variable
-if iopts.var in ['mld', 'mlotst']:
- data = data.where(data!=data.min())
-else:
- data = data.where(data!=0.)
-
-# --- get plotting arguments
-pkws = vars(iopts).copy()
-drop_items = [
- 'data', 'var', 'fpath_fig', 'dontshow',
- 'it', 'time', 'iz', 'depth',
- 'use_tgrid',
- 'catalog', 'catdict', 'model', 'zoom',
- 'factor',
-]
-for key in drop_items:
- pkws.pop(key, None)
-
-# --- identify plotting method
-if iopts.use_tgrid:
- plot_method = 'tgrid'
-elif use_healpix:
- plot_method = 'healpix'
-else:
- plot_method = 'nn'
-pkws['plot_method'] = plot_method
-
-# -------------------------
-# main plotting command
-# -------------------------
-pyic.plot(data, **pkws)
-
-# --- save figure
-fpath_fig = iopts.fpath_fig
-if fpath_fig!='none':
- if fpath_fig.startswith('~'):
- home = str(Path.home())+'/'
- fpath_fig = home + fpath_fig[1:]
- print(f'Saving figure {fpath_fig}...')
- plt.savefig(fpath_fig)
-
-# --- show figure
-if not iopts.dontshow:
- plt.show()
+def main():
+ import argparse
+ import json
+
+ help_text = """
+ Figure of horizontal lon/lat ICON data.
+
+ Usage notes:
+ ------------
+ Basic usage:
+ pyic_fig netcdf_file.nc var_name [options]
+
+ Use with HEALPix / Zarr / Intake catalog:
+ pyic_fig.py ngc3028 to --catalog="https://data.nextgems-h2020.eu/catalog.yaml"
+
+ Change color limits, colorbar:
+ pyic_fig netcdf_file.nc var_name --clim=-10,32 --cmap=viridis
+
+ Select time step and depth level by indices:
+ pyic_fig netcdf_file.nc var_name --it=3 --iz=0
+
+ Select date and depth:
+ pyic_fig netcdf_files_*.nc var_name --time=2010-03-02 --depth=1000
+
+ Change region:
+ pyic_fig netcdf_file.nc var_name --lon_reg=-20,30 --lat_reg=-45,-20
+
+ Change region accross dateline:
+ pyic_fig netcdf_file.nc var_name --lon_reg=120,90 --lat_reg=-90,90
+
+ Plot across dateline for global plot (central_longitude should probably only be specified for global plot, it is calculated otherwise):
+ pyic_fig netcdf_file.nc var_name --central_longitude=180
+
+ Plot on original triangle grid (it is recommended to cut the domain otherwise, it takes a long time):
+ pyic_fig netcdf_file.nc var_name --use_tgrid --lon_reg=-72,-68 --lat_reg=33,35
+
+ Change projection to North Polar Stereographic projection:
+ pyic_fig netcdf_file.nc var_name --projection=np
+
+ Save the figure:
+ pyic_fig netcdf_file.nc var_name --fpath_fig=/path/to/figure.png
+
+ Argument list:
+ --------------
+ """
+
+ # --- read input arguments
+ parser = argparse.ArgumentParser(description=help_text, formatter_class=argparse.RawTextHelpFormatter)
+
+ # --- necessary arguments
+ parser.add_argument('data', nargs='+', metavar='data', type=str,
+ help='Path to ICON data file or simulation name of intake catalog.')
+ parser.add_argument('var', metavar='var', type=str,
+ help='Name of variable which should be plotted.')
+ # --- optional arguments
+ # --- figure saving / showing
+ parser.add_argument('--fpath_fig', type=str, default='none',
+ help='Path to save the figure.')
+ parser.add_argument('--dontshow', action='store_true', default=False,
+ help='If dontshow is specified, the plot is not shown')
+ # --- specifying the grid
+ parser.add_argument('--gname', type=str, default='auto',
+ help='Grid name of the ICON data.')
+ parser.add_argument('--fpath_tgrid', type=str, default='auto',
+ help='Path to triangular grid file. If \'auto\' the path is guessed automatically. Only necessary if \'--use_tgrid\' is used.')
+ parser.add_argument('--fpath_ckdtree', type=str, default='auto',
+ help='Path to ckdtree interpolation file. If \'auto\' the path is guessed automatically.')
+ parser.add_argument('--coordinates', type=str, default='clat clon',
+ help='Coordinates of variable which should be plotted. Choose between \'clat clon\' (default), \'vlat vlon\' or \'elat elon\'')
+ # --- selecting time
+ parser.add_argument('--it', type=int, default=0,
+ help='Time index which should be plotted.')
+ parser.add_argument('--time', type=str, default='none',
+ help='Time string \'yyyy-mm-dd\' wich should be plotted (if specified overwrites \'it\').')
+ # --- args for color / limits and settings
+ parser.add_argument('--cmap', type=str, default='auto',
+ help='Colormap used for plot. Use "cmo.name" for cmocean colormaps.')
+ parser.add_argument('--clim', type=str, default='auto',
+ help='Color limits of the plot. Either specify one or two values.If one value is specified color limits are taken symetrically around zero. If \'auto\' is specified color limits are derived automatically.')
+ parser.add_argument('--cincr', type=float, default=-1.0,
+ help='Increment for pcolor plot to specify levels between clims.')
+ parser.add_argument('--clevs', type=str, default=None,
+ help='Color levels for pcolor plot.')
+ parser.add_argument('--conts', type=str, default=None,
+ help='Contour levels for monochromatic contours.')
+ parser.add_argument('--contfs', type=str, default=None,
+ help='Contour levels for filled contour patches.')
+ parser.add_argument('--clabel', action='store_true', default=False,
+ help='If clabel is specified, color labels will be shown.')
+ # --- args for titles and labels
+ parser.add_argument('--title_center', type=str, default='auto',
+ help='Title string center.')
+ parser.add_argument('--title_left', type=str, default='auto',
+ help='Title string left.')
+ parser.add_argument('--title_right', type=str, default='auto',
+ help='Title string right. Use --title-right="full_time" for time str without rounding.')
+ parser.add_argument('--xlabel', type=str, default='',
+ help='String for xlabel.')
+ parser.add_argument('--ylabel', type=str, default='',
+ help='String for ylabel.')
+ parser.add_argument('--cbar_str', type=str, default='auto',
+ help='String for colorbar. Default is name of variable and its units.')
+ parser.add_argument('--cbar_pos', type=str, default='bottom',
+ help='Position of colorbar. It is possible to choose between \'right\' and \'bottom\'.')
+ parser.add_argument('--fig_size_fac', type=float, default=2.,
+ help='Factor to increase the figure relative to text (default --fig_size_fac=2.).')
+ # --- manupilation of data
+ parser.add_argument('--logplot', default=False,
+ action='store_true',
+ help='Plot logarithm of the data.')
+ parser.add_argument('--factor', type=float, default=None,
+ help='Factor to mulitply data with.')
+ # --- Intake catalog
+ parser.add_argument('--catalog', type=str,
+ default='https://data.nextgems-h2020.eu/catalog.yaml',
+ help='Intake catalog which contains simulation.')
+ parser.add_argument('--model', type=str,
+ default='ICON',
+ help='Model which to choose from catalog.')
+ parser.add_argument('--catdict', type=json.loads,
+ help='Dictionary to reduce intake catalog, e.g. like this \'{"time": "P1D", "zoom": 7}\'.')
+ parser.add_argument('--zoom', type=int, default=7,
+ help='Zoom level of HEALPix grid.')
+
+ # --- specific for horizontal plot
+ parser.add_argument('--use_tgrid', default=False,
+ action='store_true',
+ help='If specified, the plot is made on the original triangular grid.')
+ parser.add_argument('--res', type=float, default=0.3,
+ help='Resolution of the interpolated data which will be plotted. So far, 1.0, 0.3, 0.1 are supported.')
+ parser.add_argument('--projection', type=str, default='pc',
+ help='Map projection, choose \'None\' to deactivate cartopy, \'pc\' for normal lon/lat projection and \'np\' or \'sp\' for Norh- South-pole stereographic projections.')
+ parser.add_argument('--iz', type=int, default=0,
+ help='Depth index which should be plotted.')
+ parser.add_argument('--depth', type=float, default=-1.,
+ help='Depth value in m which should be plotted (if specified overwrites \'iz\').')
+ parser.add_argument('--lon_reg', type=str, default=None,
+ help='Longitude range of the plot.')
+ parser.add_argument('--lat_reg', type=str, default=None,
+ help='Latitude range of the plot.')
+ parser.add_argument('--central_longitude', type=float, default=None,
+ help='Central longitude for cartopy plot.')
+ parser.add_argument('--coastlines_color', type=str, default='k',
+ help='Color of coastlines. Default is \'k\'. To disable set to \'none\'.')
+ parser.add_argument('--land_facecolor', type=str, default='0.7',
+ help='Color of land masses. Default is \'0.7\'. To disable set to \'none\'.')
+ parser.add_argument('--noland', default=False,
+ action='store_true',
+ help='If specified, continents are not filled and land_facecolor is overwritten.')
+ parser.add_argument('--lonlat_for_mask', default=False,
+ action='store_true',
+ help='If specified, mask for triangles which are swapped at periodic boundaries is calculated from clon and clat (and not only from clon). Relevant for torus setup.')
+
+ iopts = parser.parse_args()
+
+ print('Start loading modules')
+ import matplotlib
+ if iopts.dontshow:
+ matplotlib.use('Agg')
+ import numpy as np
+ import matplotlib.pyplot as plt
+ import xarray as xr
+ import glob
+ import os
+ import sys
+ from pathlib import Path
+ from ipdb import set_trace as mybreak
+ #sys.path.append(f'{Path.home()}/pyicon/')
+ import pyicon as pyic
+ print('Done loading modules.')
+
+ def str_to_array(string):
+ string = string.replace(' ', '')
+ array = np.array(string.split(','), dtype=float)
+ return array
+
+ if iopts.cmap.startswith('cmo.'):
+ import cmocean
+ iopts.cmap = getattr(cmocean.cm, iopts.cmap.split('.')[1])
+
+ # --- limits
+ if iopts.clim!='auto':
+ iopts.clim = str_to_array(iopts.clim)
+ if iopts.lon_reg:
+ iopts.lon_reg = str_to_array(iopts.lon_reg)
+ if iopts.lat_reg:
+ iopts.lat_reg = str_to_array(iopts.lat_reg)
+ if iopts.central_longitude is None:
+ iopts.central_longitude = 'auto'
+
+ # --- check whether run name or path to data is specified
+ if iopts.data[0].endswith('.nc'):
+ fpath_data = iopts.data
+ concat_dim='time'
+ elif iopts.data[0].endswith('.grb'):
+ fpath_data = iopts.data
+ concat_dim='step'
+ else:
+ run = iopts.data[0]
+ fpath_data = 'none'
+ concat_dim='time'
+
+ # --- open dataset and select data
+ mfdset_kwargs = dict(combine='nested', concat_dim=concat_dim,
+ data_vars='minimal', coords='minimal',
+ compat='override', join='override',)
+ if fpath_data!='none':
+ ds = xr.open_mfdataset(fpath_data, **mfdset_kwargs)
+ else:
+ import intake
+ cat = intake.open_catalog(iopts.catalog)
+ if iopts.catdict:
+ reduced_cat = cat[iopts.model][run](**iopts.catdict)
+ else:
+ reduced_cat = cat[iopts.model][run](zoom=iopts.zoom)
+ ds = reduced_cat.to_dask()
+ data = ds[iopts.var]
+
+ # --- get grid uuidOfHGrid
+ try:
+ data = data.assign_attrs({"uuidOfHGrid": ds.uuidOfHGrid})
+ except:
+ pass
+
+ # --- check wether data is healpix data
+ try:
+ if data.grid_mapping=='crs':
+ use_healpix = True
+ else:
+ use_healpix = False
+ except:
+ use_healpix = False
+
+ # --- convert time coordinate in case of grib data
+ if 'step' in data.dims:
+ data = data.rename(time='time_ref')
+ data = data.rename(step='time')
+ data['time'] = data.time_ref+data.time
+
+ # --- re-chunk data to allow for plotting from big files
+ chunks = dict()
+ if 'time' in data.dims:
+ chunks = dict(time=1)
+ depth_name = pyic.identify_depth_name(data)
+ if depth_name!='none':
+ chunks[depth_name] = 1
+ data = data.chunk(chunks)
+
+ # --- select time coordinate
+ if 'time' in data.dims:
+ if iopts.time=='none':
+ data = data.isel(time=iopts.it)
+ else:
+ data = data.sel(time=iops.time, method='nearest')
+ # --- select vertical coordinate
+ if depth_name!='none':
+ if iopts.depth!=-1:
+ data = data.sel({depth_name: iopts.depth}, method='nearest')
+ else:
+ data = data.isel({depth_name: iopts.iz})
+
+ # --- apply factor
+ if iopts.factor:
+ data *= iopts.factor
+
+ # --- masking variable
+ if iopts.var in ['mld', 'mlotst']:
+ data = data.where(data!=data.min())
+ else:
+ data = data.where(data!=0.)
+
+ # --- get plotting arguments
+ pkws = vars(iopts).copy()
+ drop_items = [
+ 'data', 'var', 'fpath_fig', 'dontshow',
+ 'it', 'time', 'iz', 'depth',
+ 'use_tgrid',
+ 'catalog', 'catdict', 'model', 'zoom',
+ 'factor',
+ ]
+ for key in drop_items:
+ pkws.pop(key, None)
+
+ # --- identify plotting method
+ if iopts.use_tgrid:
+ plot_method = 'tgrid'
+ elif use_healpix:
+ plot_method = 'healpix'
+ else:
+ plot_method = 'nn'
+ pkws['plot_method'] = plot_method
+
+ # -------------------------
+ # main plotting command
+ # -------------------------
+ pyic.plot(data, **pkws)
+
+ # --- save figure
+ fpath_fig = iopts.fpath_fig
+ if fpath_fig!='none':
+ if fpath_fig.startswith('~'):
+ home = str(Path.home())+'/'
+ fpath_fig = home + fpath_fig[1:]
+ print(f'Saving figure {fpath_fig}...')
+ plt.savefig(fpath_fig)
+
+ # --- show figure
+ if not iopts.dontshow:
+ plt.show()
+
+if __name__ == "__main__":
+ main()
diff --git a/tools/pyic_intake.py b/tools/pyic_intake.py
index fb5e2a9..a3d2306 100755
--- a/tools/pyic_intake.py
+++ b/tools/pyic_intake.py
@@ -258,7 +258,7 @@ def make_main(catalog):
Dmain = yaml.safe_load(file)
return
-if __name__ == "__main__":
+def main():
description_main = """
pyicon's CLI for handling ICON intake catalogs.
@@ -332,3 +332,6 @@ To get help for the individual functions use:
# fname_out=args.fname_out,
# catalog_dir=args.catalog_dir,
#)
+
+if __name__ == "__main__":
+ main()
diff --git a/tools/pyic_sec.py b/tools/pyic_sec.py
index 0852e9c..87c57d8 100755
--- a/tools/pyic_sec.py
+++ b/tools/pyic_sec.py
@@ -1,266 +1,270 @@
#!/usr/bin/env python
-import argparse
-import json
+def main():
+ import argparse
+ import json
+
+ help_text = """
+ Makes a figure from ICON data
+
+ Usage notes:
+ ------------
+ Basic usage:
+ pyic_sec.py netcdf_file.nc var_name [options]
+
+ Use with HEALPix / Zarr / Intake catalog:
+ pyic_sec.py ngc3028 to --catalog="https://data.nextgems-h2020.eu/catalog.yaml"
+
+ Specify section (with HEALPix):
+ pyic_sec.py ngc3028 to --catalog="https://data.nextgems-h2020.eu/catalog.yaml" --section='80N80W-30S20E'
+
+ Change color limits, colorbar:
+ pyic_sec.py netcdf_file.nc var_name --clim=-10,32 --cmap=viridis
+
+ Select time step by indices:
+ pyic_sec.py netcdf_file.nc var_name --it=3
+
+ Select date:
+ pyic_sec.py netcdf_files_*.nc var_name --time=2010-03-02 --depth=1000
+
+ Change x/y-limits:
+ pyic_sec.py netcdf_file.nc var_name ---xlim=-30,80 --ylim=0,3000
+
+ Add contours:
+ pyic_sec.py netcdf_file.nc var_name --clim=16 --cincr=2 --conts=auto --clabel
+
+ Save the figure:
+ pyic_sec.py netcdf_file.nc var_name --fpath_fig=/path/to/figure.png
+
+ Argument list:
+ --------------
+ """
+
+ # --- read input arguments
+ parser = argparse.ArgumentParser(description=help_text, formatter_class=argparse.RawTextHelpFormatter)
+
+ # --- necessary arguments
+ parser.add_argument('data', nargs='+', metavar='data', type=str,
+ help='Path to ICON data file or simulation name of intake catalog.')
+ parser.add_argument('var', metavar='var', type=str,
+ help='Name of variable which should be plotted.')
+ # --- optional arguments
+ # --- figure saving / showing
+ parser.add_argument('--fpath_fig', type=str, default='none',
+ help='Path to save the figure.')
+ parser.add_argument('--dontshow', action='store_true', default=False,
+ help='If dontshow is specified, the plot is not shown')
+ # --- specifying the grid
+ parser.add_argument('--gname', type=str, default='auto',
+ help='Grid name of the ICON data.')
+ parser.add_argument('--fpath_tgrid', type=str, default='auto',
+ help='Path to triangular grid file. If \'auto\' the path is guessed automatically. Only necessary if \'--use_tgrid\' is used.')
+ parser.add_argument('--fpath_ckdtree', type=str, default='auto',
+ help='Path to ckdtree interpolation file. If \'auto\' the path is guessed automatically.')
+ parser.add_argument('--coordinates', type=str, default='clat clon',
+ help='Coordinates of variable which should be plotted. Choose between \'clat clon\' (default), \'vlat vlon\' or \'elat elon\'')
+ # --- selecting time
+ parser.add_argument('--it', type=int, default=0,
+ help='Time index which should be plotted.')
+ parser.add_argument('--time', type=str, default='none',
+ help='Time string \'yyyy-mm-dd\' wich should be plotted (if specified overwrites \'it\').')
+ # --- args for color / limits and settings
+ parser.add_argument('--cmap', type=str, default='auto',
+ help='Colormap used for plot.')
+ parser.add_argument('--clim', type=str, default='auto',
+ help='Color limits of the plot. Either specify one or two values.If one value is specified color limits are taken symetrically around zero. If \'auto\' is specified color limits are derived automatically.')
+ parser.add_argument('--cincr', type=float, default=-1.0,
+ help='Increment for pcolor plot to specify levels between clims.')
+ parser.add_argument('--clevs', type=str, default=None,
+ help='Color levels for pcolor plot.')
+ parser.add_argument('--conts', type=str, default=None,
+ help='Contour levels for monochromatic contours.')
+ parser.add_argument('--contfs', type=str, default=None,
+ help='Contour levels for filled contour patches.')
+ parser.add_argument('--clabel', action='store_true', default=False,
+ help='If clabel is specified, color labels will be shown.')
+ # --- args for titles and labels
+ parser.add_argument('--title_center', type=str, default='auto',
+ help='Title string center.')
+ parser.add_argument('--title_left', type=str, default='auto',
+ help='Title string left.')
+ parser.add_argument('--title_right', type=str, default='auto',
+ help='Title string right.')
+ parser.add_argument('--xlabel', type=str, default='auto',
+ help='String for xlabel.')
+ parser.add_argument('--ylabel', type=str, default='depth [m]',
+ help='String for ylabel.')
+ parser.add_argument('--cbar_str', type=str, default='auto',
+ help='String for colorbar. Default is name of variable and its units.')
+ parser.add_argument('--cbar_pos', type=str, default='bottom',
+ help='Position of colorbar. It is possible to choose between \'right\' and \'bottom\'.')
+ # --- manupilation of data
+ parser.add_argument('--logplot', default=False,
+ action='store_true',
+ help='Plot logarithm of the data.')
+ parser.add_argument('--factor', type=float, default=None,
+ help='Factor to mulitply data with.')
+ # --- Intake catalog
+ parser.add_argument('--catalog', type=str,
+ default='https://data.nextgems-h2020.eu/catalog.yaml',
+ help='Intake catalog which contains simulation.')
+ parser.add_argument('--model', type=str,
+ default='ICON',
+ help='Model which to choose from catalog.')
+ parser.add_argument('--catdict', type=json.loads,
+ help='Dictionary to reduce intake catalog, e.g. like this \'{"time": "P1D", "zoom": 7}\'.')
+ # --- specific for section
+ parser.add_argument('--invert_yaxis', action='store_true', default=True,
+ help='Invert y-axis, starting with largest and ending with smalles value.')
+ parser.add_argument('--xdim', type=str, default='auto',
+ help='Dimension of x-axes of the plot. Choose between \{\'auto\'\}, \'lon\', or \'lat\'.')
+ parser.add_argument('--section', type=str, default='170W',
+ help='''Section which is used for interpolation.
+ For HEALPix data, specify section e.g. like this: '170W' or '65S' or '80N80W-30S20E'.
+ For regular data only the following sections are supported: \'30W\', \'170W\'
+ and zonal averages for global (\'gzave\', Atlantic \'azave\' and Indo-Pacific \'ipzave\'.'''
+ )
+ parser.add_argument('--fpath_fx', type=str, default='auto',
+ help='Path to an fx file fitting to the data.')
+ parser.add_argument('--xlim', type=str, default=None,
+ help='Limits for x-axis.')
+ parser.add_argument('--ylim', type=str, default=None,
+ help='Limits for y-axis.')
+ parser.add_argument('--facecolor', type=str, default='0.7',
+ help='Background color')
+
+ iopts = parser.parse_args()
+
+ print('Start loading modules')
+ import matplotlib
+ if iopts.dontshow:
+ matplotlib.use('Agg')
+ import numpy as np
+ import matplotlib.pyplot as plt
+ import xarray as xr
+ import glob
+ import os
+ import sys
+ from pathlib import Path
+ from ipdb import set_trace as mybreak
+ #sys.path.append(f'{Path.home()}/pyicon/')
+ import pyicon as pyic
+ print('Done loading modules.')
+
+ def str_to_array(string):
+ string = string.replace(' ', '')
+ array = np.array(string.split(','), dtype=float)
+ return array
+
+ # --- str_to_array
+ if iopts.clim!='auto':
+ iopts.clim = str_to_array(iopts.clim)
+ if iopts.xlim:
+ iopts.xlim = str_to_array(iopts.xlim)
+ if iopts.ylim:
+ iopts.ylim = str_to_array(iopts.ylim)
+ if iopts.conts and iopts.conts!='auto':
+ iopts.conts = str_to_array(iopts.conts)
+ if iopts.contfs and iopts.contfs!='auto':
+ iopts.contfs = str_to_array(iopts.contfs)
+ if iopts.clevs:
+ iopts.clevs = str_to_array(iopts.clevs)
+
+ # --- check whether run name or path to data is specified
+ if iopts.data[0].endswith('.nc') or iopts.data[0].endswith('.grb'):
+ fpath_data = iopts.data
+ else:
+ run = iopts.data[0]
+ fpath_data = 'none'
+
+ # --- open dataset and select data
+ mfdset_kwargs = dict(combine='nested', concat_dim='time',
+ data_vars='minimal', coords='minimal',
+ compat='override', join='override',)
+ if fpath_data!='none':
+ ds = xr.open_mfdataset(fpath_data, **mfdset_kwargs)
+ else:
+ import intake
+ cat = intake.open_catalog(iopts.catalog)
+ if iopts.catdict:
+ reduced_cat = cat[iopts.model][run](**iopts.catdict)
+ else:
+ reduced_cat = cat[iopts.model][run](zoom=7)
+ ds = reduced_cat.to_dask()
+ data = ds[iopts.var]
+
+ # --- check wether data is healpix data
+ try:
+ if data.grid_mapping=='crs':
+ use_healpix = True
+ else:
+ use_healpix = False
+ except:
+ use_healpix = False
+
+ # --- convert time coordinate in case of grib data
+ if 'step' in data.dims:
+ data = data.rename(time='time_ref')
+ data = data.rename(step='time')
+ data['time'] = data.time_ref+data.time
+
+ # --- re-chunk data to allow for plotting from big files
+ chunks = dict()
+ if 'time' in data.dims:
+ chunks = dict(time=1)
+ depth_name = pyic.identify_depth_name(data)
+
+ # --- select time coordinate
+ if 'time' in data.dims:
+ if iopts.time=='none':
+ data = data.isel(time=iopts.it)
+ else:
+ data = data.sel(time=iopts.time, method='nearest')
+
+ # --- apply factor
+ if iopts.factor:
+ data *= iopts.factor
+
+ # --- masking variable
+ data = data.where(data!=0)
+
+ # --- get plotting arguments
+ pkws = vars(iopts).copy()
+ drop_items = [
+ 'data', 'var', 'fpath_fig', 'dontshow',
+ 'it', 'time', 'iz', 'depth',
+ 'use_tgrid',
+ 'catalog', 'catdict', 'model',
+ 'factor',
+ 'xdim',
+ ]
+ for key in drop_items:
+ pkws.pop(key, None)
+
+ # --- identify plotting method
+ if use_healpix:
+ plot_method = 'healpix'
+ else:
+ plot_method = 'nn'
+ pkws['plot_method'] = plot_method
+
+ # -------------------------
+ # main plotting command
+ # -------------------------
+ pyic.plot_sec(data, **pkws)
+
+ # --- save figure
+ fpath_fig = iopts.fpath_fig
+ if fpath_fig!='none':
+ if fpath_fig.startswith('~'):
+ home = str(Path.home())+'/'
+ fpath_fig = home + fpath_fig[1:]
+ print(f'Saving figure {fpath_fig}...')
+ plt.savefig(fpath_fig)
+
+ # --- show figure
+ if not iopts.dontshow:
+ plt.show()
-help_text = """
-Makes a figure from ICON data
-
-Usage notes:
-------------
-Basic usage:
-pyic_sec.py netcdf_file.nc var_name [options]
-
-Use with HEALPix / Zarr / Intake catalog:
-pyic_sec.py ngc3028 to --catalog="https://data.nextgems-h2020.eu/catalog.yaml"
-
-Specify section (with HEALPix):
-pyic_sec.py ngc3028 to --catalog="https://data.nextgems-h2020.eu/catalog.yaml" --section='80N80W-30S20E'
-
-Change color limits, colorbar:
-pyic_sec.py netcdf_file.nc var_name --clim=-10,32 --cmap=viridis
-
-Select time step by indices:
-pyic_sec.py netcdf_file.nc var_name --it=3
-
-Select date:
-pyic_sec.py netcdf_files_*.nc var_name --time=2010-03-02 --depth=1000
-
-Change x/y-limits:
-pyic_sec.py netcdf_file.nc var_name ---xlim=-30,80 --ylim=0,3000
-
-Add contours:
-pyic_sec.py netcdf_file.nc var_name --clim=16 --cincr=2 --conts=auto --clabel
-
-Save the figure:
-pyic_sec.py netcdf_file.nc var_name --fpath_fig=/path/to/figure.png
-
-Argument list:
---------------
-"""
-
-# --- read input arguments
-parser = argparse.ArgumentParser(description=help_text, formatter_class=argparse.RawTextHelpFormatter)
-
-# --- necessary arguments
-parser.add_argument('data', nargs='+', metavar='data', type=str,
- help='Path to ICON data file or simulation name of intake catalog.')
-parser.add_argument('var', metavar='var', type=str,
- help='Name of variable which should be plotted.')
-# --- optional arguments
-# --- figure saving / showing
-parser.add_argument('--fpath_fig', type=str, default='none',
- help='Path to save the figure.')
-parser.add_argument('--dontshow', action='store_true', default=False,
- help='If dontshow is specified, the plot is not shown')
-# --- specifying the grid
-parser.add_argument('--gname', type=str, default='auto',
- help='Grid name of the ICON data.')
-parser.add_argument('--fpath_tgrid', type=str, default='auto',
- help='Path to triangular grid file. If \'auto\' the path is guessed automatically. Only necessary if \'--use_tgrid\' is used.')
-parser.add_argument('--fpath_ckdtree', type=str, default='auto',
- help='Path to ckdtree interpolation file. If \'auto\' the path is guessed automatically.')
-parser.add_argument('--coordinates', type=str, default='clat clon',
- help='Coordinates of variable which should be plotted. Choose between \'clat clon\' (default), \'vlat vlon\' or \'elat elon\'')
-# --- selecting time
-parser.add_argument('--it', type=int, default=0,
- help='Time index which should be plotted.')
-parser.add_argument('--time', type=str, default='none',
- help='Time string \'yyyy-mm-dd\' wich should be plotted (if specified overwrites \'it\').')
-# --- args for color / limits and settings
-parser.add_argument('--cmap', type=str, default='auto',
- help='Colormap used for plot.')
-parser.add_argument('--clim', type=str, default='auto',
- help='Color limits of the plot. Either specify one or two values.If one value is specified color limits are taken symetrically around zero. If \'auto\' is specified color limits are derived automatically.')
-parser.add_argument('--cincr', type=float, default=-1.0,
- help='Increment for pcolor plot to specify levels between clims.')
-parser.add_argument('--clevs', type=str, default=None,
- help='Color levels for pcolor plot.')
-parser.add_argument('--conts', type=str, default=None,
- help='Contour levels for monochromatic contours.')
-parser.add_argument('--contfs', type=str, default=None,
- help='Contour levels for filled contour patches.')
-parser.add_argument('--clabel', action='store_true', default=False,
- help='If clabel is specified, color labels will be shown.')
-# --- args for titles and labels
-parser.add_argument('--title_center', type=str, default='auto',
- help='Title string center.')
-parser.add_argument('--title_left', type=str, default='auto',
- help='Title string left.')
-parser.add_argument('--title_right', type=str, default='auto',
- help='Title string right.')
-parser.add_argument('--xlabel', type=str, default='auto',
- help='String for xlabel.')
-parser.add_argument('--ylabel', type=str, default='depth [m]',
- help='String for ylabel.')
-parser.add_argument('--cbar_str', type=str, default='auto',
- help='String for colorbar. Default is name of variable and its units.')
-parser.add_argument('--cbar_pos', type=str, default='bottom',
- help='Position of colorbar. It is possible to choose between \'right\' and \'bottom\'.')
-# --- manupilation of data
-parser.add_argument('--logplot', default=False,
- action='store_true',
- help='Plot logarithm of the data.')
-parser.add_argument('--factor', type=float, default=None,
- help='Factor to mulitply data with.')
-# --- Intake catalog
-parser.add_argument('--catalog', type=str,
- default='https://data.nextgems-h2020.eu/catalog.yaml',
- help='Intake catalog which contains simulation.')
-parser.add_argument('--model', type=str,
- default='ICON',
- help='Model which to choose from catalog.')
-parser.add_argument('--catdict', type=json.loads,
- help='Dictionary to reduce intake catalog, e.g. like this \'{"time": "P1D", "zoom": 7}\'.')
-# --- specific for section
-parser.add_argument('--invert_yaxis', action='store_true', default=True,
- help='Invert y-axis, starting with largest and ending with smalles value.')
-parser.add_argument('--xdim', type=str, default='auto',
- help='Dimension of x-axes of the plot. Choose between \{\'auto\'\}, \'lon\', or \'lat\'.')
-parser.add_argument('--section', type=str, default='170W',
- help='''Section which is used for interpolation.
-For HEALPix data, specify section e.g. like this: '170W' or '65S' or '80N80W-30S20E'.
-For regular data only the following sections are supported: \'30W\', \'170W\'
-and zonal averages for global (\'gzave\', Atlantic \'azave\' and Indo-Pacific \'ipzave\'.'''
-)
-parser.add_argument('--fpath_fx', type=str, default='auto',
- help='Path to an fx file fitting to the data.')
-parser.add_argument('--xlim', type=str, default=None,
- help='Limits for x-axis.')
-parser.add_argument('--ylim', type=str, default=None,
- help='Limits for y-axis.')
-parser.add_argument('--facecolor', type=str, default='0.7',
- help='Background color')
-
-iopts = parser.parse_args()
-
-print('Start loading modules')
-import matplotlib
-if iopts.dontshow:
- matplotlib.use('Agg')
-import numpy as np
-import matplotlib.pyplot as plt
-import xarray as xr
-import glob
-import os
-import sys
-from pathlib import Path
-from ipdb import set_trace as mybreak
-#sys.path.append(f'{Path.home()}/pyicon/')
-import pyicon as pyic
-print('Done loading modules.')
-
-def str_to_array(string):
- string = string.replace(' ', '')
- array = np.array(string.split(','), dtype=float)
- return array
-
-# --- str_to_array
-if iopts.clim!='auto':
- iopts.clim = str_to_array(iopts.clim)
-if iopts.xlim:
- iopts.xlim = str_to_array(iopts.xlim)
-if iopts.ylim:
- iopts.ylim = str_to_array(iopts.ylim)
-if iopts.conts and iopts.conts!='auto':
- iopts.conts = str_to_array(iopts.conts)
-if iopts.contfs and iopts.contfs!='auto':
- iopts.contfs = str_to_array(iopts.contfs)
-if iopts.clevs:
- iopts.clevs = str_to_array(iopts.clevs)
-
-# --- check whether run name or path to data is specified
-if iopts.data[0].endswith('.nc') or iopts.data[0].endswith('.grb'):
- fpath_data = iopts.data
-else:
- run = iopts.data[0]
- fpath_data = 'none'
-
-# --- open dataset and select data
-mfdset_kwargs = dict(combine='nested', concat_dim='time',
- data_vars='minimal', coords='minimal',
- compat='override', join='override',)
-if fpath_data!='none':
- ds = xr.open_mfdataset(fpath_data, **mfdset_kwargs)
-else:
- import intake
- cat = intake.open_catalog(iopts.catalog)
- if iopts.catdict:
- reduced_cat = cat[iopts.model][run](**iopts.catdict)
- else:
- reduced_cat = cat[iopts.model][run](zoom=7)
- ds = reduced_cat.to_dask()
-data = ds[iopts.var]
-
-# --- check wether data is healpix data
-try:
- if data.grid_mapping=='crs':
- use_healpix = True
- else:
- use_healpix = False
-except:
- use_healpix = False
-
-# --- convert time coordinate in case of grib data
-if 'step' in data.dims:
- data = data.rename(time='time_ref')
- data = data.rename(step='time')
- data['time'] = data.time_ref+data.time
-
-# --- re-chunk data to allow for plotting from big files
-chunks = dict()
-if 'time' in data.dims:
- chunks = dict(time=1)
-depth_name = pyic.identify_depth_name(data)
-
-# --- select time coordinate
-if 'time' in data.dims:
- if iopts.time=='none':
- data = data.isel(time=iopts.it)
- else:
- data = data.sel(time=iopts.time, method='nearest')
-
-# --- apply factor
-if iopts.factor:
- data *= iopts.factor
-
-# --- masking variable
-data = data.where(data!=0)
-
-# --- get plotting arguments
-pkws = vars(iopts).copy()
-drop_items = [
- 'data', 'var', 'fpath_fig', 'dontshow',
- 'it', 'time', 'iz', 'depth',
- 'use_tgrid',
- 'catalog', 'catdict', 'model',
- 'factor',
- 'xdim',
-]
-for key in drop_items:
- pkws.pop(key, None)
-
-# --- identify plotting method
-if use_healpix:
- plot_method = 'healpix'
-else:
- plot_method = 'nn'
-pkws['plot_method'] = plot_method
-
-# -------------------------
-# main plotting command
-# -------------------------
-pyic.plot_sec(data, **pkws)
-
-# --- save figure
-fpath_fig = iopts.fpath_fig
-if fpath_fig!='none':
- if fpath_fig.startswith('~'):
- home = str(Path.home())+'/'
- fpath_fig = home + fpath_fig[1:]
- print(f'Saving figure {fpath_fig}...')
- plt.savefig(fpath_fig)
-
-# --- show figure
-if not iopts.dontshow:
- plt.show()
+if __name__ == "__main__":
+ main()
--
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