Merge branch 'polyplot' into 'master' (aba71ba5) · Commits · CAMS / CSO

CHANGELOG

+10 −0

Original line number	Diff line number	Diff line
		@@ -539,3 +539,13 @@ v2.13

		Updates for latest python versions.
		Improved error checks.


		v2.14
		-----

		Plot pixels als polygons in case track information is not present.
		src/cso/cso_catalogue.py
		src/cso/cso_plot.py

doc/source/history.rst

+8 −13

Original line number	Diff line number	Diff line
		@@ -122,13 +122,8 @@ A summary of the versions and changes.
		* \| v2.13
		\| Minor updates to trap errors and support latest Python versions.


		To be included
		==============

		Features available in branches, that should be included in master version.

		* Create map plots as a list of pixels, in case track information is not available. (E.D.)
		* \| v2.14
		\| Plot pixels als polygons in case track information is not present.


		To be done
		@@ -162,7 +157,7 @@ A wishlist of developments.
		How to create a version tag
		===========================

		Example for tag "v2.13".
		Example for tag "v2.14".

		1. Update file formatting following conventions.

		@@ -182,17 +177,17 @@ Example for tag "v2.13".

		c. Change the release tag that will also be imported to the documenation in the `pyproject.toml <../../../pyproject.toml>`_ file::

		release = "2.13"
		release = "2.14"

		d. Commit and push these changes::

		git commit -m 'Defined v2.13' .
		git commit -m 'Defined v2.14' .
		git push

		4. Tag and push the code to the git repository::

		git tag -a 'v2.13' -m 'Tagged v2.13'
		git push origin v2.13
		git tag -a 'v2.14' -m 'Tagged v2.14'
		git push origin v2.14

pyproject.toml

+1 −1

Original line number	Diff line number	Diff line
		@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"

		[project]
		name = "cso"
		version = "2.13"
		version = "2.14"
		authors = [
		{ name = "Arjo Segers" },
		{ name = "Lewis Blake" },

src/cso/cso_catalogue.py

+131 −47

Original line number	Diff line number	Diff line
		@@ -35,6 +35,11 @@
		# Extended unit conversions.
		# Fixed reading of settings for map styles.
		#
		# 2025-09, Arjo Segers
		# Plot pixels als polygons in case track information is not present.
		# Extended unit conversions.
		# Fixed string formatting.
		#


		########################################################################
		@@ -156,6 +161,30 @@ class CSO_CatalogueBase(utopya.UtopyaRc):
		# apply factor:
		values = values * 1e6

		# vertical column density:
		elif conversion == "molec/cm2 -> umol/m2":
		# apply factor:
		# molec/cm2 / (molec/mol) umol/mol cm2/m2
		values = values / cso_constants.Avog * 1e6 * 1e4

		# vertical column density:
		elif conversion == "molec/cm2 -> 1e15 mlc/cm2":
		# apply factor:
		# molec/cm2
		values = values / 1e15

		# vertical column density:
		elif conversion == "(molec/cm2)**2 -> 1e15 mlc/cm2":
		# apply factor:
		# molec/cm2
		values = numpy.sqrt(values) / 1e15

		# vertical column density, squared
		elif conversion == "(molec/cm2)**2 -> umol/m2":
		# apply factor:
		# molec/cm2 / (molec/mol) umol/mol cm2/m2
		values = numpy.sqrt(values) / cso_constants.Avog * 1e6 * 1e4

		# vertical column density:
		elif conversion == "mol m-2 -> mmol/m2":
		# apply factor:
		@@ -383,7 +412,11 @@ class CSO_Catalogue(CSO_CatalogueBase):
		filename = os.path.join(inputdir, fname)

		# orbit key:
		if "orbit" in xlst:
		orbit = xlst.GetValue(fname, "orbit")
		else:
		orbit = ""
		#endif

		## testing ...
		# if '1200' not in filename : continue
		@@ -444,23 +477,32 @@ class CSO_Catalogue(CSO_CatalogueBase):
		# settings for this variable:
		vkey = "var.%s" % varname
		# plot type:
		ptype = self.GetSetting("var.{varname}.type", default="map")
		ptype = self.GetSetting(f"var.{varname}.type", default="map")
		# input variable:
		vname = self.GetSetting("var.{varname}.source", default=varname)
		vname = self.GetSetting(f"var.{varname}.source", default=varname)
		# target units:
		vunits = self.GetSetting("var.{varname}.units", default="None")
		vunits = self.GetSetting(f"var.{varname}.units", default="None")
		# long name used in labels:
		long_name = self.GetSetting("var.{varname}.long_name", default=varname)
		long_name = self.GetSetting(f"var.{varname}.long_name", default=varname)

		# track defined in files?
		on_track = "track_longitude" in orb.ds

		# switch:
		if ptype == "map":
		# style:
		vmin = eval(self.GetSetting("var.{varname}.vmin", default="None"))
		vmax = eval(self.GetSetting("var.{varname}.vmax", default="None"))
		colors = eval(self.GetSetting("var.{varname}.colors", default="None"))
		vmin = eval(self.GetSetting(f"var.{varname}.vmin", default="None"))
		vmax = eval(self.GetSetting(f"var.{varname}.vmax", default="None"))
		colors = eval(self.GetSetting(f"var.{varname}.colors", default="None"))

		# extract corner grids and values:
		xx, yy, values, attrs = orb.GetTrack(vname)
		if on_track:
		xx, yy, values, attrs = orb.GetTrack(sstate.ds[vname])
		else:
		xx, attrs = orb.GetData( "longitude_bounds" )
		yy, attrs = orb.GetData( "latitude_bounds" )
		values, attrs = orb.GetData( vname )
		#endif

		# adhoc, some chocho files have nans in lon/lat bound arrays,
		# these are still present because the scan line has some valid values ...
		@@ -512,6 +554,7 @@ class CSO_Catalogue(CSO_CatalogueBase):
		bmp.update(bmp_kwargs)

		# create map figure:
		if on_track:
		fig = cso_plot.QuickPat(
		values,
		x=xx,
		@@ -525,6 +568,21 @@ class CSO_Catalogue(CSO_CatalogueBase):
		title=title,
		figsize=figsize,
		)
		else:
		fig = cso_plot.QuickPoly(
		values,
		x=xx,
		y=yy,
		vmin=vmin,
		vmax=vmax,
		cmap=dict(colors=colors, color_bad=color_nan),
		bmp=bmp,
		domain=domain,
		cbar=dict(label=label),
		title=title,
		figsize=figsize,
		)
		#endif
		# save:
		fig.Export(figfile)

		@@ -812,25 +870,35 @@ class CSO_SimCatalogue(CSO_CatalogueBase):
		else:
		vfile, vname = "data", vsource
		# endif
		# track defined in files?
		on_track = "track_longitude" in sdata.ds
		# extract corner grids and values:
		if vfile == "state":
		# check ...
		if vname not in sstate.ds.keys():
		logging.error(
		"variable `%s` not found in state from file: %s"
		% (vname, statefile)
		)
		logging.error(f"variable '{vname}' not found in state from file: {statefile}")
		raise Exception
		# endif
		# extract corner grids and values:
		if on_track:
		xx, yy, values, attrs = sdata.GetTrack(sstate.ds[vname])
		else:
		xx, attrs = sdata.GetData( "longitude_bounds" )
		yy, attrs = sdata.GetData( "latitude_bounds" )
		values, attrs = sstate.GetData( vname )
		#endif
		elif vfile == "data":
		# extract corner grids and values from data file:
		if on_track:
		xx, yy, values, attrs = sdata.GetTrack(vname)
		else:
		xx, attrs = sdata.GetData( "longitude_bounds" )
		yy, attrs = sdata.GetData( "latitude_bounds" )
		values, attrs = sdata.GetData( vname )
		#endtry
		else:
		logging.error(
		'unsupported type keyword "%s" in source description "%s" for variable "%s"'
		% (vfile, vsource, varname)
		f"unsupported type keyword '{vfile}' in source description '{vsource}' for variable '{varname}'"
		)
		raise Exception
		# endif
		@@ -849,9 +917,7 @@ class CSO_SimCatalogue(CSO_CatalogueBase):
		if (len(shp) == 3) and (shp[2] == 1):
		values = values[:, :, 0]
		else:
		logging.error(
		'could not squeeze "%s" %s to 2D track' % (vname, str(shp))
		)
		logging.error(f"could not squeeze '{vname}' {shp} to 2D track")
		raise Exception
		# endif
		# endif
		@@ -866,7 +932,10 @@ class CSO_SimCatalogue(CSO_CatalogueBase):
		bmp = dict(countries=True)
		bmp.update(bmp_kwargs)

		# info ...
		logging.info(indent + " plot pattern ...")
		# create map figure:
		if on_track:
		fig = cso_plot.QuickPat(
		values,
		x=xx,
		@@ -880,6 +949,21 @@ class CSO_SimCatalogue(CSO_CatalogueBase):
		title=title,
		figsize=figsize,
		)
		else:
		fig = cso_plot.QuickPoly(
		values,
		x=xx,
		y=yy,
		vmin=vmin,
		vmax=vmax,
		cmap=dict(colors=colors, color_bad=color_nan),
		bmp=bmp,
		domain=domain,
		cbar=dict(label=label),
		title=title,
		figsize=figsize,
		)
		#endif
		# save:
		fig.Export(figfile)

		@@ -902,7 +986,7 @@ class CSO_SimCatalogue(CSO_CatalogueBase):
		# break

		else:
		logging.info(indent + " no state file: %s" % statefile)
		logging.info(f"{indent} no state file: {statefile}")
		# endif # state file present

		# next:

src/cso/cso_gridded.py

+5 −4

Original line number	Diff line number	Diff line
		@@ -40,6 +40,9 @@
		# 2025-09, Arjo Segers
		# Updated calculation of temporal means for files with time records.
		#
		# 2026-01, Arjo Segers
		# Fixed timerange setup.
		#


		########################################################################
		@@ -593,14 +596,12 @@ class CSO_GriddedAverage(utopya.UtopyaRc):
		elif tstep in ["day", "daily"]:
		# start and end of days:
		rtt1 = pandas.date_range(start=outfile_t1, end=outfile_t2, freq="D")[:-1]
		rtt2 = pandas.date_range(
		start=rtt1[0] + pandas.Timedelta(days=1), periods=len(rtt1)
		)
		rtt2 = pandas.date_range(start=rtt1[0] + pandas.Timedelta(days=1), periods=len(rtt1))
		#
		elif tstep in ["hour", "hourly"]:
		# hours, end is now the same as start ...
		rtt1 = pandas.date_range(start=outfile_t1, end=outfile_t2, freq="h")[:-1]
		rtt2 = tt1
		rtt2 = rtt1
		else:
		logging.error(f"unsupported output file frequency {tstep}")
		raise Exception