sciapy.level1c.scia_limb_nc.read_from_netcdf() - Code Metrics - Inspection of "tests l1c: Test round trips" - st-bender/sciapy - Measure and Improve Code Quality continuously with Scrutinizer

Passed

Push — master ( ed9f5a...bed583 )

by Stefan

created 2020-02-25 21:32 UTC

sciapy.level1c.scia_limb_nc.read_from_netcdf() B

↳ Parent: sciapy.level1c.scia_limb_nc

Complexity

Conditions

Size

Total Lines	73
Code Lines	51

Duplication

Lines	73
Ratio	100 %

Code Coverage

Tests	44
CRAP Score	5.0064

Importance

Changes

Metric	Value
cc	5
eloc	51
nop	2
dl	73
loc	73
ccs	44
cts	47
cp	0.9362
crap	5.0064
rs	8.1369
c	0
b	0
f	0

How to fix Long Method

# -*- coding: utf-8 -*-
# vim:fileencoding=utf-8
#
# Copyright (c) 2014-2017 Stefan Bender
#
# This file is part of sciapy.
# sciapy is free software: you can redistribute it or modify it
# under the terms of the GNU General Public License as published by
# the Free Software Foundation, version 2.
# See accompanying LICENSE file or http://www.gnu.org/licenses/gpl-2.0.html.
"""SCIAMACHY level 1c limb spectra netcdf interface
"""

from __future__ import absolute_import, division, print_function

import numpy as np
try:
	from netCDF4 import Dataset as netcdf_file
	_fmtargs = {"format": "NETCDF4"}
except ImportError:
	try:
		from scipy.io.netcdf import netcdf_file
		_fmtargs = {"version": 1}
	except ImportError:
		from pupynere import netcdf_file
		_fmtargs = {"version": 1}

from ._types import _limb_data_dtype

def read_from_netcdf(self, filename):

	"""SCIAMACHY level 1c limb scan netcdf import

	Parameters
	----------
	filename : str
		The netcdf filename to read the data from.

	Returns
	-------
	nothing
	"""
	import numpy.lib.recfunctions as rfn
	ncf = netcdf_file(filename, 'r')

	self.textheader_length = ncf.textheader_length
	self.textheader = ncf.textheader

	self.orbit_state = ncf.orbit_state
	(self.orbit, self.state_in_orbit, self.state_id,
		self.profiles_per_state, self.profile_in_state) = self.orbit_state
	self.date = ncf.date
	self.cent_lat_lon = ncf.cent_lat_lon
	self.orbit_phase = ncf.orbit_phase

	try:
		self.nalt = ncf.dimensions['limb'].size
		self.npix = ncf.dimensions['wavelength'].size
	except:
		self.nalt = ncf.dimensions['limb']
		self.npix = ncf.dimensions['wavelength']

	self.wls = ncf.variables['wavelength'][:]

	# pre-set the limb_data
	if self._limb_data_dtype is None:
		self._limb_data_dtype = _limb_data_dtype[:]
	self.limb_data = np.zeros((self.nalt), dtype=self._limb_data_dtype)

	self.limb_data["sub_sat_lat"] = ncf.variables['sub_sat_lat'][:]
	self.limb_data["sub_sat_lon"] = ncf.variables['sub_sat_lon'][:]
	self.limb_data["tp_lat"] = ncf.variables['TP latitude'][:]
	self.limb_data["tp_lon"] = ncf.variables['TP longitude'][:]
	self.limb_data["tp_alt"] = ncf.variables['TP altitude'][:]
	self.limb_data["tp_sza"] = ncf.variables['TP SZA'][:]
	self.limb_data["tp_saa"] = ncf.variables['TP SAA'][:]
	self.limb_data["tp_los"] = ncf.variables['TP LOS Zenith'][:]
	self.limb_data["toa_sza"] = ncf.variables['TOA SZA'][:]
	self.limb_data["toa_saa"] = ncf.variables['TOA SAA'][:]
	self.limb_data["toa_los"] = ncf.variables['TOA LOS Zenith'][:]
	self.limb_data["sat_sza"] = ncf.variables['SAT SZA'][:]
	self.limb_data["sat_saa"] = ncf.variables['SAT SAA'][:]
	self.limb_data["sat_los"] = ncf.variables['SAT LOS Zenith'][:]
	self.limb_data["sat_alt"] = ncf.variables['SAT altitude'][:]
	self.limb_data["earth_rad"] = ncf.variables['earthradius'][:]

	tmp_rad_arr = list(ncf.variables['radiance'][:])
	tmp_err_arr = list(ncf.variables['radiance errors'][:])

	# save to limb_data recarray
	rads = np.rec.fromarrays([tmp_rad_arr],
				dtype=np.dtype([("rad", 'f4', (self.npix,))]))
	errs = np.rec.fromarrays([tmp_err_arr],
				dtype=np.dtype([("err", 'f4', (self.npix,))]))
	self.limb_data = rfn.merge_arrays([self.limb_data, rads, errs],
			usemask=False, asrecarray=True, flatten=True)
	self._limb_data_dtype = self.limb_data.dtype

	for _k in ncf.ncattrs():
		if _k.startswith("metadata"):
			_meta_key = _k.split("::")[1]
			self.metadata[_meta_key] = getattr(ncf, _k)
	ncf.close()

def write_to_netcdf(self, filename):

	"""SCIAMACHY level 1c limb scan netcdf export

	Parameters
	----------
	filename : str
		The netcdf filename to write the data to.

	Returns
	-------
	nothing
	"""
	ncf = netcdf_file(filename, 'w', **_fmtargs)

	ncf.textheader_length = self.textheader_length
	ncf.textheader = self.textheader

	ncf.orbit_state = self.orbit_state
	ncf.date = self.date
	ncf.cent_lat_lon = self.cent_lat_lon
	ncf.orbit_phase = self.orbit_phase

	ncf.createDimension('limb', self.nalt)
	ncf.createDimension('wavelength', self.npix)

	wavs = ncf.createVariable('wavelength', np.dtype('float32').char, ('wavelength',))
	wavs.units = 'nm'
	wavs[:] = np.asarray(self.wls)

	sslat = ncf.createVariable('sub_sat_lat', np.dtype('float32').char, ('limb',))
	sslat.units = 'deg'
	sslat[:] = np.asarray(self.limb_data["sub_sat_lat"])
	sslon = ncf.createVariable('sub_sat_lon', np.dtype('float32').char, ('limb',))
	sslon.units = 'deg'
	sslon[:] = np.asarray(self.limb_data["sub_sat_lon"])
	tp_lats = ncf.createVariable('TP latitude', np.dtype('float32').char, ('limb',))
	tp_lats.units = 'deg'
	tp_lats[:] = np.asarray(self.limb_data["tp_lat"])
	tp_lons = ncf.createVariable('TP longitude', np.dtype('float32').char, ('limb',))
	tp_lons.units = 'deg'
	tp_lons[:] = np.asarray(self.limb_data["tp_lon"])
	tp_alts = ncf.createVariable('TP altitude', np.dtype('float32').char, ('limb',))
	tp_alts.units = 'km'
	tp_alts[:] = np.asarray(self.limb_data["tp_alt"])
	tp_szas = ncf.createVariable('TP SZA', np.dtype('float32').char, ('limb',))
	tp_szas.units = 'deg'
	tp_szas[:] = np.asarray(self.limb_data["tp_sza"])
	tp_saas = ncf.createVariable('TP SAA', np.dtype('float32').char, ('limb',))
	tp_saas.units = 'deg'
	tp_saas[:] = np.asarray(self.limb_data["tp_saa"])
	tp_los_zeniths = ncf.createVariable('TP LOS Zenith', np.dtype('float32').char, ('limb',))
	tp_los_zeniths.units = 'deg'
	tp_los_zeniths[:] = np.asarray(self.limb_data["tp_los"])
	toa_szas = ncf.createVariable('TOA SZA', np.dtype('float32').char, ('limb',))
	toa_szas.units = 'deg'
	toa_szas[:] = np.asarray(self.limb_data["toa_sza"])
	toa_saas = ncf.createVariable('TOA SAA', np.dtype('float32').char, ('limb',))
	toa_saas.units = 'deg'
	toa_saas[:] = np.asarray(self.limb_data["toa_saa"])
	toa_los_zeniths = ncf.createVariable('TOA LOS Zenith', np.dtype('float32').char, ('limb',))
	toa_los_zeniths.units = 'deg'
	toa_los_zeniths[:] = np.asarray(self.limb_data["toa_los"])
	sat_szas = ncf.createVariable('SAT SZA', np.dtype('float32').char, ('limb',))
	sat_szas.units = 'deg'
	sat_szas[:] = np.asarray(self.limb_data["sat_sza"])
	sat_saas = ncf.createVariable('SAT SAA', np.dtype('float32').char, ('limb',))
	sat_saas.units = 'deg'
	sat_saas[:] = np.asarray(self.limb_data["sat_saa"])
	sat_los_zeniths = ncf.createVariable('SAT LOS Zenith', np.dtype('float32').char, ('limb',))
	sat_los_zeniths.units = 'deg'
	sat_los_zeniths[:] = np.asarray(self.limb_data["sat_los"])
	sat_alts = ncf.createVariable('SAT altitude', np.dtype('float32').char, ('limb',))
	sat_alts.units = 'km'
	sat_alts[:] = np.asarray(self.limb_data["sat_alt"])
	eradii_alts = ncf.createVariable('earthradius', np.dtype('float32').char, ('limb',))
	eradii_alts.units = 'km'
	eradii_alts[:] = np.asarray(self.limb_data["earth_rad"])

	rads = ncf.createVariable('radiance', np.dtype('float32').char,
			('limb', 'wavelength'), zlib=True, complevel=1)
	errs = ncf.createVariable('radiance errors', np.dtype('float32').char,
			('limb', 'wavelength'), zlib=True, complevel=1)
	rads.units = 'ph / s / cm^2 / nm'
	errs.units = 'ph / s / cm^2 / nm'
	rads[:] = np.asarray(self.limb_data["rad"]).reshape(self.nalt, self.npix)
	errs[:] = np.asarray(self.limb_data["err"]).reshape(self.nalt, self.npix)

	for _k, _v in self.metadata.items():
		setattr(ncf, "metadata::" + _k, _v)
	ncf.close()


1			# -- coding: utf-8 --
2			# vim:fileencoding=utf-8
3			#
4			# Copyright (c) 2014-2017 Stefan Bender
5			#
6			# This file is part of sciapy.
7			# sciapy is free software: you can redistribute it or modify it
8			# under the terms of the GNU General Public License as published by
9			# the Free Software Foundation, version 2.
10			# See accompanying LICENSE file or http://www.gnu.org/licenses/gpl-2.0.html.
11	1		"""SCIAMACHY level 1c limb spectra netcdf interface
12			"""
13
14	1		from __future__ import absolute_import, division, print_function
15
16	1		import numpy as np
17	1		try:
18	1		from netCDF4 import Dataset as netcdf_file
19	1		_fmtargs = {"format": "NETCDF4"}
20			except ImportError:
21			try:
22			from scipy.io.netcdf import netcdf_file
23			_fmtargs = {"version": 1}
24			except ImportError:
25			from pupynere import netcdf_file
26			_fmtargs = {"version": 1}
27
28	1		from ._types import _limb_data_dtype
29
30	1	View Code Duplication	def read_from_netcdf(self, filename):
			0 ignored issues – show Duplication introduced 2018-07-02 09:55 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
31			"""SCIAMACHY level 1c limb scan netcdf import
32
33			Parameters
34			----------
35			filename : str
36			The netcdf filename to read the data from.
37
38			Returns
39			-------
40			nothing
41			"""
42	1		import numpy.lib.recfunctions as rfn
43	1		ncf = netcdf_file(filename, 'r')
44
45	1		self.textheader_length = ncf.textheader_length
46	1		self.textheader = ncf.textheader
47
48	1		self.orbit_state = ncf.orbit_state
49	1		(self.orbit, self.state_in_orbit, self.state_id,
50			self.profiles_per_state, self.profile_in_state) = self.orbit_state
51	1		self.date = ncf.date
52	1		self.cent_lat_lon = ncf.cent_lat_lon
53	1		self.orbit_phase = ncf.orbit_phase
54
55	1		try:
56	1		self.nalt = ncf.dimensions['limb'].size
57	1		self.npix = ncf.dimensions['wavelength'].size
58			except:
59			self.nalt = ncf.dimensions['limb']
60			self.npix = ncf.dimensions['wavelength']
61
62	1		self.wls = ncf.variables['wavelength'][:]
63
64			# pre-set the limb_data
65	1		if self._limb_data_dtype is None:
66	1		self._limb_data_dtype = _limb_data_dtype[:]
67	1		self.limb_data = np.zeros((self.nalt), dtype=self._limb_data_dtype)
68
69	1		self.limb_data["sub_sat_lat"] = ncf.variables['sub_sat_lat'][:]
70	1		self.limb_data["sub_sat_lon"] = ncf.variables['sub_sat_lon'][:]
71	1		self.limb_data["tp_lat"] = ncf.variables['TP latitude'][:]
72	1		self.limb_data["tp_lon"] = ncf.variables['TP longitude'][:]
73	1		self.limb_data["tp_alt"] = ncf.variables['TP altitude'][:]
74	1		self.limb_data["tp_sza"] = ncf.variables['TP SZA'][:]
75	1		self.limb_data["tp_saa"] = ncf.variables['TP SAA'][:]
76	1		self.limb_data["tp_los"] = ncf.variables['TP LOS Zenith'][:]
77	1		self.limb_data["toa_sza"] = ncf.variables['TOA SZA'][:]
78	1		self.limb_data["toa_saa"] = ncf.variables['TOA SAA'][:]
79	1		self.limb_data["toa_los"] = ncf.variables['TOA LOS Zenith'][:]
80	1		self.limb_data["sat_sza"] = ncf.variables['SAT SZA'][:]
81	1		self.limb_data["sat_saa"] = ncf.variables['SAT SAA'][:]
82	1		self.limb_data["sat_los"] = ncf.variables['SAT LOS Zenith'][:]
83	1		self.limb_data["sat_alt"] = ncf.variables['SAT altitude'][:]
84	1		self.limb_data["earth_rad"] = ncf.variables['earthradius'][:]
85
86	1		tmp_rad_arr = list(ncf.variables['radiance'][:])
87	1		tmp_err_arr = list(ncf.variables['radiance errors'][:])
88
89			# save to limb_data recarray
90	1		rads = np.rec.fromarrays([tmp_rad_arr],
91			dtype=np.dtype([("rad", 'f4', (self.npix,))]))
92	1		errs = np.rec.fromarrays([tmp_err_arr],
93			dtype=np.dtype([("err", 'f4', (self.npix,))]))
94	1		self.limb_data = rfn.merge_arrays([self.limb_data, rads, errs],
95			usemask=False, asrecarray=True, flatten=True)
96	1		self._limb_data_dtype = self.limb_data.dtype
97
98	1		for _k in ncf.ncattrs():
99	1		if _k.startswith("metadata"):
100	1		_meta_key = _k.split("::")[1]
101	1		self.metadata[_meta_key] = getattr(ncf, _k)
102	1		ncf.close()
103
104	1	View Code Duplication	def write_to_netcdf(self, filename):
			0 ignored issues – show Duplication introduced 2018-07-02 09:55 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
105			"""SCIAMACHY level 1c limb scan netcdf export
106
107			Parameters
108			----------
109			filename : str
110			The netcdf filename to write the data to.
111
112			Returns
113			-------
114			nothing
115			"""
116	1		ncf = netcdf_file(filename, 'w', **_fmtargs)
117
118	1		ncf.textheader_length = self.textheader_length
119	1		ncf.textheader = self.textheader
120
121	1		ncf.orbit_state = self.orbit_state
122	1		ncf.date = self.date
123	1		ncf.cent_lat_lon = self.cent_lat_lon
124	1		ncf.orbit_phase = self.orbit_phase
125
126	1		ncf.createDimension('limb', self.nalt)
127	1		ncf.createDimension('wavelength', self.npix)
128
129	1		wavs = ncf.createVariable('wavelength', np.dtype('float32').char, ('wavelength',))
130	1		wavs.units = 'nm'
131	1		wavs[:] = np.asarray(self.wls)
132
133	1		sslat = ncf.createVariable('sub_sat_lat', np.dtype('float32').char, ('limb',))
134	1		sslat.units = 'deg'
135	1		sslat[:] = np.asarray(self.limb_data["sub_sat_lat"])
136	1		sslon = ncf.createVariable('sub_sat_lon', np.dtype('float32').char, ('limb',))
137	1		sslon.units = 'deg'
138	1		sslon[:] = np.asarray(self.limb_data["sub_sat_lon"])
139	1		tp_lats = ncf.createVariable('TP latitude', np.dtype('float32').char, ('limb',))
140	1		tp_lats.units = 'deg'
141	1		tp_lats[:] = np.asarray(self.limb_data["tp_lat"])
142	1		tp_lons = ncf.createVariable('TP longitude', np.dtype('float32').char, ('limb',))
143	1		tp_lons.units = 'deg'
144	1		tp_lons[:] = np.asarray(self.limb_data["tp_lon"])
145	1		tp_alts = ncf.createVariable('TP altitude', np.dtype('float32').char, ('limb',))
146	1		tp_alts.units = 'km'
147	1		tp_alts[:] = np.asarray(self.limb_data["tp_alt"])
148	1		tp_szas = ncf.createVariable('TP SZA', np.dtype('float32').char, ('limb',))
149	1		tp_szas.units = 'deg'
150	1		tp_szas[:] = np.asarray(self.limb_data["tp_sza"])
151	1		tp_saas = ncf.createVariable('TP SAA', np.dtype('float32').char, ('limb',))
152	1		tp_saas.units = 'deg'
153	1		tp_saas[:] = np.asarray(self.limb_data["tp_saa"])
154	1		tp_los_zeniths = ncf.createVariable('TP LOS Zenith', np.dtype('float32').char, ('limb',))
155	1		tp_los_zeniths.units = 'deg'
156	1		tp_los_zeniths[:] = np.asarray(self.limb_data["tp_los"])
157	1		toa_szas = ncf.createVariable('TOA SZA', np.dtype('float32').char, ('limb',))
158	1		toa_szas.units = 'deg'
159	1		toa_szas[:] = np.asarray(self.limb_data["toa_sza"])
160	1		toa_saas = ncf.createVariable('TOA SAA', np.dtype('float32').char, ('limb',))
161	1		toa_saas.units = 'deg'
162	1		toa_saas[:] = np.asarray(self.limb_data["toa_saa"])
163	1		toa_los_zeniths = ncf.createVariable('TOA LOS Zenith', np.dtype('float32').char, ('limb',))
164	1		toa_los_zeniths.units = 'deg'
165	1		toa_los_zeniths[:] = np.asarray(self.limb_data["toa_los"])
166	1		sat_szas = ncf.createVariable('SAT SZA', np.dtype('float32').char, ('limb',))
167	1		sat_szas.units = 'deg'
168	1		sat_szas[:] = np.asarray(self.limb_data["sat_sza"])
169	1		sat_saas = ncf.createVariable('SAT SAA', np.dtype('float32').char, ('limb',))
170	1		sat_saas.units = 'deg'
171	1		sat_saas[:] = np.asarray(self.limb_data["sat_saa"])
172	1		sat_los_zeniths = ncf.createVariable('SAT LOS Zenith', np.dtype('float32').char, ('limb',))
173	1		sat_los_zeniths.units = 'deg'
174	1		sat_los_zeniths[:] = np.asarray(self.limb_data["sat_los"])
175	1		sat_alts = ncf.createVariable('SAT altitude', np.dtype('float32').char, ('limb',))
176	1		sat_alts.units = 'km'
177	1		sat_alts[:] = np.asarray(self.limb_data["sat_alt"])
178	1		eradii_alts = ncf.createVariable('earthradius', np.dtype('float32').char, ('limb',))
179	1		eradii_alts.units = 'km'
180	1		eradii_alts[:] = np.asarray(self.limb_data["earth_rad"])
181
182	1		rads = ncf.createVariable('radiance', np.dtype('float32').char,
183			('limb', 'wavelength'), zlib=True, complevel=1)
184	1		errs = ncf.createVariable('radiance errors', np.dtype('float32').char,
185			('limb', 'wavelength'), zlib=True, complevel=1)
186	1		rads.units = 'ph / s / cm^2 / nm'
187	1		errs.units = 'ph / s / cm^2 / nm'
188	1		rads[:] = np.asarray(self.limb_data["rad"]).reshape(self.nalt, self.npix)
189	1		errs[:] = np.asarray(self.limb_data["err"]).reshape(self.nalt, self.npix)
190
191	1		for _k, _v in self.metadata.items():
192	1		setattr(ncf, "metadata::" + _k, _v)
193			ncf.close()
194

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Push — master ( ed9f5a...bed583 )

sciapy.level1c.scia_limb_nc.read_from_netcdf() B

Complexity

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Duplication

Code Coverage

Importance

How to fix Long Method

Long Method

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