sciapy.level1c.scia_solar.scia_solar.write_to_textfile() - Code Metrics - Inspection of "tests l1c: Use self-made assertion function" - st-bender/sciapy - Measure and Improve Code Quality continuously with Scrutinizer

Passed

Push — master ( 021d22...fccee2 )

by Stefan

created 2020-02-27 16:10 UTC

scia_solar.write_to_textfile() B

↳ Parent: sciapy.level1c.scia_solar

Complexity

Conditions

Size

Total Lines	46
Code Lines	24

Duplication

Lines	46
Ratio	100 %

Code Coverage

Tests	14
CRAP Score	6.0702

Importance

Changes

Metric	Value
cc	6
eloc	24
nop	2
dl	46
loc	46
ccs	14
cts	16
cp	0.875
crap	6.0702
rs	8.3706
c	0
b	0
f	0

# -*- coding: utf-8 -*-
# vim:fileencoding=utf-8
#
# Copyright (c) 2014-2017 Stefan Bender
#
# This module 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 solar spectra module

This module contains the python class for SCIAMACHY level 1c solar spectra.
It include some simple conversion routines, from and to ascii and from and to netcdf.

A simple import from SRON nadc_tools (https://github.com/rmvanhees/nadc_tools)
produced HDF5 is also supported.
"""
from __future__ import absolute_import, division, print_function

__all__ = ["scia_solar", "__doc__"]

import datetime
import logging

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}

logging.basicConfig(level=logging.INFO,
		format="[%(levelname)-8s] (%(asctime)s) "
		"%(filename)s:%(lineno)d %(message)s",
		datefmt="%Y-%m-%d %H:%M:%S %z")

class scia_solar(object):

	"""SCIAMACHY solar reference spectrum class

	Contains the SCIAMACHY level 1c solar reference spectrum.
	The format is inspired by the SCIAMACHY ascii data format.

	Attributes
	----------
	textheader_length : int
		The number of lines of the text header.
	textheader : str
		The header containing the solar spectrum meta data.
	npix : int
		The number of spectral points.
	solar_id : str
		The solar reference spectrum ID,
		choices: "D0", "D1", "D2", "E0", "E1", "A0", "A1",
		"N1", "N2", "N3", "N4", "N5".
	orbit : int
		The SCIAMACHY/Envisat orbit number.
	time : :class:`datetime.datetime`
		The sensing start time of the (semi-)orbit.
	wls : (M,) array_like
		The spectral wavelengths.
	rads : (M,) array_like
		The radiances at the spectral points, M = len(wls).
	errs : (M,) array_like
		The relative radiance uncertainties at the tangent points, M = len(wls).
	"""

	def __init__(self):
		self.textheader_length = 0
		self.textheader = ""
		self.npix = 0
		self.solar_id = ""
		self.orbit = -1
		self.time = None
		self.wls = np.array([])
		self.rads = np.array([])
		self.errs = None

	def read_from_netcdf(self, filename):
		"""SCIAMACHY level 1c solar reference netcdf import

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

		Returns
		-------
		nothing
		"""
		ncf = netcdf_file(filename, 'r')
		self.textheader_length = ncf.textheader_length
		self.textheader = ncf.textheader
		if self.textheader_length > 6:
			self.solar_id = ncf.solar_id
			self.orbit = ncf.orbit
			self.time = datetime.datetime.strptime(ncf.time, '%Y-%m-%d %H:%M:%S%z')
		self.npix = len(ncf.dimensions['wavelength'])
		self.wls = ncf.variables['wavelength'][:].copy()
		self.rads = ncf.variables['radiance'][:].copy()
		try:
			self.errs = ncf.variables['radiance errors'][:].copy()
		except KeyError:
			self.errs = None
		ncf.close()

	def read_from_textfile(self, filename):
		"""SCIAMACHY level 1c solar reference text import

		Parameters
		----------
		filename : str
			The (plain) ascii table filename to read the data from.

		Returns
		-------
		nothing
		"""
		if hasattr(filename, 'seek'):
			f = filename
		else:
			f = open(filename, 'r')
		h_list = []
		try:
			nh = int(f.readline())
		except:
			nh = 6
			f.seek(0)
		for i in range(0, nh):
			h_list.append(f.readline().rstrip())
		self.textheader_length = nh
		self.textheader = '\n'.join(h_list)
		self.npix = int(f.readline())
		if nh > 6:
			self.solar_id = f.readline().rstrip()
			self.orbit = int(f.readline())
			self.time = datetime.datetime.strptime(f.readline() + "+0000", "%Y %m %d %H %M %S %z")
			self.wls, self.rads = np.genfromtxt(filename, skip_header=nh + 5, unpack=True)
			self.errs = None
		else:
			self.wls, self.rads, self.errs = np.genfromtxt(filename, skip_header=7, unpack=True)

	def read_from_hdf5(self, hf, ref="D0"):
		"""SCIAMACHY level 1c solar reference HDF5 import

		Parameters
		----------
		hf : opened file
			Pointer to the opened level 1c HDF5 file
		ref : str
			The solar reference spectra id name,
			choose from: "D0", "D1", "D2", "E0", "E1", "A0", "A1",
			"N1", "N2", "N3", "N4", "N5". Defaults to "D0".

		Returns
		-------
		success : int
			0 on success, 1 if an error occured.
		"""
		product = hf.get("/MPH")["product_name"][0].decode()
		soft_ver = hf.get("/MPH")["software_version"][0].decode()
		key_ver = hf.get("/SPH")["key_data_version"][0].decode()
		mf_ver = hf.get("/SPH")["m_factor_version"][0].decode()
		init_version = hf.get("/SPH")["init_version"][0].decode().strip()
		init_ver, decont = init_version.split(' ')
		decont = decont.lstrip("DECONT=")
		start_date = hf.get("/MPH")["sensing_start"][0].decode().rstrip('"')
		# fill some class variables
		self.time = (datetime.datetime.strptime(start_date, "%d-%b-%Y %H:%M:%S.%f")
					.replace(tzinfo=datetime.timezone.utc))
		self.orbit = hf.get("/MPH")["abs_orbit"][0]
		self.solar_id = ref

		logging.debug("product: %s, orbit: %s", product, self.orbit)
		logging.debug("soft_ver: %s, key_ver: %s, mf_ver: %s, init_ver: %s, "
				"decont_ver: %s", soft_ver, key_ver, mf_ver, init_ver, decont)

		# Prepare the header
		datatype_txt = "SCIAMACHY solar mean ref."
		n_header = 10
		line = n_header + 2
		header = ("#Data type          : {0}\n".format(datatype_txt))
		header += ("#L1b product        : {0}\n".format(product))
		header += ("#Orbit nr.          : {0:05d}\n".format(self.orbit))
		header += ("#Ver. Proc/Key/M/I/D: {0}  {1}  {2}  {3}  {4}\n"
				.format(soft_ver, key_ver, mf_ver, init_ver, decont))
		header += ("#Starttime          : {0}\n".format(start_date))
		header += ("#L.{0:2d} : Number_of_pixels\n".format(line))
		line += 1
		header += ("#L.{0:2d} : Solar ID\n".format(line))
		line += 1
		header += ("#L.{0:2d} : Orbit\n".format(line))
		line += 1
		header += ("#L.{0:2d} : Date Time : yyyy mm dd hh mm ss\n".format(line))
		line += 1
		header += ("#L.{0:2d} : Npix lines : wavelangth  irradiance  accuracy".format(line))

		sun_ref = hf.get("/GADS/SUN_REFERENCE")
		this_ref = sun_ref[sun_ref["sun_spec_id"] == ref]

		# fill the remaining class variables
		self.textheader_length = n_header
		self.textheader = header
		self.wls = this_ref["wvlen_sun"][:]
		self.npix = len(self.wls)
		self.rads = this_ref["mean_sun"][:]
		self.errs = this_ref["accuracy_sun"][:]
		return 0

	def read_from_file(self, filename):
		"""SCIAMACHY level 1c solar reference data import

		Convenience function to read the reference spectrum.
		Tries to detect the file format automatically trying netcdf first,
		and if that fails falls back to the text reader.
		Currently no HDF5 support.

		Parameters
		----------
		filename : str
			The filename to read from.

		Returns
		-------
		nothing
		"""
		try:
			# try netcdf first
			self.read_from_netcdf(filename)
		except:
			# fall back to text file
			self.read_from_textfile(filename)

	def write_to_netcdf(self, filename):
		"""SCIAMACHY level 1c solar reference 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.solar_id = self.solar_id
		ncf.orbit = self.orbit
		ncf.time = self.time.strftime('%Y-%m-%d %H:%M:%S+0000')

		ncf.createDimension('wavelength', self.npix)
		wavs = ncf.createVariable('wavelength', np.dtype('float64').char, ('wavelength',))
		wavs.units = 'nm'
		wavs[:] = self.wls

		rads = ncf.createVariable('radiance', np.dtype('float64').char, ('wavelength',))
		rads.units = 'ph / s / cm^2 / nm'
		rads[:] = self.rads

		if self.errs is not None:
			errs = ncf.createVariable('radiance errors', np.dtype('float64').char, ('wavelength',))
			errs.units = 'ph / s / cm^2 / nm'
			errs[:] = self.errs

		ncf.close()

	def write_to_textfile(self, filename):
		"""SCIAMACHY level 1c solar reference text export

		Parameters
		----------
		filename : str
			The (plain) ascii table filename to write the data to.
			Passing sys.STDOUT writes to the console.

		Returns
		-------
		nothing
		"""
		if hasattr(filename, 'seek'):
			f = filename
		else:
			f = open(filename, 'w')
		if self.textheader_length > 6:
			print("{0:2d}".format(self.textheader_length), file=f)
		print(self.textheader, file=f)
		print(self.npix, file=f)
		if self.textheader_length > 6:
			print(self.solar_id, file=f)
			print(self.orbit, file=f)
			print("%4d %2d %2d %2d %2d %2d" % (self.time.year, self.time.month,
					self.time.day, self.time.hour, self.time.minute, self.time.second),
				file=f)
		for i in range(self.npix):
			#output = []
			#output.append(self.wls[i])
			#output.append(self.rads[i])
			#output.append(self.errs[i])
			#print('\t'.join(map(str, output)), file=f)
			if self.errs is not None:
				print(
					"{0:9.4f}  {1:12.5e}  {2:12.5e}".format(
						self.wls[i], self.rads[i], self.errs[i],
					),
					file=f,
				)
			else:
				print(
					"{0:9.4f}  {1:12.5e}".format(
						self.wls[i], self.rads[i],
					),
					file=f,
				)


1			# -- coding: utf-8 --
2			# vim:fileencoding=utf-8
3			#
4			# Copyright (c) 2014-2017 Stefan Bender
5			#
6			# This module is part of sciapy.
7			# sciapy is free software: you can redistribute it or modify
8			# it under the terms of the GNU General Public License as published
9			# by 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 solar spectra module
12
13			This module contains the python class for SCIAMACHY level 1c solar spectra.
14			It include some simple conversion routines, from and to ascii and from and to netcdf.
15
16			A simple import from SRON nadc_tools (https://github.com/rmvanhees/nadc_tools)
17			produced HDF5 is also supported.
18			"""
19	1		from __future__ import absolute_import, division, print_function
20
21	1		__all__ = ["scia_solar", "__doc__"]
22
23	1		import datetime
24	1		import logging
25
26	1		import numpy as np
27	1		try:
28	1		from netCDF4 import Dataset as netcdf_file
29	1		_fmtargs = {"format": "NETCDF4"}
30			except ImportError:
31			try:
32			from scipy.io.netcdf import netcdf_file
33			_fmtargs = {"version": 1}
34			except ImportError:
35			from pupynere import netcdf_file
36			_fmtargs = {"version": 1}
37
38	1		logging.basicConfig(level=logging.INFO,
39			format="[%(levelname)-8s] (%(asctime)s) "
40			"%(filename)s:%(lineno)d %(message)s",
41			datefmt="%Y-%m-%d %H:%M:%S %z")
42
43	1	View Code Duplication	class scia_solar(object):
			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...
44			"""SCIAMACHY solar reference spectrum class
45
46			Contains the SCIAMACHY level 1c solar reference spectrum.
47			The format is inspired by the SCIAMACHY ascii data format.
48
49			Attributes
50			----------
51			textheader_length : int
52			The number of lines of the text header.
53			textheader : str
54			The header containing the solar spectrum meta data.
55			npix : int
56			The number of spectral points.
57			solar_id : str
58			The solar reference spectrum ID,
59			choices: "D0", "D1", "D2", "E0", "E1", "A0", "A1",
60			"N1", "N2", "N3", "N4", "N5".
61			orbit : int
62			The SCIAMACHY/Envisat orbit number.
63			time : :class:`datetime.datetime`
64			The sensing start time of the (semi-)orbit.
65			wls : (M,) array_like
66			The spectral wavelengths.
67			rads : (M,) array_like
68			The radiances at the spectral points, M = len(wls).
69			errs : (M,) array_like
70			The relative radiance uncertainties at the tangent points, M = len(wls).
71			"""
72
73	1		def __init__(self):
74	1		self.textheader_length = 0
75	1		self.textheader = ""
76	1		self.npix = 0
77	1		self.solar_id = ""
78	1		self.orbit = -1
79	1		self.time = None
80	1		self.wls = np.array([])
81	1		self.rads = np.array([])
82	1		self.errs = None
83
84	1		def read_from_netcdf(self, filename):
85			"""SCIAMACHY level 1c solar reference netcdf import
86
87			Parameters
88			----------
89			filename : str
90			The netcdf filename to read the data from.
91
92			Returns
93			-------
94			nothing
95			"""
96	1		ncf = netcdf_file(filename, 'r')
97	1		self.textheader_length = ncf.textheader_length
98	1		self.textheader = ncf.textheader
99	1		if self.textheader_length > 6:
100	1		self.solar_id = ncf.solar_id
101	1		self.orbit = ncf.orbit
102	1		self.time = datetime.datetime.strptime(ncf.time, '%Y-%m-%d %H:%M:%S%z')
103	1		self.npix = len(ncf.dimensions['wavelength'])
104	1		self.wls = ncf.variables['wavelength'][:].copy()
105	1		self.rads = ncf.variables['radiance'][:].copy()
106	1		try:
107	1		self.errs = ncf.variables['radiance errors'][:].copy()
108	1		except KeyError:
109	1		self.errs = None
110	1		ncf.close()
111
112	1		def read_from_textfile(self, filename):
113			"""SCIAMACHY level 1c solar reference text import
114
115			Parameters
116			----------
117			filename : str
118			The (plain) ascii table filename to read the data from.
119
120			Returns
121			-------
122			nothing
123			"""
124	1		if hasattr(filename, 'seek'):
125			f = filename
126			else:
127	1		f = open(filename, 'r')
128	1		h_list = []
129	1		try:
130	1		nh = int(f.readline())
131			except:
132			nh = 6
133			f.seek(0)
134	1		for i in range(0, nh):
135	1		h_list.append(f.readline().rstrip())
136	1		self.textheader_length = nh
137	1		self.textheader = '\n'.join(h_list)
138	1		self.npix = int(f.readline())
139	1		if nh > 6:
140	1		self.solar_id = f.readline().rstrip()
141	1		self.orbit = int(f.readline())
142	1		self.time = datetime.datetime.strptime(f.readline() + "+0000", "%Y %m %d %H %M %S %z")
143	1		self.wls, self.rads = np.genfromtxt(filename, skip_header=nh + 5, unpack=True)
144	1		self.errs = None
145			else:
146			self.wls, self.rads, self.errs = np.genfromtxt(filename, skip_header=7, unpack=True)
147
148	1		def read_from_hdf5(self, hf, ref="D0"):
149			"""SCIAMACHY level 1c solar reference HDF5 import
150
151			Parameters
152			----------
153			hf : opened file
154			Pointer to the opened level 1c HDF5 file
155			ref : str
156			The solar reference spectra id name,
157			choose from: "D0", "D1", "D2", "E0", "E1", "A0", "A1",
158			"N1", "N2", "N3", "N4", "N5". Defaults to "D0".
159
160			Returns
161			-------
162			success : int
163			0 on success, 1 if an error occured.
164			"""
165			product = hf.get("/MPH")["product_name"][0].decode()
166			soft_ver = hf.get("/MPH")["software_version"][0].decode()
167			key_ver = hf.get("/SPH")["key_data_version"][0].decode()
168			mf_ver = hf.get("/SPH")["m_factor_version"][0].decode()
169			init_version = hf.get("/SPH")["init_version"][0].decode().strip()
170			init_ver, decont = init_version.split(' ')
171			decont = decont.lstrip("DECONT=")
172			start_date = hf.get("/MPH")["sensing_start"][0].decode().rstrip('"')
173			# fill some class variables
174			self.time = (datetime.datetime.strptime(start_date, "%d-%b-%Y %H:%M:%S.%f")
175			.replace(tzinfo=datetime.timezone.utc))
176			self.orbit = hf.get("/MPH")["abs_orbit"][0]
177			self.solar_id = ref
178
179			logging.debug("product: %s, orbit: %s", product, self.orbit)
180			logging.debug("soft_ver: %s, key_ver: %s, mf_ver: %s, init_ver: %s, "
181			"decont_ver: %s", soft_ver, key_ver, mf_ver, init_ver, decont)
182
183			# Prepare the header
184			datatype_txt = "SCIAMACHY solar mean ref."
185			n_header = 10
186			line = n_header + 2
187			header = ("#Data type : {0}\n".format(datatype_txt))
188			header += ("#L1b product : {0}\n".format(product))
189			header += ("#Orbit nr. : {0:05d}\n".format(self.orbit))
190			header += ("#Ver. Proc/Key/M/I/D: {0} {1} {2} {3} {4}\n"
191			.format(soft_ver, key_ver, mf_ver, init_ver, decont))
192			header += ("#Starttime : {0}\n".format(start_date))
193			header += ("#L.{0:2d} : Number_of_pixels\n".format(line))
194			line += 1
195			header += ("#L.{0:2d} : Solar ID\n".format(line))
196			line += 1
197			header += ("#L.{0:2d} : Orbit\n".format(line))
198			line += 1
199			header += ("#L.{0:2d} : Date Time : yyyy mm dd hh mm ss\n".format(line))
200			line += 1
201			header += ("#L.{0:2d} : Npix lines : wavelangth irradiance accuracy".format(line))
202
203			sun_ref = hf.get("/GADS/SUN_REFERENCE")
204			this_ref = sun_ref[sun_ref["sun_spec_id"] == ref]
205
206			# fill the remaining class variables
207			self.textheader_length = n_header
208			self.textheader = header
209			self.wls = this_ref["wvlen_sun"][:]
210			self.npix = len(self.wls)
211			self.rads = this_ref["mean_sun"][:]
212			self.errs = this_ref["accuracy_sun"][:]
213			return 0
214
215	1		def read_from_file(self, filename):
216			"""SCIAMACHY level 1c solar reference data import
217
218			Convenience function to read the reference spectrum.
219			Tries to detect the file format automatically trying netcdf first,
220			and if that fails falls back to the text reader.
221			Currently no HDF5 support.
222
223			Parameters
224			----------
225			filename : str
226			The filename to read from.
227
228			Returns
229			-------
230			nothing
231			"""
232	1		try:
233			# try netcdf first
234	1		self.read_from_netcdf(filename)
235	1		except:
236			# fall back to text file
237	1		self.read_from_textfile(filename)
238
239	1		def write_to_netcdf(self, filename):
240			"""SCIAMACHY level 1c solar reference netcdf export
241
242			Parameters
243			----------
244			filename : str
245			The netcdf filename to write the data to.
246
247			Returns
248			-------
249			nothing
250			"""
251	1		ncf = netcdf_file(filename, 'w', **_fmtargs)
252	1		ncf.textheader_length = self.textheader_length
253	1		ncf.textheader = self.textheader
254	1		ncf.solar_id = self.solar_id
255	1		ncf.orbit = self.orbit
256	1		ncf.time = self.time.strftime('%Y-%m-%d %H:%M:%S+0000')
257
258	1		ncf.createDimension('wavelength', self.npix)
259	1		wavs = ncf.createVariable('wavelength', np.dtype('float64').char, ('wavelength',))
260	1		wavs.units = 'nm'
261	1		wavs[:] = self.wls
262
263	1		rads = ncf.createVariable('radiance', np.dtype('float64').char, ('wavelength',))
264	1		rads.units = 'ph / s / cm^2 / nm'
265	1		rads[:] = self.rads
266
267	1		if self.errs is not None:
268			errs = ncf.createVariable('radiance errors', np.dtype('float64').char, ('wavelength',))
269			errs.units = 'ph / s / cm^2 / nm'
270			errs[:] = self.errs
271
272	1		ncf.close()
273
274	1		def write_to_textfile(self, filename):
275			"""SCIAMACHY level 1c solar reference text export
276
277			Parameters
278			----------
279			filename : str
280			The (plain) ascii table filename to write the data to.
281			Passing sys.STDOUT writes to the console.
282
283			Returns
284			-------
285			nothing
286			"""
287	1		if hasattr(filename, 'seek'):
288			f = filename
289			else:
290	1		f = open(filename, 'w')
291	1		if self.textheader_length > 6:
292	1		print("{0:2d}".format(self.textheader_length), file=f)
293	1		print(self.textheader, file=f)
294	1		print(self.npix, file=f)
295	1		if self.textheader_length > 6:
296	1		print(self.solar_id, file=f)
297	1		print(self.orbit, file=f)
298	1		print("%4d %2d %2d %2d %2d %2d" % (self.time.year, self.time.month,
299			self.time.day, self.time.hour, self.time.minute, self.time.second),
300			file=f)
301	1		for i in range(self.npix):
302			#output = []
303			#output.append(self.wls[i])
304			#output.append(self.rads[i])
305			#output.append(self.errs[i])
306			#print('\t'.join(map(str, output)), file=f)
307	1		if self.errs is not None:
308			print(
309			"{0:9.4f} {1:12.5e} {2:12.5e}".format(
310			self.wls[i], self.rads[i], self.errs[i],
311			),
312			file=f,
313			)
314			else:
315	1		print(
316			"{0:9.4f} {1:12.5e}".format(
317			self.wls[i], self.rads[i],
318			),
319			file=f,
320			)
321

st-bender / sciapy

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scia_solar.write_to_textfile() B

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