[Git][debian-gis-team/pygac][upstream] New upstream version 1.3.1
Antonio Valentino
gitlab at salsa.debian.org
Sat Feb 8 08:23:08 GMT 2020
Antonio Valentino pushed to branch upstream at Debian GIS Project / pygac
Commits:
765077a8 by Antonio Valentino at 2020-02-08T08:04:27+00:00
New upstream version 1.3.1
- - - - -
10 changed files:
- .bumpversion.cfg
- + .pre-commit-config.yaml
- CHANGELOG.md
- pygac/calibration.py
- pygac/klm_reader.py
- pygac/pod_reader.py
- pygac/reader.py
- pygac/tests/test_reader.py
- pygac/version.py
- + setup.cfg
Changes:
=====================================
.bumpversion.cfg
=====================================
@@ -1,5 +1,5 @@
[bumpversion]
-current_version = 1.3.0
+current_version = 1.3.1
commit = True
tag = True
=====================================
.pre-commit-config.yaml
=====================================
@@ -0,0 +1,8 @@
+exclude: '^$'
+fail_fast: false
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+ rev: v2.2.3
+ hooks:
+ - id: flake8
+ additional_dependencies: [flake8-docstrings, flake8-debugger, flake8-bugbear]
=====================================
CHANGELOG.md
=====================================
@@ -1,3 +1,27 @@
+## Version v1.3.1 (2020/02/07)
+
+### Issues Closed
+
+* [Issue 52](https://github.com/pytroll/pygac/issues/52) - Allow gzip input files ([PR 53](https://github.com/pytroll/pygac/pull/53))
+* [Issue 49](https://github.com/pytroll/pygac/issues/49) - Calibration Coeffs Patmos-X 2017 ([PR 50](https://github.com/pytroll/pygac/pull/50))
+
+In this release 2 issues were closed.
+
+### Pull Requests Merged
+
+#### Bugs fixed
+
+* [PR 50](https://github.com/pytroll/pygac/pull/50) - Fix typo in MetOp-B calibration ([49](https://github.com/pytroll/pygac/issues/49))
+* [PR 48](https://github.com/pytroll/pygac/pull/48) - Update metadata when reading lonlat also
+
+#### Features added
+
+* [PR 53](https://github.com/pytroll/pygac/pull/53) - Allow gzip compressed files as input for klm and pod readers read method ([52](https://github.com/pytroll/pygac/issues/52))
+* [PR 51](https://github.com/pytroll/pygac/pull/51) - Use the data format name to id ARS headered files
+
+In this release 4 pull requests were closed.
+
+
## Version 1.3.0 (2019/12/05)
=====================================
pygac/calibration.py
=====================================
@@ -29,8 +29,8 @@ import numpy as np
coeffs = {
'metopb': {'ah': np.array([0.166, 0.183, 0.201]),
'al': np.array([0.055, 0.061, 0.029]),
- 'bh': np.array([2.019, 1.476, 1.478]),
- 'bl': np.array([2.019, 1.476, 1.478]),
+ 'bh': np.array([2.019, 1.476, 1.748]),
+ 'bl': np.array([2.019, 1.476, 1.748]),
'ch': np.array([-0.201, -0.137, -0.033]),
'cl': np.array([-0.201, -0.137, -0.033]),
'c_dark': np.array([39.70, 40.00, 40.30]),
@@ -405,6 +405,9 @@ coeffs = {
'b1': np.array([1 - 0.0, 1 - 0.11187, 1 - 0.05991]),
'b2': np.array([0.0, 0.00054668, 0.00024985])}}
+"""Source Patmos-X Coeffs: Version Tag 'y2017r1_sbaf'
+https://cimss.ssec.wisc.edu/patmosx/avhrr_cal.html"""
+
class Calibrator(object):
=====================================
pygac/klm_reader.py
=====================================
@@ -9,6 +9,7 @@
# Sajid Pareeth <sajid.pareeth at fmach.it>
# Martin Raspaud <martin.raspaud at smhi.se>
# Adam Dybbroe <adam.dybbroe at smhi.se>
+# Carlos Horn <carlos.horn at external.eumetsat.int>
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
@@ -587,29 +588,40 @@ class KLMReader(Reader):
The scanlines
"""
- super(KLMReader, self).read(filename=filename)
- with open(filename) as fd_:
- self.ars_head = np.fromfile(fd_, dtype=ars_header, count=1)[0]
- if not self.ars_head['data_set_name'].startswith(self.creation_site):
+ with self._open(filename) as fd_:
+ # Note that np.fromfile does not work with gzip.GzipFile
+ # objects (numpy version 1.16.4), because it restricts the
+ # file objects to (io.FileIO, io.BufferedReader, io.BufferedWriter)
+ # see: numpy.compat.py3k.isfileobj
+ self.ars_head, = np.frombuffer(
+ fd_.read(ars_header.itemsize),
+ dtype=ars_header, count=1)
+ if not self.ars_head['data_format'].startswith(b'NOAA Level 1b'):
fd_.seek(0)
self.ars_head = None
ars_offset = 0
else:
ars_offset = ars_header.itemsize
- self.head = np.fromfile(fd_, dtype=header, count=1)[0]
+ self.head, = np.frombuffer(
+ fd_.read(header.itemsize),
+ dtype=header, count=1)
self.header_version = self.head[
"noaa_level_1b_format_version_number"]
if self.header_version >= 5:
- self.analog_telemetry = np.fromfile(
- fd_, dtype=analog_telemetry_v5, count=1)[0]
+ self.analog_telemetry, = np.frombuffer(
+ fd_.read(analog_telemetry_v5.itemsize),
+ dtype=analog_telemetry_v5, count=1)
else:
- self.analog_telemetry = np.fromfile(
- fd_, dtype=analog_telemetry_v2, count=1)[0]
+ self.analog_telemetry, = np.frombuffer(
+ fd_.read(analog_telemetry_v2.itemsize),
+ dtype=analog_telemetry_v2, count=1)
# LAC: 1, GAC: 2, ...
self.data_type = self.head['data_type_code']
fd_.seek(self.offset + ars_offset, 0)
- self.scans = np.fromfile(fd_, dtype=self.scanline_type,
- count=self.head["count_of_data_records"])
+ self.scans = np.frombuffer(
+ fd_.read(),
+ dtype=self.scanline_type,
+ count=self.head["count_of_data_records"])
self.correct_scan_line_numbers()
self.spacecraft_id = self.head["noaa_spacecraft_identification_code"]
=====================================
pygac/pod_reader.py
=====================================
@@ -8,6 +8,7 @@
# Adam Dybbroe <adam.dybbroe at smhi.se>
# Sajid Pareeth <sajid.pareeth at fmach.it>
# Martin Raspaud <martin.raspaud at smhi.se>
+# Carlos Horn <carlos.horn at external.eumetsat.int>
# This work was done in the framework of ESA-CCI-Clouds phase I
@@ -216,11 +217,12 @@ class PODReader(Reader):
The scanlines
"""
- super(PODReader, self).read(filename=filename)
# choose the right header depending on the date
- with open(filename) as fd_:
+ with self._open(filename) as fd_:
# read archive header
- self.tbm_head = np.fromfile(fd_, dtype=tbm_header, count=1)[0]
+ self.tbm_head, = np.frombuffer(
+ fd_.read(tbm_header.itemsize),
+ dtype=tbm_header, count=1)
if ((not self.tbm_head['data_set_name'].startswith(self.creation_site + b'.')) and
(self.tbm_head['data_set_name'] != b'\x00' * 42 + b' ')):
fd_.seek(0)
@@ -229,7 +231,9 @@ class PODReader(Reader):
else:
tbm_offset = tbm_header.itemsize
- head = np.fromfile(fd_, dtype=header0, count=1)[0]
+ head, = np.frombuffer(
+ fd_.read(header0.itemsize),
+ dtype=header0, count=1)
year, jday, _ = self.decode_timestamps(head["start_time"])
start_date = (datetime.date(year, 1, 1) +
@@ -243,11 +247,14 @@ class PODReader(Reader):
header = header3
fd_.seek(tbm_offset, 0)
- self.head = np.fromfile(fd_, dtype=header, count=1)[0]
+ self.head, = np.frombuffer(
+ fd_.read(header.itemsize),
+ dtype=header, count=1)
fd_.seek(self.offset + tbm_offset, 0)
- self.scans = np.fromfile(fd_,
- dtype=self.scanline_type,
- count=self.head["number_of_scans"])
+ self.scans = np.frombuffer(
+ fd_.read(),
+ dtype=self.scanline_type,
+ count=self.head["number_of_scans"])
self.correct_scan_line_numbers()
self.spacecraft_id = self.head["noaa_spacecraft_identification_code"]
=====================================
pygac/reader.py
=====================================
@@ -6,6 +6,7 @@
# Author(s):
# Martin Raspaud <martin.raspaud at smhi.se>
+# Carlos Horn <carlos.horn at external.eumetsat.int>
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
@@ -30,6 +31,8 @@ import numpy as np
import os
import six
import types
+import gzip
+from contextlib import contextmanager
from pygac import (CONFIG_FILE, centered_modulus,
calculate_sun_earth_distance_correction,
@@ -120,8 +123,31 @@ class Reader(six.with_metaclass(ABCMeta)):
Args:
filename (str): Specifies the GAC/LAC file to be read.
"""
- self.filename = os.path.basename(filename)
+ raise NotImplementedError
+
+ @contextmanager
+ def _open(self, filename):
+ """Open the GAC/LAC data file and yield the filehandle.
+
+ Args:
+ filename (str): Path to GAC/LAC file to open
+
+ Note:
+ This method should be called inside the Reader.read implementation
+ """
+ basename = os.path.basename(filename)
+ root, ext = os.path.splitext(basename)
+ if ext == ".gz":
+ self.filename = root
+ file_object = gzip.open(filename, mode='rb')
+ else:
+ self.filename = basename
+ file_object = open(filename, mode='rb')
LOG.info('Reading %s', self.filename)
+ try:
+ yield file_object
+ finally:
+ file_object.close()
@abstractmethod
def get_header_timestamp(self):
@@ -385,6 +411,7 @@ class Reader(six.with_metaclass(ABCMeta)):
"""
if self.lons is None and self.lats is None:
self.lons, self.lats = self._get_lonlat()
+ self.update_meta_data()
# Interpolate from every eighth pixel to all pixels.
if self.interpolate_coords:
=====================================
pygac/tests/test_reader.py
=====================================
@@ -4,6 +4,7 @@
# Author(s):
# Stephan Finkensieper <stephan.finkensieper at dwd.de>
+# Carlos Horn <carlos.horn at external.eumetsat.int>
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
@@ -43,6 +44,17 @@ class TestGacReader(unittest.TestCase):
self.interpolator = interpolator
self.reader = GACReader()
+ @mock.patch('pygac.reader.open', mock.mock_open(read_data='normal'))
+ @mock.patch('pygac.reader.gzip.open', mock.mock_open(read_data='gzip'))
+ def test__open(self):
+ """Test if proper opener is used."""
+ with self.reader._open("test_file") as f:
+ content_normal = f.read()
+ self.assertEqual(content_normal, 'normal')
+ with self.reader._open("test_file.gz") as f:
+ content_gzip = f.read()
+ self.assertEqual(content_gzip, 'gzip')
+
def test_to_datetime64(self):
"""Test conversion from (year, jday, msec) to datetime64."""
t0 = GACReader.to_datetime64(year=np.array(1970), jday=np.array(1),
@@ -61,11 +73,13 @@ class TestGacReader(unittest.TestCase):
"""Test scanline timestamp estimation."""
self.assertEqual(self.reader.lineno2msec(12345), 6172000)
+ @mock.patch('pygac.reader.Reader.update_meta_data')
@mock.patch('pygac.gac_reader.GACReader._get_lonlat')
@mock.patch('pygac.gac_reader.GACReader._get_corrupt_mask')
@mock.patch('pygac.gac_reader.GACReader._adjust_clock_drift')
def test_get_lonlat(self, adjust_clockdrift,
- get_corrupt_mask, get_lonlat):
+ get_corrupt_mask, get_lonlat,
+ update_meta_data):
"""Test common lon/lat computation."""
lon_i = np.array([np.nan, 1, 2, 3, -180.1, 180.1])
lat_i = np.array([1, 2, 3, np.nan, -90.1, 90.1])
@@ -80,6 +94,7 @@ class TestGacReader(unittest.TestCase):
# Default
lons, lats = self.reader.get_lonlat()
get_lonlat.assert_called()
+ update_meta_data.assert_called()
adjust_clockdrift.assert_called()
numpy.testing.assert_array_equal(lons, lons_exp)
numpy.testing.assert_array_equal(lats, lats_exp)
@@ -117,11 +132,12 @@ class TestGacReader(unittest.TestCase):
for method in methods:
method.asser_not_called()
+ @mock.patch('pygac.reader.Reader.update_meta_data')
@mock.patch('pygac.gac_reader.GACReader._get_corrupt_mask')
@mock.patch('pygac.gac_reader.GACReader._adjust_clock_drift')
@mock.patch('pygac.gac_reader.GACReader._get_lonlat')
def test_interpolate(self, _get_lonlat, _adjust_clock_drift,
- _get_corrupt_mask):
+ _get_corrupt_mask, update_meta_data):
"""Test interpolate method in get_lonlat."""
self.lons = None
self.lats = None
=====================================
pygac/version.py
=====================================
@@ -22,4 +22,4 @@
"""Just holding the version of the pygac module."""
-__version__ = '1.3.0'
+__version__ = '1.3.1'
=====================================
setup.cfg
=====================================
@@ -0,0 +1,2 @@
+[flake8]
+max-line-length = 120
View it on GitLab: https://salsa.debian.org/debian-gis-team/pygac/commit/765077a83d0566606a677750009c025e5461f830
--
View it on GitLab: https://salsa.debian.org/debian-gis-team/pygac/commit/765077a83d0566606a677750009c025e5461f830
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