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commit f15522bf67c76a0d975831f91ed7194dcba8bdd0 Author: Antonio Valentino <[email protected]> Date: Sun Mar 12 08:20:29 2017 +0000 New upstream version 1.4.0 --- .bumpversion.cfg | 2 +- .travis.yml | 1 - changelog.rst | 52 +++++++++++++++++++++++ etc/Himawari-8.cfg.template | 5 +-- mpop/imageo/formats/ninjotiff.py | 36 +++++++++------- mpop/instruments/viirs.py | 9 ++-- mpop/projector.py | 76 +++++++++++++++++++++++++++++---- mpop/satin/helper_functions.py | 1 + mpop/satin/nc_osisaf_l2.py | 2 +- mpop/satin/viirs_sdr.py | 91 +++++++++++++++++++++++++++++++++++++++- mpop/tests/test_projector.py | 70 ++++++++++++++++++------------- mpop/version.py | 2 +- 12 files changed, 284 insertions(+), 63 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 8167558..3ed55f4 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 1.3.1 +current_version = 1.4.0 commit = True tag = True diff --git a/.travis.yml b/.travis.yml index e98e6be..8b12589 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,6 +1,5 @@ language: python python: -- '2.6' - '2.7' install: - pip install . diff --git a/changelog.rst b/changelog.rst index 9e2670a..4ed0c52 100644 --- a/changelog.rst +++ b/changelog.rst @@ -1,6 +1,58 @@ Changelog ========= +v1.4.0 (2017-02-20) +------------------- + +- Update changelog. [Martin Raspaud] + +- Bump version: 1.3.1 → 1.4.0. [Martin Raspaud] + +- Merge pull request #44 from pytroll/feature_bilinear. [Martin Raspaud] + + Feature bilinear + +- Clarify docstring - radius is also used with bilinear mode. [Panu + Lahtinen] + +- Test that bilinear interpolation is called. [Panu Lahtinen] + +- Mock pyresample.bilinear, autopep8 the file. [Panu Lahtinen] + +- Update docstring. [Panu Lahtinen] + +- Move imports to top of the file. [Panu Lahtinen] + +- Remove Python 2.6 from the tested versions. [Panu Lahtinen] + +- Require Pillow version < 4.0.0 for Python 2.6. [Panu Lahtinen] + +- Add mask to bilinear resampled data. [Panu Lahtinen] + +- Fix naming. [Panu Lahtinen] + +- Add implicit flag to receive un-masked parameters for bilinear + interpolation. [Panu Lahtinen] + +- Add bilinear interpolation. [Panu Lahtinen] + +- Merge branch 'pre-master' of github.com:pytroll/mpop into pre-master. + [Adam.Dybbroe] + +- Clear cache before inserting EWA parameters. [Panu Lahtinen] + +- Add EWA resampling. [Panu Lahtinen] + +- Convert maximum extent to list before modification. [Martin Raspaud] + +- Do the scaling before finalization in ninjotiff's finalize. [Martin + Raspaud] + +- Fix H8 template file's band names. [Martin Raspaud] + +- Extract elevation from viirs-sdr + Fix viirs true color. + [Adam.Dybbroe] + v1.3.1 (2016-12-12) ------------------- diff --git a/etc/Himawari-8.cfg.template b/etc/Himawari-8.cfg.template index 594b05a..f8b1dd3 100644 --- a/etc/Himawari-8.cfg.template +++ b/etc/Himawari-8.cfg.template @@ -69,13 +69,13 @@ resolution = 2000.0 size = (5500, 5500) [ahi-8] -name = 'B08' +name = 'IR3' frequency = (6.06, 6.25, 6.43) resolution = 2000.0 size = (5500, 5500) [ahi-9] -name = 'IR3' +name = 'B09' frequency = (6.89, 6.95, 7.01) resolution = 2000.0 size = (5500, 5500) @@ -121,4 +121,3 @@ name = 'B16' frequency = (13.2, 13.3, 13.4) resolution = 2000.0 size = (5500, 5500) - diff --git a/mpop/imageo/formats/ninjotiff.py b/mpop/imageo/formats/ninjotiff.py index be72489..ae0bf4f 100644 --- a/mpop/imageo/formats/ninjotiff.py +++ b/mpop/imageo/formats/ninjotiff.py @@ -311,34 +311,40 @@ def _finalize(geo_image, dtype=np.uint8, value_range_measurement_unit=None, data offset = 0 else: if value_range_measurement_unit and data_is_scaled_01: - # No additional scaling of the input data - assume that data is within [0.0, 1.0] - # and interpretate 0.0 as value_range_measurement_unit[0] - # and 1.0 as value_range_measurement_unit[1] + # No additional scaling of the input data - assume that data is + # within [0.0, 1.0] and interpret 0.0 as + # value_range_measurement_unit[0] and 1.0 as + # value_range_measurement_unit[1] + + # Make room for transparent pixel. + scale_fill_value = ( + (np.iinfo(dtype).max) / (np.iinfo(dtype).max + 1.0)) + geo_image = deepcopy(geo_image) + geo_image.channels[0] *= scale_fill_value + + geo_image.channels[0] += 1 / (np.iinfo(dtype).max + 1.0) + channels, fill_value = geo_image._finalize(dtype) - fill_value = fill_value or (0,) data = channels[0] - scale = ((value_range_measurement_unit[1] - value_range_measurement_unit[0]) / - (np.iinfo(dtype).max - 1.0)) - + scale = ((value_range_measurement_unit[1] - + value_range_measurement_unit[0]) / + (np.iinfo(dtype).max)) # Handle the case where all data has the same value. scale = scale or 1 offset = value_range_measurement_unit[0] mask = data.mask - # Make room for transparent pixel. - scale_fill_value = ( - (np.iinfo(dtype).max - 1.0) / np.iinfo(dtype).max) - data = 1 + (data.data * scale_fill_value).astype(dtype) - offset -= scale - scale /= scale_fill_value + + if fill_value is None: + fill_value = 0 else: if value_range_measurement_unit: - data.clip(value_range_measurement_unit[ - 0], value_range_measurement_unit[1], data) + data.clip(value_range_measurement_unit[0], + value_range_measurement_unit[1], data) chn_min = value_range_measurement_unit[0] chn_max = value_range_measurement_unit[1] log.debug("Scaling, using value range %.2f - %.2f" % diff --git a/mpop/instruments/viirs.py b/mpop/instruments/viirs.py index d738c55..90de50b 100644 --- a/mpop/instruments/viirs.py +++ b/mpop/instruments/viirs.py @@ -137,11 +137,13 @@ class ViirsCompositer(VisirCompositer): """Make a True Color RGB image composite from M-bands only. """ - self.check_channels('M02', 'M04', 'M05') + #elf.check_channels('M02', 'M04', 'M05') + self.check_channels('M03', 'M04', 'M05') ch1 = self['M05'].check_range() ch2 = self['M04'].check_range() - ch3 = self['M02'].check_range() + #h3 = self['M02'].check_range() + ch3 = self['M03'].check_range() img = geo_image.GeoImage((ch1, ch2, ch3), self.area, @@ -156,7 +158,8 @@ class ViirsCompositer(VisirCompositer): return img - truecolor.prerequisites = set(['M02', 'M04', 'M05']) + truecolor.prerequisites = set(['M03', 'M04', 'M05']) +# truecolor.prerequisites = set(['M02', 'M04', 'M05']) def natural(self): """Make a Natural Colors RGB image composite from diff --git a/mpop/projector.py b/mpop/projector.py index 4a11958..e31dbfd 100644 --- a/mpop/projector.py +++ b/mpop/projector.py @@ -39,6 +39,8 @@ import logging import numpy as np from pyresample import image, utils, geometry, kd_tree +from pyresample.bilinear import get_sample_from_bil_info, get_bil_info + from mpop import CONFIG_PATH logger = logging.getLogger(__name__) @@ -93,11 +95,15 @@ class Projector(object): generated projectors can be saved to disk for later reuse. Use the :meth:`save` method for this. - To define a projector object, on has to specify *in_area* and *out_area*, - and can also input the *in_lonlats* or the *mode* ('quick' which works only - if both in- and out-areas are AreaDefinitions, or 'nearest'). *radius* - defines the radius of influence for nearest neighbour search in 'nearest' - mode. + To define a projector object, on has to specify *in_area* and + *out_area*, and can also input the *in_lonlats* or the *mode*. + Available modes area: + - 'quick' (works only if both in- and out-areas are AreaDefinitions) + - 'bilinear' (out-area needs to be AreaDefinition with proj4_string) + - 'ewa' + - 'nearest'. + *radius* defines the radius of influence for nearest neighbour + search in 'nearest' and 'bilinear' modes. """ def __init__(self, in_area, out_area, @@ -105,8 +111,9 @@ class Projector(object): radius=10000, nprocs=1): if (mode is not None and - mode not in ["quick", "nearest"]): - raise ValueError("Projector mode must be 'nearest' or 'quick'") + mode not in ["quick", "nearest", "ewa", "bilinear"]): + raise ValueError("Projector mode must be one of 'nearest', " + "'quick', 'ewa', 'bilinear'") self.area_file = get_area_file() @@ -133,6 +140,7 @@ class Projector(object): self.in_area = in_area except AttributeError: try: + # TODO: Note that latlons are in order (lons, lats) self.in_area = geometry.SwathDefinition(lons=in_latlons[0], lats=in_latlons[1]) in_id = in_area @@ -160,7 +168,7 @@ class Projector(object): self.area_file + " or " "be an area object.") - #if self.in_area == self.out_area: + # if self.in_area == self.out_area: # return # choosing the right mode if necessary @@ -216,6 +224,29 @@ class Projector(object): self._cache['row_idx'] = ridx self._cache['col_idx'] = cidx + elif self.mode == "ewa": + from pyresample.ewa import ll2cr + swath_points_in_grid, cols, rows = ll2cr(self.in_area, + self.out_area) + self._cache = {} + # self._cache['ewa_swath_points_in_grid'] = \ + # swath_points_in_grid + self._cache['ewa_cols'] = cols + self._cache['ewa_rows'] = rows + + elif self.mode == "bilinear": + + bilinear_t, bilinear_s, input_idxs, idx_arr = \ + get_bil_info(self.in_area, self.out_area, + self.radius, neighbours=32, + nprocs=nprocs, masked=False) + + self._cache = {} + self._cache['bilinear_s'] = bilinear_s + self._cache['bilinear_t'] = bilinear_t + self._cache['input_idxs'] = input_idxs + self._cache['idx_arr'] = idx_arr + def save(self, resave=False): """Save the precomputation to disk, and overwrite existing file in case *resave* is true. @@ -258,4 +289,33 @@ class Projector(object): res = np.ma.array(img.get_array_from_linesample(row_idx, col_idx), dtype=data.dtype) + elif self.mode == "ewa": + from pyresample.ewa import fornav + # TODO: should be user configurable? + rows_per_scan = None + + if 'ewa_cols' not in self._cache: + self._cache['ewa_cols'] = self._file_cache['ewa_cols'] + self._cache['ewa_rows'] = self._file_cache['ewa_rows'] + num_valid_points, res = fornav(self._cache['ewa_cols'], + self._cache['ewa_rows'], + self.out_area, data, + rows_per_scan=rows_per_scan) + + elif self.mode == "bilinear": + + if 'bilinear_t' not in self._cache: + self._cache['bilinear_t'] = self._file_cache['bilinear_t'] + self._cache['bilinear_s'] = self._file_cache['bilinear_s'] + self._cache['input_idxs'] = self._file_cache['input_idxs'] + self._cache['idx_arr'] = self._file_cache['idx_arr'] + + res = get_sample_from_bil_info(data.ravel(), + self._cache['bilinear_t'], + self._cache['bilinear_s'], + self._cache['input_idxs'], + self._cache['idx_arr'], + output_shape=self.out_area.shape) + res = np.ma.masked_invalid(res) + return res diff --git a/mpop/satin/helper_functions.py b/mpop/satin/helper_functions.py index 8f6c71d..d45a4bc 100644 --- a/mpop/satin/helper_functions.py +++ b/mpop/satin/helper_functions.py @@ -87,6 +87,7 @@ def area_def_names_to_extent(area_def_names, proj4_str, if not maximum_extent: return None + maximum_extent = list(maximum_extent) maximum_extent[0] -= 10000 maximum_extent[1] -= 10000 maximum_extent[2] += 10000 diff --git a/mpop/satin/nc_osisaf_l2.py b/mpop/satin/nc_osisaf_l2.py index ac1a811..14bc34f 100644 --- a/mpop/satin/nc_osisaf_l2.py +++ b/mpop/satin/nc_osisaf_l2.py @@ -1,7 +1,7 @@ #!/usr/bin/env python # -*- coding: utf-8 -*- -# Copyright (c) 2015 Adam.Dybbroe +# Copyright (c) 2015, 2016 Adam.Dybbroe # Author(s): diff --git a/mpop/satin/viirs_sdr.py b/mpop/satin/viirs_sdr.py index e10bf65..6ee11ff 100644 --- a/mpop/satin/viirs_sdr.py +++ b/mpop/satin/viirs_sdr.py @@ -1,6 +1,6 @@ #!/usr/bin/env python # -*- coding: utf-8 -*- -# Copyright (c) 2011, 2012, 2013, 2014, 2015, 2016. +# Copyright (c) 2011, 2012, 2013, 2014, 2015, 2016, 2017. # Author(s): @@ -258,6 +258,7 @@ class ViirsGeolocationData(object): self.longitudes = None self.shape = shape self.latitudes = None + self.elevation = None self.mask = None def read(self): @@ -272,6 +273,8 @@ class ViirsGeolocationData(object): dtype=np.float32) self.latitudes = np.empty(self.shape, dtype=np.float32) + self.elevation = np.empty(self.shape, + dtype=np.float32) self.mask = np.zeros(self.shape, dtype=np.bool) @@ -286,6 +289,7 @@ class ViirsGeolocationData(object): get_lonlat_into(filename, self.longitudes[y0_:y1_, :], self.latitudes[y0_:y1_, :], + self.elevation[y0_:y1_, :], self.mask[y0_:y1_, :]) self.longitudes = np.ma.array(self.longitudes, mask=self.mask, @@ -293,6 +297,9 @@ class ViirsGeolocationData(object): self.latitudes = np.ma.array(self.latitudes, mask=self.mask, copy=False) + self.elevation = np.ma.array(self.elevation, + mask=self.mask, + copy=False) logger.debug("Geolocation read in for... " + str(self)) return self @@ -596,6 +603,66 @@ class ViirsSDRReader(Reader): return (data['sunz'], data['sun_azi'], data['satz'], data['sat_azi']) + def get_elevation(self, **kwargs): + """Get elevation/topography for a given band type (M, I, or + DNB) + Optional arguments: + bandtype = 'M', 'I', or 'DNB' + Return + elevation + + """ + + if 'bandtype' in kwargs: + bandtype = kwargs['bandtype'] + else: + bandtype = 'M' + + if bandtype.startswith('M'): + geofilenames = [geofile for geofile in self.geofiles + if os.path.basename(geofile).startswith('GMTCO')] + if len(geofilenames) == 0: + # Try the geoid instead: + geofilenames = [geofile for geofile in self.geofiles + if os.path.basename(geofile).startswith('GMODO')] + elif bandtype.startswith('I'): + geofilenames = [geofile for geofile in self.geofiles + if os.path.basename(geofile).startswith('GITCO')] + if len(geofilenames) == 0: + # Try the geoid instead: + geofilenames = [geofile for geofile in self.geofiles + if os.path.basename(geofile).startswith('GIMGO')] + elif bandtype.startswith('DNB'): + geofilenames = [geofile for geofile in self.geofiles + if os.path.basename(geofile).startswith('GDNBO')] + + else: + logger.error("Band type %s not supported", bandtype) + return None + + geofilenames = sorted(geofilenames) + + hdata = np.empty(self.shape, + dtype=np.float32) + hmask = np.zeros(self.shape, + dtype=np.bool) + + granule_length = self.shape[0] / len(geofilenames) + + for index, filename in enumerate(geofilenames): + + swath_index = index * granule_length + y0_ = swath_index + y1_ = swath_index + granule_length + + get_elevation_into(filename, + hdata[y0_:y1_, :], + hmask[y0_:y1_, :]) + + hdata = np.ma.array(hdata, mask=hmask, copy=False) + + return hdata + def load(self, satscene, calibrate=1, time_interval=None, area=None, filename=None, **kwargs): """Read viirs SDR reflectances and Tbs from file and load it into @@ -830,6 +897,10 @@ class ViirsSDRReader(Reader): lats=np.ma.masked_where(band.data.mask, band.geolocation.latitudes, copy=False)) + height = np.ma.masked_where(band.data.mask, + band.geolocation.elevation, + copy=False) + area_name = ("swath_" + satscene.fullname + "_" + str(satscene.time_slot) + "_" + str(satscene[chn].data.shape) + "_" + @@ -878,7 +949,7 @@ class ViirsSDRReader(Reader): if chn.is_loaded()]) -def get_lonlat_into(filename, out_lons, out_lats, out_mask): +def get_lonlat_into(filename, out_lons, out_lats, out_height, out_mask): """Read lon,lat from hdf5 file""" logger.debug("Geo File = " + filename) @@ -891,6 +962,22 @@ def get_lonlat_into(filename, out_lons, out_lats, out_mask): out_mask[:] = out_lats < -999 if key.endswith("Longitude"): h5f[key].read_direct(out_lons) + if key.endswith("Height"): + h5f[key].read_direct(out_height) + h5f.close() + + +def get_elevation_into(filename, out_height, out_mask): + """Read elevation/height from hdf5 file""" + logger.debug("Geo File = " + filename) + + md = HDF5MetaData(filename).read() + + h5f = h5py.File(filename, 'r') + for key in md.get_data_keys(): + if key.endswith("Height"): + h5f[key].read_direct(out_height) + out_mask[:] = out_height < -999 h5f.close() diff --git a/mpop/tests/test_projector.py b/mpop/tests/test_projector.py index bd27611..dc8ed80 100644 --- a/mpop/tests/test_projector.py +++ b/mpop/tests/test_projector.py @@ -4,11 +4,11 @@ # SMHI, # Folkborgsvägen 1, -# Norrköping, +# Norrköping, # Sweden # Author(s): - + # Martin Raspaud <[email protected]> # Adam Dybbroe <[email protected]> @@ -37,6 +37,7 @@ import numpy as np from mock import MagicMock, patch import sys sys.modules['pyresample'] = MagicMock() +sys.modules['pyresample.bilinear'] = MagicMock() from pyresample import geometry, utils @@ -44,16 +45,18 @@ from mpop.projector import Projector import mpop.projector - class TestProjector(unittest.TestCase): + """Class for testing the Projector class. """ proj = None + + @patch('mpop.projector.get_bil_info') @patch.object(utils, 'generate_quick_linesample_arrays') @patch.object(mpop.projector.kd_tree, 'get_neighbour_info') @patch.object(mpop.projector, '_get_area_hash') - def test_init(self, gah, gni, gqla): + def test_init(self, gah, gni, gqla, bil_info): """Creation of coverage. """ @@ -62,7 +65,6 @@ class TestProjector(unittest.TestCase): self.assertRaises(TypeError, Projector) self.assertRaises(TypeError, Projector, random_string(20)) - # in case of string arguments in_area_id = random_string(20) @@ -78,12 +80,9 @@ class TestProjector(unittest.TestCase): utils.parse_area_file.assert_any_call(area_file, in_area_id) utils.parse_area_file.assert_any_call(area_file, out_area_id) - - self.assertEquals(self.proj.in_area, area_type) self.assertEquals(self.proj.out_area, area_type) - # in case of undefined areas mock = MagicMock(side_effect=Exception("raise")) @@ -109,18 +108,21 @@ class TestProjector(unittest.TestCase): self.assertEquals(self.proj.in_area, in_area) in_area = geometry.SwathDefinition() - utils.parse_area_file.return_value.__getitem__.side_effect = [AttributeError, out_area_id] + utils.parse_area_file.return_value.__getitem__.side_effect = [ + AttributeError, out_area_id] self.proj = Projector(in_area, out_area_id) self.assertEquals(self.proj.in_area, in_area) out_area = geometry.AreaDefinition() - utils.parse_area_file.return_value.__getitem__.side_effect = [in_area_id, AttributeError] + utils.parse_area_file.return_value.__getitem__.side_effect = [ + in_area_id, AttributeError] self.proj = Projector(in_area_id, out_area) self.assertEquals(self.proj.out_area, out_area) # in case of lon/lat is input - utils.parse_area_file.return_value.__getitem__.side_effect = [AttributeError, out_area_id] + utils.parse_area_file.return_value.__getitem__.side_effect = [ + AttributeError, out_area_id] lonlats = ("great_lons", "even_greater_lats") self.proj = Projector("raise", out_area_id, lonlats) @@ -146,13 +148,25 @@ class TestProjector(unittest.TestCase): self.assertTrue(cache['col_idx'] is not None) # nearest mode cache - self.proj = Projector(in_area_id, out_area_id, mode="nearest") cache = getattr(self.proj, "_cache") self.assertTrue(cache['valid_index'] is not None) self.assertTrue(cache['valid_output_index'] is not None) self.assertTrue(cache['index_array'] is not None) + # bilinear mode cache + bil_info.return_value = (1, 2, 3, 4) + + def spam(val): + return 'adef' + + with patch.object(mpop.projector, 'get_area_def', spam): + self.proj = Projector(in_area_id, out_area_id, mode="bilinear") + cache = getattr(self.proj, "_cache") + self.assertTrue(cache['bilinear_t'] is not None) + self.assertTrue(cache['bilinear_s'] is not None) + self.assertTrue(cache['input_idxs'] is not None) + self.assertTrue(cache['idx_arr'] is not None) @patch.object(np.ma, "array") @patch.object(mpop.projector.kd_tree, 'get_sample_from_neighbour_info') @@ -164,35 +178,36 @@ class TestProjector(unittest.TestCase): out_area_id = random_string(20) data = np.random.standard_normal((3, 1)) - utils.parse_area_file.return_value.__getitem__.side_effect = ["a", "b", "c", "d"] + utils.parse_area_file.return_value.__getitem__.side_effect = [ + "a", "b", "c", "d"] # test quick self.proj = Projector(in_area_id, out_area_id, mode="quick") self.proj.project_array(data) - mpop.projector.image.ImageContainer.assert_called_with(\ + mpop.projector.image.ImageContainer.assert_called_with( data, "a", fill_value=None) mpop.projector.image.ImageContainer.return_value.\ - get_array_from_linesample.assert_called_with(\ - self.proj._cache["row_idx"], self.proj._cache["col_idx"]) - marray.assert_called_once_with(\ - mpop.projector.image.ImageContainer.return_value.\ + get_array_from_linesample.assert_called_with( + self.proj._cache["row_idx"], self.proj._cache["col_idx"]) + marray.assert_called_once_with( + mpop.projector.image.ImageContainer.return_value. get_array_from_linesample.return_value, dtype=np.dtype('float64')) # test nearest in_area = MagicMock() out_area = MagicMock() - utils.parse_area_file.return_value.__getitem__.side_effect = \ - [in_area, out_area] + utils.parse_area_file.return_value.__getitem__.side_effect = [ + in_area, out_area] self.proj = Projector(in_area_id, out_area_id, mode="nearest") self.proj.project_array(data) mpop.projector.kd_tree.get_sample_from_neighbour_info.\ - assert_called_with('nn', - out_area.shape, - data, - npload.return_value.__getitem__.return_value, - npload.return_value.__getitem__.return_value, - npload.return_value.__getitem__.return_value, - fill_value=None) + assert_called_with('nn', + out_area.shape, + data, + npload.return_value.__getitem__.return_value, + npload.return_value.__getitem__.return_value, + npload.return_value.__getitem__.return_value, + fill_value=None) def random_string(length, @@ -214,4 +229,3 @@ def suite(): mysuite.addTest(loader.loadTestsFromTestCase(TestProjector)) return mysuite - diff --git a/mpop/version.py b/mpop/version.py index 801da57..89fa315 100644 --- a/mpop/version.py +++ b/mpop/version.py @@ -23,4 +23,4 @@ """Version file. """ -__version__ = "v1.3.1" +__version__ = "v1.4.0" -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/pkg-grass/python-mpop.git _______________________________________________ Pkg-grass-devel mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-grass-devel
