PyThea 0.13.0__tar.gz → 0.14.0__tar.gz

{pythea-0.13.0 → pythea-0.14.0}/CHANGELOG.md

@@ -1,3 +1,13 @@
+# v0.14.0 (03-Oct-2024)
+
+## Features
+ - Adds imaging data from Solar Orbiter EUI and METIS.
+ - Implements offline fits file loading from local database.
+
+## Minor Changes
+ - Simplifies the configuration of the database directory.
+ - Improves Parker Spiral visualization.
+
 # v0.13.0 (14-Jul-2024)
 
 ## Features

{pythea-0.13.0 → pythea-0.14.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyThea
-Version: 0.13.0
+Version: 0.14.0
 Summary: PyThea: A software package to reconstruct the 3D structure of CMEs and shock waves
 Home-page: https://github.com/AthKouloumvakos/PyThea
 Author: Athanasios Kouloumvakos
@@ -29,6 +29,7 @@ Requires-Dist: astroquery
 Requires-Dist: jplephem
 Requires-Dist: numexpr
 Requires-Dist: sunpy==5.1.2
+Requires-Dist: sunpy_soar
 Requires-Dist: parfive==2.1.0
 Requires-Dist: pooch
 Requires-Dist: matplotlib

{pythea-0.13.0 → pythea-0.14.0}/PyThea/PyThea_app.py

@@ -39,6 +39,7 @@ from PyThea.modules import (date_and_event_selection, figure_streamlit,
 from PyThea.sunpy_dev.map.maputils import get_closest, maps_clims
 from PyThea.utils import (download_fits, load_fits, model_fittings,
                           plot_fitting_model, single_imager_maps_process)
+from PyThea.utils_database import get_fits_filenames_from_database
 from PyThea.version import version
 
 
@@ -84,6 +85,7 @@ def footer_text():
             More imaging data have been added:
             - SDO/AIA images from 211A channel.
             - PSP/WISPR inner and outer telescope images.
+            - SolO/EUI and METIS images.
             ''', icon='ℹ️')
     st.warning('''
            **NOTE: From PyThea >0.8.1 the JSON fitting files will be slightly different from the old ones.**
@@ -295,7 +297,15 @@ def run():
             if imager not in st.session_state.map_:
                 timerange = a.Time(st.session_state.date_process + datetime.timedelta(hours=imaging_time_range[0]),
                                    st.session_state.date_process + datetime.timedelta(hours=imaging_time_range[1]))
-                downloaded_files = download_fits(timerange, imager)
+
+                if st.session_state.offline_mode is False:
+                    downloaded_files = download_fits(timerange, imager)
+                elif st.session_state.offline_mode is True:
+                    progress_bar.desc = f'Load {imager} images from local database.'
+                    event_id = st.session_state.event_selected.replace('-', '').replace(':', '').replace('|', 'D').replace('.', 'p') \
+                        + 'M' + st.session_state.geometrical_model
+                    downloaded_files = get_fits_filenames_from_database(event_id, timerange, imager)
+
                 st.session_state.map_[imager] = load_fits(downloaded_files)
                 st.session_state.map_[imager] = single_imager_maps_process(st.session_state.map_[imager],
                                                                            **selected_imagers.imager_dict[imager]['process'],

{pythea-0.13.0 → pythea-0.14.0}/PyThea/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.13.0'
-__version_tuple__ = version_tuple = (0, 13, 0)
+__version__ = version = '0.14.0'
+__version_tuple__ = version_tuple = (0, 14, 0)

{pythea-0.13.0 → pythea-0.14.0}/PyThea/config/__init__.py

@@ -1,3 +1,8 @@
+import os
+from pathlib import Path
+
 from PyThea.config.config_sliders import *
 from PyThea.config.selected_bodies import *
 from PyThea.config.selected_imagers import *
+
+database_dir_default = os.path.join(Path.home(), 'PyThea')

{pythea-0.13.0 → pythea-0.14.0}/PyThea/config/selected_imagers.py

@@ -4,6 +4,7 @@
 
 '''
 import astropy.units as u
+import sunpy_soar  # noqa
 from sunpy.net import attrs as a
 
 imager_dict = {}
@@ -71,3 +72,11 @@ imager_dict['WISPR1'] = {'fido': (a.Instrument.wispr, a.Detector.inner),
 imager_dict['WISPR2'] = {'fido': (a.Instrument.wispr, a.Detector.outer),
                          'process': {'dimensions': (960*u.pixel, 1024*u.pixel), 'processing_level': 3, 'superpixel': 2},
                          'source': 'PSP', 'instrument': 'WISPR', 'detector': 'Outer'}
+
+imager_dict['EUI-FSI'] = {'fido': (a.Instrument('EUI'), a.soar.Product('EUI-FSI174-IMAGE'), a.Level(2)),
+                          'process': {'superpixel': 1},
+                          'source': 'SOLO', 'instrument': 'EUI-FSI', 'wavelength': '174'}
+
+imager_dict['METIS'] = {'fido': (a.Instrument('METIS'), a.soar.Product('METIS-VL-TB'), a.Level(2)),
+                        'process': {'dimensions': (1024*u.pixel, 1024*u.pixel), 'superpixel': 2},
+                        'source': 'SOLO', 'instrument': 'METIS', 'detector': 'VLD', 'wavelength': 'TB'}

{pythea-0.13.0 → pythea-0.14.0}/PyThea/data/sample_data.py

@@ -1,13 +1,13 @@
 import os
-from pathlib import Path
 
 import pooch
 
-database_dir = os.path.join(Path.home(), 'PyThea')
+from PyThea.config import database_dir_default
+
 github_main_url = 'https://github.com/AthKouloumvakos/PyThea-sample-data'
 
 aia_sample_data = pooch.create(
-    path=os.path.join(database_dir, 'sample_data'),  # The cache folder
+    path=os.path.join(database_dir_default, 'sample_data'),  # The cache folder
     base_url=f'{github_main_url}/raw/main/data/',  # The remote data url on Github
     registry={
         'aia_lev1_1600a_2012_06_06t04_07_29_12z_image_lev1.fits': 'sha256:7e88d8a277ad3dd111c1bcff3c3936d6d5ef5186e05b4bfa7749ee43c05577d5',
@@ -16,7 +16,7 @@ aia_sample_data = pooch.create(
 )
 
 stereo_sample_data = pooch.create(
-    path=os.path.join(database_dir, 'sample_data'),  # The cache folder
+    path=os.path.join(database_dir_default, 'sample_data'),  # The cache folder
     base_url=f'{github_main_url}/raw/main/data/',  # The remote data url on Github
     registry={
         '20120622_235400_d4c2a.fts': 'sha256:940680fe8bea754c9859170585d8299b9b049b631155435a31ecacf5b702d9cf',
@@ -27,7 +27,7 @@ stereo_sample_data = pooch.create(
 )
 
 wispr_sample_data = pooch.create(
-    path=os.path.join(database_dir, 'sample_data'),  # The cache folder
+    path=os.path.join(database_dir_default, 'sample_data'),  # The cache folder
     base_url=f'{github_main_url}/raw/main/data/',  # The remote data url on Github
     registry={
         'psp_l3_wispr_20210808t103707_v1_1211.fits': 'sha256:85035693c4677e8fa8a3e61b8051d6f0a46e96806b5b0cbdb3efa77652308bda',
@@ -36,7 +36,7 @@ wispr_sample_data = pooch.create(
 )
 
 json_fitting_file_sample_data = pooch.create(
-    path=os.path.join(database_dir, 'sample_data'),  # The cache folder
+    path=os.path.join(database_dir_default, 'sample_data'),  # The cache folder
     base_url=f'{github_main_url}/raw/main/data/',  # The remote data url on Github
     registry={
         'FLX1p0D20211028T153500MEllipsoid.json': 'sha256:34fced8530875110117ba27a73541d3acd0c90bc8fca99367c1ec4cdfc05ce86',

{pythea-0.13.0 → pythea-0.14.0}/PyThea/extensions/Parker_spirals/utils.py

@@ -41,3 +41,5 @@ def plot_parker_spiral(axis, map, bodies, sw_speed=350 * (u.km / u.second)):
             axis.plot_coord(spiral_coord[0], markersize=16, linewidth=10, marker='+', color='white')
 
         axis.plot_coord(spiral_coord[0], markersize=3, linewidth=4, marker='s', color=bodies_dict[body][1])
+
+        axis.plot_coord(spiral_coord[-1], markersize=8, linewidth=6, marker='x', color=bodies_dict[body][1])

{pythea-0.13.0 → pythea-0.14.0}/PyThea/modules.py

@@ -24,6 +24,7 @@ import astropy.units as u
 from sunpy.net import attrs as a
 
 from PyThea.callbacks import change_fitting_sliders, change_long_lat_sliders
+from PyThea.config import database_dir_default
 from PyThea.config.config_sliders import sliders_dict as sd
 from PyThea.extensions.hek.utils import plot_hek
 from PyThea.extensions.Parker_spirals.utils import plot_parker_spiral
@@ -121,6 +122,10 @@ def date_and_event_selection(st):
 
             st.rerun()
 
+    st.session_state.offline_mode = st.sidebar.checkbox('Work with offline mode active?', value=False)
+    if st.session_state.offline_mode:
+        st.sidebar.info(f'Fits files will be loaded from PyThea\'s database directory: {database_dir_default}', icon='ℹ️')
+
 
 def fitting_and_slider_options_container(st):
     """

{pythea-0.13.0 → pythea-0.14.0}/PyThea/sunpy_dev/map/maputils.py

@@ -305,4 +305,6 @@ def maps_clims(images):
             return [14., 14.]
         elif images[1].detector == 'Inner':
             return [13., 13.]
+    if images[1].instrument == 'Metis':
+        return [12.80, 13.00]
     return [np.nanquantile(images[1].data, 0.20)-10, np.nanquantile(images[1].data, 0.80)+10]

{pythea-0.13.0 → pythea-0.14.0}/PyThea/test/Pythea_test.py

@@ -8,7 +8,8 @@ export PYTHONPATH="${PYTHONPATH}:{top_level_dir_that_pythea_lives}/PyThea"
 """
 
 import os
-from pathlib import Path
+
+from PyThea.config import database_dir_default
 
 
 def test_database_dir_exists():
@@ -20,5 +21,4 @@ def test_database_dir_exists():
         print("Skipping test as it's running in GitHub Actions.")
         return
 
-    database_dir = os.path.join(Path.home(), 'PyThea')
-    assert os.path.exists(database_dir), f"PyThea's database directory '{database_dir}' does not exist."
+    assert os.path.exists(database_dir_default), f"PyThea's database directory '{database_dir_default}' does not exist."

{pythea-0.13.0 → pythea-0.14.0}/PyThea/utils.py

@@ -25,7 +25,6 @@ import os
 import re
 import warnings
 from copy import copy
-from pathlib import Path
 
 import astropy.units as u
 import matplotlib.colors as colors
@@ -48,6 +47,7 @@ from sunpy.net import attrs as a
 from sunpy.time import parse_time
 from sunpy.visualization import drawing
 
+from PyThea.config import database_dir_default
 from PyThea.config.selected_bodies import bodies_dict as bodies_dict_default
 from PyThea.config.selected_imagers import imager_dict as imager_dict_default
 from PyThea.geometrical_models import ellipsoid, gcs, spheroid
@@ -56,8 +56,6 @@ from PyThea.sunpy_dev.map.maputils import (filter_maps,
                                            prepare_maps)
 from PyThea.version import version
 
-database_dir_default = os.path.join(Path.home(), 'PyThea')
-
 
 def get_hek_flare(timerange, thresshold='B1.0'):
     """
@@ -133,6 +131,9 @@ def make_figure(map, cmap='Greys_r', clim=[-20, 20], clip_model=True, **kwargs):
     if map.instrument == 'WISPR':
         clim = [-10**-clim[0], 10**-clim[1]]
 
+    if map.instrument == 'Metis':
+        clim = [-10**-clim[0], 10**-clim[1]]
+
     if cmap == 'default':
         # TODO: For plain images or when EUVIA-B are used, this does not work very well.
         map.plot(norm=colors.Normalize(vmin=clim[0], vmax=clim[1]))
@@ -156,7 +157,8 @@ def make_figure(map, cmap='Greys_r', clim=[-20, 20], clip_model=True, **kwargs):
 
     axis.set_title(re.sub(r'\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}',
                           ' $T_{AGV}:$' + parse_time(map.date_average).strftime('%Y-%m-%d %H:%M:%S'),
-                          map.latex_name), fontsize=10, pad=8)
+                          map.latex_name.replace('VLD', 'METIS-VDL')),
+                   fontsize=10, pad=8)
 
     return fig, axis
 
@@ -275,7 +277,7 @@ def download_fits(timerange, imager, imager_dict=None, database_dir=None):
         'detector' (optional), and 'wavelength' (optional). The default imager_dict is from
         PyThea.config.selected_imagers.import imager_dict.
     database_dir : str, optional
-        The base directory where the data will be saved. The default is os.path.join(Path.home(), 'PyThea').
+        The base directory where the data will be saved. The default is database_dir_default from PyThea.config.
 
     Returns
     -------
@@ -340,6 +342,8 @@ def load_fits(files):
         for file_path in files:
             try:
                 map_ = sunpy.map.Map(file_path)
+                if isinstance(map_, list):  # Added because of METIS
+                    map_ = map_[0]
                 map_.meta['fits_file'] = os.path.basename(file_path)
                 maps_.append(map_)
             except RuntimeError as err:

pythea-0.14.0/PyThea/utils_database.py

@@ -0,0 +1,93 @@
+"""
+    PyThea: A software package to reconstruct the 3D structure of CMEs and
+    shock waves using multi-viewpoint remote-sensing observations.
+    Copyright (C) 2021  Athanasios Kouloumvakos
+
+    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
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+"""
+
+import collections.abc
+import json
+import os
+import re
+
+from PyThea.config import database_dir_default
+from PyThea.config.selected_imagers import imager_dict
+from PyThea.utils import download_fits
+
+
+def create_nested_dict(k, v):
+    if len(k) == 0:
+        return v
+    else:
+        return {k[0]: create_nested_dict(k[1:], v)}
+
+
+def load_nested_dict(k, d):
+    if len(k) == 0:
+        return d
+    else:
+        if k[0] in d:
+            return load_nested_dict(k[1:], d[k[0]])
+        else:
+            return None
+
+
+def update_nested_dict(d, u):
+    for k, v in u.items():
+        if isinstance(v, collections.abc.Mapping):
+            d[k] = update_nested_dict(d.get(k, {}), v)
+        else:
+            d[k] = v
+    return d
+
+
+def get_fits_filenames_from_database(event_id, timerange, imager):
+
+    db_args = [imager_dict[imager]['source'],
+               imager_dict[imager]['instrument'],
+               imager_dict[imager].get('detector', imager_dict[imager].get('wavelength'))]
+
+    # name of the JSON file with the database
+    file_id = re.search(r'D(.*?)(?=T)', event_id).group(1)
+    filename = os.path.join(database_dir_default, 'data_manager', f'{file_id}_fits_filenames.json')
+
+    if not os.path.isfile(filename):
+        # create file if it doesn't exist
+        with open(filename, 'w') as f:
+            json.dump({}, f)
+
+    # load data from file
+    with open(filename, 'r') as f:
+        database_data = json.load(f)
+
+    downloaded_files = None
+
+    if str(timerange) in database_data:
+        downloaded_files = load_nested_dict(db_args, database_data[str(timerange)])
+
+    if downloaded_files is None:
+        downloaded_files = download_fits(timerange, imager)
+
+        nested_dict_ = create_nested_dict(db_args, downloaded_files.data)
+        nested_dict_ = {str(timerange): nested_dict_}
+
+        # dictionary stored in JSON file
+        database_data = update_nested_dict(database_data, nested_dict_)
+
+        # write updated data to file
+        with open(filename, 'w') as f:
+            json.dump(database_data, f, indent=4)
+
+    return downloaded_files

{pythea-0.13.0 → pythea-0.14.0}/PyThea.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyThea
-Version: 0.13.0
+Version: 0.14.0
 Summary: PyThea: A software package to reconstruct the 3D structure of CMEs and shock waves
 Home-page: https://github.com/AthKouloumvakos/PyThea
 Author: Athanasios Kouloumvakos
@@ -29,6 +29,7 @@ Requires-Dist: astroquery
 Requires-Dist: jplephem
 Requires-Dist: numexpr
 Requires-Dist: sunpy==5.1.2
+Requires-Dist: sunpy_soar
 Requires-Dist: parfive==2.1.0
 Requires-Dist: pooch
 Requires-Dist: matplotlib

{pythea-0.13.0 → pythea-0.14.0}/PyThea.egg-info/SOURCES.txt

@@ -17,6 +17,7 @@ PyThea/geometrical_models.py
 PyThea/modules.py
 PyThea/pythea_cli.py
 PyThea/utils.py
+PyThea/utils_database.py
 PyThea/version.py
 PyThea.egg-info/.DS_Store
 PyThea.egg-info/PKG-INFO

{pythea-0.13.0 → pythea-0.14.0}/PyThea.egg-info/requires.txt

@@ -7,6 +7,7 @@ astroquery
 jplephem
 numexpr
 sunpy==5.1.2
+sunpy_soar
 parfive==2.1.0
 pooch
 matplotlib

{pythea-0.13.0 → pythea-0.14.0}/environment.yml

@@ -27,3 +27,4 @@ dependencies:
   - pip:
       - pooch
       - jplephem
+      - sunpy_soar

{pythea-0.13.0 → pythea-0.14.0}/requirements.txt

@@ -7,6 +7,7 @@ astroquery
 jplephem
 numexpr
 sunpy==5.1.2
+sunpy_soar
 parfive==2.1.0
 pooch
 matplotlib

{pythea-0.13.0 → pythea-0.14.0}/setup.py

@@ -11,6 +11,7 @@ from setuptools import find_packages, setup
 if not os.path.isdir(os.path.join(Path.home(), 'PyThea')):
     os.mkdir(os.path.join(Path.home(), 'PyThea'))
     os.mkdir(os.path.join(Path.home(), 'PyThea', 'data'))
+    os.mkdir(os.path.join(Path.home(), 'PyThea', 'data_manager'))
 
 with open('README_pypi.md', 'r', encoding='utf8') as f:
     long_description = f.read()