PyThea 0.10.0__tar.gz → 0.11.0__tar.gz

{pythea-0.10.0 → pythea-0.11.0}/CHANGELOG.md

@@ -1,3 +1,13 @@
+# v0.11.0 (17-April-2024)
+
+## Features
+ - Adds tests for ellipsoid location on AIA and STEREO COR images.
+ - Adds test_load_fitting_json_file to check the fitting file load and save.
+ - Improve PyThea tests on cli.
+
+## Major Changes
+- Change the inputs for download_fits from string dates to timerange.
+
 # v0.10.0 (17-April-2024)
 
 ## Features

{pythea-0.10.0/PyThea.egg-info → pythea-0.11.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyThea
-Version: 0.10.0
+Version: 0.11.0
 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
@@ -26,6 +26,7 @@ Requires-Dist: scipy
 Requires-Dist: aiapy
 Requires-Dist: astropy
 Requires-Dist: astroquery
+Requires-Dist: jplephem
 Requires-Dist: numexpr
 Requires-Dist: sunpy==5.1.2
 Requires-Dist: parfive==2.1.0
@@ -42,6 +43,7 @@ Requires-Dist: tqdm
 Requires-Dist: pyvista
 Requires-Dist: pytest-astropy
 Requires-Dist: pytest-sugar
+Requires-Dist: pytest-mpl
 
 # PyThea: A software package to reconstruct the 3D structure of CMEs and shock waves
 

{pythea-0.10.0 → pythea-0.11.0}/PyThea/PyThea_app.py

@@ -18,6 +18,7 @@
 """
 
 
+import datetime
 from copy import copy
 
 import astropy.units as u
@@ -26,6 +27,7 @@ import stqdm  # See also https://github.com/tqdm/tqdm
 import streamlit as st
 from astropy.coordinates import Distance, SkyCoord, SphericalRepresentation
 from sunpy.coordinates import frames
+from sunpy.net import attrs as a
 
 from PyThea.callbacks import load_or_delete_fittings
 from PyThea.config import (app_styles, config_sliders, selected_bodies,
@@ -247,8 +249,9 @@ def run():
         for imager in progress_bar:
             progress_bar.desc = f'Downloaded {imager} images from VSO'
             if imager not in st.session_state.map_:
-                st.session_state.map_[imager] = download_fits(st.session_state.date_process,
-                                                              imager, time_range=imaging_time_range)
+                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]))
+                st.session_state.map_[imager] = download_fits(timerange, imager)
                 st.session_state.map_[imager] = single_imager_maps_process(st.session_state.map_[imager],
                                                                            **selected_imagers.imager_dict[imager][1],
                                                                            skip='sequence_processing')

{pythea-0.10.0 → pythea-0.11.0}/PyThea/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.10.0'
-__version_tuple__ = version_tuple = (0, 10, 0)
+__version__ = version = '0.11.0'
+__version_tuple__ = version_tuple = (0, 11, 0)

pythea-0.11.0/PyThea/data/sample_data.py

@@ -0,0 +1,35 @@
+import os
+from pathlib import Path
+
+import pooch
+
+database_dir = os.path.join(Path.home(), 'PyThea')
+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
+    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',
+        'aia_lev1_1600a_2016_05_09t11_35_51_12z_image_lev1.fits': 'sha256:1c3bb938e9bfb3178cecead1319a92fa661eb70469715a441a849a98039f0b61'
+    },
+)
+
+stereo_sample_data = pooch.create(
+    path=os.path.join(database_dir, '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',
+        '20140221_235400_d4c2b.fts': 'sha256:13638dedeb2e510c9e2ef11d46b372acb16f9b9645ca1cabf4d0ef8444353adc',
+        '20070503_102018_s4c1a.fts': 'sha256:55cf6e3741833a82e41b46e2345bf85a0e5580a2832900eccc41f235d36fc31e',
+        '20070503_102018_s4c1b.fts': 'sha256:ca8f4aabaeb7e4bc6f4e5d4819057ddfe3f9f621716224d11acc80d701e3beb8'
+    },
+)
+
+json_fitting_file_sample_data = pooch.create(
+    path=os.path.join(database_dir, 'sample_data'),  # The cache folder
+    base_url=f'{github_main_url}/raw/main/data/',  # The remote data url on Github
+    registry={
+        'FLX1p0D20211028T153500MEllipsoid.json': 'sha256:700687ed982317400ec409390571747694237de9688a2816baa7b1770b75c9b1',
+    },
+)

{pythea-0.10.0 → pythea-0.11.0}/PyThea/pythea_cli.py

@@ -99,9 +99,28 @@ def update():
 
 
 @main.command('test')
-def main_test():
+@click.option('--mpl', is_flag=True, default=False, help='Run the test including figure tests.')
+@click.option('--remote-data', is_flag=True, default=False, help='Run the test including figure tests.')
+@click.option('--all', is_flag=True, default=False, help='Run the test including figure tests.')
+def main_test(mpl, remote_data, all):
     """Test PyThea."""
-    pytest.main(['-W', 'ignore', '--pyargs', 'PyThea'])
+
+    test_directory = os.path.dirname(__file__)
+
+    print(f'Running a test of PyThea package located in: {test_directory}')
+
+    if mpl:
+        # Run a test of the package including figure tests
+        pytest.main(['-W', 'ignore', '--mpl', '--mpl-hash-library=figure_hashes.json', '--pyargs', f'{test_directory}'])
+    elif remote_data:
+        # Run a test of the package including remote-data tests
+        pytest.main(['-W', 'ignore', '--remote-data', '--pyargs', f'{test_directory}'])
+    elif all:
+        # Run a test of the package including remote-data tests
+        pytest.main(['-W', 'ignore', '--mpl', '--mpl-hash-library=figure_hashes.json', '--remote-data', '--pyargs', f'{test_directory}'])
+    else:
+        # Run a minimum test of the package (figure tests are always true and remote-data tests are skipped)
+        pytest.main(['-W', 'ignore', '--pyargs', f'{test_directory}'])
 
 
 if __name__ == '__main__':

pythea-0.11.0/PyThea/test/figure_hashes.json

@@ -0,0 +1,6 @@
+{
+  "PyThea.test.test_figures.test_ellipsoid_on_AIA_venus": "f1ff774b483a8c934c9353c552278c8823216fc7d9dad4ccc00c74be3f30c4c3",
+  "PyThea.test.test_figures.test_ellipsoid_on_AIA_mercury": "f6afda1c769a061b7ab1fc64c4e9c0f4658cdb97c3be83828ba5d98bf1bb182c",
+  "PyThea.test.test_figures.test_ellipsoid_on_STEREO_COR1_venus": "18a3af72e9da5b60e435f83ee3ef3f8cd0eb437eaef463329552ff56968f12ff",
+  "PyThea.test.test_figures.test_ellipsoid_on_STEREO_COR2_three_planets": "231d5635f57c4d66556674a83f6cbcef7dc94b51846e977c4c2dc3dc244096ac"
+}

pythea-0.11.0/PyThea/test/test_figures.py

@@ -0,0 +1,169 @@
+import astropy.units as u
+import matplotlib.pyplot as plt
+import pytest
+import sunpy.map
+from astropy.coordinates import SkyCoord, solar_system_ephemeris
+from sunpy.coordinates import get_body_heliographic_stonyhurst
+
+from PyThea.data.sample_data import aia_sample_data, stereo_sample_data
+from PyThea.geometrical_models import ellipsoid
+from PyThea.sunpy_dev.map.maputils import prepare_maps
+
+solar_system_ephemeris.set('de432s')
+
+bodies_color_dict = {'mercury': 'darkturquoise',
+                     'venus': 'darkorchid',
+                     'earth': 'green',
+                     'mars': 'maroon',
+                     'jupiter': 'navy',
+                     'saturn': 'dodgerblue'}
+
+body_radious = {'mercury': 2440.5 * u.km,
+                'venus': 6051.8 * u.km,
+                'mars': 3396.2 * u.km,
+                'jupiter': 71492 * u.km,
+                'saturn': 60268 * u.km}  # From here: https://nssdc.gsfc.nasa.gov/planetary/factsheet/venusfact.html
+
+
+def model_from_body(body, date, observer_coordinate):
+    body_coord = get_body_heliographic_stonyhurst(body, date, observer=observer_coordinate)
+    radius =  body_radious[body]
+    center = SkyCoord(body_coord)
+    return ellipsoid(center, radius, radius, radius, 0 * u.degree)
+
+
+def make_submap(map_, center, fov):
+    center_hpc = center.transform_to(map_.coordinate_frame)
+    print(center_hpc)
+    bottom_left = SkyCoord(center_hpc.Tx - fov/2, center_hpc.Ty - fov/2, frame=map_.coordinate_frame)
+    return map_.submap(bottom_left, width=fov, height=fov)
+
+
+@pytest.mark.mpl_image_compare()
+def test_ellipsoid_on_AIA_venus():
+    """
+    Tests that the position of Venus is ploted correct at SDO/AIA images when it transited in front of the Sun.
+    """
+    fits_file = aia_sample_data.fetch('aia_lev1_1600a_2012_06_06t04_07_29_12z_image_lev1.fits')
+
+    map_ = sunpy.map.Map(fits_file, sequence=True)
+    map_ = prepare_maps(map_)[0]
+
+    model_shock = model_from_body('venus', map_.date_average, map_.observer_coordinate)
+    smap = make_submap(map_, model_shock.center, fov=200*u.arcsec)
+
+    fig = plt.figure(dpi=200)
+    ax = fig.add_subplot(projection=smap)
+    smap.plot(axes=ax)
+    smap.draw_limb(axes=ax)
+    ax.grid(False)
+    model_shock.plot(ax, mode='Full')
+    ax.set_xlim([0, smap.data.shape[0]])
+    ax.set_ylim([0, smap.data.shape[1]])
+
+    return fig
+
+
+@pytest.mark.mpl_image_compare()
+def test_ellipsoid_on_AIA_mercury():
+    """
+    Tests that the position of Mercury is ploted correct at SDO/AIA images when it transited in front of the Sun.
+    """
+    fits_file = aia_sample_data.fetch('aia_lev1_1600a_2016_05_09t11_35_51_12z_image_lev1.fits')
+
+    map_ = sunpy.map.Map(fits_file, sequence=True)
+    map_ = prepare_maps(map_)[0]
+
+    model_shock = model_from_body('mercury', map_.date_average, map_.observer_coordinate)
+    smap = make_submap(map_, model_shock.center, fov=100*u.arcsec)
+
+    fig = plt.figure(dpi=200)
+    ax = fig.add_subplot(projection=smap)
+    smap.plot(axes=ax)
+    smap.draw_limb(axes=ax)
+    ax.grid(False)
+    model_shock.plot(ax, mode='Full')
+    ax.set_xlim([0, smap.data.shape[0]])
+    ax.set_ylim([0, smap.data.shape[1]])
+
+    return fig
+
+
+@pytest.mark.mpl_image_compare()
+def test_ellipsoid_on_STEREO_COR1_venus():
+    """
+    Tests that the position of Venus is correct at STEREO COR1 images. (https://stereo.gsfc.nasa.gov/browse/2019/03/08/planets/)
+    """
+    fits_file = [stereo_sample_data.fetch('20070503_102018_s4c1b.fts'),
+                 stereo_sample_data.fetch('20070503_102018_s4c1a.fts')]
+
+    maps = sunpy.map.Map(fits_file, sequence=True)
+    maps = prepare_maps(maps, polar=True)
+
+    fig = plt.figure(figsize=(10, 5), dpi=200)
+
+    for i, map_ in enumerate(maps):
+        axis = fig.add_subplot(int(120+i+1), projection=map_)
+
+        map_.plot(axes=axis)
+        map_.draw_limb(axes=axis)
+        axis.grid(False)
+
+        model_shock = model_from_body('mercury', map_.date_average, map_.observer_coordinate)
+        axis.plot_coord(model_shock.center, 'o', color='tab:red', fillstyle='none', markersize=8)
+        x = map_.world_to_pixel(model_shock.center)[0].value
+        y = map_.world_to_pixel(model_shock.center)[1].value+40
+        axis.annotate('Mercury', (x, y), xytext=(x, y),
+                      backgroundcolor='none', color='Black', fontsize=8,
+                      horizontalalignment='center', verticalalignment='bottom')
+
+        lon, lat = axis.coords
+        lon .set_major_formatter('d.dd')
+        lat.set_major_formatter('d.dd')
+
+        axis.set_xlim([0, map_.data.shape[0]])
+        axis.set_ylim([0, map_.data.shape[1]])
+
+    fig.subplots_adjust(hspace=0.5, wspace=0.35)
+
+    return fig
+
+
+@pytest.mark.mpl_image_compare()
+def test_ellipsoid_on_STEREO_COR2_three_planets():
+    """
+    Tests that the position of three planets is correct at STEREO COR2 images. (https://stereo.gsfc.nasa.gov/browse/2021/06/22/planets/)
+    """
+    fits_file = [stereo_sample_data.fetch('20120622_235400_d4c2a.fts'),
+                 stereo_sample_data.fetch('20140221_235400_d4c2b.fts')]
+
+    maps = sunpy.map.Map(fits_file, sequence=True)
+    maps = prepare_maps(maps)
+
+    fig = plt.figure(figsize=(10, 5), dpi=200)
+
+    for i, map_ in enumerate(maps):
+        axis = fig.add_subplot(int(120+i+1), projection=map_)
+
+        map_.plot(axes=axis, vmin=300, vmax=3000)
+        map_.draw_limb(axes=axis)
+        axis.grid(False)
+
+        for body in ['mercury', 'venus', 'mars', 'saturn']:
+            model_shock = model_from_body(body, map_.date_average, map_.observer_coordinate)
+            axis.plot_coord(model_shock.center, 'o', color=bodies_color_dict[body], fillstyle='none', markersize=8)
+            x = map_.world_to_pixel(model_shock.center)[0].value
+            y = map_.world_to_pixel(model_shock.center)[1].value+40
+            axis.annotate(body.capitalize(), (x, y), xytext=(x, y),
+                          backgroundcolor='none', color='Black', fontsize=8,
+                          horizontalalignment='center', verticalalignment='bottom')
+        lon, lat = axis.coords
+        lon .set_major_formatter('d.dd')
+        lat.set_major_formatter('d.dd')
+
+        axis.set_xlim([0, map_.data.shape[0]])
+        axis.set_ylim([0, map_.data.shape[1]])
+
+    fig.subplots_adjust(hspace=0.5, wspace=0.35)
+
+    return fig

{pythea-0.10.0 → pythea-0.11.0}/PyThea/test/test_imports.py

@@ -1,3 +1,4 @@
+import os
 import pkgutil
 
 
@@ -23,6 +24,8 @@ def test_imports_all():
         except Warning:
             pass
 
-    for imper, nm, ispkg in pkgutil.walk_packages(['PyThea'], 'PyThea.',
+    test_directory = os.path.dirname(__file__)
+
+    for imper, nm, ispkg in pkgutil.walk_packages([f'{test_directory}'], 'PyThea.',
                                                   onerror=on_error):
         imper.find_spec(nm)

{pythea-0.10.0 → pythea-0.11.0}/PyThea/test/test_utils.py

@@ -2,6 +2,7 @@
 Test the utilities
 """
 
+import json
 from datetime import datetime
 
 import matplotlib.dates as mdates
@@ -12,7 +13,8 @@ from sunpy.coordinates.frames import HeliographicStonyhurst
 from sunpy.net import hek
 
 from PyThea.config.selected_bodies import bodies_dict
-from PyThea.utils import get_hek_flare, parameter_fit
+from PyThea.data.sample_data import json_fitting_file_sample_data
+from PyThea.utils import get_hek_flare, model_fittings, parameter_fit
 
 
 def test_get_hek_flare():
@@ -20,17 +22,59 @@ def test_get_hek_flare():
     Test that the get_hek_flare returns a hek.hek.HEKTable and the results are formated correct.
     """
     # This test requests the flare info for a date that returns a list of flares and compares against previous results
-    selectbox_list, flare_list = get_hek_flare(datetime(2017, 9, 10))
+    selectbox_list, flare_list = get_hek_flare(datetime(2017, 9, 10, 0, 0, 0))
     assert type(flare_list) == hek.hek.HEKTable
     assert selectbox_list == ['FLM1.1|2017-09-09T23:53:00', 'FLC9.0|2017-09-10T03:09:00', 'FLC2.9|2017-09-10T09:20:00',
                               'FLC1.6|2017-09-10T14:23:00', 'FLC1.0|2017-09-10T15:26:00', 'FLX8.2|2017-09-10T16:06:00']
 
     # This test requests the flare info for a date that returns an empty list
-    selectbox_list, flare_list = get_hek_flare(datetime(2117, 9, 10))
+    selectbox_list, flare_list = get_hek_flare(datetime(2030, 9, 10, 0, 0, 0))
     assert flare_list == []
     assert selectbox_list == ['No events returned']
 
 
+def test_load_fitting_json_file():
+    """
+    Tests that the load_fitting_json_file returns the model_fittings class and storing it to the model_fittings
+    will return the same result as the model_fittings.to_json().
+    """
+    def compare_json_objects(obj1, obj2, path='', exclude=['date_created', 'version']):
+        if exclude:
+            for key in exclude:
+                obj1.pop(key, None)
+                obj2.pop(key, None)
+
+        for key in set(obj1.keys()) | set(obj2.keys()):
+            new_path = f'{path}.{key}' if path else key
+
+            if key not in obj1 or key not in obj2:
+                print(f"Key '{new_path}' is not present in one of the objects.")
+                return False
+            elif obj1[key] != obj2[key]:
+                if isinstance(obj1[key], dict) and isinstance(obj2[key], dict):
+                    check = compare_json_objects(obj1[key], obj2[key], path=new_path)
+                    if not check:
+                        return False
+                else:
+                    print(f"Value mismatch at key '{new_path}': {obj1[key]} != {obj2[key]}")
+                    return False
+
+        return True
+
+    json_fitting_file = json_fitting_file_sample_data.fetch('FLX1p0D20211028T153500MEllipsoid.json')
+    with open(json_fitting_file, 'r') as file:
+        json_content = file.read()
+        fitting_from_json = json.loads(json_content)
+
+    model_fittings_class = model_fittings.load_from_json(json_fitting_file)
+    model_fittings_class_dict = json.loads(model_fittings_class.to_json())
+    assert isinstance(model_fittings_class, model_fittings)
+    assert model_fittings_class.event_selected == 'FLX1.0|2021-10-28T15:35:00'
+    assert model_fittings_class.date_process == '2021-10-28T15:35:00.000000'
+    assert model_fittings_class.geometrical_model == 'Ellipsoid'
+    assert compare_json_objects(model_fittings_class_dict, fitting_from_json)
+
+
 def test_get_horizons_coord():
     """
     Test that get_horizons_coord returns a Skycoord instance, in HeliographicStonyhurst frame, and returns the same coordinates every time.

{pythea-0.10.0 → pythea-0.11.0}/PyThea/utils.py

@@ -170,13 +170,10 @@ def plot_solar_reference_lines(axis, bodies_list, smap, mode='Limb from Obs.'):
         smap.draw_grid(linewidth=1, color='red', system='carrington', alpha=0.8)
 
 
-def download_fits(date_process, imager, time_range=[-1, 1]):
+def download_fits(timerange, imager):
     '''
     Downloads the imaging data (fits files) from VSO
     '''
-    timerange = a.Time(date_process + datetime.timedelta(hours=time_range[0]),
-                       date_process + datetime.timedelta(hours=time_range[1]))
-
     maps_ = []
     args = imager_dict[imager][0]
     result = Fido.search(timerange, *args)

{pythea-0.10.0 → pythea-0.11.0/PyThea.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyThea
-Version: 0.10.0
+Version: 0.11.0
 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
@@ -26,6 +26,7 @@ Requires-Dist: scipy
 Requires-Dist: aiapy
 Requires-Dist: astropy
 Requires-Dist: astroquery
+Requires-Dist: jplephem
 Requires-Dist: numexpr
 Requires-Dist: sunpy==5.1.2
 Requires-Dist: parfive==2.1.0
@@ -42,6 +43,7 @@ Requires-Dist: tqdm
 Requires-Dist: pyvista
 Requires-Dist: pytest-astropy
 Requires-Dist: pytest-sugar
+Requires-Dist: pytest-mpl
 
 # PyThea: A software package to reconstruct the 3D structure of CMEs and shock waves
 

{pythea-0.10.0 → pythea-0.11.0}/PyThea.egg-info/SOURCES.txt

@@ -49,6 +49,8 @@ PyThea/sunpy_dev/map/maputils.py
 PyThea/test/Pythea_test.py
 PyThea/test/__init__.py
 PyThea/test/conftest.py
+PyThea/test/figure_hashes.json
+PyThea/test/test_figures.py
 PyThea/test/test_geometrical_models.py
 PyThea/test/test_imports.py
 PyThea/test/test_remote_clients.py

{pythea-0.10.0 → pythea-0.11.0}/PyThea.egg-info/requires.txt

@@ -4,6 +4,7 @@ scipy
 aiapy
 astropy
 astroquery
+jplephem
 numexpr
 sunpy==5.1.2
 parfive==2.1.0
@@ -20,3 +21,4 @@ tqdm
 pyvista
 pytest-astropy
 pytest-sugar
+pytest-mpl

{pythea-0.10.0 → pythea-0.11.0}/environment.yml

@@ -22,7 +22,9 @@ dependencies:
 # - opencv-python-headless > Introdused to solve a libGL library error and no longe needed. https://github.com/AthKouloumvakos/PyThea/commit/24fa8a46fd4c4ee33aa84ee617d6f3e6628ac8e8
   - pytest-astropy
   - pytest-sugar
+  - pytest-mpl
   - pip
   - pip:
       - pooch
       - stqdm
+      - jplephem

{pythea-0.10.0 → pythea-0.11.0}/requirements.txt

@@ -4,6 +4,7 @@ scipy
 aiapy
 astropy
 astroquery
+jplephem
 numexpr
 sunpy==5.1.2
 parfive==2.1.0
@@ -20,3 +21,4 @@ tqdm
 pyvista
 pytest-astropy
 pytest-sugar
+pytest-mpl

pythea-0.10.0/PyThea/data/sample_data.py

@@ -1,15 +0,0 @@
-import os
-from pathlib import Path
-
-import pooch
-
-database_dir = os.path.join(Path.home(), 'PyThea')
-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
-    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_lowres.fits': 'sha256:396b9ef5cbc1cbe2f2af806758f449cfd36f352826b61295e6330859ac7f7652',
-    },
-)