PyThea 0.14.0__tar.gz → 1.0.0__tar.gz

{pythea-0.14.0 → pythea-1.0.0}/CHANGELOG.md

@@ -1,3 +1,19 @@
+# v1.0.0 (19-Nov-2024)
+
+## Features
+ - Adds imaging data from Solar Orbiter's SOLOHi.
+ - Implements offline fits file loading from local database.
+
+## Minor Changes
+ - Updates Test figure hashes.
+ - Final changes in README before the major release.
+
+ ## Bug Fixes
+ - Fixes a temporary bug with JSOC and AIA prep
+ - Fixes potential bug with maps loading into map sequence.
+ - Fixes a bug when fits database is selected but no files downloaded.
+ - Fixes a bug with the maps clims.
+
 # v0.14.0 (03-Oct-2024)
 
 ## Features

{pythea-0.14.0 → pythea-1.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyThea
-Version: 0.14.0
+Version: 1.0.0
 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
@@ -54,7 +54,7 @@ Requires-Dist: pytest-mpl
 ![flake8](https://github.com/AthKouloumvakos/PyThea/actions/workflows/flake8.yml/badge.svg)
 ![pytest](https://github.com/AthKouloumvakos/PyThea/actions/workflows/pytest.yml/badge.svg)
 
-_PyThea_ is an open-source software package that can be used to reconstruct the 3D structure of Coronal Mass Ejections (CMEs) and shock waves and determine their kinematics using remote-sensing observations. The tool implements the Graduated Cylindrical Shell (GCS) model that can be used to reconstruct CMEs and two geometrical models, namely a spheroid and ellipsoid model to reconstruct shock waves. It also implements remote-sensing observations from multiple viewpoints such as the Solar and Heliospheric Observatory (SoHO) and Solar Terrestrial Relations Observatory (STEREO).
+_PyThea_ is an open-source software package that can be used to reconstruct the 3D structure of Coronal Mass Ejections (CMEs) and shock waves and determine their kinematics using remote-sensing observations. The tool implements the Graduated Cylindrical Shell (GCS) model that can be used to reconstruct CMEs and two geometrical models, namely a spheroid and ellipsoid model to reconstruct shock waves. It also implements remote-sensing observations from multiple viewpoints such as the Solar and Heliospheric Observatory (SoHO), Solar Terrestrial Relations Observatory (STEREO), and Parker Solar Probe.
 
 ## 💾 Installation
 
@@ -153,3 +153,7 @@ If you use _PyThea_ for scientific work or research presented in a publication,
 ## ⓘ The mythology of Thea:
 
 In Greek mythology, Thea, also called Euryphaessa "wide-shining", is the Titaness of sight and the shining light of the clear blue sky. Her brother/consort is Hyperion, a Titan and god of the sun, and together they are the parents of Helios (the Sun), Selene (the Moon), and Eos (the Dawn).
+
+## Development Support:
+
+The lead author of this software package Athanasios Kouloumvakos acknowledges financial support from NASA Grant 80NSSC24K0071   for the further development and improvement of PyThea during 2024. This grant was part of the NASA Headquarters Heliophysics Tools and Methods Program in response to NASA ROSES–2022 (NNH22ZDA001N).

{pythea-0.14.0 → pythea-1.0.0}/PyThea/PyThea_app.py

@@ -85,7 +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.
+            - SolO/EUI, METIS, and HI(tiles 1&2) images.
             ''', icon='ℹ️')
     st.warning('''
            **NOTE: From PyThea >0.8.1 the JSON fitting files will be slightly different from the old ones.**

{pythea-0.14.0 → pythea-1.0.0}/PyThea/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.14.0'
-__version_tuple__ = version_tuple = (0, 14, 0)
+__version__ = version = '1.0.0'
+__version_tuple__ = version_tuple = (1, 0, 0)

{pythea-0.14.0 → pythea-1.0.0}/PyThea/config/selected_imagers.py

@@ -80,3 +80,10 @@ imager_dict['EUI-FSI'] = {'fido': (a.Instrument('EUI'), a.soar.Product('EUI-FSI1
 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'}
+
+for tile in range(1, 5):
+    z = 'T' if tile in [1, 2] else 'G'
+    imager_dict[f'SOLOHI-T{tile}'] = {'fido': (a.Instrument('SOLOHI'),
+                                               a.soar.Product(f'SOLOHI-{tile}F{z}'), a.Level(2)),
+                                      'process': {'superpixel': 2},
+                                      'source': 'SOLO', 'instrument': 'SOLOHI', 'detector': f'T{tile}'}

{pythea-0.14.0 → pythea-1.0.0}/PyThea/sunpy_dev/extern/sunkit_instruments/aia/utils.py

@@ -1,3 +1,4 @@
+import warnings
 from astropy.time import TimeDelta
 from aiapy.calibrate import fix_observer_location, update_pointing
 
@@ -5,7 +6,11 @@ __all__ = ['prep_aia']
 
 
 def prep_aia(map_sequence):
-    map_sequence = [update_pointing(tmap) for tmap in map_sequence]
+    try:
+        map_sequence = [update_pointing(tmap) for tmap in map_sequence]
+    except:
+        warnings.warn('Prepare AIA maps failed, script proceeded without update_pointing. Check connection with JSOC.', UserWarning)
+
     map_sequence = [fix_observer_location(tmap) for tmap in map_sequence]
 
     for map_ in map_sequence:

{pythea-0.14.0 → pythea-1.0.0}/PyThea/sunpy_dev/map/maputils.py

@@ -18,6 +18,16 @@ __all__ = ['maps_sequence_processing', 'get_closest', 'normalize_exposure',
            'prepare_maps', 'difference_maps', 'mask_occulter']
 
 
+def check_maps_sequence(map_sequence):
+    if map_sequence:
+        if isinstance(map_sequence, MapSequence):
+            return map_sequence
+        else:
+            return sunpy.map.Map(map_sequence, sequence=True)
+    else:
+        return []
+
+
 def maps_sequence_processing(map_sequence, **kwargs):
     """
     Returns a sequence of maps which is processed as plain images, running or base difference images.
@@ -36,6 +46,7 @@ def maps_sequence_processing(map_sequence, **kwargs):
         A SunPy map.
     """
 
+    map_sequence = check_maps_sequence(map_sequence)
     if len(map_sequence) == 0:
         return []
 
@@ -139,6 +150,7 @@ def filter_maps(map_sequence, **kwargs):
 
     '''
 
+    map_sequence = check_maps_sequence(map_sequence)
     if len(map_sequence) == 0:
         return []
 
@@ -155,11 +167,7 @@ def filter_maps(map_sequence, **kwargs):
         map_sequence = [tmap for tmap in map_sequence if tmap.meta['polar'] == kwargs['polar']]
 
     if len(map_sequence) != 0:
-        if isinstance(map_sequence, MapSequence):
-            return map_sequence
-        else:
-            sequence_final = sunpy.map.Map(map_sequence, sequence=True)
-
+        sequence_final = check_maps_sequence(map_sequence)
     else:
         sequence_final = []
 
@@ -188,6 +196,7 @@ def prepare_maps(map_sequence, **kwargs):
 
     '''
 
+    map_sequence = check_maps_sequence(map_sequence)
     if len(map_sequence) == 0:
         return []
 
@@ -246,6 +255,7 @@ def difference_maps(smapi, smapm):
     if smapm.exposure_time != 1*u.second:
         smapm = normalize_exposure(smapm)
     smap_difference = smapi.data - smapm.data
+
     return sunpy.map.Map(smap_difference, smapi.meta)
 
 
@@ -300,11 +310,16 @@ def mask_occulter(smap, apply_mask=True, mask_value=0):
 
 
 def maps_clims(images):
-    if images[1].instrument == 'WISPR':
-        if images[1].detector == 'Outer':
+    i = 0 if len(images) < 2 else 1
+
+    if images[i].instrument == 'WISPR':
+        if images[i].detector == 'Outer':
             return [14., 14.]
-        elif images[1].detector == 'Inner':
+        elif images[i].detector == 'Inner':
             return [13., 13.]
-    if images[1].instrument == 'Metis':
+    elif images[i].instrument == 'Metis':
         return [12.80, 13.00]
-    return [np.nanquantile(images[1].data, 0.20)-10, np.nanquantile(images[1].data, 0.80)+10]
+    elif images[i].instrument.startswith('SoloHI'):
+        return [13.95, 14.05]
+
+    return [np.nanquantile(images[i].data, 0.20)-10, np.nanquantile(images[i].data, 0.80)+10]

{pythea-0.14.0 → pythea-1.0.0}/PyThea/test/figure_hashes.json

@@ -1,9 +1,9 @@
 {
   "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_AIA_mercury": "a70589cd9c052d80532df5f9fbbc6d857333dcd3e2e7acfbe0e73f6b98a2a6ef",
   "PyThea.test.test_figures.test_ellipsoid_on_STEREO_COR1_venus": "18a3af72e9da5b60e435f83ee3ef3f8cd0eb437eaef463329552ff56968f12ff",
   "PyThea.test.test_figures.test_ellipsoid_on_STEREO_COR2_three_planets": "231d5635f57c4d66556674a83f6cbcef7dc94b51846e977c4c2dc3dc244096ac",
-  "PyThea.test.test_figures.test_kinematics_figure": "83e060de53b57e9d34fe50111ba60a44f7c7c7b20faae9a4381654ef1c9ea72d"
+  "PyThea.test.test_figures.test_kinematics_figure": "83e060de53b57e9d34fe50111ba60a44f7c7c7b20faae9a4381654ef1c9ea72d",
   "PyThea.test.test_figures.test_ellipsoid_on_WISPR_Inner_Venus": "8d831b43b0c789cacfcff8386c00af0707bb68d64fca16c6188deca93d3cba87",
   "PyThea.test.test_figures.test_ellipsoid_on_WISPR_Outer_Mercury": "f94c444f2c6f00cd5dd5deff394d0e233c9e720413fd5570b306b262915c9732"
 }

{pythea-0.14.0 → pythea-1.0.0}/PyThea/utils.py

@@ -128,10 +128,7 @@ def make_figure(map, cmap='Greys_r', clim=[-20, 20], clip_model=True, **kwargs):
     if median_filter_value != 1:
         map = sunpy.map.Map(median_filter(map.data, size=int(median_filter_value)), map.meta)
 
-    if map.instrument == 'WISPR':
-        clim = [-10**-clim[0], 10**-clim[1]]
-
-    if map.instrument == 'Metis':
+    if map.instrument in ['WISPR', 'Metis'] or map.instrument.startswith('SoloHI'):
         clim = [-10**-clim[0], 10**-clim[1]]
 
     if cmap == 'default':
@@ -155,9 +152,19 @@ def make_figure(map, cmap='Greys_r', clim=[-20, 20], clip_model=True, **kwargs):
     if cref.Ty > 0:
         axis.invert_yaxis()
 
-    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.replace('VLD', 'METIS-VDL')),
+    if map.instrument == 'SoloHI':
+        title = 'SoloHI' + f' Tile-{map.detector}' ' $T_{AGV}:$' + parse_time(map.date_average).strftime('%Y-%m-%d %H:%M:%S')
+    elif map.instrument == 'Metis':
+        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.replace('VLD', 'METIS-VDL'))
+    else:
+        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)
+    print(map.instrument)
+    print(map.latex_name)
+    axis.set_title(title,
                    fontsize=10, pad=8)
 
     return fig, axis

{pythea-0.14.0 → pythea-1.0.0}/PyThea/utils_database.py

@@ -79,7 +79,8 @@ def get_fits_filenames_from_database(event_id, timerange, imager):
 
     if downloaded_files is None:
         downloaded_files = download_fits(timerange, imager)
-
+        if not downloaded_files:
+            return None
         nested_dict_ = create_nested_dict(db_args, downloaded_files.data)
         nested_dict_ = {str(timerange): nested_dict_}
 

{pythea-0.14.0 → pythea-1.0.0}/PyThea.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyThea
-Version: 0.14.0
+Version: 1.0.0
 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
@@ -54,7 +54,7 @@ Requires-Dist: pytest-mpl
 ![flake8](https://github.com/AthKouloumvakos/PyThea/actions/workflows/flake8.yml/badge.svg)
 ![pytest](https://github.com/AthKouloumvakos/PyThea/actions/workflows/pytest.yml/badge.svg)
 
-_PyThea_ is an open-source software package that can be used to reconstruct the 3D structure of Coronal Mass Ejections (CMEs) and shock waves and determine their kinematics using remote-sensing observations. The tool implements the Graduated Cylindrical Shell (GCS) model that can be used to reconstruct CMEs and two geometrical models, namely a spheroid and ellipsoid model to reconstruct shock waves. It also implements remote-sensing observations from multiple viewpoints such as the Solar and Heliospheric Observatory (SoHO) and Solar Terrestrial Relations Observatory (STEREO).
+_PyThea_ is an open-source software package that can be used to reconstruct the 3D structure of Coronal Mass Ejections (CMEs) and shock waves and determine their kinematics using remote-sensing observations. The tool implements the Graduated Cylindrical Shell (GCS) model that can be used to reconstruct CMEs and two geometrical models, namely a spheroid and ellipsoid model to reconstruct shock waves. It also implements remote-sensing observations from multiple viewpoints such as the Solar and Heliospheric Observatory (SoHO), Solar Terrestrial Relations Observatory (STEREO), and Parker Solar Probe.
 
 ## 💾 Installation
 
@@ -153,3 +153,7 @@ If you use _PyThea_ for scientific work or research presented in a publication,
 ## ⓘ The mythology of Thea:
 
 In Greek mythology, Thea, also called Euryphaessa "wide-shining", is the Titaness of sight and the shining light of the clear blue sky. Her brother/consort is Hyperion, a Titan and god of the sun, and together they are the parents of Helios (the Sun), Selene (the Moon), and Eos (the Dawn).
+
+## Development Support:
+
+The lead author of this software package Athanasios Kouloumvakos acknowledges financial support from NASA Grant 80NSSC24K0071   for the further development and improvement of PyThea during 2024. This grant was part of the NASA Headquarters Heliophysics Tools and Methods Program in response to NASA ROSES–2022 (NNH22ZDA001N).

{pythea-0.14.0 → pythea-1.0.0}/README.md

@@ -10,10 +10,7 @@
 
 ![Logo](https://github.com/AthKouloumvakos/PyThea/blob/master/docs/logo/pythea_logo.png)
 
-_PyThea_ is an open-source software package that can be used to reconstruct the 3D structure of Coronal Mass Ejections (CMEs) and shock waves and determine their kinematics using remote-sensing observations. The tool implements the Graduated Cylindrical Shell (GCS) model that can be used to reconstruct CMEs and two geometrical models, namely a spheroid and ellipsoid model to reconstruct shock waves. It also implements remote-sensing observations from multiple viewpoints such as the Solar and Heliospheric Observatory (SoHO) and Solar Terrestrial Relations Observatory (STEREO).
-
-> [!NOTE]
-> The lead author of PyThea (A. Kouloumvakos) has been awarded a NASA Grant (80NSSC24K0071) for further developing and improving PyThea, during fiscal year 2024. The awarded proposal is part of the NASA Headquarters Heliophysics Tools and Methods Program in response to NASA ROSES–2022 (NNH22ZDA001N). The proposed software enhancements and new features encompass a range of improvements, including but not limited to: improved code documentation, expanded and improved code testing, improved image processing and visualization, and the incorporation of new solar mission imaging data.
+_PyThea_ is an open-source software package that can be used to reconstruct the 3D structure of Coronal Mass Ejections (CMEs) and shock waves and determine their kinematics using remote-sensing observations. The tool implements the Graduated Cylindrical Shell (GCS) model that can be used to reconstruct CMEs and two geometrical models, namely a spheroid and ellipsoid model to reconstruct shock waves. It also implements remote-sensing observations from multiple viewpoints such as the Solar and Heliospheric Observatory (SoHO), Solar Terrestrial Relations Observatory (STEREO), and Parker Solar Probe.
 
 ## 💾 Installation
 
@@ -112,3 +109,7 @@ If you use _PyThea_ for scientific work or research presented in a publication,
 ## ⓘ The mythology of Thea:
 
 In Greek mythology, Thea, also called Euryphaessa "wide-shining", is the Titaness of sight and the shining light of the clear blue sky. Her brother/consort is Hyperion, a Titan and god of the sun, and together they are the parents of Helios (the Sun), Selene (the Moon), and Eos (the Dawn).
+
+## Development Support:
+
+The lead author of this software package Athanasios Kouloumvakos acknowledges financial support from NASA Grant 80NSSC24K0071   for the further development and improvement of PyThea during 2024. This grant was part of the NASA Headquarters Heliophysics Tools and Methods Program in response to NASA ROSES–2022 (NNH22ZDA001N).

{pythea-0.14.0 → pythea-1.0.0}/README_pypi.md

@@ -7,7 +7,7 @@
 ![flake8](https://github.com/AthKouloumvakos/PyThea/actions/workflows/flake8.yml/badge.svg)
 ![pytest](https://github.com/AthKouloumvakos/PyThea/actions/workflows/pytest.yml/badge.svg)
 
-_PyThea_ is an open-source software package that can be used to reconstruct the 3D structure of Coronal Mass Ejections (CMEs) and shock waves and determine their kinematics using remote-sensing observations. The tool implements the Graduated Cylindrical Shell (GCS) model that can be used to reconstruct CMEs and two geometrical models, namely a spheroid and ellipsoid model to reconstruct shock waves. It also implements remote-sensing observations from multiple viewpoints such as the Solar and Heliospheric Observatory (SoHO) and Solar Terrestrial Relations Observatory (STEREO).
+_PyThea_ is an open-source software package that can be used to reconstruct the 3D structure of Coronal Mass Ejections (CMEs) and shock waves and determine their kinematics using remote-sensing observations. The tool implements the Graduated Cylindrical Shell (GCS) model that can be used to reconstruct CMEs and two geometrical models, namely a spheroid and ellipsoid model to reconstruct shock waves. It also implements remote-sensing observations from multiple viewpoints such as the Solar and Heliospheric Observatory (SoHO), Solar Terrestrial Relations Observatory (STEREO), and Parker Solar Probe.
 
 ## 💾 Installation
 
@@ -106,3 +106,7 @@ If you use _PyThea_ for scientific work or research presented in a publication,
 ## ⓘ The mythology of Thea:
 
 In Greek mythology, Thea, also called Euryphaessa "wide-shining", is the Titaness of sight and the shining light of the clear blue sky. Her brother/consort is Hyperion, a Titan and god of the sun, and together they are the parents of Helios (the Sun), Selene (the Moon), and Eos (the Dawn).
+
+## Development Support:
+
+The lead author of this software package Athanasios Kouloumvakos acknowledges financial support from NASA Grant 80NSSC24K0071   for the further development and improvement of PyThea during 2024. This grant was part of the NASA Headquarters Heliophysics Tools and Methods Program in response to NASA ROSES–2022 (NNH22ZDA001N).