PyThea 0.11.0__tar.gz → 0.12.0__tar.gz

pythea-0.12.0/.readthedocs.yaml

@@ -0,0 +1,29 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.9"
+    # You can also specify other tool versions:
+    # nodejs: "16"
+    # rust: "1.55"
+    # golang: "1.17"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/source/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+# formats:
+#    - pdf
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - requirements: docs/source/requirements.txt

{pythea-0.11.0 → pythea-0.12.0}/CHANGELOG.md

@@ -1,4 +1,29 @@
-# v0.11.0 (17-April-2024)
+# v0.12.0 (09-Jun-2024)
+
+## Features
+ - Adds more imaging data from SDO/AIA.
+ - Adds acceleration calculation in the kinematic plots.
+ - Implements acceleration plotting in the app.
+ - Includes fits file name in fitting files and dataframes.
+ - Highlights a row in the fitting table when fitting exist in table.
+
+## Major Changes
+ - Decouples the loading of fits files from download_fits function.
+
+## Minor Changes
+ - Improves configuration dictionary for selected imagers.
+ - Improves json warning message in the main app page.
+ - Adds documentation page link to the main app page.
+ - Updates README files.
+ - Improves plot_fitting_model and adds figure test.
+ - Improves application layout.
+
+## Bug Fixes
+ - Fixes a potential bug in filter_maps when no filtering is applied.
+ - Fixes a bug with progress bar with stqdm.
+ - Fixes a bug with image processing mode selection.
+
+# v0.11.0 (19-May-2024)
 
 ## Features
  - Adds tests for ellipsoid location on AIA and STEREO COR images.

{pythea-0.11.0/PyThea.egg-info → pythea-0.12.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyThea
-Version: 0.11.0
+Version: 0.12.0
 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
@@ -35,7 +35,6 @@ Requires-Dist: matplotlib
 Requires-Dist: seaborn
 Requires-Dist: streamlit
 Requires-Dist: Pillow
-Requires-Dist: stqdm
 Requires-Dist: lxml
 Requires-Dist: zeep
 Requires-Dist: drms
@@ -63,8 +62,8 @@ We recommend, creating a virtual environment for _PyThea_ and installing the pac
 If you use Anaconda or Miniconda (which we also recommend) you can create a virtual environment using ```conda``` and then install _PyThea_ using from PyPI using ```pip```. In the terminal do the following:
 
 ```python
-# Create a virtual environment. Use python=3.8 or 3.9
-conda create --name PyThea python=3.9
+# Create a virtual environment. Use python>3.9
+conda create --name PyThea python=3.10
 
 # Activate the environment
 conda activate PyThea
@@ -138,7 +137,7 @@ If there is an error when running ```PyThea streamlit``` then you can manually r
 
 ## 📙 Usage
 
-Complete documentation of the _PyThea_ is under construction.
+Complete documentation of the _PyThea_ can be found in [https://www.pythea.org/](https://www.pythea.org/).
 
 ## 📦 Useful Python packages
 

{pythea-0.11.0 → pythea-0.12.0}/PyThea/PyThea_app.py

@@ -23,7 +23,6 @@ from copy import copy
 
 import astropy.units as u
 import numpy as np
-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
@@ -38,8 +37,8 @@ from PyThea.modules import (date_and_event_selection, figure_streamlit,
                             fitting_and_slider_options_container,
                             fitting_sliders)
 from PyThea.sunpy_dev.map.maputils import get_closest, maps_clims
-from PyThea.utils import (download_fits, model_fittings, plot_fitting_model,
-                          single_imager_maps_process)
+from PyThea.utils import (download_fits, load_fits, model_fittings,
+                          plot_fitting_model, single_imager_maps_process)
 from PyThea.version import version
 
 
@@ -49,6 +48,13 @@ def delete_from_state(vars):
             del st.session_state[var]
 
 
+def highlight_row(row, row_index):
+    if row.name.strftime('%Y-%m-%dT%H:%M:%S.%f') == row_index.strftime('%Y-%m-%dT%H:%M:%S.%f').values[0]:
+        return ['background-color: lightpink']*len(row)
+    else:
+        return ['']*len(row)
+
+
 def footer_text():
     st.subheader('About this application:')
     st.markdown("""
@@ -65,16 +71,23 @@ def footer_text():
     right.markdown("""
                    **Github**: Find the latest version here
                                [![GitHub](https://img.shields.io/badge/github-%23121011.svg?style=for-the-badge&logo=github&logoColor=white)](https://github.com/AthKouloumvakos/PyThea) \n
-                   **Citation**: Cite PyThea as [![https://doi.org/10.5281/zenodo.5713659](https://zenodo.org/badge/DOI/10.5281/zenodo.5713659.svg)](https://doi.org/10.5281/zenodo.5713659) \n
+                   **Documentation Page**: https://www.pythea.org/
                    """ +
                    f"""
                    **Version**: {version} (latest release [![Version](https://img.shields.io/github/v/release/AthKouloumvakos/PyThea)](https://github.com/AthKouloumvakos/PyThea/releases))
                    """)
     left.image('https://github.com/AthKouloumvakos/PyThea/blob/master/docs/logo/pythea_logo.png?raw=true')
+    st.markdown("""
+                **Citation**: Please cite the following paper [![https://www.frontiersin.org/articles/10.3389/fspas.2022.974137/](https://img.shields.io/static/v1?label=Paper&message=Frontiers&color=red)](https://www.frontiersin.org/articles/10.3389/fspas.2022.974137/) and [![https://doi.org/10.5281/zenodo.5713659](https://zenodo.org/badge/DOI/10.5281/zenodo.5713659.svg)](https://doi.org/10.5281/zenodo.5713659)
+                """)
+    st.info('''
+            More imaging data have been added:
+            - SDO/AIA images from 211A channel have been added.
+            ''', icon='ℹ️')
     st.warning('''
-           ⚠️ **NOTE: From PyThea >0.8.1 the JSON fitting files will be slightly different from the old ones.** ⚠️
-           * Due to a change in the fitting time input, the new fitting files may have slightly different times for the same images (see further information [here](https://github.com/AthKouloumvakos/PyThea/discussions/24)).
-           ''')
+           **NOTE: From PyThea >0.8.1 the JSON fitting files will be slightly different from the old ones.**
+           Due to a change in the fitting time input, the new fitting files may have slightly different times for the same images (see further information [here](https://github.com/AthKouloumvakos/PyThea/discussions/24)).
+           ''', icon='⚠️')
     st.markdown('---')
 
 
@@ -86,7 +99,10 @@ def run():
     #############################################################
     # set page config
     st.set_page_config(page_title='PyThea', page_icon=':rocket:',
-                       initial_sidebar_state='expanded')
+                       initial_sidebar_state='expanded',
+                       menu_items={
+                           'Get Help': 'https://www.pythea.org/',
+                           'Report a Bug': 'https://github.com/AthKouloumvakos/PyThea'})
 
     #############################################################
     # HTML Styles
@@ -94,7 +110,7 @@ def run():
 
     #############################################################
     # Main page information text
-    st.title('PyThea: Reconstruct CMEs & Shocks')
+    st.header('PyThea: Reconstruct CMEs & Shocks')
 
     #############################################################
     # Startup Variables
@@ -106,7 +122,6 @@ def run():
 
     if 'date_process' not in st.session_state:
         date_and_event_selection(st)
-        st.markdown(""" #### ⏻ Select a day & solar event. """)
     else:
         st.sidebar.markdown('## Processing Event|Date:')
         st.sidebar.info(f'{st.session_state.event_selected}')
@@ -194,7 +209,8 @@ def run():
                                                     on_change=delete_from_state,
                                                     kwargs={'vars': ['map', 'imagers_list_', 'clim', 'clim_manual_low', 'clim_manual_high']})
         if image_mode in ['Running Diff.', 'Base Diff.']:
-            diff_value = procoption_container.number_input('Select Step/Image for Running/Base Diff.', 1, 5, key='diff_value',
+            min_diff = 1 if image_mode == 'Running Diff.' else 0
+            diff_value = procoption_container.number_input('Select Step/Image for Running/Base Diff.', min_diff, 5, key='diff_value',
                                                            on_change=delete_from_state,
                                                            kwargs={'vars': ['map', 'imagers_list_', 'clim', 'clim_manual_low', 'clim_manual_high']})
         else:
@@ -245,15 +261,16 @@ def run():
         st.session_state.map_ = {} if 'map_' not in st.session_state else st.session_state.map_
         st.session_state.map = {} if 'map' not in st.session_state else st.session_state.map
         st.session_state['imagers_list_'] = imagers_list
-        progress_bar = stqdm.stqdm(imager_added, desc='Preparing to Download data')
-        for imager in progress_bar:
-            progress_bar.desc = f'Downloaded {imager} images from VSO'
+        progress_bar = st.progress(0, text='Preparing to Download data')
+        for i, imager in enumerate(imager_added):
+            progress_bar.progress(i/len(imager_added), text=f'Download {imager} images from VSO')
             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]))
-                st.session_state.map_[imager] = download_fits(timerange, imager)
+                downloaded_files = download_fits(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][1],
+                                                                           **selected_imagers.imager_dict[imager]['process'],
                                                                            skip='sequence_processing')
             processed_images = single_imager_maps_process(st.session_state.map_[imager],
                                                           skip=['filter', 'prepare'],
@@ -265,6 +282,7 @@ def run():
             else:
                 st.session_state.imagers_list_.remove(imager)
                 st.session_state.map_colormap_limits.pop(imager, None)
+        progress_bar.empty()
 
     if imager_removed != []:
         st.session_state['imagers_list_'] = imagers_list
@@ -374,6 +392,7 @@ def run():
     # Store the fitting
     single_fit = model.to_dataframe()
     single_fit['imager'] = imager_select
+    single_fit['fits_file'] = running_map.meta['fits_file']
 
     if store_fit_button_pressed:
         if 'model_fittings' not in st.session_state:
@@ -390,10 +409,13 @@ def run():
         st.markdown('---')
         st.markdown('### Parameters Table')
         st.markdown('**Running Fitting Table:**')
-        st.dataframe(single_fit)
+        col_formats = {col: '{:,.2f}'.format for col in single_fit.select_dtypes(include='number').columns}
+        st.dataframe(single_fit.style.format(col_formats))
         if 'model_fittings' in st.session_state:
             st.markdown('**Stored Fitting Table:**')
-            st.dataframe(st.session_state.model_fittings.parameters)
+            st.dataframe(st.session_state.model_fittings.parameters.style.apply(highlight_row,
+                                                                                row_index=single_fit.index, axis=1).format(col_formats)
+                         )
             col1, col2 = st.columns((2, 2))
             col2.selectbox('Select a fitting',
                            options=st.session_state.model_fittings.parameters.index,
@@ -413,7 +435,7 @@ def run():
         st.markdown('### Plots of kinematics ')
         col1, col2, col3 = st.columns(3)
         plt_kinematics_select = col1.selectbox('Select Plots',
-                                               options=['All', 'HeightT', 'SpeedT', 'Long-LatT'])
+                                               options=['All', 'HeightT', 'SpeedT', 'AccelerationT', 'Long-LatT'])
 
         fit_mode = col2.selectbox('Select Fitting Mode',
                                   options=['polynomial', 'spline', 'custom'],

{pythea-0.11.0 → pythea-0.12.0}/PyThea/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.11.0'
-__version_tuple__ = version_tuple = (0, 11, 0)
+__version__ = version = '0.12.0'
+__version_tuple__ = version_tuple = (0, 12, 0)

{pythea-0.11.0 → pythea-0.12.0}/PyThea/config/app_styles.py

@@ -1,9 +1,4 @@
 def apply(st):
-    # Hide the menu button
-    st.markdown(""" <style>
-                #MainMenu {visibility: hidden;}
-                footer {visibility: hidden;}
-                </style> """, unsafe_allow_html=True)
     # Do some css styling tricks here (e.g. remove the padding)
     # https://discuss.streamlit.io/t/reduce-white-space-top-of-the-page/21737/3
     st.markdown("""

pythea-0.12.0/PyThea/config/selected_imagers.py

@@ -0,0 +1,65 @@
+'''
+ A dictionary of the selected imagers
+ How to use this:
+
+'''
+import astropy.units as u
+from sunpy.net import attrs as a
+
+imager_dict = {}
+
+imager_dict['LC2'] = {'fido': (a.Instrument.lasco, a.Detector.c2),
+                      'process': {'dimensions': (1024*u.pixel, 1024*u.pixel), 'polar': 'Clear', 'superpixel': 2},
+                      'source': 'SOHO', 'instrument': 'LASCO', 'detector': 'C2'}
+
+imager_dict['LC3'] = {'fido': (a.Instrument.lasco, a.Detector.c3),
+                      'process': {'dimensions': (1024*u.pixel, 1024*u.pixel), 'polar': 'Clear', 'superpixel': 2},
+                      'source': 'SOHO', 'instrument': 'LASCO', 'detector': 'C3'}
+
+imager_dict['AIA-193'] = {'fido': (a.Instrument.aia, a.Wavelength(19.3 * u.nm), a.Sample(1*u.minute)),
+                          'process': {'dimensions': (4096*u.pixel, 4096*u.pixel), 'superpixel': 8, 'exposure': 1.90},
+                          'source': 'SDO', 'instrument': 'AIA', 'wavelength': '193'}
+
+imager_dict['AIA-211'] = {'fido': (a.Instrument.aia, a.Wavelength(21.1 * u.nm), a.Sample(1*u.minute)),
+                          'process': {'dimensions': (4096*u.pixel, 4096*u.pixel), 'superpixel': 8, 'exposure': 1.90},
+                          'source': 'SDO', 'instrument': 'AIA', 'wavelength': '211'}
+
+imager_dict['COR2A'] = {'fido': (a.Source('STEREO_A'), a.Detector.cor2),
+                        'process': {'dimensions': (2048*u.pixel, 2048*u.pixel), 'polar': 1001, 'superpixel': 4},
+                        'source': 'STEREO_A', 'instrument': 'SECCHI', 'detector': 'COR2'}
+
+imager_dict['COR2B'] = {'fido': (a.Source('STEREO_B'), a.Detector.cor2),
+                        'process': {'dimensions': (2048*u.pixel, 2048*u.pixel), 'polar': 1001, 'superpixel': 4},
+                        'source': 'STEREO_B', 'instrument': 'SECCHI', 'detector': 'COR2'}
+
+imager_dict['EUVIA'] = {'fido': (a.Source('STEREO_A'), a.Detector.euvi, a.Wavelength(19.5 * u.nm)),
+                        'process': {'dimensions': (2048*u.pixel, 2048*u.pixel), 'superpixel': 4},
+                        'source': 'STEREO_A', 'instrument': 'SECCHI', 'detector': 'EUVI'}
+
+imager_dict['EUVIB'] = {'fido': (a.Source('STEREO_B'), a.Detector.euvi, a.Wavelength(19.5 * u.nm)),
+                        'process': {'dimensions': (2048*u.pixel, 2048*u.pixel), 'superpixel': 4},
+                        'source': 'STEREO_B', 'instrument': 'SECCHI', 'detector': 'EUVI'}
+
+imager_dict['COR1A'] = {'fido': (a.Source('STEREO_A'), a.Detector.cor1),
+                        'process': {'dimensions': (512*u.pixel, 512*u.pixel)},
+                        'source': 'STEREO_A', 'instrument': 'SECCHI', 'detector': 'COR1'}
+
+imager_dict['COR1B'] = {'fido': (a.Source('STEREO_B'), a.Detector.cor1),
+                        'process': {'dimensions': (512*u.pixel, 512*u.pixel)},
+                        'source': 'STEREO_B', 'instrument': 'SECCHI', 'detector': 'COR1'}
+
+imager_dict['HI1A'] = {'fido': (a.Source('STEREO_A'), a.Detector.hi1),
+                       'process': {'dimensions': (1024*u.pixel, 1024*u.pixel), 'superpixel': 2},
+                       'source': 'STEREO_A', 'instrument': 'SECCHI', 'detector': 'HI1'}
+
+imager_dict['HI1B'] = {'fido': (a.Source('STEREO_B'), a.Detector.hi1),
+                       'process': {'dimensions': (1024*u.pixel, 1024*u.pixel), 'superpixel': 2},
+                       'source': 'STEREO_B', 'instrument': 'SECCHI', 'detector': 'HI1'}
+
+imager_dict['HI2A'] = {'fido': (a.Source('STEREO_A'), a.Detector.hi2),
+                       'process': {'dimensions': (1024*u.pixel, 1024*u.pixel), 'superpixel': 2},
+                       'source': 'STEREO_A', 'instrument': 'SECCHI', 'detector': 'HI2'}
+
+imager_dict['HI2B'] = {'fido': (a.Source('STEREO_B'), a.Detector.hi2),
+                       'process': {'dimensions': (1024*u.pixel, 1024*u.pixel), 'superpixel': 2},
+                       'source': 'STEREO_B', 'instrument': 'SECCHI', 'detector': 'HI2'}

{pythea-0.11.0 → pythea-0.12.0}/PyThea/data/sample_data.py

@@ -30,6 +30,6 @@ 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',
+        'FLX1p0D20211028T153500MEllipsoid.json': 'sha256:34fced8530875110117ba27a73541d3acd0c90bc8fca99367c1ec4cdfc05ce86',
     },
 )

{pythea-0.11.0 → pythea-0.12.0}/PyThea/sunpy_dev/map/maputils.py

@@ -8,6 +8,7 @@ import warnings
 import astropy.units as u
 import numpy as np
 import sunpy.map
+from sunpy.map.mapsequence import MapSequence
 
 import PyThea.sunpy_dev.extern.sunkit_instruments.aia.utils  # noqa
 import PyThea.sunpy_dev.extern.sunkit_instruments.lasco.utils  # noqa
@@ -47,7 +48,7 @@ def maps_sequence_processing(map_sequence, **kwargs):
 
     smap = []
     if seq_type == 'Running Diff.':
-        for i in range(1+diff_num, len(map_sequence)):
+        for i in range(diff_num, len(map_sequence)):
             smap_diff = difference_maps(map_sequence[i], map_sequence[i-diff_num])
             smap.append(smap_diff)
     if seq_type == 'Base Diff.':
@@ -151,7 +152,11 @@ 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:
-        sequence_final = sunpy.map.Map(map_sequence, sequence=True)
+        if isinstance(map_sequence, MapSequence):
+            return map_sequence
+        else:
+            sequence_final = sunpy.map.Map(map_sequence, sequence=True)
+
     else:
         sequence_final = []
 

{pythea-0.11.0 → pythea-0.12.0}/PyThea/test/figure_hashes.json

@@ -2,5 +2,6 @@
   "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.test.test_figures.test_ellipsoid_on_STEREO_COR2_three_planets": "231d5635f57c4d66556674a83f6cbcef7dc94b51846e977c4c2dc3dc244096ac",
+  "PyThea.test.test_figures.test_kinematics_figure": "83e060de53b57e9d34fe50111ba60a44f7c7c7b20faae9a4381654ef1c9ea72d"
 }

{pythea-0.11.0 → pythea-0.12.0}/PyThea/test/test_figures.py

@@ -5,9 +5,12 @@ 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.data.sample_data import (aia_sample_data,
+                                     json_fitting_file_sample_data,
+                                     stereo_sample_data)
 from PyThea.geometrical_models import ellipsoid
 from PyThea.sunpy_dev.map.maputils import prepare_maps
+from PyThea.utils import model_fittings, plot_fitting_model
 
 solar_system_ephemeris.set('de432s')
 
@@ -167,3 +170,27 @@ def test_ellipsoid_on_STEREO_COR2_three_planets():
     fig.subplots_adjust(hspace=0.5, wspace=0.35)
 
     return fig
+
+
+@pytest.mark.mpl_image_compare()
+def test_kinematics_figure():
+    json_fitting_file = json_fitting_file_sample_data.fetch('FLX1p0D20211028T153500MEllipsoid.json')
+    model_fittings_class = model_fittings.load_from_json(json_fitting_file)
+
+    fit_method = {'type': 'polynomial', 'order': 2}
+
+    fig, (ax1, ax2, ax3) = plt.subplots(1, 3, figsize=(18, 5), tight_layout=True)
+
+    fig, ax1 = plot_fitting_model(model_fittings_class,
+                                  fit_args=fit_method,
+                                  plt_type='HeightT',
+                                  fig=fig, axis=ax1)
+    fig, ax2 = plot_fitting_model(model_fittings_class,
+                                  fit_args=fit_method,
+                                  plt_type='SpeedT',
+                                  fig=fig, axis=ax2)
+    fig, ax3 = plot_fitting_model(model_fittings_class,
+                                  fit_args=fit_method,
+                                  plt_type='AccelerationT',
+                                  fig=fig, axis=ax3)
+    return fig

{pythea-0.11.0 → pythea-0.12.0}/PyThea/test/test_remote_clients.py

@@ -68,7 +68,7 @@ def test_vso_search(imager):
     """
     Tests that the Fido.search returns always the same number of files from VSO.
     """
-    file_num = {'AIA': [60, 61],
+    file_num = {'AIA-193': [60, 61], 'AIA-211': [60, 61],
                 'LC2': [5], 'LC3': [5],
                 'COR2A': [7], 'COR2B': [7],
                 'EUVIA': [11], 'EUVIB': [11],
@@ -79,7 +79,7 @@ def test_vso_search(imager):
     for query in [a.Time('2011/01/01 00:00:00', '2011/01/01 01:00:00'),
                   a.Time('2012/01/01 00:00:00', '2012/01/01 01:00:00'),
                   a.Time('2013/01/01 00:00:00', '2013/01/01 01:00:00'), ]:
-        args = imager_dict[imager][0]
+        args = imager_dict[imager]['fido']
         result = Fido.search(query, *args)
 
         assert len(result) == 1

{pythea-0.11.0 → pythea-0.12.0}/PyThea/utils.py

@@ -174,15 +174,32 @@ def download_fits(timerange, imager):
     '''
     Downloads the imaging data (fits files) from VSO
     '''
-    maps_ = []
-    args = imager_dict[imager][0]
-    result = Fido.search(timerange, *args)
+    imager_prop = imager_dict[imager]
+    result = Fido.search(timerange, *imager_prop['fido'])
     print(result)
     if result:
-        downloaded_files = Fido.fetch(result, path=f'{database_dir}'+'/data/{source}/{instrument}/'+'/{file}')
-        for file_path in downloaded_files:
+        if 'detector' in imager_prop:
+            sub_path = imager_prop['detector']
+        elif 'wavelength' in imager_prop:
+            sub_path = imager_prop['wavelength']
+        path_str = f'{database_dir}/data/{imager_prop["source"]}/{imager_prop["instrument"]}/{sub_path}'+'/{file}'
+        downloaded_files = Fido.fetch(result, path=path_str)
+    else:
+        downloaded_files = []
+
+    return downloaded_files
+
+
+def load_fits(files):
+    '''
+    Loads the imaging data (fits files) from a list of files.
+    '''
+    maps_ = []
+    if files:
+        for file_path in files:
             try:
                 map_ = sunpy.map.Map(file_path)
+                map_.meta['fits_file'] = os.path.basename(file_path)
                 maps_.append(map_)
             except RuntimeError as err:
                 print('Handling RuntimeError error:', err)
@@ -192,7 +209,6 @@ def download_fits(timerange, imager):
                 print(f"File '{file_path}' has been removed.")
         if maps_:
             maps_ = sunpy.map.Map(maps_, sequence=True)
-
     return maps_
 
 
@@ -210,7 +226,7 @@ def maps_process(maps_dict_in, imagers_list_in, image_mode, **kwargs):
     for imager in imagers_list_in:
         if imager in maps_dict_in and maps_dict_in[imager] != []:
             if not kwargs:
-                extras = imager_dict[imager][1]
+                extras = imager_dict[imager]['process']
             else:
                 if imager in kwargs:
                     extras = kwargs[imager]
@@ -277,6 +293,14 @@ class model_fittings:
                             the old file with the new one. This will not alter your fittings.')
             kinematics = {'fit_method': {'type': 'polynomial', 'order': 1}}
 
+        if fitting['version'] <= '0.11.0':
+            # In version >0.11.0 more AIA channels added so this will update the fitting files
+            # prodused at earlier versions by replasing the imager values from "AIA" to "AIA-193".
+            parameters['imager'] = parameters['imager'].replace('AIA', 'AIA-193')
+            # In version >0.11.0 the fits file name is added to the single fits
+            if 'fits_file' not in parameters.columns:
+                parameters['fits_file'] = ''
+
         model_fittings_class = model_fittings(fitting['event_selected'],
                                               fitting['date_process'],
                                               fitting['geometrical_model']['type'],
@@ -315,11 +339,15 @@ class model_fittings:
             return json.dumps(model_dict, indent=' ')
 
 
-def plot_fitting_model(model, fit_args, plt_type='HeightT'):
+def plot_fitting_model(model, fit_args, plt_type='HeightT', fig=None, axis=None):
     '''
     Plot the height(speed)--time evolution of the fitting parameters.
     '''
     palete = sns.color_palette('deep')
+
+    Rs2km = (1 * u.R_sun).to_value(u.km)
+    sec = 24*60*60
+
     parameters = {
         'Spheroid':
             {'height': ['+', '', palete[3], 'h-apex'],
@@ -335,9 +363,14 @@ def plot_fitting_model(model, fit_args, plt_type='HeightT'):
              'rapex': ['x', '', palete[0], 'r-apex'],
              },
     }
+
     parameters = parameters[model.geometrical_model]
-    # Height vs time
-    fig, axis = plt.subplots(figsize=(5.5, 5.5), tight_layout=True)
+
+    if fig is None and axis is None:
+        fig, axis = plt.subplots(figsize=(5.5, 5.5), tight_layout=True)
+    else:
+        fig, axis = fig, axis
+
     if plt_type == 'HeightT':
         for p in parameters.keys():
             axis.plot(model.parameters.index,
@@ -345,7 +378,7 @@ def plot_fitting_model(model, fit_args, plt_type='HeightT'):
                       marker=parameters[p][0],
                       linestyle=parameters[p][1],
                       color=parameters[p][2],
-                      label=parameters[p][3])  # label='fit: a=%5.3f, b=%5.3f, c=%5.3f' % tuple(popt)
+                      label=parameters[p][3])
             if len(model.parameters[p])-1 > fit_args['order']:
                 # How to get confidence intervals from curve_fit?
                 fit = parameter_fit(model.parameters.index, model.parameters[p], fit_args)
@@ -359,26 +392,45 @@ def plot_fitting_model(model, fit_args, plt_type='HeightT'):
                 axis.plot(model.parameters.index, model.parameters[p], '--', color=parameters[p][2])
         ylabel = 'Height of apex and length of flanks [Rsun]'
         axis.set_ylim(bottom=0)
-    elif plt_type == 'SpeedT':
+    elif plt_type in ('SpeedT', 'AccelerationT'):
+        gradient_power = {'SpeedT': 1, 'AccelerationT': 2}
+        const = {'SpeedT': Rs2km/sec, 'AccelerationT': Rs2km/sec**2}
         for p in parameters.keys():
-            if len(model.parameters[p])-1 > fit_args['order']:
+            if len(model.parameters[p])-gradient_power[plt_type] > fit_args['order']:
                 # How to get confidence intervals from curve_fit?
                 fit = parameter_fit(model.parameters.index, model.parameters[p], fit_args)
-                Rs2km = (1 * u.R_sun).to_value(u.km)
-                sec = 24*60*60
-                speed_best_fit = (Rs2km/sec) * np.gradient(fit['best_fit_y'], fit['best_fit_x_num'])
-                speed_bound_upper = (Rs2km/sec) * np.gradient(fit['sigma_bounds']['up'], fit['best_fit_x_num'])
-                speed_bound_lower = (Rs2km/sec) * np.gradient(fit['sigma_bounds']['low'], fit['best_fit_x_num'])
-                axis.plot(fit['best_fit_x'], speed_best_fit, '-', color=parameters[p][2], label=parameters[p][3])
-                axis.fill_between(fit['best_fit_x'], speed_bound_lower, speed_bound_upper,
+                if plt_type == 'SpeedT':
+                    best_fit = const[plt_type] * np.gradient(fit['best_fit_y'], fit['best_fit_x_num'])
+                    upper_bound = const[plt_type] * np.gradient(fit['sigma_bounds']['up'], fit['best_fit_x_num'])
+                    lower_bound = const[plt_type] * np.gradient(fit['sigma_bounds']['low'], fit['best_fit_x_num'])
+                    if fit_args['type'] == 'spline':
+                        axis.fill_between(fit['best_fit_x'], const[plt_type] * fit['sigv_bounds']['dlow'], const[plt_type] * fit['sigv_bounds']['dup'],
+                                          color=parameters[p][2], alpha=0.05)
+                    ylabel = 'Speed [km/s]'
+                elif plt_type == 'AccelerationT':
+                    best_fit = const[plt_type] * np.gradient(np.gradient(fit['best_fit_y'], fit['best_fit_x_num'], edge_order=2), fit['best_fit_x_num'], edge_order=2)
+                    upper_bound = const[plt_type] * np.gradient(np.gradient(fit['sigma_bounds']['up'], fit['best_fit_x_num'], edge_order=2), fit['best_fit_x_num'], edge_order=2)
+                    lower_bound = const[plt_type] * np.gradient(np.gradient(fit['sigma_bounds']['low'], fit['best_fit_x_num'], edge_order=2), fit['best_fit_x_num'], edge_order=2)
+                    if fit_args['type'] == 'spline':
+                        axis.fill_between(fit['best_fit_x'], const[plt_type] * fit['sigv_bounds']['ddlow'], const[plt_type] * fit['sigv_bounds']['ddup'],
+                                          color=parameters[p][2], alpha=0.05)
+                    ylabel = 'Acceleration [km/s$^2$]'
+
+                axis.plot(fit['best_fit_x'], best_fit, '-', color=parameters[p][2], label=parameters[p][3])
+                axis.fill_between(fit['best_fit_x'], lower_bound, upper_bound,
                                   color=parameters[p][2], alpha=0.20)
-                if fit_args['type'] == 'spline':
-                    axis.fill_between(fit['best_fit_x'], (Rs2km/sec) * fit['sigv_bounds']['dlow'], (Rs2km/sec) * fit['sigv_bounds']['dup'],
-                                      color=parameters[p][2], alpha=0.05)
+
             else:
-                pass
-        ylabel = 'Speed [km/s]'
+                ylabel = ' '
+                axis.text(0.5, 0.5, f'Not enough points for \n fitting with order {fit_args["order"]}.',
+                          transform=axis.transAxes,
+                          fontsize=20, color='gray', alpha=0.5,
+                          ha='center', va='center', rotation=30)
+                break
+
+    if plt_type != 'AccelerationT':
         axis.set_ylim(bottom=0)
+
     if plt_type == 'LongT' or plt_type == 'LatT':
         parameters = {'LongT': ['hgln', '+', palete[3], 'Longitude'],
                       'LatT': ['hglt', '+', palete[2], 'Latitude']}
@@ -411,8 +463,16 @@ def plot_fitting_model(model, fit_args, plt_type='HeightT'):
     axis.xaxis.set_major_formatter(formatter)
     axis.minorticks_on()
     xlim = axis.get_xlim()
-    if xlim[1] - xlim[0] <= 0.5:
-        axis.xaxis.set_minor_locator(mdates.MinuteLocator(byminute=[0, 10, 20, 30, 40, 50]))
+
+    hour_threshold = 24 * (xlim[1] - xlim[0])
+
+    if hour_threshold <= 2:
+        axis.xaxis.set_minor_locator(mdates.MinuteLocator(byminute=np.arange(0, 61, 1)))
+    elif hour_threshold <= 6:
+        axis.xaxis.set_minor_locator(mdates.MinuteLocator(byminute=np.arange(0, 61, 5)))
+    else:
+        axis.xaxis.set_minor_locator(mdates.HourLocator(byhour=np.arange(0, 25, 1)))
+
     fig.autofmt_xdate(bottom=0, rotation=0, ha='center')
     axis.legend(loc='lower right')
 
@@ -453,13 +513,17 @@ def parameter_fit(x, y, fit_args):
         sigma_bound_up = best_fit + sigma
         sigma_bound_low = best_fit - sigma
 
-        sv_bound_up, sv_bound_low, sv_bound_dup, sv_bound_dlow = best_fit, best_fit, np.gradient(best_fit, xxx), np.gradient(best_fit, xxx)
+        sv_bound_up, sv_bound_low, sv_bound_dup, sv_bound_dlow, sv_bound_ddup, sv_bound_ddlow = \
+            best_fit, best_fit, np.gradient(best_fit, xxx), np.gradient(best_fit, xxx), \
+            np.gradient(np.gradient(best_fit, xxx)), np.gradient(np.gradient(best_fit, xxx))
         for i in range(2, 100):
             spl = UnivariateSpline(xx, y, s=i/100, k=fit_args['order'])
             sv_bound_up = np.maximum(sv_bound_up, spl(xxx))
             sv_bound_low = np.minimum(sv_bound_low, spl(xxx))
             sv_bound_dup = np.maximum(sv_bound_dup, np.gradient(spl(xxx), xxx))
             sv_bound_dlow = np.minimum(sv_bound_dlow, np.gradient(spl(xxx), xxx))
+            sv_bound_ddup = np.maximum(sv_bound_ddup, np.gradient(np.gradient(spl(xxx), xxx)))
+            sv_bound_ddlow = np.minimum(sv_bound_ddlow, np.gradient(np.gradient(spl(xxx), xxx)))
 
         fitting = {'spl': spl,
                    'sigma': sigma,
@@ -471,7 +535,9 @@ def parameter_fit(x, y, fit_args):
                    'sigv_bounds': {'up': sv_bound_up,
                                    'low': sv_bound_low,
                                    'dup': sv_bound_dup,
-                                   'dlow': sv_bound_dlow},
+                                   'dlow': sv_bound_dlow,
+                                   'ddup': sv_bound_ddup,
+                                   'ddlow': sv_bound_ddlow},
                    }
     elif fit_args['type'] == 'custom':
         expression = fit_args['expression']  # 'a * exp(-b * x) + c'

{pythea-0.11.0 → pythea-0.12.0/PyThea.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyThea
-Version: 0.11.0
+Version: 0.12.0
 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
@@ -35,7 +35,6 @@ Requires-Dist: matplotlib
 Requires-Dist: seaborn
 Requires-Dist: streamlit
 Requires-Dist: Pillow
-Requires-Dist: stqdm
 Requires-Dist: lxml
 Requires-Dist: zeep
 Requires-Dist: drms
@@ -63,8 +62,8 @@ We recommend, creating a virtual environment for _PyThea_ and installing the pac
 If you use Anaconda or Miniconda (which we also recommend) you can create a virtual environment using ```conda``` and then install _PyThea_ using from PyPI using ```pip```. In the terminal do the following:
 
 ```python
-# Create a virtual environment. Use python=3.8 or 3.9
-conda create --name PyThea python=3.9
+# Create a virtual environment. Use python>3.9
+conda create --name PyThea python=3.10
 
 # Activate the environment
 conda activate PyThea
@@ -138,7 +137,7 @@ If there is an error when running ```PyThea streamlit``` then you can manually r
 
 ## 📙 Usage
 
-Complete documentation of the _PyThea_ is under construction.
+Complete documentation of the _PyThea_ can be found in [https://www.pythea.org/](https://www.pythea.org/).
 
 ## 📦 Useful Python packages
 

{pythea-0.11.0 → pythea-0.12.0}/PyThea.egg-info/SOURCES.txt

@@ -1,3 +1,4 @@
+.readthedocs.yaml
 CHANGELOG.md
 LICENSE.md
 MANIFEST.in

{pythea-0.11.0 → pythea-0.12.0}/PyThea.egg-info/requires.txt

@@ -13,7 +13,6 @@ matplotlib
 seaborn
 streamlit
 Pillow
-stqdm
 lxml
 zeep
 drms

{pythea-0.11.0 → pythea-0.12.0}/README.md

@@ -22,8 +22,8 @@ We recommend, creating a virtual environment for _PyThea_ and installing the pac
 If you use Anaconda or Miniconda (which we also recommend) you can create a virtual environment using ```conda``` and then install _PyThea_ using from PyPI using ```pip```. In the terminal do the following:
 
 ```python
-# Create a virtual environment. Use python=3.8 or 3.9
-conda create --name PyThea python=3.9
+# Create a virtual environment. Use python>3.9
+conda create --name PyThea python=3.10
 
 # Activate the environment
 conda activate PyThea
@@ -97,7 +97,7 @@ If there is an error when running ```PyThea streamlit``` then you can manually r
 
 ## 📙 Usage
 
-Complete documentation of the _PyThea_ can be found in (under construction)
+Complete documentation of the _PyThea_ can be found in [https://www.pythea.org/](https://www.pythea.org/).
 
 ## 📦 Useful Python packages
 

{pythea-0.11.0 → pythea-0.12.0}/README_pypi.md

@@ -16,8 +16,8 @@ We recommend, creating a virtual environment for _PyThea_ and installing the pac
 If you use Anaconda or Miniconda (which we also recommend) you can create a virtual environment using ```conda``` and then install _PyThea_ using from PyPI using ```pip```. In the terminal do the following:
 
 ```python
-# Create a virtual environment. Use python=3.8 or 3.9
-conda create --name PyThea python=3.9
+# Create a virtual environment. Use python>3.9
+conda create --name PyThea python=3.10
 
 # Activate the environment
 conda activate PyThea
@@ -91,7 +91,7 @@ If there is an error when running ```PyThea streamlit``` then you can manually r
 
 ## 📙 Usage
 
-Complete documentation of the _PyThea_ is under construction.
+Complete documentation of the _PyThea_ can be found in [https://www.pythea.org/](https://www.pythea.org/).
 
 ## 📦 Useful Python packages
 

{pythea-0.11.0 → pythea-0.12.0}/environment.yml

@@ -26,5 +26,4 @@ dependencies:
   - pip
   - pip:
       - pooch
-      - stqdm
       - jplephem

{pythea-0.11.0 → pythea-0.12.0}/requirements.txt

@@ -13,7 +13,6 @@ matplotlib
 seaborn
 streamlit
 Pillow
-stqdm
 lxml
 zeep
 drms

{pythea-0.11.0 → pythea-0.12.0}/setup.cfg

@@ -34,6 +34,10 @@ exclude =
 	.md,
 	PyThea/extensions/
 
+[tool:pytest]
+addopts = 
+	--ignore=docs/
+
 [egg_info]
 tag_build = 
 tag_date = 0

pythea-0.11.0/PyThea/config/selected_imagers.py

@@ -1,34 +0,0 @@
-'''
- A dictionary of the selected imagers
- How to use this:
-
-'''
-import astropy.units as u
-from sunpy.net import attrs as a
-
-imager_dict = dict.fromkeys(['LC2'], [(a.Instrument.lasco, a.Detector.c2),
-                                      {'dimensions': (1024*u.pixel, 1024*u.pixel), 'polar': 'Clear', 'superpixel': 2}, 'LASCO-C2'])
-imager_dict.update(dict.fromkeys(['LC3'], [(a.Instrument.lasco, a.Detector.c3),
-                                           {'dimensions': (1024*u.pixel, 1024*u.pixel), 'polar': 'Clear', 'superpixel': 2}, 'LASCO-C3']))
-imager_dict.update(dict.fromkeys(['AIA'], [(a.Instrument.aia, a.Wavelength(19.3 * u.nm), a.Sample(1*u.minute)),
-                                           {'dimensions': (4096*u.pixel, 4096*u.pixel), 'superpixel': 8, 'exposure': 1.90}, 'SDO-AIA']))
-imager_dict.update(dict.fromkeys(['COR2A'], [(a.Source('STEREO_A'), a.Detector.cor2),
-                                             {'dimensions': (2048*u.pixel, 2048*u.pixel), 'polar': 1001, 'superpixel': 4}, 'STA-COR2']))
-imager_dict.update(dict.fromkeys(['COR2B'], [(a.Source('STEREO_B'), a.Detector.cor2),
-                                             {'dimensions': (2048*u.pixel, 2048*u.pixel), 'polar': 1001, 'superpixel': 4}, 'STB-COR2']))
-imager_dict.update(dict.fromkeys(['EUVIA'], [(a.Source('STEREO_A'), a.Detector.euvi, a.Wavelength(19.5 * u.nm)),
-                                             {'dimensions': (2048*u.pixel, 2048*u.pixel), 'superpixel': 4}, 'STA-EUVI']))
-imager_dict.update(dict.fromkeys(['EUVIB'], [(a.Source('STEREO_B'), a.Detector.euvi, a.Wavelength(19.5 * u.nm)),
-                                             {'dimensions': (2048*u.pixel, 2048*u.pixel), 'superpixel': 4}, 'STB-EUVI']))
-imager_dict.update(dict.fromkeys(['COR1A'], [(a.Source('STEREO_A'), a.Detector.cor1),
-                                             {'dimensions': (512*u.pixel, 512*u.pixel)}, 'STA-COR1']))  # 'polar':0
-imager_dict.update(dict.fromkeys(['COR1B'], [(a.Source('STEREO_B'), a.Detector.cor1),
-                                             {'dimensions': (512*u.pixel, 512*u.pixel)}, 'STB-COR1']))  # 'polar':0
-imager_dict.update(dict.fromkeys(['HI1A'], [(a.Source('STEREO_A'), a.Detector.hi1),
-                                            {'dimensions': (1024*u.pixel, 1024*u.pixel), 'superpixel': 2}, 'STA-HI1']))
-imager_dict.update(dict.fromkeys(['HI1B'], [(a.Source('STEREO_B'), a.Detector.hi1),
-                                            {'dimensions': (1024*u.pixel, 1024*u.pixel), 'superpixel': 2}, 'STB-HI1']))
-imager_dict.update(dict.fromkeys(['HI2A'], [(a.Source('STEREO_A'), a.Detector.hi2),
-                                            {'dimensions': (1024*u.pixel, 1024*u.pixel), 'superpixel': 2}, 'STA-HI2']))
-imager_dict.update(dict.fromkeys(['HI2B'], [(a.Source('STEREO_B'), a.Detector.hi2),
-                                            {'dimensions': (1024*u.pixel, 1024*u.pixel)}, 'STB-HI2']))