seppy 0.1.12__py3-none-any.whl → 0.1.14__py3-none-any.whl

seppy/tools/__init__.py

@@ -19,7 +19,7 @@ from seppy.loader.solo import epd_load
 from seppy.loader.stereo import calc_av_en_flux_HET as calc_av_en_flux_ST_HET
 from seppy.loader.stereo import calc_av_en_flux_SEPT, stereo_load
 from seppy.loader.wind import wind3dp_load
-from seppy.util import *
+from seppy.util import bepi_sixs_load, calc_av_en_flux_sixs, custom_warning, flux2series, resample_df
 
 
 # This is to get rid of this specific warning:
@@ -92,10 +92,8 @@ class Event:
         # names from the dataframe.
         self.load_all_viewing()
 
-        # JG: This is NOT enough to just check this at this position! This needs to be aborting the process if the specific combination is chosen!
-        # JG: Removed here and moved to appropriate positions.
         # # Check that the data that was loaded is valid. If not, give a warning.
-        # self.validate_data()
+        self.validate_data()
 
         # Download radio cdf files ONLY if asked to
         if self.radio_spacecraft is not None:
@@ -107,15 +105,21 @@ class Event:
         Provide an error msg if this object is initialized with a combination that yields invalid data products.
         """
 
-        # Data products for SolO/STEP before 22 Oct 2021 are no reliable for non-Pixel Averaged data
+        # SolO/STEP data before 22 Oct 2021 is not supported yet for non-'Pixel averaged' viewing
+        warn_mess_step_pixels_old = "SolO/STEP data is not included yet for individual Pixels for dates preceding Oct 22, 2021. Only 'Pixel averaged' is supported."
         if self.spacecraft == "solo" and self.sensor == "step":
             if self.start_date < pd.to_datetime("2021-10-22").date():
                 if not self.viewing == 'Pixel averaged':
-                    raise Warning("WARNING! SolO/STEP data is not included yet for individual Pixels for dates preceding Oct 22, 2021.")
+                    # when 'viewing' is undefined, only give a warning; if it's wrong defined, abort with warning
+                    if not self.viewing:
+                        # warnings.warn(message=warn_mess_step_pixels_old)
+                        custom_warning(message=warn_mess_step_pixels_old)
+                    else:
+                        raise Warning(warn_mess_step_pixels_old)
 
         # Electron data for SolO/STEP is removed for now (Feb 2024, JG)
         if self.spacecraft == "solo" and self.sensor == "step" and self.species.lower()[0] == 'e':
-            raise Warning("WARNING! SolO/STEP electron data is not implemented yet!")
+            raise Warning("SolO/STEP electron data is not implemented yet!")
 
     def update_onset_attributes(self, flux_series, onset_stats, onset_found, peak_flux, peak_time, fig, bg_mean):
         """
@@ -269,6 +273,10 @@ class Event:
                 meta = {"E5": "0.45 - 0.50 MeV",
                         "E15": "0.70 - 1.10 MeV"}
 
+                # TODO:
+                # - add resample_df here?
+                # - add pos_timestamp here
+
                 self.update_viewing(viewing)
                 return df, meta
 
@@ -341,7 +349,8 @@ class Event:
             df, meta = bepi_sixs_load(startdate=self.start_date,
                                       enddate=self.end_date,
                                       side=viewing,
-                                      path=self.data_path)
+                                      path=self.data_path,
+                                      pos_timestamp='center')
             df_i = df[[f"P{i}" for i in range(1, 10)]]
             df_e = df[[f"E{i}" for i in range(1, 8)]]
             return df_i, df_e, meta
@@ -472,7 +481,10 @@ class Event:
         self.update_viewing(viewing)
 
         if self.spacecraft == 'solo':
-            if viewing == 'sun':
+            if not viewing:
+                raise Exception("For this operation, the instrument's 'viewing' direction must be defined in the call of 'Event'!")
+
+            elif viewing == 'sun':
 
                 self.current_df_i = self.df_i_sun
                 self.current_df_e = self.df_e_sun
@@ -1094,7 +1106,7 @@ class Event:
 
             if (self.spacecraft == 'solo' or self.spacecraft == 'psp'):
                 plabel = AnchoredText(f"Onset time: {str(onset_stats[-1])[:19]}\n"
-                                      f"Peak flux: {df_flux_peak['flux'][0]:.2E}",
+                                      f"Peak flux: {df_flux_peak['flux'].iloc[0]:.2E}",
                                       prop=dict(size=13), frameon=True,
                                       loc=(4))
             # if(self.spacecraft[:2].lower() == 'st' or self.spacecraft == 'soho' or self.spacecraft == 'wind'):
@@ -1178,8 +1190,9 @@ class Event:
             # Check if background is separated from plot range by over a day, issue a warning if so, but don't
             if (background_range[0] < xlim[0] - datetime.timedelta(days=1) and background_range[0] < xlim[1] - datetime.timedelta(days=1)) or \
                (background_range[1] > xlim[0] + datetime.timedelta(days=1) and background_range[1] > xlim[1] + datetime.timedelta(days=1)):
-                background_warning = "NOTICE that your background_range is separated from plot_range by over a day.\nIf this was intentional you may ignore this warning."
-                warnings.warn(message=background_warning)
+                background_warning = "Your background_range is separated from plot_range by over a day. If this was intentional you may ignore this warning."
+                # warnings.warn(message=background_warning)
+                custom_warning(message=background_warning)
 
         if (self.spacecraft[:2].lower() == 'st' and self.sensor == 'sept') \
                 or (self.spacecraft.lower() == 'psp' and self.sensor.startswith('isois')) \
@@ -1503,6 +1516,8 @@ class Event:
             return yaxis_bin_boundaries * y_multiplier
 
         def combine_grids_and_ybins(grid, grid1, y_arr, y_arr1):
+            # TODO: Which bin exactly is removed here? HET? EPT? (JG)
+
             # solo/het lowest electron channel partially overlaps with ept highest channel -> erase the "extra" bin where overlapping hapens
             if self.spacecraft == "solo" and (self.sensor == "het" or other.sensor == "het") and self.species in ("electrons", "electron", 'e'):
 
@@ -1545,6 +1560,8 @@ class Event:
         if self.spacecraft == "solo":
 
             if instrument == "step":
+                # custom_warning('The lower STEP energy channels are partly overlapping, which is not correctly implemented at the moment!')
+                raise Warning('SolO/STEP is not implemented yet in the dynamic spectrum tool!')
 
                 # All viewings are contained in the same dataframe, choose the pixel (viewing) here
                 pixel = self.viewing.split(' ')[1]
@@ -1599,8 +1616,13 @@ class Event:
                 s_identifier = "protons"
             if instrument.lower() == "ephin":
                 particle_data = self.current_df_e
+                # Here drop the E300 channel altogether from the dataframe if the data is produced after Oct 4, 2017,
+                # for it contains no valid data. Keyword axis==1 refers to the columns axis.
+                if self.start_date > pd.to_datetime("2017-10-04").date():
+                    particle_data = particle_data.drop("E300", axis=1)
+
                 s_identifier = "electrons"
-                raise Warning('SOHO/EPHIN is not implemented yet in the dynamic spectrum tool!')
+                # raise Warning('SOHO/EPHIN is not implemented yet in the dynamic spectrum tool!')
 
         if spacecraft == "psp":
             if instrument.lower() == "isois-epihi":
@@ -2285,11 +2307,11 @@ class Event:
                 energy_ranges = self.current_energies["channels_dict_df_p"]["ch_strings"].values
             if self.sensor.lower() == "ephin":
                 # Choose only the first 4 channels (E150, E300, E1300 and E3000)
-                # This are the only electron channels (rest p and He), and we
+                # These are the only electron channels (rest are p and He), and we
                 # use only electron data here.
                 energy_ranges = [val for val in self.current_energies.values()][:4]
             if self.sensor.lower() in ("ephin-5", "ephin-15"):
-                energy_ranges = [value for key, value in self.current_energies.items()]
+                energy_ranges = [value for _, value in self.current_energies.items()]
 
         if self.spacecraft == "psp":
             energy_dict = self.meta
@@ -2442,9 +2464,13 @@ class Event:
         from IPython.display import display
 
         # This has to be run first, otherwise self.current_df does not exist
-        # Note that PSP will by default have its viewing=="all", which does not yield proper dataframes
-        if self.viewing != "all":
-            self.choose_data(self.viewing)
+        # Note that PSP will by default have its viewing=='all', which does not yield proper dataframes
+        if self.viewing != 'all':
+            if self.spacecraft == 'solo' and not self.viewing:
+                raise Warning("For this operation the instrument's 'viewing' direction must be defined in the call of 'Event'! Please define and re-run.")
+                return
+            else:
+                self.choose_data(self.viewing)
         else:
             if self.sensor == "isois-epihi":
                 # Just choose data with either ´A´ or ´B´. I'm not sure if there's a difference
@@ -2521,6 +2547,7 @@ class Event:
                                'display.max_columns', None,
                                ):
             display(df)
+        return
 
     def save_and_update_rcparams(self, plotting_function: str):
         """

seppy/tools/widgets.py

@@ -61,7 +61,7 @@ radio_dict = {
     "None": None,
     "STEREO-A": ("ahead", "STEREO-A"),
     "STEREO-B": ("behind", "STEREO-B"),
-    "WIND (Coming soon!)": ("wind", "WIND")
+    # "WIND (Coming soon!)": ("wind", "WIND")  # TODO: re-add when supported!
 }
 
 # Drop-downs for dynamic particle spectrum:

seppy/util/__init__.py

@@ -1,16 +1,33 @@
 
-import numpy as np
-import pandas as pd
+import datetime
+import warnings
+
 import astropy.constants as const
 import astropy.units as u
+import numpy as np
+import pandas as pd
 import sunpy.sun.constants as sconst
-
-import datetime
 from sunpy.coordinates import get_horizons_coord
 
 # Utilities toolbox, contains helpful functions
 
 
+def custom_formatwarning(message, *args, **kwargs):
+    # ignore everything except the message
+    FAIL = '\033[91m'
+    ENDC = '\033[0m'
+    BOLD = "\033[1m"
+    return BOLD+FAIL+'WARNING: '+ENDC+ str(message) + '\n'
+
+
+def custom_warning(message):
+    formatwarning_orig = warnings.formatwarning
+    warnings.formatwarning = custom_formatwarning
+    warnings.warn(message)
+    warnings.formatwarning = formatwarning_orig
+    return
+
+
 def resample_df(df, resample, pos_timestamp="center", origin="start"):
     """
     Resamples a Pandas Dataframe or Series to a new frequency.
@@ -25,8 +42,9 @@ def resample_df(df, resample, pos_timestamp="center", origin="start"):
             Controls if the timestamp is at the center of the time bin, or at
             the start of it
     origin : str, default 'start'
-            Controls if the origin of resampling is at the start of the day
-            (midnight) or at the first entry of the input dataframe/series
+            Controls if the origin of resampling is at the first entry of the
+            input dataframe/series (‘start’), or at the start of the day
+            (‘start_day’)
 
     Returns:
     ----------
@@ -75,7 +93,7 @@ def flux2series(flux, dates, cadence=None):
     return flux_series
 
 
-def bepicolombo_sixs_stack(path, date, side):
+def bepicolombo_sixs_stack(path, date, side, pos_timestamp='center'):
     # side is the index of the file here
     try:
         try:
@@ -90,6 +108,26 @@ def bepicolombo_sixs_stack(path, date, side):
         times = [t.tz_convert(None) for t in times]
         df.index = np.array(times)
         df = df.drop(columns=['TimeUTC'])
+
+        # TODO: (as it's not really nicely done so far)
+        # careful!
+        # adjusting the position of the timestamp manually.
+        # requires knowledge of the original time resolution and timestamp position!
+        if type(date) is datetime.datetime:
+            change_date = pd.Timestamp(2022, 8, 29)
+        elif type(date) is datetime.date:
+            change_date = pd.Timestamp(2022, 8, 29).date()
+        if date < change_date:
+            cadence = 8
+        elif date >= change_date:
+            cadence = 24
+        #
+        if pos_timestamp == 'center':
+            df.index = df.index+pd.Timedelta(f'{cadence/2}s')
+            # warnings.warn("Assuming cadence of 8s before 2022-08-29 and 24s after!")
+            custom_warning("Assuming cadence of 8s before 2022-08-29 and 24s after!")
+        elif pos_timestamp == 'start':
+            pass
     except FileNotFoundError:
         print(f'Unable to open {filename}')
         df = pd.DataFrame()
@@ -97,14 +135,14 @@ def bepicolombo_sixs_stack(path, date, side):
     return df, filename
 
 
-def bepi_sixs_load(startdate, enddate, side, path):
+def bepi_sixs_load(startdate, enddate, side, path, pos_timestamp='center'):
     dates = pd.date_range(startdate, enddate)
 
     # read files into Pandas dataframes:
-    df, file = bepicolombo_sixs_stack(path, startdate, side=side)
+    df, file = bepicolombo_sixs_stack(path, startdate, side=side, pos_timestamp=pos_timestamp)
     if len(dates) > 1:
         for date in dates[1:]:
-            t_df, file = bepicolombo_sixs_stack(path, date.date(), side=side)
+            t_df, file = bepicolombo_sixs_stack(path, date.date(), side=side, pos_timestamp=pos_timestamp)
             df = pd.concat([df, t_df])
 
     channels_dict = {"Energy_Bin_str": {'E1': '71 keV', 'E2': '106 keV', 'E3': '169 keV', 'E4': '280 keV', 'E5': '960 keV', 'E6': '2240 keV', 'E7': '8170 keV',
@@ -146,6 +184,9 @@ def calc_av_en_flux_sixs(df, channel, species):
     GEOMFACTOR_PROT_COMB89 = 3.34
     GEOMFACTOR_ELEC_COMB56 = 0.0972
 
+    if type(channel) is list and len(channel) == 1:
+        channel = channel[0]
+
     if species in ['p', 'protons']:
         if channel == [8, 9]:
             countrate = df['P8'] * GEOMFACTOR_PROT8 + df['P9'] * GEOMFACTOR_PROT9
@@ -313,7 +354,7 @@ def speed2energy(species, speed):
     mass_dict = {'p': const.m_p, 'e': const.m_e}
     gamma = 1/np.sqrt(1-speed**2/const.c**2)
     K = (gamma-1)*mass_dict[species]*const.c**2
-    return K.to(u.MeV) 
+    return K.to(u.MeV)
 
 
 def speed2momentum(species, speed):

seppy/version.py

@@ -5,4 +5,4 @@ try:
     from setuptools_scm import get_version
     __version__ = get_version(root='..', relative_to=__file__)
 except Exception:
-    __version__ = '0.1.12'
+    __version__ = '0.1.14'

{seppy-0.1.12.dist-info → seppy-0.1.14.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: seppy
-Version: 0.1.12
+Version: 0.1.14
 Summary: SEPpy
 Home-page: https://github.com/serpentine-h2020/SEPpy
 Author: Jan Gieseler
@@ -14,34 +14,33 @@ Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering :: Physics
 Requires-Python: >=3.8
 License-File: licenses/LICENSE.rst
 Requires-Dist: astropy
+Requires-Dist: astroquery
 Requires-Dist: bs4
 Requires-Dist: cdflib
-Requires-Dist: datetime
-Requires-Dist: drms
-Requires-Dist: h5netcdf
 Requires-Dist: ipykernel
 Requires-Dist: ipywidgets
-Requires-Dist: lxml
 Requires-Dist: matplotlib
+Requires-Dist: mpl-animators>=1.0.0
 Requires-Dist: numpy
 Requires-Dist: pandas
 Requires-Dist: pooch
 Requires-Dist: requests
 Requires-Dist: solo-epd-loader
-Requires-Dist: sunpy >=4.1.0
-Requires-Dist: zeep
+Requires-Dist: sunpy>=4.1.0
 Provides-Extra: all
 Provides-Extra: docs
-Requires-Dist: sphinx ; extra == 'docs'
-Requires-Dist: sphinx-automodapi ; extra == 'docs'
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinx-automodapi; extra == "docs"
 Provides-Extra: test
-Requires-Dist: pytest ; extra == 'test'
-Requires-Dist: pytest-doctestplus ; extra == 'test'
-Requires-Dist: pytest-cov ; extra == 'test'
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-doctestplus; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
 
 seppy
 =====

seppy-0.1.14.dist-info/RECORD

@@ -0,0 +1,29 @@
+seppy/__init__.py,sha256=M8ZBbGj0r_XdNVLzaSXF38M4wyzAgUX32LXcSYh5O5A,254
+seppy/version.py,sha256=Yt0zY5AwafNxgEo2ms3qwU0OMj3CY7uImiooX_Os2jQ,346
+seppy/data/test/20230719_side0.csv,sha256=0htTQcdQydRc92bkO26lxK8tDRSeN6uov13VfsqmUFQ,72368
+seppy/data/test/20230719_side1.csv,sha256=iHCfHmOIltJatncWpns_zq3ym_-2yRu0twmDvQDbmJw,72368
+seppy/data/test/20230719_side2.csv,sha256=eYyEQX5fNDO4E57KwKN3bHs6u5-lHaAhIHt-3f20Urg,72368
+seppy/data/test/epi21106.rl2,sha256=Fhq5A5D1pKqEfV9mx6T8tjEei4HmSfmWBR0XaLJl_JI,180858
+seppy/data/test/sept_ahead_ele_sun_2006_318_1min_l2_v03.dat,sha256=ReZ7cvIcC4Z_nDJ-oJQ7lsKSziA_qlZsAG74F5n3M2o,167882
+seppy/data/test/soho_erne-hed_l2-1min_20211028_v01.cdf,sha256=RX1XX6eQevCuXqc1tTAEjPsXtlgbDeP2DsmRFVbsGwg,278505
+seppy/data/test/solo_l2_mag-rtn-normal-1-minute_20210712_v01.cdf,sha256=Tc_-3YQMVGDwJgN1td2iqTPGfCF7YwmuyYZ2G0NiSoY,59249
+seppy/data/test/sta_l1_het_20211028_v01.cdf,sha256=429TIPXSQI5heQVNqyRYLF7HUDZPByzk-xYf9IzSJ0U,215082
+seppy/data/test/wi_sfsp_3dp_00000000_v01.cdf,sha256=ifAM0FiB2tepHmlpsqbotJMyQqSB3bwpPcKD6VhukFA,30939
+seppy/data/test/wi_sfsp_3dp_20200213_v01.cdf,sha256=UiKcBPcWZkh3KIBigoZubTJ3Fw90E8p7XhbA9uW6VWk,67008
+seppy/loader/psp.py,sha256=PbxCEW-06d2I_JGIfIAqqXMU_uPdQFhmh-fUoXpzz9k,31535
+seppy/loader/soho.py,sha256=EIFKde1dGpT9yU6bU-XtTsHUCvTEkzHhdPOOMtqVrDU,20262
+seppy/loader/solo.py,sha256=Nst2ZJU2yH5NHsB6M_69ryVfzt978hbmqhxaHZJREVg,3054
+seppy/loader/stereo.py,sha256=S0_IRIFbFxLH00bSIt1uZMflmuG5dAU5sKw0w9NL9oM,24583
+seppy/loader/wind.py,sha256=3rWV_EOcY7sY69eqtCQCZxL5GxAQZuMm1-wpJJxrej8,18460
+seppy/tests/__init__.py,sha256=1D-l3TVbwIZHY78A-sB7kc4ldldX8ZaEq-Ntph51WVw,108
+seppy/tests/test_loader.py,sha256=mt52vrAeSEtJ-od4Cqt0HrscN_ykKNHklGZm8OTZjLs,7767
+seppy/tests/test_tools.py,sha256=NrKXrlgCsy9RRx2V7fUGRtB1l8N0_CXasyGjoB_lSNU,31518
+seppy/tools/__init__.py,sha256=Ge3lQ9zVRJ27aaHSet2I1wQ9tD4emVfjnn49pUGcoiY,116086
+seppy/tools/swaves.py,sha256=OcohPXLko0ik9FLyYMVkYxI75W4XzOKvQ2Ylnwi-wlQ,3139
+seppy/tools/widgets.py,sha256=atQj9vvus0UgrUV6vlPcTdjpaidnERUevOp6FUmGLSI,6820
+seppy/util/__init__.py,sha256=0J3DNmOdh9X8a-uZy0yfFe1ubFSfcF5b7K4RMSJvGHA,15705
+seppy-0.1.14.dist-info/LICENSE.rst,sha256=SxptLPCIHKdfDjyguGdC7ai6Eze-Vz_t1jdqC8h19js,1473
+seppy-0.1.14.dist-info/METADATA,sha256=adiL7bpY08aZg2c5uC_o_8j5hTlWn-8nksTv8v9KEcU,4399
+seppy-0.1.14.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
+seppy-0.1.14.dist-info/top_level.txt,sha256=G2Op1GREPmbCX81isNhYY_7ZZyLWLIm-MJC04J4Fgc4,6
+seppy-0.1.14.dist-info/RECORD,,

{seppy-0.1.12.dist-info → seppy-0.1.14.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.42.0)
+Generator: setuptools (72.2.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

seppy-0.1.12.dist-info/RECORD

@@ -1,27 +0,0 @@
-seppy/__init__.py,sha256=M8ZBbGj0r_XdNVLzaSXF38M4wyzAgUX32LXcSYh5O5A,254
-seppy/version.py,sha256=BdI0483CKw5g6ZLk-JrMdNNQTyX9GkavgloDI4wsv2Y,346
-seppy/data/test/epi21106.rl2,sha256=Fhq5A5D1pKqEfV9mx6T8tjEei4HmSfmWBR0XaLJl_JI,180858
-seppy/data/test/psp_isois-epihi_l2-het-rates60_20210531_v15.cdf,sha256=u0XcZ9SpocPwuKAmu7w2qDU_yLXxg3eyf0VXvayWlT4,401828
-seppy/data/test/sept_ahead_ele_sun_2006_318_1min_l2_v03.dat,sha256=ReZ7cvIcC4Z_nDJ-oJQ7lsKSziA_qlZsAG74F5n3M2o,167882
-seppy/data/test/soho_erne-hed_l2-1min_20211028_v01.cdf,sha256=RX1XX6eQevCuXqc1tTAEjPsXtlgbDeP2DsmRFVbsGwg,278505
-seppy/data/test/solo_l2_mag-rtn-normal-1-minute_20210712_v01.cdf,sha256=Tc_-3YQMVGDwJgN1td2iqTPGfCF7YwmuyYZ2G0NiSoY,59249
-seppy/data/test/sta_l1_het_20211028_v01.cdf,sha256=429TIPXSQI5heQVNqyRYLF7HUDZPByzk-xYf9IzSJ0U,215082
-seppy/data/test/wi_sfsp_3dp_00000000_v01.cdf,sha256=ifAM0FiB2tepHmlpsqbotJMyQqSB3bwpPcKD6VhukFA,30939
-seppy/data/test/wi_sfsp_3dp_20200213_v01.cdf,sha256=UiKcBPcWZkh3KIBigoZubTJ3Fw90E8p7XhbA9uW6VWk,67008
-seppy/loader/psp.py,sha256=PbxCEW-06d2I_JGIfIAqqXMU_uPdQFhmh-fUoXpzz9k,31535
-seppy/loader/soho.py,sha256=j3cwsrJ2orWIMD_V5_bh0SUti1B53bOgUGu64lZj7o4,19466
-seppy/loader/solo.py,sha256=Nst2ZJU2yH5NHsB6M_69ryVfzt978hbmqhxaHZJREVg,3054
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