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Merge pull request serpentine-h2020#37 from jgieseler/main
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Temporary fix cdflib<1.0 to avoid incompatibility
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@jgieseler
jgieseler authored Jun 5, 2023
2 parents 2645ee0 + 2d3e5b6 commit 3946042
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Showing 7 changed files with 154 additions and 62 deletions.
1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -39,6 +39,7 @@ pip-delete-this-directory.txt

# Unit test / coverage reports
htmlcov/
.tmp/
.tox/
.nox/
.coverage
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2 changes: 1 addition & 1 deletion requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
astropy
bs4
cdflib
cdflib < 1.0.0
datetime
drms
h5netcdf
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105 changes: 47 additions & 58 deletions seppy/tools/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,10 +27,10 @@
# cell centers, but are not monotonically increasing or decreasing. This may lead to incorrectly calculated cell edges, in which
# case, please supply explicit cell edges to pcolormesh.
# colormesh = ax.pcolormesh( time_arr, freq[::-1], data_arr[::-1], vmin = 0, vmax = 0.5*np.max(data_arr), cmap = 'inferno' )
warnings.filterwarnings(action = "ignore",
message = "The input coordinates to pcolormesh are interpreted as cell centers, but are not monotonically increasing or \
warnings.filterwarnings(action="ignore",
message="The input coordinates to pcolormesh are interpreted as cell centers, but are not monotonically increasing or \
decreasing. This may lead to incorrectly calculated cell edges, in which case, please supply explicit cell edges to pcolormesh.",
category = UserWarning)
category=UserWarning)


class Event:
Expand Down Expand Up @@ -100,7 +100,6 @@ def __init__(self, start_date, end_date, spacecraft, sensor,
from seppy.tools.swaves import get_swaves
self.radio_files = get_swaves(start_date, end_date)


def validate_data(self):
"""
Provide an error msg if this object is initialized with a combination that yields invalid data products.
Expand Down Expand Up @@ -148,7 +147,6 @@ def update_viewing(self, viewing):
except AttributeError:
self.viewing = '0' # A placeholder viewing that should not cause any trouble


# I suggest we at some point erase the arguments ´spacecraft´ and ´threshold´ due to them not being used.
# `viewing` and `autodownload` are actually the only necessary input variables for this function, the rest
# are class attributes, and should probably be cleaned up at some point
Expand All @@ -165,19 +163,19 @@ def load_data(self, spacecraft, sensor, viewing, data_level,
enddate=self.end_date,
path=self.data_path,
autodownload=autodownload)
#self.update_viewing(viewing) Why is viewing updated here?
# self.update_viewing(viewing) Why is viewing updated here?
return df_i, df_e, meta

elif self.sensor == "step":
df, meta = epd_load(sensor=sensor,
viewing="None",
level=data_level,
startdate=self.start_date,
enddate=self.end_date,
path=self.data_path,
autodownload=autodownload)

#self.update_viewing(viewing) Why is viewing updated here?
viewing="None",
level=data_level,
startdate=self.start_date,
enddate=self.end_date,
path=self.data_path,
autodownload=autodownload)

# self.update_viewing(viewing) Why is viewing updated here?
return df, meta

if self.spacecraft[:2].lower() == 'st':
Expand Down Expand Up @@ -490,7 +488,7 @@ def choose_data(self, viewing):
self.current_df_i = self.df_i_south
self.current_df_e = self.df_e_south
self.current_energies = self.energies_south

elif "Pixel" in viewing:

# All viewings are contained in the same dataframe, choose the pixel (viewing) here
Expand All @@ -504,8 +502,8 @@ def choose_data(self, viewing):
elif len(pixel) > 2:
pixel = "Avg"

self.current_df_i = self.df_step[[ col for col in self.df_step.columns if f"Magnet_{pixel}_Flux" in col]]
self.current_df_e = self.df_step[[ col for col in self.df_step.columns if f"Electron_{pixel}_Flux" in col]]
self.current_df_i = self.df_step[[col for col in self.df_step.columns if f"Magnet_{pixel}_Flux" in col]]
self.current_df_e = self.df_step[[col for col in self.df_step.columns if f"Electron_{pixel}_Flux" in col]]
self.current_energies = self.energies_step

if self.spacecraft[:2].lower() == 'st':
Expand Down Expand Up @@ -1238,14 +1236,14 @@ def find_onset(self, viewing, bg_start=None, bg_length=None, background_range=No
if self.species in ('p', 'i'):
channel_id = self.current_df_i.columns[channels[0]]
df_flux = pd.DataFrame(data={
"flux" : self.current_df_i[channel_id]
}, index = self.current_df_i.index)
"flux": self.current_df_i[channel_id]
}, index=self.current_df_i.index)

elif self.species == 'e':
channel_id = self.current_df_e.columns[channels[0]]
df_flux = pd.DataFrame(data={
"flux" : self.current_df_e[channel_id]
}, index = self.current_df_e.index)
"flux": self.current_df_e[channel_id]
}, index=self.current_df_e.index)

else:
invalid_sensor_msg = "Invalid sensor!"
Expand Down Expand Up @@ -1434,9 +1432,8 @@ def find_onset(self, viewing, bg_start=None, bg_length=None, background_range=No
# For backwards compatibility, make a copy of the `find_onset` function that is called `analyse` (which was its old name).
analyse = copy.copy(find_onset)


def dynamic_spectrum(self, view, cmap: str = 'magma', xlim: tuple = None, resample: str = None, save: bool = False,
other = None) -> None:
other=None) -> None:
"""
Shows all the different energy channels in a single 2D plot, and color codes the corresponding intensity*energy^2 by a colormap.
Expand All @@ -1463,12 +1460,11 @@ def get_yaxis_bin_boundaries(e_lows, e_highs, y_multiplier, is_solohetions):
if not is_solohetions:
return np.append(e_lows, e_highs[-1]) * y_multiplier


# Init the boundaries. For SolO/HET there are more boundaries than channels
yaxis_bin_boundaries = np.zeros(len(e_lows)+2)
yaxis_idx = 0
chooser_idx = yaxis_idx
while yaxis_idx < len(yaxis_bin_boundaries)-1: # this loop will not go to the final index of the array
while yaxis_idx < len(yaxis_bin_boundaries)-1: # this loop will not go to the final index of the array

# Set the first boundary as simply the first val of lower energy boundaries and continue
if yaxis_idx==0:
Expand All @@ -1490,40 +1486,37 @@ def get_yaxis_bin_boundaries(e_lows, e_highs, y_multiplier, is_solohetions):

yaxis_idx += 2
chooser_idx += 1

# Finally the last boundary is the final boundary of e_highs:
yaxis_bin_boundaries[-1] = e_highs[-1]

return yaxis_bin_boundaries * y_multiplier


def combine_grids_and_ybins(grid, grid1, y_arr, y_arr1):
# 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'):

# 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'):
grid1 = np.append(grid, grid1, axis=0)[:-1]

grid1 = np.append(grid, grid1, axis=0)[:-1]
# This deletes the first entry of y_arr1
y_arr1 = np.delete(y_arr1, 0, axis=0)
y_arr1 = np.append(y_arr, y_arr1)

# This deletes the first entry of y_arr1
y_arr1 = np.delete(y_arr1, 0, axis=0)
y_arr1 = np.append(y_arr, y_arr1)
# There is a gap between the highest solo/ept proton channel and the lowest het ion channel -> add extra row to grid
# filled with nans to compensate
elif self.spacecraft == "solo" and (self.sensor == "het" or other.sensor == "het") and self.species == 'p':

# There is a gap between the highest solo/ept proton channel and the lowest het ion channel -> add extra row to grid
# filled with nans to compensate
elif self.spacecraft == "solo" and (self.sensor == "het" or other.sensor == "het") and self.species == 'p':
nans = np.array([[np.nan for i in range(len(grid[0]))]])
grid = np.append(grid, nans, axis=0)
grid1 = np.append(grid, grid1, axis=0)[:-2]
y_arr1 = np.append(y_arr, y_arr1)

nans = np.array([[np.nan for i in range(len(grid[0]))]])
grid = np.append(grid, nans, axis=0)
grid1 = np.append(grid, grid1, axis=0)[:-2]
y_arr1 = np.append(y_arr, y_arr1)

else:
else:

grid1 = np.append(grid,grid1, axis=0)
y_arr1 = np.append(y_arr, y_arr1)

return grid1, y_arr1
grid1 = np.append(grid, grid1, axis=0)
y_arr1 = np.append(y_arr, y_arr1)

return grid1, y_arr1

# Event attributes
spacecraft = self.spacecraft.lower()
Expand Down Expand Up @@ -1552,12 +1545,12 @@ def combine_grids_and_ybins(grid, grid1, y_arr, y_arr1):
pixel = "Avg"

if species in ("electron", 'e'):
particle_data = self.df_step[[ col for col in self.df_step.columns if f"Electron_{pixel}_Flux" in col]]
particle_data = self.df_step[[col for col in self.df_step.columns if f"Electron_{pixel}_Flux" in col]]
s_identifier = "electrons"

# Step's "Magnet" channel deflects electrons -> measures all positive ions
else:
particle_data = self.df_step[[ col for col in self.df_step.columns if f"Magnet_{pixel}_Flux" in col]]
particle_data = self.df_step[[col for col in self.df_step.columns if f"Magnet_{pixel}_Flux" in col]]
s_identifier = "ions"

# EPT and HET data come in almost identical containers, they need not be differentiated
Expand Down Expand Up @@ -1633,7 +1626,7 @@ def combine_grids_and_ybins(grid, grid1, y_arr, y_arr1):
y_multiplier = 1e-6 # MeV
y_unit = "MeV"
else:
y_multiplier = 1e-6 # MeV
y_multiplier = 1e-6 # MeV
y_unit = "MeV"

# Resample only if requested
Expand Down Expand Up @@ -1767,7 +1760,6 @@ def combine_grids_and_ybins(grid, grid1, y_arr, y_arr1):
ax[DYN_SPEC_INDX].xaxis.set_major_formatter(utc_dt_format1)
# ax.xaxis.set_minor_locator(mdates.MinuteLocator(interval = 5))


# Expand the spectrum to a second instrument (for now only for solo/ept + step or het)
if other and self.sensor == "ept" and other.sensor == "het":

Expand All @@ -1785,14 +1777,13 @@ def combine_grids_and_ybins(grid, grid1, y_arr, y_arr1):
except KeyError:
particle_data1 = other.current_df_i["H_Flux"]


# Resample only if requested
if resample is not None:
particle_data1 = resample_df(df=particle_data1, resample=resample)

if xlim is None:
df1 = particle_data1[:]
#t_start, t_end = df.index[0], df.index[-1]
# t_start, t_end = df.index[0], df.index[-1]
else:
# td is added to the start and the end to avert white pixels at the end of the plot
td_str = resample if resample is not None else '0s'
Expand All @@ -1813,7 +1804,7 @@ def combine_grids_and_ybins(grid, grid1, y_arr, y_arr1):
y_arr1 = get_yaxis_bin_boundaries(e_lows1, e_highs1, y_multiplier, is_solohetions)

# Set image pixel height (length was already set before)
# For solohet+ions we do not subtract 1 here, because there is an energy gap between EPT highest channel and
# For solohet+ions we do not subtract 1 here, because there is an energy gap between EPT highest channel and
# HET lowest channel, hence requiring one "empty" bin in between
image_hei1 = len(y_arr1)+1 if is_solohetions else len(y_arr1)

Expand Down Expand Up @@ -1847,7 +1838,7 @@ def combine_grids_and_ybins(grid, grid1, y_arr, y_arr1):
maskedgrid1 = np.where(grid1 == 0, 0, 1)
maskedgrid1= np.ma.masked_where(maskedgrid1 == 1, maskedgrid1)

#return time1, y_arr1, grid1
# return time1, y_arr1, grid1
# Colormesh
cplot1 = ax[DYN_SPEC_INDX].pcolormesh(time1, y_arr1, grid1, shading='auto', cmap=cmap, norm=normscale)
greymesh1 = ax[DYN_SPEC_INDX].pcolormesh(time1, y_arr1, maskedgrid1, shading='auto', cmap='Greys', vmin=-1, vmax=1)
Expand All @@ -1862,7 +1853,7 @@ def combine_grids_and_ybins(grid, grid1, y_arr, y_arr1):
ax[DYN_SPEC_INDX].set_ylim(np.nanmin(y_arr), np.nanmax(y_arr1))

# Set a rougher tickscale
energy_tick_powers = (-1,1,3) if species in ("electron", 'e') else (-1,2,4)
energy_tick_powers = (-1, 1, 3) if species in ("electron", 'e') else (-1, 2, 4)
yticks = np.logspace(start=energy_tick_powers[0], stop=energy_tick_powers[1], num=energy_tick_powers[2])

# First one sets the ticks in place and the second one enlarges the tick labels (not the ticks, the numbers next to them)
Expand All @@ -1874,8 +1865,7 @@ def combine_grids_and_ybins(grid, grid1, y_arr, y_arr1):
# Introduce minor ticks back
ax[DYN_SPEC_INDX].yaxis.set_tick_params(length=8., width=1.2, which='minor', labelsize=0.)

fig.set_size_inches((27,18))

fig.set_size_inches((27, 18))

# Title
if view is not None and other:
Expand All @@ -1901,7 +1891,6 @@ def combine_grids_and_ybins(grid, grid1, y_arr, y_arr1):
# Finally return plotting options to what they were before plotting
rcParams.update(original_rcparams)


def tsa_plot(self, view, selection=None, xlim=None, resample=None):
"""
Makes an interactive time-shift plot
Expand Down
2 changes: 1 addition & 1 deletion seppy/tools/widgets.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@
("STEREO-A", "SEPT"): ("sun", "asun", "north", "south"),
("STEREO-B", "SEPT"): ("sun", "asun", "north", "south"),
("Solar Orbiter", "STEP"): ("Pixel averaged", "Pixel 1", "Pixel 2", "Pixel 3", "Pixel 4", "Pixel 5", "Pixel 6", "Pixel 7", "Pixel 8", "Pixel 9", "Pixel 10",
"Pixel 11", "Pixel 12", "Pixel 13", "Pixel 14", "Pixel 15"),
"Pixel 11", "Pixel 12", "Pixel 13", "Pixel 14", "Pixel 15"),
("Solar Orbiter", "EPT"): ("sun", "asun", "north", "south"),
("Solar Orbiter", "HET"): ("sun", "asun", "north", "south"),
("Bepicolombo", "SIXS-P"): (0, 1, 2, 3, 4),
Expand Down
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