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alhomalhom
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Merge branch 'master' into fileindex_interfaces
2 parents e48157d + 50fe4ca commit e17775c

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Lines changed: 221 additions & 137 deletions

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‎.github/workflows/check_contributors.yml‎

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name: Contributors check
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on:
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push:
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branches: [ master ]
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pull_request:
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branches: [ master ]
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workflow_dispatch:
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jobs:
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latest:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Check contributor changes
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run: |
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cd $GITHUB_WORKSPACE
22+
current_gitlog=$(git shortlog -s -n | sed -En "s/^\W*[0-9]+\W//p")
23+
n_current=$(echo "$current_gitlog" | wc -l)
24+
git_diff=$(git diff --name-only origin/master... | grep -Po 'CITATION.cff' || echo "Citations not modified")
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git checkout origin/master
26+
previous_gitlog=$(git shortlog -s -n | sed -En "s/^\W*[0-9]+\W//p")
27+
n_prev=$(echo "$previous_gitlog" | wc -l)
28+
if [[ ! $git_diff ]]; then
29+
if [ $n_current -ne $n_prev ]; then
30+
echo "$current_gitlog" >current_gitlog.txt
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echo "$previous_gitlog" >previous_gitlog.txt
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echo "::warning::Found new contributors, check the citations file!"
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sort current_gitlog.txt previous_gitlog.txt | uniq -u
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exit 1;
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fi
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fi

‎.github/workflows/make_sbatch_job.sh‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@ fi
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# first with srun (in case the file has not yet updated on the front end)
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# second if srun fails (in case communication failure) it tries to cat it on the frontend (may be empty if file has not been updated pyproject)
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11-
sbatch -W --array=1-$ARRAY_SIZE -o "$1" ./testpackage/$1.sh $2 > jobid_$1 || (srun cat $1 || cat $1 || echo "cat failed exit code $?" && exit 1)
11+
sbatch -W --array=1-$ARRAY_SIZE -o "$1" ./testpackage/$1.sh $2 > jobid_$1 || true
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1313
#in case we do exit 0 successfully
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LOG=$(srun cat $1 || cat $1)

‎analysator/calculations/__init__.py‎

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@@ -37,7 +37,8 @@
3737
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'''
3939
#for usage with "from (package) import *"
40-
__all__=["ids3d","intpol_file","intpol_points","cutthrough","fourier","spectra","variable","timeevolution","pitchangle","gyrophaseangle","themis_observation","cut3d","lineout","fit","fieldtracer","non_maxwellianity","null_lines","interpolator_amr"]
40+
__all__=["ids3d","intpol_file","intpol_points","cutthrough","fourier","spectra","variable","timeevolution","pitchangle","gyrophaseangle","cut3d","lineout","fit","fieldtracer","non_maxwellianity","null_lines","interpolator_amr"
41+
"spacecraft_to_simulation_frame","simulation_to_spacecraft_frame","simulation_to_observation_frame"]
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4243

4344
# List of functions and classes that should be imported into the interface
@@ -53,10 +54,6 @@
5354
from .pitchangle import pitch_angles
5455
#from .backstream import extract_velocity_cells_sphere, extract_velocity_cells_non_sphere
5556
from .gyrophaseangle import gyrophase_angles_from_file
56-
from .themis_observation import themis_observation_from_file
57-
from .themis_observation import themis_plot_detector
58-
from .themis_observation import themis_plot_phasespace_contour
59-
from .themis_observation import themis_plot_phasespace_helistyle
6057
#from .themis_observation import simulation_to_spacecraft_frame
6158
from .cut3d import cut3d
6259
from .lineout import lineout
@@ -66,3 +63,4 @@
6663
from .non_maxwellianity import epsilon_M
6764
from .null_lines import LMN_null_lines_FOTE
6865
from .interpolator_amr import AMRInterpolator, supported_amr_interpolators
66+
from .virtual_observations import spacecraft_to_simulation_frame,simulation_to_spacecraft_frame,simulation_to_observation_frame

‎analysator/calculations/virtual_observations.py‎

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,40 @@
1+
2+
import numpy as np
3+
def simulation_to_spacecraft_frame(spinvector, detector_axis, phi=0):
4+
''' Builds a matrix to transform coordinates from simulation frame into spaceraft frame
5+
:param spinvector Spacecraft spin axis, in simulation coordinates
6+
:param detector_axis Detector plane normal axis
7+
:param phi Rotate spacecraft around spin axis after setting up coordinate system
8+
'''
9+
# TODO: Normalize vectors?
10+
y = np.cross(detector_axis,spinvector)
11+
z = np.cross(spinvector, y)
12+
yr = np.cos(phi)*y - np.sin(phi)*z
13+
zr = np.sin(phi)*y + np.cos(phi)*z
14+
m = np.array([spinvector, yr, zr])
15+
16+
return m
17+
18+
def spacecraft_to_simulation_frame(spinvector, detector_axis, phi=0):
19+
''' Builds a matrix to transform coordinates from spaceraft frame back to simulation frame
20+
:param spinvector Spacecraft spin axis, in simulation coordinates
21+
:param detector_axis Detector plane normal axis
22+
:param phi Rotate spacecraft around spin axis after setting up coordinate system
23+
'''
24+
return simulation_to_spacecraft_frame(spinvector,detector_axis,phi).T
25+
26+
def simulation_to_observation_frame(x_axis,y_axis):
27+
''' Builds a 3x3 matrix to transform velocities into an observation plane
28+
:param x_axis: x-axis of the observation plane (in simulation coordinates)
29+
:param y_axis: y-axis of the observation plane (gets orthonormalized)
30+
'''
31+
xn = np.linalg.norm(x_axis)
32+
x_axis /= xn
33+
p = x_axis.dot(y_axis)
34+
y_axis -= p*x_axis
35+
yn = np.linalg.norm(y_axis)
36+
y_axis /= yn
37+
z_axis = np.cross(x_axis,y_axis)
38+
return np.array([x_axis,y_axis,z_axis])
39+
40+

‎analysator/plot/__init__.py‎

Lines changed: 5 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -36,7 +36,10 @@
3636
#for usage with "from (package) import *"
3737
__all__ = ['plot_colormap', 'plot_vdf', 'plot_vdfdiff', 'plot_vdf_profiles', 'plot_colormap3dslice',
3838
'plot_threeslice', 'plot_ionosphere', 'plot_isosurface', 'plot_neutral_sheet',
39-
'plot_variables','colormaps', 'plot_helpers']
39+
'plot_variables','colormaps', 'plot_helpers'
40+
'themis_plot_phasespace_contour','themis_plot_detector','themis_observation_from_file'
41+
'themis_plot_phasespace_helistyle',"themis_observation"
42+
]
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4144
from .plot_variables import plot_variables, plot_multiple_variables
4245

@@ -46,7 +49,7 @@
4649
import matplotlib.pyplot as plt
4750
import matplotlib
4851
from . import colormaps
49-
52+
from .plot_themis_observation import themis_plot_detector,themis_plot_phasespace_contour,themis_plot_phasespace_helistyle,themis_observation,themis_observation_from_file
5053
from . import plot_helpers
5154
from .plot_colormap import plot_colormap
5255
from .plot_vdf import plot_vdf

analysator/calculations/themis_observation.py renamed to analysator/plot/plot_themis_observation.py

Lines changed: 34 additions & 71 deletions
Original file line numberDiff line numberDiff line change
@@ -25,11 +25,10 @@
2525
import analysator as pt
2626
import matplotlib.pyplot as plt
2727
import matplotlib
28-
from .rotation import rotateVectorToVector
2928
from scipy.interpolate import griddata
3029
from scipy.signal import sepfir2d
31-
from packaging.version import Version
3230
import logging
31+
from analysator.calculations import virtual_observations as vsc
3332

3433
# Detector data obtained from the Themis ESA instrument paper
3534
# http://dx.doi.org/10.1007/s11214-008-9440-2
@@ -48,73 +47,19 @@
4847
themis_colors=[(0,0,0),(.5,0,.5),(0,0,1),(0,1,1),(0,1,0),(1,1,0),(1,0,0)]
4948
themis_colormap = matplotlib.colors.LinearSegmentedColormap.from_list("themis",themis_colors)
5049

51-
def get_dv(vlsvReader,pop="proton"):
52-
# Get velocity grid sizes:
53-
vel_mesh_size = vlsvReader.get_velocity_mesh_size(pop=pop)
54-
vel_block_size = vlsvReader.get_velocity_block_size(pop=pop)
55-
vxcells = vel_mesh_size[0]*vel_block_size[0]
56-
vycells = vel_mesh_size[1]*vel_block_size[1]
57-
vzcells = vel_mesh_size[2]*vel_block_size[2]
58-
59-
vel_mesh_limits = vlsvReader.get_velocity_mesh_extent(pop=pop)
60-
vxmin = vel_mesh_limits[0]
61-
vymin = vel_mesh_limits[1]
62-
vzmin = vel_mesh_limits[2]
63-
vxmax = vel_mesh_limits[3]
64-
vymax = vel_mesh_limits[4]
65-
vzmax = vel_mesh_limits[5]
66-
67-
dvx = (vxmax - vxmin) / (float)(vxcells)
68-
dvy = (vymax - vymin) / (float)(vycells)
69-
dvz = (vzmax - vzmin) / (float)(vzcells)
70-
return [dvx,dvy,dvz]
71-
72-
def simulation_to_spacecraft_frame(spinvector, detector_axis, phi=0):
73-
''' Builds a matrix to transform coordinates from simulation frame into spaceraft frame
74-
:param spinvector Spacecraft spin axis, in simulation coordinates
75-
:param detector_axis Detector plane normal axis
76-
:param phi Rotate spacecraft around spin axis after setting up coordinate system
77-
'''
78-
# TODO: Normalize vectors?
79-
y = np.cross(detector_axis,spinvector)
80-
z = np.cross(spinvector, y)
81-
yr = np.cos(phi)*y - np.sin(phi)*z
82-
zr = np.sin(phi)*y + np.cos(phi)*z
83-
m = np.array([spinvector, yr, zr])
84-
85-
return m
86-
87-
def spacecraft_to_simulation_frame(spinvector, detector_axis, phi=0):
88-
''' Builds a matrix to transform coordinates from spaceraft frame back to simulation frame
89-
:param spinvector Spacecraft spin axis, in simulation coordinates
90-
:param detector_axis Detector plane normal axis
91-
:param phi Rotate spacecraft around spin axis after setting up coordinate system
92-
'''
93-
return simulation_to_spacecraft_frame(spinvector,detector_axis,phi).T
94-
95-
def simulation_to_observation_frame(x_axis,y_axis):
96-
''' Builds a 3x3 matrix to transform velocities into an observation plane
97-
:param x_axis: x-axis of the observation plane (in simulation coordinates)
98-
:param y_axis: y-axis of the observation plane (gets orthonormalized)
99-
'''
100-
xn = np.linalg.norm(x_axis)
101-
x_axis /= xn
102-
p = x_axis.dot(y_axis)
103-
y_axis -= p*x_axis
104-
yn = np.linalg.norm(y_axis)
105-
y_axis /= yn
106-
z_axis = np.cross(x_axis,y_axis)
107-
return np.array([x_axis,y_axis,z_axis])
108-
109-
def themis_plot_detector(vlsvReader, cellID, detector_axis=np.array([0,1,0]), pop="proton"):
50+
def themis_plot_detector(vlsvReader, cellID,outputfile="./themis_plot_detector.png",nooverwrite=False,draw=True, detector_axis=np.array([0,1,0]), pop="proton"):
11051
''' Plots a view of the detector countrates using matplotlib
11152
:param vlsvReader: Some VlsvReader class with a file open
11253
:type vlsvReader: :class:`vlsvfile.VlsvReader`
11354
:param cellid: The cell id where the distribution is supposet to be sampled NOTE: The cell id must have a velocity distribution!
11455
:param detector_axis: detector axis direction (note: this is not spacecraft spin axis!)
56+
:param draw: Set to false to save to file instead of drawing on screen
57+
:kward outputfile: File to output the image to if Draw=False
58+
:kward nooverwrite: Whether to allow overwriting of files when saving, Default False
59+
11560
'''
11661

117-
matrix = spacecraft_to_simulation_frame(np.cross(np.array([1.,0,0]),detector_axis),detector_axis)
62+
matrix = vsc.spacecraft_to_simulation_frame(np.cross(np.array([1.,0,0]),detector_axis),detector_axis)
11863

11964
logging.info("Getting phasespace data...")
12065
angles, energies, vmin, vmax, values = themis_observation_from_file( vlsvReader=vlsvReader,
@@ -133,17 +78,24 @@ def themis_plot_detector(vlsvReader, cellID, detector_axis=np.array([0,1,0]), po
13378
cax = ax.pcolormesh(grid_theta,grid_r,values, norm=matplotlib.colors.LogNorm(vmin=vmin,vmax=vmax), cmap=themis_colormap)
13479
ax.grid(True)
13580
fig.colorbar(cax)
136-
plt.show()
81+
if not draw:
82+
outputpath=pt.plot.output_path(outputfile,None,None,nooverwrite)
83+
plt.savefig(outputpath)
84+
else:
85+
plt.show()
13786

138-
def themis_plot_phasespace_contour(vlsvReader, cellID, plane_x=np.array([1.,0,0]), plane_y=np.array([0,0,1.]), smooth=False, xlabel="Vx", ylabel="Vy", pop="proton"):
87+
def themis_plot_phasespace_contour(vlsvReader, cellID,outputfile='./themis_plot_phasespace_contour.png', nooverwrite=False, draw=True, plane_x=np.array([1.,0,0]), plane_y=np.array([0,0,1.]), smooth=False, xlabel="Vx", ylabel="Vy", pop="proton"):
13988
''' Plots a contour view of phasespace, as seen by a themis detector, at the given cellID
14089
:param vlsvReader: Some VlsvReader class with a file open
14190
:type vlsvReader: :class:`vlsvfile.VlsvReader`
14291
:param cellid: The cell id where the distribution is supposet to be sampled NOTE: The cell id must have a velocity distribution!
92+
:param draw: Set to false to save to file instead of drawing on screen
93+
:kward outputfile: File to output the image to if Draw=False
94+
:kward nooverwrite: Whether to allow overwriting of files when saving, Default False
14395
:param plane_x and plane_y: x and y direction of the resulting plot plane
14496
'''
14597

146-
matrix = simulation_to_observation_frame(plane_x,plane_y)
98+
matrix = vsc.simulation_to_observation_frame(plane_x,plane_y)
14799

148100
angles, energies, vmin, vmax, values = themis_observation_from_file( vlsvReader=vlsvReader, cellid=cellID, matrix=matrix,pop=pop)
149101

@@ -176,18 +128,25 @@ def themis_plot_phasespace_contour(vlsvReader, cellID, plane_x=np.array([1.,0,0]
176128
cax = ax.contour(xi,yi,vi.T, levels=np.logspace(np.log10(vmin),np.log10(vmax),20), norm=matplotlib.colors.LogNorm(vmin=vmin,vmax=vmax))
177129
ax.grid(True)
178130
fig.colorbar(cax)
179-
plt.show()
131+
if not draw:
132+
outputpath=pt.plot.output_path(outputfile,None,None,nooverwrite)
133+
plt.savefig(outputpath)
134+
else:
135+
plt.show()
180136

181-
def themis_plot_phasespace_helistyle(vlsvReader, cellID, plane_x=np.array([1.,0,0]), plane_y=np.array([0,0,1.]), smooth=True, xlabel="Vx", ylabel="Vy"):
137+
def themis_plot_phasespace_helistyle(vlsvReader, cellID,outputfile='./themis_plot_phasespace_helistyle',plane_x=np.array([1.,0,0]), plane_y=np.array([0,0,1.]), smooth=True, xlabel="Vx", ylabel="Vy",draw=True,nooverwrite=False):
182138
''' Plots a view of phasespace, as seen by a themis detector, at the given cellID, in the style that heli likes.
183139
:param vlsvReader: Some VlsvReader class with a file open
184140
:type vlsvReader: :class:`vlsvfile.VlsvReader`
185141
:param cellid: The cell id where the distribution is supposet to be sampled NOTE: The cell id must have a velocity distribution!
186142
:param smooth: Smooth re-gridded phasespace before plotting
143+
:param draw: Set to false to save to file instead of drawing on screen
144+
:kward outputfile: File to output the image to if Draw=False
145+
:kward nooverwrite: Whether to allow overwriting of files when saving, Default False
187146
:param plane_x and plane_y: x and y direction of the resulting plot plane
188147
'''
189148

190-
matrix = simulation_to_observation_frame(plane_x,plane_y)
149+
matrix = vsc.simulation_to_observation_frame(plane_x,plane_y)
191150

192151
angles, energies, vmin, vmax, values = themis_observation_from_file( vlsvReader=vlsvReader, cellid=cellID, matrix=matrix, countrates=False)
193152
if vmin == 0:
@@ -218,12 +177,16 @@ def themis_plot_phasespace_helistyle(vlsvReader, cellID, plane_x=np.array([1.,0,
218177
ax.set_ylabel(ylabel+" (km/s)")
219178
cmapuse=pt.plot.get_cmap("Blues")
220179

221-
cax = ax.pcolormesh(xi,yi,vi.T, norm=matplotlib.colors.LogNorm(vmin=vmin,vmax=vmax), vmin=vmin, vmax=vmax, cmap=cmapuse, shading='flat')
180+
cax = ax.pcolormesh(xi,yi,vi.T, norm=matplotlib.colors.LogNorm(vmin=vmin,vmax=vmax), cmap=cmapuse)
222181
cax2 = ax.contourf(xi,yi,vi.T, levels=np.logspace(np.log10(vmin),np.log10(vmax),20), norm=matplotlib.colors.LogNorm(vmin=vmin,vmax=vmax), vmin=vmin, vmax=vmax, cmap=cmapuse)
223182
#cax3 = ax.contour(xi,yi,vi.T, levels=np.logspace(np.log10(vmin),np.log10(vmax),20), norm=matplotlib.colors.LogNorm(vmin=vmin,vmax=vmax), cmap=pl.get_cmap("binary"))
224183
ax.grid(True)
225184
fig.colorbar(cax)
226-
plt.show()
185+
if not draw:
186+
outputpath=pt.plot.output_path(outputfile,None,None,nooverwrite)
187+
fig.savefig(outputpath)
188+
else:
189+
plt.show()
227190
def themis_observation_from_file( vlsvReader, cellid, matrix=np.array([[1,0,0],[0,1,0],[0,0,1]]), countrates=True, interpolate=True,binOffset=[0.,0.],pop='proton'):
228191
''' Calculates artificial THEMIS EMS observation from the given cell
229192
:param vlsvReader: Some VlsvReader class with a file open
@@ -248,7 +211,7 @@ def themis_observation_from_file( vlsvReader, cellid, matrix=np.array([[1,0,0],[
248211
pl.show()
249212
'''
250213
# Get velocity space resolution
251-
dvx,dvy,dvz = get_dv(vlsvReader,pop=pop)
214+
dvx,dvy,dvz = vlsvReader.get_velocity_mesh_dv(pop=pop)
252215

253216
# Read the velocity cells:
254217
velocity_cell_data = vlsvReader.read_velocity_cells(cellid,pop=pop)

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