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jonas.sinjan
hrt_pipeline
Commits
060f3bab
Commit
060f3bab
authored
Jul 27, 2021
by
jonas
Browse files
input as jsons, flat 6 and 4 fix
parent
cd7a5f7c
Changes
5
Hide whitespace changes
Inline
Side-by-side
.gitignore
View file @
060f3bab
...
...
@@ -18,3 +18,4 @@ _RTE.npz
run.py
P-MILOS/*
utils.py
file_names.txt
create_input_json.py
0 → 100644
View file @
060f3bab
import
json
science_april
=
[
'solo_L0_phi-hrt-ilam_20200420T141752_V202004221450C_0024160030000.fits'
,
'solo_L0_phi-hrt-ilam_20200420T142022_V202004221451C_0024160031000.fits'
,
'solo_L0_phi-hrt-ilam_20200420T142252_V202004221452C_0024160032000.fits'
,
'solo_L0_phi-hrt-ilam_20200420T142522_V202004221457C_0024160033000.fits'
,
'solo_L0_phi-hrt-ilam_20200420T142752_V202004221511C_0024160034000.fits'
,
'solo_L0_phi-hrt-ilam_20200420T143023_V202004221517C_0024160035000.fits'
,
'solo_L0_phi-hrt-ilam_20200420T143253_V202004221518C_0024160036000.fits'
,
'solo_L0_phi-hrt-ilam_20200420T143523_V202004221522C_0024160037000.fits'
,
'solo_L0_phi-hrt-ilam_20200420T143753_V202004231605C_0024160038000.fits'
,
'solo_L0_phi-hrt-ilam_20200420T144023_V202004231605C_0024160039000.fits'
]
flatfield_fits_filename
=
'/data/slam/home/sinjan/fits_files/april_avgd_2020_flat.fits'
#solo_L0_phi-hrt-flat_0667134081_V202103221851C_0162201100.fits'
darkfield_fits_filename
=
'../fits_files/solo_L0_phi-fdt-ilam_20200228T155100_V202002281636_0022210004_000.fits'
science_april
=
[
'/data/slam/home/sinjan/fits_files/'
+
i
for
i
in
science_april
]
input_dict
=
{
'data_f'
:
science_april
,
'flat_f'
:
flatfield_fits_filename
,
'dark_f'
:
darkfield_fits_filename
}
json
.
dump
(
input_dict
,
open
(
f
"./input_jsons/april_2020.txt"
,
"w"
))
\ No newline at end of file
hrt_pipe.py
View file @
060f3bab
...
...
@@ -547,7 +547,7 @@ def phihrt_pipe(data_f, dark_f = '', flat_f = '', scale_data = True, bit_flat =
tmp
=
np
.
mean
(
flat
,
axis
=-
2
)
#avg over pol states for the wavelength
data
/=
tmp
[
start_row
:
start_row
+
data_size
[
0
],
start_col
:
start_col
+
data_size
[
1
],
np
.
newaxis
,
np
.
newaxis
]
data
/=
tmp
[
start_row
:
start_row
+
data_size
[
0
],
start_col
:
start_col
+
data_size
[
1
],
np
.
newaxis
,
:,
np
.
newaxis
]
elif
flat_states
==
24
:
...
...
@@ -562,7 +562,7 @@ def phihrt_pipe(data_f, dark_f = '', flat_f = '', scale_data = True, bit_flat =
tmp
=
np
.
mean
(
flat
,
axis
=-
1
)
#avg over wavelength
data
/=
tmp
[
start_row
:
start_row
+
data_size
[
0
],
start_col
:
start_col
+
data_size
[
1
],
np
.
newaxis
,
np
.
newaxis
]
data
/=
tmp
[
start_row
:
start_row
+
data_size
[
0
],
start_col
:
start_col
+
data_size
[
1
],
:,
np
.
newaxis
,
np
.
newaxis
]
printc
(
'--------------------------------------------------------------'
,
bcolors
.
OKGREEN
)
printc
(
f
"------------- Flat Field correction time:
{
np
.
round
(
time
.
time
()
-
start_time
,
3
)
}
seconds "
,
bcolors
.
OKGREEN
)
...
...
input_jsons/april_2020.txt
0 → 100644
View file @
060f3bab
{"data_f": ["/data/slam/home/sinjan/fits_files/solo_L0_phi-hrt-ilam_20200420T141752_V202004221450C_0024160030000.fits", "/data/slam/home/sinjan/fits_files/solo_L0_phi-hrt-ilam_20200420T142022_V202004221451C_0024160031000.fits", "/data/slam/home/sinjan/fits_files/solo_L0_phi-hrt-ilam_20200420T142252_V202004221452C_0024160032000.fits", "/data/slam/home/sinjan/fits_files/solo_L0_phi-hrt-ilam_20200420T142522_V202004221457C_0024160033000.fits", "/data/slam/home/sinjan/fits_files/solo_L0_phi-hrt-ilam_20200420T142752_V202004221511C_0024160034000.fits", "/data/slam/home/sinjan/fits_files/solo_L0_phi-hrt-ilam_20200420T143023_V202004221517C_0024160035000.fits", "/data/slam/home/sinjan/fits_files/solo_L0_phi-hrt-ilam_20200420T143253_V202004221518C_0024160036000.fits", "/data/slam/home/sinjan/fits_files/solo_L0_phi-hrt-ilam_20200420T143523_V202004221522C_0024160037000.fits", "/data/slam/home/sinjan/fits_files/solo_L0_phi-hrt-ilam_20200420T143753_V202004231605C_0024160038000.fits", "/data/slam/home/sinjan/fits_files/solo_L0_phi-hrt-ilam_20200420T144023_V202004231605C_0024160039000.fits"], "flat_f": "/data/slam/home/sinjan/fits_files/april_avgd_2020_flat.fits", "dark_f": "../fits_files/solo_L0_phi-fdt-ilam_20200228T155100_V202002281636_0022210004_000.fits"}
\ No newline at end of file
run.py
View file @
060f3bab
from
hrt_pipe
import
phihrt_pipe
import
numpy
as
np
import
json
sciencedata_fits_filenames
=
[
'solo_L0_phi-hrt-ilam_20201117T170209_V202106300922C_0051170001.fits'
]
#
['solo_L0_phi-hrt-ilam_20200420T142022_V202004221451C_0024160031000.fits']#,'solo_L0_phi-hrt-ilam_20200420T142252_V202004221452C_0024160032000.fits','solo_L0_phi-hrt-ilam_20200420T142522_V202004221457C_0024160033000.fits','solo_L0_phi-hrt-ilam_20200420T142752_V202004221511C_0024160034000.fits','solo_L0_phi-hrt-ilam_20200420T143023_V202004221517C_0024160035000.fits', 'solo_L0_phi-hrt-ilam_20200420T143253_V202004221518C_0024160036000.fits','solo_L0_phi-hrt-ilam_20200420T143523_V202004221522C_0024160037000.fits', 'solo_L0_phi-hrt-ilam_20200420T143753_V202004231605C_0024160038000.fits','solo_L0_phi-hrt-ilam_20200420T144023_V202004231605C_0024160039000.fits']
#'/data/slam/home/sinjan/fits_files/solo_L0_phi-hrt-ilam_20200420T141752_V202004221450C_0024160030000.fits'#solo_L1_phi-hrt-ilam_20201117T170209_V202107090920C_0051170001.fits'#solo_L1_phi-hrt-ilam_20201117T170209_V202107060746C_0051170001.fits'#['solo_L1_phi-hrt-ilam_20200528T171109_V202106111600C_0045140102.fits']
#
sciencedata_fits_filenames = ['solo_L0_phi-hrt-ilam_20201117T170209_V202106300922C_0051170001.fits']##'/data/slam/home/sinjan/fits_files/solo_L0_phi-hrt-ilam_20200420T141752_V202004221450C_0024160030000.fits'#solo_L1_phi-hrt-ilam_20201117T170209_V202107090920C_0051170001.fits'#solo_L1_phi-hrt-ilam_20201117T170209_V202107060746C_0051170001.fits'#['solo_L1_phi-hrt-ilam_20200528T171109_V202106111600C_0045140102.fits']
# ['solo_L0_phi-hrt-ilam_20210421T120003_V202106080929C_0144210101.fits', 'solo_L0_phi-hrt-ilam_20210424T120003_V202106141014C_0144240101.fits',
# 'solo_L0_phi-hrt-ilam_20210425T120002_V202106141020C_0144250101.fits', 'solo_L0_phi-hrt-ilam_20210426T120002_V202106162118C_0144260101.fits',
# 'solo_L0_phi-hrt-ilam_20210427T120002_V202106162052C_0144270101.fits', 'solo_L0_phi-hrt-ilam_20210427T120002_V202106171444C_0144270101.fits',
# 'solo_L0_phi-hrt-ilam_20210427T120002_V202106171517C_0144270101.fits'] ##['solo_L1_phi-hrt-ilam_20210223T170002_V202106111612C_0142230201.fits']
#['solo_L0_phi-hrt-ilam_0667414748_V202103221851C_0142230201.fits']#['solo_L0_phi-hrt-ilam_0667414905_V202103221851C_0142230602.fits', 'solo_L0_phi-hrt-ilam_0667415054_V202103221851C_0142230603.fits', 'solo_L0_phi-hrt-ilam_0667415205_V202103221851C_0142230604.fits', 'solo_L0_phi-hrt-ilam_0667415354_V202103221851C_0142230605.fits', 'solo_L0_phi-hrt-ilam_0667415505_V202103221851C_0142230606.fits', 'solo_L0_phi-hrt-ilam_0667415654_V202103221851C_0142230607.fits', 'solo_L0_phi-hrt-ilam_0667415805_V202103221851C_0142230608.fits']#['../fits_files/solo_L0_phi-hrt-ilam_0667414748_V202103221851C_0142230201.fits']
#sciencedata_fits_filenames = ['solo_L0_phi-hrt-ilam_0667414748_V202103221851C_0142230201.fits']
#sciencedata_fits_filenames = ['solo_L0_phi-hrt-ilam_0667414905_V202103221851C_0142230602.fits', 'solo_L0_phi-hrt-ilam_0667415054_V202103221851C_0142230603.fits', 'solo_L0_phi-hrt-ilam_0667415205_V202103221851C_0142230604.fits', 'solo_L0_phi-hrt-ilam_0667415354_V202103221851C_0142230605.fits', 'solo_L0_phi-hrt-ilam_0667415505_V202103221851C_0142230606.fits', 'solo_L0_phi-hrt-ilam_0667415654_V202103221851C_0142230607.fits', 'solo_L0_phi-hrt-ilam_0667415805_V202103221851C_0142230608.fits']
#
#['solo_L0_phi-hrt-ilam_0667414748_V202103221851C_0142230201.fits']#['solo_L0_phi-hrt-ilam_0667414905_V202103221851C_0142230602.fits', 'solo_L0_phi-hrt-ilam_0667415054_V202103221851C_0142230603.fits', 'solo_L0_phi-hrt-ilam_0667415205_V202103221851C_0142230604.fits', 'solo_L0_phi-hrt-ilam_0667415354_V202103221851C_0142230605.fits', 'solo_L0_phi-hrt-ilam_0667415505_V202103221851C_0142230606.fits', 'solo_L0_phi-hrt-ilam_0667415654_V202103221851C_0142230607.fits', 'solo_L0_phi-hrt-ilam_0667415805_V202103221851C_0142230608.fits']#['../fits_files/solo_L0_phi-hrt-ilam_0667414748_V202103221851C_0142230201.fits']
#
sciencedata_fits_filenames =
['solo_L0_phi-hrt-ilam_0667414905_V202103221851C_0142230602.fits']#
['solo_L0_phi-hrt-ilam_0667414748_V202103221851C_0142230201.fits']
#
#sciencedata_fits_filenames = ['solo_L0_phi-hrt-ilam_0667414905_V202103221851C_0142230602.fits', 'solo_L0_phi-hrt-ilam_0667415054_V202103221851C_0142230603.fits', 'solo_L0_phi-hrt-ilam_0667415205_V202103221851C_0142230604.fits', 'solo_L0_phi-hrt-ilam_0667415354_V202103221851C_0142230605.fits', 'solo_L0_phi-hrt-ilam_0667415505_V202103221851C_0142230606.fits', 'solo_L0_phi-hrt-ilam_0667415654_V202103221851C_0142230607.fits', 'solo_L0_phi-hrt-ilam_0667415805_V202103221851C_0142230608.fits']
flatfield_fits_filename
=
'/data/slam/home/sinjan/fits_files/solo_L0_phi-hrt-flat_0667134081_V202103221851C_0162201100.fits'
#solo_L0_phi-hrt-ilam_20200417T174529_V202004241516C_0024150020000.fits'#solo_L0_phi-hrt-flat_0667134081_V202103221851C_0162201100.fits' #solo_L0_phi-hrt-ilam_20200417T174529_V202004241516C_0024150020000.fits'#solo_L1_phi-hrt-ilam_20200417T174538_V202106111549C_0024150020.fits'#solo_L0_phi-hrt-flat_0667134081_V202103221851C_0162201100.fits'
darkfield_fits_filename
=
'../fits_files/solo_L0_phi-fdt-ilam_20200228T155100_V202002281636_0022210004_000.fits'
# science_april = ['solo_L0_phi-hrt-ilam_20200420T142022_V202004221451C_0024160031000.fits','solo_L0_phi-hrt-ilam_20200420T142252_V202004221452C_0024160032000.fits','solo_L0_phi-hrt-ilam_20200420T142522_V202004221457C_0024160033000.fits','solo_L0_phi-hrt-ilam_20200420T142752_V202004221511C_0024160034000.fits','solo_L0_phi-hrt-ilam_20200420T143023_V202004221517C_0024160035000.fits', 'solo_L0_phi-hrt-ilam_20200420T143253_V202004221518C_0024160036000.fits','solo_L0_phi-hrt-ilam_20200420T143523_V202004221522C_0024160037000.fits', 'solo_L0_phi-hrt-ilam_20200420T143753_V202004231605C_0024160038000.fits','solo_L0_phi-hrt-ilam_20200420T144023_V202004231605C_0024160039000.fits']
sciencedata_fits_filenames
=
[
'/data/slam/home/sinjan/fits_files/'
+
i
for
i
in
sciencedata_fits_filenames
]
# flatfield_fits_filename = '/data/slam/home/sinjan/fits_files/solo_L0_phi-hrt-flat_0667134081_V202103221851C_0162201100.fits'#solo_L0_phi-hrt-flat_0667134081_V202103221851C_0162201100.fits'#solo_L0_phi-hrt-ilam_20200417T174529_V202004241516C_0024150020000.fits' #solo_L0_phi-hrt-ilam_20200417T174529_V202004241516C_0024150020000.fits'#solo_L1_phi-hrt-ilam_20200417T174538_V202106111549C_0024150020.fits'#solo_L0_phi-hrt-flat_0667134081_V202103221851C_0162201100.fits'
# darkfield_fits_filename = '../fits_files/solo_L0_phi-fdt-ilam_20200228T155100_V202002281636_0022210004_000.fits'
# sciencedata_fits_filenames = ['/data/slam/home/sinjan/fits_files/' + i for i in science_april]
input_json_file
=
'./input_jsons/april_2020.txt'
input_dict
=
json
.
load
(
open
(
input_json_file
))
data_f
=
input_dict
[
'data_f'
]
flat_f
=
input_dict
[
'flat_f'
]
dark_f
=
input_dict
[
'dark_f'
]
prefilter_f
=
'../fits_files/fitted_prefilter.fits'
...
...
@@ -29,13 +41,13 @@ prefilter_f = '../fits_files/fitted_prefilter.fits'
c_talk_params
=
np
.
zeros
((
2
,
3
))
q_slope
=
-
0.0
09
8
#0.00
38
u_slope
=
-
0.000
3
#-0.0077
v_slope
=
-
0.007
0
#-0.00
09
q_slope
=
-
0.0
141
#0.003
8#
-
0.00
98#
u_slope
=
-
0.000
8
#-0.0077
#-0.0003#
v_slope
=
-
0.007
5
#-0.0009
#-0.00
70#
q_int
=
-
0.001
5
#-0.0056 #the offset, normalised to I_c
u_int
=
0.00
0
7
#0.0031
v_int
=
0.00
06
#-0.0002
q_int
=
0.001
8
#-0.0056
#-0.0015#
#the offset, normalised to I_c
u_int
=
0.00
1
7
#0.0031
#0.0007#
v_int
=
0.00
1
#-0.0002
#0.0006#
c_talk_params
[
0
,
0
]
=
q_slope
c_talk_params
[
0
,
1
]
=
u_slope
...
...
@@ -45,12 +57,13 @@ c_talk_params[1,0] = q_int
c_talk_params
[
1
,
1
]
=
u_int
c_talk_params
[
1
,
2
]
=
v_int
out_names
=
[
'nov_17_0051170001'
]
#, '0024160032000_noflat', '0024160033000_noflat', '0024160034000_noflat', '0024160035000_noflat', '0024160036000_noflat', '0024160037000_noflat', '0024160038000_noflat', '0024160039000_noflat']
#
out_names = ['nov_17_0051170001']#, '0024160032000_noflat', '0024160033000_noflat', '0024160034000_noflat', '0024160035000_noflat', '0024160036000_noflat', '0024160037000_noflat', '0024160038000_noflat', '0024160039000_noflat']
phihrt_pipe
(
sciencedata_fits_filenames
,
flat_f
=
flatfield_fits_filename
,
dark_f
=
darkfield_fits_filename
,
scale_data
=
True
,
bit_flat
=
True
,
norm_f
=
True
,
clean_f
=
True
,
sigma
=
59
,
flat_states
=
24
,
norm_stokes
=
True
,
prefilter_f
=
None
,
dark_c
=
True
,
flat_c
=
True
,
fs_c
=
True
,
demod
=
True
,
ctalk_params
=
c_talk_params
,
ItoQUV
=
False
,
out_demod_file
=
True
,
out_demod_filename
=
out_names
,
out_dir
=
'/data/slam/home/sinjan/hrt_pipe_results/nov_17_2020/'
,
rte
=
'RTE'
,
phihrt_pipe
(
data_f
,
flat_f
=
flat_f
,
dark_f
=
dark_f
,
scale_data
=
False
,
bit_flat
=
True
,
norm_f
=
True
,
clean_f
=
False
,
sigma
=
59
,
flat_states
=
6
,
norm_stokes
=
True
,
prefilter_f
=
None
,
dark_c
=
True
,
flat_c
=
True
,
fs_c
=
True
,
demod
=
True
,
ctalk_params
=
c_talk_params
,
ItoQUV
=
False
,
out_demod_file
=
True
,
out_demod_filename
=
None
,
out_dir
=
'/data/slam/home/sinjan/hrt_pipe_results/april_2020_6f/'
,
rte
=
'-'
,
out_rte_filename
=
None
,
p_milos
=
False
,
config_file
=
True
)
"""
Input Parameters:
...
...
@@ -119,6 +132,6 @@ ctalk_params: numpy arr, DEFAULT: None
rte: str, DEFAULT: False
invert using cmilos, options: 'RTE' for Milne Eddington Inversion, 'CE' for Classical Estimates, 'CE+RTE' for combined
out_rte_filename: str, DEFAULT = ''
if '', takes last 10 characters of input scan filename (assumes its a DID), change if want other name
out_rte_filename: str
or list
, DEFAULT = ''
if '', takes last 10 characters of input scan filename (assumes its a DID), change if want other name
(s) for each scan
"""
\ No newline at end of file
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