In [1]:
# import
import os
from configobj import ConfigObj
from pypit.par import pypitpar
In [2]:
# To get the default parameters, declare the parameters set
# without arguments
p = pypitpar.ProcessImagesPar()
# Use print() to get a short-form representation
print('Print output:')
print(p)
# Use the info() method to get a long-form representation
print('.info() output:')
p.info()
# Both of these can go haywire for complex constructions of
# parameter sets (sets within sets) but are well formatted
# in the simplest cases
# Use the to_config() method to output to a *.cfg file with
# comments for each item. You have to provide a section
# name in most cases.
p.to_config('test_process.cfg', section_name='process')
# You can also use the to_config() method to just get the
# list of strings that are then written to the file. This
# is useful when you want to reconstruct a ConfigObj.
p_cfgobj = ConfigObj(p.to_config(cfg_file=None, section_name='process'))
print(p_cfgobj)
Print output:
Parameter Value Default Type Callable
----------------------------------------------------------
overscan savgol savgol str False
overscan_par 5, 65 5, 65 int, list False
match -1 -1 int, float False
combine weightmean weightmean str False
satpix reject reject str False
sigrej 20.0 20.0 int, float False
n_lohi 0, 0 0, 0 list False
sig_lohi 3.0, 3.0 3.0, 3.0 list False
replace maxnonsat maxnonsat str False
lamaxiter 1 1 int False
grow 1.5 1.5 int, float False
rmcompact True True bool False
sigclip 5.0 5.0 int, float False
sigfrac 0.3 0.3 int, float False
objlim 5.0 5.0 int, float False
.info() output:
overscan
Value: savgol
Default: savgol
Options: polynomial, savgol, median
Valid Types: str
Callable: False
Description: Method used to fit the overscan. Options are: polynomial, savgol, median
overscan_par
Value: [5, 65]
Default: [5, 65]
Options: None
Valid Types: int, list
Callable: False
Description: Parameters for the overscan subtraction. For 'polynomial', set overcan_par = order, number of pixels, number of repeats ; for 'savgol', set overscan_par = order, window size ; for 'median', set overscan_par = None or omit the keyword.
match
Value: -1
Default: -1
Options: None
Valid Types: int, float
Callable: False
Description: (Deprecate?) Match frames with pixel counts that are within N-sigma of one another, where match=N below. If N < 0, nothing is matched.
combine
Value: weightmean
Default: weightmean
Options: mean, median, weightmean
Valid Types: str
Callable: False
Description: Method used to combine frames. Options are: mean, median, weightmean
satpix
Value: reject
Default: reject
Options: reject, force, nothing
Valid Types: str
Callable: False
Description: Handling of saturated pixels. Options are: reject, force, nothing
sigrej
Value: 20.0
Default: 20.0
Options: None
Valid Types: int, float
Callable: False
Description: Sigma level to reject cosmic rays (<= 0.0 means no CR removal)
n_lohi
Value: [0, 0]
Default: [0, 0]
Options: None
Valid Types: list
Callable: False
Description: Number of pixels to reject at the lowest and highest ends of the distribution; i.e., n_lohi = low, high. Use None for no limit.
sig_lohi
Value: [3.0, 3.0]
Default: [3.0, 3.0]
Options: None
Valid Types: list
Callable: False
Description: Sigma-clipping level at the low and high ends of the distribution; i.e., sig_lohi = low, high. Use None for no limit.
replace
Value: maxnonsat
Default: maxnonsat
Options: min, max, mean, median, weightmean, maxnonsat
Valid Types: str
Callable: False
Description: If all pixels are rejected, replace them using this method. Options are: min, max, mean, median, weightmean, maxnonsat
lamaxiter
Value: 1
Default: 1
Options: None
Valid Types: int
Callable: False
Description: Maximum number of iterations for LA cosmics routine.
grow
Value: 1.5
Default: 1.5
Options: None
Valid Types: int, float
Callable: False
Description: Factor by which to expand regions with cosmic rays detected by the LA cosmics routine.
rmcompact
Value: True
Default: True
Options: None
Valid Types: bool
Callable: False
Description: Remove compact detections in LA cosmics routine
sigclip
Value: 5.0
Default: 5.0
Options: None
Valid Types: int, float
Callable: False
Description: Sigma level for rejection in LA cosmics routine
sigfrac
Value: 0.3
Default: 0.3
Options: None
Valid Types: int, float
Callable: False
Description: Fraction for the lower clipping threshold in LA cosmics routine.
objlim
Value: 5.0
Default: 5.0
Options: None
Valid Types: int, float
Callable: False
Description: Object detection limit in LA cosmics routine
{'process': {'overscan': 'savgol', 'overscan_par': ['5', '65'], 'match': '-1', 'combine': 'weightmean', 'satpix': 'reject', 'sigrej': '20.0', 'n_lohi': ['0', '0'], 'sig_lohi': ['3.0', '3.0'], 'replace': 'maxnonsat', 'lamaxiter': '1', 'grow': '1.5', 'rmcompact': 'True', 'sigclip': '5.0', 'sigfrac': '0.3', 'objlim': '5.0'}}
In [3]:
pypitpar.ReducePar()
Out[3]:
Parameter Value Default Type Callable
----------------------------------------------------
spectrograph None None str False
pipeline None None str False
detnum None None list False
sortroot None None str False
calwin 0 0 int, float False
scidir Science Science str False
qadir QA QA str False
Parameters used for each frame type (bias, pixelflat, etc) are abstracted to a single "Frame-Group" parameter set. The default is 'bias'; valid frame types are shown using the static method valid_frame_types (see below). The parameters used to process the images in the frame group is a subset of FrameGroupPar, called ProcessImagesPar.
In [4]:
pypitpar.ProcessImagesPar()
Out[4]:
Parameter Value Default Type Callable
----------------------------------------------------------
overscan savgol savgol str False
overscan_par 5, 65 5, 65 int, list False
match -1 -1 int, float False
combine weightmean weightmean str False
satpix reject reject str False
sigrej 20.0 20.0 int, float False
n_lohi 0, 0 0, 0 list False
sig_lohi 3.0, 3.0 3.0, 3.0 list False
replace maxnonsat maxnonsat str False
lamaxiter 1 1 int False
grow 1.5 1.5 int, float False
rmcompact True True bool False
sigclip 5.0 5.0 int, float False
sigfrac 0.3 0.3 int, float False
objlim 5.0 5.0 int, float False
In [5]:
pypitpar.FrameGroupPar.valid_frame_types()
Out[5]:
['bias', 'pixelflat', 'arc', 'pinhole', 'trace', 'standard', 'science', 'all']
In [6]:
pypitpar.FrameGroupPar()
Out[6]:
Parameter Value Default Type Callable
-------------------------------------------------------
frametype bias bias str False
useframe bias None str False
number 0 0 int False
process see below see below ParSet, dict False
process
Parameter Value Default Type Callable
----------------------------------------------------------
overscan savgol savgol str False
overscan_par 5, 65 5, 65 int, list False
match -1 -1 int, float False
combine weightmean weightmean str False
satpix reject reject str False
sigrej 20.0 20.0 int, float False
n_lohi 0, 0 0, 0 list False
sig_lohi 3.0, 3.0 3.0, 3.0 list False
replace maxnonsat maxnonsat str False
lamaxiter 1 1 int False
grow 1.5 1.5 int, float False
rmcompact True True bool False
sigclip 5.0 5.0 int, float False
sigfrac 0.3 0.3 int, float False
objlim 5.0 5.0 int, float False
CalibrationsPar is a super set of other parameter groups that are needed for the calibration data. It is built up of 10 other parameter sets, plus a few additional single parameters like where to save the master frames. Six of these are instances of FrameGroupPar for the bias, arc, pixelflat, pinhole, trace and standard frames (see above). The remaining four set how to peform the field flattening (FlatFieldPar), determine the wavelength solution (WavelengthSolutionPar), trace the spatial position of the slits along the dispersion axis (TraceSlitsPar), and trace the shift in the wavelength solution as a function of spatial position within a slit (WaveTiltsPar)
In [7]:
pypitpar.FlatFieldPar()
Out[7]:
Parameter Value Default Type Callable
------------------------------------------------------
frame pixelflat pixelflat str False
slitprofile True True bool False
method bspline bspline str False
params 20 20 int, list False
twodpca 0 0 int False
In [8]:
pypitpar.WavelengthSolutionPar()
Out[8]:
Parameter Value Default Type Callable
-----------------------------------------------------------------
reference arc arc str False
method arclines arclines str False
lamps None None list False
detection 6.0 6.0 int, float False
numsearch 20 20 int False
nfitpix 5 5 int False
IDpixels None None int, list False
IDwaves None None int, float, list False
medium vacuum vacuum str False
frame heliocentric heliocentric str False
In [9]:
pypitpar.TraceSlitsPar()
Out[9]:
Parameter Value Default Type Callable
-----------------------------------------------------------------------
function legendre legendre str False
polyorder 3 3 int False
medrep 0 0 int False
number -1 -1 int False
trim 3, 3 3, 3 tuple False
maxgap None None int False
maxshift 0.15 0.15 int, float False
pad 0 0 int False
sigdetect 20.0 20.0 int, float False
fracignore 0.01 0.01 float False
diffpolyorder 2 2 int False
single [] [] list False
sobel_mode nearest nearest str False
pcatype pixel pixel str False
pcapar 3, 2, 1, 0, 0, 0 3, 2, 1, 0, 0, 0 list False
pcaextrap 0, 0 0, 0 list False
In [10]:
pypitpar.WaveTiltsPar()
Out[10]:
Parameter Value Default Type Callable
--------------------------------------------------------------------
idsonly False False bool False
tracethresh 1000.0 1000.0 int, float, list, ndarray False
order 2 2 int False
function legendre legendre str False
yorder 4 4 int False
func2D legendre legendre str False
method spca spca str False
params 1, 1, 0 1, 1, 0 int, list False
In [11]:
# Putting it all together, the CalibrationsPar parameter set looks like this:
pypitpar.CalibrationsPar()
Out[11]:
Parameter Value Default Type Callable
------------------------------------------------------------
caldir MF MF str False
masters None None str False
setup None None str False
trim True True bool False
badpix True True bool False
biasframe see below see below ParSet, dict False
arcframe see below see below ParSet, dict False
pixelflatframe see below see below ParSet, dict False
pinholeframe see below see below ParSet, dict False
traceframe see below see below ParSet, dict False
standardframe see below see below ParSet, dict False
flatfield see below see below ParSet, dict False
wavelengths see below see below ParSet, dict False
slits see below see below ParSet, dict False
tilts see below see below ParSet, dict False
biasframe
Parameter Value Default Type Callable
-------------------------------------------------------
frametype bias bias str False
useframe bias None str False
number 5 0 int False
process see below see below ParSet, dict False
biasframe:process
Parameter Value Default Type Callable
----------------------------------------------------------
overscan savgol savgol str False
overscan_par 5, 65 5, 65 int, list False
match -1 -1 int, float False
combine weightmean weightmean str False
satpix reject reject str False
sigrej 20.0 20.0 int, float False
n_lohi 0, 0 0, 0 list False
sig_lohi 3.0, 3.0 3.0, 3.0 list False
replace maxnonsat maxnonsat str False
lamaxiter 1 1 int False
grow 1.5 1.5 int, float False
rmcompact True True bool False
sigclip 5.0 5.0 int, float False
sigfrac 0.3 0.3 int, float False
objlim 5.0 5.0 int, float False
arcframe
Parameter Value Default Type Callable
-------------------------------------------------------
frametype arc bias str False
useframe arc None str False
number 1 0 int False
process see below see below ParSet, dict False
arcframe:process
Parameter Value Default Type Callable
----------------------------------------------------------
overscan savgol savgol str False
overscan_par 5, 65 5, 65 int, list False
match -1 -1 int, float False
combine weightmean weightmean str False
satpix reject reject str False
sigrej -1 20.0 int, float False
n_lohi 0, 0 0, 0 list False
sig_lohi 3.0, 3.0 3.0, 3.0 list False
replace maxnonsat maxnonsat str False
lamaxiter 1 1 int False
grow 1.5 1.5 int, float False
rmcompact True True bool False
sigclip 5.0 5.0 int, float False
sigfrac 0.3 0.3 int, float False
objlim 5.0 5.0 int, float False
pixelflatframe
Parameter Value Default Type Callable
-------------------------------------------------------
frametype pixelflat bias str False
useframe pixelflat None str False
number 5 0 int False
process see below see below ParSet, dict False
pixelflatframe:process
Parameter Value Default Type Callable
----------------------------------------------------------
overscan savgol savgol str False
overscan_par 5, 65 5, 65 int, list False
match -1 -1 int, float False
combine weightmean weightmean str False
satpix reject reject str False
sigrej 20.0 20.0 int, float False
n_lohi 0, 0 0, 0 list False
sig_lohi 3.0, 3.0 3.0, 3.0 list False
replace maxnonsat maxnonsat str False
lamaxiter 1 1 int False
grow 1.5 1.5 int, float False
rmcompact True True bool False
sigclip 5.0 5.0 int, float False
sigfrac 0.3 0.3 int, float False
objlim 5.0 5.0 int, float False
pinholeframe
Parameter Value Default Type Callable
-------------------------------------------------------
frametype pinhole bias str False
useframe pinhole None str False
number 0 0 int False
process see below see below ParSet, dict False
pinholeframe:process
Parameter Value Default Type Callable
----------------------------------------------------------
overscan savgol savgol str False
overscan_par 5, 65 5, 65 int, list False
match -1 -1 int, float False
combine weightmean weightmean str False
satpix reject reject str False
sigrej 20.0 20.0 int, float False
n_lohi 0, 0 0, 0 list False
sig_lohi 3.0, 3.0 3.0, 3.0 list False
replace maxnonsat maxnonsat str False
lamaxiter 1 1 int False
grow 1.5 1.5 int, float False
rmcompact True True bool False
sigclip 5.0 5.0 int, float False
sigfrac 0.3 0.3 int, float False
objlim 5.0 5.0 int, float False
traceframe
Parameter Value Default Type Callable
-------------------------------------------------------
frametype trace bias str False
useframe trace None str False
number 3 0 int False
process see below see below ParSet, dict False
traceframe:process
Parameter Value Default Type Callable
----------------------------------------------------------
overscan savgol savgol str False
overscan_par 5, 65 5, 65 int, list False
match -1 -1 int, float False
combine weightmean weightmean str False
satpix reject reject str False
sigrej 20.0 20.0 int, float False
n_lohi 0, 0 0, 0 list False
sig_lohi 3.0, 3.0 3.0, 3.0 list False
replace maxnonsat maxnonsat str False
lamaxiter 1 1 int False
grow 1.5 1.5 int, float False
rmcompact True True bool False
sigclip 5.0 5.0 int, float False
sigfrac 0.3 0.3 int, float False
objlim 5.0 5.0 int, float False
standardframe
Parameter Value Default Type Callable
-------------------------------------------------------
frametype standard bias str False
useframe standard None str False
number 1 0 int False
process see below see below ParSet, dict False
standardframe:process
Parameter Value Default Type Callable
----------------------------------------------------------
overscan savgol savgol str False
overscan_par 5, 65 5, 65 int, list False
match -1 -1 int, float False
combine weightmean weightmean str False
satpix reject reject str False
sigrej 20.0 20.0 int, float False
n_lohi 0, 0 0, 0 list False
sig_lohi 3.0, 3.0 3.0, 3.0 list False
replace maxnonsat maxnonsat str False
lamaxiter 1 1 int False
grow 1.5 1.5 int, float False
rmcompact True True bool False
sigclip 5.0 5.0 int, float False
sigfrac 0.3 0.3 int, float False
objlim 5.0 5.0 int, float False
flatfield
Parameter Value Default Type Callable
------------------------------------------------------
frame pixelflat pixelflat str False
slitprofile True True bool False
method bspline bspline str False
params 20 20 int, list False
twodpca 0 0 int False
wavelengths
Parameter Value Default Type Callable
-----------------------------------------------------------------
reference arc arc str False
method arclines arclines str False
lamps None None list False
detection 6.0 6.0 int, float False
numsearch 20 20 int False
nfitpix 5 5 int False
IDpixels None None int, list False
IDwaves None None int, float, list False
medium vacuum vacuum str False
frame heliocentric heliocentric str False
slits
Parameter Value Default Type Callable
-----------------------------------------------------------------------
function legendre legendre str False
polyorder 3 3 int False
medrep 0 0 int False
number -1 -1 int False
trim 3, 3 3, 3 tuple False
maxgap None None int False
maxshift 0.15 0.15 int, float False
pad 0 0 int False
sigdetect 20.0 20.0 int, float False
fracignore 0.01 0.01 float False
diffpolyorder 2 2 int False
single [] [] list False
sobel_mode nearest nearest str False
pcatype pixel pixel str False
pcapar 3, 2, 1, 0, 0, 0 3, 2, 1, 0, 0, 0 list False
pcaextrap 0, 0 0, 0 list False
tilts
Parameter Value Default Type Callable
--------------------------------------------------------------------
idsonly False False bool False
tracethresh 1000.0 1000.0 int, float, list, ndarray False
order 2 2 int False
function legendre legendre str False
yorder 4 4 int False
func2D legendre legendre str False
method spca spca str False
params 1, 1, 0 1, 1, 0 int, list False
In [12]:
pypitpar.TraceObjectsPar()
Out[12]:
Parameter Value Default Type Callable
---------------------------------------------------
function legendre legendre str False
order 2 2 int False
find standard standard str False
nsmooth 3 3 int, float False
xedge 0.03 0.03 float False
method pca pca str False
params 1, 0 1, 0 int, list False
In [13]:
pypitpar.ManualExtractionPar()
Out[13]:
Parameter Value Default Type Callable
-----------------------------------------
frame None None str False
params None None list False
Then the manual parameter in the ExtractObjectsPar is a list of the ManualExtractionPar objects for all the manual extractions to perform. The number of manual extractions is just the length of the list or 0 if the element is None.
In [14]:
p = pypitpar.ExtractObjectsPar()
print(p) # The printing goes a bit wrong for 'manual'
nmanual = 0 if p['manual'] is None else len(p['manual'])
print('Manual extractions to perform: {0}'.format(nmanual))
Parameter Value Default Type Callable
----------------------------------------------------
pixelmap None None str False
pixelwidth 2.5 2.5 int, float False
reuse False False bool False
profile gaussian gaussian str False
maxnumber None None int False
manual None None list False
Manual extractions to perform: 0
Finally, there are parameter sets that used for the sky subtraction, flexure correction, and flux calibration.
In [15]:
#6
pypitpar.SkySubtractionPar()
Out[15]:
Parameter Value Default Type Callable
-----------------------------------------------------
bspline_spacing 0.6 0.6 int, float False
nodding False False bool False
In [16]:
#3
pypitpar.FlexurePar()
Out[16]:
Parameter Value Default Type Callable
------------------------------------------------
method boxcar boxcar str False
maxshift 20 20 int, float False
spectrum None None str False
In [17]:
#5
pypitpar.FluxCalibrationPar()
Out[17]:
Parameter Value Default Type Callable
-----------------------------------------
nonlinear False False bool False
sensfunc None None str False
All of the above are expected to be parameter subsets that are passed to individual methods. Sticking with the idea of having a single object that provides all the parameters needed for a run of pypit, the PypitPar object just collects all the above objects into a single parameter set.
In [18]:
pypitpar.PypitPar()
Out[18]:
Parameter Value Default Type Callable
----------------------------------------------------------
rdx see below see below ParSet, dict False
calibrations see below see below ParSet, dict False
scienceframe see below see below ParSet, dict False
objects see below see below ParSet, dict False
extract see below see below ParSet, dict False
skysubtract None None ParSet, dict False
flexure None None ParSet, dict False
fluxcalib None None ParSet, dict False
rdx
Parameter Value Default Type Callable
----------------------------------------------------
spectrograph None None str False
pipeline None None str False
detnum None None list False
sortroot None None str False
calwin 0 0 int, float False
scidir Science Science str False
qadir QA QA str False
calibrations
Parameter Value Default Type Callable
------------------------------------------------------------
caldir MF MF str False
masters None None str False
setup None None str False
trim True True bool False
badpix True True bool False
biasframe see below see below ParSet, dict False
arcframe see below see below ParSet, dict False
pixelflatframe see below see below ParSet, dict False
pinholeframe see below see below ParSet, dict False
traceframe see below see below ParSet, dict False
standardframe see below see below ParSet, dict False
flatfield see below see below ParSet, dict False
wavelengths see below see below ParSet, dict False
slits see below see below ParSet, dict False
tilts see below see below ParSet, dict False
calibrations:biasframe
Parameter Value Default Type Callable
-------------------------------------------------------
frametype bias bias str False
useframe bias None str False
number 5 0 int False
process see below see below ParSet, dict False
calibrations:biasframe:process
Parameter Value Default Type Callable
----------------------------------------------------------
overscan savgol savgol str False
overscan_par 5, 65 5, 65 int, list False
match -1 -1 int, float False
combine weightmean weightmean str False
satpix reject reject str False
sigrej 20.0 20.0 int, float False
n_lohi 0, 0 0, 0 list False
sig_lohi 3.0, 3.0 3.0, 3.0 list False
replace maxnonsat maxnonsat str False
lamaxiter 1 1 int False
grow 1.5 1.5 int, float False
rmcompact True True bool False
sigclip 5.0 5.0 int, float False
sigfrac 0.3 0.3 int, float False
objlim 5.0 5.0 int, float False
calibrations:arcframe
Parameter Value Default Type Callable
-------------------------------------------------------
frametype arc bias str False
useframe arc None str False
number 1 0 int False
process see below see below ParSet, dict False
calibrations:arcframe:process
Parameter Value Default Type Callable
----------------------------------------------------------
overscan savgol savgol str False
overscan_par 5, 65 5, 65 int, list False
match -1 -1 int, float False
combine weightmean weightmean str False
satpix reject reject str False
sigrej -1 20.0 int, float False
n_lohi 0, 0 0, 0 list False
sig_lohi 3.0, 3.0 3.0, 3.0 list False
replace maxnonsat maxnonsat str False
lamaxiter 1 1 int False
grow 1.5 1.5 int, float False
rmcompact True True bool False
sigclip 5.0 5.0 int, float False
sigfrac 0.3 0.3 int, float False
objlim 5.0 5.0 int, float False
calibrations:pixelflatframe
Parameter Value Default Type Callable
-------------------------------------------------------
frametype pixelflat bias str False
useframe pixelflat None str False
number 5 0 int False
process see below see below ParSet, dict False
calibrations:pixelflatframe:process
Parameter Value Default Type Callable
----------------------------------------------------------
overscan savgol savgol str False
overscan_par 5, 65 5, 65 int, list False
match -1 -1 int, float False
combine weightmean weightmean str False
satpix reject reject str False
sigrej 20.0 20.0 int, float False
n_lohi 0, 0 0, 0 list False
sig_lohi 3.0, 3.0 3.0, 3.0 list False
replace maxnonsat maxnonsat str False
lamaxiter 1 1 int False
grow 1.5 1.5 int, float False
rmcompact True True bool False
sigclip 5.0 5.0 int, float False
sigfrac 0.3 0.3 int, float False
objlim 5.0 5.0 int, float False
calibrations:pinholeframe
Parameter Value Default Type Callable
-------------------------------------------------------
frametype pinhole bias str False
useframe pinhole None str False
number 0 0 int False
process see below see below ParSet, dict False
calibrations:pinholeframe:process
Parameter Value Default Type Callable
----------------------------------------------------------
overscan savgol savgol str False
overscan_par 5, 65 5, 65 int, list False
match -1 -1 int, float False
combine weightmean weightmean str False
satpix reject reject str False
sigrej 20.0 20.0 int, float False
n_lohi 0, 0 0, 0 list False
sig_lohi 3.0, 3.0 3.0, 3.0 list False
replace maxnonsat maxnonsat str False
lamaxiter 1 1 int False
grow 1.5 1.5 int, float False
rmcompact True True bool False
sigclip 5.0 5.0 int, float False
sigfrac 0.3 0.3 int, float False
objlim 5.0 5.0 int, float False
calibrations:traceframe
Parameter Value Default Type Callable
-------------------------------------------------------
frametype trace bias str False
useframe trace None str False
number 3 0 int False
process see below see below ParSet, dict False
calibrations:traceframe:process
Parameter Value Default Type Callable
----------------------------------------------------------
overscan savgol savgol str False
overscan_par 5, 65 5, 65 int, list False
match -1 -1 int, float False
combine weightmean weightmean str False
satpix reject reject str False
sigrej 20.0 20.0 int, float False
n_lohi 0, 0 0, 0 list False
sig_lohi 3.0, 3.0 3.0, 3.0 list False
replace maxnonsat maxnonsat str False
lamaxiter 1 1 int False
grow 1.5 1.5 int, float False
rmcompact True True bool False
sigclip 5.0 5.0 int, float False
sigfrac 0.3 0.3 int, float False
objlim 5.0 5.0 int, float False
calibrations:standardframe
Parameter Value Default Type Callable
-------------------------------------------------------
frametype standard bias str False
useframe standard None str False
number 1 0 int False
process see below see below ParSet, dict False
calibrations:standardframe:process
Parameter Value Default Type Callable
----------------------------------------------------------
overscan savgol savgol str False
overscan_par 5, 65 5, 65 int, list False
match -1 -1 int, float False
combine weightmean weightmean str False
satpix reject reject str False
sigrej 20.0 20.0 int, float False
n_lohi 0, 0 0, 0 list False
sig_lohi 3.0, 3.0 3.0, 3.0 list False
replace maxnonsat maxnonsat str False
lamaxiter 1 1 int False
grow 1.5 1.5 int, float False
rmcompact True True bool False
sigclip 5.0 5.0 int, float False
sigfrac 0.3 0.3 int, float False
objlim 5.0 5.0 int, float False
calibrations:flatfield
Parameter Value Default Type Callable
------------------------------------------------------
frame pixelflat pixelflat str False
slitprofile True True bool False
method bspline bspline str False
params 20 20 int, list False
twodpca 0 0 int False
calibrations:wavelengths
Parameter Value Default Type Callable
-----------------------------------------------------------------
reference arc arc str False
method arclines arclines str False
lamps None None list False
detection 6.0 6.0 int, float False
numsearch 20 20 int False
nfitpix 5 5 int False
IDpixels None None int, list False
IDwaves None None int, float, list False
medium vacuum vacuum str False
frame heliocentric heliocentric str False
calibrations:slits
Parameter Value Default Type Callable
-----------------------------------------------------------------------
function legendre legendre str False
polyorder 3 3 int False
medrep 0 0 int False
number -1 -1 int False
trim 3, 3 3, 3 tuple False
maxgap None None int False
maxshift 0.15 0.15 int, float False
pad 0 0 int False
sigdetect 20.0 20.0 int, float False
fracignore 0.01 0.01 float False
diffpolyorder 2 2 int False
single [] [] list False
sobel_mode nearest nearest str False
pcatype pixel pixel str False
pcapar 3, 2, 1, 0, 0, 0 3, 2, 1, 0, 0, 0 list False
pcaextrap 0, 0 0, 0 list False
calibrations:tilts
Parameter Value Default Type Callable
--------------------------------------------------------------------
idsonly False False bool False
tracethresh 1000.0 1000.0 int, float, list, ndarray False
order 2 2 int False
function legendre legendre str False
yorder 4 4 int False
func2D legendre legendre str False
method spca spca str False
params 1, 1, 0 1, 1, 0 int, list False
scienceframe
Parameter Value Default Type Callable
-------------------------------------------------------
frametype science bias str False
useframe science None str False
number 0 0 int False
process see below see below ParSet, dict False
scienceframe:process
Parameter Value Default Type Callable
----------------------------------------------------------
overscan savgol savgol str False
overscan_par 5, 65 5, 65 int, list False
match -1 -1 int, float False
combine weightmean weightmean str False
satpix reject reject str False
sigrej 20.0 20.0 int, float False
n_lohi 0, 0 0, 0 list False
sig_lohi 3.0, 3.0 3.0, 3.0 list False
replace maxnonsat maxnonsat str False
lamaxiter 1 1 int False
grow 1.5 1.5 int, float False
rmcompact True True bool False
sigclip 5.0 5.0 int, float False
sigfrac 0.3 0.3 int, float False
objlim 5.0 5.0 int, float False
objects
Parameter Value Default Type Callable
---------------------------------------------------
function legendre legendre str False
order 2 2 int False
find standard standard str False
nsmooth 3 3 int, float False
xedge 0.03 0.03 float False
method pca pca str False
params 1, 0 1, 0 int, list False
extract
Parameter Value Default Type Callable
----------------------------------------------------
pixelmap None None str False
pixelwidth 2.5 2.5 int, float False
reuse False False bool False
profile gaussian gaussian str False
maxnumber None None int False
manual None None list False
Like all the other pypit parameter sets, PypitPar has a from_dict method, but it also has a from_cfg_file that allows you to read and write the full parameter sets to a *.cfg config file. However, for runs of pypit, we're most often going to be reading the configuration from a group of lines in the *.pypit file. Here's a short demo of how to read and write the pypit parameters to a *.cfg; writing may be useful to see the full set of parameters along with the description of each parameter.
In [19]:
help(pypitpar.PypitPar.from_cfg_file)
Help on method from_cfg_file in module pypit.par.pypitpar:
from_cfg_file(cfg_file=None, merge_with=None, evaluate=True) method of builtins.type instance
Construct the parameter set using a configuration file.
Note that::
default = PypitPar()
nofile = PypitPar.from_cfg_file()
assert default.data == nofile.data, 'This should always pass.'
Args:
cfg_file (:obj:`str`, optional):
The name of the configuration file that defines the
default parameters. This can be used to load a pypit
config file from a previous run that was constructed and
output by pypit. This has to contain the full set of
parameters, not just the subset you want to change. For
the latter, use :arg:`merge_with` to provide one or more
config files to merge with the defaults to construct the
full parameter set.
merge_with (:obj:`str`, :obj:`list`, optional):
One or more config files with the modifications to
either default parameters (:arg:`cfg_file` is None) or
the parameters provided by :arg:`cfg_file`. The
modifications are performed in series so the list order
of the config files is important.
evaluate (:obj:`bool`, optional):
Evaluate the values in the config object before
assigning them in the subsequent parameter sets. The
parameters in the config file are *always* read as
strings, so this should almost always be true; however,
see the warning below.
.. warning::
When :arg:`evaluate` is true, the function runs `eval()` on
all the entries in the `ConfigObj` dictionary, done using
:func:`_recursive_dict_evaluate`. This has the potential to
go haywire if the name of a parameter unintentionally
happens to be identical to an imported or system-level
function. Of course, this can be useful by allowing one to
define the function to use as a parameter, but it also means
one has to be careful with the values that the parameters
should be allowed to have. The current way around this is
to provide a list of strings that should be ignored during
the evaluation, done using :func:`_eval_ignore`.
.. todo::
Allow the user to add to the ignored strings.
Returns:
:class:`pypit.par.core.PypitPar`: The instance of the
parameter set.
You can get the default parameters and print the result like this.
In [20]:
# Write the defaults
p = pypitpar.PypitPar.from_cfg_file()
p.to_config('default.cfg')
You can then read it back in. The expand_spectrograph option allows you to set all the spectrograph setting using the spectrograph keyword in the input config file (this is KECK_LRISb by default). If you just want to use what's in the config file without finding the spectrograph configuration file (because those keywords are already in the configuration file in this example), you would set expand_spectrograph=False.
In [21]:
# Read them in
p = pypitpar.PypitPar.from_cfg_file('default.cfg')
p['rdx']['spectrograph'] is None
Out[21]:
True
In [22]:
from pypit.par import PypitPar
In [23]:
from pypit import pypitsetup
pypit_file = '../../pypit/tests/files/example_pypit_file.pypit'
setup = pypitsetup.PypitSetup.from_pypit_file(pypit_file)
par, spectrograph, fitstbl, setup_dict = setup.run()
[INFO] :: Loading the reduction file
[INFO] :: Found 2 raw data frames
[INFO] :: Input file loaded successfully
[WARNING] :: UTC is not listed as a header keyword in file:
/Users/westfall/Work/packages/PYPIT/pypit/tests/files/b1.fits.gz
[WARNING] :: BINNING keyword not in header. Setting to None
[INFO] :: Successfully loaded headers for file:
/Users/westfall/Work/packages/PYPIT/pypit/tests/files/b1.fits.gz
[WARNING] :: UTC is not listed as a header keyword in file:
/Users/westfall/Work/packages/PYPIT/pypit/tests/files/b27.fits.gz
[WARNING] :: BINNING keyword not in header. Setting to None
[INFO] :: Successfully loaded headers for file:
/Users/westfall/Work/packages/PYPIT/pypit/tests/files/b27.fits.gz
[INFO] :: Checking spectrograph settings for required header information
[INFO] :: Headers loaded for 2 files successfully
[INFO] :: Typing files
[INFO] :: Adding file type information to the fitstbl
[INFO] :: Matching calibrations to Science frames
[INFO] :: =================================================
[INFO] :: Matching calibrations to J1217p3905: b27.fits.gz
[INFO] :: Found 1 arc frame for J1217p3905 (1 required)
[INFO] :: No bias frames are required. Not matching..
[INFO] :: Dark frames not required. Not matching..
[INFO] :: No pinhole frames are required. Not matching..
[INFO] :: No pixelflat frames are required. Not matching..
[INFO] :: No standard frames are required. Not matching..
[INFO] :: No trace frames are required. Not matching..
[INFO] :: Science frames successfully matched to calibration frames
In [24]:
# The compiled parameter set is in par
print(par)
Parameter Value Default Type Callable
----------------------------------------------------------
rdx see below see below ParSet, dict False
calibrations see below see below ParSet, dict False
scienceframe see below see below ParSet, dict False
objects see below see below ParSet, dict False
extract see below see below ParSet, dict False
skysubtract see below see below ParSet, dict False
flexure see below see below ParSet, dict False
fluxcalib see below see below ParSet, dict False
rdx
Parameter Value Default Type Callable
--------------------------------------------------------------------
spectrograph shane_kast_blue None str False
pipeline ARMS None str False
detnum None None list False
sortroot shane_kast_blue_setup_A None str False
calwin 0 0 int, float False
scidir Science Science str False
qadir QA QA str False
calibrations
Parameter Value Default Type Callable
------------------------------------------------------------
caldir MF MF str False
masters None None str False
setup None None str False
trim True True bool False
badpix True True bool False
biasframe see below see below ParSet, dict False
arcframe see below see below ParSet, dict False
pixelflatframe see below see below ParSet, dict False
pinholeframe see below see below ParSet, dict False
traceframe see below see below ParSet, dict False
standardframe see below see below ParSet, dict False
flatfield see below see below ParSet, dict False
wavelengths see below see below ParSet, dict False
slits see below see below ParSet, dict False
tilts see below see below ParSet, dict False
calibrations:biasframe
Parameter Value Default Type Callable
-------------------------------------------------------
frametype bias bias str False
useframe bias None str False
number 0 0 int False
process see below see below ParSet, dict False
calibrations:biasframe:process
Parameter Value Default Type Callable
---------------------------------------------------------
overscan savgol savgol str False
overscan_par 5, 65 5, 65 int, list False
match -1 -1 int, float False
combine mean weightmean str False
satpix reject reject str False
sigrej 30 20.0 int, float False
n_lohi 0, 0 0, 0 list False
sig_lohi 10, 10 3.0, 3.0 list False
replace maxnonsat maxnonsat str False
lamaxiter 1 1 int False
grow 1.5 1.5 int, float False
rmcompact True True bool False
sigclip 5.0 5.0 int, float False
sigfrac 0.3 0.3 int, float False
objlim 5.0 5.0 int, float False
calibrations:arcframe
Parameter Value Default Type Callable
-------------------------------------------------------
frametype arc bias str False
useframe arc None str False
number 1 0 int False
process see below see below ParSet, dict False
calibrations:arcframe:process
Parameter Value Default Type Callable
---------------------------------------------------------
overscan savgol savgol str False
overscan_par 5, 65 5, 65 int, list False
match -1 -1 int, float False
combine mean weightmean str False
satpix reject reject str False
sigrej -1 20.0 int, float False
n_lohi 0, 0 0, 0 list False
sig_lohi 3.0, 3.0 3.0, 3.0 list False
replace maxnonsat maxnonsat str False
lamaxiter 1 1 int False
grow 1.5 1.5 int, float False
rmcompact True True bool False
sigclip 5.0 5.0 int, float False
sigfrac 0.3 0.3 int, float False
objlim 5.0 5.0 int, float False
calibrations:pixelflatframe
Parameter Value Default Type Callable
-------------------------------------------------------
frametype pixelflat bias str False
useframe pixelflat None str False
number 0 0 int False
process see below see below ParSet, dict False
calibrations:pixelflatframe:process
Parameter Value Default Type Callable
---------------------------------------------------------
overscan savgol savgol str False
overscan_par 5, 65 5, 65 int, list False
match -1 -1 int, float False
combine mean weightmean str False
satpix reject reject str False
sigrej 30 20.0 int, float False
n_lohi 0, 0 0, 0 list False
sig_lohi 3.0, 3.0 3.0, 3.0 list False
replace maxnonsat maxnonsat str False
lamaxiter 1 1 int False
grow 1.5 1.5 int, float False
rmcompact True True bool False
sigclip 5.0 5.0 int, float False
sigfrac 0.3 0.3 int, float False
objlim 5.0 5.0 int, float False
calibrations:pinholeframe
Parameter Value Default Type Callable
-------------------------------------------------------
frametype pinhole bias str False
useframe pinhole None str False
number 0 0 int False
process see below see below ParSet, dict False
calibrations:pinholeframe:process
Parameter Value Default Type Callable
---------------------------------------------------------
overscan savgol savgol str False
overscan_par 5, 65 5, 65 int, list False
match -1 -1 int, float False
combine mean weightmean str False
satpix reject reject str False
sigrej 30 20.0 int, float False
n_lohi 0, 0 0, 0 list False
sig_lohi 3.0, 3.0 3.0, 3.0 list False
replace maxnonsat maxnonsat str False
lamaxiter 1 1 int False
grow 1.5 1.5 int, float False
rmcompact True True bool False
sigclip 5.0 5.0 int, float False
sigfrac 0.3 0.3 int, float False
objlim 5.0 5.0 int, float False
calibrations:traceframe
Parameter Value Default Type Callable
-------------------------------------------------------
frametype trace bias str False
useframe trace None str False
number 0 0 int False
process see below see below ParSet, dict False
calibrations:traceframe:process
Parameter Value Default Type Callable
---------------------------------------------------------
overscan savgol savgol str False
overscan_par 5, 65 5, 65 int, list False
match -1 -1 int, float False
combine mean weightmean str False
satpix reject reject str False
sigrej 30 20.0 int, float False
n_lohi 0, 0 0, 0 list False
sig_lohi 3.0, 3.0 3.0, 3.0 list False
replace maxnonsat maxnonsat str False
lamaxiter 1 1 int False
grow 1.5 1.5 int, float False
rmcompact True True bool False
sigclip 5.0 5.0 int, float False
sigfrac 0.3 0.3 int, float False
objlim 5.0 5.0 int, float False
calibrations:standardframe
Parameter Value Default Type Callable
-------------------------------------------------------
frametype standard bias str False
useframe standard None str False
number 0 0 int False
process see below see below ParSet, dict False
calibrations:standardframe:process
Parameter Value Default Type Callable
---------------------------------------------------------
overscan savgol savgol str False
overscan_par 5, 65 5, 65 int, list False
match -1 -1 int, float False
combine mean weightmean str False
satpix reject reject str False
sigrej 30 20.0 int, float False
n_lohi 0, 0 0, 0 list False
sig_lohi 3.0, 3.0 3.0, 3.0 list False
replace maxnonsat maxnonsat str False
lamaxiter 1 1 int False
grow 1.5 1.5 int, float False
rmcompact True True bool False
sigclip 5.0 5.0 int, float False
sigfrac 0.3 0.3 int, float False
objlim 5.0 5.0 int, float False
calibrations:flatfield
Parameter Value Default Type Callable
------------------------------------------------------
frame pixelflat pixelflat str False
slitprofile True True bool False
method bspline bspline str False
params 20 20 int, list False
twodpca 0 0 int False
calibrations:wavelengths
Parameter Value Default Type Callable
-----------------------------------------------------------------
reference arc arc str False
method arclines arclines str False
lamps None None list False
detection 6.0 6.0 int, float False
numsearch 20 20 int False
nfitpix 5 5 int False
IDpixels None None int, list False
IDwaves None None int, float, list False
medium vacuum vacuum str False
frame heliocentric heliocentric str False
calibrations:slits
Parameter Value Default Type Callable
-----------------------------------------------------------------------
function legendre legendre str False
polyorder 3 3 int False
medrep 0 0 int False
number -1 -1 int False
trim 3, 3 3, 3 tuple False
maxgap None None int False
maxshift 0.15 0.15 int, float False
pad 0 0 int False
sigdetect 20.0 20.0 int, float False
fracignore 0.01 0.01 float False
diffpolyorder 2 2 int False
single [] [] list False
sobel_mode nearest nearest str False
pcatype pixel pixel str False
pcapar 3, 2, 1, 0, 0, 0 3, 2, 1, 0, 0, 0 list False
pcaextrap 0, 0 0, 0 list False
calibrations:tilts
Parameter Value Default Type Callable
--------------------------------------------------------------------
idsonly False False bool False
tracethresh 1000.0 1000.0 int, float, list, ndarray False
order 2 2 int False
function legendre legendre str False
yorder 4 4 int False
func2D legendre legendre str False
method spca spca str False
params 1, 1, 0 1, 1, 0 int, list False
scienceframe
Parameter Value Default Type Callable
-------------------------------------------------------
frametype science bias str False
useframe science None str False
number 0 0 int False
process see below see below ParSet, dict False
scienceframe:process
Parameter Value Default Type Callable
---------------------------------------------------------
overscan savgol savgol str False
overscan_par 5, 65 5, 65 int, list False
match -1 -1 int, float False
combine mean weightmean str False
satpix reject reject str False
sigrej 30 20.0 int, float False
n_lohi 8, 8 0, 0 list False
sig_lohi 3.0, 3.0 3.0, 3.0 list False
replace maxnonsat maxnonsat str False
lamaxiter 1 1 int False
grow 1.5 1.5 int, float False
rmcompact True True bool False
sigclip 5.0 5.0 int, float False
sigfrac 0.3 0.3 int, float False
objlim 5.0 5.0 int, float False
objects
Parameter Value Default Type Callable
---------------------------------------------------
function legendre legendre str False
order 2 2 int False
find standard standard str False
nsmooth 3 3 int, float False
xedge 0.03 0.03 float False
method pca pca str False
params 1, 0 1, 0 int, list False
extract
Parameter Value Default Type Callable
----------------------------------------------------
pixelmap None None str False
pixelwidth 2.5 2.5 int, float False
reuse False False bool False
profile gaussian gaussian str False
maxnumber None None int False
manual None None list False
skysubtract
Parameter Value Default Type Callable
-----------------------------------------------------
bspline_spacing 0.6 0.6 int, float False
nodding False False bool False
flexure
Parameter Value Default Type Callable
------------------------------------------------
method boxcar boxcar str False
maxshift 20 20 int, float False
spectrum None None str False
fluxcalib
Parameter Value Default Type Callable
-----------------------------------------
nonlinear False False bool False
sensfunc None None str False
In [25]:
from pypit.par.util import parse_pypit_file
from pypit.spectrographs.util import load_spectrograph
# Read the PypeIt file
cfg, data, frametype, setups = parse_pypit_file(pypit_file) #,file_check=False)
# Long-winded way of getting the spectrograph name
name = pypitpar.PypitPar.from_cfg_lines(merge_with=cfg)['rdx']['spectrograph']
# Instantiate the spectrograph
spectrograph = load_spectrograph(name)
# Get the spectrograph specific configuration
spec_cfg = spectrograph.default_pypit_par().to_config()
# Initialize the PypeIt parameters merge in the user config
par = pypitpar.PypitPar.from_cfg_lines(cfg_lines=spec_cfg, merge_with=cfg)
print(par)
Parameter Value Default Type Callable
----------------------------------------------------------
rdx see below see below ParSet, dict False
calibrations see below see below ParSet, dict False
scienceframe see below see below ParSet, dict False
objects see below see below ParSet, dict False
extract see below see below ParSet, dict False
skysubtract see below see below ParSet, dict False
flexure see below see below ParSet, dict False
fluxcalib see below see below ParSet, dict False
rdx
Parameter Value Default Type Callable
--------------------------------------------------------------------
spectrograph shane_kast_blue None str False
pipeline ARMS None str False
detnum None None list False
sortroot shane_kast_blue_setup_A None str False
calwin 0 0 int, float False
scidir Science Science str False
qadir QA QA str False
calibrations
Parameter Value Default Type Callable
------------------------------------------------------------
caldir MF MF str False
masters None None str False
setup None None str False
trim True True bool False
badpix True True bool False
biasframe see below see below ParSet, dict False
arcframe see below see below ParSet, dict False
pixelflatframe see below see below ParSet, dict False
pinholeframe see below see below ParSet, dict False
traceframe see below see below ParSet, dict False
standardframe see below see below ParSet, dict False
flatfield see below see below ParSet, dict False
wavelengths see below see below ParSet, dict False
slits see below see below ParSet, dict False
tilts see below see below ParSet, dict False
calibrations:biasframe
Parameter Value Default Type Callable
-------------------------------------------------------
frametype bias bias str False
useframe bias None str False
number 0 0 int False
process see below see below ParSet, dict False
calibrations:biasframe:process
Parameter Value Default Type Callable
---------------------------------------------------------
overscan savgol savgol str False
overscan_par 5, 65 5, 65 int, list False
match -1 -1 int, float False
combine mean weightmean str False
satpix reject reject str False
sigrej 30 20.0 int, float False
n_lohi 0, 0 0, 0 list False
sig_lohi 10, 10 3.0, 3.0 list False
replace maxnonsat maxnonsat str False
lamaxiter 1 1 int False
grow 1.5 1.5 int, float False
rmcompact True True bool False
sigclip 5.0 5.0 int, float False
sigfrac 0.3 0.3 int, float False
objlim 5.0 5.0 int, float False
calibrations:arcframe
Parameter Value Default Type Callable
-------------------------------------------------------
frametype arc bias str False
useframe arc None str False
number 1 0 int False
process see below see below ParSet, dict False
calibrations:arcframe:process
Parameter Value Default Type Callable
---------------------------------------------------------
overscan savgol savgol str False
overscan_par 5, 65 5, 65 int, list False
match -1 -1 int, float False
combine mean weightmean str False
satpix reject reject str False
sigrej -1 20.0 int, float False
n_lohi 0, 0 0, 0 list False
sig_lohi 3.0, 3.0 3.0, 3.0 list False
replace maxnonsat maxnonsat str False
lamaxiter 1 1 int False
grow 1.5 1.5 int, float False
rmcompact True True bool False
sigclip 5.0 5.0 int, float False
sigfrac 0.3 0.3 int, float False
objlim 5.0 5.0 int, float False
calibrations:pixelflatframe
Parameter Value Default Type Callable
-------------------------------------------------------
frametype pixelflat bias str False
useframe pixelflat None str False
number 0 0 int False
process see below see below ParSet, dict False
calibrations:pixelflatframe:process
Parameter Value Default Type Callable
---------------------------------------------------------
overscan savgol savgol str False
overscan_par 5, 65 5, 65 int, list False
match -1 -1 int, float False
combine mean weightmean str False
satpix reject reject str False
sigrej 30 20.0 int, float False
n_lohi 0, 0 0, 0 list False
sig_lohi 3.0, 3.0 3.0, 3.0 list False
replace maxnonsat maxnonsat str False
lamaxiter 1 1 int False
grow 1.5 1.5 int, float False
rmcompact True True bool False
sigclip 5.0 5.0 int, float False
sigfrac 0.3 0.3 int, float False
objlim 5.0 5.0 int, float False
calibrations:pinholeframe
Parameter Value Default Type Callable
-------------------------------------------------------
frametype pinhole bias str False
useframe pinhole None str False
number 0 0 int False
process see below see below ParSet, dict False
calibrations:pinholeframe:process
Parameter Value Default Type Callable
---------------------------------------------------------
overscan savgol savgol str False
overscan_par 5, 65 5, 65 int, list False
match -1 -1 int, float False
combine mean weightmean str False
satpix reject reject str False
sigrej 30 20.0 int, float False
n_lohi 0, 0 0, 0 list False
sig_lohi 3.0, 3.0 3.0, 3.0 list False
replace maxnonsat maxnonsat str False
lamaxiter 1 1 int False
grow 1.5 1.5 int, float False
rmcompact True True bool False
sigclip 5.0 5.0 int, float False
sigfrac 0.3 0.3 int, float False
objlim 5.0 5.0 int, float False
calibrations:traceframe
Parameter Value Default Type Callable
-------------------------------------------------------
frametype trace bias str False
useframe trace None str False
number 0 0 int False
process see below see below ParSet, dict False
calibrations:traceframe:process
Parameter Value Default Type Callable
---------------------------------------------------------
overscan savgol savgol str False
overscan_par 5, 65 5, 65 int, list False
match -1 -1 int, float False
combine mean weightmean str False
satpix reject reject str False
sigrej 30 20.0 int, float False
n_lohi 0, 0 0, 0 list False
sig_lohi 3.0, 3.0 3.0, 3.0 list False
replace maxnonsat maxnonsat str False
lamaxiter 1 1 int False
grow 1.5 1.5 int, float False
rmcompact True True bool False
sigclip 5.0 5.0 int, float False
sigfrac 0.3 0.3 int, float False
objlim 5.0 5.0 int, float False
calibrations:standardframe
Parameter Value Default Type Callable
-------------------------------------------------------
frametype standard bias str False
useframe standard None str False
number 0 0 int False
process see below see below ParSet, dict False
calibrations:standardframe:process
Parameter Value Default Type Callable
---------------------------------------------------------
overscan savgol savgol str False
overscan_par 5, 65 5, 65 int, list False
match -1 -1 int, float False
combine mean weightmean str False
satpix reject reject str False
sigrej 30 20.0 int, float False
n_lohi 0, 0 0, 0 list False
sig_lohi 3.0, 3.0 3.0, 3.0 list False
replace maxnonsat maxnonsat str False
lamaxiter 1 1 int False
grow 1.5 1.5 int, float False
rmcompact True True bool False
sigclip 5.0 5.0 int, float False
sigfrac 0.3 0.3 int, float False
objlim 5.0 5.0 int, float False
calibrations:flatfield
Parameter Value Default Type Callable
------------------------------------------------------
frame pixelflat pixelflat str False
slitprofile True True bool False
method bspline bspline str False
params 20 20 int, list False
twodpca 0 0 int False
calibrations:wavelengths
Parameter Value Default Type Callable
-----------------------------------------------------------------
reference arc arc str False
method arclines arclines str False
lamps None None list False
detection 6.0 6.0 int, float False
numsearch 20 20 int False
nfitpix 5 5 int False
IDpixels None None int, list False
IDwaves None None int, float, list False
medium vacuum vacuum str False
frame heliocentric heliocentric str False
calibrations:slits
Parameter Value Default Type Callable
-----------------------------------------------------------------------
function legendre legendre str False
polyorder 3 3 int False
medrep 0 0 int False
number -1 -1 int False
trim 3, 3 3, 3 tuple False
maxgap None None int False
maxshift 0.15 0.15 int, float False
pad 0 0 int False
sigdetect 20.0 20.0 int, float False
fracignore 0.01 0.01 float False
diffpolyorder 2 2 int False
single [] [] list False
sobel_mode nearest nearest str False
pcatype pixel pixel str False
pcapar 3, 2, 1, 0, 0, 0 3, 2, 1, 0, 0, 0 list False
pcaextrap 0, 0 0, 0 list False
calibrations:tilts
Parameter Value Default Type Callable
--------------------------------------------------------------------
idsonly False False bool False
tracethresh 1000.0 1000.0 int, float, list, ndarray False
order 2 2 int False
function legendre legendre str False
yorder 4 4 int False
func2D legendre legendre str False
method spca spca str False
params 1, 1, 0 1, 1, 0 int, list False
scienceframe
Parameter Value Default Type Callable
-------------------------------------------------------
frametype science bias str False
useframe science None str False
number 0 0 int False
process see below see below ParSet, dict False
scienceframe:process
Parameter Value Default Type Callable
---------------------------------------------------------
overscan savgol savgol str False
overscan_par 5, 65 5, 65 int, list False
match -1 -1 int, float False
combine mean weightmean str False
satpix reject reject str False
sigrej 30 20.0 int, float False
n_lohi 8, 8 0, 0 list False
sig_lohi 3.0, 3.0 3.0, 3.0 list False
replace maxnonsat maxnonsat str False
lamaxiter 1 1 int False
grow 1.5 1.5 int, float False
rmcompact True True bool False
sigclip 5.0 5.0 int, float False
sigfrac 0.3 0.3 int, float False
objlim 5.0 5.0 int, float False
objects
Parameter Value Default Type Callable
---------------------------------------------------
function legendre legendre str False
order 2 2 int False
find standard standard str False
nsmooth 3 3 int, float False
xedge 0.03 0.03 float False
method pca pca str False
params 1, 0 1, 0 int, list False
extract
Parameter Value Default Type Callable
----------------------------------------------------
pixelmap None None str False
pixelwidth 2.5 2.5 int, float False
reuse False False bool False
profile gaussian gaussian str False
maxnumber None None int False
manual None None list False
skysubtract
Parameter Value Default Type Callable
-----------------------------------------------------
bspline_spacing 0.6 0.6 int, float False
nodding False False bool False
flexure
Parameter Value Default Type Callable
------------------------------------------------
method boxcar boxcar str False
maxshift 20 20 int, float False
spectrum None None str False
fluxcalib
Parameter Value Default Type Callable
-----------------------------------------
nonlinear False False bool False
sensfunc None None str False
[INFO] :: Loading the reduction file
[INFO] :: Found 2 raw data frames
[INFO] :: Input file loaded successfully
In [26]:
p = PypitPar.from_cfg_file(merge_with='keck_lris_blue_long_400_3400_d560.cfg')
I actually had to comment out the definition of the flexure spectrum because I can't find it on my disk, and the declaration above faults when it can't find the file.
With the declaration above, all the default parameters are set, the spectrograph key (KECK_LRISb) is used to find the appropriate spectrograph definition file (../../pypit/config/spectrographs/KECK_LRISb_spectrograph.cfg), and both are merged with the alterations in the local keck_lris_blue_long_400_3400_d560.cfg file.
You can print the compiled parameters using the to_config method.
In [27]:
p.to_config('compiled_example.cfg')
In [ ]:
Content source: PYPIT/PYPIT
Similar notebooks: