Contents

rscd step

For MIRI multiple integration data, the reset switch decay causes the the initial groups in integrations after the first one to be offset from their expected linear accumulation of signal. The most significant deviations occur in groups 1 and 2. This step corrects for these effects.

Official documentation for rscd can be found here:

https://jwst-pipeline.readthedocs.io/en/latest/jwst/rscd/index.html

Input data

An example of running the rscd step is now shown using a simple simulated observation of a galaxy with the MIRI Imager (F1130W filter) produced with MIRISim v2.3, with precending pipeline steps applied, i.e. linearity output.

Python

Start by importing what will be used and set the CRDS_CONTEXT

# imports
import os, glob, shutil
import numpy as np
from matplotlib.colors import LogNorm
import matplotlib.pyplot as plt
from jwst import datamodels

# set the CRDS_CONTEXT
os.environ["CRDS_CONTEXT"] = "jwst_0641.pmap"

Import rscd and print the docstring and spec to show some information

# import the step
from jwst.rscd import rscd_step

# print the description and options
print(rscd_step.RSCD_Step.__doc__)
print(rscd_step.RSCD_Step.spec)

    RSCD_Step: Performs an RSCD correction to MIRI data.
    Baseline version flags the first N groups as 'DO_NOT_USE' in
    the 2nd and later integrations in a copy of the input
    science data model.
    Enhanced version is not ready nor enabled.
    

         type = option('baseline','enhanced',default = 'baseline') # Type of correction

Set the name of the input file and run the step. This will produce an output file ending with _rscd_step.fits

Parameters used:

output_use_model : boolean, optional, default=False
     propagate the input filename to the output

save_results: boolean, optional, default=False
     save the results to file

Note that the rscd will return the output datamodel so we set this to the dm variable.

# user specified
my_input_file = 'det_image_seq1_MIRIMAGE_F1130Wexp1_linearitystep.fits'

# run the step
dm = rscd_step.RSCD_Step.call(my_input_file, output_use_model=True, save_results=True)

2020-10-29 14:07:39,118 - CRDS - ERROR -  Error determining best reference for 'pars-rscd_step'  =   Unknown reference type 'pars-rscd_step'
2020-10-29 14:07:39,120 - stpipe.RSCD_Step - INFO - RSCD_Step instance created.
2020-10-29 14:07:39,203 - stpipe.RSCD_Step - INFO - Step RSCD_Step running with args ('det_image_seq1_MIRIMAGE_F1130Wexp1_linearitystep.fits',).
2020-10-29 14:07:39,205 - stpipe.RSCD_Step - INFO - Step RSCD_Step parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': True, 'output_use_index': True, 'save_results': True, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'type': 'baseline'}
2020-10-29 14:07:39,524 - stpipe.RSCD_Step - INFO - Using RSCD reference file /Users/patrickkavanagh/crds_mirror/references/jwst/miri/jwst_miri_rscd_0010.fits
2020-10-29 14:07:41,887 - stpipe.RSCD_Step - INFO - Saved model in det_image_seq1_MIRIMAGE_F1130Wexp1_rscd_step.fits
2020-10-29 14:07:41,888 - stpipe.RSCD_Step - INFO - Step RSCD_Step done

Since rscd only applies a correction to integrations >1, we can check one of these to see the correction. If there is only one integration, then rscd doesn’t do anything.

# set the sample pixel
pixel = [600,500]

# define group numbers for integration ramps
group = range(1,dm.data[0,:,pixel[0],pixel[1]].shape[0]+1,1)

# open the input file as a datamodel
in_dm = datamodels.open(my_input_file)

# first check that there is more than one integration
if dm.data.shape[0] > 1:

    # plot
    fig, axs = plt.subplots(2, 1, figsize=(10, 8), sharex=True)

    # plot input and output ramps of the second integration
    axs[0].plot(group, in_dm.data[-1,:,pixel[1],pixel[0]], c='r', marker='^', markersize=6, 
                linestyle='-', linewidth=2, label='input ramp')
    axs[0].plot(group, dm.data[-1,:,pixel[1],pixel[0]], c='b', marker='o', linestyle='-', 
                linewidth=2, label='RSCD calibrated ramp')
    axs[0].set_title('RSCD correction',fontsize=15)
    axs[0].set_ylabel('DN',fontsize=15)
    axs[0].set_xlim(-1,max(group)+1)
    axs[0].legend(prop={'size':12}, loc=0)

    # plot ratio between the two
    axs[1].plot(group, in_dm.data[-1,:,pixel[1],pixel[0]] / dm.data[-1,:,pixel[1],pixel[0]], c='g', 
                marker='s', markersize=6, linestyle='-', linewidth=2, label='ratio')
    axs[1].set_ylabel('DN',fontsize=15)
    axs[1].set_xlabel('group',fontsize=15)
    axs[1].legend(prop={'size':12}, loc=0)

    plt.tight_layout(h_pad=0)
    plt.show()

else: 
    print("RSCD step only operates on exposures with more than one integration.")
../_images/RSCD_9_0.png

Command line

To achieve the same result from the command line there are a couple of options.

Option 1: Run the RSCD_Step class using the strun command:

strun jwst.rscd.RSCD_Step det_image_seq1_MIRIMAGE_F1130Wexp1_linearitystep.fits

Option 2: If they don’t already exist, collect the pipeline configuration files in your working directory using collect_pipeline_configs and then run the RSCD_Step using the strun command with the associated rscd.cfg file.

collect_pipeline_cfgs cfgs/

strun cfgs/rscd.cfg det_image_seq1_MIRIMAGE_F1130Wexp1_linearitystep.fits

This will produce the same output file ending with _rscd_step.fits

A full list of the command line options are given by running the following:

strun jwst.rscd.RSCD_Step -h

or

strun cfgs/rscd.cfg -h

Override reference file

To override the reference file for this step in Python:

# set the override reference file name
my_ref = 'my_rscd.fits'

dm = rscd.RSCD_Step.call(my_input_file, output_use_model=True, save_results=True, 
                         override_rscd=my_ref)

and using the command line:

strun jwst.rscd.RSCD_Step det_image_seq1_MIRIMAGE_F1130Wexp1_linearitystep.fits  --override_rscd my_rscd.fits

or

strun cfgs/rscd.cfg det_image_seq1_MIRIMAGE_F1130Wexp1_linearitystep.fits --override_rscd my_rscd.fits
linearity step dark_current step