Contents

lastframe step

This step flags the final group as bad if the number of groups is greater than 3. No correction or flagging is done otherwise.

Official documentation for lastframe can be found here:

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

Input data

An example of running the lastframe 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. firstframe 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 lastframe and print the docstring and spec to show some information

#import the step
from jwst.lastframe import lastframe_step

# print the description and options
print(lastframe_step.LastFrameStep.__doc__)
print(lastframe_step.LastFrameStep.spec)

    LastFrameStep: This is a MIRI specific task.  If the number of groups
    is greater than 2, the GROUP data quality flags for the final group will
    be set to DO_NOT_USE.
    

    pre_hooks          = string_list(default=list())
    post_hooks         = string_list(default=list())
    output_file        = output_file(default=None)   # File to save output to.
    output_dir         = string(default=None)        # Directory path for output files
    output_ext         = string(default='.fits')     # Default type of output
    output_use_model   = boolean(default=False)      # When saving use `DataModel.meta.filename`
    output_use_index   = boolean(default=True)       # Append index.
    save_results       = boolean(default=False)      # Force save results
    skip               = boolean(default=False)      # Skip this step
    suffix             = string(default=None)        # Default suffix for output files
    search_output_file = boolean(default=True)       # Use outputfile define in parent step
    input_dir          = string(default=None)        # Input directory

Set the name of the input file and run the step. This will produce an output file ending with _lastframestep.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 firstframe will return the output datamodel so we set this to the dm variable.

# user specified
my_input_file = 'det_image_seq1_MIRIMAGE_F1130Wexp1_firstframestep.fits'

# run the step
dm = lastframe_step.LastFrameStep.call(my_input_file, output_use_model=True, save_results=True)

2020-10-29 14:05:47,900 - CRDS - ERROR -  Error determining best reference for 'pars-lastframestep'  =   Unknown reference type 'pars-lastframestep'
2020-10-29 14:05:47,902 - stpipe.LastFrameStep - INFO - LastFrameStep instance created.
2020-10-29 14:05:47,984 - stpipe.LastFrameStep - INFO - Step LastFrameStep running with args ('det_image_seq1_MIRIMAGE_F1130Wexp1_firstframestep.fits',).
2020-10-29 14:05:47,985 - stpipe.LastFrameStep - INFO - Step LastFrameStep 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': ''}
2020-10-29 14:05:50,174 - stpipe.LastFrameStep - INFO - Saved model in det_image_seq1_MIRIMAGE_F1130Wexp1_lastframestep.fits
2020-10-29 14:05:50,175 - stpipe.LastFrameStep - INFO - Step LastFrameStep done

We can plot the GROUPDQ last frame image and the GROUPDQ 1D array for a sample pixel to check the step has flagged the last frame in the ramps with a value of 1

# set the sample pixel
pixel = [688,511]

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

# plot
fig, axs = plt.subplots(1, 2, figsize=(12, 5))

# plot the first frame of the first integration of the GROUPDQ extension
axs[0].imshow(dm.groupdq[0][-1], cmap='jet', interpolation='nearest', origin='lower')
axs[0].annotate('first frame of GROUPDQ', xy=(0.0, 1.02), xycoords='axes fraction', 
                fontsize=12, fontweight='bold', color='k')

# determine the values in this GROUPDQ frame
flag_values = np.unique(dm.groupdq[0][-1])
axs[0].annotate('Flag values in last frame: %s' % flag_values, xy=(0.05, 0.92), 
                xycoords='axes fraction', fontsize=12, fontweight='bold', color='w')

# input and output ramps (setting a slight offset for the output ramp)
axs[1].plot(group, dm.groupdq[-1,:,pixel[1],pixel[0]], c='b', marker='o', linestyle='-', 
            linewidth=2, label='lastframe flagged')

axs[1].set_ylabel('flag values',fontsize=15)
axs[1].set_xlim(-1,max(group)+1)
axs[1].set_ylim(-0.5,1.5)
axs[1].legend(prop={'size':12}, loc=2)

plt.tight_layout(h_pad=0)
plt.show()
../_images/lastframe_9_0.png

Command line

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

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

strun jwst.lastframe.LastFrameStep det_image_seq1_MIRIMAGE_F1130Wexp1_firststep.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 LastFrameStep using the strun command with the associated lastframe.cfg file.

collect_pipeline_cfgs cfgs/

strun cfgs/lastframe.cfg det_image_seq1_MIRIMAGE_F1130Wexp1_firstframestep.fits

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

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

strun jwst.lastframe.LastFrameStep -h

or

strun cfgs/lastframe.cfg -h

Override reference file

There is currently no reference file for the lastframe step.

firstframe step linearity step