images.imutil

The images.imutil package provides general FITS image tools such as header editing and image arithmetic.

Notes

For questions or comments please see our github page. We encourage and appreciate user feedback.

Most of these notebooks rely on basic knowledge of the Astropy FITS I/O module. If you are unfamiliar with this module please see the Astropy FITS I/O user documentation before using this documentation.

Contents:

chpixtype

Please review the Notes section above before running any examples in this notebook

Chpixtype is a task that allows you to change the pixel type of a FITS image. There is built in functionality in astropy.io.fits to preform this task with the scale method. Below you will find a table that translates the chpixtype newpixtype options into their equivalent numpy/astropy type.

Type Conversions

Chpixtype

Numpy/Astropy Type

ushort

uint16

short

int16

int

int32

long

int64

real

float32

double

float64

# Standard Imports
import numpy as np

# Astronomy Specific Imports
from astropy.io import fits
from astroquery.mast import Observations
# Download test file using astroquery, this only needs to be run once
# and can be skipped if using your own data.
# Astroquery will only download file if not already present.
obsid = '2004615006'
Observations.download_products(obsid,productFilename="iczgs3ygq_flt.fits")
Downloading URL https://mast.stsci.edu/api/v0/download/file?uri=mast:HST/product/iczgs3ygq/iczgs3ygq_flt.fits to ./mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fits ... [Done]
Table length=1
Local PathStatusMessageURL
str47str5str87str93
./mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fitsERRORDownloaded filesize is 16531200,but should be 16534080, file may be partial or corrupt.https://mast.stsci.edu/api/v0/download/file?uri=mast:HST/product/iczgs3ygq/iczgs3ygq_flt.fits
# Change this value to your desired data file, here were creating a filename
# for our new changed data
orig_data = './mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fits'
new_data = 'iczgs3ygq_newdtype_flt.fits'

# Read in your FITS file
hdu = fits.open(orig_data)

# Print info about FITS file
hdu.info()

# Edit the datatype for the first sci extension
hdu[1].scale(type='int32')

# Save changed hdu object to new file
# The overwrite argument tells the writeto method to overwrite if file already exists
hdu.writeto(new_data, overwrite=True)
hdu.close()
Filename: ./mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fits
No.    Name      Ver    Type      Cards   Dimensions   Format
  0  PRIMARY       1 PrimaryHDU     265   ()
  1  SCI           1 ImageHDU       140   (1014, 1014)   float32
  2  ERR           1 ImageHDU        51   (1014, 1014)   float32
  3  DQ            1 ImageHDU        43   (1014, 1014)   int16
  4  SAMP          1 ImageHDU        37   (1014, 1014)   int16
  5  TIME          1 ImageHDU        37   (1014, 1014)   float32
  6  WCSCORR       1 BinTableHDU     59   7R x 24C   [40A, I, A, 24A, 24A, 24A, 24A, D, D, D, D, D, D, D, D, 24A, 24A, D, D, D, D, J, 40A, 128A]

hedit

Please review the Notes section above before running any examples in this notebook

The hedit task allows users to edit an image header. This functioanlity is covered in astropy.io.fits. Take note that to make changes to a FITS file, you must use the mode='update' keyword in the fits.open call. The default mode for fits.open is readonly. Below you’ll find examples of editing a keyword if it does/doesn’t exist, and how to delete keywords from the header. Also provided is an example of updating multiple files at once using the convience function setval.

For examples on printing/viewing header keywords please see hselect

# Standard Imports
from glob import glob

# Astronomy Specific Imports
from astropy.io import fits
from astroquery.mast import Observations
# Download test file using astroquery, this only needs to be run once
# and can be skipped if using your own data.
# Astroquery will only download file if not already present.
obsid = '2004615006'
Observations.download_products(obsid,productFilename="iczgs3ygq_flt.fits")
INFO: Found cached file ./mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fits with expected size 16534080. [astroquery.query]
Table length=1
Local PathStatusMessageURL
str47str5str87str93
./mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fitsERRORDownloaded filesize is 16531200,but should be 16534080, file may be partial or corrupt.https://mast.stsci.edu/api/v0/download/file?uri=mast:HST/product/iczgs3ygq/iczgs3ygq_flt.fits
# Change this value to your desired data file
test_data = './mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fits'

# Open FITS file, include the mode='update' keyword
hdu = fits.open(test_data, mode='update')

# Simple header change, will add keyword if it doesn't exist
hdu[0].header['MYKEY1'] = 'Editing this keyword'

# Only add keyword if it does not already exist:
if 'MYKEY2' not in hdu[0].header:
    hdu[0].header['MYKEY2'] = 'Also editing this'

# To delete keywords, first check if they exist:
if 'MYKEY2' in hdu[0].header:
    del hdu[0].header['MYKEY2']

# Close FITS file, this will save your changes
hdu.close()

Below we will show an example of how to update a keyword in multiple FITS files using the Astropy convenience function astropy.io.fits.setval and the glob function. Astropy.io.fits.setval will add the keyword if it does not already exist.

# Change this value to your desired search
data_list = glob('./mastDownload/HST/ICZGS3YGQ/*.fits')

# Now we loop over the list of file and use the setval function to update keywords
# Here we update the keyword MYKEY1 value to the integer 5.
for filename in data_list:
    fits.setval(filename, 'MYKEY1', value=5)

hselect

Please review the Notes section above before running any examples in this notebook

The hselect task allows users to search for keyword values in the FITS headers. This functionality has been replaced by the CCDProc ImageFileCollection class. This class stores the header keyword values in an Astropy Table object. There is also an executable script provided by Astropy called fitsheader. You’ll find examples of both below.

If you wish to save your output to a text file, please see the Astropy Table Documentation and the Astropy Unified I/O page.

# Astronomy Specific Imports
from ccdproc import ImageFileCollection
from astroquery.mast import Observations
# Download test file using astroquery, this only needs to be run once
# and can be skipped if using your own data.
# Astroquery will only download file if not already present.
obsid = '2004663553'
Observations.download_products(obsid, productFilename="jczgx1ppq_flc.fits")
obsid = '2004663554'
Observations.download_products(obsid, productFilename="jczgx1ptq_flc.fits")
obsid = '2004663556'
Observations.download_products(obsid, productFilename="jczgx1q1q_flc.fits")

import shutil
shutil.move('./mastDownload/HST/JCZGX1PPQ/jczgx1ppq_flc.fits','../data/')
shutil.move('./mastDownload/HST/JCZGX1PTQ/jczgx1ptq_flc.fits','../data/')
shutil.move('./mastDownload/HST/JCZGX1Q1Q/jczgx1q1q_flc.fits','../data/')
INFO:astropy:Found cached file ./mastDownload/HST/JCZGX1PPQ/jczgx1ppq_flc.fits with expected size 167964480.
INFO: Found cached file ./mastDownload/HST/JCZGX1PPQ/jczgx1ppq_flc.fits with expected size 167964480. [astroquery.query]
INFO:astropy:Found cached file ./mastDownload/HST/JCZGX1PTQ/jczgx1ptq_flc.fits with expected size 167964480.
INFO: Found cached file ./mastDownload/HST/JCZGX1PTQ/jczgx1ptq_flc.fits with expected size 167964480. [astroquery.query]
INFO:astropy:Found cached file ./mastDownload/HST/JCZGX1Q1Q/jczgx1q1q_flc.fits with expected size 167964480.
INFO: Found cached file ./mastDownload/HST/JCZGX1Q1Q/jczgx1q1q_flc.fits with expected size 167964480. [astroquery.query]
'../data/jczgx1q1q_flc.fits'
# first we make the ImageFileCollection object
collec = ImageFileCollection('../data/',
                             keywords=["filetype","date","exptime","filter2"],
                             glob_include="jcz*.fits", ext=0)

# header keywords values are stored in an Astropy Table in the summary attribute
out_table = collec.summary
out_table
Table masked=True length=3
filefiletypedateexptimefilter2
str18str3str10float64str5
jczgx1ppq_flc.fitsSCI2017-12-03578.0F814W
jczgx1ptq_flc.fitsSCI2017-12-03607.0F814W
jczgx1q1q_flc.fitsSCI2017-12-03578.0F814W
# Now we can filter our table based on keyword values using Python bitwise operators
filtered_table = out_table[(out_table['exptime'] < 600) & (out_table['filter2'] == 'F814W')]
filtered_table
Table masked=True length=2
filefiletypedateexptimefilter2
str18str3str10float64str5
jczgx1ppq_flc.fitsSCI2017-12-03578.0F814W
jczgx1q1q_flc.fitsSCI2017-12-03578.0F814W
# Now let's extract the filename list from our filtered table into a python List object
filelist = filtered_table['file'].data
print(filelist)

for filename in filelist:
    print(filename)
    # Do your analysis here
['jczgx1ppq_flc.fits' 'jczgx1q1q_flc.fits']
jczgx1ppq_flc.fits
jczgx1q1q_flc.fits

Also available is the Astropy executable script fitsheader. Fitsheader can be run from the command line.

# the "!" character tells the notebook to run this command as if it were in a terminal window
!fitsheader --help
usage: fitsheader [-h] [-e HDU] [-k KEYWORD] [-t [FORMAT]] [-c]
                  filename [filename ...]

Print the header(s) of a FITS file. Optional arguments allow the desired
extension(s), keyword(s), and output format to be specified. Note that in the
case of a compressed image, the decompressed header is shown by default.

positional arguments:
  filename              path to one or more files; wildcards are supported

optional arguments:
  -h, --help            show this help message and exit
  -e HDU, --extension HDU
                        specify the extension by name or number; this argument
                        can be repeated to select multiple extensions
  -k KEYWORD, --keyword KEYWORD
                        specify a keyword; this argument can be repeated to
                        select multiple keywords; also supports wildcards
  -t [FORMAT], --table [FORMAT]
                        print the header(s) in machine-readable table format;
                        the default format is "ascii.fixed_width" (can be
                        "ascii.csv", "ascii.html", "ascii.latex", "fits", etc)
  -c, --compressed      for compressed image data, show the true header which
                        describes the compression rather than the data
# print out only the keyword names that match FILE* or NAXIS*
!fitsheader --keyword FILE* --keyword NAXIS* ../data/*.fits
# HDU 0 in ../data/imstack_out.fits:
NAXIS   =                    3 / number of array dimensions
NAXIS1  =                 4096
NAXIS2  =                 2048
NAXIS3  =                    2
# HDU 0 in ../data/jczgx1ppq_flc.fits:
FILENAME= 'jczgx1ppq_flc.fits' / name of file
FILETYPE= 'SCI      '          / type of data found in data file
NAXIS   =                    0 / number of data axes

# HDU 1 in ../data/jczgx1ppq_flc.fits:
NAXIS   =                    2 / number of data axes
NAXIS1  =                 4096 / length of data axis 1
NAXIS2  =                 2048 / length of data axis 2

# HDU 2 in ../data/jczgx1ppq_flc.fits:
NAXIS   =                    2 / number of data axes
NAXIS1  =                 4096 / length of data axis 1
NAXIS2  =                 2048 / length of data axis 2

# HDU 3 in ../data/jczgx1ppq_flc.fits:
NAXIS   =                    2 / number of data axes
NAXIS1  =                 4096 / length of data axis 1
NAXIS2  =                 2048 / length of data axis 2

# HDU 4 in ../data/jczgx1ppq_flc.fits:
NAXIS   =                    2 / number of data axes
NAXIS1  =                 4096 / length of data axis 1
NAXIS2  =                 2048 / length of data axis 2

# HDU 5 in ../data/jczgx1ppq_flc.fits:
NAXIS   =                    2 / number of data axes
NAXIS1  =                 4096 / length of data axis 1
NAXIS2  =                 2048 / length of data axis 2

# HDU 6 in ../data/jczgx1ppq_flc.fits:
NAXIS   =                    2 / number of data axes
NAXIS1  =                 4096 / length of data axis 1
NAXIS2  =                 2048 / length of data axis 2

# HDU 7 in ../data/jczgx1ppq_flc.fits:
NAXIS   =                    2 / number of array dimensions
NAXIS1  =                   64
NAXIS2  =                   32

# HDU 8 in ../data/jczgx1ppq_flc.fits:
NAXIS   =                    2 / number of array dimensions
NAXIS1  =                   64
NAXIS2  =                   32

# HDU 9 in ../data/jczgx1ppq_flc.fits:
NAXIS   =                    2 / number of array dimensions
NAXIS1  =                   64
NAXIS2  =                   32

# HDU 10 in ../data/jczgx1ppq_flc.fits:
NAXIS   =                    2 / number of array dimensions
NAXIS1  =                   64
NAXIS2  =                   32

# HDU 11 in ../data/jczgx1ppq_flc.fits:
NAXIS   =                    2 / number of array dimensions
NAXIS1  =                   64
NAXIS2  =                   32

# HDU 12 in ../data/jczgx1ppq_flc.fits:
NAXIS   =                    2 / number of array dimensions
NAXIS1  =                   64
NAXIS2  =                   32

# HDU 13 in ../data/jczgx1ppq_flc.fits:
NAXIS   =                    2 / number of array dimensions
NAXIS1  =                   64
NAXIS2  =                   32

# HDU 14 in ../data/jczgx1ppq_flc.fits:
NAXIS   =                    2 / number of array dimensions
NAXIS1  =                   64
NAXIS2  =                   32

# HDU 15 in ../data/jczgx1ppq_flc.fits:
NAXIS   =                    2 / number of array dimensions
NAXIS1  =                  455 / length of dimension 1
NAXIS2  =                   14 / length of dimension 2
# HDU 0 in ../data/jczgx1ptq_flc.fits:
FILENAME= 'jczgx1ptq_flc.fits' / name of file
FILETYPE= 'SCI      '          / type of data found in data file
NAXIS   =                    0 / number of data axes

# HDU 1 in ../data/jczgx1ptq_flc.fits:
NAXIS   =                    2 / number of data axes
NAXIS1  =                 4096 / length of data axis 1
NAXIS2  =                 2048 / length of data axis 2

# HDU 2 in ../data/jczgx1ptq_flc.fits:
NAXIS   =                    2 / number of data axes
NAXIS1  =                 4096 / length of data axis 1
NAXIS2  =                 2048 / length of data axis 2

# HDU 3 in ../data/jczgx1ptq_flc.fits:
NAXIS   =                    2 / number of data axes
NAXIS1  =                 4096 / length of data axis 1
NAXIS2  =                 2048 / length of data axis 2

# HDU 4 in ../data/jczgx1ptq_flc.fits:
NAXIS   =                    2 / number of data axes
NAXIS1  =                 4096 / length of data axis 1
NAXIS2  =                 2048 / length of data axis 2

# HDU 5 in ../data/jczgx1ptq_flc.fits:
NAXIS   =                    2 / number of data axes
NAXIS1  =                 4096 / length of data axis 1
NAXIS2  =                 2048 / length of data axis 2

# HDU 6 in ../data/jczgx1ptq_flc.fits:
NAXIS   =                    2 / number of data axes
NAXIS1  =                 4096 / length of data axis 1
NAXIS2  =                 2048 / length of data axis 2

# HDU 7 in ../data/jczgx1ptq_flc.fits:
NAXIS   =                    2 / number of array dimensions
NAXIS1  =                   64
NAXIS2  =                   32

# HDU 8 in ../data/jczgx1ptq_flc.fits:
NAXIS   =                    2 / number of array dimensions
NAXIS1  =                   64
NAXIS2  =                   32

# HDU 9 in ../data/jczgx1ptq_flc.fits:
NAXIS   =                    2 / number of array dimensions
NAXIS1  =                   64
NAXIS2  =                   32

# HDU 10 in ../data/jczgx1ptq_flc.fits:
NAXIS   =                    2 / number of array dimensions
NAXIS1  =                   64
NAXIS2  =                   32

# HDU 11 in ../data/jczgx1ptq_flc.fits:
NAXIS   =                    2 / number of array dimensions
NAXIS1  =                   64
NAXIS2  =                   32

# HDU 12 in ../data/jczgx1ptq_flc.fits:
NAXIS   =                    2 / number of array dimensions
NAXIS1  =                   64
NAXIS2  =                   32

# HDU 13 in ../data/jczgx1ptq_flc.fits:
NAXIS   =                    2 / number of array dimensions
NAXIS1  =                   64
NAXIS2  =                   32

# HDU 14 in ../data/jczgx1ptq_flc.fits:
NAXIS   =                    2 / number of array dimensions
NAXIS1  =                   64
NAXIS2  =                   32

# HDU 15 in ../data/jczgx1ptq_flc.fits:
NAXIS   =                    2 / number of array dimensions
NAXIS1  =                  455 / length of dimension 1
NAXIS2  =                   14 / length of dimension 2
# HDU 0 in ../data/jczgx1q1q_flc.fits:
FILENAME= 'jczgx1q1q_flc.fits' / name of file
FILETYPE= 'SCI      '          / type of data found in data file
NAXIS   =                    0 / number of data axes

# HDU 1 in ../data/jczgx1q1q_flc.fits:
NAXIS   =                    2 / number of data axes
NAXIS1  =                 4096 / length of data axis 1
NAXIS2  =                 2048 / length of data axis 2

# HDU 2 in ../data/jczgx1q1q_flc.fits:
NAXIS   =                    2 / number of data axes
NAXIS1  =                 4096 / length of data axis 1
NAXIS2  =                 2048 / length of data axis 2

# HDU 3 in ../data/jczgx1q1q_flc.fits:
NAXIS   =                    2 / number of data axes
NAXIS1  =                 4096 / length of data axis 1
NAXIS2  =                 2048 / length of data axis 2

# HDU 4 in ../data/jczgx1q1q_flc.fits:
NAXIS   =                    2 / number of data axes
NAXIS1  =                 4096 / length of data axis 1
NAXIS2  =                 2048 / length of data axis 2

# HDU 5 in ../data/jczgx1q1q_flc.fits:
NAXIS   =                    2 / number of data axes
NAXIS1  =                 4096 / length of data axis 1
NAXIS2  =                 2048 / length of data axis 2

# HDU 6 in ../data/jczgx1q1q_flc.fits:
NAXIS   =                    2 / number of data axes
NAXIS1  =                 4096 / length of data axis 1
NAXIS2  =                 2048 / length of data axis 2

# HDU 7 in ../data/jczgx1q1q_flc.fits:
NAXIS   =                    2 / number of array dimensions
NAXIS1  =                   64
NAXIS2  =                   32

# HDU 8 in ../data/jczgx1q1q_flc.fits:
NAXIS   =                    2 / number of array dimensions
NAXIS1  =                   64
NAXIS2  =                   32

# HDU 9 in ../data/jczgx1q1q_flc.fits:
NAXIS   =                    2 / number of array dimensions
NAXIS1  =                   64
NAXIS2  =                   32

# HDU 10 in ../data/jczgx1q1q_flc.fits:
NAXIS   =                    2 / number of array dimensions
NAXIS1  =                   64
NAXIS2  =                   32

# HDU 11 in ../data/jczgx1q1q_flc.fits:
NAXIS   =                    2 / number of array dimensions
NAXIS1  =                   64
NAXIS2  =                   32

# HDU 12 in ../data/jczgx1q1q_flc.fits:
NAXIS   =                    2 / number of array dimensions
NAXIS1  =                   64
NAXIS2  =                   32

# HDU 13 in ../data/jczgx1q1q_flc.fits:
NAXIS   =                    2 / number of array dimensions
NAXIS1  =                   64
NAXIS2  =                   32

# HDU 14 in ../data/jczgx1q1q_flc.fits:
NAXIS   =                    2 / number of array dimensions
NAXIS1  =                   64
NAXIS2  =                   32

# HDU 15 in ../data/jczgx1q1q_flc.fits:
NAXIS   =                    2 / number of array dimensions
NAXIS1  =                  455 / length of dimension 1
NAXIS2  =                   14 / length of dimension 2
# print out only the first extension and keyword names that match FILE* or NAXIS*
!fitsheader --extension 0 --keyword FILE* --keyword NAXIS* ../data/*.fits
# HDU 0 in ../data/imstack_out.fits:
NAXIS   =                    3 / number of array dimensions
NAXIS1  =                 4096
NAXIS2  =                 2048
NAXIS3  =                    2
# HDU 0 in ../data/jczgx1ppq_flc.fits:
FILENAME= 'jczgx1ppq_flc.fits' / name of file
FILETYPE= 'SCI      '          / type of data found in data file
NAXIS   =                    0 / number of data axes
# HDU 0 in ../data/jczgx1ptq_flc.fits:
FILENAME= 'jczgx1ptq_flc.fits' / name of file
FILETYPE= 'SCI      '          / type of data found in data file
NAXIS   =                    0 / number of data axes
# HDU 0 in ../data/jczgx1q1q_flc.fits:
FILENAME= 'jczgx1q1q_flc.fits' / name of file
FILETYPE= 'SCI      '          / type of data found in data file
NAXIS   =                    0 / number of data axes

imarith-imdivide

Please review the Notes section above before running any examples in this notebook

Imarith and imdivide both provide functionality to apply basic operators to whole image arrays. This task can be achieved with basic astropy.io.fits functionality along with numpy array functionality. We show a few examples below. In the first code cell we adding and dividing two image arrays together. In the second code cell we show how to use a data quality array to decide which image array values to replace with zero.

The basic operands (+,-,/,*) can all be used with an assignment operator in python (+=,-=,/=,*=). See http://www.tutorialspoint.com/python/python_basic_operators.htm for more details

# Astronomy Specific Imports
from astropy.io import fits
from astroquery.mast import Observations
# Download test file using astroquery, this only needs to be run once
# and can be skipped if using your own data.
# Astroquery will only download file if not already present.
obsid = '2004615003'
Observations.download_products(obsid,productFilename="iczgs3y5q_flt.fits")
obsid = '2004615006'
Observations.download_products(obsid,productFilename="iczgs3ygq_flt.fits")
INFO:astropy:Found cached file ./mastDownload/HST/ICZGS3Y5Q/iczgs3y5q_flt.fits with expected size 16534080.
INFO: Found cached file ./mastDownload/HST/ICZGS3Y5Q/iczgs3y5q_flt.fits with expected size 16534080. [astroquery.query]
INFO:astropy:Found cached file ./mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fits with expected size 16534080.
INFO: Found cached file ./mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fits with expected size 16534080. [astroquery.query]
Table length=1
Local PathStatusMessageURL
str47str5str87str93
./mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fitsERRORDownloaded filesize is 16531200,but should be 16534080, file may be partial or corrupt.https://mast.stsci.edu/api/v0/download/file?uri=mast:HST/product/iczgs3ygq/iczgs3ygq_flt.fits
# Basic operands (+,-,/,*)
# Change these values to your desired data files
test_data1 = './mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fits'
test_data2 = './mastDownload/HST/ICZGS3Y5Q/iczgs3y5q_flt.fits'
output_data = 'imarith_out.fits'
output_data2 = 'imarith_new.fits'


# Open FITS file
hdu1 = fits.open(test_data1)
hdu2 = fits.open(test_data2)

# Print information about the FITS file we opened
hdu1.info()
hdu2.info()

# Here we add hdu2-ext1 to hdu1-ext1 by using the shortcut += operator
hdu1[1].data += hdu2[1].data

# If you are dividing and need to avoid zeros in the image use indexing
indx_zeros = hdu2[1].data == 0
indx_nonzeros = hdu2[1].data != 0

# Set this value as you would the divzero parameter in imarith
# Here we're working with the error arrays of the image
set_zeros = 999.9
hdu1[2].data[indx_nonzeros] /= hdu2[2].data[indx_nonzeros]
hdu1[2].data[indx_zeros] = 999.9

# Save your new file
# The overwrite argument tells the writeto method to overwrite if file already exists
hdu1.writeto(output_data, overwrite=True)

# If you want to save you updated array to a new file with just the updated image array
# we can repackage the extension into a new HDUList
image_array = hdu1[1].data
new_hdu = fits.PrimaryHDU(image_array)
new_hdu.writeto(output_data2, overwrite=True)

# Close hdu files
hdu1.close()
hdu2.close()
Filename: ./mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fits
No.    Name      Ver    Type      Cards   Dimensions   Format
  0  PRIMARY       1 PrimaryHDU     266   ()
  1  SCI           1 ImageHDU       140   (1014, 1014)   float32
  2  ERR           1 ImageHDU        51   (1014, 1014)   float32
  3  DQ            1 ImageHDU        43   (1014, 1014)   int16
  4  SAMP          1 ImageHDU        37   (1014, 1014)   int16
  5  TIME          1 ImageHDU        37   (1014, 1014)   float32
  6  WCSCORR       1 BinTableHDU     59   7R x 24C   [40A, I, A, 24A, 24A, 24A, 24A, D, D, D, D, D, D, D, D, 24A, 24A, D, D, D, D, J, 40A, 128A]
Filename: ./mastDownload/HST/ICZGS3Y5Q/iczgs3y5q_flt.fits
No.    Name      Ver    Type      Cards   Dimensions   Format
  0  PRIMARY       1 PrimaryHDU     265   ()
  1  SCI           1 ImageHDU       140   (1014, 1014)   float32
  2  ERR           1 ImageHDU        51   (1014, 1014)   float32
  3  DQ            1 ImageHDU        43   (1014, 1014)   int16
  4  SAMP          1 ImageHDU        37   (1014, 1014)   int16
  5  TIME          1 ImageHDU        37   (1014, 1014)   float32
  6  WCSCORR       1 BinTableHDU     59   7R x 24C   [40A, I, A, 24A, 24A, 24A, 24A, D, D, D, D, D, D, D, D, 24A, 24A, D, D, D, D, J, 40A, 128A]
# Here we show an example of using an HST DQ array to
# replace only certain values with zero in an image array

# Change these values to your desired data files
test_data1 = './mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fits'
output_file = 'iczgs3ygq_updated.fits'

# Open FITS file
hdulist = fits.open(test_data1)

# First we should use the DQ array to make a boolean mask
DQ_mask = hdulist[3].data > 16384

# Now we can use the mask to replace values in the image array
# with 0.
hdulist[1].data[DQ_mask] = 0

# Now we can save out the edited FITS to a new file
hdulist.writeto(output_file)

# And finally, close the original FITS file
# The orignially file will not be updated since we did not
# open the file in 'update' mode
hdulist.close()

imcopy

Please review the Notes section above before running any examples in this notebook

Imcopy allows users to copy a FITS image to a new file. We can accomplish this using astropy.io.fits by saving our FITS file to a new filename.

Imcopy will also make a cutout of an image and save the cutout to a new file with an updated WCS. We show an exampe of this in Python using the Cutout2D tool in Astropy. For more information on how to use Cutout2D please see this tutorial page.

# Astronomy Specific Imports
from astropy import wcs
from astropy.io import fits
from astropy.nddata import Cutout2D
from astroquery.mast import Observations
# Download test file using astroquery, this only needs to be run once
# and can be skipped if using your own data.
# Astroquery will only download file if not already present.
obsid = '2004615006'
Observations.download_products(obsid,productFilename="iczgs3ygq_flt.fits")
obsid = '2004345211'
Observations.download_products(obsid,productFilename="jcw505010_drz.fits")
INFO:astropy:Found cached file ./mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fits with expected size 16534080.
INFO: Found cached file ./mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fits with expected size 16534080. [astroquery.query]
INFO:astropy:Found cached file ./mastDownload/HST/JCW505010/jcw505010_drz.fits with expected size 219404160.
INFO: Found cached file ./mastDownload/HST/JCW505010/jcw505010_drz.fits with expected size 219404160. [astroquery.query]
Table length=1
Local PathStatusMessageURL
str47str5str89str93
./mastDownload/HST/JCW505010/jcw505010_drz.fitsERRORDownloaded filesize is 219456000,but should be 219404160, file may be partial or corrupt.https://mast.stsci.edu/api/v0/download/file?uri=mast:HST/product/jcw505010/jcw505010_drz.fits

Simple example of a file copy

# Change these values to your desired filenames
test_data = './mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fits'
output_data = 'imcopy_out.fits'

hdulist = fits.open(test_data)
# The overwrite argument tells the writeto method to overwrite if file already exists
hdulist.writeto(output_data, overwrite=True)
hdulist.close()

Example using a new cutout, here we will take a 50x50 pixel cutout from all image extensions centered at x:200, y:300

# Change these values to your desired filenames
test_data = './mastDownload/HST/JCW505010/jcw505010_drz.fits'
output_data = 'imcopy_cutout_out.fits'

hdulist = fits.open(test_data)

# Create iterable list of tuples to feed into Cutout2D,
# seperate list for extensions with wcs, as feeding the wcs
# back into the FITS file takes more work.
ext_list = [1,2]
for ext in ext_list:
    orig_wcs = wcs.WCS(hdulist[ext].header)
    cutout = Cutout2D(hdulist[ext].data, (200,300), (50,50), wcs=orig_wcs)
    hdulist[ext].data = cutout.data
    hdulist[ext].header.update(cutout.wcs.to_header())

hdulist.writeto(output_data, overwrite=True)

hdulist.close()

imfunction-imexpr

Please review the Notes section above before running any examples in this notebook

Imfunction will apply a function to the image pixel values in an image array. Imexpr gives you similiar functionality with the added capability to combine different images using a user created expression. We can accomplish this using the built in funcitonality of the numpy library.

If there is a particular function you would like to apply to your image array that you cannot find in the numpy library you can use the np.vectorize function, which can make any python function apply to each element of your array. But keep in mind that np.vectorize is esentially looping over the array, and may not be the most efficient method.

Example using exsisting numpy function:

# Standard Imports
import numpy as np

# Astronomy Specific Imports
from astropy.io import fits
from astroquery.mast import Observations
# Download test file using astroquery, this only needs to be run once
# and can be skipped if using your own data.
# Astroquery will only download file if not already present.
obsid = '2004615006'
Observations.download_products(obsid,productFilename="iczgs3ygq_flt.fits")
INFO:astropy:Found cached file ./mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fits with expected size 16534080.
INFO: Found cached file ./mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fits with expected size 16534080. [astroquery.query]
Table length=1
Local PathStatusMessageURL
str47str5str87str93
./mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fitsERRORDownloaded filesize is 16531200,but should be 16534080, file may be partial or corrupt.https://mast.stsci.edu/api/v0/download/file?uri=mast:HST/product/iczgs3ygq/iczgs3ygq_flt.fits
# Change these values to your desired data files
test_data = './mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fits'
output_data = 'imfunction_out.fits'

# Here we use the cosine function as an example
hdu = fits.open(test_data)
sci = hdu[1].data

# When you call your new function, make sure to reassign the array to
# the new values if the original function is not changing values in place
hdu[1].data = np.cos(hdu[1].data)

# Now save out to a new file, and close the original file, changes will
# not be applied to the oiginal FITS file.
hdu.writeto(output_data, overwrite=True)
hdu.close()

Example using user defined function and np.vectorize:

# Change these values to your desired data files
test_data = './mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fits'
output_data = 'imfunction2_out.fits'

# Here we use the following custom function as an example
def my_func(x):
    return (x**2)+(x**3)

# Now we open our file, and vectorize our function
hdu = fits.open(test_data)
sci = hdu[1].data
vector_func = np.vectorize(my_func)

# When you call your new function, make sure to reassign the array to
# the new values if the original function is not changing values in place
hdu[1].data = vector_func(hdu[1].data)

# Now save out to a new file, and close the original file, changes will
# not be applied to the oiginal FITS file.
hdu.writeto(output_data, overwrite=True)
hdu.close()

imheader

Please review the Notes section above before running any examples in this notebook

The imheader task allows the user to list header parameters for a list of images. Here we can use the astropy convenience function, fits.getheader(). We also show in this example how to save a header to a text file, see the Python file I/O documentation for more details.

# Standard Imports
import numpy as np
import glob

# Astronomy Specific Imports
from astropy.io import fits
from astroquery.mast import Observations
# Download test file using astroquery, this only needs to be run once
# and can be skipped if using your own data.
# Astroquery will only download file if not already present.
obsid = '2004663553'
Observations.download_products(obsid, productFilename="jczgx1ppq_flc.fits")
obsid = '2004663554'
Observations.download_products(obsid, productFilename="jczgx1ptq_flc.fits")
obsid = '2004663556'
Observations.download_products(obsid, productFilename="jczgx1q1q_flc.fits")

import shutil
shutil.move('./mastDownload/HST/JCZGX1PPQ/jczgx1ppq_flc.fits','../data/')
shutil.move('./mastDownload/HST/JCZGX1PTQ/jczgx1ptq_flc.fits','../data/')
shutil.move('./mastDownload/HST/JCZGX1Q1Q/jczgx1q1q_flc.fits','../data/')
# Change these values to your desired data files, glob will capture all wildcard matches
test_data = glob.glob('../data/jczgx*')
out_text = 'imheader_out.txt'

for filename in test_data:
    # Pull the header from extension 1 using FITS convenience function.
    # To access multiple header it's better to use the fits.open() function.
    head = fits.getheader(filename, ext=1)

    # Using repr function to format output
    print(repr(head))

    # Save header to text file
    with open(out_text, mode='a') as out_file:
        out_file.write(repr(head))
        out_file.write('\n\n')
XTENSION= 'IMAGE   '           / IMAGE extension
BITPIX  =                  -32 / number of bits per data pixel
NAXIS   =                    2 / number of data axes
NAXIS1  =                 4096 / length of data axis 1
NAXIS2  =                 2048 / length of data axis 2
PCOUNT  =                    0 / required keyword; must = 0
GCOUNT  =                    1 / required keyword; must = 1
ORIGIN  = 'HSTIO/CFITSIO March 2010' / FITS file originator
DATE    = '2017-12-03' / date this file was written (yyyy-mm-dd)
INHERIT =                    T / inherit the primary header
EXTNAME = 'SCI     '           / extension name
EXTVER  =                    1 / extension version number
ROOTNAME= 'jczgx1ppq                         ' / rootname of the observation set
EXPNAME = 'jczgx1ppq                ' / exposure identifier
BUNIT   = 'ELECTRONS'          / brightness units

              / WFC CCD CHIP IDENTIFICATION

CCDCHIP =                    2 / CCD chip (1 or 2)

              / World Coordinate System and Related Parameters

WCSAXES =                    2 / number of World Coordinate System axes
CRPIX1  =               2048.0 / x-coordinate of reference pixel
CRPIX2  =               1024.0 / y-coordinate of reference pixel
CRVAL1  =    127.7729653461655 / first axis value at reference pixel
CRVAL2  =    65.84354161173992 / second axis value at reference pixel
CTYPE1  = 'RA---TAN-SIP'       / the coordinate type for the first axis
CTYPE2  = 'DEC--TAN-SIP'       / the coordinate type for the second axis
CD1_1   = 1.90483532036217E-08 / partial of first axis coordinate w.r.t. x
CD1_2   = -1.3940675227771E-05 / partial of first axis coordinate w.r.t. y
CD2_1   = -1.3846187057971E-05 / partial of second axis coordinate w.r.t. x
CD2_2   = -9.8508094364170E-07 / partial of second axis coordinate w.r.t. y
LTV1    =        0.0000000E+00 / offset in X to subsection start
LTV2    =        0.0000000E+00 / offset in Y to subsection start
RAW_LTV1=                  0.0 / original offset in X to subsection start
RAW_LTV2=                  0.0 / original offset in Y to subsection start
LTM1_1  =                  1.0 / reciprocal of sampling rate in X
LTM2_2  =                  1.0 / reciprocal of sampling rate in Y
ORIENTAT=             -94.0229 / position angle of image y axis (deg. e of n)
RA_APER =   1.277389583333E+02 / RA of aperture reference position
DEC_APER=   6.584194444444E+01 / Declination of aperture reference position
PA_APER =             -94.3071 / Position Angle of reference aperture center (de
VAFACTOR=   1.000063780568E+00 / velocity aberration plate scale factor

              / READOUT DEFINITION PARAMETERS

CENTERA1=                 2073 / subarray axis1 center pt in unbinned dect. pix
CENTERA2=                 1035 / subarray axis2 center pt in unbinned dect. pix
SIZAXIS1=                 4096 / subarray axis1 size in unbinned detector pixels
SIZAXIS2=                 2048 / subarray axis2 size in unbinned detector pixels
BINAXIS1=                    1 / axis1 data bin size in unbinned detector pixels
BINAXIS2=                    1 / axis2 data bin size in unbinned detector pixels

              / PHOTOMETRY KEYWORDS

PHOTMODE= 'ACS WFC1 F814W MJD#57677.0450' / observation con
PHOTFLAM=        7.0486380E-20 / inverse sensitivity, ergs/cm2/Ang/electron
PHOTZPT =       -2.1100000E+01 / ST magnitude zero point
PHOTPLAM=        8.0449937E+03 / Pivot wavelength (Angstroms)
PHOTBW  =        6.5305701E+02 / RMS bandwidth of filter plus detector

              / REPEATED EXPOSURES INFO

NCOMBINE=                    1 / number of image sets combined during CR rejecti

              / DATA PACKET INFORMATION

FILLCNT =                    0 / number of segments containing fill
ERRCNT  =                    0 / number of segments containing errors
PODPSFF =                    F / podps fill present (T/F)
STDCFFF =                    F / science telemetry fill data present (T=1/F=0)
STDCFFP = '0x5569'             / science telemetry fill pattern (hex)

              / ON-BOARD COMPRESSION INFORMATION

WFCMPRSD=                    F / was WFC data compressed? (T/F)
CBLKSIZ =                    0 / size of compression block in 2-byte words
LOSTPIX =                    0 / #pixels lost due to buffer overflow
COMPTYP = 'None    '           / compression type performed (Partial/Full/None)

              / IMAGE STATISTICS AND DATA QUALITY FLAGS

NGOODPIX=              7987438 / number of good pixels
SDQFLAGS=                31743 / serious data quality flags
GOODMIN =       -2.4801433E+02 / minimum value of good pixels
GOODMAX =        9.0880914E+04 / maximum value of good pixels
GOODMEAN=        5.3076767E+01 / mean value of good pixels
SOFTERRS=                    0 / number of soft error pixels (DQF=1)
SNRMIN  =       -7.5930123E+00 / minimum signal to noise of good pixels
SNRMAX  =        2.2929968E+02 / maximum signal to noise of good pixels
SNRMEAN =        5.1801496E+00 / mean value of signal to noise of good pixels
MEANDARK=        6.1097779E+00 / average of the dark values subtracted
MEANBLEV=       -1.3650392E-01 / average of all bias levels subtracted
MEANFLSH=             0.000000 / Mean number of counts in post flash exposure
RADESYS = 'ICRS    '
OCX10   = 0.001964245000000002
OCX11   =  0.04982054148069229
OCY10   =  0.05027000100000004
OCY11   = 0.001500803312490457
IDCSCALE=                 0.05
IDCTHETA=                  0.0
IDCXREF =               2048.0
IDCYREF =               1024.0
IDCV2REF=    257.1520000000001
IDCV3REF=    302.6619900000002
D2IMERR1=  0.04199999943375587 / Maximum error of NPOL correction for axis 1
D2IMDIS1= 'Lookup  '           / Detector to image correction type
D2IM1   = 'EXTVER: 1' / Version number of WCSDVARR extension containing d2im loo
D2IM1   = 'NAXES: 2' / Number of independent variables in d2im function
D2IM1   = 'AXIS.1: 1' / Axis number of the jth independent variable in a d2im fu
D2IM1   = 'AXIS.2: 2' / Axis number of the jth independent variable in a d2im fu
D2IMERR2=  0.06400000303983688 / Maximum error of NPOL correction for axis 2
D2IMDIS2= 'Lookup  '           / Detector to image correction type
D2IM2   = 'EXTVER: 2' / Version number of WCSDVARR extension containing d2im loo
D2IM2   = 'NAXES: 2' / Number of independent variables in d2im function
D2IM2   = 'AXIS.1: 1' / Axis number of the jth independent variable in a d2im fu
D2IM2   = 'AXIS.2: 2' / Axis number of the jth independent variable in a d2im fu
D2IMEXT = 'jref$02c1450oj_d2i.fits'
WCSNAMEO= 'OPUS    '
WCSAXESO=                    2
CRPIX1O =               2100.0
CRPIX2O =               1024.0
CDELT1O =                  1.0
CDELT2O =                  1.0
CUNIT1O = 'deg     '
CUNIT2O = 'deg     '
CTYPE1O = 'RA---TAN'
CTYPE2O = 'DEC--TAN'
CRVAL1O =       127.7729685204
CRVAL2O =       65.84282090734
LONPOLEO=                180.0
LATPOLEO=       65.84282090734
RADESYSO= 'ICRS    '
CD1_1O  =          2.49806E-08
CD1_2O  =         -1.39456E-05
CD2_1O  =         -1.38597E-05
CD2_2O  =         -9.80762E-07
TDDALPHA= ''
TDD_CXA = ''
TDD_CXB =    -1.0658206323E-06
TDD_CTB =     1.5787128139E-06
TDD_CYA = ''
TDD_CYB = ''
TDDBETA = ''
TDD_CTA = ''
IDCTAB  = 'jref$11d1433lj_idc.fits'
A_2_2   = 3.78731328537869E-14
B_0_3   = -3.8365982324508E-10
A_ORDER =                    5
A_0_2   = 2.16316670266357E-06
B_5_0   = -2.9216557962212E-18
A_4_1   = -2.2975314425693E-18
B_3_1   = -9.2662863736411E-16
B_1_1   = 6.18673688121303E-06
A_4_0   = 2.49648430134054E-14
B_2_0   = -1.7485625426539E-06
A_3_2   = 1.79076698558529E-18
B_0_2   = -7.2366916752762E-06
B_2_3   = -4.0303373428367E-19
A_2_1   = -3.3923056140854E-11
B_3_0   = 9.85440944815669E-11
B_ORDER =                    5
A_3_0   = -4.9299373340579E-10
B_2_1   = -5.1770017201658E-10
B_3_2   = -6.5749429811757E-19
A_2_0   = 8.55757690624103E-06
B_0_4   = 4.80879850209643E-15
B_1_3   = 1.17049370338725E-14
A_1_2   = -5.3116725265518E-10
B_0_5   = -3.0673060246341E-17
A_0_5   = 6.02661866571512E-18
A_5_0   = 3.34396903040512E-18
B_4_1   = 1.26957713407563E-18
A_2_3   = 2.16524457164329E-18
A_1_3   = -7.8672443613644E-15
B_2_2   = -2.9754427958761E-14
B_1_4   = 1.23793339962009E-17
B_1_2   = -7.2577430975755E-11
A_1_1   = -5.2167190331715E-06
A_0_4   = 2.30261315411602E-14
B_4_0   = -1.7435196173764E-14
A_3_1   = 6.55120590759313E-15
A_1_4   = -1.4386444581929E-18
A_0_3   = -1.4678926146950E-13
WCSNAME = 'IDC_11d1433lj'
CPERR1  =  0.02756105922162533 / Maximum error of NPOL correction for axis 1
CPDIS1  = 'Lookup  '           / Prior distortion function type
DP1     = 'EXTVER: 1' / Version number of WCSDVARR extension containing lookup d
DP1     = 'NAXES: 2' / Number of independent variables in distortion function
DP1     = 'AXIS.1: 1' / Axis number of the jth independent variable in a distort
DP1     = 'AXIS.2: 2' / Axis number of the jth independent variable in a distort
CPERR2  =  0.01880022883415222 / Maximum error of NPOL correction for axis 2
CPDIS2  = 'Lookup  '           / Prior distortion function type
DP2     = 'EXTVER: 2' / Version number of WCSDVARR extension containing lookup d
DP2     = 'NAXES: 2' / Number of independent variables in distortion function
DP2     = 'AXIS.1: 1' / Axis number of the jth independent variable in a distort
DP2     = 'AXIS.2: 2' / Axis number of the jth independent variable in a distort
NPOLEXT = 'jref$02c1450rj_npl.fits'
MDRIZSKY=    40.54545593261719 / Sky value computed by AstroDrizzle
XTENSION= 'IMAGE   '           / IMAGE extension
BITPIX  =                  -32 / number of bits per data pixel
NAXIS   =                    2 / number of data axes
NAXIS1  =                 4096 / length of data axis 1
NAXIS2  =                 2048 / length of data axis 2
PCOUNT  =                    0 / required keyword; must = 0
GCOUNT  =                    1 / required keyword; must = 1
ORIGIN  = 'HSTIO/CFITSIO March 2010' / FITS file originator
DATE    = '2017-12-03' / date this file was written (yyyy-mm-dd)
INHERIT =                    T / inherit the primary header
EXTNAME = 'SCI     '           / extension name
EXTVER  =                    1 / extension version number
ROOTNAME= 'jczgx1ptq                         ' / rootname of the observation set
EXPNAME = 'jczgx1ptq                ' / exposure identifier
BUNIT   = 'ELECTRONS'          / brightness units

              / WFC CCD CHIP IDENTIFICATION

CCDCHIP =                    2 / CCD chip (1 or 2)

              / World Coordinate System and Related Parameters

WCSAXES =                    2 / number of World Coordinate System axes
CRPIX1  =               2048.0 / x-coordinate of reference pixel
CRPIX2  =               1024.0 / y-coordinate of reference pixel
CRVAL1  =     127.774971972961 / first axis value at reference pixel
CRVAL2  =    65.84362363894992 / second axis value at reference pixel
CTYPE1  = 'RA---TAN-SIP'       / the coordinate type for the first axis
CTYPE2  = 'DEC--TAN-SIP'       / the coordinate type for the second axis
CD1_1   = 1.86049319494035E-08 / partial of first axis coordinate w.r.t. x
CD1_2   = -1.3940697878041E-05 / partial of first axis coordinate w.r.t. y
CD2_1   = -1.3846178828081E-05 / partial of second axis coordinate w.r.t. x
CD2_2   = -9.8463386768576E-07 / partial of second axis coordinate w.r.t. y
LTV1    =        0.0000000E+00 / offset in X to subsection start
LTV2    =        0.0000000E+00 / offset in Y to subsection start
RAW_LTV1=                  0.0 / original offset in X to subsection start
RAW_LTV2=                  0.0 / original offset in Y to subsection start
LTM1_1  =                  1.0 / reciprocal of sampling rate in X
LTM2_2  =                  1.0 / reciprocal of sampling rate in Y
ORIENTAT=              -94.021 / position angle of image y axis (deg. e of n)
RA_APER =   1.277409647262E+02 / RA of aperture reference position
DEC_APER=   6.584202691721E+01 / Declination of aperture reference position
PA_APER =             -94.3053 / Position Angle of reference aperture center (de
VAFACTOR=   1.000063143039E+00 / velocity aberration plate scale factor

              / READOUT DEFINITION PARAMETERS

CENTERA1=                 2073 / subarray axis1 center pt in unbinned dect. pix
CENTERA2=                 1035 / subarray axis2 center pt in unbinned dect. pix
SIZAXIS1=                 4096 / subarray axis1 size in unbinned detector pixels
SIZAXIS2=                 2048 / subarray axis2 size in unbinned detector pixels
BINAXIS1=                    1 / axis1 data bin size in unbinned detector pixels
BINAXIS2=                    1 / axis2 data bin size in unbinned detector pixels

              / PHOTOMETRY KEYWORDS

PHOTMODE= 'ACS WFC1 F814W MJD#57677.0536' / observation con
PHOTFLAM=        7.0486380E-20 / inverse sensitivity, ergs/cm2/Ang/electron
PHOTZPT =       -2.1100000E+01 / ST magnitude zero point
PHOTPLAM=        8.0449937E+03 / Pivot wavelength (Angstroms)
PHOTBW  =        6.5305701E+02 / RMS bandwidth of filter plus detector

              / REPEATED EXPOSURES INFO

NCOMBINE=                    1 / number of image sets combined during CR rejecti

              / DATA PACKET INFORMATION

FILLCNT =                    0 / number of segments containing fill
ERRCNT  =                    0 / number of segments containing errors
PODPSFF =                    F / podps fill present (T/F)
STDCFFF =                    F / science telemetry fill data present (T=1/F=0)
STDCFFP = '0x5569'             / science telemetry fill pattern (hex)

              / ON-BOARD COMPRESSION INFORMATION

WFCMPRSD=                    F / was WFC data compressed? (T/F)
CBLKSIZ =                    0 / size of compression block in 2-byte words
LOSTPIX =                    0 / #pixels lost due to buffer overflow
COMPTYP = 'None    '           / compression type performed (Partial/Full/None)

              / IMAGE STATISTICS AND DATA QUALITY FLAGS

NGOODPIX=              7987448 / number of good pixels
SDQFLAGS=                31743 / serious data quality flags
GOODMIN =       -5.6858374E+02 / minimum value of good pixels
GOODMAX =        8.4768180E+04 / maximum value of good pixels
GOODMEAN=        4.5566620E+01 / mean value of good pixels
SOFTERRS=                    0 / number of soft error pixels (DQF=1)
SNRMIN  =       -6.5290461E+00 / minimum signal to noise of good pixels
SNRMAX  =        2.3049573E+02 / maximum signal to noise of good pixels
SNRMEAN =        4.5304279E+00 / mean value of signal to noise of good pixels
MEANDARK=        6.4147372E+00 / average of the dark values subtracted
MEANBLEV=        6.4909774E-01 / average of all bias levels subtracted
MEANFLSH=             0.000000 / Mean number of counts in post flash exposure
RADESYS = 'ICRS    '
OCX10   = 0.001964245000000002
OCX11   =  0.04982054148069229
OCY10   =  0.05027000100000004
OCY11   = 0.001500803312490457
IDCSCALE=                 0.05
IDCTHETA=                  0.0
IDCXREF =               2048.0
IDCYREF =               1024.0
IDCV2REF=    257.1520000000001
IDCV3REF=    302.6619900000002
D2IMERR1=  0.04199999943375587 / Maximum error of NPOL correction for axis 1
D2IMDIS1= 'Lookup  '           / Detector to image correction type
D2IM1   = 'EXTVER: 1' / Version number of WCSDVARR extension containing d2im loo
D2IM1   = 'NAXES: 2' / Number of independent variables in d2im function
D2IM1   = 'AXIS.1: 1' / Axis number of the jth independent variable in a d2im fu
D2IM1   = 'AXIS.2: 2' / Axis number of the jth independent variable in a d2im fu
D2IMERR2=  0.06400000303983688 / Maximum error of NPOL correction for axis 2
D2IMDIS2= 'Lookup  '           / Detector to image correction type
D2IM2   = 'EXTVER: 2' / Version number of WCSDVARR extension containing d2im loo
D2IM2   = 'NAXES: 2' / Number of independent variables in d2im function
D2IM2   = 'AXIS.1: 1' / Axis number of the jth independent variable in a d2im fu
D2IM2   = 'AXIS.2: 2' / Axis number of the jth independent variable in a d2im fu
D2IMEXT = 'jref$02c1450oj_d2i.fits'
WCSNAMEO= 'OPUS    '
WCSAXESO=                    2
CRPIX1O =               2100.0
CRPIX2O =               1024.0
CDELT1O =                  1.0
CDELT2O =                  1.0
CUNIT1O = 'deg     '
CUNIT2O = 'deg     '
CTYPE1O = 'RA---TAN'
CTYPE2O = 'DEC--TAN'
CRVAL1O =       127.7749750908
CRVAL2O =       65.84290293455
LONPOLEO=                180.0
LATPOLEO=       65.84290293455
RADESYSO= 'ICRS    '
CD1_1O  =          2.45367E-08
CD1_2O  =         -1.39456E-05
CD2_1O  =         -1.38597E-05
CD2_2O  = -9.8031499999999E-07
TDDALPHA= ''
TDD_CXA = ''
TDD_CXB =    -1.0658206323E-06
TDD_CTB =     1.5787128139E-06
TDD_CYA = ''
TDD_CYB = ''
TDDBETA = ''
TDD_CTA = ''
IDCTAB  = 'jref$11d1433lj_idc.fits'
A_2_2   = 3.78731328537869E-14
B_0_3   = -3.8365982324508E-10
A_ORDER =                    5
A_0_2   = 2.16316670266357E-06
B_5_0   = -2.9216557962212E-18
A_4_1   = -2.2975314425693E-18
B_3_1   = -9.2662863736411E-16
B_1_1   = 6.18673688121303E-06
A_4_0   = 2.49648430134054E-14
B_2_0   = -1.7485625426539E-06
A_3_2   = 1.79076698558529E-18
B_0_2   = -7.2366916752762E-06
B_2_3   = -4.0303373428367E-19
A_2_1   = -3.3923056140854E-11
B_3_0   = 9.85440944815669E-11
B_ORDER =                    5
A_3_0   = -4.9299373340579E-10
B_2_1   = -5.1770017201658E-10
B_3_2   = -6.5749429811757E-19
A_2_0   = 8.55757690624103E-06
B_0_4   = 4.80879850209643E-15
B_1_3   = 1.17049370338725E-14
A_1_2   = -5.3116725265518E-10
B_0_5   = -3.0673060246341E-17
A_0_5   = 6.02661866571512E-18
A_5_0   = 3.34396903040512E-18
B_4_1   = 1.26957713407563E-18
A_2_3   = 2.16524457164329E-18
A_1_3   = -7.8672443613644E-15
B_2_2   = -2.9754427958761E-14
B_1_4   = 1.23793339962009E-17
B_1_2   = -7.2577430975755E-11
A_1_1   = -5.2167190331715E-06
A_0_4   = 2.30261315411602E-14
B_4_0   = -1.7435196173764E-14
A_3_1   = 6.55120590759313E-15
A_1_4   = -1.4386444581929E-18
A_0_3   = -1.4678926146950E-13
WCSNAME = 'IDC_11d1433lj'
CPERR1  =  0.02756105922162533 / Maximum error of NPOL correction for axis 1
CPDIS1  = 'Lookup  '           / Prior distortion function type
DP1     = 'EXTVER: 1' / Version number of WCSDVARR extension containing lookup d
DP1     = 'NAXES: 2' / Number of independent variables in distortion function
DP1     = 'AXIS.1: 1' / Axis number of the jth independent variable in a distort
DP1     = 'AXIS.2: 2' / Axis number of the jth independent variable in a distort
CPERR2  =  0.01880022883415222 / Maximum error of NPOL correction for axis 2
CPDIS2  = 'Lookup  '           / Prior distortion function type
DP2     = 'EXTVER: 2' / Version number of WCSDVARR extension containing lookup d
DP2     = 'NAXES: 2' / Number of independent variables in distortion function
DP2     = 'AXIS.1: 1' / Axis number of the jth independent variable in a distort
DP2     = 'AXIS.2: 2' / Axis number of the jth independent variable in a distort
NPOLEXT = 'jref$02c1450rj_npl.fits'
MDRIZSKY=    33.60466766357422 / Sky value computed by AstroDrizzle
XTENSION= 'IMAGE   '           / IMAGE extension
BITPIX  =                  -32 / number of bits per data pixel
NAXIS   =                    2 / number of data axes
NAXIS1  =                 4096 / length of data axis 1
NAXIS2  =                 2048 / length of data axis 2
PCOUNT  =                    0 / required keyword; must = 0
GCOUNT  =                    1 / required keyword; must = 1
ORIGIN  = 'HSTIO/CFITSIO March 2010' / FITS file originator
DATE    = '2017-12-03' / date this file was written (yyyy-mm-dd)
INHERIT =                    T / inherit the primary header
EXTNAME = 'SCI     '           / extension name
EXTVER  =                    1 / extension version number
ROOTNAME= 'jczgx1q1q                         ' / rootname of the observation set
EXPNAME = 'jczgx1q1q                ' / exposure identifier
BUNIT   = 'ELECTRONS'          / brightness units

              / WFC CCD CHIP IDENTIFICATION

CCDCHIP =                    2 / CCD chip (1 or 2)

              / World Coordinate System and Related Parameters

WCSAXES =                    2 / number of World Coordinate System axes
CRPIX1  =               2048.0 / x-coordinate of reference pixel
CRPIX2  =               1024.0 / y-coordinate of reference pixel
CRVAL1  =    127.7790008405421 / first axis value at reference pixel
CRVAL2  =     65.8438018528099 / second axis value at reference pixel
CTYPE1  = 'RA---TAN-SIP'       / the coordinate type for the first axis
CTYPE2  = 'DEC--TAN-SIP'       / the coordinate type for the second axis
CD1_1   = 1.77165941042396E-08 / partial of first axis coordinate w.r.t. x
CD1_2   = -1.3940911726204E-05 / partial of first axis coordinate w.r.t. y
CD2_1   = -1.3846329672062E-05 / partial of second axis coordinate w.r.t. x
CD2_2   = -9.8374991384276E-07 / partial of second axis coordinate w.r.t. y
LTV1    =        0.0000000E+00 / offset in X to subsection start
LTV2    =        0.0000000E+00 / offset in Y to subsection start
RAW_LTV1=                  0.0 / original offset in X to subsection start
RAW_LTV2=                  0.0 / original offset in Y to subsection start
LTM1_1  =                  1.0 / reciprocal of sampling rate in X
LTM2_2  =                  1.0 / reciprocal of sampling rate in Y
ORIENTAT=             -94.0174 / position angle of image y axis (deg. e of n)
RA_APER =   1.277449931071E+02 / RA of aperture reference position
DEC_APER=   6.584220602391E+01 / Declination of aperture reference position
PA_APER =             -94.3016 / Position Angle of reference aperture center (de
VAFACTOR=   1.000073952797E+00 / velocity aberration plate scale factor

              / READOUT DEFINITION PARAMETERS

CENTERA1=                 2073 / subarray axis1 center pt in unbinned dect. pix
CENTERA2=                 1035 / subarray axis2 center pt in unbinned dect. pix
SIZAXIS1=                 4096 / subarray axis1 size in unbinned detector pixels
SIZAXIS2=                 2048 / subarray axis2 size in unbinned detector pixels
BINAXIS1=                    1 / axis1 data bin size in unbinned detector pixels
BINAXIS2=                    1 / axis2 data bin size in unbinned detector pixels

              / PHOTOMETRY KEYWORDS

PHOTMODE= 'ACS WFC1 F814W MJD#57677.0946' / observation con
PHOTFLAM=        7.0486386E-20 / inverse sensitivity, ergs/cm2/Ang/electron
PHOTZPT =       -2.1100000E+01 / ST magnitude zero point
PHOTPLAM=        8.0449937E+03 / Pivot wavelength (Angstroms)
PHOTBW  =        6.5305701E+02 / RMS bandwidth of filter plus detector

              / REPEATED EXPOSURES INFO

NCOMBINE=                    1 / number of image sets combined during CR rejecti

              / DATA PACKET INFORMATION

FILLCNT =                    0 / number of segments containing fill
ERRCNT  =                    0 / number of segments containing errors
PODPSFF =                    F / podps fill present (T/F)
STDCFFF =                    F / science telemetry fill data present (T=1/F=0)
STDCFFP = '0x5569'             / science telemetry fill pattern (hex)

              / ON-BOARD COMPRESSION INFORMATION

WFCMPRSD=                    F / was WFC data compressed? (T/F)
CBLKSIZ =                    0 / size of compression block in 2-byte words
LOSTPIX =                    0 / #pixels lost due to buffer overflow
COMPTYP = 'None    '           / compression type performed (Partial/Full/None)

              / IMAGE STATISTICS AND DATA QUALITY FLAGS

NGOODPIX=              7987459 / number of good pixels
SDQFLAGS=                31743 / serious data quality flags
GOODMIN =       -4.6811813E+02 / minimum value of good pixels
GOODMAX =        8.6860820E+04 / maximum value of good pixels
GOODMEAN=        5.8565811E+01 / mean value of good pixels
SOFTERRS=                    0 / number of soft error pixels (DQF=1)
SNRMIN  =       -5.3112264E+00 / minimum signal to noise of good pixels
SNRMAX  =        2.3047971E+02 / maximum signal to noise of good pixels
SNRMEAN =        5.8733592E+00 / mean value of signal to noise of good pixels
MEANDARK=        6.1097779E+00 / average of the dark values subtracted
MEANBLEV=       -8.4848583E-01 / average of all bias levels subtracted
MEANFLSH=             0.000000 / Mean number of counts in post flash exposure
RADESYS = 'ICRS    '
OCX10   = 0.001964245000000002
OCX11   =  0.04982054148069229
OCY10   =  0.05027000100000004
OCY11   = 0.001500803312490457
IDCSCALE=                 0.05
IDCTHETA=                  0.0
IDCXREF =               2048.0
IDCYREF =               1024.0
IDCV2REF=    257.1520000000001
IDCV3REF=    302.6619900000002
D2IMERR1=  0.04199999943375587 / Maximum error of NPOL correction for axis 1
D2IMDIS1= 'Lookup  '           / Detector to image correction type
D2IM1   = 'EXTVER: 1' / Version number of WCSDVARR extension containing d2im loo
D2IM1   = 'NAXES: 2' / Number of independent variables in d2im function
D2IM1   = 'AXIS.1: 1' / Axis number of the jth independent variable in a d2im fu
D2IM1   = 'AXIS.2: 2' / Axis number of the jth independent variable in a d2im fu
D2IMERR2=  0.06400000303983688 / Maximum error of NPOL correction for axis 2
D2IMDIS2= 'Lookup  '           / Detector to image correction type
D2IM2   = 'EXTVER: 2' / Version number of WCSDVARR extension containing d2im loo
D2IM2   = 'NAXES: 2' / Number of independent variables in d2im function
D2IM2   = 'AXIS.1: 1' / Axis number of the jth independent variable in a d2im fu
D2IM2   = 'AXIS.2: 2' / Axis number of the jth independent variable in a d2im fu
D2IMEXT = 'jref$02c1450oj_d2i.fits'
WCSNAMEO= 'OPUS    '
WCSAXESO=                    2
CRPIX1O =               2100.0
CRPIX2O =               1024.0
CDELT1O =                  1.0
CDELT2O =                  1.0
CUNIT1O = 'deg     '
CUNIT2O = 'deg     '
CTYPE1O = 'RA---TAN'
CTYPE2O = 'DEC--TAN'
CRVAL1O =       127.7790038454
CRVAL2O =    65.84308114840999
LONPOLEO=                180.0
LATPOLEO=    65.84308114840999
RADESYSO= 'ICRS    '
CD1_1O  =          2.36474E-08
CD1_2O  =         -1.39456E-05
CD2_1O  =         -1.38597E-05
CD2_2O  =          -9.7942E-07
TDDALPHA= ''
TDD_CXA = ''
TDD_CXB =    -1.0658206323E-06
TDD_CTB =     1.5787128139E-06
TDD_CYA = ''
TDD_CYB = ''
TDDBETA = ''
TDD_CTA = ''
IDCTAB  = 'jref$11d1433lj_idc.fits'
A_2_2   = 3.78731328537869E-14
B_0_3   = -3.8365982324508E-10
A_ORDER =                    5
A_0_2   = 2.16316670266357E-06
B_5_0   = -2.9216557962212E-18
A_4_1   = -2.2975314425693E-18
B_3_1   = -9.2662863736411E-16
B_1_1   = 6.18673688121303E-06
A_4_0   = 2.49648430134054E-14
B_2_0   = -1.7485625426539E-06
A_3_2   = 1.79076698558529E-18
B_0_2   = -7.2366916752762E-06
B_2_3   = -4.0303373428367E-19
A_2_1   = -3.3923056140854E-11
B_3_0   = 9.85440944815669E-11
B_ORDER =                    5
A_3_0   = -4.9299373340579E-10
B_2_1   = -5.1770017201658E-10
B_3_2   = -6.5749429811757E-19
A_2_0   = 8.55757690624103E-06
B_0_4   = 4.80879850209643E-15
B_1_3   = 1.17049370338725E-14
A_1_2   = -5.3116725265518E-10
B_0_5   = -3.0673060246341E-17
A_0_5   = 6.02661866571512E-18
A_5_0   = 3.34396903040512E-18
B_4_1   = 1.26957713407563E-18
A_2_3   = 2.16524457164329E-18
A_1_3   = -7.8672443613644E-15
B_2_2   = -2.9754427958761E-14
B_1_4   = 1.23793339962009E-17
B_1_2   = -7.2577430975755E-11
A_1_1   = -5.2167190331715E-06
A_0_4   = 2.30261315411602E-14
B_4_0   = -1.7435196173764E-14
A_3_1   = 6.55120590759313E-15
A_1_4   = -1.4386444581929E-18
A_0_3   = -1.4678926146950E-13
WCSNAME = 'IDC_11d1433lj'
CPERR1  =  0.02756105922162533 / Maximum error of NPOL correction for axis 1
CPDIS1  = 'Lookup  '           / Prior distortion function type
DP1     = 'EXTVER: 1' / Version number of WCSDVARR extension containing lookup d
DP1     = 'NAXES: 2' / Number of independent variables in distortion function
DP1     = 'AXIS.1: 1' / Axis number of the jth independent variable in a distort
DP1     = 'AXIS.2: 2' / Axis number of the jth independent variable in a distort
CPERR2  =  0.01880022883415222 / Maximum error of NPOL correction for axis 2
CPDIS2  = 'Lookup  '           / Prior distortion function type
DP2     = 'EXTVER: 2' / Version number of WCSDVARR extension containing lookup d
DP2     = 'NAXES: 2' / Number of independent variables in distortion function
DP2     = 'AXIS.1: 1' / Axis number of the jth independent variable in a distort
DP2     = 'AXIS.2: 2' / Axis number of the jth independent variable in a distort
NPOLEXT = 'jref$02c1450rj_npl.fits'
MDRIZSKY=    50.43417358398437 / Sky value computed by AstroDrizzle

imhistogram

Please review the Notes section above before running any examples in this notebook

Imhistogram will plot a customized histogram of the provided image data. To make a histogram in Python we are going to use Matplotlib’s hist function. See the hist documentation for options to change the histogram type, scaling, bin sizes, and more.

# Standard Imports
import numpy as np

# Astronomy Specific Imports
from astropy.io import fits
from astroquery.mast import Observations

# Plotting Imports/Setup
import matplotlib.pyplot as plt
%matplotlib inline
# Download test file using astroquery, this only needs to be run once
# and can be skipped if using your own data.
# Astroquery will only download file if not already present.
obsid = '2004615006'
Observations.download_products(obsid,productFilename="iczgs3ygq_flt.fits")
INFO:astropy:Found cached file ./mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fits with expected size 16534080.
INFO: Found cached file ./mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fits with expected size 16534080. [astroquery.query]
Table length=1
Local PathStatusMessageURL
str47str5str87str93
./mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fitsERRORDownloaded filesize is 16531200,but should be 16534080, file may be partial or corrupt.https://mast.stsci.edu/api/v0/download/file?uri=mast:HST/product/iczgs3ygq/iczgs3ygq_flt.fits
# Change these values to your desired data files
test_data = './mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fits'

# Pull out the first science array, we also need to flatten the data to a
# 1D array before sending it to hist
sci1 = fits.getdata(test_data,ext=1)
sci1f = sci1.flatten()

# Now we can plot our histogram, using some of the optional keywords in hist
# The hist function returns the values of the histogram bins (n), the edges
# of the bins (obins), and the patches used to create the histogram
fig = plt.figure()
n, obins, patches = plt.hist(sci1f,bins=100,range=(0,2))

# Save resulting figure to png file
fig.savefig('hist.png')
_images/images.imutil_67_0.png

imreplace

Please review the Notes section above before running any examples in this notebook

Imreplace is used to replace array sections with a constant. We can use simple numpy array manipulation to replicate imreplace. For details on how to grow the boolean array for replacement see crgrow, or the skimage.dilation documentation.

# Standard Imports
import numpy as np

# Astronomy Specific Imports
from astropy.io import fits
from astroquery.mast import Observations
# Download test file using astroquery, this only needs to be run once
# and can be skipped if using your own data.
# Astroquery will only download file if not already present.
obsid = '2004615006'
Observations.download_products(obsid,productFilename="iczgs3ygq_flt.fits")
INFO:astropy:Found cached file ./mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fits with expected size 16534080.
INFO: Found cached file ./mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fits with expected size 16534080. [astroquery.query]
Table length=1
Local PathStatusMessageURL
str47str5str87str93
./mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fitsERRORDownloaded filesize is 16531200,but should be 16534080, file may be partial or corrupt.https://mast.stsci.edu/api/v0/download/file?uri=mast:HST/product/iczgs3ygq/iczgs3ygq_flt.fits
# Change these values to your desired data files
test_data = './mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fits'
out_file = 'imreplace_out.fits'

# Pull out the first science array
hdu = fits.open(test_data)
sci1 = hdu[1].data

print("cutout of array before replacements:")
print(sci1[50:55, 50:55])

# Make boolean mask with your requirements, here we produce a boolean mask
# where all array elements with values >0.5 and <0.6 are set to True.
mask1 = np.logical_and(sci1>0.8, sci1<0.82)

# Use mask to replace values
sci1[mask1] = 99

print("\ncoutout of array after replacements:")
print(sci1[50:55, 50:55])

# Take updated array and write out new FITS file
hdu[1].data = sci1
hdu.writeto(out_file, overwrite=True)

# Close FITS file
hdu.close()
cutout of array before replacements:
[[ 0.89118606  0.87640154  0.81239933  0.77495182  0.80048275]
 [ 0.83939391  0.79715788  0.71130604  0.83452195  0.74553812]
 [ 0.82984501  0.82536161  0.82937354  0.82661521  0.80760878]
 [ 0.88277584  0.78050691  0.85906219  0.80846858  0.8092978 ]
 [ 0.85532236  0.73028219  0.81455106  0.76300722  0.85437953]]

coutout of array after replacements:
[[  0.89118606   0.87640154  99.           0.77495182  99.        ]
 [  0.83939391   0.79715788   0.71130604   0.83452195   0.74553812]
 [  0.82984501   0.82536161   0.82937354   0.82661521  99.        ]
 [  0.88277584   0.78050691   0.85906219  99.          99.        ]
 [  0.85532236   0.73028219  99.           0.76300722   0.85437953]]
# We can also use numpy where to pull out index numbers
mask2 = np.where(sci1 > 1000)
print("Index values where sci1 is > 1,000")
print(mask2)
Index values where sci1 is > 1,000
(array([ 474,  474,  606,  607,  607,  607,  608,  608,  608,  608,  609,
        609,  609,  609,  610,  610,  610,  804,  804,  809,  809,  810,
        883,  883, 1002, 1013]), array([455, 456, 285, 284, 285, 286, 284, 285, 286, 287, 284, 285, 286,
       287, 284, 285, 286, 349, 350,  53, 575,  53, 161, 162, 104, 460]))

imstack-imslice

Please review the Notes section above before running any examples in this notebook

Imstack can take multiple FITS images and stack the data, writing out a new file where the FITS data is 1-dimension higher then the input images. Here we show that manipulation using the astropy library and numpy.stack.

Imslice can take a 3-D datacube FITS image and return multiple 2D images sliced through the chosen dimension. Keep in mind for the python equivalent workflow that the header file from the original input image will be used for all output images, including WCS information. We will be using numpy.split.

Below we first produced a 3-D datacube with by stacking, then split the output.

# Standard Imports
import numpy as np

# Astronomy Specific Imports
from astropy.io import fits
from astroquery.mast import Observations
# Download test file using astroquery, this only needs to be run once
# and can be skipped if using your own data.
# Astroquery will only download file if not already present.
obsid = '2004663553'
Observations.download_products(obsid,productFilename="jczgx1ppq_flc.fits")
obsid = '2004663556'
Observations.download_products(obsid, productFilename="jczgx1q1q_flc.fits")
INFO: Found cached file ./mastDownload/HST/JCZGX1PPQ/jczgx1ppq_flc.fits with expected size 167964480. [astroquery.query]
INFO: Found cached file ./mastDownload/HST/JCZGX1Q1Q/jczgx1q1q_flc.fits with expected size 167964480. [astroquery.query]
Table length=1
Local PathStatusMessageURL
str47str8objectobject
./mastDownload/HST/JCZGX1Q1Q/jczgx1q1q_flc.fitsCOMPLETENoneNone

Here is an example that stacks arrays into a 3-D datacube

# Pull two image data arrays and an image header
header1 = fits.getheader('./mastDownload/HST/JCZGX1PPQ/jczgx1ppq_flc.fits',ext=1)
image1 = fits.getdata('./mastDownload/HST/JCZGX1PPQ/jczgx1ppq_flc.fits')
image2 = fits.getdata('./mastDownload/HST/JCZGX1Q1Q/jczgx1q1q_flc.fits')

# Stack arrays, the new dimension will be put first, unless otherwise specified with the axis keyword
outstack = np.stack((image1,image2))
print("final shape is:")
print(outstack.shape)

# Now we can write this new array into a new FITS file by packing it back into an HDU object
hdu = fits.PrimaryHDU(outstack,header1)
hdu.writeto('imstack_out.fits', overwrite=True)
final shape is:
(2, 2048, 4096)

Now we take that output and break it back down to 2-D arrays.

# Pull image data array and image header
orig_hdu = fits.open('imstack_out.fits')

print("Here's the extensions in our input file:")
orig_hdu.info()

header1 = orig_hdu[0].header
image1 = orig_hdu[0].data
orig_hdu.close()

print("\noriginal array - the dimension order is listed " +
      "in reverse order \nnow that we have read the array into a numpy array:")
print(image1.shape)

# Slice images easily by using numpy.split, which returns a list of the output arrays
# THen numpy.squeeze is used to remove the extra length one dimensions left over from
# numpy.split.
arr_list = np.split(image1, 2)
arr_list = np.squeeze(arr_list)
print("\nfinal shape of a slice is:")
print(arr_list[0].shape)

# Now we can write this new array into a new FITS files by packing it back into an HDU object
hdu1 = fits.PrimaryHDU(arr_list[0],header1)
hdu1.writeto('imslice_out1.fits', overwrite=True)
hdu2 = fits.PrimaryHDU(arr_list[1],header1)
hdu2.writeto('imslice_out2.fits', overwrite=True)
Here's the extensions in our input file:
Filename: imstack_out.fits
No.    Name      Ver    Type      Cards   Dimensions   Format
  0  SCI           1 PrimaryHDU     199   (4096, 2048, 2)   float32

original array - the dimension order is listed in reverse order
now that we have read the array into a numpy array:
(2, 2048, 4096)

final shape of a slice is:
(2048, 4096)

imstatistics

Please review the Notes section above before running any examples in this notebook

We will use the astropy.stats.sigma_clipped_stats function here, which has some wider capabilites then the imstatistics function. Please see the stats package documentation for details on the advanced usage. We also use some Numpy functions for additional statistics.

Important Note to Users: There are some small differences in algorithms between the IRAF and Python statistical calculations. Both the centering function used for the clipping as well as the degrees of freedom may vary. For example, astropy.stats.sigma_clipped_stats uses a simple median for the clipping center. However a custom centering function can be provided through the cenfunc parameter. Proceed with care if you are comparing prior IRAF results to Python results.

# Standard Imports
import numpy as np

# Astronomy Specific Imports
from astropy.io import fits
from astropy import stats
from astroquery.mast import Observations
# Download test file using astroquery, this only needs to be run once
# and can be skipped if using your own data.
# Astroquery will only download file if not already present.
obsid = '2004615006'
Observations.download_products(obsid,productFilename="iczgs3ygq_flt.fits")
INFO:astropy:Found cached file ./mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fits with expected size 16534080.
INFO: Found cached file ./mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fits with expected size 16534080. [astroquery.query]
Table length=1
Local PathStatusMessageURL
str47str5str87str93
./mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fitsERRORDownloaded filesize is 16531200,but should be 16534080, file may be partial or corrupt.https://mast.stsci.edu/api/v0/download/file?uri=mast:HST/product/iczgs3ygq/iczgs3ygq_flt.fits
# Change these values to your desired data files
test_data = './mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fits'
sci1 = fits.getdata(test_data, ext=1)

# The sigma_clipped_stats function returns the mean, median, and stddev respectively
# To more closely replicate the IRAF version that is using n-1 in it's calculations
# we use the std_ddof parameter
output = stats.sigma_clipped_stats(sci1, sigma=3.0, iters=3, std_ddof=1)
print("mean, median, standard deviation:")
print(output)

# To see the min and max of an array we can use numpy.min and numpy.max
array_min = np.min(sci1)
array_max = np.max(sci1)
print("\nmin, max")
print("{}, {}".format(array_min, array_max))

# To find out how many pixels are greater then a particular value we can use numpy.where
where_result = np.where(sci1 > 1000)
count = len(where_result[0])
print("\nNumber of pixels above 1,000:")
print(count)
mean, median, standard deviation:
(0.82595410841884809, 0.81768394, 0.074634554991261454)

min, max
-4007.712890625, 27569.6015625

Number of pixels above 1,000:
26

imsum

Please review the Notes section above before running any examples in this notebook

Imsum is used to compute the sum, average, or mean of a set of images. We will be using the ccdproc Combiner class here. Keep in mind that the original FITS header is not retained in the CCDData object. Please see the ccdproc documentation for more details.

# Astronomy Specific Imports
from astropy.io import fits
from astropy import units
from ccdproc import CCDData, Combiner
from astroquery.mast import Observations
# Download test file using astroquery, this only needs to be run once
# and can be skipped if using your own data.
# Astroquery will only download file if not already present.
obsid = '2004615003'
Observations.download_products(obsid,productFilename="iczgs3y5q_flt.fits")
obsid = '2004615006'
Observations.download_products(obsid,productFilename="iczgs3ygq_flt.fits")
INFO:astropy:Found cached file ./mastDownload/HST/ICZGS3Y5Q/iczgs3y5q_flt.fits with expected size 16534080.
INFO: Found cached file ./mastDownload/HST/ICZGS3Y5Q/iczgs3y5q_flt.fits with expected size 16534080. [astroquery.query]
INFO:astropy:Found cached file ./mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fits with expected size 16534080.
INFO: Found cached file ./mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fits with expected size 16534080. [astroquery.query]
Table length=1
Local PathStatusMessageURL
str47str5str87str93
./mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fitsERRORDownloaded filesize is 16531200,but should be 16534080, file may be partial or corrupt.https://mast.stsci.edu/api/v0/download/file?uri=mast:HST/product/iczgs3ygq/iczgs3ygq_flt.fits
# Change these values to your desired data files
test_data1 = './mastDownload/HST/ICZGS3Y5Q/iczgs3y5q_flt.fits'
test_data2 = './mastDownload/HST/ICZGS3YGQ/iczgs3ygq_flt.fits'

# First we need to pull out the science arrays to create CCDData objects
# Our actual unit is electrons/sec, this is not accepted by the current
# set of units
cdata1 = CCDData.read(test_data1, hdu=1, unit=units.electron/units.s)
cdata2 = cdata1.copy()
cdata3 = CCDData.read(test_data2, hdu=1, unit=units.electron/units.s)
cdata4 = cdata3.copy()
combiner = Combiner([cdata1, cdata2, cdata3, cdata4])

# Now we can make our mask for extrema clipping
# The equivalent of low_reject, high_reject parameter
combiner.clip_extrema(nlow=1, nhigh=1)

# And finally to combine...
final_combine = combiner.average_combine()
print(final_combine.data)
INFO:astropy:using the unit electron / s passed to the FITS reader instead of the unit ELECTRONS/S in the FITS file.
INFO:astropy:using the unit electron / s passed to the FITS reader instead of the unit ELECTRONS/S in the FITS file.
INFO: using the unit electron / s passed to the FITS reader instead of the unit ELECTRONS/S in the FITS file. [astropy.nddata.ccddata]
INFO: using the unit electron / s passed to the FITS reader instead of the unit ELECTRONS/S in the FITS file. [astropy.nddata.ccddata]
[[  0.87720111   0.82106587   0.79521415 ...,   3.87308204   7.41545987
    9.01969481]
 [  0.89028609   0.7884455    0.8240625  ...,   0.86163342   4.53510189
    0.99109203]
 [  0.81683022   0.83273572   0.82175627 ...,   3.60699821  -7.82266164
    2.95994186]
 ...,
 [ 40.72796059  15.36561799  -8.79329443 ...,  22.68277168  25.31048012
   28.829813  ]
 [ 46.28870392  -4.50218874   1.74757147 ...,  13.24364138  25.70440292
   11.0971849 ]
 [ 42.8106432   29.66250706  63.18441772 ...,   0.           9.80057049
   22.66858006]]

listpixels

Please review the Notes section above before running any examples in this notebook

Listpixels was used to list an indexed section of a FITS data array. This is easy to do using astropy, but keep in mind that Python indexes from zero, and with the y-axis leading, i.e. [y,x]. You also want to end the cut with the pixel after the end pixel. So to get 1-10 in x and 5-15 in y, you will index like so: array[4:15,0:10]. To see listpixels results for more then one file, you will need to loop over a list of files, see information about Python loops here.

# Astronomy Specific Imports
from astropy.io import fits
from astroquery.mast import Observations
# Download test file using astroquery, this only needs to be run once
# and can be skipped if using your own data.
# Astroquery will only download file if not already present.
obsid = '2004615003'
Observations.download_products(obsid,productFilename="iczgs3y5q_flt.fits")
INFO:astropy:Found cached file ./mastDownload/HST/ICZGS3Y5Q/iczgs3y5q_flt.fits with expected size 16534080.
INFO: Found cached file ./mastDownload/HST/ICZGS3Y5Q/iczgs3y5q_flt.fits with expected size 16534080. [astroquery.query]
Table length=1
Local PathStatusMessageURL
str47str5str87str93
./mastDownload/HST/ICZGS3Y5Q/iczgs3y5q_flt.fitsERRORDownloaded filesize is 16531200,but should be 16534080, file may be partial or corrupt.https://mast.stsci.edu/api/v0/download/file?uri=mast:HST/product/iczgs3y5q/iczgs3y5q_flt.fits
# Change this value to your desired data files
test_data1 = './mastDownload/HST/ICZGS3Y5Q/iczgs3y5q_flt.fits'

# To quickly pull out the data array you can use the astropy convenience function
data_arr = fits.getdata(test_data1,ext=1)

# Now we can index the array as desired
# We're cutting out 5 in y, and 2 in x
print(data_arr[0:5,0:2])
[[ 0.86692303  0.80678135]
 [ 0.83312052  0.76854318]
 [ 0.77341086  0.80276382]
 [ 0.80539584  0.78261763]
 [ 0.78274417  0.82206035]]

Not Replacing

  • imrename - can use command line utilities or the Python os package for this functionality.

  • imdelete - can use command line utilities or the Python os package for this functionality.

  • imtile - may replace infuture

  • sections - IRAF utility function

  • imgets - see images.imutil.hselect

  • minmax - see images.imutil.imstatistics