{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# SEIP MIPS map homogenisation\n",
"\n",
"\n",
"The original MIPS maps have been produced by IPAC. This code takes the individual image files and adds them into a single multi-layered fits files to have the homogeneous HELP format. \n",
"\n",
"## Caveats \n",
"* Although many of the longer wavelength MIPS maps are available I've only run this on the MIPS 24micron maps at the moment\n",
"* Some of the SEIP maps may not have successfully down-loaded, this hasn't been checked\n",
"* only puts in image, error and coverage files (and adds blank PSF extension)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
" Guide
\n",
"Steps:
\n",
"* Obtain list of fields from sub-folders\n",
"for each field:\n",
"* read in coverage, image and noise\n",
"* attach meta data\n",
"* create PSF extension\n",
"* Save out\n",
"\n",
"Things you may wish to edit
\n",
"* You'll need to change the folder path in the 2nd code block to point you where the files are in your system\n",
"* Add in a specifc field (or switch to wild chracter) in the path to pick field(s)\n",
"* change the 1.mosaic pattern to 2.mosaic for MIPS 70 micron or 3.mosaic for MIPS 160.\n",
"* read in more of the available files and add as additional extensions"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Importing libraries"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"from datetime import datetime\n",
"from itertools import product\n",
"import glob\n",
"\n",
"import numpy as np\n",
"import astropy as astropy\n",
"\n",
"from astropy.io import fits\n",
"from astropy.table import Table\n",
"from astropy.table import Column\n",
"from astropy import wcs\n",
"VERSION = \"0.9\""
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# This is where you set up the field and folders to work on\n",
"the notebook needs to be run for each field in turn - commenting in/out as appropriate"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"#field_specified='HDF-N' \n",
"#field_specified='XMM-LSS' \n",
"#field_specified='AKARI-NEP' \n",
"#field_specified='AKARI-SEP' \n",
"#field_specified='Bootes' \n",
"#field_specified='CDFS-SWIRE' \n",
"#field_specified='COSMOS' \n",
"#field_specified='EGS' \n",
"#field_specified='ELAIS-N1' \n",
"#field_specified='ELAIS-N2' \n",
"#field_specified='ELAIS-S1' \n",
"#field_specified='GAMA-09' \n",
"#field_specified='GAMA-12' \n",
"#field_specified='GAMA-15' \n",
"#field_specified='NGP' \n",
"#field_specified='SGP' \n",
"#field_specified='Lockman-SWIRE' \n",
"#field_specified='SA13' \n",
"#field_specified='SPIRE-NEP' \n",
"#field_specified='SSDF' \n",
"#field_specified='xFLS' \n",
"#field_specified='XMM-13hr' \n",
"#field_specified='Herschel-Stripe-82' \n",
"\n",
"\n",
"#mainfolder='/Volumes/Seagate Backup Plus Drive/HELP/mips_fields'\n",
"#moc_dir='/Volumes/Seagate Backup Plus Drive/HELP/dmu_products/dmu2/dmu2_field_coverages/'\n",
"\n",
"#mainfolder='/Users/sjo/Data/SEIP/mips_fields'\n",
"#moc_dir='/Users/sjo/Data/dmu2_field_coverages/'\n",
"\n",
"mainfolder='../../dmu17/dmu17_SEIP_maps/'\n",
"moc_dir= '../../dmu2/dmu2_field_coverages/'"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# finding all the SEIP mosaic files in the folder"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Number of files found: 466\n"
]
}
],
"source": [
"# finding all the SEIP mosaic files (other files should be there if the mosaic file is)\n",
"filelist= glob.glob(f\"{mainfolder}/{field_specified}/data/*1.mosaic.fits\", recursive=True)\n",
"print(\"Number of files found:\", len(filelist))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# opening the table which logs the SEIP files"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Filename: ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/mosaic_tiles_Herschel-Stripe-82.fits\n",
"No. Name Ver Type Cards Dimensions Format\n",
" 0 PRIMARY 1 PrimaryHDU 4 () \n",
" 1 mosaic_tiles.cat 1 BinTableHDU 104 2161R x 37C [J, 20A, 4A, I, J, D, D, D, D, D, D, D, I, J, I, I, I, I, 22A, 29A, D, D, D, D, D, D, D, D, D, D, E, D, 18A, L, 143A, 44A, L] \n"
]
}
],
"source": [
"# opening the table of SEIP in which we will update some records\n",
"seip_table = fits.open(f\"{mainfolder}/{field_specified}/mosaic_tiles_{field_specified}.fits\", mode='update')\n",
"seip_table.info()\n",
"seip_hd=seip_table[1].header\n",
"seip_data=seip_table[1].data\n",
"#print(repr(seip_hd))\n",
"seip_table2=Table.read(f\"{mainfolder}/{field_specified}/mosaic_tiles_{field_specified}.fits\")\n",
"seip_table2['areahelp']=np.zeros(len(seip_table2['EXPTIME']))\n",
"#t.add_column(aa, index=0) \n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# MOC libraries\n",
"This next block of code comes from Peter Hurley's XID libraray and allows us to create a MOC from the error array"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
"import pymoc as pymoc\n",
"from pymoc import MOC\n",
"from pymoc import io\n",
"\n",
"from healpy import pixelfunc\n",
"from pymoc.util import catalog\n",
"\n",
"import numpy as np\n",
"def get_HEALPix_pixels(order,ra,dec,unique=True):\n",
"\n",
"\n",
" \"\"\"Work out what HEALPix a source is in\n",
" :param order: order of HEALPix\n",
" :param ra: Right Ascension\n",
" :param dec: Declination\n",
" :param unique: if unique is true, removes duplicate pixels\n",
" :return: list of HEALPix pixels :rtype:\n",
" \"\"\"\n",
" HPX_D2R=np.pi/180.0\n",
" #Convert catalogue to polar co-ords in radians\n",
" phi = ra*HPX_D2R\n",
" theta = np.pi/2.0 - dec*HPX_D2R\n",
" #calculate what pixel each object is in\n",
" ipix = pixelfunc.ang2pix(2**order, theta, phi, nest=True)\n",
" #return unique pixels (i.e. remove duplicates)\n",
" if unique is True:\n",
" return np.unique(ipix)\n",
" else:\n",
" return ipix\n",
"\n",
"\n",
"def create_MOC_from_map(good,wcs):\n",
" \"\"\"Generate MOC from map\n",
" :param good: boolean array associated with map\n",
" :param wcs: wcs information\n",
" :return: MOC :rtype: pymoc.MOC\n",
" \"\"\"\n",
" x_pix,y_pix=np.meshgrid(np.arange(0,wcs._naxis1),np.arange(0,wcs._naxis2))\n",
" ra,dec= wcs.wcs_pix2world(x_pix,y_pix,0)\n",
"\n",
" pixels=get_HEALPix_pixels(15,ra[good],dec[good])\n",
" map_moc=MOC()\n",
" map_moc.add(15,pixels)\n",
" return map_moc"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# setting up global MOCS"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
"# sum of all SEIP MOCS\n",
"total_moc=MOC()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Performing the homogenisation\n",
"i.e. merging component files into a single multi-extension file and adding some keywords\n",
"traps errors so that it can continue, e.g. if a file is missing\n",
"skips over files if they've already been logged as \"downloaded\" (this could be improved to be an option"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"----------------\n",
"0 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000861.20000861-140.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000861.20000861-140.MIPS.1.mosaic.fits ['20000861.20000861-140.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 1.4663315547854497e-05\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"1 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000821.20000821-576.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000821.20000821-576.MIPS.1.mosaic.fits ['20000821.20000821-576.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 0.0\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"2 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000861.20000861-627.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000861.20000861-627.MIPS.1.mosaic.fits ['20000861.20000861-627.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 0.0\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"3 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000801.20000801-314.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000801.20000801-314.MIPS.1.mosaic.fits ['20000801.20000801-314.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 2.0513037307484113e-05\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"4 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/50064590.50064590-0.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"50064590.50064590-0.MIPS.1.mosaic.fits ['50064590.50064590-0.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 9.294406196944022e-06\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"5 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20001201.20001201-75.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20001201.20001201-75.MIPS.1.mosaic.fits ['20001201.20001201-75.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 1.031747357371152e-05\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"6 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000141.20000141-14.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000141.20000141-14.MIPS.1.mosaic.fits ['20000141.20000141-14.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 0.0001045040406318093\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"7 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000861.20000861-506.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000861.20000861-506.MIPS.1.mosaic.fits ['20000861.20000861-506.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 0.0\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"8 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20001201.20001201-16.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20001201.20001201-16.MIPS.1.mosaic.fits ['20001201.20001201-16.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 1.0093159468223889e-05\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"9 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000861.20000861-261.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000861.20000861-261.MIPS.1.mosaic.fits ['20000861.20000861-261.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 1.8964294700899948e-05\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"10 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000821.20000821-488.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000821.20000821-488.MIPS.1.mosaic.fits ['20000821.20000821-488.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 0.0\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"11 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000821.20000821-505.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000821.20000821-505.MIPS.1.mosaic.fits ['20000821.20000821-505.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 0.0\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"12 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000801.20000801-367.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000801.20000801-367.MIPS.1.mosaic.fits ['20000801.20000801-367.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 2.634227821400399e-06\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"13 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000861.20000861-349.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000861.20000861-349.MIPS.1.mosaic.fits ['20000861.20000861-349.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 2.0104395524008818e-05\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"14 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000821.20000821-262.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000821.20000821-262.MIPS.1.mosaic.fits ['20000821.20000821-262.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 2.4143999980225204e-05\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"15 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/50063780.50063780-0.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"50063780.50063780-0.MIPS.1.mosaic.fits ['50063780.50063780-0.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 4.3829025654844096e-06\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"16 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000821.20000821-453.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000821.20000821-453.MIPS.1.mosaic.fits ['20000821.20000821-453.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 0.0\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"17 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20001201.20001201-68.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20001201.20001201-68.MIPS.1.mosaic.fits ['20001201.20001201-68.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 9.20565583346848e-06\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"18 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000791.20000791-401.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000791.20000791-401.MIPS.1.mosaic.fits ['20000791.20000791-401.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 2.253088897815328e-05\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"19 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000861.20000861-575.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000861.20000861-575.MIPS.1.mosaic.fits ['20000861.20000861-575.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 0.0\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"20 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000861.20000861-70.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000861.20000861-70.MIPS.1.mosaic.fits ['20000861.20000861-70.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 1.604626077212172e-05\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"21 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20001541.20001541-39.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20001541.20001541-39.MIPS.1.mosaic.fits ['20001541.20001541-39.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 0.0\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"22 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000791.20000791-366.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000791.20000791-366.MIPS.1.mosaic.fits ['20000791.20000791-366.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 2.2324129889616856e-05\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"23 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000271.20000271-1.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000271.20000271-1.MIPS.1.mosaic.fits ['20000271.20000271-1.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Area 7.327269019689447e-05\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"24 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20001201.20001201-58.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20001201.20001201-58.MIPS.1.mosaic.fits ['20001201.20001201-58.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 4.492133782069692e-06\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"25 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000821.20000821-173.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000821.20000821-173.MIPS.1.mosaic.fits ['20000821.20000821-173.MIPS.1.mosaic.fits']\n",
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"27 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20001201.20001201-93.MIPS.1.mosaic.fits\n",
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"44 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20001141.20001141-64.MIPS.1.mosaic.fits\n",
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]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
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]
},
{
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]
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]
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]
},
{
"name": "stdout",
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"text": [
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]
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]
},
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]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
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]
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]
},
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]
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"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 0.0\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"443 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20001551.20001551-0.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20001551.20001551-0.MIPS.1.mosaic.fits ['20001551.20001551-0.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 1.3755331059989345e-05\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"444 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000801.20000801-210.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000801.20000801-210.MIPS.1.mosaic.fits ['20000801.20000801-210.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 9.953694611333754e-06\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"445 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000791.20000791-488.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000791.20000791-488.MIPS.1.mosaic.fits ['20000791.20000791-488.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 4.186871542862611e-06\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"446 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000801.20000801-489.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000801.20000801-489.MIPS.1.mosaic.fits ['20000801.20000801-489.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 0.0\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"447 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20001321.20001321-65.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20001321.20001321-65.MIPS.1.mosaic.fits ['20001321.20001321-65.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 6.8308521514581236e-06\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"448 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20001141.20001141-65.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20001141.20001141-65.MIPS.1.mosaic.fits ['20001141.20001141-65.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 9.103251567919778e-06\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"449 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000791.20000791-576.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000791.20000791-576.MIPS.1.mosaic.fits ['20000791.20000791-576.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 0.0\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"450 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000821.20000821-524.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000821.20000821-524.MIPS.1.mosaic.fits ['20000821.20000821-524.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 0.0\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"451 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000021.20000021-1.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000021.20000021-1.MIPS.1.mosaic.fits ['20000021.20000021-1.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 3.189844107906066e-05\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"452 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000791.20000791-453.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000791.20000791-453.MIPS.1.mosaic.fits ['20000791.20000791-453.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 2.3670014522542642e-05\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"453 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20001201.20001201-92.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20001201.20001201-92.MIPS.1.mosaic.fits ['20001201.20001201-92.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 1.4736461451817854e-05\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"454 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000861.20000861-87.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000861.20000861-87.MIPS.1.mosaic.fits ['20000861.20000861-87.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 2.404062043595699e-05\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"455 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20001201.20001201-59.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20001201.20001201-59.MIPS.1.mosaic.fits ['20001201.20001201-59.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Area 2.8243096438331784e-05\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"456 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000271.20000271-0.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000271.20000271-0.MIPS.1.mosaic.fits ['20000271.20000271-0.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 5.578496747733483e-05\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"457 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000821.20000821-401.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000821.20000821-401.MIPS.1.mosaic.fits ['20000821.20000821-401.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 2.2728870558214102e-05\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"458 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000821.20000821-366.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000821.20000821-366.MIPS.1.mosaic.fits ['20000821.20000821-366.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 2.216320890089747e-05\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"459 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000791.20000791-505.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000791.20000791-505.MIPS.1.mosaic.fits ['20000791.20000791-505.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 0.0\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"460 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/40004930.40004930-0.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"40004930.40004930-0.MIPS.1.mosaic.fits ['40004930.40004930-0.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 9.297332033102555e-06\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"461 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/40006150.40006150-0.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"40006150.40006150-0.MIPS.1.mosaic.fits ['40006150.40006150-0.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 1.3180891894197107e-05\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"462 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000801.20000801-628.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000801.20000801-628.MIPS.1.mosaic.fits ['20000801.20000801-628.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 0.0\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"463 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20001201.20001201-9.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20001201.20001201-9.MIPS.1.mosaic.fits ['20001201.20001201-9.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 3.1052874429244244e-06\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"464 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000791.20000791-262.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000791.20000791-262.MIPS.1.mosaic.fits ['20000791.20000791-262.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 1.81421347403518e-05\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n",
"----------------\n",
"465 ../../dmu17/dmu17_SEIP_maps//Herschel-Stripe-82/data/20000861.20000861-471.MIPS.1.mosaic.fits\n",
"Herschel-Stripe-82\n",
"20000861.20000861-471.MIPS.1.mosaic.fits ['20000861.20000861-471.MIPS.1.mosaic.fits']\n",
"../../dmu2/dmu2_field_coverages/Herschel-Stripe-82_MOC.fits\n",
"Area 0.0\n",
"downloaded: [ True]\n",
"updating intersection with HELP\n"
]
}
],
"source": [
"for i, file in enumerate(filelist):\n",
" print('----------------')\n",
" print(i,file)\n",
" folders=file.split('/')\n",
" print(folders[len(folders)-3])\n",
" field=folders[len(folders)-3]\n",
" filename=folders[len(folders)-1]\n",
" seip_id=(filename==seip_data.field('file')) \n",
" print(filename,seip_data.field('file')[seip_id])\n",
"# actual HELP SPIRE MOC\n",
" print(f'{moc_dir}{field}_MOC.fits')\n",
"# help_moc_hdu = fits.open(f'{moc_dir}{field}_MOC.fits')\n",
" help_moc=MOC()\n",
"# pymoc.io.fits.read_moc_fits(help_moc, f'{moc_dir}{field}_MOC.fits',include_meta=False)\n",
" help_moc.read(f'{moc_dir}{field}_MOC.fits')\n",
"\n",
" if seip_data.field('downloaded')[seip_id]:\n",
" print(\"Already downloaded skipping file\",filename)\n",
" else:\n",
" ext=0\n",
" \n",
" try:\n",
"\n",
" # Load in image map\n",
" image_map=fits.open(file)\n",
" image_hdu = fits.ImageHDU(header=image_map[ext].header,\n",
" data=image_map[ext].data)\n",
" image_hdu.header['EXTNAME'] = \"IMAGE\"\n",
" \n",
" # Load in uncertainty map\n",
" noise_map=fits.open(file.replace('mosaic','unc'))\n",
" noise_hdu = fits.ImageHDU(header=noise_map[ext].header,\n",
" data=noise_map[ext].data)\n",
" noise_hdu.header['EXTNAME'] = \"ERROR\"\n",
" \n",
" # we'll use the uncertainty map to generate a MOC\n",
" good=~np.isnan(noise_map[ext].data)\n",
" w = wcs.WCS(noise_map[ext].header) \n",
" m=create_MOC_from_map(good,w)\n",
" total_moc=total_moc+m\n",
" \n",
" intersect=m.intersection(help_moc)\n",
" print('Area',repr(intersect.area))\n",
" \n",
"# moc_hdu=io.fits.write_moc_fits_hdu(m)\n",
"# io.fits.write_moc_fits(m,file.replace('mosaic','moc3'),overwrite=True)\n",
" \n",
" m.write(file.replace('mosaic','moc'), overwrite=True)\n",
" \n",
" # Load in coverage map\n",
" cov_map=fits.open(file.replace('mosaic','cov'))\n",
" cov_hdu = fits.ImageHDU(header=cov_map[ext].header,\n",
" data=cov_map[ext].data)\n",
" cov_hdu.header['EXTNAME'] = \"COVERAGE\"\n",
"\n",
" # Mark this tile as successfully downloaded\n",
" \n",
" seip_data.field('downloaded')[seip_id]=True\n",
" print('downloaded:',seip_data.field('downloaded')[seip_id])\n",
"\n",
"# ----------------------------\n",
" # mark this tile with area of overlap with HELP\n",
" seip_data.field('inhelp')[seip_id]=(intersect.area>0.)\n",
" seip_table2.field('areahelp')[seip_id]=(intersect.area)\n",
" print('updating intersection with HELP')\n",
" #print(seip_id) \n",
"# ----------------------------\n",
"\n",
" except:\n",
" # update the SEIP file to clearly indicate that this file is not there\n",
" seip_data.field('downloaded')[seip_id]=False\n",
" print,'error'\n",
"# stop\n",
" #fits.close(file)\n",
" pass\n",
" \n",
" #Create primary header\n",
" primary_hdu = fits.PrimaryHDU()\n",
" primary_hdu.header.append((\n",
" \"CREATOR\", \"Herschel Extragalactic Legacy Project\"\n",
" ))\n",
" primary_hdu.header.append((\n",
" \"TIMESYS\", \"UTC\", \"All dates are in UTC time\"\n",
" ))\n",
" primary_hdu.header.append((\n",
" \"DATE\", datetime.now().replace(microsecond=0).isoformat(),\n",
" \"Date of file creation\"\n",
" ))\n",
" primary_hdu.header.append((\n",
" \"VERSION\", VERSION, \"HELP product version\"\n",
" ))\n",
" primary_hdu.header.append((\n",
" \"TELESCOP\", \"Spitzer\", \"Name of the telescope\"\n",
" ))\n",
" primary_hdu.header.append((\n",
" \"INSTRUME\", \"MIPS\", \"Name of the instrument\"\n",
" ))\n",
" primary_hdu.header.append((\n",
" \"FILTER\", \"MIPS-24\", \"Name of the filter\"\n",
" ))\n",
" primary_hdu.header.append((\n",
" \"FIELD\", field, \"Name of the HELP field\"\n",
" ))\n",
"\n",
"\n",
" #Add empty extension for PSF\n",
" psf_hdu = fits.ImageHDU()\n",
" psf_hdu.header['EXTNAME'] = \"PSF\"\n",
" psf_hdu.header.add_comment(\"The PSF is not available.\")\n",
"\n",
" hdu_list = fits.HDUList([primary_hdu, image_hdu, noise_hdu, cov_hdu, psf_hdu])\n",
" hdu_list.writeto(file.replace('mosaic','help'),\n",
" checksum=True, overwrite=True)\n",
" # print(f\"{file} / processed...\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Wrapping up some output files"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [],
"source": [
"# writing out the SEIP Table\n",
"seip_table.flush()\n",
"seip_table2.write(f\"{mainfolder}/{field_specified}/mosaic_tiles_{field_specified}_new.fits\", overwrite=True)\n",
"\n",
"# writing out the combined moc\n",
"total_moc.write('help_moc.fits', overwrite=True)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
" Finding MOC files and writing an Aladin Script for plotting then up
"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Number of MOC files found: 466\n"
]
}
],
"source": [
"# writing a file for plotting up MOCS in aladin\n",
"\n",
"moc_filelist= glob.glob(f\"{mainfolder}/{field_specified}/data/*1.moc.fits\", recursive=True)\n",
"print(\"Number of MOC files found:\", len(moc_filelist))\n",
"\n",
"\n",
"f=open(f\"{mainfolder}/{field_specified}/aladin_script_{field_specified}.txt\", 'w')\n",
"f.write(\"# This script can be loaded into Aladin using the Tools>Script Console (F5)\\n\")\n",
"f.write(\"# you will need to alter the file paths to be correct relative to your Aladin installation\\n\")\n",
"f.write(\"load \"+moc_dir+field+\"_MOC.fits \\n\")\n",
"# help_moc_hdu = fits.open(f'{moc_dir}{field}_MOC.fits')\n",
"\n",
"for i, file in enumerate(moc_filelist):\n",
" f.write(\"load \"+file.replace('mosaic','moc')+\"\\n\")\n",
"f.write(\"save \"+f\"{mainfolder}/{field_specified}/{field_specified}_moc_plots.eps\")\n",
"f.close()\n",
" "
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"\n",
"-------------------------------------------------------------------------------\n",
"\n",
"\n",
"\n",
"**Authors**: This code was adapted from code used for SPIRE homogenisaton (Yannick Roehlly) and in turn adapted for PACS data (Peter Hurley). [Seb Oliver](http://www.sussex.ac.uk/profiles/91548)\n",
"\n",
" \n",
"For a full description of the database and how it is organised in to `dmu_products` please the top level [readme](../readme.md).\n",
" \n",
"The Herschel Extragalactic Legacy Project, ([HELP](http://herschel.sussex.ac.uk/)), is a [European Commission Research Executive Agency](https://ec.europa.eu/info/departments/research-executive-agency_en)\n",
"funded project under the SP1-Cooperation, Collaborative project, Small or medium-scale focused research project, FP7-SPACE-2013-1 scheme, Grant Agreement\n",
"Number 607254.\n",
"\n",
"[Acknowledgements](http://herschel.sussex.ac.uk/acknowledgements)\n",
"\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python (herschelhelp_internal)",
"language": "python",
"name": "helpint"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.5"
}
},
"nbformat": 4,
"nbformat_minor": 2
}