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Merged
merged 11 commits into from
Jun 6, 2025
Merged

45 save intermediate files #82

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fc0c06e
using a keep_intermediate property in the config file, we can now add…
laldoroty Jun 5, 2025
c65cf76
add files to optional intermediate file output
laldoroty Jun 5, 2025
1103eba
changelog
Jun 5, 2025
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ruff
laldoroty Jun 5, 2025
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changelog
laldoroty Jun 5, 2025
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changelog
laldoroty Jun 5, 2025
2dc8978
Move intermediate file save location to /pscratch/sd/l/laldorot. Upda…
laldoroty Jun 5, 2025
9dbad03
minor edits in accordance with review comments
laldoroty Jun 6, 2025
224db67
Update phrosty_config.yaml in examples/perlmutter to reflect keep_int…
laldoroty Jun 6, 2025
1b31de0
remove vestigial docstring
laldoroty Jun 6, 2025
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add comment about defining variables early on
laldoroty Jun 6, 2025
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9 changes: 9 additions & 0 deletions changes/45.feature.rst
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Original file line number Diff line number Diff line change
@@ -0,0 +1,9 @@
Added ability to output the following intermediate files:
- Sky-subtracted science and template
- Cross-convolved science and template
- Science and template input PSFs
- Science and template detection masks
- Aligned template image
- Aligned template PSF
- Aligned template detection mask
- Decorrelation kernel
131 changes: 99 additions & 32 deletions phrosty/pipeline.py
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Original file line number Diff line number Diff line change
@@ -1,39 +1,38 @@
import nvtx

import re
import pathlib
# Imports STANDARD
import argparse
import cupy as cp
from functools import partial
import logging
import matplotlib.pyplot as plt
from multiprocessing import Pool
from functools import partial

import numpy as np
import cupy as cp

import matplotlib.pyplot as plt
import nvtx
import pathlib
import re

# Imports ASTRO
from astropy.coordinates import SkyCoord
from astropy.io import fits
import astropy.table
from astropy.table import Table
import astropy.units as u
from astropy.wcs import WCS
from astropy.coordinates import SkyCoord
from astropy.wcs.utils import skycoord_to_pixel
import astropy.units as u

from sfft.SpaceSFFTCupyFlow import SpaceSFFT_CupyFlow
from galsim import roman

from snpit_utils.logger import SNLogger
from snpit_utils.config import Config
from snappl.psf import PSF
from snappl.image import OpenUniverse2024FITSImage
from phrosty.utils import read_truth_txt, get_exptime
# Imports INTERNAL
from phrosty.imagesubtraction import sky_subtract, stampmaker
from phrosty.photometry import ap_phot, psfmodel, psf_phot

from galsim import roman
from phrosty.utils import get_exptime, read_truth_txt
from sfft.SpaceSFFTCupyFlow import SpaceSFFT_CupyFlow
from snappl.image import OpenUniverse2024FITSImage
from snappl.psf import PSF
from snpit_utils.config import Config
from snpit_utils.logger import SNLogger


class PipelineImage:

"""Holds a snappl.image.Image, with some other stuff the pipeline needs."""

def __init__( self, imagepath, pointing, sca ):
Expand All @@ -56,6 +55,11 @@ def __init__( self, imagepath, pointing, sca ):
# self.psf is a object of a subclass of snappl.psf.PSF
self.config = Config.get()
self.temp_dir = pathlib.Path( self.config.value( 'photometry.phrosty.paths.temp_dir' ) )
self.keep_intermediate = self.config.value( 'photometry.phrosty.keep_intermediate' )
if not self.keep_intermediate:
self.save_dir = pathlib.Path( self.config.value( 'photometry.phrosty.paths.temp_dir' ) )
elif self.keep_intermediate:
self.save_dir = pathlib.Path( self.config.value( 'photometry.phrosty.paths.dia_out_dir' ) )

if self.config.value( 'photometry.phrosty.image_type' ) == 'ou2024fits':
self.image = OpenUniverse2024FITSImage( imagepath, None, sca )
Expand All @@ -65,14 +69,28 @@ def __init__( self, imagepath, pointing, sca ):

self.pointing = pointing

# Intermediate files
if self.keep_intermediate:
self.skysub_path = None
self.detmask_path = None
self.input_sci_psf_path = None
self.input_templ_psf_path = None
self.aligned_sci_img_path = None
self.aligned_templ_img_path = None
self.aligned_sci_psf_path = None
self.aligned_templ_psf_path = None
self.crossconv_sci_path = None
self.crossconv_templ_path = None
self.decorr_kernel_path = None

# Always save and output these
self.decorr_psf_path = {}
self.decorr_zptimg_path = {}
self.decorr_diff_path = {}
self.zpt_stamp_path = {}
self.diff_stamp_path = {}

self.skysub_path = None
self.detmas_path = None
# Used internally, held in-memory
self.skyrms = None
self.psfobj = None
self.psf_data = None
Expand All @@ -95,9 +113,10 @@ def run_sky_subtract( self, mp=True ):
if mp:
SNLogger.multiprocessing_replace()
SNLogger.debug( f"run_sky_subtract on {imname}" )
self.skysub_path = self.temp_dir / f"skysub_{imname}"
self.detmask_path = self.temp_dir / f"detmask_{imname}"
self.skyrms = sky_subtract( self.image.path, self.skysub_path, self.detmask_path, temp_dir=self.temp_dir,

self.skysub_path = self.save_dir / f"skysub_{imname}"
self.detmask_path = self.save_dir / f"detmask_{imname}"
self.skyrms = sky_subtract( self.image.path, self.skysub_path, self.detmask_path, temp_dir=self.save_dir,
force=self.config.value( 'photometry.phrosty.force_sky_subtract' ) )
SNLogger.debug( f"...done running sky subtraction on {self.image.name}" )
return ( self.skysub_path, self.detmask_path, self.skyrms )
Expand Down Expand Up @@ -131,6 +150,9 @@ def get_psf( self, ra, dec, dump_file=False ):
# the psf... and it's different for each type of
# PSF. We need to fix that... somehow....

if self.keep_intermediate:
dump_file = True

if self.psfobj is None:
psftype = self.config.value( 'photometry.phrosty.psf.type' )
self.psfobj = PSF.get_psf_object( psftype, pointing=self.pointing, sca=self.image.sca )
Expand Down Expand Up @@ -200,6 +222,8 @@ def __init__( self, object_id, ra, dec, band, science_images, template_images, n
if self.nuke_temp_dir:
SNLogger.warning( "nuke_temp_dir not implemented" )

self.keep_intermediate = self.config.value( 'photometry.phrosty.keep_intermediate' )


def sky_sub_all_images( self ):
# Currently, this writes out a bunch of FITS files. Further refactoring needed
Expand All @@ -224,7 +248,6 @@ def log_error( img, x ):
img.save_sky_subtract_info( img.run_sky_subtract( mp=False ) )



def get_psfs( self ):
all_imgs = self.science_images.copy() # shallow copy
all_imgs.extend( self.template_images )
Expand Down Expand Up @@ -489,9 +512,9 @@ def do_stamps( self, sci_image, templ_image ):

diffname = sci_image.decorr_diff_path[ templ_image.image.name ]
diff_stampname = stampmaker( self.ra, self.dec, np.array([100, 100]),
diffname,
savedir=self.dia_out_dir,
savename=f"stamp_{diffname.name}" )
diffname,
savedir=self.dia_out_dir,
savename=f"stamp_{diffname.name}" )

SNLogger.info(f"Decorrelated stamp path: {pathlib.Path( diff_stampname )}")
SNLogger.info(f"Zpt image stamp path: {pathlib.Path( zpt_stampname )}")
Expand Down Expand Up @@ -614,9 +637,53 @@ def log_fits_write_error( savepath, x ):
fits_writer_pool.apply_async( self.write_fits_file,
( cp.asnumpy( decorimg ).T, hdr, savepath ), {},
error_callback=partial(log_fits_write_error, savepath) )
sci_image.decorr_psf_path[ templ_image.image.name ]= decorr_psf_path
sci_image.decorr_zptimg_path[ templ_image.image.name ]= decorr_zptimg_path
sci_image.decorr_diff_path[ templ_image.image.name ]= decorr_diff_path
sci_image.decorr_psf_path[ templ_image.image.name ] = decorr_psf_path
sci_image.decorr_zptimg_path[ templ_image.image.name ] = decorr_zptimg_path
sci_image.decorr_diff_path[ templ_image.image.name ] = decorr_diff_path

if self.keep_intermediate:
# Each key is the file prefix addition.
# Each list has [descriptive filetype, image file name, data, header].
# The 'convolved' images have that [:-8] in their image file name and combined
# names because LNA thinks it's important that we keep track of which images
# have been convolved with which. Because also then if you use the same template
# image more than once, it gets overwritten. Also, [:-8] and [:-3] assume that
# image.image.name ends in fits.gz.

# TODO: Include score and variance images. Include multiprocessing.
write_filepaths = {'aligned': [['img',
templ_image.image.name,
cp.asnumpy(sfftifier.PixA_resamp_object_GPU),
sfftifier.hdr_target],
['psf',
templ_image.image.name,
cp.asnumpy(sfftifier.PSF_resamp_object_GPU),
sfftifier.hdr_target],
['detmask',
sci_image.image.name,
cp.asnumpy(sfftifier.PixA_resamp_object_DMASK_GPU),
sfftifier.hdr_target]
],
'convolved': [['img',
f'{sci_image.image.name[:-8]}_{templ_image.image.name[:-3]}',
cp.asnumpy(sfftifier.PixA_Ctarget_GPU),
sfftifier.hdr_target],
['img',
f'{templ_image.image.name[:-8]}_{sci_image.image.name[:-3]}',
cp.asnumpy(sfftifier.PixA_Cresamp_object_GPU),
sfftifier.hdr_target]
],
'decorr': [['kernel',
sci_image.image.name,
cp.asnumpy(sfftifier.FKDECO_GPU),
sfftifier.hdr_target]
]
}
# Write the aligned images
for key in write_filepaths.keys():
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@wmwv wmwv Jun 5, 2025

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Does waiting until here mean that all the steps have to have been successful to get any of the images to be written out?

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@laldoroty laldoroty Jun 5, 2025

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Only for the portions on GPU.

for (imgtype, name, data, header) in write_filepaths[key]:
savepath = self.dia_out_dir / f'{key}_{imgtype}_{name}'
self.write_fits_file( data, header, savepath=savepath)

SNLogger.info( f"DONE processing {sci_image.image.name} minus {templ_image.image.name}" )

Expand Down
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