References (#582)

mirar/data/utils/coords.py

@@ -3,7 +3,9 @@
 """
 import logging
 
+from astropy import units as u
 from astropy.io import fits
+from astropy.units import Quantity
 from astropy.wcs import WCS
 
 from mirar.data import Image
@@ -90,3 +92,18 @@ def write_regions_file(
         regions_f.write(f"{system}\n")
         for ind, x in enumerate(x_coords):
             regions_f.write(f"CIRCLE({x},{y_coords[ind]},{region_radius})\n")
+
+
+def get_image_dims_from_header(header: fits.Header) -> (Quantity, Quantity):
+    """
+    Get image dimensions from the header
+    Args:
+        header:
+
+    Returns:
+
+    """
+    nx, ny = header["NAXIS1"], header["NAXIS2"]
+    dx, dy = header["CD1_1"], header["CD2_2"]
+    img_dims = (dx * nx * u.deg, dy * ny * u.deg)
+    return img_dims

mirar/io.py

@@ -15,7 +15,7 @@
 from astropy.utils.exceptions import AstropyUserWarning, AstropyWarning
 
 from mirar.data import Image
-from mirar.paths import BASE_NAME_KEY, RAW_IMG_KEY, core_fields
+from mirar.paths import BASE_NAME_KEY, LATEST_SAVE_KEY, RAW_IMG_KEY, core_fields
 
 logger = logging.getLogger(__name__)
 
@@ -93,7 +93,9 @@ def open_fits(path: str | Path) -> tuple[np.ndarray, fits.Header]:
     :param path: path of fits file
     :return: tuple containing image data and image header
     """
-    with fits.open(path, memmap=False) as img:
+    if isinstance(path, str):
+        path = Path(path)
+    with fits.open(path, memmap=False, ignore_missing_simple=True) as img:
         hdu = img.pop(0)
         hdu.verify("silentfix+ignore")
         data = hdu.data
@@ -103,11 +105,33 @@ def open_fits(path: str | Path) -> tuple[np.ndarray, fits.Header]:
         header[BASE_NAME_KEY] = Path(path).name
 
     if RAW_IMG_KEY not in header.keys():
-        header[RAW_IMG_KEY] = path
+        header[RAW_IMG_KEY] = path.as_posix()
 
     return data, header
 
 
+def save_fits(
+    image: Image,
+    path: str | Path,
+):
+    """
+    Save an Image to path
+
+    :param image: Image to save
+    :param path: path
+    :return: None
+    """
+    if isinstance(path, str):
+        path = Path(path)
+    check_image_has_core_fields(image)
+    data = image.get_data()
+    header = image.get_header()
+    if header is not None:
+        header[LATEST_SAVE_KEY] = path.as_posix()
+    logger.debug(f"Saving to {path.as_posix()}")
+    save_to_path(data, header, path)
+
+
 def open_raw_image(
     path: str | Path,
     open_f: Callable[[str | Path], tuple[np.ndarray, fits.Header]] = open_fits,
@@ -119,6 +143,9 @@ def open_raw_image(
     :param open_f: function to open the raw image
     :return: Image object
     """
+    if isinstance(path, str):
+        path = Path(path)
+
     data, header = open_f(path)
 
     new_img = Image(data.astype(np.float64), header)
@@ -292,10 +319,14 @@ def check_image_has_core_fields(img: Image):
         if key not in img.keys():
             if BASE_NAME_KEY in img.keys():
                 msg = f"({img[BASE_NAME_KEY]}) "
-
-            err = (
-                f"New image {msg}is missing the core field {key}. "
-                f"Available fields are {list(img.keys())}."
-            )
+                err = (
+                    f"New image {msg}is missing the core field {key}. "
+                    f"Available fields are {list(img.keys())}."
+                )
+            else:
+                err = (
+                    f"New image is missing the core field {BASE_NAME_KEY}. Available "
+                    f"fields are {list(img.keys())}."
+                )
             logger.error(err)
             raise MissingCoreFieldError(err)

mirar/paths.py

@@ -265,6 +265,8 @@ def get_astrometry_keys() -> list:
 GAIN_KEY = "GAIN"
 EXPTIME_KEY = "EXPTIME"
 ZP_KEY = "ZP"
+ZP_STD_KEY = "ZPSTD"
+ZP_NSTARS_KEY = "ZPNSTARS"
 SATURATE_KEY = "SATURATE"
 PSF_FLUX_KEY = "psf_flux"
 PSF_FLUXUNC_KEY = "psf_fluxunc"

mirar/pipelines/sedmv2/blocks.py

@@ -18,6 +18,7 @@
     sedmv2_reference_image_resampler,
     sedmv2_reference_psfex,
     sedmv2_reference_sextractor,
+    sedmv2_zogy_catalogs_purifier,
 )
 from mirar.pipelines.sedmv2.load_sedmv2_image import load_sedmv2_mef_image
 from mirar.processors import BiasCalibrator, FlatCalibrator
@@ -44,11 +45,7 @@
 
 # from mirar.processors.utils.cal_hunter import CalHunter
 from mirar.processors.utils.header_annotate import HeaderEditor
-from mirar.processors.zogy.zogy import (
-    ZOGY,
-    ZOGYPrepare,
-    default_sedmv2_catalog_purifier,
-)
+from mirar.processors.zogy.zogy import ZOGY, ZOGYPrepare
 
 load_raw = [
     MEFLoader(
@@ -218,7 +215,7 @@
     ZOGYPrepare(
         output_sub_dir="subtract",
         sci_zp_header_key="ZP_AUTO",
-        catalog_purifier=default_sedmv2_catalog_purifier,
+        catalog_purifier=sedmv2_zogy_catalogs_purifier,
     ),
     ZOGY(output_sub_dir="subtract"),
 ]

mirar/pipelines/sedmv2/generator.py

@@ -110,7 +110,9 @@ def sedmv2_reference_image_resampler(**kwargs) -> Swarp:
     :param kwargs: kwargs
     :return: Swarp processor
     """
-    return Swarp(swarp_config_path=swarp_config_path, cache=True, **kwargs)
+    return Swarp(
+        swarp_config_path=swarp_config_path, cache=True, subtract_bkg=True, **kwargs
+    )
 
 
 def sedmv2_reference_sextractor(output_sub_dir: str, gain: float) -> Sextractor:
@@ -142,3 +144,24 @@ def sedmv2_reference_psfex(output_sub_dir: str, norm_fits: bool) -> PSFex:
         output_sub_dir=output_sub_dir,
         norm_fits=norm_fits,
     )
+
+
+def sedmv2_zogy_catalogs_purifier(sci_catalog, ref_catalog):
+    """
+    TODO: This should be in sedmv2?
+    """
+    good_sci_sources = (
+        (sci_catalog["FLAGS"] == 0)
+        & (sci_catalog["SNR_WIN"] > 5)
+        & (sci_catalog["FWHM_WORLD"] < 4.0 / 3600)
+        & (sci_catalog["FWHM_WORLD"] > 0.5 / 3600)
+        & (sci_catalog["SNR_WIN"] < 1000)
+    )
+
+    good_ref_sources = (
+        (ref_catalog["SNR_WIN"] > 5)
+        & (ref_catalog["FWHM_WORLD"] < 5.0 / 3600)
+        & (ref_catalog["FWHM_WORLD"] > 0.5 / 3600)
+    )
+
+    return good_sci_sources, good_ref_sources

mirar/pipelines/summer/blocks.py

@@ -28,6 +28,7 @@
     summer_reference_image_resampler,
     summer_reference_psfex,
     summer_reference_sextractor,
+    summer_zogy_catalogs_purifier,
 )
 from mirar.pipelines.summer.load_summer_image import (
     load_proc_summer_image,
@@ -56,11 +57,7 @@
 from mirar.processors.utils.cal_hunter import CalHunter
 from mirar.processors.utils.header_annotate import HeaderEditor
 from mirar.processors.utils.simulate_realtime import RealtimeImageSimulator
-from mirar.processors.zogy.zogy import (
-    ZOGY,
-    ZOGYPrepare,
-    default_summer_catalog_purifier,
-)
+from mirar.processors.zogy.zogy import ZOGY, ZOGYPrepare
 
 load_raw = [
     ImageLoader(load_image=load_raw_summer_image),
@@ -231,7 +228,7 @@
         output_sub_dir="subtract",
         sci_zp_header_key="ZP_AUTO",
         ref_zp_header_key="ZP",
-        catalog_purifier=default_summer_catalog_purifier,
+        catalog_purifier=summer_zogy_catalogs_purifier,
     ),
     ZOGY(output_sub_dir="subtract"),
 ]

mirar/pipelines/summer/generator.py

@@ -138,7 +138,9 @@ def summer_reference_image_resampler(**kwargs) -> Swarp:
     :param kwargs: kwargs
     :return: Swarp processor
     """
-    return Swarp(swarp_config_path=swarp_config_path, cache=True, **kwargs)
+    return Swarp(
+        swarp_config_path=swarp_config_path, cache=True, subtract_bkg=True, **kwargs
+    )
 
 
 def summer_reference_sextractor(output_sub_dir: str, gain: float) -> Sextractor:
@@ -170,3 +172,29 @@ def summer_reference_psfex(output_sub_dir: str, norm_fits: bool) -> PSFex:
         output_sub_dir=output_sub_dir,
         norm_fits=norm_fits,
     )
+
+
+def summer_zogy_catalogs_purifier(sci_catalog: Table, ref_catalog: Table):
+    """
+    :param sci_catalog: science catalog
+    :param ref_catalog: reference catalog
+    :return: good_sci_sources, good_ref_sources
+    """
+    # Need to do this because the summer data is typically much
+    # shallower than the PS1 data, and only the brightest
+    # sources in PS1 xmatch to it.
+    good_sci_sources = (
+        (sci_catalog["FLAGS"] == 0)
+        & (sci_catalog["SNR_WIN"] > 5)
+        & (sci_catalog["FWHM_WORLD"] < 4.0 / 3600)
+        & (sci_catalog["FWHM_WORLD"] > 0.5 / 3600)
+        & (sci_catalog["SNR_WIN"] < 1000)
+    )
+
+    good_ref_sources = (
+        (ref_catalog["SNR_WIN"] > 5)
+        & (ref_catalog["FWHM_WORLD"] < 5.0 / 3600)
+        & (ref_catalog["FWHM_WORLD"] > 0.5 / 3600)
+    )
+
+    return good_sci_sources, good_ref_sources

mirar/pipelines/summer/load_summer_image.py

@@ -2,7 +2,6 @@
 Module with functions to load raw and processed summer images
 """
 import logging
-import os
 import warnings
 from pathlib import Path
 
@@ -31,7 +30,7 @@
 logger = logging.getLogger(__name__)
 
 
-def load_raw_summer_fits(path: str) -> tuple[np.array, astropy.io.fits.Header]:
+def load_raw_summer_fits(path: str | Path) -> tuple[np.array, astropy.io.fits.Header]:
     """
     Function to load a raw summer image and add/modify the required headers
     Args:
@@ -40,6 +39,8 @@ def load_raw_summer_fits(path: str) -> tuple[np.array, astropy.io.fits.Header]:
     Returns: [image data, image header]
 
     """
+    if isinstance(path, str):
+        path = Path(path)
     data, header = open_fits(path)
 
     with warnings.catch_warnings():
@@ -85,8 +86,8 @@ def load_raw_summer_fits(path: str) -> tuple[np.array, astropy.io.fits.Header]:
         header["TELDEC"] = tel_crd.dec.deg
         header["BZERO"] = 0
 
-        header[LATEST_SAVE_KEY] = path
-        header[RAW_IMG_KEY] = path
+        header[LATEST_SAVE_KEY] = path.as_posix()
+        header[RAW_IMG_KEY] = path.as_posix()
 
         data = data * 1.0  # pylint: disable=no-member
 
@@ -95,7 +96,7 @@ def load_raw_summer_fits(path: str) -> tuple[np.array, astropy.io.fits.Header]:
 
         header[PROC_HISTORY_KEY] = ""
 
-        base_name = os.path.basename(path)
+        base_name = path.name
         header[BASE_NAME_KEY] = base_name
 
         pipeline_version = __version__

mirar/pipelines/winter/blocks.py

@@ -10,6 +10,7 @@
     MAX_DITHER_KEY,
     OBSCLASS_KEY,
     TARGET_KEY,
+    ZP_KEY,
     base_output_dir,
 )
 from mirar.pipelines.winter.config import (
@@ -31,9 +32,8 @@
     winter_astrostat_catalog_purifier,
     winter_fourier_filtered_image_generator,
     winter_photometric_catalog_generator,
-    winter_refbuild_reference_generator,
     winter_reference_generator,
-    winter_reference_image_resampler,
+    winter_reference_image_resampler_for_zogy,
     winter_reference_psfex,
     winter_reference_sextractor,
     winter_stackid_annotator,
@@ -134,7 +134,7 @@
 ]
 
 refbuild = [
-    GetReferenceImage(ref_image_generator=winter_refbuild_reference_generator),
+    GetReferenceImage(ref_image_generator=winter_reference_generator),
     ImageSaver(output_dir_name="stacked_ref"),
 ]
 
@@ -350,22 +350,29 @@
 load_stack = [
     ImageLoader(input_sub_dir="final"),
     ImageBatcher(["BOARD_ID", "FILTER", TARGET_KEY, "SUBCOORD"]),
+    # ImageSelector(
+    #     (BASE_NAME_KEY, "WINTERcamera_20230727-035357-778_mef_4_0_0.fits_stack.fits")
+    # ),
 ]
 
 imsub = [
     HeaderAnnotator(input_keys=[SUB_ID_KEY], output_key="SUBDETID"),
     ProcessReference(
         ref_image_generator=winter_reference_generator,
-        swarp_resampler=winter_reference_image_resampler,
+        swarp_resampler=winter_reference_image_resampler_for_zogy,
         sextractor=winter_reference_sextractor,
         ref_psfex=winter_reference_psfex,
     ),
     Sextractor(**sextractor_reference_config, output_sub_dir="subtract", cache=False),
     PSFex(config_path=psfex_path, output_sub_dir="subtract", norm_fits=True),
     # ImageSaver(output_dir_name="presubtract"),
-    ZOGYPrepare(output_sub_dir="subtract", sci_zp_header_key="ZP_AUTO"),
+    ZOGYPrepare(
+        output_sub_dir="subtract", sci_zp_header_key="ZP_AUTO", ref_zp_header_key=ZP_KEY
+    ),
     # ImageSaver(output_dir_name="prezogy"),
-    ZOGY(output_sub_dir="subtract", sci_zp_header_key="ZP_AUTO"),
+    ZOGY(
+        output_sub_dir="subtract", sci_zp_header_key="ZP_AUTO", ref_zp_header_key=ZP_KEY
+    ),
     ImageSaver(output_dir_name="diffs"),
 ]