Update zogy

winterdrp/pipelines/sedmv2/blocks.py

@@ -21,7 +21,10 @@
     sedmv2_reference_psfex,
     sedmv2_reference_sextractor,
 )
-from winterdrp.pipelines.sedmv2.load_sedmv2_image import load_raw_sedmv2_image
+from winterdrp.pipelines.sedmv2.load_sedmv2_image import (
+    load_proc_sedmv2_image,
+    load_raw_sedmv2_image,
+)
 from winterdrp.processors import BiasCalibrator, FlatCalibrator
 from winterdrp.processors.anet import AstrometryNet
 from winterdrp.processors.astromatic import PSFex, Sextractor, Swarp
@@ -57,6 +60,10 @@
     ImageLoader(load_image=load_raw_sedmv2_image),
 ]
 
+load_proc = [
+    ImageLoader(load_image=load_proc_sedmv2_image),
+]
+
 cal_hunter = [
     CalHunter(load_image=load_raw_sedmv2_image, requirements=sedmv2_cal_requirements),
 ]
@@ -193,18 +200,22 @@
     ),
     Sextractor(
         output_sub_dir="subtract",
-        cache=False,
+        cache=True,
         write_regions_bool=True,
         **sextractor_photometry_config
     ),
     PSFex(config_path=psfex_config_path, output_sub_dir="subtract", norm_fits=True),
-    ImageSaver(output_dir_name="ref"),
+    # ImageSaver(output_dir_name="ref"),
     ZOGYPrepare(
         output_sub_dir="subtract",
         sci_zp_header_key="ZP_AUTO",
         catalog_purifier=default_sedmv2_catalog_purifier,
+        write_region_bool=True,
+    ),
+    ZOGY(
+        output_sub_dir="subtract",
+        sci_zp_header_key="ZP_AUTO",
     ),
-    ZOGY(output_sub_dir="subtract"),
 ]
 
 imsub = subtract  # + export_diff_to_db + extract_candidates

winterdrp/pipelines/sedmv2/generator.py

@@ -125,6 +125,7 @@ def sedmv2_reference_sextractor(output_sub_dir: str, gain: float) -> Sextractor:
         gain=gain,
         output_sub_dir=output_sub_dir,
         cache=True,
+        write_regions_bool=True,
         **sextractor_photometry_config,
     )
 

winterdrp/pipelines/sedmv2/load_sedmv2_image.py

@@ -86,6 +86,67 @@ def load_raw_sedmv2_image(path: str) -> tuple[np.array, astropy.io.fits.Header]:
     return data[0].data, data[0].header  # pylint: disable=no-member
 
 
+def load_proc_sedmv2_image(path: str) -> tuple[np.array, astropy.io.fits.Header]:
+    """
+    Function to load a raw SEDMv2 image
+
+    :param path:- path of file
+    :return: data and header of image
+    """
+
+    with fits.open(path) as data:
+        header = data[0].header  # pylint: disable=no-member
+
+        if "PREPTAG" not in header.keys():
+            if "IMGTYPE" in header.keys():
+                path_new = prepare_science(path)
+            else:  # IMGTYPE not in cal; may change w updated cal files
+                path_new = prepare_cal(path)
+            data = fits.open(path_new)
+            header = data[0].header  # pylint: disable=no-member
+
+        header["TARGET"] = header["OBSTYPE"].lower()
+        data[0].data = data[0].data * 1.0  # pylint: disable=no-member
+        header.append(("GAIN", 1.0, "Gain in electrons / ADU"), end=True)
+
+        # positions
+        header["RA"] = header["RAD"]
+        header["DEC"] = header["DECD"]
+        header["TELRA"] = header["TELRAD"]
+        header["TELDEC"] = header["TELDECD"]
+
+        # keys, IDs
+        base_name = os.path.basename(path)
+        header[BASE_NAME_KEY] = base_name
+        header[LATEST_SAVE_KEY] = path
+        header[RAW_IMG_KEY] = path
+        header[PROC_HISTORY_KEY] = ""
+        header[PROC_FAIL_KEY] = ""
+        pipeline_version = __version__
+        pipeline_version_padded_str = "".join(
+            [x.rjust(2, "0") for x in pipeline_version.split(".")]
+        )
+        header["PROCID"] = int(str(header["EXPID"]) + str(pipeline_version_padded_str))
+        header["OBSID"] = 0
+        header["PROGID"] = int(3)  # sedmv2's ID
+        header["FIELDID"] = 999999999
+        header["COADDS"] = 1
+        header["BZERO"] = 0
+
+        header["UTC"] = "20221223_00:00:00"
+        header["UTCTIME"] = header["UTC"]
+        header["TIMEUTC"] = header["UTCTIME"]
+        header["OBSDATE"] = int(header["UTC"].split("_")[0])
+        header["NIGHT"] = int(Time(header["DATE"], format="isot").jd) - int(
+            Time("2018-01-01", format="iso").jd
+        )  # integer value, night 1, night 2...
+        header["EXPMJD"] = header["OBSDATE"]
+
+        image_data = data[0].data
+        image_data[image_data == 0] = np.nan
+    return image_data, data[0].header  # pylint: disable=no-member
+
+
 def prepare_science(filepath: str) -> str:
     """
     Additional steps to get sedmv2 science files into working order

winterdrp/pipelines/sedmv2/sedmv2_pipeline.py

@@ -11,6 +11,8 @@
 from winterdrp.pipelines.base_pipeline import Pipeline
 from winterdrp.pipelines.sedmv2.blocks import (
     cal_hunter,
+    imsub,
+    load_proc,
     load_raw,
     process,
     process_stellar,
@@ -37,6 +39,7 @@ class SEDMv2Pipeline(Pipeline):
         "default": load_raw + cal_hunter + process,
         "default_stellar": load_raw + cal_hunter + process_stellar,  # +image_photometry
         "default_transient": load_raw + cal_hunter + process_transient,  # +imsub,
+        "imsub": load_proc + imsub,
     }
 
     @staticmethod

winterdrp/processors/zogy/zogy.py

@@ -270,6 +270,7 @@ def _apply_to_images(self, batch: ImageBatch) -> ImageBatch:
             sci_catalog_path = image["SRCCAT"]  # convert to key
             sci_mask_path = image[LATEST_WEIGHT_SAVE_KEY]
 
+            logger.debug(f"{self.get_path(sci_mask_path)}")
             ref_weight_data = self.open_fits(self.get_path(ref_mask_path))
             sci_weight_data = self.open_fits(self.get_path(sci_mask_path))
 
@@ -291,14 +292,15 @@ def _apply_to_images(self, batch: ImageBatch) -> ImageBatch:
             scorr_weight_path = sci_img_path.replace(".fits", ".scorr.weight.fits")
             self.save_fits(scorr_weight_img, path=self.get_path(scorr_weight_path))
 
+            logger.info(f"{sci_weight_data.get_data()}")
+
             ast_unc_x, ast_unc_y, flux_scale = self.get_ast_fluxscale(
                 ref_catalog_path, sci_catalog_path
             )
 
             # Scale reference image
             ref_data *= flux_scale
             ref_img.set_data(ref_data)
-
             ref_unscaled_zp = ref_img["ZP"]
             ref_img["ZP"] = float(ref_img["ZP"]) + 2.5 * np.log10(flux_scale)
 
@@ -329,6 +331,14 @@ def _apply_to_images(self, batch: ImageBatch) -> ImageBatch:
             sci_rms_image = self.get_rms_image(image, sci_rms)
             ref_rms_image = self.get_rms_image(ref_img, ref_rms)
 
+            sci_rms_data = sci_rms_image.get_data()
+            sci_rms_data[image_mask] = 0
+            sci_rms_image.set_data(sci_rms_data)
+
+            ref_rms_data = ref_rms_image.get_data()
+            ref_rms_data[image_mask] = 0
+            ref_rms_image.set_data(ref_rms_data)
+
             sci_rms_path = sci_img_path + ".unc"
             ref_rms_path = ref_img_path + ".unc"