Combined

sdi/combine.py

@@ -33,7 +33,7 @@ def combine(hduls, name="ALGN"):
         raise KeyError(str(f"Name {name} not found in HDUList! Try running again with `combine -n [name]` from above")) from None
 
     comb = np.median(data, axis=0)
-    hdu = fits.PrimaryHDU(comb)
+    hdu = fits.PrimaryHDU(data = comb, header =  hduls_list[0][name].header)
 
     # We do not need to create a list of HDUL's here. We return a single median image.
 

sdi/subtract.py

@@ -4,13 +4,16 @@
 from astropy.io.fits import CompImageHDU
 from . import _cli as cli
 from .combine import combine
-import os                                             #sfft specific
-from sfft.EasyCrowdedPacket import Easy_CrowdedPacket #sfft specific
+import os
+#from .sfft.sfft.EasyCrowdedPacket import Easy_CrowdedPacket #sfft specific
 from sfft.CustomizedPacket import Customized_Packet   #sfft specific
 from sfft.EasySparsePacket import Easy_SparsePacket   #sfft specific
 import time
 import numpy as np                                           #sfft specific
 import sys
+import os.path as pa
+from sfft.utils.SExSkySubtract import SEx_SkySubtract
+
 
 def subtract(hduls, name="ALGN", method: ("sfft", "ois", "numpy")="sfft"):
     """
@@ -29,12 +32,12 @@ def subtract(hduls, name="ALGN", method: ("sfft", "ois", "numpy")="sfft"):
         temp_image_fits_filenames = []
         venv_file_path = sys.prefix
         for i, hdu in enumerate(hduls): #Write the science hduls into temporary fits files
-            temp_filename = venv_file_path + "/sdi_pipeline/sdi/temp_image{}.fits".format(i)
+            temp_filename = venv_file_path + "/temp_image{}.fits".format(i)
             temp_data = hdu[name].data
-            primary = fits.PrimaryHDU(temp_data)
+            primary = fits.PrimaryHDU(data= temp_data, header =  hduls[i][name].header)
             primary.writeto(temp_filename, overwrite = True)
             temp_image_fits_filenames.append(temp_filename)
-        temp_ref_path = venv_file_path + "/sdi_pipeline/temp_ref.fits"
+        temp_ref_path = venv_file_path + "/temp_ref.fits"
         template_fits = combine(hduls, name) # Create the reference image
         template_fits.writeto(temp_ref_path, overwrite = True) # Write the reference image into temporary fits file
 
@@ -49,25 +52,48 @@ def subtract(hduls, name="ALGN", method: ("sfft", "ois", "numpy")="sfft"):
         size += os.path.getsize(temp_ref_path)
         print("Total size of temporary files is {} mb".format(size/1024**2))
         outputs = []
+    #Sky-Subtraction
+        print("Performing Sky-Subtraction")
+        skysub_fits = []
+        for i, FITS_obj in enumerate(temp_image_fits_filenames):
+            FITS_skysub = venv_file_path + "/temp_skysub_image{}.fits".format(i)
+            skysub_fits.append(FITS_skysub)
+            SEx_SkySubtract.SSS(FITS_obj=FITS_obj, FITS_skysub=FITS_skysub, FITS_sky=None, FITS_skyrms=None, \
+                SATUR_KEY='SATURATE', ESATUR_KEY='ESATUR', BACK_SIZE=64, BACK_FILTERSIZE=3, \
+                DETECT_THRESH=1.5, DETECT_MINAREA=5, DETECT_MAXAREA=0)
+        REF_skysub = venv_file_path + "/temp_skysub_ref.fits".format(i)
+        SEx_SkySubtract.SSS(FITS_obj=temp_ref_path, FITS_skysub=REF_skysub, FITS_sky=None, FITS_skyrms=None, \
+            SATUR_KEY='SATURATE', ESATUR_KEY='ESATUR', BACK_SIZE=64, BACK_FILTERSIZE=3, \
+            DETECT_THRESH=1.5, DETECT_MINAREA=5, DETECT_MAXAREA=0)
 
     #Subtract
         start = time.perf_counter()
         print("Method = sfft")  #TODO Incorperate input masks for when we take real data
-        for i, fits_name in enumerate(temp_image_fits_filenames):       
-            sol, diff = Customized_Packet.CP(FITS_REF = temp_ref_path, FITS_SCI = fits_name, 
-                                    FITS_mREF = temp_ref_path, FITS_mSCI = fits_name,
-                                    ForceConv = "REF", GKerHW = 4, BGPolyOrder = 2, KerPolyOrder = 2)    
+
+
+        # for i, fits_name in enumerate(temp_image_fits_filenames):       
+        #     sol, diff = Customized_Packet.CP(FITS_REF = temp_ref_path, FITS_SCI = fits_name, 
+        #                             FITS_mREF = temp_ref_path, FITS_mSCI = fits_name,
+        #                             ForceConv = "REF", GKerHW = 4, BGPolyOrder = 2, KerPolyOrder = 2)
+
+        #     if np.isnan(np.sum(diff)) == True:
+        #         raise ValueError("Residual contains NaN")
+        #     else:
+        #         hduls[i].insert(1,CompImageHDU(data = diff, header =  hduls[i][name].header, name = "SUB"))
+        #     outputs.append(hduls[i])
+        for i, fits_name in enumerate(skysub_fits):       
+            dic, sol, diff = Easy_SparsePacket.ESP(FITS_REF = REF_skysub, FITS_SCI = fits_name)    						    
 
             if np.isnan(np.sum(diff)) == True:
                 raise ValueError("Residual contains NaN")
             else:
                 hduls[i].insert(1,CompImageHDU(data = diff, header =  hduls[i][name].header, name = "SUB"))
-            outputs.append(hduls[i])
+            outputs.append(hduls[i])	
         stop = time.perf_counter()
         print("Subtraction Complete")
         print("Time Elapsed: {} sec".format(round(stop-start, 4)))
         print("Removing Temporary Fits Files")    
-        for i, fits_name in enumerate(temp_image_fits_filenames): #Remove Temporary Fits files from disc  
+        for i, fits_name in enumerate(skysub_fits): #Remove Temporary Fits files from disc  
             if os.path.exists(fits_name):
                 os.remove(fits_name)
             else:

setup.py

@@ -1,4 +1,18 @@
+import os
+import sys
 from setuptools import setup, find_packages
+
+DESCRIPTION = "Pipeline to Take a Stack of Images and Extract Residuals"
+NAME = "sdi-pipeline"
+AUTHOR = "Kyle Lam"
+AUTHOR_EMAIL = "[email protected]"
+MAINTAINER = "Kyle Lama"
+MAINTAINER_EMAIL = "[email protected]"
+DOWNLOAD_URL = "https://github.com/ucsbdeepspace/sdi_pipeline.git"
+
+LICENSE = 'MIT Licence'
+VERSION = '0.99'
+=======
 import subprocess
 import sys
 
@@ -18,15 +32,38 @@
 
 subprocess.run(sys.executable + " -m pip install --upgrade pip setuptools==56.0.0 setuptools_rust numpy", shell=True)
 
-setup(
-    name="sdi-cli",
-    version="0.99",
-    py_modules=["sdi"],
-    # packages=find_packages(include=["openfits"]),
-    include_package_data=True,
-    install_requires=["click", "astropy", "photutils", "ois", "astroalign", "astroquery", "sklearn"],
-    entry_points="""
-        [console_scripts]
-        sdi=sdi._cli:cli
-    """,
-)
+install_reqs = ["numpy",
+				"setuptools_rust",
+				"click", 
+				"astropy", 
+				"photutils", 
+				"ois", 
+				"astroalign", 
+				"astroquery", 
+				"sklearn",
+				]
+setup_reqs = ["numpy", 
+				"setuptools_rust"]
+
+setup(name = NAME,
+      version = VERSION,
+      description = DESCRIPTION,
+	  setup_requires = setup_reqs,
+      install_requires = install_reqs,
+      author = AUTHOR,
+      author_email = AUTHOR_EMAIL,
+      maintainer = MAINTAINER,
+      maintainer_email = MAINTAINER_EMAIL,
+      download_url = DOWNLOAD_URL,
+      license = LICENSE,
+      packages = find_packages(),
+      include_package_data = True,
+    #   classifiers = [
+    #     'Development Status :: 4 - Beta',
+    #     'Environment :: Console',
+    #     'Intended Audience :: Science/Research',
+    #     'Natural Language :: English',
+    #     'Programming Language :: Python :: 3.7',
+    #     'Programming Language :: Python :: 3 :: Only',
+    #     'Topic :: Scientific/Engineering :: Astronomy'],
+     )