diff --git a/CHANGELOG.rst b/CHANGELOG.rst new file mode 100644 index 0000000..0bf7cfc --- /dev/null +++ b/CHANGELOG.rst @@ -0,0 +1,3 @@ +Changes from v0.0.0 to v0.0.1 +========================= +Made repo public. \ No newline at end of file diff --git a/config/README.md b/config/README.md deleted file mode 100644 index bc79c08..0000000 --- a/config/README.md +++ /dev/null @@ -1,41 +0,0 @@ -## Config imsim - -`was.yaml`: _euclidlike_imsim exemple_ config file. -You will want to update the following entries: - -- `input.obseq_data.file_name`: path to the observing sequence. Link to `euclidlike/data/euclid_obseq.fits` -- `input.sky_catalog.file_name`: path to the skyCatalog to use -- `output.dir`: path to the output directory for the simulated images -- `output.truth.dir`: path to the ouput directory for the true catalogs - -To run the code: -```bash -galsim was.yaml -``` - -You might want to specify some config entries in the command line, likes: -```bash -galsim was.yaml input.obseq_data.visit=33690 image.CCD=1 -``` - -## Config SLURM - -`slurm_runner.sh` contain the SLURM configuration to run "large scale" simulations. -You will want to update the following line: -- `#!/bin/zsh`: depending on the shell you are using you might want to change it to: `#!/bin/bash` -- `#SBATCH --output=/path/to/slurm-%A-%a.out`: slurm stdout file -- `#SBATCH --error=/path/to/slurm-%A-%a.err`: slurm stderr file -- `source activate [env_name]`: conda environment to use -- `file_list='/path/to/run_list.txt'`: file containing the pointings to simulate (see note below) - -the `run_list.txt` is a 2 columns file with the pointing and the CCD_ID to simulate. It should lookq like: -``` -33688 0 -33688 1 -33688 2 -[...] -33688 35 -33689 0 -33689 1 -[...] -``` diff --git a/config/README.rst b/config/README.rst new file mode 100644 index 0000000..fb823c3 --- /dev/null +++ b/config/README.rst @@ -0,0 +1,49 @@ +Config imsim +============ + +``was.yaml``: *euclidlike_imsim example* config file. +You will want to update the following entries: + +- ``input.obseq_data.file_name``: path to the observing sequence. Link to ``euclidlike/data/euclid_obseq.fits`` +- ``input.sky_catalog.file_name``: path to the skyCatalog to use +- ``output.dir``: path to the output directory for the simulated images +- ``output.truth.dir``: path to the output directory for the true catalogs + +To run the code: + +.. code-block:: bash + + galsim was.yaml + +You might want to specify some config entries on the command line, like: + +.. code-block:: bash + + galsim was.yaml input.obseq_data.visit=33690 image.CCD=1 + + +Config SLURM +============ + +``slurm_runner.sh`` contains the SLURM configuration to run "large scale" simulations. +You will want to update the following lines: + +- ``#!/bin/zsh``: depending on the shell you are using, you might want to change it to: ``#!/bin/bash`` +- ``#SBATCH --output=/path/to/slurm-%A-%a.out``: SLURM stdout file +- ``#SBATCH --error=/path/to/slurm-%A-%a.err``: SLURM stderr file +- ``source activate [env_name]``: conda environment to use +- ``file_list='/path/to/run_list.txt'``: file containing the pointings to simulate (see note below) + +The ``run_list.txt`` is a 2-column file with the pointing and the ``CCD_ID`` to simulate. It should look like: + +.. code-block:: text + + 33688 0 + 33688 1 + 33688 2 + [...] + 33688 35 + 33689 0 + 33689 1 + [...] + diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle index 2d9ec1c..d38556f 100644 Binary files a/docs/_build/doctrees/environment.pickle and b/docs/_build/doctrees/environment.pickle differ diff --git a/docs/_build/doctrees/euclidlike.doctree b/docs/_build/doctrees/euclidlike.doctree index 3147a25..a6e6f7e 100644 Binary files a/docs/_build/doctrees/euclidlike.doctree and b/docs/_build/doctrees/euclidlike.doctree differ diff --git a/docs/_build/doctrees/euclidlike_imsim.doctree b/docs/_build/doctrees/euclidlike_imsim.doctree index 590b7be..f46c640 100644 Binary files a/docs/_build/doctrees/euclidlike_imsim.doctree and b/docs/_build/doctrees/euclidlike_imsim.doctree differ diff --git a/docs/_build/doctrees/examples.doctree b/docs/_build/doctrees/examples.doctree new file mode 100644 index 0000000..f39ec92 Binary files /dev/null and b/docs/_build/doctrees/examples.doctree differ diff --git a/docs/_build/doctrees/history.doctree b/docs/_build/doctrees/history.doctree new file mode 100644 index 0000000..68423cc Binary files /dev/null and b/docs/_build/doctrees/history.doctree differ diff --git a/docs/_build/doctrees/index.doctree b/docs/_build/doctrees/index.doctree index e619b1a..79b0e2b 100644 Binary files a/docs/_build/doctrees/index.doctree and b/docs/_build/doctrees/index.doctree differ diff --git a/docs/_build/doctrees/install.doctree b/docs/_build/doctrees/install.doctree new file mode 100644 index 0000000..895b106 Binary files /dev/null and b/docs/_build/doctrees/install.doctree differ diff --git a/docs/_build/doctrees/modules.doctree b/docs/_build/doctrees/modules.doctree index 186a5a8..696c7e8 100644 Binary files a/docs/_build/doctrees/modules.doctree and b/docs/_build/doctrees/modules.doctree differ diff --git a/docs/_build/doctrees/overview.doctree b/docs/_build/doctrees/overview.doctree new file mode 100644 index 0000000..6efbd28 Binary files /dev/null and b/docs/_build/doctrees/overview.doctree differ diff --git a/docs/_build/doctrees/scripts.doctree b/docs/_build/doctrees/scripts.doctree index 13bc54c..37d1451 100644 Binary files a/docs/_build/doctrees/scripts.doctree and b/docs/_build/doctrees/scripts.doctree differ diff --git a/docs/_build/html/.buildinfo b/docs/_build/html/.buildinfo index acd1aed..cbbaf3d 100644 --- a/docs/_build/html/.buildinfo +++ b/docs/_build/html/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file records the configuration used when building these files. When it is not found, a full rebuild will be done. -config: cec21682d6cc0df78936fbd198ac0c57 +config: 11d168bc3ba21763cf541d100b9a19c3 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/_build/html/_modules/euclidlike/backgrounds.html b/docs/_build/html/_modules/euclidlike/backgrounds.html index 1041421..82899f6 100644 --- a/docs/_build/html/_modules/euclidlike/backgrounds.html +++ b/docs/_build/html/_modules/euclidlike/backgrounds.html @@ -38,7 +38,7 @@

Source code for euclidlike.backgrounds

 import galsim
 
 

-[docs]
+[docs]
 def getSkyLevel(bandpass, world_pos=None, exptime=None, epoch=2025, date=None):
     """
     Get the expected sky level for a Euclid observation due to zodiacal light for this bandpass
@@ -121,8 +121,6 @@ 
Source code for euclidlike.backgrounds
     return sky_val  

 
 
-

-[docs]
 def getZodiBackground(ecl_lat, ecl_dlon, lambda_min, lambda_max, Tlambda, T):
     """
     This helper routine is used with permission from Chris Hirata's Exposure Time Calculator and enables the
@@ -258,8 +256,7 @@ 
Source code for euclidlike.backgrounds
             5.03411747e10*lambda_* np.interp(lambda_,Tlambda,T)
 
     # We now have the zodi level in photons/m^2/sr/sec. Convert to photons/m^2/arcsec^2/sec.
-    return (zodi_tot / 4.2545170296152206e10)

-
+    return (zodi_tot / 4.2545170296152206e10)
@@ -288,6 +285,14 @@

GalSim-Euclid-Like

Navigation

+

Related Topics

diff --git a/docs/_build/html/_modules/euclidlike/bandpass.html b/docs/_build/html/_modules/euclidlike/bandpass.html index 05560f0..76a7977 100644 --- a/docs/_build/html/_modules/euclidlike/bandpass.html +++ b/docs/_build/html/_modules/euclidlike/bandpass.html @@ -52,7 +52,7 @@

Source code for euclidlike.bandpass

 from . import vis_red_limit, vis_blue_limit
 
 

-[docs]
+[docs]
 def getBandpasses(AB_zeropoint=True, default_thin_trunc=True, full_bandpass=False, **kwargs):
     """
     Function to get the bandpass information for the Euclid VIS band and the three Euclid NISP passbands.
@@ -185,6 +185,14 @@ 
GalSim-Euclid-Like

     

 
 
Navigation

+
 
 

 
Related Topics

diff --git a/docs/_build/html/_modules/euclidlike/euclidlike_psf.html b/docs/_build/html/_modules/euclidlike/euclidlike_psf.html
index 47409b6..3b5022b 100644
--- a/docs/_build/html/_modules/euclidlike/euclidlike_psf.html
+++ b/docs/_build/html/_modules/euclidlike/euclidlike_psf.html
@@ -100,7 +100,7 @@ 
Source code for euclidlike.euclidlike_psf
 _get_quadrant_psf = LRU_Cache(__get_quadrant_psf)
 
 

-[docs]
+[docs]
 def getPSF(
         ccd, bandpass,
         ccd_pos=None, wcs=None,
@@ -231,7 +231,7 @@ 
Source code for euclidlike.euclidlike_psf
 
 
 

-[docs]
+[docs]
 def getBrightPSF(
        ccd,
     bandpass,
@@ -433,6 +433,14 @@ 
GalSim-Euclid-Like

     

 
 
Navigation

+
 
 

 
Related Topics

diff --git a/docs/_build/html/_modules/euclidlike/euclidlike_wcs.html b/docs/_build/html/_modules/euclidlike/euclidlike_wcs.html
index 284db9a..ae3388b 100644
--- a/docs/_build/html/_modules/euclidlike/euclidlike_wcs.html
+++ b/docs/_build/html/_modules/euclidlike/euclidlike_wcs.html
@@ -119,7 +119,7 @@ 
Source code for euclidlike.euclidlike_wcs
 
 
 

-[docs]
+[docs]
 def getWCS(world_pos, PA=None, date=None, CCDs=None, PA_is_FPA=False, SAA=None):
     """
     This routine returns a dict containing a WCS for each of the Euclid CCDs.
@@ -246,8 +246,6 @@ 
Source code for euclidlike.euclidlike_wcs
 
 
 
-

-[docs]
 def convertCenter(world_pos, CCD, PA=None, date=None, SAA=None, PA_is_FPA=False, tol=0.5*coord.arcsec):
     """
     This is a simple helper routine that takes an input position ``world_pos`` that is meant to
@@ -316,12 +314,11 @@ 
Source code for euclidlike.euclidlike_wcs
         shift_val = np.abs(world_pos.distanceTo(test_sca_pos)/coord.arcsec)
         fpa_cent = coord.CelestialCoord(fpa_cent.ra + delta_ra, fpa_cent.dec + delta_dec)
 
-    return fpa_cent

-
+    return fpa_cent
 
 
 

-[docs]
+[docs]
 def findCCD(wcs_dict, world_pos, include_border=False):
     """
     This is a subroutine to take a dict of WCS (one per CCD) from euclidlike.getWCS() and query
@@ -583,8 +580,6 @@ 
Source code for euclidlike.euclidlike_wcs
     return date, CCDs, pa_fpa, pa_obsy
 
 
-

-[docs]
 def allowedPos(world_pos, date, SAA=None):
     """
     This routine can be used to check whether Euclid would be allowed to look at a particular
@@ -623,12 +618,9 @@ 
Source code for euclidlike.euclidlike_wcs
     # Check if it's within tolerance.
     min_ang = 90. - min_sun_angle/coord.degrees
     max_ang = 90. + max_sun_angle/coord.degrees
-    return min_ang <= angle_deg <= max_ang

-
+    return min_ang <= angle_deg <= max_ang
 
 
-

-[docs]
 def bestPA(world_pos, date, SAA=None):
     """
     This routine determines the best position angle for the observatory for a given observation date
@@ -671,8 +663,7 @@ 
Source code for euclidlike.euclidlike_wcs
     # celestial north pole.  It is defined as position angle east of north.
     north = coord.CelestialCoord(y_obs.ra, 90.*coord.degrees)
     obs_pa = world_pos.angleBetween(y_obs, north)
-    return obs_pa

-
+    return obs_pa
 

 
           

@@ -700,6 +691,14 @@ 
GalSim-Euclid-Like

     

 
 
Navigation

+
 
 

 
Related Topics

diff --git a/docs/_build/html/_modules/euclidlike_imsim/bandpass.html b/docs/_build/html/_modules/euclidlike_imsim/bandpass.html
new file mode 100644
index 0000000..5c34fef
--- /dev/null
+++ b/docs/_build/html/_modules/euclidlike_imsim/bandpass.html
@@ -0,0 +1,144 @@
+
+
+
+  
+    
+    
+    euclidlike_imsim.bandpass — GalSim-Euclid-Like 0.0.1 documentation
+    
+    
+    
+    
+    
+    
+    
+    
+   
+  
+  
+
+  
+  
+
+  
+  
+
+    

+      

+        

+          
+
+          

+            
+  
Source code for euclidlike_imsim.bandpass
+import euclidlike
+from galsim.config import BandpassBuilder, RegisterBandpassType, GetAllParams
+
+
+

+[docs]
+class EuclidlikeBandpassBuilder(BandpassBuilder):
+    """A class for loading a Bandpass from a file
+
+    FileBandpass expected the following parameter:
+
+        name (str)          The name of the Euclid filter to get. (required)
+    """
+

+[docs]
+    def buildBandpass(self, config, base, logger):
+        """Build the Bandpass based on the specifications in the config dict.
+
+        Parameters:
+            config:     The configuration dict for the bandpass type.
+            base:       The base configuration dict.
+            logger:     If provided, a logger for logging debug statements.
+
+        Returns:
+            the constructed Bandpass object.
+        """
+        req = {'name': str}
+        kwargs, safe = GetAllParams(config, base, req=req)
+
+        name = kwargs['name']
+        # Hard set the limit due to PSF definition
+        bandpass = euclidlike.getBandpasses()[name]
+
+        return bandpass, safe

+

+
+
+
+RegisterBandpassType('EuclidlikeBandpass', EuclidlikeBandpassBuilder())
+RegisterBandpassType('EuclidlikeBandpassTrimmed', EuclidlikeBandpassBuilder())
+

+
+          

+          
+        

+      

+      
+      

+    

+    

+      ©2024, Rachel Mandelbaum, Axel Guinot, Federico Berlfein, Andy Park, Xiangchong Li, Michael Troxel, Tianqing Zhang.
+      
+      |
+      Powered by Sphinx 8.1.3
+      & Alabaster 1.0.0
+      
+    

+
+    
+
+    
+  
+
\ No newline at end of file
diff --git a/docs/_build/html/_modules/euclidlike_imsim/ccd.html b/docs/_build/html/_modules/euclidlike_imsim/ccd.html
new file mode 100644
index 0000000..db285cb
--- /dev/null
+++ b/docs/_build/html/_modules/euclidlike_imsim/ccd.html
@@ -0,0 +1,331 @@
+
+
+
+  
+    
+    
+    euclidlike_imsim.ccd — GalSim-Euclid-Like 0.0.1 documentation
+    
+    
+    
+    
+    
+    
+    
+    
+   
+  
+  
+
+  
+  
+
+  
+  
+
+    

+      

+        

+          
+
+          

+            
+  
Source code for euclidlike_imsim.ccd
+import galsim
+import galsim.config
+from galsim.config import RegisterImageType
+from galsim.config.image_scattered import ScatteredImageBuilder
+from galsim.errors import GalSimConfigValueError
+from galsim.image import Image
+from astropy.time import Time
+import numpy as np
+
+import euclidlike
+from euclidlike.instrument_params import gain, saturation
+from .noise import cfg_noise_key, parse_noise_config, get_noise
+
+
+

+[docs]
+class EuclidlikeCCDImageBuilder(ScatteredImageBuilder):
+
+

+[docs]
+    def setup(self, config, base, image_num, obj_num, ignore, logger):
+        """Do the initialization and setup for building the image.
+
+        This figures out the size that the image will be, but doesn't actually build it yet.
+
+        Parameters:
+            config:     The configuration dict for the image field.
+            base:       The base configuration dict.
+            image_num:  The current image number.
+            obj_num:    The first object number in the image.
+            ignore:     A list of parameters that are allowed to be in config that we can
+                        ignore here. i.e. it won't be an error if these parameters are present.
+            logger:     If given, a logger object to log progress.
+
+        Returns:
+            xsize, ysize
+        """
+        logger.debug(
+            "image %d: Building EuclidlikeCCD: image, obj = %d,%d",
+            image_num,
+            image_num,
+            obj_num,
+        )
+
+        self.nobjects = self.getNObj(config, base, image_num, logger=logger)
+        logger.debug("image %d: nobj = %d", image_num, self.nobjects)
+
+        # These are allowed for Scattered, but we don't use them here.
+        extra_ignore = [
+            "image_pos",
+            "world_pos",
+            "stamp_size",
+            "stamp_xsize",
+            "stamp_ysize",
+            "nobjects",
+        ]
+        req = {"CCD": int, "filter": str, "mjd": float, "exptime": float}
+        opt = {
+            "draw_method": str,
+        }
+        opt.update({key: bool for key in cfg_noise_key})
+        params = galsim.config.GetAllParams(
+            config, base, req=req, opt=opt, ignore=ignore + extra_ignore
+        )[0]
+
+        self.ccd = params["CCD"]
+        base["CCD"] = self.ccd
+        self.filter = params["filter"]
+        self.mjd = params["mjd"]
+        self.exptime = params["exptime"]
+
+        self.cfg_noise = parse_noise_config(params)
+
+        # If draw_method isn't in image field, it may be in stamp.  Check.
+        self.draw_method = params.get(
+            "draw_method", base.get("stamp", {}).get("draw_method", "auto")
+        )
+
+        # If user hasn't overridden the bandpass to use, get the standard one.
+        if "bandpass" not in config:
+            base["bandpass"] = galsim.config.BuildBandpass(
+                base["image"], "bandpass", base, logger=logger
+            )
+
+        return euclidlike.n_pix_col, euclidlike.n_pix_row

+
+
+

+[docs]
+    def buildImage(self, config, base, image_num, obj_num, logger):
+        """Build an Image containing multiple objects placed at arbitrary locations.
+
+        Parameters:
+            config:     The configuration dict for the image field.
+            base:       The base configuration dict.
+            image_num:  The current image number.
+            obj_num:    The first object number in the image.
+            logger:     If given, a logger object to log progress.
+
+        Returns:
+            the final image and the current noise variance in the image as a tuple
+        """
+        full_xsize = base["image_xsize"]
+        full_ysize = base["image_ysize"]
+        wcs = base["wcs"]
+
+        full_image = Image(full_xsize, full_ysize, dtype=float)
+        full_image.setOrigin(base["image_origin"])
+        full_image.wcs = wcs
+        full_image.setZero()
+
+        full_image.header = galsim.FitsHeader()
+        full_image.header["EXPTIME"] = self.exptime
+        full_image.header["MJD-OBS"] = self.mjd
+        full_image.header["DATE-OBS"] = str(Time(self.mjd, format="mjd").datetime)
+        full_image.header["FILTER"] = self.filter
+        full_image.header["GAIN"] = gain
+        full_image.header["ZPTMAG"] = 2.5 * np.log10(
+            self.exptime * euclidlike.collecting_area
+        )
+
+        base["current_image"] = full_image
+
+        if "image_pos" in config and "world_pos" in config:
+            raise GalSimConfigValueError(
+                "Both image_pos and world_pos specified for Scattered image.",
+                (config["image_pos"], config["world_pos"]),
+            )
+
+        if "image_pos" not in config and "world_pos" not in config:
+            xmin = base["image_origin"].x
+            xmax = xmin + full_xsize - 1
+            ymin = base["image_origin"].y
+            ymax = ymin + full_ysize - 1
+            config["image_pos"] = {
+                "type": "XY",
+                "x": {"type": "Random", "min": xmin, "max": xmax},
+                "y": {"type": "Random", "min": ymin, "max": ymax},
+            }
+
+        nbatch = self.nobjects // 1000 + 1
+        for batch in range(nbatch):
+            start_obj_num = self.nobjects * batch // nbatch
+            end_obj_num = self.nobjects * (batch + 1) // nbatch
+            nobj_batch = end_obj_num - start_obj_num
+            if nbatch > 1:
+                logger.warning(
+                    "Start batch %d/%d with %d objects [%d, %d)",
+                    batch + 1,
+                    nbatch,
+                    nobj_batch,
+                    start_obj_num,
+                    end_obj_num,
+                )
+            stamps, current_vars = galsim.config.BuildStamps(
+                nobj_batch, base, logger=logger, obj_num=start_obj_num, do_noise=False
+            )
+            base["index_key"] = "image_num"
+
+            for k in range(nobj_batch):
+                # This is our signal that the object was skipped.
+                if stamps[k] is None:
+                    continue
+                bounds = stamps[k].bounds & full_image.bounds
+                if not bounds.isDefined():  # pragma: no cover
+                    # These noramlly show up as stamp==None, but technically it is possible
+                    # to get a stamp that is off the main image, so check for that here to
+                    # avoid an error.  But this isn't covered in the imsim test suite.
+                    continue
+
+                logger.debug(
+                    "image %d: full bounds = %s", image_num, str(full_image.bounds)
+                )
+                logger.debug(
+                    "image %d: stamp %d bounds = %s",
+                    image_num,
+                    k + start_obj_num,
+                    str(stamps[k].bounds),
+                )
+                logger.debug("image %d: Overlap = %s", image_num, str(bounds))
+                full_image[bounds] += stamps[k][bounds]
+            stamps = None
+
+        return full_image, None

+
+
+

+[docs]
+    def addNoise(self, image, config, base, image_num, obj_num, current_var, logger):
+        """Add the final noise to a Scattered image
+
+        Parameters:
+            image:          The image onto which to add the noise.
+            config:         The configuration dict for the image field.
+            base:           The base configuration dict.
+            image_num:      The current image number.
+            obj_num:        The first object number in the image.
+            current_var:    The current noise variance in each postage stamps.
+            logger:         If given, a logger object to log progress.
+        """
+        # check ignore noise
+        if self.cfg_noise["ignore_noise"]:
+            return
+
+        if "noise_image" not in base.keys():
+            get_noise(self.cfg_noise, config, base, logger)
+
+        # We first have to apply gain and quantize the image
+        image /= gain
+        image.quantize()
+
+        image += base["noise_image"]
+        
+        # Apply saturation
+        saturation_ADU = np.round(saturation/gain)
+        mask_saturated = image.array > saturation_ADU
+        base["saturated_mask"] = mask_saturated
+        image.array[mask_saturated] = saturation_ADU
+        
+        if self.cfg_noise["sky_subtract"]:
+            image -= base["sky_image"]

+

+
+
+
+# Register this as a valid type
+RegisterImageType("euclidlike_ccd", EuclidlikeCCDImageBuilder())
+

+
+          

+          
+        

+      

+      
+      

+    

+    

+      ©2024, Rachel Mandelbaum, Axel Guinot, Federico Berlfein, Andy Park, Xiangchong Li, Michael Troxel, Tianqing Zhang.
+      
+      |
+      Powered by Sphinx 8.1.3
+      & Alabaster 1.0.0
+      
+    

+
+    
+
+    
+  
+
\ No newline at end of file
diff --git a/docs/_build/html/_modules/euclidlike_imsim/noise.html b/docs/_build/html/_modules/euclidlike_imsim/noise.html
new file mode 100644
index 0000000..36a03a4
--- /dev/null
+++ b/docs/_build/html/_modules/euclidlike_imsim/noise.html
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+
+
+
+  
+    
+    
+    euclidlike_imsim.noise — GalSim-Euclid-Like 0.0.1 documentation
+    
+    
+    
+    
+    
+    
+    
+    
+   
+  
+  
+
+  
+  
+
+  
+  
+
+    

+      

+        

+          
+
+          

+            
+  
Source code for euclidlike_imsim.noise
+import numpy as np
+
+from astropy.time import Time
+
+import galsim
+from galsim.errors import GalSimConfigError
+
+import euclidlike
+from euclidlike.instrument_params import gain, read_noise
+
+# Some place holder stuff, will need to update later in euclidlike
+# This is just to avoid changing the code and don't have "errors"
+stray_light_fraction = 0.
+dark_current = 0.
+
+cfg_noise_key = [
+    "ignore_noise",
+    "stray_light",
+    "thermal_background",
+    "reciprocity_failure",
+    "dark_current",
+    "nonlinearity",
+    "ipc",
+    "read_noise",
+    "sky_subtract",
+]
+
+
+

+[docs]
+def parse_noise_config(params):
+
+    cfg_noise = {}
+    for key in cfg_noise_key:
+        cfg_noise[key] = params.get(key, False)
+
+    cfg_noise["exptime"] = params["exptime"]
+    cfg_noise["mjd"] = params["mjd"]
+
+    return cfg_noise

+
+
+
+

+[docs]
+def get_noise(cfg_noise, cfg_image, base, logger):
+
+    noise_img = base["current_image"].copy()
+    noise_img.fill(0)
+
+    wcs = base["wcs"]
+    bp = base["bandpass"]
+    rng = galsim.config.GetRNG(cfg_image, base)
+    logger.info(
+        "image %d: Start EuclidlikeCCD detector effects", base.get("image_num", 0)
+    )
+
+    # Things that will eventually be subtracted (if sky_subtract) will have their expectation
+    # value added to sky_image.  So technically, this includes things that aren't just sky.
+    # E.g. includes dark_current and thermal backgrounds.
+    sky_image = noise_img.copy()
+    sky_level = euclidlike.getSkyLevel(
+        bp,
+        world_pos=wcs.toWorld(noise_img.true_center),
+        date=Time(cfg_noise["mjd"], format="mjd").datetime,
+    )
+    logger.debug("Adding sky_level = %s", sky_level)
+    if cfg_noise["stray_light"]:
+        logger.debug("Stray light fraction = %s", stray_light_fraction)
+        sky_level *= 1.0 + stray_light_fraction
+    wcs.makeSkyImage(sky_image, sky_level)
+
+    # The image up to here is an expectation value.
+    # Realize it as an integer number of photons.
+    poisson_noise = galsim.noise.PoissonNoise(rng)
+    logger.debug("Adding poisson noise to sky photons")
+    sky_image1 = sky_image.copy()
+    sky_image1.addNoise(poisson_noise)
+    noise_img.quantize()
+    # the image won't necessarily be integers.
+    noise_img += sky_image1
+
+    # Apply the detector effects here.  Not all of these are "noise" per se, but they
+    # happen interspersed with various noise effects, so apply them all in this step.
+
+    if cfg_noise["dark_current"]:
+        dc = dark_current * cfg_noise["exptime"]
+        logger.debug("Adding dark current: %s", dc)
+        sky_image += dc
+        dark_noise = galsim.noise.DeviateNoise(
+            galsim.random.PoissonDeviate(rng, dc)
+        )
+        noise_img.addNoise(dark_noise)
+
+    if cfg_noise["read_noise"]:
+        logger.debug("Adding read noise %s", read_noise)
+        noise_img.addNoise(galsim.GaussianNoise(rng, sigma=read_noise))
+
+    logger.debug("Applying gain %s", gain)
+    noise_img /= gain
+
+    # Make integer ADU now.
+    noise_img.quantize()
+
+    sky_image /= gain
+    sky_image.quantize()
+
+    base["noise_image"] = noise_img
+    base["sky_image"] = sky_image

+
+
+
+

+[docs]
+class NoiseImageBuilder(galsim.config.ExtraOutputBuilder):
+
+

+[docs]
+    def initialize(self, data, scratch, config, base, logger):
+        """Do any initial setup for this builder at the start of a new output file.
+
+        The base class implementation saves two work space items into self.data and self.scratch
+        that can be used to safely communicate across multiple processes.
+
+        Parameters:
+            data:       An empty list of length nimages to use as work space.
+            scratch:    An empty dict that can be used as work space.
+            config:     The configuration field for this output object.
+            base:       The base configuration dict.
+            logger:     If given, a logger object to log progress. [default: None]
+        """
+        req = {"CCD": int, "filter": str, "mjd": float, "exptime": float}
+        opt = {key: bool for key in cfg_noise_key}
+        ignore = galsim.config.image.image_ignore
+        extra_ignore = [
+            "image_pos",
+            "world_pos",
+            "stamp_size",
+            "stamp_xsize",
+            "stamp_ysize",
+            "nobjects",
+        ]
+        params = galsim.config.GetAllParams(
+            base["image"], base, req=req, opt=opt, ignore=ignore+extra_ignore,
+        )[0]
+        self.cfg_noise = parse_noise_config(params)
+
+        self._check_input()
+
+        self.data = data
+        self.scratch = scratch
+        self.final_data = None

+
+
+    def _check_input(self):
+        if self.cfg_noise["ignore_noise"]:
+            raise GalSimConfigError(
+                "You cannot ignore the noise and request the noise image at the same time."
+                " Either active the noise or remove the output noise image."
+            )
+
+

+[docs]
+    def processImage(self, index, obj_nums, config, base, logger):
+        """Perform any necessary processing at the end of each image construction.
+
+        This function will be called after each full image is built.
+
+        Compute the noise for the current image and add it to the image.
+        It will also create an independent noise image.
+        The code optionally subtract the background if requested.
+
+        Parameters:
+            index:      The index in self.data to use for this image.  This isn't the image_num
+                        (which can be accessed at base['image_num'] if needed), but rather
+                        an index that starts at 0 for the first image being worked on and
+                        goes up to nimages-1.
+            obj_nums:   The object numbers that were used for this image.
+            config:     The configuration field for this output object.
+            base:       The base configuration dict.
+            logger:     If given, a logger object to log progress. [default: None]
+        """
+        if "noise_image" not in base.keys():
+            get_noise(self.cfg_noise, config, base, logger)
+
+        noise_image = base["noise_image"].copy()
+
+        if self.cfg_noise["sky_subtract"]:
+            noise_image -= base["sky_image"]
+
+        self.data[index] = noise_image

+

+
+
+
+

+[docs]
+class SkyImageBuilder(NoiseImageBuilder):
+
+    def _check_input(self):
+        if self.cfg_noise["ignore_noise"]:
+            raise GalSimConfigError(
+                "You cannot ignore the noise and request the sky image at the same time."
+                " Either activate the noise or remove the output sky image."
+            )
+
+

+[docs]
+    def processImage(self, index, obj_nums, config, base, logger):
+        """Perform any necessary processing at the end of each image construction.
+
+        This function will be called after each full image is built.
+
+        Compute the sky background and return it in an image.
+
+        Parameters:
+            index:      The index in self.data to use for this image.  This isn't the image_num
+                        (which can be accessed at base['image_num'] if needed), but rather
+                        an index that starts at 0 for the first image being worked on and
+                        goes up to nimages-1.
+            obj_nums:   The object numbers that were used for this image.
+            config:     The configuration field for this output object.
+            base:       The base configuration dict.
+            logger:     If given, a logger object to log progress. [default: None]
+        """
+        if "noise_image" not in base.keys():
+            get_noise(self.cfg_noise, config, base, logger)
+
+        self.data[index] = base["sky_image"].copy()

+

+
+
+
+

+[docs]
+class WeightImageBuilder(NoiseImageBuilder):
+
+    def _check_input(self):
+        if self.cfg_noise["ignore_noise"]:
+            raise GalSimConfigError(
+                "You cannot ignore the noise and request the weight image at the same time."
+                " Either activate the noise or remove the output sky image."
+            )
+
+

+[docs]
+    def processImage(self, index, obj_nums, config, base, logger):
+        """Perform any necessary processing at the end of each image construction.
+
+        This function will be called after each full image is built.
+
+        Compute the weight map from the noise image and return it in an image.
+
+        Parameters:
+            index:      The index in self.data to use for this image.  This isn't the image_num
+                        (which can be accessed at base['image_num'] if needed), but rather
+                        an index that starts at 0 for the first image being worked on and
+                        goes up to nimages-1.
+            obj_nums:   The object numbers that were used for this image.
+            config:     The configuration field for this output object.
+            base:       The base configuration dict.
+            logger:     If given, a logger object to log progress. [default: None]
+        """
+        if "noise_image" not in base.keys():
+            get_noise(self.cfg_noise, config, base, logger)
+
+        noise_var = np.var(base["noise_image"].array)
+
+        weight_image = galsim.ImageF(base["image_bounds"])
+        weight_image += noise_var
+        weight_image.invertSelf()
+
+        self.data[index] = weight_image

+

+
+
+
+galsim.config.RegisterExtraOutput('noise_image', NoiseImageBuilder())
+galsim.config.RegisterExtraOutput('sky_image', SkyImageBuilder())
+galsim.config.RegisterExtraOutput('weight_image', WeightImageBuilder())
+

+
+          

+          
+        

+      

+      
+      

+    

+    

+      ©2024, Rachel Mandelbaum, Axel Guinot, Federico Berlfein, Andy Park, Xiangchong Li, Michael Troxel, Tianqing Zhang.
+      
+      |
+      Powered by Sphinx 8.1.3
+      & Alabaster 1.0.0
+      
+    

+
+    
+
+    
+  
+
\ No newline at end of file
diff --git a/docs/_build/html/_modules/euclidlike_imsim/obseq.html b/docs/_build/html/_modules/euclidlike_imsim/obseq.html
new file mode 100644
index 0000000..74ece02
--- /dev/null
+++ b/docs/_build/html/_modules/euclidlike_imsim/obseq.html
@@ -0,0 +1,227 @@
+
+
+
+  
+    
+    
+    euclidlike_imsim.obseq — GalSim-Euclid-Like 0.0.1 documentation
+    
+    
+    
+    
+    
+    
+    
+    
+   
+  
+  
+
+  
+  
+
+  
+  
+
+    

+      

+        

+          
+
+          

+            
+  
Source code for euclidlike_imsim.obseq
+from astropy.time import Time
+import pandas as pd
+import galsim
+import galsim.config
+from galsim.angle import Angle
+from galsim.config import InputLoader, RegisterValueType, RegisterInputType
+from galsim.errors import GalSimConfigValueError
+
+
+OBS_KIND = [
+    "VIS_LONG",
+    "VIS_SHORT",
+    "NISP_J",
+    "NISP_H",
+    "NISP_Y",
+]
+
+

+[docs]
+class ObSeqDataLoader(object):
+    """Read the exposure information from the observation sequence."""
+
+    _req_params = {"file_name": str, "visit": int, "obs_kind": str, "CCD": int}
+
+    def __init__(self, file_name, visit, obs_kind, CCD, logger=None):
+        self.logger = galsim.config.LoggerWrapper(logger)
+        self.file_name = file_name
+        self.visit = visit
+        self.ccd = CCD
+
+        if obs_kind not in OBS_KIND:
+            raise GalSimConfigValueError(
+                "Invalid obs_kind.", obs_kind, OBS_KIND
+            )
+        self.obs_kind = obs_kind
+
+        # try:
+        self.read_obseq()
+        # except:
+        #     # Read visit info from the config file.
+        #     self.logger.warning('Reading visit info from config file.')
+
+

+[docs]
+    def read_obseq(self):
+        """Read visit info from the obseq file."""
+        if self.file_name is None:
+            raise ValueError(
+                "No obseq filename provided, trying to build from config information."
+            )
+        if self.visit is None:
+            raise ValueError(
+                "The visit must be set when reading visit info from an obseq file."
+            )
+
+        self.logger.warning(
+            "Reading info from obseq file %s for visit %s", self.file_name, self.visit
+        )
+
+        ob = pd.read_pickle(self.file_name).loc[self.visit]
+
+        self.ob = {}
+        for obs_kind in OBS_KIND:
+            _ob = {}
+            _ob["visit"] = self.visit
+            _ob["ccd"] = self.ccd
+            _ob["ra"] = ob.loc[obs_kind]["ra"] * galsim.degrees
+            _ob["dec"] = ob.loc[obs_kind]["dec"] * galsim.degrees
+            _ob["pa"] = ob.loc[obs_kind]["pa"] * galsim.degrees
+            _ob["saa"] = ob.loc[obs_kind]["saa"] * galsim.degrees
+            _ob["date"] = Time(ob.loc[obs_kind]["date"], format="mjd").datetime
+            _ob["mjd"] = ob.loc[obs_kind]["date"]
+            _ob["filter"] = ob.loc[obs_kind]["filter"]
+            _ob["exptime"] = ob.loc[obs_kind]["exptime"]
+            self.ob[obs_kind] = _ob

+
+
+

+[docs]
+    def get(self, field, default=None, obs_kind=None):
+
+        if obs_kind is None:
+            obs_kind = self.obs_kind
+        else:
+            if obs_kind not in OBS_KIND:
+                raise KeyError(
+                    f"OpsimData obs_kind {obs_kind} not present in ob, "
+                    f"must be in {OBS_KIND}."
+                )
+        ob = self.ob[obs_kind]
+
+        if field not in ob and default is None:
+            raise KeyError("OpsimData field %s not present in ob" % field)
+
+        return ob.get(field, default)

+

+
+
+
+

+[docs]
+def ObSeqData(config, base, value_type):
+    """Returns the obseq data for a pointing."""
+    pointing = galsim.config.GetInputObj("obseq_data", config, base, "OpSeqDataLoader")
+
+    req = {"field": str}
+    opt = {"obs_kind": str}
+
+    kwargs, safe = galsim.config.GetAllParams(config, base, req=req, opt=opt)
+    field = kwargs["field"]
+    obs_kind = kwargs.get("obs_kind", None)
+
+    val = value_type(pointing.get(field, obs_kind=obs_kind))
+    return val, safe

+
+
+
+RegisterInputType(
+    "obseq_data", InputLoader(ObSeqDataLoader, file_scope=True, takes_logger=True)
+)
+RegisterValueType(
+    "ObSeqData", ObSeqData, [float, int, str, Angle], input_type="obseq_data"
+)
+

+
+          

+          
+        

+      

+      
+      

+    

+    

+      ©2024, Rachel Mandelbaum, Axel Guinot, Federico Berlfein, Andy Park, Xiangchong Li, Michael Troxel, Tianqing Zhang.
+      
+      |
+      Powered by Sphinx 8.1.3
+      & Alabaster 1.0.0
+      
+    

+
+    
+
+    
+  
+
\ No newline at end of file
diff --git a/docs/_build/html/_modules/euclidlike_imsim/photonOps.html b/docs/_build/html/_modules/euclidlike_imsim/photonOps.html
new file mode 100644
index 0000000..e60a325
--- /dev/null
+++ b/docs/_build/html/_modules/euclidlike_imsim/photonOps.html
@@ -0,0 +1,194 @@
+
+
+
+  
+    
+    
+    euclidlike_imsim.photonOps — GalSim-Euclid-Like 0.0.1 documentation
+    
+    
+    
+    
+    
+    
+    
+    
+   
+  
+  
+
+  
+  
+
+  
+  
+
+    

+      

+        

+          
+
+          

+            
+  
Source code for euclidlike_imsim.photonOps
+_w1 = 0.17519
+_w2 = 0.53146
+_w3 = 0.29335
+_s  = 0.3279
+_s1 = 0.4522*_s
+_s2 = 0.8050*_s
+_s3 = 1.4329*_s
+
+import numpy as np
+from galsim import PhotonOp,UniformDeviate,GaussianDeviate
+from galsim.config import PhotonOpBuilder,RegisterPhotonOpType,get_cls_params,GetAllParams,GetRNG
+
+

+[docs]
+class ChargeDiff(PhotonOp):
+    """A photon operator that applies the effect of charge diffusion via a probablistic model limit.
+    """
+    def __init__(self, rng=None, **kwargs):
+
+        self.ud   = UniformDeviate(rng)
+        self.gd1  = GaussianDeviate(rng, sigma=_s1)
+        self.gd2  = GaussianDeviate(rng, sigma=_s2)
+        self.gd3  = GaussianDeviate(rng, sigma=_s3)
+
+

+[docs]
+    def applyTo(self, photon_array, local_wcs=None, rng=None):
+        """Apply the charge diffusion effect to the photons
+
+        Parameters:
+            photon_array:   A `PhotonArray` to apply the operator to.
+            local_wcs:      A `LocalWCS` instance defining the local WCS for the current photon
+                            bundle in case the operator needs this information.  [default: None]
+            rng:            A random number generator to use if needed. [default: None]
+        """
+
+        # Choose which weighted Gausian to use in sech model approximation
+        u  = np.empty(len(photon_array.x))
+        self.ud.generate(u)
+
+        # Selects appropriate fraction of photons corresponding to the first gaussian in the sech model
+        mask = u<_w1
+        dx = np.empty(np.sum(mask))
+        dy = np.empty(np.sum(mask))
+        # Generate and apply the 2D gaussian shifts corresponding to the first gaussian
+        self.gd1.generate(dx)
+        self.gd1.generate(dy)
+        photon_array.x[mask] += dx
+        photon_array.y[mask] += dy
+
+        # Selects appropriate fraction of photons corresponding to the second gaussian in the sech model
+        mask = (u>=_w1)&(u<=(1.-_w3))
+        dx = np.empty(np.sum(mask))
+        dy = np.empty(np.sum(mask))
+        # Generate and apply the 2D gaussian shifts corresponding to the second gaussian
+        self.gd2.generate(dx)
+        self.gd2.generate(dy)
+        photon_array.x[mask] += dx
+        photon_array.y[mask] += dy
+
+        # Selects appropriate fraction of photons corresponding to the third gaussian in the sech model 
+        mask = u>(1.-_w3)
+        dx = np.empty(np.sum(mask))
+        dy = np.empty(np.sum(mask))
+        # Generate and apply the 2D gaussian shifts corresponding to the second gaussian
+        self.gd3.generate(dx)
+        self.gd3.generate(dy)
+        photon_array.x[mask] += dx
+        photon_array.y[mask] += dy

+

+
+
+
+

+[docs]
+class ChargeDiffBuilder(PhotonOpBuilder):
+    """Build ChargeDiff photonOp
+    """
+

+[docs]
+    def buildPhotonOp(self, config, base, logger):
+        req, opt, single, takes_rng = get_cls_params(ChargeDiff)
+        kwargs, safe = GetAllParams(config, base, req, opt, single)
+        rng = GetRNG(config, base, logger, "Roman_stamp")
+        kwargs['rng'] = rng
+        return ChargeDiff(**kwargs)

+

+
+
+RegisterPhotonOpType('ChargeDiff', ChargeDiffBuilder())
+

+
+          

+          
+        

+      

+      
+      

+    

+    

+      ©2024, Rachel Mandelbaum, Axel Guinot, Federico Berlfein, Andy Park, Xiangchong Li, Michael Troxel, Tianqing Zhang.
+      
+      |
+      Powered by Sphinx 8.1.3
+      & Alabaster 1.0.0
+      
+    

+
+    
+
+    
+  
+
\ No newline at end of file
diff --git a/docs/_build/html/_modules/euclidlike_imsim/psf.html b/docs/_build/html/_modules/euclidlike_imsim/psf.html
new file mode 100644
index 0000000..361ca93
--- /dev/null
+++ b/docs/_build/html/_modules/euclidlike_imsim/psf.html
@@ -0,0 +1,304 @@
+
+
+
+  
+    
+    
+    euclidlike_imsim.psf — GalSim-Euclid-Like 0.0.1 documentation
+    
+    
+    
+    
+    
+    
+    
+    
+   
+  
+  
+
+  
+  
+
+  
+  
+
+    

+      

+        

+          
+
+          

+            
+  
Source code for euclidlike_imsim.psf
+import galsim
+import euclidlike
+import galsim.config
+from galsim.config import RegisterObjectType, RegisterInputType, OpticalPSF, InputLoader
+
+import euclidlike
+
+
+

+[docs]
+class EuclidlikePSF(object):
+    """Class building needed Euclidlike PSFs."""
+
+    def __init__(
+        self,
+        CCD=None,
+        WCS=None,
+        n_waves=None,
+        bpass=None,
+        extra_aberrations=None,
+        logger=None,
+    ):
+
+        logger = galsim.config.LoggerWrapper(logger)
+        # n_waves parameter is only used for treatment of bright objects. In here we use n_waves = 5
+        # to speed up computation of the ChromaticOpticalPSF used for bright objects. 
+        if n_waves == -1:
+            n_waves = 5
+
+        corners = [
+            galsim.PositionD(1, 1),
+            galsim.PositionD(1, euclidlike.n_pix_row),
+            galsim.PositionD(euclidlike.n_pix_col, 1),
+            galsim.PositionD(euclidlike.n_pix_col, euclidlike.n_pix_row),
+        ]
+        cc = galsim.PositionD(euclidlike.n_pix_col / 2, euclidlike.n_pix_row/ 2)
+        tags = ["ll", "lu", "ul", "uu"]
+        self.PSF = {}
+        pupil_bin = 8
+        self.PSF[pupil_bin] = {}
+        for tag, CCD_pos in tuple(zip(tags, corners)):
+            self.PSF[pupil_bin][tag] = self._psf_call(
+                CCD, bpass, CCD_pos, WCS, pupil_bin, n_waves, logger, extra_aberrations
+            )
+        for pupil_bin in [4, 2, "achromatic"]:
+            self.PSF[pupil_bin] = self._psf_call(
+                CCD, bpass, cc, WCS, pupil_bin, n_waves, logger, extra_aberrations
+            )
+
+    def _parse_pupil_bin(self, pupil_bin):
+        if pupil_bin == "achromatic":
+            return 8
+        else:
+            return pupil_bin
+
+    def _psf_call(
+        self, CCD, bpass, CCD_pos, WCS, pupil_bin, n_waves, logger, extra_aberrations
+    ):
+
+        if pupil_bin == 8:
+            psf = euclidlike.getPSF(
+                CCD,
+                bpass.name,
+                ccd_pos=CCD_pos,
+                wcs=WCS,
+                # pupil_bin=pupil_bin,
+                # n_waves=n_waves,
+                logger=logger,
+                # Don't set wavelength for this one.
+                # We want this to be chromatic for photon shooting.
+                # wavelength          = bpass.effective_wavelength,
+                # extra_aberrations=extra_aberrations,
+            )
+        else:
+            psf = euclidlike.getBrightPSF(
+                CCD,
+                bpass.name,
+                ccd_pos=CCD_pos,
+                wcs=WCS,
+                pupil_bin=self._parse_pupil_bin(pupil_bin),
+                n_waves=n_waves,
+                logger=logger,
+                # Note: setting wavelength makes it achromatic.
+                # We only use pupil_bin = 2,4 for FFT objects.
+                wavelength=bpass.effective_wavelength,
+            )
+
+            # psf = euclidlike.getPSF(
+            #     CCD,
+            #     bpass.name,
+            #     ccd_pos=CCD_pos,
+            #     wcs=WCS,
+            #     # pupil_bin=self._parse_pupil_bin(pupil_bin),
+            #     # n_waves=n_waves,
+            #     logger=logger,
+            #     # Note: setting wavelength makes it achromatic.
+            #     # We only use pupil_bin = 2,4 for FFT objects.
+            #     wavelength=bpass.effective_wavelength,
+            #     # extra_aberrations=extra_aberrations,
+            # )
+        if pupil_bin == 4:
+            return psf.withGSParams(maximum_fft_size=16384, folding_threshold=1e-3)
+        elif pupil_bin == 2:
+            return psf.withGSParams(maximum_fft_size=16384, folding_threshold=1e-4)
+        else:
+            return psf.withGSParams(maximum_fft_size=16384)
+
+

+[docs]
+    def getPSF(self, pupil_bin, pos):
+        """
+        Return a PSF to be convolved with sources.
+        PSF is sampled at 4 quadrants for each CCD. Returned PSF
+        corresponds to that of the quadrant of the CCD position.
+
+        @param [in] what pupil binning to request.
+        """
+        ## For now no interpolation is used
+        #wll = (euclidlike.n_pix_col - pos.x) * (euclidlike.n_pix_row - pos.y)
+        #wlu = (euclidlike.n_pix_col - pos.x) * (pos.y - 1)
+        #wul = (pos.x - 1) * (euclidlike.n_pix_row - pos.y)
+        #wuu = (pos.x - 1) * (pos.y - 1)
+        #return (
+        #    wll * psf["ll"] + wlu * psf["lu"] + wul * psf["ul"] + wuu * psf["uu"]
+        #) / ((euclidlike.n_pix_row - 1) * (euclidlike.n_pix_col - 1))
+
+
+        psf = self.PSF[pupil_bin]
+        if pupil_bin != 8:
+            return psf
+
+        quad_row = 'l'
+        quad_col = 'l'
+        if pos.y > euclidlike.n_pix_row/2:
+            quad_row = 'u'
+        if pos.x > euclidlike.n_pix_col/2:
+            quad_col = 'u'   
+        quad_pos = quad_col + quad_row
+        return psf[quad_pos]

+

+
+        
+
+
+
+

+[docs]
+class PSFLoader(InputLoader):
+    """PSF loader."""
+
+    def __init__(self):
+        # Override some defaults in the base init.
+        super().__init__(init_func=EuclidlikePSF, takes_logger=True, use_proxy=False)
+
+

+[docs]
+    def getKwargs(self, config, base, logger):
+        logger.debug("Get kwargs for PSF")
+
+        req = {}
+        opt = {
+            "n_waves": int,
+        }
+        ignore = ["extra_aberrations"]
+
+        # If CCD is in base, then don't require it in the config file.
+        # (Presumably because using Euclidlike image type, which sets it there for convenience.)
+        if "CCD" in base:
+            opt["CCD"] = int
+        else:
+            req["CCD"] = int
+
+        kwargs, safe = galsim.config.GetAllParams(
+            config, base, req=req, opt=opt, ignore=ignore
+        )
+
+        # If not given in kwargs, then it must have been in base, so this is ok.
+        if "CCD" not in kwargs:
+            kwargs["CCD"] = base["CCD"]
+
+        kwargs["extra_aberrations"] = galsim.config.ParseAberrations(
+            "extra_aberrations", config, base, "EuclidlikePSF"
+        )
+        kwargs["WCS"] = galsim.config.BuildWCS(
+            base["image"], "wcs", base, logger=logger
+        )
+        kwargs["bpass"] = galsim.config.BuildBandpass(
+            base["image"], "bandpass", base, logger
+        )[0]
+
+        logger.debug("kwargs = %s", kwargs)
+
+        return kwargs, False

+

+
+
+
+# Register this as a valid type
+RegisterInputType("euclidlike_psf", PSFLoader())
+# RegisterObjectType('euclidlike_psf', BuildEuclidlikePSF, input_type='euclidlikepsf_loader')
+

+
+          

+          
+        

+      

+      
+      

+    

+    

+      ©2024, Rachel Mandelbaum, Axel Guinot, Federico Berlfein, Andy Park, Xiangchong Li, Michael Troxel, Tianqing Zhang.
+      
+      |
+      Powered by Sphinx 8.1.3
+      & Alabaster 1.0.0
+      
+    

+
+    
+
+    
+  
+
\ No newline at end of file
diff --git a/docs/_build/html/_modules/euclidlike_imsim/skycat.html b/docs/_build/html/_modules/euclidlike_imsim/skycat.html
new file mode 100644
index 0000000..f31c627
--- /dev/null
+++ b/docs/_build/html/_modules/euclidlike_imsim/skycat.html
@@ -0,0 +1,631 @@
+
+
+
+  
+    
+    
+    euclidlike_imsim.skycat — GalSim-Euclid-Like 0.0.1 documentation
+    
+    
+    
+    
+    
+    
+    
+    
+   
+  
+  
+
+  
+  
+
+  
+  
+
+    

+      

+        

+          
+
+          

+            
+  
Source code for euclidlike_imsim.skycat
+"""
+Interface to obtain objects from skyCatalogs.
+"""
+
+import os
+import numpy as np
+import galsim
+from galsim.config import (
+    InputLoader,
+    RegisterInputType,
+    RegisterValueType,
+    RegisterObjectType,
+)
+
+import euclidlike
+
+
+

+[docs]
+class SkyCatalogInterface:
+    """Interface to skyCatalogs package."""
+
+    _trivial_sed = galsim.SED(
+        galsim.LookupTable([100, 2600], [1, 1], interpolant="linear"),
+        wave_type="nm",
+        flux_type="fphotons",
+    )
+
+    def __init__(
+        self,
+        file_name,
+        exptime,
+        wcs=None,
+        mjd=None,
+        bandpass=None,
+        xsize=None,
+        ysize=None,
+        obj_types=None,
+        edge_pix=100,
+        max_flux=None,
+        logger=None,
+    ):
+        """
+        Parameters
+        ----------
+        file_name : str
+            Name of skyCatalogs yaml config file.
+        wcs : galsim.WCS
+            WCS of the image to render.
+        mjd : float
+            MJD of the midpoint of the exposure.
+        exptime : float
+            Exposure time.
+        xsize : int
+            Size in pixels of CCD in x-direction.
+        ysize : int
+            Size in pixels of CCD in y-direction.
+        obj_types : list-like [None]
+            List or tuple of object types to render, e.g., ('star', 'galaxy').
+            If None, then consider all object types.
+        edge_pix : float [100]
+            Size in pixels of the buffer region around nominal image
+            to consider objects.
+        logger : logging.Logger [None]
+            Logger object.
+        """
+        self.file_name = file_name
+        self.wcs = wcs
+        self.mjd = mjd
+        self.exptime = exptime
+        self.bandpass = bandpass
+        if xsize is not None:
+            self.xsize = xsize
+        else:
+            self.xsize = euclidlike.n_pix_col
+        if ysize is not None:
+            self.ysize = ysize
+        else:
+            self.ysize = euclidlike.n_pix_row
+        self.obj_types = obj_types
+        self.edge_pix = edge_pix
+        self.logger = galsim.config.LoggerWrapper(logger)
+
+        if obj_types is not None:
+            self.logger.warning(f"Object types restricted to {obj_types}")
+        self.ccd_center = wcs.toWorld(
+            galsim.PositionD(self.xsize / 2.0, self.ysize / 2.0)
+        )
+        self._objects = None
+
+    @property
+    def objects(self):
+        from skycatalogs import skyCatalogs
+
+        if self._objects is None:
+
+            # Select objects from polygonal region bounded by CCD edges
+            corners = (
+                (-self.edge_pix, -self.edge_pix),
+                (self.xsize + self.edge_pix, -self.edge_pix),
+                (self.xsize + self.edge_pix, self.ysize + self.edge_pix),
+                (-self.edge_pix, self.ysize + self.edge_pix),
+            )
+            vertices = []
+            for x, y in corners:
+                sky_coord = self.wcs.toWorld(galsim.PositionD(x, y))
+                vertices.append(
+                    (sky_coord.ra / galsim.degrees, sky_coord.dec / galsim.degrees)
+                )
+            region = skyCatalogs.PolygonalRegion(vertices)
+            sky_cat = skyCatalogs.open_catalog(self.file_name)
+            self._objects = sky_cat.get_objects_by_region(
+                region, obj_type_set=self.obj_types, mjd=self.mjd
+            )
+            if not self._objects:
+                self.logger.warning("No objects found on image.")
+            else:
+                self._build_dtype_dict()
+        return self._objects
+
+    def _build_dtype_dict(self):
+        self._dtype_dict = {}
+        obj_types = []
+        for coll in self._objects.get_collections():
+            objects_type = coll._object_type_unique
+            if objects_type in obj_types:
+                continue
+            col_names = list(coll.native_columns)
+            for col_name in col_names:
+                try:
+                    # Some columns cannot be read in snana
+                    np_type = coll.get_native_attribute(col_name).dtype.type()
+                except Exception as e:
+                    self.logger.warning(
+                        f"The column {col_name} could not be read from skyCatalog."
+                    )
+                    continue
+                if np_type is None:
+                    py_type = str
+                else:
+                    py_type = type(np_type.astype(object))
+                self._dtype_dict[col_name] = py_type
+
+

+[docs]
+    def get_ccd_center(self):
+        """
+        Return the CCD center.
+        """
+        return self.ccd_center

+
+
+

+[docs]
+    def getNObjects(self):
+        """
+        Return the number of GSObjects to render
+        """
+        return len(self.objects)

+
+
+

+[docs]
+    def getApproxNObjects(self):
+        """
+        Return the approximate number of GSObjects to render, as set in
+        the class initializer.
+        """
+        return self.getNObjects()

+
+
+

+[docs]
+    def getWorldPos(self, index):
+        """
+        Return the sky coordinates of the skyCatalog object
+        corresponding to the specified index.
+
+        Parameters
+        ----------
+        index : int
+            Index of the (object_index, subcomponent) combination.
+
+        Returns
+        -------
+        galsim.CelestialCoord
+        """
+        skycat_obj = self.objects[index]
+        ra, dec = skycat_obj.ra, skycat_obj.dec
+        return galsim.CelestialCoord(ra * galsim.degrees, dec * galsim.degrees)

+
+
+

+[docs]
+    def getFlux(self, index, filter=None, mjd=None, exptime=None):
+        """
+        Return the flux associated to an object.
+
+        Parameters
+        ----------
+        index : int
+            Index of the object in the self.objects catalog.
+        filter : str, optional
+            Name of the filter for which the flux is computed. If None, use the
+            filter provided during initialization. [Default: None]
+        mjd : float, optional
+            Date of the observation in MJD format. If None, use the
+            mjd provided during initialization. [Default: None]
+        exptime : int or float, optional
+            Exposure time of the observation. If None, use the
+            exptime provided during initialization. [Default: None]
+
+        Returns
+        -------
+        flux
+            Computer flux at the given date for the requested exposure time and
+            filter.
+        """
+
+        if filter is None:
+            filter = self.bandpass.name
+        if mjd is None:
+            mjd = self.mjd
+        if exptime is None:
+            exptime = self.exptime
+
+        skycat_obj = self.objects[index]
+        # We cache the SEDs for potential later use
+        self._seds = skycat_obj.get_observer_sed_components()
+        for i, sed in enumerate(self._seds.values()):
+            if i == 0:
+                sed_sum = sed
+            else:
+                sed_sum += sed
+        raw_flux = skycat_obj.get_euclid_flux(
+            filter,
+            sed_sum,
+            mjd=mjd,
+            cache=False
+        )
+        if hasattr(skycat_obj, "get_wl_params"):
+            _, _, mu = skycat_obj.get_wl_params()
+        else:
+            mu = 1.
+        flux = raw_flux * mu * exptime * euclidlike.collecting_area
+
+        return flux

+
+
+

+[docs]
+    def getValue(self, index, field):
+        """
+        Return a skyCatalog value for the an object.
+
+        Parameters
+        ----------
+        index : int
+            Index of the object in the self.objects catalog.
+        field : str
+            Name of the field for which you want the value.
+
+        Returns
+        -------
+        int or float or str or None
+            The value associated to the field or None if the field do not exist.
+        """
+
+        skycat_obj = self.objects[index]
+
+        if field not in self._dtype_dict:
+            # We cannot raise an error because one could have a field for snana
+            # in the config and we don't want to crash because there are no SN
+            # in this particular image. We then default to False which might not
+            # be the right type for the required column but we have no way of knowing
+            # the correct type if the column do not exist.
+            self.logger.warning(f"The field {field} was not found in skyCatalog.")
+            return None
+        elif field not in skycat_obj.native_columns:
+            if self._dtype_dict[field] is int:
+                # There are no "special value" for integer so we default to
+                # hopefully something completely off
+                return -9999
+            elif self._dtype_dict[field] is float:
+                return np.nan
+            elif self._dtype_dict[field] is str:
+                return None
+        else:
+            return skycat_obj.get_native_attribute(field)

+
+
+

+[docs]
+    def getObj(self, index, gsparams=None, rng=None, exptime=30):
+        """
+        Return the galsim object for the skyCatalog object
+        corresponding to the specified index.  If the skyCatalog
+        object is a galaxy, the returned galsim object will be
+        a galsim.Sum.
+
+        Parameters
+        ----------
+        index : int
+            Index of the object in the self.objects catalog.
+
+        Returns
+        -------
+        galsim.GSObject
+        """
+        if not self.objects:
+            raise RuntimeError("Trying to get an object from an empty sky catalog")
+
+        faint = False
+        skycat_obj = self.objects[index]
+        gsobjs = skycat_obj.get_gsobject_components(gsparams)
+
+        # Compute the flux or get the cached value.
+        flux = self.getFlux(index)
+        if np.isnan(flux):
+            return None
+
+        # Set up simple SED if too faint
+        if flux < 40:
+            faint = True
+        if not faint:
+            seds = skycat_obj.get_observer_sed_components(mjd=self.mjd)
+
+        gs_obj_list = []
+        for component in gsobjs:
+            if faint:
+                gsobjs[component] = gsobjs[component].evaluateAtWavelength(
+                    self.bandpass
+                )
+                gs_obj_list.append(
+                    gsobjs[component]
+                    * self._trivial_sed
+                    * self.exptime
+                    * euclidlike.collecting_area
+                )
+            else:
+                if component in seds:
+                    gs_obj_list.append(
+                        gsobjs[component]
+                        * seds[component]
+                        * self.exptime
+                        * euclidlike.collecting_area
+                    )
+
+        if not gs_obj_list:
+            return None
+
+        if len(gs_obj_list) == 1:
+            gs_object = gs_obj_list[0]
+        else:
+            gs_object = galsim.Add(gs_obj_list)
+
+        # Give the object the right flux
+        gs_object.flux = flux
+        gs_object.withFlux(gs_object.flux, self.bandpass)
+
+        # Get the object type
+        if (skycat_obj.object_type == "diffsky_galaxy") | (
+            skycat_obj.object_type == "galaxy"
+        ):
+            gs_object.object_type = "galaxy"
+        if skycat_obj.object_type == "star":
+            gs_object.object_type = "star"
+        if skycat_obj.object_type == "snana":
+            gs_object.object_type = "transient"
+
+        return gs_object

+

+
+
+
+

+[docs]
+class SkyCatalogLoader(InputLoader):
+    """
+    Class to load SkyCatalogInterface object.
+    """
+
+

+[docs]
+    def getKwargs(self, config, base, logger):
+        req = {"file_name": str, "exptime": float}
+        opt = {
+            "edge_pix": float,
+            "obj_types": list,
+            "mjd": float,
+        }
+        kwargs, safe = galsim.config.GetAllParams(config, base, req=req, opt=opt)
+        wcs = galsim.config.BuildWCS(base["image"], "wcs", base, logger=logger)
+        kwargs["wcs"] = wcs
+        kwargs["logger"] = logger
+
+        if "bandpass" not in config:
+            base["bandpass"] = galsim.config.BuildBandpass(
+                base["image"], "bandpass", base, logger=logger
+            )[0]
+
+        kwargs["bandpass"] = base["bandpass"]
+        # Sky catalog object lists are created per CCD, so they are
+        # not safe to reuse.
+        safe = False
+        return kwargs, safe

+

+
+
+
+

+[docs]
+def SkyCatObj(config, base, ignore, gsparams, logger):
+    """
+    Build an object according to info in the sky catalog.
+    """
+    skycat = galsim.config.GetInputObj("sky_catalog", config, base, "SkyCatObj")
+
+    # Ensure that this sky catalog matches the CCD being simulated by
+    # comparing center locations on the sky.
+    world_center = base["world_center"]
+    ccd_center = skycat.get_ccd_center()
+    sep = ccd_center.distanceTo(base["world_center"]) / galsim.arcsec
+    # Centers must agree to within at least 1 arcsec:
+    if sep > 1.0:
+        message = (
+            "skyCatalogs selection and CCD center do not agree: \n"
+            "skycat.ccd_center: "
+            f"{ccd_center.ra/galsim.degrees:.5f}, "
+            f"{ccd_center.dec/galsim.degrees:.5f}\n"
+            "world_center: "
+            f"{world_center.ra/galsim.degrees:.5f}, "
+            f"{world_center.dec/galsim.degrees:.5f} \n"
+            f"Separation: {sep:.2e} arcsec"
+        )
+        raise RuntimeError(message)
+
+    # Setup the indexing sequence if it hasn't been specified.  The
+    # normal thing with a catalog is to just use each object in order,
+    # so we don't require the user to specify that by hand.  We can do
+    # it for them.
+    galsim.config.SetDefaultIndex(config, skycat.getNObjects())
+
+    req = {"index": int}
+    opt = {"num": int}
+    kwargs, safe = galsim.config.GetAllParams(config, base, req=req, opt=opt)
+    index = kwargs["index"]
+
+    rng = galsim.config.GetRNG(config, base, logger, "SkyCatObj")
+
+    obj = skycat.getObj(index, gsparams=gsparams, rng=rng)
+    base["object_id"] = skycat.objects[index].id
+
+    return obj, safe

+
+
+
+

+[docs]
+def SkyCatWorldPos(config, base, value_type):
+    """Return a value from the object part of the skyCatalog"""
+    skycat = galsim.config.GetInputObj("sky_catalog", config, base, "SkyCatWorldPos")
+
+    # Setup the indexing sequence if it hasn't been specified.  The
+    # normal thing with a catalog is to just use each object in order,
+    # so we don't require the user to specify that by hand.  We can do
+    # it for them.
+    galsim.config.SetDefaultIndex(config, skycat.getNObjects())
+
+    req = {"index": int}
+    opt = {"num": int}
+    kwargs, safe = galsim.config.GetAllParams(config, base, req=req, opt=opt)
+    index = kwargs["index"]
+
+    pos = skycat.getWorldPos(index)
+    return pos, safe

+
+
+
+

+[docs]
+def SkyCatValue(config, base, value_type):
+    """Return a value from the object part of the skyCatalog
+    """
+
+    skycat = galsim.config.GetInputObj("sky_catalog", config, base, "SkyCatValue")
+
+    # Setup the indexing sequence if it hasn't been specified.  The
+    # normal thing with a catalog is to just use each object in order,
+    # so we don't require the user to specify that by hand.  We can do
+    # it for them.
+    galsim.config.SetDefaultIndex(config, skycat.getNObjects())
+
+    req = {"field": str, "index": int}
+    opt = {"obs_kind": str}
+    params, safe = galsim.config.GetAllParams(config, base, req=req, opt=opt)
+    field = params["field"]
+    index = params["index"]
+    obs_kind = params.get("obs_kind", None)
+
+    if field == "flux":
+        if obs_kind is None:
+            val = skycat.getFlux(index)
+        else:
+            pointing = galsim.config.GetInputObj("obseq_data", config, base, "OpSeqDataLoader")
+            filter = pointing.get("filter", obs_kind=obs_kind)
+            exptime = pointing.get("exptime", obs_kind=obs_kind)
+            mjd = pointing.get("mjd", obs_kind=obs_kind)
+            val = skycat.getFlux(index, filter=filter, exptime=exptime, mjd=mjd)
+    else:
+        val = skycat.getValue(index, field)
+
+    return val, safe

+
+
+
+
+RegisterInputType("sky_catalog", SkyCatalogLoader(SkyCatalogInterface, has_nobj=True))
+RegisterObjectType("SkyCatObj", SkyCatObj, input_type="sky_catalog")
+RegisterValueType(
+    "SkyCatWorldPos", SkyCatWorldPos, [galsim.CelestialCoord], input_type="sky_catalog"
+)
+
+# Here we have to provide None as a type otherwise Galsim complains but I don't know why..
+RegisterValueType(
+    "SkyCatValue", SkyCatValue, [float, int, str, None]  # , input_type="sky_catalog"
+)
+

+
+          

+          
+        

+      

+      
+      

+    

+    

+      ©2024, Rachel Mandelbaum, Axel Guinot, Federico Berlfein, Andy Park, Xiangchong Li, Michael Troxel, Tianqing Zhang.
+      
+      |
+      Powered by Sphinx 8.1.3
+      & Alabaster 1.0.0
+      
+    

+
+    
+
+    
+  
+
\ No newline at end of file
diff --git a/docs/_build/html/_modules/euclidlike_imsim/stamp.html b/docs/_build/html/_modules/euclidlike_imsim/stamp.html
new file mode 100644
index 0000000..00c4a59
--- /dev/null
+++ b/docs/_build/html/_modules/euclidlike_imsim/stamp.html
@@ -0,0 +1,454 @@
+
+
+
+  
+    
+    
+    euclidlike_imsim.stamp — GalSim-Euclid-Like 0.0.1 documentation
+    
+    
+    
+    
+    
+    
+    
+    
+   
+  
+  
+
+  
+  
+
+  
+  
+
+    

+      

+        

+          
+
+          

+            
+  
Source code for euclidlike_imsim.stamp
+import numpy as np
+import galsim
+import euclidlike
+import galsim.config
+from galsim.config import RegisterStampType, StampBuilder
+# import os, psutil
+# process = psutil.Process()
+
+# Parameter below determines the flux at which we switch from using Euclid-like PSF to the bright star PSF
+# This is done to avoid visual artifacts from using the Euclid-like PSF for very bright objects.
+# Tests to determine this value can be found here: https://github.com/GalSim-developers/GalSim-Euclid-Like/issues/46
+psf_switch_limit = 8e5
+
+

+[docs]
+class Euclidlike_stamp(StampBuilder):
+    """This performs the tasks necessary for building the stamp for a single object.
+
+    It uses the regular Basic functions for most things.
+    It specializes the quickSkip, buildProfile, and draw methods.
+    """
+    _trivial_sed = galsim.SED(
+        galsim.LookupTable(
+            [100, 2600],
+            [1, 1],
+            interpolant='linear'
+        ),
+        wave_type='nm', flux_type='fphotons'
+    )
+
+

+[docs]
+    def setup(self, config, base, xsize, ysize, ignore, logger):
+        """
+        Do the initialization and setup for building a postage stamp.
+
+        In the base class, we check for and parse the appropriate size and position values in
+        config (aka base['stamp'] or base['image'].
+
+        Values given in base['stamp'] take precedence if these are given in both places (which
+        would be confusing, so probably shouldn't do that, but there might be a use case where it
+        would make sense).
+
+        Parameters:
+            config:     The configuration dict for the stamp field.
+            base:       The base configuration dict.
+            xsize:      The xsize of the image to build (if known).
+            ysize:      The ysize of the image to build (if known).
+            ignore:     A list of parameters that are allowed to be in config that we can
+                        ignore here. i.e. it won't be an error if these parameters are present.
+            logger:     A logger object to log progress.
+
+        Returns:
+            xsize, ysize, image_pos, world_pos
+        """
+        # print('stamp setup',process.memory_info().rss)
+
+        gal = galsim.config.BuildGSObject(base, 'gal', logger=logger)[0]
+        if gal is None:
+            raise galsim.config.SkipThisObject('gal is None (invalid parameters)')
+        base['object_type'] = gal.object_type
+        bandpass = base['bandpass']
+        if not hasattr(gal, 'flux'):
+            # In this case, the object flux has not been precomputed
+            # or cached by the skyCatalogs code.
+            gal.flux = gal.calculateFlux(bandpass)
+        self.flux = gal.flux
+        # Cap (star) flux at 30M photons to avoid gross artifacts when trying to draw the Euclid PSF in finite time and memory
+        flux_cap = 3e7
+        if self.flux > flux_cap:
+            if (hasattr(gal, 'original') and hasattr(gal.original, 'original') and isinstance(gal.original.original, galsim.DeltaFunction)) or (isinstance(gal, galsim.DeltaFunction)):
+                gal = gal.withFlux(flux_cap, bandpass)
+                self.flux = flux_cap
+                gal.flux = flux_cap
+        base['flux'] = gal.flux
+        base['mag'] = -2.5 * np.log10(gal.flux) + bandpass.zeropoint
+        # print('stamp setup2',process.memory_info().rss)
+
+        # Compute or retrieve the realized flux.
+        self.rng = galsim.config.GetRNG(config, base, logger, "Euclidlike_stamp")
+        self.realized_flux = galsim.PoissonDeviate(self.rng, mean=self.flux)()
+        base['realized_flux'] = self.realized_flux
+
+        # Check if the realized flux is 0.
+        if self.realized_flux == 0:
+            # If so, we'll skip everything after this.
+            # The mechanism within GalSim to do this is to raise a special SkipThisObject class.
+            raise galsim.config.SkipThisObject('realized flux=0')
+
+        # Otherwise figure out the stamp size
+        if self.flux < 10:
+            # For really faint things, don't try too hard.  Just use 32x32.
+            image_size = 32
+            self.pupil_bin = 'achromatic'
+
+        else:
+            gal_achrom = gal.evaluateAtWavelength(bandpass.effective_wavelength)
+            if (hasattr(gal_achrom, 'original') and isinstance(gal_achrom.original, galsim.DeltaFunction)):
+                # For bright stars, set the following stamp size limits
+                if self.flux < psf_switch_limit:
+                    image_size = 500
+                    self.pupil_bin = 8
+                elif self.flux < 6e6:
+                    image_size = 1000
+                    self.pupil_bin = 4
+                else:
+                    image_size = 1600
+                    self.pupil_bin = 2
+            else:
+                self.pupil_bin = 8
+                # # Get storead achromatic PSF
+                # psf = galsim.config.BuildGSObject(base, 'psf', logger=logger)[0]['achromatic']
+                # obj = galsim.Convolve(gal_achrom, psf).withFlux(self.flux)
+                obj = gal_achrom.withGSParams(galsim.GSParams(stepk_minimum_hlr=20))
+                image_size = obj.getGoodImageSize(euclidlike.pixel_scale)
+
+        # print('stamp setup3',process.memory_info().rss)
+        base['pupil_bin'] = self.pupil_bin
+        logger.info('Object flux is %d', self.flux)
+        logger.info('Object %d will use stamp size = %s', base.get('obj_num', 0), image_size)
+
+        # Determine where this object is going to go:
+        # This is the same as what the base StampBuilder does:
+        if 'image_pos' in config:
+            image_pos = galsim.config.ParseValue(config, 'image_pos', base, galsim.PositionD)[0]
+        else:
+            image_pos = None
+
+        if 'world_pos' in config:
+            world_pos = galsim.config.ParseWorldPos(config, 'world_pos', base, logger)
+        else:
+            world_pos = None
+
+        return image_size, image_size, image_pos, world_pos

+
+
+

+[docs]
+    def buildPSF(self, config, base, gsparams, logger):
+        """Build the PSF object.
+
+        For the Basic stamp type, this builds a PSF from the base['psf'] dict, if present,
+        else returns None.
+
+        Parameters:
+            config:     The configuration dict for the stamp field.
+            base:       The base configuration dict.
+            gsparams:   A dict of kwargs to use for a GSParams.  More may be added to this
+                        list by the galaxy object.
+            logger:     A logger object to log progress.
+
+        Returns:
+            the PSF
+        """
+        if base.get('psf', {}).get('type', 'euclidlike_psf') != 'euclidlike_psf':
+            return galsim.config.BuildGSObject(base, 'psf', gsparams=gsparams, logger=logger)[0]
+
+        euclidlike_psf = galsim.config.GetInputObj('euclidlike_psf', config, base, 'buildPSF')
+        psf = euclidlike_psf.getPSF(self.pupil_bin, base['image_pos'])
+        return psf

+
+
+

+[docs]
+    def getDrawMethod(self, config, base, logger):
+        """Determine the draw method to use.
+
+        @param config       The configuration dict for the stamp field.
+        @param base         The base configuration dict.
+        @param logger       A logger object to log progress.
+
+        @returns method
+        """
+        method = galsim.config.ParseValue(config,'draw_method',base,str)[0]
+        if method not in galsim.config.valid_draw_methods:
+            raise galsim.GalSimConfigValueError("Invalid draw_method.", method,
+                                                galsim.config.valid_draw_methods)
+        if method  == 'auto':
+            if self.pupil_bin in [4,2]:
+                logger.info('Auto -> Use FFT drawing for object %d.',base['obj_num'])
+                return 'fft'
+            else:
+                logger.info('Auto -> Use photon shooting for object %d.',base['obj_num'])
+                return 'phot'
+        else:
+            # If user sets something specific for the method, rather than auto,
+            # then respect their wishes.
+            logger.info('Use specified method=%s for object %d.',method,base['obj_num'])
+            return method

+
+
+

+[docs]
+    @classmethod
+    def fix_seds(cls, prof, bandpass):
+        # If any SEDs are not currently using a LookupTable for the function or if they are
+        # using spline interpolation, then the codepath is quite slow.
+        # Better to fix them before doing WavelengthSampler.
+
+        if (isinstance(prof, galsim.SimpleChromaticTransformation) and
+            (not isinstance(prof._flux_ratio._spec, galsim.LookupTable)
+             or prof._flux_ratio._spec.interpolant != 'linear')):
+            original = prof._original
+            sed = prof._flux_ratio
+            wave_list, _, _ = galsim.utilities.combine_wave_list(sed, bandpass)
+            f = np.broadcast_to(sed(wave_list), wave_list.shape)
+            new_spec = galsim.LookupTable(wave_list, f, interpolant='linear')
+            new_sed = galsim.SED(
+                new_spec,
+                'nm',
+                'fphotons' if sed.spectral else '1'
+            )
+            prof._flux_ratio = new_sed
+
+        # Also recurse onto any components.
+        if isinstance(prof, galsim.ChromaticObject):
+            if hasattr(prof, 'obj_list'):
+                for obj in prof.obj_list:
+                    cls.fix_seds(obj, bandpass)
+            if hasattr(prof, 'original'):
+                cls.fix_seds(prof.original, bandpass)

+
+
+

+[docs]
+    def draw(self, prof, image, method, offset, config, base, logger):
+        """Draw the profile on the postage stamp image.
+
+        Parameters:
+            prof:       The profile to draw.
+            image:      The image onto which to draw the profile (which may be None).
+            method:     The method to use in drawImage.
+            offset:     The offset to apply when drawing.
+            config:     The configuration dict for the stamp field.
+            base:       The base configuration dict.
+            logger:     A logger object to log progress.
+
+        Returns:
+            the resulting image
+        """
+        if prof is None:
+            # If was decide to do any rejection steps, this could be set to None, in which case,
+            # don't draw anything.
+            return image
+
+        # Prof is normally a convolution here with obj_list being [gal, psf1, psf2,...]
+        # for some number of component PSFs.
+        # print('stamp draw',process.memory_info().rss)
+
+        gal, *psfs = prof.obj_list if hasattr(prof, 'obj_list') else [prof]
+
+        faint = self.flux < 40
+        bandpass = base['bandpass']
+        if faint:
+            logger.info("Flux = %.0f  Using trivial sed", self.flux)
+        else:
+            self.fix_seds(gal, bandpass)
+
+        image.wcs = base['wcs']
+
+        # Set limit on the size of photons batches to consider when
+        # calling gsobject.drawImage.
+        maxN = int(1e6)
+        if 'maxN' in config:
+            maxN = galsim.config.ParseValue(config, 'maxN', base, int)[0]
+        # print('stamp draw2',process.memory_info().rss)
+
+        if method == 'fft':
+            fft_image = image.copy()
+            fft_offset = offset
+            kwargs = dict(
+                method='fft',
+                offset=fft_offset,
+                image=fft_image,
+            )
+            if not faint and config.get('fft_photon_ops'):
+                kwargs.update({
+                    "photon_ops": galsim.config.BuildPhotonOps(config, 'fft_photon_ops', base, logger),
+                    "maxN": maxN,
+                    "rng": self.rng,
+                    "n_subsample": 1,
+                })
+
+            # Go back to a combined convolution for fft drawing.
+            gal = gal.withFlux(self.flux, bandpass)
+            prof = galsim.Convolve([gal] + psfs)
+            try:
+                prof.drawImage(bandpass, **kwargs)
+            except galsim.errors.GalSimFFTSizeError as e:
+                # I think this shouldn't happen with the updates I made to how the image size
+                # is calculated, even for extremely bright things.  So it should be ok to
+                # just report what happened, give some extra information to diagonose the problem
+                # and raise the error.
+                logger.error('Caught error trying to draw using FFT:')
+                logger.error('%s', e)
+                logger.error('You may need to add a gsparams field with maximum_fft_size to')
+                logger.error('either the psf or gal field to allow larger FFTs.')
+                logger.info('prof = %r', prof)
+                logger.info('fft_image = %s', fft_image)
+                logger.info('offset = %r', offset)
+                logger.info('wcs = %r', image.wcs)
+                raise
+            # Some pixels can end up negative from FFT numerics.  Just set them to 0.
+            fft_image.array[fft_image.array < 0] = 0.
+            fft_image.addNoise(galsim.PoissonNoise(rng=self.rng))
+            # In case we had to make a bigger image, just copy the part we need.
+            image += fft_image[image.bounds]
+
+        else:
+            # We already calculated realized_flux above.  Use that now and tell GalSim not
+            # recalculate the Poisson realization of the flux.
+            gal = gal.withFlux(self.realized_flux, bandpass)
+            # print('stamp draw3b ',process.memory_info().rss)
+
+            if not faint and 'photon_ops' in config:
+                photon_ops = galsim.config.BuildPhotonOps(config, 'photon_ops', base, logger)
+            else:
+                photon_ops = []
+
+            # Put the psfs at the start of the photon_ops.
+            # Probably a little better to put them a bit later than the start in some cases
+            # (e.g. after TimeSampler, PupilAnnulusSampler), but leave that as a todo for now.
+            photon_ops = psfs + photon_ops
+
+            # prof = galsim.Convolve([gal] + psfs)
+
+            # print('-------- gal ----------',gal)
+            # print('-------- psf ----------',psfs)
+
+            # print('stamp draw3a',process.memory_info().rss)
+            gal.drawImage(bandpass,
+                          method='phot',
+                          offset=offset,
+                          rng=self.rng,
+                          maxN=maxN,
+                          n_photons=self.realized_flux,
+                          image=image,
+                          photon_ops=photon_ops,
+                          sensor=None,
+                          add_to_image=True,
+                          poisson_flux=False)
+        # print('stamp draw3',process.memory_info().rss)
+
+        return image

+

+
+
+
+# Register this as a valid type
+RegisterStampType('Euclidlike_stamp', Euclidlike_stamp())
+

+
+          

+          
+        

+      

+      
+      

+    

+    

+      ©2024, Rachel Mandelbaum, Axel Guinot, Federico Berlfein, Andy Park, Xiangchong Li, Michael Troxel, Tianqing Zhang.
+      
+      |
+      Powered by Sphinx 8.1.3
+      & Alabaster 1.0.0
+      
+    

+
+    
+
+    
+  
+
\ No newline at end of file
diff --git a/docs/_build/html/_modules/euclidlike_imsim/utils.html b/docs/_build/html/_modules/euclidlike_imsim/utils.html
new file mode 100644
index 0000000..dfadbec
--- /dev/null
+++ b/docs/_build/html/_modules/euclidlike_imsim/utils.html
@@ -0,0 +1,250 @@
+
+
+
+  
+    
+    
+    euclidlike_imsim.utils — GalSim-Euclid-Like 0.0.1 documentation
+    
+    
+    
+    
+    
+    
+    
+    
+   
+  
+  
+
+  
+  
+
+  
+  
+
+    

+      

+        

+          
+
+          

+            
+  
Source code for euclidlike_imsim.utils
+import numpy as np
+import galsim
+import galsim.config
+import galsim.roman as roman
+
+

+[docs]
+class roman_utils(object):
+    """
+    Class to contain a variety of helper routines to work with the simulation data.
+    """
+    def __init__(self, config_file,visit=None,sca=None,image_name=None,setup_skycat=False):
+        """
+        Setup information about a simulated Roman image.
+        Parameters:
+            config_file: the GalSim config file that produced the simulation
+            visit: the visit (observation sequence) number of the pointing 
+            sca: the SCA number
+            image_name: the filename of the image (can be used instead of visit, sca)
+            setup_skycat: setup the skycatalog information to have access to
+        """
+        config = galsim.config.ReadConfig(config_file)[0]
+
+        self.visit,self.sca = self.check_input(visit,sca,image_name)
+
+        if not setup_skycat:
+            del config['input']['sky_catalog']
+        config['input']['obseq_data']['visit'] = self.visit
+        config['image']['SCA'] = self.sca
+        galsim.config.ProcessInput(config)
+        if setup_skycat:
+            self.skycat = galsim.config.GetInputObj('sky_catalog',config['input']['sky_catalog'],config,'sky_catalog')
+        self.PSF        = galsim.config.GetInputObj('roman_psf',config['input']['roman_psf'],config,'roman_psf')
+        self.wcs        = galsim.config.BuildWCS(config['image'], 'wcs', config)
+        self.bpass      = galsim.config.BuildBandpass(config['image'], 'bandpass', config, None)[0]
+        self.photon_ops = galsim.config.BuildPhotonOps(config['stamp'], 'photon_ops', config, None)
+        self.rng        = galsim.config.GetRNG(config, config['image'], None, "psf_image")
+
+

+[docs]
+    def check_input(self,visit,sca,image_name):
+        if image_name is not None:
+            print('Inferring visit and sca from image_name.')
+            start = 21
+            end = -5
+            if 'simple_model' in image_name:
+                start = 28
+            if 'gz' in image_name:
+                end = -8
+            tmp = np.array(image_name[start:end].split('_')).astype(int)
+            return tmp[0],tmp[1]
+        if (visit is None) | (sca is None):
+            raise ValueError('Insufficient information to construct visit info - all inputs are None.')
+        return visit,sca

+
+
+

+[docs]
+    def getPSF(self,x=None,y=None,pupil_bin=8):
+        """
+        Return Roman PSF for some image position.
+        Parameters:
+            x: x-position in SCA
+            y: y-position in SCA
+            pupil_bin: pupil image binning factor
+        Returns:
+            the chromatic GalSim PSF model object (does not include additional effects like charge diffusion!)
+        """
+        if pupil_bin!=8:
+            if (x is not None)|(y is not None):
+                raise ValueError('x,y position for pupil_bin values other than 8 not supported. Using SCA center.')
+            return self.PSF.getPSF(pupil_bin,galsim.PositionD(roman.n_pix/2,roman.n_pix/2))
+        if (x is None) | (y is None):
+            return self.PSF.getPSF(8,galsim.PositionD(roman.n_pix/2,roman.n_pix/2))
+        return self.PSF.getPSF(8,galsim.PositionD(x,y))

+
+
+

+[docs]
+    def getWCS(self):
+        """
+        Return Roman WCS for image
+        """
+        return self.wcs

+
+
+

+[docs]
+    def getLocalWCS(self,x,y):
+        """
+        Return Roman WCS for image
+        """
+        return self.wcs.local(galsim.PositionD(x,y))

+
+
+

+[docs]
+    def getBandpass(self):
+        """
+        Return Roman bandpass for image
+        """
+        return self.bpass

+
+
+

+[docs]
+    def getPSF_Image(self,stamp_size,x=None,y=None,pupil_bin=8,sed=None,
+                        oversampling_factor=1,include_photonOps=False,n_phot=1e6):
+        """
+        Return a Roman PSF image for some image position
+        Parameters:
+            stamp_size: size of output PSF model stamp in native roman pixel_scale (oversampling_factor=1)
+            x: x-position in SCA
+            y: y-position in SCA
+            pupil_bin: pupil image binning factor
+            sed: SED to be used to draw the PSF - default is a flat SED.
+            oversampling_factor: factor by which to oversample native roman pixel_scale
+            include_photonOps: include additional contributions from other photon operators in effective psf image
+        Returns:
+            the PSF GalSim image object (use image.array to get a numpy array representation)
+        """
+        if sed is None:
+            sed = galsim.SED(galsim.LookupTable([100, 2600], [1,1], interpolant='linear'),
+                              wave_type='nm', flux_type='fphotons')
+        point = galsim.DeltaFunction()*sed
+        point = point.withFlux(1,self.bpass)
+        local_wcs = self.getLocalWCS(x,y)
+        wcs = galsim.JacobianWCS(dudx=local_wcs.dudx/oversampling_factor,
+                                 dudy=local_wcs.dudy/oversampling_factor,
+                                 dvdx=local_wcs.dvdx/oversampling_factor,
+                                 dvdy=local_wcs.dvdy/oversampling_factor)
+        stamp = galsim.Image(stamp_size*oversampling_factor,stamp_size*oversampling_factor,wcs=wcs)
+        if not include_photonOps:
+            psf = galsim.Convolve(point, self.getPSF(x,y,pupil_bin))
+            return psf.drawImage(self.bpass,image=stamp,wcs=wcs,method='no_pixel')
+        photon_ops = [self.getPSF(x,y,pupil_bin)] + self.photon_ops
+        return point.drawImage(self.bpass,
+                                method='phot',
+                                rng=self.rng,
+                                maxN=1e6,
+                                n_photons=1e6,
+                                image=stamp,
+                                photon_ops=photon_ops,
+                                poisson_flux=False)

+

+
+

+
+          

+          
+        

+      

+      
+      

+    

+    

+      ©2024, Rachel Mandelbaum, Axel Guinot, Federico Berlfein, Andy Park, Xiangchong Li, Michael Troxel, Tianqing Zhang.
+      
+      |
+      Powered by Sphinx 8.1.3
+      & Alabaster 1.0.0
+      
+    

+
+    
+
+    
+  
+
\ No newline at end of file
diff --git a/docs/_build/html/_modules/euclidlike_imsim/wcs.html b/docs/_build/html/_modules/euclidlike_imsim/wcs.html
new file mode 100644
index 0000000..9c8bdad
--- /dev/null
+++ b/docs/_build/html/_modules/euclidlike_imsim/wcs.html
@@ -0,0 +1,169 @@
+
+
+
+  
+    
+    
+    euclidlike_imsim.wcs — GalSim-Euclid-Like 0.0.1 documentation
+    
+    
+    
+    
+    
+    
+    
+    
+   
+  
+  
+
+  
+  
+
+  
+  
+
+    

+      

+        

+          
+
+          

+            
+  
Source code for euclidlike_imsim.wcs
+from astropy.time import Time
+import galsim
+import euclidlike
+from galsim.config import WCSBuilder, RegisterWCSType
+from galsim.angle import Angle
+from galsim.celestial import CelestialCoord
+
+
+

+[docs]
+class EuclidlikeWCS(WCSBuilder):
+
+

+[docs]
+    def buildWCS(self, config, base, logger):
+
+        req = {
+            "CCD": int,
+            "ra": Angle,
+            "dec": Angle,
+            "pa": Angle,
+            "mjd": float,
+        }
+        opt = {
+            "saa": Angle,
+            "min_sun_angle": float,
+            "max_sun_angle": float,
+            "force_cvz": bool,
+        }
+
+        kwargs, safe = galsim.config.GetAllParams(
+            config,
+            base,
+            req=req,
+            opt=opt,
+        )
+        if "min_sun_angle" in kwargs:
+            euclidlike.instrument_params.min_sun_angle = \
+                kwargs["min_sun_angle"] * galsim.degrees
+            euclidlike.euclidlike_wcs.min_sun_angle = \
+                kwargs["min_sun_angle"] * galsim.degrees
+        if "max_sun_angle" in kwargs:
+            euclidlike.instrument_params.max_sun_angle = \
+                kwargs["max_sun_angle"] * galsim.degrees
+            euclidlike.euclidlike_wcs.max_sun_angle = \
+                kwargs["max_sun_angle"] * galsim.degrees
+        if "saa" in kwargs:
+            SAA = kwargs["saa"]
+        else:
+            SAA = None
+        pointing = CelestialCoord(ra=kwargs["ra"], dec=kwargs["dec"])
+        wcs = euclidlike.getWCS(
+            world_pos=pointing,
+            PA=kwargs["pa"],
+            date=Time(kwargs["mjd"], format="mjd").datetime,
+            CCDs=kwargs["CCD"],
+            PA_is_FPA=True,
+            SAA=SAA,
+        )[kwargs["CCD"]]
+        return wcs

+

+
+
+
+RegisterWCSType("EuclidlikeWCS", EuclidlikeWCS())
+

+
+          

+          
+        

+      

+      
+      

+    

+    

+      ©2024, Rachel Mandelbaum, Axel Guinot, Federico Berlfein, Andy Park, Xiangchong Li, Michael Troxel, Tianqing Zhang.
+      
+      |
+      Powered by Sphinx 8.1.3
+      & Alabaster 1.0.0
+      
+    

+
+    
+
+    
+  
+
\ No newline at end of file
diff --git a/docs/_build/html/_modules/index.html b/docs/_build/html/_modules/index.html
index 4b0a73d..5eea8e7 100644
--- a/docs/_build/html/_modules/index.html
+++ b/docs/_build/html/_modules/index.html
@@ -35,6 +35,18 @@ 
All modules for which code is available

 
  • euclidlike.bandpass
    • 
 
  • euclidlike.euclidlike_psf
    • 
 
  • euclidlike.euclidlike_wcs
    • 
+
  • euclidlike_imsim.bandpass
    • 
+
  • euclidlike_imsim.ccd
    • 
+
  • euclidlike_imsim.noise
    • 
+
  • euclidlike_imsim.obseq
    • 
+
  • euclidlike_imsim.photonOps
    • 
+
  • euclidlike_imsim.psf
    • 
+
  • euclidlike_imsim.skycat
    • 
+
  • euclidlike_imsim.stamp
    • 
+
  • euclidlike_imsim.utils
    • 
+
  • euclidlike_imsim.wcs
    • 
+
  • scripts.download_psf
    • 
+
  • scripts.make_euclidlike_pupil_plane
    • 
 
 
           
    
@@ -62,6 +74,14 @@ 
    GalSim-Euclid-Like
    
     
    
 
 
    Navigation
    
+
 
 
    
 
    Related Topics
    
diff --git a/docs/_build/html/_modules/scripts/download_psf.html b/docs/_build/html/_modules/scripts/download_psf.html
new file mode 100644
index 0000000..f4f4a05
--- /dev/null
+++ b/docs/_build/html/_modules/scripts/download_psf.html
@@ -0,0 +1,619 @@
+
+
+
+  
+    
+    
+    scripts.download_psf — GalSim-Euclid-Like 0.0.1 documentation
+    
+    
+    
+    
+    
+    
+    
+    
+   
+  
+  
+
+  
+  
+
+  
+  
+
+    
    
+      
    
+        
    
+          
+
+          
    
+            
+  
    Source code for scripts.download_psf
    +
+"""
+A program to download the Euclid-like PSF sampled across the focal plane for discrete wavelengths.
+The code below was adapted from: https://github.com/GalSim-developers/GalSim/blob/releases/2.5/galsim/download_cosmos.py
+"""
+
+import os, sys, zipfile, subprocess, shutil, json
+import argparse
+import logging
+from urllib.request import urlopen
+
+from galsim._version import __version__ as version
+#from .meta_data import share_dir
+from galsim.utilities import ensure_dir
+from galsim.main import make_logger
+
+script_name = 'euclidlike_download_psf'
+script_dir = os.path.dirname(__file__)
+share_dir = os.path.join(script_dir, '..', 'euclidlike', 'data')
+
+
    
+[docs]
+def parse_args(command_args):
+    """Handle the command line arguments using either argparse (if available) or optparse.
+    """
+    # Another potential option we might want to add is to download the smaller training sample
+    # rather than the full 4 GB file.  Right now, this just downloads the larger catalog.
+
+    # Short description strings common to both parsing mechanisms
+    description = "This program will download the Euclid-like PSF \n"
+    description += "and place them in the GalSim-Euclid-Like data directory so they can be used as\n "
+    description += "the default files for the euclid-like PSF.\n"
+    description += "See https://github.com/GalSim-developers/GalSim-Euclid-Like/wiki/Euclid-Like-PSF\n"
+    description += "for more details about the files being downloaded."
+    epilog = "Note: The unpacked files total almost 4 GB in size!\n"
+
+    # Build the parser and add arguments
+    parser = argparse.ArgumentParser(description=description, epilog=epilog, add_help=True)
+    parser.add_argument(
+        '-v', '--verbosity', type=int, action='store', default=2, choices=(0, 1, 2, 3),
+        help='Integer verbosity level: min=0, max=3 [default=2]')
+    parser.add_argument(
+        '-f', '--force', action='store_const', default=False, const=True,
+        help='Force overwriting the current file if one exists')
+    parser.add_argument(
+        '-q', '--quiet', action='store_const', default=False, const=True,
+        help="Don't ask about re-downloading an existing file. (implied by verbosity=0)")
+    parser.add_argument(
+        '-u', '--unpack', action='store_const', default=False, const=True,
+        help='Re-unpack the tar file if not downloading')
+    parser.add_argument(
+        '--save', action='store_const', default=False, const=True,
+        help="Save the tarball after unpacking.")
+    parser.add_argument(
+        '-d', '--dir', action='store', default=None,
+        help="Install into an alternate directory and link from the euclidlike/data directory")
+    parser.add_argument(
+        '--nolink', action='store_const', default=False, const=True,
+        help="Don't link to the alternate directory from euclidlike/data")
+    args = parser.parse_args(command_args)
+    args.log_file = None
+    args.log_format = None
+
+    # Return the args
+    return args
    
+
+
+
    
+[docs]
+def get_input():  # pragma: no cover
+    # A level of indirection to make it easier to test functions using input.
+    # This one isn't covered, since we always mock it.
+    return input()
    
+
+
+# Based on recipe 577058: http://code.activestate.com/recipes/577058/
+
    
+[docs]
+def query_yes_no(question, default="yes"):
+    """Ask a yes/no question via input() and return their answer.
+
+    "question" is a string that is presented to the user.
+    "default" is the presumed answer if the user just hits <Enter>.
+        It must be "yes" (the default), "no" or None (meaning
+        an answer is required of the user).
+
+    The "answer" return value is one of "yes" or "no".
+    """
+    valid = {"yes":"yes",   "y":"yes",  "ye":"yes",
+             "no":"no",     "n":"no"}
+    if default == None:
+        prompt = " [y/n] "
+    elif default == "yes":
+        prompt = " [Y/n] "
+    elif default == "no":
+        prompt = " [y/N] "
+    else:
+        raise ValueError("invalid default answer: '%s'" % default)
+
+    while 1:
+        sys.stdout.write(question + prompt)
+        choice = get_input().lower()
+        if default is not None and choice == '':
+            choice = default
+            break
+        elif choice in valid.keys():
+            break
+        else:
+            sys.stdout.write("Please respond with 'yes' or 'no' "\
+                             "(or 'y' or 'n').\n")
+    return valid[choice]
    
+
+
+
+
    
+[docs]
+def get_names(args, logger):
+    if args.dir is not None:
+        target_dir = os.path.expanduser(args.dir)
+        do_link = not args.nolink
+    else:
+        target_dir = share_dir
+        do_link = False
+
+    url ='https://cosmo.vera.psc.edu/Euclid-like-PSFs/monopsfs_euclidlike.zip'
+    file_name = os.path.basename(url)
+    target = os.path.join(target_dir, file_name)
+    link_dir = os.path.join(share_dir, file_name)[:-len('.zip')]
+    unpack_dir = target[:-len('.zip')]
+    logger.warning('Downloading from url:\n  %s',url)
+    logger.warning('Target location is:\n  %s',target)
+    target_dir = unpack_dir
+
+    return url, target, target_dir, link_dir, unpack_dir, do_link
    
+
+
+
+
+
    
+[docs]
+def get_meta(url, args, logger):
+    logger.info('')
+
+    # See how large the file to be downloaded is.
+    u = urlopen(url)
+    meta = u.info()
+    logger.debug("Meta information about url:\n%s",str(meta))
+    file_name = os.path.basename(url)
+    file_size = int(meta.get("Content-Length"))
+    logger.info("Size of %s: %d MBytes" , file_name, file_size/1024**2)
+
+    return meta
    
+
+
+
    
+[docs]
+def check_existing(target, unpack_dir, meta, args, logger):
+    # Make sure the directory we want to put this file exists.
+    ensure_dir(target)
+
+    do_download = True
+    # If file already exists
+    if os.path.isfile(target):
+        file_size = int(meta.get("Content-Length"))
+        logger.info("")
+        existing_file_size = os.path.getsize(target)
+        if args.force:
+            logger.info("Target file already exists.  Size = %d MBytes.  Forced re-download.",
+                        existing_file_size/1024**2)
+        elif file_size == existing_file_size:
+            if args.quiet:
+                logger.info("Target file already exists.  Not re-downloading.")
+                do_download = False
+            else:
+                q = "Target file already exists.  Overwrite?"
+                yn = query_yes_no(q, default='no')
+                if yn == 'no':
+                    do_download = False
+        else:
+            logger.warning("Target file already exists, but it seems to be either incomplete, "
+                           "corrupt, or obsolete")
+            if args.quiet:
+                logger.info("Size of existing file = %d MBytes.  Re-downloading.",
+                            existing_file_size/1024**2)
+            else:
+                q = "Size of existing file = %d MBytes.  Re-download?"%(existing_file_size/1024**2)
+                yn = query_yes_no(q, default='yes')
+                if yn == 'no':
+                    do_download = False
+    elif unpack_dir is not None and os.path.isdir(unpack_dir):
+        logger.info("")
+
+        # Check that this is the current version.
+        meta_file = os.path.join(unpack_dir, 'meta.json')
+        logger.debug('meta_file = %s',meta_file)
+        if os.path.isfile(meta_file):
+            logger.debug('meta_file exists')
+            with open(meta_file) as fp:
+                saved_meta_dict = json.load(fp)
+                # Get rid of the unicode
+                saved_meta_dict = dict([ (str(k),str(v)) for k,v in saved_meta_dict.items()])
+            saved_meta_dict = {k.lower():v for k,v in saved_meta_dict.items()}
+            logger.debug("current meta information is %s",saved_meta_dict)
+            meta_dict = dict(meta)
+            meta_dict = {k.lower():v for k,v in meta_dict.items()}
+            logger.debug("url's meta information is %s",meta_dict)
+
+            # There are several checksum tags.  If any of them are present and match,
+            # then file is current.  If they don't match, file is obsolete.
+            # If none are present, then they changed something, so do a longer check.
+            # (And try to get around to updating this list of checksum keys.)
+            checksum_keys = ['oc-checksum', 'content-md5', 'etag']
+            obsolete = None
+            for k in checksum_keys:
+                if k in saved_meta_dict and k in meta_dict:
+                    if saved_meta_dict[k] == meta_dict[k]:
+                        logger.info("Checksum key %s matches.  File is up to date."%k)
+                        obsolete = False
+                    else:
+                        logger.info("Checksum key %s doesn't matches.  File is obsolete."%k)
+                        obsolete = True
+                    break
+
+            if obsolete is None:
+                # Check all meta data.  If it all matches, then it's fine.
+                # Otherwise, the file is obsolete.
+                obsolete = False
+                for k in meta_dict:
+                    # Skip some keys that don't imply obselescence.
+                    if k.startswith('x-') or k.startswith('retry') or k.startswith('set-cookie'):
+                        continue
+                    if k == 'date' or k == 'last-modified' or k == 'server':
+                        continue
+                    # Others that are missing or different imply obsolete
+                    if k not in saved_meta_dict:
+                        logger.debug("key %s is missing in saved meta information",k)
+                        obsolete = True
+                    elif meta_dict[k] != saved_meta_dict[k]:
+                        logger.debug("key %s differs: %s != %s",k,meta_dict[k],saved_meta_dict[k])
+                        obsolete = True
+                    else:
+                        logger.debug("key %s matches",k)
+        else:
+            logger.debug('meta_file does not exist')
+            obsolete = True
+
+        if obsolete:
+            if args.quiet or args.force:
+                logger.warning("The version currently on disk is obsolete.  "
+                               "Downloading new version.")
+            else:
+                q = "The version currently on disk is obsolete.  Download new version?"
+                yn = query_yes_no(q, default='yes')
+                if yn == 'no':
+                    do_download = False
+        elif args.force:
+            logger.info("Target file has already been downloaded and unpacked.  "
+                        "Forced re-download.")
+        elif args.quiet:
+            logger.info("Target file has already been downloaded and unpacked.  "
+                        "Not re-downloading.")
+            args.save = True  # Don't delete it!
+            do_download = False
+        else:
+            q = "Target file has already been downloaded and unpacked.  Re-download?"
+            yn = query_yes_no(q, default='no')
+            if yn == 'no':
+                args.save = True
+                do_download = False
+    return do_download
    
+
+
+
    
+[docs]
+def download(do_download, url, target, meta, args, logger):
+    if not do_download: return
+    logger.info("")
+    u = urlopen(url)
+    # This bit is based on one of the answers here: (by PabloG)
+    # http://stackoverflow.com/questions/22676/how-do-i-download-a-file-over-http-using-python
+    # The progress feature in that answer is important here, since downloading such a large file
+    # will take a while.
+    file_size = int(meta.get("Content-Length"))
+    try:
+        with open(target, 'wb') as f:
+            file_size_dl = 0
+            block_sz = 32 * 1024
+            next_dot = file_size/100.  # For verbosity==1, the next size for writing a dot.
+            while True:
+                buffer = u.read(block_sz)
+                if not buffer:
+                    break
+
+                file_size_dl += len(buffer)
+                f.write(buffer)
+
+                # Status bar
+                if args.verbosity >= 2:
+                    status = r"Downloading: %5d / %d MBytes  [%3.2f%%]" % (
+                        file_size_dl/1024**2, file_size/1024**2, file_size_dl*100./file_size)
+                    status = status + '\b'*len(status)
+                    sys.stdout.write(status)
+                    sys.stdout.flush()
+                elif args.verbosity >= 1 and file_size_dl > next_dot:
+                    sys.stdout.write('.')
+                    sys.stdout.flush()
+                    next_dot += file_size/100.
+        logger.info("Download complete.")
+        logger.info("")
+    except OSError as e:
+        # Try to give a reasonable suggestion for some common OSErrors.
+        logger.error("\n\nOSError: %s",str(e))
+        if 'Permission denied' in str(e):
+            logger.error("Rerun using sudo %s",script_name)
+            logger.error("If this is not possible, you can download to an alternate location:")
+            logger.error("    %s -d dir_name --nolink\n",script_name)
+        elif 'Disk quota' in str(e) or 'No space' in str(e):
+            logger.error("You might need to download this in an alternate location and link:")
+            logger.error("    %s -d dir_name\n",script_name)
+        raise
    
+
+
+
    
+[docs]
+def check_unpack(do_download, unpack_dir, target, args):
+    # Usually we unpack if we downloaded the tarball or if specified by the command line option.
+    do_unpack = do_download or args.unpack
+
+    # If the unpack dir is missing, then need to unpack
+    if not os.path.exists(unpack_dir):
+        do_unpack = True
+
+    # But of course if there is no tarball, we can't unpack it
+    if not os.path.isfile(target):
+        do_unpack = False
+
+    # If we have a downloaded tar file, ask if it should be re-unpacked.
+    if not do_unpack and not args.quiet and os.path.isfile(target):
+        q = "Zip file is already unpacked.  Re-unpack?"
+        yn = query_yes_no(q, default='no')
+        if yn == 'yes':
+            do_unpack=True
+    return do_unpack
    
+
+
+
    
+[docs]
+def unpack(do_unpack, target, target_dir, unpack_dir, meta, args, logger):
+    if not do_unpack: return
+    logger.info("Unpacking the zip file...")
+    with zipfile.ZipFile(target, 'r') as zip_ref:
+        if args.verbosity >= 3:
+            zip_ref.printdir()
+        elif args.verbosity >= 2:
+            zip_ref.printdir()
+
+        def is_within_directory(directory, target):
+            abs_directory = os.path.abspath(directory)
+            abs_target = os.path.abspath(target)
+            prefix = os.path.commonprefix([abs_directory, abs_target])
+            return prefix == abs_directory
+
+        def safe_extract(zip_ref, path=".", members=None):
+            # This is somewhat gratuitous for our use case, since we directly control the zip file,
+            # but it's a good practice to avoid security vulnerabilities.
+            members = []
+            for member in zip_ref.namelist():
+                if member != 'VIS_response.fits.gz': # not interested in downloading this file
+                    members.append(member)
+                    member_path = os.path.join(path, member)
+                    if not is_within_directory(path, member_path):  # pragma: no cover
+                        raise Exception("Attempted Path Traversal in Zip File")
+
+            zip_ref.extractall(path, members)
+
+        safe_extract(zip_ref, target_dir)
+
+    # Write the meta information to a file, meta.json to mark what version this all is.
+    meta_file = os.path.join(unpack_dir, 'meta.json')
+    with open(meta_file, 'w') as fp:
+        json.dump(dict(meta), fp)
+
+    logger.info("Extracted contents of zip file.")
+    logger.info("")
    
+
+
+
+
    
+[docs]
+def check_remove(do_unpack, target, args):
+    # Usually, we remove the tarball if we unpacked it and command line doesn't specify to save it.
+    do_remove = do_unpack and not args.save
+
+    # But if we didn't unpack it, and they didn't say to save it, ask if we should remove it.
+    if os.path.isfile(target) and not do_remove and not args.save and not args.quiet:
+        q = "Remove the zipfile?"
+        yn = query_yes_no(q, default='no')
+        if yn == 'yes':
+            do_remove = True
+    return do_remove
    
+
+
+
    
+[docs]
+def remove_tarball(do_remove, target, logger):
+    if do_remove:
+        logger.info("Removing the zipfile to save space")
+        os.remove(target)
    
+
+
+
+
+
+
+
    
+[docs]
+def download_psf(args, logger):
+    """The main script given the ArgParsed args and a logger
+    """
+    # Give diagnostic about GalSim version
+    logger.debug("GalSim version: %s",version)
+    logger.debug("This download script is: %s",__file__)
+    logger.info("Type %s -h to see command line options.\n",script_name)
+
+    # Some definitions:
+    # share_dir is the base galsim share directory, e.g. /usr/local/share/galsim/
+    # url is the url from which we will download the tarball.
+    # target is the full path of the downloaded tarball
+    # target_dir is where we will put the downloaded file, usually == share_dir.
+    # link_dir is the directory where this would normally have been unpacked.
+    # unpack_dir is the directory that the tarball will unpack into.
+
+    # caution about storage and ask user if they want to proceed.
+    q = "You are about to download 4Gb, do you want to proceed?"
+    yn = query_yes_no(q, default='no')
+    if yn == 'no':
+        return
+
+    url, target, target_dir, link_dir, unpack_dir, do_link = get_names(args, logger)
+
+    meta = get_meta(url, args, logger)
+
+    # Check if the file already exists and if it is the right size
+    do_download = check_existing(target, unpack_dir, meta, args, logger)
+
+    # Download the tarball
+    download(do_download, url, target, meta, args, logger)
+
+    # Unpack the tarball
+    do_unpack = check_unpack(do_download, unpack_dir, target, args)
+    unpack(do_unpack, target, target_dir, unpack_dir, meta, args, logger)
+
+    # Remove the tarball
+    do_remove = check_remove(do_unpack, target, args)
+    remove_tarball(do_remove, target, logger)
+
+    # If we are downloading to an alternate directory, we (usually) link to it from share/galsim
+    make_link(do_link, unpack_dir, link_dir, args, logger)
    
+
+
+
    
+[docs]
+def main(command_args):
+    """The whole process given command-line parameters in their native (non-ArgParse) form.
+    """
+    args = parse_args(command_args)
+    logger = make_logger(args)
+    download_psf(args, logger)
    
+
+
+
    
+[docs]
+def run_main():
+    """Kick off the process grabbing the command-line parameters from sys.argv
+    """
+    main(sys.argv[1:])
    
+
+
    
+
+          
    
+          
+        
    
+      
    
+      
+      
    
+    
    
+    
    
+      ©2024, Rachel Mandelbaum, Axel Guinot, Federico Berlfein, Andy Park, Xiangchong Li, Michael Troxel, Tianqing Zhang.
+      
+      |
+      Powered by Sphinx 8.1.3
+      & Alabaster 1.0.0
+      
+    
    
+
+    
+
+    
+  
+
\ No newline at end of file
diff --git a/docs/_build/html/_modules/scripts/make_euclidlike_pupil_plane.html b/docs/_build/html/_modules/scripts/make_euclidlike_pupil_plane.html
new file mode 100644
index 0000000..39caf0c
--- /dev/null
+++ b/docs/_build/html/_modules/scripts/make_euclidlike_pupil_plane.html
@@ -0,0 +1,295 @@
+
+
+
+  
+    
+    
+    scripts.make_euclidlike_pupil_plane — GalSim-Euclid-Like 0.0.1 documentation
+    
+    
+    
+    
+    
+    
+    
+    
+   
+  
+  
+
+  
+  
+
+  
+  
+
+    
    
+      
    
+        
    
+          
+
+          
    
+            
+  
    Source code for scripts.make_euclidlike_pupil_plane
    +"""
+This code has been taken from https://github.com/CosmoStat/wf-psf Liaudat et al.
+
+This is an implementation of the function `generate_pupil_obscurations` https://github.com/CosmoStat/wf-psf/blob/87e0c8e9770199cd276f5f0551054cb4902d53bb/src/wf_psf/sims/SimPSFToolkit.py#L233
+
+NOTE from Tobias Liaudat:
+"Simple procedure considering only the 2D plane.
+No 3D projections wrt the angle of the FoV is done."
+"""  # noqa
+from argparse import ArgumentParser
+import os
+import importlib.util
+from importlib.resources import files
+
+import numpy as np
+from scipy.signal import convolve2d
+
+import galsim
+
+
+# Telescope parameters
+AS_diam = 1200  # Aperture stop diameter [mm]
+M1_diam = 395  # Mirror 1 cap stopper diameter [mm]
+
+sp_lenght = 700  # Spider length [mm]
+sp_width = 12  # Spider width [mm]
+
+AS_centre = [0, 0]
+M1_centre = [0, 51]
+
+sp1_angle = 106.78 - 90  # [degrees]
+sp2_angle = 50.11 - 90  # [degrees]
+sp3_angle = -10.76 - 90  # [degrees]
+
+sp1_x_pos = 260  # [mm]
+sp1_y_pos = 240  # [mm]
+sp2_x_pos = -330  # [mm]
+sp2_y_pos = 130  # [mm]
+sp3_x_pos = 70  # [mm]
+sp3_y_pos = -330  # [mm]
+
+
+
    
+[docs]
+def make_EuclidLike_pupil_plane(N_pix=2048, do_filter=True, N_filter=3):
+    # Build pupil plane
+    pupil_plane = np.ones((N_pix, N_pix))
+
+    # coordinates of map in [mm]
+    W, H = np.meshgrid(
+        np.linspace(-AS_diam // 2, AS_diam // 2, N_pix),
+        np.linspace(-AS_diam // 2, AS_diam // 2, N_pix),
+    )
+
+    # Calculate the Aperture stop and draw it ###
+    aperture_stop_mask = np.sqrt(
+        (W - AS_centre[0]) ** 2 + (H - AS_centre[1]) ** 2
+    ) <= (AS_diam / 2)
+    pupil_plane[~aperture_stop_mask] = 0
+
+    # Calculate the M1/M2 obscurations and draw them ###
+    M1_mask = np.sqrt((W - M1_centre[0]) ** 2 + (H - M1_centre[1]) ** 2) <= (
+        M1_diam / 2
+    )
+    pupil_plane[M1_mask] = 0
+
+    # Calculate the spiders and draw them
+    # Spider 1
+    sp1_a = np.tan(sp1_angle * (np.pi / 180))
+    sp1_b = sp1_y_pos - sp1_a * sp1_x_pos
+
+    sp1_mask_1 = sp1_a * W + sp1_b - sp_width / 2 * np.sqrt(1 + sp1_a**2) < H
+    sp1_mask_2 = sp1_a * W + sp1_b + sp_width / 2 * np.sqrt(1 + sp1_a**2) > H
+    sp1_mask = np.logical_and(sp1_mask_1, sp1_mask_2)
+
+    sp1_length_mask = np.sqrt((W - sp1_x_pos) ** 2 + (H - sp1_y_pos) ** 2) <= (
+        sp_lenght / 2
+    )
+    sp1_mask = np.logical_and(sp1_mask, sp1_length_mask)
+
+    # Spider 2
+    sp2_a = np.tan(sp2_angle * (np.pi / 180))
+    sp2_b = sp2_y_pos - sp2_a * sp2_x_pos
+
+    sp2_mask_1 = sp2_a * W + sp2_b - sp_width / 2 * np.sqrt(1 + sp2_a**2) < H
+    sp2_mask_2 = sp2_a * W + sp2_b + sp_width / 2 * np.sqrt(1 + sp2_a**2) > H
+    sp2_mask = np.logical_and(sp2_mask_1, sp2_mask_2)
+
+    sp2_length_mask = np.sqrt((W - sp2_x_pos) ** 2 + (H - sp2_y_pos) ** 2) <= (
+        sp_lenght / 2
+    )
+    sp2_mask = np.logical_and(sp2_mask, sp2_length_mask)
+
+    # Spider 3
+    sp3_a = np.tan(sp3_angle * (np.pi / 180))
+    sp3_b = sp3_y_pos - sp3_a * sp3_x_pos
+
+    sp3_mask_1 = sp3_a * W + sp3_b - sp_width / 2 * np.sqrt(1 + sp3_a**2) < H
+    sp3_mask_2 = sp3_a * W + sp3_b + sp_width / 2 * np.sqrt(1 + sp3_a**2) > H
+    sp3_mask = np.logical_and(sp3_mask_1, sp3_mask_2)
+
+    sp3_length_mask = np.sqrt((W - sp3_x_pos) ** 2 + (H - sp3_y_pos) ** 2) <= (
+        sp_lenght / 2
+    )
+    sp3_mask = np.logical_and(sp3_mask, sp3_length_mask)
+
+    # Draw the three spider arms
+    pupil_plane[sp1_mask] = 0
+    pupil_plane[sp2_mask] = 0
+    pupil_plane[sp3_mask] = 0
+
+    # Low-pass filter the image
+    if do_filter:
+        top_hat_filter = np.ones((N_filter, N_filter))
+
+        pupil_plane = convolve2d(
+            pupil_plane,
+            top_hat_filter,
+            boundary="fill",
+            mode="same",
+            fillvalue=0,
+        )
+        pupil_plane /= np.sum(top_hat_filter)
+
+    # Get pupil scale
+    pupil_scale = AS_diam / N_pix
+
+    return pupil_plane, pupil_scale
    
+
+
+
+if __name__ == "__main__":
+    parser = ArgumentParser()
+    parser.add_argument(
+        "-o",
+        "--output",
+        dest="output_path",
+        help="Path where to save the pupil plane. Default to the euclidlike"
+        " data directory if it exist.",
+        type=str,
+    )
+    parser.add_argument(
+        "-N",
+        "--N_pix",
+        dest="Npix",
+        help="N pixels used to save the pupil plane. [Default: 2048]",
+        type=int,
+        default=2048,
+    )
+    parser.add_argument(
+        "-filter",
+        "--do_filter",
+        dest="DoFilter",
+        help="Wether to apply a Top-Hat filter. [Default: True]",
+        type=bool,
+        default=True,
+    )
+    parser.add_argument(
+        "-Nf",
+        "--N_filter",
+        dest="Nfilter",
+        help="N pixels used for the Top-Hat filter. [Default: 3]",
+        type=int,
+        default=3,
+    )
+
+    args = parser.parse_args()
+
+    # Deal with the output
+    if args.output_path is None:
+        if importlib.util.find_spec("euclidlike") is None:
+            raise ValueError(
+                "No output path provided and euclidlike not found."
+                " Please provide an output path."
+            )
+        output_path = str(
+            files("euclidlike.data").joinpath("euclid_pupil_plane.fits.gz")
+        )
+    else:
+        output_path = os.path.abspath(args.output_path)
+
+    pupil_plane, pupil_scale = make_EuclidLike_pupil_plane(
+        args.Npix,
+        args.DoFilter,
+        args.Nfilter,
+    )
+
+    # Galsim need the pupil scale in m/pixel
+    pupil_img = galsim.Image(pupil_plane, scale=pupil_scale / 1000)
+    pupil_img.write(output_path)
+    print(f"Pupil plane saved at: {output_path}")
+
    
+
+          
    
+          
+        
    
+      
    
+      
+      
    
+    
    
+    
    
+      ©2024, Rachel Mandelbaum, Axel Guinot, Federico Berlfein, Andy Park, Xiangchong Li, Michael Troxel, Tianqing Zhang.
+      
+      |
+      Powered by Sphinx 8.1.3
+      & Alabaster 1.0.0
+      
+    
    
+
+    
+
+    
+  
+
\ No newline at end of file
diff --git a/docs/_build/html/_sources/euclidlike.rst.txt b/docs/_build/html/_sources/euclidlike.rst.txt
index c09a526..d4f2d47 100644
--- a/docs/_build/html/_sources/euclidlike.rst.txt
+++ b/docs/_build/html/_sources/euclidlike.rst.txt
@@ -1,53 +1,153 @@
-euclidlike package
-==================
+The Euclid-like Module
+################################
 
-Submodules
-----------
+The ``euclidlike`` module contains telescope information and functionality needed for image simulations.
+The demo script end_to_end_demo.py shows how to use many of the atrributes and functions described here.
 
-euclidlike.backgrounds module
------------------------------
 
-.. automodule:: euclidlike.backgrounds
-   :members:
-   :undoc-members:
-   :show-inheritance:
+Module-level Attributes
+=======================
 
-euclidlike.bandpass module
---------------------------
+There are several of attributes of the ``euclidlike`` module which define some numerical
+parameters related to a Euclid-like geometry.  Some of these parameters relate to the entire
+wide-field imager.  Others, especially the return values of the functions to get the
+PSF and WCS, are specific to each CCD and therefore are indexed based on the detector number. 
+All detector-related arrays are 0-indexed, which might differ from the CCD indices for Euclid,
+which run 1-1 to n_row-n_col.
 
-.. automodule:: euclidlike.bandpass
-   :members:
-   :undoc-members:
-   :show-inheritance:
+gain
+    The gain for all CCDs is expected to be the roughly the same.
 
-euclidlike.euclidlike\_psf module
----------------------------------
+pixel_scale
+    The pixel scale in units of arcsec/pixel. 
 
-.. automodule:: euclidlike.euclidlike_psf
-   :members:
-   :undoc-members:
-   :show-inheritance:
+diameter
+    The telescope diameter in meters.
 
-euclidlike.euclidlike\_wcs module
----------------------------------
+obscuration
+    The linear obscuration of the telescope, expressed as a fraction of the diameter.
 
-.. automodule:: euclidlike.euclidlike_wcs
-   :members:
-   :undoc-members:
-   :show-inheritance:
+collecting_area
+    The actual collecting area after accounting for obscuration, struts, etc. in
+        units of cm^2.
 
-euclidlike.instrument\_params module
-------------------------------------
+long_exptime
+    The typical exposure time for the longer exposures used for VIS images, in units of seconds.  
+    The number that is stored is for a single dither.
 
-.. automodule:: euclidlike.instrument_params
-   :members:
-   :undoc-members:
-   :show-inheritance:
+short_exptime_nisp
+    The typical exposure time for the shorter NISP imaging exposures used for VIS images, in units of seconds.  
+    The number that is stored is for a single dither.
 
-Module contents
----------------
+short_exptime_vis
+    The typical exposure time for the shorter exposures with VIS taken in parallel with NISP imaging, in units of seconds.  
+    The number that is stored is for a single dither.
 
-.. automodule:: euclidlike
-   :members:
-   :undoc-members:
-   :show-inheritance:
+n_dithers
+    The number of dithers per filter.
+
+n_ccd
+    The number of CCDs in the focal plane.
+    
+n_ccd_row
+    The number of CCDs in the each focal plane row.
+
+n_ccd_col
+    The number of CCDs in the each focal plane column.
+
+n_pix_row
+    Each CCD has n_pix_row total pixels in each row.
+n_pix_col
+    Each CCD has n_pix_col total pixels in each column.
+
+pixel_scale_mm
+    The physical pixel size, in units of mm.
+
+plate_scale
+    The plate scale, in units of arcsec / mm
+
+read_noise
+    Total readout noise, in units of e-. 
+
+saturation
+    Pixel saturation, in units of e-. 
+
+det2ccd
+    Mapping from DETID to CCDID.
+
+ccd2det
+    Mapping from CCDID to DETID.
+
+min_sun_angle
+    Minimum allowed angle from the telescope solar panels to the sun, in degrees.
+
+max_sun_angle
+    Maximum allowed angle from the telescope solar panels to the sun, in degrees.
+
+vis_bands
+    List of available VIS bands
+nisp_bands
+    List of available NISP bands
+
+vis_blue_limit
+    Bandpass blue limit  needed for consistency with the wavelength range covered by ur tabulated 
+    PSF images, in nm.
+
+vis_red_limit
+    Bandpass red limit  needed for consistency with the wavelength range covered by ur tabulated 
+    PSF images, in nm.
+
+For example, to get the gain value, use euclidlike.gain.
+
+#.. automodule:: euclidlike.instrument_params
+#   :members:
+#   :undoc-members:
+
+
+Euclid-like Functions
+===============
+
+This module also contains the following routines:
+
+`euclidlike.getBandpasses`
+    A utility to get a dictionary containing galsim.Bandpass objects for each of
+    the Euclid-like imaging bandpasses, which by default have AB zeropoints given using
+    the GalSim zeropoint convention (see `getBandpasses` docstring for more details).
+
+`euclidlike.getSkyLevel`
+    A utility to find the expected sky level due to zodiacal light at a given
+    position, in a given band.
+
+`euclidlike.getZodiBackground`
+    This helper routine is enables the calculation of the zodiacal light, in photons/m^2/arcsec^2/sec
+
+`euclidlike.getPSF`
+    A routine to get a chromatic representation of the PSF in a single CCD.
+    PSFs are based on precomputed, oversampled (by 3x) PSF images on a grid in wavelength and
+    focal plane position.
+
+`euclidlike.getBrightPSF`
+    Get a fake optical PSF for very bright objects.
+
+`euclidlike.getWCS`
+    This routine returns a dict containing a WCS for each of the Euclid CCDs.
+
+`euclidlike.findCCD`
+    This is a helper routine to calculate the minimum and maximum pixel values that should be
+    considered within a CCD.
+
+
+
+.. autofunction:: euclidlike.getBandpasses
+
+.. autofunction:: euclidlike.getSkyLevel
+
+.. autofunction:: euclidlike.getZodiBackground
+
+.. autofunction:: euclidlike.getPSF
+
+.. autofunction:: euclidlike.getBrightPSF
+
+.. autofunction:: euclidlike.getWCS
+
+.. autofunction:: euclidlike.findCCD
diff --git a/docs/_build/html/_sources/euclidlike_imsim.rst.txt b/docs/_build/html/_sources/euclidlike_imsim.rst.txt
index bc6626f..244a9b5 100644
--- a/docs/_build/html/_sources/euclidlike_imsim.rst.txt
+++ b/docs/_build/html/_sources/euclidlike_imsim.rst.txt
@@ -1,109 +1,64 @@
-euclidlike\_imsim package
-=========================
+The Euclid-like ImSim Module
+################################
 
-Submodules
-----------
+This module contains configuration scripts to produce large-scale Euclid-like simulation runs based on the information in ``euclidlike``.
+It is based heavily on `roman_imsim `_.
 
-euclidlike\_imsim.bandpass module
----------------------------------
+Classes and Functions
+=====================
 
 .. automodule:: euclidlike_imsim.bandpass
    :members:
    :undoc-members:
-   :show-inheritance:
-
-euclidlike\_imsim.ccd module
-----------------------------
 
 .. automodule:: euclidlike_imsim.ccd
    :members:
    :undoc-members:
-   :show-inheritance:
-
-euclidlike\_imsim.detector\_physics module
-------------------------------------------
 
 .. automodule:: euclidlike_imsim.detector_physics
    :members:
    :undoc-members:
-   :show-inheritance:
-
-euclidlike\_imsim.noise module
-------------------------------
 
 .. automodule:: euclidlike_imsim.noise
    :members:
    :undoc-members:
-   :show-inheritance:
-
-euclidlike\_imsim.obseq module
-------------------------------
 
 .. automodule:: euclidlike_imsim.obseq
    :members:
    :undoc-members:
-   :show-inheritance:
-
-euclidlike\_imsim.photonOps module
-----------------------------------
 
 .. automodule:: euclidlike_imsim.photonOps
    :members:
    :undoc-members:
-   :show-inheritance:
-
-euclidlike\_imsim.psf module
-----------------------------
 
 .. automodule:: euclidlike_imsim.psf
    :members:
    :undoc-members:
-   :show-inheritance:
-
-euclidlike\_imsim.scafile module
---------------------------------
 
 .. automodule:: euclidlike_imsim.scafile
    :members:
    :undoc-members:
-   :show-inheritance:
-
-euclidlike\_imsim.skycat module
--------------------------------
 
 .. automodule:: euclidlike_imsim.skycat
    :members:
    :undoc-members:
-   :show-inheritance:
-
-euclidlike\_imsim.stamp module
-------------------------------
 
 .. automodule:: euclidlike_imsim.stamp
    :members:
    :undoc-members:
-   :show-inheritance:
-
-euclidlike\_imsim.utils module
-------------------------------
 
 .. automodule:: euclidlike_imsim.utils
    :members:
    :undoc-members:
-   :show-inheritance:
-
-euclidlike\_imsim.wcs module
-----------------------------
 
 .. automodule:: euclidlike_imsim.wcs
    :members:
    :undoc-members:
-   :show-inheritance:
 
-Module contents
----------------
 
-.. automodule:: euclidlike_imsim
-   :members:
-   :undoc-members:
-   :show-inheritance:
+Use
+====
+Example files needed for large-scale Euclid-like simulation runs are included in ``GalSim-Euclid-Like/config``.
+
+.. include:: ../config/README.rst
+
diff --git a/docs/_build/html/_sources/examples.rst.txt b/docs/_build/html/_sources/examples.rst.txt
new file mode 100644
index 0000000..07f898e
--- /dev/null
+++ b/docs/_build/html/_sources/examples.rst.txt
@@ -0,0 +1,29 @@
+Examples
+=========
+
+The ``GalSim-Euclid-Like/examples`` directory contains example files for how use the euclidlike module.  
+
+End-to-end demo 
+---------------
+
+`end_to_end_demo.py.py <../examples/end_to_end_demo.py>`_
+
+This first demo is the euclidlike-equivalent of  `demo 13 `_ in ``GalSim``. This demo uses the Euclid-like PSF, WCS, and background noise to produce a realistic scene of galaxies and stars as observed from a Euclid-like Telescope. 
+
+** Features introduced in the Python file**:
+
+- euclidlike.getBandpasses(AB_zeropoint)
+- euclidlike.getWCS(world_pos, CCDs_CCD, date)
+- euclidlike.getPSF(use_CCD, filter_name, wcs)
+- euclidlike.getSkyLevel(bandpass, world_pos)
+
+The output generated from this file can be visualized by running the script `end_to_end_demo.py.py <../examples/end_to_end_demo.py>`_
+
+
+Focal Plane Layout 
+------------------
+
+`plot_VIS.py <../examples/plot_VIS.py>`_
+
+This Jupyter Notebook shows the display of the focal plane used in the euclidlike package, along with the CCD centers and ID convention.
+
diff --git a/docs/_build/html/_sources/history.rst.txt b/docs/_build/html/_sources/history.rst.txt
new file mode 100644
index 0000000..d35e38d
--- /dev/null
+++ b/docs/_build/html/_sources/history.rst.txt
@@ -0,0 +1,11 @@
+Revision History
+################
+
+.. include:: ../CHANGELOG.rst
+
+
+Older Versions
+==============
+
+.. toctree::
+    older
\ No newline at end of file
diff --git a/docs/_build/html/_sources/index.rst.txt b/docs/_build/html/_sources/index.rst.txt
index 55d881e..3f160f3 100644
--- a/docs/_build/html/_sources/index.rst.txt
+++ b/docs/_build/html/_sources/index.rst.txt
@@ -1,63 +1,24 @@
-GalSim-Euclid-Like
-==================
-
-Helper functions to generate simulations of Euclid-like images using GalSim.
-
-This repository contains information about the Euclid space telescope and survey that is needed to
-produce simulations using `GalSim `_.  Some of the
-information provided is approximate, aimed towards fast simulations rather than full accuracy in
-representation of Euclid images.  Places where the information is only approximate are flagged and
-described in the docstring, and we particularly highlight that the PSF is only approximate;
-for details, see the docstring of the ``getPSF()`` method.  This library should enable generation of
-Euclid-like images of sufficient fidelity for preliminary exploration of object detection,
-photometry, deblending, and joint analysis with ground-based observatories.  For
-applications requiring high precision such as weak lensing, the higher fidelity simulations
-available within the Euclid Consortium should be used.
-
-This repository includes two distinct packages:
-
-* ``euclidlike``: has basic observatory, instrumentation, and survey information for Euclid.
-  This package can be used on its own along with GalSim to produce Euclid-like simulations.
-
-* ``euclidlike_imsim``: has configuration scripts to produce large-scale Euclid-like simulation runs
-  based on the information in ``euclidlike``. It is based heavily on `roman_imsim `_.
-
-
-References
-==================
+.. GalSim-Euclid-Like documentation master file 
+   
 
-For more information about `GalSim `_, please see its README and documentation.
+GalSim-Euclid-Like: Euclid-like images using GalSim
+==============================================
 
-For more information about Euclid, please see the `Euclid Consortium website `_ and papers linked from there.
+.. toctree::
+    :maxdepth: 2
 
-Attribution for software and data used by particular routines in this library is given in the docstring for the relevant routine.
+    overview
+    install
+    euclidlike
+    euclidlike_imsim
+    examples
+    history
 
-Installation
-==================
-
-Please view the `installation instructions `_ for details on how to install GalSim-Euclid-Like.
-
-Downloading relevant data
-==================                                                                              
-The Euclid-like PSF is constructed from precomputed oversampled images on a grid in focal plane position and wavelength. To use the full FOV PSF within GalSim-Euclid-Like, the images must be downloaded by running::
-
-    $ euclidlike_download_psf
-
-in the terminal after installation of GalSim-Euclid-Like. To install in an alternative directory to the default, use the ``--dir`` argument. Refer to the ``getPSF`` documentation for further details about the PSF. 
 
-Getting started
-==================                                                                             
 
-Please see the examples/ directory for demos illustrating the use of this code.
-
-Communicating with the developers
+Indices and tables
 ==================
-Feel free to `open a GitHub issue `_ to reach the developers with questions, comments, and bug reports.  New contributors are also welcome and can indicate their interest in developing this code base through the Issues.
-
-Attribution
-==================                                   
-
-This software is open source and may be used according to the terms of its `license `_.
-
-When using this software, please provide the URL to the repository in the resulting paper or note.  Once there is a Zenodo DOI or journal article, this README will be updated and we will ask those using the code in their research to cite the relevant journal article.
 
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/docs/_build/html/_sources/install.rst.txt b/docs/_build/html/_sources/install.rst.txt
new file mode 100644
index 0000000..63b62ca
--- /dev/null
+++ b/docs/_build/html/_sources/install.rst.txt
@@ -0,0 +1,4 @@
+Installation
+########
+
+.. include:: ../INSTALL.rst
\ No newline at end of file
diff --git a/docs/_build/html/_sources/modules.rst.txt b/docs/_build/html/_sources/modules.rst.txt
index 269fdea..dc909a1 100644
--- a/docs/_build/html/_sources/modules.rst.txt
+++ b/docs/_build/html/_sources/modules.rst.txt
@@ -1,9 +1,6 @@
-GalSim-Euclid-Like
-==================
-
 .. toctree::
    :maxdepth: 4
 
    euclidlike
    euclidlike_imsim
-   scripts
+   scripts
\ No newline at end of file
diff --git a/docs/_build/html/_sources/overview.rst.txt b/docs/_build/html/_sources/overview.rst.txt
new file mode 100644
index 0000000..803a9ee
--- /dev/null
+++ b/docs/_build/html/_sources/overview.rst.txt
@@ -0,0 +1,4 @@
+Overview
+########
+
+.. include:: ../README.rst
\ No newline at end of file
diff --git a/docs/_build/html/_sources/scripts.rst.txt b/docs/_build/html/_sources/scripts.rst.txt
index 28a2437..11b271d 100644
--- a/docs/_build/html/_sources/scripts.rst.txt
+++ b/docs/_build/html/_sources/scripts.rst.txt
@@ -1,6 +1,11 @@
 scripts package
 ===============
 
+.. automodule:: scripts
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 Submodules
 ----------
 
@@ -19,11 +24,3 @@ scripts.make\_euclidlike\_pupil\_plane module
    :members:
    :undoc-members:
    :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: scripts
-   :members:
-   :undoc-members:
-   :show-inheritance:
diff --git a/docs/_build/html/euclidlike.html b/docs/_build/html/euclidlike.html
index ae374c6..f539977 100644
--- a/docs/_build/html/euclidlike.html
+++ b/docs/_build/html/euclidlike.html
@@ -5,7 +5,7 @@
     
     
 
-    euclidlike package — GalSim-Euclid-Like 0.0.1 documentation
+    The Euclid-like Module — GalSim-Euclid-Like 0.0.1 documentation
     
     
     
@@ -14,6 +14,8 @@
     
     
     
+    
+    
    
   
   
@@ -31,17 +33,142 @@
 
           
    
             
-  
    
-
    euclidlike package
    
-
    
-
    Submodules
    
+  
    
+
    The Euclid-like Module
    
+
    The euclidlike module contains telescope information and functionality needed for image simulations.
+The demo script end_to_end_demo.py shows how to use many of the atrributes and functions described here.
    
+
    
+
    Module-level Attributes
    
+
    There are several of attributes of the euclidlike module which define some numerical
+parameters related to a Euclid-like geometry.  Some of these parameters relate to the entire
+wide-field imager.  Others, especially the return values of the functions to get the
+PSF and WCS, are specific to each CCD and therefore are indexed based on the detector number.
+All detector-related arrays are 0-indexed, which might differ from the CCD indices for Euclid,
+which run 1-1 to n_row-n_col.
    
+
    
+
    gain
    The gain for all CCDs is expected to be the roughly the same.
    
+
    
+
    pixel_scale
    The pixel scale in units of arcsec/pixel.
    
+
    
+
    diameter
    The telescope diameter in meters.
    
+
    
+
    obscuration
    The linear obscuration of the telescope, expressed as a fraction of the diameter.
    
+
    
+
    collecting_area
    
+
    The actual collecting area after accounting for obscuration, struts, etc. in
    units of cm^2.
    
+
    
+
    
+
    
+
    long_exptime
    The typical exposure time for the longer exposures used for VIS images, in units of seconds.
+The number that is stored is for a single dither.
    
+
    
+
    short_exptime_nisp
    The typical exposure time for the shorter NISP imaging exposures used for VIS images, in units of seconds.
+The number that is stored is for a single dither.
    
+
    
+
    short_exptime_vis
    The typical exposure time for the shorter exposures with VIS taken in parallel with NISP imaging, in units of seconds.
+The number that is stored is for a single dither.
    
+
    
+
    n_dithers
    The number of dithers per filter.
    
+
    
+
    n_ccd
    The number of CCDs in the focal plane.
    
+
    
+
    n_ccd_row
    The number of CCDs in the each focal plane row.
    
+
    
+
    n_ccd_col
    The number of CCDs in the each focal plane column.
    
+
    
+
    n_pix_row
    Each CCD has n_pix_row total pixels in each row.
    
+
    
+
    n_pix_col
    Each CCD has n_pix_col total pixels in each column.
    
+
    
+
    pixel_scale_mm
    The physical pixel size, in units of mm.
    
+
    
+
    plate_scale
    The plate scale, in units of arcsec / mm
    
+
    
+
    read_noise
    Total readout noise, in units of e-.
    
+
    
+
    saturation
    Pixel saturation, in units of e-.
    
+
    
+
    det2ccd
    Mapping from DETID to CCDID.
    
+
    
+
    ccd2det
    Mapping from CCDID to DETID.
    
+
    
+
    min_sun_angle
    Minimum allowed angle from the telescope solar panels to the sun, in degrees.
    
+
    
+
    max_sun_angle
    Maximum allowed angle from the telescope solar panels to the sun, in degrees.
    
+
    
+
    vis_bands
    List of available VIS bands
    
+
    
+
    nisp_bands
    List of available NISP bands
    
+
    
+
    vis_blue_limit
    Bandpass blue limit  needed for consistency with the wavelength range covered by ur tabulated
+PSF images, in nm.
    
+
    
+
    vis_red_limit
    Bandpass red limit  needed for consistency with the wavelength range covered by ur tabulated
+PSF images, in nm.
    
+
    
+
    
+
    For example, to get the gain value, use euclidlike.gain.
    
+
    #.. automodule:: euclidlike.instrument_params
+#   :members:
+#   :undoc-members:
    
 
    
-
    
-
    euclidlike.backgrounds module
    
-
    This file includes any routines needed to define the background level, for which the main contribution (currently the only one implemented) is zodiacal light.
    
+
    
+
    Euclid-like Functions
    
+
    This module also contains the following routines:
    
+
    
+
    euclidlike.getBandpasses
    A utility to get a dictionary containing galsim.Bandpass objects for each of
+the Euclid-like imaging bandpasses, which by default have AB zeropoints given using
+the GalSim zeropoint convention (see getBandpasses docstring for more details).
    
+
    
+
    euclidlike.getSkyLevel
    A utility to find the expected sky level due to zodiacal light at a given
+position, in a given band.
    
+
    
+
    euclidlike.getZodiBackground
    This helper routine is enables the calculation of the zodiacal light, in photons/m^2/arcsec^2/sec
    
+
    
+
    euclidlike.getPSF
    A routine to get a chromatic representation of the PSF in a single CCD.
+PSFs are based on precomputed, oversampled (by 3x) PSF images on a grid in wavelength and
+focal plane position.
    
+
    
+
    euclidlike.getBrightPSF
    Get a fake optical PSF for very bright objects.
    
+
    
+
    euclidlike.getWCS
    This routine returns a dict containing a WCS for each of the Euclid CCDs.
    
+
    
+
    euclidlike.findCCD
    This is a helper routine to calculate the minimum and maximum pixel values that should be
+considered within a CCD.
    
+
    
+
    
+
    
+
    
+euclidlike.getBandpasses(AB_zeropoint=True, default_thin_trunc=True, full_bandpass=False, **kwargs)[source]
    
+
    Function to get the bandpass information for the Euclid VIS band and the three Euclid NISP passbands.
    
+
    This routine reads in files containing a list of wavelengths and
+transmission values for the Euclid bands. The files are located in the
+euclidlike.data directory. The routine then creates a Bandpass object
+using the LookupTable class from the GalSim package, and returns a dict with bandpasses for the
+keys.
    
+
    The bandpasses are publicly available from IPAC:
+http://svo2.cab.inta-csic.es/svo/theory/fps3/index.php?mode=browse&gname=Euclid&gname2=VIS&asttype=.
+https://euclid.esac.esa.int/msp/refdata/nisp/NISP-PHOTO-PASSBANDS-V1
    
+
    These are relatively old files that do not include the latest estimates of system response.
+They correspond to end-of-life estimates, with some expected degradation of the QE and filter
+transmission over time.  This can lead to flux estimates that are suppressed by 5-10% from
+beginning-of-life flux estimates.
    
+
    The VIS bandpass red and blue limits are set not by the transmission curve but by the range of
+wavelengths over which we have tabulated PSF images.  The wavelength range is read in from the
+instrument parameter file.
    
+
    Args:
+AB_zeropoint (bool) : If True, set the zeropoint of the bandpass to the AB magnitude system. [default: True]
+default_thin_trunc (bool) : If True, use the default thinning and truncation parameters. [default: True]
+full_bandpass (bool): if True, use the full bandpass without red/blue limits needed for PSF
    
+
    
+
    calculations. [default: False]
    
+
    
+
    kwargs : Additional keyword arguments to pass to either Bandpass.thin or Bandpass.truncate.
    
+
    
+
 
    
-
    
-euclidlike.backgrounds.getSkyLevel(bandpass, world_pos=None, exptime=None, epoch=2025, date=None)[source]
    
+
    
+euclidlike.getSkyLevel(bandpass, world_pos=None, exptime=None, epoch=2025, date=None)[source]
    
 
    Get the expected sky level for a Euclid observation due to zodiacal light for this bandpass
 and position.
    
 
    This routine can take an arbitray galsim.Bandpass() and calculate the zodiacal background
@@ -82,123 +209,8 @@ 
    Submodules
-
    
-euclidlike.backgrounds.getZodiBackground(ecl_lat, ecl_dlon, lambda_min, lambda_max, Tlambda, T)[source]
    
-
    This helper routine is used with permission from Chris Hirata’s Exposure Time Calculator and enables the
-calculation of the zodiacal light in photons/m^2/arcsec^2/sec. The ETC may be found here:
    
-
    http://www.tapir.caltech.edu/~chirata/web/software/space-etc/
    
-
    The code was ported from C to python by Michael Troxel (matroxel on GitHub).  The units are
-exactly as in the original C code, and we convert to any other needed units outside of this
-routine, in user-facing code.
    
-
    
-
    Parameters:
    
-
      
-
    • ecl_lat – Ecliptic latitude (degrees)
      • 
-
    • ecl_dlon – Ecliptic longitude (degrees)
      • 
-
    • lambda_min – Minimum wavelength for the bandpass (microns)
      • 
-
    • lambda_max – Maximum wavelength for the bandpass (microns)
      • 
-
    • Tlambda – Numpy array containing a grid of wavelength values for the bandpass (microns)
      • 
-
    • T – Numpy array containing the throughput (normalized to be between 0-1) for the
-bandpass
      • 
-
    
-
    
-
    Returns:
    
-
    A floating point value for the zodiacal light in photons/m^2/arcsec^2/sec
    
-
    
-
    
-
    
-
-
    
-
    
-
    euclidlike.bandpass module
    
-
    @file bandpass.py
    
-
    This file includes any routines needed to define the Euclid bandpasses.
-This module is heavily based on the roman bandpass.py file from the GalSim package.
-https://github.com/GalSim-developers/GalSim/blob/releases/2.5/galsim/roman/roman_bandpass.py
    
-
    The Euclid VIS bandpass is read in from the Euclid_VIS.vis.dat file which can be downloaded from
-http://svo2.cab.inta-csic.es/svo/theory/fps3/index.php?mode=browse&gname=Euclid&gname2=VIS&asttype=.
    
-
    The Euclid NISP bandpasses are read in from files downloaded from
-https://euclid.esac.esa.int/msp/refdata/nisp/NISP-PHOTO-PASSBANDS-V1
    
-
    
-
    
-euclidlike.bandpass.getBandpasses(AB_zeropoint=True, default_thin_trunc=True, full_bandpass=False, **kwargs)[source]
    
-
    Function to get the bandpass information for the Euclid VIS band and the three Euclid NISP passbands.
    
-
    This routine reads in files containing a list of wavelengths and
-transmission values for the Euclid bands. The files are located in the
-euclidlike.data directory. The routine then creates a Bandpass object
-using the LookupTable class from the GalSim package, and returns a dict with bandpasses for the
-keys.
    
-
    The bandpasses are publicly available from IPAC:
-http://svo2.cab.inta-csic.es/svo/theory/fps3/index.php?mode=browse&gname=Euclid&gname2=VIS&asttype=.
-https://euclid.esac.esa.int/msp/refdata/nisp/NISP-PHOTO-PASSBANDS-V1
    
-
    These are relatively old files that do not include the latest estimates of system response.
-They correspond to end-of-life estimates, with some expected degradation of the QE and filter
-transmission over time.  This can lead to flux estimates that are suppressed by 5-10% from
-beginning-of-life flux estimates.
    
-
    The VIS bandpass red and blue limits are set not by the transmission curve but by the range of
-wavelengths over which we have tabulated PSF images.  The wavelength range is read in from the
-instrument parameter file.
    
-
    Args:
-AB_zeropoint (bool) : If True, set the zeropoint of the bandpass to the AB magnitude system. [default: True]
-default_thin_trunc (bool) : If True, use the default thinning and truncation parameters. [default: True]
-full_bandpass (bool): if True, use the full bandpass without red/blue limits needed for PSF
    
-
    
-
    calculations. [default: False]
    
-
    
-
    kwargs : Additional keyword arguments to pass to either Bandpass.thin or Bandpass.truncate.
    
-
    
-
-
    
-
    
-
    euclidlike.euclidlike_psf module
    
-
    
-
    
-euclidlike.euclidlike_psf.getBrightPSF(ccd, bandpass, ccd_pos=None, pupil_bin=4, wcs=None, n_waves=None, wavelength=None, gsparams=None, logger=None)[source]
    
-
    Get a fake optical PSF for very bright objects in Euclid-like simulations.
-Depending on the inputs, this routine returns a chromatic or achromatic PSF using the
-Euclid telescope diameter and Euclid-like aperture.
    
-
    Args:
-ccd (int):  Single value specifying the CCD for which the PSF should be
    
-
    
-
    loaded.
    
-
    
-
    
-
    bandpass (str): Single string specifying the bandpass to use when
    defining the pupil plane configuration and/or interpolation of
-chromatic PSFs.
    
-
    
-
    ccd_pos:  Single galsim.PositionD indicating the position within the CCD
    for which the PSF should be created. If None, the exact center of the
-CCD is chosen. [default: None]
    
-
    
-
    wcs:  The WCS to use to project the PSF into world coordinates. [default:
    galsim.PixelScale(euclidlike.pixel_scale)]
    
-
    
-
    n_waves (int): Number of wavelengths to use for setting up interpolation of the
    chromatic PSF objects, which can lead to much faster image
-rendering.  If None, then no interpolation is used. Note that
-users who want to interpolate can always set up the interpolation
-later on even if they do not do so when calling getPSF.
-[default: None]
    
-
    
-
    wavelength (float):  An option to get an achromatic PSF for a single
    wavelength, for users who do not care about chromaticity of the PSF. If
-None, then the fully chromatic PSF is returned as an
-InterpolatedChromaticObject. Alternatively the user should supply
-either (a) a wavelength in nanometers, and they will get an
-InterpolatedImage object for that wavelength, or (b) a bandpass object,
-in which case they will get an InterpolatedImage objects defined at the
-effective wavelength of that bandpass. [default: None]
    
-
    
-
    gsparams:  An optional GSParams argument.  See the docstring for GSParams
    for details. [default: None]
    
-
    
-
    
-
    
-
    Returns:
    
-
    A single PSF object (either an InterpolatedChromaticObject or an
-InterpolatedImage depending on the inputs).
    
-
    
-
    
-
    
-
-
    
-
    
-euclidlike.euclidlike_psf.getPSF(ccd, bandpass, ccd_pos=None, wcs=None, wavelength=None, gsparams=None, logger=None, psf_dir=None)[source]
    
+
    
+euclidlike.getPSF(ccd, bandpass, ccd_pos=None, wcs=None, wavelength=None, gsparams=None, logger=None, psf_dir=None)[source]
    
 
    Get a single PSF for a Euclid-like simulation.
    
 
    These PSFs are based on precomputed, oversampled (by 3x) PSF images on a grid in wavelength and
 focal plane position.  These images were provided by Lance Miller and Chris Duncan.  They are
@@ -276,152 +288,54 @@ 
    Submodules
-
    euclidlike.euclidlike_wcs module
    
-
    @file euclidlike_wcs.py
    
-
    This file includes any routines needed to define and use the Euclid-like WCS.
-Current version is based on the focal plane description detailed in
-Scaramella et al. (Fig. 2 and Table 1).
-The distortion coefficients were derived from the ERO release.
    
-
    Scaramella et al.: https://arxiv.org/abs/2108.01201
    
 
    
-
    
-euclidlike.euclidlike_wcs.allowedPos(world_pos, date, SAA=None)[source]
    
-
    This routine can be used to check whether Euclid would be allowed to look at a particular
-position (world_pos) on a given date.   This is determined by the angle of this position
-relative to the Sun.
    
-
    In general, Euclid can point at angles relative to the Sun in the range 90+20 & 90-3 degrees.
-Obviously, pointing too close to the Sun would result in overly high sky backgrounds.  It is
-less obvious why Euclid cannot look at a spot directly opposite from the Sun (180 degrees on the
-sky).  The reason is that the observatory is aligned such that if the observer is looking at
-some sky position, the solar panels are oriented at 90 degrees from that position.  So it’s
-always optimal for the observatory to be pointing at an angle of 90 degrees relative to the
-Sun.  It is also permitted to look within [-3, + 20] degrees of that optimal position.
    
-
    
-
    Parameters:
    
-
      
-
    • world_pos – A galsim.CelestialCoord indicating the position at which the observer
-wishes to look.
      • 
-
    • date – A python datetime object indicating the desired date of observation.
      • 
-
    • SAA – A galsim.Angle representing the Solar Aspect Angle
-of the telescope for the observation. If not provided,
-it will be computed internally.
      • 
-
    
+
    
+euclidlike.getBrightPSF(ccd, bandpass, ccd_pos=None, pupil_bin=4, wcs=None, n_waves=None, wavelength=None, gsparams=None, logger=None)[source]
    
+
    Get a fake optical PSF for very bright objects in Euclid-like simulations.
+Depending on the inputs, this routine returns a chromatic or achromatic PSF using the
+Euclid telescope diameter and Euclid-like aperture.
    
+
    Args:
+ccd (int):  Single value specifying the CCD for which the PSF should be
    
+
    
+
    loaded.
    
+
    
+
    
+
    bandpass (str): Single string specifying the bandpass to use when
    defining the pupil plane configuration and/or interpolation of
+chromatic PSFs.
    
 
    
-
    Returns:
    
-
    True or False, indicating whether it is permitted to look at this position on this date.
    
+
    ccd_pos:  Single galsim.PositionD indicating the position within the CCD
    for which the PSF should be created. If None, the exact center of the
+CCD is chosen. [default: None]
    
 
    
-
    
-
    
-
-
    
-
    
-euclidlike.euclidlike_wcs.bestPA(world_pos, date, SAA=None)[source]
    
-
    This routine determines the best position angle for the observatory for a given observation date
-and position on the sky.
    
-
    The best/optimal position angle is determined by the fact that the solar panels are at 90
-degrees to the position being observed, and it is best to have those facing the Sun as directly
-as possible.  Note that if a given world_pos is not actually observable on the given
-date, then this routine will return None.
    
-
    
-
    Parameters:
    
-
      
-
    • world_pos – A galsim.CelestialCoord indicating the position at which the observer
-wishes to look.
      • 
-
    • date – A python datetime object indicating the desired date of observation.
      • 
-
    • SAA – A galsim.Angle representing the Solar Aspect Angle
-of the telescope for the observation. If not provided,
-it will be computed internally.
      • 
-
    
+
    wcs:  The WCS to use to project the PSF into world coordinates. [default:
    galsim.PixelScale(euclidlike.pixel_scale)]
    
 
    
-
    Returns:
    
-
    the best position angle for the observatory, as a galsim.Angle, or None if the position
-is not observable.
    
+
    n_waves (int): Number of wavelengths to use for setting up interpolation of the
    chromatic PSF objects, which can lead to much faster image
+rendering.  If None, then no interpolation is used. Note that
+users who want to interpolate can always set up the interpolation
+later on even if they do not do so when calling getPSF.
+[default: None]
    
 
    
-
    
-
    
-
-
    
-
    
-euclidlike.euclidlike_wcs.convertCenter(world_pos, CCD, PA=None, date=None, SAA=None, PA_is_FPA=False, tol=coord.Angle(2.42406840554768e-06, coord.radians))[source]
    
-
    This is a simple helper routine that takes an input position world_pos that is meant to
-correspond to the position of the center of an CCD, and tells where the center of the focal
-plane array should be.  The goal is to provide a position that can be used as an input to
-getWCS(), which wants the center of the focal plane array.
    
-
    The results of the calculation are deterministic if given a fixed position angle (PA).  If it’s
-not given one, it will try to determine the best one for this location and date, like getWCS()
-does.
    
-
    Because of distortions varying across the focal plane, this routine has to iteratively correct
-its initial result based on empirical tests.  The tol kwarg can be used to adjust how
-careful it will be, but it always does at least one iteration.
    
-
    
-
    Parameters:
    
-
      
-
    • world_pos – A galsim.CelestialCoord indicating the position to observe at the center of the
-given CCD.  Note that if the given position is not observable on
-the given date, then the routine will raise an exception.
      • 
-
    • CCD – A single number giving the CCD for which the center should be located at
-world_pos.
      • 
-
    • PA – galsim.Angle representing the position angle of the observatory +Y axis, unless
-PA_is_FPA=True, in which case it’s the position angle of the FPA.  For
-users to do not care about this, then leaving this as None will result in the
-routine using the supplied date and world_pos to select the optimal
-orientation for the observatory.  Note that if a user supplies a PA value,
-the routine does not check whether this orientation is actually allowed.
-[default: None]
      • 
-
    • SAA – A galsim.Angle representing the Solar Aspect Angle
-of the telescope for the observation. If not provided,
-it will be computed internally.
      • 
-
    • date – The date of the observation, as a python datetime object.  If None, then the
-vernal equinox in 2025 will be used.  [default: None]
      • 
-
    • PA_is_FPA – If True, then the position angle that was provided was the PA of the focal
-plane array, not the observatory. [default: False]
      • 
-
    • tol – Tolerance for errors due to distortions, as a galsim.Angle.
-[default: 0.5*galsim.arcsec]
      • 
-
    
+
    wavelength (float):  An option to get an achromatic PSF for a single
    wavelength, for users who do not care about chromaticity of the PSF. If
+None, then the fully chromatic PSF is returned as an
+InterpolatedChromaticObject. Alternatively the user should supply
+either (a) a wavelength in nanometers, and they will get an
+InterpolatedImage object for that wavelength, or (b) a bandpass object,
+in which case they will get an InterpolatedImage objects defined at the
+effective wavelength of that bandpass. [default: None]
    
 
    
-
    Returns:
    
-
    A CelestialCoord object indicating the center of the focal plane array.
    
+
    gsparams:  An optional GSParams argument.  See the docstring for GSParams
    for details. [default: None]
    
 
    
 
    
-
    
-
-
    
-
    
-euclidlike.euclidlike_wcs.findCCD(wcs_dict, world_pos, include_border=False)[source]
    
-
    This is a subroutine to take a dict of WCS (one per CCD) from euclidlike.getWCS() and query
-which CCD a particular real-world coordinate would be located on.  The position (world_pos)
-should be specified as a galsim.CelestialCoord.  If the position is not located on any of the
-CCDs, the result will be None.  Note that if wcs_dict does not include all CCDs in it, then
-it’s possible the position might lie on one of the CCDs that was not included.
    
-
    Depending on what the user wants to do with the results, they may wish to use the
-include_border keyword.  This keyword determines whether or not to include an additional
-border corresponding to half of the gaps between CCDs.  For example, if a user is drawing a
-single image they may wish to only know whether a given position falls onto a CCD, and if so,
-which one (ignoring everything in the gaps).  In contrast, a user who plans to make a sequence
-of dithered images might find it most useful to know whether the position is either on a CCD or
-close enough that in a small dither sequence it might appear on the CCD at some point.  Use of
-include_border switches between these scenarios.
    
 
    
-
    Parameters:
    
-
      
-
    • wcs_dict – The dict of WCS’s output from euclidlike.getWCS().
      • 
-
    • world_pos – A galsim.CelestialCoord indicating the sky position of interest.
      • 
-
    • include_border – If True, then include the half-border around CCD to cover the gap
-between each sensor. [default: False]
      • 
-
    
-
    
-
    Returns:
    
-
    an integer value of the CCD on which the position falls, or None if the position is not
-on any CCD.
    
+
    Returns:
    
+
    A single PSF object (either an InterpolatedChromaticObject or an
+InterpolatedImage depending on the inputs).
    
 
    
 
    
 
    
 
 
    
-
    
-euclidlike.euclidlike_wcs.getWCS(world_pos, PA=None, date=None, CCDs=None, PA_is_FPA=False, SAA=None)[source]
    
+
    
+euclidlike.getWCS(world_pos, PA=None, date=None, CCDs=None, PA_is_FPA=False, SAA=None)[source]
    
 
    This routine returns a dict containing a WCS for each of the Euclid CCDs.
 The Euclid CCDs are labeled 0-35, so these numbers are used as the keys in
 the dict.  Alternatively the user can request a subset of the CCDs using
@@ -475,14 +389,38 @@ 
    Submodules
-
    euclidlike.instrument_params module
    
-
    Basic information GalSim needs to produce Euclid-like simulations.
    
-
    When editing this file, you should also modify the imports in __init__.py
    
-
    
-
    
-
    Module contents
    
+
    
+
    
+euclidlike.findCCD(wcs_dict, world_pos, include_border=False)[source]
    
+
    This is a subroutine to take a dict of WCS (one per CCD) from euclidlike.getWCS() and query
+which CCD a particular real-world coordinate would be located on.  The position (world_pos)
+should be specified as a galsim.CelestialCoord.  If the position is not located on any of the
+CCDs, the result will be None.  Note that if wcs_dict does not include all CCDs in it, then
+it’s possible the position might lie on one of the CCDs that was not included.
    
+
    Depending on what the user wants to do with the results, they may wish to use the
+include_border keyword.  This keyword determines whether or not to include an additional
+border corresponding to half of the gaps between CCDs.  For example, if a user is drawing a
+single image they may wish to only know whether a given position falls onto a CCD, and if so,
+which one (ignoring everything in the gaps).  In contrast, a user who plans to make a sequence
+of dithered images might find it most useful to know whether the position is either on a CCD or
+close enough that in a small dither sequence it might appear on the CCD at some point.  Use of
+include_border switches between these scenarios.
    
+
    
+
    Parameters:
    
+
      
+
    • wcs_dict – The dict of WCS’s output from euclidlike.getWCS().
      • 
+
    • world_pos – A galsim.CelestialCoord indicating the sky position of interest.
      • 
+
    • include_border – If True, then include the half-border around CCD to cover the gap
+between each sensor. [default: False]
      • 
+
    
+
    
+
    Returns:
    
+
    an integer value of the CCD on which the position falls, or None if the position is not
+on any CCD.
    
+
    
+
    
+
    
+
 
    
 
    
 
@@ -512,11 +450,25 @@ 
    GalSim-Euclid-Like
    
     
    
 
 
    Navigation
    
+
 
 
    
 
    Related Topics
    
 
 
    
diff --git a/docs/_build/html/euclidlike_imsim.html b/docs/_build/html/euclidlike_imsim.html
index b9034a0..e6d31e5 100644
--- a/docs/_build/html/euclidlike_imsim.html
+++ b/docs/_build/html/euclidlike_imsim.html
@@ -5,7 +5,7 @@
     
     
 
-    euclidlike_imsim package — GalSim-Euclid-Like 0.0.1 documentation
+    The Euclid-like ImSim Module — GalSim-Euclid-Like 0.0.1 documentation
     
     
     
@@ -14,6 +14,8 @@
     
     
     
+    
+    
    
   
   
@@ -31,49 +33,736 @@
 
           
    
             
-  
    
-
    euclidlike_imsim package
    
-
    
-
    Submodules
    
-
    
-
    
-
    euclidlike_imsim.bandpass module
    
-
    
-
    
-
    euclidlike_imsim.ccd module
    
-
    
-
    
-
    euclidlike_imsim.detector_physics module
    
-
    
-
    
-
    euclidlike_imsim.noise module
    
-
    
-
    
-
    euclidlike_imsim.obseq module
    
-
    
-
    
-
    euclidlike_imsim.photonOps module
    
-
    
-
    
-
    euclidlike_imsim.psf module
    
-
    
-
    
-
    euclidlike_imsim.scafile module
    
-
    
-
    
-
    euclidlike_imsim.skycat module
    
-
    
-
    
-
    euclidlike_imsim.stamp module
    
+  
    
+
    The Euclid-like ImSim Module
    
+
    This module contains configuration scripts to produce large-scale Euclid-like simulation runs based on the information in euclidlike.
+It is based heavily on roman_imsim.
    
+
    
+
    Classes and Functions
    
+
    
+
    
+class euclidlike_imsim.bandpass.EuclidlikeBandpassBuilder[source]
    
+
    A class for loading a Bandpass from a file
    
+
    FileBandpass expected the following parameter:
    
+
    
+
    name (str)          The name of the Euclid filter to get. (required)
    
+
    
+
    
+
    
+buildBandpass(config, base, logger)[source]
    
+
    Build the Bandpass based on the specifications in the config dict.
    
+
    
+
    Parameters:
    
+
      
+
    • config – The configuration dict for the bandpass type.
      • 
+
    • base – The base configuration dict.
      • 
+
    • logger – If provided, a logger for logging debug statements.
      • 
+
    
+
    
+
    Returns:
    
+
    the constructed Bandpass object.
    
+
    
+
    
+
    
+
+
    
+
+
    
+
    
+class euclidlike_imsim.ccd.EuclidlikeCCDImageBuilder[source]
    
+
    
+
    
+addNoise(image, config, base, image_num, obj_num, current_var, logger)[source]
    
+
    Add the final noise to a Scattered image
    
+
    
+
    Parameters:
    
+
      
+
    • image – The image onto which to add the noise.
      • 
+
    • config – The configuration dict for the image field.
      • 
+
    • base – The base configuration dict.
      • 
+
    • image_num – The current image number.
      • 
+
    • obj_num – The first object number in the image.
      • 
+
    • current_var – The current noise variance in each postage stamps.
      • 
+
    • logger – If given, a logger object to log progress.
      • 
+
    
+
    
+
    
+
    
+
+
    
+
    
+buildImage(config, base, image_num, obj_num, logger)[source]
    
+
    Build an Image containing multiple objects placed at arbitrary locations.
    
+
    
+
    Parameters:
    
+
      
+
    • config – The configuration dict for the image field.
      • 
+
    • base – The base configuration dict.
      • 
+
    • image_num – The current image number.
      • 
+
    • obj_num – The first object number in the image.
      • 
+
    • logger – If given, a logger object to log progress.
      • 
+
    
+
    
+
    Returns:
    
+
    the final image and the current noise variance in the image as a tuple
    
+
    
+
    
+
    
+
+
    
+
    
+setup(config, base, image_num, obj_num, ignore, logger)[source]
    
+
    Do the initialization and setup for building the image.
    
+
    This figures out the size that the image will be, but doesn’t actually build it yet.
    
+
    
+
    Parameters:
    
+
      
+
    • config – The configuration dict for the image field.
      • 
+
    • base – The base configuration dict.
      • 
+
    • image_num – The current image number.
      • 
+
    • obj_num – The first object number in the image.
      • 
+
    • ignore – A list of parameters that are allowed to be in config that we can
+ignore here. i.e. it won’t be an error if these parameters are present.
      • 
+
    • logger – If given, a logger object to log progress.
      • 
+
    
+
    
+
    Returns:
    
+
    xsize, ysize
    
+
    
+
    
+
    
+
+
    
+
+
    
+
    
+class euclidlike_imsim.noise.NoiseImageBuilder[source]
    
+
    
+
    
+initialize(data, scratch, config, base, logger)[source]
    
+
    Do any initial setup for this builder at the start of a new output file.
    
+
    The base class implementation saves two work space items into self.data and self.scratch
+that can be used to safely communicate across multiple processes.
    
+
    
+
    Parameters:
    
+
      
+
    • data – An empty list of length nimages to use as work space.
      • 
+
    • scratch – An empty dict that can be used as work space.
      • 
+
    • config – The configuration field for this output object.
      • 
+
    • base – The base configuration dict.
      • 
+
    • logger – If given, a logger object to log progress. [default: None]
      • 
+
    
+
    
+
    
+
    
+
+
    
+
    
+processImage(index, obj_nums, config, base, logger)[source]
    
+
    Perform any necessary processing at the end of each image construction.
    
+
    This function will be called after each full image is built.
    
+
    Compute the noise for the current image and add it to the image.
+It will also create an independent noise image.
+The code optionally subtract the background if requested.
    
+
    
+
    Parameters:
    
+
      
+
    • index – The index in self.data to use for this image.  This isn’t the image_num
+(which can be accessed at base[‘image_num’] if needed), but rather
+an index that starts at 0 for the first image being worked on and
+goes up to nimages-1.
      • 
+
    • obj_nums – The object numbers that were used for this image.
      • 
+
    • config – The configuration field for this output object.
      • 
+
    • base – The base configuration dict.
      • 
+
    • logger – If given, a logger object to log progress. [default: None]
      • 
+
    
+
    
+
    
+
    
+
+
    
+
+
    
+
    
+class euclidlike_imsim.noise.SkyImageBuilder[source]
    
+
    
+
    
+processImage(index, obj_nums, config, base, logger)[source]
    
+
    Perform any necessary processing at the end of each image construction.
    
+
    This function will be called after each full image is built.
    
+
    Compute the sky background and return it in an image.
    
+
    
+
    Parameters:
    
+
      
+
    • index – The index in self.data to use for this image.  This isn’t the image_num
+(which can be accessed at base[‘image_num’] if needed), but rather
+an index that starts at 0 for the first image being worked on and
+goes up to nimages-1.
      • 
+
    • obj_nums – The object numbers that were used for this image.
      • 
+
    • config – The configuration field for this output object.
      • 
+
    • base – The base configuration dict.
      • 
+
    • logger – If given, a logger object to log progress. [default: None]
      • 
+
    
+
    
+
    
+
    
+
+
    
+
+
    
+
    
+class euclidlike_imsim.noise.WeightImageBuilder[source]
    
+
    
+
    
+processImage(index, obj_nums, config, base, logger)[source]
    
+
    Perform any necessary processing at the end of each image construction.
    
+
    This function will be called after each full image is built.
    
+
    Compute the weight map from the noise image and return it in an image.
    
+
    
+
    Parameters:
    
+
      
+
    • index – The index in self.data to use for this image.  This isn’t the image_num
+(which can be accessed at base[‘image_num’] if needed), but rather
+an index that starts at 0 for the first image being worked on and
+goes up to nimages-1.
      • 
+
    • obj_nums – The object numbers that were used for this image.
      • 
+
    • config – The configuration field for this output object.
      • 
+
    • base – The base configuration dict.
      • 
+
    • logger – If given, a logger object to log progress. [default: None]
      • 
+
    
+
    
+
    
+
    
+
+
    
+
+
    
+
    
+euclidlike_imsim.noise.get_noise(cfg_noise, cfg_image, base, logger)[source]
    
+
    
+
+
    
+
    
+euclidlike_imsim.noise.parse_noise_config(params)[source]
    
+
    
+
+
    
+
    
+euclidlike_imsim.obseq.ObSeqData(config, base, value_type)[source]
    
+
    Returns the obseq data for a pointing.
    
+
    
+
+
    
+
    
+class euclidlike_imsim.obseq.ObSeqDataLoader(file_name, visit, obs_kind, CCD, logger=None)[source]
    
+
    Read the exposure information from the observation sequence.
    
+
    
+
    
+get(field, default=None, obs_kind=None)[source]
    
+
    
+
+
    
+
    
+read_obseq()[source]
    
+
    Read visit info from the obseq file.
    
+
    
+
+
    
+
+
    
+
    
+class euclidlike_imsim.photonOps.ChargeDiff(rng=None, **kwargs)[source]
    
+
    A photon operator that applies the effect of charge diffusion via a probablistic model limit.
    
+
    
+
    
+applyTo(photon_array, local_wcs=None, rng=None)[source]
    
+
    Apply the charge diffusion effect to the photons
    
+
    
+
    Parameters:
    
+
      
+
    • photon_array – A PhotonArray to apply the operator to.
      • 
+
    • local_wcs – A LocalWCS instance defining the local WCS for the current photon
+bundle in case the operator needs this information.  [default: None]
      • 
+
    • rng – A random number generator to use if needed. [default: None]
      • 
+
    
+
    
+
    
+
    
+
+
    
+
+
    
+
    
+class euclidlike_imsim.photonOps.ChargeDiffBuilder[source]
    
+
    Build ChargeDiff photonOp
    
+
    
+
    
+buildPhotonOp(config, base, logger)[source]
    
+
    Build the PhotonOp based on the specifications in the config dict.
    
+
    Note: Sub-classes must override this function with a real implementation.
    
+
    
+
    Parameters:
    
+
      
+
    • config – The configuration dict for the PhotonOp
      • 
+
    • base – The base configuration dict.
      • 
+
    • logger – If provided, a logger for logging debug statements.
      • 
+
    
+
    
+
    Returns:
    
+
    the constructed PhotonOp object.
    
+
    
+
    
+
    
+
+
    
+
+
    
+
    
+class euclidlike_imsim.psf.EuclidlikePSF(CCD=None, WCS=None, n_waves=None, bpass=None, extra_aberrations=None, logger=None)[source]
    
+
    Class building needed Euclidlike PSFs.
    
+
    
+
    
+getPSF(pupil_bin, pos)[source]
    
+
    Return a PSF to be convolved with sources.
+PSF is sampled at 4 quadrants for each CCD. Returned PSF
+corresponds to that of the quadrant of the CCD position.
    
+
    @param [in] what pupil binning to request.
    
+
    
+
+
    
+
+
    
+
    
+class euclidlike_imsim.psf.PSFLoader[source]
    
+
    PSF loader.
    
+
    
+
    
+getKwargs(config, base, logger)[source]
    
+
    Parse the config dict and return the kwargs needed to build the input object.
    
+
    The default implementation looks for special class attributes called:
    
+
    
+
    _req_params
    A dict of required parameters and their types.
    
+
    
+
    _opt_params
    A dict of optional parameters and their types.
    
+
    
+
    _single_params
    A list of dicts of parameters such that one and only one of
+parameter in each dict is required.
    
+
    
+
    _takes_rng
    A bool value saying whether an rng object is required.
    
+
    
+
    
+
    See galsim.Catalog for an example of a class that sets these attributes.
    
+
    In addition to the kwargs, we also return a bool value, safe, that indicates whether
+the constructed object will be safe to keep around for multiple files (True) of if
+it will need to be rebuilt for each output file (False).
    
+
    
+
    Parameters:
    
+
      
+
    • config – The config dict for this input item
      • 
+
    • base – The base config dict
      • 
+
    • logger – If given, a logger object to log progress. [default: None]
      • 
+
    
+
    
+
    Returns:
    
+
    kwargs, safe
    
+
    
+
    
+
    
+
+
    
+
+
    Interface to obtain objects from skyCatalogs.
    
+
    
+
    
+euclidlike_imsim.skycat.SkyCatObj(config, base, ignore, gsparams, logger)[source]
    
+
    Build an object according to info in the sky catalog.
    
+
    
+
+
    
+
    
+euclidlike_imsim.skycat.SkyCatValue(config, base, value_type)[source]
    
+
    Return a value from the object part of the skyCatalog
    
+
    
+
+
    
+
    
+euclidlike_imsim.skycat.SkyCatWorldPos(config, base, value_type)[source]
    
+
    Return a value from the object part of the skyCatalog
    
+
    
+
+
    
+
    
+class euclidlike_imsim.skycat.SkyCatalogInterface(file_name, exptime, wcs=None, mjd=None, bandpass=None, xsize=None, ysize=None, obj_types=None, edge_pix=100, max_flux=None, logger=None)[source]
    
+
    Interface to skyCatalogs package.
    
+
    
+
    
+getApproxNObjects()[source]
    
+
    Return the approximate number of GSObjects to render, as set in
+the class initializer.
    
+
    
+
+
    
+
    
+getFlux(index, filter=None, mjd=None, exptime=None)[source]
    
+
    Return the flux associated to an object.
    
+
    
+
    Parameters:
    
+
      
+
    • index (int) – Index of the object in the self.objects catalog.
      • 
+
    • filter (str, optional) – Name of the filter for which the flux is computed. If None, use the
+filter provided during initialization. [Default: None]
      • 
+
    • mjd (float, optional) – Date of the observation in MJD format. If None, use the
+mjd provided during initialization. [Default: None]
      • 
+
    • exptime (int or float, optional) – Exposure time of the observation. If None, use the
+exptime provided during initialization. [Default: None]
      • 
+
    
+
    
+
    Returns:
    
+
    Computer flux at the given date for the requested exposure time and
+filter.
    
+
    
+
    Return type:
    
+
    flux
    
+
    
+
    
+
    
+
+
    
+
    
+getNObjects()[source]
    
+
    Return the number of GSObjects to render
    
+
    
+
+
    
+
    
+getObj(index, gsparams=None, rng=None, exptime=30)[source]
    
+
    Return the galsim object for the skyCatalog object
+corresponding to the specified index.  If the skyCatalog
+object is a galaxy, the returned galsim object will be
+a galsim.Sum.
    
+
    
+
    Parameters:
    
+
    index (int) – Index of the object in the self.objects catalog.
    
+
    
+
    Return type:
    
+
    galsim.GSObject
    
+
    
+
    
+
    
+
+
    
+
    
+getValue(index, field)[source]
    
+
    Return a skyCatalog value for the an object.
    
+
    
+
    Parameters:
    
+
      
+
    • index (int) – Index of the object in the self.objects catalog.
      • 
+
    • field (str) – Name of the field for which you want the value.
      • 
+
    
+
    
+
    Returns:
    
+
    The value associated to the field or None if the field do not exist.
    
+
    
+
    Return type:
    
+
    int or float or str or None
    
+
    
+
    
+
    
+
+
    
+
    
+getWorldPos(index)[source]
    
+
    Return the sky coordinates of the skyCatalog object
+corresponding to the specified index.
    
+
    
+
    Parameters:
    
+
    index (int) – Index of the (object_index, subcomponent) combination.
    
+
    
+
    Return type:
    
+
    galsim.CelestialCoord
    
+
    
+
    
+
    
+
+
    
+
    
+get_ccd_center()[source]
    
+
    Return the CCD center.
    
+
    
+
+
    
+
    
+property objects
    
+
    
+
+
    
+
+
    
+
    
+class euclidlike_imsim.skycat.SkyCatalogLoader(init_func, has_nobj=False, file_scope=False, takes_logger=False, use_proxy=True, worker_init=None, worker_initargs=None)[source]
    
+
    Class to load SkyCatalogInterface object.
    
+
    
+
    
+getKwargs(config, base, logger)[source]
    
+
    Parse the config dict and return the kwargs needed to build the input object.
    
+
    The default implementation looks for special class attributes called:
    
+
    
+
    _req_params
    A dict of required parameters and their types.
    
+
    
+
    _opt_params
    A dict of optional parameters and their types.
    
+
    
+
    _single_params
    A list of dicts of parameters such that one and only one of
+parameter in each dict is required.
    
+
    
+
    _takes_rng
    A bool value saying whether an rng object is required.
    
+
    
+
    
+
    See galsim.Catalog for an example of a class that sets these attributes.
    
+
    In addition to the kwargs, we also return a bool value, safe, that indicates whether
+the constructed object will be safe to keep around for multiple files (True) of if
+it will need to be rebuilt for each output file (False).
    
+
    
+
    Parameters:
    
+
      
+
    • config – The config dict for this input item
      • 
+
    • base – The base config dict
      • 
+
    • logger – If given, a logger object to log progress. [default: None]
      • 
+
    
+
    
+
    Returns:
    
+
    kwargs, safe
    
+
    
+
    
+
    
+
+
    
+
+
    
+
    
+class euclidlike_imsim.stamp.Euclidlike_stamp[source]
    
+
    This performs the tasks necessary for building the stamp for a single object.
    
+
    It uses the regular Basic functions for most things.
+It specializes the quickSkip, buildProfile, and draw methods.
    
+
    
+
    
+buildPSF(config, base, gsparams, logger)[source]
    
+
    Build the PSF object.
    
+
    For the Basic stamp type, this builds a PSF from the base[‘psf’] dict, if present,
+else returns None.
    
+
    
+
    Parameters:
    
+
      
+
    • config – The configuration dict for the stamp field.
      • 
+
    • base – The base configuration dict.
      • 
+
    • gsparams – A dict of kwargs to use for a GSParams.  More may be added to this
+list by the galaxy object.
      • 
+
    • logger – A logger object to log progress.
      • 
+
    
+
    
+
    Returns:
    
+
    the PSF
    
+
    
+
    
+
    
+
+
    
+
    
+draw(prof, image, method, offset, config, base, logger)[source]
    
+
    Draw the profile on the postage stamp image.
    
+
    
+
    Parameters:
    
+
      
+
    • prof – The profile to draw.
      • 
+
    • image – The image onto which to draw the profile (which may be None).
      • 
+
    • method – The method to use in drawImage.
      • 
+
    • offset – The offset to apply when drawing.
      • 
+
    • config – The configuration dict for the stamp field.
      • 
+
    • base – The base configuration dict.
      • 
+
    • logger – A logger object to log progress.
      • 
+
    
+
    
+
    Returns:
    
+
    the resulting image
    
+
    
+
    
+
    
+
+
    
+
    
+classmethod fix_seds(prof, bandpass)[source]
    
+
    
+
+
    
+
    
+getDrawMethod(config, base, logger)[source]
    
+
    Determine the draw method to use.
    
+
    @param config       The configuration dict for the stamp field.
+@param base         The base configuration dict.
+@param logger       A logger object to log progress.
    
+
    @returns method
    
+
    
+
+
    
+
    
+setup(config, base, xsize, ysize, ignore, logger)[source]
    
+
    Do the initialization and setup for building a postage stamp.
    
+
    In the base class, we check for and parse the appropriate size and position values in
+config (aka base[‘stamp’] or base[‘image’].
    
+
    Values given in base[‘stamp’] take precedence if these are given in both places (which
+would be confusing, so probably shouldn’t do that, but there might be a use case where it
+would make sense).
    
+
    
+
    Parameters:
    
+
      
+
    • config – The configuration dict for the stamp field.
      • 
+
    • base – The base configuration dict.
      • 
+
    • xsize – The xsize of the image to build (if known).
      • 
+
    • ysize – The ysize of the image to build (if known).
      • 
+
    • ignore – A list of parameters that are allowed to be in config that we can
+ignore here. i.e. it won’t be an error if these parameters are present.
      • 
+
    • logger – A logger object to log progress.
      • 
+
    
+
    
+
    Returns:
    
+
    xsize, ysize, image_pos, world_pos
    
+
    
+
    
+
    
+
+
    
+
+
    
+
    
+class euclidlike_imsim.utils.roman_utils(config_file, visit=None, sca=None, image_name=None, setup_skycat=False)[source]
    
+
    Class to contain a variety of helper routines to work with the simulation data.
    
+
    
+
    
+check_input(visit, sca, image_name)[source]
    
+
    
+
+
    
+
    
+getBandpass()[source]
    
+
    Return Roman bandpass for image
    
+
    
+
+
    
+
    
+getLocalWCS(x, y)[source]
    
+
    Return Roman WCS for image
    
+
    
+
+
    
+
    
+getPSF(x=None, y=None, pupil_bin=8)[source]
    
+
    Return Roman PSF for some image position.
+:param x: x-position in SCA
+:param y: y-position in SCA
+:param pupil_bin: pupil image binning factor
    
+
    
+
    Returns:
    
+
    the chromatic GalSim PSF model object (does not include additional effects like charge diffusion!)
    
+
    
+
    
+
    
+
+
    
+
    
+getPSF_Image(stamp_size, x=None, y=None, pupil_bin=8, sed=None, oversampling_factor=1, include_photonOps=False, n_phot=1000000.0)[source]
    
+
    Return a Roman PSF image for some image position
+:param stamp_size: size of output PSF model stamp in native roman pixel_scale (oversampling_factor=1)
+:param x: x-position in SCA
+:param y: y-position in SCA
+:param pupil_bin: pupil image binning factor
+:param sed: SED to be used to draw the PSF - default is a flat SED.
+:param oversampling_factor: factor by which to oversample native roman pixel_scale
+:param include_photonOps: include additional contributions from other photon operators in effective psf image
    
+
    
+
    Returns:
    
+
    the PSF GalSim image object (use image.array to get a numpy array representation)
    
+
    
+
    
+
    
+
+
    
+
    
+getWCS()[source]
    
+
    Return Roman WCS for image
    
+
    
+
+
    
+
+
    
+
    
+class euclidlike_imsim.wcs.EuclidlikeWCS[source]
    
+
    
+
    
+buildWCS(config, base, logger)[source]
    
+
    Build the WCS based on the specifications in the config dict.
    
+
    Note: Sub-classes must override this function with a real implementation.
    
+
    
+
    Parameters:
    
+
      
+
    • config – The configuration dict for the wcs type.
      • 
+
    • base – The base configuration dict.
      • 
+
    • logger – If provided, a logger for logging debug statements.
      • 
+
    
+
    
+
    Returns:
    
+
    the constructed WCS object.
    
+
    
+
    
+
    
+
+
    
+
 
    
-
    
-
    euclidlike_imsim.utils module
    
+
    
+
    Use
    
+
    Example files needed for large-scale Euclid-like simulation runs are included in GalSim-Euclid-Like/config.
    
 
    
-
    
-
    euclidlike_imsim.wcs module
    
+
    
+
    Config imsim
    
+
    was.yaml: euclidlike_imsim example config file.
+You will want to update the following entries:
    
+
      
+
    • input.obseq_data.file_name: path to the observing sequence. Link to euclidlike/data/euclid_obseq.fits
      • 
+
    • input.sky_catalog.file_name: path to the skyCatalog to use
      • 
+
    • output.dir: path to the output directory for the simulated images
      • 
+
    • output.truth.dir: path to the output directory for the true catalogs
      • 
+
    
+
    To run the code:
    
+
    galsim was.yaml
+
    
+
    
+
    You might want to specify some config entries on the command line, like:
    
+
    galsim was.yaml input.obseq_data.visit=33690 image.CCD=1
+
    
+
    
 
    
-
    
-
    Module contents
    
+
    
+
    Config SLURM
    
+
    slurm_runner.sh contains the SLURM configuration to run “large scale” simulations.
+You will want to update the following lines:
    
+
      
+
    • #!/bin/zsh: depending on the shell you are using, you might want to change it to: #!/bin/bash
      • 
+
    • #SBATCH --output=/path/to/slurm-%A-%a.out: SLURM stdout file
      • 
+
    • #SBATCH --error=/path/to/slurm-%A-%a.err: SLURM stderr file
      • 
+
    • source activate [env_name]: conda environment to use
      • 
+
    • file_list='/path/to/run_list.txt': file containing the pointings to simulate (see note below)
      • 
+
    
+
    The run_list.txt is a 2-column file with the pointing and the CCD_ID to simulate. It should look like:
    
+
    33688 0
+33688 1
+33688 2
+[...]
+33688 35
+33689 0
+33689 1
+[...]
+
    
+
    
 
    
 
    
 
@@ -103,11 +792,27 @@ 
    GalSim-Euclid-Like
    
     
    
 
 
    Navigation
    
+
 
 
    
 
    Related Topics
    
 
 
    
diff --git a/docs/_build/html/examples.html b/docs/_build/html/examples.html
new file mode 100644
index 0000000..4fd9454
--- /dev/null
+++ b/docs/_build/html/examples.html
@@ -0,0 +1,135 @@
+
+
+
+  
+    
+    
+
+    Examples — GalSim-Euclid-Like 0.0.1 documentation
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
+   
+  
+  
+
+  
+  
+
+  
+  
+
+    
    
+      
    
+        
    
+          
+
+          
    
+            
+  
    
+
    Examples
    
+
    The GalSim-Euclid-Like/examples directory contains example files for how use the euclidlike module.
    
+
    
+
    End-to-end demo
    
+
    end_to_end_demo.py.py
    
+
    This first demo is the euclidlike-equivalent of  demo 13 in GalSim. This demo uses the Euclid-like PSF, WCS, and background noise to produce a realistic scene of galaxies and stars as observed from a Euclid-like Telescope.
    
+
    ** Features introduced in the Python file**:
    
+
      
+
    • euclidlike.getBandpasses(AB_zeropoint)
      • 
+
    • euclidlike.getWCS(world_pos, CCDs_CCD, date)
      • 
+
    • euclidlike.getPSF(use_CCD, filter_name, wcs)
      • 
+
    • euclidlike.getSkyLevel(bandpass, world_pos)
      • 
+
    
+
    The output generated from this file can be visualized by running the script end_to_end_demo.py.py
    
+
    
+
    
+
    Focal Plane Layout
    
+
    plot_VIS.py
    
+
    This Jupyter Notebook shows the display of the focal plane used in the euclidlike package, along with the CCD centers and ID convention.
    
+
    
+
    
+
+
+          
    
+          
+        
    
+      
    
+      
+      
    
+    
    
+    
    
+      ©2024, Rachel Mandelbaum, Axel Guinot, Federico Berlfein, Andy Park, Xiangchong Li, Michael Troxel, Tianqing Zhang.
+      
+      |
+      Powered by Sphinx 8.1.3
+      & Alabaster 1.0.0
+      
+      |
+      Page source
+    
    
+
+    
+
+    
+  
+
\ No newline at end of file
diff --git a/docs/_build/html/genindex.html b/docs/_build/html/genindex.html
index 9c9d874..5f05424 100644
--- a/docs/_build/html/genindex.html
+++ b/docs/_build/html/genindex.html
@@ -37,16 +37,30 @@ 
    Index
    
  A
  | B
  | C
+ | D
  | E
  | F
  | G
+ | I
  | M
+ | N
+ | O
+ | P
+ | Q
+ | R
+ | S
+ | U
+ | W
  
 
    
 
    A
    
 
+  
    
   
 
    
@@ -54,7 +68,17 @@ 
    A
    
 
    B
    
 
+  
    
   
 
    
@@ -62,7 +86,33 @@ 
    B
    
 
    C
    
 
+  
+
    
   
    
+
+
    D
    
+
+  
+  
    
 
    
@@ -71,56 +121,98 @@ 
    E
    
 
    
   
   
 
    
 
 
    F
    
 
+  
    
   
 
    
@@ -128,19 +220,73 @@ 
    F
    
 
    G
    
 
+
    
   
   
    
+
+
    I
    
+
+  
    
 
    
@@ -148,23 +294,174 @@ 
    G
    
 
    M
    
 
+
    
   
    
+
+
    N
    
+
+  
+
    
+
+
    O
    
+
+  
+  
+
    
+
+
    P
    
+
+  
+  
+
    
+
+
    Q
    
+
+  
+
    
+
+
    R
    
+
+  
+  
+
    
+
+
    S
    
+
+  
+  
+
    
+
+
    U
    
+
+  
+
    
+
+
    W
    
+
+  
    
 
    
 
@@ -195,6 +492,14 @@ 
    GalSim-Euclid-Like
    
     
    
 
 
    Navigation
    
+
 
 
    
 
    Related Topics
    
diff --git a/docs/_build/html/history.html b/docs/_build/html/history.html
new file mode 100644
index 0000000..9f69abb
--- /dev/null
+++ b/docs/_build/html/history.html
@@ -0,0 +1,123 @@
+
+
+
+  
+    
+    
+
+    Revision History — GalSim-Euclid-Like 0.0.1 documentation
+    
+    
+    
+    
+    
+    
+    
+    
+    
+   
+  
+  
+
+  
+  
+
+  
+  
+
+    
    
+      
    
+        
    
+          
+
+          
    
+            
+  
    
+
    Revision History
    
+
    
+
    Changes from v0.0.0 to v0.0.1
    
+
    Made repo public.
    
+
    
+
    
+
    Older Versions
    
+
    
+
    
+
    
+
    
+
+
+          
    
+          
+        
    
+      
    
+      
+      
    
+    
    
+    
    
+      ©2024, Rachel Mandelbaum, Axel Guinot, Federico Berlfein, Andy Park, Xiangchong Li, Michael Troxel, Tianqing Zhang.
+      
+      |
+      Powered by Sphinx 8.1.3
+      & Alabaster 1.0.0
+      
+      |
+      Page source
+    
    
+
+    
+
+    
+  
+
\ No newline at end of file
diff --git a/docs/_build/html/index.html b/docs/_build/html/index.html
index 5cb8389..73125c7 100644
--- a/docs/_build/html/index.html
+++ b/docs/_build/html/index.html
@@ -5,7 +5,7 @@
     
     
 
-    GalSim-Euclid-Like — GalSim-Euclid-Like 0.0.1 documentation
+    GalSim-Euclid-Like: Euclid-like images using GalSim — GalSim-Euclid-Like 0.0.1 documentation
     
     
     
@@ -14,6 +14,7 @@
     
     
     
+    
    
   
   
@@ -31,57 +32,56 @@
 
           
    
             
-  
    
-
    GalSim-Euclid-Like
    
-
    Helper functions to generate simulations of Euclid-like images using GalSim.
    
-
    This repository contains information about the Euclid space telescope and survey that is needed to
-produce simulations using GalSim.  Some of the
-information provided is approximate, aimed towards fast simulations rather than full accuracy in
-representation of Euclid images.  Places where the information is only approximate are flagged and
-described in the docstring, and we particularly highlight that the PSF is only approximate;
-for details, see the docstring of the getPSF() method.  This library should enable generation of
-Euclid-like images of sufficient fidelity for preliminary exploration of object detection,
-photometry, deblending, and joint analysis with ground-based observatories.  For
-applications requiring high precision such as weak lensing, the higher fidelity simulations
-available within the Euclid Consortium should be used.
    
-
    This repository includes two distinct packages:
    
-
    
 
 
    Navigation
    
+
 
 
    
 
    Related Topics
    
 
 
    
diff --git a/docs/_build/html/install.html b/docs/_build/html/install.html
new file mode 100644
index 0000000..11726e8
--- /dev/null
+++ b/docs/_build/html/install.html
@@ -0,0 +1,150 @@
+
+
+
+  
+    
+    
+
+    Installation — GalSim-Euclid-Like 0.0.1 documentation
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
+   
+  
+  
+
+  
+  
+
+  
+  
+
+    
    
+      
    
+        
    
+          
+
+          
    
+            
+  
    
+
    Installation
    
+
    
+
    Installation Instructions
    
+
    The GalSim-Euclid-Like repository contains two python libraries and currently supports Python versions 3.10 and above.
    
+
    System requirements: Given the heavy dependance on GalSim, GalSim-Euclid-Like currently only supports Linux and Mac OSX. For
+further details on system requirements for GalSim see GalSim Installation.
    
+
    
+
    Dependencies
    
+
    GalSim-Euclid-Like requires python>=3.10 and the following dependencies:
    
+
    numpy>=1.17,
+galsim>=2.6,
+astropy>=2.0
+
    
+
    
+
    
+
    
+
    Installation
    
+
    The source code for GalSim-Euclid-Like has not been published to pypi. To install from source code:
    
+
    git clone git@github.com:GalSim-developers/GalSim-Euclid-Like.git
+
    
+
    
+
    and install by running:
    
+
    conda create -n euclidlike python=3.10
+cd GalSim-Euclid-Like
+conda activate euclidlike
+pip install .
+
    
+
    
+
    To make sure the installation is successful, do the following:
    
+
    $ python
+>>> import euclidlike
+>>> euclidlike.getBandpasses()
+
    
+
    
+
    
+
    
+
    
+
+
+          
    
+          
+        
    
+      
    
+      
+      
    
+    
    
+    
    
+      ©2024, Rachel Mandelbaum, Axel Guinot, Federico Berlfein, Andy Park, Xiangchong Li, Michael Troxel, Tianqing Zhang.
+      
+      |
+      Powered by Sphinx 8.1.3
+      & Alabaster 1.0.0
+      
+      |
+      Page source
+    
    
+
+    
+
+    
+  
+
\ No newline at end of file
diff --git a/docs/_build/html/modules.html b/docs/_build/html/modules.html
index 71109a5..b8967d7 100644
--- a/docs/_build/html/modules.html
+++ b/docs/_build/html/modules.html
@@ -5,7 +5,7 @@
     
     
 
-    GalSim-Euclid-Like — GalSim-Euclid-Like 0.0.1 documentation
+    <no title> — GalSim-Euclid-Like 0.0.1 documentation
     
     
     
@@ -31,65 +31,144 @@
 
           
    
             
-  
    
-
    GalSim-Euclid-Like
    
-
    
+  
    
 
    
-
    
 
 
           
    
@@ -117,6 +196,14 @@ 
    GalSim-Euclid-Like
    
     
    
 
 
    Navigation
    
+
 
 
    
 
    Related Topics
    
diff --git a/docs/_build/html/objects.inv b/docs/_build/html/objects.inv
index 5e4256b..24e0d91 100644
Binary files a/docs/_build/html/objects.inv and b/docs/_build/html/objects.inv differ
diff --git a/docs/_build/html/overview.html b/docs/_build/html/overview.html
new file mode 100644
index 0000000..47dd1b5
--- /dev/null
+++ b/docs/_build/html/overview.html
@@ -0,0 +1,173 @@
+
+
+
+  
+    
+    
+
+    Overview — GalSim-Euclid-Like 0.0.1 documentation
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
+   
+  
+  
+
+  
+  
+
+  
+  
+
+    
    
+      
    
+        
    
+          
+
+          
    
+            
+  
    
+
    Overview
    
+
    
+
    GalSim-Euclid-Like
    
+
    Helper functions to generate simulations of Euclid-like images using GalSim.
    
+
    This repository contains information about the Euclid space telescope and survey that is needed to
+produce simulations using GalSim.  Some of the
+information provided is approximate, aimed towards fast simulations rather than full accuracy in
+representation of Euclid images.  Places where the information is only approximate are flagged and
+described in the docstring, and we particularly highlight that the PSF is only approximate;
+for details, see the docstring of the getPSF() method.  This library should enable generation of
+Euclid-like images of sufficient fidelity for preliminary exploration of object detection,
+photometry, deblending, and joint analysis with ground-based observatories.  For
+applications requiring high precision such as weak lensing, the higher fidelity simulations
+available within the Euclid Consortium should be used.
    
+
    This repository includes two distinct packages:
    
+
      
+
    • euclidlike: has basic observatory, instrumentation, and survey information for Euclid.
+This package can be used on its own along with GalSim to produce Euclid-like simulations.
      • 
+
    • euclidlike_imsim: has configuration scripts to produce large-scale Euclid-like simulation runs
+based on the information in euclidlike. It is based heavily on roman_imsim.
      • 
+
    
+
    
+
    
+
    References
    
+
    For more information about GalSim, please see its README and documentation.
    
+
    For more information about Euclid, please see the Euclid Consortium website and papers linked from there.
    
+
    Attribution for software and data used by particular routines in this library is given in the docstring for the relevant routine.
    
+
    
+
    
+
    Installation
    
+
    Please view the installation instructions for details on how to install GalSim-Euclid-Like.
    
+
    
+
    
+
    Downloading relevant data
    
+
    The Euclid-like PSF is constructed from precomputed oversampled images on a grid in focal plane position and wavelength. To use the full FOV PSF within GalSim-Euclid-Like, the images must be downloaded by running:
    
+
    $ euclidlike_download_psf
+
    
+
    
+
    in the terminal after installation of GalSim-Euclid-Like. To install in an alternative directory to the default, use the --dir argument. Refer to the getPSF documentation for further details about the PSF.
    
+
    
+
    
+
    Getting started
    
+
    Please see the examples/ directory for demos illustrating the use of this code.
    
+
    
+
    
+
    Communicating with the developers
    
+
    Feel free to open a GitHub issue to reach the developers with questions, comments, and bug reports.  New contributors are also welcome and can indicate their interest in developing this code base through the Issues.
    
+
    
+
    
+
    Attribution
    
+
    This software is open source and may be used according to the terms of its license.
    
+
    When using this software, please provide the URL to the repository in the resulting paper or note.  Once there is a Zenodo DOI or journal article, this README will be updated and we will ask those using the code in their research to cite the relevant journal article.
    
+
    
+
    
+
+
+          
    
+          
+        
    
+      
    
+      
+      
    
+    
    
+    
    
+      ©2024, Rachel Mandelbaum, Axel Guinot, Federico Berlfein, Andy Park, Xiangchong Li, Michael Troxel, Tianqing Zhang.
+      
+      |
+      Powered by Sphinx 8.1.3
+      & Alabaster 1.0.0
+      
+      |
+      Page source
+    
    
+
+    
+
+    
+  
+
\ No newline at end of file
diff --git a/docs/_build/html/py-modindex.html b/docs/_build/html/py-modindex.html
index f0b916e..9330300 100644
--- a/docs/_build/html/py-modindex.html
+++ b/docs/_build/html/py-modindex.html
@@ -37,7 +37,8 @@
    
    Python Module Index
    
 
    
    
-   e
+   e | 
+   s
    
    
 
    
@@ -48,32 +49,76 @@ 
    Python Module Index
    
+     
+       
+       
+     
+       
+       
+     
+       
+       
+     
+       
+       
+     
+       
+       
+     
+     
+     
+       
+       
+     
+       
+       
+     
+       
+       
    
        
    
        
-       euclidlike
+       euclidlike_imsim
        
    
      
    
        
           
-       euclidlike.backgrounds
+       euclidlike_imsim.bandpass
        
    
      
    
        
           
-       euclidlike.bandpass
+       euclidlike_imsim.ccd
        
    
      
    
        
           
-       euclidlike.euclidlike_psf
+       euclidlike_imsim.noise
        
    
      
    
        
           
-       euclidlike.euclidlike_wcs
+       euclidlike_imsim.obseq
        
    
      
    
        
           
-       euclidlike.instrument_params
+       euclidlike_imsim.photonOps
+       
       
+       euclidlike_imsim.psf
+       
       
+       euclidlike_imsim.skycat
+       
       
+       euclidlike_imsim.stamp
+       
       
+       euclidlike_imsim.utils
+       
       
+       euclidlike_imsim.wcs
+       
     
    
+       s
    
+       scripts
+       
       
+       scripts.download_psf
+       
       
+       scripts.make_euclidlike_pupil_plane
        
    
    
    
 
@@ -103,6 +148,14 @@ 
    GalSim-Euclid-Like
    
     
    
 
 
    Navigation
    
+
 
 
    
 
    Related Topics
    
diff --git a/docs/_build/html/scripts.html b/docs/_build/html/scripts.html
index bd95c86..87be1ee 100644
--- a/docs/_build/html/scripts.html
+++ b/docs/_build/html/scripts.html
@@ -31,19 +31,115 @@
 
           
    
             
-  
    
-
    scripts package
    
+  
    
+
    scripts package
    
 
    
 
    Submodules
    
 
    
-
    
-
    scripts.download_psf module
    
-
    
-
    
-
    scripts.make_euclidlike_pupil_plane module
    
+
    
+
    scripts.download_psf module
    
+
    A program to download the Euclid-like PSF sampled across the focal plane for discrete wavelengths.
+The code below was adapted from: https://github.com/GalSim-developers/GalSim/blob/releases/2.5/galsim/download_cosmos.py
    
+
    
+
    
+scripts.download_psf.check_existing(target, unpack_dir, meta, args, logger)[source]
    
+
    
+
+
    
+
    
+scripts.download_psf.check_remove(do_unpack, target, args)[source]
    
+
    
+
+
    
+
    
+scripts.download_psf.check_unpack(do_download, unpack_dir, target, args)[source]
    
+
    
+
+
    
+
    
+scripts.download_psf.download(do_download, url, target, meta, args, logger)[source]
    
+
    
+
+
    
+
    
+scripts.download_psf.download_psf(args, logger)[source]
    
+
    The main script given the ArgParsed args and a logger
    
+
    
+
+
    
+
    
+scripts.download_psf.get_input()[source]
    
+
    
+
+
    
+
    
+scripts.download_psf.get_meta(url, args, logger)[source]
    
+
    
+
+
    
+
    
+scripts.download_psf.get_names(args, logger)[source]
    
+
    
+
+
    
+
    
+scripts.download_psf.main(command_args)[source]
    
+
    The whole process given command-line parameters in their native (non-ArgParse) form.
    
+
    
+
+
    
+
+
    
+
+
    
+
    
+scripts.download_psf.parse_args(command_args)[source]
    
+
    Handle the command line arguments using either argparse (if available) or optparse.
    
+
    
+
+
    
+
    
+scripts.download_psf.query_yes_no(question, default='yes')[source]
    
+
    Ask a yes/no question via input() and return their answer.
    
+
    “question” is a string that is presented to the user.
+“default” is the presumed answer if the user just hits <Enter>.
    
+
    
+
    It must be “yes” (the default), “no” or None (meaning
+an answer is required of the user).
    
+
    
+
    The “answer” return value is one of “yes” or “no”.
    
+
    
+
+
    
+
    
+scripts.download_psf.remove_tarball(do_remove, target, logger)[source]
    
+
    
+
+
    
+
    
+scripts.download_psf.run_main()[source]
    
+
    Kick off the process grabbing the command-line parameters from sys.argv
    
+
    
+
+
    
+
    
+scripts.download_psf.unpack(do_unpack, target, target_dir, unpack_dir, meta, args, logger)[source]
    
+
    
+
 
    
-
    
-
    Module contents
    
+
    
+
    scripts.make_euclidlike_pupil_plane module
    
+
    This code has been taken from https://github.com/CosmoStat/wf-psf Liaudat et al.
    
+
    This is an implementation of the function generate_pupil_obscurations https://github.com/CosmoStat/wf-psf/blob/87e0c8e9770199cd276f5f0551054cb4902d53bb/src/wf_psf/sims/SimPSFToolkit.py#L233
    
+
    NOTE from Tobias Liaudat:
+“Simple procedure considering only the 2D plane.
+No 3D projections wrt the angle of the FoV is done.”
    
+
    
+
    
+scripts.make_euclidlike_pupil_plane.make_EuclidLike_pupil_plane(N_pix=2048, do_filter=True, N_filter=3)[source]
    
+
    
+
 
    
 
    
 
@@ -73,6 +169,14 @@ 
    GalSim-Euclid-Like
    
     
    
 
 
    Navigation
    
+
 
 
    
 
    Related Topics
    
diff --git a/docs/_build/html/search.html b/docs/_build/html/search.html
index 8a6504c..e5c04c5 100644
--- a/docs/_build/html/search.html
+++ b/docs/_build/html/search.html
@@ -81,6 +81,14 @@ 
    GalSim-Euclid-Like
    
 
 
 
    Navigation
    
+
 
 
    
 
    Related Topics
    
diff --git a/docs/_build/html/searchindex.js b/docs/_build/html/searchindex.js
index bd0afe7..ea6848e 100644
--- a/docs/_build/html/searchindex.js
+++ b/docs/_build/html/searchindex.js
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/docs/conf.py b/docs/conf.py
index d38c79e..3220f77 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -10,6 +10,9 @@
 import sys
 sys.path.insert(0,os.path.abspath('.'))
 
+import euclidlike
+import euclidlike_imsim
+
 project = 'GalSim-Euclid-Like'
 copyright = '2024, Rachel Mandelbaum, Axel Guinot, Federico Berlfein, Andy Park, Xiangchong Li, Michael Troxel, Tianqing Zhang'
 author = 'Rachel Mandelbaum, Axel Guinot, Federico Berlfein, Andy Park, Xiangchong Li, Michael Troxel, Tianqing Zhang'
@@ -21,7 +24,7 @@
 extensions = []
 
 templates_path = ['_templates']
-exclude_patterns = []
+exclude_patterns = ['**/.ipynb_checkpoints']
 
 
 
diff --git a/docs/euclidlike.rst b/docs/euclidlike.rst
index c09a526..d4f2d47 100644
--- a/docs/euclidlike.rst
+++ b/docs/euclidlike.rst
@@ -1,53 +1,153 @@
-euclidlike package
-==================
+The Euclid-like Module
+################################
 
-Submodules
-----------
+The ``euclidlike`` module contains telescope information and functionality needed for image simulations.
+The demo script end_to_end_demo.py shows how to use many of the atrributes and functions described here.
 
-euclidlike.backgrounds module
------------------------------
 
-.. automodule:: euclidlike.backgrounds
-   :members:
-   :undoc-members:
-   :show-inheritance:
+Module-level Attributes
+=======================
 
-euclidlike.bandpass module
---------------------------
+There are several of attributes of the ``euclidlike`` module which define some numerical
+parameters related to a Euclid-like geometry.  Some of these parameters relate to the entire
+wide-field imager.  Others, especially the return values of the functions to get the
+PSF and WCS, are specific to each CCD and therefore are indexed based on the detector number. 
+All detector-related arrays are 0-indexed, which might differ from the CCD indices for Euclid,
+which run 1-1 to n_row-n_col.
 
-.. automodule:: euclidlike.bandpass
-   :members:
-   :undoc-members:
-   :show-inheritance:
+gain
+    The gain for all CCDs is expected to be the roughly the same.
 
-euclidlike.euclidlike\_psf module
----------------------------------
+pixel_scale
+    The pixel scale in units of arcsec/pixel. 
 
-.. automodule:: euclidlike.euclidlike_psf
-   :members:
-   :undoc-members:
-   :show-inheritance:
+diameter
+    The telescope diameter in meters.
 
-euclidlike.euclidlike\_wcs module
----------------------------------
+obscuration
+    The linear obscuration of the telescope, expressed as a fraction of the diameter.
 
-.. automodule:: euclidlike.euclidlike_wcs
-   :members:
-   :undoc-members:
-   :show-inheritance:
+collecting_area
+    The actual collecting area after accounting for obscuration, struts, etc. in
+        units of cm^2.
 
-euclidlike.instrument\_params module
-------------------------------------
+long_exptime
+    The typical exposure time for the longer exposures used for VIS images, in units of seconds.  
+    The number that is stored is for a single dither.
 
-.. automodule:: euclidlike.instrument_params
-   :members:
-   :undoc-members:
-   :show-inheritance:
+short_exptime_nisp
+    The typical exposure time for the shorter NISP imaging exposures used for VIS images, in units of seconds.  
+    The number that is stored is for a single dither.
 
-Module contents
----------------
+short_exptime_vis
+    The typical exposure time for the shorter exposures with VIS taken in parallel with NISP imaging, in units of seconds.  
+    The number that is stored is for a single dither.
 
-.. automodule:: euclidlike
-   :members:
-   :undoc-members:
-   :show-inheritance:
+n_dithers
+    The number of dithers per filter.
+
+n_ccd
+    The number of CCDs in the focal plane.
+    
+n_ccd_row
+    The number of CCDs in the each focal plane row.
+
+n_ccd_col
+    The number of CCDs in the each focal plane column.
+
+n_pix_row
+    Each CCD has n_pix_row total pixels in each row.
+n_pix_col
+    Each CCD has n_pix_col total pixels in each column.
+
+pixel_scale_mm
+    The physical pixel size, in units of mm.
+
+plate_scale
+    The plate scale, in units of arcsec / mm
+
+read_noise
+    Total readout noise, in units of e-. 
+
+saturation
+    Pixel saturation, in units of e-. 
+
+det2ccd
+    Mapping from DETID to CCDID.
+
+ccd2det
+    Mapping from CCDID to DETID.
+
+min_sun_angle
+    Minimum allowed angle from the telescope solar panels to the sun, in degrees.
+
+max_sun_angle
+    Maximum allowed angle from the telescope solar panels to the sun, in degrees.
+
+vis_bands
+    List of available VIS bands
+nisp_bands
+    List of available NISP bands
+
+vis_blue_limit
+    Bandpass blue limit  needed for consistency with the wavelength range covered by ur tabulated 
+    PSF images, in nm.
+
+vis_red_limit
+    Bandpass red limit  needed for consistency with the wavelength range covered by ur tabulated 
+    PSF images, in nm.
+
+For example, to get the gain value, use euclidlike.gain.
+
+#.. automodule:: euclidlike.instrument_params
+#   :members:
+#   :undoc-members:
+
+
+Euclid-like Functions
+===============
+
+This module also contains the following routines:
+
+`euclidlike.getBandpasses`
+    A utility to get a dictionary containing galsim.Bandpass objects for each of
+    the Euclid-like imaging bandpasses, which by default have AB zeropoints given using
+    the GalSim zeropoint convention (see `getBandpasses` docstring for more details).
+
+`euclidlike.getSkyLevel`
+    A utility to find the expected sky level due to zodiacal light at a given
+    position, in a given band.
+
+`euclidlike.getZodiBackground`
+    This helper routine is enables the calculation of the zodiacal light, in photons/m^2/arcsec^2/sec
+
+`euclidlike.getPSF`
+    A routine to get a chromatic representation of the PSF in a single CCD.
+    PSFs are based on precomputed, oversampled (by 3x) PSF images on a grid in wavelength and
+    focal plane position.
+
+`euclidlike.getBrightPSF`
+    Get a fake optical PSF for very bright objects.
+
+`euclidlike.getWCS`
+    This routine returns a dict containing a WCS for each of the Euclid CCDs.
+
+`euclidlike.findCCD`
+    This is a helper routine to calculate the minimum and maximum pixel values that should be
+    considered within a CCD.
+
+
+
+.. autofunction:: euclidlike.getBandpasses
+
+.. autofunction:: euclidlike.getSkyLevel
+
+.. autofunction:: euclidlike.getZodiBackground
+
+.. autofunction:: euclidlike.getPSF
+
+.. autofunction:: euclidlike.getBrightPSF
+
+.. autofunction:: euclidlike.getWCS
+
+.. autofunction:: euclidlike.findCCD
diff --git a/docs/euclidlike_imsim.rst b/docs/euclidlike_imsim.rst
index bc6626f..244a9b5 100644
--- a/docs/euclidlike_imsim.rst
+++ b/docs/euclidlike_imsim.rst
@@ -1,109 +1,64 @@
-euclidlike\_imsim package
-=========================
+The Euclid-like ImSim Module
+################################
 
-Submodules
-----------
+This module contains configuration scripts to produce large-scale Euclid-like simulation runs based on the information in ``euclidlike``.
+It is based heavily on `roman_imsim `_.
 
-euclidlike\_imsim.bandpass module
----------------------------------
+Classes and Functions
+=====================
 
 .. automodule:: euclidlike_imsim.bandpass
    :members:
    :undoc-members:
-   :show-inheritance:
-
-euclidlike\_imsim.ccd module
-----------------------------
 
 .. automodule:: euclidlike_imsim.ccd
    :members:
    :undoc-members:
-   :show-inheritance:
-
-euclidlike\_imsim.detector\_physics module
-------------------------------------------
 
 .. automodule:: euclidlike_imsim.detector_physics
    :members:
    :undoc-members:
-   :show-inheritance:
-
-euclidlike\_imsim.noise module
-------------------------------
 
 .. automodule:: euclidlike_imsim.noise
    :members:
    :undoc-members:
-   :show-inheritance:
-
-euclidlike\_imsim.obseq module
-------------------------------
 
 .. automodule:: euclidlike_imsim.obseq
    :members:
    :undoc-members:
-   :show-inheritance:
-
-euclidlike\_imsim.photonOps module
-----------------------------------
 
 .. automodule:: euclidlike_imsim.photonOps
    :members:
    :undoc-members:
-   :show-inheritance:
-
-euclidlike\_imsim.psf module
-----------------------------
 
 .. automodule:: euclidlike_imsim.psf
    :members:
    :undoc-members:
-   :show-inheritance:
-
-euclidlike\_imsim.scafile module
---------------------------------
 
 .. automodule:: euclidlike_imsim.scafile
    :members:
    :undoc-members:
-   :show-inheritance:
-
-euclidlike\_imsim.skycat module
--------------------------------
 
 .. automodule:: euclidlike_imsim.skycat
    :members:
    :undoc-members:
-   :show-inheritance:
-
-euclidlike\_imsim.stamp module
-------------------------------
 
 .. automodule:: euclidlike_imsim.stamp
    :members:
    :undoc-members:
-   :show-inheritance:
-
-euclidlike\_imsim.utils module
-------------------------------
 
 .. automodule:: euclidlike_imsim.utils
    :members:
    :undoc-members:
-   :show-inheritance:
-
-euclidlike\_imsim.wcs module
-----------------------------
 
 .. automodule:: euclidlike_imsim.wcs
    :members:
    :undoc-members:
-   :show-inheritance:
 
-Module contents
----------------
 
-.. automodule:: euclidlike_imsim
-   :members:
-   :undoc-members:
-   :show-inheritance:
+Use
+====
+Example files needed for large-scale Euclid-like simulation runs are included in ``GalSim-Euclid-Like/config``.
+
+.. include:: ../config/README.rst
+
diff --git a/docs/examples.rst b/docs/examples.rst
new file mode 100644
index 0000000..07f898e
--- /dev/null
+++ b/docs/examples.rst
@@ -0,0 +1,29 @@
+Examples
+=========
+
+The ``GalSim-Euclid-Like/examples`` directory contains example files for how use the euclidlike module.  
+
+End-to-end demo 
+---------------
+
+`end_to_end_demo.py.py <../examples/end_to_end_demo.py>`_
+
+This first demo is the euclidlike-equivalent of  `demo 13 `_ in ``GalSim``. This demo uses the Euclid-like PSF, WCS, and background noise to produce a realistic scene of galaxies and stars as observed from a Euclid-like Telescope. 
+
+** Features introduced in the Python file**:
+
+- euclidlike.getBandpasses(AB_zeropoint)
+- euclidlike.getWCS(world_pos, CCDs_CCD, date)
+- euclidlike.getPSF(use_CCD, filter_name, wcs)
+- euclidlike.getSkyLevel(bandpass, world_pos)
+
+The output generated from this file can be visualized by running the script `end_to_end_demo.py.py <../examples/end_to_end_demo.py>`_
+
+
+Focal Plane Layout 
+------------------
+
+`plot_VIS.py <../examples/plot_VIS.py>`_
+
+This Jupyter Notebook shows the display of the focal plane used in the euclidlike package, along with the CCD centers and ID convention.
+
diff --git a/docs/history.rst b/docs/history.rst
new file mode 100644
index 0000000..d35e38d
--- /dev/null
+++ b/docs/history.rst
@@ -0,0 +1,11 @@
+Revision History
+################
+
+.. include:: ../CHANGELOG.rst
+
+
+Older Versions
+==============
+
+.. toctree::
+    older
\ No newline at end of file
diff --git a/docs/index.rst b/docs/index.rst
index 55d881e..3f160f3 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -1,63 +1,24 @@
-GalSim-Euclid-Like
-==================
-
-Helper functions to generate simulations of Euclid-like images using GalSim.
-
-This repository contains information about the Euclid space telescope and survey that is needed to
-produce simulations using `GalSim `_.  Some of the
-information provided is approximate, aimed towards fast simulations rather than full accuracy in
-representation of Euclid images.  Places where the information is only approximate are flagged and
-described in the docstring, and we particularly highlight that the PSF is only approximate;
-for details, see the docstring of the ``getPSF()`` method.  This library should enable generation of
-Euclid-like images of sufficient fidelity for preliminary exploration of object detection,
-photometry, deblending, and joint analysis with ground-based observatories.  For
-applications requiring high precision such as weak lensing, the higher fidelity simulations
-available within the Euclid Consortium should be used.
-
-This repository includes two distinct packages:
-
-* ``euclidlike``: has basic observatory, instrumentation, and survey information for Euclid.
-  This package can be used on its own along with GalSim to produce Euclid-like simulations.
-
-* ``euclidlike_imsim``: has configuration scripts to produce large-scale Euclid-like simulation runs
-  based on the information in ``euclidlike``. It is based heavily on `roman_imsim `_.
-
-
-References
-==================
+.. GalSim-Euclid-Like documentation master file 
+   
 
-For more information about `GalSim `_, please see its README and documentation.
+GalSim-Euclid-Like: Euclid-like images using GalSim
+==============================================
 
-For more information about Euclid, please see the `Euclid Consortium website `_ and papers linked from there.
+.. toctree::
+    :maxdepth: 2
 
-Attribution for software and data used by particular routines in this library is given in the docstring for the relevant routine.
+    overview
+    install
+    euclidlike
+    euclidlike_imsim
+    examples
+    history
 
-Installation
-==================
-
-Please view the `installation instructions `_ for details on how to install GalSim-Euclid-Like.
-
-Downloading relevant data
-==================                                                                              
-The Euclid-like PSF is constructed from precomputed oversampled images on a grid in focal plane position and wavelength. To use the full FOV PSF within GalSim-Euclid-Like, the images must be downloaded by running::
-
-    $ euclidlike_download_psf
-
-in the terminal after installation of GalSim-Euclid-Like. To install in an alternative directory to the default, use the ``--dir`` argument. Refer to the ``getPSF`` documentation for further details about the PSF. 
 
-Getting started
-==================                                                                             
 
-Please see the examples/ directory for demos illustrating the use of this code.
-
-Communicating with the developers
+Indices and tables
 ==================
-Feel free to `open a GitHub issue `_ to reach the developers with questions, comments, and bug reports.  New contributors are also welcome and can indicate their interest in developing this code base through the Issues.
-
-Attribution
-==================                                   
-
-This software is open source and may be used according to the terms of its `license `_.
-
-When using this software, please provide the URL to the repository in the resulting paper or note.  Once there is a Zenodo DOI or journal article, this README will be updated and we will ask those using the code in their research to cite the relevant journal article.
 
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/docs/install.rst b/docs/install.rst
new file mode 100644
index 0000000..63b62ca
--- /dev/null
+++ b/docs/install.rst
@@ -0,0 +1,4 @@
+Installation
+########
+
+.. include:: ../INSTALL.rst
\ No newline at end of file
diff --git a/docs/modules.rst b/docs/modules.rst
index 269fdea..dc909a1 100644
--- a/docs/modules.rst
+++ b/docs/modules.rst
@@ -1,9 +1,6 @@
-GalSim-Euclid-Like
-==================
-
 .. toctree::
    :maxdepth: 4
 
    euclidlike
    euclidlike_imsim
-   scripts
+   scripts
\ No newline at end of file
diff --git a/docs/overview.rst b/docs/overview.rst
new file mode 100644
index 0000000..803a9ee
--- /dev/null
+++ b/docs/overview.rst
@@ -0,0 +1,4 @@
+Overview
+########
+
+.. include:: ../README.rst
\ No newline at end of file
diff --git a/docs/scripts.rst b/docs/scripts.rst
index 28a2437..11b271d 100644
--- a/docs/scripts.rst
+++ b/docs/scripts.rst
@@ -1,6 +1,11 @@
 scripts package
 ===============
 
+.. automodule:: scripts
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 Submodules
 ----------
 
@@ -19,11 +24,3 @@ scripts.make\_euclidlike\_pupil\_plane module
    :members:
    :undoc-members:
    :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: scripts
-   :members:
-   :undoc-members:
-   :show-inheritance:
diff --git a/euclidlike/instrument_params.py b/euclidlike/instrument_params.py
index a3fc12a..8371047 100644
--- a/euclidlike/instrument_params.py
+++ b/euclidlike/instrument_params.py
@@ -136,4 +136,4 @@
 # this module.  However, pointing errors / jitter are quantified in the VIS paper.
 #
 # The impact of the dichroic and of charge transfer inefficiency are not included.  Same for
-# saturation (200000 e-).
+# saturation (200000 e-).
\ No newline at end of file