Merge remote-tracking branch 'origin/develop' into develop

config/obs_config_SCI.yaml

@@ -62,10 +62,10 @@ call_sequence:
     hot_pixels: YES
     dead_pixels: YES
     bad_columns: YES
-  # Apply response nonlinearity
-  nonlinearity: {}
   # Apply CCD Saturation & Blooming
   blooming: {}
+  # Apply response nonlinearity
+  nonlinearity: {}
   # Run CTE simulation
   # CTE_effect: {}
   # Add prescan and overscan

observation_sim/ObservationSim.py

@@ -154,13 +154,12 @@ class Observation(object):
                 chip_output.Log_error(e)
                 chip_output.Log_error("Failed simulation on step: %s" % (step))
                 break
-
-        chip_output.Log_info("check running:1: pointing-%d chip-%d pid-%d memory-%6.2fGB" % (pointing.id,
-                             chip.chipID, os.getpid(), (psutil.Process(os.getpid()).memory_info().rss / 1024 / 1024 / 1024)))
         del chip.img
         del chip.flat_img
         del chip.prnu_img
         del chip.shutter_img
+        chip_output.Log_info("check running:1: pointing-%d chip-%d pid-%d memory-%6.2fGB" % (pointing.id,
+                             chip.chipID, os.getpid(), (psutil.Process(os.getpid()).memory_info().rss / 1024 / 1024 / 1024)))
 
     def runExposure_MPI_PointingList(self, pointing_list, chips=None):
         comm = MPI.COMM_WORLD
@@ -239,5 +238,6 @@ class Observation(object):
                     "finished running chip#%d..." % (chip.chipID))
                 for handler in chip_output.logger.handlers[:]:
                     chip_output.logger.removeHandler(handler)
+                del chip_output
                 gc.collect()
             process_counter += nchips_per_fp

observation_sim/instruments/chip/libBF/diffusion_X1.c

@@ -37,7 +37,7 @@ void addEffects(int ngx_ima, int ngy_ima, float *arr_ima, float *arr_imc, int bi
   {
     printf("Adding BF effect...\n");
     //setup BF correlation fliter
-    float neX;
+    float neX, neXtemp;
     float neP1 = 50000;
     float bfaP1[9]={0.9707182, 0.002143905, 0.004131103, 0.001149542, 0.0005501739, 0.0005469659, 0.0003726081, 0.0003795207, 0.0001633302};
     float neP2 = 10000;
@@ -56,15 +56,18 @@ void addEffects(int ngx_ima, int ngy_ima, float *arr_ima, float *arr_imc, int bi
         neX = arr_ima[j+i*ny];
         if(neX >= 10000)
         {
+          neXtemp = neX;
+          if(neXtemp > 100000)
+              neXtemp = 100000;
           bfa[0][0]=0; //linearInterp(neX, neP1, bfaP1[0], neP2, bfaP2[0]); //0;
-          bfa[0][1]=bfa[0][-1]=linearInterp(neX, neP1, bfaP1[1], neP2, bfaP2[1]); //0.01575;
-          bfa[-1][0]=bfa[1][0]=linearInterp(neX, neP1, bfaP1[2], neP2, bfaP2[2]); //0.00652;
-          bfa[-1][-1]=bfa[1][1]=bfa[-1][1]=bfa[1][-1]=linearInterp(neX, neP1, bfaP1[3], neP2, bfaP2[3]); //0.00335;
-          bfa[0][-2]=bfa[0][2]=linearInterp(neX, neP1, bfaP1[4], neP2, bfaP2[4]);
-          bfa[-2][0]=bfa[2][0]=linearInterp(neX, neP1, bfaP1[5], neP2, bfaP2[5]); //0.00118;
-          bfa[-2][-1]=bfa[-2][1]=bfa[2][1]=bfa[2][-1]=linearInterp(neX, neP1, bfaP1[6], neP2, bfaP2[6]);
-          bfa[-1][-2]=bfa[1][2]=bfa[-1][2]=bfa[1][-2]=linearInterp(neX, neP1, bfaP1[7], neP2, bfaP2[7]); //0.00083;
-          bfa[-2][-2]=bfa[-2][2]=bfa[2][-2]=bfa[2][2]=linearInterp(neX, neP1, bfaP1[8], neP2, bfaP2[8]); //0.00043;
+          bfa[0][1]=bfa[0][-1]=linearInterp(neXtemp, neP1, bfaP1[1], neP2, bfaP2[1]); //0.01575;
+          bfa[-1][0]=bfa[1][0]=linearInterp(neXtemp, neP1, bfaP1[2], neP2, bfaP2[2]); //0.00652;
+          bfa[-1][-1]=bfa[1][1]=bfa[-1][1]=bfa[1][-1]=linearInterp(neXtemp, neP1, bfaP1[3], neP2, bfaP2[3]); //0.00335;
+          bfa[0][-2]=bfa[0][2]=linearInterp(neXtemp, neP1, bfaP1[4], neP2, bfaP2[4]);
+          bfa[-2][0]=bfa[2][0]=linearInterp(neXtemp, neP1, bfaP1[5], neP2, bfaP2[5]); //0.00118;
+          bfa[-2][-1]=bfa[-2][1]=bfa[2][1]=bfa[2][-1]=linearInterp(neXtemp, neP1, bfaP1[6], neP2, bfaP2[6]);
+          bfa[-1][-2]=bfa[1][2]=bfa[-1][2]=bfa[1][-2]=linearInterp(neXtemp, neP1, bfaP1[7], neP2, bfaP2[7]); //0.00083;
+          bfa[-2][-2]=bfa[-2][2]=bfa[2][-2]=bfa[2][2]=linearInterp(neXtemp, neP1, bfaP1[8], neP2, bfaP2[8]); //0.00043;
         }
         else
         {

observation_sim/mock_objects/Galaxy.py

@@ -115,7 +115,7 @@ class Galaxy(MockObject):
 
         # Set Galsim Parameters
         if self.getMagFilter(filt) <= 15 and (not big_galaxy):
-            folding_threshold = 5.e-4
+            folding_threshold = 5.e-8
         else:
             folding_threshold = 5.e-3
         gsp = galsim.GSParams(folding_threshold=folding_threshold)
@@ -170,8 +170,11 @@ class Galaxy(MockObject):
             # print("nphotons_sub-band_%d = %.2f"%(i, nphotons))
 
             # Get PSF model
+            EXTRA = False
+            if self.getMagFilter(filt) <= filt.mag_saturation-1.:
+                EXTRA = True
             psf, pos_shear = psf_model.get_PSF(
-                chip=chip, pos_img=pos_img, bandpass=bandpass, folding_threshold=folding_threshold)
+                chip=chip, pos_img=pos_img, bandpass=bandpass, folding_threshold=folding_threshold, extrapolate=EXTRA)
 
             if self.bfrac == 0:
                 gal_temp = disk
@@ -198,7 +201,7 @@ class Galaxy(MockObject):
             # gal = self.bfrac * bulge + (1.0 - self.bfrac - kfrac) * disk + kfrac * knots
 
         # stamp = gal.drawImage(wcs=chip_wcs_local, method='phot', offset=offset, save_photons=True)
-        stamp = gal.drawImage(wcs=chip_wcs_local, offset=offset)
+        stamp = gal.drawImage(method='no_pixel', wcs=chip_wcs_local, offset=offset)
         if np.sum(np.isnan(stamp.array)) > 0:
             # ERROR happens
             return 2, pos_shear

observation_sim/mock_objects/MockObject.py

@@ -122,7 +122,7 @@ class MockObject(object):
             return 2, None
         # Set Galsim Parameters
         if self.getMagFilter(filt) <= 15:
-            folding_threshold = 5.e-4
+            folding_threshold = 5.e-8
         else:
             folding_threshold = 5.e-3
         gsp = galsim.GSParams(folding_threshold=folding_threshold)
@@ -160,14 +160,17 @@ class MockObject(object):
             # print("nphotons_sub-band_%d = %.2f"%(i, nphotons))
 
             # Get PSF model
+            EXTRA = False
+            if self.getMagFilter(filt) <= filt.mag_saturation-1.:
+                EXTRA = True
             psf, pos_shear = psf_model.get_PSF(chip=chip, pos_img=pos_img, bandpass=bandpass,
-                                               folding_threshold=folding_threshold)
+                                               folding_threshold=folding_threshold, extrapolate=EXTRA)
             # star = galsim.DeltaFunction(gsparams=gsp)
             # star = star.withFlux(nphotons)
             # star = galsim.Convolve(psf, star)
             star = psf.withFlux(nphotons)
 
-            stamp = star.drawImage(wcs=chip_wcs_local, offset=offset)
+            stamp = star.drawImage(method='no_pixel', wcs=chip_wcs_local, offset=offset)
             if np.sum(np.isnan(stamp.array)) > 0:
                 continue
             stamp.setCenter(x_nominal, y_nominal)

observation_sim/mock_objects/Stamp.py

@@ -92,7 +92,7 @@ class Stamp(MockObject):
             else:
                 gal = gal + gal_temp
 
-        stamp = gal.drawImage(wcs=chip_wcs_local, offset=offset)
+        stamp = gal.drawImage(method='no_pixel', wcs=chip_wcs_local, offset=offset)
         if np.sum(np.isnan(stamp.array)) > 0:
             # ERROR happens
             return 2, pos_shear

observation_sim/psf/PSFInterp.py

@@ -13,6 +13,7 @@ import galsim
 import h5py
 
 from observation_sim.psf.PSFModel import PSFModel
+from observation_sim.psf._util import psf_extrapolate
 
 
 NPSF = 900  # ***# 30*30
@@ -324,7 +325,7 @@ class PSFInterp(PSFModel):
                 return twave
         return -1
 
-    def get_PSF(self, chip, pos_img, bandpass, galsimGSObject=True, findNeighMode='treeFind', folding_threshold=5.e-3, pointing_pa=0.0):
+    def get_PSF(self, chip, pos_img, bandpass, galsimGSObject=True, findNeighMode='treeFind', folding_threshold=5.e-3, pointing_pa=0.0, extrapolate=False, ngg=2048):
         """
         Get the PSF at a given image position
 
@@ -358,20 +359,18 @@ class PSFInterp(PSFModel):
             imPSF = psfMaker_IDW(px, py, PSFMat, cen_col, cen_row, IDWindex=2, OnlyNeighbors=True,
                                  hoc=self.hoc[twave], hoclist=self.hoclist[twave], PSFCentroidWgt=True)
 
-        '''
-        ############TEST: START
-        TestGaussian = False
-        if TestGaussian:
-            gsx  = galsim.Gaussian(sigma=0.04)
-            #pointing_pa = -23.433333
-            imPSF= gsx.shear(g1=0.8, g2=0.).rotate(0.*galsim.degrees).drawImage(nx = 256, ny=256, scale=pixSize).array
-        ############TEST: END
-        '''
+        if extrapolate is True:
+            ccdList = [6,  7,  8,  9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25]
+            rr_trim_list = [72, 64, 96, 88, 64, 72, 72, 76, 72, 72, 76, 72, 72, 64, 88, 96, 64, 72]
+            imPSF = psf_extrapolate(imPSF, rr_trim=rr_trim_list[ccdList.index(chip.chipID)], ngg=ngg)
 
         if galsimGSObject:
-            imPSFt = np.zeros([257, 257])
-            imPSFt[0:256, 0:256] = imPSF
-            # imPSFt[120:130, 0:256] = 1.
+            if extrapolate is True:
+                imPSFt = np.zeros([ngg+1, ngg+1])
+                imPSFt[:-1, :-1] = imPSF
+            else:
+                imPSFt = np.zeros([257, 257])
+                imPSFt[0:256, 0:256] = imPSF
 
             img = galsim.ImageF(imPSFt, scale=pixSize)
             gsp = galsim.GSParams(folding_threshold=folding_threshold)

observation_sim/psf/_util.py

+import numpy as np
+from scipy.interpolate import interp1d
+
+
+def binningPSF(img, ngg):
+    imgX = img.reshape(ngg, img.shape[0]//ngg, ngg, img.shape[1]//ngg).mean(-1).mean(1)
+    return imgX
+
+
+def radial_average_at_pixel(image, center_x, center_y, dr=10):
+    # Get coordinates relative to the specified center pixel (x, y)
+    y, x = np.indices(image.shape)
+    r = np.sqrt((x - center_x)**2 + (y - center_y)**2)
+
+    # Set up bins
+    max_radius = int(r.max())  # Maximum distance from the center pixel
+    radial_bins = np.arange(0, max_radius, dr)
+
+    # Compute average value in each bin
+    radial_means = []
+    for i in range(len(radial_bins) - 1):
+        mask = (r >= radial_bins[i]) & (r < radial_bins[i + 1])
+        if np.any(mask):
+            radial_means.append(image[mask].mean())
+        else:
+            radial_means.append(0)  # In case no pixels are in the bin
+    return radial_bins[:-1], radial_means  # Exclude last bin since no mean calculated
+
+
+def psf_extrapolate(psf, rr_trim=64, ngg=256):
+    # ngg = 256
+    # extrapolate PSF
+    if True:
+        xim = np.arange(256)-128
+        xim, yim = np.meshgrid(xim, xim)
+        rim = np.sqrt(xim**2 + yim**2)
+
+        # rr_trim  = 96
+        psf_temp = psf
+        psf_temp[rim > rr_trim] = 0
+        radii, means = radial_average_at_pixel(psf_temp, 128, 128, dr=4)
+
+        radii_log = np.log(radii[1:])
+        means_log = np.log(means[1:])
+
+        finite_mask = np.isfinite(means_log)
+        f_interp = interp1d(radii_log[finite_mask][:-1], means_log[finite_mask][:-1], kind='linear', fill_value="extrapolate")
+
+        # ngg = 1024
+        xim = np.arange(ngg)-int(ngg/2)
+        xim, yim = np.meshgrid(xim, xim)
+        rim = np.sqrt(xim**2 + yim**2)
+        rim[int(ngg/2), int(ngg/2)] = np.finfo(float).eps  # 1e-7
+        rim_log = np.log(rim)
+        y_new = f_interp(rim_log)
+
+        arr = np.zeros([ngg, ngg])
+        arr[int(ngg/2-128):int(ngg/2+128), int(ngg/2-128):int(ngg/2+128)] = np.log(psf_temp + np.finfo(float).eps)
+        arr[rim > rr_trim] = 0
+        arr[arr == 0] = y_new[arr == 0]
+        psf = np.exp(arr)
+        psf[rim > int(ngg/2)] = 0
+    imPSF = psf  # binningPSF(psf, int(ngg/2))
+    imPSF = imPSF/np.nansum(imPSF)
+    return imPSF

observation_sim/sim_steps/add_objects.py

@@ -238,11 +238,12 @@ def add_objects(self, chip, filt, tel, pointing, catalog, obs_param):
                 self.chip_output.Log_error("obj id: %s" % (obj.param['id']))
                 self.chip_output.Log_error("    e1: %.5f\n    e2: %.5f\n    size: %f\n    bfrac: %f\n    detA: %f\n    g1: %.5f\n    g2: %.5f\n" % (
                     obj.param['e1'], obj.param['e2'], obj.param['size'], obj.param['bfrac'], obj.param['detA'], obj.param['g1'], obj.param['g2']))
-
         # Unload SED:
         obj.unload_SED()
         del obj
         # gc.collect()
+    cat.starDDL.freeGlobeData()
+    del cat.starDDL
 
     if chip.survey_type == "spectroscopic" and not self.overall_config["run_option"]["out_cat_only"] and chip.slsPSFOptim:
         # from observation_sim.instruments.chip import chip_utils as chip_utils

tools/setConfig/reset_obs.py

+from flask import Flask, render_template, request, redirect
+import yaml
+import ast
+
+app = Flask(__name__)
+
+
+key_type_map = {
+    'obs_type': str,
+    'obs_type_code': str,
+    'obs_id': str,
+    'run_chips': list,
+    'call_sequence': {
+        'scie_obs': {
+          'shutter_effect': bool,
+          'flat_fielding': bool,
+          'field_dist': bool,
+        },
+        'sky_background': {
+            'shutter_effect': bool,
+            'flat_fielding': bool,
+            'enable_straylight_model': bool,
+            'flat_level': None,
+            'flat_level_filt': None,
+        },
+        'PRNU_effect': {},
+        'cosmic_rays': {
+            'save_cosmic_img':  bool,
+        },
+        'poisson_and_dark': {
+            'add_dark': bool,
+        },
+        'bright_fatter': {},
+        'detector_defects': {
+            'hot_pixels': bool,
+            'dead_pixels': bool,
+            'bad_columns': bool,
+        },
+        'nonlinearity': {},
+        'blooming': {},
+        'prescan_overscan': {
+            'add_dark': bool,
+        },
+        'bias': {
+            'bias_16channel': bool,
+        },
+        'readout_noise': {},
+        'gain': {
+            'gain_16channel': bool,
+        },
+        'quantization_and_output': {
+            'format_output': bool,
+        },
+    },
+}
+
+
+def convert_dict_values(d, key_type_map):
+    for key, value in d.items():
+        if isinstance(value, dict):
+            convert_dict_values(value, key_type_map[key])
+        elif key in key_type_map:
+            if key_type_map[key] is int:
+                d[key] = int(value)
+            if key_type_map[key] is float:
+                d[key] = float(value)
+            if key_type_map[key] is bool:
+                if d[key].lower() == 'yes' or d[key].lower() == 'true':
+                    d[key] = True
+                else:
+                    d[key] = False
+            if key_type_map[key] is str:
+                d[key] = str(value)
+            if key_type_map[key] is list:
+                d[key] = ast.literal_eval(value)
+            if key_type_map[key] is None:
+                d[key] = None
+
+
+def load_yaml():
+    with open('templates/obs_config_SCI.yaml', 'r') as file:
+        return yaml.safe_load(file)
+
+
+def save_yaml(data):
+    convert_dict_values(data, key_type_map)
+    with open('config_reset/obs_config_SCI_reset.yaml', 'w') as file:
+        yaml.dump(data, file, default_flow_style=False, sort_keys=False)
+
+
+def render_form(data, parent_key=''):
+    form_html = ''
+    for key, value in data.items():
+        full_key = f"{parent_key}.{key}" if parent_key else key
+        if isinstance(value, dict):  # 处理字典
+            form_html += f"<div class='block'><h2>{key}</h2>{render_form(value, full_key)}</div>"
+        else:
+            form_html += f"<label for='{full_key}'>{key}:</label>"
+            form_html += f"<input type='text' id='{full_key}' name='{full_key}' value='{value}'><br>"
+    return form_html
+
+
+@app.route('/', methods=['GET', 'POST'])
+def index():
+    if request.method == 'POST':
+        data = load_yaml()
+        for key in request.form:
+            keys = key.split('.')
+            temp = data
+            for k in keys[:-1]:
+                temp = temp[k]
+            temp[keys[-1]] = request.form[key]
+        save_yaml(data)
+        return redirect('/')
+
+    data = load_yaml()
+    form_html = render_form(data)
+    return render_template('index_obs.html', form_html=form_html)
+
+
+if __name__ == '__main__':
+    app.run(debug=True)

tools/setConfig/reset_overall.py

+from flask import Flask, render_template, request, redirect
+import yaml
+import ast
+
+app = Flask(__name__)
+
+key_type_map = {
+    'work_dir': str,
+    'run_name': str,
+    'project_cycle': int,
+    'run_counter': int,
+    'run_option': {
+        'out_cat_only': bool,
+    },
+    'catalog_options': {
+        'input_path': {
+            'cat_dir': str,
+            'star_cat': str,
+            'galaxy_cat': str,
+        },
+        'SED_templates_path': {
+            'star_SED': str,
+            'galaxy_SED': str,
+            'AGN_SED': str,
+        },
+        'star_only': bool,
+        'galaxy_only': bool,
+        'rotateEll': float,
+        'enable_mw_ext_gal': bool,
+        'planck_ebv_map': str,
+    },
+    'obs_setting': {
+        'pointing_file': str,
+        'obs_config_file': str,
+        'run_pointings': list,
+        'enable_astrometric_model': bool,
+        'cut_in_band': str,
+        'mag_sat_margin': float,
+        'mag_lim_margin': float,
+    },
+    'psf_setting': {
+        'psf_model': str,
+        'psf_pho_dir': str,
+        'psf_sls_dir': str,
+    },
+    'shear_setting': {
+        'shear_type': str,
+        'reduced_g1': float,
+        'reduced_g2': float,
+    },
+    'output_setting': {
+        'output_format': str,
+        'shutter_output': bool,
+        'prnu_output': bool,
+    },
+    'random_seeds': {
+        'seed_poisson': int,
+        'seed_CR': int,
+        'seed_flat': int,
+        'seed_prnu': int,
+        'seed_gainNonUniform': int,
+        'seed_biasNonUniform': int,
+        'seed_rnNonUniform': int,
+        'seed_badcolumns': int,
+        'seed_defective': int,
+        'seed_readout': int,
+    },
+}
+
+
+def convert_dict_values(d, key_type_map):
+    for key, value in d.items():
+        if isinstance(value, dict):
+            convert_dict_values(value, key_type_map[key])
+        elif key in key_type_map:
+            if key_type_map[key] is int:
+                d[key] = int(value)
+            if key_type_map[key] is float:
+                d[key] = float(value)
+            if key_type_map[key] is bool:
+                if d[key].lower() == 'yes' or d[key].lower() == 'true':
+                    d[key] = True
+                else:
+                    d[key] = False
+            if key_type_map[key] is str:
+                d[key] = str(value)
+            if key_type_map[key] is list:
+                d[key] = ast.literal_eval(value)
+
+
+def load_yaml():
+    with open('templates/config_overall.yaml', 'r') as file:
+        return yaml.safe_load(file)
+
+
+def save_yaml(data):
+    convert_dict_values(data, key_type_map)
+    with open('config_reset/config_overall_reset.yaml', 'w') as file:
+        yaml.dump(data, file, default_flow_style=False, sort_keys=False)
+
+
+def render_form(data, parent_key=''):
+    form_html = ''
+    for key, value in data.items():
+        full_key = f"{parent_key}.{key}" if parent_key else key
+        if isinstance(value, dict):  # 处理字典
+            form_html += f"<div class='block'><h2>{key}</h2>{render_form(value, full_key)}</div>"
+        else:
+            form_html += f"<label for='{full_key}'>{key}:</label>"
+            form_html += f"<input type='text' id='{full_key}' name='{full_key}' value='{value}'><br>"
+    return form_html
+
+
+@app.route('/', methods=['GET', 'POST'])
+def index():
+    if request.method == 'POST':
+        data = load_yaml()
+        for key in request.form:
+            keys = key.split('.')
+            temp = data
+            for k in keys[:-1]:
+                temp = temp[k]
+            temp[keys[-1]] = request.form[key]
+        save_yaml(data)
+        return redirect('/')
+
+    data = load_yaml()
+    form_html = render_form(data)
+    return render_template('index_overall.html', form_html=form_html)
+
+
+if __name__ == '__main__':
+    app.run(debug=True)

tools/setConfig/templates/config_overall.yaml

+---
+###############################################
+#
+#  Configuration file for CSST simulation
+#           Overall settings
+#  CSST-Sim Group, 2024/01/08
+#
+###############################################
+
+# Base diretories and naming setup
+# can add some of the command-line arguments here as well;
+# ok to pass either way or both, as long as they are consistent
+work_dir: "/public/home/fangyuedong/project/workplace/"
+run_name: "ext_on"
+
+# Project cycle and run counter are used to name the outputs
+project_cycle: 9
+run_counter: 1
+
+# Run options
+run_option:
+  # Output catalog only?
+  # If yes, no imaging simulation will be run. Only the catalogs
+  # of corresponding footprints will be generated.
+  out_cat_only: NO
+
+###############################################
+# Catalog setting
+###############################################
+# Configure the input catalog: options should be implemented
+# in the corresponding (user defined) 'Catalog' class
+catalog_options:
+  input_path:
+    cat_dir: "/public/share/yangxuliu/CSSOSDataProductsSims/data_50sqDeg/"
+    star_cat: "starcat_C9/"
+    galaxy_cat: "qsocat/cat2CSSTSim_bundle-50sqDeg/"
+
+  SED_templates_path:
+    star_SED: "/public/share/yangxuliu/CSSOSDataProductsSims/data_50sqDeg/starcat_C9/"
+    galaxy_SED: "/public/share/yangxuliu/CSSOSDataProductsSims/data_50sqDeg/sedlibs/"
+    AGN_SED: "/public/share/yangxuliu/CSSOSDataProductsSims/data_50sqDeg/qsocat/qsosed/"
+
+  # Only simulate stars?
+  star_only: NO
+
+  # Only simulate galaxies?
+  galaxy_only: NO
+
+  # rotate galaxy ellipticity
+  rotateEll: 0. # [degree]
+
+  # Whether to apply milky way extinction to galaxies
+  enable_mw_ext_gal: YES
+  planck_ebv_map: "/public/home/fangyuedong/project/ext_maps/planck/HFI_CompMap_ThermalDustModel_2048_R1.20.fits"
+
+###############################################
+# Observation setting
+###############################################
+obs_setting:
+  # (Optional) a file of point list 
+  # if you just want to run default pointing:
+  # - pointing_dir: null
+  # - pointing_file: null
+  pointing_file: "/public/share/yangxuliu/CSSOSDataProductsSims/data_50sqDeg/pointing50_C9/pointing_50_1_n.dat"
+
+  obs_config_file: "/public/home/fangyuedong/project/csst_msc_sim/config/obs_config_SCI.yaml"
+
+  # Run specific pointing(s):
+  # - give a list of indexes of pointings: [ip_1, ip_2...]
+  # - run all pointings: null
+  # Note: only valid when a pointing list is specified
+  run_pointings: [0, 1, 2, 3, 4]
+
+  # Whether to enable astrometric modeling
+  enable_astrometric_model: YES
+
+  # Cut by saturation magnitude in which band?
+  cut_in_band: "z"
+
+  # saturation magnitude margin
+  mag_sat_margin: -2.5
+  # mag_sat_margin: -15.
+
+  # limiting magnitude margin
+  mag_lim_margin: +1.0
+
+###############################################
+# PSF setting
+###############################################
+psf_setting:
+  
+  # Which PSF model to use:
+  # "Gauss": simple gaussian profile
+  # "Interp": Interpolated PSF from sampled ray-tracing data
+  psf_model: "Interp"
+
+  # PSF size [arcseconds]
+  # radius of 80% energy encircled
+  # NOTE: only valid for "Gauss" PSF
+  # psf_rcont: 0.15
+
+  # path to PSF data
+  # NOTE: only valid for "Interp" PSF
+  # PSF models for photometry survey simulation
+  psf_pho_dir: "/public/share/yangxuliu/CSSOSDataProductsSims/dataC6/psfCube1"
+  # PSF models for slitless spectrum survey simulation
+  psf_sls_dir: "/public/share/yangxuliu/CSSOSDataProductsSims/data_50sqDeg/SLS_PSF_PCA_fp/"
+
+###############################################
+# Shear setting
+###############################################
+
+shear_setting:
+  # Options to generate mock shear field:
+  # "constant": all galaxies are assigned a constant reduced shear
+  # "catalog": get shear values from catalog
+  shear_type: "constant"
+
+  # For constant shear field
+  reduced_g1: 0.
+  reduced_g2: 0.
+
+###############################################
+# Output options
+###############################################
+output_setting:
+  output_format:  "channels" # Whether to export as 16 channels (subimages) with pre- and over-scan ("image"/"channels")
+  shutter_output: NO # Whether to export shutter effect 16-bit image
+  prnu_output:    NO # Whether to export the PRNU (pixel-to-pixel flat-fielding) files
+
+###############################################
+# Random seeds
+###############################################
+random_seeds:
+  seed_poisson:         20210601  # Seed for Poisson noise
+  seed_CR:              20210317  # Seed for generating random cosmic ray maps
+  seed_flat:            20210101  # Seed for generating random flat fields
+  seed_prnu:            20210102  # Seed for photo-response non-uniformity
+  seed_gainNonUniform:  20210202  # Seed for gain nonuniformity
+  seed_biasNonUniform:  20210203  # Seed for bias nonuniformity
+  seed_rnNonUniform:    20210204  # Seed for readout-noise nonuniformity
+  seed_badcolumns:      20240309  # Seed for bad columns
+  seed_defective:       20210304  # Seed for defective (bad) pixels
+  seed_readout:         20210601  # Seed for read-out gaussian noise
+...
\ No newline at end of file

tools/setConfig/templates/index_obs.html

+<!DOCTYPE html>
+<html lang="zh">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>csst_msc_sim_CONF</title>
+    <link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/all.min.css" rel="stylesheet">
+    <style>
+        body {
+            font-family: Arial, sans-serif;
+            margin: 0;
+            padding: 20px;
+            background-color: #f4f4f4;
+            color: #333;
+        }
+        h1 {
+            text-align: center;
+            color: #4CAF50;
+        }
+        .container {
+            max-width: 800px;
+            margin: 0 auto;
+            background: #fff;
+            padding: 20px;
+            border-radius: 8px;
+            box-shadow: 0 2px 10px rgba(0, 0, 0, 0.1);
+        }
+        .block {
+            margin-bottom: 20px;
+            border: 1px solid #ccc;
+            border-radius: 4px;
+            padding: 10px;
+            background-color: #fafafa;
+        }
+        h2 {
+            color: #4CAF50;
+            font-size: 1.2em;
+            margin-bottom: 10px;
+        }
+        label {
+            display: block;
+            margin: 5px 0;
+        }
+        input[type="text"] {
+            width: calc(100% - 22px);
+            padding: 10px;
+            border: 1px solid #ccc;
+            border-radius: 4px;
+            margin-bottom: 10px;
+            transition: border 0.3s;
+        }
+        input[type="text"]:focus {
+            border-color: #4CAF50;
+            outline: none;
+        }
+        input[type="submit"] {
+            background-color: #4CAF50;
+            color: white;
+            border: none;
+            padding: 10px 15px;
+            border-radius: 4px;
+            cursor: pointer;
+            font-size: 1em;
+            transition: background-color 0.3s;
+        }
+        input[type="submit"]:hover {
+            background-color: #45a049;
+        }
+        table {
+            width: 100%;
+            border: 1px solid #ddd;
+            border-radius: 8px; /* 圆角 */
+            overflow: hidden; /* 隐藏超出表格的内容 */
+            box-shadow: 0 0 10px rgba(0, 0, 0, 0.1); /* 添加阴影 */
+        }
+
+        th, td {
+            border-bottom: 1px solid #ddd; /* 单元格底部边框 */
+            padding: 12px; /* 内边距 */
+            text-align: left;
+        }
+        tr:hover {
+            background-color: #ADD8E6; /* 悬停时背景颜色 */
+        }
+    </style>
+</head>
+<body>
+    <div class="container">
+        <h1>配置obs_config_SCI.yaml</h1>
+        <p><strong>说明:</strong>
+        1,该脚本可用于生成CSST主巡天成像仿真的参数文件,相关参数说明见本页脚注;2,用户必须修改相关路径参数，其他参数可参考默认值
+.
+        </p>
+        <hr style="border: 2px solid green;">
+        <form method="POST">
+            {{ form_html | safe }}
+            <input type="submit" value="保存">
+        </form>
+    </div>
+
+    <footer class="mt-4">
+        <p class="text-center">这是一个有用的网页</p>
+        <table>
+            <tr>
+                <th>KEYS</th>
+                <th>VALUES</th>
+                <th>COMMENTS</th>
+            </tr>
+            <tr>
+                <th>obs_type</th>
+                <td>"SCI", [str]</td>
+                <td>仿真图像类型</td>
+            </tr>
+            <tr>
+                <th>obs_type_code</th>
+                <td>"101", [str]</td>
+                <td>数据系统内部标号</td>
+            </tr>
+            <tr>
+                <th>obs_id</th>
+                <td>"00000001", [str]</td>
+                <td>this setting will only be used if pointing list file is not given</td>
+            </tr>
+            <tr>
+                <th>run_chips</th>
+                <td>[7,8,9], [list]</td>
+                <td>Define list of chips</td>
+            </tr>
+            <tr>
+                <th>scie_obs:<span style="font-weight: normal;">shutter_effect</span></th>
+                <td>YES, [bool]</td>
+                <td>是否应用快门效应</td>
+            </tr>
+            <tr>
+                <th>scie_obs:<span style="font-weight: normal;">flat_fielding</span></th>
+                <td>YES, [bool]</td>
+                <td>是否应用平场模块</td>
+            </tr>
+            <tr>
+                <th>scie_obs:<span style="font-weight: normal;">field_dist</span></th>
+                <td>YES, [bool]</td>
+                <td> </td>
+            </tr>
+            <tr>
+                <th>sky_background:<span style="font-weight: normal;">shutter_effect</span></th>
+                <td>YES, [bool]</td>
+                <td>是否应用快门效应</td>
+            </tr>
+            <tr>
+                <th>sky_background:<span style="font-weight: normal;">flat_fielding</span></th>
+                <td>YES, [bool]</td>
+                <td>是否应用平场模块</td>
+            </tr>
+            <tr>
+                <th>sky_background:<span style="font-weight: normal;">enable_straylight_model</span></th>
+                <td>YES, [bool]</td>
+                <td>是否应用杂散光模块</td>
+            </tr>
+            <tr>
+                <th>sky_background:<span style="font-weight: normal;">flat_level</span></th>
+                <td>null [null or int]</td>
+                <td>set the total skybackground value (e-) in the exptime,if none,set null, or delete the key</td>
+            </tr>
+            <tr>
+                <th>sky_background:<span style="font-weight: normal;">flat_level_filt</span></th>
+                <td>null, [str]</td>
+                <td>the vale of "flat_level" is in the filter "flat_level_filt", can set NUV, u, g, r, i, z, y, if none,set null,or delete the key</td>
+            </tr>
+            <tr>
+                <th>PRNU_effect<span style="font-weight: normal;"></span></th>
+                <td>---</td>
+                <td>应用像素间不均匀响应模块；如果需关闭，请在生成的yaml文件中直接注释</td>
+            </tr>
+            <tr>
+                <th>cosmic_rays:<span style="font-weight: normal;">save_cosmic_img</span></th>
+                <td>YES, [bool]</td>
+                <td>是否保存宇宙线图像</td>
+            </tr>
+            <tr>
+                <th>poisson_and_dark:<span style="font-weight: normal;">add_dark</span></th>
+                <td>YES, [bool]</td>
+                <td>是否添加暗电流</td>
+            </tr>
+            <tr>
+                <th>bright_fatter<span style="font-weight: normal;"></span></th>
+                <td>YES, [bool]</td>
+                <td>应用亮胖效应模块；如果需关闭，请在生成的yaml文件中直接注释</td>
+            </tr>
+            <tr>
+                <th>detector_defects:<span style="font-weight: normal;">hot_pixels</span></th>
+                <td>YES, [bool]</td>
+                <td>是否添加热像元</td>
+            </tr>
+            <tr>
+                <th>detector_defects:<span style="font-weight: normal;">dead_pixels</span></th>
+                <td>YES, [bool]</td>
+                <td>是否添加坏像元</td>
+            </tr>
+            <tr>
+                <th>detector_defects:<span style="font-weight: normal;">bad_columns</span></th>
+                <td>YES, [bool]</td>
+                <td>是否添加坏像列</td>
+            </tr>
+            <tr>
+                <th>nonlinearity<span style="font-weight: normal;"></span></th>
+                <td>---</td>
+                <td>应用非线性响应模块；如果需关闭，请在生成的yaml文件中直接注释</td>
+            </tr>
+            <tr>
+                <th>blooming<span style="font-weight: normal;"></span></th>
+                <td>---</td>
+                <td>是否应用饱和溢出模块;如果需关闭，请在生成的yaml文件中直接注释</td>
+            </tr>
+            <tr>
+                <th>prescan_overscan:<span style="font-weight: normal;">add_dark</span></th>
+                <td>YES, [bool]</td>
+                <td> 是否在pre/over-scan区域添加暗电流/</td>
+            </tr>
+            <tr>
+                <th>bias:<span style="font-weight: normal;">bias_16channel</span></th>
+                <td>YES, [bool]</td>
+                <td>是否添加16通道的偏置电压</td>
+            </tr>
+            <tr>
+                <th>readout_noise<span style="font-weight: normal;"></span></th>
+                <td>---</td>
+                <td>添加读出噪声；如果需关闭，请在生成的yaml文件中直接注释</td>
+            </tr>
+            <tr>
+                <th>gain:<span style="font-weight: normal;">gain_16channel</span></th>
+                <td>YES, [bool]</td>
+                <td>是否应用增益</td>
+            </tr>
+            <tr>
+                <th>quantization_and_output:<span style="font-weight: normal;">format_output</span></th>
+                <td>YES, [bool]</td>
+                <td>是否按0级数据格式定义输出图像</td>
+            </tr>
+
+
+
+        </table>
+    </footer>
+</body>
+</html>
+

tools/setConfig/templates/index_overall.html

+<!DOCTYPE html>
+<html lang="zh">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>csst_msc_sim_CONF</title>
+    <link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/all.min.css" rel="stylesheet">
+    <style>
+        body {
+            font-family: Arial, sans-serif;
+            margin: 0;
+            padding: 20px;
+            background-color: #f4f4f4;
+            color: #333;
+        }
+        h1 {
+            text-align: center;
+            color: #4CAF50;
+        }
+        .container {
+            max-width: 800px;
+            margin: 0 auto;
+            background: #fff;
+            padding: 20px;
+            border-radius: 8px;
+            box-shadow: 0 2px 10px rgba(0, 0, 0, 0.1);
+        }
+        .block {
+            margin-bottom: 20px;
+            border: 1px solid #ccc;
+            border-radius: 4px;
+            padding: 10px;
+            background-color: #fafafa;
+        }
+        h2 {
+            color: #4CAF50;
+            font-size: 1.2em;
+            margin-bottom: 10px;
+        }
+        label {
+            display: block;
+            margin: 5px 0;
+        }
+        input[type="text"] {
+            width: calc(100% - 22px);
+            padding: 10px;
+            border: 1px solid #ccc;
+            border-radius: 4px;
+            margin-bottom: 10px;
+            transition: border 0.3s;
+        }
+        input[type="text"]:focus {
+            border-color: #4CAF50;
+            outline: none;
+        }
+        input[type="submit"] {
+            background-color: #4CAF50;
+            color: white;
+            border: none;
+            padding: 10px 15px;
+            border-radius: 4px;
+            cursor: pointer;
+            font-size: 1em;
+            transition: background-color 0.3s;
+        }
+        input[type="submit"]:hover {
+            background-color: #45a049;
+        }
+        table {  
+            width: 100%;  
+            border: 1px solid #ddd;  
+            border-radius: 8px; /* 圆角 */  
+            overflow: hidden; /* 隐藏超出表格的内容 */  
+            box-shadow: 0 0 10px rgba(0, 0, 0, 0.1); /* 添加阴影 */  
+        }  
+          
+        th, td {  
+            border-bottom: 1px solid #ddd; /* 单元格底部边框 */  
+            padding: 12px; /* 内边距 */  
+            text-align: left;
+        }
+        tr:hover {  
+            background-color: #ADD8E6; /* 悬停时背景颜色 */  
+        }
+    </style>
+</head>
+<body>
+    <div class="container">
+        <h1>配置config_overall.yaml</h1>
+        <p><strong>说明:</strong>
+        1,该脚本可用于生成CSST主巡天成像仿真的参数文件,相关参数说明见本页脚注;2,用户必须修改相关路径参数，其他参数可参考默认值.
+        </p>
+        <hr style="border: 2px solid green;">
+        <form method="POST">
+            {{ form_html | safe }}
+            <input type="submit" value="保存">
+        </form>
+    </div>
+
+    <footer class="mt-4">
+        <p class="text-center">这是一个有用的网页</p>
+        <table>  
+            <tr>  
+                <th>KEYS</th>  
+                <th>VALUES</th>  
+                <th>COMMENTS</th>  
+            </tr>  
+            <tr>  
+                <th>work_dir</th>  
+                <td>/localpath, [str]</td>  
+                <td>工作目录-仿真输出的文件路径</td>  
+            </tr>  
+            <tr>  
+                <th>run_name</th>  
+                <td>testRun, [str]</td>  
+                <td>当前仿真目录</td>  
+            </tr>  
+            <tr>  
+                <th>project_cycle</th>  
+                <td>10, [int]</td>  
+                <td>CSST数据系统开发阶段-C10</td>  
+            </tr>  
+            <tr>  
+                <th>project_cycle</th>  
+                <td>0, [int]</td>  
+                <td>仿真次数标号-0</td>  
+            </tr>  
+            <tr>
+                <th>run_option:<span style="font-weight: normal;">out_cat_only</span></th>
+                <td>NO, [bool]</td>
+                <td>是否仅输出星表-YES,不产生开展成像仿真，直接输出星表文件；NO,开展成像仿真</td>
+            </tr>
+            <tr>
+                <th>catalog_options:<span style="font-weight: normal;">input_path</span></th>
+                <td>/localpath, [str]</td>
+                <td>"cat_dir": 输入星表路径, "star_cat": 恒星星表目录, "galaxy_cat": 星系星表目录</td>
+            </tr>
+            <tr>
+                <th>catalog_options:<span style="font-weight: normal;">SED_templates_path</span></th>
+                <td>/localpath, [str]</td>
+                <td>"star_SED": 恒星SED路径,"galaxy_SED": 星系SED路径,"AGN_SED": 类星体SED路径</td>
+            </tr>
+            <tr>
+                <th>catalog_options:<span style="font-weight: normal;">star_only</span></th>
+                <td>NO, [bool]</td>
+                <td>YES,只对恒星成像；NO,包含其他天体成像</td>
+            </tr>
+            <tr>
+                <th>catalog_options:<span style="font-weight: normal;">galaxy_only</span></th>
+                <td>NO, [bool]</td>
+                <td>YES,只对星系成像；NO,包含其他天体成像</td>
+            </tr>
+            <tr>
+                <th>catalog_options:<span style="font-weight: normal;">rotateEll</span></th>
+                <td>0.0, [float]</td>
+                <td>旋转星系指向（度）</td>
+            </tr>
+            <tr>
+                <th>catalog_options:<span style="font-weight: normal;">enable_mw_ext_gal</span></th>
+                <td>NO, [bool]</td>
+                <td>是否应用银河系消光</td>
+            </tr>
+            <tr>
+                <th>catalog_options:<span style="font-weight: normal;">planck_ebv_map</span></th>
+                <td>/localpath, [str]</td>
+                <td>消光模型</td>
+            </tr>
+            <tr>
+                <th>obs_setting:<span style="font-weight: normal;">pointing_file</span></th>
+                <td>/localpath, [str]</td>
+                <td>曝光指向文件路径</td>
+            </tr>
+            <tr>
+                <th>obs_setting:<span style="font-weight: normal;">obs_config_file</span></th>
+                <td>/localpath, [str]</td>
+                <td>观测配置文件路径</td>
+            </tr>
+            <tr>
+                <th>obs_setting:<span style="font-weight: normal;">run_pointings</span></th>
+                <td>[0], [int]</td>
+                <td>give a list of indexes of pointings</td>
+            </tr>
+            <tr>
+                <th>obs_setting:<span style="font-weight: normal;">enable_astrometric_model</span></th>
+                <td>YES, [bool]</td>
+                <td>是否应用天测模块</td>
+            </tr>
+            <tr>
+                <th>obs_setting:<span style="font-weight: normal;">cut_in_band</span></th>
+                <td>"z", [str]</td>
+                <td>Cut by saturation magnitude in which band</td>
+            </tr>
+            <tr>
+                <th>obs_setting:<span style="font-weight: normal;">mag_sat_margin</span></th>
+                <td>-2.5, [float]</td>
+                <td>saturation magnitude margin</td>
+            </tr>
+            <tr>
+                <th>obs_setting:<span style="font-weight: normal;">mag_lim_margin</span></th>
+                <td>+1.0, [float]</td>
+                <td>limiting magnitude margin</td>
+            </tr>
+            <tr>
+                <th>psf_setting:<span style="font-weight: normal;">psf_model</span></th>
+                <td>"Interp", [str]</td>
+                <td>Interp-Interpolated PSF from sampled ray-tracing data; Gauss-simple gaussian profile</td>
+            </tr>
+            <tr>
+                <th>psf_setting:<span style="font-weight: normal;">psf_pho_dir</span></th>
+                <td>/localpath, [str]</td>
+                <td>多色成像PSF数据库路径</td>
+            </tr>
+            <tr>
+                <th>psf_setting:<span style="font-weight: normal;">psf_sls_dir</span></th>
+                <td>/localpath, [str]</td>
+                <td>无缝光谱PSF数据库路径</td>
+            </tr>
+            <tr>
+                <th>shear_setting:<span style="font-weight: normal;">shear_type</span></th>
+                <td>constant, [str]</td>
+                <td>constant-all galaxies are assigned a constant reduced shear; catalog-get shear values from catalog</td>
+            </tr>
+            <tr>
+                <th>shear_setting:<span style="font-weight: normal;">reduced_g1</span></th>
+                <td>0.0, [float]</td>
+                <td>weak lensing shear, gamma_1</td>
+            </tr>
+            <tr>
+                <th>shear_setting:<span style="font-weight: normal;"></span>reduced_g1</th>
+                <td>0.0, [float]</td>
+                <td>weak lensing shear, gamma_2</td>
+            </tr>
+            <tr>
+                <th>output_setting:<span style="font-weight: normal;">output_format</span></th>
+                <td>channels, [str]</td>
+                <td>Whether to export as 16 channels (subimages) with pre- and over-scan (\"image\"/\"channels\")</td>
+            </tr>
+            <tr>
+                <th>output_setting:<span style="font-weight: normal;">shutter_output</span></th>
+                <td>NO, [bool]</td>
+                <td>Whether to export shutter effect 16-bit image</td>
+            </tr>
+            <tr>
+                <th>output_setting:<span style="font-weight: normal;">prnu_output</span></th>
+                <td>NO, [bool]</td>
+                <td>Whether to export the PRNU (pixel-to-pixel flat-fielding) files</td>
+            </tr>
+        
+            <tr>
+                <th>random_seeds</th>
+                <td>[int]</td>
+                <td>设置随机数种子</td>
+            </tr>
+        </table>  
+    </footer>
+</body>
+</html>
+

tools/setConfig/templates/obs_config_SCI.yaml

+---
+###############################################
+#
+#  Configuration file for CSST simulation
+#  For single exposure type:
+#                SCI-WIDE
+#  CSST-Sim Group, 2024/01/08
+#
+###############################################
+
+# Observation type
+obs_type: "SCI"
+obs_type_code: "101"
+obs_id: "00000001" # this setting will only be used if pointing list file is not given
+
+# Define list of chips
+# run_chips: [6,7,8,9,11,12,13,14,15,16,17,18,19,20,22,23,24,25] # Photometric chips
+#run_chips: [1,2,3,4,5,10,21,26,27,28,29,30] # Spectroscopic chips
+run_chips: [17, 22]
+
+# Define observation sequence
+call_sequence:
+  # Accumulate fluxes from objects
+  scie_obs:
+    # [Optional]: exposure time of the pointing will be used as default.
+    # Set it here is you want to override the default
+    # exptime: 150. # [s] 
+    shutter_effect: YES
+    flat_fielding: YES
+    field_dist: YES
+  # Accumulate fluxes from sky background
+  sky_background:
+    # [Optional]: exposure time of the pointing will be used as default.
+    # Set it here is you want to override the default
+    # exptime: 150. # [s]
+    shutter_effect: YES
+    flat_fielding: YES
+    enable_straylight_model: YES
+    # flat_level: set the total skybackground value (e-) in the exptime,if none,set null, or delete the key
+    # flat_level_filt: the vale of "flat_level" is in the filter "flat_level_filt", can set NUV, u, g, r, i, z, y, if 
+    # none,set null,or delete the key
+    flat_level: null
+    flat_level_filt: null
+  # Apply PRNU to accumulated photons
+  PRNU_effect: {}
+  # Accumulate photons caused by cosmic rays
+  cosmic_rays: 
+    # [Optional]: exposure time of the pointing will be used as default.
+    # Set it here is you want to override the default
+    # exptime: 150. # [s]
+    save_cosmic_img:  YES # # Whether to export cosmic ray image
+  # Add Poission noise and dark current
+  poisson_and_dark:
+    # [Optional]: exposure time of the pointing will be used as default.
+    # Set it here is you want to override the default
+    # exptime: 150. # [s]
+    add_dark: YES
+  # Simulate brighter fatter effects
+  bright_fatter: {}
+  # Add detector defects: hot/warm pixels, bad columns
+  detector_defects:
+    hot_pixels: YES
+    dead_pixels: YES
+    bad_columns: YES
+  # Apply response nonlinearity
+  nonlinearity: {}
+  # Apply CCD Saturation & Blooming
+  blooming: {}
+  # Run CTE simulation
+  # CTE_effect: {}
+  # Add prescan and overscan
+  prescan_overscan:
+    add_dark: YES
+  # Add bias
+  bias:
+    bias_16channel: YES
+  # Add readout noise
+  readout_noise: {}
+  # Apply gain
+  gain:
+    gain_16channel: YES
+  # Output the final image
+  quantization_and_output:
+    format_output: YES
+...