move input & output options to config_injection.yaml

README.md

 # Pipeline for source injection on CSST images
 
 ## Installation
+1. First make sure CSST simulation package is installed
+2. Install the source injection packages:
 ```
-python setup.py install --user
-```
+    python setup.py install --user
+ ```
\ No newline at end of file
+
+## Usage
+### Run Source Injection
+```
+    python ./injection_pipeline/injection_pipeline.py /path/to/config_injection.yaml
+```
+### Run L1 Detrending pipeline
+### Run L1 Detection & Photometry pipeline
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config/config_injection.yaml

@@ -19,7 +19,10 @@ pos_sampling:
   # type: "uniform"
   # object_density: 37 # arcmin^-2
 
-# output_img_dir: "/public/home/fangyuedong/project/injection_pipeline/workspace"
+input_dir: "/public/home/fangyuedong/project/50sqDeg_L1_outputs/50sqDeg_Photo_W2/"
+output_dir: "/public/home/fangyuedong/project/demo_csst_injection/50sqDeg_Photo_W2/"
+pointing_label_list: ["MSC_0000000"]
+chip_label_list: ["07"]
 
 ###############################################
 # PSF setting
@@ -63,7 +66,7 @@ catalog_options:
 # observation_sim.instruments.chip object
 # (TODO) Should readout from header
 ###############################################
-ins_effects:
+# ins_effects:
   # switches
   # bright_fatter:  ON # Whether to simulate Brighter-Fatter (also diffusion) effect
 
@@ -82,16 +85,16 @@ ins_effects:
 # random_seeds:
 #   seed_Av:              121212    # Seed for generating random intrinsic extinction
 
-###############################################
-# Measurement setting
-###############################################
-measurement_setting:
-  input_img_list: "/share/home/fangyuedong/injection_pipeline/injected_L1_img_MSC_0000000.list"
-  # input_img_list: "/share/home/fangyuedong/injection_pipeline/input_L1_img_MSC_0000000.list"
-  input_wht_list: "/share/home/fangyuedong/injection_pipeline/L1_wht_img_MSC_0000000.list"
-  input_flg_list: "/share/home/fangyuedong/injection_pipeline/L1_flg_img_MSC_0000000.list"
-  input_psf_list: "/share/home/fangyuedong/injection_pipeline/psf_img_MSC_0000000.list"
-  sex_config: "/share/home/fangyuedong/injection_pipeline/config/default.config"
-  sex_param: "/share/home/fangyuedong/injection_pipeline/config/default.param"
-  n_jobs: 8
-  output_dir: "/share/home/fangyuedong/injection_pipeline/workspace"
+# ###############################################
+# # Measurement setting
+# ###############################################
+# measurement_setting:
+#   input_img_list: "/share/home/fangyuedong/injection_pipeline/injected_L1_img_MSC_0000000.list"
+#   # input_img_list: "/share/home/fangyuedong/injection_pipeline/input_L1_img_MSC_0000000.list"
+#   input_wht_list: "/share/home/fangyuedong/injection_pipeline/L1_wht_img_MSC_0000000.list"
+#   input_flg_list: "/share/home/fangyuedong/injection_pipeline/L1_flg_img_MSC_0000000.list"
+#   input_psf_list: "/share/home/fangyuedong/injection_pipeline/psf_img_MSC_0000000.list"
+#   sex_config: "/share/home/fangyuedong/injection_pipeline/config/default.config"
+#   sex_param: "/share/home/fangyuedong/injection_pipeline/config/default.param"
+#   n_jobs: 8
+#   output_dir: "/share/home/fangyuedong/injection_pipeline/workspace"
\ No newline at end of file

injection_pipeline/config.py

@@ -7,7 +7,6 @@ def parse_args():
     '''
     parser = argparse.ArgumentParser()
     parser.add_argument('config_file', help='.yaml config file for injection settings.')
-    parser.add_argument('-c', '--config_dir', help='Directory that houses the .yaml config file.')
     # parser.add_argument('-d', '--data_dir', help='Directory that houses the input data.')
     # parser.add_argument('-w', '--work_dir', help='The path for output.')
     return parser.parse_args()
\ No newline at end of file

injection_pipeline/injection_pipeline.py

@@ -15,10 +15,6 @@ class InjectionPipeline(object):
         # Load configuration
         if config_file is None:
             args = parse_args()
-            if args.config_dir is None:
-                args.config_dir = ''
-            args.config_dir = os.path.abspath(args.config_dir)
-            args.config_file = os.path.join(args.config_dir, args.config_file)
             config_file = args.config_file
 
         with open(config_file, "r") as stream:
@@ -29,6 +25,11 @@ class InjectionPipeline(object):
             except yaml.YAMLError as exc:
                 print(exc)
 
+        self.input_dir = self.config['input_dir']
+        self.output_dir = self.config['output_dir']
+        self.pointing_label_list = self.config['pointing_label_list']
+        self.chip_label_list = self.config['chip_label_list']
+
     def genearte_path_list_for_one_pointing(self,
                                             input_dir,
                                             pointing_label,
@@ -57,11 +58,20 @@ class InjectionPipeline(object):
         return image_path_list
 
     def run_pointing_list(self,
-                          input_dir,
-                          pointing_label_list,
-                          output_dir,
                           Catalog,
+                          input_dir=None,
+                          pointing_label_list=None,
+                          output_dir=None,
                           chip_label_list=None):
+        if input_dir is None:
+            input_dir = self.input_dir
+        if pointing_label_list is None:
+            pointing_label_list = self.pointing_label_list
+        if output_dir is None:
+            output_dir = self.output_dir
+        if chip_label_list is None:
+            chip_label_list = self.chip_label_list
+        
         image_path_list = []
         output_path_list = []
         try:
@@ -110,19 +120,21 @@ class InjectionPipeline(object):
 
 
 if __name__ == "__main__":
-    input_dir = "/public/home/fangyuedong/project/50sqDeg_L1_outputs/50sqDeg_Photo_W2/"
-    # pointing_label_list = ["MSC_0000000", "MSC_0000001",
-    #                        "MSC_0000002", "MSC_0000003", "MSC_0000004", "MSC_0000005", "MSC_0000006", "MSC_0000007", "MSC_0000008", "MSC_0000009"]
-    chip_label_list = None
-    pointing_label_list = ["MSC_0000000"]
-    chip_label_list = ["07"]
-    # output_dir = "/public/home/fangyuedong/project/injected_50sqDeg_L1_outputs/50sqDeg_Photo_W3/"
-    output_dir = "/public/home/fangyuedong/project/test_photometry/50sqDeg_Photo_W2/"
-    config_file = "/public/home/fangyuedong/project/injection_pipeline/config/config_injection.yaml"
-
-    pipeline = InjectionPipeline(config_file=config_file)
-    pipeline.run_pointing_list(input_dir=input_dir,
-                               pointing_label_list=pointing_label_list,
-                               output_dir=output_dir,
-                               chip_label_list=chip_label_list,
-                               Catalog=SimCat)
+    # input_dir = "/public/home/fangyuedong/project/50sqDeg_L1_outputs/50sqDeg_Photo_W2/"
+    # # pointing_label_list = ["MSC_0000000", "MSC_0000001",
+    # #                        "MSC_0000002", "MSC_0000003", "MSC_0000004", "MSC_0000005", "MSC_0000006", "MSC_0000007", "MSC_0000008", "MSC_0000009"]
+    # chip_label_list = None
+    # pointing_label_list = ["MSC_0000000"]
+    # chip_label_list = ["07"]
+    # # output_dir = "/public/home/fangyuedong/project/injected_50sqDeg_L1_outputs/50sqDeg_Photo_W3/"
+    # output_dir = "/public/home/fangyuedong/project/test_photometry/50sqDeg_Photo_W2/"
+    # config_file = "/public/home/fangyuedong/project/injection_pipeline/config/config_injection.yaml"
+
+    # pipeline = InjectionPipeline(config_file=config_file)
+    pipeline = InjectionPipeline()
+    # pipeline.run_pointing_list(input_dir=input_dir,
+    #                            pointing_label_list=pointing_label_list,
+    #                            output_dir=output_dir,
+    #                            chip_label_list=chip_label_list,
+    #                            Catalog=SimCat)
+    pipeline.run_pointing_list(Catalog=SimCat)