add configuration files for detrending and photometry

README.md

@@ -8,9 +8,22 @@
  ```
 
 ## Usage
+### Run L1 Detrending pipeline (optional)
+* If the L1 images are not available, we need first to run the CSST detrending pipeline on the raw images to get the L1 calibrated products. Otherwise this step can be ignored.
+* This step removes all the instrumental related effects as well as cosmoic rays
+* modify the corresponding ```config_detrending.yaml``` file to configure all running options
+```
+    python ./measurement_pipeline/run_csst_msc_instrument.py /path/to/config_detrending.yaml
+```
 ### Run Source Injection
+* Inject souces onto the L1 (detrended)
+* modify the corresponding ```config_injection.yaml``` file to configure all running options
 ```
     python ./injection_pipeline/injection_pipeline.py /path/to/config_injection.yaml
 ```
-### Run L1 Detrending pipeline
-### Run L1 Detection & Photometry pipeline
\ No newline at end of file
+### Run L1 Detection & Photometry pipeline
+* Re-detect and redo the photometry measurements on the injected images
+* modify the corresponding ```config_photometry.yaml``` file to configure all running options
+```
+    python ./measurement_pipeline/run_csst_msc_mbi_photometry.py /path/to/config_photometry.yaml
+```
\ No newline at end of file

config/config_detrending.yaml

+input_dir: "/public/share/yangxuliu/CSSOSDataProductsSims/outputs_50sqDeg/50sqDeg_Photo_W2/"
+output_dir: "/public/home/fangyuedong/project/demo_csst_injection/50sqDeg_Photo_W2/"
+pointing_label_list: ["MSC_0000000"]
+chip_label_list: ["07"]
\ No newline at end of file

config/config_photometry.yaml

+input_dir: "/public/home/fangyuedong/project/demo_csst_injection/50sqDeg_Photo_W2/"
+flag_weight_dir: "/public/home/fangyuedong/project/demo_csst_injection/L1_products/50sqDeg_Photo_W2/"
+output_dir: "/public/home/fangyuedong/project/demo_csst_injection/50sqDeg_Photo_W2/"
+pointing_label_list: ["MSC_0000000"]
+chip_label_list: ["07"]
+calib_data_path: "/public/home/fangyuedong/project/calib_data/"
\ No newline at end of file

measurement_pipeline/config.py

+import argparse
+
+def parse_args():
+    '''
+    Parse command line arguments. Many of the following
+    can be set in the .yaml config file as well.
+    '''
+    parser = argparse.ArgumentParser()
+    parser.add_argument('config_file', help='.yaml config file for injection settings.')
+    # 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

measurement_pipeline/run_csst_msc_instrument.py

 """_summary_
 """
 import os
+import yaml
 from glob import glob
 import mpi4py.MPI as MPI
 # from .L1_pipeline.csst_msc_instrument.csst_msc_mbi_instrument import core_msc_l1_mbi_instrument
 from L1_pipeline.csst_msc_instrument.csst_msc_mbi_instrument import core_msc_l1_mbi_instrument
+from config import parse_args
 
 
 def run_csst_msc_instrument(image_path,
@@ -126,13 +128,24 @@ if __name__ == "__main__":
     # output_dir = "/public/home/fangyuedong/project/test_deepcr"
     # input_dir = "/public/share/yangxuliu/CSSOSDataProductsSims/outputs_50sqDeg/50sqDeg_Photo_W2/"
     # output_dir = "/public/home/fangyuedong/project/50sqDeg_L1_outputs/50sqDeg_Photo_W2/"
-    input_dir = "/public/share/yangxuliu/CSSOSDataProductsSims/outputs_50sqDeg/50sqDeg_Photo_W3/"
-    output_dir = "/public/home/fangyuedong/project/50sqDeg_L1_outputs/50sqDeg_Photo_W3/"
-    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
-
-    run_pointing_list(input_dir=input_dir,
-                      pointing_label_list=pointing_label_list,
-                      output_dir=output_dir,
-                      chip_label_list=chip_label_list)
+    # input_dir = "/public/share/yangxuliu/CSSOSDataProductsSims/outputs_50sqDeg/50sqDeg_Photo_W3/"
+    # output_dir = "/public/home/fangyuedong/project/50sqDeg_L1_outputs/50sqDeg_Photo_W3/"
+    # 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
+
+    args = parse_args()
+    config_file = args.config_file
+    with open(config_file, "r") as stream:
+        try:
+            config = yaml.safe_load(stream)
+            for key, value in config.items():
+                print(key + " : " + str(value))
+        except yaml.YAMLError as exc:
+            print(exc)
+
+    run_pointing_list(input_dir=config["input_dir"],
+                      pointing_label_list=config["pointing_label_list"],
+                      output_dir=config["output_dir"],
+                      chip_label_list=config["chip_label_list"],
+                      calib_data_path=config["calib_data_path"])

measurement_pipeline/run_csst_msc_mbi_photometry.py

 """_summary_
 """
 import os
+import yaml
 from glob import glob
 import mpi4py.MPI as MPI
 from L1_pipeline.csst_msc_mbi_photometry.csst_photometry import core_msc_l1_mbi_phot
 from typing import Optional
-
+from config import parse_args
 
 def run_csst_msc_mbi_photometry(image_path,
                                 output_dir,
@@ -135,17 +136,28 @@ if __name__ == "__main__":
     # chip_label_list = None
     # output_dir = "/public/home/fangyuedong/project/processed_injected_50sqDeg_L1_outputs"
     # flag_weight_dir = "/public/home/fangyuedong/project/50sqDeg_L1_outputs/50sqDeg_Photo_W2/"
-    flag_weight_dir = "/public/home/fangyuedong/project/50sqDeg_L1_outputs/50sqDeg_Photo_W3/"
-
-    # input_dir = "/public/home/fangyuedong/project/50sqDeg_L1_outputs/50sqDeg_Photo_W3/"
-    input_dir = "/public/home/fangyuedong/project/injected_50sqDeg_L1_outputs/50sqDeg_Photo_W3/"
-    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
-    # output_dir = "/public/home/fangyuedong/project/50sqDeg_L1_outputs/50sqDeg_Photo_W3/"
-    output_dir = "/public/home/fangyuedong/project/processed_injected_50sqDeg_L1_outputs/50sqDeg_Photo_W3/"
-    run_pointing_list(input_dir=input_dir,
-                      flag_weight_dir=flag_weight_dir,
-                      pointing_label_list=pointing_label_list,
-                      output_dir=output_dir,
-                      chip_label_list=chip_label_list)
+    # flag_weight_dir = "/public/home/fangyuedong/project/50sqDeg_L1_outputs/50sqDeg_Photo_W3/"
+
+    # # input_dir = "/public/home/fangyuedong/project/50sqDeg_L1_outputs/50sqDeg_Photo_W3/"
+    # input_dir = "/public/home/fangyuedong/project/injected_50sqDeg_L1_outputs/50sqDeg_Photo_W3/"
+    # 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
+    # # output_dir = "/public/home/fangyuedong/project/50sqDeg_L1_outputs/50sqDeg_Photo_W3/"
+    # output_dir = "/public/home/fangyuedong/project/processed_injected_50sqDeg_L1_outputs/50sqDeg_Photo_W3/"
+
+    args = parse_args()
+    config_file = args.config_file
+    with open(config_file, "r") as stream:
+        try:
+            config = yaml.safe_load(stream)
+            for key, value in config.items():
+                print(key + " : " + str(value))
+        except yaml.YAMLError as exc:
+            print(exc)
+    
+    run_pointing_list(input_dir=config["input_dir"],
+                      flag_weight_dir=config["flag_weight_dir"],
+                      pointing_label_list=config["pointing_label_list"],
+                      output_dir=config["output_dir"],
+                      chip_label_list=config["chip_label_list"])