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Commit 05b89e5d authored by Fang Yuedong's avatar Fang Yuedong
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move input & output options to config_injection.yaml

parent 1e98863d
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README.md
View file @ 05b89e5d
# 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
```
## Usage
### Run Source Injection
```
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
config/config_injection.yaml
View file @ 05b89e5d
......@@ -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"
\ No newline at end of file
# ###############################################
# # 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
View file @ 05b89e5d
......@@ -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
View file @ 05b89e5d
......@@ -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)
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