move input & output options to config_injection.yaml (05b89e5d) · Commits · Fang Yuedong / injection_pipeline

README.md

+12 −2

Original line number	Diff line number	Diff line
		# 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
		```

		## 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

+18 −15

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		@@ -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

+0 −1

Original line number	Diff line number	Diff line
		@@ -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

+35 −23

Original line number	Diff line number	Diff line
		@@ -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)