add deep_cr module

measurement_pipeline/L1_pipeline/csst_msc_instrument/csst_msc_mbi_instrument.py

@@ -24,6 +24,7 @@ from astropy.stats import sigma_clipped_stats
 #     FlagConfig,
 # )
 from L1_pipeline.csst_msc_instrument.image import (
+    remove_cr_deepcr,
     subtract_bias,
     subtract_dark,
     FlagConfig,
@@ -46,7 +47,7 @@ def core_msc_l1_mbi_instrument(
     config_ccd_info: Optional[str] = None,
     config_bad_pixel: Optional[str] = None,
     device: Optional[str] = "CPU",
-): #-> CsstResult:
+):  # -> CsstResult:
     """
     Make the instrument correction for one chip of CSST data.
 
@@ -91,7 +92,8 @@ def core_msc_l1_mbi_instrument(
         hdu = fits.HDUList(
             [
                 fits.PrimaryHDU(header=raw[0].header.copy()),
-                fits.ImageHDU(header=raw[1].header.copy(), data=raw[1].data.copy()),
+                fits.ImageHDU(header=raw[1].header.copy(),
+                              data=raw[1].data.copy()),
             ]
         )
         # 创建wht[1].data hdulist
@@ -153,8 +155,10 @@ def core_msc_l1_mbi_instrument(
         )
         # 过饱和检测
         saturate = SATURATE
-        flg[1].data = _check_over_saturation(flg[1].data, hdu[1].data, saturate)
-        saturate = saturate * hdu[1].header["GAIN01"] / hdu[0].header["EXPTIME"]
+        flg[1].data = _check_over_saturation(
+            flg[1].data, hdu[1].data, saturate)
+        saturate = saturate * \
+            hdu[1].header["GAIN01"] / hdu[0].header["EXPTIME"]
         status_header.set("SATURATE", saturate)
         # 时间归一
         hdu[1].data = hdu[1].data / hdu[0].header["EXPTIME"]
@@ -163,17 +167,18 @@ def core_msc_l1_mbi_instrument(
         # hdu[1].header.set('BUNIT', 'electron/s')
         status_header.set("BUNIT", "electron/s")
         # 检测宇宙线
-        # hdu[1].data, flg[1].data, cr_count = remove_cr_deepcr(
-        #     hdu[1].data,
-        #     flg[1].data,
-        #     device,
-        #     hdu[1].header["CHIPID"],
-        # )
-        # status_header.set("S_CRS", 0)
-        # status_header.set("CRCOUNT", cr_count)
-        
+        hdu[1].data, flg[1].data, cr_count = remove_cr_deepcr(
+            hdu[1].data,
+            flg[1].data,
+            device,
+            hdu[1].header["CHIPID"],
+        )
+        status_header.set("S_CRS", 0)
+        status_header.set("CRCOUNT", cr_count)
+
         # 记录BKG与RMS
-        _, bkg, rms = sigma_clipped_stats(data=hdu[1].data, mask=(flg[1].data == 16))
+        _, bkg, rms = sigma_clipped_stats(
+            data=hdu[1].data, mask=(flg[1].data == 16))
         status_header.set("SKY_BKG", bkg)
         status_header.set("SKY_RMS", rms)
         # 检测卫星拖尾
@@ -185,7 +190,7 @@ def core_msc_l1_mbi_instrument(
         )
         # 数据类型
         hdu[1].data = hdu[1].data.astype(np.float32)
-        
+
         # # 快门改正
         # hdu[1].data = _fix_shutter(hdu[1].data, shutter, hdu[0].header["EXPTIME"])
         # status_header.set("S_SHUT", 0)
@@ -243,7 +248,8 @@ def _set_status_header():
 
     status_header = fits.Header()  # template Header
     status_header.append(("COMMENT", "=" * 66), bottom=True)
-    status_header.append(("COMMENT", "INSTRUMENT CORRECTION INFORMATION"), bottom=True)
+    status_header.append(
+        ("COMMENT", "INSTRUMENT CORRECTION INFORMATION"), bottom=True)
     status_header.append(("COMMENT", "=" * 66), bottom=True)
 
     for card in demo_header.cards:
@@ -369,8 +375,10 @@ def _dilation(array_orig: np.ndarray, iterations: int = 1):
     """
     from scipy import ndimage
 
-    struct1 = ndimage.generate_binary_structure(2, 1)  # give a saturate structure
-    struct_ext = ndimage.iterate_structure(struct1, iterations)  # make a dilation
+    struct1 = ndimage.generate_binary_structure(
+        2, 1)  # give a saturate structure
+    struct_ext = ndimage.iterate_structure(
+        struct1, iterations)  # make a dilation
     if iterations == 0:
         array_out = array_orig
     else:

measurement_pipeline/L1_pipeline/csst_msc_instrument/image/__init__.py

@@ -15,6 +15,9 @@ from .gain import apply_gain
 from .overscan import correct_overscan
 from .config import FlagConfig, CameraConfig, CCDArrayConfig, get_array_config
 from .format import convert_format
+from .cosmicray.deepcr import remove_cr_deepcr
+from .cosmicray.lacosmic import remove_cr_la
 
-__all__ = ['correct_overscan', 'apply_gain', 'subtract_bias', 'remove_crosstalk', 'subtract_dark', 
-'FlagConfig', 'CameraConfig', 'CCDArrayConfig', 'get_array_config','convert_format', ]
\ No newline at end of file
+
+__all__ = ['correct_overscan', 'apply_gain', 'subtract_bias', 'remove_crosstalk', 'subtract_dark',
+           'FlagConfig', 'CameraConfig', 'CCDArrayConfig', 'get_array_config', 'convert_format', 'remove_cr_deepcr', 'remove_cr_la']

measurement_pipeline/L1_pipeline/csst_msc_instrument/image/cosmicray/__init__.py

+"""
+Identifier:     csst-l1/msc/csst_msc_common/csst_msc_common/cosmicray/__init__.py
+Name:           __init__.py
+Description:    Cosmic ray module.
+Author:         Li Shao (shaoli@nao.cas.cn)
+Created:        2023-11-27
+Modified-History:
+    2023-11-27, Li Shao, created
+"""
+
+from .deepcr import remove_cr_deepcr
+from .lacosmic import remove_cr_la
+
+__all__ = ['remove_cr_deepcr', 'remove_cr_la', ]