finished pipeline for instrumental correction

csst/__init__.py

 import os
 
 __version__ = "0.0.5"
+
 PACKAGE_PATH = os.path.dirname(__file__)

csst/msc/astrometry.py

 from ..core.processor import CsstProcessor
+from .. import PACKAGE_PATH
+
+CONFIG_SCAMP = PACKAGE_PATH + "/msc/config/test.txt"
 
 
 class CsstProcMscPositionCalibration(CsstProcessor):
@@ -10,9 +13,13 @@ class CsstProcMscPositionCalibration(CsstProcessor):
 
     def run(self, data, *args, **kwargs):
         # run your pipeline here
-        # make sure that your input data should be a child class instance of CsstData.
+        # make sure that your input raw should be a child class instance of CsstData.
         pass
 
     def cleanup(self, **kwargs):
         # clean up environment
         pass
+
+
+def test_dir():
+    print(CONFIG_SCAMP)
\ No newline at end of file

csst/msc/instrument.py

@@ -94,7 +94,7 @@ class CsstMscInstrumentProc(CsstProcessor):
             inpaint_model = 'ACS-WFC-F606W-2-32'
             model = deepCR(clean_model, inpaint_model, device='CPU', hidden=50)
             masked, cleaned = model.clean(
-                self.__img, threshold=0.5, inpaint=True, segment=True, patch=256, parallel=True, n_jobs=2)
+                self.__img, threshold=0.5, inpaint=True, segment=True, patch=256, parallel=True, n_jobs=self.n_jobs)
         else:
             cleaned, masked = cosmicray_lacosmic(ccd=self.__img,
                                                  sigclip=3.,  # cr_threshold
@@ -137,7 +137,8 @@ class CsstMscInstrumentProc(CsstProcessor):
         weight[self.__flg > 0] = 0
         self.__wht = weight
 
-    def prepare(self, **kwargs):
+    def prepare(self, n_jobs=2, **kwargs):
+        self.n_jobs = n_jobs
         for name in kwargs:
             self._switches[name] = kwargs[name]
 
@@ -165,6 +166,9 @@ class CsstMscInstrumentProc(CsstProcessor):
         img = raw.deepcopy(name="SCI", data=self.__img)
         wht = raw.deepcopy(name="WHT", data=self.__wht)
         flg = raw.deepcopy(name="FLG", data=self.__flg)
+        img.set_keyword("FILENAME", img.get_keyword("FILENAME", hdu=0).replace("_raw", "_img"), hdu=0)
+        wht.set_keyword("FILENAME", wht.get_keyword("FILENAME", hdu=0).replace("_raw", "_img"), hdu=0)
+        flg.set_keyword("FILENAME", flg.get_keyword("FILENAME", hdu=0).replace("_raw", "_img"), hdu=0)
 
         return img, wht, flg
 

csst/msc/pipeline.py

@@ -4,82 +4,48 @@
 # node name
 HOST = "tulip"
 # working directory
-DIR_WORKING = ""
+DIR_WORK = "/share/HDD7/csstpipeline/msc"
 # gaia catalog directory (for position calibration)
 DIR_GAIA_CATALOG = ""
 
+DIR_TEST = "/share/Cycle-3-SimuData/multipleBandsImaging/CSST_shearOFF/MSC_0000020/"  #  MSC_MS_210525220000_100000020_06_raw.fits
+PATH_BIAS = "/share/HDD7/csstpipeline/ref/MSC_CLB_210525200000_100000016_{:02d}_combine.fits"
+PATH_DARK = "/share/HDD7/csstpipeline/ref/MSC_CLD_210525202000_100000016_{:02d}_combine.fits"
+PATH_FLAT = "/share/HDD7/csstpipeline/ref/MSC_CLF_210525201000_100000016_{:02d}_combine.fits"
 
-# raw images
-fp_list = ["MSC_MS_210527171000_100000279_6_raw.fits",
-           "MSC_MS_210527171000_100000279_7_raw.fits",
-           "MSC_MS_210527171000_100000279_8_raw.fits",
-           "MSC_MS_210527171000_100000279_9_raw.fits",
-           "MSC_MS_210527171000_100000279_10_raw.fits",
-           "MSC_MS_210527171000_100000279_11_raw.fits",
-           "MSC_MS_210527171000_100000279_12_raw.fits",
-           "MSC_MS_210527171000_100000279_13_raw.fits",
-           "MSC_MS_210527171000_100000279_14_raw.fits",
-           "MSC_MS_210527171000_100000279_15_raw.fits",
-           "MSC_MS_210527171000_100000279_16_raw.fits",
-           "MSC_MS_210527171000_100000279_17_raw.fits",
-           "MSC_MS_210527171000_100000279_18_raw.fits",
-           "MSC_MS_210527171000_100000279_19_raw.fits",
-           "MSC_MS_210527171000_100000279_20_raw.fits",
-           "MSC_MS_210527171000_100000279_21_raw.fits",
-           "MSC_MS_210527171000_100000279_22_raw.fits",
-           "MSC_MS_210527171000_100000279_23_raw.fits",
-           "MSC_MS_210527171000_100000279_24_raw.fits",
-           "MSC_MS_210527171000_100000279_25_raw.fits",
-           ]
+import os
+os.chdir(DIR_WORK)
 
+import glob
 from csst.msc.data import CsstMscImgData
 from csst.msc.instrument import CsstMscInstrumentProc
-from astropy.io import fits
+# from astropy.io import fits
 
-# get aux raw
-bs = fits.getdata("/raw/ref/MSC_CLB_210525190000_100000014_13_combine.fits")
-dk = fits.getdata("/raw/ref/MSC_CLD_210525192000_100000014_13_combine.fits")
-ft = fits.getdata("/raw/ref/MSC_CLF_210525191000_100000014_13_combine.fits")
+for i_ccd in range(6, 26):
+    # i_ccd = 6
+    print("processing CCD {}".format(i_ccd))
+    fp_raw = glob.glob("{}/MSC_MS_*{:02}_raw.fits".format(DIR_TEST, i_ccd))
+    assert len(fp_raw) == 1
+    fp_raw = fp_raw[0]
 
-fp_img_list = []
-fp_flg_list = []
-fp_wht_list = []
-data_list = []
-
-for fp in fp_list:
-    # read image raw
-    data = CsstMscImgData.read(fp)
-
-    # set aux raw
-    data.set_bias(bs)
-    data.set_dark(dk)
-    data.set_flat(ft)
+    raw = CsstMscImgData.read(fp_raw)
+    bias = raw.get_bias(PATH_BIAS.format(i_ccd))
+    dark = raw.get_bias(PATH_DARK.format(i_ccd))
+    flat = raw.get_bias(PATH_FLAT.format(i_ccd))
 
     # initialize Instrument Processor
     instProc = CsstMscInstrumentProc()
-    instProc.prepare()
-    instProc.run(data)
+    instProc.prepare(n_jobs=2)
+    img, wht, flg = instProc.run(raw, bias, dark, flat)
     instProc.cleanup()
 
-    # output filepath
-    fp_img = fp.replace("raw.fits", "img.fits")
-    fp_flg = fp.replace("raw.fits", "flg.fits")
-    fp_wht = fp.replace("raw.fits", "wht.fits")
-
-    # save l1 raw
-    data.save_l1data('sci', fp_img)
-    data.save_l1data('flag', fp_flg)
-    data.save_l1data('weight', fp_wht)
-
-    # store in a list for position calibration
-    fp_img_list.append(fp_img)
-    fp_flg_list.append(fp_flg)
-    fp_wht_list.append(fp_wht)
-
-    data_list.append(data)
+    # save img, wht, flg to somewhere
+    img.writeto("{}/{}.fits".format(DIR_WORK, img.get_keyword("FILENAME")))
+    wht.writeto("{}/{}.fits".format(DIR_WORK, wht.get_keyword("FILENAME")))
+    flg.writeto("{}/{}.fits".format(DIR_WORK, flg.get_keyword("FILENAME")))
 
 
-# position calibration
+# TODO:  position calibration
 from csst.msc.astrometry import CsstProcMscPositionCalibration
 pcProc = CsstProcMscPositionCalibration()
 pcProc.prepare(search_radius=2.,)