add wrapper for photometry calls

measurement_pipeline/L1_pipeline/csst_msc_mbi_photometry/csst_photometry.py

@@ -84,6 +84,10 @@ prog_dir = os.path.dirname(__file__)
 config_path = os.path.join(prog_dir, 'data/')
 __version__ = "1.4.3"
 
+# [TODO]
+zero_points = {'NUV': 24.8, 'u': 25.22, 'g': 26.23,
+               'r': 26.04, 'i': 25.85, 'z': 25.27, 'y': 23.92}
+
 
 def pick_psfstars(psffile, remove_polution=False, min_nstar=10, max_nstar=1500, class_star=0.7, match_dist=10,
                   min_sn=20, max_elp=0.3, fwhm_range=[1.5, 20]):
@@ -134,12 +138,15 @@ def pick_psfstars(psffile, remove_polution=False, min_nstar=10, max_nstar=1500,
             cat = cat[index]
             print("selecting isolated stars:", len(cat))
 
-    mask = (cat['flags'] == 0) & (cat['nimaflags_iso'] < 3) & (cat['CLASS_STAR'] > class_star) & (cat['ELLIPTICITY'] < max_elp) & (
+    # mask = (cat['flags'] == 0) & (cat['nimaflags_iso'] < 3) & (cat['CLASS_STAR'] > class_star) & (cat['ELLIPTICITY'] < max_elp) & (
+    #     cat['SNR_WIN'] > min_sn) & (cat['FWHM_IMAGE'] > fwhm_range[0]) & (cat['FWHM_IMAGE'] < fwhm_range[1])
+    # [TODO]
+    mask = (cat['flags'] == 0) & (cat['CLASS_STAR'] > class_star) & (cat['ELLIPTICITY'] < max_elp) & (
         cat['SNR_WIN'] > min_sn) & (cat['FWHM_IMAGE'] > fwhm_range[0]) & (cat['FWHM_IMAGE'] < fwhm_range[1])
     cat = cat[mask]
 
     if len(cat) < min_nstar:
-        print("too few psf stars...")
+        print("too few psf stars... , got %d" % (len(cat)))
         hdulist.close()
         return False
 
@@ -224,7 +231,8 @@ def get_psf(imgfile, whtfile, flgfile, psffile, psf_size=101, degree=3, variabil
     # fitsname = dm.l1_detector(detector=detector, post="")
 
     head = fits.getheader(imgfile, 0)
-    gain = head['exptime']
+    # gain = head['exptime']
+    gain = head['EXPTIME']
     saturate = 50000.0 / gain
 
     # fitsname,_=os.path.splitext(imgfile)
@@ -324,7 +332,9 @@ def photometry(imgfile, whtfile, flgfile, psffile, fluxfile, catfile, skyfile, s
 
     if zp_name not in head or head[zp_name] <= 0:
         print("No zeropoint in the header or bad zeropoint")
-        return False
+        # return False
+        # [TODO]
+
     # date=head['date-obs']
     # ccd=head['ccd_no']
 
@@ -335,7 +345,8 @@ def photometry(imgfile, whtfile, flgfile, psffile, fluxfile, catfile, skyfile, s
     # flagfile=rootname[:indpos]+'_flg.fits'
     # weightfile=rootname[:indpos]+'_wht.fits'
 
-    gain = head['exptime']
+    # gain = head['exptime']
+    gain = head['EXPTIME']
     saturate = 50000.0 / gain
 
     # types = {'sky': 'BACKGROUND', 'seg': 'SEGMENTATION', 'mod': 'MODELS', 'res': '-MODELS'}
@@ -655,12 +666,12 @@ def clean_catalog(cat, head, sep=2.0, star_thresh=0.005):
     # add IDs
     bits = 6
     objid = np.array(cat['ObjID'])
-    if 'ccdchip' in head:
-        ccdno = int(str.strip(head['ccdchip'])[3:])
+    if 'CCDCHIP' in head:
+        ccdno = int(str.strip(head['CCDCHIP'])[3:])
     else:
-        ccdno = int(str.strip(head['chipid']))
+        ccdno = int(str.strip(head['CHIPID']))
 
-    obsid = int(head['obsid'])
+    obsid = int(head['OBSID'])
     ids = np.array(cat['ObjID'], dtype=int) + ccdno * \
         10 ** bits + obsid * 10 ** (bits + 2)
     col = Table.Column(
@@ -670,7 +681,7 @@ def clean_catalog(cat, head, sep=2.0, star_thresh=0.005):
     cat.add_column(col, index=0)
     col = Table.Column(ids, name='ID')
     cat.add_column(col, index=0)
-    filt = head['filter']
+    filt = head['FILTER']
     ff = np.zeros(len(cat), dtype='<U3')
     ff[:] = filt
     col = Table.Column(ff, name='Filter')
@@ -728,7 +739,9 @@ def calibrate_fluxadu(fluxadu, head, head_zpt=None, zp_name='ZP'):
         c = head_zpt
     else:
         if zp_name not in head or head[zp_name] <= 0:
-            return False
+            # return False
+            # [TODO]
+            c = zero_points[head['FILTER']]
         else:
             c = head[zp_name]
 

measurement_pipeline/run_csst_msc_mbi_photometry

+"""_summary_
+"""
+import os
+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
+
+
+def run_csst_msc_mbi_photometry(image_path,
+                                output_dir,
+                                weight_path: str = None,
+                                flag_path: str = None,
+                                psf_ccds_path: Optional[str] = None,
+                                plot_flag: bool = False,
+                                getpsf_flag: bool = False,):
+
+    input_dir = os.path.dirname(image_path)
+    img_filename = os.path.basename(image_path)
+
+    if weight_path is None:
+        weight_path = os.path.join(
+            input_dir, img_filename.replace("img", "wht"))
+    if flag_path is None:
+        flag_path = os.path.join(input_dir, img_filename.replace("img", "flg"))
+
+    psf_local_path = os.path.join(
+        output_dir, img_filename.replace("img", "psf"))
+    flux_path = os.path.join(
+        output_dir, img_filename.replace("img", "flux"))
+    cat_path = os.path.join(
+        output_dir, img_filename.replace("img", "cat"))
+    seg_path = os.path.join(
+        output_dir, img_filename.replace("img", "seg"))
+    sky_path = os.path.join(
+        output_dir, img_filename.replace("img", "sky"))
+
+    core_msc_l1_mbi_phot(
+        image_path=image_path,
+        weight_path=weight_path,
+        flag_path=flag_path,
+        psf_ccds_path=None,
+        psf_local_path=psf_local_path,
+        flux_path=flux_path,
+        cat_path=cat_path,
+        seg_path=seg_path,
+        sky_path=sky_path,
+        plot_flag=plot_flag,
+        getpsf_flag=getpsf_flag)
+
+
+def genearte_path_list_for_one_pointing(input_dir,
+                                        pointing_label,
+                                        chip_label_list=None):
+    """_summary_
+
+    Args:
+        input_dir (_type_): _description_
+        pointing_label (_type_): _description_
+        chip_label_list (_type_, optional): _description_. Defaults to None.
+
+    Returns:
+        _type_: _description_
+    """
+    pointing_dir = os.path.join(input_dir, pointing_label)
+    if chip_label_list is None:
+        image_path_list = glob(
+            pointing_dir + '/CSST_MSC_MS_SCIE_*_' + '*_img_*')
+    else:
+        image_path_list = []
+        for chip_label in chip_label_list:
+            image_path = glob(pointing_dir + '/CSST_MSC_MS_SCIE_*_' +
+                              chip_label + '_img_*')[0]
+            image_path_list.append(image_path)
+
+    return image_path_list
+
+
+def run_pointing_list(input_dir,
+                      pointing_label_list,
+                      output_dir,
+                      chip_label_list=None):
+    image_path_list = []
+    output_path_list = []
+    try:
+        if not os.path.exists(output_dir):
+            os.makedirs(output_dir)
+    except OSError:
+        pass
+
+    for pointing_label in pointing_label_list:
+        output_pointing_dir = os.path.join(output_dir, pointing_label)
+        try:
+            if not os.path.exists(output_pointing_dir):
+                os.makedirs(output_pointing_dir)
+        except OSError:
+            pass
+        temp_img_path_list = genearte_path_list_for_one_pointing(input_dir=input_dir,
+                                                                 pointing_label=pointing_label,
+                                                                 chip_label_list=chip_label_list)
+        image_path_list = image_path_list + temp_img_path_list
+        output_path_list = output_path_list + \
+            [output_pointing_dir] * len(temp_img_path_list)
+
+    comm = MPI.COMM_WORLD
+    ind_thread = comm.Get_rank()
+    num_thread = comm.Get_size()
+
+    for i in range(len(image_path_list)):
+        if i % num_thread != ind_thread:
+            continue
+        image_path = image_path_list[i]
+        output_path = output_path_list[i]
+        run_csst_msc_mbi_photometry(image_path=image_path,
+                                    output_dir=output_path)
+
+
+if __name__ == "__main__":
+    input_dir = "/public/home/fangyuedong/project/50sqDeg_L1_outputs"
+    # pointing_label_list = ["MSC_0000000", "MSC_0000001",
+    #                        "MSC_0000002", "MSC_0000003", "MSC_0000004", "MSC_0000005"]
+    # chip_label_list = None
+    pointing_label_list = ["MSC_0000000"]
+    chip_label_list = ["08"]
+    output_dir = "/public/home/fangyuedong/project/test_photometry"
+    run_pointing_list(input_dir=input_dir,
+                      pointing_label_list=pointing_label_list,
+                      output_dir=output_dir,
+                      chip_label_list=chip_label_list)