added code to run se and psfex on Bok images but currently segfaults …

…when psfex called. It does not look like se is running correctly either as I usually see it count up the sources as it finds them....

py/legacypipe/bok.py

@@ -4,6 +4,8 @@
 import fitsio
 import numpy as np
 
+from legacypipe.image import LegacySurveyImage, CalibMixin
+#from legacypipe.cpimage import CPImage
 from image import LegacySurveyImage
 from common import create_temp
 from astrometry.util.util import Tan, Sip, anwcs_t
@@ -16,21 +18,21 @@
 from tractor.image import Image
 from tractor.tractortime import TAITime
 
-from legacypipe.ptf import zeropoint_for_ptf
-
 
 '''
 Code specific to images from the 90prime camera on the Bok telescope.
 '''
-
-class BokImage(LegacySurveyImage):
+
+#class BokImage(LegacySurveyImage):
+class BokImage(LegacySurveyImage, CalibMixin):
     '''
     A LegacySurveyImage subclass to handle images from the 90prime
     camera on the Bok telescope.
     '''
     def __init__(self, survey, t):
         super(BokImage, self).__init__(survey, t)
         self.pixscale= 0.455
+        self.dqfn= self.read_dq() #array of 0s for now
         self.whtfn= self.imgfn.replace('.fits','.wht.fits')
 
         self.calname = os.path.basename(self.imgfn).replace('.fits','') 
@@ -94,70 +96,56 @@ def get_wcs(self):
         wcs.plver = ''
         return wcs
 
-    def run_calibs(self, psfex=True, sky=True, funpack=False, git_version=None,
-                       force=False,
-                       **kwargs):
+    def run_calibs(self, psfex=True, sky=True, se=False,
+                   funpack=False, fcopy=False, use_mask=True,
+                   force=False, just_check=False, git_version=None,
+                   splinesky=False,**kwargs):
+
+        '''
+        Run calibration pre-processing steps.
+
+        Parameters
+        ----------
+        just_check: boolean
+            If True, returns True if calibs need to be run.
+        '''
         print('run_calibs for', self.name, ': sky=', sky, 'kwargs', kwargs) 
-        se = False
+        ##################
+        #from decam.py
+        from .common import (create_temp, get_version_header,
+                             get_git_version)
+
         if psfex and os.path.exists(self.psffn) and (not force):
-            psfex = False
+            if self.check_psf(self.psffn):
+                psfex = False
         if psfex:
             se = True
-
+            
         if se and os.path.exists(self.sefn) and (not force):
-            se = False
+            if self.check_se_cat(self.sefn):
+                se = False
         if se:
-            sedir = self.survey.get_se_dir()
-            trymakedirs(self.sefn, dir=True)
-            ####
-            trymakedirs('junk',dir=True) #need temp dir for mask-2 and invvar map
-            hdu=0
-            maskfn= self.imgfn.replace('_scie_','_mask_')
-            #invvar= self.read_invvar(self.imgfn,maskfn,hdu) #note, all post processing on image,mask done in read_invvar
-            invvar= self.read_invvar()
-            mask= self.read_dq()
-            maskfn= os.path.join('junk',os.path.basename(maskfn))
-            invvarfn= maskfn.replace('_mask_','_invvar_')
-            fitsio.write(maskfn, mask)
-            fitsio.write(invvarfn, invvar)
-            print('wrote mask-2 to %s, invvar to %s' % (maskfn,invvarfn))
-            #run se 
-            hdr=fitsio.read_header(self.imgfn,ext=hdu)
-            magzp  = zeropoint_for_ptf(hdr)
-            seeing = hdr['PIXSCALE'] * hdr['MEDFWHM']
-            gain= hdr['GAIN']
-            cmd = ' '.join(['sex','-c', os.path.join(sedir,'ptf.se'),
-                            '-WEIGHT_IMAGE %s' % invvarfn, '-WEIGHT_TYPE MAP_WEIGHT',
-                            '-GAIN %f' % gain,
-                            '-FLAG_IMAGE %s' % maskfn,
-                            '-FLAG_TYPE OR',
-                            '-SEEING_FWHM %f' % seeing,
-                            '-DETECT_MINAREA 3',
-                            '-PARAMETERS_NAME', os.path.join(sedir,'ptf.param'),
-                            '-FILTER_NAME', os.path.join(sedir, 'ptf_gauss_3.0_5x5.conv'),
-                            '-STARNNW_NAME', os.path.join(sedir, 'ptf_default.nnw'),
-                            '-PIXEL_SCALE 0',
-                            # SE has a *bizarre* notion of "sigma"
-                            '-DETECT_THRESH 1.0',
-                            '-ANALYSIS_THRESH 1.0',
-                            '-MAG_ZEROPOINT %f' % magzp,
-                            '-CATALOG_NAME', self.sefn,
-                            self.imgfn])
-            print(cmd)
-            if os.system(cmd):
-                raise RuntimeError('Command failed: ' + cmd)
-        if psfex:
-            sedir = self.survey.get_se_dir()
-            trymakedirs(self.psffn, dir=True)
-            # If we wrote *.psf instead of *.fits in a previous run...
-            oldfn = self.psffn.replace('.fits', '.psf')
-            if os.path.exists(oldfn):
-                print('Moving', oldfn, 'to', self.psffn)
-                os.rename(oldfn, self.psffn)
-            else: 
-                cmd= ' '.join(['psfex',self.sefn,'-c', os.path.join(sedir,'ptf.psfex'),
-                    '-PSF_DIR',os.path.dirname(self.psffn)])
-                print(cmd)
-                if os.system(cmd):
-                    raise RuntimeError('Command failed: ' + cmd)
-
+            funpack = True
+
+        if just_check:
+            return (se or psfex)
+
+        todelete = []
+        #if funpack:
+        #    # The image & mask files to process (funpacked if necessary)
+        #    imgfn,maskfn = self.funpack_files(self.imgfn, self.dqfn, self.hdu, todelete)
+        #else:
+        #    imgfn,maskfn = self.imgfn,self.dqfn
+        imgfn,maskfn = self.imgfn,self.dqfn
+        print('----TEMPORARILY FORCING se and psfex to run for testing ------') 
+        #if se:
+        self.run_se('90prime', imgfn, 'junkname')
+        #if psfex:
+        self.run_psfex('90prime')
+
+        print('exiting early')
+        import sys
+        sys.exit()
+
+        #############
+

py/legacypipe/image.py

@@ -681,23 +681,26 @@ def run_se(self, surveyname, imgfn, maskfn):
 
         sedir = self.survey.get_se_dir()
         trymakedirs(self.sefn, dir=True)
-
         cmd = ' '.join([
             'sex',
             '-c', os.path.join(sedir, surveyname + '.se'),
-            '-FLAG_IMAGE ' + maskfn,
             '-SEEING_FWHM %f' % seeing,
             '-PARAMETERS_NAME', os.path.join(sedir, surveyname + '.param'),
-            '-FILTER_NAME', os.path.join(sedir, 'gauss_5.0_9x9.conv'),
             '-STARNNW_NAME', os.path.join(sedir, 'default.nnw'),
             '-PIXEL_SCALE 0',
             # SE has a *bizarre* notion of "sigma"
             '-DETECT_THRESH 1.0',
             '-ANALYSIS_THRESH 1.0',
-            '-MAG_ZEROPOINT %f' % magzp,
-            '-CATALOG_NAME', self.sefn,
-            imgfn])
+            '-MAG_ZEROPOINT %f' % magzp])
+        if surveyname == '90prime': 
+            cmd+= ' -PHOT_APERTURES 7.5,15.0,22.0'
+            cmd+= ' -FILTER_NAME %s' % os.path.join(sedir, surveyname + '.conv') #sextractor default .conv file
+        else: 
+            cmd+= ' -FLAG_IMAGE %s' % maskfn #Bok does not have this
+            cmd+= ' -FILTER_NAME %s' % os.path.join(sedir, 'gauss_5.0_9x9.conv')
+        cmd+= ' -CATALOG_NAME %s %s' % (self.sefn,imgfn)
         print(cmd)
+
         if os.system(cmd):
             raise RuntimeError('Command failed: ' + cmd)
 
@@ -709,12 +712,16 @@ def run_psfex(self, surveyname):
         primhdr = self.read_image_primary_header()
         plver = primhdr.get('PLVER', '')
         verstr = get_git_version()
-        cmds = ['psfex -c %s -PSF_DIR %s %s' %
-                (os.path.join(sedir, surveyname + '.psfex'),
-                 os.path.dirname(self.psffn), self.sefn),
-                'modhead %s LEGPIPEV %s "legacypipe git version"' %
-                (self.psffn, verstr),
-                'modhead %s PLVER %s "CP ver of image file"' % (self.psffn, plver)]
+        if surveyname == '90prime':
+            cmds = ['psfex %s -c %s -PSF_DIR %s' % \
+                (self.sefn, os.path.join(sedir, surveyname + '.psfex'), os.path.dirname(self.psffn))]
+        else: 
+            cmds = ['psfex -c %s -PSF_DIR %s %s' %
+                    (os.path.join(sedir, surveyname + '.psfex'),
+                     os.path.dirname(self.psffn), self.sefn),
+                    'modhead %s LEGPIPEV %s "legacypipe git version"' %
+                    (self.psffn, verstr),
+                    'modhead %s PLVER %s "CP ver of image file"' % (self.psffn, plver)]
         for cmd in cmds:
             print(cmd)
             rtn = os.system(cmd)