port obs_subaru to python3 Tickets/dm 7306

bin.src/displayCamera.py

@@ -6,6 +6,7 @@
 import lsst.afw.cameraGeom.utils as cameraGeomUtils
 from lsst.afw.cameraGeom import Camera
 
+
 def checkStr(strVal, level):
     """Check if a string is a valid identifier
     @param[in] strVal: String containing the identifier
@@ -54,8 +55,8 @@ def displayCamera(args):
                 cameraGeomUtils.showCcd(detector, frame=frame)
                 frame += 1
 
-    raftMap = {'0':[],
-               '1':[]}
+    raftMap = {'0': [],
+               '1': []}
     for det in camera:
         dName = det.getName()
         if dName.startswith('1'):
@@ -87,16 +88,16 @@ def displayCamera(args):
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description='Display the Subaru cameras')
-    parser.add_argument('--showAmp', help='Show an amplifier segment in ds9  May have multiple arguments. '\
-                                          'Format like ccd_name amp_name e.g. '\
+    parser.add_argument('--showAmp', help='Show an amplifier segment in ds9  May have multiple arguments. '
+                                          'Format like ccd_name amp_name e.g. '
                                           '\"1_53 0,0\"', type=str, nargs='+')
-    parser.add_argument('--showCcd', help='Show a CCD from the mosaic in ds9.  May have multiple arguments. '\
+    parser.add_argument('--showCcd', help='Show a CCD from the mosaic in ds9.  May have multiple arguments. '
                                           'Format like ccd_name e.g. \"0_17\"', type=str,
                                           nargs='+')
-    parser.add_argument('--showRaft', help='Show a raft from the mosaic in ds9.  May have multiple arguments. '\
-                                          'May be 0 or 1', type=str)
+    parser.add_argument('--showRaft', help='Show a raft from the mosaic in ds9.  May have multiple arguments. '
+                        'May be 0 or 1', type=str)
     parser.add_argument('--showCamera', help='Show the camera mosaic in ds9.', action='store_true')
-    parser.add_argument('--cameraBinSize', type= int, default=20,
+    parser.add_argument('--cameraBinSize', type=int, default=20,
                         help='Size of binning when displaying the full camera mosaic')
     parser.add_argument('--plotFocalPlane', action='store_true',
                         help='Plot the focalplane in an interactive matplotlib window')

bin.src/genDefectFits.py

@@ -1,5 +1,6 @@
 #!/usr/bin/env python
 
+from __future__ import print_function
 import sys
 import os.path
 import re
@@ -14,6 +15,7 @@
 Defect = collections.namedtuple('Defect', ['x0', 'y0', 'width', 'height'])
 mapperMap = {'hsc': HscMapper, 'suprimecam': SuprimecamMapper, 'suprimecam_mit': SuprimecamMapperMit}
 
+
 def genDefectFits(cameraName, source, targetDir):
     mapper = mapperMap[cameraName.lower()](root=".")
     camera = mapper.camera
@@ -32,16 +34,16 @@ def genDefectFits(cameraName, source, targetDir):
             continue
         ccd, x0, y0, width, height = re.split("\s+", line)
         ccd = int(ccd)
-        if not ccds.has_key(ccd):
+        if ccd not in ccds:
             raise RuntimeError("Unrecognised ccd: %d" % ccd)
-        if not defects.has_key(ccd):
+        if ccd not in defects:
             defects[ccd] = list()
         defects[ccd].append(Defect(x0=int(x0), y0=int(y0), width=int(width), height=int(height)))
     f.close()
 
     for ccd in ccds:
         # Make empty defect FITS file for CCDs with no defects
-        if not defects.has_key(ccd):
+        if ccd not in defects:
             defects[ccd] = list()
 
         columns = list()
@@ -56,12 +58,12 @@ def genDefectFits(cameraName, source, targetDir):
         table.header['NAME'] = ccd
 
         name = os.path.join(targetDir, "defects_%d.fits" % ccd)
-        print "Writing %d defects from CCD %d (%s) to %s" % (table.header['NAXIS2'], ccd, ccds[ccd], name)
+        print("Writing %d defects from CCD %d (%s) to %s" % (table.header['NAXIS2'], ccd, ccds[ccd], name))
         if os.path.exists(name):
             if args.force:
                 os.unlink(name)
             else:
-                print >> sys.stderr, "File %s already exists; use --force to overwrite" % name
+                print("File %s already exists; use --force to overwrite" % name, file=sys.stderr)
                 continue
 
         table.writeto(name)

bin.src/genDefectRegistry.py

@@ -1,5 +1,7 @@
 #!/usr/bin/env python
 
+from __future__ import print_function
+from builtins import zip
 import glob
 import os
 import re
@@ -13,7 +15,9 @@
 
 from lsst.pipe.base import Struct
 
+
 class Row(Struct):
+
     def __init__(self, path, version, validStart, validEnd=None):
         super(Row, self).__init__(path=path, version=version, validStart=validStart, validEnd=validEnd)
 
@@ -45,7 +49,7 @@ def __init__(self, path, version, validStart, validEnd=None):
 for f in glob.glob(os.path.join(args.root, "*", "defects*.fits")):
     m = re.search(r'(\S+)/defects_(\d+)\.fits', f)
     if not m:
-        print >>sys.stderr, "Unrecognized file: %s" % (f,)
+        print("Unrecognized file: %s" % (f,), file=sys.stderr)
         continue
     #
     # Convert f to be relative to the location of the registry
@@ -62,7 +66,7 @@ def __init__(self, path, version, validStart, validEnd=None):
 # Fix up end dates so there are no collisions.
 # Defects files for a CCD are valid from the date they are registered until the next date.
 # This means that any defects file should carry ALL the defects that are present at that time.
-for ccd, rowList in rowsPerCcd.iteritems():
+for ccd, rowList in rowsPerCcd.items():
     rowList.sort(key=lambda row: row.validStart) # ISO-8601 will sort just fine without conversion from str
     for thisRow, nextRow in zip(rowList[:-1], rowList[1:]):
         thisRow.validEnd = (datetime.datetime.strptime(nextRow.validStart, "%Y-%m-%d") -
@@ -71,7 +75,7 @@ def __init__(self, path, version, validStart, validEnd=None):
 
     for row in rowList:
         if args.verbose:
-            print "Registering %s" % row.path
+            print("Registering %s" % row.path)
         conn.execute(cmd, (row.path, row.version, ccd, row.validStart, row.validEnd))
 
 conn.commit()

bin.src/makeGeom.py

@@ -21,6 +21,9 @@
 # the GNU General Public License along with this program.  If not,
 # see <https://www.lsstcorp.org/LegalNotices/>.
 #
+from __future__ import print_function
+from builtins import map
+from builtins import range
 import pyfits
 import sys
 import re
@@ -36,10 +39,11 @@
 
 hack = True
 
+
 def getSecCenter(sec):
     sec = re.sub('\'', '', sec)
     sec = re.sub('\[|\:|\,|\]', ' ', sec)
-    fields = map(int, sec.split())
+    fields = list(map(int, sec.split()))
     # these indices run from 1..N
     # to run from 0..N-1 subtract off 2 from each sum
     return 0.5 * (fields[0] + fields[1] - 2), 0.5 * (fields[2] + fields[3] - 2)
@@ -59,6 +63,7 @@ def printCameraGeom(filename, buff):
     buff.write('    } \n')
     buff.write('} \n')
 
+
 def printAmpDefaults(buff):
     # http://cfht.hawaii.edu/Instruments/Imaging/MegaPrime/rawdata.html
     #
@@ -72,6 +77,7 @@ def printAmpDefaults(buff):
     buff.write('    overclockV: 32 \n')
     buff.write('} \n')
 
+
 def printCcdAmpDefaults(buff):
     # Depending on how much we need to undo the imsplice operation
     # here are the defaults from straight off the camera
@@ -104,6 +110,7 @@ def printCcdAmpDefaults(buff):
     buff.write('    } \n')
     buff.write('} \n')
 
+
 def printCcdDiskLayout(buff):
     buff.write('CcdDiskLayout: { \n')
     buff.write('    HduPerAmp: true \n')
@@ -149,6 +156,7 @@ def printRaftCcdGeom(buff, ccdId, ccdname, xidx, yidx, xpos, ypos):
     buff.write('        orientation: 0.000000 0.000000 0.000000 \n')
     buff.write('    } \n')
 
+
 def printElectronics(buff, ccdId, ccdname, xidx, yidx, infoA, infoB):
     # http://www.cfht.hawaii.edu/Instruments/Imaging/Megacam/specsinformation.html
 
@@ -215,11 +223,11 @@ def printElectronics(buff, ccdId, ccdname, xidx, yidx, infoA, infoB):
     # everything else.  Raft w.r.t. boresight; CCD w.r.t. Raft center; Amp
     # w.r.t CCD center.
 
-    buffCamera  = open('Camera.paf', 'w')
+    buffCamera = open('Camera.paf', 'w')
     buffElectro = open('Electronics.paf', 'w')
 
     infile = sys.argv[1]           # full MEF file; e.g. 871034p.fits
-    ptr    = pyfits.open(infile)
+    ptr = pyfits.open(infile)
 
     printCameraGeom(infile, buffCamera)
     printAmpDefaults(buffCamera)
@@ -228,29 +236,29 @@ def printElectronics(buff, ccdId, ccdname, xidx, yidx, infoA, infoB):
 
     # 0th layer is pure metadata
     for ccd in range(1, len(ptr)):
-    #for ccd in [1, 28]:
-        ccdId        = ptr[ccd].header['EXTVER']
-        ccdBoundary  = ptr[ccd].header['DETSEC']
-        ccdName      = ptr[ccd].header['CCDNAME']
+        #for ccd in [1, 28]:
+        ccdId = ptr[ccd].header['EXTVER']
+        ccdBoundary = ptr[ccd].header['DETSEC']
+        ccdName = ptr[ccd].header['CCDNAME']
         amp1Boundary = ptr[ccd].header['DETSECA']
         amp2Boundary = ptr[ccd].header['DETSECB']
 
         ccdxc, ccdyc = getSecCenter(ccdBoundary)
-        xpos         = (ccdxc - detCenterX) * cfhtPixelScale
-        ypos         = (ccdyc - detCenterY) * cfhtPixelScale
+        xpos = (ccdxc - detCenterX) * cfhtPixelScale
+        ypos = (ccdyc - detCenterY) * cfhtPixelScale
 
-        gain1        = ptr[ccd].header['GAINA']
-        gain2        = ptr[ccd].header['GAINB']
+        gain1 = ptr[ccd].header['GAINA']
+        gain2 = ptr[ccd].header['GAINB']
 
-        rdnoise1     = ptr[ccd].header['RDNOISEA']
-        rdnoise2     = ptr[ccd].header['RDNOISEB']
+        rdnoise1 = ptr[ccd].header['RDNOISEA']
+        rdnoise2 = ptr[ccd].header['RDNOISEB']
 
         # assume non-linear = saturation since we have no non-linearity curves
-        saturate1    = ptr[ccd].header['MAXLINA']
-        saturate2    = ptr[ccd].header['MAXLINB']
+        saturate1 = ptr[ccd].header['MAXLINA']
+        saturate2 = ptr[ccd].header['MAXLINB']
 
-        print ccdId, ccdBoundary, amp1Boundary, amp2Boundary, gain1, gain2, rdnoise1, rdnoise2, \
-            saturate1, saturate2
+        print(ccdId, ccdBoundary, amp1Boundary, amp2Boundary, gain1, gain2, rdnoise1, rdnoise2, \
+            saturate1, saturate2)
 
         # flip y
         xidx = ccdId % 9

bin.src/refileFocus.py

@@ -12,8 +12,7 @@
     108		110
     114		108
 """
-
-#!/usr/bin/env python
+from __future__ import print_function
 
 import glob
 import os
@@ -37,17 +36,19 @@
 #
 # Desired remapping
 #
-remap = {112 : 106,
+remap = {112: 106,
          #104 : 104
-         107 : 105,
-         113 : 107,
-         115 : 109,
+         107: 105,
+         113: 107,
+         115: 109,
          #111 : 111,
-         108 : 110,
-         114 : 108,
+         108: 110,
+         114: 108,
          }
 
 # Gather list of files
+
+
 def globber(field="*", filename="*.fits"):
     return glob.glob(os.path.join(args.root, field, "*-*-*", "*", "*", filename))
 
@@ -61,7 +62,7 @@ def globber(field="*", filename="*.fits"):
     if args.fields:
         for f in args.fields:
             files += globber(field=f)
-print 'Processing %d files...' % len(files)
+print('Processing %d files...' % len(files))
 
 # Set up regex for parsing directory structure
 reField = r'([\w .+-]+)'
@@ -75,13 +76,13 @@ def globber(field="*", filename="*.fits"):
 for fileNo, fits in enumerate(files):
     m = re.search(regex, fits)
     if not m:
-        print "Warning: skipping unrecognized filename:", fits
+        print("Warning: skipping unrecognized filename:", fits)
         continue
 
     field, dateObs, pointing, filterId, visit, ccd = m.groups()
     visit = int(visit)
     ccd = int(ccd)
-    if not visits.has_key(visit):
+    if visit not in visits:
         visits[visit] = set()
     visits[visit].add(ccd)
     #print "Processing %s" % fits
@@ -91,14 +92,14 @@ def globber(field="*", filename="*.fits"):
 #
 for visit, ccds in visits.items():
     if 105 in ccds:                     # already refiled
-        print "%d is already refiled" % visit
+        print("%d is already refiled" % visit)
         del visits[visit]
         continue
 
     if set(remap.keys()) != set([_ for _ in ccds if remap.get(_)]): # no focus chips are available
         continue
 
-    print visit
+    print(visit)
     try:
         tmpDir = None
         for old, new in remap.items():
@@ -120,4 +121,3 @@ def globber(field="*", filename="*.fits"):
             os.rmdir(tmpDir)
 #
 #
-