DM-7886: pyfits to astropy

bin.src/genDefectFits.py

@@ -6,7 +6,7 @@
 import re
 
 import numpy
-import pyfits
+from astropy.io import fits
 import collections
 
 from lsst.obs.hsc import HscMapper
@@ -27,19 +27,18 @@ def genDefectFits(cameraName, source, targetDir):
 
     defects = dict()
 
-    f = open(source, "r")
-    for line in f:
-        line = re.sub("\#.*", "", line).strip()
-        if len(line) == 0:
-            continue
-        ccd, x0, y0, width, height = re.split("\s+", line)
-        ccd = int(ccd)
-        if ccd not in ccds:
-            raise RuntimeError("Unrecognised ccd: %d" % 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()
+    with open(source, "r") as f:
+        for line in f:
+            line = re.sub("\#.*", "", line).strip()
+            if len(line) == 0:
+                continue
+            ccd, x0, y0, width, height = re.split("\s+", line)
+            ccd = int(ccd)
+            if ccd not in ccds:
+                raise RuntimeError("Unrecognised ccd: %d" % 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)))
 
     for ccd in ccds:
         # Make empty defect FITS file for CCDs with no defects
@@ -49,11 +48,11 @@ def genDefectFits(cameraName, source, targetDir):
         columns = list()
         for colName in Defect._fields:
             colData = numpy.array([d._asdict()[colName] for d in defects[ccd]])
-            col = pyfits.Column(name=colName, format="I", array=colData)
+            col = fits.Column(name=colName, format="I", array=colData)
             columns.append(col)
 
-        cols = pyfits.ColDefs(columns)
-        table = pyfits.BinTableHDU.from_columns(cols)
+        cols = fits.ColDefs(columns)
+        table = fits.BinTableHDU.from_columns(cols)
 
         table.header['NAME'] = ccd
 

bin.src/makeGeom.py

@@ -24,7 +24,7 @@
 from __future__ import absolute_import, division, print_function
 from builtins import map
 from builtins import range
-import pyfits
+from astropy.io import fits
 import sys
 import re
 import os
@@ -227,7 +227,7 @@ def printElectronics(buff, ccdId, ccdname, xidx, yidx, infoA, infoB):
     buffElectro = open('Electronics.paf', 'w')
 
     infile = sys.argv[1]           # full MEF file; e.g. 871034p.fits
-    ptr = pyfits.open(infile)
+    ptr = fits.open(infile)
 
     printCameraGeom(infile, buffCamera)
     printAmpDefaults(buffCamera)

bin.src/showPsfs.py

@@ -7,6 +7,7 @@
 import re
 import sys
 
+from astropy.io import fits
 import numpy as np
 from matplotlib.mlab import griddata
 import matplotlib.pyplot as plt
@@ -249,8 +250,7 @@ def main(dataDir, visit, title="", outputTxtFileName=None,
     plt.axis([-20000, 20000, -20000, 20000])
 
     def frameInfoFrom(filepath):
-        import pyfits
-        with pyfits.open(filepath) as hdul:
+        with fits.open(filepath) as hdul:
             h = hdul[0].header
             'object=ABELL2163 filter=HSC-I exptime=360.0 alt=62.11143274 azm=202.32265181 hst=(23:40:08.363-23:40:48.546)'
             return 'object=%s filter=%s exptime=%.1f azm=%.2f hst=%s' % (h['OBJECT'], h['FILTER01'], h['EXPTIME'], h['AZIMUTH'], h['HST'])

python/lsst/obs/subaru/strayLight/rotatorAngle.py

@@ -22,7 +22,7 @@
 
 import sys
 import numpy as np
-import astropy.io.fits as pyfits
+from astropy.io import fits
 
 ### fixed parameters
 ltt_d = 19.82556  # dome latitude in degree
@@ -203,7 +203,7 @@ def _gsCPposNorth(ra_t_d, de_t_d, inr_d, mjd):
 
 def _getDataArrayFromFITSFileWithHeader(pathToFITSFile):
     """return array of pixel data"""
-    fitsfile   = pyfits.open(pathToFITSFile)
+    fitsfile   = fits.open(pathToFITSFile)
     dataArray  = fitsfile[0].data
     fitsHeader = fitsfile[0].header
     fitsfile.close()

python/lsst/obs/subaru/strayLight/yStrayLight.py

@@ -21,7 +21,7 @@
 import os
 
 import numpy
-import astropy.io.fits as pyfits
+from astropy.io import fits
 import scipy.interpolate
 
 from lsst.pex.config import Config, Field
@@ -144,7 +144,7 @@ def get_ybackground(filename, angle_start, angle_end=None):
 
     @return (numpy.array[][])
     """
-    hdulist = pyfits.open(filename)
+    hdulist = fits.open(filename)
     header = hdulist[0].header
 
     # full-size ccd height & channel width

ups/obs_subaru.table

@@ -2,7 +2,7 @@ setupRequired(daf_persistence)
 setupRequired(obs_base)
 setupRequired(pipe_tasks)
 setupRequired(meas_astrom)
-setupRequired(pyfits)
+setupRequired(astropy)
 setupRequired(sconsUtils)
 setupRequired(pybind11)
 setupRequired(numpy)
@@ -18,4 +18,3 @@ envPrepend(DYLD_LIBRARY_PATH, ${PRODUCT_DIR}/lib)
 envPrepend(LSST_LIBRARY_PATH, ${PRODUCT_DIR}/lib)
 envPrepend(PYTHONPATH, ${PRODUCT_DIR}/python)
 envPrepend(PATH, ${PRODUCT_DIR}/bin)
-