HLA-1254: Address issues caught by SonarQube (#1802)

CHANGELOG.rst

@@ -20,6 +20,15 @@ number of the code change for that issue.  These PRs can be viewed at:
 
 3.7.1 (unreleased)
 ======================
+- Addressed bugs caught by SonarQube static code analysis.  Interface
+  changes listed here: Added missing input data parameter to the create_output
+  calls, Added missing log level to run function, Removed the deprecated 
+  parameter, dao_threshold, from astrometric_utils.py/extract_sources, removed 
+  "ivmlist" parameter from the interface of multiple functions in processInput.py 
+  as it is an output parameter (buildFileListOrig, buildFileList, checkMultipleFiles,
+  and process_input), and addressed missing parameters in the calls to
+  get_ci_info and get_ci_from_file.. [#1802]
+
 - Exclude single filter images from the generation of the total detection
   image to minimize cosmic ray contamination, unless there are only single
   filter images in the visit. [#1797]

drizzlepac/haputils/align_utils.py

@@ -714,7 +714,6 @@ def find_alignment_sources(self, output=True, dqname='DQ', crclean=False,
                                                                  outroot=outroot,
                                                                  kernel=self.kernel,
                                                                  segment_threshold=self.threshold[chip],
-                                                                 dao_threshold=self.bkg_rms_mean[chip],
                                                                  fwhm=self.kernel_fwhm,
                                                                  **extract_pars)
             if crclean and crmap is not None:

drizzlepac/haputils/astrometric_utils.py

@@ -958,8 +958,7 @@ def build_gaussian_kernel(fwhm, npixels):
 
 
 def extract_sources(img, dqmask=None, fwhm=3.0, kernel=None, photmode=None,
-                    segment_threshold=None, dao_threshold=None,
-                    dao_nsigma=3.0, source_box=7,
+                    segment_threshold=None, dao_nsigma=3.0, source_box=7,
                     classify=True, centering_mode="starfind", nlargest=None,
                     outroot=None, plot=False, vmax=None, deblend=False,
                     log_level=logutil.logging.INFO):
@@ -988,10 +987,6 @@ def extract_sources(img, dqmask=None, fwhm=3.0, kernel=None, photmode=None,
     segment_threshold : ndarray or None
         Value from the image which serves as the limit for determining sources.
         If None, compute a default value of (background+5*rms(background)).
-    dao_threshold : float, optional
-        [Deprecated] This parameter is not used.  In fact, it now gets computed
-        internally using the ``sigma_clipped_bkg()`` function which uses the
-        ``dao_nsigma`` parameter.
     dao_nsigma : float
         This number gets used to determine the threshold for detection of point
         sources.  The threshold gets computed using a simple ``mean + dao_nsigma * rms``,
@@ -1456,7 +1451,6 @@ def generate_source_catalog(image, dqname="DQ", output=False, fwhm=3.0,
 
         bkg_ra, bkg_median, bkg_rms_ra, bkg_rms_median = compute_2d_background(imgarr, box_size, win_size)
         threshold = nsigma * bkg_rms_ra
-        dao_threshold = nsigma * bkg_rms_median
 
         (kernel, kernel_psf), kernel_fwhm = build_auto_kernel(imgarr - bkg_ra, whtarr,
                                                               threshold=threshold,
@@ -1470,7 +1464,6 @@ def generate_source_catalog(image, dqname="DQ", output=False, fwhm=3.0,
                                                  outroot=outroot, kernel=kernel,
                                                  photmode=photmode,
                                                  segment_threshold=threshold,
-                                                 dao_threshold=dao_threshold,
                                                  fwhm=kernel_fwhm, **detector_pars)
         del crmap
         source_cats[chip] = seg_tab

drizzlepac/haputils/ci_table.py

@@ -207,10 +207,10 @@ def get_ci_from_file(drzfile, ci_lookup_file_path, log_level, **kw):
     inst, detect, filt = parse_file(drzfile)
     return get_ci_info(inst, detect, filt, ci_lookup_file_path, **kw)
 
-
 if __name__ == '__main__':
+    ci_lookup_file_path = 'svm_parameters/any'
     inst, detect, filt = ('wfc3', 'uvis', 'f606w')
-    ciap_dict = get_ci_info(inst, detect, filt)
+    ciap_dict = get_ci_info(inst, detect, filt, ci_lookup_file_path)
     log.info("configuration:  {}".format(inst, detect, filt))
     log.info("eff_wave:       {}".format(ciap_dict['eff_wave']))
     log.info("ci_lower:       {}".format(ciap_dict['ci_lower_limit']))
@@ -220,7 +220,7 @@ def get_ci_from_file(drzfile, ci_lookup_file_path, log_level, **kw):
 
     drizzled_image = 'hst_12311_03_wfc3_uvis_f275w_drz.fits'
     inst, detect, filt = parse_file(drizzled_image)
-    ciap_dict = get_ci_from_file(drizzled_image)
+    ciap_dict = get_ci_from_file(drizzled_image, ci_lookup_file_path, logutil.logging.INFO)
     log.info("drizzled image: {}".format(drizzled_image))
     log.info("configuration:  {}".format(inst, detect, filt))
     log.info("eff_wave:       {}".format(ciap_dict['eff_wave']))
@@ -231,7 +231,7 @@ def get_ci_from_file(drzfile, ci_lookup_file_path, log_level, **kw):
 
     drizzled_image = 'hst_11969_04_wfpc2_f606w_pc_drz.fits'
     inst, detect, filt = parse_file(drizzled_image)
-    ciap_dict = get_ci_from_file(drizzled_image)
+    ciap_dict = get_ci_from_file(drizzled_image, ci_lookup_file_path, logutil.logging.INFO)
     log.info("drizzled image: {}".format(drizzled_image))
     log.info("configuration:  {}".format(inst, detect, filt))
     log.info("eff_wave:       {}".format(ciap_dict['eff_wave']))

drizzlepac/haputils/hapcut_utils.py

@@ -113,11 +113,6 @@ def mvm_id_filenames(sky_coord, cutout_size, log_level=logutil.logging.INFO):
     del acs_query_table
     del wfc3_query_table
 
-    # Catch the case where no files are found which satisfied the Query
-    if not query_table:
-        log.warning("Query for objects within {} of {} returned NO RESULTS!".format(radius, (str_ra, str_dec)))
-        return query_table
-
     # Compute the limits of the cutout region
     deg_cutout_size = cutout_size.to(u.deg)
     ra_min = sky_coord.ra.degree - deg_cutout_size.value[0]
@@ -127,6 +122,11 @@ def mvm_id_filenames(sky_coord, cutout_size, log_level=logutil.logging.INFO):
     str_ra = "{:.4f}".format(sky_coord.ra.degree)
     str_dec = "{:.4f}".format(sky_coord.dec.degree)
 
+    # Catch the case where no files are found which satisfied the Query
+    if not query_table:
+        log.warning("Query for objects within {} of {} returned NO RESULTS!".format(radius, (str_ra, str_dec)))
+        return query_table
+
     # Filter the output as necessary to include only MVM filenames (MVM prefix: hst_skycell).
     # Also, filter out images which are not actually in the requested cutout region as the
     # archive search had to be done using a radius.

drizzlepac/haputils/product.py

@@ -199,7 +199,6 @@ def align_to_gaia(
 
         exposure_filenames = []
         headerlet_filenames = {}
-        align_table = None
         crclean = []
 
         # If no catalog list has been provided, use the list defined in the configuration file

drizzlepac/nicmosData.py

@@ -423,10 +423,10 @@ def fromcalfile(filename):
     hdulist = fileutil.openImage(filename)
 
     if 'TEMPFILE' in hdulist[0].header:
+        tddfile = hdulist[0].header['TEMPFILE']
         if tddfile == 'N/A':
             return None
         else:
-            tddfile = hdulist[0].header['TEMPFILE']
             tddhdulist = fileutil.openImage(tddfile)
             return darkobject(tddhdulist)
     else:

drizzlepac/processInput.py

@@ -533,15 +533,15 @@ def processFilenames(input=None,output=None,infilesOnly=False):
     return filelist, output, ivmlist, oldasndict
 
 
-def process_input(input, output=None, ivmlist=None, updatewcs=True,
+def process_input(input, output=None, updatewcs=True,
                   prodonly=False,  wcskey=None, **workinplace):
     """
     Create the full input list of filenames after verifying and converting
     files as needed.
     """
 
     newfilelist, ivmlist, output, oldasndict, origflist = buildFileListOrig(
-            input, output=output, ivmlist=ivmlist, wcskey=wcskey,
+            input, output=output, wcskey=wcskey,
             updatewcs=updatewcs, **workinplace)
 
     if not newfilelist:
@@ -655,19 +655,19 @@ def _process_input_wcs_single(fname, wcskey, updatewcs):
         wcscorr.init_wcscorr(fname)
 
 
-def buildFileList(input, output=None, ivmlist=None,
+def buildFileList(input, output=None, 
                 wcskey=None, updatewcs=True, **workinplace):
     """
     Builds a file list which has undergone various instrument-specific
     checks for input to MultiDrizzle, including splitting STIS associations.
     """
     newfilelist, ivmlist, output, oldasndict, filelist = \
-        buildFileListOrig(input=input, output=output, ivmlist=ivmlist,
+        buildFileListOrig(input=input, output=output, 
                     wcskey=wcskey, updatewcs=updatewcs, **workinplace)
     return newfilelist, ivmlist, output, oldasndict
 
 
-def buildFileListOrig(input, output=None, ivmlist=None,
+def buildFileListOrig(input, output=None,
                 wcskey=None, updatewcs=True, **workinplace):
     """
     Builds a file list which has undergone various instrument-specific