Merge pull request #49 from PaulHancock/dev-codacy

dev-codacy

AegeanTools/BANE.py

@@ -62,7 +62,7 @@ def sigmaclip(arr, lo, hi, reps=3):
 
     std = np.std(clipped)
     mean = np.mean(clipped)
-    for i in range(int(reps)):
+    for _ in range(int(reps)):
         clipped = clipped[np.where(clipped > mean-std*lo)]
         clipped = clipped[np.where(clipped < mean+std*hi)]
         pstd = std

AegeanTools/MIMAS.py

@@ -4,11 +4,8 @@
 """
 MIMAS - The Multi-resolution Image Mask for Aegean Software
 
-Created: Paul Hancock, Oct 2014
-
 TODO: Write an in/out reader for MOC formats described by
 http://arxiv.org/abs/1505.02937
-
 """
 
 import logging
@@ -174,9 +171,9 @@ def mask_file(regionfile, infile, outfile, negate=False):
     :func:`AegeanTools.MIMAS.mask_plane`
     """
     # Check that the input file is accessible and then open it
-    assert os.path.exists(infile), "Cannot locate fits file {0}".format(infile)
+    if not os.path.exists(infile): raise AssertionError("Cannot locate fits file {0}".format(infile))
     im = pyfits.open(infile)
-    assert os.path.exists(regionfile), "Cannot locate region file {0}".format(regionfile)
+    if not os.path.exists(regionfile): raise AssertionError("Cannot locate region file {0}".format(regionfile))
     region = cPickle.load(open(regionfile, 'rb'))
     try:
         wcs = pywcs.WCS(im[0].header, naxis=2)

AegeanTools/catalogs.py

@@ -10,7 +10,6 @@
 __date__ = "2016-07-26"
 
 # Standard imports
-import sys
 import os
 import numpy as np
 import re
@@ -21,9 +20,7 @@
 from .models import OutputSource, classify_catalog
 
 # input/output table formats
-import astropy
 from astropy.table.table import Table
-from astropy.table import Column
 from astropy.io import ascii
 from astropy.io import fits
 from astropy.io.votable import from_table, parse_single_table
@@ -62,7 +59,7 @@ def check_table_formats(files):
     cont = True
     formats = get_table_formats()
     for t in files.split(','):
-        name, ext = os.path.splitext(t)
+        _, ext = os.path.splitext(t)
         ext = ext[1:].lower()
         if ext not in formats:
             cont = False
@@ -336,7 +333,7 @@ def table_to_source_list(table, src_type=OutputSource):
                 # copy the value to our object
                 val = row[param]
                 # hack around float32's broken-ness
-                if type(val) == np.float32:
+                if isinstance(val, np.float32):
                     val = np.float64(val)
                 setattr(src, param, val)
         # save this object to our list of sources

AegeanTools/fits_image.py

@@ -179,7 +179,7 @@ def __init__(self, filename=None, hdu_index=0, beam=None, slice=None):
             self.bscale = self._header["BSCALE"]
         else:
             self.bscale = 1
-            
+
         self.filename = filename
         # fix possible problems with miriad generated fits files % HT John Morgan.
         try:
@@ -242,7 +242,8 @@ def set_pixels(self, pixels):
         -------
         None
         """
-        assert pixels.shape == self._pixels.shape, "Shape mismatch between pixels supplied {0} and existing image pixels {1}".format(pixels.shape,self._pixels.shape)
+        if not (pixels.shape == self._pixels.shape):
+            raise AssertionError("Shape mismatch between pixels supplied {0} and existing image pixels {1}".format(pixels.shape,self._pixels.shape))
         self._pixels = pixels
         # reset this so that it is calculated next time the function is called
         self._rms = None
@@ -319,7 +320,7 @@ def sky2pix(self, skypos):
         """
         skybox = [skypos, skypos]
         pixbox = self.wcs.all_world2pix(skybox, 1)
-        return [float(pixbox[0][0]), float(pixbox[0][1])] 
+        return [float(pixbox[0][0]), float(pixbox[0][1])]
 
 
 class Beam(object):
@@ -328,8 +329,8 @@ class Beam(object):
     Properties are a,b,pa. No assumptions are made as to the units, but both a and b have to be >0.
     """
     def __init__(self, a, b, pa, pixa=None, pixb=None):
-        assert a > 0, "major axis must be >0"
-        assert b > 0, "minor axis must be >0"
+        if not (a > 0): raise AssertionError("major axis must be >0")
+        if not (b > 0): raise AssertionError("minor axis must be >0")
         self.a = a
         self.b = b
         self.pa = pa

AegeanTools/fitting.py

@@ -356,7 +356,7 @@ def hessian(pars, x, y):
 
             if yo_var:
                 # H(amp,yo)/G =  1.0*(-sx**2*((x - xo)*sin(t) + (-y + yo)*cos(t))*cos(t) + sy**2*((x - xo)*cos(t) + (y - yo)*sin(t))*sin(t))/(amp*sx**2*sy**2)
-                hmat[j][k] = -(xsin - ycos)*cost/sy2 + (xcos + ysin)*sint/sx2 
+                hmat[j][k] = -(xsin - ycos)*cost/sy2 + (xcos + ysin)*sint/sx2
                 hmat[j][k] *= model/amp
                 k += 1
 
@@ -1077,7 +1077,7 @@ def new_errors(source, model, wcshelper):  # pragma: no cover
             (a, b), e = np.linalg.eig(mat)
             pa = np.degrees(np.arctan2(*e[0]))
             # transform this ellipse into sky coordinates
-            ra, dec, major, minor, pa = wcshelper.pix2sky_ellipse([xo, yo], a, b, pa)
+            _, dec, major, minor, pa = wcshelper.pix2sky_ellipse([xo, yo], a, b, pa)
 
             # now determine the radius of the ellipse along the ra/dec directions.
             source.err_ra = major*minor / np.hypot(major*np.sin(np.radians(pa)), minor*np.cos(np.radians(pa)))
@@ -1255,15 +1255,15 @@ def covar_errors(params, data, errs, B, C=None):
             J = lmfit_jacobian(params, mask[0], mask[1], errs=errs)
             covar = np.transpose(J).dot(inv(C)).dot(J)
             onesigma = np.sqrt(np.diag(inv(covar)))
-        except (np.linalg.linalg.LinAlgError, ValueError) as e:
+        except (np.linalg.linalg.LinAlgError, ValueError) as _:
             C = None
 
     if C is None:
         try:
             J = lmfit_jacobian(params, mask[0], mask[1], B=B, errs=errs)
             covar = np.transpose(J).dot(J)
             onesigma = np.sqrt(np.diag(inv(covar)))
-        except (np.linalg.linalg.LinAlgError, ValueError) as e:
+        except (np.linalg.linalg.LinAlgError, ValueError) as _:
             onesigma = [-2] * len(mask[0])
 
     for i in range(params['components'].value):
@@ -1357,18 +1357,18 @@ def test_hessian_plots():
         kwargs = {"interpolation": "nearest", 'aspect': 1, 'vmin': -1, 'vmax': 1}
         fig, ax = pyplot.subplots(6, 6, squeeze=True, sharex=True, sharey=True, figsize=(5, 6))
         Hemp = emp_hessian(model, x, y)
-        vars = ['amp', 'xo', 'yo', 'sx', 'sy', 'theta']
+        params = ['amp', 'xo', 'yo', 'sx', 'sy', 'theta']
         for i, row in enumerate(ax):
             for j, ax in enumerate(row):
                 im = Hemp[i, j, :, :]
                 # im[np.where(abs(im) < 1e-5)] = 0
-                # print vars[i],vars[j], np.amax(im)
+                # print params[i],params[j], np.amax(im)
                 im /= np.amax(im)
                 ax.imshow(im, **kwargs)
                 if j == 0:
-                    ax.set_ylabel(vars[i])
+                    ax.set_ylabel(params[i])
                 if i == 5:
-                    ax.set_xlabel(vars[j])
+                    ax.set_xlabel(params[j])
                 clx(ax)
         fig.suptitle('Empirical Hessian')
 
@@ -1379,13 +1379,13 @@ def test_hessian_plots():
             for j, ax in enumerate(row):
                 im = Hana[i, j, :, :]
                 # im[np.where(abs(im) < 1e-5)] = 0
-                # print vars[i],vars[j], np.amax(im)
+                # print params[i],params[j], np.amax(im)
                 im /= np.amax(im)
                 ax.imshow(im, **kwargs)
                 if j == 0:
-                    ax.set_ylabel(vars[i])
+                    ax.set_ylabel(params[i])
                 if i == 5:
-                    ax.set_xlabel(vars[j])
+                    ax.set_xlabel(params[j])
                 clx(ax)
         fig.suptitle('Analytical Hessian')
 
@@ -1400,9 +1400,9 @@ def test_hessian_plots():
                 im2 /= np.amax(im2)
                 ax.imshow(im1-im2, **kwargs)
                 if j == 0:
-                    ax.set_ylabel(vars[i])
+                    ax.set_ylabel(params[i])
                 if i == 5:
-                    ax.set_xlabel(vars[j])
+                    ax.set_xlabel(params[j])
                 clx(ax)
         fig.suptitle('Difference')
         pyplot.show()

AegeanTools/models.py

@@ -76,7 +76,7 @@ def _sanitise(self):
         Convert attributes of type npumpy.float32 to numpy.float64 so that they will print properly.
         """
         for k in self.__dict__:
-            if type(self.__dict__[k]) in [np.float32]:  # np.float32 has a broken __str__ method
+            if isinstance(self.__dict__[k], np.float32):  # np.float32 has a broken __str__ method
                 self.__dict__[k] = np.float64(self.__dict__[k])
 
     def __str__(self):

AegeanTools/msq2.py

@@ -32,7 +32,7 @@ def find_start_point(self):
         Find the first location in our array that is not empty
         """
         for i, row in enumerate(self.data):
-            for j, col in enumerate(row):
+            for j, _ in enumerate(row):
                 if self.data[i, j] != 0:  # or not np.isfinite(self.data[i,j]):
                     return i, j
 
@@ -213,7 +213,7 @@ def do_march_all(self):
         """
         # copy the data since we are going to be modifying it
         data_copy = copy(self.data)
-        
+
         # iterate through finding an island, creating a perimeter,
         # and then blanking the island
         perimeters = []
@@ -225,6 +225,6 @@ def do_march_all(self):
             self._blank_within(perim)
             p = self.find_start_point()
 
-        # restore the data 
+        # restore the data
         self.data = data_copy
         return perimeters

AegeanTools/regions.py

@@ -82,7 +82,7 @@ def add_poly(self, positions, depth=None):
         depth : int
             The deepth at which the polygon will be inserted.
         """
-        assert len(positions) >= 3, "A minimum of three coordinate pairs are required"
+        if not (len(positions) >= 3): raise AssertionError("A minimum of three coordinate pairs are required")
 
         if depth is None or depth > self.maxdepth:
             depth = self.maxdepth
@@ -109,7 +109,6 @@ def add_pixels(self, pix, depth):
         if depth not in self.pixeldict:
             self.pixeldict[depth] = set()
         self.pixeldict[depth].update(set(pix))
-        pass
 
     def get_area(self, degrees=True):
         """
@@ -259,7 +258,7 @@ def without(self, other):
         """
         # work only on the lowest level
         # TODO: Allow this to be done for regions with different depths.
-        assert self.maxdepth == other.maxdepth, "Regions must have the same maxdepth"
+        if not (self.maxdepth == other.maxdepth): raise AssertionError("Regions must have the same maxdepth")
         self._demote_all()
         opd = set(other.get_demoted())
         self.pixeldict[self.maxdepth].difference_update(opd)
@@ -279,7 +278,7 @@ def intersect(self, other):
         """
         # work only on the lowest level
         # TODO: Allow this to be done for regions with different depths.
-        assert self.maxdepth == other.maxdepth, "Regions must have the same maxdepth"
+        if not (self.maxdepth == other.maxdepth): raise AssertionError("Regions must have the same maxdepth")
         self._demote_all()
         opd = set(other.get_demoted())
         self.pixeldict[self.maxdepth].intersection_update(opd)
@@ -299,7 +298,7 @@ def symmetric_difference(self, other):
         """
         # work only on the lowest level
         # TODO: Allow this to be done for regions with different depths.
-        assert self.maxdepth == other.maxdepth, "Regions must have the same maxdepth"
+        if not (self.maxdepth == other.maxdepth): raise AssertionError("Regions must have the same maxdepth")
         self._demote_all()
         opd = set(other.get_demoted())
         self.pixeldict[self.maxdepth].symmetric_difference_update(opd)
@@ -420,7 +419,7 @@ def sky2ang(sky):
         """
         try:
             theta_phi = sky.copy()
-        except AttributeError as e:
+        except AttributeError as _:
             theta_phi = np.array(sky)
         theta_phi[:, [1, 0]] = theta_phi[:, [0, 1]]
         theta_phi[:, 0] = np.pi/2 - theta_phi[:, 0]

AegeanTools/source_finder.py

@@ -1466,7 +1466,7 @@ def find_sources_in_image(self, filename, hdu_index=0, outfile=None, rms=None, m
         # Tell numpy to be quiet
         np.seterr(invalid='ignore')
         if cores is not None:
-            assert (cores >= 1), "cores must be one or more"
+            if not (cores >= 1): raise AssertionError("cores must be one or more")
 
         self.load_globals(filename, hdu_index=hdu_index, bkgin=bkgin, rmsin=rmsin, beam=beam, rms=rms, cores=cores,
                           verb=True, mask=mask, lat=lat, psf=imgpsf, blank=blank, docov=docov, slice=slice)
@@ -1732,7 +1732,7 @@ def priorized_fit_islands(self, filename, catalogue, hdu_index=0, outfile=None,
 
         components = 0
         for source in sources:
-            if type(source) == OutputSource:
+            if isinstance(source, OutputSource):
                 components += 1
                 if outfile:
                     print(str(source), file=outfile)
@@ -1885,7 +1885,7 @@ def check_cores(cores):
         cores = 1
     else:
         try:
-            temp = queue.manage(pprocess.MakeReusable(fix_shape))
+            _ = queue.manage(pprocess.MakeReusable(fix_shape))
         except:
             cores = 1
     return cores

AegeanTools/wcs_helpers.py

@@ -14,7 +14,6 @@
 from .fits_image import Beam, get_beam, get_pixinfo
 
 # the glory of astropy
-import astropy
 import astropy.wcs as pywcs
 from astropy.io import fits
 

tests/test_BANE.py

@@ -2,8 +2,6 @@
 from __future__ import print_function
 
 from AegeanTools import BANE
-from AegeanTools import fits_interp
-from astropy.io import fits
 import numpy as np
 import os
 

tests/test_cluster.py

@@ -6,7 +6,7 @@
 
 from AegeanTools import cluster
 from AegeanTools.models import SimpleSource
-from copy import deepcopy, copy
+from copy import deepcopy
 import math
 import numpy as np
 
@@ -65,7 +65,7 @@ def test_regroup():
     # this should throw an attribute error
     try:
         cluster.regroup([1], eps=1)
-    except AttributeError as e:
+    except AttributeError as _:
         pass
 
     # this should result in 51 groups

tests/test_fits_image.py

@@ -64,25 +64,25 @@ def test_get_beam():
 def test_fix_aips_header():
     header = fits.getheader('tests/test_files/1904-66_SIN.fits')
     # test when this function is not needed
-    newhead = fi.fix_aips_header(header)
+    _ = fi.fix_aips_header(header)
 
     # test when beam params are not present, but there is no aips history
     del header['BMAJ'], header['BMIN'], header['BPA']
-    newhead = fi.fix_aips_header(header)
+    _ = fi.fix_aips_header(header)
 
     # test with some aips history
     header['HISTORY'] = 'AIPS   CLEAN BMAJ=  1.2500E-02 BMIN=  1.2500E-02 BPA=   0.00'
-    newhead = fi.fix_aips_header(header)
+    _ = fi.fix_aips_header(header)
 
 
 def test_init():
     filename = 'tests/test_files/1904-66_SIN.fits'
     # normal invocation
-    im = fi.FitsImage(filename)
+    _ = fi.FitsImage(filename)
 
     # call with an already opened hdu instead of a file name
     hdu = fits.open(filename)
-    im = fi.FitsImage(hdu)
+    _ = fi.FitsImage(hdu)
 
     # set bzero/bscale
     hdu[0].header['BZERO'] = 1