pep8fixes

setup.py

@@ -49,17 +49,27 @@
 # If third party package is found compile as well
 if os.path.isdir(relaxPath):
     print('Installing ARIA-tools with support for RelaxIV')
-    module1 = Extension('ARIAtools.demo', sources=['tools/bindings/relaxIVdriver.cpp',
-                                                   'tools/bindings/unwcompmodule.cpp',
-                                                   os.path.join(relaxPath, 'RelaxIV/RelaxIV.C')], include_dirs=['tools/include', os.path.join(relaxPath, 'MCFClass'), os.path.join(relaxPath, 'OPTUtils'), os.path.join(relaxPath, 'RelaxIV')])
+    module1 = Extension(
+        'ARIAtools.demo',
+        sources=[
+            'tools/bindings/relaxIVdriver.cpp',
+            'tools/bindings/unwcompmodule.cpp',
+            os.path.join(relaxPath, 'RelaxIV/RelaxIV.C')],
+        include_dirs=[
+            'tools/include', os.path.join(relaxPath, 'MCFClass'),
+            os.path.join(relaxPath, 'OPTUtils'),
+            os.path.join(relaxPath, 'RelaxIV')])
 
     setup(name='ARIAtools',
           version=version0,
           description='This is the ARIA tools package with RelaxIV support',
           ext_modules=[module1],
           packages=['ARIAtools'],
           package_dir={'': 'tools'},
-          scripts=['tools/bin/ariaPlot.py', 'tools/bin/ariaDownload.py', 'tools/bin/ariaExtract.py', 'tools/bin/ariaTSsetup.py', 'tools/bin/ariaAOIassist.py', 'tools/bin/ariaMisclosure.py'])
+          scripts=['tools/bin/ariaPlot.py', 'tools/bin/ariaDownload.py',
+                   'tools/bin/ariaExtract.py', 'tools/bin/ariaTSsetup.py',
+                   'tools/bin/ariaAOIassist.py', 'tools/bin/ariaMisclosure.py'
+                   'tools/bin/export_product.py'])
 else:
     # Third party package RelaxIV not found
     print('Installing ARIA-tools without support for RelaxIV')
@@ -69,4 +79,7 @@
           description='This is the ARIA tools package without RelaxIV support',
           packages=['ARIAtools'],
           package_dir={'': 'tools'},
-          scripts=['tools/bin/ariaPlot.py', 'tools/bin/ariaDownload.py', 'tools/bin/ariaExtract.py', 'tools/bin/ariaTSsetup.py', 'tools/bin/ariaAOIassist.py', 'tools/bin/ariaMisclosure.py'])
+          scripts=['tools/bin/ariaPlot.py', 'tools/bin/ariaDownload.py',
+                   'tools/bin/ariaExtract.py', 'tools/bin/ariaTSsetup.py',
+                   'tools/bin/ariaAOIassist.py', 'tools/bin/ariaMisclosure.py',
+                   'tools/bin/export_product.py'])

tests/regression/validate_test.py

@@ -233,7 +233,7 @@ class AriaToolsScriptTester():
     @pytest.fixture(scope='class')
     def tester(self):
         with tarfile.open(os.path.join(
-                'golden_test_outputs', self.FLAVOR+'.tar.gz')) as tar:
+                'golden_test_outputs', self.FLAVOR + '.tar.gz')) as tar:
             tar.extractall(os.path.join('golden_test_outputs'))
 
         test_dir = os.path.join('test_outputs', self.FLAVOR)
@@ -271,7 +271,7 @@ class TestAriaDownload():
     @pytest.fixture(scope='class')
     def tester(self):
         with tarfile.open(os.path.join(
-                'golden_test_outputs', self.FLAVOR+'.tar.gz')) as tar:
+                'golden_test_outputs', self.FLAVOR + '.tar.gz')) as tar:
             tar.extractall(os.path.join('golden_test_outputs'))
 
         test_dir = os.path.join('test_outputs', self.FLAVOR)

tools/ARIAtools/extractProduct.py

@@ -530,25 +530,25 @@ def merged_productbbox(
 def create_raster_from_gunw(fname, data_lis, proj, driver, hgt_field=None):
     """Wrapper to create raster and apply projection"""
     # open original raster
-    osgeo.gdal.BuildVRT(fname+'_temp.vrt', data_lis)
-    da = rioxarray.open_rasterio(fname+'_temp.vrt', masked=True)
+    osgeo.gdal.BuildVRT(fname + '_temp.vrt', data_lis)
+    da = rioxarray.open_rasterio(fname + '_temp.vrt', masked=True)
 
     # Reproject the raster to the desired projection
     reproj_da = da.rio.reproject(f'EPSG:{proj}',
                                  resampling=rasterio.enums.Resampling.nearest,
                                  nodata=0)
     reproj_da.rio.to_raster(fname, driver=driver, crs=f'EPSG:{proj}')
-    os.remove(fname+'_temp.vrt')
+    os.remove(fname + '_temp.vrt')
     da.close()
     reproj_da.close()
     buildvrt_options = osgeo.gdal.BuildVRTOptions(outputSRS=f'EPSG:{proj}')
-    osgeo.gdal.BuildVRT(fname+'.vrt', fname, options=buildvrt_options)
+    osgeo.gdal.BuildVRT(fname + '.vrt', fname, options=buildvrt_options)
 
     if hgt_field is not None:
         # write height layers
         hgt_meta = osgeo.gdal.Open(data_lis[0]).GetMetadataItem(hgt_field)
         osgeo.gdal.Open(
-            fname+'.vrt').SetMetadataItem(hgt_field, hgt_meta)
+            fname + '.vrt').SetMetadataItem(hgt_field, hgt_meta)
 
     return
 
@@ -1374,7 +1374,7 @@ def export_products(
 
     end_time = time.time()
     LOGGER.debug(
-        "export_product_worker took %f seconds" % (end_time-start_time))
+        "export_product_worker took %f seconds" % (end_time - start_time))
 
     # delete directory for quality control plots if empty
     plots_subdir = os.path.abspath(
@@ -1398,7 +1398,6 @@ def finalize_metadata(outname, bbox_bounds, arrres, dem_bounds, prods_TOTbbox,
     3D layers with a DEM.
     Lat/lon arrays must also be passed for this process.
     """
-    #arrshape = [dem.RasterYSize, dem.RasterXSize]
     ref_geotrans = dem.GetGeoTransform()
     dem_arrres = [abs(ref_geotrans[1]), abs(ref_geotrans[-1])]
 
@@ -1498,8 +1497,9 @@ def finalize_metadata(outname, bbox_bounds, arrres, dem_bounds, prods_TOTbbox,
     gdal_warp_kwargs = {
         'format': outputFormat, 'cutlineDSName': prods_TOTbbox,
         'outputBounds': dem_bounds, 'dstNodata': data_array_nodata,
-        'xRes': dem_arrres[0], 'yRes': dem_arrres[1], 'targetAlignedPixels': True,
-        'multithread': True, 'options': [f'NUM_THREADS={num_threads}']}
+        'xRes': dem_arrres[0], 'yRes': dem_arrres[1],
+        'targetAlignedPixels': True, 'multithread': True,
+        'options': [f'NUM_THREADS={num_threads}']}
     warp_options = osgeo.gdal.WarpOptions(**gdal_warp_kwargs)
     osgeo.gdal.Warp(tmp_name + '_temp', tmp_name, options=warp_options)
 

tools/ARIAtools/phaseMinimization.py

@@ -392,7 +392,8 @@ def __init__(self, x=None, y=None, phase=None, compNum=None, redArcs=0):
             else:
                 self.loops = self.__createTriangulation(
                     delauneyTri, vertices, edges)
-                self.neutralResidue, self.neutralNodeIdx = self.__computeNeutralResidue()
+                self.neutralResidue, self.neutralNodeIdx = (
+                    self.__computeNeutralResidue())
 
             # Saving some variables for plotting
             self.__redArcs = redArcs
@@ -420,16 +421,19 @@ def __getTriSeq(va, vb, vc):
         '''
         Get Sequence of triangle points
         '''
-        def line(va, vb, vc): return (((vc.y - va.y) * (vb.x - va.x))
-                                      ) - ((vc.x - va.x) * (vb.y - va.y))
+        def line(va, vb, vc):
+            return (((vc.y - va.y) * (vb.x - va.x)) -
+                    ((vc.x - va.x) * (vb.y - va.y)))
 
         # Line equation through pt0 and pt1
         # Test for pt3 - Does it lie to the left or to the right ?
         pos3 = line(va, vb, vc)
-        if(pos3 > 0):
-            # left
+
+        # left
+        if pos3 > 0:
             return (va, vc, vb)
-        else:  # right
+        # right
+        else:
             return (va, vb, vc)
 
     # Create Delaunay Triangulation.
@@ -578,8 +582,9 @@ def __createTriangulation(self, delauneyTri, vertices, edges):
 
         # Generate the points in a sequence
         def getSeq(va, vb, vc):
-            def line(va, vb, vc): return (
-                ((vc.y - va.y) * (vb.x - va.x))) - ((vc.x - va.x) * (vb.y - va.y))
+            def line(va, vb, vc):
+                return (((vc.y - va.y) * (vb.x - va.x)) -
+                        ((vc.x - va.x) * (vb.y - va.y)))
 
             # Line equation through pt0 and pt1
             # Test for pt3 - Does it lie to the left or to the right ?
@@ -739,8 +744,8 @@ def __MCFRelaxIV(edgeLen, fileName="network.dmx"):
         try:
             from . import unwcomp
         except BaseException:
-            raise Exception("MCF requires RelaxIV solver - Please drop the RelaxIV software \
-                          into the src folder and re-make")
+            raise Exception("MCF requires RelaxIV solver - Please drop the "
+                            "RelaxIV software into the src folder and re-make")
         return unwcomp.relaxIVwrapper_Py(fileName)
 
     def solve(self, solver, filename="network.dmx"):
@@ -764,19 +769,24 @@ def __solveEdgeCost__(self, solver, fileName="network.dmx"):
         # Solve the objective function
         if solver == 'glpk':
             LOGGER.info('Using GLPK MIP solver')
-            def MIPsolver(): return self.__prob__.solve(pulp.GLPK(msg=0))
+
+            def MIPsolver():
+                return self.__prob__.solve(pulp.GLPK(msg=0))
+
         elif solver == 'pulp':
             LOGGER.info('Using PuLP MIP solver')
-            def MIPsolver(): return self.__prob__.solve()
+
+            def MIPsolver():
+                return self.__prob__.solve()
+
         elif solver == 'gurobi':
             LOGGER.info('Using Gurobi MIP solver')
-            def MIPsolver(): return self.__prob__.solve(pulp.GUROBI_CMD())
+
+            def MIPsolver():
+                return self.__prob__.solve(pulp.GUROBI_CMD())
 
         LOGGER.info(
-            'Time Taken (in sec) to solve: %f',
-            T.timeit(
-                MIPsolver,
-                number=1))
+            'Time Taken (in sec) to solve: %f', T.timeit(MIPsolver, number=1))
 
         # Get solution
         for v, edge in self.__edges.items():
@@ -916,18 +926,24 @@ def firstPassCommandLine():
     parser = argparse.ArgumentParser(description='Phase Unwrapping')
 
     # Positional argument - Input XML file
-    parser.add_argument('--inputType', choices=['plane', 'sinc', 'sine'],
-                        help='Type of input to unwrap', default='plane', dest='inputType')
-    parser.add_argument('--dim', type=int, default=100,
-                        help='Dimension of the image (square)', dest='dim')
-    parser.add_argument('-c', action='store_true',
-                        help='Component-wise unwrap test', dest='compTest')
-    parser.add_argument('-MCF', action='store_true',
-                        help='Minimum Cost Flow', dest='mcf')
-    parser.add_argument('--redArcs', type=int, default=0,
-                        help='Redundant Arcs', dest='redArcs')
-    parser.add_argument('--solver', choices=['glpk', 'pulp', 'gurobi'],
-                        help='Type of solver', default='pulp', dest='solver')
+    parser.add_argument(
+        '--inputType', choices=['plane', 'sinc', 'sine'],
+        help='Type of input to unwrap', default='plane', dest='inputType')
+    parser.add_argument(
+        '--dim', type=int, default=100,
+        help='Dimension of the image (square)', dest='dim')
+    parser.add_argument(
+        '-c', action='store_true',
+        help='Component-wise unwrap test', dest='compTest')
+    parser.add_argument(
+        '-MCF', action='store_true',
+        help='Minimum Cost Flow', dest='mcf')
+    parser.add_argument(
+        '--redArcs', type=int, default=0,
+        help='Redundant Arcs', dest='redArcs')
+    parser.add_argument(
+        '--solver', choices=['glpk', 'pulp', 'gurobi'],
+        help='Type of solver', default='pulp', dest='solver')
 
     # Parse input
     args = parser.parse_args()
@@ -1011,7 +1027,8 @@ def main():
             xidx, yidx, wrapImg[xidx, yidx], redArcs=redArcs)
     else:
         phaseunwrap = PhaseUnwrap(
-            xidx, yidx, wrapImg[xidx, yidx], compImg[xidx, yidx], redArcs=redArcs)
+            xidx, yidx, wrapImg[xidx, yidx], compImg[xidx, yidx],
+            redArcs=redArcs)
 
     # Including the neutral node for min cost flow
     phaseunwrap.solve(solver)
@@ -1022,10 +1039,6 @@ def main():
     # phaseunwrap.plotSpanningTree("spanningTree%d.png"%(redArcs))
     phaseunwrap.plotResult("final%d.png" % (redArcs))
 
-    #import pdb; pdb.set_trace()
-    #fig = plt.figure()
-    #ax = fig.add_subplot(111, projection='3d')
-
 
 if __name__ == '__main__':
 

tools/ARIAtools/product.py

@@ -87,8 +87,9 @@ def package_dict(scene, new_scene, scene_ind,
     # IFG corresponding to reference product already exists, append to dict
     if sorted_dict:
         dict_vals = [[
-            subitem for item in a for subitem in (item if
-            isinstance(item, list) else [item])] for a in zip(
+            subitem for item in a for subitem in (
+                item if isinstance(item, list) else [item])]
+            for a in zip(
                 sorted_dict[dict_ind][scene_ind].values(),
                 new_scene[scene_ind].values())]
 
@@ -924,7 +925,7 @@ def __NISARmappingData__(self, fname, rdrmetadata_dict, sdskeys, version):
         datalyr_dict[
             'productBoundingBoxFrames'] = fname + '":' + sdskeys[0]
         for i in enumerate(layerkeys):
-            datalyr_dict[i[1]] = fname + '":'+sdskeys[i[0]]
+            datalyr_dict[i[1]] = fname + '":' + sdskeys[i[0]]
 
         # Rewrite tropo and iono keys
         datalyr_dict['ionosphere'] = datalyr_dict.pop(

tools/ARIAtools/stack.py

@@ -19,6 +19,7 @@
 
 LOGGER = logging.getLogger(__name__)
 
+
 # STACK OBJECT ---
 class Stack:
     '''
@@ -170,7 +171,8 @@ def __formatDates__(self):
     def __formatExcludePairs__(self):
         '''
         Check that exclude dates are in one of two formats:
-        1. a string containing the pairs in YOUNGER_OLDER format, space-separated
+        1. a string containing the pairs in YOUNGER_OLDER format,
+           space-separated
         2. a .txt file with lines of the same formatting
         Formatting should match "pair" formatting: [[master,slave]]
         '''
@@ -231,8 +233,9 @@ def plotPairs(self):
         # Legend
         handles, labels = pairAx.get_legend_handles_labels()
         uniqueLabels = dict(zip(labels, handles))
-        pairAx.legend(uniqueLabels.values(), uniqueLabels.keys(),
-                      bbox_to_anchor=(0.005, 0.99), loc='upper left', borderaxespad=0.)
+        pairAx.legend(
+            uniqueLabels.values(), uniqueLabels.keys(),
+            bbox_to_anchor=(0.005, 0.99), loc='upper left', borderaxespad=0.)
 
         # Other formatting
         pairAx.set_yticks([])
@@ -279,22 +282,23 @@ def createTriplets(self, minTime=None, maxTime=None, printTriplets=False):
         self.nTriplets = len(self.triplets)
 
         # Print to text file
-        with open(os.path.join(self.workdir, 'ValidTriplets.txt'), 'w') as tripletFile:
+        with open(os.path.join(
+                self.workdir, 'ValidTriplets.txt'), 'w') as tripletFile:
             for triplet in self.triplets:
                 strPair = [self.__datePair2strPair__(pair) for pair in triplet]
                 tripletFile.write('{}\n'.format(strPair))
             tripletFile.close()
 
         # Report if requested
-        if printTriplets == True:
+        if printTriplets:
 
             # Print to screen
             LOGGER.info('Existing triplets:')
             for triplet in self.triplets:
                 LOGGER.info([
                     self.__datePair2strPair__(pair) for pair in triplet])
 
-        if self.verbose == True:
+        if self.verbose:
             LOGGER.info(
                 '%s existing triplets found based on search criteria',
                 self.nTriplets)
@@ -425,11 +429,11 @@ def XY2LoLa(self, x, y):
     # Reference point formatting
     def __referencePoint__(self, refXY, refLoLa):
         '''
-        Determine the reference point in XY coordinates. The reference point can be
-        automatically or manually selected by the user and is subtracted
-        from each interferogram.
-        The point can be given in pixels or lon/lat coordinates. If given in Lat/Lon, determine
-        the location in XY.
+        Determine the reference point in XY coordinates. The reference point
+        can be automatically or manually selected by the user and is
+        subtracted from each interferogram.
+        The point can be given in pixels or lon/lat coordinates. If given in
+        Lat/Lon, determine the location in XY.
         '''
         LOGGER.debug('Determining reference point...')
 
@@ -460,7 +464,8 @@ def __referencePoint__(self, refXY, refLoLa):
     # Random reference point
     def __autoReferencePoint__(self):
         '''
-        Use the coherence stack to automatically determine a suitable reference point.
+        Use the coherence stack to automatically determine a suitable
+        reference point.
         '''
         # Load coherence data from cohStack.vrt
         cohfile = os.path.join(self.imgdir, 'cohStack.vrt')
@@ -479,7 +484,7 @@ def __autoReferencePoint__(self):
 
         # Loop until suitable reference point is found
         n = 0
-        while cohMask[self.refY, self.refX] == False:
+        while not cohMask[self.refY, self.refX]:
 
             # Reselect reference points
             self.refX = np.random.randint(cohDS.RasterXSize)
@@ -606,7 +611,7 @@ def __plotSeries__(self, ax, data, title):
         Plot misclosure timeseries.
         '''
         # Plot data
-        if self.plotTimeIntervals == False:
+        if not self.plotTimeIntervals:
             ax.plot([tripletDate[1]
                     for tripletDate in self.tripletDates], data, '-k.')
         else:
@@ -760,7 +765,8 @@ def __misclosureQuery__(self, queryXY=None, queryLoLa=None):
             qLon, qLat = self.XY2LoLa(queryXY[0], queryXY[1])
 
         LOGGER.debug(
-            'Query point: X %s / Y %s; Lon %.4f / Lat %.4f', qx, qy, qLon, qLat)
+            'Query point: X %s / Y %s; Lon %.4f / Lat %.4f',
+            qx, qy, qLon, qLat)
 
         # Plot query points on map
         self.netMscAx.plot(