SKA-ScienceDataProcessor · timcornwell · Jun 3, 2018 · May 28, 2018 · May 29, 2018
diff --git a/Makefile b/Makefile
@@ -18,7 +18,6 @@ WORKER_REPLICAS ?= 1
 WORKER_ARL_DATA ?= /arl/data
 CURRENT_DIR = $(shell pwd)
 JUPYTER_PASSWORD ?= changeme
-CONTAINER_EXISTS = $(shell $(DOCKER) ps -aqf ancestor=itsthenetwork/nfs-server-alpine)
 SERVER_DEVICE ?= $(shell ip link | grep BROADCAST | head -1 | awk '{print $$2}' | sed 's/://')
 NFS_SERVER ?= "127.0.0.1"
 
@@ -100,9 +99,8 @@ docker_push: docker_build
 	docker push $(DOCKER_REPO)$(DOCKER_IMAGE)
 
 docker_nfs_arl_data:
-ifneq "$(strip $(CONTAINER_EXISTS))" ""
-	$(DOCKER) rm -f $(CONTAINER_EXISTS)
-endif
+	CONTAINER_EXISTS=$$($(DOCKER) ps -aqf ancestor=itsthenetwork/nfs-server-alpine) && \
+	if [ -n "$${CONTAINER_EXISTS}" ]; then $(DOCKER) rm -f $${CONTAINER_EXISTS}; fi
 	docker run -d --name nfs --privileged -p 2049:2049 \
 	-v $(CURRENT_DIR)/:/arl \
 	-e SHARED_DIRECTORY=/arl itsthenetwork/nfs-server-alpine:latest

diff --git a/libs/calibration/solvers.py b/libs/calibration/solvers.py
@@ -315,7 +315,7 @@ def solution_residual_scalar(gain, x, xwt):
         for ant2 in range(nants):
             for chan in range(nchan):
                 error = x[ant2, ant1, chan, 0, 0] - \
-                        gain[ant1, chan, 0, 0] * numpy.conjugate(gain[ant2, chan, 0, 0])
+                    gain[ant1, chan, 0, 0] * numpy.conjugate(gain[ant2, chan, 0, 0])
                 residual += (error * xwt[ant2, ant1, chan, 0, 0] * numpy.conjugate(error)).real
                 sumwt += xwt[ant2, ant1, chan, 0, 0]
 
@@ -353,7 +353,7 @@ def solution_residual_vector(gain, x, xwt):
             for chan in range(nchan):
                 for rec in range(nrec):
                     error = x[ant2, ant1, chan, rec, rec] - \
-                            gain[ant1, chan, rec, rec] * numpy.conjugate(gain[ant2, chan, rec, rec])
+                        gain[ant1, chan, rec, rec] * numpy.conjugate(gain[ant2, chan, rec, rec])
                     residual += (error * xwt[ant2, ant1, chan, rec, rec] * numpy.conjugate(error)).real
                     sumwt += xwt[ant2, ant1, chan, rec, rec]
 
@@ -385,7 +385,7 @@ def solution_residual_matrix(gain, x, xwt):
                 for rec1 in range(nrec):
                     for rec2 in range(nrec):
                         error = x[ant2, ant1, chan, rec2, rec1] - \
-                                gain[ant1, chan, rec2, rec1] * numpy.conjugate(gain[ant2, chan, rec2, rec1])
+                            gain[ant1, chan, rec2, rec1] * numpy.conjugate(gain[ant2, chan, rec2, rec1])
                         residual[chan, rec2, rec1] += (error * xwt[ant2, ant1, chan, rec2, rec1] * numpy.conjugate(
                             error)).real
                         sumwt[chan, rec2, rec1] += xwt[ant2, ant1, chan, rec2, rec1]

diff --git a/libs/fourier_transforms/convolutional_gridding.py b/libs/fourier_transforms/convolutional_gridding.py
@@ -358,7 +358,7 @@ def visibility_recentre(uvw, dl, dm):
     :returns: Visibility coordinates re-centrered on the peak of their w-kernel
     """
 
-    u, v, w = numpy.hsplit(uvw, 3)
+    u, v, w = numpy.hsplit(uvw, 3)  # pylint: disable=unbalanced-tuple-unpacking
     return numpy.hstack([u - w * dl, v - w * dm, w])
 
 

diff --git a/libs/fourier_transforms/fft_support.py b/libs/fourier_transforms/fft_support.py
@@ -62,8 +62,8 @@ def pad_mid(ff, npixel):
     if npixel == nx:
         return ff
     assert npixel > nx and npixel > ny
-    pw = [(0, 0)] * (ff.ndim-2)  + [(npixel // 2 - cy, npixel // 2 - cy),
-                                    (npixel // 2 - cx, npixel // 2 - cx)]
+    pw = [(0, 0)] * (ff.ndim - 2) + [(npixel // 2 - cy, npixel // 2 - cy),
+                                     (npixel // 2 - cx, npixel // 2 - cx)]
     return numpy.pad(ff,
                      pad_width=pw,
                      mode='constant',
@@ -94,7 +94,6 @@ def extract_mid(a, npixel):
         return a[..., cx - s:cx + s, cy - s:cy + s]
 
 
-
 def extract_oversampled(a, xf, yf, kernel_oversampling, kernelwidth):
     """
     Extract the (xf-th,yf-th) w-kernel from the oversampled parent

diff --git a/libs/image/cleaners.py b/libs/image/cleaners.py
@@ -29,23 +29,22 @@ def hogbom(dirty, psf, window, gain, thresh, niter, fracthresh, prefix=''):
     assert 0.0 < gain < 2.0
     assert niter > 0
 
-
     log.info("hogbom %s Max abs in dirty image = %.6f Jy/beam" % (prefix, numpy.max(numpy.abs(dirty))))
     absolutethresh = max(thresh, fracthresh * numpy.fabs(dirty).max())
     log.info("hogbom %s Start of minor cycle" % prefix)
-    log.info("hogbom %s This minor cycle will stop at %d iterations or peak < %.6f (Jy/beam)" % (prefix, niter,
-                                                                                          absolutethresh))
+    log.info("hogbom %s This minor cycle will stop at %d iterations or peak < %.6f (Jy/beam)" %
+             (prefix, niter, absolutethresh))
 
     comps = numpy.zeros(dirty.shape)
     res = numpy.array(dirty)
     pmax = psf.max()
     assert pmax > 0.0
     log.info('hogbom %s: Timing for setup: %.3f (s) for dirty shape %s, PSF shape %s' %
-              (prefix, time.time() - starttime, str(dirty.shape), str(psf.shape)))
+             (prefix, time.time() - starttime, str(dirty.shape), str(psf.shape)))
     starttime = time.time()
     aiter = 0
     for i in range(niter):
-        aiter = i+1
+        aiter = i + 1
         if window is not None:
             mx, my = numpy.unravel_index((numpy.fabs(res * window)).argmax(), dirty.shape)
         else:
@@ -63,7 +62,7 @@ def hogbom(dirty, psf, window, gain, thresh, niter, fracthresh, prefix=''):
 
     dtime = time.time() - starttime
     log.info('%s Timing for clean: %.3f (s) for dirty %s, PSF %s , %d iterations, time per clean %.3f (ms)' %
-              (prefix, dtime, str(dirty.shape), str(psf.shape), aiter, 1000.0 * dtime/aiter))
+             (prefix, dtime, str(dirty.shape), str(psf.shape), aiter, 1000.0 * dtime / aiter))
 
     return comps, res
 
@@ -173,11 +172,11 @@ def msclean(dirty, psf, window, gain, thresh, niter, scales, fracthresh, prefix=
     log.info("msclean %s: Max abs in dirty Image = %.6f Jy/beam" % (prefix, numpy.fabs(res_scalestack[0, :, :]).max()))
     absolutethresh = max(thresh, fracthresh * numpy.fabs(res_scalestack[0, :, :]).max())
     log.info("msclean %s: Start of minor cycle" % prefix)
-    log.info("msclean %s: This minor cycle will stop at %d iterations or peak < %.6f (Jy/beam)" % (prefix, niter,
-                                                                                          absolutethresh))
+    log.info("msclean %s: This minor cycle will stop at %d iterations or peak < %.6f (Jy/beam)" %
+             (prefix, niter, absolutethresh))
 
     log.info('msclean %s: Timing for setup: %.3f (s) for dirty shape %s, PSF shape %s , scales %s' %
-              (prefix, time.time() - starttime, str(dirty.shape), str(psf.shape), str(scales)))
+             (prefix, time.time() - starttime, str(dirty.shape), str(psf.shape), str(scales)))
     starttime = time.time()
     aiter = 0
     for i in range(niter):
@@ -211,7 +210,7 @@ def msclean(dirty, psf, window, gain, thresh, niter, scales, fracthresh, prefix=
     dtime = time.time() - starttime
     log.info('msclean %s: Timing for clean: %.3f (s) for dirty shape %s, PSF shape %s , scales %s, %d iterations, '
              'time per clean %.3f (ms)' %
-              (prefix, dtime, str(dirty.shape), str(psf.shape), str(scales), aiter, 1000.0 * dtime/aiter))
+             (prefix, dtime, str(dirty.shape), str(psf.shape), str(scales), aiter, 1000.0 * dtime / aiter))
 
     return comps, pmax * res_scalestack[0, :, :]
 
@@ -442,7 +441,6 @@ def msmfsclean(dirty, psf, window, gain, thresh, niter, scales, fracthresh, find
     pmax = psf.max()
     assert pmax > 0.0
 
-
     psfpeak = argmax(numpy.fabs(psf))
     log.info("mmclean %s: Peak of PSF = %s at %s" % (prefix, pmax, psfpeak))
     dmax = dirty.max()
@@ -471,7 +469,6 @@ def msmfsclean(dirty, psf, window, gain, thresh, niter, scales, fracthresh, find
     ssmmpsf = calculate_scale_scale_moment_moment_psf(lpsf, pscalestack)
     hsmmpsf, ihsmmpsf = calculate_scale_inverse_moment_moment_hessian(ssmmpsf)
 
-
     for scale in range(nscales):
         log.debug("mmclean %s: Moment-moment coupling matrix[scale %d] =\n %s" % (prefix, scale, hsmmpsf[scale]))
 
@@ -488,16 +485,16 @@ def msmfsclean(dirty, psf, window, gain, thresh, niter, scales, fracthresh, find
     log.info("mmclean %s: Max abs in dirty Image = %.6f Jy/beam" % (prefix, numpy.fabs(smresidual[0, 0, :, :]).max()))
     absolutethresh = max(thresh, fracthresh * numpy.fabs(smresidual[0, 0, :, :]).max())
     log.info("mmclean %s: Start of minor cycle" % prefix)
-    log.info("mmclean %s: This minor cycle will stop at %d iterations or peak < %.6f (Jy/beam)" % (prefix, niter,
-                                                                                          absolutethresh))
+    log.info("mmclean %s: This minor cycle will stop at %d iterations or peak < %.6f (Jy/beam)" %
+             (prefix, niter, absolutethresh))
 
     # Start iterations
     scale_counts = numpy.zeros(nscales, dtype='int')
     scale_flux = numpy.zeros(nscales)
 
     aiter = 0
     log.info('mmclean %s: Timing for setup: %.3f (s) for dirty shape %s, PSF shape %s , scales %s, %d moments' %
-              (prefix, time.time() - starttime, str(dirty.shape), str(psf.shape), str(scales), nmoments))
+             (prefix, time.time() - starttime, str(dirty.shape), str(psf.shape), str(scales), nmoments))
     starttime = time.time()
     for i in range(niter):
         aiter = i + 1
@@ -533,8 +530,7 @@ def msmfsclean(dirty, psf, window, gain, thresh, niter, scales, fracthresh, find
     dtime = time.time() - starttime
     log.info('mmclean %s: Timing for clean: %.3f (s) for dirty shape %s, PSF shape %s , scales %s, %d moments, '
              '%d iterations, time per clean %.3f (ms)' %
-              (prefix, dtime, str(dirty.shape), str(psf.shape), str(scales), nmoments, aiter, 1000.0 * dtime/aiter))
-
+             (prefix, dtime, str(dirty.shape), str(psf.shape), str(scales), nmoments, aiter, 1000.0 * dtime / aiter))
 
     return m_model, pmax * smresidual[0, :, :, :]
 

diff --git a/libs/image/operations.py b/libs/image/operations.py
@@ -336,4 +336,4 @@ def create_w_term_like(im: Image, w, phasecentre=None, remove_shift=False, dopol
     fresnel = numpy.abs(w) * (0.5 * fov) ** 2
     log.debug('create_w_term_image: For w = %.1f, field of view = %.6f, Fresnel number = %.2f' % (w, fov, fresnel))
 
-    return fim
+    return fim
diff --git a/libs/util/array_functions.py b/libs/util/array_functions.py
@@ -172,4 +172,4 @@ def insert_array(im, x, y, flux, bandwidth=1.0, support=7, insert_function=inser
         for pol in range(npol):
             im[chan, pol, inty - support:inty + support, intx - support:intx + support] += flux[chan, pol] * insert
 
-    return im
+    return im
diff --git a/libs/util/coordinate_support.py b/libs/util/coordinate_support.py
@@ -47,7 +47,7 @@ def xyz_at_latitude(local_xyz, lat):
     :return: Celestial XYZ coordinates
     """
 
-    x, y, z = numpy.hsplit(local_xyz, 3)
+    x, y, z = numpy.hsplit(local_xyz, 3)  # pylint: disable=unbalanced-tuple-unpacking
 
     lat2 = numpy.pi / 2 - lat
     y2 = -z * numpy.sin(lat2) + y * numpy.cos(lat2)
@@ -72,7 +72,7 @@ def xyz_to_uvw(xyz, ha, dec):
     :param dec: declination of phase tracking centre.
     """
 
-    x, y, z = numpy.hsplit(xyz, 3)
+    x, y, z = numpy.hsplit(xyz, 3)  # pylint: disable=unbalanced-tuple-unpacking
 
     # Two rotations:
     #  1. by 'ha' along the z axis
@@ -100,7 +100,7 @@ def uvw_to_xyz(uvw, ha, dec):
     :param dec: declination of phase tracking centre
     """
 
-    u, v, w = numpy.hsplit(uvw, 3)
+    u, v, w = numpy.hsplit(uvw, 3)  # pylint: disable=unbalanced-tuple-unpacking
 
     # Two rotations:
     #  1. by 'dec-90' along the u axis
@@ -168,6 +168,7 @@ def skycoord_to_lmn(pos: SkyCoord, phasecentre: SkyCoord):
     # not quite follow imaging conventions
     return dc.y.value, dc.z.value, dc.x.value - 1
 
+
 def lmn_to_skycoord(lmn, phasecentre: SkyCoord):
     """
     Convert l,m,n coordinate system + phascentre to astropy sky coordinate
@@ -182,7 +183,7 @@ def lmn_to_skycoord(lmn, phasecentre: SkyCoord):
     """
 
     # Convert l,m,n to SkyCoord convention, also enforce celestial sphere
-    n = numpy.sqrt(1-lmn[0]**2-lmn[1]**2)-1.0
+    n = numpy.sqrt(1 - lmn[0] ** 2 - lmn[1] ** 2) - 1.0
     dc = n + 1, lmn[0], lmn[1]
     target = SkyCoord(x=dc[0], y=dc[1], z=dc[2], representation='cartesian', frame=phasecentre.skyoffset_frame())
     return target.transform_to(phasecentre.frame)