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Fix a few minor issues with stacking #453

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Dec 21, 2017
Merged

Fix a few minor issues with stacking #453

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20 changes: 11 additions & 9 deletions spectral_cube/analysis_utilities.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,8 @@ def fourier_shift(x, shift, axis=0, add_pad=False, pad_size=None):
nanmask = ~np.isfinite(x)

# If all NaNs, there is nothing to shift
if nanmask.all():
# But only if there is no added padding. Otherwise we need to pad
if nanmask.all() and not add_pad:
return x

nonan = x.copy()
Expand Down Expand Up @@ -64,6 +65,10 @@ def fourier_shift(x, shift, axis=0, add_pad=False, pad_size=None):
pad_nonan = nonan
pad_mask = nanmask

# Check if there are all NaNs before shifting
if nanmask.all():
return np.array([np.NaN] * pad_mask.size)

nonan_shift = _fourier_shifter(pad_nonan, shift, axis)
if shift_mask:
mask_shift = _fourier_shifter(pad_mask, shift, axis) > 0.5
Expand Down Expand Up @@ -105,7 +110,7 @@ def get_chunks(num_items, chunk):
items = np.arange(num_items)

if num_items == chunk:
return items
return [items]

chunks = \
np.array_split(items,
Expand Down Expand Up @@ -221,8 +226,8 @@ def stack_spectra(cube, velocity_surface, v0=None,
# component that the velocity surface is derived from.

# Find max +/- pixel shifts, rounding up to the nearest integer
max_pos_shift = np.ceil(pix_shifts.max()).astype(int)
max_neg_shift = np.ceil(pix_shifts.min()).astype(int)
max_pos_shift = np.ceil(np.nanmax(pix_shifts)).astype(int)
max_neg_shift = np.ceil(np.nanmin(pix_shifts)).astype(int)

# The total pixel size of the new spectral axis
num_vel_pix = cube.spectral_axis.size + max_pos_shift - max_neg_shift
Expand All @@ -236,13 +241,10 @@ def stack_spectra(cube, velocity_surface, v0=None,
else:
pad_size = None

# Adjust the header to have velocities centered at v0.
# new_header["CRVAL1"] = new_header["CRVAL1"] - v0.to(u.m / u.s).value

all_shifted_spectra = []

if chunk_size == -1:
chunk_size = len(xy_posns)
chunk_size = len(xy_posns[0])

# Create chunks of spectra for read-out.
chunks = get_chunks(len(xy_posns[0]), chunk_size)
Expand All @@ -253,7 +255,7 @@ def stack_spectra(cube, velocity_surface, v0=None,

for i, chunk in enumerate(iterat):

gen = ((cube.unmasked_data[:, y, x], shift, pad_edges, pad_size)
gen = ((cube.filled_data[:, y, x].value, shift, pad_edges, pad_size)
for y, x, shift in
zip(xy_posns[0][chunk], xy_posns[1][chunk], pix_shifts[chunk]))

Expand Down