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Fix usage of incorrect trace extraction function
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(cherry picked from commit 57df30b)
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@sergiopasra
sergiopasra committed May 2, 2018
1 parent 1805a0c commit 1a1fd90
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Showing 2 changed files with 70 additions and 234 deletions.
135 changes: 70 additions & 65 deletions megaradrp/processing/aperture.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,93 +32,64 @@ def apextract(data, trace):
return rss


def apextract_tracemap_old(data, tracemap):
"""Extract apertures using a tracemap."""

pols = [t.polynomial for t in tracemap.contents]

borders = []

# These are polynomial, they can be summed

# Estimate left border for the first trace
pix_12 = 0.5 * (pols[0] + pols[1])
# Use the half distance in the first trace
pix_01 = 1.5 * pols[0] - 0.5 * pols[1]

borders.append((pix_01, pix_12))

for idx in range(1, len(pols)-1):
if pols[idx].order!=0:
pix_01 = pix_12
pix_12 = 0.5 * (pols[idx] + pols[idx+1])
borders.append((pix_01, pix_12))
else:
empty = nppol.Polynomial([0.0])
borders.append((empty, empty))
# else:
# if pols[idx].order==0:
# borders.append((pix_01, pols[idx+1]))
# else:
# borders.append((pix_01, pols[idx+1]))

# borders.append((pix_01, pix_12))
# Estimate right border for the last trace
pix_01 = pix_12
# Use the half distance in last trace
pix_12 = 1.5 * pols[-1] - 0.5 * pols[-2]

borders.append((pix_01, pix_12))

out = numpy.zeros((len(pols), data.shape[1]), dtype='float')

rss = extract.extract_simple_rss(data, borders, out=out)

return rss


def apextract_tracemap(data, tracemap):
"""Extract apertures using a tracemap.
Consider that the nearest fiber could be far away if there
are missing fibers.
Parameters
----------
data: ndarray
tracemap: TraceMap
"""

existing = [None]
for t in tracemap.contents:
if t.fitparms: # This is a check if the trace is valid
if t.valid:
existing.append(t)

existing.append(None)
# Compute borders
borders = []
far_dist = 100

# Handle the first and last using centinels
for t1, t2, t3 in zip(existing, existing[1:], existing[2:]):
# Distance to contfibers # in box
if t1 is None:
d21 = 100
d21 = far_dist
else:
d21 = (t2.fibid - t1.fibid) + (t2.boxid - t1.boxid)
if t3 is None:
d32 = 100
d32 = far_dist
else:
d32 = (t3.fibid - t2.fibid) + (t3.boxid - t2.boxid)

y2_off = t2.polynomial(tracemap.ref_column)
t2_off = tracemap.global_offset(y2_off)
t2_pol_off = t2.polynomial + t2_off

# Right border
if d32 == 1:
pix_32 = 0.5 * (t2.polynomial + t3.polynomial)
elif d32 == 2:
pix_32 = 0.5 * (t2.polynomial + t3.polynomial)
pix_32 = 0.5 * (pix_32 + t2.polynomial)
pix_32 = None
if d32 <= 2:
y3_off = t3.polynomial(tracemap.ref_column)
t3_off = tracemap.global_offset(y3_off)
pix_32 = 0.5 * (t2_pol_off + t3.polynomial + t3_off)
if d32 == 2:
pix_32 = 0.5 * (pix_32 + t2_pol_off)
elif d32 > 2:
pix_32 = None

if d21 == 1:
pix_21 = 0.5 * (t2.polynomial + t1.polynomial)
elif d21 == 2:
pix_21 = 0.5 * (t2.polynomial + t1.polynomial)
pix_21 = 0.5 * (pix_21 + t2.polynomial)
pix_21 = None
if d21 <= 2:
y1_off = t1.polynomial(tracemap.ref_column)
t1_off = tracemap.global_offset(y1_off)
pix_21 = 0.5 * (t2_pol_off + t1.polynomial + t1_off)
if d21 == 2:
pix_21 = 0.5 * (pix_21 + t2_pol_off)
elif d21 > 2:
pix_21 = None

Expand All @@ -127,22 +98,56 @@ def apextract_tracemap(data, tracemap):

if pix_32 is None:
# Recompute pix32 using pix_21
pix_32 = t2.polynomial + (t2.polynomial - pix_21)
pix_32 = t2_pol_off + (t2_pol_off - pix_21)

if pix_21 is None:
# Recompute pix21 using pix_32
pix_21 = t2.polynomial - (pix_32 - t2.polynomial)
pix_21 = t2_pol_off - (pix_32 - t2_pol_off)

#
borders.append((t2.fibid - 1, (pix_21, pix_32)))
borders.append((t2.fibid, pix_21, pix_32))

mm = 623 # FIXME, hardcoded
out = numpy.zeros((mm, data.shape[1]), dtype='float32')
rss = extract.extract_simple_rss(data, borders, out=out)
nfibers = tracemap.total_fibers
out = numpy.zeros((nfibers, data.shape[1]), dtype='float')
rss = extract_simple_rss2(data, borders, out=out)

return rss


def extract_simple_rss(arr, borders2, axis=0, out=None):

# FIXME, this should be changed in numina
# If arr is not in native byte order, the C-extension won't work
if arr.dtype.byteorder != '=':
arr2 = arr.byteswap().newbyteorder()
else:
arr2 = arr

if axis == 0:
arr3 = arr2
elif axis == 1:
arr3 = arr2.T
else:
raise ValueError("'axis' must be 0 or 1")

if out is None:
out = numpy.zeros((borders2[-1][0], arr3.shape[1]), dtype='float')

xx = numpy.arange(arr3.shape[1])

# Borders contains a list of function objects
for idx, b1, b2 in borders2:
bb1 = b1(xx)
bb1[bb1 < -0.5] = -0.5
bb2 = b2(xx)
bb2[bb2 > arr3.shape[0] - 0.5] = arr3.shape[0] - 0.5
extract.extract_simple_intl(arr3, xx, bb1, bb2, out[idx-1])
return out


apextract_tracemap_2 = apextract_tracemap
extract_simple_rss2 = extract_simple_rss


class ApertureExtractor(numina.processing.Corrector):
"""A Node that extracts apertures."""

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169 changes: 0 additions & 169 deletions megaradrp/processing/trimover.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -94,175 +94,6 @@ def get_conf_value(confFile, key):
return confFile[key]


def apextract(data, trace):
"""Extract apertures."""
rss = numpy.empty((trace.shape[0], data.shape[1]), dtype='float32')
for idx, r in enumerate(trace):
l = r[0]
r = r[2] + 1
sl = (slice(l, r), )
m = data[sl].sum(axis=0)
rss[idx] = m
return rss


def apextract_tracemap_2(data, tracemap):
"""Extract apertures using a tracemap.
Consider that the nearest fiber could be far away if there
are missing fibers.
Parameters
----------
data: ndarray
tracemap: TraceMap
"""

existing = [None]
for t in tracemap.contents:
if t.valid:
existing.append(t)

existing.append(None)
# Compute borders
borders = []
far_dist = 100

# Handle the first and last using centinels
for t1, t2, t3 in zip(existing, existing[1:], existing[2:]):
# Distance to contfibers # in box
if t1 is None:
d21 = far_dist
else:
d21 = (t2.fibid - t1.fibid) + (t2.boxid - t1.boxid)
if t3 is None:
d32 = far_dist
else:
d32 = (t3.fibid - t2.fibid) + (t3.boxid - t2.boxid)

y2_off = t2.polynomial(tracemap.ref_column)
t2_off = tracemap.global_offset(y2_off)
t2_pol_off = t2.polynomial + t2_off

# Right border
pix_32 = None
if d32 <= 2:
y3_off = t3.polynomial(tracemap.ref_column)
t3_off = tracemap.global_offset(y3_off)
pix_32 = 0.5 * (t2_pol_off + t3.polynomial + t3_off)
if d32 == 2:
pix_32 = 0.5 * (pix_32 + t2_pol_off)
elif d32 > 2:
pix_32 = None

pix_21 = None
if d21 <= 2:
y1_off = t1.polynomial(tracemap.ref_column)
t1_off = tracemap.global_offset(y1_off)
pix_21 = 0.5 * (t2_pol_off + t1.polynomial + t1_off)
if d21 == 2:
pix_21 = 0.5 * (pix_21 + t2_pol_off)
elif d21 > 2:
pix_21 = None

if pix_32 is None and pix_21 is None:
continue

if pix_32 is None:
# Recompute pix32 using pix_21
pix_32 = t2_pol_off + (t2_pol_off - pix_21)

if pix_21 is None:
# Recompute pix21 using pix_32
pix_21 = t2_pol_off - (pix_32 - t2_pol_off)

borders.append((t2.fibid, pix_21, pix_32))

nfibers = tracemap.total_fibers
out = numpy.zeros((nfibers, data.shape[1]), dtype='float')
rss = extract_simple_rss2(data, borders, out=out)

return rss


def extract_simple_rss2(arr, borders2, axis=0, out=None):

# FIXME, this should be changed in numina
# If arr is not in native byte order, the C-extension won't work
if arr.dtype.byteorder != '=':
arr2 = arr.byteswap().newbyteorder()
else:
arr2 = arr

if axis == 0:
arr3 = arr2
elif axis == 1:
arr3 = arr2.T
else:
raise ValueError("'axis' must be 0 or 1")

if out is None:
out = numpy.zeros((borders2[-1][0], arr3.shape[1]), dtype='float')

xx = numpy.arange(arr3.shape[1])

# Borders contains a list of function objects
for idx, b1, b2 in borders2:
bb1 = b1(xx)
bb1[bb1 < -0.5] = -0.5
bb2 = b2(xx)
bb2[bb2 > arr3.shape[0] - 0.5] = arr3.shape[0] - 0.5
extract.extract_simple_intl(arr3, xx, bb1, bb2, out[idx-1])
return out


def apextract_tracemap(data, tracemap):
"""Extract apertures using a tracemap."""

pols = [t.polynomial for t in tracemap.contents]

borders = []

# These are polynomial, they can be summed

# Estimate left border for the first trace
pix_12 = 0.5 * (pols[0] + pols[1])
# Use the half distance in the first trace
pix_01 = 1.5 * pols[0] - 0.5 * pols[1]

borders.append((pix_01, pix_12))

for idx in range(1, len(pols)-1):
if pols[idx].order!=0:
pix_01 = pix_12
pix_12 = 0.5 * (pols[idx] + pols[idx+1])
borders.append((pix_01, pix_12))
else:
empty = nppol.Polynomial([0.0])
borders.append((empty, empty))
# else:
# if pols[idx].order==0:
# borders.append((pix_01, pols[idx+1]))
# else:
# borders.append((pix_01, pols[idx+1]))

# borders.append((pix_01, pix_12))
# Estimate right border for the last trace
pix_01 = pix_12
# Use the half distance in last trace
pix_12 = 1.5 * pols[-1] - 0.5 * pols[-2]

borders.append((pix_01, pix_12))

out = numpy.zeros((len(pols), data.shape[1]), dtype='float')

rss = extract.extract_simple_rss(data, borders, out=out)

return rss


def apextract_weights(data, weights, size=4096):
"""Extract apertures using a map of weights."""

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