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difference image option #22

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4 changes: 3 additions & 1 deletion README.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -88,7 +88,7 @@ To see all the options, use the `--help` argument to see the full usage informat
[--step STEP] [--fps FPS] [--binning BINNING] [--dpi DPI]
[--stretch STRETCH] [--min_cut MIN_CUT] [--max_cut MAX_CUT]
[--min_percent %] [--max_percent %] [--cmap CMAP] [--flags]
[--raw | --background | --cosmic]
[--label LABEL] [--difference] [--raw | --background | --cosmic]
[--ut | --jd | --mjd | --bkjd | --cadence]
tpf_filename [tpf_filename ...]

Expand Down Expand Up @@ -122,6 +122,8 @@ To see all the options, use the `--help` argument to see the full usage informat
--max_percent % maximum cut percentile (default: 95)
--cmap CMAP matplotlib color map name (default: gray)
--flags show the quality flags
--label LABEL label to show in the bottom left corner (default: objectname)
--difference show the median-subtracted difference image
--raw show the uncalibrated pixel counts ('RAW_CNTS')
--background show the background flux ('FLUX_BKG')
--cosmic show the cosmic rays ('COSMIC_RAYS')
Expand Down
59 changes: 45 additions & 14 deletions k2flix/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -114,7 +114,7 @@ def __init__(self, filename, cache=True, verbose=False):
@property
def objectname(self):
return self.hdulist[0].header.get('OBJECT', '')

@property
def ra(self):
return self.hdulist[0].header.get('RA_OBJ', '')
Expand Down Expand Up @@ -215,34 +215,40 @@ def quality_flags(self, frameno):
flags.append(KEPLER_QUALITY_FLAGS[flag])
return flags

def flux(self, frameno=0, data_col='FLUX', pedestal=1000.):
def flux(self, frameno=0, data_col='FLUX', pedestal=1000.,
difference=False):
"""Returns the data for a given frame.

Parameters
----------
frameno : int
Frame number.

raw : bool
If `True` return the raw counts, if `False` return the calibrated
flux. (Default: `False`.)
data_col : str
Image data to be displayed. (Default: `FLUX`.)

pedestal : float
Value to add to the pixel counts. This is useful to help prevent
the counts from being negative after background subtraction.
(Default: 1000.)

difference : bool
Whether to subtract data median before displaying.
"""
# Quick hack for TESS simulated data:
if (data_col == 'COSMIC_RAYS') and (data_col not in self.hdulist[1].data.columns.names) and ('COSMICS' in self.hdulist[1].data.columns.names):
data_col = 'COSMICS'
flux = self.hdulist[1].data[data_col][frameno].copy() + pedestal
if difference:
flux -= self.subtracted_img
with warnings.catch_warnings():
warnings.filterwarnings('ignore', message="(.*)invalid value(.*)")
if data_col != 'COSMIC_RAYS' and np.all(np.isnan(flux)):
raise BadKeplerFrame('frame {0}: bad frame'.format(frameno))
return flux

def flux_binned(self, frameno=0, binning=1, data_col='FLUX', pedestal=1000):
def flux_binned(self, frameno=0, binning=1, data_col='FLUX', pedestal=1000,
difference=False):
"""Returns the co-added data centered on a frame.

Parameters
Expand All @@ -262,7 +268,8 @@ def flux_binned(self, frameno=0, binning=1, data_col='FLUX', pedestal=1000):
the counts from being negative after background subtraction.
(Default: 1000.)
"""
flx = self.flux(frameno, data_col=data_col, pedestal=pedestal)
flx = self.flux(frameno, data_col=data_col, pedestal=pedestal,
difference=difference)
framecount = 1
# Add additional frames if binning was requested
if binning > 1:
Expand All @@ -272,15 +279,17 @@ def flux_binned(self, frameno=0, binning=1, data_col='FLUX', pedestal=1000):
frameno_to_add = frameno + frameno_offset
if frameno_to_add < 0 or frameno_to_add > self.no_frames - 1:
continue # Avoid going out of bounds
flx += self.flux(frameno_to_add, data_col=data_col, pedestal=pedestal)
flx += self.flux(frameno_to_add, data_col=data_col,
pedestal=pedestal, difference=difference)
framecount += 1
flx = flx / framecount
if self.verbose:
print('Frame {}: co-adding {} cadences.'.format(frameno, framecount))
return flx

def cut_levels(self, min_percent=1., max_percent=95., data_col='FLUX',
sample_start=None, sample_stop=None, n_samples=3):
sample_start=None, sample_stop=None, n_samples=3,
difference=False):
"""Determine the cut levels for contrast stretching.

For speed, the levels are determined using only `n_samples` number
Expand All @@ -301,7 +310,8 @@ def cut_levels(self, min_percent=1., max_percent=95., data_col='FLUX',
try:
sample = np.concatenate(
[
self.flux(frameno, data_col=data_col)
self.flux(frameno, data_col=data_col,
difference=difference)
for frameno
in np.linspace(sample_start, sample_stop,
n_samples).astype(int)
Expand All @@ -315,7 +325,8 @@ def cut_levels(self, min_percent=1., max_percent=95., data_col='FLUX',
try:
sample = np.concatenate(
[
self.flux(frameno, data_col=data_col)
self.flux(frameno, data_col=data_col,
difference=difference)
for frameno
in np.random.choice(np.arange(sample_start,
sample_stop+1),
Expand All @@ -338,7 +349,8 @@ def cut_levels(self, min_percent=1., max_percent=95., data_col='FLUX',
def create_figure(self, frameno=0, binning=1, dpi=None,
stretch='log', vmin=1, vmax=5000,
cmap='gray', data_col='FLUX', annotate=True,
time_format='ut', show_flags=False, label=None):
time_format='ut', show_flags=False, label=None,
difference=False):
"""Returns a matplotlib Figure object that visualizes a frame.

Parameters
Expand Down Expand Up @@ -378,14 +390,19 @@ def create_figure(self, frameno=0, binning=1, dpi=None,
label : str
Label text to show in the bottom left corner of the movie.

difference : boolean, optiona
Show median-subtracted difference image?
(Default: `False`.)

Returns
-------
image : array
An array of unisgned integers of shape (x, y, 3),
representing an RBG colour image x px wide and y px high.
"""
# Get the flux data to visualize
flx = self.flux_binned(frameno=frameno, binning=binning, data_col=data_col)
flx = self.flux_binned(frameno=frameno, binning=binning,
data_col=data_col, difference=difference)

# Determine the figsize and dpi
shape = list(flx.shape)
Expand Down Expand Up @@ -497,7 +514,7 @@ def save_movie(self, output_fn=None, start=None, stop=None, step=None,
binning=1, fps=15., dpi=None, stretch='log',
min_cut=None, max_cut=None, min_percent=1., max_percent=95.,
cmap='gray', time_format='ut', show_flags=False, data_col='FLUX',
ignore_bad_frames=True, label=None):
difference=False, ignore_bad_frames=True, label=None):
"""Save an animation.

Parameters
Expand Down Expand Up @@ -556,6 +573,10 @@ def save_movie(self, output_fn=None, start=None, stop=None, step=None,
show_flags : boolean, optional
If `True`, annotate the quality flags if set.

difference : boolean, optional
If `True`, show median-subtracted difference images. Default:
`False`.

ignore_bad_frames : boolean, optional
If `True`, any frames which cannot be rendered will be ignored
without raising a ``BadKeplerFrame`` exception. Default: `True`.
Expand All @@ -571,12 +592,18 @@ def save_movie(self, output_fn=None, start=None, stop=None, step=None,
step = int((frameno_stop - frameno_start) / 100)
if step < 1:
step = 1
# If doing difference imaging, store median image in self
if difference:
self.subtracted_img = np.nanmedian(self.hdulist[1].data[data_col].copy(),
axis=0)

# Determine cut levels for contrast stretching from a sample of pixels
if min_cut is None or max_cut is None:
vmin, vmax = self.cut_levels(min_percent=min_percent,
max_percent=max_percent,
sample_start=frameno_start,
sample_stop=frameno_stop,
difference=difference,
data_col=data_col)
if min_cut is not None:
vmin = min_cut
Expand All @@ -591,6 +618,7 @@ def save_movie(self, output_fn=None, start=None, stop=None, step=None,
dpi=dpi, stretch=stretch,
vmin=vmin, vmax=vmax, cmap=cmap,
data_col=data_col, time_format=time_format,
difference=difference,
show_flags=show_flags, label=label)
img = np.fromstring(fig.canvas.tostring_rgb(), dtype=np.uint8, sep='')
img = img.reshape(fig.canvas.get_width_height()[::-1] + (3,))
Expand Down Expand Up @@ -653,6 +681,8 @@ def k2flix_main(args=None):
help='label to show in the bottom left corner (default: objectname)')
parser.add_argument('tpf_filename', nargs='+',
help='path to one or more Target Pixel Files (TPF)')
parser.add_argument('--difference', action='store_true',
help="show the median-subtracted difference image")

datagroup = parser.add_mutually_exclusive_group()
datagroup.add_argument('--raw', action='store_true',
Expand Down Expand Up @@ -719,6 +749,7 @@ def k2flix_main(args=None):
time_format=time_format,
show_flags=args.flags,
data_col=data_col,
difference=args.difference,
label=args.label)
except Exception as e:
if args.verbose:
Expand Down