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Log the absence of a filter from the ghost gap file only once #667

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merged 2 commits into from
Apr 23, 2021
Merged

Log the absence of a filter from the ghost gap file only once #667

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6f2d77c
Log the absence of a filter from the ghost gap file only once
bhilbert4 Apr 21, 2021
7078255
In docs, note the filters for which ghosts are added
bhilbert4 Apr 22, 2021
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2 changes: 1 addition & 1 deletion docs/ghosts.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ If **add_ghosts** is True, Mirage will calculate, for each point source in your

.. tip::

If you wish to run Mirage with a "gap summary" file other than that in the config directory, you can either replace the file in the config directory with your own, or update the value of NIRISS_GHOST_GAP_FILE in the constants.py file of the repository to point to your file. This may be useful for testing new ghost position calibration results.
The current "gap summary" file allows for the addition of ghost sources for observations that use F090W, F115W, F140M, F150W, and F200W. For other filters, the ghost positions and/or magnitudes have not been characterized, and therefore ghosts will not be added. If you wish to run Mirage with a "gap summary" file other than that in the config directory, you can either replace the file in the config directory with your own, or update the value of NIRISS_GHOST_GAP_FILE in the constants.py file of the repository to point to your file. This may be useful for testing new ghost position calibration results.

Mirage currently carries one fits file in its collection of :ref:`reference files <reference_files>` that provides an image of an optical ghost from a point source on the NIRISS detector. This image was created from ground testing data. By default, this file is used when adding ghosts to the data. **NOTE that this stamp image applies to point sources only. By default, no ghosts are added for galaxy or extended sources.**

Expand Down
42 changes: 30 additions & 12 deletions mirage/seed_image/catalog_seed_image.py
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Expand Up @@ -1626,7 +1626,8 @@ def movingTargetInputs(self, filename, input_type, MT_tracking=False,
# frame individually.
if add_ghosts:
ghost_x_frames, ghost_y_frames, ghost_mags, ghost_countrate, ghost_file = self.locate_ghost(x_frames, y_frames, rate,
magsys, entry, input_type)
magsys, entry, input_type,
log_skipped_filters=False)
if ghost_file is not None:
ghost_stamp, ghost_header = self.basic_get_image(ghost_file)

Expand Down Expand Up @@ -2677,7 +2678,8 @@ def get_point_source_list(self, filename, source_type='pointsources', segment_of
# If this is a NIRISS simulation and the user wants to add ghosts,
# do that here.
if self.params['Inst']['instrument'].lower() == 'niriss' and self.params['simSignals']['add_ghosts']:
gx, gy, gmag, gcounts, gfile = self.locate_ghost(pixelx, pixely, countrate, magsys, values, 'point_source')
gx, gy, gmag, gcounts, gfile = self.locate_ghost(pixelx, pixely, countrate, magsys, values, 'point_source',
log_skipped_filters=log_ghost_err)
if np.isfinite(gx) and gfile is not None:
ghost_source_index.append(index)
ghost_x.append(gx)
Expand All @@ -2686,14 +2688,17 @@ def get_point_source_list(self, filename, source_type='pointsources', segment_of
ghost_filename.append(gfile)

ghost_src, skipped_non_niriss = source_mags_to_ghost_mags(values, self.params['Reffiles']['flux_cal'],
magsys, NIRISS_GHOST_GAP_FILE, log_skipped_filters=log_ghost_err)
ghost_i += 1
magsys, NIRISS_GHOST_GAP_FILE, log_skipped_filters=False)

if ghost_mags is None:
ghost_mags = copy.deepcopy(ghost_src)
else:
ghost_mags = vstack([ghost_mags, ghost_src])

# Increment the counter to control the logging regardless of whether the source
# is on the detector or not.
ghost_i += 1

psf_len = self.find_psf_size(countrate)
edgex = np.int(psf_len // 2)
edgey = np.int(psf_len // 2)
Expand Down Expand Up @@ -3920,7 +3925,8 @@ def filterGalaxyList(self, galaxylist, pixelflag, radiusflag, magsystem, catfile
# If this is a NIRISS simulation and the user wants to add ghosts,
# do that here.
if self.params['Inst']['instrument'].lower() == 'niriss' and self.params['simSignals']['add_ghosts']:
gx, gy, gmag, gcounts, gfile = self.locate_ghost(pixelx, pixely, rate, magsystem, source, 'galaxies')
gx, gy, gmag, gcounts, gfile = self.locate_ghost(pixelx, pixely, rate, magsystem, source, 'galaxies',
log_skipped_filters=log_ghost_err)
if np.isfinite(gx) and gfile is not None:
ghost_source_index.append(index)
ghost_x.append(gx)
Expand All @@ -3929,14 +3935,17 @@ def filterGalaxyList(self, galaxylist, pixelflag, radiusflag, magsystem, catfile
ghost_filename.append(gfile)

ghost_src, skipped_non_niriss = source_mags_to_ghost_mags(source, self.params['Reffiles']['flux_cal'], magsystem,
NIRISS_GHOST_GAP_FILE, log_skipped_filters=log_ghost_err)
ghost_i += 1
NIRISS_GHOST_GAP_FILE, log_skipped_filters=False)

if ghost_mags is None:
ghost_mags = copy.deepcopy(ghost_src)
else:
ghost_mags = vstack([ghost_mags, ghost_src])

# Increment the counter to control the logging regardless of whether the source
# is on the detector or not.
ghost_i += 1

# only keep the source if the peak will fall within the subarray
if pixely > outminy and pixely < outmaxy and pixelx > outminx and pixelx < outmaxx:

Expand Down Expand Up @@ -4328,7 +4337,7 @@ def calc_x_position_angle(self, v2_value, v3_value, position_angle):
+ 90. - self.params['Telescope']['rotation'])
return x_posang

def locate_ghost(self, pixel_x, pixel_y, count_rate, magnitude_system, source_row, obj_type):
def locate_ghost(self, pixel_x, pixel_y, count_rate, magnitude_system, source_row, obj_type, log_skipped_filters=True):
"""Calculate the ghost location, brightness, and stamp image file name
for the input source.

Expand Down Expand Up @@ -4368,6 +4377,10 @@ def locate_ghost(self, pixel_x, pixel_y, count_rate, magnitude_system, source_ro

ghost_file : str
Name of fits file containing the stamp image to use for the ghost source

log_skipped_filters : bool
If True, any filter magnitudes that are not converted because
the filter is not in the gap summary file will be logged.
"""
allowed_types = ['point_source', 'galaxies', 'extended']
if obj_type not in allowed_types:
Expand All @@ -4382,7 +4395,8 @@ def locate_ghost(self, pixel_x, pixel_y, count_rate, magnitude_system, source_ro
count_rate,
search_filter,
self.params['Readout']['pupil'],
NIRISS_GHOST_GAP_FILE
NIRISS_GHOST_GAP_FILE,
log_skipped_filters=log_skipped_filters
)
if isinstance(ghost_pixelx, np.float):
if not np.isfinite(ghost_pixelx):
Expand Down Expand Up @@ -4629,7 +4643,8 @@ def getExtendedSourceList(self, filename, ghost_search=True):
# This is done outside the if statement below because sources outside the
# detector can potentially produce ghosts on the detector
if ghost_search and self.params['Inst']['instrument'].lower() == 'niriss' and self.params['simSignals']['add_ghosts']:
gx, gy, gmag, gcounts, gfile = self.locate_ghost(pixelx, pixely, countrate, magsys, values, 'extended')
gx, gy, gmag, gcounts, gfile = self.locate_ghost(pixelx, pixely, countrate, magsys, values, 'extended',
log_skipped_filters=log_ghost_err)
if np.isfinite(gx) and gfile is not None:
ghost_source_index.append(indexnum)
ghost_x.append(gx)
Expand All @@ -4638,14 +4653,17 @@ def getExtendedSourceList(self, filename, ghost_search=True):
ghost_filename.append(gfile)

ghost_src, skipped_non_niriss = source_mags_to_ghost_mags(values, self.params['Reffiles']['flux_cal'],
magsys, NIRISS_GHOST_GAP_FILE, log_skipped_filters=log_ghost_err)
ghost_i += 1
magsys, NIRISS_GHOST_GAP_FILE, log_skipped_filters=False)

if ghost_mags is None:
ghost_mags = copy.deepcopy(ghost_src)
else:
ghost_mags = vstack([ghost_mags, ghost_src])

# Increment the counter to control the logging regardless of whether the source
# is on the detector or not.
ghost_i += 1

# Keep only sources within the appropriate bounds
if pixely > miny and pixely < maxy and pixelx > minx and pixelx < maxx:

Expand Down