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OSSOS/MOP | src/ossos/web/web/initiate/populate_ossuary.py | main | def main():
"""
Update the ossuary Postgres db with images observed for OSSOS.
iq: Go through and check all ossuary's images for new existence of IQs/zeropoints.
comment: Go through all ossuary and
Then updates ossuary with new images that are at any stage of processing.
Constructs full image entries, including header and info in the vtags, and inserts to ossuary.
TODO: a CLUSTER after data is inserted - maybe once a week, depending how much there is
CLUSTER images; need to sqlalchemy this one
"""
parser = argparse.ArgumentParser()
parser.add_argument("-iq", "--iq", action="store_true",
help="Check existing images in ossuary that do not yet have "
"IQ/zeropoint information; update where possible.")
parser.add_argument("-comment", action="store_true",
help="Add comments on images provided by S. Gwyn to database.")
parser.add_argument("-snr", action="store_true",
help="Update existing images in ossuary for SNR info where that exists in a vtag.")
args = parser.parse_args()
images = web.field_obs.queries.ImagesQuery()
processed_images, iqs = retrieve_processed_images(images) # straight list of primary keys
commdict = parse_sgwn_comments()
if args.iq:
unmeasured_iqs = iq_unmeasured_images(images)
sys.stdout.write('%d images in ossuary; updating %d with new IQ/zeropoint information.\n' %
(len(processed_images), len(unmeasured_iqs)))
for n, image in enumerate(unmeasured_iqs): # it's in the db, so has already passed the other checks
update_values(images, image)
sys.stdout.write('%s %d/%d...ossuary updated.\n' % (image, n + 1, len(unmeasured_iqs)))
if args.snr:
unmeasured = snr_unmeasured_images(images)
sys.stdout.write('%d images in ossuary; updating %d with new SNR information.\n' %
(len(processed_images), len(unmeasured)))
for n, image in enumerate(unmeasured): # it's in the db, so has already passed the other checks
update_values(images, image, iq_zeropt=False, snr=True)
sys.stdout.write('%s %d/%d...ossuary updated.\n' % (image, n + 1, len(unmeasured)))
if args.comment:
sys.stdout.write('%d images in ossuary; updating with new comment information.\n' %
len(processed_images))
for image in commdict.keys():
if int(image) in processed_images:
update_values(images, image, iq_zeropt=False, comment=True, commdict=commdict)
sys.stdout.write('%s has comment...\n' % image)
unprocessed_images = parse_unprocessed_images(storage.list_dbimages(), processed_images)
sys.stdout.write('%d images in ossuary; updating with %d new in VOspace.\n' %
(len(processed_images), len(unprocessed_images)))
for n, image in enumerate(unprocessed_images):
sys.stdout.write('%s %d/%d ' % (image, n + 1, len(unprocessed_images)))
try:
subheader, fullheader = get_header(image)
if subheader is not None:
sys.stdout.write('Header obtained. ')
verify_ossos_image(fullheader)
header = get_iq_and_zeropoint(image, subheader)
header = get_snr(image, header)
if image in commdict.keys():
header['comment'] = commdict[image]
put_image_in_database(header, images)
sys.stdout.write('...added to ossuary...\n')
# generate_MegaCam_previews(image)
# sys.stdout.write(' .gif preview saved.\n')
else:
sys.stdout.write('Header is not available: skipping.\n')
except Exception, e:
sys.stdout.write('... %s\n' % e) | python | def main():
"""
Update the ossuary Postgres db with images observed for OSSOS.
iq: Go through and check all ossuary's images for new existence of IQs/zeropoints.
comment: Go through all ossuary and
Then updates ossuary with new images that are at any stage of processing.
Constructs full image entries, including header and info in the vtags, and inserts to ossuary.
TODO: a CLUSTER after data is inserted - maybe once a week, depending how much there is
CLUSTER images; need to sqlalchemy this one
"""
parser = argparse.ArgumentParser()
parser.add_argument("-iq", "--iq", action="store_true",
help="Check existing images in ossuary that do not yet have "
"IQ/zeropoint information; update where possible.")
parser.add_argument("-comment", action="store_true",
help="Add comments on images provided by S. Gwyn to database.")
parser.add_argument("-snr", action="store_true",
help="Update existing images in ossuary for SNR info where that exists in a vtag.")
args = parser.parse_args()
images = web.field_obs.queries.ImagesQuery()
processed_images, iqs = retrieve_processed_images(images) # straight list of primary keys
commdict = parse_sgwn_comments()
if args.iq:
unmeasured_iqs = iq_unmeasured_images(images)
sys.stdout.write('%d images in ossuary; updating %d with new IQ/zeropoint information.\n' %
(len(processed_images), len(unmeasured_iqs)))
for n, image in enumerate(unmeasured_iqs): # it's in the db, so has already passed the other checks
update_values(images, image)
sys.stdout.write('%s %d/%d...ossuary updated.\n' % (image, n + 1, len(unmeasured_iqs)))
if args.snr:
unmeasured = snr_unmeasured_images(images)
sys.stdout.write('%d images in ossuary; updating %d with new SNR information.\n' %
(len(processed_images), len(unmeasured)))
for n, image in enumerate(unmeasured): # it's in the db, so has already passed the other checks
update_values(images, image, iq_zeropt=False, snr=True)
sys.stdout.write('%s %d/%d...ossuary updated.\n' % (image, n + 1, len(unmeasured)))
if args.comment:
sys.stdout.write('%d images in ossuary; updating with new comment information.\n' %
len(processed_images))
for image in commdict.keys():
if int(image) in processed_images:
update_values(images, image, iq_zeropt=False, comment=True, commdict=commdict)
sys.stdout.write('%s has comment...\n' % image)
unprocessed_images = parse_unprocessed_images(storage.list_dbimages(), processed_images)
sys.stdout.write('%d images in ossuary; updating with %d new in VOspace.\n' %
(len(processed_images), len(unprocessed_images)))
for n, image in enumerate(unprocessed_images):
sys.stdout.write('%s %d/%d ' % (image, n + 1, len(unprocessed_images)))
try:
subheader, fullheader = get_header(image)
if subheader is not None:
sys.stdout.write('Header obtained. ')
verify_ossos_image(fullheader)
header = get_iq_and_zeropoint(image, subheader)
header = get_snr(image, header)
if image in commdict.keys():
header['comment'] = commdict[image]
put_image_in_database(header, images)
sys.stdout.write('...added to ossuary...\n')
# generate_MegaCam_previews(image)
# sys.stdout.write(' .gif preview saved.\n')
else:
sys.stdout.write('Header is not available: skipping.\n')
except Exception, e:
sys.stdout.write('... %s\n' % e) | [
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JohnVinyard/zounds | zounds/spectral/frequencyadaptive.py | FrequencyAdaptive.square | def square(self, n_coeffs, do_overlap_add=False):
"""
Compute a "square" view of the frequency adaptive transform, by
resampling each frequency band such that they all contain the same
number of samples, and performing an overlap-add procedure in the
case where the sample frequency and duration differ
:param n_coeffs: The common size to which each frequency band should
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"""
resampled_bands = [
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for band in self.iter_bands()]
stacked = np.vstack(resampled_bands).T
fdim = FrequencyDimension(self.scale)
# TODO: This feels like it could be wrapped up nicely elsewhere
chunk_frequency = Picoseconds(int(np.round(
self.time_dimension.duration / Picoseconds(1) / n_coeffs)))
td = TimeDimension(frequency=chunk_frequency)
arr = ConstantRateTimeSeries(ArrayWithUnits(
stacked.reshape(-1, n_coeffs, self.n_bands),
dimensions=[self.time_dimension, td, fdim]))
if not do_overlap_add:
return arr
# Begin the overlap add procedure
overlap_ratio = self.time_dimension.overlap_ratio
if overlap_ratio == 0:
# no overlap add is necessary
return ArrayWithUnits(stacked, [td, fdim])
step_size_samples = int(n_coeffs * overlap_ratio)
first_dim = int(np.round(
(stacked.shape[0] * overlap_ratio) + (n_coeffs * overlap_ratio)))
output = ArrayWithUnits(
np.zeros((first_dim, self.n_bands)),
dimensions=[td, fdim])
for i, chunk in enumerate(arr):
start = step_size_samples * i
stop = start + n_coeffs
output[start: stop] += chunk.reshape((-1, self.n_bands))
return output | python | def square(self, n_coeffs, do_overlap_add=False):
"""
Compute a "square" view of the frequency adaptive transform, by
resampling each frequency band such that they all contain the same
number of samples, and performing an overlap-add procedure in the
case where the sample frequency and duration differ
:param n_coeffs: The common size to which each frequency band should
be resampled
"""
resampled_bands = [
self._resample(band, n_coeffs)
for band in self.iter_bands()]
stacked = np.vstack(resampled_bands).T
fdim = FrequencyDimension(self.scale)
# TODO: This feels like it could be wrapped up nicely elsewhere
chunk_frequency = Picoseconds(int(np.round(
self.time_dimension.duration / Picoseconds(1) / n_coeffs)))
td = TimeDimension(frequency=chunk_frequency)
arr = ConstantRateTimeSeries(ArrayWithUnits(
stacked.reshape(-1, n_coeffs, self.n_bands),
dimensions=[self.time_dimension, td, fdim]))
if not do_overlap_add:
return arr
# Begin the overlap add procedure
overlap_ratio = self.time_dimension.overlap_ratio
if overlap_ratio == 0:
# no overlap add is necessary
return ArrayWithUnits(stacked, [td, fdim])
step_size_samples = int(n_coeffs * overlap_ratio)
first_dim = int(np.round(
(stacked.shape[0] * overlap_ratio) + (n_coeffs * overlap_ratio)))
output = ArrayWithUnits(
np.zeros((first_dim, self.n_bands)),
dimensions=[td, fdim])
for i, chunk in enumerate(arr):
start = step_size_samples * i
stop = start + n_coeffs
output[start: stop] += chunk.reshape((-1, self.n_bands))
return output | [
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OSSOS/MOP | src/ossos/core/ossos/downloads/cutouts/calculator.py | CoordinateConverter.convert | def convert(self, point):
"""
Convert a point from one coordinate system to another.
Args:
point: tuple(int x, int y)
The point in the original coordinate system.
Returns:
converted_point: tuple(int x, int y)
The point in the new coordinate system.
Example: convert coordinate from original image into a pixel location
within a cutout image.
@rtype: list(float,float)
"""
x, y = point
(x1, y1) = x - self.x_offset, y - self.y_offset
logger.debug("converted {} {} ==> {} {}".format(x, y, x1, y1))
return x1, y1 | python | def convert(self, point):
"""
Convert a point from one coordinate system to another.
Args:
point: tuple(int x, int y)
The point in the original coordinate system.
Returns:
converted_point: tuple(int x, int y)
The point in the new coordinate system.
Example: convert coordinate from original image into a pixel location
within a cutout image.
@rtype: list(float,float)
"""
x, y = point
(x1, y1) = x - self.x_offset, y - self.y_offset
logger.debug("converted {} {} ==> {} {}".format(x, y, x1, y1))
return x1, y1 | [
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JohnVinyard/zounds | zounds/learn/util.py | simple_settings | def simple_settings(cls):
"""
Create sane default persistence settings for learning pipelines
:param cls: The class to decorate
"""
class Settings(ff.PersistenceSettings):
_id = cls.__name__
id_provider = ff.StaticIdProvider(_id)
key_builder = ff.StringDelimitedKeyBuilder()
database = ff.FileSystemDatabase(
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class Model(cls, Settings):
pass
Model.__name__ = cls.__name__
Model.__module__ = cls.__module__
return Model | python | def simple_settings(cls):
"""
Create sane default persistence settings for learning pipelines
:param cls: The class to decorate
"""
class Settings(ff.PersistenceSettings):
_id = cls.__name__
id_provider = ff.StaticIdProvider(_id)
key_builder = ff.StringDelimitedKeyBuilder()
database = ff.FileSystemDatabase(
path=_id, key_builder=key_builder, createdirs=True)
class Model(cls, Settings):
pass
Model.__name__ = cls.__name__
Model.__module__ = cls.__module__
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JohnVinyard/zounds | zounds/learn/util.py | apply_network | def apply_network(network, x, chunksize=None):
"""
Apply a pytorch network, potentially in chunks
"""
network_is_cuda = next(network.parameters()).is_cuda
x = torch.from_numpy(x)
with torch.no_grad():
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if chunksize is None:
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for i in range(0, len(x), chunksize)]) | python | def apply_network(network, x, chunksize=None):
"""
Apply a pytorch network, potentially in chunks
"""
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x = torch.from_numpy(x)
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JohnVinyard/zounds | zounds/learn/util.py | sample_norm | def sample_norm(x):
"""
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https://arxiv.org/pdf/1710.10196.pdf
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# square
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OSSOS/MOP | src/ossos/core/ossos/downloads/cutouts/source.py | SourceCutout.reset_coord | def reset_coord(self):
"""
Reset the source location based on the init_skycoord values
@return:
"""
(x, y, idx) = self.world2pix(self.init_skycoord.ra,
self.init_skycoord.dec,
usepv=True)
self.update_pixel_location((x, y), idx) | python | def reset_coord(self):
"""
Reset the source location based on the init_skycoord values
@return:
"""
(x, y, idx) = self.world2pix(self.init_skycoord.ra,
self.init_skycoord.dec,
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OSSOS/MOP | src/ossos/core/ossos/downloads/cutouts/source.py | SourceCutout.pixel_coord | def pixel_coord(self):
"""
Return the coordinates of the source in the cutout reference frame.
@return:
"""
return self.get_pixel_coordinates(self.reading.pix_coord, self.reading.get_ccd_num()) | python | def pixel_coord(self):
"""
Return the coordinates of the source in the cutout reference frame.
@return:
"""
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OSSOS/MOP | src/ossos/core/ossos/downloads/cutouts/source.py | SourceCutout.get_hdulist_idx | def get_hdulist_idx(self, ccdnum):
"""
The SourceCutout is a list of HDUs, this method returns the index of the HDU that corresponds to the given
ccd number. CCDs are numbers from 0, but the first CCD (CCDNUM=0) is often in extension 1 of an MEF.
@param ccdnum: the number of the CCD in the MEF that is being referenced.
@return: the index of in self.hdulist that corresponds to the given CCD number.
"""
for (extno, hdu) in enumerate(self.hdulist):
if ccdnum == int(hdu.header.get('EXTVER', -1)) or str(ccdnum) in hdu.header.get('AMPNAME', ''):
return extno
raise ValueError("Failed to find requested CCD Number {} in cutout {}".format(ccdnum,
self)) | python | def get_hdulist_idx(self, ccdnum):
"""
The SourceCutout is a list of HDUs, this method returns the index of the HDU that corresponds to the given
ccd number. CCDs are numbers from 0, but the first CCD (CCDNUM=0) is often in extension 1 of an MEF.
@param ccdnum: the number of the CCD in the MEF that is being referenced.
@return: the index of in self.hdulist that corresponds to the given CCD number.
"""
for (extno, hdu) in enumerate(self.hdulist):
if ccdnum == int(hdu.header.get('EXTVER', -1)) or str(ccdnum) in hdu.header.get('AMPNAME', ''):
return extno
raise ValueError("Failed to find requested CCD Number {} in cutout {}".format(ccdnum,
self)) | [
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OSSOS/MOP | src/ossos/core/ossos/downloads/cutouts/source.py | SourceCutout.flip_flip | def flip_flip(self, point):
"""
Sometimes we 'flipped' the X/Y coordinates of the image during processing. This function takes an
(x,y) location from the processing pipeline and returns the x/y location relative to the original
reference frame. (Correctly checks if the coordinate is flipped to begin with.)
This is only for use on the original X/Y coordinates as provided by an input reading.
@param point: an x/y location on the image.
@type point: [x, y]
@return: the x/y location on the un-fliped frame
"""
x, y = point
if self.reading.compute_inverted():
naxis1 = self.reading.obs.header.get(self.reading.obs.HEADER_IMG_SIZE_X,
self.reading.obs.header.get('NAXIS1', 256))
naxis2 = self.reading.obs.header.get(self.reading.obs.HEADER_IMG_SIZE_Y,
self.reading.obs.header.get('NAXIS2', 256))
logger.debug("Got that image has size {}, {}".format(naxis1, naxis2))
x1 = x
y1 = y
x = int(naxis1) - x + 1
y = int(naxis2) - y + 1
logger.debug("Inverted source location from {},{} to {},{}".format(x1, y1, x, y))
return x, y | python | def flip_flip(self, point):
"""
Sometimes we 'flipped' the X/Y coordinates of the image during processing. This function takes an
(x,y) location from the processing pipeline and returns the x/y location relative to the original
reference frame. (Correctly checks if the coordinate is flipped to begin with.)
This is only for use on the original X/Y coordinates as provided by an input reading.
@param point: an x/y location on the image.
@type point: [x, y]
@return: the x/y location on the un-fliped frame
"""
x, y = point
if self.reading.compute_inverted():
naxis1 = self.reading.obs.header.get(self.reading.obs.HEADER_IMG_SIZE_X,
self.reading.obs.header.get('NAXIS1', 256))
naxis2 = self.reading.obs.header.get(self.reading.obs.HEADER_IMG_SIZE_Y,
self.reading.obs.header.get('NAXIS2', 256))
logger.debug("Got that image has size {}, {}".format(naxis1, naxis2))
x1 = x
y1 = y
x = int(naxis1) - x + 1
y = int(naxis2) - y + 1
logger.debug("Inverted source location from {},{} to {},{}".format(x1, y1, x, y))
return x, y | [
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OSSOS/MOP | src/ossos/core/ossos/downloads/cutouts/source.py | SourceCutout.update_pixel_location | def update_pixel_location(self, new_pixel_location, hdu_index):
"""
Update the x/y location of the associated reading by using new_pixel_location and transforming from cutout
reference frame to observation refrence frame.
@param new_pixel_location: (x, y) location of the source in cutout pixel reference frame
@param hdu_index: index of the associate hdu in the hdulist for this cutout
"""
self.reading.pix_coord = self.get_observation_coordinates(new_pixel_location[0],
new_pixel_location[1],
hdu_index)
new_ccd = self.get_ccdnum(hdu_index)
if new_ccd != self.reading.get_ccd_num():
self._apcor = None
self._zmag = None
self.reading.obs.ccdnum = self.get_ccdnum(hdu_index)
self.reading.sky_coord = self.pix2world(new_pixel_location[0],
new_pixel_location[1],
hdu_index) | python | def update_pixel_location(self, new_pixel_location, hdu_index):
"""
Update the x/y location of the associated reading by using new_pixel_location and transforming from cutout
reference frame to observation refrence frame.
@param new_pixel_location: (x, y) location of the source in cutout pixel reference frame
@param hdu_index: index of the associate hdu in the hdulist for this cutout
"""
self.reading.pix_coord = self.get_observation_coordinates(new_pixel_location[0],
new_pixel_location[1],
hdu_index)
new_ccd = self.get_ccdnum(hdu_index)
if new_ccd != self.reading.get_ccd_num():
self._apcor = None
self._zmag = None
self.reading.obs.ccdnum = self.get_ccdnum(hdu_index)
self.reading.sky_coord = self.pix2world(new_pixel_location[0],
new_pixel_location[1],
hdu_index) | [
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OSSOS/MOP | src/ossos/core/ossos/downloads/cutouts/source.py | SourceCutout.get_pixel_coordinates | def get_pixel_coordinates(self, point, ccdnum):
"""
Retrieves the pixel location of a point within the current HDUList given the
location in the original FITS image. This takes into account that
the image may be a cutout of a larger original.
Args:
point: tuple(float, float)
(x, y) in original.
Returns:
(x, y) pixel in this image.
@param extno: the extno from the original Mosaic that the x/y coordinates are from.
"""
hdulist_index = self.get_hdulist_idx(ccdnum)
if isinstance(point[0], Quantity) and isinstance(point[1], Quantity):
pix_point = point[0].value, point[1].value
else:
pix_point = point
if self.reading.inverted:
pix_point = self.reading.obs.naxis1 - pix_point[0] +1 , self.reading.obs.naxis2 - pix_point[1] + 1
(x, y) = self.hdulist[hdulist_index].converter.convert(pix_point)
return x, y, hdulist_index | python | def get_pixel_coordinates(self, point, ccdnum):
"""
Retrieves the pixel location of a point within the current HDUList given the
location in the original FITS image. This takes into account that
the image may be a cutout of a larger original.
Args:
point: tuple(float, float)
(x, y) in original.
Returns:
(x, y) pixel in this image.
@param extno: the extno from the original Mosaic that the x/y coordinates are from.
"""
hdulist_index = self.get_hdulist_idx(ccdnum)
if isinstance(point[0], Quantity) and isinstance(point[1], Quantity):
pix_point = point[0].value, point[1].value
else:
pix_point = point
if self.reading.inverted:
pix_point = self.reading.obs.naxis1 - pix_point[0] +1 , self.reading.obs.naxis2 - pix_point[1] + 1
(x, y) = self.hdulist[hdulist_index].converter.convert(pix_point)
return x, y, hdulist_index | [
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OSSOS/MOP | src/ossos/core/ossos/downloads/cutouts/source.py | SourceCutout.get_observation_coordinates | def get_observation_coordinates(self, x, y, hdulist_index):
"""
Retrieves the location of a point using the coordinate system of
the original observation, i.e. the original image before any
cutouts were done.
Returns:
(x, y) in the original image coordinate system.
@param x: x-pixel location in the cutout frame of reference
@param y: y-pixel location in the cutout frame of reference
@param idx: index of hdu in hdulist that the given x/y corresponds to.
"""
return self.hdulist[hdulist_index].converter.get_inverse_converter().convert((x, y)) | python | def get_observation_coordinates(self, x, y, hdulist_index):
"""
Retrieves the location of a point using the coordinate system of
the original observation, i.e. the original image before any
cutouts were done.
Returns:
(x, y) in the original image coordinate system.
@param x: x-pixel location in the cutout frame of reference
@param y: y-pixel location in the cutout frame of reference
@param idx: index of hdu in hdulist that the given x/y corresponds to.
"""
return self.hdulist[hdulist_index].converter.get_inverse_converter().convert((x, y)) | [
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OSSOS/MOP | src/ossos/core/ossos/downloads/cutouts/source.py | SourceCutout.world2pix | def world2pix(self, ra, dec, usepv=True):
"""
Convert a given RA/DEC position to the X/Y/HDULIST_INDEX in the cutout frame.
Here we loop over the hdulist to find the extension is RA/DEC are from and then return the appropriate X/Y
:param ra: The Right Ascension of the point
:type ra: Quantity
:param dec: The Declination of the point
:type dec: Quantity
:return: X, Y, Extension position of source in cutout reference frame
:rtype: (float, float, int)
@param usepv: Should the non-linear part of the WCS be using to compute the transformation? (default: True)
"""
x, y, idx = (0, 0, 0)
for idx in range(1, len(self.hdulist)):
hdu = self.hdulist[idx]
x, y = hdu.wcs.sky2xy(ra, dec, usepv=usepv)
if 0 < x < hdu.header['NAXIS1'] and 0 < y < hdu.header['NAXIS2']:
# print "Inside the frame."
return x, y, idx
return x, y, idx | python | def world2pix(self, ra, dec, usepv=True):
"""
Convert a given RA/DEC position to the X/Y/HDULIST_INDEX in the cutout frame.
Here we loop over the hdulist to find the extension is RA/DEC are from and then return the appropriate X/Y
:param ra: The Right Ascension of the point
:type ra: Quantity
:param dec: The Declination of the point
:type dec: Quantity
:return: X, Y, Extension position of source in cutout reference frame
:rtype: (float, float, int)
@param usepv: Should the non-linear part of the WCS be using to compute the transformation? (default: True)
"""
x, y, idx = (0, 0, 0)
for idx in range(1, len(self.hdulist)):
hdu = self.hdulist[idx]
x, y = hdu.wcs.sky2xy(ra, dec, usepv=usepv)
if 0 < x < hdu.header['NAXIS1'] and 0 < y < hdu.header['NAXIS2']:
# print "Inside the frame."
return x, y, idx
return x, y, idx | [
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OSSOS/MOP | src/ossos/core/ossos/downloads/cutouts/source.py | SourceCutout.zmag | def zmag(self,):
"""
Return the photometric zeropoint of the CCD associated with the reading.
@return: float
"""
if self._zmag is None:
hdulist_index = self.get_hdulist_idx(self.reading.get_ccd_num())
self._zmag = self.hdulist[hdulist_index].header.get('PHOTZP', 0.0)
return self._zmag | python | def zmag(self,):
"""
Return the photometric zeropoint of the CCD associated with the reading.
@return: float
"""
if self._zmag is None:
hdulist_index = self.get_hdulist_idx(self.reading.get_ccd_num())
self._zmag = self.hdulist[hdulist_index].header.get('PHOTZP', 0.0)
return self._zmag | [
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OSSOS/MOP | src/ossos/core/ossos/downloads/cutouts/source.py | SourceCutout.apcor | def apcor(self):
"""
return the aperture correction of for the CCD assocated with the reading.
@return: Apcor
"""
if self._apcor is None:
try:
self._apcor = Downloader().download_apcor(self.reading.get_apcor_uri())
except:
self._apcor = ApcorData.from_string("5 15 99.99 99.99")
return self._apcor | python | def apcor(self):
"""
return the aperture correction of for the CCD assocated with the reading.
@return: Apcor
"""
if self._apcor is None:
try:
self._apcor = Downloader().download_apcor(self.reading.get_apcor_uri())
except:
self._apcor = ApcorData.from_string("5 15 99.99 99.99")
return self._apcor | [
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OSSOS/MOP | src/ossos/core/ossos/downloads/cutouts/source.py | SourceCutout.get_observed_magnitude | def get_observed_magnitude(self, centroid=True):
# NOTE: this import is only here so that we don't load up IRAF
# unnecessarily (ex: for candidates processing).
"""
Get the magnitude at the current pixel x/y location.
:return: Table
"""
max_count = float(self.astrom_header.get("MAXCOUNT", 30000))
(x, y, hdulist_index) = self.pixel_coord
tmp_file = self._hdu_on_disk(hdulist_index)
try:
from ossos import daophot
phot = daophot.phot_mag(tmp_file,
x, y,
aperture=self.apcor.aperture,
sky=self.apcor.sky,
swidth=self.apcor.swidth,
apcor=self.apcor.apcor,
zmag=self.zmag,
maxcount=max_count, extno=1,
centroid=centroid)
if not self.apcor.valid:
phot['PIER'][0] = 1
return phot
except Exception as ex:
print ex
raise ex
finally:
self.close() | python | def get_observed_magnitude(self, centroid=True):
# NOTE: this import is only here so that we don't load up IRAF
# unnecessarily (ex: for candidates processing).
"""
Get the magnitude at the current pixel x/y location.
:return: Table
"""
max_count = float(self.astrom_header.get("MAXCOUNT", 30000))
(x, y, hdulist_index) = self.pixel_coord
tmp_file = self._hdu_on_disk(hdulist_index)
try:
from ossos import daophot
phot = daophot.phot_mag(tmp_file,
x, y,
aperture=self.apcor.aperture,
sky=self.apcor.sky,
swidth=self.apcor.swidth,
apcor=self.apcor.apcor,
zmag=self.zmag,
maxcount=max_count, extno=1,
centroid=centroid)
if not self.apcor.valid:
phot['PIER'][0] = 1
return phot
except Exception as ex:
print ex
raise ex
finally:
self.close() | [
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OSSOS/MOP | src/ossos/core/ossos/downloads/cutouts/source.py | SourceCutout._hdu_on_disk | def _hdu_on_disk(self, hdulist_index):
"""
IRAF routines such as daophot need input on disk.
Returns:
filename: str
The name of the file containing the FITS data.
"""
if self._tempfile is None:
self._tempfile = tempfile.NamedTemporaryFile(
mode="r+b", suffix=".fits")
self.hdulist[hdulist_index].writeto(self._tempfile.name)
return self._tempfile.name | python | def _hdu_on_disk(self, hdulist_index):
"""
IRAF routines such as daophot need input on disk.
Returns:
filename: str
The name of the file containing the FITS data.
"""
if self._tempfile is None:
self._tempfile = tempfile.NamedTemporaryFile(
mode="r+b", suffix=".fits")
self.hdulist[hdulist_index].writeto(self._tempfile.name)
return self._tempfile.name | [
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OSSOS/MOP | src/ossos/core/ossos/downloads/cutouts/source.py | SourceCutout.comparison_image_list | def comparison_image_list(self):
"""
returns a list of possible comparison images for the current cutout. Will query CADC to create the list when
first called.
@rtype: Table
"""
if self._comparison_image_list is not None:
return self._comparison_image_list
ref_ra = self.reading.ra * units.degree
ref_dec = self.reading.dec * units.degree
radius = self.radius is not None and self.radius or config.read('CUTOUTS.SINGLETS.RADIUS') * units.arcminute
print("Querying CADC for list of possible comparison images at RA: {}, DEC: {}, raidus: {}".format(ref_ra,
ref_dec,
radius))
query_result = storage.cone_search(ref_ra, ref_dec, radius, radius) # returns an astropy.table.table.Table
print("Got {} possible images".format(len(query_result)))
ans = raw_input("Do you want to lookup IQ? (y/n)")
print("Building table for presentation and selection")
if ans == "y":
print("Including getting fwhm which is a bit slow.")
comparison_image_list = []
if len(query_result['collectionID']) > 0: # are there any comparison images even available on that sky?
index = -1
for row in query_result:
expnum = row['collectionID']
if expnum in self._bad_comparison_images:
continue
date = Time(row['mjdate'], format='mjd').mpc
if Time(row['mjdate'], format='mjd') < Time('2013-01-01 00:00:00', format='iso'):
continue
exptime = row['exptime']
if float(exptime) < 250:
continue
filter_name = row['filter']
if 'U' in filter_name:
continue
if filter_name.lower() in self.hdulist[-1].header['FILTER'].lower():
filter_name = "* {:8s}".format(filter_name)
fwhm = -1.0
if ans == 'y':
try:
fwhm = "{:5.2f}".format(float(storage.get_fwhm_tag(expnum, 22)))
except:
pass
index += 1
comparison_image_list.append([index, expnum, date, exptime, filter_name, fwhm, None])
self._comparison_image_list = Table(data=numpy.array(comparison_image_list),
names=["ID", "EXPNUM", "DATE-OBS", "EXPTIME", "FILTER", "FWHM", "REFERENCE"])
return self._comparison_image_list | python | def comparison_image_list(self):
"""
returns a list of possible comparison images for the current cutout. Will query CADC to create the list when
first called.
@rtype: Table
"""
if self._comparison_image_list is not None:
return self._comparison_image_list
ref_ra = self.reading.ra * units.degree
ref_dec = self.reading.dec * units.degree
radius = self.radius is not None and self.radius or config.read('CUTOUTS.SINGLETS.RADIUS') * units.arcminute
print("Querying CADC for list of possible comparison images at RA: {}, DEC: {}, raidus: {}".format(ref_ra,
ref_dec,
radius))
query_result = storage.cone_search(ref_ra, ref_dec, radius, radius) # returns an astropy.table.table.Table
print("Got {} possible images".format(len(query_result)))
ans = raw_input("Do you want to lookup IQ? (y/n)")
print("Building table for presentation and selection")
if ans == "y":
print("Including getting fwhm which is a bit slow.")
comparison_image_list = []
if len(query_result['collectionID']) > 0: # are there any comparison images even available on that sky?
index = -1
for row in query_result:
expnum = row['collectionID']
if expnum in self._bad_comparison_images:
continue
date = Time(row['mjdate'], format='mjd').mpc
if Time(row['mjdate'], format='mjd') < Time('2013-01-01 00:00:00', format='iso'):
continue
exptime = row['exptime']
if float(exptime) < 250:
continue
filter_name = row['filter']
if 'U' in filter_name:
continue
if filter_name.lower() in self.hdulist[-1].header['FILTER'].lower():
filter_name = "* {:8s}".format(filter_name)
fwhm = -1.0
if ans == 'y':
try:
fwhm = "{:5.2f}".format(float(storage.get_fwhm_tag(expnum, 22)))
except:
pass
index += 1
comparison_image_list.append([index, expnum, date, exptime, filter_name, fwhm, None])
self._comparison_image_list = Table(data=numpy.array(comparison_image_list),
names=["ID", "EXPNUM", "DATE-OBS", "EXPTIME", "FILTER", "FWHM", "REFERENCE"])
return self._comparison_image_list | [
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OSSOS/MOP | src/ossos/core/ossos/downloads/cutouts/source.py | SourceCutout.retrieve_comparison_image | def retrieve_comparison_image(self):
"""
Search the DB for a comparison image for this cutout.
"""
# selecting comparator when on a comparator should load a new one.
collectionID = self.comparison_image_list[self.comparison_image_index]['EXPNUM']
ref_ra = self.reading.ra * units.degree
ref_dec = self.reading.dec * units.degree
radius = self.radius is not None and self.radius or config.read('CUTOUTS.SINGLETS.RADIUS') * units.arcminute
try:
comparison = collectionID
hdu_list = storage.ra_dec_cutout(storage.dbimages_uri(comparison),
SkyCoord(ref_ra, ref_dec), radius)
ccd = int(hdu_list[-1].header.get('EXTVER', 0))
obs = Observation(str(comparison), 'p',
ccdnum=ccd)
x = hdu_list[-1].header.get('NAXIS1', 0) // 2.0
y = hdu_list[-1].header.get('NAXIS2', 0) // 2.0
ref_ra = self.reading.ra * units.degree
ref_dec = self.reading.dec * units.degree
reading = SourceReading(x, y, self.reading.x, self.reading.y,
ref_ra, ref_dec, self.reading.x, self.reading.y, obs)
self.comparison_image_list[self.comparison_image_index]["REFERENCE"] = SourceCutout(reading, hdu_list)
except Exception as ex:
print traceback.format_exc()
print ex
print "Failed to load comparison image;"
self.comparison_image_index = None
logger.error("{} {}".format(type(ex), str(ex)))
logger.error(traceback.format_exc()) | python | def retrieve_comparison_image(self):
"""
Search the DB for a comparison image for this cutout.
"""
# selecting comparator when on a comparator should load a new one.
collectionID = self.comparison_image_list[self.comparison_image_index]['EXPNUM']
ref_ra = self.reading.ra * units.degree
ref_dec = self.reading.dec * units.degree
radius = self.radius is not None and self.radius or config.read('CUTOUTS.SINGLETS.RADIUS') * units.arcminute
try:
comparison = collectionID
hdu_list = storage.ra_dec_cutout(storage.dbimages_uri(comparison),
SkyCoord(ref_ra, ref_dec), radius)
ccd = int(hdu_list[-1].header.get('EXTVER', 0))
obs = Observation(str(comparison), 'p',
ccdnum=ccd)
x = hdu_list[-1].header.get('NAXIS1', 0) // 2.0
y = hdu_list[-1].header.get('NAXIS2', 0) // 2.0
ref_ra = self.reading.ra * units.degree
ref_dec = self.reading.dec * units.degree
reading = SourceReading(x, y, self.reading.x, self.reading.y,
ref_ra, ref_dec, self.reading.x, self.reading.y, obs)
self.comparison_image_list[self.comparison_image_index]["REFERENCE"] = SourceCutout(reading, hdu_list)
except Exception as ex:
print traceback.format_exc()
print ex
print "Failed to load comparison image;"
self.comparison_image_index = None
logger.error("{} {}".format(type(ex), str(ex)))
logger.error(traceback.format_exc()) | [
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OSSOS/MOP | src/ossos/web/web/auth/model.py | User.check_password | def check_password(self, passwd, group):
# This provides authentication via CADC.
"""check that the passwd provided matches the required password."""
return gms.isMember(self.login, passwd, group) | python | def check_password(self, passwd, group):
# This provides authentication via CADC.
"""check that the passwd provided matches the required password."""
return gms.isMember(self.login, passwd, group) | [
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JohnVinyard/zounds | zounds/timeseries/timeseries.py | TimeDimension.integer_based_slice | def integer_based_slice(self, ts):
"""
Transform a :class:`TimeSlice` into integer indices that numpy can work
with
Args:
ts (slice, TimeSlice): the time slice to translate into integer
indices
"""
if isinstance(ts, slice):
try:
start = Seconds(0) if ts.start is None else ts.start
if start < Seconds(0):
start = self.end + start
stop = self.end if ts.stop is None else ts.stop
if stop < Seconds(0):
stop = self.end + stop
duration = stop - start
ts = TimeSlice(start=start, duration=duration)
except (ValueError, TypeError):
pass
if not isinstance(ts, TimeSlice):
return ts
diff = self.duration - self.frequency
start_index = \
max(0, np.floor((ts.start - diff) / self.frequency))
end = self.end if ts.duration is None else ts.end
# KLUDGE: This is basically arbitrary, but the motivation is that we'd
# like to differentiate between cases where the slice
# actually/intentionally overlaps a particular sample, and cases where
# the slice overlaps the sample by a tiny amount, due to rounding or
# lack of precision (e.g. Seconds(1) / SR44100().frequency).
ratio = np.round(end / self.frequency, 2)
stop_index = np.ceil(ratio)
return slice(int(start_index), int(stop_index)) | python | def integer_based_slice(self, ts):
"""
Transform a :class:`TimeSlice` into integer indices that numpy can work
with
Args:
ts (slice, TimeSlice): the time slice to translate into integer
indices
"""
if isinstance(ts, slice):
try:
start = Seconds(0) if ts.start is None else ts.start
if start < Seconds(0):
start = self.end + start
stop = self.end if ts.stop is None else ts.stop
if stop < Seconds(0):
stop = self.end + stop
duration = stop - start
ts = TimeSlice(start=start, duration=duration)
except (ValueError, TypeError):
pass
if not isinstance(ts, TimeSlice):
return ts
diff = self.duration - self.frequency
start_index = \
max(0, np.floor((ts.start - diff) / self.frequency))
end = self.end if ts.duration is None else ts.end
# KLUDGE: This is basically arbitrary, but the motivation is that we'd
# like to differentiate between cases where the slice
# actually/intentionally overlaps a particular sample, and cases where
# the slice overlaps the sample by a tiny amount, due to rounding or
# lack of precision (e.g. Seconds(1) / SR44100().frequency).
ratio = np.round(end / self.frequency, 2)
stop_index = np.ceil(ratio)
return slice(int(start_index), int(stop_index)) | [
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OSSOS/MOP | src/ossos/core/ossos/pipeline/build_astrometry_report.py | load_observations | def load_observations((observations, regex, rename), path, filenames):
"""
Returns a provisional name based dictionary of observations of the object.
Each observations is keyed on the date. ie. a dictionary of dictionaries.
@param path: the directory where filenames are.
@type path str
@param filenames: list of files in path.
@type filenames list
@rtype None
"""
for filename in filenames:
if re.search(regex, filename) is None:
logging.error("Skipping {}".format(filename))
continue
obs = mpc.MPCReader().read(os.path.join(path, filename))
for ob in obs:
if "568" not in ob.observatory_code:
continue
if not isinstance(ob.comment, mpc.OSSOSComment):
continue
if ob.date < Time("2013-01-01 00:00:00"):
continue
if rename:
new_provisional_name = os.path.basename(filename)
new_provisional_name = new_provisional_name[0:new_provisional_name.find(".")]
rename_map[ob.provisional_name] = new_provisional_name
try:
key1 = ob.comment.frame.split('p')[0]
except Exception as ex:
logger.warning(str(ex))
logger.warning(ob.to_string())
continue
key2 = ob.provisional_name
if key1 not in observations:
observations[key1] = {}
if key2 in observations[key1]:
if observations[key1][key2]:
continue
if not observation.null_observation:
logger.error(filename)
logger.error(str(observations[key1][key2]))
raise ValueError("conflicting observations for {} in {}".format(key2, key1))
observations[key1][key2] = ob | python | def load_observations((observations, regex, rename), path, filenames):
"""
Returns a provisional name based dictionary of observations of the object.
Each observations is keyed on the date. ie. a dictionary of dictionaries.
@param path: the directory where filenames are.
@type path str
@param filenames: list of files in path.
@type filenames list
@rtype None
"""
for filename in filenames:
if re.search(regex, filename) is None:
logging.error("Skipping {}".format(filename))
continue
obs = mpc.MPCReader().read(os.path.join(path, filename))
for ob in obs:
if "568" not in ob.observatory_code:
continue
if not isinstance(ob.comment, mpc.OSSOSComment):
continue
if ob.date < Time("2013-01-01 00:00:00"):
continue
if rename:
new_provisional_name = os.path.basename(filename)
new_provisional_name = new_provisional_name[0:new_provisional_name.find(".")]
rename_map[ob.provisional_name] = new_provisional_name
try:
key1 = ob.comment.frame.split('p')[0]
except Exception as ex:
logger.warning(str(ex))
logger.warning(ob.to_string())
continue
key2 = ob.provisional_name
if key1 not in observations:
observations[key1] = {}
if key2 in observations[key1]:
if observations[key1][key2]:
continue
if not observation.null_observation:
logger.error(filename)
logger.error(str(observations[key1][key2]))
raise ValueError("conflicting observations for {} in {}".format(key2, key1))
observations[key1][key2] = ob | [
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OSSOS/MOP | src/ossos/core/scripts/plant.py | plant_kbos | def plant_kbos(filename, psf, kbos, shifts, prefix):
"""
Add KBOs to an image
:param filename: name of the image to add KBOs to
:param psf: the Point Spread Function in IRAF/DAOPHOT format to be used by ADDSTAR
:param kbos: list of KBOs to add, has format as returned by KBOGenerator
:param shifts: dictionary with shifts to transfer to coordinates to reference frame.
:param prefix: an estimate FWHM of the image, used to determine trailing.
:return: None
"""
iraf.set(uparm="./")
iraf.digiphot()
iraf.apphot()
iraf.daophot(_doprint=0)
iraf.images()
if shifts['nmag'] < 4:
logging.warning("Mag shift based on fewer than 4 common stars.")
fd = open("plant.WARNING", 'a')
fd.write("Mag shift based on fewer than 4 common stars.")
fd.close()
if shifts['emag'] > 0.05:
logging.warning("Mag shift has large uncertainty.")
fd = open("plant.WARNING", 'a')
fd.write("Mag shift hsa large uncertainty.")
fd.close()
addstar = tempfile.NamedTemporaryFile(suffix=".add")
# transform KBO locations to this frame using the shifts provided.
w = get_wcs(shifts)
header = fits.open(filename)[0].header
# set the rate of motion in units of pixels/hour instead of ''/hour
scale = header['PIXSCAL1']
rate = kbos['sky_rate']/scale
# compute the location of the KBOs in the current frame.
# offset magnitudes from the reference frame to the current one.
mag = kbos['mag'] - shifts['dmag']
angle = radians(kbos['angle'])
# Move the x/y locations to account for the sky motion of the source.
x = kbos['x'] - rate*24.0*shifts['dmjd']*cos(angle)
y = kbos['y'] - rate*24.0*shifts['dmjd']*sin(angle)
x, y = w.wcs_world2pix(x, y, 1)
# Each source will be added as a series of PSFs so that a new PSF is added for each pixel the source moves.
itime = float(header['EXPTIME'])/3600.0
npsf = fabs(rint(rate * itime)) + 1
mag += 2.5*log10(npsf)
dt_per_psf = itime/npsf
# Build an addstar file to be used in the planting of source.
idx = 0
for record in transpose([x, y, mag, npsf, dt_per_psf, rate, angle]):
x = record[0]
y = record[1]
mag = record[2]
npsf = record[3]
dt = record[4]
rate = record[5]
angle = record[6]
for i in range(int(npsf)):
idx += 1
x += dt*rate*math.cos(angle)
y += dt*rate*math.sin(angle)
addstar.write("{} {} {} {}\n".format(x, y, mag, idx))
addstar.flush()
fk_image = prefix+filename
try:
os.unlink(fk_image)
except OSError as err:
if err.errno == errno.ENOENT:
pass
else:
raise
# add the sources to the image.
iraf.daophot.addstar(filename, addstar.name, psf, fk_image,
simple=True, verify=False, verbose=False)
# convert the image to short integers.
iraf.images.chpix(fk_image, fk_image, 'ushort') | python | def plant_kbos(filename, psf, kbos, shifts, prefix):
"""
Add KBOs to an image
:param filename: name of the image to add KBOs to
:param psf: the Point Spread Function in IRAF/DAOPHOT format to be used by ADDSTAR
:param kbos: list of KBOs to add, has format as returned by KBOGenerator
:param shifts: dictionary with shifts to transfer to coordinates to reference frame.
:param prefix: an estimate FWHM of the image, used to determine trailing.
:return: None
"""
iraf.set(uparm="./")
iraf.digiphot()
iraf.apphot()
iraf.daophot(_doprint=0)
iraf.images()
if shifts['nmag'] < 4:
logging.warning("Mag shift based on fewer than 4 common stars.")
fd = open("plant.WARNING", 'a')
fd.write("Mag shift based on fewer than 4 common stars.")
fd.close()
if shifts['emag'] > 0.05:
logging.warning("Mag shift has large uncertainty.")
fd = open("plant.WARNING", 'a')
fd.write("Mag shift hsa large uncertainty.")
fd.close()
addstar = tempfile.NamedTemporaryFile(suffix=".add")
# transform KBO locations to this frame using the shifts provided.
w = get_wcs(shifts)
header = fits.open(filename)[0].header
# set the rate of motion in units of pixels/hour instead of ''/hour
scale = header['PIXSCAL1']
rate = kbos['sky_rate']/scale
# compute the location of the KBOs in the current frame.
# offset magnitudes from the reference frame to the current one.
mag = kbos['mag'] - shifts['dmag']
angle = radians(kbos['angle'])
# Move the x/y locations to account for the sky motion of the source.
x = kbos['x'] - rate*24.0*shifts['dmjd']*cos(angle)
y = kbos['y'] - rate*24.0*shifts['dmjd']*sin(angle)
x, y = w.wcs_world2pix(x, y, 1)
# Each source will be added as a series of PSFs so that a new PSF is added for each pixel the source moves.
itime = float(header['EXPTIME'])/3600.0
npsf = fabs(rint(rate * itime)) + 1
mag += 2.5*log10(npsf)
dt_per_psf = itime/npsf
# Build an addstar file to be used in the planting of source.
idx = 0
for record in transpose([x, y, mag, npsf, dt_per_psf, rate, angle]):
x = record[0]
y = record[1]
mag = record[2]
npsf = record[3]
dt = record[4]
rate = record[5]
angle = record[6]
for i in range(int(npsf)):
idx += 1
x += dt*rate*math.cos(angle)
y += dt*rate*math.sin(angle)
addstar.write("{} {} {} {}\n".format(x, y, mag, idx))
addstar.flush()
fk_image = prefix+filename
try:
os.unlink(fk_image)
except OSError as err:
if err.errno == errno.ENOENT:
pass
else:
raise
# add the sources to the image.
iraf.daophot.addstar(filename, addstar.name, psf, fk_image,
simple=True, verify=False, verbose=False)
# convert the image to short integers.
iraf.images.chpix(fk_image, fk_image, 'ushort') | [
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:param kbos: list of KBOs to add, has format as returned by KBOGenerator
:param shifts: dictionary with shifts to transfer to coordinates to reference frame.
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OSSOS/MOP | src/ossos/core/scripts/plant.py | plant | def plant(expnums, ccd, rmin, rmax, ang, width, number=10, mmin=21.0, mmax=25.5, version='s', dry_run=False):
"""Plant artificial sources into the list of images provided.
:param expnums: list of MegaPrime exposure numbers to add artificial KBOs to
:param ccd: which ccd to work on.
:param rmin: The minimum rate of motion to add sources at (''/hour)
:param rmax: The maximum rate of motion to add sources at (''/hour)
:param ang: The mean angle of motion to add sources
:param width: The +/- range of angles of motion
:param version: Add sources to the 'o', 'p' or 's' images
:param dry_run: don't push results to VOSpace.
"""
# Construct a list of artificial KBOs with positions in the image
# and rates of motion within the bounds given by the caller.
filename = storage.get_image(expnums[0],
ccd=ccd,
version=version)
header = fits.open(filename)[0].header
bounds = util.get_pixel_bounds_from_datasec_keyword(header.get('DATASEC', '[33:2080,1:4612]'))
# generate a set of artificial KBOs to add to the image.
kbos = KBOGenerator.get_kbos(n=number,
rate=(rmin, rmax),
angle=(ang - width, ang + width),
mag=(mmin, mmax),
x=(bounds[0][0], bounds[0][1]),
y=(bounds[1][0], bounds[1][1]),
filename='Object.planted')
for expnum in expnums:
filename = storage.get_image(expnum, ccd, version)
psf = storage.get_file(expnum, ccd, version, ext='psf.fits')
plant_kbos(filename, psf, kbos, get_shifts(expnum, ccd, version), "fk")
if dry_run:
return
uri = storage.get_uri('Object', ext='planted', version='',
subdir=str(
expnums[0]) + "/ccd%s" % (str(ccd).zfill(2)))
storage.copy('Object.planted', uri)
for expnum in expnums:
uri = storage.get_uri(expnum,
ccd=ccd,
version=version,
ext='fits', prefix='fk')
filename = os.path.basename(uri)
storage.copy(filename, uri)
return | python | def plant(expnums, ccd, rmin, rmax, ang, width, number=10, mmin=21.0, mmax=25.5, version='s', dry_run=False):
"""Plant artificial sources into the list of images provided.
:param expnums: list of MegaPrime exposure numbers to add artificial KBOs to
:param ccd: which ccd to work on.
:param rmin: The minimum rate of motion to add sources at (''/hour)
:param rmax: The maximum rate of motion to add sources at (''/hour)
:param ang: The mean angle of motion to add sources
:param width: The +/- range of angles of motion
:param version: Add sources to the 'o', 'p' or 's' images
:param dry_run: don't push results to VOSpace.
"""
# Construct a list of artificial KBOs with positions in the image
# and rates of motion within the bounds given by the caller.
filename = storage.get_image(expnums[0],
ccd=ccd,
version=version)
header = fits.open(filename)[0].header
bounds = util.get_pixel_bounds_from_datasec_keyword(header.get('DATASEC', '[33:2080,1:4612]'))
# generate a set of artificial KBOs to add to the image.
kbos = KBOGenerator.get_kbos(n=number,
rate=(rmin, rmax),
angle=(ang - width, ang + width),
mag=(mmin, mmax),
x=(bounds[0][0], bounds[0][1]),
y=(bounds[1][0], bounds[1][1]),
filename='Object.planted')
for expnum in expnums:
filename = storage.get_image(expnum, ccd, version)
psf = storage.get_file(expnum, ccd, version, ext='psf.fits')
plant_kbos(filename, psf, kbos, get_shifts(expnum, ccd, version), "fk")
if dry_run:
return
uri = storage.get_uri('Object', ext='planted', version='',
subdir=str(
expnums[0]) + "/ccd%s" % (str(ccd).zfill(2)))
storage.copy('Object.planted', uri)
for expnum in expnums:
uri = storage.get_uri(expnum,
ccd=ccd,
version=version,
ext='fits', prefix='fk')
filename = os.path.basename(uri)
storage.copy(filename, uri)
return | [
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:param rmax: The maximum rate of motion to add sources at (''/hour)
:param ang: The mean angle of motion to add sources
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OSSOS/MOP | src/ossos/core/ossos/kbo.py | Orbfit._fit_radec | def _fit_radec(self):
"""
call fit_radec of BK passing in the observations.
"""
# call fitradec with mpcfile, abgfile, resfile
self.orbfit.fitradec.restype = ctypes.c_int
self.orbfit.fitradec.argtypes = [ ctypes.c_char_p, ctypes.c_char_p, ctypes.c_char_p ]
mpc_file = tempfile.NamedTemporaryFile(suffix='.mpc')
for observation in self.observations:
mpc_file.write("{}\n".format(str(observation)))
mpc_file.seek(0)
abg_file = tempfile.NamedTemporaryFile()
res_file = tempfile.NamedTemporaryFile()
self.orbfit.fitradec(ctypes.c_char_p(mpc_file.name),
ctypes.c_char_p(abg_file.name),
ctypes.c_char_p(res_file.name))
self.abg = abg_file
self.abg.seek(0)
self.residuals = res_file
self.residuals.seek(0) | python | def _fit_radec(self):
"""
call fit_radec of BK passing in the observations.
"""
# call fitradec with mpcfile, abgfile, resfile
self.orbfit.fitradec.restype = ctypes.c_int
self.orbfit.fitradec.argtypes = [ ctypes.c_char_p, ctypes.c_char_p, ctypes.c_char_p ]
mpc_file = tempfile.NamedTemporaryFile(suffix='.mpc')
for observation in self.observations:
mpc_file.write("{}\n".format(str(observation)))
mpc_file.seek(0)
abg_file = tempfile.NamedTemporaryFile()
res_file = tempfile.NamedTemporaryFile()
self.orbfit.fitradec(ctypes.c_char_p(mpc_file.name),
ctypes.c_char_p(abg_file.name),
ctypes.c_char_p(res_file.name))
self.abg = abg_file
self.abg.seek(0)
self.residuals = res_file
self.residuals.seek(0) | [
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OSSOS/MOP | src/ossos/core/ossos/kbo.py | Orbfit.predict | def predict(self, date, obs_code=568):
"""
use the bk predict method to compute the location of the source on the given date.
"""
time = Time(date, scale='utc', precision=6)
jd = ctypes.c_double(time.jd)
# call predict with agbfile, jdate, obscode
self.orbfit.predict.restype = ctypes.POINTER(ctypes.c_double * 5)
self.orbfit.predict.argtypes = [ ctypes.c_char_p, ctypes.c_double, ctypes.c_int ]
predict = self.orbfit.predict(ctypes.c_char_p(self.abg.name),
jd,
ctypes.c_int(obs_code))
self.coordinate = coordinates.SkyCoord(predict.contents[0],
predict.contents[1],
unit=(units.degree, units.degree))
self.dra = predict.contents[2]
self.ddec = predict.contents[3]
self.pa = predict.contents[4]
self.date = str(time) | python | def predict(self, date, obs_code=568):
"""
use the bk predict method to compute the location of the source on the given date.
"""
time = Time(date, scale='utc', precision=6)
jd = ctypes.c_double(time.jd)
# call predict with agbfile, jdate, obscode
self.orbfit.predict.restype = ctypes.POINTER(ctypes.c_double * 5)
self.orbfit.predict.argtypes = [ ctypes.c_char_p, ctypes.c_double, ctypes.c_int ]
predict = self.orbfit.predict(ctypes.c_char_p(self.abg.name),
jd,
ctypes.c_int(obs_code))
self.coordinate = coordinates.SkyCoord(predict.contents[0],
predict.contents[1],
unit=(units.degree, units.degree))
self.dra = predict.contents[2]
self.ddec = predict.contents[3]
self.pa = predict.contents[4]
self.date = str(time) | [
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OSSOS/MOP | src/ossos/core/ossos/gui/views/appview.py | guithread | def guithread(function):
"""
Decorator to make sure the function is called from wx's main GUI
thread. This is needed when trying to trigger UI updates from a thread
other than the main GUI thread (such as some asynchronous data loading
thread).
I learned about doing this from:
wxPython 2.8 Application Development Cookbook, Chapter 11
"""
def new_guithread_function(*args, **kwargs):
if wx.Thread_IsMain():
return function(*args, **kwargs)
else:
wx.CallAfter(function, *args, **kwargs)
return new_guithread_function | python | def guithread(function):
"""
Decorator to make sure the function is called from wx's main GUI
thread. This is needed when trying to trigger UI updates from a thread
other than the main GUI thread (such as some asynchronous data loading
thread).
I learned about doing this from:
wxPython 2.8 Application Development Cookbook, Chapter 11
"""
def new_guithread_function(*args, **kwargs):
if wx.Thread_IsMain():
return function(*args, **kwargs)
else:
wx.CallAfter(function, *args, **kwargs)
return new_guithread_function | [
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wxPython 2.8 Application Development Cookbook, Chapter 11 | [
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OSSOS/MOP | src/jjk/preproc/MOPfiles.py | write | def write(file,hdu,order=None,format=None):
"""Write a file in the crazy MOP format given an mop data hdu."""
if order or format:
warnings.warn('Use of <order> and <format> depricated',DeprecationWarning)
## if the order of the columns isn't constrained just use the keys in what ever order
data='data'
if not order:
if not hdu.has_key('order'):
hdu['order']=hdu[data].keys()
else:
hdu['order']=order
if not format:
if not hdu.has_key('format'):
hdu['format']={}
for o in hdu['order']:
if not hdu['format'].has_key(o):
hdu['format'][o]='%10s'
else:
hdu['format']=format
f=open(file,'w')
kline='## '
vline='# '
header='header'
num=0
for keyword in hdu[header]:
kline+='%10s ' % (keyword, )
vline+='%10s ' % str(hdu[header][keyword])
num+=1
if not ( num % 6 ) :
num=0
f.write(kline+'\n')
f.write(vline+'\n')
kline='## '
vline='# '
if num > 0:
f.write(kline+'\n')
f.write(vline+'\n')
f.write('## ')
for column in hdu['order']:
f.write(' %10s' % (column))
f.write('\n')
dlen=len(hdu[data][hdu['order'][0]])
for i in range(dlen):
f.write(' ')
for column in hdu['order']:
f.write(hdu['format'][column] % (hdu[data][column][i]))
f.write(' ')
f.write('\n')
f.close()
return | python | def write(file,hdu,order=None,format=None):
"""Write a file in the crazy MOP format given an mop data hdu."""
if order or format:
warnings.warn('Use of <order> and <format> depricated',DeprecationWarning)
## if the order of the columns isn't constrained just use the keys in what ever order
data='data'
if not order:
if not hdu.has_key('order'):
hdu['order']=hdu[data].keys()
else:
hdu['order']=order
if not format:
if not hdu.has_key('format'):
hdu['format']={}
for o in hdu['order']:
if not hdu['format'].has_key(o):
hdu['format'][o]='%10s'
else:
hdu['format']=format
f=open(file,'w')
kline='## '
vline='# '
header='header'
num=0
for keyword in hdu[header]:
kline+='%10s ' % (keyword, )
vline+='%10s ' % str(hdu[header][keyword])
num+=1
if not ( num % 6 ) :
num=0
f.write(kline+'\n')
f.write(vline+'\n')
kline='## '
vline='# '
if num > 0:
f.write(kline+'\n')
f.write(vline+'\n')
f.write('## ')
for column in hdu['order']:
f.write(' %10s' % (column))
f.write('\n')
dlen=len(hdu[data][hdu['order'][0]])
for i in range(dlen):
f.write(' ')
for column in hdu['order']:
f.write(hdu['format'][column] % (hdu[data][column][i]))
f.write(' ')
f.write('\n')
f.close()
return | [
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OSSOS/MOP | src/jjk/preproc/MOPfiles.py | store | def store(hdu,dbase='cfeps',duser='cfhls',dtype='MYSQL',table='source'):
"""Write the contents of a MOP data structure to a SQL table"""
import MOPdbaccess
db=MOPdbaccess.connect(dbase,duser,dbSystem=dtype)
dbc=db.cursor()
### INSERT THE 'HEADER' in the meta-data table
file_id=hdu['header']['image']
for key in hdu['header'].keys():
if key == 'image':
continue
value=hdu['header'][key]
### require that the file_id+keyword is unique
sql="DELETE FROM metadata WHERE file_id='%s' and keyword='%s' " % ( file_id, key)
dbc.execute(sql)
sql="INSERT INTO metadata (file_id, keyword, value) values ('%s','%s','%s' ) "% ( file_id, key, value)
dbc.execute(sql)
db.commit()
sql="DELETE FROM source WHERE file_id LIKE '%s' " % ( file_id )
dbc.execute(sql)
sql="INSERT INTO %s ( " % ( table)
sep=" "
values="("
cols=hdu['hdu2sql'].keys()
for col in cols:
sql+=sep+hdu['hdu2sql'][col]
values+=sep+" %s "
sep=', '
values+=", '%s', %d, %d )" % ( file_id, int(hdu['header']['EXPNUM']), int(hdu['header']['CHIP'] )-1 )
sql+=", file_id, expnum, ccd ) VALUES "+values
#print sql
#sys.exit()
#values=[]
for row in range(len(hdu['data'][cols[0]])):
value=[]
for col in cols:
value.append(hdu['data'][col][row])
dbc.execute(sql,value)
sql="""insert into source_idx ( sourceID, x, y, z ) SELECT sourceID,
(360.0*COS(RADIANS(raDeg))*COS(RADIANS(decDeg))),
(360.0*SIN(RADIANS(raDeg))*COS(RADIANS(decDeg))),
(360.0*SIN(RADIANS(decDeg))) FROM source WHERE file_id='%s'""" % (file_id)
dbc.execute(sql)
db.commit()
return | python | def store(hdu,dbase='cfeps',duser='cfhls',dtype='MYSQL',table='source'):
"""Write the contents of a MOP data structure to a SQL table"""
import MOPdbaccess
db=MOPdbaccess.connect(dbase,duser,dbSystem=dtype)
dbc=db.cursor()
### INSERT THE 'HEADER' in the meta-data table
file_id=hdu['header']['image']
for key in hdu['header'].keys():
if key == 'image':
continue
value=hdu['header'][key]
### require that the file_id+keyword is unique
sql="DELETE FROM metadata WHERE file_id='%s' and keyword='%s' " % ( file_id, key)
dbc.execute(sql)
sql="INSERT INTO metadata (file_id, keyword, value) values ('%s','%s','%s' ) "% ( file_id, key, value)
dbc.execute(sql)
db.commit()
sql="DELETE FROM source WHERE file_id LIKE '%s' " % ( file_id )
dbc.execute(sql)
sql="INSERT INTO %s ( " % ( table)
sep=" "
values="("
cols=hdu['hdu2sql'].keys()
for col in cols:
sql+=sep+hdu['hdu2sql'][col]
values+=sep+" %s "
sep=', '
values+=", '%s', %d, %d )" % ( file_id, int(hdu['header']['EXPNUM']), int(hdu['header']['CHIP'] )-1 )
sql+=", file_id, expnum, ccd ) VALUES "+values
#print sql
#sys.exit()
#values=[]
for row in range(len(hdu['data'][cols[0]])):
value=[]
for col in cols:
value.append(hdu['data'][col][row])
dbc.execute(sql,value)
sql="""insert into source_idx ( sourceID, x, y, z ) SELECT sourceID,
(360.0*COS(RADIANS(raDeg))*COS(RADIANS(decDeg))),
(360.0*SIN(RADIANS(raDeg))*COS(RADIANS(decDeg))),
(360.0*SIN(RADIANS(decDeg))) FROM source WHERE file_id='%s'""" % (file_id)
dbc.execute(sql)
db.commit()
return | [
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OSSOS/MOP | src/jjk/preproc/MOPfiles.py | read | def read(file):
"""Read in a file and create a data strucuture that is a hash with members 'header'
and 'data'. The 'header' is a hash of header keywords, the data is a hash of columns.
To get to the nth element of column NAME use hdu[data][NAME][n]. To get the header
information use hdu[header][KEYWORD]. """
f = open(file,'r')
lines=f.readlines()
f.close()
import re, string
keywords=[]
values=[]
formats={}
header={}
cdata={}
for line in lines:
if ( re.match(r'^##',line)):
## header line
m=string.split(string.lstrip(line[2:]))
if not m:
sys.stderr.write( "Ill formed header line in %s \ n " % ( file, ))
sys.stderr.write( line)
continue
keywords=m
add_id=False
continue
if ( re.match(r'^# ',line)):
## this is a keyword value line, must match the previous keyword line
m=string.split(string.lstrip(line[1:]))
values=m
if len(values)!= len(keywords):
sys.stderr.write( "Ill formed header, keyword/value missmatach\n")
for index in range(len(values)):
header[keywords[index]]=values[index]
## blank the arrays, we've already stuck this into the header
keywords=[]
values=[]
continue
if ( re.match(r'^#F',line)):
## this is a format line for the columns needs to be a keyword line first
if not keywords:
sys.stderr.write("Cann't have formats without column names...\n")
continue
f=string.split(string.lstrip(line))
if add_id:
f.append('%8d')
for col in keywords:
formats[col]=f.pop(0)
### must be the actual data
### expect a previous header line to define column headers
if not keywords:
sys.stderr.write( "No keywords for data columns, assuming x,y,mag,msky\n")
keywords=('X','Y','MAG','MSKY')
values = string.split(string.lstrip(line))
### add the id value to the values array if needed
if not 'ID' in keywords:
keywords.append('ID')
add_id=True
if not cdata:
for keyword in keywords:
cdata[keyword]=[]
if add_id:
values.append(len(cdata[keywords[0]])+1)
if len(values)!=len(keywords):
sys.stderr.write("Keyword and value index have different length?\n")
continue
for index in range(len(values)):
cdata[keywords[index]].append(values[index])
hdu={'data': cdata, 'header': header, 'format': formats, 'order': keywords}
### the hdu is a dictionary with the header and data
return hdu | python | def read(file):
"""Read in a file and create a data strucuture that is a hash with members 'header'
and 'data'. The 'header' is a hash of header keywords, the data is a hash of columns.
To get to the nth element of column NAME use hdu[data][NAME][n]. To get the header
information use hdu[header][KEYWORD]. """
f = open(file,'r')
lines=f.readlines()
f.close()
import re, string
keywords=[]
values=[]
formats={}
header={}
cdata={}
for line in lines:
if ( re.match(r'^##',line)):
## header line
m=string.split(string.lstrip(line[2:]))
if not m:
sys.stderr.write( "Ill formed header line in %s \ n " % ( file, ))
sys.stderr.write( line)
continue
keywords=m
add_id=False
continue
if ( re.match(r'^# ',line)):
## this is a keyword value line, must match the previous keyword line
m=string.split(string.lstrip(line[1:]))
values=m
if len(values)!= len(keywords):
sys.stderr.write( "Ill formed header, keyword/value missmatach\n")
for index in range(len(values)):
header[keywords[index]]=values[index]
## blank the arrays, we've already stuck this into the header
keywords=[]
values=[]
continue
if ( re.match(r'^#F',line)):
## this is a format line for the columns needs to be a keyword line first
if not keywords:
sys.stderr.write("Cann't have formats without column names...\n")
continue
f=string.split(string.lstrip(line))
if add_id:
f.append('%8d')
for col in keywords:
formats[col]=f.pop(0)
### must be the actual data
### expect a previous header line to define column headers
if not keywords:
sys.stderr.write( "No keywords for data columns, assuming x,y,mag,msky\n")
keywords=('X','Y','MAG','MSKY')
values = string.split(string.lstrip(line))
### add the id value to the values array if needed
if not 'ID' in keywords:
keywords.append('ID')
add_id=True
if not cdata:
for keyword in keywords:
cdata[keyword]=[]
if add_id:
values.append(len(cdata[keywords[0]])+1)
if len(values)!=len(keywords):
sys.stderr.write("Keyword and value index have different length?\n")
continue
for index in range(len(values)):
cdata[keywords[index]].append(values[index])
hdu={'data': cdata, 'header': header, 'format': formats, 'order': keywords}
### the hdu is a dictionary with the header and data
return hdu | [
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OSSOS/MOP | src/jjk/preproc/MOPfiles.py | xymatch | def xymatch(outfile, filenames, tol=2):
"""Given a list of MOPfiles merge them based on x/y coordinates matching.."""
import math
import sys
output={}
files=[]
for filename in filenames:
this_file=read(filename)
## match files based on the 'X' and 'Y' column.
## if those don't exist then skip this file
if not this_file['data'].has_key('X') or not this_file['data'].has_key('Y'):
continue
if not output.has_key('data'):
output=this_file
continue
delete_list=[]
for keyword in this_file['header']:
if not keyword in output['header']:
output['header'][keyword]=this_file['header'][keyword]
for col in this_file['data'].keys():
if not output['data'].has_key(col):
output['order'].append(col)
output['data'][col]=[]
output['order'].append(col)
if this_file['format'].has_key(col):
output['format'][col]=this_file['format'][col]
else:
output['format'][col]='%10s'
### pad previously values with empties..
for i in range(len(output['data']['X'])):
output['data'][col].append(None)
for i in xrange(len(output['data']['X'])):
x1=float(output['data']['X'][i])
y1=float(output['data']['Y'][i])
matched=False
for j in xrange(len(this_file['data']['X'])):
x2=float(this_file['data']['X'][j])
y2=float(this_file['data']['Y'][j])
if ( ((x1-x2)**2+(y1-y2)**2) < tol**2):
for col in this_file['data'].keys():
if output['data'][col][i] is None:
output['data'][col][i]=this_file['data'][col][j]
matched=True
break
if not matched:
delete_list.append(i)
delete_list.sort()
delete_list.reverse()
for i in delete_list:
for col in output['data'].keys():
del output['data'][col][i]
write(outfile,output) | python | def xymatch(outfile, filenames, tol=2):
"""Given a list of MOPfiles merge them based on x/y coordinates matching.."""
import math
import sys
output={}
files=[]
for filename in filenames:
this_file=read(filename)
## match files based on the 'X' and 'Y' column.
## if those don't exist then skip this file
if not this_file['data'].has_key('X') or not this_file['data'].has_key('Y'):
continue
if not output.has_key('data'):
output=this_file
continue
delete_list=[]
for keyword in this_file['header']:
if not keyword in output['header']:
output['header'][keyword]=this_file['header'][keyword]
for col in this_file['data'].keys():
if not output['data'].has_key(col):
output['order'].append(col)
output['data'][col]=[]
output['order'].append(col)
if this_file['format'].has_key(col):
output['format'][col]=this_file['format'][col]
else:
output['format'][col]='%10s'
### pad previously values with empties..
for i in range(len(output['data']['X'])):
output['data'][col].append(None)
for i in xrange(len(output['data']['X'])):
x1=float(output['data']['X'][i])
y1=float(output['data']['Y'][i])
matched=False
for j in xrange(len(this_file['data']['X'])):
x2=float(this_file['data']['X'][j])
y2=float(this_file['data']['Y'][j])
if ( ((x1-x2)**2+(y1-y2)**2) < tol**2):
for col in this_file['data'].keys():
if output['data'][col][i] is None:
output['data'][col][i]=this_file['data'][col][j]
matched=True
break
if not matched:
delete_list.append(i)
delete_list.sort()
delete_list.reverse()
for i in delete_list:
for col in output['data'].keys():
del output['data'][col][i]
write(outfile,output) | [
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playpauseandstop/rororo | rororo/logger.py | default_logging_dict | def default_logging_dict(*loggers: str, **kwargs: Any) -> DictStrAny:
r"""Prepare logging dict suitable with ``logging.config.dictConfig``.
**Usage**::
from logging.config import dictConfig
dictConfig(default_logging_dict('yourlogger'))
:param \*loggers: Enable logging for each logger in sequence.
:param \*\*kwargs: Setup additional logger params via keyword arguments.
"""
kwargs.setdefault('level', 'INFO')
return {
'version': 1,
'disable_existing_loggers': True,
'filters': {
'ignore_errors': {
'()': IgnoreErrorsFilter,
},
},
'formatters': {
'default': {
'format': '%(asctime)s [%(levelname)s:%(name)s] %(message)s',
},
'naked': {
'format': u'%(message)s',
},
},
'handlers': {
'stdout': {
'class': 'logging.StreamHandler',
'filters': ['ignore_errors'],
'formatter': 'default',
'level': 'DEBUG',
'stream': sys.stdout,
},
'stderr': {
'class': 'logging.StreamHandler',
'formatter': 'default',
'level': 'WARNING',
'stream': sys.stderr,
},
},
'loggers': {
logger: dict(handlers=['stdout', 'stderr'], **kwargs)
for logger in loggers
},
} | python | def default_logging_dict(*loggers: str, **kwargs: Any) -> DictStrAny:
r"""Prepare logging dict suitable with ``logging.config.dictConfig``.
**Usage**::
from logging.config import dictConfig
dictConfig(default_logging_dict('yourlogger'))
:param \*loggers: Enable logging for each logger in sequence.
:param \*\*kwargs: Setup additional logger params via keyword arguments.
"""
kwargs.setdefault('level', 'INFO')
return {
'version': 1,
'disable_existing_loggers': True,
'filters': {
'ignore_errors': {
'()': IgnoreErrorsFilter,
},
},
'formatters': {
'default': {
'format': '%(asctime)s [%(levelname)s:%(name)s] %(message)s',
},
'naked': {
'format': u'%(message)s',
},
},
'handlers': {
'stdout': {
'class': 'logging.StreamHandler',
'filters': ['ignore_errors'],
'formatter': 'default',
'level': 'DEBUG',
'stream': sys.stdout,
},
'stderr': {
'class': 'logging.StreamHandler',
'formatter': 'default',
'level': 'WARNING',
'stream': sys.stderr,
},
},
'loggers': {
logger: dict(handlers=['stdout', 'stderr'], **kwargs)
for logger in loggers
},
} | [
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playpauseandstop/rororo | rororo/logger.py | update_sentry_logging | def update_sentry_logging(logging_dict: DictStrAny,
sentry_dsn: Optional[str],
*loggers: str,
level: Union[str, int] = None,
**kwargs: Any) -> None:
r"""Enable Sentry logging if Sentry DSN passed.
.. note::
Sentry logging requires `raven <http://pypi.python.org/pypi/raven>`_
library to be installed.
**Usage**::
from logging.config import dictConfig
LOGGING = default_logging_dict()
SENTRY_DSN = '...'
update_sentry_logging(LOGGING, SENTRY_DSN)
dictConfig(LOGGING)
**Using AioHttpTransport for SentryHandler**
This will allow to use ``aiohttp.client`` for pushing data to Sentry in
your ``aiohttp.web`` app, which means elimination of sync calls to Sentry.
::
from raven_aiohttp import AioHttpTransport
update_sentry_logging(LOGGING, SENTRY_DSN, transport=AioHttpTransport)
:param logging_dict: Logging dict.
:param sentry_dsn:
Sentry DSN value. If ``None`` do not update logging dict at all.
:param \*loggers:
Use Sentry logging for each logger in the sequence. If the sequence is
empty use Sentry logging to each available logger.
:param \*\*kwargs: Additional kwargs to be passed to ``SentryHandler``.
"""
# No Sentry DSN, nothing to do
if not sentry_dsn:
return
# Add Sentry handler
kwargs['class'] = 'raven.handlers.logging.SentryHandler'
kwargs['dsn'] = sentry_dsn
logging_dict['handlers']['sentry'] = dict(
level=level or 'WARNING',
**kwargs)
loggers = tuple(logging_dict['loggers']) if not loggers else loggers
for logger in loggers:
# Ignore missing loggers
logger_dict = logging_dict['loggers'].get(logger)
if not logger_dict:
continue
# Ignore logger from logger config
if logger_dict.pop('ignore_sentry', False):
continue
# Handlers list should exist
handlers = list(logger_dict.setdefault('handlers', []))
handlers.append('sentry')
logger_dict['handlers'] = tuple(handlers) | python | def update_sentry_logging(logging_dict: DictStrAny,
sentry_dsn: Optional[str],
*loggers: str,
level: Union[str, int] = None,
**kwargs: Any) -> None:
r"""Enable Sentry logging if Sentry DSN passed.
.. note::
Sentry logging requires `raven <http://pypi.python.org/pypi/raven>`_
library to be installed.
**Usage**::
from logging.config import dictConfig
LOGGING = default_logging_dict()
SENTRY_DSN = '...'
update_sentry_logging(LOGGING, SENTRY_DSN)
dictConfig(LOGGING)
**Using AioHttpTransport for SentryHandler**
This will allow to use ``aiohttp.client`` for pushing data to Sentry in
your ``aiohttp.web`` app, which means elimination of sync calls to Sentry.
::
from raven_aiohttp import AioHttpTransport
update_sentry_logging(LOGGING, SENTRY_DSN, transport=AioHttpTransport)
:param logging_dict: Logging dict.
:param sentry_dsn:
Sentry DSN value. If ``None`` do not update logging dict at all.
:param \*loggers:
Use Sentry logging for each logger in the sequence. If the sequence is
empty use Sentry logging to each available logger.
:param \*\*kwargs: Additional kwargs to be passed to ``SentryHandler``.
"""
# No Sentry DSN, nothing to do
if not sentry_dsn:
return
# Add Sentry handler
kwargs['class'] = 'raven.handlers.logging.SentryHandler'
kwargs['dsn'] = sentry_dsn
logging_dict['handlers']['sentry'] = dict(
level=level or 'WARNING',
**kwargs)
loggers = tuple(logging_dict['loggers']) if not loggers else loggers
for logger in loggers:
# Ignore missing loggers
logger_dict = logging_dict['loggers'].get(logger)
if not logger_dict:
continue
# Ignore logger from logger config
if logger_dict.pop('ignore_sentry', False):
continue
# Handlers list should exist
handlers = list(logger_dict.setdefault('handlers', []))
handlers.append('sentry')
logger_dict['handlers'] = tuple(handlers) | [
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OSSOS/MOP | src/ossos/core/scripts/preproc.py | trim | def trim(hdu, datasec='DATASEC'):
"""TRIM a CFHT MEGAPRIME frame using the DATASEC keyword"""
datasec = re.findall(r'(\d+)',
hdu.header.get(datasec))
l = int(datasec[0]) - 1
r = int(datasec[1])
b = int(datasec[2]) - 1
t = int(datasec[3])
logger.info("Trimming [%d:%d,%d:%d]" % ( l, r, b, t))
hdu.data = hdu.data[b:t, l:r]
hdu.header.update('DATASEC',
"[%d:%d,%d:%d]" % (1, r - l + 1, 1, t - b + 1),
comment="Image was trimmed")
hdu.header.update('ODATASEC',
"[%d:%d,%d:%d]" % (l + 1, r, b + 1, t),
comment="previous DATASEC")
return | python | def trim(hdu, datasec='DATASEC'):
"""TRIM a CFHT MEGAPRIME frame using the DATASEC keyword"""
datasec = re.findall(r'(\d+)',
hdu.header.get(datasec))
l = int(datasec[0]) - 1
r = int(datasec[1])
b = int(datasec[2]) - 1
t = int(datasec[3])
logger.info("Trimming [%d:%d,%d:%d]" % ( l, r, b, t))
hdu.data = hdu.data[b:t, l:r]
hdu.header.update('DATASEC',
"[%d:%d,%d:%d]" % (1, r - l + 1, 1, t - b + 1),
comment="Image was trimmed")
hdu.header.update('ODATASEC',
"[%d:%d,%d:%d]" % (l + 1, r, b + 1, t),
comment="previous DATASEC")
return | [
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OSSOS/MOP | src/ossos/core/ossos/parsers.py | ossos_release_parser | def ossos_release_parser(table=False, data_release=parameters.RELEASE_VERSION):
"""
extra fun as this is space-separated so using CSV parsers is not an option
"""
names = ['cl', 'p', 'j', 'k', 'sh', 'object', 'mag', 'e_mag', 'Filt', 'Hsur', 'dist', 'e_dist', 'Nobs',
'time', 'av_xres', 'av_yres', 'max_x', 'max_y', 'a', 'e_a', 'e', 'e_e', 'i', 'e_i', 'Omega', 'e_Omega',
'omega', 'e_omega', 'tperi', 'e_tperi', 'RAdeg', 'DEdeg', 'JD', 'rate']#, 'eff', 'm_lim']
if table:
retval = Table.read(parameters.RELEASE_DETECTIONS[data_release], format='ascii', guess=False,
delimiter=' ', data_start=0, comment='#', names=names, header_start=None)
else:
retval = []
with open(data_release, 'r') as detectionsfile:
for line in detectionsfile.readlines()[1:]: # first line is column definitions
obj = TNO.from_string(line, version=parameters.RELEASE_DETECTIONS[data_release])
retval.append(obj)
return retval | python | def ossos_release_parser(table=False, data_release=parameters.RELEASE_VERSION):
"""
extra fun as this is space-separated so using CSV parsers is not an option
"""
names = ['cl', 'p', 'j', 'k', 'sh', 'object', 'mag', 'e_mag', 'Filt', 'Hsur', 'dist', 'e_dist', 'Nobs',
'time', 'av_xres', 'av_yres', 'max_x', 'max_y', 'a', 'e_a', 'e', 'e_e', 'i', 'e_i', 'Omega', 'e_Omega',
'omega', 'e_omega', 'tperi', 'e_tperi', 'RAdeg', 'DEdeg', 'JD', 'rate']#, 'eff', 'm_lim']
if table:
retval = Table.read(parameters.RELEASE_DETECTIONS[data_release], format='ascii', guess=False,
delimiter=' ', data_start=0, comment='#', names=names, header_start=None)
else:
retval = []
with open(data_release, 'r') as detectionsfile:
for line in detectionsfile.readlines()[1:]: # first line is column definitions
obj = TNO.from_string(line, version=parameters.RELEASE_DETECTIONS[data_release])
retval.append(obj)
return retval | [
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OSSOS/MOP | src/ossos/core/ossos/parsers.py | ossos_discoveries | def ossos_discoveries(directory=parameters.REAL_KBO_AST_DIR,
suffix='ast',
no_nt_and_u=False,
single_object=None,
all_objects=True,
data_release=None,
):
"""
Returns a list of objects holding orbfit.Orbfit objects with the observations in the Orbfit.observations field.
Default is to return only the objects corresponding to the current Data Release.
"""
retval = []
# working_context = context.get_context(directory)
# files = working_context.get_listing(suffix)
files = [f for f in os.listdir(directory) if (f.endswith('mpc') or f.endswith('ast') or f.endswith('DONE'))]
if single_object is not None:
files = filter(lambda name: name.startswith(single_object), files)
elif all_objects and data_release is not None:
# only return the objects corresponding to a particular Data Release
data_release = ossos_release_parser(table=True, data_release=data_release)
objects = data_release['object']
files = filter(lambda name: name.partition(suffix)[0].rstrip('.') in objects, files)
for filename in files:
# keep out the not-tracked and uncharacteried.
if no_nt_and_u and (filename.__contains__('nt') or filename.startswith('u')):
continue
# observations = mpc.MPCReader(directory + filename)
mpc_filename = directory + filename
abg_filename = os.path.abspath(directory + '/../abg/') + "/" + os.path.splitext(filename)[0] + ".abg"
obj = TNO(None, ast_filename=mpc_filename, abg_filename=abg_filename)
retval.append(obj)
return retval | python | def ossos_discoveries(directory=parameters.REAL_KBO_AST_DIR,
suffix='ast',
no_nt_and_u=False,
single_object=None,
all_objects=True,
data_release=None,
):
"""
Returns a list of objects holding orbfit.Orbfit objects with the observations in the Orbfit.observations field.
Default is to return only the objects corresponding to the current Data Release.
"""
retval = []
# working_context = context.get_context(directory)
# files = working_context.get_listing(suffix)
files = [f for f in os.listdir(directory) if (f.endswith('mpc') or f.endswith('ast') or f.endswith('DONE'))]
if single_object is not None:
files = filter(lambda name: name.startswith(single_object), files)
elif all_objects and data_release is not None:
# only return the objects corresponding to a particular Data Release
data_release = ossos_release_parser(table=True, data_release=data_release)
objects = data_release['object']
files = filter(lambda name: name.partition(suffix)[0].rstrip('.') in objects, files)
for filename in files:
# keep out the not-tracked and uncharacteried.
if no_nt_and_u and (filename.__contains__('nt') or filename.startswith('u')):
continue
# observations = mpc.MPCReader(directory + filename)
mpc_filename = directory + filename
abg_filename = os.path.abspath(directory + '/../abg/') + "/" + os.path.splitext(filename)[0] + ".abg"
obj = TNO(None, ast_filename=mpc_filename, abg_filename=abg_filename)
retval.append(obj)
return retval | [
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OSSOS/MOP | src/ossos/core/ossos/parsers.py | ossos_release_with_metadata | def ossos_release_with_metadata():
"""
Wrap the objects from the Version Releases together with the objects instantiated from fitting their mpc lines
"""
# discoveries = ossos_release_parser()
discoveries = []
observations = ossos_discoveries()
for obj in observations:
discov = [n for n in obj[0].mpc_observations if n.discovery.is_discovery][0]
tno = parameters.tno()
tno.dist = obj[1].distance
tno.ra_discov = discov.coordinate.ra.degrees
tno.mag = discov.mag
tno.name = discov.provisional_name
discoveries.append(tno)
# for obj in discoveries:
# observation = [n for n in observations if n.observations[-1].provisional_name == obj.name][0]
# for obs in observation.observations:
# if obs.discovery.is_discovery:
# if obj.mag is not None:
# H = obj.mag + 2.5 * math.log10(1. / ((obj.dist ** 2) * ((obj.dist - 1.) ** 2)))
# else:
# H = None
# obj.H = H
# obj.T = observation.T
# obj.discovery_date = obs.date
# obj.observations = observation
return discoveries | python | def ossos_release_with_metadata():
"""
Wrap the objects from the Version Releases together with the objects instantiated from fitting their mpc lines
"""
# discoveries = ossos_release_parser()
discoveries = []
observations = ossos_discoveries()
for obj in observations:
discov = [n for n in obj[0].mpc_observations if n.discovery.is_discovery][0]
tno = parameters.tno()
tno.dist = obj[1].distance
tno.ra_discov = discov.coordinate.ra.degrees
tno.mag = discov.mag
tno.name = discov.provisional_name
discoveries.append(tno)
# for obj in discoveries:
# observation = [n for n in observations if n.observations[-1].provisional_name == obj.name][0]
# for obs in observation.observations:
# if obs.discovery.is_discovery:
# if obj.mag is not None:
# H = obj.mag + 2.5 * math.log10(1. / ((obj.dist ** 2) * ((obj.dist - 1.) ** 2)))
# else:
# H = None
# obj.H = H
# obj.T = observation.T
# obj.discovery_date = obs.date
# obj.observations = observation
return discoveries | [
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OSSOS/MOP | src/ossos/core/ossos/parsers.py | _kbos_from_survey_sym_model_input_file | def _kbos_from_survey_sym_model_input_file(model_file):
"""
Load a Survey Simulator model file as an array of ephem EllipticalBody objects.
@param model_file:
@return:
"""
lines = storage.open_vos_or_local(model_file).read().split('\n')
kbos = []
for line in lines:
if len(line) == 0 or line[0] == '#': # skip initial column descriptors and the final blank line
continue
kbo = ephem.EllipticalBody()
values = line.split()
kbo.name = values[8]
kbo.j = values[9]
kbo.k = values[10]
kbo._a = float(values[0])
kbo._e = float(values[1])
kbo._inc = float(values[2])
kbo._Om = float(values[3])
kbo._om = float(values[4])
kbo._M = float(values[5])
kbo._H = float(values[6])
epoch = ephem.date(2453157.50000 - ephem.julian_date(0))
kbo._epoch_M = epoch
kbo._epoch = epoch
kbos.append(kbo)
return kbos | python | def _kbos_from_survey_sym_model_input_file(model_file):
"""
Load a Survey Simulator model file as an array of ephem EllipticalBody objects.
@param model_file:
@return:
"""
lines = storage.open_vos_or_local(model_file).read().split('\n')
kbos = []
for line in lines:
if len(line) == 0 or line[0] == '#': # skip initial column descriptors and the final blank line
continue
kbo = ephem.EllipticalBody()
values = line.split()
kbo.name = values[8]
kbo.j = values[9]
kbo.k = values[10]
kbo._a = float(values[0])
kbo._e = float(values[1])
kbo._inc = float(values[2])
kbo._Om = float(values[3])
kbo._om = float(values[4])
kbo._M = float(values[5])
kbo._H = float(values[6])
epoch = ephem.date(2453157.50000 - ephem.julian_date(0))
kbo._epoch_M = epoch
kbo._epoch = epoch
kbos.append(kbo)
return kbos | [
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OSSOS/MOP | src/ossos/core/ossos/parsers.py | round_sig_error | def round_sig_error(num, uncert, pm=False):
"""
Return a string of the number and its uncertainty to the right sig figs via uncertainty's print methods.
The uncertainty determines the sig fig rounding of the number.
https://pythonhosted.org/uncertainties/user_guide.html
"""
u = ufloat(num, uncert)
if pm:
return '{:.1uL}'.format(u)
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return '{:.1uLS}'.format(u) | python | def round_sig_error(num, uncert, pm=False):
"""
Return a string of the number and its uncertainty to the right sig figs via uncertainty's print methods.
The uncertainty determines the sig fig rounding of the number.
https://pythonhosted.org/uncertainties/user_guide.html
"""
u = ufloat(num, uncert)
if pm:
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else:
return '{:.1uLS}'.format(u) | [
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openstack/python-scciclient | scciclient/irmc/elcm.py | _parse_elcm_response_body_as_json | def _parse_elcm_response_body_as_json(response):
"""parse eLCM response body as json data
eLCM response should be in form of:
_
Key1: value1 <-- optional -->
Key2: value2 <-- optional -->
KeyN: valueN <-- optional -->
- CRLF -
JSON string
-
:param response: eLCM response
:return: json object if success
:raise ELCMInvalidResponse: if the response does not contain valid
json data.
"""
try:
body = response.text
body_parts = body.split('\r\n')
if len(body_parts) > 0:
return jsonutils.loads(body_parts[-1])
else:
return None
except (TypeError, ValueError):
raise ELCMInvalidResponse('eLCM response does not contain valid json '
'data. Response is "%s".' % body) | python | def _parse_elcm_response_body_as_json(response):
"""parse eLCM response body as json data
eLCM response should be in form of:
_
Key1: value1 <-- optional -->
Key2: value2 <-- optional -->
KeyN: valueN <-- optional -->
- CRLF -
JSON string
-
:param response: eLCM response
:return: json object if success
:raise ELCMInvalidResponse: if the response does not contain valid
json data.
"""
try:
body = response.text
body_parts = body.split('\r\n')
if len(body_parts) > 0:
return jsonutils.loads(body_parts[-1])
else:
return None
except (TypeError, ValueError):
raise ELCMInvalidResponse('eLCM response does not contain valid json '
'data. Response is "%s".' % body) | [
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openstack/python-scciclient | scciclient/irmc/elcm.py | elcm_request | def elcm_request(irmc_info, method, path, **kwargs):
"""send an eLCM request to the server
:param irmc_info: dict of iRMC params to access the server node
{
'irmc_address': host,
'irmc_username': user_id,
'irmc_password': password,
'irmc_port': 80 or 443, default is 443,
'irmc_auth_method': 'basic' or 'digest', default is 'basic',
'irmc_client_timeout': timeout, default is 60,
...
}
:param method: request method such as 'GET', 'POST'
:param path: url path for eLCM request
:returns: requests.Response from SCCI server
:raises SCCIInvalidInputError: if port and/or auth_method params
are invalid
:raises SCCIClientError: if SCCI failed
"""
host = irmc_info['irmc_address']
port = irmc_info.get('irmc_port', 443)
auth_method = irmc_info.get('irmc_auth_method', 'basic')
userid = irmc_info['irmc_username']
password = irmc_info['irmc_password']
client_timeout = irmc_info.get('irmc_client_timeout', 60)
# Request headers, params, and data
headers = kwargs.get('headers', {'Accept': 'application/json'})
params = kwargs.get('params')
data = kwargs.get('data')
auth_obj = None
try:
protocol = {80: 'http', 443: 'https'}[port]
auth_obj = {
'basic': requests.auth.HTTPBasicAuth(userid, password),
'digest': requests.auth.HTTPDigestAuth(userid, password)
}[auth_method.lower()]
except KeyError:
raise scci.SCCIInvalidInputError(
("Invalid port %(port)d or " +
"auth_method for method %(auth_method)s") %
{'port': port, 'auth_method': auth_method})
try:
r = requests.request(method,
protocol + '://' + host + path,
headers=headers,
params=params,
data=data,
verify=False,
timeout=client_timeout,
allow_redirects=False,
auth=auth_obj)
except requests.exceptions.RequestException as requests_exception:
raise scci.SCCIClientError(requests_exception)
# Process status_code 401
if r.status_code == 401:
raise scci.SCCIClientError('UNAUTHORIZED')
return r | python | def elcm_request(irmc_info, method, path, **kwargs):
"""send an eLCM request to the server
:param irmc_info: dict of iRMC params to access the server node
{
'irmc_address': host,
'irmc_username': user_id,
'irmc_password': password,
'irmc_port': 80 or 443, default is 443,
'irmc_auth_method': 'basic' or 'digest', default is 'basic',
'irmc_client_timeout': timeout, default is 60,
...
}
:param method: request method such as 'GET', 'POST'
:param path: url path for eLCM request
:returns: requests.Response from SCCI server
:raises SCCIInvalidInputError: if port and/or auth_method params
are invalid
:raises SCCIClientError: if SCCI failed
"""
host = irmc_info['irmc_address']
port = irmc_info.get('irmc_port', 443)
auth_method = irmc_info.get('irmc_auth_method', 'basic')
userid = irmc_info['irmc_username']
password = irmc_info['irmc_password']
client_timeout = irmc_info.get('irmc_client_timeout', 60)
# Request headers, params, and data
headers = kwargs.get('headers', {'Accept': 'application/json'})
params = kwargs.get('params')
data = kwargs.get('data')
auth_obj = None
try:
protocol = {80: 'http', 443: 'https'}[port]
auth_obj = {
'basic': requests.auth.HTTPBasicAuth(userid, password),
'digest': requests.auth.HTTPDigestAuth(userid, password)
}[auth_method.lower()]
except KeyError:
raise scci.SCCIInvalidInputError(
("Invalid port %(port)d or " +
"auth_method for method %(auth_method)s") %
{'port': port, 'auth_method': auth_method})
try:
r = requests.request(method,
protocol + '://' + host + path,
headers=headers,
params=params,
data=data,
verify=False,
timeout=client_timeout,
allow_redirects=False,
auth=auth_obj)
except requests.exceptions.RequestException as requests_exception:
raise scci.SCCIClientError(requests_exception)
# Process status_code 401
if r.status_code == 401:
raise scci.SCCIClientError('UNAUTHORIZED')
return r | [
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:param irmc_info: dict of iRMC params to access the server node
{
'irmc_address': host,
'irmc_username': user_id,
'irmc_password': password,
'irmc_port': 80 or 443, default is 443,
'irmc_auth_method': 'basic' or 'digest', default is 'basic',
'irmc_client_timeout': timeout, default is 60,
...
}
:param method: request method such as 'GET', 'POST'
:param path: url path for eLCM request
:returns: requests.Response from SCCI server
:raises SCCIInvalidInputError: if port and/or auth_method params
are invalid
:raises SCCIClientError: if SCCI failed | [
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openstack/python-scciclient | scciclient/irmc/elcm.py | elcm_profile_get_versions | def elcm_profile_get_versions(irmc_info):
"""send an eLCM request to get profile versions
:param irmc_info: node info
:returns: dict object of profiles if succeed
{
"Server":{
"@Version": "1.01",
"AdapterConfigIrmc":{
"@Version": "1.00"
},
"HWConfigurationIrmc":{
"@Version": "1.00"
},
"SystemConfig":{
"IrmcConfig":{
"@Version": "1.02"
},
"BiosConfig":{
"@Version": "1.02"
}
}
}
}
:raises: SCCIClientError if SCCI failed
"""
# Send GET request to the server
resp = elcm_request(irmc_info,
method='GET',
path=URL_PATH_PROFILE_MGMT + 'version')
if resp.status_code == 200:
return _parse_elcm_response_body_as_json(resp)
else:
raise scci.SCCIClientError(('Failed to get profile versions with '
'error code %s' % resp.status_code)) | python | def elcm_profile_get_versions(irmc_info):
"""send an eLCM request to get profile versions
:param irmc_info: node info
:returns: dict object of profiles if succeed
{
"Server":{
"@Version": "1.01",
"AdapterConfigIrmc":{
"@Version": "1.00"
},
"HWConfigurationIrmc":{
"@Version": "1.00"
},
"SystemConfig":{
"IrmcConfig":{
"@Version": "1.02"
},
"BiosConfig":{
"@Version": "1.02"
}
}
}
}
:raises: SCCIClientError if SCCI failed
"""
# Send GET request to the server
resp = elcm_request(irmc_info,
method='GET',
path=URL_PATH_PROFILE_MGMT + 'version')
if resp.status_code == 200:
return _parse_elcm_response_body_as_json(resp)
else:
raise scci.SCCIClientError(('Failed to get profile versions with '
'error code %s' % resp.status_code)) | [
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openstack/python-scciclient | scciclient/irmc/elcm.py | elcm_profile_get | def elcm_profile_get(irmc_info, profile_name):
"""send an eLCM request to get profile data
:param irmc_info: node info
:param profile_name: name of profile
:returns: dict object of profile data if succeed
:raises: ELCMProfileNotFound if profile does not exist
:raises: SCCIClientError if SCCI failed
"""
# Send GET request to the server
resp = elcm_request(irmc_info,
method='GET',
path=URL_PATH_PROFILE_MGMT + profile_name)
if resp.status_code == 200:
return _parse_elcm_response_body_as_json(resp)
elif resp.status_code == 404:
raise ELCMProfileNotFound('Profile "%s" not found '
'in the profile store.' % profile_name)
else:
raise scci.SCCIClientError(('Failed to get profile "%(profile)s" with '
'error code %(error)s' %
{'profile': profile_name,
'error': resp.status_code})) | python | def elcm_profile_get(irmc_info, profile_name):
"""send an eLCM request to get profile data
:param irmc_info: node info
:param profile_name: name of profile
:returns: dict object of profile data if succeed
:raises: ELCMProfileNotFound if profile does not exist
:raises: SCCIClientError if SCCI failed
"""
# Send GET request to the server
resp = elcm_request(irmc_info,
method='GET',
path=URL_PATH_PROFILE_MGMT + profile_name)
if resp.status_code == 200:
return _parse_elcm_response_body_as_json(resp)
elif resp.status_code == 404:
raise ELCMProfileNotFound('Profile "%s" not found '
'in the profile store.' % profile_name)
else:
raise scci.SCCIClientError(('Failed to get profile "%(profile)s" with '
'error code %(error)s' %
{'profile': profile_name,
'error': resp.status_code})) | [
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openstack/python-scciclient | scciclient/irmc/elcm.py | elcm_profile_create | def elcm_profile_create(irmc_info, param_path):
"""send an eLCM request to create profile
To create a profile, a new session is spawned with status 'running'.
When profile is created completely, the session ends.
:param irmc_info: node info
:param param_path: path of profile
:returns: dict object of session info if succeed
{
'Session':
{
'Id': id
'Status': 'activated'
...
}
}
:raises: SCCIClientError if SCCI failed
"""
# Send POST request to the server
# NOTE: This task may take time, so set a timeout
_irmc_info = dict(irmc_info)
_irmc_info['irmc_client_timeout'] = PROFILE_CREATE_TIMEOUT
resp = elcm_request(_irmc_info,
method='POST',
path=URL_PATH_PROFILE_MGMT + 'get',
params={'PARAM_PATH': param_path})
if resp.status_code == 202:
return _parse_elcm_response_body_as_json(resp)
else:
raise scci.SCCIClientError(('Failed to create profile for path '
'"%(param_path)s" with error code '
'%(error)s' %
{'param_path': param_path,
'error': resp.status_code})) | python | def elcm_profile_create(irmc_info, param_path):
"""send an eLCM request to create profile
To create a profile, a new session is spawned with status 'running'.
When profile is created completely, the session ends.
:param irmc_info: node info
:param param_path: path of profile
:returns: dict object of session info if succeed
{
'Session':
{
'Id': id
'Status': 'activated'
...
}
}
:raises: SCCIClientError if SCCI failed
"""
# Send POST request to the server
# NOTE: This task may take time, so set a timeout
_irmc_info = dict(irmc_info)
_irmc_info['irmc_client_timeout'] = PROFILE_CREATE_TIMEOUT
resp = elcm_request(_irmc_info,
method='POST',
path=URL_PATH_PROFILE_MGMT + 'get',
params={'PARAM_PATH': param_path})
if resp.status_code == 202:
return _parse_elcm_response_body_as_json(resp)
else:
raise scci.SCCIClientError(('Failed to create profile for path '
'"%(param_path)s" with error code '
'%(error)s' %
{'param_path': param_path,
'error': resp.status_code})) | [
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openstack/python-scciclient | scciclient/irmc/elcm.py | elcm_profile_set | def elcm_profile_set(irmc_info, input_data):
"""send an eLCM request to set param values
To apply param values, a new session is spawned with status 'running'.
When values are applied or error, the session ends.
:param irmc_info: node info
:param input_data: param values to apply, eg.
{
'Server':
{
'SystemConfig':
{
'BiosConfig':
{
'@Processing': 'execute',
-- config data --
}
}
}
}
:returns: dict object of session info if succeed
{
'Session':
{
'Id': id
'Status': 'activated'
...
}
}
:raises: SCCIClientError if SCCI failed
"""
# Prepare the data to apply
if isinstance(input_data, dict):
data = jsonutils.dumps(input_data)
else:
data = input_data
# Send POST request to the server
# NOTE: This task may take time, so set a timeout
_irmc_info = dict(irmc_info)
_irmc_info['irmc_client_timeout'] = PROFILE_SET_TIMEOUT
content_type = 'application/x-www-form-urlencoded'
if input_data['Server'].get('HWConfigurationIrmc'):
content_type = 'application/json'
resp = elcm_request(_irmc_info,
method='POST',
path=URL_PATH_PROFILE_MGMT + 'set',
headers={'Content-type': content_type},
data=data)
if resp.status_code == 202:
return _parse_elcm_response_body_as_json(resp)
else:
raise scci.SCCIClientError(('Failed to apply param values with '
'error code %(error)s' %
{'error': resp.status_code})) | python | def elcm_profile_set(irmc_info, input_data):
"""send an eLCM request to set param values
To apply param values, a new session is spawned with status 'running'.
When values are applied or error, the session ends.
:param irmc_info: node info
:param input_data: param values to apply, eg.
{
'Server':
{
'SystemConfig':
{
'BiosConfig':
{
'@Processing': 'execute',
-- config data --
}
}
}
}
:returns: dict object of session info if succeed
{
'Session':
{
'Id': id
'Status': 'activated'
...
}
}
:raises: SCCIClientError if SCCI failed
"""
# Prepare the data to apply
if isinstance(input_data, dict):
data = jsonutils.dumps(input_data)
else:
data = input_data
# Send POST request to the server
# NOTE: This task may take time, so set a timeout
_irmc_info = dict(irmc_info)
_irmc_info['irmc_client_timeout'] = PROFILE_SET_TIMEOUT
content_type = 'application/x-www-form-urlencoded'
if input_data['Server'].get('HWConfigurationIrmc'):
content_type = 'application/json'
resp = elcm_request(_irmc_info,
method='POST',
path=URL_PATH_PROFILE_MGMT + 'set',
headers={'Content-type': content_type},
data=data)
if resp.status_code == 202:
return _parse_elcm_response_body_as_json(resp)
else:
raise scci.SCCIClientError(('Failed to apply param values with '
'error code %(error)s' %
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openstack/python-scciclient | scciclient/irmc/elcm.py | elcm_profile_delete | def elcm_profile_delete(irmc_info, profile_name):
"""send an eLCM request to delete a profile
:param irmc_info: node info
:param profile_name: name of profile
:raises: ELCMProfileNotFound if the profile does not exist
:raises: SCCIClientError if SCCI failed
"""
# Send DELETE request to the server
resp = elcm_request(irmc_info,
method='DELETE',
path=URL_PATH_PROFILE_MGMT + profile_name)
if resp.status_code == 200:
# Profile deleted
return
elif resp.status_code == 404:
# Profile not found
raise ELCMProfileNotFound('Profile "%s" not found '
'in the profile store.' % profile_name)
else:
raise scci.SCCIClientError(('Failed to delete profile "%(profile)s" '
'with error code %(error)s' %
{'profile': profile_name,
'error': resp.status_code})) | python | def elcm_profile_delete(irmc_info, profile_name):
"""send an eLCM request to delete a profile
:param irmc_info: node info
:param profile_name: name of profile
:raises: ELCMProfileNotFound if the profile does not exist
:raises: SCCIClientError if SCCI failed
"""
# Send DELETE request to the server
resp = elcm_request(irmc_info,
method='DELETE',
path=URL_PATH_PROFILE_MGMT + profile_name)
if resp.status_code == 200:
# Profile deleted
return
elif resp.status_code == 404:
# Profile not found
raise ELCMProfileNotFound('Profile "%s" not found '
'in the profile store.' % profile_name)
else:
raise scci.SCCIClientError(('Failed to delete profile "%(profile)s" '
'with error code %(error)s' %
{'profile': profile_name,
'error': resp.status_code})) | [
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openstack/python-scciclient | scciclient/irmc/elcm.py | elcm_session_list | def elcm_session_list(irmc_info):
"""send an eLCM request to list all sessions
:param irmc_info: node info
:returns: dict object of sessions if succeed
{
'SessionList':
{
'Contains':
[
{ 'Id': id1, 'Name': name1 },
{ 'Id': id2, 'Name': name2 },
{ 'Id': idN, 'Name': nameN },
]
}
}
:raises: SCCIClientError if SCCI failed
"""
# Send GET request to the server
resp = elcm_request(irmc_info,
method='GET',
path='/sessionInformation/')
if resp.status_code == 200:
return _parse_elcm_response_body_as_json(resp)
else:
raise scci.SCCIClientError(('Failed to list sessions with '
'error code %s' % resp.status_code)) | python | def elcm_session_list(irmc_info):
"""send an eLCM request to list all sessions
:param irmc_info: node info
:returns: dict object of sessions if succeed
{
'SessionList':
{
'Contains':
[
{ 'Id': id1, 'Name': name1 },
{ 'Id': id2, 'Name': name2 },
{ 'Id': idN, 'Name': nameN },
]
}
}
:raises: SCCIClientError if SCCI failed
"""
# Send GET request to the server
resp = elcm_request(irmc_info,
method='GET',
path='/sessionInformation/')
if resp.status_code == 200:
return _parse_elcm_response_body_as_json(resp)
else:
raise scci.SCCIClientError(('Failed to list sessions with '
'error code %s' % resp.status_code)) | [
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openstack/python-scciclient | scciclient/irmc/elcm.py | elcm_session_get_status | def elcm_session_get_status(irmc_info, session_id):
"""send an eLCM request to get session status
:param irmc_info: node info
:param session_id: session id
:returns: dict object of session info if succeed
{
'Session':
{
'Id': id
'Status': status
...
}
}
:raises: ELCMSessionNotFound if the session does not exist
:raises: SCCIClientError if SCCI failed
"""
# Send GET request to the server
resp = elcm_request(irmc_info,
method='GET',
path='/sessionInformation/%s/status' % session_id)
if resp.status_code == 200:
return _parse_elcm_response_body_as_json(resp)
elif resp.status_code == 404:
raise ELCMSessionNotFound('Session "%s" does not exist' % session_id)
else:
raise scci.SCCIClientError(('Failed to get status of session '
'"%(session)s" with error code %(error)s' %
{'session': session_id,
'error': resp.status_code})) | python | def elcm_session_get_status(irmc_info, session_id):
"""send an eLCM request to get session status
:param irmc_info: node info
:param session_id: session id
:returns: dict object of session info if succeed
{
'Session':
{
'Id': id
'Status': status
...
}
}
:raises: ELCMSessionNotFound if the session does not exist
:raises: SCCIClientError if SCCI failed
"""
# Send GET request to the server
resp = elcm_request(irmc_info,
method='GET',
path='/sessionInformation/%s/status' % session_id)
if resp.status_code == 200:
return _parse_elcm_response_body_as_json(resp)
elif resp.status_code == 404:
raise ELCMSessionNotFound('Session "%s" does not exist' % session_id)
else:
raise scci.SCCIClientError(('Failed to get status of session '
'"%(session)s" with error code %(error)s' %
{'session': session_id,
'error': resp.status_code})) | [
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openstack/python-scciclient | scciclient/irmc/elcm.py | elcm_session_terminate | def elcm_session_terminate(irmc_info, session_id):
"""send an eLCM request to terminate a session
:param irmc_info: node info
:param session_id: session id
:raises: ELCMSessionNotFound if the session does not exist
:raises: SCCIClientError if SCCI failed
"""
# Send DELETE request to the server
resp = elcm_request(irmc_info,
method='DELETE',
path='/sessionInformation/%s/terminate' % session_id)
if resp.status_code == 200:
return
elif resp.status_code == 404:
raise ELCMSessionNotFound('Session "%s" does not exist' % session_id)
else:
raise scci.SCCIClientError(('Failed to terminate session '
'"%(session)s" with error code %(error)s' %
{'session': session_id,
'error': resp.status_code})) | python | def elcm_session_terminate(irmc_info, session_id):
"""send an eLCM request to terminate a session
:param irmc_info: node info
:param session_id: session id
:raises: ELCMSessionNotFound if the session does not exist
:raises: SCCIClientError if SCCI failed
"""
# Send DELETE request to the server
resp = elcm_request(irmc_info,
method='DELETE',
path='/sessionInformation/%s/terminate' % session_id)
if resp.status_code == 200:
return
elif resp.status_code == 404:
raise ELCMSessionNotFound('Session "%s" does not exist' % session_id)
else:
raise scci.SCCIClientError(('Failed to terminate session '
'"%(session)s" with error code %(error)s' %
{'session': session_id,
'error': resp.status_code})) | [
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openstack/python-scciclient | scciclient/irmc/elcm.py | elcm_session_delete | def elcm_session_delete(irmc_info, session_id, terminate=False):
"""send an eLCM request to remove a session from the session list
:param irmc_info: node info
:param session_id: session id
:param terminate: a running session must be terminated before removing
:raises: ELCMSessionNotFound if the session does not exist
:raises: SCCIClientError if SCCI failed
"""
# Terminate the session first if needs to
if terminate:
# Get session status to check
session = elcm_session_get_status(irmc_info, session_id)
status = session['Session']['Status']
# Terminate session if it is activated or running
if status == 'running' or status == 'activated':
elcm_session_terminate(irmc_info, session_id)
# Send DELETE request to the server
resp = elcm_request(irmc_info,
method='DELETE',
path='/sessionInformation/%s/remove' % session_id)
if resp.status_code == 200:
return
elif resp.status_code == 404:
raise ELCMSessionNotFound('Session "%s" does not exist' % session_id)
else:
raise scci.SCCIClientError(('Failed to remove session '
'"%(session)s" with error code %(error)s' %
{'session': session_id,
'error': resp.status_code})) | python | def elcm_session_delete(irmc_info, session_id, terminate=False):
"""send an eLCM request to remove a session from the session list
:param irmc_info: node info
:param session_id: session id
:param terminate: a running session must be terminated before removing
:raises: ELCMSessionNotFound if the session does not exist
:raises: SCCIClientError if SCCI failed
"""
# Terminate the session first if needs to
if terminate:
# Get session status to check
session = elcm_session_get_status(irmc_info, session_id)
status = session['Session']['Status']
# Terminate session if it is activated or running
if status == 'running' or status == 'activated':
elcm_session_terminate(irmc_info, session_id)
# Send DELETE request to the server
resp = elcm_request(irmc_info,
method='DELETE',
path='/sessionInformation/%s/remove' % session_id)
if resp.status_code == 200:
return
elif resp.status_code == 404:
raise ELCMSessionNotFound('Session "%s" does not exist' % session_id)
else:
raise scci.SCCIClientError(('Failed to remove session '
'"%(session)s" with error code %(error)s' %
{'session': session_id,
'error': resp.status_code})) | [
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openstack/python-scciclient | scciclient/irmc/elcm.py | _process_session_data | def _process_session_data(irmc_info, operation, session_id,
session_timeout=BIOS_CONFIG_SESSION_TIMEOUT):
"""process session for Bios config backup/restore or RAID config operation
:param irmc_info: node info
:param operation: one of 'BACKUP_BIOS', 'RESTORE_BIOS' or 'CONFIG_RAID'
:param session_id: session id
:param session_timeout: session timeout
:return: a dict with following values:
{
'bios_config': <data in case of BACKUP/RESTORE_BIOS operation>,
'warning': <warning message if there is>
}
or
{
'raid_config': <data of raid adapter profile>,
'warning': <warning message if there is>
}
"""
session_expiration = time.time() + session_timeout
while time.time() < session_expiration:
# Get session status to check
session = elcm_session_get_status(irmc_info=irmc_info,
session_id=session_id)
status = session['Session']['Status']
if status == 'running' or status == 'activated':
# Sleep a bit
time.sleep(5)
elif status == 'terminated regularly':
result = {}
if operation == 'BACKUP_BIOS':
# Bios profile is created, get the data now
result['bios_config'] = elcm_profile_get(
irmc_info=irmc_info,
profile_name=PROFILE_BIOS_CONFIG)
elif operation == 'RESTORE_BIOS':
# Bios config applied successfully
pass
elif operation == 'CONFIG_RAID':
# Getting raid config
result['raid_config'] = elcm_profile_get(irmc_info,
PROFILE_RAID_CONFIG)
# Cleanup operation by deleting related session and profile.
# In case of error, report it as warning instead of error.
try:
elcm_session_delete(irmc_info=irmc_info,
session_id=session_id,
terminate=True)
if operation == 'CONFIG_RAID':
return result
elcm_profile_delete(irmc_info=irmc_info,
profile_name=PROFILE_BIOS_CONFIG)
except scci.SCCIError as e:
result['warning'] = e
return result
else:
# Error occurred, get session log to see what happened
session_log = elcm_session_get_log(irmc_info=irmc_info,
session_id=session_id)
raise scci.SCCIClientError(
('Failed to %(operation)s config. '
'Session log is "%(session_log)s".' %
{'operation': operation,
'session_log': jsonutils.dumps(session_log)}))
else:
raise ELCMSessionTimeout(
('Failed to %(operation)s config. '
'Session %(session_id)s log is timeout.' %
{'operation': operation,
'session_id': session_id})) | python | def _process_session_data(irmc_info, operation, session_id,
session_timeout=BIOS_CONFIG_SESSION_TIMEOUT):
"""process session for Bios config backup/restore or RAID config operation
:param irmc_info: node info
:param operation: one of 'BACKUP_BIOS', 'RESTORE_BIOS' or 'CONFIG_RAID'
:param session_id: session id
:param session_timeout: session timeout
:return: a dict with following values:
{
'bios_config': <data in case of BACKUP/RESTORE_BIOS operation>,
'warning': <warning message if there is>
}
or
{
'raid_config': <data of raid adapter profile>,
'warning': <warning message if there is>
}
"""
session_expiration = time.time() + session_timeout
while time.time() < session_expiration:
# Get session status to check
session = elcm_session_get_status(irmc_info=irmc_info,
session_id=session_id)
status = session['Session']['Status']
if status == 'running' or status == 'activated':
# Sleep a bit
time.sleep(5)
elif status == 'terminated regularly':
result = {}
if operation == 'BACKUP_BIOS':
# Bios profile is created, get the data now
result['bios_config'] = elcm_profile_get(
irmc_info=irmc_info,
profile_name=PROFILE_BIOS_CONFIG)
elif operation == 'RESTORE_BIOS':
# Bios config applied successfully
pass
elif operation == 'CONFIG_RAID':
# Getting raid config
result['raid_config'] = elcm_profile_get(irmc_info,
PROFILE_RAID_CONFIG)
# Cleanup operation by deleting related session and profile.
# In case of error, report it as warning instead of error.
try:
elcm_session_delete(irmc_info=irmc_info,
session_id=session_id,
terminate=True)
if operation == 'CONFIG_RAID':
return result
elcm_profile_delete(irmc_info=irmc_info,
profile_name=PROFILE_BIOS_CONFIG)
except scci.SCCIError as e:
result['warning'] = e
return result
else:
# Error occurred, get session log to see what happened
session_log = elcm_session_get_log(irmc_info=irmc_info,
session_id=session_id)
raise scci.SCCIClientError(
('Failed to %(operation)s config. '
'Session log is "%(session_log)s".' %
{'operation': operation,
'session_log': jsonutils.dumps(session_log)}))
else:
raise ELCMSessionTimeout(
('Failed to %(operation)s config. '
'Session %(session_id)s log is timeout.' %
{'operation': operation,
'session_id': session_id})) | [
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:param session_id: session id
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openstack/python-scciclient | scciclient/irmc/elcm.py | backup_bios_config | def backup_bios_config(irmc_info):
"""backup current bios configuration
This function sends a BACKUP BIOS request to the server. Then when the bios
config data are ready for retrieving, it will return the data to the
caller. Note that this operation may take time.
:param irmc_info: node info
:return: a dict with following values:
{
'bios_config': <bios config data>,
'warning': <warning message if there is>
}
"""
# 1. Make sure there is no BiosConfig profile in the store
try:
# Get the profile first, if not found, then an exception
# will be raised.
elcm_profile_get(irmc_info=irmc_info,
profile_name=PROFILE_BIOS_CONFIG)
# Profile found, delete it
elcm_profile_delete(irmc_info=irmc_info,
profile_name=PROFILE_BIOS_CONFIG)
except ELCMProfileNotFound:
# Ignore this error as it's not an error in this case
pass
# 2. Send request to create a new profile for BiosConfig
session = elcm_profile_create(irmc_info=irmc_info,
param_path=PARAM_PATH_BIOS_CONFIG)
# 3. Profile creation is in progress, we monitor the session
session_timeout = irmc_info.get('irmc_bios_session_timeout',
BIOS_CONFIG_SESSION_TIMEOUT)
return _process_session_data(
irmc_info=irmc_info,
operation='BACKUP_BIOS',
session_id=session['Session']['Id'],
session_timeout=session_timeout) | python | def backup_bios_config(irmc_info):
"""backup current bios configuration
This function sends a BACKUP BIOS request to the server. Then when the bios
config data are ready for retrieving, it will return the data to the
caller. Note that this operation may take time.
:param irmc_info: node info
:return: a dict with following values:
{
'bios_config': <bios config data>,
'warning': <warning message if there is>
}
"""
# 1. Make sure there is no BiosConfig profile in the store
try:
# Get the profile first, if not found, then an exception
# will be raised.
elcm_profile_get(irmc_info=irmc_info,
profile_name=PROFILE_BIOS_CONFIG)
# Profile found, delete it
elcm_profile_delete(irmc_info=irmc_info,
profile_name=PROFILE_BIOS_CONFIG)
except ELCMProfileNotFound:
# Ignore this error as it's not an error in this case
pass
# 2. Send request to create a new profile for BiosConfig
session = elcm_profile_create(irmc_info=irmc_info,
param_path=PARAM_PATH_BIOS_CONFIG)
# 3. Profile creation is in progress, we monitor the session
session_timeout = irmc_info.get('irmc_bios_session_timeout',
BIOS_CONFIG_SESSION_TIMEOUT)
return _process_session_data(
irmc_info=irmc_info,
operation='BACKUP_BIOS',
session_id=session['Session']['Id'],
session_timeout=session_timeout) | [
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:param irmc_info: node info
:return: a dict with following values:
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openstack/python-scciclient | scciclient/irmc/elcm.py | restore_bios_config | def restore_bios_config(irmc_info, bios_config):
"""restore bios configuration
This function sends a RESTORE BIOS request to the server. Then when the
bios
is ready for restoring, it will apply the provided settings and return.
Note that this operation may take time.
:param irmc_info: node info
:param bios_config: bios config
"""
def _process_bios_config():
try:
if isinstance(bios_config, dict):
input_data = bios_config
else:
input_data = jsonutils.loads(bios_config)
# The input data must contain flag "@Processing":"execute" in the
# equivalent section.
bios_cfg = input_data['Server']['SystemConfig']['BiosConfig']
bios_cfg['@Processing'] = 'execute'
return input_data
except (TypeError, ValueError, KeyError):
raise scci.SCCIInvalidInputError(
('Invalid input bios config "%s".' % bios_config))
# 1. Parse the bios config and create the input data
input_data = _process_bios_config()
# 2. Make sure there is no BiosConfig profile in the store
try:
# Get the profile first, if not found, then an exception
# will be raised.
elcm_profile_get(irmc_info=irmc_info,
profile_name=PROFILE_BIOS_CONFIG)
# Profile found, delete it
elcm_profile_delete(irmc_info=irmc_info,
profile_name=PROFILE_BIOS_CONFIG)
except ELCMProfileNotFound:
# Ignore this error as it's not an error in this case
pass
# 3. Send a request to apply the param values
session = elcm_profile_set(irmc_info=irmc_info,
input_data=input_data)
# 4. Param values applying is in progress, we monitor the session
session_timeout = irmc_info.get('irmc_bios_session_timeout',
BIOS_CONFIG_SESSION_TIMEOUT)
_process_session_data(irmc_info=irmc_info,
operation='RESTORE_BIOS',
session_id=session['Session']['Id'],
session_timeout=session_timeout) | python | def restore_bios_config(irmc_info, bios_config):
"""restore bios configuration
This function sends a RESTORE BIOS request to the server. Then when the
bios
is ready for restoring, it will apply the provided settings and return.
Note that this operation may take time.
:param irmc_info: node info
:param bios_config: bios config
"""
def _process_bios_config():
try:
if isinstance(bios_config, dict):
input_data = bios_config
else:
input_data = jsonutils.loads(bios_config)
# The input data must contain flag "@Processing":"execute" in the
# equivalent section.
bios_cfg = input_data['Server']['SystemConfig']['BiosConfig']
bios_cfg['@Processing'] = 'execute'
return input_data
except (TypeError, ValueError, KeyError):
raise scci.SCCIInvalidInputError(
('Invalid input bios config "%s".' % bios_config))
# 1. Parse the bios config and create the input data
input_data = _process_bios_config()
# 2. Make sure there is no BiosConfig profile in the store
try:
# Get the profile first, if not found, then an exception
# will be raised.
elcm_profile_get(irmc_info=irmc_info,
profile_name=PROFILE_BIOS_CONFIG)
# Profile found, delete it
elcm_profile_delete(irmc_info=irmc_info,
profile_name=PROFILE_BIOS_CONFIG)
except ELCMProfileNotFound:
# Ignore this error as it's not an error in this case
pass
# 3. Send a request to apply the param values
session = elcm_profile_set(irmc_info=irmc_info,
input_data=input_data)
# 4. Param values applying is in progress, we monitor the session
session_timeout = irmc_info.get('irmc_bios_session_timeout',
BIOS_CONFIG_SESSION_TIMEOUT)
_process_session_data(irmc_info=irmc_info,
operation='RESTORE_BIOS',
session_id=session['Session']['Id'],
session_timeout=session_timeout) | [
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:param irmc_info: node info
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openstack/python-scciclient | scciclient/irmc/elcm.py | get_secure_boot_mode | def get_secure_boot_mode(irmc_info):
"""Get the status if secure boot is enabled or not.
:param irmc_info: node info.
:raises: SecureBootConfigNotFound, if there is no configuration for secure
boot mode in the bios.
:return: True if secure boot mode is enabled on the node, False otherwise.
"""
result = backup_bios_config(irmc_info=irmc_info)
try:
bioscfg = result['bios_config']['Server']['SystemConfig']['BiosConfig']
return bioscfg['SecurityConfig']['SecureBootControlEnabled']
except KeyError:
msg = ("Failed to get secure boot mode from server %s. Upgrading iRMC "
"firmware may resolve this issue." % irmc_info['irmc_address'])
raise SecureBootConfigNotFound(msg) | python | def get_secure_boot_mode(irmc_info):
"""Get the status if secure boot is enabled or not.
:param irmc_info: node info.
:raises: SecureBootConfigNotFound, if there is no configuration for secure
boot mode in the bios.
:return: True if secure boot mode is enabled on the node, False otherwise.
"""
result = backup_bios_config(irmc_info=irmc_info)
try:
bioscfg = result['bios_config']['Server']['SystemConfig']['BiosConfig']
return bioscfg['SecurityConfig']['SecureBootControlEnabled']
except KeyError:
msg = ("Failed to get secure boot mode from server %s. Upgrading iRMC "
"firmware may resolve this issue." % irmc_info['irmc_address'])
raise SecureBootConfigNotFound(msg) | [
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openstack/python-scciclient | scciclient/irmc/elcm.py | set_secure_boot_mode | def set_secure_boot_mode(irmc_info, enable):
"""Enable/Disable secure boot on the server.
:param irmc_info: node info
:param enable: True, if secure boot needs to be
enabled for next boot, else False.
"""
bios_config_data = {
'Server': {
'@Version': '1.01',
'SystemConfig': {
'BiosConfig': {
'@Version': '1.01',
'SecurityConfig': {
'SecureBootControlEnabled': enable
}
}
}
}
}
restore_bios_config(irmc_info=irmc_info, bios_config=bios_config_data) | python | def set_secure_boot_mode(irmc_info, enable):
"""Enable/Disable secure boot on the server.
:param irmc_info: node info
:param enable: True, if secure boot needs to be
enabled for next boot, else False.
"""
bios_config_data = {
'Server': {
'@Version': '1.01',
'SystemConfig': {
'BiosConfig': {
'@Version': '1.01',
'SecurityConfig': {
'SecureBootControlEnabled': enable
}
}
}
}
}
restore_bios_config(irmc_info=irmc_info, bios_config=bios_config_data) | [
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openstack/python-scciclient | scciclient/irmc/elcm.py | _update_raid_input_data | def _update_raid_input_data(target_raid_config, raid_input):
"""Process raid input data.
:param target_raid_config: node raid info
:param raid_input: raid information for creating via eLCM
:raises ELCMValueError: raise msg if wrong input
:return: raid_input: raid input data which create raid configuration
{
"Server":{
"HWConfigurationIrmc":{
"@Processing":"execute",
"Adapters":{
"RAIDAdapter":[
{
"@AdapterId":"RAIDAdapter0",
"@ConfigurationType":"Addressing",
"LogicalDrives":{
"LogicalDrive":[
{
"@Number":0,
"@Action":"Create",
"RaidLevel":"1"
}
]
}
}
]
},
"@Version":"1.00"
},
"@Version":"1.01"
}
}
"""
logical_disk_list = target_raid_config['logical_disks']
raid_input['Server']['HWConfigurationIrmc'].update({'@Processing':
'execute'})
array_info = raid_input['Server']['HWConfigurationIrmc']['Adapters'][
'RAIDAdapter'][0]
array_info['LogicalDrives'] = {'LogicalDrive': []}
array_info['Arrays'] = {'Array': []}
for i, logical_disk in enumerate(logical_disk_list):
physical_disks = logical_disk.get('physical_disks')
# Auto create logical drive along with random physical disks.
# Allow auto create along with raid 10 and raid 50
# with specific physical drive.
if not physical_disks or logical_disk['raid_level'] \
in ('10', '50'):
array_info['LogicalDrives']['LogicalDrive'].append(
{'@Action': 'Create',
'RaidLevel': logical_disk['raid_level'],
'InitMode': 'slow'})
array_info['LogicalDrives']['LogicalDrive'][i].update({
"@Number": i})
else:
# Create array disks with specific physical servers
arrays = {
"@Number": i,
"@ConfigurationType": "Setting",
"PhysicalDiskRefs": {
"PhysicalDiskRef": []
}
}
lo_drive = {
"@Number": i,
"@Action": "Create",
"RaidLevel": "",
"ArrayRefs": {
"ArrayRef": [
]
},
"InitMode": "slow"
}
array_info['Arrays']['Array'].append(arrays)
array_info['LogicalDrives']['LogicalDrive'].append(lo_drive)
lo_drive.update({'RaidLevel': logical_disk['raid_level']})
lo_drive['ArrayRefs']['ArrayRef'].append({"@Number": i})
for element in logical_disk['physical_disks']:
arrays['PhysicalDiskRefs']['PhysicalDiskRef'].append({
'@Number': element})
if logical_disk['size_gb'] != "MAX":
# Ensure correctly order these items in dict
size = collections.OrderedDict()
size['@Unit'] = 'GB'
size['#text'] = logical_disk['size_gb']
array_info['LogicalDrives']['LogicalDrive'][i]['Size'] = size
return raid_input | python | def _update_raid_input_data(target_raid_config, raid_input):
"""Process raid input data.
:param target_raid_config: node raid info
:param raid_input: raid information for creating via eLCM
:raises ELCMValueError: raise msg if wrong input
:return: raid_input: raid input data which create raid configuration
{
"Server":{
"HWConfigurationIrmc":{
"@Processing":"execute",
"Adapters":{
"RAIDAdapter":[
{
"@AdapterId":"RAIDAdapter0",
"@ConfigurationType":"Addressing",
"LogicalDrives":{
"LogicalDrive":[
{
"@Number":0,
"@Action":"Create",
"RaidLevel":"1"
}
]
}
}
]
},
"@Version":"1.00"
},
"@Version":"1.01"
}
}
"""
logical_disk_list = target_raid_config['logical_disks']
raid_input['Server']['HWConfigurationIrmc'].update({'@Processing':
'execute'})
array_info = raid_input['Server']['HWConfigurationIrmc']['Adapters'][
'RAIDAdapter'][0]
array_info['LogicalDrives'] = {'LogicalDrive': []}
array_info['Arrays'] = {'Array': []}
for i, logical_disk in enumerate(logical_disk_list):
physical_disks = logical_disk.get('physical_disks')
# Auto create logical drive along with random physical disks.
# Allow auto create along with raid 10 and raid 50
# with specific physical drive.
if not physical_disks or logical_disk['raid_level'] \
in ('10', '50'):
array_info['LogicalDrives']['LogicalDrive'].append(
{'@Action': 'Create',
'RaidLevel': logical_disk['raid_level'],
'InitMode': 'slow'})
array_info['LogicalDrives']['LogicalDrive'][i].update({
"@Number": i})
else:
# Create array disks with specific physical servers
arrays = {
"@Number": i,
"@ConfigurationType": "Setting",
"PhysicalDiskRefs": {
"PhysicalDiskRef": []
}
}
lo_drive = {
"@Number": i,
"@Action": "Create",
"RaidLevel": "",
"ArrayRefs": {
"ArrayRef": [
]
},
"InitMode": "slow"
}
array_info['Arrays']['Array'].append(arrays)
array_info['LogicalDrives']['LogicalDrive'].append(lo_drive)
lo_drive.update({'RaidLevel': logical_disk['raid_level']})
lo_drive['ArrayRefs']['ArrayRef'].append({"@Number": i})
for element in logical_disk['physical_disks']:
arrays['PhysicalDiskRefs']['PhysicalDiskRef'].append({
'@Number': element})
if logical_disk['size_gb'] != "MAX":
# Ensure correctly order these items in dict
size = collections.OrderedDict()
size['@Unit'] = 'GB'
size['#text'] = logical_disk['size_gb']
array_info['LogicalDrives']['LogicalDrive'][i]['Size'] = size
return raid_input | [
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openstack/python-scciclient | scciclient/irmc/elcm.py | _get_existing_logical_drives | def _get_existing_logical_drives(raid_adapter):
"""Collect existing logical drives on the server.
:param raid_adapter: raid adapter info
:returns: existing_logical_drives: get logical drive on server
"""
existing_logical_drives = []
logical_drives = raid_adapter['Server']['HWConfigurationIrmc'][
'Adapters']['RAIDAdapter'][0].get('LogicalDrives')
if logical_drives is not None:
for drive in logical_drives['LogicalDrive']:
existing_logical_drives.append(drive['@Number'])
return existing_logical_drives | python | def _get_existing_logical_drives(raid_adapter):
"""Collect existing logical drives on the server.
:param raid_adapter: raid adapter info
:returns: existing_logical_drives: get logical drive on server
"""
existing_logical_drives = []
logical_drives = raid_adapter['Server']['HWConfigurationIrmc'][
'Adapters']['RAIDAdapter'][0].get('LogicalDrives')
if logical_drives is not None:
for drive in logical_drives['LogicalDrive']:
existing_logical_drives.append(drive['@Number'])
return existing_logical_drives | [
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openstack/python-scciclient | scciclient/irmc/elcm.py | _create_raid_adapter_profile | def _create_raid_adapter_profile(irmc_info):
"""Attempt delete exist adapter then create new raid adapter on the server.
:param irmc_info: node info
:returns: result: a dict with following values:
{
'raid_config': <data of raid adapter profile>,
'warning': <warning message if there is>
}
"""
try:
# Attempt erase exist adapter on BM Server
elcm_profile_delete(irmc_info, PROFILE_RAID_CONFIG)
except ELCMProfileNotFound:
# Ignore this error as it's not an error in this case
pass
session = elcm_profile_create(irmc_info, PARAM_PATH_RAID_CONFIG)
# Monitoring currently session until done.
session_timeout = irmc_info.get('irmc_raid_session_timeout',
RAID_CONFIG_SESSION_TIMEOUT)
return _process_session_data(irmc_info, 'CONFIG_RAID',
session['Session']['Id'],
session_timeout) | python | def _create_raid_adapter_profile(irmc_info):
"""Attempt delete exist adapter then create new raid adapter on the server.
:param irmc_info: node info
:returns: result: a dict with following values:
{
'raid_config': <data of raid adapter profile>,
'warning': <warning message if there is>
}
"""
try:
# Attempt erase exist adapter on BM Server
elcm_profile_delete(irmc_info, PROFILE_RAID_CONFIG)
except ELCMProfileNotFound:
# Ignore this error as it's not an error in this case
pass
session = elcm_profile_create(irmc_info, PARAM_PATH_RAID_CONFIG)
# Monitoring currently session until done.
session_timeout = irmc_info.get('irmc_raid_session_timeout',
RAID_CONFIG_SESSION_TIMEOUT)
return _process_session_data(irmc_info, 'CONFIG_RAID',
session['Session']['Id'],
session_timeout) | [
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openstack/python-scciclient | scciclient/irmc/elcm.py | create_raid_configuration | def create_raid_configuration(irmc_info, target_raid_config):
"""Process raid_input then perform raid configuration into server.
:param irmc_info: node info
:param target_raid_config: node raid information
"""
if len(target_raid_config['logical_disks']) < 1:
raise ELCMValueError(message="logical_disks must not be empty")
# Check RAID config in the new RAID adapter. Must be erased before
# create new RAID config.
raid_adapter = get_raid_adapter(irmc_info)
logical_drives = raid_adapter['Server']['HWConfigurationIrmc'][
'Adapters']['RAIDAdapter'][0].get('LogicalDrives')
session_timeout = irmc_info.get('irmc_raid_session_timeout',
RAID_CONFIG_SESSION_TIMEOUT)
if logical_drives is not None:
# Delete exist logical drives in server.
# NOTE(trungnv): Wait session complete and raise error if
# delete raid config during FGI(Foreground Initialization) in-progress
# in previous mechanism.
delete_raid_configuration(irmc_info)
# Updating raid adapter profile after deleted profile.
raid_adapter = get_raid_adapter(irmc_info)
# Create raid configuration based on target_raid_config of node
raid_input = _update_raid_input_data(target_raid_config, raid_adapter)
session = elcm_profile_set(irmc_info, raid_input)
# Monitoring raid creation session until done.
_process_session_data(irmc_info, 'CONFIG_RAID',
session['Session']['Id'],
session_timeout) | python | def create_raid_configuration(irmc_info, target_raid_config):
"""Process raid_input then perform raid configuration into server.
:param irmc_info: node info
:param target_raid_config: node raid information
"""
if len(target_raid_config['logical_disks']) < 1:
raise ELCMValueError(message="logical_disks must not be empty")
# Check RAID config in the new RAID adapter. Must be erased before
# create new RAID config.
raid_adapter = get_raid_adapter(irmc_info)
logical_drives = raid_adapter['Server']['HWConfigurationIrmc'][
'Adapters']['RAIDAdapter'][0].get('LogicalDrives')
session_timeout = irmc_info.get('irmc_raid_session_timeout',
RAID_CONFIG_SESSION_TIMEOUT)
if logical_drives is not None:
# Delete exist logical drives in server.
# NOTE(trungnv): Wait session complete and raise error if
# delete raid config during FGI(Foreground Initialization) in-progress
# in previous mechanism.
delete_raid_configuration(irmc_info)
# Updating raid adapter profile after deleted profile.
raid_adapter = get_raid_adapter(irmc_info)
# Create raid configuration based on target_raid_config of node
raid_input = _update_raid_input_data(target_raid_config, raid_adapter)
session = elcm_profile_set(irmc_info, raid_input)
# Monitoring raid creation session until done.
_process_session_data(irmc_info, 'CONFIG_RAID',
session['Session']['Id'],
session_timeout) | [
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openstack/python-scciclient | scciclient/irmc/elcm.py | delete_raid_configuration | def delete_raid_configuration(irmc_info):
"""Delete whole raid configuration or one of logical drive on the server.
:param irmc_info: node info
"""
# Attempt to get raid configuration on BM Server
raid_adapter = get_raid_adapter(irmc_info)
existing_logical_drives = _get_existing_logical_drives(raid_adapter)
# Ironic requires delete_configuration first. Will pass if blank raid
# configuration in server.
if not existing_logical_drives:
return
raid_adapter['Server']['HWConfigurationIrmc'].update({
'@Processing': 'execute'})
logical_drive = raid_adapter['Server']['HWConfigurationIrmc'][
'Adapters']['RAIDAdapter'][0]['LogicalDrives']['LogicalDrive']
for drive in logical_drive:
drive['@Action'] = 'Delete'
# Attempt to delete logical drive in the raid config
session = elcm_profile_set(irmc_info, raid_adapter)
# Monitoring raid config delete session until done.
session_timeout = irmc_info.get('irmc_raid_session_timeout',
RAID_CONFIG_SESSION_TIMEOUT)
_process_session_data(irmc_info, 'CONFIG_RAID', session['Session']['Id'],
session_timeout)
# Attempt to delete raid adapter
elcm_profile_delete(irmc_info, PROFILE_RAID_CONFIG) | python | def delete_raid_configuration(irmc_info):
"""Delete whole raid configuration or one of logical drive on the server.
:param irmc_info: node info
"""
# Attempt to get raid configuration on BM Server
raid_adapter = get_raid_adapter(irmc_info)
existing_logical_drives = _get_existing_logical_drives(raid_adapter)
# Ironic requires delete_configuration first. Will pass if blank raid
# configuration in server.
if not existing_logical_drives:
return
raid_adapter['Server']['HWConfigurationIrmc'].update({
'@Processing': 'execute'})
logical_drive = raid_adapter['Server']['HWConfigurationIrmc'][
'Adapters']['RAIDAdapter'][0]['LogicalDrives']['LogicalDrive']
for drive in logical_drive:
drive['@Action'] = 'Delete'
# Attempt to delete logical drive in the raid config
session = elcm_profile_set(irmc_info, raid_adapter)
# Monitoring raid config delete session until done.
session_timeout = irmc_info.get('irmc_raid_session_timeout',
RAID_CONFIG_SESSION_TIMEOUT)
_process_session_data(irmc_info, 'CONFIG_RAID', session['Session']['Id'],
session_timeout)
# Attempt to delete raid adapter
elcm_profile_delete(irmc_info, PROFILE_RAID_CONFIG) | [
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openstack/python-scciclient | scciclient/irmc/elcm.py | set_bios_configuration | def set_bios_configuration(irmc_info, settings):
"""Set BIOS configurations on the server.
:param irmc_info: node info
:param settings: Dictionary containing the BIOS configuration.
:raise: BiosConfigNotFound, if there is wrong settings for bios
configuration.
"""
bios_config_data = {
'Server': {
'SystemConfig': {
'BiosConfig': {}
}
}
}
versions = elcm_profile_get_versions(irmc_info)
server_version = versions['Server'].get('@Version')
bios_version = \
versions['Server']['SystemConfig']['BiosConfig'].get('@Version')
if server_version:
bios_config_data['Server']['@Version'] = server_version
if bios_version:
bios_config_data['Server']['SystemConfig']['BiosConfig']['@Version'] = \
bios_version
configs = {}
for setting_param in settings:
setting_name = setting_param.get("name")
setting_value = setting_param.get("value")
# Revert-conversion from a string of True/False to boolean.
# It will be raise failed if put "True" or "False" string value.
if isinstance(setting_value, six.string_types):
if setting_value.lower() == "true":
setting_value = True
elif setting_value.lower() == "false":
setting_value = False
try:
type_config, config = BIOS_CONFIGURATION_DICTIONARY[
setting_name].split("_")
if type_config in configs.keys():
configs[type_config][config] = setting_value
else:
configs.update({type_config: {config: setting_value}})
except KeyError:
raise BiosConfigNotFound("Invalid BIOS setting: %s"
% setting_param)
bios_config_data['Server']['SystemConfig']['BiosConfig'].update(configs)
restore_bios_config(irmc_info, bios_config_data) | python | def set_bios_configuration(irmc_info, settings):
"""Set BIOS configurations on the server.
:param irmc_info: node info
:param settings: Dictionary containing the BIOS configuration.
:raise: BiosConfigNotFound, if there is wrong settings for bios
configuration.
"""
bios_config_data = {
'Server': {
'SystemConfig': {
'BiosConfig': {}
}
}
}
versions = elcm_profile_get_versions(irmc_info)
server_version = versions['Server'].get('@Version')
bios_version = \
versions['Server']['SystemConfig']['BiosConfig'].get('@Version')
if server_version:
bios_config_data['Server']['@Version'] = server_version
if bios_version:
bios_config_data['Server']['SystemConfig']['BiosConfig']['@Version'] = \
bios_version
configs = {}
for setting_param in settings:
setting_name = setting_param.get("name")
setting_value = setting_param.get("value")
# Revert-conversion from a string of True/False to boolean.
# It will be raise failed if put "True" or "False" string value.
if isinstance(setting_value, six.string_types):
if setting_value.lower() == "true":
setting_value = True
elif setting_value.lower() == "false":
setting_value = False
try:
type_config, config = BIOS_CONFIGURATION_DICTIONARY[
setting_name].split("_")
if type_config in configs.keys():
configs[type_config][config] = setting_value
else:
configs.update({type_config: {config: setting_value}})
except KeyError:
raise BiosConfigNotFound("Invalid BIOS setting: %s"
% setting_param)
bios_config_data['Server']['SystemConfig']['BiosConfig'].update(configs)
restore_bios_config(irmc_info, bios_config_data) | [
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openstack/python-scciclient | scciclient/irmc/elcm.py | get_bios_settings | def get_bios_settings(irmc_info):
"""Get the current BIOS settings on the server
:param irmc_info: node info.
:returns: a list of dictionary BIOS settings
"""
bios_config = backup_bios_config(irmc_info)['bios_config']
bios_config_data = bios_config['Server']['SystemConfig']['BiosConfig']
settings = []
# TODO(trungnv): Allow working with multi levels of BIOS dictionary.
for setting_param in BIOS_CONFIGURATION_DICTIONARY:
type_config, config = BIOS_CONFIGURATION_DICTIONARY[
setting_param].split("_")
if config in bios_config_data.get(type_config, {}):
value = six.text_type(bios_config_data[type_config][config])
settings.append({'name': setting_param, 'value': value})
return settings | python | def get_bios_settings(irmc_info):
"""Get the current BIOS settings on the server
:param irmc_info: node info.
:returns: a list of dictionary BIOS settings
"""
bios_config = backup_bios_config(irmc_info)['bios_config']
bios_config_data = bios_config['Server']['SystemConfig']['BiosConfig']
settings = []
# TODO(trungnv): Allow working with multi levels of BIOS dictionary.
for setting_param in BIOS_CONFIGURATION_DICTIONARY:
type_config, config = BIOS_CONFIGURATION_DICTIONARY[
setting_param].split("_")
if config in bios_config_data.get(type_config, {}):
value = six.text_type(bios_config_data[type_config][config])
settings.append({'name': setting_param, 'value': value})
return settings | [
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playpauseandstop/rororo | rororo/aio.py | add_resource_context | def add_resource_context(router: web.AbstractRouter,
url_prefix: str = None,
name_prefix: str = None) -> Iterator[Any]:
"""Context manager for adding resources for given router.
Main goal of context manager to easify process of adding resources with
routes to the router. This also allow to reduce amount of repeats, when
supplying new resources by reusing URL & name prefixes for all routes
inside context manager.
Behind the scene, context manager returns a function which calls::
resource = router.add_resource(url, name)
resource.add_route(method, handler)
**Usage**::
with add_resource_context(app.router, '/api', 'api') as add_resource:
add_resource('/', get=views.index)
add_resource('/news', get=views.list_news, post=views.create_news)
:param router: Route to add resources to.
:param url_prefix: If supplied prepend this prefix to each resource URL.
:param name_prefix: If supplied prepend this prefix to each resource name.
"""
def add_resource(url: str,
get: View = None,
*,
name: str = None,
**kwargs: Any) -> web.Resource:
"""Inner function to create resource and add necessary routes to it.
Support adding routes of all methods, supported by aiohttp, as
GET/POST/PUT/PATCH/DELETE/HEAD/OPTIONS/*, e.g.,
::
with add_resource_context(app.router) as add_resource:
add_resource('/', get=views.get, post=views.post)
add_resource('/wildcard', **{'*': views.wildcard})
:param url:
Resource URL. If ``url_prefix`` setup in context it will be
prepended to URL with ``/``.
:param get:
GET handler. Only handler to be setup without explicit call.
:param name: Resource name.
:type name: str
:rtype: aiohttp.web.Resource
"""
kwargs['get'] = get
if url_prefix:
url = '/'.join((url_prefix.rstrip('/'), url.lstrip('/')))
if not name and get:
name = get.__name__
if name_prefix and name:
name = '.'.join((name_prefix.rstrip('.'), name.lstrip('.')))
resource = router.add_resource(url, name=name)
for method, handler in kwargs.items():
if handler is None:
continue
resource.add_route(method.upper(), handler)
return resource
yield add_resource | python | def add_resource_context(router: web.AbstractRouter,
url_prefix: str = None,
name_prefix: str = None) -> Iterator[Any]:
"""Context manager for adding resources for given router.
Main goal of context manager to easify process of adding resources with
routes to the router. This also allow to reduce amount of repeats, when
supplying new resources by reusing URL & name prefixes for all routes
inside context manager.
Behind the scene, context manager returns a function which calls::
resource = router.add_resource(url, name)
resource.add_route(method, handler)
**Usage**::
with add_resource_context(app.router, '/api', 'api') as add_resource:
add_resource('/', get=views.index)
add_resource('/news', get=views.list_news, post=views.create_news)
:param router: Route to add resources to.
:param url_prefix: If supplied prepend this prefix to each resource URL.
:param name_prefix: If supplied prepend this prefix to each resource name.
"""
def add_resource(url: str,
get: View = None,
*,
name: str = None,
**kwargs: Any) -> web.Resource:
"""Inner function to create resource and add necessary routes to it.
Support adding routes of all methods, supported by aiohttp, as
GET/POST/PUT/PATCH/DELETE/HEAD/OPTIONS/*, e.g.,
::
with add_resource_context(app.router) as add_resource:
add_resource('/', get=views.get, post=views.post)
add_resource('/wildcard', **{'*': views.wildcard})
:param url:
Resource URL. If ``url_prefix`` setup in context it will be
prepended to URL with ``/``.
:param get:
GET handler. Only handler to be setup without explicit call.
:param name: Resource name.
:type name: str
:rtype: aiohttp.web.Resource
"""
kwargs['get'] = get
if url_prefix:
url = '/'.join((url_prefix.rstrip('/'), url.lstrip('/')))
if not name and get:
name = get.__name__
if name_prefix and name:
name = '.'.join((name_prefix.rstrip('.'), name.lstrip('.')))
resource = router.add_resource(url, name=name)
for method, handler in kwargs.items():
if handler is None:
continue
resource.add_route(method.upper(), handler)
return resource
yield add_resource | [
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playpauseandstop/rororo | rororo/aio.py | parse_aioredis_url | def parse_aioredis_url(url: str) -> DictStrAny:
"""
Convert Redis URL string to dict suitable to pass to
``aioredis.create_redis(...)`` call.
**Usage**::
async def connect_redis(url=None):
url = url or 'redis://localhost:6379/0'
return await create_redis(**get_aioredis_parts(url))
:param url: URL to access Redis instance, started with ``redis://``.
"""
parts = urlparse(url)
db = parts.path[1:] or None # type: Optional[Union[str, int]]
if db:
db = int(db)
return {
'address': (parts.hostname, parts.port or 6379),
'db': db,
'password': parts.password} | python | def parse_aioredis_url(url: str) -> DictStrAny:
"""
Convert Redis URL string to dict suitable to pass to
``aioredis.create_redis(...)`` call.
**Usage**::
async def connect_redis(url=None):
url = url or 'redis://localhost:6379/0'
return await create_redis(**get_aioredis_parts(url))
:param url: URL to access Redis instance, started with ``redis://``.
"""
parts = urlparse(url)
db = parts.path[1:] or None # type: Optional[Union[str, int]]
if db:
db = int(db)
return {
'address': (parts.hostname, parts.port or 6379),
'db': db,
'password': parts.password} | [
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OSSOS/MOP | src/ossos/core/ossos/mpc_time.py | TimeMPC.str_kwargs | def str_kwargs(self):
"""
Generator that yields a dict of values corresponding to the
calendar date and time for the internal JD values.
Here we provide the additional 'fracday' element needed by 'mpc' format
"""
iys, ims, ids, ihmsfs = sofa_time.jd_dtf(self.scale.upper()
.encode('utf8'),
6,
self.jd1, self.jd2)
# Get the str_fmt element of the first allowed output subformat
_, _, str_fmt = self._select_subfmts(self.out_subfmt)[0]
yday = None
has_yday = '{yday:' in str_fmt or False
for iy, im, iday, ihmsf in itertools.izip(iys, ims, ids, ihmsfs):
ihr, imin, isec, ifracsec = ihmsf
if has_yday:
yday = datetime(iy, im, iday).timetuple().tm_yday
# MPC uses day fraction as time part of datetime
fracday = (((((ifracsec / 1000000.0 + isec) / 60.0 + imin) / 60.0) + ihr) / 24.0) * (10 ** 6)
fracday = '{0:06g}'.format(fracday)[0:self.precision]
#format_str = '{{0:g}}'.format(self.precision)
#fracday = int(format_str.format(fracday))
yield dict(year=int(iy), mon=int(im), day=int(iday), hour=int(ihr), min=int(imin), sec=int(isec),
fracsec=int(ifracsec), yday=yday, fracday=fracday) | python | def str_kwargs(self):
"""
Generator that yields a dict of values corresponding to the
calendar date and time for the internal JD values.
Here we provide the additional 'fracday' element needed by 'mpc' format
"""
iys, ims, ids, ihmsfs = sofa_time.jd_dtf(self.scale.upper()
.encode('utf8'),
6,
self.jd1, self.jd2)
# Get the str_fmt element of the first allowed output subformat
_, _, str_fmt = self._select_subfmts(self.out_subfmt)[0]
yday = None
has_yday = '{yday:' in str_fmt or False
for iy, im, iday, ihmsf in itertools.izip(iys, ims, ids, ihmsfs):
ihr, imin, isec, ifracsec = ihmsf
if has_yday:
yday = datetime(iy, im, iday).timetuple().tm_yday
# MPC uses day fraction as time part of datetime
fracday = (((((ifracsec / 1000000.0 + isec) / 60.0 + imin) / 60.0) + ihr) / 24.0) * (10 ** 6)
fracday = '{0:06g}'.format(fracday)[0:self.precision]
#format_str = '{{0:g}}'.format(self.precision)
#fracday = int(format_str.format(fracday))
yield dict(year=int(iy), mon=int(im), day=int(iday), hour=int(ihr), min=int(imin), sec=int(isec),
fracsec=int(ifracsec), yday=yday, fracday=fracday) | [
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JohnVinyard/zounds | zounds/spectral/sliding_window.py | oggvorbis | def oggvorbis(s):
"""
This is taken from the ogg vorbis spec
(http://xiph.org/vorbis/doc/Vorbis_I_spec.html)
:param s: the total length of the window, in samples
"""
try:
s = np.arange(s)
except TypeError:
s = np.arange(s[0])
i = np.sin((s + .5) / len(s) * np.pi) ** 2
f = np.sin(.5 * np.pi * i)
return f * (1. / f.max()) | python | def oggvorbis(s):
"""
This is taken from the ogg vorbis spec
(http://xiph.org/vorbis/doc/Vorbis_I_spec.html)
:param s: the total length of the window, in samples
"""
try:
s = np.arange(s)
except TypeError:
s = np.arange(s[0])
i = np.sin((s + .5) / len(s) * np.pi) ** 2
f = np.sin(.5 * np.pi * i)
return f * (1. / f.max()) | [
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OSSOS/MOP | src/ossos/core/ossos/downloads/cutouts/focus.py | FocusCalculator.convert_source_location | def convert_source_location(self, source_reading, reference_reading):
"""
Converts the source (x, y) location from reading into the coordinate
system of reference_reading.
"""
offset_x, offset_y = reference_reading.get_coordinate_offset(source_reading)
focus = source_reading.x + offset_x, source_reading.y + offset_y
return focus | python | def convert_source_location(self, source_reading, reference_reading):
"""
Converts the source (x, y) location from reading into the coordinate
system of reference_reading.
"""
offset_x, offset_y = reference_reading.get_coordinate_offset(source_reading)
focus = source_reading.x + offset_x, source_reading.y + offset_y
return focus | [
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OSSOS/MOP | src/ossos/core/ossos/downloads/cutouts/focus.py | SingletFocusCalculator.calculate_focus | def calculate_focus(self, reading):
"""
Determines what the focal point of the downloaded image should be.
Returns:
focal_point: (x, y)
The location of the source in the middle observation, in the
coordinate system of the current source reading.
"""
middle_index = len(self.source.get_readings()) // 2
middle_reading = self.source.get_reading(middle_index)
return self.convert_source_location(middle_reading, reading) | python | def calculate_focus(self, reading):
"""
Determines what the focal point of the downloaded image should be.
Returns:
focal_point: (x, y)
The location of the source in the middle observation, in the
coordinate system of the current source reading.
"""
middle_index = len(self.source.get_readings()) // 2
middle_reading = self.source.get_reading(middle_index)
return self.convert_source_location(middle_reading, reading) | [
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OSSOS/MOP | src/ossos/plotting/scripts/rose_topdown.py | top_down_SolarSystem | def top_down_SolarSystem(discoveries,
inner_limit=6, # truncate at 8 AU to show that we don't have sensitivity in close
extent=83, # extend to 83 AU as indicative only, sensitivity is to ~300 AU
plot_discoveries=None,
plot_colossos=False,
plot_blocks=None,
plot_galaxy=False,
feature_blocks=None,
plot_Ijiraq=False, # detected Ijiraq at 9.80 AU in the 13AE block
label_blocks=True,
savefilename=None):
"""
Plot the OSSOS discoveries on a top-down Solar System showing the position of Neptune and model TNOs.
Discoveries are plotted each at their time of discovery according to the value in the Version Release.
Coordinates should be polar to account for RA hours, radial axis is in AU.
:return: a saved plot
This is not a 'projection' of the particles into any common plane. Each wedge is a different latitude above
the plane, but inside each wedge it is heliocentric distance vs RA.
That is fine. It's just important to know that if someone asks we know this is NOT (for example) a projection of each
object down into the ecliptic.
A very minor future long-term improvement is that the galactic
plane wedge is not (I don't think) symmetric around 18h and 6h.
I think that lines of constant (say 15 degree galactic lat) are
centered a little off (I think the wedge would 'twist' a little
bit counter-clockwise). I am not absolutely sure along the
ecliptic where the b= +/- 15 degree lines are but I don't
think they are symmetric?
"""
fig = plt.figure(figsize=(6, 6))
rect = [0.01, 0.01, 0.95, .95] # the plot occupies not all the figspace
ax1 = fig.add_axes(rect, polar=True, frameon=False) # theta (RA) is zero at E, increases anticlockwise
ax1.set_aspect('equal')
ax1.set_rlim(0, extent)
ax1.set_rgrids([20, 40, 60, 80], labels=["", "", '20 au', '40 au', '60 au', '80 au'], angle=190, alpha=0.45) # angle = 308
ax1.yaxis.set_major_locator(MultipleLocator(20))
ax1.xaxis.set_major_locator(MultipleLocator(math.radians(15))) # every 2 hours
ax1.grid(axis='x', color='k', linestyle='--', alpha=0.2)
ax1.set_xticklabels(['', '0h', "", '2h', "", '4h', "", '6h', "", '8h', "", '10h', "", '12h', "", '14h', "", '16h',
"", '18h', "", '20h', "", '22h', "", ],
# ""]) # str(r)+'h' for r in range(-1,24)],
# ['', '0h', '2h', '4h', '6h', '8h', '10h', '12h', '14h', '16h', '18h', '20h', '22h'],
color='b', alpha=0.6) # otherwise they get in the way
if plot_galaxy:
# plot exclusion zones due to Galactic plane: RAs indicate where bar starts, rather than its centre angle
width = math.radians(3 * 15)
plt.bar(math.radians(4.5 * 15), extent, width=width, color=plot_fanciness.ALMOST_BLACK, linewidth=0, alpha=0.2)
plt.bar(math.radians(16.5 * 15), extent, width=width, color=plot_fanciness.ALMOST_BLACK, linewidth=0, alpha=0.2)
ax1.annotate('galactic plane', (math.radians(6.9 * 15), extent - 15), size=10, color='k', alpha=0.45)
ax1.annotate(' galactic plane\navoidance zone', (math.radians(16.9 * 15), extent - 12), size=10, color='k', alpha=0.45)
# again RAs indicate where bar starts, so subtract half the block width from the block centrepoints
# and approximate blocks as math.radians(7) degrees wide.
for blockname, block in parameters.BLOCKS.items():
if plot_blocks:
if blockname in plot_blocks:
if feature_blocks is not None and blockname in feature_blocks:
colour = 'm' #'#E47833'
alpha = 0.25
else:
colour = 'b'
alpha = 0.1
# if blockname.startswith('13') or blockname.startswith('14'):
width = math.radians(7) # the 3 x 7 field layout
# else:
# width = math.radians(5) # the 4 x 5 field layout
# cmap = plt.get_cmap('Blues')
# if blockname.endswith('AO'):
# colour = '#E47833'
# alpha = 0.17
# cmap = plt.get_cmap('Oranges') # colorbrewer.sequential.Oranges_3.mpl_colors
ax1.bar(ephem.hours(block["RA"]) - math.radians(3.5), extent, linewidth=0.1,
width=width, bottom=inner_limit, zorder=0, color=colour, alpha=alpha)
if label_blocks:
ax1.annotate(blockname[3], (ephem.hours(block["RA"]) + math.radians(0.36), extent - 3.), size=15,
color='b')
# No optional on these just yet
plot_planets_plus_Pluto(ax1)
ra, dist, hlat, Hmag = parsers.synthetic_model_kbos(kbotype='resonant', arrays=True, maglimit=24.7)
# can't plot Hmag as marker size in current setup.
ax1.scatter(ra, dist, marker='o', s=2, facecolor=plot_fanciness.ALMOST_BLACK,
edgecolor=plot_fanciness.ALMOST_BLACK, linewidth=0.1, alpha=0.12, zorder=1)
if plot_discoveries is not None:
plot_ossos_discoveries(ax1, discoveries, plot_discoveries, plot_colossos=plot_colossos)
# special detection in 13AE: Saturn's moon Ijiraq at 2013-04-09 shows inner limit of sensitivity.
if plot_Ijiraq:
# Position from Horizons as it's excluded from the list of detections
ax1.scatter(ephem.hours('14 29 46.57'), 9.805,
marker='o', s=4, facecolor='b', edgecolor=plot_fanciness.ALMOST_BLACK, linewidth=0.15, alpha=0.8)
plt.draw()
if savefilename is not None:
outfile = '{}.pdf'.format(savefilename)
else:
outfile = 'topdown_RA_d_OSSOS_v{}.pdf'.format(parameters.RELEASE_VERSION)
plt.savefig(outfile, transparent=True, bbox_inches='tight')
return | python | def top_down_SolarSystem(discoveries,
inner_limit=6, # truncate at 8 AU to show that we don't have sensitivity in close
extent=83, # extend to 83 AU as indicative only, sensitivity is to ~300 AU
plot_discoveries=None,
plot_colossos=False,
plot_blocks=None,
plot_galaxy=False,
feature_blocks=None,
plot_Ijiraq=False, # detected Ijiraq at 9.80 AU in the 13AE block
label_blocks=True,
savefilename=None):
"""
Plot the OSSOS discoveries on a top-down Solar System showing the position of Neptune and model TNOs.
Discoveries are plotted each at their time of discovery according to the value in the Version Release.
Coordinates should be polar to account for RA hours, radial axis is in AU.
:return: a saved plot
This is not a 'projection' of the particles into any common plane. Each wedge is a different latitude above
the plane, but inside each wedge it is heliocentric distance vs RA.
That is fine. It's just important to know that if someone asks we know this is NOT (for example) a projection of each
object down into the ecliptic.
A very minor future long-term improvement is that the galactic
plane wedge is not (I don't think) symmetric around 18h and 6h.
I think that lines of constant (say 15 degree galactic lat) are
centered a little off (I think the wedge would 'twist' a little
bit counter-clockwise). I am not absolutely sure along the
ecliptic where the b= +/- 15 degree lines are but I don't
think they are symmetric?
"""
fig = plt.figure(figsize=(6, 6))
rect = [0.01, 0.01, 0.95, .95] # the plot occupies not all the figspace
ax1 = fig.add_axes(rect, polar=True, frameon=False) # theta (RA) is zero at E, increases anticlockwise
ax1.set_aspect('equal')
ax1.set_rlim(0, extent)
ax1.set_rgrids([20, 40, 60, 80], labels=["", "", '20 au', '40 au', '60 au', '80 au'], angle=190, alpha=0.45) # angle = 308
ax1.yaxis.set_major_locator(MultipleLocator(20))
ax1.xaxis.set_major_locator(MultipleLocator(math.radians(15))) # every 2 hours
ax1.grid(axis='x', color='k', linestyle='--', alpha=0.2)
ax1.set_xticklabels(['', '0h', "", '2h', "", '4h', "", '6h', "", '8h', "", '10h', "", '12h', "", '14h', "", '16h',
"", '18h', "", '20h', "", '22h', "", ],
# ""]) # str(r)+'h' for r in range(-1,24)],
# ['', '0h', '2h', '4h', '6h', '8h', '10h', '12h', '14h', '16h', '18h', '20h', '22h'],
color='b', alpha=0.6) # otherwise they get in the way
if plot_galaxy:
# plot exclusion zones due to Galactic plane: RAs indicate where bar starts, rather than its centre angle
width = math.radians(3 * 15)
plt.bar(math.radians(4.5 * 15), extent, width=width, color=plot_fanciness.ALMOST_BLACK, linewidth=0, alpha=0.2)
plt.bar(math.radians(16.5 * 15), extent, width=width, color=plot_fanciness.ALMOST_BLACK, linewidth=0, alpha=0.2)
ax1.annotate('galactic plane', (math.radians(6.9 * 15), extent - 15), size=10, color='k', alpha=0.45)
ax1.annotate(' galactic plane\navoidance zone', (math.radians(16.9 * 15), extent - 12), size=10, color='k', alpha=0.45)
# again RAs indicate where bar starts, so subtract half the block width from the block centrepoints
# and approximate blocks as math.radians(7) degrees wide.
for blockname, block in parameters.BLOCKS.items():
if plot_blocks:
if blockname in plot_blocks:
if feature_blocks is not None and blockname in feature_blocks:
colour = 'm' #'#E47833'
alpha = 0.25
else:
colour = 'b'
alpha = 0.1
# if blockname.startswith('13') or blockname.startswith('14'):
width = math.radians(7) # the 3 x 7 field layout
# else:
# width = math.radians(5) # the 4 x 5 field layout
# cmap = plt.get_cmap('Blues')
# if blockname.endswith('AO'):
# colour = '#E47833'
# alpha = 0.17
# cmap = plt.get_cmap('Oranges') # colorbrewer.sequential.Oranges_3.mpl_colors
ax1.bar(ephem.hours(block["RA"]) - math.radians(3.5), extent, linewidth=0.1,
width=width, bottom=inner_limit, zorder=0, color=colour, alpha=alpha)
if label_blocks:
ax1.annotate(blockname[3], (ephem.hours(block["RA"]) + math.radians(0.36), extent - 3.), size=15,
color='b')
# No optional on these just yet
plot_planets_plus_Pluto(ax1)
ra, dist, hlat, Hmag = parsers.synthetic_model_kbos(kbotype='resonant', arrays=True, maglimit=24.7)
# can't plot Hmag as marker size in current setup.
ax1.scatter(ra, dist, marker='o', s=2, facecolor=plot_fanciness.ALMOST_BLACK,
edgecolor=plot_fanciness.ALMOST_BLACK, linewidth=0.1, alpha=0.12, zorder=1)
if plot_discoveries is not None:
plot_ossos_discoveries(ax1, discoveries, plot_discoveries, plot_colossos=plot_colossos)
# special detection in 13AE: Saturn's moon Ijiraq at 2013-04-09 shows inner limit of sensitivity.
if plot_Ijiraq:
# Position from Horizons as it's excluded from the list of detections
ax1.scatter(ephem.hours('14 29 46.57'), 9.805,
marker='o', s=4, facecolor='b', edgecolor=plot_fanciness.ALMOST_BLACK, linewidth=0.15, alpha=0.8)
plt.draw()
if savefilename is not None:
outfile = '{}.pdf'.format(savefilename)
else:
outfile = 'topdown_RA_d_OSSOS_v{}.pdf'.format(parameters.RELEASE_VERSION)
plt.savefig(outfile, transparent=True, bbox_inches='tight')
return | [
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Discoveries are plotted each at their time of discovery according to the value in the Version Release.
Coordinates should be polar to account for RA hours, radial axis is in AU.
:return: a saved plot
This is not a 'projection' of the particles into any common plane. Each wedge is a different latitude above
the plane, but inside each wedge it is heliocentric distance vs RA.
That is fine. It's just important to know that if someone asks we know this is NOT (for example) a projection of each
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A very minor future long-term improvement is that the galactic
plane wedge is not (I don't think) symmetric around 18h and 6h.
I think that lines of constant (say 15 degree galactic lat) are
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bit counter-clockwise). I am not absolutely sure along the
ecliptic where the b= +/- 15 degree lines are but I don't
think they are symmetric? | [
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OSSOS/MOP | src/ossos/plotting/scripts/rose_topdown.py | plot_ossos_discoveries | def plot_ossos_discoveries(ax, discoveries, plot_discoveries,
plot_colossos=False, split_plutinos=False):
"""
plotted at their discovery locations, provided by the Version Releases in decimal degrees.
"""
fc = ['b', '#E47833', 'k']
alpha = [0.85, 0.6, 1.]
marker = ['o', 'd']
size = [7, 25]
plottable = [] # Which blocks' discoveries to include?
for d in discoveries:
for n in plot_discoveries:
if d['object'].startswith(n): # can for sure be better, but this hack works. Need to get where going
plottable.append(d)
# Hack to get in the O15BD objects
# directory_name = '/Users/bannisterm/Dropbox/OSSOS/measure3/ossin/D_tmp/'
# kbos = parsers.ossos_discoveries(directory_name, all_objects=False, data_release=None)
# for kbo in kbos:
# plottable_kbo = {'RAdeg': kbo.discovery.coordinate.ra.to_string(unit=units.degree, sep=':'),
# 'dist': kbo.orbit.distance.value}
# plottable.append(plottable_kbo)
if plot_colossos:
fainter = []
colossos = []
for n in plottable:
if n['object'] in parameters.COLOSSOS:
colossos.append(n)
else:
fainter.append(n)
plot_ossos_points(fainter, ax, marker[0], size[0], fc[0], alpha[1], 1)
plot_ossos_points(colossos, ax, marker[1], size[1], fc[2], alpha[2], 2)
elif split_plutinos:
# plutino_index = np.where((plottable['cl'] == 'res') & (plottable['j'] == 3) & (plottable['k'] == 2))
raise NotImplementedError
else:
plot_ossos_points(plottable, ax, marker[0], size[0], fc[0], alpha[0], 2)
return | python | def plot_ossos_discoveries(ax, discoveries, plot_discoveries,
plot_colossos=False, split_plutinos=False):
"""
plotted at their discovery locations, provided by the Version Releases in decimal degrees.
"""
fc = ['b', '#E47833', 'k']
alpha = [0.85, 0.6, 1.]
marker = ['o', 'd']
size = [7, 25]
plottable = [] # Which blocks' discoveries to include?
for d in discoveries:
for n in plot_discoveries:
if d['object'].startswith(n): # can for sure be better, but this hack works. Need to get where going
plottable.append(d)
# Hack to get in the O15BD objects
# directory_name = '/Users/bannisterm/Dropbox/OSSOS/measure3/ossin/D_tmp/'
# kbos = parsers.ossos_discoveries(directory_name, all_objects=False, data_release=None)
# for kbo in kbos:
# plottable_kbo = {'RAdeg': kbo.discovery.coordinate.ra.to_string(unit=units.degree, sep=':'),
# 'dist': kbo.orbit.distance.value}
# plottable.append(plottable_kbo)
if plot_colossos:
fainter = []
colossos = []
for n in plottable:
if n['object'] in parameters.COLOSSOS:
colossos.append(n)
else:
fainter.append(n)
plot_ossos_points(fainter, ax, marker[0], size[0], fc[0], alpha[1], 1)
plot_ossos_points(colossos, ax, marker[1], size[1], fc[2], alpha[2], 2)
elif split_plutinos:
# plutino_index = np.where((plottable['cl'] == 'res') & (plottable['j'] == 3) & (plottable['k'] == 2))
raise NotImplementedError
else:
plot_ossos_points(plottable, ax, marker[0], size[0], fc[0], alpha[0], 2)
return | [
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OSSOS/MOP | src/ossos/plotting/scripts/rose_topdown.py | orbit_fit_residuals | def orbit_fit_residuals(discoveries, blockID='O13AE'):
"""Brett: What are relevant and stunning are the actual orbit fit residuals
for orbits with d(a)/a<1%. I would be happy with a simple histogram of all those numbers,
although the 'tail' (probably blended and not yet completely flagged) should
perhaps be excluded. There will be a pretty clear gaussian I would think, peaking near 0.07".
"""
ra_residuals = []
dec_residuals = []
ressum = []
for i, orbit in enumerate(discoveries):
if (orbit.da / orbit.a) < 0.01:
print i, len(discoveries), orbit.observations[0].provisional_name, orbit.da / orbit.a
res = orbit.residuals.split('\n')
for r in res:
rr = r.split(' ')
if (len(rr) > 1) and not (rr[0].startswith('!')):
ra_residuals.append(float(r.split(' ')[4]))
dec_residuals.append(float(r.split(' ')[5]))
ressum.append(1000 * (float(r.split(' ')[4]) ** 2 + float(r.split(' ')[5]) ** 2))
plt.figure(figsize=(6, 6))
bins = [r for r in range(-25, 150, 25)]
n, bins, patches = plt.hist(ressum, histtype='step', color='b', bins=bins, label='$dra^{2}+ddec^{2}$')
# midpoints = [r/1000. for r in range(-350,350,50)]
# popt, pcov = curve_fit(gaussian, midpoints, n)
# print 'a', popt[0], 'mu', popt[1], 'sigma', popt[2]
# xm = np.linspace(-.375, .375, 100) # 100 evenly spaced points
# plt.plot(xm, gaussian(xm, popt[0], popt[1], popt[2]), ls='--', color='#E47833', linewidth=2)
# sigma = r'$\sigma = %.2f \pm %.2f$' % (popt[2], np.sqrt(pcov[2, 2]))
# plt.annotate(sigma, (0.12, 50), color='#E47833')
plt.xlim((-25, 150)) # sufficient for 13AE data
plt.ylabel('observations of orbits with d(a)/a < 1% (i.e 3-5 month arcs)')
plt.xlabel('orbit fit residuals (milliarcsec)')
plt.legend()
# clean_legend()
plt.draw()
outfile = 'orbit_fit_residuals_13AE_corrected'
plt.savefig('/ossos_sequence/'+ outfile + '.pdf', transparent=True)
return | python | def orbit_fit_residuals(discoveries, blockID='O13AE'):
"""Brett: What are relevant and stunning are the actual orbit fit residuals
for orbits with d(a)/a<1%. I would be happy with a simple histogram of all those numbers,
although the 'tail' (probably blended and not yet completely flagged) should
perhaps be excluded. There will be a pretty clear gaussian I would think, peaking near 0.07".
"""
ra_residuals = []
dec_residuals = []
ressum = []
for i, orbit in enumerate(discoveries):
if (orbit.da / orbit.a) < 0.01:
print i, len(discoveries), orbit.observations[0].provisional_name, orbit.da / orbit.a
res = orbit.residuals.split('\n')
for r in res:
rr = r.split(' ')
if (len(rr) > 1) and not (rr[0].startswith('!')):
ra_residuals.append(float(r.split(' ')[4]))
dec_residuals.append(float(r.split(' ')[5]))
ressum.append(1000 * (float(r.split(' ')[4]) ** 2 + float(r.split(' ')[5]) ** 2))
plt.figure(figsize=(6, 6))
bins = [r for r in range(-25, 150, 25)]
n, bins, patches = plt.hist(ressum, histtype='step', color='b', bins=bins, label='$dra^{2}+ddec^{2}$')
# midpoints = [r/1000. for r in range(-350,350,50)]
# popt, pcov = curve_fit(gaussian, midpoints, n)
# print 'a', popt[0], 'mu', popt[1], 'sigma', popt[2]
# xm = np.linspace(-.375, .375, 100) # 100 evenly spaced points
# plt.plot(xm, gaussian(xm, popt[0], popt[1], popt[2]), ls='--', color='#E47833', linewidth=2)
# sigma = r'$\sigma = %.2f \pm %.2f$' % (popt[2], np.sqrt(pcov[2, 2]))
# plt.annotate(sigma, (0.12, 50), color='#E47833')
plt.xlim((-25, 150)) # sufficient for 13AE data
plt.ylabel('observations of orbits with d(a)/a < 1% (i.e 3-5 month arcs)')
plt.xlabel('orbit fit residuals (milliarcsec)')
plt.legend()
# clean_legend()
plt.draw()
outfile = 'orbit_fit_residuals_13AE_corrected'
plt.savefig('/ossos_sequence/'+ outfile + '.pdf', transparent=True)
return | [
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openstack/python-scciclient | scciclient/irmc/snmp.py | get_irmc_firmware_version | def get_irmc_firmware_version(snmp_client):
"""Get irmc firmware version of the node.
:param snmp_client: an SNMP client object.
:raises: SNMPFailure if SNMP operation failed.
:returns: a string of bmc name and irmc firmware version.
"""
try:
bmc_name = snmp_client.get(BMC_NAME_OID)
irmc_firm_ver = snmp_client.get(IRMC_FW_VERSION_OID)
return ('%(bmc)s%(sep)s%(firm_ver)s' %
{'bmc': bmc_name if bmc_name else '',
'firm_ver': irmc_firm_ver if irmc_firm_ver else '',
'sep': '-' if bmc_name and irmc_firm_ver else ''})
except SNMPFailure as e:
raise SNMPIRMCFirmwareFailure(
SNMP_FAILURE_MSG % ("GET IRMC FIRMWARE VERSION", e)) | python | def get_irmc_firmware_version(snmp_client):
"""Get irmc firmware version of the node.
:param snmp_client: an SNMP client object.
:raises: SNMPFailure if SNMP operation failed.
:returns: a string of bmc name and irmc firmware version.
"""
try:
bmc_name = snmp_client.get(BMC_NAME_OID)
irmc_firm_ver = snmp_client.get(IRMC_FW_VERSION_OID)
return ('%(bmc)s%(sep)s%(firm_ver)s' %
{'bmc': bmc_name if bmc_name else '',
'firm_ver': irmc_firm_ver if irmc_firm_ver else '',
'sep': '-' if bmc_name and irmc_firm_ver else ''})
except SNMPFailure as e:
raise SNMPIRMCFirmwareFailure(
SNMP_FAILURE_MSG % ("GET IRMC FIRMWARE VERSION", e)) | [
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:raises: SNMPFailure if SNMP operation failed.
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openstack/python-scciclient | scciclient/irmc/snmp.py | get_bios_firmware_version | def get_bios_firmware_version(snmp_client):
"""Get bios firmware version of the node.
:param snmp_client: an SNMP client object.
:raises: SNMPFailure if SNMP operation failed.
:returns: a string of bios firmware version.
"""
try:
bios_firmware_version = snmp_client.get(BIOS_FW_VERSION_OID)
return six.text_type(bios_firmware_version)
except SNMPFailure as e:
raise SNMPBIOSFirmwareFailure(
SNMP_FAILURE_MSG % ("GET BIOS FIRMWARE VERSION", e)) | python | def get_bios_firmware_version(snmp_client):
"""Get bios firmware version of the node.
:param snmp_client: an SNMP client object.
:raises: SNMPFailure if SNMP operation failed.
:returns: a string of bios firmware version.
"""
try:
bios_firmware_version = snmp_client.get(BIOS_FW_VERSION_OID)
return six.text_type(bios_firmware_version)
except SNMPFailure as e:
raise SNMPBIOSFirmwareFailure(
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openstack/python-scciclient | scciclient/irmc/snmp.py | get_server_model | def get_server_model(snmp_client):
"""Get server model of the node.
:param snmp_client: an SNMP client object.
:raises: SNMPFailure if SNMP operation failed.
:returns: a string of server model.
"""
try:
server_model = snmp_client.get(SERVER_MODEL_OID)
return six.text_type(server_model)
except SNMPFailure as e:
raise SNMPServerModelFailure(
SNMP_FAILURE_MSG % ("GET SERVER MODEL", e)) | python | def get_server_model(snmp_client):
"""Get server model of the node.
:param snmp_client: an SNMP client object.
:raises: SNMPFailure if SNMP operation failed.
:returns: a string of server model.
"""
try:
server_model = snmp_client.get(SERVER_MODEL_OID)
return six.text_type(server_model)
except SNMPFailure as e:
raise SNMPServerModelFailure(
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openstack/python-scciclient | scciclient/irmc/snmp.py | SNMPClient._get_auth | def _get_auth(self):
"""Return the authorization data for an SNMP request.
:returns: A
:class:`pysnmp.entity.rfc3413.oneliner.cmdgen.CommunityData`
object.
"""
if self.version == SNMP_V3:
# Handling auth/encryption credentials is not (yet) supported.
# This version supports a security name analogous to community.
return cmdgen.UsmUserData(self.security)
else:
mp_model = 1 if self.version == SNMP_V2C else 0
return cmdgen.CommunityData(self.community, mpModel=mp_model) | python | def _get_auth(self):
"""Return the authorization data for an SNMP request.
:returns: A
:class:`pysnmp.entity.rfc3413.oneliner.cmdgen.CommunityData`
object.
"""
if self.version == SNMP_V3:
# Handling auth/encryption credentials is not (yet) supported.
# This version supports a security name analogous to community.
return cmdgen.UsmUserData(self.security)
else:
mp_model = 1 if self.version == SNMP_V2C else 0
return cmdgen.CommunityData(self.community, mpModel=mp_model) | [
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openstack/python-scciclient | scciclient/irmc/snmp.py | SNMPClient.get | def get(self, oid):
"""Use PySNMP to perform an SNMP GET operation on a single object.
:param oid: The OID of the object to get.
:raises: SNMPFailure if an SNMP request fails.
:returns: The value of the requested object.
"""
try:
results = self.cmd_gen.getCmd(self._get_auth(),
self._get_transport(),
oid)
except snmp_error.PySnmpError as e:
raise SNMPFailure(SNMP_FAILURE_MSG % ("GET", e))
error_indication, error_status, error_index, var_binds = results
if error_indication:
# SNMP engine-level error.
raise SNMPFailure(SNMP_FAILURE_MSG % ("GET", error_indication))
if error_status:
# SNMP PDU error.
raise SNMPFailure(
"SNMP operation '%(operation)s' failed: %(error)s at"
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{'operation': "GET", 'error': error_status.prettyPrint(),
'index':
error_index and var_binds[int(error_index) - 1]
or '?'})
# We only expect a single value back
name, val = var_binds[0]
return val | python | def get(self, oid):
"""Use PySNMP to perform an SNMP GET operation on a single object.
:param oid: The OID of the object to get.
:raises: SNMPFailure if an SNMP request fails.
:returns: The value of the requested object.
"""
try:
results = self.cmd_gen.getCmd(self._get_auth(),
self._get_transport(),
oid)
except snmp_error.PySnmpError as e:
raise SNMPFailure(SNMP_FAILURE_MSG % ("GET", e))
error_indication, error_status, error_index, var_binds = results
if error_indication:
# SNMP engine-level error.
raise SNMPFailure(SNMP_FAILURE_MSG % ("GET", error_indication))
if error_status:
# SNMP PDU error.
raise SNMPFailure(
"SNMP operation '%(operation)s' failed: %(error)s at"
" %(index)s" %
{'operation': "GET", 'error': error_status.prettyPrint(),
'index':
error_index and var_binds[int(error_index) - 1]
or '?'})
# We only expect a single value back
name, val = var_binds[0]
return val | [
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openstack/python-scciclient | scciclient/irmc/snmp.py | SNMPClient.get_next | def get_next(self, oid):
"""Use PySNMP to perform an SNMP GET NEXT operation on a table object.
:param oid: The OID of the object to get.
:raises: SNMPFailure if an SNMP request fails.
:returns: A list of values of the requested table object.
"""
try:
results = self.cmd_gen.nextCmd(self._get_auth(),
self._get_transport(),
oid)
except snmp_error.PySnmpError as e:
raise SNMPFailure(SNMP_FAILURE_MSG % ("GET_NEXT", e))
error_indication, error_status, error_index, var_binds = results
if error_indication:
# SNMP engine-level error.
raise SNMPFailure(
SNMP_FAILURE_MSG % ("GET_NEXT", error_indication))
if error_status:
# SNMP PDU error.
raise SNMPFailure(
"SNMP operation '%(operation)s' failed: %(error)s at"
" %(index)s" %
{'operation': "GET_NEXT", 'error': error_status.prettyPrint(),
'index':
error_index and var_binds[int(error_index) - 1]
or '?'})
return [val for row in var_binds for name, val in row] | python | def get_next(self, oid):
"""Use PySNMP to perform an SNMP GET NEXT operation on a table object.
:param oid: The OID of the object to get.
:raises: SNMPFailure if an SNMP request fails.
:returns: A list of values of the requested table object.
"""
try:
results = self.cmd_gen.nextCmd(self._get_auth(),
self._get_transport(),
oid)
except snmp_error.PySnmpError as e:
raise SNMPFailure(SNMP_FAILURE_MSG % ("GET_NEXT", e))
error_indication, error_status, error_index, var_binds = results
if error_indication:
# SNMP engine-level error.
raise SNMPFailure(
SNMP_FAILURE_MSG % ("GET_NEXT", error_indication))
if error_status:
# SNMP PDU error.
raise SNMPFailure(
"SNMP operation '%(operation)s' failed: %(error)s at"
" %(index)s" %
{'operation': "GET_NEXT", 'error': error_status.prettyPrint(),
'index':
error_index and var_binds[int(error_index) - 1]
or '?'})
return [val for row in var_binds for name, val in row] | [
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openstack/python-scciclient | scciclient/irmc/snmp.py | SNMPClient.set | def set(self, oid, value):
"""Use PySNMP to perform an SNMP SET operation on a single object.
:param oid: The OID of the object to set.
:param value: The value of the object to set.
:raises: SNMPFailure if an SNMP request fails.
"""
try:
results = self.cmd_gen.setCmd(self._get_auth(),
self._get_transport(),
(oid, value))
except snmp_error.PySnmpError as e:
raise SNMPFailure(SNMP_FAILURE_MSG % ("SET", e))
error_indication, error_status, error_index, var_binds = results
if error_indication:
# SNMP engine-level error.
raise SNMPFailure(SNMP_FAILURE_MSG % ("SET", error_indication))
if error_status:
# SNMP PDU error.
raise SNMPFailure(
"SNMP operation '%(operation)s' failed: %(error)s at"
" %(index)s" %
{'operation': "SET", 'error': error_status.prettyPrint(),
'index':
error_index and var_binds[int(error_index) - 1]
or '?'}) | python | def set(self, oid, value):
"""Use PySNMP to perform an SNMP SET operation on a single object.
:param oid: The OID of the object to set.
:param value: The value of the object to set.
:raises: SNMPFailure if an SNMP request fails.
"""
try:
results = self.cmd_gen.setCmd(self._get_auth(),
self._get_transport(),
(oid, value))
except snmp_error.PySnmpError as e:
raise SNMPFailure(SNMP_FAILURE_MSG % ("SET", e))
error_indication, error_status, error_index, var_binds = results
if error_indication:
# SNMP engine-level error.
raise SNMPFailure(SNMP_FAILURE_MSG % ("SET", error_indication))
if error_status:
# SNMP PDU error.
raise SNMPFailure(
"SNMP operation '%(operation)s' failed: %(error)s at"
" %(index)s" %
{'operation': "SET", 'error': error_status.prettyPrint(),
'index':
error_index and var_binds[int(error_index) - 1]
or '?'}) | [
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OSSOS/MOP | src/ossos/core/ossos/mop_file.py | MOPFile.filename | def filename(self):
"""
Name if the MOP formatted file to parse.
@rtype: basestring
@return: filename
"""
if self._filename is None:
self._filename = storage.get_file(self.basename,
self.ccd,
ext=self.extension,
version=self.type,
prefix=self.prefix)
return self._filename | python | def filename(self):
"""
Name if the MOP formatted file to parse.
@rtype: basestring
@return: filename
"""
if self._filename is None:
self._filename = storage.get_file(self.basename,
self.ccd,
ext=self.extension,
version=self.type,
prefix=self.prefix)
return self._filename | [
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OSSOS/MOP | src/ossos/core/ossos/mop_file.py | MOPFile._parse | def _parse(self):
"""read in a file and return a MOPFile object."""
with open(self.filename, 'r') as fobj:
lines = fobj.read().split('\n')
# Create a header object with content at start of file
self.header = MOPHeader(self.subfmt).parser(lines)
# Create a data attribute to hold an astropy.table.Table object
self.data = MOPDataParser(self.header).parse(lines) | python | def _parse(self):
"""read in a file and return a MOPFile object."""
with open(self.filename, 'r') as fobj:
lines = fobj.read().split('\n')
# Create a header object with content at start of file
self.header = MOPHeader(self.subfmt).parser(lines)
# Create a data attribute to hold an astropy.table.Table object
self.data = MOPDataParser(self.header).parse(lines) | [
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OSSOS/MOP | src/ossos/core/ossos/mop_file.py | MOPDataParser.table | def table(self):
"""
The astropy.table.Table object that will contain the data result
@rtype: Table
@return: data table
"""
if self._table is None:
column_names = []
for fileid in self.header.file_ids:
for column_name in self.header.column_names:
column_names.append("{}_{}".format(column_name, fileid))
column_names.append("ZP_{}".format(fileid))
if len(column_names) > 0:
self._table = Table(names=column_names)
else:
self._table = Table()
return self._table | python | def table(self):
"""
The astropy.table.Table object that will contain the data result
@rtype: Table
@return: data table
"""
if self._table is None:
column_names = []
for fileid in self.header.file_ids:
for column_name in self.header.column_names:
column_names.append("{}_{}".format(column_name, fileid))
column_names.append("ZP_{}".format(fileid))
if len(column_names) > 0:
self._table = Table(names=column_names)
else:
self._table = Table()
return self._table | [
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OSSOS/MOP | src/ossos/core/ossos/mop_file.py | MOPHeader.parser | def parser(self, lines):
"""Given a set of lines parse the into a MOP Header"""
while len(lines) > 0:
if lines[0].startswith('##') and lines[1].startswith('# '):
# A two-line keyword/value line starts here.
self._header_append(lines.pop(0), lines.pop(0))
elif lines[0].startswith('# '):
# Lines with single comments are exposure numbers unless preceeded by double comment line
self._append_file_id(lines.pop(0))
elif lines[0].startswith('##'):
# Double comment lines without a single comment following are column headers for dataset.
self._set_column_names(lines.pop(0)[2:])
else:
# Last line of the header reached.
return self
raise IOError("Failed trying to read header") | python | def parser(self, lines):
"""Given a set of lines parse the into a MOP Header"""
while len(lines) > 0:
if lines[0].startswith('##') and lines[1].startswith('# '):
# A two-line keyword/value line starts here.
self._header_append(lines.pop(0), lines.pop(0))
elif lines[0].startswith('# '):
# Lines with single comments are exposure numbers unless preceeded by double comment line
self._append_file_id(lines.pop(0))
elif lines[0].startswith('##'):
# Double comment lines without a single comment following are column headers for dataset.
self._set_column_names(lines.pop(0)[2:])
else:
# Last line of the header reached.
return self
raise IOError("Failed trying to read header") | [
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OSSOS/MOP | src/ossos/core/ossos/mop_file.py | MOPHeader._compute_mjd | def _compute_mjd(self, kw, val):
"""
Sometimes that MJD-OBS-CENTER keyword maps to a three component string, instead of a single value.
@param kw: a list of keywords
@param val: a list of matching values
@return: the MJD-OBS-CENTER as a julian date.
"""
try:
idx = kw.index('MJD-OBS-CENTER')
except ValueError:
return
if len(val) == len(kw):
return
if len(val) - 2 != len(kw):
raise ValueError("convert: keyword/value lengths don't match: {}/{}".format(kw, val))
val.insert(idx, Time("{} {} {}".format(val.pop(idx), val.pop(idx), val.pop(idx)),
format='mpc',
scale='utc').mjd)
logging.debug("Computed MJD: {}".format(val[idx])) | python | def _compute_mjd(self, kw, val):
"""
Sometimes that MJD-OBS-CENTER keyword maps to a three component string, instead of a single value.
@param kw: a list of keywords
@param val: a list of matching values
@return: the MJD-OBS-CENTER as a julian date.
"""
try:
idx = kw.index('MJD-OBS-CENTER')
except ValueError:
return
if len(val) == len(kw):
return
if len(val) - 2 != len(kw):
raise ValueError("convert: keyword/value lengths don't match: {}/{}".format(kw, val))
val.insert(idx, Time("{} {} {}".format(val.pop(idx), val.pop(idx), val.pop(idx)),
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OSSOS/MOP | src/jjk/preproc/findTriplets.py | getExpInfo | def getExpInfo(expnum):
"""Return a dictionary of information about a particular exposure"""
col_names=['object',
'e.expnum',
'mjdate',
'uttime',
'filter',
'elongation',
'obs_iq_refccd',
'triple', 'qso_status']
sql="SELECT "
sep=" "
for col_name in col_names:
sql=sql+sep+col_name
sep=","
sql=sql+" FROM bucket.exposure e "
sql=sql+" JOIN bucket.circumstance c ON e.expnum=c.expnum "
sql=sql+" LEFT JOIN triple_members t ON e.expnum=t.expnum "
sql=sql+" WHERE e.expnum=%d " % ( expnum )
#sys.stderr.write(sql);
cfeps.execute(sql)
rows=cfeps.fetchall()
#print rows
result={}
#import datetime
for idx in range(len(rows[0])):
result[col_names[idx]]=rows[0][idx]
return(result) | python | def getExpInfo(expnum):
"""Return a dictionary of information about a particular exposure"""
col_names=['object',
'e.expnum',
'mjdate',
'uttime',
'filter',
'elongation',
'obs_iq_refccd',
'triple', 'qso_status']
sql="SELECT "
sep=" "
for col_name in col_names:
sql=sql+sep+col_name
sep=","
sql=sql+" FROM bucket.exposure e "
sql=sql+" JOIN bucket.circumstance c ON e.expnum=c.expnum "
sql=sql+" LEFT JOIN triple_members t ON e.expnum=t.expnum "
sql=sql+" WHERE e.expnum=%d " % ( expnum )
#sys.stderr.write(sql);
cfeps.execute(sql)
rows=cfeps.fetchall()
#print rows
result={}
#import datetime
for idx in range(len(rows[0])):
result[col_names[idx]]=rows[0][idx]
return(result) | [
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OSSOS/MOP | src/jjk/preproc/findTriplets.py | getTripInfo | def getTripInfo(triple):
"""Return a dictionary of information about a particular triple"""
col_names=['mjdate', 'filter', 'elongation', 'discovery','checkup', 'recovery', 'iq','block' ]
sql="SELECT mjdate md,"
sql=sql+" filter, avg(elongation), d.id, checkup.checkup, recovery.recovery , avg(obs_iq_refccd), b.qname "
sql=sql+"FROM triple_members t JOIN bucket.exposure e ON t.expnum=e.expnum "
sql=sql+"JOIN bucket.blocks b ON b.expnum=e.expnum "
sql=sql+"JOIN bucket.circumstance c on e.expnum=c.expnum "
sql=sql+"LEFT JOIN discovery d ON t.triple=d.triple "
sql=sql+"LEFT JOIN checkup ON t.triple=checkup.triple "
sql=sql+"LEFT JOIN recovery ON t.triple=recovery.triple "
sql=sql+"WHERE t.triple=%s "
sql=sql+"GROUP BY t.triple ORDER BY t.triple "
cfeps.execute(sql,(triple, ) )
rows=cfeps.fetchall()
result={}
#import datetime
for idx in range(len(rows[0])):
result[col_names[idx]]=rows[0][idx]
return result | python | def getTripInfo(triple):
"""Return a dictionary of information about a particular triple"""
col_names=['mjdate', 'filter', 'elongation', 'discovery','checkup', 'recovery', 'iq','block' ]
sql="SELECT mjdate md,"
sql=sql+" filter, avg(elongation), d.id, checkup.checkup, recovery.recovery , avg(obs_iq_refccd), b.qname "
sql=sql+"FROM triple_members t JOIN bucket.exposure e ON t.expnum=e.expnum "
sql=sql+"JOIN bucket.blocks b ON b.expnum=e.expnum "
sql=sql+"JOIN bucket.circumstance c on e.expnum=c.expnum "
sql=sql+"LEFT JOIN discovery d ON t.triple=d.triple "
sql=sql+"LEFT JOIN checkup ON t.triple=checkup.triple "
sql=sql+"LEFT JOIN recovery ON t.triple=recovery.triple "
sql=sql+"WHERE t.triple=%s "
sql=sql+"GROUP BY t.triple ORDER BY t.triple "
cfeps.execute(sql,(triple, ) )
rows=cfeps.fetchall()
result={}
#import datetime
for idx in range(len(rows[0])):
result[col_names[idx]]=rows[0][idx]
return result | [
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OSSOS/MOP | src/jjk/preproc/findTriplets.py | getExpnums | def getExpnums(pointing,night=None):
"""Get all exposures of specified pointing ID.
Default is to return a list of all exposure numbers"""
if night:
night=" floor(e.mjdate-0.0833)=%d " % ( night )
else:
night=''
sql="SELECT e.expnum "
sql=sql+"FROM bucket.exposure e "
sql=sql+"JOIN bucket.association a on e.expnum=a.expnum "
sql=sql+"WHERE a.pointing="+str(pointing)+" AND "+night
sql=sql+" ORDER BY mjdate, uttime DESC "
cfeps.execute(sql)
return(cfeps.fetchall()) | python | def getExpnums(pointing,night=None):
"""Get all exposures of specified pointing ID.
Default is to return a list of all exposure numbers"""
if night:
night=" floor(e.mjdate-0.0833)=%d " % ( night )
else:
night=''
sql="SELECT e.expnum "
sql=sql+"FROM bucket.exposure e "
sql=sql+"JOIN bucket.association a on e.expnum=a.expnum "
sql=sql+"WHERE a.pointing="+str(pointing)+" AND "+night
sql=sql+" ORDER BY mjdate, uttime DESC "
cfeps.execute(sql)
return(cfeps.fetchall()) | [
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OSSOS/MOP | src/jjk/preproc/findTriplets.py | getTriples | def getTriples(pointing):
"""Get all triples of a specified pointing ID.
Defaults is to return a complete list triples."""
sql="SELECT id FROM triples t join triple_members m ON t.id=m.triple"
sql+=" join bucket.exposure e on e.expnum=m.expnum "
sql+=" WHERE pointing=%s group by id order by e.expnum "
cfeps.execute(sql, ( pointing, ) )
return(cfeps.fetchall()) | python | def getTriples(pointing):
"""Get all triples of a specified pointing ID.
Defaults is to return a complete list triples."""
sql="SELECT id FROM triples t join triple_members m ON t.id=m.triple"
sql+=" join bucket.exposure e on e.expnum=m.expnum "
sql+=" WHERE pointing=%s group by id order by e.expnum "
cfeps.execute(sql, ( pointing, ) )
return(cfeps.fetchall()) | [
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OSSOS/MOP | src/jjk/preproc/findTriplets.py | createNewTriples | def createNewTriples(Win):
"""Add entries to the triples tables based on new images in the db"""
win.help("Building list of exposures to look for triples")
cols=('e.expnum', 'object',
'mjdate',
'uttime',
'elongation',
'filter',
'obs_iq_refccd','qso_status' )
header='%6s %-10s%-12s%10s%10s%10s%8s%10s' % cols
pointings=getNewTriples()
num_p=len(pointings)
for pointing in pointings:
pid=pointing[0]
mjd=pointing[1]
expnums=getExpnums(pointing=pid,night=mjd)
num_p=num_p-1
while (1):
### Loop over this pointing until keystroke gets us out
win.help("Select (space) members of triplets - %d remaining" % num_p )
## start with an empty list
explist=[]
choices=[]
current_date=''
for expnum in expnums:
info=getExpInfo(expnum[0])
row=()
if not str(info['triple'])=='None' :
continue
if str(info['obs_iq_refccd'])=='None':
info['obs_iq_refccd']=-1.0
choices.append('%6d %10s %15s %10s %8.2f %10s %8.2f %10s' % (
int(info['e.expnum']),
str(info['object']),
str(info['mjdate']),
str(info['uttime']),
float(str(info['elongation'])),
str(info['filter']),
float(str(info['obs_iq_refccd'])),
str(info['qso_status'])
))
explist.append(expnum[0])
if len(choices)<3:
### we need to provide at least 3 choices,
### otherwise this isn't a triple (is it)
break
### win.list returns the user's choices as a list.
choice_list=win.list(header,choices)
### zero length list implies were done.
if choice_list==None:
break
### is this actually a triple?
if len(choice_list)!=3:
win.help("Must have 3 members to make a tripple")
continue
### Create a new line in the triple table
sql = "INSERT INTO triples (id, pointing ) VALUES ( NULL, %s ) "
cfeps.execute(sql, ( pid, ) )
sql = "SELECT id FROM triples WHERE pointing=%s order by id desc"
cfeps.execute(sql, ( pid, ) )
ttt=cfeps.fetchall()
triple= ttt[0][0]
win.help(str(triple))
### record the members of this new triple.
sql = "INSERT INTO triple_members (triple, expnum) VALUES ( %s, %s)";
win.help(sql)
for exp in choice_list:
cfeps.execute(sql,(triple,explist[exp]))
return(0) | python | def createNewTriples(Win):
"""Add entries to the triples tables based on new images in the db"""
win.help("Building list of exposures to look for triples")
cols=('e.expnum', 'object',
'mjdate',
'uttime',
'elongation',
'filter',
'obs_iq_refccd','qso_status' )
header='%6s %-10s%-12s%10s%10s%10s%8s%10s' % cols
pointings=getNewTriples()
num_p=len(pointings)
for pointing in pointings:
pid=pointing[0]
mjd=pointing[1]
expnums=getExpnums(pointing=pid,night=mjd)
num_p=num_p-1
while (1):
### Loop over this pointing until keystroke gets us out
win.help("Select (space) members of triplets - %d remaining" % num_p )
## start with an empty list
explist=[]
choices=[]
current_date=''
for expnum in expnums:
info=getExpInfo(expnum[0])
row=()
if not str(info['triple'])=='None' :
continue
if str(info['obs_iq_refccd'])=='None':
info['obs_iq_refccd']=-1.0
choices.append('%6d %10s %15s %10s %8.2f %10s %8.2f %10s' % (
int(info['e.expnum']),
str(info['object']),
str(info['mjdate']),
str(info['uttime']),
float(str(info['elongation'])),
str(info['filter']),
float(str(info['obs_iq_refccd'])),
str(info['qso_status'])
))
explist.append(expnum[0])
if len(choices)<3:
### we need to provide at least 3 choices,
### otherwise this isn't a triple (is it)
break
### win.list returns the user's choices as a list.
choice_list=win.list(header,choices)
### zero length list implies were done.
if choice_list==None:
break
### is this actually a triple?
if len(choice_list)!=3:
win.help("Must have 3 members to make a tripple")
continue
### Create a new line in the triple table
sql = "INSERT INTO triples (id, pointing ) VALUES ( NULL, %s ) "
cfeps.execute(sql, ( pid, ) )
sql = "SELECT id FROM triples WHERE pointing=%s order by id desc"
cfeps.execute(sql, ( pid, ) )
ttt=cfeps.fetchall()
triple= ttt[0][0]
win.help(str(triple))
### record the members of this new triple.
sql = "INSERT INTO triple_members (triple, expnum) VALUES ( %s, %s)";
win.help(sql)
for exp in choice_list:
cfeps.execute(sql,(triple,explist[exp]))
return(0) | [
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OSSOS/MOP | src/jjk/preproc/findTriplets.py | setDiscoveryTriples | def setDiscoveryTriples(win,table="discovery"):
"""Provide user with a list of triples that could be discovery triples"""
win.help("Getting a list of pointings with triples from the CFEPS db")
pointings=getPointingsWithTriples()
win.help("Select the "+table+" triple form the list...")
import time
for pointing in pointings:
header="%10s %10s %8s %10s %8s" % (pointing[1],'mjdate','Elongation','Filter', 'IQ')
triples=getTriples(pointing=pointing[0])
choices=[]
triplist=[]
no_type=0
previous_list=[]
for triple in triples:
#win.help(str(triple))
tripinfo=getTripInfo(triple[0])
if not tripinfo[table]==None:
previous_list.append(triple[0])
#if not abs(180-tripinfo['elongation'])< 20:
# continue
triplist.append(triple)
if str(tripinfo['iq'])=='None':
tripinfo['iq']=-1.0
obs_type=' '
if tripinfo['discovery']:
obs_type='D'
elif tripinfo['checkup']:
obs_type='C'
elif tripinfo['recovery']:
obs_type='R'
if obs_type==' ':
no_type+=1
line=(obs_type,tripinfo['mjdate'], tripinfo['elongation'],
tripinfo['filter'], tripinfo['iq'], tripinfo['block'] )
choices.append('%10s %10s %8.2f %10s %8.2f %8s' % line)
if len(choices)==0 or no_type==0:
continue
#if len(previous_list)==1:
# continue
win.help("Choose a "+table+" triple (space) [no choice means skip] then press enter\n (q) to exit")
choice=win.list(header,choices)
if choice==None:
win.help("Loading next triple")
break
### Record which triplet is a discovery triplet
if len(choice)!=1:
win.help("Loading next triple\n")
continue
discovery_triple=triplist[choice[0]]
for triple in previous_list:
sql="DELETE FROM "+table+" WHERE triple=%s "
cfeps.execute(sql,triple)
sql="INSERT INTO "+table+" ( triple ) VALUES ( %s ) "
cfeps.execute(sql,discovery_triple) | python | def setDiscoveryTriples(win,table="discovery"):
"""Provide user with a list of triples that could be discovery triples"""
win.help("Getting a list of pointings with triples from the CFEPS db")
pointings=getPointingsWithTriples()
win.help("Select the "+table+" triple form the list...")
import time
for pointing in pointings:
header="%10s %10s %8s %10s %8s" % (pointing[1],'mjdate','Elongation','Filter', 'IQ')
triples=getTriples(pointing=pointing[0])
choices=[]
triplist=[]
no_type=0
previous_list=[]
for triple in triples:
#win.help(str(triple))
tripinfo=getTripInfo(triple[0])
if not tripinfo[table]==None:
previous_list.append(triple[0])
#if not abs(180-tripinfo['elongation'])< 20:
# continue
triplist.append(triple)
if str(tripinfo['iq'])=='None':
tripinfo['iq']=-1.0
obs_type=' '
if tripinfo['discovery']:
obs_type='D'
elif tripinfo['checkup']:
obs_type='C'
elif tripinfo['recovery']:
obs_type='R'
if obs_type==' ':
no_type+=1
line=(obs_type,tripinfo['mjdate'], tripinfo['elongation'],
tripinfo['filter'], tripinfo['iq'], tripinfo['block'] )
choices.append('%10s %10s %8.2f %10s %8.2f %8s' % line)
if len(choices)==0 or no_type==0:
continue
#if len(previous_list)==1:
# continue
win.help("Choose a "+table+" triple (space) [no choice means skip] then press enter\n (q) to exit")
choice=win.list(header,choices)
if choice==None:
win.help("Loading next triple")
break
### Record which triplet is a discovery triplet
if len(choice)!=1:
win.help("Loading next triple\n")
continue
discovery_triple=triplist[choice[0]]
for triple in previous_list:
sql="DELETE FROM "+table+" WHERE triple=%s "
cfeps.execute(sql,triple)
sql="INSERT INTO "+table+" ( triple ) VALUES ( %s ) "
cfeps.execute(sql,discovery_triple) | [
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OSSOS/MOP | src/ossos/core/ossos/pipeline/step1.py | run | def run(expnum,
ccd,
prefix='',
version='p',
sex_thresh=_SEX_THRESHOLD,
wave_thresh=_WAVE_THRESHOLD,
maxcount=_MAX_COUNT,
dry_run=False,
force=True):
"""run the actual step1jmp/matt codes.
expnum: the CFHT expousre to process
ccd: which ccd in the mosaic to process
fwhm: the image quality, FWHM, of the image. In pixels.
sex_thresh: the detection threhold to run sExtractor at
wave_thresh: the detection threshold for wavelet
maxcount: saturation level
"""
message = storage.SUCCESS
if storage.get_status(task, prefix, expnum, version, ccd) and not force:
logging.info("{} completed successfully for {} {} {} {}".format(task, prefix, expnum, version, ccd))
return
with storage.LoggingManager(task, prefix, expnum, ccd, version, dry_run):
try:
if not storage.get_status(dependency, prefix, expnum, version, ccd):
raise IOError(35, "Cannot start {} as {} not yet completed for {}{}{}{:02d}".format(
task, dependency, prefix, expnum, version, ccd))
logging.info("Retrieving imaging and input parameters from VOSpace")
storage.get_file(expnum, ccd, prefix=prefix, version=version, ext='mopheader')
filename = storage.get_image(expnum, ccd, version=version, prefix=prefix)
fwhm = storage.get_fwhm(expnum, ccd, prefix=prefix, version=version)
basename = os.path.splitext(filename)[0]
_get_weight_map(filename, ccd)
logging.info("Launching step1jmp")
logging.info(util.exec_prog(['step1jmp',
'-f', basename,
'-t', str(wave_thresh),
'-w', str(fwhm),
'-m', str(maxcount)]))
logging.info(util.exec_prog(['step1matt',
'-f', basename,
'-t', str(sex_thresh),
'-w', str(fwhm),
'-m', str(maxcount)]))
if os.access('weight.fits', os.R_OK):
os.unlink('weight.fits')
if not dry_run:
for ext in ['obj.jmp', 'obj.matt']:
obj_uri = storage.get_uri(expnum, ccd, version=version, ext=ext,
prefix=prefix)
obj_filename = basename + "." + ext
count = 0
with open(obj_filename, 'r'):
while True:
try:
count += 1
logging.info("Attempt {} to copy {} -> {}".format(count, obj_filename, obj_uri))
storage.copy(obj_filename, obj_uri)
break
except Exception as ex:
if count > 10:
raise ex
logging.info(message)
except Exception as ex:
message = str(ex)
logging.error(message)
if not dry_run:
storage.set_status(task, prefix, expnum, version, ccd, status=message) | python | def run(expnum,
ccd,
prefix='',
version='p',
sex_thresh=_SEX_THRESHOLD,
wave_thresh=_WAVE_THRESHOLD,
maxcount=_MAX_COUNT,
dry_run=False,
force=True):
"""run the actual step1jmp/matt codes.
expnum: the CFHT expousre to process
ccd: which ccd in the mosaic to process
fwhm: the image quality, FWHM, of the image. In pixels.
sex_thresh: the detection threhold to run sExtractor at
wave_thresh: the detection threshold for wavelet
maxcount: saturation level
"""
message = storage.SUCCESS
if storage.get_status(task, prefix, expnum, version, ccd) and not force:
logging.info("{} completed successfully for {} {} {} {}".format(task, prefix, expnum, version, ccd))
return
with storage.LoggingManager(task, prefix, expnum, ccd, version, dry_run):
try:
if not storage.get_status(dependency, prefix, expnum, version, ccd):
raise IOError(35, "Cannot start {} as {} not yet completed for {}{}{}{:02d}".format(
task, dependency, prefix, expnum, version, ccd))
logging.info("Retrieving imaging and input parameters from VOSpace")
storage.get_file(expnum, ccd, prefix=prefix, version=version, ext='mopheader')
filename = storage.get_image(expnum, ccd, version=version, prefix=prefix)
fwhm = storage.get_fwhm(expnum, ccd, prefix=prefix, version=version)
basename = os.path.splitext(filename)[0]
_get_weight_map(filename, ccd)
logging.info("Launching step1jmp")
logging.info(util.exec_prog(['step1jmp',
'-f', basename,
'-t', str(wave_thresh),
'-w', str(fwhm),
'-m', str(maxcount)]))
logging.info(util.exec_prog(['step1matt',
'-f', basename,
'-t', str(sex_thresh),
'-w', str(fwhm),
'-m', str(maxcount)]))
if os.access('weight.fits', os.R_OK):
os.unlink('weight.fits')
if not dry_run:
for ext in ['obj.jmp', 'obj.matt']:
obj_uri = storage.get_uri(expnum, ccd, version=version, ext=ext,
prefix=prefix)
obj_filename = basename + "." + ext
count = 0
with open(obj_filename, 'r'):
while True:
try:
count += 1
logging.info("Attempt {} to copy {} -> {}".format(count, obj_filename, obj_uri))
storage.copy(obj_filename, obj_uri)
break
except Exception as ex:
if count > 10:
raise ex
logging.info(message)
except Exception as ex:
message = str(ex)
logging.error(message)
if not dry_run:
storage.set_status(task, prefix, expnum, version, ccd, status=message) | [
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OSSOS/MOP | src/ossos/utils/2MASS_Vizier.py | query | def query(ra ,dec, rad=0.1, query=None):
"""Query the CADC TAP service to determine the list of images for the
NewHorizons Search. Things to determine:
a- Images to have the reference subtracted from.
b- Image to use as the 'REFERENCE' image.
c- Images to be used for input into the reference image
Logic: Given a particular Image/CCD find all the CCDs of the same field that
overlap that CCD but are taken more than 7 days later or earlier than
that image.
"""
if query is None:
query=( """ SELECT """
""" "II/246/out".raj2000 as ra, "II/246/out".dej2000 as dec, "II/246/out".jmag as jmag """
""" FROM "II/246/out" """
""" WHERE """
""" CONTAINS(POINT('ICRS', raj2000, dej2000), CIRCLE('ICRS', {}, {}, {})) = 1 """.format(ra,dec,rad) )
tapURL = "http://TAPVizieR.u-strasbg.fr/TAPVizieR/tap/sync"
## Some default parameters for that TAP service queries.
tapParams={'REQUEST': 'doQuery',
'LANG': 'ADQL',
'FORMAT': 'votable',
'QUERY': query}
response = requests.get(tapURL, params=tapParams)
data = StringIO(response.text)
data.seek(0)
data.seek(0)
T = votable.parse_single_table(data).to_table()
return T | python | def query(ra ,dec, rad=0.1, query=None):
"""Query the CADC TAP service to determine the list of images for the
NewHorizons Search. Things to determine:
a- Images to have the reference subtracted from.
b- Image to use as the 'REFERENCE' image.
c- Images to be used for input into the reference image
Logic: Given a particular Image/CCD find all the CCDs of the same field that
overlap that CCD but are taken more than 7 days later or earlier than
that image.
"""
if query is None:
query=( """ SELECT """
""" "II/246/out".raj2000 as ra, "II/246/out".dej2000 as dec, "II/246/out".jmag as jmag """
""" FROM "II/246/out" """
""" WHERE """
""" CONTAINS(POINT('ICRS', raj2000, dej2000), CIRCLE('ICRS', {}, {}, {})) = 1 """.format(ra,dec,rad) )
tapURL = "http://TAPVizieR.u-strasbg.fr/TAPVizieR/tap/sync"
## Some default parameters for that TAP service queries.
tapParams={'REQUEST': 'doQuery',
'LANG': 'ADQL',
'FORMAT': 'votable',
'QUERY': query}
response = requests.get(tapURL, params=tapParams)
data = StringIO(response.text)
data.seek(0)
data.seek(0)
T = votable.parse_single_table(data).to_table()
return T | [
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a- Images to have the reference subtracted from.
b- Image to use as the 'REFERENCE' image.
c- Images to be used for input into the reference image
Logic: Given a particular Image/CCD find all the CCDs of the same field that
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OSSOS/MOP | src/jjk/preproc/objIngest.py | objIngest | def objIngest(obj_file):
import sys,os,math,re
import pyfits
import MOPfiles
obj=MOPfiles.read(obj_file)
"""
The SQL description of the source table
+-------------+---------+------+-----+---------+----------------+
| Field | Type | Null | Key | Default | Extra |
+-------------+---------+------+-----+---------+----------------+
| sourceID | int(11) | | PRI | NULL | auto_increment |
| x_pix | float | YES | MUL | NULL | |
| y_pix | float | YES | | NULL | |
| iso_flux | float | YES | | NULL | |
| iso_err | float | YES | | NULL | |
| aper_flux | float | YES | | NULL | |
| aper_err | float | YES | | NULL | |
| iso_area | float | YES | | NULL | |
| kron_radius | float | YES | MUL | NULL | |
| elongation | float | YES | | NULL | |
| cxx | float | YES | | NULL | |
| cyy | float | YES | | NULL | |
| cxy | float | YES | | NULL | |
| max_flux | float | YES | | NULL | |
| max_int | float | YES | | NULL | |
| mag_dao | float | YES | MUL | NULL | |
| merr_dao | float | YES | | NULL | |
| sky_cts | float | YES | | NULL | |
| chi2 | float | YES | | NULL | |
| npix | float | YES | | NULL | |
| sharp | float | YES | | NULL | |
| ra_deg | float | YES | MUL | NULL | |
| dec_deg | float | YES | | NULL | |
+-------------+---------+------+-----+---------+----------------+
"""
"""
Columns in the SOURCE table...
## X Y FLUX_ISO FLUXERR_ISO FLUX_APER FLUXERR_APER ISOAREA_IMAGE KRON_RADIUS ELONGATION CXX_IMAGE CYY_IMAGE CXY_IMAGE FLUX_MAX ID MAX_INT FLUX MERR SKY ELON X^2 N_PIX MAG SHARP SIZE
"""
### The mapping
obj['hdu2sql']={'MAX_INT': 'peak',
'FLUX': 'flux',
'MAG': 'mag',
'MERR': 'merr',
'SKY': 'sky',
'ELON': 'elongation',
'X^2': 'chi2',
'N_PIX': 'npix',
'SHARP': 'sharpness',
'Y': 'yPix',
'X': 'xPix',
'SIZE': 'size',
'RA': 'raDeg',
'DEC': 'decDeg',
}
MOPfiles.store(obj)
return | python | def objIngest(obj_file):
import sys,os,math,re
import pyfits
import MOPfiles
obj=MOPfiles.read(obj_file)
"""
The SQL description of the source table
+-------------+---------+------+-----+---------+----------------+
| Field | Type | Null | Key | Default | Extra |
+-------------+---------+------+-----+---------+----------------+
| sourceID | int(11) | | PRI | NULL | auto_increment |
| x_pix | float | YES | MUL | NULL | |
| y_pix | float | YES | | NULL | |
| iso_flux | float | YES | | NULL | |
| iso_err | float | YES | | NULL | |
| aper_flux | float | YES | | NULL | |
| aper_err | float | YES | | NULL | |
| iso_area | float | YES | | NULL | |
| kron_radius | float | YES | MUL | NULL | |
| elongation | float | YES | | NULL | |
| cxx | float | YES | | NULL | |
| cyy | float | YES | | NULL | |
| cxy | float | YES | | NULL | |
| max_flux | float | YES | | NULL | |
| max_int | float | YES | | NULL | |
| mag_dao | float | YES | MUL | NULL | |
| merr_dao | float | YES | | NULL | |
| sky_cts | float | YES | | NULL | |
| chi2 | float | YES | | NULL | |
| npix | float | YES | | NULL | |
| sharp | float | YES | | NULL | |
| ra_deg | float | YES | MUL | NULL | |
| dec_deg | float | YES | | NULL | |
+-------------+---------+------+-----+---------+----------------+
"""
"""
Columns in the SOURCE table...
## X Y FLUX_ISO FLUXERR_ISO FLUX_APER FLUXERR_APER ISOAREA_IMAGE KRON_RADIUS ELONGATION CXX_IMAGE CYY_IMAGE CXY_IMAGE FLUX_MAX ID MAX_INT FLUX MERR SKY ELON X^2 N_PIX MAG SHARP SIZE
"""
### The mapping
obj['hdu2sql']={'MAX_INT': 'peak',
'FLUX': 'flux',
'MAG': 'mag',
'MERR': 'merr',
'SKY': 'sky',
'ELON': 'elongation',
'X^2': 'chi2',
'N_PIX': 'npix',
'SHARP': 'sharpness',
'Y': 'yPix',
'X': 'xPix',
'SIZE': 'size',
'RA': 'raDeg',
'DEC': 'decDeg',
}
MOPfiles.store(obj)
return | [
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| x_pix | float | YES | MUL | NULL | |
| y_pix | float | YES | | NULL | |
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| iso_err | float | YES | | NULL | |
| aper_flux | float | YES | | NULL | |
| aper_err | float | YES | | NULL | |
| iso_area | float | YES | | NULL | |
| kron_radius | float | YES | MUL | NULL | |
| elongation | float | YES | | NULL | |
| cxx | float | YES | | NULL | |
| cyy | float | YES | | NULL | |
| cxy | float | YES | | NULL | |
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| merr_dao | float | YES | | NULL | |
| sky_cts | float | YES | | NULL | |
| chi2 | float | YES | | NULL | |
| npix | float | YES | | NULL | |
| sharp | float | YES | | NULL | |
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OSSOS/MOP | src/jjk/preproc/MOPplot.py | load_edbfile | def load_edbfile(file=None):
"""Load the targets from a file"""
import ephem,string,math
if file is None:
import tkFileDialog
try:
file=tkFileDialog.askopenfilename()
except:
return
if file is None or file == '':
return
f=open(file)
lines=f.readlines()
f.close()
for line in lines:
p=line.split(',')
name=p[0].strip().upper()
mpc_objs[name]=ephem.readdb(line)
mpc_objs[name].compute()
objInfoDict[name]="%6s %6s %6s\n" % ( string.center("a",6),
string.center("e",6),
string.center("i",6) )
objInfoDict[name]+="%6.2f %6.3f %6.2f\n" % (mpc_objs[name]._a,mpc_objs[name]._e,math.degrees(mpc_objs[name]._inc))
objInfoDict[name]+="%7.2f %7.2f\n" % ( mpc_objs[name].earth_distance, mpc_objs[name].mag)
doplot(mpc_objs) | python | def load_edbfile(file=None):
"""Load the targets from a file"""
import ephem,string,math
if file is None:
import tkFileDialog
try:
file=tkFileDialog.askopenfilename()
except:
return
if file is None or file == '':
return
f=open(file)
lines=f.readlines()
f.close()
for line in lines:
p=line.split(',')
name=p[0].strip().upper()
mpc_objs[name]=ephem.readdb(line)
mpc_objs[name].compute()
objInfoDict[name]="%6s %6s %6s\n" % ( string.center("a",6),
string.center("e",6),
string.center("i",6) )
objInfoDict[name]+="%6.2f %6.3f %6.2f\n" % (mpc_objs[name]._a,mpc_objs[name]._e,math.degrees(mpc_objs[name]._inc))
objInfoDict[name]+="%7.2f %7.2f\n" % ( mpc_objs[name].earth_distance, mpc_objs[name].mag)
doplot(mpc_objs) | [
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OSSOS/MOP | src/jjk/preproc/MOPplot.py | load_abgfiles | def load_abgfiles(dir=None):
"""Load the targets from a file"""
import ephem,string
if dir is None:
import tkFileDialog
try:
dir=tkFileDialog.askdirectory()
except:
return
if dir is None:
return None
from glob import glob
files=glob(dir+"/*.abg")
import os
for f in files:
(name,ext)=os.path.splitext(os.path.basename(f))
NAME=name.strip().upper()
kbos[name]=f
#print name
aei=file(dir+"/"+name+".aei")
lines=aei.readlines()
aei.close()
objInfoDict[name]="%6s %6s %6s\n" % ( string.center("a",6),
string.center("e",6),
string.center("i",6) )
try:
(a,e,i,N,w,T) = lines[4].split()
except:
print lines[4]
(a,e,i,N,w,T) = (0,0,0,0,0,0)
objInfoDict[name]+="%6.2f %6.3f %6.2f\n" % (float(a),float(e),float(i))
s=lines[5][0:2]
(a,e,i,N,w,T) = lines[5][2:-1].split()
objInfoDict[name]+=" %6.3f %6.3f %6.3f\n" % (float(a),float(e),float(i))
abg = file(dir+"/"+name+".abg")
lines = abg.readlines()
abg.close()
for line in lines:
if not line[0:5] == "# Bar":
continue
objInfoDict[name]+=line[2:-1]+"\n"
break
res=file(dir+"/"+name+".res")
lines=res.readlines()
res.close()
line=lines.pop()
values=line.split()
s = "[nobs: "+values[0]+" dt: "+values[1]+"]\n"
objInfoDict[name]+=s
mpc = file(dir+"/../mpc/"+name+".mpc")
lines=mpc.readlines()
mpc.close()
last_date=0
for line in lines:
if len(line)==0:
continue
if line[0]=="#":
continue
this_year=int(line[15:19])
this_month=int(line[20:22])
this_day = int(line[23:25])
this_date = this_year+this_month/12.0 +this_day/365.25
if last_date < this_date:
last_date=this_date
year=this_year
day = this_day
month=this_month
mag={}
for line in lines:
try:
mags=line[65:69].strip()
if len(mags)==0:
continue
filter=line[70]
if filter not in mag:
mag[filter]=[]
mag[filter].append(float(mags))
except:
continue
mags=''
for filter in mag:
magv=0
for m in mag[filter]:
magv = magv+m/len(mag[filter])
mags = mags+ "%4.1f-%s " % ( magv , filter)
if len(mags)==0:
mags= "N/A"
objInfoDict[name]+="MAG: "+mags+"\n"
objInfoDict[name]+="Last obs: %s %s %s \n" % (year,month, day)
doplot(kbos) | python | def load_abgfiles(dir=None):
"""Load the targets from a file"""
import ephem,string
if dir is None:
import tkFileDialog
try:
dir=tkFileDialog.askdirectory()
except:
return
if dir is None:
return None
from glob import glob
files=glob(dir+"/*.abg")
import os
for f in files:
(name,ext)=os.path.splitext(os.path.basename(f))
NAME=name.strip().upper()
kbos[name]=f
#print name
aei=file(dir+"/"+name+".aei")
lines=aei.readlines()
aei.close()
objInfoDict[name]="%6s %6s %6s\n" % ( string.center("a",6),
string.center("e",6),
string.center("i",6) )
try:
(a,e,i,N,w,T) = lines[4].split()
except:
print lines[4]
(a,e,i,N,w,T) = (0,0,0,0,0,0)
objInfoDict[name]+="%6.2f %6.3f %6.2f\n" % (float(a),float(e),float(i))
s=lines[5][0:2]
(a,e,i,N,w,T) = lines[5][2:-1].split()
objInfoDict[name]+=" %6.3f %6.3f %6.3f\n" % (float(a),float(e),float(i))
abg = file(dir+"/"+name+".abg")
lines = abg.readlines()
abg.close()
for line in lines:
if not line[0:5] == "# Bar":
continue
objInfoDict[name]+=line[2:-1]+"\n"
break
res=file(dir+"/"+name+".res")
lines=res.readlines()
res.close()
line=lines.pop()
values=line.split()
s = "[nobs: "+values[0]+" dt: "+values[1]+"]\n"
objInfoDict[name]+=s
mpc = file(dir+"/../mpc/"+name+".mpc")
lines=mpc.readlines()
mpc.close()
last_date=0
for line in lines:
if len(line)==0:
continue
if line[0]=="#":
continue
this_year=int(line[15:19])
this_month=int(line[20:22])
this_day = int(line[23:25])
this_date = this_year+this_month/12.0 +this_day/365.25
if last_date < this_date:
last_date=this_date
year=this_year
day = this_day
month=this_month
mag={}
for line in lines:
try:
mags=line[65:69].strip()
if len(mags)==0:
continue
filter=line[70]
if filter not in mag:
mag[filter]=[]
mag[filter].append(float(mags))
except:
continue
mags=''
for filter in mag:
magv=0
for m in mag[filter]:
magv = magv+m/len(mag[filter])
mags = mags+ "%4.1f-%s " % ( magv , filter)
if len(mags)==0:
mags= "N/A"
objInfoDict[name]+="MAG: "+mags+"\n"
objInfoDict[name]+="Last obs: %s %s %s \n" % (year,month, day)
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OSSOS/MOP | src/jjk/preproc/MOPplot.py | fits_list | def fits_list(filter,root,fnames):
"""Get a list of files matching filter in directory root"""
import re, pyfits, wcsutil
for file in fnames:
if re.match(filter,file):
fh=pyfits.open(file)
for ext in fh:
obj=ext.header.get('OBJECT',file)
dx=ext.header.get('NAXIS1',None)
dy=ext.header.get('NAXIS2',None)
wcs=wcsutil.WCSObject(ext)
(x1,y1)=wcs.xy2rd((1,1,))
(x2,y2)=wcs.xy2rd((dx,dy))
ccds=[x1,y1,x2,y2]
pointing={'label': obj, 'camera': ccds}
return files | python | def fits_list(filter,root,fnames):
"""Get a list of files matching filter in directory root"""
import re, pyfits, wcsutil
for file in fnames:
if re.match(filter,file):
fh=pyfits.open(file)
for ext in fh:
obj=ext.header.get('OBJECT',file)
dx=ext.header.get('NAXIS1',None)
dy=ext.header.get('NAXIS2',None)
wcs=wcsutil.WCSObject(ext)
(x1,y1)=wcs.xy2rd((1,1,))
(x2,y2)=wcs.xy2rd((dx,dy))
ccds=[x1,y1,x2,y2]
pointing={'label': obj, 'camera': ccds}
return files | [
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OSSOS/MOP | src/jjk/preproc/MOPplot.py | load_fis | def load_fis(dir=None):
"""Load fits images in a directory"""
if dir is None:
import tkFileDialog
try:
dir=tkFileDialog.askdirectory()
except:
return
if dir is None:
return None
from os.path import walk
walk(dir,fits_list,"*.fits") | python | def load_fis(dir=None):
"""Load fits images in a directory"""
if dir is None:
import tkFileDialog
try:
dir=tkFileDialog.askdirectory()
except:
return
if dir is None:
return None
from os.path import walk
walk(dir,fits_list,"*.fits") | [
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OSSOS/MOP | src/jjk/preproc/MOPplot.py | do_objs | def do_objs(kbos):
"""Draw the actual plot"""
import orbfit, ephem, math
import re
re_string=w.FilterVar.get()
vlist=[]
for name in kbos:
if not re.search(re_string,name):
continue
vlist.append(name)
if type(kbos[name])==type(ephem.EllipticalBody()):
kbos[name].compute(w.date.get())
ra=kbos[name].ra
dec=kbos[name].dec
a=math.radians(10.0/3600.0)
b=a
ang=0.0
color='blue'
yoffset=+10
xoffset=+10
else:
yoffset=-10
xoffset=-10
file=kbos[name]
jdate=ephem.julian_date(w.date.get())
obs=568
try:
position=orbfit.predict(file,jdate,obs)
except:
continue
ra=math.radians(position[0])
dec=math.radians(position[1])
a=math.radians(position[2]/3600.0)
b=math.radians(position[3]/3600.0)
ang=math.radians(position[4])
if ( a> math.radians(1.0) ):
color='green'
else:
color='black'
if w.show_ellipse.get()==1 :
if ( a < math.radians(5.0) ):
w.create_ellipse(ra,dec,a,b,ang)
if ( a < math.radians(1.0) ):
w.create_point(ra,dec,size=2,color=color)
if w.show_labels.get()==1:
w.label(ra,dec,name,offset=[xoffset,yoffset])
vlist.sort()
for v in vlist:
w.objList.insert(END,v)
w.plot_pointings() | python | def do_objs(kbos):
"""Draw the actual plot"""
import orbfit, ephem, math
import re
re_string=w.FilterVar.get()
vlist=[]
for name in kbos:
if not re.search(re_string,name):
continue
vlist.append(name)
if type(kbos[name])==type(ephem.EllipticalBody()):
kbos[name].compute(w.date.get())
ra=kbos[name].ra
dec=kbos[name].dec
a=math.radians(10.0/3600.0)
b=a
ang=0.0
color='blue'
yoffset=+10
xoffset=+10
else:
yoffset=-10
xoffset=-10
file=kbos[name]
jdate=ephem.julian_date(w.date.get())
obs=568
try:
position=orbfit.predict(file,jdate,obs)
except:
continue
ra=math.radians(position[0])
dec=math.radians(position[1])
a=math.radians(position[2]/3600.0)
b=math.radians(position[3]/3600.0)
ang=math.radians(position[4])
if ( a> math.radians(1.0) ):
color='green'
else:
color='black'
if w.show_ellipse.get()==1 :
if ( a < math.radians(5.0) ):
w.create_ellipse(ra,dec,a,b,ang)
if ( a < math.radians(1.0) ):
w.create_point(ra,dec,size=2,color=color)
if w.show_labels.get()==1:
w.label(ra,dec,name,offset=[xoffset,yoffset])
vlist.sort()
for v in vlist:
w.objList.insert(END,v)
w.plot_pointings() | [
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OSSOS/MOP | src/jjk/preproc/MOPplot.py | plot.eps | def eps(self):
"""Print the canvas to a postscript file"""
import tkFileDialog,tkMessageBox
filename=tkFileDialog.asksaveasfilename(message="save postscript to file",filetypes=['eps','ps'])
if filename is None:
return
self.postscript(file=filename) | python | def eps(self):
"""Print the canvas to a postscript file"""
import tkFileDialog,tkMessageBox
filename=tkFileDialog.asksaveasfilename(message="save postscript to file",filetypes=['eps','ps'])
if filename is None:
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OSSOS/MOP | src/jjk/preproc/MOPplot.py | plot.c2s | def c2s(self,p=[0,0]):
"""Convert from canvas to screen coordinates"""
return((p[0]-self.canvasx(self.cx1),p[1]-self.canvasy(self.cy1))) | python | def c2s(self,p=[0,0]):
"""Convert from canvas to screen coordinates"""
return((p[0]-self.canvasx(self.cx1),p[1]-self.canvasy(self.cy1))) | [
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