def make_normalized_image(self, newname, image):
header = image.get_header()
# normalize the data
coadds = header.get('COADDS', 1)
ndr = header.get('NDR', 1)
divisor = coadds * ndr
data_np = image.get_data()
data_np = data_np / divisor
# create a new image
new_image = AstroImage.AstroImage(data_np=data_np, logger=self.logger)
new_image.set(name=newname)
new_image.update_keywords(header)
new_image.update_keywords(
dict(COADD=1, COADDS=1, NDR=1, FRAMEID=newname))
if self.settings.get('cache_normalized_images', True):
# write out a cached copy so we can reload as necessary
try:
prefix = os.path.join(os.environ['GEN2COMMON'], 'data_cache')
except KeyError:
prefix = '/tmp'
cached_path = os.path.join(prefix, newname + '.fits')
new_image.set(path=cached_path)
if not os.path.exists(cached_path):
new_image.save_as_file(cached_path)
return new_image
def load_file(self, filepath):
image = AstroImage.AstroImage(logger=self.logger)
image.load_file(filepath)
self.fitsimage.set_image(image)
self.setWindowTitle(filepath)
# create compass
try:
try:
self.fitsimage.deleteObjectByTag(self.cp_tag)
except KeyError:
pass
(x, y, xn, yn, xe, ye) = image.calc_compass_center()
self.logger.debug("x=%d y=%d xn=%d yn=%d xe=%d ye=%d" %
(x, y, xn, yn, xe, ye))
Compass = self.fitsimage.getDrawClass('compass')
self.fitsimage.add(Compass(x,
y,
xn,
yn,
xe,
ye,
color='skyblue',
fontsize=14),
tag=self.cp_tag)
except Exception as e:
self.logger.warn("Can't calculate compass: %s" % (str(e)))
def load_image(self, filepath):
# Create an image. Assume type to be an AstroImage unless
# the MIME association says it is something different.
try:
typ, subtyp = self.guess_filetype(filepath)
except Exception:
# Can't determine file type: assume and attempt FITS
typ, subtyp = 'image', 'fits'
if (typ == 'image') and (subtyp != 'fits'):
image = RGBImage.RGBImage(logger=self.logger)
else:
image = AstroImage.AstroImage(logger=self.logger)
try:
self.logger.info("Loading image from %s" % (filepath))
image.load_file(filepath)
#self.gui_do(chinfo.fitsimage.onscreen_message, "")
except Exception as e:
errmsg = "Failed to load file '%s': %s" % (filepath, str(e))
self.logger.error(errmsg)
try:
(type, value, tb) = sys.exc_info()
tb_str = "\n".join(traceback.format_tb(tb))
except Exception as e:
tb_str = "Traceback information unavailable."
self.gui_do(self.show_error, errmsg + '\n' + tb_str)
#chinfo.fitsimage.onscreen_message("Failed to load file", delay=1.0)
raise ControlError(errmsg)
self.logger.debug("Successfully loaded file into image object.")
return image
def create_blank_image(ra_deg,
dec_deg,
fov_deg,
px_scale,
rot_deg,
cdbase=[1, 1],
dtype=None,
logger=None,
pfx='dp'):
# ra and dec in traditional format
ra_txt = wcs.raDegToString(ra_deg, format='%02d:%02d:%06.3f')
dec_txt = wcs.decDegToString(dec_deg, format='%s%02d:%02d:%05.2f')
# Create an empty image
imagesize = int(round(fov_deg / px_scale))
# round to an even size
if imagesize % 2 != 0:
imagesize += 1
## # round to an odd size
## if imagesize % 2 == 0:
## imagesize += 1
width = height = imagesize
if dtype is None:
dtype = numpy.float32
data = numpy.zeros((height, width), dtype=dtype)
crpix = float(imagesize // 2)
header = OrderedDict((
('SIMPLE', True),
('BITPIX', -32),
('EXTEND', True),
('NAXIS', 2),
('NAXIS1', imagesize),
('NAXIS2', imagesize),
('RA', ra_txt),
('DEC', dec_txt),
('EQUINOX', 2000.0),
('OBJECT', 'MOSAIC'),
('LONPOLE', 180.0),
))
# Add basic WCS keywords
wcshdr = wcs.simple_wcs(crpix,
crpix,
ra_deg,
dec_deg,
px_scale,
rot_deg,
cdbase=cdbase)
header.update(wcshdr)
# Create image container
image = AstroImage.AstroImage(data, logger=logger)
image.update_keywords(header)
# give the image a name
get_image_name(image, pfx=pfx)
return image
def _data_to_image(data):
ids = data.component_ids()
data_np = data[ids[0]]
data_meta = {}
if hasattr(data.coords, 'header'):
h = AstroImage.AstroHeader()
h.update(data.coords.header)
data_meta['header'] = h
image = AstroImage.AstroImage(data_np=data_np, metadata=data_meta)
if hasattr(data.coords, 'wcs'):
image.wcs.load_header(data.coords.wcs.to_header())
return image
def load_file(self, filepath):
image = AstroImage.AstroImage(logger=self.logger)
image.load_file(filepath)
self.fitsimage.set_image(image)
self.setWindowTitle(filepath)
# create compass
try:
try:
self.fitsimage.delete_object_by_tag(self.cp_tag)
except KeyError:
pass
width, height = image.get_size()
x, y = width / 2.0, height / 2.0
# radius we want the arms to be (approx 1/4 the largest dimension)
radius = float(max(width, height)) / 4.0
Compass = self.fitsimage.get_draw_class('compass')
self.fitsimage.add(Compass(x,
y,
radius,
color='skyblue',
fontsize=14),
tag=self.cp_tag)
except Exception as e:
self.logger.warning("Can't calculate compass: %s" % (str(e)))
def mosaic_some(self, paths, image_loader=None):
if image_loader is None:
image_loader = self.fv.load_image
for url in paths:
if self.ev_intr.isSet():
break
mosaic_hdus = self.settings.get('mosaic_hdus', False)
if mosaic_hdus:
self.logger.debug("mosaicing hdus")
# User wants us to mosaic HDUs
# TODO: do this in a different thread?
with pyfits.open(url, 'readonly') as in_f:
i = 0
for hdu in in_f:
i += 1
# TODO: I think we need a little more rigorous test
# than just whether the data section is empty
if hdu.data is None:
continue
self.logger.debug("ingesting hdu #%d" % (i))
image = AstroImage.AstroImage(logger=self.logger)
image.load_hdu(hdu)
image.set(name='hdu%d' % (i))
image = self.preprocess(image)
self.ingest_one(image)
else:
image = image_loader(url)
image = self.preprocess(image)
self.ingest_one(image)
def load_hdu(self, hdu, dstobj=None, **kwargs):
from ginga import AstroImage # Put here to avoid circular import
typ = self.get_hdu_type(hdu)
if typ == 'image':
# <-- data is an image
ahdr = AstroImage.AstroHeader()
self.fromHDU(hdu, ahdr)
metadata = dict(header=ahdr)
data = hdu.read()
if dstobj is None:
# get model class for this type of object
obj_class = self.factory_dict.get('image', None)
if obj_class is None:
raise FITSError(
"I don't know how to load objects of kind 'image'")
dstobj = obj_class(logger=self.logger)
dstobj.load_data(data, metadata=metadata)
elif typ == 'table':
# <-- data is a table
raise FITSError(
"FITS tables are not yet readable using ginga/fitsio")
return dstobj
def setup_module():
"""Create objects once and re-use throughout this module."""
global img_dict
if minversion(astropy, '3.1'):
USE_APE14 = True
else:
USE_APE14 = False
img_dict = {}
for modname in _wcsmods:
if modname == 'astropy_ape14' and not USE_APE14:
continue
if not wcsmod.use(modname, raise_err=False):
continue
img_dict[modname] = {}
for dim in _hdr.keys():
w = wcsmod.WCS(_logger)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
w.load_header(_hdr[dim])
img = AstroImage.AstroImage(logger=_logger)
img.wcs = w
if dim == '2d':
img.revnaxis = []
img.naxispath = []
else: # 3d
img.revnaxis = [0]
img.naxispath = [0]
img_dict[modname][dim] = img
def load_hdu(self, hdu, dstobj=None, **kwargs):
from ginga import AstroImage # Put here to avoid circular import
hduinfo = hdu.get_info()
hdutype = hduinfo.get('hdutype', None)
ahdr = AstroImage.AstroHeader()
self.fromHDU(hdu, ahdr)
metadata = dict(header=ahdr)
data = hdu.read()
if hdutype == fitsio.IMAGE_HDU:
# <-- data is an image
if dstobj is None:
# get model class for this type of object
obj_class = self.factory_dict.get('image', None)
if obj_class is None:
raise FITSError(
"I don't know how to load objects of kind 'image'")
dstobj = obj_class(logger=self.logger)
dstobj.load_data(data, metadata=metadata)
elif hdutype in (fitsio.ASCII_TBL, fitsio.BINARY_TBL):
# <-- data is a table
raise FITSError(
"FITS tables are not yet readable using ginga/fitsio")
return dstobj
def load_idx(self, idx, **kwargs):
if idx is None:
idx = self.find_first_good_idx()
typ = self.get_idx_type(idx)
if typ == 'image':
from ginga import AstroImage, RGBImage
header = self.get_header(idx)
data_np = np.copy(self._f[idx].value)
if 'PALETTE' in header:
p_idx = header['PALETTE']
p_data = self._f[p_idx].value
data_np = p_data[data_np]
image = RGBImage.RGBImage(logger=self.logger)
else:
image = AstroImage.AstroImage(logger=self.logger)
image.update_keywords(header)
image.set_data(data_np)
name = iohelper.name_image_from_path(self._path, idx=idx)
image.set(path=self._path, name=name, idx=idx,
image_loader=load_file)
return image
raise ValueError("I don't know how to read dataset '{}'".format(idx))
def load_file(self, filepath):
image = AstroImage.AstroImage(logger=self.logger)
with asdf.open(filepath) as asdf_f:
image.load_asdf(asdf_f)
self.fitsimage.set_image(image)
self.setWindowTitle(filepath)
def set_data(self, data, metadata=None, redraw=True):
dims = data.shape
## assert (len(dims) == 2), \
## FitsImageError("Only 2D images are supported!")
image = AstroImage.AstroImage(data,
metadata=metadata,
logger=self.logger)
self.set_image(image, redraw=redraw)
def load_hdu(self, hdu):
"""
Load an HDU into the viewer.
"""
image = AstroImage.AstroImage(logger=self.logger)
image.load_hdu(hdu)
self.set_image(image)
def load_data(self, data_np):
"""
Load raw numpy data into the viewer.
"""
image = AstroImage.AstroImage(logger=self.logger)
image.set_data(data_np)
self.set_image(image)
def load_fits(self, filepath):
"""
Load a FITS file into the viewer.
"""
image = AstroImage.AstroImage(logger=self.logger)
image.load_file(filepath)
self.set_image(image)
def load_hdu(self, hdu, dstobj=None, **kwargs):
if isinstance(hdu, (
pyfits.ImageHDU,
pyfits.CompImageHDU,
pyfits.PrimaryHDU,
)):
# <-- data is an image
if dstobj is None:
# get model class for this type of object
obj_class = self.factory_dict.get('image', None)
if obj_class is None:
raise FITSError(
"I don't know how to load objects of kind 'image'")
dstobj = obj_class(logger=self.logger)
# For now, call back into the object to load it from pyfits-style
# HDU in future migrate to storage-neutral format
dstobj.load_hdu(hdu, **kwargs)
elif isinstance(hdu, (pyfits.TableHDU, pyfits.BinTableHDU)):
# <-- data is a table
# Handle ASDF embedded in FITS.
# TODO: Populate EXTNAME, EXTVER, NAXISn in ASDF meta from HDU?
# TODO: How to read from all the different ASDF layouts?
# TODO: Cache the ASDF object?
from ginga.util import io_asdf
if io_asdf.have_asdf and hdu.name == 'ASDF':
from asdf.fits_embed import AsdfInFits
from ginga import AstroImage
self.logger.debug('Attempting to load {} extension from '
'FITS'.format(hdu.name))
dstobj = AstroImage.AstroImage()
with AsdfInFits.open(self.fits_f) as asdf_f:
dstobj.load_asdf(asdf_f)
return dstobj
if dstobj is None:
self.logger.debug('Attempting to load table from FITS')
# get model class for this type of object
obj_class = self.factory_dict.get('table', None)
if obj_class is None:
raise FITSError(
"I don't know how to load objects of kind 'table'")
dstobj = obj_class(logger=self.logger)
# For now, call back into the object to load it from pyfits-style
# HDU in future migrate to storage-neutral format
dstobj.load_hdu(hdu, **kwargs)
else:
raise FITSError("I don't know how to read this HDU")
return dstobj
def loadImage(self, data_np):
"""Load image array."""
# Set image
self.image = data_np
aimg = AstroImage.AstroImage(self.logger)
aimg.set_data(self.image)
self.set_image(aimg)
def _load(self):
"""
Loads an image into the viewer, applying appropriate transformations for proper display.
Checks if an HDU has been loaded already and retrieves if needed and then displays that HDU.
Uses multiprocessing techniques for simultaneous downloads and dictionaries to keep track of which images
have been already loaded for faster image switching.
"""
# load the image if not already available, for now we'll put this in here.
if self.candidates is None:
self.logger.info("No candidates loaded.")
return
# loads first candidate
if self.candidate is None:
self.next()
return
key = self.key
while True:
# noinspection PyBroadException
try:
if key not in self.astro_images:
# TODO: MEF
image = AstroImage.AstroImage(logger=self.logger)
image.load_hdu(self.loaded_hdu)
self.astro_images[key] = image
self.set_image(self.astro_images[key])
if self.zoom is not None:
self.zoom_to(self.zoom)
self._rotate()
if self.center is not None:
self._align()
# the image cutout is considered the first object on the canvas, this deletes everything over top of it
self.canvas.delete_objects(self.canvas.get_objects()[1:])
if key not in self.null_observation:
self.mark_aperture()
self.header_box.set_text("Header:" + self.info)
self.logger.info("Loaded: {}".format(
self.candidate[self.obs_number].comment.frame))
break
except Exception as ex:
self.logger.info(str(ex))
self.logger.info(
"Skipping candidate {} due to load failure.".format(
self.candidate[0].provisional_name))
self.next()
break
self._center = WCS(self.header).all_pix2world(
self.get_data_size()[0] / 2,
self.get_data_size()[1] / 2, 0)
def make_image(data_np, oldimage, header, pfx='dp'):
# Prepare a new image with the numpy array as data
image = AstroImage.AstroImage()
image.set_data(data_np)
# Set the header to be the old image header updated
# with items from the new header
oldhdr = oldimage.get_header()
oldhdr.update(header)
image.update_keywords(oldhdr)
# give the image a name
get_image_name(image, pfx=pfx)
return image
def mosaic(paths, logger, outfile=None):
logger.info("Mosaicing images...")
image = AstroImage.AstroImage(logger=logger)
mosaic = image.mosaic(paths)
if outfile:
try:
os.remove(outfile)
except:
pass
logger.info("Writing mosaic file to %s ..." % (outfile))
mosaic.write_fits(outfile)
def load_file(self, filepath):
log.info(f'Loading image: {filepath}')
self.clear_overlays()
image = AstroImage.AstroImage(logger=self.logger)
image.load_file(filepath)
if self.medfilt is True:
log.info('Median filtering image for display')
data = image.get_data()
filtered_image = medfilt(data, (3, 3))
image.set_data(filtered_image)
self.image = image
self.fitsimage.set_image(image)
self.setWindowTitle(f'{filepath} {self.medfilt_str}')
self.overlay_catalog()
def test_pixtoradec_scalar(self, modname):
if not wcsmod.use(modname, raise_err=False):
pytest.skip("WCS '{}' not available".format(modname))
wcs = wcsmod.WCS(self.logger)
#if wcs.wcs is None:
# pytest.skip("WCS '{}' not available".format(modname))
wcs.load_header(self.header)
img = AstroImage.AstroImage(logger=self.logger)
img.wcs = wcs
img.revnaxis = []
ra_deg_v1 = 300.2308791294835
dec_deg_v1 = 22.691653517073615
ra_deg, dec_deg = img.pixtoradec(120, 100)
np.testing.assert_allclose(ra_deg, ra_deg_v1),
np.testing.assert_allclose(dec_deg, dec_deg_v1)
def test_radectopix_scalar(self, modname):
if not wcsmod.use(modname, raise_err=False):
pytest.skip("WCS '{}' not available".format(modname))
wcs = wcsmod.WCS(self.logger)
#if wcs.wcs is None:
# pytest.skip("WCS '{}' not available".format(modname))
wcs.load_header(self.header)
img = AstroImage.AstroImage(logger=self.logger)
img.wcs = wcs
img.naxispath = []
x_v1 = 120
y_v1 = 100
x, y = img.radectopix(300.2308791294835, 22.691653517073615)
np.testing.assert_allclose(x, x_v1)
np.testing.assert_allclose(y, y_v1)
def load_asdf(asdf_obj, idx=None, logger=None):
"""
Load data from an open ASDF object.
Parameters
----------
asdf_obj : obj
ASDF or ASDF-in-FITS object.
idx : None
Currently unused. Reserved for future use to identify specific
data set of an ASDF object containing the data of interest.
logger : python logging object
Currently unused. Reserved for future use in logging
Returns
-------
data : ndarray or `None`
Image data, if found.
wcs : obj or `None`
GWCS object or models, if found.
ahdr : dict
Header containing metadata.
"""
# TODO: support other types, like AstroTable, if ASDF can contain them
data_obj = AstroImage.AstroImage(logger=logger)
# TODO: idx may contain info about what part of the file to load
# e.g. should we pass as 'data_key' parameter?
data, wcs, ahdr = load_from_asdf(asdf_obj)
data_obj.setup_data(data, naxispath=None)
wcsinfo = wcsmod.get_wcs_class('astropy_ape14')
data_obj.wcs = wcsinfo.wrapper_class(logger=logger)
data_obj.wcs.wcs = wcs
if wcs is not None:
data_obj.wcs.coordsys = wcs.output_frame.name
return data_obj
def loader(filepath, logger=None, **kwargs):
"""
Load an object from an ASDF file.
See :func:`ginga.util.loader` for more info.
TODO: kwargs may contain info about what part of the file to load
"""
# see ginga.util.loader module
# TODO: return an AstroTable if loading a table, etc.
# for now, assume always an image
from ginga import AstroImage
image = AstroImage.AstroImage(logger=logger)
with asdf.open(filepath) as asdf_f:
#image.load_asdf(asdf_f, **kwargs)
image.load_asdf(asdf_f)
return image
def radectopix_scalar_runtest(self, modname):
if not wcsmod.use(modname, raise_err=False):
return False
wcs = wcsmod.WCS(self.logger)
wcs.load_header(self.header)
img = AstroImage.AstroImage(logger=self.logger)
img.wcs = wcs
img.naxispath = []
x_v1 = 120
y_v1 = 100
x, y = img.radectopix(300.2308791294835, 22.691653517073615)
assert numpy.isclose(x, x_v1), \
ValueError("x does not match (%f != %f)" % (x, x_v1))
assert numpy.isclose(y, y_v1), \
ValueError("y does not match (%f != %f)" % (y, y_v1))
return True
def mosaic_some(self, paths, image_loader=None):
if image_loader == None:
image_loader = self.fv.load_image
for url in paths:
if self.ev_intr.isSet():
break
mosaic_hdus = self.settings.get('mosaic_hdus', False)
if mosaic_hdus:
self.logger.debug("mosaicing hdus")
# User wants us to mosaic HDUs
# TODO: do this in a different thread?
with pyfits.open(url, 'readonly') as in_f:
i = 0
for hdu in in_f:
i += 1
if hdu.data == None:
continue
self.logger.debug("ingesting hdu #%d" % (i))
image = AstroImage.AstroImage(logger=self.logger)
image.load_hdu(hdu)
image.set(name='hdu%d' % (i))
with self.lock:
self.fv.gui_call(self.fv.error_wrap, self.ingest_one, image)
with self.lock:
count = self.ingest_count
else:
image = image_loader(url)
with self.lock:
self.fv.gui_call(self.fv.error_wrap, self.ingest_one, image)
count = self.ingest_count
self.update_progress(float(count)/self.total_files)
if count == self.total_files:
self.end_progress()
total_elapsed = time.time() - self.start_time
msg = "Done. Total=%.2f Process=%.2f (sec)" % (
total_elapsed, self.process_elapsed)
self.update_status(msg)
def set_hdu(self, idx):
self.logger.debug("Loading fits hdu #%d" % (idx))
image = AstroImage.AstroImage(logger=self.logger)
try:
hdu = self.fits_f[idx - 1]
dims = list(hdu.data.shape)
dims.reverse()
image.load_hdu(hdu)
image.set(path=self.path)
self.fitsimage.set_image(image)
self.build_naxis(dims)
self.curhdu = idx - 1
self.logger.debug("HDU #%d loaded." % (idx))
except Exception as e:
errmsg = "Error loading FITS HDU #%d: %s" % (idx, str(e))
self.logger.error(errmsg)
self.fv.show_error(errmsg)
def pixtoradec_scalar_runtest(self, modname):
if not wcsmod.use(modname, raise_err=False):
return False
wcs = wcsmod.WCS(self.logger)
wcs.load_header(self.header)
img = AstroImage.AstroImage(logger=self.logger)
img.wcs = wcs
img.revnaxis = []
ra_deg_v1 = 300.2308791294835
dec_deg_v1 = 22.691653517073615
ra_deg, dec_deg = img.pixtoradec(120, 100)
assert numpy.isclose(ra_deg, ra_deg_v1), \
ValueError("RA deg does not match (%f != %f)" % (ra_deg,
ra_deg_v1))
assert numpy.isclose(dec_deg, dec_deg_v1), \
ValueError("DEC deg does not match (%f != %f)" % (dec_deg,
dec_deg_v1))
return True