def load(filename, center=None, **kw):
"""Imports an AIPs clean component list file
"""
srclist = []
dprint(1, "importing AIPS clean component table", filename)
# read file
ff = open(filename)
if center is None:
raise ValueError("field centre must be specified")
# now process file line-by-line
linenum = 0
for line in ff:
linenum += 1
# parse one line
dprint(4, "read line:", line)
ff = line.split()
if len(ff) != 5:
continue
try:
num = int(ff[0])
dx, dy, i, i_tot = list(map(float, ff[1:]))
except:
continue
try:
# convert dx/dy to real positions
l, m = sin(dx * ARCSEC), sin(dy * ARCSEC)
ra, dec = lm_to_radec(l, m, *center)
pos = ModelClasses.Position(ra, dec)
except Exception as exc:
print("CC %d: error converting coordinates (%s), skipping" %
(num, str(exc)))
continue
flux = ModelClasses.Flux(i)
# now create a source object
src = SkyModel.Source('cc%d' % num, pos, flux)
src.setAttribute('r', math.sqrt(l * l + m * m))
srclist.append(src)
dprintf(2, "imported %d sources from file %s\n", len(srclist), filename)
# create model
model = ModelClasses.SkyModel(*srclist)
# setup model center
model.setFieldCenter(*center)
# setup radial distances
projection = Coordinates.Projection.SinWCS(*model.fieldCenter())
for src in model.sources:
l, m = projection.lm(src.pos.ra, src.pos.dec)
src.setAttribute('r', math.sqrt(l * l + m * m))
return model
def load(filename, center=None, **kw):
"""Imports an AIPS clean component list from FITS table
"""
srclist = []
dprint(1, "importing AIPS clean component FITS table", filename)
# read file
ff = pyfits.open(filename)
if center is None:
hdr = ff[0].header
ra = hdr['CRVAL1'] * _units[hdr.get('CUNIT1', 'DEG').strip()]
dec = hdr['CRVAL2'] * _units[hdr.get('CUNIT2', 'DEG').strip()]
print("Using FITS image centre (%.4f, %.4f deg) as field centre" %
(ra / DEG, dec / DEG))
center = ra, dec
# now process file line-by-line
cclist = ff[1].data
hdr = ff[1].header
ux = _units[hdr.get('TUNIT2', 'DEG').strip()]
uy = _units[hdr.get('TUNIT3', 'DEG').strip()]
for num, ccrec in enumerate(cclist):
stokes_i, dx, dy = list(map(float, ccrec))
# convert dx/dy to real positions
l, m = sin(dx * ux), sin(dy * uy)
ra, dec = lm_to_radec(l, m, *center)
pos = ModelClasses.Position(ra, dec)
flux = ModelClasses.Flux(stokes_i)
# now create a source object
src = SkyModel.Source('cc%d' % num, pos, flux)
src.setAttribute('r', math.sqrt(l * l + m * m))
srclist.append(src)
dprintf(2, "imported %d sources from file %s\n", len(srclist), filename)
# create model
model = ModelClasses.SkyModel(*srclist)
# setup model center
model.setFieldCenter(*center)
# setup radial distances
projection = Coordinates.Projection.SinWCS(*model.fieldCenter())
for src in model.sources:
l, m = projection.lm(src.pos.ra, src.pos.dec)
src.setAttribute('r', math.sqrt(l * l + m * m))
return model
def load (filename,center=None,**kw):
"""Imports an AIPs clean component list file
"""
srclist = [];
dprint(1,"importing AIPS clean component table",filename);
# read file
ff = file(filename);
if center is None:
raise ValueError,"field centre must be specified";
# now process file line-by-line
linenum = 0;
for line in ff:
linenum += 1;
# parse one line
dprint(4,"read line:",line);
ff = line.split();
if len(ff) != 5:
continue;
try:
num = int(ff[0]);
dx,dy,i,i_tot = map(float,ff[1:]);
except:
continue;
try:
# convert dx/dy to real positions
l,m = sin(dx*ARCSEC),sin(dy*ARCSEC);
ra,dec = lm_to_radec(l,m,*center);
pos = ModelClasses.Position(ra,dec);
except Exception,exc:
print "CC %d: error converting coordinates (%s), skipping"%(num,str(exc));
continue;
flux = ModelClasses.Flux(i);
# now create a source object
src = SkyModel.Source('cc%d'%num,pos,flux);
src.setAttribute('r',math.sqrt(l*l+m*m));
srclist.append(src);
def load(filename, center=None, **kw):
"""Imports an AIPS clean component list from FITS table
"""
srclist = []
dprint(1, "importing AIPS clean component FITS table", filename)
# read file
ff = pyfits.open(filename)
if center is None:
ra = ff[0].header['CRVAL1']
dec = ff[0].header['CRVAL2']
print "Using FITS image centre (%.4f, %.4f deg) as field centre" % (
ra, dec)
center = ra * DEG, dec * DEG
# now process file line-by-line
cclist = ff[1].data
for num, ccrec in enumerate(cclist):
stokes_i, dx, dy = map(float, ccrec)
# convert dx/dy to real positions
l, m = sin(dx * ARCSEC), sin(dy * ARCSEC)
ra, dec = lm_to_radec(l, m, *center)
pos = ModelClasses.Position(ra, dec)
flux = ModelClasses.Flux(stokes_i)
# now create a source object
src = SkyModel.Source('cc%d' % num, pos, flux)
src.setAttribute('r', math.sqrt(l * l + m * m))
srclist.append(src)
dprintf(2, "imported %d sources from file %s\n", len(srclist), filename)
# create model
model = ModelClasses.SkyModel(*srclist)
# setup model center
model.setFieldCenter(*center)
# setup radial distances
projection = Coordinates.Projection.SinWCS(*model.fieldCenter())
return model
def accept(self):
"""Tries to make a brick, and closes the dialog if successful."""
sources = [
src for src in self.model.sources
if src.selected and src.typecode == 'pnt'
]
filename = self.wfile.filename()
if not self._fileSelected(filename):
return
# get PB expression
pbfunc = None
if self.wpb_apply.isChecked():
pbexp = str(self.wpb_exp.text())
try:
pbfunc = eval("lambda r,fq:" + pbexp)
except Exception as err:
QMessageBox.warning(
self, "Error parsing PB experssion",
"Error parsing primary beam expression %s: %s" %
(pbexp, str(err)))
return
# get frequency
freq = str(self.wfreq.text())
freq = float(freq) * 1e+6 if freq else None
# get pad factor
pad = str(self.wpad.text())
pad = max(float(pad), 1) if pad else 1
# read fits file
busy = BusyIndicator()
try:
input_hdu = pyfits.open(filename)[0]
except Exception as err:
busy = None
QMessageBox.warning(
self, "Error reading FITS",
"Error reading FITS file %s: %s" % (filename, str(err)))
return
# reset data if asked to
if self.woverwrite.isChecked():
input_hdu.data[...] = 0
# insert sources
Imaging.restoreSources(input_hdu,
sources,
0,
primary_beam=pbfunc,
freq=freq)
# save fits file
try:
# pyfits seems to produce an exception:
# TypeError: formatwarning() takes exactly 4 arguments (5 given)
# when attempting to overwrite a file. As a workaround, remove the file first.
if os.path.exists(filename):
os.remove(filename)
input_hdu.writeto(filename)
except Exception as err:
traceback.print_exc()
busy = None
QMessageBox.warning(
self, "Error writing FITS",
"Error writing FITS file %s: %s" % (filename, str(err)))
return
changed = False
sources = self.model.sources
# remove sources from model if asked to
if self.wdel.isChecked():
sources = [
src for src in sources
if not (src.selected and src.typecode == 'pnt')
]
changed = True
# add image to model if asked to
if self.wadd.isChecked():
hdr = input_hdu.header
# get image parameters
max_flux = float(input_hdu.data.max())
wcs = WCS(hdr, mode='pyfits')
# Get reference pixel coordinates
# wcs.getCentreWCSCoords() doesn't work, as that gives us the middle of the image
# So scan the header to get the CRPIX values
ra0 = dec0 = 1
for iaxis in range(hdr['NAXIS']):
axs = str(iaxis + 1)
name = hdr.get('CTYPE' + axs, axs).upper()
if name.startswith("RA"):
ra0 = hdr.get('CRPIX' + axs, 1) - 1
elif name.startswith("DEC"):
dec0 = hdr.get('CRPIX' + axs, 1) - 1
# convert pixel to degrees
ra0, dec0 = wcs.pix2wcs(ra0, dec0)
ra0 *= DEG
dec0 *= DEG
sx, sy = wcs.getHalfSizeDeg()
sx *= DEG
sy *= DEG
nx, ny = input_hdu.data.shape[-1:-3:-1]
# check if this image is already contained in the model
for src in sources:
if isinstance(getattr(src, 'shape', None),
ModelClasses.FITSImage) and os.path.samefile(
src.shape.filename, filename):
# update source parameters
src.pos.ra, src.pos.dec = ra0, dec0
src.flux.I = max_flux
src.shape.ex, src.shape.ey = sx, sy
src.shape.nx, src.shape.ny = nx, ny
src.shape.pad = pad
break
# not contained, make new source object
else:
pos = ModelClasses.Position(ra0, dec0)
flux = ModelClasses.Flux(max_flux)
shape = ModelClasses.FITSImage(sx,
sy,
0,
os.path.basename(filename),
nx,
ny,
pad=pad)
img_src = SkyModel.Source(os.path.splitext(
os.path.basename(filename))[0],
pos,
flux,
shape=shape)
sources.append(img_src)
changed = True
if changed:
self.model.setSources(sources)
self.model.emitUpdate(SkyModel.SkyModel.UpdateAll, origin=self)
self.parent().showMessage("Wrote %d sources to FITS file %s" %
(len(sources), filename))
busy = None
return QDialog.accept(self)
class AddBrickDialog(QDialog):
def __init__(self, parent, modal=True, flags=Qt.WindowFlags()):
QDialog.__init__(self, parent, flags)
self.setModal(modal)
self.setWindowTitle("Add FITS brick")
lo = QVBoxLayout(self)
lo.setMargin(10)
lo.setSpacing(5)
# file selector
self.wfile = FileSelector(self,
label="FITS filename:",
dialog_label="FITS file",
default_suffix="fits",
file_types="FITS files (*.fits *.FITS)",
file_mode=QFileDialog.ExistingFile)
lo.addWidget(self.wfile)
# overwrite or add mode
lo1 = QGridLayout()
lo.addLayout(lo1)
lo1.setContentsMargins(0, 0, 0, 0)
lo1.addWidget(QLabel("Padding factor:", self), 0, 0)
self.wpad = QLineEdit("2", self)
self.wpad.setValidator(QDoubleValidator(self))
lo1.addWidget(self.wpad, 0, 1)
lo1.addWidget(QLabel("Assign source name:", self), 1, 0)
self.wname = QLineEdit(self)
lo1.addWidget(self.wname, 1, 1)
# OK/cancel buttons
lo.addSpacing(10)
lo2 = QHBoxLayout()
lo.addLayout(lo2)
lo2.setContentsMargins(0, 0, 0, 0)
lo2.setMargin(5)
self.wokbtn = QPushButton("OK", self)
self.wokbtn.setMinimumWidth(128)
QObject.connect(self.wokbtn, SIGNAL("clicked()"), self.accept)
self.wokbtn.setEnabled(False)
cancelbtn = QPushButton("Cancel", self)
cancelbtn.setMinimumWidth(128)
QObject.connect(cancelbtn, SIGNAL("clicked()"), self.reject)
lo2.addWidget(self.wokbtn)
lo2.addStretch(1)
lo2.addWidget(cancelbtn)
self.setMinimumWidth(384)
# signals
QObject.connect(self.wfile, SIGNAL("filenameSelected"),
self._fileSelected)
# internal state
self.qerrmsg = QErrorMessage(self)
def setModel(self, model):
self.model = model
if model.filename():
self._model_dir = os.path.dirname(os.path.abspath(
model.filename()))
else:
self._model_dir = os.path.abspath('.')
self.wfile.setDirectory(self._model_dir)
self._fileSelected(self.wfile.filename(), quiet=True)
def _fileSelected(self, filename, quiet=False):
self.wokbtn.setEnabled(False)
if not filename:
return None
# check that filename matches model
if not os.path.samefile(self._model_dir, os.path.dirname(filename)):
self.wfile.setFilename('')
if not quiet:
QMessageBox.warning(
self, "Directory mismatch",
"""<P>The FITS file must reside in the same directory
as the current sky model.</P>""")
self.wfile.setDirectory(self._model_dir)
return None
# if filename is not in model already, enable the "add to model" control
for src in self.model.sources:
if isinstance(getattr(src, 'shape', None), ModelClasses.FITSImage):
if os.path.exists(src.shape.filename) and os.path.samefile(
src.shape.filename, filename):
if not quiet:
QMessageBox.warning(
self, "Already in model",
"This FITS brick is already present in the model.")
self.wfile.setFilename('')
return None
if not str(self.wname.text()):
self.wname.setText(
os.path.splitext(os.path.basename(str(filename)))[0])
self.wokbtn.setEnabled(True)
return filename
def accept(self):
"""Tries to add brick, and closes the dialog if successful."""
filename = self.wfile.filename()
# read fits file
busy = BusyIndicator()
try:
input_hdu = pyfits.open(filename)[0]
except Exception, err:
busy = None
QMessageBox.warning(
self, "Error reading FITS",
"Error reading FITS file %s: %s" % (filename, str(err)))
return
# check name
srcname = str(self.wname.text()) or os.path.splitext(
os.path.basename(str(filename)))[0]
if srcname in set([src.name for src in self.model.sources]):
QMessageBox.warning(
self, "Already in model",
"<p>The model already contains a source named '%s'. Please select a different name.</p>"
% srcname)
return
# get image parameters
hdr = input_hdu.header
max_flux = float(input_hdu.data.max())
wcs = WCS(hdr, mode='pyfits')
# Get reference pixel coordinates
# wcs.getCentreWCSCoords() doesn't work, as that gives us the middle of the image
# So scan the header to get the CRPIX values
ra0 = dec0 = 1
for iaxis in range(hdr['NAXIS']):
axs = str(iaxis + 1)
name = hdr.get('CTYPE' + axs, axs).upper()
if name.startswith("RA"):
ra0 = hdr.get('CRPIX' + axs, 1) - 1
elif name.startswith("DEC"):
dec0 = hdr.get('CRPIX' + axs, 1) - 1
# convert pixel to degrees
# print ra0,dec0;
ra0, dec0 = wcs.pix2wcs(ra0, dec0)
ra0 *= DEG
dec0 *= DEG
# print ModelClasses.Position.ra_hms_static(ra0);
# print ModelClasses.Position.dec_sdms_static(dec0);
sx, sy = wcs.getHalfSizeDeg()
sx *= DEG
sy *= DEG
nx, ny = input_hdu.data.shape[-1:-3:-1]
pos = ModelClasses.Position(ra0, dec0)
flux = ModelClasses.Flux(max_flux)
shape = ModelClasses.FITSImage(sx,
sy,
0,
os.path.basename(filename),
nx,
ny,
pad=float(str(self.wpad.text()) or "1"))
img_src = SkyModel.Source(srcname, pos, flux, shape=shape)
self.model.setSources(self.model.sources + [img_src])
self.model.emitUpdate(SkyModel.SkyModel.UpdateAll, origin=self)
busy = None
return QDialog.accept(self)
def accept(self):
"""Tries to add brick, and closes the dialog if successful."""
filename = self.wfile.filename()
# read fits file
busy = BusyIndicator()
try:
input_hdu = pyfits.open(filename)[0]
except Exception as err:
busy.reset_cursor()
QMessageBox.warning(
self, "Error reading FITS",
"Error reading FITS file %s: %s" % (filename, str(err)))
return
# check name
srcname = str(self.wname.text()) or os.path.splitext(
os.path.basename(str(filename)))[0]
if srcname in set([src.name for src in self.model.sources]):
QMessageBox.warning(
self, "Already in model",
"<p>The model already contains a source named '%s'. Please select a different name.</p>"
% srcname)
return
# get image parameters
hdr = input_hdu.header
max_flux = float(input_hdu.data.max())
wcs = WCS(hdr, mode='pyfits')
# Get reference pixel coordinates
# wcs.getCentreWCSCoords() doesn't work, as that gives us the middle of the image
# So scan the header to get the CRPIX values
ra0 = dec0 = 1
for iaxis in range(hdr['NAXIS']):
axs = str(iaxis + 1)
name = hdr.get('CTYPE' + axs, axs).upper()
if name.startswith("RA"):
ra0 = hdr.get('CRPIX' + axs, 1) - 1
elif name.startswith("DEC"):
dec0 = hdr.get('CRPIX' + axs, 1) - 1
# convert pixel to degrees
# print ra0,dec0
ra0, dec0 = wcs.pix2wcs(ra0, dec0)
ra0 *= DEG
dec0 *= DEG
# print ModelClasses.Position.ra_hms_static(ra0)
# print ModelClasses.Position.dec_sdms_static(dec0)
sx, sy = wcs.getHalfSizeDeg()
sx *= DEG
sy *= DEG
nx, ny = input_hdu.data.shape[-1:-3:-1]
pos = ModelClasses.Position(ra0, dec0)
flux = ModelClasses.Flux(max_flux)
shape = ModelClasses.FITSImage(sx,
sy,
0,
os.path.basename(filename),
nx,
ny,
pad=float(str(self.wpad.text()) or "1"))
img_src = SkyModel.Source(srcname, pos, flux, shape=shape)
self.model.setSources(self.model.sources + [img_src])
self.model.emitUpdate(SkyModel.SkyModel.UpdateAll, origin=self)
busy.reset_cursor()
return QDialog.accept(self)
sy *= DEG;
nx,ny = input_hdu.data.shape[-1:-3:-1];
# check if this image is already contained in the model
for src in sources:
if isinstance(getattr(src,'shape',None),ModelClasses.FITSImage) and os.path.samefile(src.shape.filename,filename):
# update source parameters
src.pos.ra,src.pos.dec = ra0,dec0;
src.flux.I = max_flux;
src.shape.ex,src.shape.ey = sx,sy;
src.shape.nx,src.shape.ny = nx,ny;
src.shape.pad = pad;
break;
# not contained, make new source object
else:
pos = ModelClasses.Position(ra0,dec0);
flux = ModelClasses.Flux(max_flux);
shape = ModelClasses.FITSImage(sx,sy,0,os.path.basename(filename),nx,ny,pad=pad);
img_src = SkyModel.Source(os.path.splitext(os.path.basename(filename))[0],pos,flux,shape=shape);
sources.append(img_src);
changed = True;
if changed:
self.model.setSources(sources);
self.model.emitUpdate(SkyModel.SkyModel.UpdateAll,origin=self);
self.parent().showMessage("Wrote %d sources to FITS file %s"%(len(sources),filename));
busy = None;
return QDialog.accept(self);
def make_brick (mainwin,model):
# check that something is selected
if not [ src for src in model.sources if src.selected ]:
mainwin.showErrorMessage("Cannot make FITS brick without a source selection. Please select some sources first.");