class ExportKarmaDialog(QDialog):
def __init__(self, parent, modal=True, flags=Qt.WindowFlags()):
QDialog.__init__(self, parent, flags)
self.setModal(modal)
self.setWindowTitle("Export Karma annotations")
lo = QVBoxLayout(self)
lo.setMargin(10)
lo.setSpacing(5)
# file selector
self.wfile = FileSelector(self,
label="Filename:",
dialog_label="Karma annotations filename",
default_suffix="ann",
file_types="Karma annotations (*.ann)")
lo.addWidget(self.wfile)
# selected sources checkbox
self.wsel = QCheckBox("selected sources only", self)
lo.addWidget(self.wsel)
# 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("valid"), self.wokbtn.setEnabled)
# internal state
self.qerrmsg = QErrorMessage(self)
self._model_filename = None
def setModel(self, model):
self.model = model
# set the default annotations filename, whenever a new model filename is set
filename = self.model.filename()
if filename and filename != self._model_filename:
self._model_filename = filename
self.wfile.setFilename(os.path.splitext(filename)[0] + ".ann")
def accept(self):
"""Tries to export annotations, and closes the dialog if successful."""
try:
filename = self.wfile.filename()
if os.path.exists(filename) and QMessageBox.question(
self, "Exporting Karma annotations",
"<P>Overwrite the file %s?</P>" % filename, QMessageBox.Yes
| QMessageBox.No, QMessageBox.Yes) != QMessageBox.Yes:
return
f = file(self.wfile.filename(), "wt")
f.write('COORD W\nPA STANDARD\nCOLOR GREEN\nFONT hershey12\n')
# source list
if self.wsel.isChecked():
sources = [src for src in self.model.sources if src.selected]
else:
sources = self.model.sources
# calculate basis size for crosses (TODO: replace min_size with something more sensible, as this value is in degrees)
brightnesses = [
abs(src.brightness()) for src in sources
if src.brightness() != 0
]
min_bright = brightnesses and min(brightnesses)
min_size = 0.01
# loop over sources
busy = BusyIndicator()
for src in sources:
ra = src.pos.ra / DEG
dec = src.pos.dec / DEG
# figure out source size
if src.brightness() and min_bright:
ysize = (math.log10(abs(src.brightness())) -
math.log10(min_bright) + 1) * min_size
else:
ysize = min_size
xsize = ysize / (math.cos(src.pos.dec) or 1)
# figure out source style
style, label = self.model.getSourcePlotStyle(src)
if style:
f.write('# %s\n' % src.name)
# write symbol for source
f.write('COLOR %s\n' % style.symbol_color)
if style.symbol == "plus":
f.write('CROSS %.12f %.12f %f %f\n' %
(ra, dec, xsize, ysize))
elif style.symbol == "cross":
f.write('CROSS %.12f %.12f %f %f 45\n' %
(ra, dec, ysize, ysize))
elif style.symbol == "circle":
f.write('CIRCLE %.12f %.12f %f\n' % (ra, dec, ysize))
elif style.symbol == "dot":
f.write('DOT %.12f %.12f\n' % (ra, dec))
elif style.symbol == "square":
f.write('CBOX %.12f %.12f %f %f\n' %
(ra, dec, xsize, ysize))
elif style.symbol == "diamond":
f.write('CBOX %.12f %.12f %f %f 45\n' %
(ra, dec, xsize, ysize))
# write label
if label:
f.write('FONT hershey%d\n' % (style.label_size * 2))
f.write('COLOR %s\n' % style.label_color)
f.write('TEXT %.12f %.12f %s\n' % (ra, dec, label))
f.close()
except IOError as err:
busy = None
self.qerrmsg.showMessage(
"Error writing Karma annotations file %s: %s" %
(filename, str(err)))
return
busy = None
self.parent().showMessage(
"Wrote Karma annotations for %d sources to file %s" %
(len(sources), filename))
return QDialog.accept(self)
class MakeBrickDialog(QDialog):
def __init__(self, parent, modal=True, flags=Qt.WindowFlags()):
QDialog.__init__(self, parent, flags)
self.setModal(modal)
self.setWindowTitle("Convert sources to FITS brick")
lo = QVBoxLayout(self)
lo.setMargin(10)
lo.setSpacing(5)
# file selector
self.wfile = FileSelector(self,
label="FITS filename:",
dialog_label="Output FITS file",
default_suffix="fits",
file_types="FITS files (*.fits *.FITS)",
file_mode=QFileDialog.ExistingFile)
lo.addWidget(self.wfile)
# reference frequency
lo1 = QHBoxLayout()
lo.addLayout(lo1)
lo1.setContentsMargins(0, 0, 0, 0)
label = QLabel("Frequency, MHz:", self)
lo1.addWidget(label)
tip = """<P>If your sky model contains spectral information (such as spectral indices), then a brick may be generated
for a specific frequency. If a frequency is not specified here, the reference frequency of the model sources will be assumed.</P>"""
self.wfreq = QLineEdit(self)
self.wfreq.setValidator(QDoubleValidator(self))
label.setToolTip(tip)
self.wfreq.setToolTip(tip)
lo1.addWidget(self.wfreq)
# beam gain
lo1 = QHBoxLayout()
lo.addLayout(lo1)
lo1.setContentsMargins(0, 0, 0, 0)
self.wpb_apply = QCheckBox("Apply primary beam expression:", self)
self.wpb_apply.setChecked(True)
lo1.addWidget(self.wpb_apply)
tip = """<P>If this option is specified, a primary power beam gain will be applied to the sources before inserting
them into the brick. This can be any valid Python expression making use of the variables 'r' (corresponding
to distance from field centre, in radians) and 'fq' (corresponding to frequency.)</P>"""
self.wpb_exp = QLineEdit(self)
self.wpb_apply.setToolTip(tip)
self.wpb_exp.setToolTip(tip)
lo1.addWidget(self.wpb_exp)
# overwrite or add mode
lo1 = QHBoxLayout()
lo.addLayout(lo1)
lo1.setContentsMargins(0, 0, 0, 0)
self.woverwrite = QRadioButton("overwrite image", self)
self.woverwrite.setChecked(True)
lo1.addWidget(self.woverwrite)
self.waddinto = QRadioButton("add into image", self)
lo1.addWidget(self.waddinto)
# add to model
self.wadd = QCheckBox(
"Add resulting brick to sky model as a FITS image component", self)
lo.addWidget(self.wadd)
lo1 = QHBoxLayout()
lo.addLayout(lo1)
lo1.setContentsMargins(0, 0, 0, 0)
self.wpad = QLineEdit(self)
self.wpad.setValidator(QDoubleValidator(self))
self.wpad.setText("1.1")
lab = QLabel("...with padding factor:", self)
lab.setToolTip(
"""<P>The padding factor determines the amount of null padding inserted around the image during
the prediction stage. Padding alleviates the effects of tapering and detapering in the uv-brick, which can show
up towards the edges of the image. For a factor of N, the image will be padded out to N times its original size.
This increases memory use, so if you have no flux at the edges of the image anyway, then a pad factor of 1 is
perfectly fine.</P>""")
self.wpad.setToolTip(lab.toolTip())
QObject.connect(self.wadd, SIGNAL("toggled(bool)"),
self.wpad.setEnabled)
QObject.connect(self.wadd, SIGNAL("toggled(bool)"), lab.setEnabled)
self.wpad.setEnabled(False)
lab.setEnabled(False)
lo1.addStretch(1)
lo1.addWidget(lab, 0)
lo1.addWidget(self.wpad, 1)
self.wdel = QCheckBox(
"Remove from the sky model sources that go into the brick", self)
lo.addWidget(self.wdel)
# 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
pb = self.model.primaryBeam()
if pb:
self.wpb_exp.setText(pb)
else:
self.wpb_apply.setChecked(False)
self.wpb_exp.setText("")
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
# read fits file
busy = BusyIndicator()
try:
input_hdu = pyfits.open(filename)[0]
hdr = input_hdu.header
# get frequency, if specified
for axis in range(1, hdr['NAXIS'] + 1):
if hdr['CTYPE%d' % axis].upper() == 'FREQ':
self.wfreq.setText(str(hdr['CRVAL%d' % axis] / 1e+6))
break
except Exception as err:
busy = None
self.wfile.setFilename('')
if not quiet:
QMessageBox.warning(
self, "Error reading FITS",
"Error reading FITS file %s: %s" % (filename, str(err)))
return None
self.wokbtn.setEnabled(True)
# 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) \
and os.path.exists(src.shape.filename) and os.path.exists(filename) \
and os.path.samefile(src.shape.filename, filename):
self.wadd.setChecked(True)
self.wadd.setEnabled(False)
self.wadd.setText("image already in sky model")
break
else:
self.wadd.setText("add image to sky model")
return filename
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 RestoreImageDialog (QDialog):
def __init__ (self,parent,modal=True,flags=Qt.WindowFlags()):
QDialog.__init__(self,parent,flags);
self.setModal(modal);
self.setWindowTitle("Restore model into image");
lo = QVBoxLayout(self);
lo.setMargin(10);
lo.setSpacing(5);
# file selector
self.wfile_in = FileSelector(self,label="Input FITS file:",dialog_label="Input FITS file",default_suffix="fits",file_types="FITS files (*.fits *.FITS)",file_mode=QFileDialog.ExistingFile);
lo.addWidget(self.wfile_in);
self.wfile_out = FileSelector(self,label="Output FITS file:",dialog_label="Output FITS file",default_suffix="fits",file_types="FITS files (*.fits *.FITS)",file_mode=QFileDialog.AnyFile);
lo.addWidget(self.wfile_out);
# beam size
lo1 = QHBoxLayout();
lo.addLayout(lo1);
lo1.setContentsMargins(0,0,0,0);
lo1.addWidget(QLabel("Restoring beam FWHM, major axis:",self));
self.wbmaj = QLineEdit(self);
lo1.addWidget(self.wbmaj);
lo1.addWidget(QLabel("\" minor axis:",self));
self.wbmin = QLineEdit(self);
lo1.addWidget(self.wbmin);
lo1.addWidget(QLabel("\" P.A.:",self));
self.wbpa = QLineEdit(self);
lo1.addWidget(self.wbpa);
lo1.addWidget(QLabel(u"\u00B0",self));
for w in self.wbmaj,self.wbmin,self.wbpa:
w.setValidator(QDoubleValidator(self));
lo1 = QHBoxLayout();
lo.addLayout(lo1);
lo1.setContentsMargins(0,0,0,0);
self.wfile_psf = FileSelector(self,label="Set restoring beam by fitting PSF image:",dialog_label="PSF FITS file",default_suffix="fits",file_types="FITS files (*.fits *.FITS)",file_mode=QFileDialog.ExistingFile);
lo1.addSpacing(32);
lo1.addWidget(self.wfile_psf);
# selection only
self.wselonly = QCheckBox("restore selected model sources only",self);
lo.addWidget(self.wselonly );
# 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_in,SIGNAL("filenameSelected"),self._fileSelected);
QObject.connect(self.wfile_in,SIGNAL("filenameSelected"),self._inputFileSelected);
QObject.connect(self.wfile_out,SIGNAL("filenameSelected"),self._fileSelected);
QObject.connect(self.wfile_psf,SIGNAL("filenameSelected"),self._psfFileSelected);
# internal state
self.qerrmsg = QErrorMessage(self);
def setModel (self,model):
nsel = len([ src for src in model.sources if src.selected ]);
self.wselonly.setVisible(nsel>0 and nsel<len(model.sources));
self.model = model;
self._fileSelected(None);
def _fileSelected (self,filename):
self.wokbtn.setEnabled(bool(self.wfile_in.filename() and self.wfile_out.filename()));
def _inputFileSelected (self,filename):
if filename:
try:
header = pyfits.open(filename)[0].header;
except:
self.qerrmsg.showMessage("Error reading FITS file %s: %s"%(filename,str(err)));
self.wfile_in.setFilename("");
return;
# try to get beam extents
gx,gy,grot = [ header.get(x,None) for x in 'BMAJ','BMIN','BPA' ];
if all([x is not None for x in gx,gy,grot]):
# if beam size is already set, ask before overwriting
print [ str(x.text()) for x in self.wbmaj,self.wbmin,self.wbpa ]
class RestoreImageDialog(QDialog):
def __init__(self, parent, modal=True, flags=Qt.WindowFlags()):
QDialog.__init__(self, parent, flags)
self.setModal(modal)
self.setWindowTitle("Restore model into image")
lo = QVBoxLayout(self)
lo.setMargin(10)
lo.setSpacing(5)
# file selector
self.wfile_in = FileSelector(self, label="Input FITS file:", dialog_label="Input FITS file",
default_suffix="fits", file_types="FITS files (*.fits *.FITS)",
file_mode=QFileDialog.ExistingFile)
lo.addWidget(self.wfile_in)
self.wfile_out = FileSelector(self, label="Output FITS file:", dialog_label="Output FITS file",
default_suffix="fits", file_types="FITS files (*.fits *.FITS)",
file_mode=QFileDialog.AnyFile)
lo.addWidget(self.wfile_out)
# beam size
lo1 = QHBoxLayout()
lo.addLayout(lo1)
lo1.setContentsMargins(0, 0, 0, 0)
lo1.addWidget(QLabel("Restoring beam FWHM, major axis:", self))
self.wbmaj = QLineEdit(self)
lo1.addWidget(self.wbmaj)
lo1.addWidget(QLabel("\" minor axis:", self))
self.wbmin = QLineEdit(self)
lo1.addWidget(self.wbmin)
lo1.addWidget(QLabel("\" P.A.:", self))
self.wbpa = QLineEdit(self)
lo1.addWidget(self.wbpa)
lo1.addWidget(QLabel("\u00B0", self))
for w in self.wbmaj, self.wbmin, self.wbpa:
w.setValidator(QDoubleValidator(self))
lo1 = QHBoxLayout()
lo.addLayout(lo1)
lo1.setContentsMargins(0, 0, 0, 0)
self.wfile_psf = FileSelector(self, label="Set restoring beam by fitting PSF image:",
dialog_label="PSF FITS file", default_suffix="fits",
file_types="FITS files (*.fits *.FITS)", file_mode=QFileDialog.ExistingFile)
lo1.addSpacing(32)
lo1.addWidget(self.wfile_psf)
# selection only
self.wselonly = QCheckBox("restore selected model sources only", self)
lo.addWidget(self.wselonly)
# 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_in, SIGNAL("filenameSelected"), self._fileSelected)
QObject.connect(self.wfile_in, SIGNAL("filenameSelected"), self._inputFileSelected)
QObject.connect(self.wfile_out, SIGNAL("filenameSelected"), self._fileSelected)
QObject.connect(self.wfile_psf, SIGNAL("filenameSelected"), self._psfFileSelected)
# internal state
self.qerrmsg = QErrorMessage(self)
def setModel(self, model):
nsel = len([src for src in model.sources if src.selected])
self.wselonly.setVisible(nsel > 0 and nsel < len(model.sources))
self.model = model
self._fileSelected(None)
def _fileSelected(self, filename):
self.wokbtn.setEnabled(bool(self.wfile_in.filename() and self.wfile_out.filename()))
def _inputFileSelected(self, filename):
if filename:
try:
header = pyfits.open(filename)[0].header
except Exception as err:
self.qerrmsg.showMessage("Error reading FITS file %s: %s" % (filename, str(err)))
self.wfile_in.setFilename("")
return
# try to get beam extents
gx, gy, grot = [header.get(x, None) for x in ('BMAJ', 'BMIN', 'BPA')]
if all([x is not None for x in (gx, gy, grot)]):
# if beam size is already set, ask before overwriting
print([str(x.text()) for x in (self.wbmaj, self.wbmin, self.wbpa)])
if any([bool(str(x.text())) for x in (self.wbmaj, self.wbmin, self.wbpa)]) and \
QMessageBox.question(self, "Set restoring beam",
"Also reset restoring beam size from this FITS file?",
QMessageBox.Yes | QMessageBox.No) != QMessageBox.Yes:
return
self.wbmaj.setText("%.2f" % (gx * 3600))
self.wbmin.setText("%.2f" % (gy * 3600))
self.wbpa.setText("%.2f" % grot)
def _psfFileSelected(self, filename):
busy = BusyIndicator()
filename = str(filename)
self.parent().showMessage("Fitting gaussian to PSF file %s" % filename)
try:
bmaj, bmin, pa = [x / DEG for x in Imaging.fitPsf(filename)]
except Exception as err:
busy = None
self.qerrmsg.showMessage("Error fitting PSF file %s: %s" % (filename, str(err)))
return
bmaj *= 3600 * Imaging.FWHM
bmin *= 3600 * Imaging.FWHM
self.wbmaj.setText(str(bmaj))
self.wbmin.setText(str(bmin))
self.wbpa.setText(str(pa))
def accept(self):
"""Tries to restore the image, and closes the dialog if successful."""
# get list of sources to restore
sources = self.model.sources
sel_sources = [src for src in sources if src.selected]
if len(sel_sources) > 0 and len(sel_sources) < len(sources) and self.wselonly.isChecked():
sources = sel_sources
if not sources:
self.qerrmsg.showMessage("No sources to restore.")
return
busy = BusyIndicator()
# get filenames
infile = self.wfile_in.filename()
outfile = self.wfile_out.filename()
self.parent().showMessage(
"Restoring %d model sources to image %s, writing to %s" % (len(sources), infile, outfile))
# read fits file
try:
input_hdu = pyfits.open(infile)[0]
except Exception as err:
busy = None
self.qerrmsg.showMessage("Error reading FITS file %s: %s" % (infile, str(err)))
return
# get beam sizes
try:
bmaj = float(str(self.wbmaj.text()))
bmin = float(str(self.wbmin.text()))
pa = float(str(self.wbpa.text()) or "0")
except Exception as err:
busy = None
self.qerrmsg.showMessage("Invalid beam size specified")
return
bmaj = bmaj / (Imaging.FWHM * 3600) * DEG
bmin = bmin / (Imaging.FWHM * 3600) * DEG
pa = pa * DEG
# restore
try:
Imaging.restoreSources(input_hdu, sources, bmaj, bmin, pa)
except Exception as err:
busy = None
self.qerrmsg.showMessage("Error restoring model into image: %s" % str(err))
return
# save fits file
try:
input_hdu.writeto(outfile, clobber=True)
except Exception as err:
busy = None
self.qerrmsg.showMessage("Error writing FITS file %s: %s" % (outfile, str(err)))
return
self.parent().loadImage(outfile)
busy = None
return QDialog.accept(self)
class MakeBrickDialog(QDialog):
def __init__(self, parent, modal=True, flags=Qt.WindowFlags()):
QDialog.__init__(self, parent, flags)
self.setModal(modal)
self.setWindowTitle("Convert sources to FITS brick")
lo = QVBoxLayout(self)
lo.setMargin(10)
lo.setSpacing(5)
# file selector
self.wfile = FileSelector(self, label="FITS filename:", dialog_label="Output FITS file", default_suffix="fits",
file_types="FITS files (*.fits *.FITS)", file_mode=QFileDialog.ExistingFile)
lo.addWidget(self.wfile)
# reference frequency
lo1 = QHBoxLayout()
lo.addLayout(lo1)
lo1.setContentsMargins(0, 0, 0, 0)
label = QLabel("Frequency, MHz:", self)
lo1.addWidget(label)
tip = """<P>If your sky model contains spectral information (such as spectral indices), then a brick may be generated
for a specific frequency. If a frequency is not specified here, the reference frequency of the model sources will be assumed.</P>"""
self.wfreq = QLineEdit(self)
self.wfreq.setValidator(QDoubleValidator(self))
label.setToolTip(tip)
self.wfreq.setToolTip(tip)
lo1.addWidget(self.wfreq)
# beam gain
lo1 = QHBoxLayout()
lo.addLayout(lo1)
lo1.setContentsMargins(0, 0, 0, 0)
self.wpb_apply = QCheckBox("Apply primary beam expression:", self)
self.wpb_apply.setChecked(True)
lo1.addWidget(self.wpb_apply)
tip = """<P>If this option is specified, a primary power beam gain will be applied to the sources before inserting
them into the brick. This can be any valid Python expression making use of the variables 'r' (corresponding
to distance from field centre, in radians) and 'fq' (corresponding to frequency.)</P>"""
self.wpb_exp = QLineEdit(self)
self.wpb_apply.setToolTip(tip)
self.wpb_exp.setToolTip(tip)
lo1.addWidget(self.wpb_exp)
# overwrite or add mode
lo1 = QHBoxLayout()
lo.addLayout(lo1)
lo1.setContentsMargins(0, 0, 0, 0)
self.woverwrite = QRadioButton("overwrite image", self)
self.woverwrite.setChecked(True)
lo1.addWidget(self.woverwrite)
self.waddinto = QRadioButton("add into image", self)
lo1.addWidget(self.waddinto)
# add to model
self.wadd = QCheckBox("Add resulting brick to sky model as a FITS image component", self)
lo.addWidget(self.wadd)
lo1 = QHBoxLayout()
lo.addLayout(lo1)
lo1.setContentsMargins(0, 0, 0, 0)
self.wpad = QLineEdit(self)
self.wpad.setValidator(QDoubleValidator(self))
self.wpad.setText("1.1")
lab = QLabel("...with padding factor:", self)
lab.setToolTip("""<P>The padding factor determines the amount of null padding inserted around the image during
the prediction stage. Padding alleviates the effects of tapering and detapering in the uv-brick, which can show
up towards the edges of the image. For a factor of N, the image will be padded out to N times its original size.
This increases memory use, so if you have no flux at the edges of the image anyway, then a pad factor of 1 is
perfectly fine.</P>""")
self.wpad.setToolTip(lab.toolTip())
QObject.connect(self.wadd, SIGNAL("toggled(bool)"), self.wpad.setEnabled)
QObject.connect(self.wadd, SIGNAL("toggled(bool)"), lab.setEnabled)
self.wpad.setEnabled(False)
lab.setEnabled(False)
lo1.addStretch(1)
lo1.addWidget(lab, 0)
lo1.addWidget(self.wpad, 1)
self.wdel = QCheckBox("Remove from the sky model sources that go into the brick", self)
lo.addWidget(self.wdel)
# 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
pb = self.model.primaryBeam()
if pb:
self.wpb_exp.setText(pb)
else:
self.wpb_apply.setChecked(False)
self.wpb_exp.setText("")
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
# read fits file
busy = BusyIndicator()
try:
input_hdu = pyfits.open(filename)[0]
hdr = input_hdu.header
# get frequency, if specified
for axis in range(1, hdr['NAXIS'] + 1):
if hdr['CTYPE%d' % axis].upper() == 'FREQ':
self.wfreq.setText(str(hdr['CRVAL%d' % axis] / 1e+6))
break
except Exception as err:
busy = None
self.wfile.setFilename('')
if not quiet:
QMessageBox.warning(self, "Error reading FITS",
"Error reading FITS file %s: %s" % (filename, str(err)))
return None
self.wokbtn.setEnabled(True)
# 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) \
and os.path.exists(src.shape.filename) and os.path.exists(filename) \
and os.path.samefile(src.shape.filename, filename):
self.wadd.setChecked(True)
self.wadd.setEnabled(False)
self.wadd.setText("image already in sky model")
break
else:
self.wadd.setText("add image to sky model")
return filename
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.model = None
self._model_dir = None
self.setModal(modal)
self.setWindowTitle("Add FITS brick")
lo = QVBoxLayout(self)
lo.setContentsMargins(10, 10, 10, 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.setContentsMargins(5, 5, 5, 5)
self.wokbtn = QPushButton("OK", self)
self.wokbtn.setMinimumWidth(128)
self.wokbtn.clicked.connect(self.accept)
self.wokbtn.setEnabled(False)
cancelbtn = QPushButton("Cancel", self)
cancelbtn.setMinimumWidth(128)
cancelbtn.clicked.connect(self.reject)
lo2.addWidget(self.wokbtn)
lo2.addStretch(1)
lo2.addWidget(cancelbtn)
self.setMinimumWidth(384)
# signals
self.wfile.filenameSelected.connect(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 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)
class ExportKarmaDialog (QDialog):
def __init__ (self,parent,modal=True,flags=Qt.WindowFlags()):
QDialog.__init__(self,parent,flags);
self.setModal(modal);
self.setWindowTitle("Export Karma annotations");
lo = QVBoxLayout(self);
lo.setMargin(10);
lo.setSpacing(5);
# file selector
self.wfile = FileSelector(self,label="Filename:",dialog_label="Karma annotations filename",default_suffix="ann",file_types="Karma annotations (*.ann)");
lo.addWidget(self.wfile);
# selected sources checkbox
self.wsel = QCheckBox("selected sources only",self);
lo.addWidget(self.wsel);
# 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("valid"),self.wokbtn.setEnabled);
# internal state
self.qerrmsg = QErrorMessage(self);
self._model_filename = None;
def setModel (self,model):
self.model = model;
# set the default annotations filename, whenever a new model filename is set
filename = self.model.filename();
if filename and filename != self._model_filename:
self._model_filename = filename;
self.wfile.setFilename(os.path.splitext(filename)[0] + ".ann");
def accept (self):
"""Tries to export annotations, and closes the dialog if successful.""";
try:
filename = self.wfile.filename();
if os.path.exists(filename) and QMessageBox.question(self,"Exporting Karma annotations","<P>Overwrite the file %s?</P>"%filename,
QMessageBox.Yes|QMessageBox.No,QMessageBox.Yes) != QMessageBox.Yes:
return;
f = file(self.wfile.filename(),"wt");
f.write('COORD W\nPA STANDARD\nCOLOR GREEN\nFONT hershey12\n');
# source list
if self.wsel.isChecked():
sources = [ src for src in self.model.sources if src.selected ];
else:
sources = self.model.sources;
# calculate basis size for crosses (TODO: replace min_size with something more sensible, as this value is in degrees)
brightnesses = [ abs(src.brightness()) for src in sources if src.brightness() != 0 ];
min_bright = brightnesses and min(brightnesses) ;
min_size = 0.01;
# loop over sources
busy = BusyIndicator();
for src in sources:
ra = src.pos.ra/DEG;
dec = src.pos.dec/DEG;
# figure out source size
if src.brightness() and min_bright:
ysize = (math.log10(abs(src.brightness())) - math.log10(min_bright) + 1)*min_size;
else:
ysize = min_size;
xsize = ysize/(math.cos(src.pos.dec) or 1);
# figure out source style
style,label = self.model.getSourcePlotStyle(src);
if style:
f.write('# %s\n'%src.name);
# write symbol for source
f.write('COLOR %s\n'%style.symbol_color);
if style.symbol == "plus":
f.write('CROSS %.12f %.12f %f %f\n'%(ra,dec,xsize,ysize));
elif style.symbol == "cross":
f.write('CROSS %.12f %.12f %f %f 45\n'%(ra,dec,ysize,ysize));
elif style.symbol == "circle":
f.write('CIRCLE %.12f %.12f %f\n'%(ra,dec,ysize));
elif style.symbol == "dot":
f.write('DOT %.12f %.12f\n'%(ra,dec));
elif style.symbol == "square":
f.write('CBOX %.12f %.12f %f %f\n'%(ra,dec,xsize,ysize));
elif style.symbol == "diamond":
f.write('CBOX %.12f %.12f %f %f 45\n'%(ra,dec,xsize,ysize));
# write label
if label:
f.write('FONT hershey%d\n'%(style.label_size*2));
f.write('COLOR %s\n'%style.label_color);
f.write('TEXT %.12f %.12f %s\n'%(ra,dec,label));
f.close();
except IOError,err:
busy = None;
self.qerrmsg.showMessage("Error writing Karma annotations file %s: %s"%(filename,str(err)));
return;
busy = None;
self.parent().showMessage("Wrote Karma annotations for %d sources to file %s"%(len(sources),filename));
return QDialog.accept(self);