def retrieve(self, filetype, run, camcol, field=None, band=None, skipExisting=True,
tempsuffix='.tmp', rerun=None):
outfn = self.getPath(filetype, run, camcol, field, band,
rerun=rerun)
print('Checking for file', outfn)
if outfn is None:
return None
if skipExisting and os.path.exists(outfn):
#print('Exists')
return outfn
outdir = os.path.dirname(outfn)
if not os.path.exists(outdir):
try:
os.makedirs(outdir)
except:
pass
url = self.get_url(filetype, run, camcol, field, band=band, rerun=rerun)
#print 'Did not find file:', outfn
print('Retrieving from URL:', url)
if self.curl:
cmd = "curl -o '%(outfn)s' '%(url)s'"
else:
cmd = "wget --continue -nv -O %(outfn)s '%(url)s'"
# suffix to add to the downloaded filename
suff = self.dassuffix.get(filetype, '')
oo = outfn + suff
if tempsuffix is not None:
oo += tempsuffix
cmd = cmd % dict(outfn=oo, url=url)
self.logger.debug('cmd: %s' % cmd)
(rtn,out,err) = run_command(cmd)
if rtn:
print('Command failed: command', cmd)
print('Output:', out)
print('Error:', err)
print('Return val:', rtn)
return None
if tempsuffix is not None:
#
self.logger.debug('Renaming %s to %s' % (oo, outfn+suff))
os.rename(oo, outfn + suff)
if filetype in self.processcmds:
cmd = self.processcmds[filetype]
cmd = cmd % dict(input = outfn + suff, output = outfn)
self.logger.debug('cmd: %s' % cmd)
(rtn,out,err) = run_command(cmd)
if rtn:
print('Command failed: command', cmd)
print('Output:', out)
print('Error:', err)
print('Return val:', rtn)
return None
return outfn
def new_fits_file(req, jobid=None):
job = get_object_or_404(Job, pk=jobid)
wcsfn = job.get_wcs_file()
img = job.user_image.image
df = img.disk_file
infn = df.get_path()
if df.is_fits_image():
fitsinfn = infn
else:
## FIXME -- could convert other formats to FITS...
pnmfn = get_temp_file()
fitsinfn = get_temp_file()
cmd = 'image2pnm.py -i %s -o %s && an-pnmtofits %s > %s' % (infn, pnmfn, pnmfn, fitsinfn)
logmsg('Running: ' + cmd)
(rtn, out, err) = run_command(cmd)
if rtn:
logmsg('out: ' + out)
logmsg('err: ' + err)
return HttpResponse('image2pnm.py failed: out ' + out + ', err ' + err)
outfn = get_temp_file()
cmd = 'new-wcs -i %s -w %s -o %s -d' % (fitsinfn, wcsfn, outfn)
logmsg('Running: ' + cmd)
(rtn, out, err) = run_command(cmd)
if rtn:
logmsg('out: ' + out)
logmsg('err: ' + err)
return HttpResponse('plot failed: out ' + out + ', err ' + err)
res = HttpResponse(open(outfn))
res['Content-Type'] = 'application/fits'
res['Content-Length'] = file_size(outfn)
res['Content-Disposition'] = 'attachment; filename=new-image.fits'
return res
def retrieve(self, filetype, run, camcol, field=None, band=None, skipExisting=True,
tempsuffix='.tmp', rerun=None):
outfn = self.getPath(filetype, run, camcol, field, band,
rerun=rerun)
print('Checking for file', outfn)
if outfn is None:
return None
if skipExisting and os.path.exists(outfn):
#print('Exists')
return outfn
outdir = os.path.dirname(outfn)
if not os.path.exists(outdir):
try:
os.makedirs(outdir)
except:
pass
url = self.get_url(filetype, run, camcol, field, band=band, rerun=rerun)
#print 'Did not find file:', outfn
print('Retrieving from URL:', url)
if self.curl:
cmd = "curl -o '%(outfn)s' '%(url)s'"
else:
cmd = "wget --continue -nv -O %(outfn)s '%(url)s'"
# suffix to add to the downloaded filename
suff = self.dassuffix.get(filetype, '')
oo = outfn + suff
if tempsuffix is not None:
oo += tempsuffix
cmd = cmd % dict(outfn=oo, url=url)
self.logger.debug('cmd: %s' % cmd)
(rtn,out,err) = run_command(cmd)
if rtn:
print('Command failed: command', cmd)
print('Output:', out)
print('Error:', err)
print('Return val:', rtn)
return None
if tempsuffix is not None:
#
self.logger.debug('Renaming %s to %s' % (oo, outfn+suff))
os.rename(oo, outfn + suff)
if filetype in self.processcmds:
cmd = self.processcmds[filetype]
cmd = cmd % dict(input = outfn + suff, output = outfn)
self.logger.debug('cmd: %s' % cmd)
(rtn,out,err) = run_command(cmd)
if rtn:
print('Command failed: command', cmd)
print('Output:', out)
print('Error:', err)
print('Return val:', rtn)
return None
return outfn
def new_fits_file(req, jobid=None):
job = get_object_or_404(Job, pk=jobid)
wcsfn = job.get_wcs_file()
img = job.user_image.image
df = img.disk_file
infn = df.get_path()
if df.is_fits_image():
fitsinfn = infn
else:
## FIXME -- could convert other formats to FITS...
pnmfn = get_temp_file()
fitsinfn = get_temp_file()
cmd = 'image2pnm.py -i %s -o %s && an-pnmtofits %s > %s' % (
infn, pnmfn, pnmfn, fitsinfn)
logmsg('Running: ' + cmd)
(rtn, out, err) = run_command(cmd)
if rtn:
logmsg('out: ' + out)
logmsg('err: ' + err)
return HttpResponse('image2pnm.py failed: out ' + out + ', err ' +
err)
outfn = get_temp_file()
cmd = 'new-wcs -i %s -w %s -o %s -d' % (fitsinfn, wcsfn, outfn)
logmsg('Running: ' + cmd)
(rtn, out, err) = run_command(cmd)
if rtn:
logmsg('out: ' + out)
logmsg('err: ' + err)
return HttpResponse('plot failed: out ' + out + ', err ' + err)
res = HttpResponse(open(outfn))
res['Content-Type'] = 'application/fits'
res['Content-Length'] = file_size(outfn)
res['Content-Disposition'] = 'attachment; filename=new-image.fits'
return res
def retrieve(self,
filetype,
run,
camcol,
field=None,
band=None,
skipExisting=True,
tempsuffix='.tmp'):
outfn = self.getPath(filetype, run, camcol, field, band)
if outfn is None:
return None
if skipExisting and os.path.exists(outfn):
return outfn
print 'Did not find file:', outfn
url = self.get_url(filetype, run, camcol, field, band=band)
#print 'URL:', url
if self.curl:
cmd = "curl -o '%(outfn)s' '%(url)s'"
else:
cmd = "wget --continue -nv -O %(outfn)s '%(url)s'"
# suffix to add to the downloaded filename
suff = self.dassuffix.get(filetype, '')
oo = outfn + suff
if tempsuffix is not None:
oo += tempsuffix
cmd = cmd % dict(outfn=oo, url=url)
self.logger.debug('cmd: %s' % cmd)
(rtn, out, err) = run_command(cmd)
if rtn:
print 'Command failed: command', cmd
print 'Output:', out
print 'Error:', err
print 'Return val:', rtn
return None
if tempsuffix is not None:
#
os.rename(oo, outfn + suff)
if filetype in self.processcmds:
cmd = self.processcmds[filetype]
cmd = cmd % dict(input=outfn + suff, output=outfn)
self.logger.debug('cmd: %s' % cmd)
(rtn, out, err) = run_command(cmd)
if rtn:
print 'Command failed: command', cmd
print 'Output:', out
print 'Error:', err
print 'Return val:', rtn
return None
return outfn
def retrieve(self, filetype, run, camcol, field=None, band=None, skipExisting=True,
tempsuffix='.tmp'):
outfn = self.getPath(filetype, run, camcol, field, band)
if outfn is None:
return None
if skipExisting and os.path.exists(outfn):
return outfn
url = self.get_url(filetype, run, camcol, field, band=band)
#print 'URL:', url
if self.curl:
cmd = "curl -o '%(outfn)s' '%(url)s'"
else:
cmd = "wget --continue -nv -O %(outfn)s '%(url)s'"
# suffix to add to the downloaded filename
suff = self.dassuffix.get(filetype, '')
oo = outfn + suff
if tempsuffix is not None:
oo += tempsuffix
cmd = cmd % dict(outfn=oo, url=url)
self.logger.debug('cmd: %s' % cmd)
(rtn,out,err) = run_command(cmd)
if rtn:
print 'Command failed: command', cmd
print 'Output:', out
print 'Error:', err
print 'Return val:', rtn
return None
if tempsuffix is not None:
#
os.rename(oo, outfn + suff)
if filetype in self.processcmds:
cmd = self.processcmds[filetype]
cmd = cmd % dict(input = outfn + suff, output = outfn)
self.logger.debug('cmd: %s' % cmd)
(rtn,out,err) = run_command(cmd)
if rtn:
print 'Command failed: command', cmd
print 'Output:', out
print 'Error:', err
print 'Return val:', rtn
return None
return outfn
def filetype(fn):
filecmd = 'file -b -N -L -k %s'
cmd = filecmd % shell_escape(fn)
(rtn,out,err) = run_command(cmd)
if rtn:
logverb('"file" command failed. Command: "%s"' % cmd)
logverb(' ', out)
logverb(' ', err)
return None
out = out.strip()
logverb('File: "%s"' % out)
lst = []
# The "file -r" flag, removed in some Ubuntu versions, used to
# tell it not to convert non-printable characters to octal. Without -r,
# some versions print the string r'\012- ' instead of "\n- ". Do that
# manually here.
out = out.replace(r'\012- ', '\n- ')
for line in out.split('\n- '):
if line.endswith('\n-'):
line = line[:-2]
if len(line) == 0:
continue
p = line.split(', ', 1)
if len(p) == 2:
lst.append(tuple(p))
else:
lst.append((p[0], ''))
return lst
def get_git_version(dir=None):
'''
Runs 'git describe' in the current directory (or given dir) and
returns the result as a string.
Parameters
----------
dir : string
If non-None, "cd" to the given directory before running 'git describe'
Returns
-------
Git version string
'''
from astrometry.util.run_command import run_command
cmd = ''
if dir is not None:
cmd = "cd '%s' && " % dir
cmd += 'git describe'
rtn,version,err = run_command(cmd)
if rtn:
raise RuntimeError('Failed to get version string (%s): ' % cmd +
version + err)
version = version.strip()
return version
def filetype(fn):
filecmd = 'file -b -N -L -k %s'
cmd = filecmd % shell_escape(fn)
(rtn, out, err) = run_command(cmd)
if rtn:
logverb('"file" command failed. Command: "%s"' % cmd)
logverb(' ', out)
logverb(' ', err)
return None
out = out.strip()
logverb('File: "%s"' % out)
lst = []
# The "file -r" flag, removed in some Ubuntu versions, used to
# tell it not to convert non-printable characters to octal. Without -r,
# some versions print the string r'\012- ' instead of "\n- ". Do that
# manually here.
out = out.replace(r'\012- ', '\n- ')
for line in out.split('\n- '):
if line.endswith('\n-'):
line = line[:-2]
if len(line) == 0:
continue
p = line.split(', ', 1)
if len(p) == 2:
lst.append(tuple(p))
else:
lst.append((p[0], ''))
return lst
def sdss_das_get(filetype, outfn, run, camcol, field, band=None, reruns=None, suffix=None, gunzip=True, curl=False, ):
if reruns is None:
reruns = [40,41,42,44]
urls = []
for rerun in reruns:
url = sdss_das_get_url(filetype, run, camcol, field, rerun, band,
suffix=suffix)
if url is None:
return False
urls.append(url)
if suffix is None:
suffix = sdss_das_get_suffix(filetype)
if outfn:
outfn = outfn % { 'run':run, 'camcol':camcol, 'field':field, 'band':band } + suffix
else:
outfn = sdss_filename(filetype, run, camcol, field, band) + suffix
if not get_urls(urls, outfn, curl):
return False
if suffix == '.gz' and gunzip:
print 'gzipped file; outfn=', outfn
gzipfn = outfn
outfn = gzipfn.replace('.gz', '')
if os.path.exists(gzipfn):
cmd = 'gunzip -cd %s > %s' % (gzipfn, outfn)
print 'Running:', cmd
(rtn, out, err) = run_command(cmd)
if rtn:
print 'Command failed: command', cmd
print 'Output:', out
print 'Error:', err
print 'Return val:', rtn
return outfn
def render(self, f):
if hasattr(self, 'sourcelist'):
# image is a source list
self.sourcelist.render(f)
else:
if self.disk_file.is_fits_image():
# convert fits image to jpg for browser rendering
key = 'jpg_image%i' % self.id
df = CachedFile.get(key)
if df is None:
imagefn = get_temp_file()
pnmfn = self.get_pnm_path()
cmd = 'pnmtojpeg < %s > %s' % (pnmfn, imagefn)
logmsg("Making resized image: %s" % cmd)
rtn, out, err = run_command(cmd)
if rtn:
logmsg('pnmtojpeg failed: rtn %i' % rtn)
logmsg('out: ' + out)
logmsg('err: ' + err)
raise RuntimeError(
'Failed to make jpg image for %s: pnmtojpeg: %s' %
(str(self), err))
# cache
logmsg('Caching key "%s"' % key)
df = CachedFile.add(key, imagefn)
else:
logmsg('Cache hit for key "%s"' % key)
else:
df = self.disk_file
dfile = open(df.get_path())
f.write(dfile.read())
dfile.close()
def render(self, f):
if hasattr(self, 'sourcelist'):
# image is a source list
self.sourcelist.render(f)
else:
if self.disk_file.is_fits_image():
# convert fits image to jpg for browser rendering
key = 'jpg_image%i' % self.id
df = CachedFile.get(key)
if df is None:
imagefn = get_temp_file()
pnmfn = self.get_pnm_path()
cmd = 'pnmtojpeg < %s > %s' % (pnmfn, imagefn)
logmsg("Making resized image: %s" % cmd)
rtn,out,err = run_command(cmd)
if rtn:
logmsg('pnmtojpeg failed: rtn %i' % rtn)
logmsg('out: ' + out)
logmsg('err: ' + err)
raise RuntimeError('Failed to make jpg image for %s: pnmtojpeg: %s' % (str(self), err))
# cache
logmsg('Caching key "%s"' % key)
df = CachedFile.add(key, imagefn)
else:
logmsg('Cache hit for key "%s"' % key)
else:
df = self.disk_file
dfile = open(df.get_path())
f.write(dfile.read())
dfile.close()
def filetype(fn):
filecmd = 'file -b -N -L -k -r %s'
cmd = filecmd % shell_escape(fn)
(rtn, out, err) = run_command(cmd)
if rtn:
logverb('"file" command failed. Command: "%s"' % cmd)
logverb(' ', out)
logverb(' ', err)
return None
out = out.strip()
logverb('File: "%s"' % out)
lst = []
for line in out.split('\n- '):
if line.endswith('\n-'):
line = line[:-2]
if len(line) == 0:
continue
p = line.split(', ', 1)
if len(p) == 2:
lst.append(tuple(p))
else:
lst.append((p[0], ''))
return lst
def filetype(fn):
filecmd = 'file -b -N -L -k -r %s'
cmd = filecmd % shell_escape(fn)
(rtn,out,err) = run_command(cmd)
if rtn:
logverb('"file" command failed. Command: "%s"' % cmd)
logverb(' ', out)
logverb(' ', err)
return None
out = out.strip()
logverb('File: "%s"' % out)
lst = []
for line in out.split('\n- '):
if line.endswith('\n-'):
line = line[:-2]
if len(line) == 0:
continue
p = line.split(', ', 1)
if len(p) == 2:
lst.append(tuple(p))
else:
lst.append((p[0], ''))
return lst
def create_resized_image(self, maxsize):
if max(self.width, self.height) <= maxsize:
return self
pnmfn = self.get_pnm_path()
imagefn = get_temp_file()
# find scale
scale = float(maxsize) / float(max(self.width, self.height))
W, H = int(round(scale * self.width)), int(round(scale * self.height))
cmd = 'pnmscale -width %i -height %i %s | pnmtojpeg > %s' % (
W, H, pnmfn, imagefn)
logmsg("Making resized image: %s" % cmd)
rtn, out, err = run_command(cmd)
if rtn:
logmsg('pnmscale failed: rtn %i' % rtn)
logmsg('out: ' + out)
logmsg('err: ' + err)
raise RuntimeError(
'Failed to make resized image for %s: pnmscale: %s' %
(str(self), err))
df = DiskFile.from_file(imagefn, Image.RESIZED_COLLECTION)
#logmsg('Resized disk file:', df)
try:
image, created = Image.objects.get_or_create(disk_file=df,
width=W,
height=H)
#if created:
# logmsg('Created:', created)
except Image.MultipleObjectsReturned:
image = Image.objects.filter(disk_file=df, width=W, height=H)
image = image[0]
return image
def run_convert_command(cmd, deleteonfail=None):
logmsg('Command: ' + cmd)
(rtn, stdout, stderr) = run_command(cmd)
if rtn:
errmsg = 'Command failed: ' + cmd + ': ' + stderr
logmsg(errmsg + '; rtn val %d' % rtn)
logmsg('out: ' + stdout)
logmsg('err: ' + stderr)
if deleteonfail:
os.unlink(deleteonfail)
raise FileConversionError(errmsg)
def run_convert_command(cmd, deleteonfail=None):
logmsg('Command: ' + cmd)
(rtn, stdout, stderr) = run_command(cmd)
if rtn:
errmsg = 'Command failed: ' + cmd + ': ' + stderr
logmsg(errmsg + '; rtn val %d' % rtn)
logmsg('out: ' + stdout);
logmsg('err: ' + stderr);
if deleteonfail:
os.unlink(deleteonfail)
raise FileConversionError(errmsg)
def _unzip_frame(self, fn, run, camcol):
if self.readBz2:
return None, True
# No, PJM reported that pyfits failed on SDSS frame*.bz2 files
# if not fitsio:
# # pyfits can read .bz2
# return None,True
tempfn = None
keep = False
filetype = 'frame'
if not (filetype in self.postprocesscmds and fn.endswith('.bz2')):
return None, True
cmd = self.postprocesscmds[filetype]
if self.unzip_dir is not None:
udir = os.path.join(self.unzip_dir, '%i' % run, '%i' % camcol)
if not os.path.exists(udir):
try:
os.makedirs(udir)
except:
pass
tempfn = os.path.join(udir,
os.path.basename(fn).replace('.bz2', ''))
#print 'Checking', tempfn
if os.path.exists(tempfn):
print 'File exists:', tempfn
return tempfn, True
else:
print 'Saving to', tempfn
keep = True
else:
fid, tempfn = tempfile.mkstemp()
os.close(fid)
cmd = cmd % dict(input=fn, output=tempfn)
self.logger.debug('cmd: %s' % cmd)
print 'command:', cmd
(rtn, out, err) = run_command(cmd)
if rtn:
print 'Command failed: command', cmd
print 'Output:', out
print 'Error:', err
print 'Return val:', rtn
raise RuntimeError('Command failed (return val %i): %s' %
(rtn, cmd))
print out
print err
return tempfn, keep
def _unzip_frame(self, fn, run, camcol):
if self.readBz2:
return None,True
# No, PJM reported that pyfits failed on SDSS frame*.bz2 files
# if not fitsio:
# # pyfits can read .bz2
# return None,True
tempfn = None
keep = False
filetype = 'frame'
if not(filetype in self.postprocesscmds and fn.endswith('.bz2')):
return None,True
cmd = self.postprocesscmds[filetype]
if self.unzip_dir is not None:
udir = os.path.join(self.unzip_dir, '%i' % run, '%i' % camcol)
if not os.path.exists(udir):
try:
os.makedirs(udir)
except:
pass
tempfn = os.path.join(udir, os.path.basename(fn).replace('.bz2', ''))
#print 'Checking', tempfn
if os.path.exists(tempfn):
print 'File exists:', tempfn
return tempfn,True
else:
print 'Saving to', tempfn
keep = True
else:
fid,tempfn = tempfile.mkstemp()
os.close(fid)
cmd = cmd % dict(input = fn, output = tempfn)
self.logger.debug('cmd: %s' % cmd)
print 'command:', cmd
(rtn,out,err) = run_command(cmd)
if rtn:
print 'Command failed: command', cmd
print 'Output:', out
print 'Error:', err
print 'Return val:', rtn
raise RuntimeError('Command failed (return val %i): %s' % (rtn, cmd))
print out
print err
return tempfn,keep
def get_urls(urls, outfn):
for url in urls:
cmd = 'wget --continue -nv '
if outfn:
cmd += '-O %s ' % outfn
cmd += '\"%s\"' % url
print 'Running:', cmd
(rtn, out, err) = run_command(cmd)
if rtn == 0:
return True
if rtn:
print 'Command failed: command', cmd
print 'Output:', out
print 'Error:', err
print 'Return val:', rtn
return False
def sdss_das_get(filetype,
outfn,
run,
camcol,
field,
band=None,
reruns=None,
suffix=None,
gunzip=True):
if suffix is None:
suffix = sdss_das_get_suffix(filetype)
if reruns is None:
reruns = [40, 41, 42, 44]
urls = []
for rerun in reruns:
path = sdss_path(filetype, run, camcol, field, band, rerun)
if path is None:
print 'Unknown SDSS filetype', filetype
return False
urls.append('http://das.sdss.org/imaging/' + path + suffix)
if outfn:
outfn = outfn % {
'run': run,
'camcol': camcol,
'field': field,
'band': band
}
else:
outfn = sdss_filename(filetype, run, camcol, field, band) + suffix
if not get_urls(urls, outfn):
return False
if suffix == '.gz' and gunzip:
print 'gzipped file; outfn=', outfn
gzipfn = outfn
outfn = gzipfn.replace('.gz', '')
if os.path.exists(gzipfn):
cmd = 'gunzip -cd %s > %s' % (gzipfn, outfn)
print 'Running:', cmd
(rtn, out, err) = run_command(cmd)
if rtn == 0:
return True
if rtn:
print 'Command failed: command', cmd
print 'Output:', out
print 'Error:', err
print 'Return val:', rtn
def kml_file(req, jobid=None):
#return HttpResponse('KMZ requests are off for now. Post at https://groups.google.com/forum/#!forum/astrometry for help.')
import tempfile
import PIL.Image
job = get_object_or_404(Job, pk=jobid)
wcsfn = job.get_wcs_file()
img = job.user_image.image
df = img.disk_file
pnmfn = img.get_pnm_path(tempfiles=req.tempfiles)
imgfn = get_temp_file(tempfiles=req.tempfiles)
image = PIL.Image.open(pnmfn)
image.save(imgfn, 'PNG')
dirnm = tempfile.mkdtemp()
req.tempdirs.append(dirnm)
warpedimgfn = 'image.png'
kmlfn = 'doc.kml'
outfn = get_temp_file(tempfiles=req.tempfiles)
cmd = ('cd %(dirnm)s'
'; %(wcs2kml)s '
'--input_image_origin_is_upper_left '
'--fitsfile=%(wcsfn)s '
'--imagefile=%(imgfn)s '
'--kmlfile=%(kmlfn)s '
'--outfile=%(warpedimgfn)s '
'; zip -j - %(warpedimgfn)s %(kmlfn)s > %(outfn)s ' %
dict(dirnm=dirnm,
wcsfn=wcsfn,
imgfn=imgfn,
kmlfn=kmlfn,
wcs2kml=settings.WCS2KML,
warpedimgfn=warpedimgfn,
outfn=outfn))
logmsg('Running: ' + cmd)
(rtn, out, err) = run_command(cmd)
if rtn:
logmsg('out: ' + out)
logmsg('err: ' + err)
return HttpResponse('kml generation failed: ' + err)
res = HttpResponse(open(outfn, 'rb'))
res['Content-Type'] = 'application/x-zip-compressed'
res['Content-Length'] = file_size(outfn)
res['Content-Disposition'] = 'attachment; filename=image.kmz'
return res
def create_resized_image(self, maxsize):
if max(self.width, self.height) <= maxsize:
return self
pnmfn = self.get_pnm_path()
imagefn = get_temp_file()
# find scale
scale = float(maxsize) / float(max(self.width, self.height))
W,H = int(round(scale * self.width)), int(round(scale * self.height))
cmd = 'pnmscale -width %i -height %i %s | pnmtojpeg > %s' % (W, H, pnmfn, imagefn)
logmsg("Making resized image: %s" % cmd)
rtn,out,err = run_command(cmd)
if rtn:
logmsg('pnmscale failed: rtn %i' % rtn)
logmsg('out: ' + out)
logmsg('err: ' + err)
raise RuntimeError('Failed to make resized image for %s: pnmscale: %s' % (str(self), err))
df = DiskFile.from_file(imagefn, Image.RESIZED_COLLECTION)
image, created = Image.objects.get_or_create(disk_file=df, width=W, height=H)
return image
def kml_file(req, jobid=None):
job = get_object_or_404(Job, pk=jobid)
wcsfn = job.get_wcs_file()
img = job.user_image.image
df = img.disk_file
pnmfn = img.get_pnm_path()
imgfn = get_temp_file()
image = PIL.Image.open(pnmfn)
image.save(imgfn, 'PNG')
dirnm = tempfile.mkdtemp()
warpedimgfn = 'image.png'
kmlfn = 'doc.kml'
outfn = get_temp_file()
cmd = ('cd %(dirnm)s'
'; /usr/local/wcs2kml/bin/wcs2kml '
'--input_image_origin_is_upper_left '
'--fitsfile=%(wcsfn)s '
'--imagefile=%(imgfn)s '
'--kmlfile=%(kmlfn)s '
'--outfile=%(warpedimgfn)s '
'; zip -j - %(warpedimgfn)s %(kmlfn)s > %(outfn)s ' %
dict(dirnm=dirnm,
wcsfn=wcsfn,
imgfn=imgfn,
kmlfn=kmlfn,
warpedimgfn=warpedimgfn,
outfn=outfn))
logmsg('Running: ' + cmd)
(rtn, out, err) = run_command(cmd)
if rtn:
logmsg('out: ' + out)
logmsg('err: ' + err)
return HttpResponse('kml generation failed: ' + err)
res = HttpResponse(open(outfn))
res['Content-Type'] = 'application/x-zip-compressed'
res['Content-Length'] = file_size(outfn)
res['Content-Disposition'] = 'attachment; filename=image.kmz'
return res
def filetype(fn):
filecmd = 'file -b -N -L -k -r %s'
cmd = filecmd % shell_escape(fn)
(rtn, out, err) = run_command(cmd)
if rtn:
logverb('"file" command failed. Command: "%s"' % cmd)
logverb(' ', out)
logverb(' ', err)
return None
out = out.strip()
logverb('File: "%s"' % out)
parts = [line.split(', ', 1) for line in out.split('\n- ')]
lst = []
for p in parts:
if len(p) == 2:
lst.append(tuple(p))
else:
lst.append((p[0], ''))
return lst
def kml_file(req, jobid=None):
import PIL.Image
job = get_object_or_404(Job, pk=jobid)
wcsfn = job.get_wcs_file()
img = job.user_image.image
df = img.disk_file
pnmfn = img.get_pnm_path()
imgfn = get_temp_file()
image = PIL.Image.open(pnmfn)
image.save(imgfn, 'PNG')
dirnm = tempfile.mkdtemp()
warpedimgfn = 'image.png'
kmlfn = 'doc.kml'
outfn = get_temp_file()
cmd = ('cd %(dirnm)s'
'; %(wcs2kml)s '
'--input_image_origin_is_upper_left '
'--fitsfile=%(wcsfn)s '
'--imagefile=%(imgfn)s '
'--kmlfile=%(kmlfn)s '
'--outfile=%(warpedimgfn)s '
'; zip -j - %(warpedimgfn)s %(kmlfn)s > %(outfn)s ' %
dict(dirnm=dirnm, wcsfn=wcsfn, imgfn=imgfn, kmlfn=kmlfn,
wcs2kml=settings.WCS2KML,
warpedimgfn=warpedimgfn, outfn=outfn))
logmsg('Running: ' + cmd)
(rtn, out, err) = run_command(cmd)
if rtn:
logmsg('out: ' + out)
logmsg('err: ' + err)
return HttpResponse('kml generation failed: ' + err)
res = HttpResponse(open(outfn))
res['Content-Type'] = 'application/x-zip-compressed'
res['Content-Length'] = file_size(outfn)
res['Content-Disposition'] = 'attachment; filename=image.kmz'
return res
def get_tarball_files(fn, tempdirs=None):
# create temp dir to extract tarfile.
tempdir = tempfile.mkdtemp()
if tempdirs is not None:
tempdirs.append(tempdir)
cmd = 'tar xvf %s -C %s' % (fn, tempdir)
print('Extracting tarball: %s' % cmd)
(rtn, out, err) = run_command(cmd)
if rtn:
print('Failed to un-tar file:\n' + err)
#bailout(submission, 'failed to extract tar file')
print('failed to extract tar file')
return None
fns = out.strip('\n').split('\n')
validpaths = []
for fn in fns:
path = os.path.join(tempdir, fn)
logmsg('Path "%s"' % path)
if not os.path.exists(path):
logmsg('Path "%s" does not exist.' % path)
continue
if os.path.islink(path):
logmsg('Path "%s" is a symlink.' % path)
continue
if os.path.isfile(path):
validpaths.append(path)
else:
logmsg('Path "%s" is not a file.' % path)
if len(validpaths) == 0:
#userlog('Tar file contains no regular files.')
#bailout(submission, "tar file contains no regular files.")
#return -1
logmsg('No real files in tar file')
return None
logmsg('Got %i paths.' % len(validpaths))
return validpaths
def get_tarball_files(fn):
# create temp dir to extract tarfile.
tempdir = tempfile.mkdtemp()
cmd = 'tar xvf %s -C %s' % (fn, tempdir)
#userlog('Extracting tarball...')
(rtn, out, err) = run_command(cmd)
if rtn:
#userlog('Failed to un-tar file:\n' + err)
#bailout(submission, 'failed to extract tar file')
print 'failed to extract tar file'
return None
fns = out.strip('\n').split('\n')
validpaths = []
for fn in fns:
path = os.path.join(tempdir, fn)
logmsg('Path "%s"' % path)
if not os.path.exists(path):
logmsg('Path "%s" does not exist.' % path)
continue
if os.path.islink(path):
logmsg('Path "%s" is a symlink.' % path)
continue
if os.path.isfile(path):
validpaths.append(path)
else:
logmsg('Path "%s" is not a file.' % path)
if len(validpaths) == 0:
#userlog('Tar file contains no regular files.')
#bailout(submission, "tar file contains no regular files.")
#return -1
logmsg('No real files in tar file')
return None
logmsg('Got %i paths.' % len(validpaths))
return validpaths
def get_urls(urls, outfn, curl=False): for url in urls: if curl: cmd = 'curl ' if outfn: cmd += '-o %s ' % outfn else: cmd += '-O ' else: cmd = 'wget --continue -nv ' if outfn: cmd += '-O %s ' % outfn cmd += '\"%s\"' % url print 'Running:', cmd (rtn, out, err) = run_command(cmd) if rtn == 0: return True if rtn: print 'Command failed: command', cmd print 'Output:', out print 'Error:', err print 'Return val:', rtn return False
def get_urls(urls, outfn, curl=False):
for url in urls:
if curl:
cmd = 'curl '
if outfn:
cmd += '-o %s ' % outfn
else:
cmd += '-O '
else:
cmd = 'wget --continue -nv '
if outfn:
cmd += '-O %s ' % outfn
cmd += '\"%s\"' % url
print('Running:', cmd)
(rtn, out, err) = run_command(cmd)
if rtn == 0:
return True
if rtn:
print('Command failed: command', cmd)
print('Output:', out)
print('Error:', err)
print('Return val:', rtn)
return False
def get_git_version(dir=None):
'''
Runs 'git describe' in the current directory (or given dir) and
returns the result as a string.
Parameters
----------
dir : string
If non-None, "cd" to the given directory before running 'git describe'
Returns
-------
Git version string
'''
from astrometry.util.run_command import run_command
cmd = ''
if dir is not None:
cmd = "cd '%s' && " % dir
cmd += 'git describe'
rtn,version,err = run_command(cmd)
if rtn:
raise RuntimeError('Failed to get version string (%s): ' % cmd + version + err)
version = version.strip()
return version
def read_photoobjs(sdss, wcs, margin, cols=None, pa=None, wfn='window_flist.fits'):
'''
Read photoObjs that are inside the given 'wcs', plus 'margin' in degrees.
If 'pa' is not None, assume it is a PrimaryArea object.
'''
log = logging.getLogger('read_photoobjs')
#wfn = os.path.join(resolvedir, 'window_flist.fits')
ra,dec = wcs.radec_center()
rad = wcs.radius()
rad += np.hypot(13., 9.) / 2 / 60.
# a little extra margin
rad += margin
print 'Searching for run,camcol,fields with radius', rad, 'deg'
RCF = radec_to_sdss_rcf(ra, dec, radius=rad*60., tablefn=wfn)
log.debug('Found %i fields possibly in range' % len(RCF))
RCF = [(run,camcol,field) for (run,camcol,field,r,d) in RCF]
pixmargin = margin * 3600. / wcs.pixel_scale()
W,H = wcs.get_width(), wcs.get_height()
RR = '301'
RCF = [(run,camcol,field) for (run,camcol,field) in RCF
if (sdss.get_rerun(run, field=field) == RR)]
log.debug('Found %i fields with rerun = %s' % (len(RCF), RR))
if pa is not None:
rr = RR
RCF = [(run,camcol,field) for (run,camcol,field) in RCF
if (pa.get(rr, run, camcol, field) > 0)]
log.debug('Found %i fields with positive primaryArea' % (len(RCF)))
TT = []
for run,camcol,field in RCF:
log.debug('RCF %i/%i/%i' % (run, camcol, field))
rr = sdss.get_rerun(run, field=field)
fn = get_photoobj_filename(rr, run, camcol, field)
if not os.path.exists(fn):
url = sdss.get_url('photoObj', run, camcol, field)
cmd = "wget --continue -nv -O %(outfn)s '%(url)s'"
cmd = cmd % dict(outfn=fn, url=url)
dirnm = os.path.dirname(fn)
print 'Directory:', dirnm
if not os.path.exists(dirnm):
print 'Creating', dirnm
try:
os.makedirs(dirnm)
except:
pass
log.debug('Retrieving photoObj from %s to %s' % (url, fn))
(rtn,out,err) = run_command(cmd)
if rtn:
print 'Command failed: command', cmd
print 'Output:', out
print 'Error:', err
print 'Return val:', rtn
return None
T = fits_table(fn, columns=cols)
if T is None:
log.debug('read 0 from %s' % fn)
continue
log.debug('read %i from %s' % (len(T), fn))
# while we're reading it, record its length for later...
#get_photoobj_length(rr, run, camcol, field)
ok,x,y = wcs.radec2pixelxy(T.ra, T.dec)
x -= 1
y -= 1
T.cut((x > -pixmargin) * (x < (W + pixmargin)) *
(y > -pixmargin) * (y < (H + pixmargin)) *
(T.resolve_status & 256) > 0)
log.debug('cut to %i within target area and PRIMARY.' % len(T))
if len(T) == 0:
continue
TT.append(T)
if not len(TT):
return None
T = merge_tables(TT)
return T
def read_photoobjs(sdss,
wcs,
margin,
cols=None,
pa=None,
wfn='window_flist.fits'):
'''
Read photoObjs that are inside the given 'wcs', plus 'margin' in degrees.
If 'pa' is not None, assume it is a PrimaryArea object.
'''
log = logging.getLogger('read_photoobjs')
#wfn = os.path.join(resolvedir, 'window_flist.fits')
ra, dec = wcs.radec_center()
rad = wcs.radius()
rad += np.hypot(13., 9.) / 2 / 60.
# a little extra margin
rad += margin
print 'Searching for run,camcol,fields with radius', rad, 'deg'
RCF = radec_to_sdss_rcf(ra, dec, radius=rad * 60., tablefn=wfn)
log.debug('Found %i fields possibly in range' % len(RCF))
RCF = [(run, camcol, field) for (run, camcol, field, r, d) in RCF]
pixmargin = margin * 3600. / wcs.pixel_scale()
W, H = wcs.get_width(), wcs.get_height()
RR = '301'
RCF = [(run, camcol, field) for (run, camcol, field) in RCF
if (sdss.get_rerun(run, field=field) == RR)]
log.debug('Found %i fields with rerun = %s' % (len(RCF), RR))
if pa is not None:
rr = RR
RCF = [(run, camcol, field) for (run, camcol, field) in RCF
if (pa.get(rr, run, camcol, field) > 0)]
log.debug('Found %i fields with positive primaryArea' % (len(RCF)))
TT = []
for run, camcol, field in RCF:
log.debug('RCF %i/%i/%i' % (run, camcol, field))
rr = sdss.get_rerun(run, field=field)
fn = get_photoobj_filename(rr, run, camcol, field)
if not os.path.exists(fn):
url = sdss.get_url('photoObj', run, camcol, field)
cmd = "wget --continue -nv -O %(outfn)s '%(url)s'"
cmd = cmd % dict(outfn=fn, url=url)
dirnm = os.path.dirname(fn)
print 'Directory:', dirnm
if not os.path.exists(dirnm):
print 'Creating', dirnm
try:
os.makedirs(dirnm)
except:
pass
log.debug('Retrieving photoObj from %s to %s' % (url, fn))
(rtn, out, err) = run_command(cmd)
if rtn:
print 'Command failed: command', cmd
print 'Output:', out
print 'Error:', err
print 'Return val:', rtn
return None
T = fits_table(fn, columns=cols)
if T is None:
log.debug('read 0 from %s' % fn)
continue
log.debug('read %i from %s' % (len(T), fn))
# while we're reading it, record its length for later...
#get_photoobj_length(rr, run, camcol, field)
ok, x, y = wcs.radec2pixelxy(T.ra, T.dec)
x -= 1
y -= 1
T.cut((x > -pixmargin) * (x < (W + pixmargin)) * (y > -pixmargin) *
(y < (H + pixmargin)) * (T.resolve_status & 256) > 0)
log.debug('cut to %i within target area and PRIMARY.' % len(T))
if len(T) == 0:
continue
TT.append(T)
if not len(TT):
return None
T = merge_tables(TT)
return T
cmd = 'augment-xylist '
def join(terms):
return ' '.join(terms)
cmd = 'augment-xylist {}'.format(
join([
join([' '.join([str(y) for y in x]) for x in axyargs.iteritems()]),
join(axyflags)
]))
logger.info('running: ' + cmd)
xylist_start = time.time()
(rtn, out, err) = run_command(cmd, tee=True)
xylist_end = time.time()
if rtn:
logger.info('out: ' + out)
logger.info('err: ' + err)
logger.critical('augment-xylist failed: rtn val: {} err: {}'.format(
rtn, err))
sys.exit(-1)
logger.info('created axy file: {} in {:0.2f} seconds'.format(
axypath, xylist_end - xylist_start))
cmd = 'astrometry-engine {}'.format(axypath)
astrometry_engine_start = time.time()
(rtn, out, err) = run_command(cmd, tee=True)
astrometry_engine_end = time.time()
if rtn:
def run_ps_thread(pid, ppid, fn):
from astrometry.util.run_command import run_command
import time
import re
import fitsio
#print('run_ps_thread starting:', pid, ppid, fn)
#print('My pid:', os.getpid())
TT = []
step = 0
trex = re.compile('(((?P<days>\d*)-)?(?P<hours>\d*):)?(?P<minutes>\d*):(?P<seconds>[\d\.]*)')
def parse_time_strings(ss):
etime = []
any_failed = None
for s in ss:
m = trex.match(s)
if m is None:
any_failed = s
break
days,hours,mins,secs = m.group('days', 'hours', 'minutes',
'seconds')
# print('Elapsed time', s, 'parsed to', days,hours,mins,secs)
days = int(days, 10) if days is not None else 0
hours = int(hours, 10) if hours is not None else 0
mins = int(mins, 10)
if secs.startswith('0'):
secs = secs[1:]
secs = float(secs)
tt = days * 24 * 3600 + hours * 3600 + mins * 60 + secs
#print('->', tt, 'seconds')
etime.append(tt)
return any_failed, etime
fitshdr = fitsio.FITSHDR()
fitshdr['PPID'] = pid
while True:
time.sleep(5)
step += 1
#cmd = ('ps ax -o "user pcpu pmem state cputime etime pgid pid ppid ' +
# 'psr rss session vsize args"')
# OSX-compatible
cmd = ('ps ax -o "user pcpu pmem state cputime etime pgid pid ppid ' +
'rss vsize command"')
#print('Command:', cmd)
rtn,out,err = run_command(cmd)
if rtn:
print('FAILED to run ps:', rtn, out, err)
time.sleep(1)
break
#print('Got PS output')
#print(out)
#print('Err')
#print(err)
if len(err):
print('Error string from ps:', err)
lines = out.split('\n')
hdr = lines.pop(0)
cols = hdr.split()
cols = [c.replace('%','P') for c in cols]
cols = [c.lower() for c in cols]
#print('Columns:', cols)
vals = [[] for c in cols]
# maximum length for 'command', command-line args field
maxlen = 128
for line in lines:
words = line.split()
# "command" column can contain spaces; it is last
if len(words) == 0:
continue
words = (words[:len(cols)-1] +
[' '.join(words[len(cols)-1:])[:maxlen]])
assert(len(words) == len(cols))
for v,w in zip(vals, words):
v.append(w)
parsetypes = dict(pcpu = np.float32,
pmem = np.float32,
pgid = np.int32,
pid = np.int32,
ppid = np.int32,
rs = np.float32,
vsz = np.float32,
)
T = fits_table()
for c,v in zip(cols, vals):
# print('Col', c, 'Values:', v[:3], '...')
v = np.array(v)
tt = parsetypes.get(c, None)
if tt is not None:
v = v.astype(tt)
T.set(c, v)
# Apply cuts!
T.cut(reduce(np.logical_or, [
T.pcpu > 5, T.pmem > 5,
(T.ppid == pid) * [not c.startswith('ps ax') for c in T.command]]))
#print('Cut to', len(T), 'with significant CPU/MEM use or my PPID')
if len(T) == 0:
continue
T.unixtime = np.zeros(len(T), np.float64) + time.time()
T.step = np.zeros(len(T), np.int16) + step
any_failed,etime = parse_time_strings(T.elapsed)
if any_failed is not None:
print('Failed to parse elapsed time string:', any_failed)
else:
T.elapsed = np.array(etime)
any_failed,ctime = parse_time_strings(T.time)
if any_failed is not None:
print('Failed to parse elapsed time string:', any_failed)
else:
T.time = np.array(ctime)
T.rename('time', 'cputime')
TT.append(T)
if step % 12 == 0:
# Write out results every ~ minute.
T = merge_tables(TT, columns='fillzero')
tmpfn = os.path.join(os.path.dirname(fn), 'tmp-' + os.path.basename(fn))
T.writeto(tmpfn, header=fitshdr)
os.rename(tmpfn, fn)
print('Wrote', fn)
TT = [T]
def run_ps_thread(parent_pid, parent_ppid, fn, shutdown, event_queue):
from astrometry.util.run_command import run_command
from astrometry.util.fits import fits_table, merge_tables
import time
import re
import fitsio
from functools import reduce
# my pid = parent pid -- this is a thread.
print('run_ps_thread starting: parent PID', parent_pid, ', my PID',
os.getpid(), fn)
TT = []
step = 0
events = []
trex = re.compile(
'(((?P<days>\d*)-)?(?P<hours>\d*):)?(?P<minutes>\d*):(?P<seconds>[\d\.]*)'
)
def parse_time_strings(ss):
etime = []
any_failed = None
for s in ss:
m = trex.match(s)
if m is None:
any_failed = s
break
days, hours, mins, secs = m.group('days', 'hours', 'minutes',
'seconds')
#print('Elapsed time', s, 'parsed to', days,hours,mins,secs)
days = int(days, 10) if days is not None else 0
hours = int(hours, 10) if hours is not None else 0
mins = int(mins, 10)
if secs.startswith('0'):
secs = secs[1:]
secs = float(secs)
tt = days * 24 * 3600 + hours * 3600 + mins * 60 + secs
#print('->', tt, 'seconds')
etime.append(tt)
return any_failed, etime
def write_results(fn, T, events, hdr):
T.mine = np.logical_or(T.pid == parent_pid, T.ppid == parent_pid)
T.main = (T.pid == parent_pid)
tmpfn = os.path.join(os.path.dirname(fn),
'tmp-' + os.path.basename(fn))
T.writeto(tmpfn, header=hdr)
if len(events):
E = fits_table()
E.unixtime = np.array([e[0] for e in events])
E.event = np.array([e[1] for e in events])
E.step = np.array([e[2] for e in events])
E.writeto(tmpfn, append=True)
os.rename(tmpfn, fn)
print('Wrote', fn)
fitshdr = fitsio.FITSHDR()
fitshdr['PPID'] = parent_pid
last_time = {}
last_proc_time = {}
clock_ticks = os.sysconf('SC_CLK_TCK')
#print('Clock times:', clock_ticks)
if clock_ticks == -1:
#print('Failed to get clock times per second; assuming 100')
clock_ticks = 100
while True:
shutdown.wait(5.0)
if shutdown.is_set():
print('ps shutdown flag set. Quitting.')
break
if event_queue is not None:
while True:
try:
(t, msg) = event_queue.popleft()
events.append((t, msg, step))
#print('Popped event', t,msg)
except IndexError:
# no events
break
step += 1
#cmd = ('ps ax -o "user pcpu pmem state cputime etime pgid pid ppid ' +
# 'psr rss session vsize args"')
# OSX-compatible
cmd = ('ps ax -o "user pcpu pmem state cputime etime pgid pid ppid ' +
'rss vsize wchan command"')
#print('Command:', cmd)
rtn, out, err = run_command(cmd)
if rtn:
print('FAILED to run ps:', rtn, out, err)
time.sleep(1)
break
# print('Got PS output')
# print(out)
# print('Err')
# print(err)
if len(err):
print('Error string from ps:', err)
lines = out.split('\n')
hdr = lines.pop(0)
cols = hdr.split()
cols = [c.replace('%', 'P') for c in cols]
cols = [c.lower() for c in cols]
#print('Columns:', cols)
vals = [[] for c in cols]
# maximum length for 'command', command-line args field
maxlen = 128
for line in lines:
words = line.split()
# "command" column can contain spaces; it is last
if len(words) == 0:
continue
words = (words[:len(cols) - 1] +
[' '.join(words[len(cols) - 1:])[:maxlen]])
assert (len(words) == len(cols))
for v, w in zip(vals, words):
v.append(w)
parsetypes = dict(
pcpu=np.float32,
pmem=np.float32,
pgid=np.int32,
pid=np.int32,
ppid=np.int32,
rs=np.float32,
vsz=np.float32,
)
T = fits_table()
for c, v in zip(cols, vals):
# print('Col', c, 'Values:', v[:3], '...')
v = np.array(v)
tt = parsetypes.get(c, None)
if tt is not None:
v = v.astype(tt)
T.set(c, v)
any_failed, etime = parse_time_strings(T.elapsed)
if any_failed is not None:
print('Failed to parse elapsed time string:', any_failed)
else:
T.elapsed = np.array(etime)
any_failed, ctime = parse_time_strings(T.time)
if any_failed is not None:
print('Failed to parse elapsed time string:', any_failed)
else:
T.time = np.array(ctime)
T.rename('time', 'cputime')
# Compute 'instantaneous' (5-sec averaged) %cpu
# BUT this only counts whole seconds in the 'ps' output.
T.icpu = np.zeros(len(T), np.float32)
icpu = T.icpu
for i, (p, etime, ctime) in enumerate(zip(T.pid, T.elapsed,
T.cputime)):
try:
elast, clast = last_time[p]
# new process with an existing PID?
if etime > elast:
icpu[i] = 100. * (ctime - clast) / (etime - elast)
except:
pass
last_time[p] = (etime, ctime)
# print('Processes:')
# J = np.argsort(-T.icpu)
# for j in J:
# p = T.pid[j]
# pp = T.ppid[j]
# print(' PID', p, '(main)' if p == parent_pid else '',
# '(worker)' if pp == parent_pid else '',
# 'pcpu', T.pcpu[j], 'pmem', T.pmem[j], 'icpu', T.icpu[j],
# T.command[j][:20])
# Apply cuts!
T.cut(
reduce(np.logical_or, [
T.pcpu > 5, T.pmem > 5, T.icpu > 5, T.pid == parent_pid,
(T.ppid == parent_pid) *
np.array([not c.startswith('ps ax') for c in T.command])
]))
#print('Cut to', len(T), 'with significant CPU/MEM use or my PPID')
# print('Kept:')
# J = np.argsort(-T.icpu)
# for j in J:
# p = T.pid[j]
# pp = T.ppid[j]
# print(' PID', p, '(main)' if p == parent_pid else '',
# '(worker)' if pp == parent_pid else '',
# 'pcpu', T.pcpu[j], 'pmem', T.pmem[j], 'icpu', T.icpu[j],
# T.command[j][:20])
if len(T) == 0:
continue
timenow = time.time()
T.unixtime = np.zeros(len(T), np.float64) + timenow
T.step = np.zeros(len(T), np.int16) + step
if os.path.exists('/proc'):
# Try to grab higher-precision CPU timing info from /proc/PID/stat
T.proc_utime = np.zeros(len(T), np.float32)
T.proc_stime = np.zeros(len(T), np.float32)
T.processor = np.zeros(len(T), np.int16)
T.proc_icpu = np.zeros(len(T), np.float32)
for i, p in enumerate(T.pid):
try:
# See:
# http://man7.org/linux/man-pages/man5/proc.5.html
procfn = '/proc/%i/stat' % p
txt = open(procfn).read()
#print('Read', procfn, ':', txt)
words = txt.split()
utime = int(words[13]) / float(clock_ticks)
stime = int(words[14]) / float(clock_ticks)
proc = int(words[38])
#print('utime', utime, 'stime', stime, 'processor', proc)
ctime = utime + stime
try:
tlast, clast = last_proc_time[p]
#print('pid', p, 'Tnow,Cnow', timenow, ctime, 'Tlast,Clast', tlast,clast)
if ctime >= clast:
T.proc_icpu[i] = 100. * (
ctime - clast) / float(timenow - tlast)
except:
pass
last_proc_time[p] = (timenow, ctime)
T.proc_utime[i] = utime
T.proc_stime[i] = stime
T.processor[i] = proc
except:
pass
TT.append(T)
#print('ps -- step', step)
if (step % 12 == 0) and len(TT) > 0:
# Write out results every ~ minute.
print('ps -- writing', fn)
T = merge_tables(TT, columns='fillzero')
write_results(fn, T, events, fitshdr)
TT = [T]
# Just before returning, write out results.
if len(TT) > 0:
print('ps -- writing', fn)
T = merge_tables(TT, columns='fillzero')
write_results(fn, T, events, fitshdr)
def annotated_image(req, jobid=None, size='full'):
job = get_object_or_404(Job, pk=jobid)
ui = job.user_image
img = ui.image
if size == 'display':
scale = float(img.get_display_image().width) / img.width
img = img.get_display_image()
else:
scale = 1.0
wcsfn = job.get_wcs_file()
pnmfn = img.get_pnm_path()
annfn = get_temp_file()
#datadir = os.path.join(os.path.dirname(os.path.dirname(settings.WEB_DIR)), 'data')
catdir = settings.CAT_DIR
uzcfn = os.path.join(catdir, 'uzc2000.fits')
abellfn = os.path.join(catdir, 'abell-all.fits')
#hdfn = os.path.join(os.path.dirname(os.path.dirname(settings.WEB_DIR)),
#'net', 'hd.fits')
hdfn = settings.HENRY_DRAPER_CAT
tycho2fn = settings.TYCHO2_KD
rad = job.calibration.get_radius()
#logmsg('pnm file: %s' % pnmfn)
args = [
'plotann.py --no-grid --toy -10',
'--scale %s' % (str(scale)),
]
#if rad < 10.:
if rad < 1.:
args.extend([ #'--uzccat %s' % uzcfn,
'--abellcat %s' % abellfn,
'--hdcat %s' % hdfn
])
if rad < 0.25:
args.append('--tycho2cat %s' % tycho2fn)
#if rad > 20:
if rad > 10:
args.append('--no-ngc')
if rad > 30:
args.append('--no-bright')
cmd = ' '.join(args + ['%s %s %s' % (wcsfn, pnmfn, annfn)])
#cmd = 'plot-constellations -w %s -i %s -o %s -s %s -N -C -B -c' % (wcsfn, pnmfn, annfn, str(scale))
import sys
# (rtn,out,err) = run_command('which plotann.py; echo pyp $PYTHONPATH; echo path $PATH; echo llp $LD_LIBRARY_PATH; echo "set"; set')
# return HttpResponse('which: ' + out + err + '<br>sys.path<br>' + '<br>'.join(sys.path) +
# "<br>PATH " + os.environ['PATH'] +
# "<br>LLP " + os.environ['LD_LIBRARY_PATH'] +
# "<br>sys.path " + ':'.join(sys.path) +
# "<br>cmd " + cmd)
os.environ['PYTHONPATH'] = ':'.join(sys.path)
logmsg('Running: ' + cmd)
#logmsg('PYTHONPATH: ' + os.environ['PYTHONPATH'])
#logmsg('PATH: ' + os.environ['PATH'])
#(rtn,out,err) = run_command('which plotann.py')
#logmsg('which plotann.py: ' + out)
(rtn, out, err) = run_command(cmd)
if rtn:
logmsg('out: ' + out)
logmsg('err: ' + err)
return HttpResponse('plot failed: ' + err + "<br><pre>" + out +
"</pre><br><pre>" + err + "</pre>")
f = open(annfn)
res = HttpResponse(f)
#res['Content-Type'] = 'image/png'
# plotann.py produces jpeg by default
res['Content-Type'] = 'image/jpeg'
return res
def readFrame(self, run, camcol, field, band, filename=None):
'''
http://data.sdss3.org/datamodel/files/BOSS_PHOTOOBJ/frames/RERUN/RUN/CAMCOL/frame.html
'''
f = Frame(run, camcol, field, band)
# ...
if filename is None:
fn = self.getPath('frame', run, camcol, field, band)
else:
fn = filename
#print 'reading file', fn
if fitsio:
print 'Frame filename', fn
# eg /clusterfs/riemann/raid006/dr10/boss/photoObj/frames/301/2825/1/frame-u-002825-1-0126.fits.bz2
tempfn = None
keep = False
cmd = None
# bunzip2
filetype = 'frame'
if filetype in self.processcmds:
cmd = self.processcmds[filetype]
if cmd is not None and self.unzip_dir is not None:
udir = os.path.join(self.unzip_dir, '%i' % run, '%i' % camcol)
if not os.path.exists(udir):
try:
os.makedirs(udir)
except:
pass
tempfn = os.path.join(udir,
os.path.basename(fn).replace('.bz2', ''))
#print 'Checking', tempfn
if os.path.exists(tempfn):
print 'File exists:', tempfn
fn = tempfn
cmd = None
else:
print 'Saving to', tempfn
keep = True
elif cmd is not None and self.unzip_dir is None:
fid, tempfn = tempfile.mkstemp()
os.close(fid)
if cmd is not None:
cmd = cmd % dict(input=fn, output=tempfn)
self.logger.debug('cmd: %s' % cmd)
(rtn, out, err) = run_command(cmd)
if rtn:
print 'Command failed: command', cmd
print 'Output:', out
print 'Error:', err
print 'Return val:', rtn
return None
fn = tempfn
#f.image, f.header = fitsio.read(fn, header=True)
#print 'Reading header...'
f.header = fitsio.read_header(fn, 0)
#print 'Reading image HDU...'
# Allow later reading of just the ROI slice...
f.image_proxy = fitsio.FITS(fn)[0]
f.calib = fitsio.read(fn, ext=1)
sky = fitsio.read(fn,
ext=2,
columns=['allsky', 'xinterp', 'yinterp'])
#print 'sky', type(sky)
# ... supposed to be a recarray, but it's not...
f.sky, f.skyxi, f.skyyi = sky.tolist()[0]
tab = fits_table(fn, hdu=3)
if not keep and tempfn is not None:
os.remove(tempfn)
else:
p = pyfits.open(fn)
# in nanomaggies
f.image = p[0].data
f.header = p[0].header
# converts counts -> nanomaggies
f.calib = p[1].data
# table with val,x,y -- binned; use bilinear interpolation to expand
sky = p[2].data
# table -- asTrans structure
tab = fits_table(p[3].data)
f.sky = sky.field('allsky')[0]
f.skyxi = sky.field('xinterp')[0]
f.skyyi = sky.field('yinterp')[0]
#print 'sky shape', f.sky.shape
if len(f.sky.shape) != 2:
f.sky = f.sky.reshape((-1, 256))
assert (len(tab) == 1)
tab = tab[0]
# DR7 has NODE, INCL in radians...
f.astrans = AsTrans(run,
camcol,
field,
band,
node=np.deg2rad(tab.node),
incl=np.deg2rad(tab.incl),
astrans=tab,
cut_to_band=False)
return f
def dojob(job,
userimage,
log=None,
solve_command=None,
solve_locally=None,
tempfiles=None):
print('dojob: tempdir:', tempfile.gettempdir())
jobdir = job.make_dir()
#print('Created job dir', jobdir)
#log = create_job_logger(job)
#jobdir = job.get_dir()
if log is None:
log = create_job_logger(job)
log.msg('Starting Job processing for', job)
job.set_start_time()
job.save()
#os.chdir(dirnm) - not thread safe (working directory is global)!
log.msg('Creating directory', jobdir)
axyfn = 'job.axy'
axypath = os.path.join(jobdir, axyfn)
sub = userimage.submission
log.msg('submission id', sub.id)
df = userimage.image.disk_file
img = userimage.image
# Build command-line arguments for the augment-xylist program, which
# detects sources in the image and adds processing arguments to the header
# to produce a "job.axy" file.
slo, shi = sub.get_scale_bounds()
# Note, this must match Job.get_wcs_file().
wcsfile = 'wcs.fits'
corrfile = 'corr.fits'
axyflags = []
axyargs = {
'--out': axypath,
'--scale-low': slo,
'--scale-high': shi,
'--scale-units': sub.scale_units,
'--wcs': wcsfile,
'--corr': corrfile,
'--rdls': 'rdls.fits',
'--pixel-error': sub.positional_error,
'--ra': sub.center_ra,
'--dec': sub.center_dec,
'--radius': sub.radius,
'--downsample': sub.downsample_factor,
# tuning-up maybe fixed; if not, turn it off with:
#'--odds-to-tune': 1e9,
# Other things we might want include...
# --invert
# -g / --guess-scale: try to guess the image scale from the FITS headers
# --crpix-x <pix>: set the WCS reference point to the given position
# --crpix-y <pix>: set the WCS reference point to the given position
# -w / --width <pixels>: specify the field width
# -e / --height <pixels>: specify the field height
# -X / --x-column <column-name>: the FITS column name
# -Y / --y-column <column-name>
}
if hasattr(img, 'sourcelist'):
# image is a source list; use --xylist
axyargs['--xylist'] = img.sourcelist.get_fits_path(tempfiles=tempfiles)
w, h = img.width, img.height
if sub.image_width:
w = sub.image_width
if sub.image_height:
h = sub.image_height
axyargs['--width'] = w
axyargs['--height'] = h
else:
axyargs['--image'] = df.get_path()
# UGLY
if sub.parity == 0:
axyargs['--parity'] = 'pos'
elif sub.parity == 1:
axyargs['--parity'] = 'neg'
if sub.tweak_order == 0:
axyflags.append('--no-tweak')
else:
axyargs['--tweak-order'] = '%i' % sub.tweak_order
if sub.use_sextractor:
axyflags.append('--use-source-extractor')
if sub.crpix_center:
axyflags.append('--crpix-center')
if sub.invert:
axyflags.append('--invert')
cmd = 'augment-xylist '
for (k, v) in list(axyargs.items()):
if v:
cmd += k + ' ' + str(v) + ' '
for k in axyflags:
cmd += k + ' '
log.msg('running: ' + cmd)
(rtn, out, err) = run_command(cmd)
if rtn:
log.msg('out: ' + out)
log.msg('err: ' + err)
logmsg('augment-xylist failed: rtn val', rtn, 'err', err)
raise Exception
log.msg('created axy file', axypath)
# shell into compute server...
logfn = job.get_log_file()
# the "tar" commands both use "-C" to chdir, and the ssh command
# and redirect uses absolute paths.
if solve_locally is not None:
cmd = (('cd %(jobdir)s && %(solvecmd)s %(jobid)s %(axyfile)s >> ' +
'%(logfile)s') % dict(jobid='job-%s-%i' %
(settings.sitename, job.id),
solvecmd=solve_locally,
axyfile=axyfn,
jobdir=jobdir,
logfile=logfn))
log.msg('command:', cmd)
w = os.system(cmd)
if not os.WIFEXITED(w):
log.msg('Solver failed (sent signal?)')
logmsg('Call to solver failed for job', job.id)
raise Exception
rtn = os.WEXITSTATUS(w)
if rtn:
log.msg('Solver failed with return value %i' % rtn)
logmsg('Call to solver failed for job', job.id, 'with return val',
rtn)
raise Exception
log.msg('Solver completed successfully.')
else:
if solve_command is None:
solve_command = 'ssh -x -T %(sshconfig)s'
cmd = ((
'(echo %(jobid)s; '
'tar cf - --ignore-failed-read -C %(jobdir)s %(axyfile)s) | ' +
solve_command + ' 2>>%(logfile)s | '
'tar xf - --atime-preserve -m --exclude=%(axyfile)s -C %(jobdir)s '
'>>%(logfile)s 2>&1') % dict(jobid='job-%s-%i' %
(settings.sitename, job.id),
axyfile=axyfn,
jobdir=jobdir,
sshconfig=settings.ssh_solver_config,
logfile=logfn))
log.msg('command:', cmd)
w = os.system(cmd)
if not os.WIFEXITED(w):
log.msg('Solver failed (sent signal?)')
logmsg('Call to solver failed for job', job.id)
raise Exception
rtn = os.WEXITSTATUS(w)
if rtn:
log.msg('Solver failed with return value %i' % rtn)
logmsg('Call to solver failed for job', job.id, 'with return val',
rtn)
raise Exception
log.msg('Solver completed successfully.')
# Solved?
wcsfn = os.path.join(jobdir, wcsfile)
log.msg('Checking for WCS file', wcsfn)
if os.path.exists(wcsfn):
log.msg('WCS file exists')
# Parse the wcs.fits file
wcs = Tan(wcsfn, 0)
# Convert to database model...
tan = TanWCS(crval1=wcs.crval[0],
crval2=wcs.crval[1],
crpix1=wcs.crpix[0],
crpix2=wcs.crpix[1],
cd11=wcs.cd[0],
cd12=wcs.cd[1],
cd21=wcs.cd[2],
cd22=wcs.cd[3],
imagew=img.width,
imageh=img.height)
tan.save()
log.msg('Created TanWCS:', tan)
# Find field's healpix nside and index
ra, dec, radius = tan.get_center_radecradius()
nside = anutil.healpix_nside_for_side_length_arcmin(radius * 60)
nside = int(2**round(math.log(nside, 2)))
nside = max(1, nside)
healpix = anutil.radecdegtohealpix(ra, dec, nside)
try:
sky_location, created = SkyLocation.objects.get_or_create(
nside=nside, healpix=healpix)
except MultipleObjectsReturned:
log.msg('Multiple SkyLocations for nside %i, healpix %i' %
(nside, healpix))
# arbitrarily take the first one.
sky_location = SkyLocation.objects.filter(nside=nside,
healpix=healpix)[0]
log.msg('SkyLocation:', sky_location)
# Find bounds for the Calibration object.
r0, r1, d0, d1 = wcs.radec_bounds()
# Find cartesian coordinates
ra *= math.pi / 180
dec *= math.pi / 180
tempr = math.cos(dec)
x = tempr * math.cos(ra)
y = tempr * math.sin(ra)
z = math.sin(dec)
r = radius / 180 * math.pi
calib = Calibration(raw_tan=tan,
ramin=r0,
ramax=r1,
decmin=d0,
decmax=d1,
x=x,
y=y,
z=z,
r=r,
sky_location=sky_location)
calib.save()
log.msg('Created Calibration', calib)
job.calibration = calib
job.save() # save calib before adding machine tags
job.status = 'S'
job.user_image.add_machine_tags(job)
job.user_image.add_sky_objects(job)
else:
job.status = 'F'
job.set_end_time()
job.save()
log.msg('Finished job', job.id)
logmsg('Finished job', job.id)
return job.id
def annotated_image(req, jobid=None, size='full'):
job = get_object_or_404(Job, pk=jobid)
ui = job.user_image
img = ui.image
if size == 'display':
scale = float(img.get_display_image().width)/img.width
img = img.get_display_image()
else:
scale = 1.0
wcsfn = job.get_wcs_file()
pnmfn = img.get_pnm_path()
annfn = get_temp_file()
#datadir = os.path.join(os.path.dirname(os.path.dirname(settings.WEB_DIR)), 'data')
catdir = settings.CAT_DIR
uzcfn = os.path.join(catdir, 'uzc2000.fits')
abellfn = os.path.join(catdir, 'abell-all.fits')
#hdfn = os.path.join(os.path.dirname(os.path.dirname(settings.WEB_DIR)),
#'net', 'hd.fits')
hdfn = settings.HENRY_DRAPER_CAT
tycho2fn = settings.TYCHO2_KD
rad = job.calibration.get_radius()
#logmsg('pnm file: %s' % pnmfn)
args = ['plotann.py --no-grid --toy -10',
'--scale %s' % (str(scale)),]
#if rad < 10.:
if rad < 1.:
args.extend([#'--uzccat %s' % uzcfn,
'--abellcat %s' % abellfn,
'--hdcat %s' % hdfn
])
if rad < 0.25:
args.append('--tycho2cat %s' % tycho2fn)
#if rad > 20:
if rad > 10:
args.append('--no-ngc')
if rad > 30:
args.append('--no-bright')
cmd = ' '.join(args + ['%s %s %s' % (wcsfn, pnmfn, annfn)])
#cmd = 'plot-constellations -w %s -i %s -o %s -s %s -N -C -B -c' % (wcsfn, pnmfn, annfn, str(scale))
import sys
# (rtn,out,err) = run_command('which plotann.py; echo pyp $PYTHONPATH; echo path $PATH; echo llp $LD_LIBRARY_PATH; echo "set"; set')
# return HttpResponse('which: ' + out + err + '<br>sys.path<br>' + '<br>'.join(sys.path) +
# "<br>PATH " + os.environ['PATH'] +
# "<br>LLP " + os.environ['LD_LIBRARY_PATH'] +
# "<br>sys.path " + ':'.join(sys.path) +
# "<br>cmd " + cmd)
os.environ['PYTHONPATH'] = ':'.join(sys.path)
logmsg('Running: ' + cmd)
#logmsg('PYTHONPATH: ' + os.environ['PYTHONPATH'])
#logmsg('PATH: ' + os.environ['PATH'])
#(rtn,out,err) = run_command('which plotann.py')
#logmsg('which plotann.py: ' + out)
(rtn, out, err) = run_command(cmd)
if rtn:
logmsg('out: ' + out)
logmsg('err: ' + err)
return HttpResponse('plot failed: ' + err + "<br><pre>" + out + "</pre><br><pre>" + err + "</pre>")
f = open(annfn)
res = HttpResponse(f)
#res['Content-Type'] = 'image/png'
# plotann.py produces jpeg by default
res['Content-Type'] = 'image/jpeg'
return res
def dojob(job, userimage, log=None):
jobdir = job.make_dir()
#print 'Created job dir', jobdir
#log = create_job_logger(job)
#jobdir = job.get_dir()
if log is None:
log = create_job_logger(job)
log.msg('Starting Job processing for', job)
job.set_start_time()
job.save()
#os.chdir(dirnm) - not thread safe (working directory is global)!
log.msg('Creating directory', jobdir)
axyfn = 'job.axy'
axypath = os.path.join(jobdir, axyfn)
sub = userimage.submission
log.msg('submission id', sub.id)
df = userimage.image.disk_file
img = userimage.image
# Build command-line arguments for the augment-xylist program, which
# detects sources in the image and adds processing arguments to the header
# to produce a "job.axy" file.
slo,shi = sub.get_scale_bounds()
# Note, this must match Job.get_wcs_file().
wcsfile = 'wcs.fits'
axyflags = []
axyargs = {
'--out': axypath,
'--scale-low': slo,
'--scale-high': shi,
'--scale-units': sub.scale_units,
'--wcs': wcsfile,
'--rdls': 'rdls.fits',
'--pixel-error': sub.positional_error,
'--ra': sub.center_ra,
'--dec': sub.center_dec,
'--radius': sub.radius,
'--downsample': sub.downsample_factor,
# tuning-up maybe fixed; if not, turn it off with:
#'--odds-to-tune': 1e9,
# Other things we might want include...
# --invert
# -g / --guess-scale: try to guess the image scale from the FITS headers
# --crpix-x <pix>: set the WCS reference point to the given position
# --crpix-y <pix>: set the WCS reference point to the given position
# -w / --width <pixels>: specify the field width
# -e / --height <pixels>: specify the field height
# -X / --x-column <column-name>: the FITS column name
# -Y / --y-column <column-name>
}
if hasattr(img,'sourcelist'):
# image is a source list; use --xylist
axyargs['--xylist'] = img.sourcelist.get_fits_path()
w,h = img.width, img.height
if sub.image_width:
w = sub.image_width
if sub.image_height:
h = sub.image_height
axyargs['--width' ] = w
axyargs['--height'] = h
else:
axyargs['--image'] = df.get_path()
# UGLY
if sub.parity == 0:
axyargs['--parity'] = 'pos'
elif sub.parity == 1:
axyargs['--parity'] = 'neg'
if sub.tweak_order == 0:
axyflags.append('--no-tweak')
else:
axyargs['--tweak-order'] = '%i' % sub.tweak_order
if sub.use_sextractor:
axyflags.append('--use-sextractor')
if sub.crpix_center:
axyflags.append('--crpix-center')
if sub.invert:
axyflags.append('--invert')
cmd = 'augment-xylist '
for (k,v) in axyargs.items():
if v:
cmd += k + ' ' + str(v) + ' '
for k in axyflags:
cmd += k + ' '
log.msg('running: ' + cmd)
(rtn, out, err) = run_command(cmd)
if rtn:
log.msg('out: ' + out)
log.msg('err: ' + err)
logmsg('augment-xylist failed: rtn val', rtn, 'err', err)
raise Exception
log.msg('created axy file', axypath)
# shell into compute server...
logfn = job.get_log_file()
# the "tar" commands both use "-C" to chdir, and the ssh command
# and redirect uses absolute paths.
cmd = ('(echo %(jobid)s; '
'tar cf - --ignore-failed-read -C %(jobdir)s %(axyfile)s) | '
'ssh -x -T %(sshconfig)s 2>>%(logfile)s | '
'tar xf - --atime-preserve -m --exclude=%(axyfile)s -C %(jobdir)s '
'>>%(logfile)s 2>&1' %
dict(jobid='job-%s-%i' % (settings.sitename, job.id),
axyfile=axyfn, jobdir=jobdir,
sshconfig=settings.ssh_solver_config,
logfile=logfn))
log.msg('command:', cmd)
w = os.system(cmd)
if not os.WIFEXITED(w):
log.msg('Solver failed (sent signal?)')
logmsg('Call to solver failed for job', job.id)
raise Exception
rtn = os.WEXITSTATUS(w)
if rtn:
log.msg('Solver failed with return value %i' % rtn)
logmsg('Call to solver failed for job', job.id, 'with return val', rtn)
raise Exception
log.msg('Solver completed successfully.')
# Solved?
wcsfn = os.path.join(jobdir, wcsfile)
log.msg('Checking for WCS file', wcsfn)
if os.path.exists(wcsfn):
log.msg('WCS file exists')
# Parse the wcs.fits file
wcs = Tan(wcsfn, 0)
# Convert to database model...
tan = TanWCS(crval1=wcs.crval[0], crval2=wcs.crval[1],
crpix1=wcs.crpix[0], crpix2=wcs.crpix[1],
cd11=wcs.cd[0], cd12=wcs.cd[1],
cd21=wcs.cd[2], cd22=wcs.cd[3],
imagew=img.width, imageh=img.height)
tan.save()
log.msg('Created TanWCS:', tan)
# Find field's healpix nside and index
ra, dec, radius = tan.get_center_radecradius()
nside = anutil.healpix_nside_for_side_length_arcmin(radius*60)
nside = int(2**round(math.log(nside, 2)))
healpix = anutil.radecdegtohealpix(ra, dec, nside)
sky_location, created = SkyLocation.objects.get_or_create(nside=nside, healpix=healpix)
log.msg('SkyLocation:', sky_location)
# Find bounds for the Calibration object.
r0,r1,d0,d1 = wcs.radec_bounds()
# Find cartesian coordinates
ra *= math.pi/180
dec *= math.pi/180
tempr = math.cos(dec)
x = tempr*math.cos(ra)
y = tempr*math.sin(ra)
z = math.sin(dec)
r = radius/180*math.pi
calib = Calibration(raw_tan=tan, ramin=r0, ramax=r1, decmin=d0, decmax=d1,
x=x,y=y,z=z,r=r,
sky_location=sky_location)
calib.save()
log.msg('Created Calibration', calib)
job.calibration = calib
job.save() # save calib before adding machine tags
job.status = 'S'
job.user_image.add_machine_tags(job)
job.user_image.add_sky_objects(job)
else:
job.status = 'F'
job.set_end_time()
job.save()
log.msg('Finished job', job.id)
logmsg('Finished job',job.id)
return job.id
