def peak(so, mapdir):
src = '{}/{}.cnt'.format(mapdir, so)
for li in ['ll.nocal', 'rr.nocal', 'll.nopol', 'rr.nopol']:
miriad.maxfit({
'in': '{}.{}.cm'.format(src, li),
'log': 'maxfit_{}.{}'.format(so, li)
})
miriad.maxfit({
'in': '{}.i.cm'.format(src),
'log': 'maxfit_{}.stokesI'.format(so)
})
def getMapData(uncorrectedMap,
correctedMap,
line,
stokes,
peakStokes,
regionWidth=1,
useFull=True,
imspectOptions={},
maxfitOptions={}):
"""
Returns two numpy arrays representing the uncorrected and corrected spectra for each given stokes
these arrays in turn are of length 2*len(stokes).
ex:
```
freqs, amps = getMapData('/path/to/uncorrected/map', '/path/to/corrected/map', 'co3-2', ['i', 'v'], 'v', regionWidth=1)
# freqs[0], amps[0] is the frequency vs. amplitude for the uncorrected map of stokes i through the max peak of stokes i
# since getMapData was called with stokes = ['i', 'v'] len(freqs) = 4 and len(amps) = 4
```
"""
corrText = ['uncorr', 'corr']
frequencies = []
amplitudes = []
for i, mapdir in enumerate([uncorrectedMap, correctedMap]):
if useFull:
peakLineMap = (mapdir + '.' + peakStokes + '.full.cm').replace(
'usb', line)
else:
peakLineMap = (mapdir + '.' + peakStokes + '.cm').replace(
'usb', line)
try:
maxPixel = miriad.maxfit({
**{
'in': peakLineMap
},
**maxfitOptions
},
stdout=subprocess.PIPE).stdout
maxPixel = str(maxPixel).split('\\n')[4]
maxPixel = maxPixel[maxPixel.find('(') +
1:maxPixel.find(')')].split(',')[0:2]
maxPixel = list(map(int, maxPixel))
except:
maxPixel = [64, 64]
if 'OrionKL' in correctedMap:
maxPixel = [90, 111]
if 'sio' in line and 'OrionKL' in correctedMap:
maxPixel = [124, 75]
# make a box around the peak (by finding a bottom left corner 'blc' and top right corner 'trc')
blc = (maxPixel[0] - regionWidth / 2, maxPixel[1] - regionWidth / 2)
blc = tuple(map(int, blc))
trc = (maxPixel[0] + regionWidth / 2, maxPixel[1] + regionWidth / 2)
trc = tuple(map(int, trc))
region = 'abspixel,box({},{},{},{})'.format(blc[0], blc[1], trc[0],
trc[1])
print(peakLineMap)
print('peak at:', str(maxPixel))
# save overlay file
overlayFile = '{}.{}.cmap.olay'.format(
mapdir.split('/')[1], peakStokes)
output = 'star abspix abspix Peak_V yes {} {} 6 6'.format(
maxPixel[0], maxPixel[1])
with open(overlayFile, 'w') as f:
f.write('color 1\n')
f.write(output)
for stk in stokes:
mapsuffix = '.{}.full.cm'.format(stk)
mappath = mapdir + mapsuffix
miriad.velsw({'in': mappath, 'axis': 'FREQ'})
# get i and v spectra through the point where v peaks in the line map
imspectDefaults = {
'in': mappath,
'region': region,
}
x, y, _ = miriad.dumpImspect(mappath,
options={
**imspectDefaults,
**imspectOptions
})
frequencies.append(x)
amplitudes.append(y)
return frequencies, amplitudes