| 1 | import _asap |
|---|
| 2 | |
|---|
| 3 | class linefinder: |
|---|
| 4 | """ |
|---|
| 5 | The class for automated spectral line search in ASAP. |
|---|
| 6 | """ |
|---|
| 7 | |
|---|
| 8 | def __init__(self): |
|---|
| 9 | """ |
|---|
| 10 | Create a line finder object. |
|---|
| 11 | """ |
|---|
| 12 | self.finder = _asap.linefinder() |
|---|
| 13 | return |
|---|
| 14 | |
|---|
| 15 | def set_options(self,threshold=1.7320508075688772,min_nchan=3, |
|---|
| 16 | avg_limit=8,box_size=0.2): |
|---|
| 17 | """ |
|---|
| 18 | Set the parameters of the algorithm |
|---|
| 19 | Parameters: |
|---|
| 20 | threshold a single channel S/N ratio above which the |
|---|
| 21 | channel is considered to be a detection |
|---|
| 22 | Default is sqrt(3), which together with |
|---|
| 23 | min_nchan=3 gives a 3-sigma criterion |
|---|
| 24 | min_nchan a minimal number of consequtive channels, |
|---|
| 25 | which should satisfy a threshold criterion to |
|---|
| 26 | be a detection. Default is 3. |
|---|
| 27 | avg_limit A number of consequtive channels not greater than |
|---|
| 28 | this parameter can be averaged to search for |
|---|
| 29 | broad lines. Default is 8. |
|---|
| 30 | box_size A running mean box size specified as a fraction |
|---|
| 31 | of the total spectrum length. Default is 1/5 |
|---|
| 32 | Note: For bad baselines threshold should be increased, |
|---|
| 33 | and avg_limit decreased (or even switched off completely by |
|---|
| 34 | setting this parameter to 1) to avoid detecting baseline |
|---|
| 35 | undulations instead of real lines. |
|---|
| 36 | """ |
|---|
| 37 | self.finder.setoptions(threshold,min_nchan,avg_limit,box_size) |
|---|
| 38 | return |
|---|
| 39 | |
|---|
| 40 | def set_scan(self,scan,mask=None,edge=(0,0)): |
|---|
| 41 | """ |
|---|
| 42 | Set the 'data' (scantable) to work with. |
|---|
| 43 | Parameters: |
|---|
| 44 | scan: a scantable |
|---|
| 45 | mask: an optional mask retreived from scantable |
|---|
| 46 | edge: an optional number of channel to drop at |
|---|
| 47 | the edge of spectrum. If only one value is |
|---|
| 48 | specified, the same number will be dropped from |
|---|
| 49 | both sides of the spectrum. Default is to keep |
|---|
| 50 | all channels |
|---|
| 51 | """ |
|---|
| 52 | if not scan: |
|---|
| 53 | raise RuntimeError, 'Please give a correct scan' |
|---|
| 54 | if len(edge)>2: |
|---|
| 55 | raise RuntimeError, "The edge parameter should have two \ |
|---|
| 56 | or less elements" |
|---|
| 57 | if mask is None: |
|---|
| 58 | from numarray import ones |
|---|
| 59 | self.finder.setscan(scan,ones(scan.nchan()),edge) |
|---|
| 60 | else: |
|---|
| 61 | self.finder.setscan(scan,mask,edge) |
|---|
| 62 | return |
|---|
| 63 | def find_lines(self): |
|---|
| 64 | """ |
|---|
| 65 | Search for spectral lines in the scan assigned in set_scan. |
|---|
| 66 | A number of lines found will be returned |
|---|
| 67 | """ |
|---|
| 68 | return self.finder.findlines() |
|---|
| 69 | def get_mask(self,invert=False): |
|---|
| 70 | """ |
|---|
| 71 | Get the mask to mask out all lines that have been found (default) |
|---|
| 72 | |
|---|
| 73 | Parameters: |
|---|
| 74 | invert if True, only channels belong to lines will be unmasked |
|---|
| 75 | |
|---|
| 76 | Note: all channels originally masked by the input mask or |
|---|
| 77 | dropped out by the edge parameter will still be excluded |
|---|
| 78 | regardless on the invert option |
|---|
| 79 | """ |
|---|
| 80 | return self.finder.getmask(invert) |
|---|
| 81 | def get_ranges(self,defunits=True): |
|---|
| 82 | """ |
|---|
| 83 | Get ranges (start and end channels or velocities) for all spectral |
|---|
| 84 | lines found. |
|---|
| 85 | |
|---|
| 86 | Parameters: |
|---|
| 87 | defunits if True (default), the range will use the same units |
|---|
| 88 | as set for the scan (e.g. LSR velocity) |
|---|
| 89 | if False, the range will be expressed in channels |
|---|
| 90 | """ |
|---|
| 91 | return self.finder.getlineranges(defunits) |
|---|
