1 | import _asap |
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2 | |
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3 | class linefinder: |
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4 | """ |
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5 | The class for automated spectral line search in ASAP. |
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6 | |
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7 | Example: |
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8 | fl=linefinder() |
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9 | fl.set_scan(sc) |
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10 | fl.set_options(threshold=3) |
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11 | nlines=fl.find_lines(edge=(50,0)) |
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12 | if nlines!=0: |
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13 | print "Found ",nlines," spectral lines" |
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14 | print fl.get_ranges(False) |
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15 | else: |
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16 | print "No lines found!" |
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17 | sc2=sc.poly_baseline(fl.get_mask(),7) |
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18 | |
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19 | The algorithm involves a simple threshold criterion. The line is |
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20 | considered to be detected if a specified number of consequtive |
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21 | channels (default is 3) is brighter (with respect to the current baseline |
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22 | estimate) than the threshold times the noise level. This criterion is |
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23 | applied in the iterative procedure updating baseline estimate and trying |
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24 | reduced spectral resolutions to detect broad lines as well. The off-line |
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25 | noise level is determined at each iteration as an average of 80% of the |
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26 | lowest variances across the spectrum (i.e. histogram equalization is |
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27 | used to avoid missing weak lines if strong ones are present). For |
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28 | bad baseline shapes it is recommended to increase the threshold and |
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29 | possibly switch the averaging option off (see set_options) to |
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30 | detect strong lines only, fit a high order baseline and repeat the line |
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31 | search. |
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32 | |
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33 | """ |
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34 | |
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35 | def __init__(self): |
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36 | """ |
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37 | Create a line finder object. |
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38 | """ |
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39 | self.finder = _asap.linefinder() |
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40 | return |
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41 | |
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42 | def set_options(self,threshold=1.7320508075688772,min_nchan=3, |
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43 | avg_limit=8,box_size=0.2,noise_box='all',noise_stat='mean80'): |
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44 | """ |
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45 | Set the parameters of the algorithm |
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46 | Parameters: |
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47 | threshold a single channel S/N ratio above which the |
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48 | channel is considered to be a detection |
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49 | Default is sqrt(3), which together with |
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50 | min_nchan=3 gives a 3-sigma criterion |
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51 | min_nchan a minimal number of consequtive channels, |
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52 | which should satisfy a threshold criterion to |
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53 | be a detection. Default is 3. |
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54 | avg_limit A number of consequtive channels not greater than |
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55 | this parameter can be averaged to search for |
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56 | broad lines. Default is 8. |
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57 | box_size A running mean/median box size specified as a fraction |
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58 | of the total spectrum length. Default is 1/5 |
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59 | noise_box Area of the spectrum used to estimate noise stats |
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60 | Both string values and numbers are allowed |
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61 | Allowed string values: |
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62 | 'all' use all the spectrum (default) |
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63 | 'box' noise box is the same as running mean/median |
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64 | box |
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65 | Numeric values are defined as a fraction from the |
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66 | spectrum size. Values should be positive. |
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67 | (noise_box == box_size has the same effect as |
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68 | noise_box = 'box') |
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69 | noise_stat Statistics used to estimate noise, allowed values: |
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70 | 'mean80' use the 80% of the lowest deviations |
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71 | in the noise box (default) |
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72 | 'median' median of deviations in the noise box |
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73 | |
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74 | Note: For bad baselines threshold should be increased, |
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75 | and avg_limit decreased (or even switched off completely by |
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76 | setting this parameter to 1) to avoid detecting baseline |
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77 | undulations instead of real lines. |
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78 | """ |
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79 | if noise_stat.lower() not in ["mean80",'median']: |
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80 | raise RuntimeError, "noise_stat argument in linefinder.set_options can only be mean80 or median" |
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81 | nStat = (noise_stat.lower() == "median") |
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82 | nBox = -1. |
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83 | if isinstance(noise_box,str): |
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84 | if noise_box.lower() not in ['all','box']: |
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85 | raise RuntimeError, "string-valued noise_box in linefinder.set_options can only be all or box" |
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86 | if noise_box.lower() == 'box': |
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87 | nBox = box_size |
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88 | else: |
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89 | nBox = float(noise_box) |
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90 | self.finder.setoptions(threshold,min_nchan,avg_limit,box_size,nBox,nStat) |
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91 | return |
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92 | |
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93 | def set_scan(self, scan): |
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94 | """ |
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95 | Set the 'data' (scantable) to work with. |
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96 | Parameters: |
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97 | scan: a scantable |
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98 | """ |
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99 | if not scan: |
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100 | raise RuntimeError, 'Please give a correct scan' |
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101 | self.finder.setscan(scan) |
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102 | |
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103 | def find_lines(self,nRow=0,mask=[],edge=(0,0)): |
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104 | """ |
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105 | Search for spectral lines in the scan assigned in set_scan. |
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106 | Parameters: |
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107 | nRow: a row in the scantable to work with |
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108 | mask: an optional mask (e.g. retreived from scantable) |
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109 | edge: an optional number of channels to drop at |
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110 | the edge of the spectrum. If only one value is |
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111 | specified, the same number will be dropped from |
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112 | both sides of the spectrum. Default is to keep |
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113 | all channels |
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114 | A number of lines found will be returned |
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115 | """ |
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116 | if isinstance(edge,int): |
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117 | edge=(edge,) |
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118 | |
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119 | from asap import _is_sequence_or_number as _is_valid |
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120 | |
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121 | if not _is_valid(edge, int): |
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122 | raise RuntimeError, "Parameter 'edge' has to be an integer or \ |
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123 | a pair of integers specified as a tuple" |
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124 | |
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125 | if len(edge)>2: |
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126 | raise RuntimeError, "The edge parameter should have two \ |
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127 | or less elements" |
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128 | return self.finder.findlines(mask,list(edge),nRow) |
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129 | def get_mask(self,invert=False): |
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130 | """ |
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131 | Get the mask to mask out all lines that have been found (default) |
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132 | |
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133 | Parameters: |
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134 | invert if True, only channels belong to lines will be unmasked |
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135 | |
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136 | Note: all channels originally masked by the input mask or |
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137 | dropped out by the edge parameter will still be excluded |
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138 | regardless on the invert option |
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139 | """ |
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140 | return self.finder.getmask(invert) |
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141 | def get_ranges(self,defunits=True): |
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142 | """ |
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143 | Get ranges (start and end channels or velocities) for all spectral |
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144 | lines found. |
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145 | |
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146 | Parameters: |
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147 | defunits if True (default), the range will use the same units |
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148 | as set for the scan (e.g. LSR velocity) |
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149 | if False, the range will be expressed in channels |
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150 | """ |
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151 | if (defunits): |
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152 | return self.finder.getlineranges() |
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153 | else: |
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154 | return self.finder.getlinerangesinchannels() |
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