[1846] | 1 | """This module defines the scantable class.""" |
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| 2 | |
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[1697] | 3 | import os |
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[2751] | 4 | import re |
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[2315] | 5 | import tempfile |
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[1948] | 6 | import numpy |
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[1691] | 7 | try: |
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| 8 | from functools import wraps as wraps_dec |
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| 9 | except ImportError: |
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| 10 | from asap.compatibility import wraps as wraps_dec |
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| 11 | |
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[1824] | 12 | from asap.env import is_casapy |
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[876] | 13 | from asap._asap import Scantable |
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[2004] | 14 | from asap._asap import filler, msfiller |
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[1824] | 15 | from asap.parameters import rcParams |
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[1862] | 16 | from asap.logging import asaplog, asaplog_post_dec |
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[1824] | 17 | from asap.selector import selector |
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| 18 | from asap.linecatalog import linecatalog |
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[1600] | 19 | from asap.coordinate import coordinate |
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[1859] | 20 | from asap.utils import _n_bools, mask_not, mask_and, mask_or, page |
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[1907] | 21 | from asap.asapfitter import fitter |
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[102] | 22 | |
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[1689] | 23 | def preserve_selection(func): |
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[1691] | 24 | @wraps_dec(func) |
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[1689] | 25 | def wrap(obj, *args, **kw): |
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| 26 | basesel = obj.get_selection() |
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[1857] | 27 | try: |
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| 28 | val = func(obj, *args, **kw) |
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| 29 | finally: |
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| 30 | obj.set_selection(basesel) |
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[1689] | 31 | return val |
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| 32 | return wrap |
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| 33 | |
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[1846] | 34 | def is_scantable(filename): |
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| 35 | """Is the given file a scantable? |
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[1689] | 36 | |
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[1846] | 37 | Parameters: |
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| 38 | |
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| 39 | filename: the name of the file/directory to test |
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| 40 | |
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| 41 | """ |
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[1883] | 42 | if ( os.path.isdir(filename) |
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| 43 | and os.path.exists(filename+'/table.info') |
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| 44 | and os.path.exists(filename+'/table.dat') ): |
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| 45 | f=open(filename+'/table.info') |
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| 46 | l=f.readline() |
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| 47 | f.close() |
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[2753] | 48 | match_pattern = '^Type = (Scantable)? *$' |
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[2751] | 49 | if re.match(match_pattern,l): |
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[1883] | 50 | return True |
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| 51 | else: |
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| 52 | return False |
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| 53 | else: |
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| 54 | return False |
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| 55 | ## return (os.path.isdir(filename) |
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| 56 | ## and not os.path.exists(filename+'/table.f1') |
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| 57 | ## and os.path.exists(filename+'/table.info')) |
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[1697] | 58 | |
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[1883] | 59 | def is_ms(filename): |
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| 60 | """Is the given file a MeasurementSet? |
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[1697] | 61 | |
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[1883] | 62 | Parameters: |
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| 63 | |
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| 64 | filename: the name of the file/directory to test |
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| 65 | |
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| 66 | """ |
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| 67 | if ( os.path.isdir(filename) |
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| 68 | and os.path.exists(filename+'/table.info') |
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| 69 | and os.path.exists(filename+'/table.dat') ): |
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| 70 | f=open(filename+'/table.info') |
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| 71 | l=f.readline() |
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| 72 | f.close() |
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| 73 | if ( l.find('Measurement Set') != -1 ): |
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| 74 | return True |
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| 75 | else: |
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| 76 | return False |
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| 77 | else: |
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| 78 | return False |
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[2186] | 79 | |
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| 80 | def normalise_edge_param(edge): |
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| 81 | """\ |
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| 82 | Convert a given edge value to a one-dimensional array that can be |
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| 83 | given to baseline-fitting/subtraction functions. |
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| 84 | The length of the output value will be an even because values for |
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| 85 | the both sides of spectra are to be contained for each IF. When |
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| 86 | the length is 2, the values will be applied to all IFs. If the length |
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| 87 | is larger than 2, it will be 2*ifnos(). |
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| 88 | Accepted format of edge include: |
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| 89 | * an integer - will be used for both sides of spectra of all IFs. |
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| 90 | e.g. 10 is converted to [10,10] |
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[2277] | 91 | * an empty list/tuple [] - converted to [0, 0] and used for all IFs. |
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[2186] | 92 | * a list/tuple containing an integer - same as the above case. |
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| 93 | e.g. [10] is converted to [10,10] |
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| 94 | * a list/tuple containing two integers - will be used for all IFs. |
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| 95 | e.g. [5,10] is output as it is. no need to convert. |
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| 96 | * a list/tuple of lists/tuples containing TWO integers - |
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| 97 | each element of edge will be used for each IF. |
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[2277] | 98 | e.g. [[5,10],[15,20]] - [5,10] for IF[0] and [15,20] for IF[1]. |
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| 99 | |
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| 100 | If an element contains the same integer values, the input 'edge' |
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| 101 | parameter can be given in a simpler shape in the following cases: |
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[2186] | 102 | ** when len(edge)!=2 |
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[2277] | 103 | any elements containing the same values can be replaced |
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| 104 | to single integers. |
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| 105 | e.g. [[15,15]] can be simplified to [15] (or [15,15] or 15 also). |
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| 106 | e.g. [[1,1],[2,2],[3,3]] can be simplified to [1,2,3]. |
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[2186] | 107 | ** when len(edge)=2 |
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| 108 | care is needed for this case: ONLY ONE of the |
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| 109 | elements can be a single integer, |
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| 110 | e.g. [[5,5],[10,10]] can be simplified to [5,[10,10]] |
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[2277] | 111 | or [[5,5],10], but can NOT be simplified to [5,10]. |
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[2186] | 112 | when [5,10] given, it is interpreted as |
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[2277] | 113 | [[5,10],[5,10],[5,10],...] instead, as shown before. |
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[2186] | 114 | """ |
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| 115 | from asap import _is_sequence_or_number as _is_valid |
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| 116 | if isinstance(edge, list) or isinstance(edge, tuple): |
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| 117 | for edgepar in edge: |
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| 118 | if not _is_valid(edgepar, int): |
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| 119 | raise ValueError, "Each element of the 'edge' tuple has \ |
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| 120 | to be a pair of integers or an integer." |
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| 121 | if isinstance(edgepar, list) or isinstance(edgepar, tuple): |
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| 122 | if len(edgepar) != 2: |
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| 123 | raise ValueError, "Each element of the 'edge' tuple has \ |
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| 124 | to be a pair of integers or an integer." |
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| 125 | else: |
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| 126 | if not _is_valid(edge, int): |
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| 127 | raise ValueError, "Parameter 'edge' has to be an integer or a \ |
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| 128 | pair of integers specified as a tuple. \ |
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| 129 | Nested tuples are allowed \ |
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| 130 | to make individual selection for different IFs." |
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| 131 | |
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| 132 | |
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| 133 | if isinstance(edge, int): |
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| 134 | edge = [ edge, edge ] # e.g. 3 => [3,3] |
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| 135 | elif isinstance(edge, list) or isinstance(edge, tuple): |
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| 136 | if len(edge) == 0: |
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| 137 | edge = [0, 0] # e.g. [] => [0,0] |
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| 138 | elif len(edge) == 1: |
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| 139 | if isinstance(edge[0], int): |
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| 140 | edge = [ edge[0], edge[0] ] # e.g. [1] => [1,1] |
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| 141 | |
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| 142 | commonedge = True |
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| 143 | if len(edge) > 2: commonedge = False |
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| 144 | else: |
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| 145 | for edgepar in edge: |
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| 146 | if isinstance(edgepar, list) or isinstance(edgepar, tuple): |
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| 147 | commonedge = False |
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| 148 | break |
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| 149 | |
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| 150 | if commonedge: |
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| 151 | if len(edge) > 1: |
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| 152 | norm_edge = edge |
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| 153 | else: |
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| 154 | norm_edge = edge + edge |
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| 155 | else: |
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| 156 | norm_edge = [] |
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| 157 | for edgepar in edge: |
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| 158 | if isinstance(edgepar, int): |
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| 159 | norm_edge += [edgepar, edgepar] |
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| 160 | else: |
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| 161 | norm_edge += edgepar |
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| 162 | |
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| 163 | return norm_edge |
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| 164 | |
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| 165 | def raise_fitting_failure_exception(e): |
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| 166 | msg = "The fit failed, possibly because it didn't converge." |
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| 167 | if rcParams["verbose"]: |
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| 168 | asaplog.push(str(e)) |
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| 169 | asaplog.push(str(msg)) |
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| 170 | else: |
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| 171 | raise RuntimeError(str(e)+'\n'+msg) |
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| 172 | |
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[2189] | 173 | def pack_progress_params(showprogress, minnrow): |
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| 174 | return str(showprogress).lower() + ',' + str(minnrow) |
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| 175 | |
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[2767] | 176 | def pack_blinfo(blinfo, maxirow): |
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| 177 | """\ |
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| 178 | convert a dictionary or a list of dictionaries of baseline info |
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| 179 | into a list of comma-separated strings. |
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| 180 | """ |
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| 181 | if isinstance(blinfo, dict): |
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| 182 | res = do_pack_blinfo(blinfo, maxirow) |
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| 183 | return [res] if res != '' else [] |
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| 184 | elif isinstance(blinfo, list) or isinstance(blinfo, tuple): |
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| 185 | res = [] |
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| 186 | for i in xrange(len(blinfo)): |
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| 187 | resi = do_pack_blinfo(blinfo[i], maxirow) |
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| 188 | if resi != '': |
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| 189 | res.append(resi) |
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| 190 | return res |
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| 191 | |
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| 192 | def do_pack_blinfo(blinfo, maxirow): |
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| 193 | """\ |
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| 194 | convert a dictionary of baseline info for a spectrum into |
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| 195 | a comma-separated string. |
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| 196 | """ |
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| 197 | dinfo = {} |
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| 198 | for key in ['row', 'blfunc', 'masklist']: |
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| 199 | if blinfo.has_key(key): |
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| 200 | val = blinfo[key] |
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| 201 | if key == 'row': |
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| 202 | irow = val |
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| 203 | if isinstance(val, list) or isinstance(val, tuple): |
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| 204 | slval = [] |
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| 205 | for i in xrange(len(val)): |
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| 206 | if isinstance(val[i], list) or isinstance(val[i], tuple): |
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| 207 | for j in xrange(len(val[i])): |
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| 208 | slval.append(str(val[i][j])) |
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| 209 | else: |
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| 210 | slval.append(str(val[i])) |
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| 211 | sval = ",".join(slval) |
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| 212 | else: |
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| 213 | sval = str(val) |
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| 214 | |
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| 215 | dinfo[key] = sval |
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| 216 | else: |
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| 217 | raise ValueError("'"+key+"' is missing in blinfo.") |
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| 218 | |
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| 219 | if irow >= maxirow: return '' |
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| 220 | |
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| 221 | for key in ['order', 'npiece', 'nwave']: |
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| 222 | if blinfo.has_key(key): |
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| 223 | val = blinfo[key] |
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| 224 | if isinstance(val, list) or isinstance(val, tuple): |
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| 225 | slval = [] |
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| 226 | for i in xrange(len(val)): |
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| 227 | slval.append(str(val[i])) |
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| 228 | sval = ",".join(slval) |
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| 229 | else: |
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| 230 | sval = str(val) |
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| 231 | dinfo[key] = sval |
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| 232 | |
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| 233 | blfunc = dinfo['blfunc'] |
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| 234 | fspec_keys = {'poly': 'order', 'chebyshev': 'order', 'cspline': 'npiece', 'sinusoid': 'nwave'} |
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| 235 | |
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| 236 | fspec_key = fspec_keys[blfunc] |
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| 237 | if not blinfo.has_key(fspec_key): |
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| 238 | raise ValueError("'"+fspec_key+"' is missing in blinfo.") |
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| 239 | |
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| 240 | clip_params_n = 0 |
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| 241 | for key in ['clipthresh', 'clipniter']: |
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| 242 | if blinfo.has_key(key): |
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| 243 | clip_params_n += 1 |
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| 244 | dinfo[key] = str(blinfo[key]) |
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| 245 | |
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| 246 | if clip_params_n == 0: |
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| 247 | dinfo['clipthresh'] = '0.0' |
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| 248 | dinfo['clipniter'] = '0' |
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| 249 | elif clip_params_n != 2: |
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| 250 | raise ValueError("both 'clipthresh' and 'clipniter' must be given for n-sigma clipping.") |
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| 251 | |
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| 252 | lf_params_n = 0 |
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| 253 | for key in ['thresh', 'edge', 'chan_avg_limit']: |
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| 254 | if blinfo.has_key(key): |
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| 255 | lf_params_n += 1 |
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| 256 | val = blinfo[key] |
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| 257 | if isinstance(val, list) or isinstance(val, tuple): |
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| 258 | slval = [] |
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| 259 | for i in xrange(len(val)): |
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| 260 | slval.append(str(val[i])) |
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| 261 | sval = ",".join(slval) |
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| 262 | else: |
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| 263 | sval = str(val) |
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| 264 | dinfo[key] = sval |
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| 265 | |
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| 266 | if lf_params_n == 3: |
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| 267 | dinfo['use_linefinder'] = 'true' |
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[2810] | 268 | elif lf_params_n == 0: |
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[2767] | 269 | dinfo['use_linefinder'] = 'false' |
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| 270 | dinfo['thresh'] = '' |
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| 271 | dinfo['edge'] = '' |
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| 272 | dinfo['chan_avg_limit'] = '' |
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| 273 | else: |
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| 274 | raise ValueError("all of 'thresh', 'edge' and 'chan_avg_limit' must be given to use linefinder.") |
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| 275 | |
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| 276 | slblinfo = [dinfo['row'], blfunc, dinfo[fspec_key], dinfo['masklist'], \ |
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| 277 | dinfo['clipthresh'], dinfo['clipniter'], \ |
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| 278 | dinfo['use_linefinder'], dinfo['thresh'], dinfo['edge'], dinfo['chan_avg_limit']] |
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| 279 | |
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| 280 | return ":".join(slblinfo) |
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| 281 | |
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| 282 | def parse_fitresult(sres): |
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| 283 | """\ |
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| 284 | Parse the returned value of apply_bltable() or sub_baseline() and |
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| 285 | extract row number, the best-fit coefficients and rms, then pack |
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| 286 | them into a dictionary. |
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| 287 | The input value is generated by Scantable::packFittingResults() and |
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| 288 | formatted as 'row:coeff[0],coeff[1],..,coeff[n-1]:rms'. |
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| 289 | """ |
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| 290 | res = [] |
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| 291 | for i in xrange(len(sres)): |
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| 292 | (srow, scoeff, srms) = sres[i].split(":") |
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| 293 | row = int(srow) |
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| 294 | rms = float(srms) |
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| 295 | lscoeff = scoeff.split(",") |
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| 296 | coeff = [] |
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| 297 | for j in xrange(len(lscoeff)): |
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| 298 | coeff.append(float(lscoeff[j])) |
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| 299 | res.append({'row': row, 'coeff': coeff, 'rms': rms}) |
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| 300 | |
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| 301 | return res |
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| 302 | |
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[876] | 303 | class scantable(Scantable): |
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[1846] | 304 | """\ |
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| 305 | The ASAP container for scans (single-dish data). |
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[102] | 306 | """ |
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[1819] | 307 | |
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[1862] | 308 | @asaplog_post_dec |
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[2315] | 309 | def __init__(self, filename, average=None, unit=None, parallactify=None, |
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| 310 | **args): |
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[1846] | 311 | """\ |
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[102] | 312 | Create a scantable from a saved one or make a reference |
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[1846] | 313 | |
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[102] | 314 | Parameters: |
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[1846] | 315 | |
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| 316 | filename: the name of an asap table on disk |
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| 317 | or |
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| 318 | the name of a rpfits/sdfits/ms file |
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| 319 | (integrations within scans are auto averaged |
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| 320 | and the whole file is read) or |
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| 321 | [advanced] a reference to an existing scantable |
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| 322 | |
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| 323 | average: average all integrations withinb a scan on read. |
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| 324 | The default (True) is taken from .asaprc. |
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| 325 | |
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[484] | 326 | unit: brightness unit; must be consistent with K or Jy. |
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[1846] | 327 | Over-rides the default selected by the filler |
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| 328 | (input rpfits/sdfits/ms) or replaces the value |
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| 329 | in existing scantables |
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| 330 | |
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[1920] | 331 | antenna: for MeasurementSet input data only: |
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[2349] | 332 | Antenna selection. integer (id) or string |
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| 333 | (name or id). |
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[1846] | 334 | |
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[2349] | 335 | parallactify: Indicate that the data had been parallactified. |
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| 336 | Default (false) is taken from rc file. |
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[1846] | 337 | |
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[2754] | 338 | getpt: Whether to import direction from MS/POINTING |
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| 339 | table properly or not. |
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| 340 | This is effective only when filename is MS. |
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| 341 | The default (True) is to import direction |
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| 342 | from MS/POINTING. |
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[710] | 343 | """ |
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[976] | 344 | if average is None: |
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[710] | 345 | average = rcParams['scantable.autoaverage'] |
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[1593] | 346 | parallactify = parallactify or rcParams['scantable.parallactify'] |
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[1259] | 347 | varlist = vars() |
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[876] | 348 | from asap._asap import stmath |
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[1819] | 349 | self._math = stmath( rcParams['insitu'] ) |
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[876] | 350 | if isinstance(filename, Scantable): |
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| 351 | Scantable.__init__(self, filename) |
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[181] | 352 | else: |
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[1697] | 353 | if isinstance(filename, str): |
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[976] | 354 | filename = os.path.expandvars(filename) |
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| 355 | filename = os.path.expanduser(filename) |
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| 356 | if not os.path.exists(filename): |
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| 357 | s = "File '%s' not found." % (filename) |
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| 358 | raise IOError(s) |
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[1697] | 359 | if is_scantable(filename): |
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| 360 | ondisk = rcParams['scantable.storage'] == 'disk' |
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| 361 | Scantable.__init__(self, filename, ondisk) |
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| 362 | if unit is not None: |
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| 363 | self.set_fluxunit(unit) |
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[2008] | 364 | if average: |
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| 365 | self._assign( self.average_time( scanav=True ) ) |
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[1819] | 366 | # do not reset to the default freqframe |
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| 367 | #self.set_freqframe(rcParams['scantable.freqframe']) |
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[1883] | 368 | elif is_ms(filename): |
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[1916] | 369 | # Measurement Set |
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| 370 | opts={'ms': {}} |
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[2844] | 371 | mskeys=['getpt','antenna'] |
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[1916] | 372 | for key in mskeys: |
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| 373 | if key in args.keys(): |
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| 374 | opts['ms'][key] = args[key] |
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| 375 | self._fill([filename], unit, average, opts) |
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[1893] | 376 | elif os.path.isfile(filename): |
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[2761] | 377 | opts={'nro': {}} |
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| 378 | nrokeys=['freqref'] |
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| 379 | for key in nrokeys: |
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| 380 | if key in args.keys(): |
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| 381 | opts['nro'][key] = args[key] |
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| 382 | self._fill([filename], unit, average, opts) |
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[2350] | 383 | # only apply to new data not "copy constructor" |
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| 384 | self.parallactify(parallactify) |
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[1883] | 385 | else: |
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[1819] | 386 | msg = "The given file '%s'is not a valid " \ |
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| 387 | "asap table." % (filename) |
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[1859] | 388 | raise IOError(msg) |
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[1118] | 389 | elif (isinstance(filename, list) or isinstance(filename, tuple)) \ |
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[976] | 390 | and isinstance(filename[-1], str): |
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[1916] | 391 | self._fill(filename, unit, average) |
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[1586] | 392 | self.parallactify(parallactify) |
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[1259] | 393 | self._add_history("scantable", varlist) |
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[102] | 394 | |
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[1862] | 395 | @asaplog_post_dec |
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[876] | 396 | def save(self, name=None, format=None, overwrite=False): |
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[1846] | 397 | """\ |
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[1280] | 398 | Store the scantable on disk. This can be an asap (aips++) Table, |
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| 399 | SDFITS or MS2 format. |
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[1846] | 400 | |
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[116] | 401 | Parameters: |
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[1846] | 402 | |
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[2431] | 403 | name: the name of the outputfile. For format 'ASCII' |
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[1093] | 404 | this is the root file name (data in 'name'.txt |
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[497] | 405 | and header in 'name'_header.txt) |
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[1855] | 406 | |
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[116] | 407 | format: an optional file format. Default is ASAP. |
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[1855] | 408 | Allowed are: |
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| 409 | |
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| 410 | * 'ASAP' (save as ASAP [aips++] Table), |
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| 411 | * 'SDFITS' (save as SDFITS file) |
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| 412 | * 'ASCII' (saves as ascii text file) |
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| 413 | * 'MS2' (saves as an casacore MeasurementSet V2) |
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[2315] | 414 | * 'FITS' (save as image FITS - not readable by |
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| 415 | class) |
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[1855] | 416 | * 'CLASS' (save as FITS readable by CLASS) |
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| 417 | |
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[411] | 418 | overwrite: If the file should be overwritten if it exists. |
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[256] | 419 | The default False is to return with warning |
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[411] | 420 | without writing the output. USE WITH CARE. |
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[1855] | 421 | |
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[1846] | 422 | Example:: |
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| 423 | |
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[116] | 424 | scan.save('myscan.asap') |
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[1118] | 425 | scan.save('myscan.sdfits', 'SDFITS') |
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[1846] | 426 | |
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[116] | 427 | """ |
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[411] | 428 | from os import path |
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[1593] | 429 | format = format or rcParams['scantable.save'] |
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[256] | 430 | suffix = '.'+format.lower() |
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[1118] | 431 | if name is None or name == "": |
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[256] | 432 | name = 'scantable'+suffix |
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[718] | 433 | msg = "No filename given. Using default name %s..." % name |
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| 434 | asaplog.push(msg) |
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[411] | 435 | name = path.expandvars(name) |
---|
[256] | 436 | if path.isfile(name) or path.isdir(name): |
---|
| 437 | if not overwrite: |
---|
[718] | 438 | msg = "File %s exists." % name |
---|
[1859] | 439 | raise IOError(msg) |
---|
[451] | 440 | format2 = format.upper() |
---|
| 441 | if format2 == 'ASAP': |
---|
[116] | 442 | self._save(name) |
---|
[2029] | 443 | elif format2 == 'MS2': |
---|
| 444 | msopt = {'ms': {'overwrite': overwrite } } |
---|
| 445 | from asap._asap import mswriter |
---|
| 446 | writer = mswriter( self ) |
---|
| 447 | writer.write( name, msopt ) |
---|
[116] | 448 | else: |
---|
[989] | 449 | from asap._asap import stwriter as stw |
---|
[1118] | 450 | writer = stw(format2) |
---|
| 451 | writer.write(self, name) |
---|
[116] | 452 | return |
---|
| 453 | |
---|
[102] | 454 | def copy(self): |
---|
[1846] | 455 | """Return a copy of this scantable. |
---|
| 456 | |
---|
| 457 | *Note*: |
---|
| 458 | |
---|
[1348] | 459 | This makes a full (deep) copy. scan2 = scan1 makes a reference. |
---|
[1846] | 460 | |
---|
| 461 | Example:: |
---|
| 462 | |
---|
[102] | 463 | copiedscan = scan.copy() |
---|
[1846] | 464 | |
---|
[102] | 465 | """ |
---|
[876] | 466 | sd = scantable(Scantable._copy(self)) |
---|
[113] | 467 | return sd |
---|
| 468 | |
---|
[1093] | 469 | def drop_scan(self, scanid=None): |
---|
[1846] | 470 | """\ |
---|
[1093] | 471 | Return a new scantable where the specified scan number(s) has(have) |
---|
| 472 | been dropped. |
---|
[1846] | 473 | |
---|
[1093] | 474 | Parameters: |
---|
[1846] | 475 | |
---|
[1093] | 476 | scanid: a (list of) scan number(s) |
---|
[1846] | 477 | |
---|
[1093] | 478 | """ |
---|
| 479 | from asap import _is_sequence_or_number as _is_valid |
---|
| 480 | from asap import _to_list |
---|
| 481 | from asap import unique |
---|
| 482 | if not _is_valid(scanid): |
---|
[2315] | 483 | raise RuntimeError( 'Please specify a scanno to drop from the' |
---|
| 484 | ' scantable' ) |
---|
[1859] | 485 | scanid = _to_list(scanid) |
---|
| 486 | allscans = unique([ self.getscan(i) for i in range(self.nrow())]) |
---|
| 487 | for sid in scanid: allscans.remove(sid) |
---|
| 488 | if len(allscans) == 0: |
---|
| 489 | raise ValueError("Can't remove all scans") |
---|
| 490 | sel = selector(scans=allscans) |
---|
| 491 | return self._select_copy(sel) |
---|
[1093] | 492 | |
---|
[1594] | 493 | def _select_copy(self, selection): |
---|
| 494 | orig = self.get_selection() |
---|
| 495 | self.set_selection(orig+selection) |
---|
| 496 | cp = self.copy() |
---|
| 497 | self.set_selection(orig) |
---|
| 498 | return cp |
---|
| 499 | |
---|
[102] | 500 | def get_scan(self, scanid=None): |
---|
[1855] | 501 | """\ |
---|
[102] | 502 | Return a specific scan (by scanno) or collection of scans (by |
---|
| 503 | source name) in a new scantable. |
---|
[1846] | 504 | |
---|
| 505 | *Note*: |
---|
| 506 | |
---|
[1348] | 507 | See scantable.drop_scan() for the inverse operation. |
---|
[1846] | 508 | |
---|
[102] | 509 | Parameters: |
---|
[1846] | 510 | |
---|
[513] | 511 | scanid: a (list of) scanno or a source name, unix-style |
---|
| 512 | patterns are accepted for source name matching, e.g. |
---|
| 513 | '*_R' gets all 'ref scans |
---|
[1846] | 514 | |
---|
| 515 | Example:: |
---|
| 516 | |
---|
[513] | 517 | # get all scans containing the source '323p459' |
---|
| 518 | newscan = scan.get_scan('323p459') |
---|
| 519 | # get all 'off' scans |
---|
| 520 | refscans = scan.get_scan('*_R') |
---|
| 521 | # get a susbset of scans by scanno (as listed in scan.summary()) |
---|
[1118] | 522 | newscan = scan.get_scan([0, 2, 7, 10]) |
---|
[1846] | 523 | |
---|
[102] | 524 | """ |
---|
| 525 | if scanid is None: |
---|
[1859] | 526 | raise RuntimeError( 'Please specify a scan no or name to ' |
---|
| 527 | 'retrieve from the scantable' ) |
---|
[102] | 528 | try: |
---|
[946] | 529 | bsel = self.get_selection() |
---|
| 530 | sel = selector() |
---|
[102] | 531 | if type(scanid) is str: |
---|
[946] | 532 | sel.set_name(scanid) |
---|
[1594] | 533 | return self._select_copy(sel) |
---|
[102] | 534 | elif type(scanid) is int: |
---|
[946] | 535 | sel.set_scans([scanid]) |
---|
[1594] | 536 | return self._select_copy(sel) |
---|
[381] | 537 | elif type(scanid) is list: |
---|
[946] | 538 | sel.set_scans(scanid) |
---|
[1594] | 539 | return self._select_copy(sel) |
---|
[381] | 540 | else: |
---|
[718] | 541 | msg = "Illegal scanid type, use 'int' or 'list' if ints." |
---|
[1859] | 542 | raise TypeError(msg) |
---|
[102] | 543 | except RuntimeError: |
---|
[1859] | 544 | raise |
---|
[102] | 545 | |
---|
| 546 | def __str__(self): |
---|
[2315] | 547 | tempFile = tempfile.NamedTemporaryFile() |
---|
| 548 | Scantable._summary(self, tempFile.name) |
---|
| 549 | tempFile.seek(0) |
---|
| 550 | asaplog.clear() |
---|
| 551 | return tempFile.file.read() |
---|
[102] | 552 | |
---|
[2315] | 553 | @asaplog_post_dec |
---|
[976] | 554 | def summary(self, filename=None): |
---|
[1846] | 555 | """\ |
---|
[102] | 556 | Print a summary of the contents of this scantable. |
---|
[1846] | 557 | |
---|
[102] | 558 | Parameters: |
---|
[1846] | 559 | |
---|
[1931] | 560 | filename: the name of a file to write the putput to |
---|
[102] | 561 | Default - no file output |
---|
[1846] | 562 | |
---|
[102] | 563 | """ |
---|
| 564 | if filename is not None: |
---|
[256] | 565 | if filename is "": |
---|
| 566 | filename = 'scantable_summary.txt' |
---|
[415] | 567 | from os.path import expandvars, isdir |
---|
[411] | 568 | filename = expandvars(filename) |
---|
[2286] | 569 | if isdir(filename): |
---|
[718] | 570 | msg = "Illegal file name '%s'." % (filename) |
---|
[1859] | 571 | raise IOError(msg) |
---|
[2286] | 572 | else: |
---|
| 573 | filename = "" |
---|
| 574 | Scantable._summary(self, filename) |
---|
[710] | 575 | |
---|
[1512] | 576 | def get_spectrum(self, rowno): |
---|
[1471] | 577 | """Return the spectrum for the current row in the scantable as a list. |
---|
[1846] | 578 | |
---|
[1471] | 579 | Parameters: |
---|
[1846] | 580 | |
---|
[1573] | 581 | rowno: the row number to retrieve the spectrum from |
---|
[1846] | 582 | |
---|
[1471] | 583 | """ |
---|
| 584 | return self._getspectrum(rowno) |
---|
[946] | 585 | |
---|
[1471] | 586 | def get_mask(self, rowno): |
---|
| 587 | """Return the mask for the current row in the scantable as a list. |
---|
[1846] | 588 | |
---|
[1471] | 589 | Parameters: |
---|
[1846] | 590 | |
---|
[1573] | 591 | rowno: the row number to retrieve the mask from |
---|
[1846] | 592 | |
---|
[1471] | 593 | """ |
---|
| 594 | return self._getmask(rowno) |
---|
| 595 | |
---|
| 596 | def set_spectrum(self, spec, rowno): |
---|
[1938] | 597 | """Set the spectrum for the current row in the scantable. |
---|
[1846] | 598 | |
---|
[1471] | 599 | Parameters: |
---|
[1846] | 600 | |
---|
[1855] | 601 | spec: the new spectrum |
---|
[1846] | 602 | |
---|
[1855] | 603 | rowno: the row number to set the spectrum for |
---|
| 604 | |
---|
[1471] | 605 | """ |
---|
[2348] | 606 | assert(len(spec) == self.nchan(self.getif(rowno))) |
---|
[1471] | 607 | return self._setspectrum(spec, rowno) |
---|
| 608 | |
---|
[1600] | 609 | def get_coordinate(self, rowno): |
---|
| 610 | """Return the (spectral) coordinate for a a given 'rowno'. |
---|
[1846] | 611 | |
---|
| 612 | *Note*: |
---|
| 613 | |
---|
[1600] | 614 | * This coordinate is only valid until a scantable method modifies |
---|
| 615 | the frequency axis. |
---|
| 616 | * This coordinate does contain the original frequency set-up |
---|
| 617 | NOT the new frame. The conversions however are done using the user |
---|
| 618 | specified frame (e.g. LSRK/TOPO). To get the 'real' coordinate, |
---|
| 619 | use scantable.freq_align first. Without it there is no closure, |
---|
[1846] | 620 | i.e.:: |
---|
[1600] | 621 | |
---|
[1846] | 622 | c = myscan.get_coordinate(0) |
---|
| 623 | c.to_frequency(c.get_reference_pixel()) != c.get_reference_value() |
---|
| 624 | |
---|
[1600] | 625 | Parameters: |
---|
[1846] | 626 | |
---|
[1600] | 627 | rowno: the row number for the spectral coordinate |
---|
| 628 | |
---|
| 629 | """ |
---|
| 630 | return coordinate(Scantable.get_coordinate(self, rowno)) |
---|
| 631 | |
---|
[946] | 632 | def get_selection(self): |
---|
[1846] | 633 | """\ |
---|
[1005] | 634 | Get the selection object currently set on this scantable. |
---|
[1846] | 635 | |
---|
| 636 | Example:: |
---|
| 637 | |
---|
[1005] | 638 | sel = scan.get_selection() |
---|
| 639 | sel.set_ifs(0) # select IF 0 |
---|
| 640 | scan.set_selection(sel) # apply modified selection |
---|
[1846] | 641 | |
---|
[946] | 642 | """ |
---|
| 643 | return selector(self._getselection()) |
---|
| 644 | |
---|
[1576] | 645 | def set_selection(self, selection=None, **kw): |
---|
[1846] | 646 | """\ |
---|
[1005] | 647 | Select a subset of the data. All following operations on this scantable |
---|
| 648 | are only applied to thi selection. |
---|
[1846] | 649 | |
---|
[1005] | 650 | Parameters: |
---|
[1697] | 651 | |
---|
[1846] | 652 | selection: a selector object (default unset the selection), or |
---|
[2431] | 653 | any combination of 'pols', 'ifs', 'beams', 'scans', |
---|
| 654 | 'cycles', 'name', 'query' |
---|
[1697] | 655 | |
---|
[1846] | 656 | Examples:: |
---|
[1697] | 657 | |
---|
[1005] | 658 | sel = selector() # create a selection object |
---|
[1118] | 659 | self.set_scans([0, 3]) # select SCANNO 0 and 3 |
---|
[1005] | 660 | scan.set_selection(sel) # set the selection |
---|
| 661 | scan.summary() # will only print summary of scanno 0 an 3 |
---|
| 662 | scan.set_selection() # unset the selection |
---|
[1697] | 663 | # or the equivalent |
---|
| 664 | scan.set_selection(scans=[0,3]) |
---|
| 665 | scan.summary() # will only print summary of scanno 0 an 3 |
---|
| 666 | scan.set_selection() # unset the selection |
---|
[1846] | 667 | |
---|
[946] | 668 | """ |
---|
[1576] | 669 | if selection is None: |
---|
| 670 | # reset |
---|
| 671 | if len(kw) == 0: |
---|
| 672 | selection = selector() |
---|
| 673 | else: |
---|
| 674 | # try keywords |
---|
| 675 | for k in kw: |
---|
| 676 | if k not in selector.fields: |
---|
[2320] | 677 | raise KeyError("Invalid selection key '%s', " |
---|
| 678 | "valid keys are %s" % (k, |
---|
| 679 | selector.fields)) |
---|
[1576] | 680 | selection = selector(**kw) |
---|
[946] | 681 | self._setselection(selection) |
---|
| 682 | |
---|
[1819] | 683 | def get_row(self, row=0, insitu=None): |
---|
[1846] | 684 | """\ |
---|
[1819] | 685 | Select a row in the scantable. |
---|
| 686 | Return a scantable with single row. |
---|
[1846] | 687 | |
---|
[1819] | 688 | Parameters: |
---|
[1846] | 689 | |
---|
| 690 | row: row no of integration, default is 0. |
---|
| 691 | insitu: if False a new scantable is returned. Otherwise, the |
---|
| 692 | scaling is done in-situ. The default is taken from .asaprc |
---|
| 693 | (False) |
---|
| 694 | |
---|
[1819] | 695 | """ |
---|
[2349] | 696 | if insitu is None: |
---|
| 697 | insitu = rcParams['insitu'] |
---|
[1819] | 698 | if not insitu: |
---|
| 699 | workscan = self.copy() |
---|
| 700 | else: |
---|
| 701 | workscan = self |
---|
| 702 | # Select a row |
---|
[2349] | 703 | sel = selector() |
---|
[1992] | 704 | sel.set_rows([row]) |
---|
[1819] | 705 | workscan.set_selection(sel) |
---|
| 706 | if not workscan.nrow() == 1: |
---|
[2349] | 707 | msg = "Could not identify single row. %d rows selected." \ |
---|
| 708 | % (workscan.nrow()) |
---|
[1819] | 709 | raise RuntimeError(msg) |
---|
| 710 | if insitu: |
---|
| 711 | self._assign(workscan) |
---|
| 712 | else: |
---|
| 713 | return workscan |
---|
| 714 | |
---|
[1862] | 715 | @asaplog_post_dec |
---|
[1907] | 716 | def stats(self, stat='stddev', mask=None, form='3.3f', row=None): |
---|
[1846] | 717 | """\ |
---|
[135] | 718 | Determine the specified statistic of the current beam/if/pol |
---|
[102] | 719 | Takes a 'mask' as an optional parameter to specify which |
---|
| 720 | channels should be excluded. |
---|
[1846] | 721 | |
---|
[102] | 722 | Parameters: |
---|
[1846] | 723 | |
---|
[1819] | 724 | stat: 'min', 'max', 'min_abc', 'max_abc', 'sumsq', 'sum', |
---|
| 725 | 'mean', 'var', 'stddev', 'avdev', 'rms', 'median' |
---|
[1855] | 726 | |
---|
[135] | 727 | mask: an optional mask specifying where the statistic |
---|
[102] | 728 | should be determined. |
---|
[1855] | 729 | |
---|
[1819] | 730 | form: format string to print statistic values |
---|
[1846] | 731 | |
---|
[1907] | 732 | row: row number of spectrum to process. |
---|
| 733 | (default is None: for all rows) |
---|
[1846] | 734 | |
---|
[1907] | 735 | Example: |
---|
[113] | 736 | scan.set_unit('channel') |
---|
[1118] | 737 | msk = scan.create_mask([100, 200], [500, 600]) |
---|
[135] | 738 | scan.stats(stat='mean', mask=m) |
---|
[1846] | 739 | |
---|
[102] | 740 | """ |
---|
[1593] | 741 | mask = mask or [] |
---|
[876] | 742 | if not self._check_ifs(): |
---|
[1118] | 743 | raise ValueError("Cannot apply mask as the IFs have different " |
---|
| 744 | "number of channels. Please use setselection() " |
---|
| 745 | "to select individual IFs") |
---|
[1819] | 746 | rtnabc = False |
---|
| 747 | if stat.lower().endswith('_abc'): rtnabc = True |
---|
| 748 | getchan = False |
---|
| 749 | if stat.lower().startswith('min') or stat.lower().startswith('max'): |
---|
| 750 | chan = self._math._minmaxchan(self, mask, stat) |
---|
| 751 | getchan = True |
---|
| 752 | statvals = [] |
---|
[1907] | 753 | if not rtnabc: |
---|
| 754 | if row == None: |
---|
| 755 | statvals = self._math._stats(self, mask, stat) |
---|
| 756 | else: |
---|
| 757 | statvals = self._math._statsrow(self, mask, stat, int(row)) |
---|
[256] | 758 | |
---|
[1819] | 759 | #def cb(i): |
---|
| 760 | # return statvals[i] |
---|
[256] | 761 | |
---|
[1819] | 762 | #return self._row_callback(cb, stat) |
---|
[102] | 763 | |
---|
[1819] | 764 | label=stat |
---|
| 765 | #callback=cb |
---|
| 766 | out = "" |
---|
| 767 | #outvec = [] |
---|
| 768 | sep = '-'*50 |
---|
[1907] | 769 | |
---|
| 770 | if row == None: |
---|
| 771 | rows = xrange(self.nrow()) |
---|
| 772 | elif isinstance(row, int): |
---|
| 773 | rows = [ row ] |
---|
| 774 | |
---|
| 775 | for i in rows: |
---|
[1819] | 776 | refstr = '' |
---|
| 777 | statunit= '' |
---|
| 778 | if getchan: |
---|
| 779 | qx, qy = self.chan2data(rowno=i, chan=chan[i]) |
---|
| 780 | if rtnabc: |
---|
| 781 | statvals.append(qx['value']) |
---|
| 782 | refstr = ('(value: %'+form) % (qy['value'])+' ['+qy['unit']+'])' |
---|
| 783 | statunit= '['+qx['unit']+']' |
---|
| 784 | else: |
---|
| 785 | refstr = ('(@ %'+form) % (qx['value'])+' ['+qx['unit']+'])' |
---|
| 786 | |
---|
| 787 | tm = self._gettime(i) |
---|
| 788 | src = self._getsourcename(i) |
---|
| 789 | out += 'Scan[%d] (%s) ' % (self.getscan(i), src) |
---|
| 790 | out += 'Time[%s]:\n' % (tm) |
---|
[1907] | 791 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (self.getbeam(i)) |
---|
| 792 | if self.nif(-1) > 1: out += ' IF[%d] ' % (self.getif(i)) |
---|
| 793 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (self.getpol(i)) |
---|
[1819] | 794 | #outvec.append(callback(i)) |
---|
[1907] | 795 | if len(rows) > 1: |
---|
| 796 | # out += ('= %'+form) % (outvec[i]) +' '+refstr+'\n' |
---|
| 797 | out += ('= %'+form) % (statvals[i]) +' '+refstr+'\n' |
---|
| 798 | else: |
---|
| 799 | # out += ('= %'+form) % (outvec[0]) +' '+refstr+'\n' |
---|
| 800 | out += ('= %'+form) % (statvals[0]) +' '+refstr+'\n' |
---|
[1819] | 801 | out += sep+"\n" |
---|
| 802 | |
---|
[1859] | 803 | import os |
---|
| 804 | if os.environ.has_key( 'USER' ): |
---|
| 805 | usr = os.environ['USER'] |
---|
| 806 | else: |
---|
| 807 | import commands |
---|
| 808 | usr = commands.getoutput( 'whoami' ) |
---|
| 809 | tmpfile = '/tmp/tmp_'+usr+'_casapy_asap_scantable_stats' |
---|
| 810 | f = open(tmpfile,'w') |
---|
| 811 | print >> f, sep |
---|
| 812 | print >> f, ' %s %s' % (label, statunit) |
---|
| 813 | print >> f, sep |
---|
| 814 | print >> f, out |
---|
| 815 | f.close() |
---|
| 816 | f = open(tmpfile,'r') |
---|
| 817 | x = f.readlines() |
---|
| 818 | f.close() |
---|
| 819 | asaplog.push(''.join(x), False) |
---|
| 820 | |
---|
[1819] | 821 | return statvals |
---|
| 822 | |
---|
| 823 | def chan2data(self, rowno=0, chan=0): |
---|
[1846] | 824 | """\ |
---|
[1819] | 825 | Returns channel/frequency/velocity and spectral value |
---|
| 826 | at an arbitrary row and channel in the scantable. |
---|
[1846] | 827 | |
---|
[1819] | 828 | Parameters: |
---|
[1846] | 829 | |
---|
[1819] | 830 | rowno: a row number in the scantable. Default is the |
---|
| 831 | first row, i.e. rowno=0 |
---|
[1855] | 832 | |
---|
[1819] | 833 | chan: a channel in the scantable. Default is the first |
---|
| 834 | channel, i.e. pos=0 |
---|
[1846] | 835 | |
---|
[1819] | 836 | """ |
---|
| 837 | if isinstance(rowno, int) and isinstance(chan, int): |
---|
| 838 | qx = {'unit': self.get_unit(), |
---|
| 839 | 'value': self._getabcissa(rowno)[chan]} |
---|
| 840 | qy = {'unit': self.get_fluxunit(), |
---|
| 841 | 'value': self._getspectrum(rowno)[chan]} |
---|
| 842 | return qx, qy |
---|
| 843 | |
---|
[1118] | 844 | def stddev(self, mask=None): |
---|
[1846] | 845 | """\ |
---|
[135] | 846 | Determine the standard deviation of the current beam/if/pol |
---|
| 847 | Takes a 'mask' as an optional parameter to specify which |
---|
| 848 | channels should be excluded. |
---|
[1846] | 849 | |
---|
[135] | 850 | Parameters: |
---|
[1846] | 851 | |
---|
[135] | 852 | mask: an optional mask specifying where the standard |
---|
| 853 | deviation should be determined. |
---|
| 854 | |
---|
[1846] | 855 | Example:: |
---|
| 856 | |
---|
[135] | 857 | scan.set_unit('channel') |
---|
[1118] | 858 | msk = scan.create_mask([100, 200], [500, 600]) |
---|
[135] | 859 | scan.stddev(mask=m) |
---|
[1846] | 860 | |
---|
[135] | 861 | """ |
---|
[1118] | 862 | return self.stats(stat='stddev', mask=mask); |
---|
[135] | 863 | |
---|
[1003] | 864 | |
---|
[1259] | 865 | def get_column_names(self): |
---|
[1846] | 866 | """\ |
---|
[1003] | 867 | Return a list of column names, which can be used for selection. |
---|
| 868 | """ |
---|
[1259] | 869 | return list(Scantable.get_column_names(self)) |
---|
[1003] | 870 | |
---|
[1730] | 871 | def get_tsys(self, row=-1): |
---|
[1846] | 872 | """\ |
---|
[113] | 873 | Return the System temperatures. |
---|
[1846] | 874 | |
---|
| 875 | Parameters: |
---|
| 876 | |
---|
| 877 | row: the rowno to get the information for. (default all rows) |
---|
| 878 | |
---|
[113] | 879 | Returns: |
---|
[1846] | 880 | |
---|
[876] | 881 | a list of Tsys values for the current selection |
---|
[1846] | 882 | |
---|
[113] | 883 | """ |
---|
[1730] | 884 | if row > -1: |
---|
| 885 | return self._get_column(self._gettsys, row) |
---|
[876] | 886 | return self._row_callback(self._gettsys, "Tsys") |
---|
[256] | 887 | |
---|
[2406] | 888 | def get_tsysspectrum(self, row=-1): |
---|
| 889 | """\ |
---|
| 890 | Return the channel dependent system temperatures. |
---|
[1730] | 891 | |
---|
[2406] | 892 | Parameters: |
---|
| 893 | |
---|
| 894 | row: the rowno to get the information for. (default all rows) |
---|
| 895 | |
---|
| 896 | Returns: |
---|
| 897 | |
---|
| 898 | a list of Tsys values for the current selection |
---|
| 899 | |
---|
| 900 | """ |
---|
| 901 | return self._get_column( self._gettsysspectrum, row ) |
---|
| 902 | |
---|
[2791] | 903 | def set_tsys(self, values, row=-1): |
---|
| 904 | """\ |
---|
| 905 | Set the Tsys value(s) of the given 'row' or the whole scantable |
---|
| 906 | (selection). |
---|
| 907 | |
---|
| 908 | Parameters: |
---|
| 909 | |
---|
| 910 | values: a scalar or list (if Tsys is a vector) of Tsys value(s) |
---|
| 911 | row: the row number to apply Tsys values to. |
---|
| 912 | (default all rows) |
---|
| 913 | |
---|
| 914 | """ |
---|
| 915 | |
---|
| 916 | if not hasattr(values, "__len__"): |
---|
| 917 | values = [values] |
---|
| 918 | self._settsys(values, row) |
---|
| 919 | |
---|
[1730] | 920 | def get_weather(self, row=-1): |
---|
[1846] | 921 | """\ |
---|
| 922 | Return the weather informations. |
---|
| 923 | |
---|
| 924 | Parameters: |
---|
| 925 | |
---|
| 926 | row: the rowno to get the information for. (default all rows) |
---|
| 927 | |
---|
| 928 | Returns: |
---|
| 929 | |
---|
| 930 | a dict or list of of dicts of values for the current selection |
---|
| 931 | |
---|
| 932 | """ |
---|
| 933 | |
---|
[1730] | 934 | values = self._get_column(self._get_weather, row) |
---|
| 935 | if row > -1: |
---|
| 936 | return {'temperature': values[0], |
---|
| 937 | 'pressure': values[1], 'humidity' : values[2], |
---|
| 938 | 'windspeed' : values[3], 'windaz' : values[4] |
---|
| 939 | } |
---|
| 940 | else: |
---|
| 941 | out = [] |
---|
| 942 | for r in values: |
---|
| 943 | |
---|
| 944 | out.append({'temperature': r[0], |
---|
| 945 | 'pressure': r[1], 'humidity' : r[2], |
---|
| 946 | 'windspeed' : r[3], 'windaz' : r[4] |
---|
| 947 | }) |
---|
| 948 | return out |
---|
| 949 | |
---|
[876] | 950 | def _row_callback(self, callback, label): |
---|
| 951 | out = "" |
---|
[1118] | 952 | outvec = [] |
---|
[1590] | 953 | sep = '-'*50 |
---|
[876] | 954 | for i in range(self.nrow()): |
---|
| 955 | tm = self._gettime(i) |
---|
| 956 | src = self._getsourcename(i) |
---|
[1590] | 957 | out += 'Scan[%d] (%s) ' % (self.getscan(i), src) |
---|
[876] | 958 | out += 'Time[%s]:\n' % (tm) |
---|
[1590] | 959 | if self.nbeam(-1) > 1: |
---|
| 960 | out += ' Beam[%d] ' % (self.getbeam(i)) |
---|
| 961 | if self.nif(-1) > 1: out += ' IF[%d] ' % (self.getif(i)) |
---|
| 962 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (self.getpol(i)) |
---|
[876] | 963 | outvec.append(callback(i)) |
---|
| 964 | out += '= %3.3f\n' % (outvec[i]) |
---|
[1590] | 965 | out += sep+'\n' |
---|
[1859] | 966 | |
---|
| 967 | asaplog.push(sep) |
---|
| 968 | asaplog.push(" %s" % (label)) |
---|
| 969 | asaplog.push(sep) |
---|
| 970 | asaplog.push(out) |
---|
[1861] | 971 | asaplog.post() |
---|
[1175] | 972 | return outvec |
---|
[256] | 973 | |
---|
[1947] | 974 | def _get_column(self, callback, row=-1, *args): |
---|
[1070] | 975 | """ |
---|
| 976 | """ |
---|
| 977 | if row == -1: |
---|
[1947] | 978 | return [callback(i, *args) for i in range(self.nrow())] |
---|
[1070] | 979 | else: |
---|
[1819] | 980 | if 0 <= row < self.nrow(): |
---|
[1947] | 981 | return callback(row, *args) |
---|
[256] | 982 | |
---|
[1070] | 983 | |
---|
[1948] | 984 | def get_time(self, row=-1, asdatetime=False, prec=-1): |
---|
[1846] | 985 | """\ |
---|
[113] | 986 | Get a list of time stamps for the observations. |
---|
[1938] | 987 | Return a datetime object or a string (default) for each |
---|
| 988 | integration time stamp in the scantable. |
---|
[1846] | 989 | |
---|
[113] | 990 | Parameters: |
---|
[1846] | 991 | |
---|
[1348] | 992 | row: row no of integration. Default -1 return all rows |
---|
[1855] | 993 | |
---|
[1348] | 994 | asdatetime: return values as datetime objects rather than strings |
---|
[1846] | 995 | |
---|
[2349] | 996 | prec: number of digits shown. Default -1 to automatic |
---|
| 997 | calculation. |
---|
[1948] | 998 | Note this number is equals to the digits of MVTime, |
---|
| 999 | i.e., 0<prec<3: dates with hh:: only, |
---|
| 1000 | <5: with hh:mm:, <7 or 0: with hh:mm:ss, |
---|
[1947] | 1001 | and 6> : with hh:mm:ss.tt... (prec-6 t's added) |
---|
| 1002 | |
---|
[113] | 1003 | """ |
---|
[1175] | 1004 | from datetime import datetime |
---|
[1948] | 1005 | if prec < 0: |
---|
| 1006 | # automagically set necessary precision +1 |
---|
[2349] | 1007 | prec = 7 - \ |
---|
| 1008 | numpy.floor(numpy.log10(numpy.min(self.get_inttime(row)))) |
---|
[1948] | 1009 | prec = max(6, int(prec)) |
---|
| 1010 | else: |
---|
| 1011 | prec = max(0, prec) |
---|
| 1012 | if asdatetime: |
---|
| 1013 | #precision can be 1 millisecond at max |
---|
| 1014 | prec = min(12, prec) |
---|
| 1015 | |
---|
[1947] | 1016 | times = self._get_column(self._gettime, row, prec) |
---|
[1348] | 1017 | if not asdatetime: |
---|
[1392] | 1018 | return times |
---|
[1947] | 1019 | format = "%Y/%m/%d/%H:%M:%S.%f" |
---|
| 1020 | if prec < 7: |
---|
| 1021 | nsub = 1 + (((6-prec)/2) % 3) |
---|
| 1022 | substr = [".%f","%S","%M"] |
---|
| 1023 | for i in range(nsub): |
---|
| 1024 | format = format.replace(substr[i],"") |
---|
[1175] | 1025 | if isinstance(times, list): |
---|
[1947] | 1026 | return [datetime.strptime(i, format) for i in times] |
---|
[1175] | 1027 | else: |
---|
[1947] | 1028 | return datetime.strptime(times, format) |
---|
[102] | 1029 | |
---|
[1348] | 1030 | |
---|
| 1031 | def get_inttime(self, row=-1): |
---|
[1846] | 1032 | """\ |
---|
[1348] | 1033 | Get a list of integration times for the observations. |
---|
| 1034 | Return a time in seconds for each integration in the scantable. |
---|
[1846] | 1035 | |
---|
[1348] | 1036 | Parameters: |
---|
[1846] | 1037 | |
---|
[1348] | 1038 | row: row no of integration. Default -1 return all rows. |
---|
[1846] | 1039 | |
---|
[1348] | 1040 | """ |
---|
[1573] | 1041 | return self._get_column(self._getinttime, row) |
---|
[1348] | 1042 | |
---|
[1573] | 1043 | |
---|
[714] | 1044 | def get_sourcename(self, row=-1): |
---|
[1846] | 1045 | """\ |
---|
[794] | 1046 | Get a list source names for the observations. |
---|
[714] | 1047 | Return a string for each integration in the scantable. |
---|
| 1048 | Parameters: |
---|
[1846] | 1049 | |
---|
[1348] | 1050 | row: row no of integration. Default -1 return all rows. |
---|
[1846] | 1051 | |
---|
[714] | 1052 | """ |
---|
[1070] | 1053 | return self._get_column(self._getsourcename, row) |
---|
[714] | 1054 | |
---|
[794] | 1055 | def get_elevation(self, row=-1): |
---|
[1846] | 1056 | """\ |
---|
[794] | 1057 | Get a list of elevations for the observations. |
---|
| 1058 | Return a float for each integration in the scantable. |
---|
[1846] | 1059 | |
---|
[794] | 1060 | Parameters: |
---|
[1846] | 1061 | |
---|
[1348] | 1062 | row: row no of integration. Default -1 return all rows. |
---|
[1846] | 1063 | |
---|
[794] | 1064 | """ |
---|
[1070] | 1065 | return self._get_column(self._getelevation, row) |
---|
[794] | 1066 | |
---|
| 1067 | def get_azimuth(self, row=-1): |
---|
[1846] | 1068 | """\ |
---|
[794] | 1069 | Get a list of azimuths for the observations. |
---|
| 1070 | Return a float for each integration in the scantable. |
---|
[1846] | 1071 | |
---|
[794] | 1072 | Parameters: |
---|
[1348] | 1073 | row: row no of integration. Default -1 return all rows. |
---|
[1846] | 1074 | |
---|
[794] | 1075 | """ |
---|
[1070] | 1076 | return self._get_column(self._getazimuth, row) |
---|
[794] | 1077 | |
---|
| 1078 | def get_parangle(self, row=-1): |
---|
[1846] | 1079 | """\ |
---|
[794] | 1080 | Get a list of parallactic angles for the observations. |
---|
| 1081 | Return a float for each integration in the scantable. |
---|
[1846] | 1082 | |
---|
[794] | 1083 | Parameters: |
---|
[1846] | 1084 | |
---|
[1348] | 1085 | row: row no of integration. Default -1 return all rows. |
---|
[1846] | 1086 | |
---|
[794] | 1087 | """ |
---|
[1070] | 1088 | return self._get_column(self._getparangle, row) |
---|
[794] | 1089 | |
---|
[1070] | 1090 | def get_direction(self, row=-1): |
---|
| 1091 | """ |
---|
| 1092 | Get a list of Positions on the sky (direction) for the observations. |
---|
[1594] | 1093 | Return a string for each integration in the scantable. |
---|
[1855] | 1094 | |
---|
[1070] | 1095 | Parameters: |
---|
[1855] | 1096 | |
---|
[1070] | 1097 | row: row no of integration. Default -1 return all rows |
---|
[1855] | 1098 | |
---|
[1070] | 1099 | """ |
---|
| 1100 | return self._get_column(self._getdirection, row) |
---|
| 1101 | |
---|
[1391] | 1102 | def get_directionval(self, row=-1): |
---|
[1846] | 1103 | """\ |
---|
[1391] | 1104 | Get a list of Positions on the sky (direction) for the observations. |
---|
| 1105 | Return a float for each integration in the scantable. |
---|
[1846] | 1106 | |
---|
[1391] | 1107 | Parameters: |
---|
[1846] | 1108 | |
---|
[1391] | 1109 | row: row no of integration. Default -1 return all rows |
---|
[1846] | 1110 | |
---|
[1391] | 1111 | """ |
---|
| 1112 | return self._get_column(self._getdirectionvec, row) |
---|
| 1113 | |
---|
[1862] | 1114 | @asaplog_post_dec |
---|
[102] | 1115 | def set_unit(self, unit='channel'): |
---|
[1846] | 1116 | """\ |
---|
[102] | 1117 | Set the unit for all following operations on this scantable |
---|
[1846] | 1118 | |
---|
[102] | 1119 | Parameters: |
---|
[1846] | 1120 | |
---|
| 1121 | unit: optional unit, default is 'channel'. Use one of '*Hz', |
---|
| 1122 | 'km/s', 'channel' or equivalent '' |
---|
| 1123 | |
---|
[102] | 1124 | """ |
---|
[484] | 1125 | varlist = vars() |
---|
[1118] | 1126 | if unit in ['', 'pixel', 'channel']: |
---|
[113] | 1127 | unit = '' |
---|
| 1128 | inf = list(self._getcoordinfo()) |
---|
| 1129 | inf[0] = unit |
---|
| 1130 | self._setcoordinfo(inf) |
---|
[1118] | 1131 | self._add_history("set_unit", varlist) |
---|
[113] | 1132 | |
---|
[1862] | 1133 | @asaplog_post_dec |
---|
[484] | 1134 | def set_instrument(self, instr): |
---|
[1846] | 1135 | """\ |
---|
[1348] | 1136 | Set the instrument for subsequent processing. |
---|
[1846] | 1137 | |
---|
[358] | 1138 | Parameters: |
---|
[1846] | 1139 | |
---|
[710] | 1140 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA', |
---|
[407] | 1141 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART' |
---|
[1846] | 1142 | |
---|
[358] | 1143 | """ |
---|
| 1144 | self._setInstrument(instr) |
---|
[1118] | 1145 | self._add_history("set_instument", vars()) |
---|
[358] | 1146 | |
---|
[1862] | 1147 | @asaplog_post_dec |
---|
[1190] | 1148 | def set_feedtype(self, feedtype): |
---|
[1846] | 1149 | """\ |
---|
[1190] | 1150 | Overwrite the feed type, which might not be set correctly. |
---|
[1846] | 1151 | |
---|
[1190] | 1152 | Parameters: |
---|
[1846] | 1153 | |
---|
[1190] | 1154 | feedtype: 'linear' or 'circular' |
---|
[1846] | 1155 | |
---|
[1190] | 1156 | """ |
---|
| 1157 | self._setfeedtype(feedtype) |
---|
| 1158 | self._add_history("set_feedtype", vars()) |
---|
| 1159 | |
---|
[1862] | 1160 | @asaplog_post_dec |
---|
[276] | 1161 | def set_doppler(self, doppler='RADIO'): |
---|
[1846] | 1162 | """\ |
---|
[276] | 1163 | Set the doppler for all following operations on this scantable. |
---|
[1846] | 1164 | |
---|
[276] | 1165 | Parameters: |
---|
[1846] | 1166 | |
---|
[276] | 1167 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA' |
---|
[1846] | 1168 | |
---|
[276] | 1169 | """ |
---|
[484] | 1170 | varlist = vars() |
---|
[276] | 1171 | inf = list(self._getcoordinfo()) |
---|
| 1172 | inf[2] = doppler |
---|
| 1173 | self._setcoordinfo(inf) |
---|
[1118] | 1174 | self._add_history("set_doppler", vars()) |
---|
[710] | 1175 | |
---|
[1862] | 1176 | @asaplog_post_dec |
---|
[226] | 1177 | def set_freqframe(self, frame=None): |
---|
[1846] | 1178 | """\ |
---|
[113] | 1179 | Set the frame type of the Spectral Axis. |
---|
[1846] | 1180 | |
---|
[113] | 1181 | Parameters: |
---|
[1846] | 1182 | |
---|
[591] | 1183 | frame: an optional frame type, default 'LSRK'. Valid frames are: |
---|
[1819] | 1184 | 'TOPO', 'LSRD', 'LSRK', 'BARY', |
---|
[1118] | 1185 | 'GEO', 'GALACTO', 'LGROUP', 'CMB' |
---|
[1846] | 1186 | |
---|
| 1187 | Example:: |
---|
| 1188 | |
---|
[113] | 1189 | scan.set_freqframe('BARY') |
---|
[1846] | 1190 | |
---|
[113] | 1191 | """ |
---|
[1593] | 1192 | frame = frame or rcParams['scantable.freqframe'] |
---|
[484] | 1193 | varlist = vars() |
---|
[1819] | 1194 | # "REST" is not implemented in casacore |
---|
| 1195 | #valid = ['REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', \ |
---|
| 1196 | # 'GEO', 'GALACTO', 'LGROUP', 'CMB'] |
---|
| 1197 | valid = ['TOPO', 'LSRD', 'LSRK', 'BARY', \ |
---|
[1118] | 1198 | 'GEO', 'GALACTO', 'LGROUP', 'CMB'] |
---|
[591] | 1199 | |
---|
[989] | 1200 | if frame in valid: |
---|
[113] | 1201 | inf = list(self._getcoordinfo()) |
---|
| 1202 | inf[1] = frame |
---|
| 1203 | self._setcoordinfo(inf) |
---|
[1118] | 1204 | self._add_history("set_freqframe", varlist) |
---|
[102] | 1205 | else: |
---|
[1118] | 1206 | msg = "Please specify a valid freq type. Valid types are:\n", valid |
---|
[1859] | 1207 | raise TypeError(msg) |
---|
[710] | 1208 | |
---|
[1862] | 1209 | @asaplog_post_dec |
---|
[989] | 1210 | def set_dirframe(self, frame=""): |
---|
[1846] | 1211 | """\ |
---|
[989] | 1212 | Set the frame type of the Direction on the sky. |
---|
[1846] | 1213 | |
---|
[989] | 1214 | Parameters: |
---|
[1846] | 1215 | |
---|
[989] | 1216 | frame: an optional frame type, default ''. Valid frames are: |
---|
| 1217 | 'J2000', 'B1950', 'GALACTIC' |
---|
[1846] | 1218 | |
---|
| 1219 | Example: |
---|
| 1220 | |
---|
[989] | 1221 | scan.set_dirframe('GALACTIC') |
---|
[1846] | 1222 | |
---|
[989] | 1223 | """ |
---|
| 1224 | varlist = vars() |
---|
[1859] | 1225 | Scantable.set_dirframe(self, frame) |
---|
[1118] | 1226 | self._add_history("set_dirframe", varlist) |
---|
[989] | 1227 | |
---|
[113] | 1228 | def get_unit(self): |
---|
[1846] | 1229 | """\ |
---|
[113] | 1230 | Get the default unit set in this scantable |
---|
[1846] | 1231 | |
---|
[113] | 1232 | Returns: |
---|
[1846] | 1233 | |
---|
[113] | 1234 | A unit string |
---|
[1846] | 1235 | |
---|
[113] | 1236 | """ |
---|
| 1237 | inf = self._getcoordinfo() |
---|
| 1238 | unit = inf[0] |
---|
| 1239 | if unit == '': unit = 'channel' |
---|
| 1240 | return unit |
---|
[102] | 1241 | |
---|
[1862] | 1242 | @asaplog_post_dec |
---|
[158] | 1243 | def get_abcissa(self, rowno=0): |
---|
[1846] | 1244 | """\ |
---|
[158] | 1245 | Get the abcissa in the current coordinate setup for the currently |
---|
[113] | 1246 | selected Beam/IF/Pol |
---|
[1846] | 1247 | |
---|
[113] | 1248 | Parameters: |
---|
[1846] | 1249 | |
---|
[226] | 1250 | rowno: an optional row number in the scantable. Default is the |
---|
| 1251 | first row, i.e. rowno=0 |
---|
[1846] | 1252 | |
---|
[113] | 1253 | Returns: |
---|
[1846] | 1254 | |
---|
[1348] | 1255 | The abcissa values and the format string (as a dictionary) |
---|
[1846] | 1256 | |
---|
[113] | 1257 | """ |
---|
[256] | 1258 | abc = self._getabcissa(rowno) |
---|
[710] | 1259 | lbl = self._getabcissalabel(rowno) |
---|
[158] | 1260 | return abc, lbl |
---|
[113] | 1261 | |
---|
[1862] | 1262 | @asaplog_post_dec |
---|
[2322] | 1263 | def flag(self, mask=None, unflag=False, row=-1): |
---|
[1846] | 1264 | """\ |
---|
[1001] | 1265 | Flag the selected data using an optional channel mask. |
---|
[1846] | 1266 | |
---|
[1001] | 1267 | Parameters: |
---|
[1846] | 1268 | |
---|
[1001] | 1269 | mask: an optional channel mask, created with create_mask. Default |
---|
| 1270 | (no mask) is all channels. |
---|
[1855] | 1271 | |
---|
[1819] | 1272 | unflag: if True, unflag the data |
---|
[1846] | 1273 | |
---|
[2322] | 1274 | row: an optional row number in the scantable. |
---|
| 1275 | Default -1 flags all rows |
---|
| 1276 | |
---|
[1001] | 1277 | """ |
---|
| 1278 | varlist = vars() |
---|
[1593] | 1279 | mask = mask or [] |
---|
[1994] | 1280 | self._flag(row, mask, unflag) |
---|
[1001] | 1281 | self._add_history("flag", varlist) |
---|
| 1282 | |
---|
[1862] | 1283 | @asaplog_post_dec |
---|
[2322] | 1284 | def flag_row(self, rows=None, unflag=False): |
---|
[1846] | 1285 | """\ |
---|
[1819] | 1286 | Flag the selected data in row-based manner. |
---|
[1846] | 1287 | |
---|
[1819] | 1288 | Parameters: |
---|
[1846] | 1289 | |
---|
[1843] | 1290 | rows: list of row numbers to be flagged. Default is no row |
---|
[2322] | 1291 | (must be explicitly specified to execute row-based |
---|
| 1292 | flagging). |
---|
[1855] | 1293 | |
---|
[1819] | 1294 | unflag: if True, unflag the data. |
---|
[1846] | 1295 | |
---|
[1819] | 1296 | """ |
---|
| 1297 | varlist = vars() |
---|
[2322] | 1298 | if rows is None: |
---|
| 1299 | rows = [] |
---|
[1859] | 1300 | self._flag_row(rows, unflag) |
---|
[1819] | 1301 | self._add_history("flag_row", varlist) |
---|
| 1302 | |
---|
[1862] | 1303 | @asaplog_post_dec |
---|
[1819] | 1304 | def clip(self, uthres=None, dthres=None, clipoutside=True, unflag=False): |
---|
[1846] | 1305 | """\ |
---|
[1819] | 1306 | Flag the selected data outside a specified range (in channel-base) |
---|
[1846] | 1307 | |
---|
[1819] | 1308 | Parameters: |
---|
[1846] | 1309 | |
---|
[1819] | 1310 | uthres: upper threshold. |
---|
[1855] | 1311 | |
---|
[1819] | 1312 | dthres: lower threshold |
---|
[1846] | 1313 | |
---|
[2322] | 1314 | clipoutside: True for flagging data outside the range |
---|
| 1315 | [dthres:uthres]. |
---|
[1928] | 1316 | False for flagging data inside the range. |
---|
[1855] | 1317 | |
---|
[1846] | 1318 | unflag: if True, unflag the data. |
---|
| 1319 | |
---|
[1819] | 1320 | """ |
---|
| 1321 | varlist = vars() |
---|
[1859] | 1322 | self._clip(uthres, dthres, clipoutside, unflag) |
---|
[1819] | 1323 | self._add_history("clip", varlist) |
---|
| 1324 | |
---|
[1862] | 1325 | @asaplog_post_dec |
---|
[1584] | 1326 | def lag_flag(self, start, end, unit="MHz", insitu=None): |
---|
[1846] | 1327 | """\ |
---|
[1192] | 1328 | Flag the data in 'lag' space by providing a frequency to remove. |
---|
[2177] | 1329 | Flagged data in the scantable get interpolated over the region. |
---|
[1192] | 1330 | No taper is applied. |
---|
[1846] | 1331 | |
---|
[1192] | 1332 | Parameters: |
---|
[1846] | 1333 | |
---|
[1579] | 1334 | start: the start frequency (really a period within the |
---|
| 1335 | bandwidth) or period to remove |
---|
[1855] | 1336 | |
---|
[1579] | 1337 | end: the end frequency or period to remove |
---|
[1855] | 1338 | |
---|
[2431] | 1339 | unit: the frequency unit (default 'MHz') or '' for |
---|
[1579] | 1340 | explicit lag channels |
---|
[1846] | 1341 | |
---|
| 1342 | *Notes*: |
---|
| 1343 | |
---|
[1579] | 1344 | It is recommended to flag edges of the band or strong |
---|
[1348] | 1345 | signals beforehand. |
---|
[1846] | 1346 | |
---|
[1192] | 1347 | """ |
---|
| 1348 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1349 | self._math._setinsitu(insitu) |
---|
| 1350 | varlist = vars() |
---|
[1579] | 1351 | base = { "GHz": 1000000000., "MHz": 1000000., "kHz": 1000., "Hz": 1.} |
---|
| 1352 | if not (unit == "" or base.has_key(unit)): |
---|
[1192] | 1353 | raise ValueError("%s is not a valid unit." % unit) |
---|
[1859] | 1354 | if unit == "": |
---|
| 1355 | s = scantable(self._math._lag_flag(self, start, end, "lags")) |
---|
| 1356 | else: |
---|
| 1357 | s = scantable(self._math._lag_flag(self, start*base[unit], |
---|
| 1358 | end*base[unit], "frequency")) |
---|
[1192] | 1359 | s._add_history("lag_flag", varlist) |
---|
| 1360 | if insitu: |
---|
| 1361 | self._assign(s) |
---|
| 1362 | else: |
---|
| 1363 | return s |
---|
[1001] | 1364 | |
---|
[1862] | 1365 | @asaplog_post_dec |
---|
[2349] | 1366 | def fft(self, rowno=None, mask=None, getrealimag=False): |
---|
[2177] | 1367 | """\ |
---|
| 1368 | Apply FFT to the spectra. |
---|
| 1369 | Flagged data in the scantable get interpolated over the region. |
---|
| 1370 | |
---|
| 1371 | Parameters: |
---|
[2186] | 1372 | |
---|
| 1373 | rowno: The row number(s) to be processed. int, list |
---|
[2349] | 1374 | and tuple are accepted. By default (None), FFT |
---|
[2186] | 1375 | is applied to the whole data. |
---|
| 1376 | |
---|
| 1377 | mask: Auxiliary channel mask(s). Given as a boolean |
---|
| 1378 | list, it is applied to all specified rows. |
---|
| 1379 | A list of boolean lists can also be used to |
---|
| 1380 | apply different masks. In the latter case, the |
---|
| 1381 | length of 'mask' must be the same as that of |
---|
[2349] | 1382 | 'rowno'. The default is None. |
---|
[2177] | 1383 | |
---|
| 1384 | getrealimag: If True, returns the real and imaginary part |
---|
| 1385 | values of the complex results. |
---|
| 1386 | If False (the default), returns the amplitude |
---|
| 1387 | (absolute value) normalised with Ndata/2 and |
---|
| 1388 | phase (argument, in unit of radian). |
---|
| 1389 | |
---|
| 1390 | Returns: |
---|
| 1391 | |
---|
[2186] | 1392 | A list of dictionaries containing the results for each spectrum. |
---|
| 1393 | Each dictionary contains two values, the real and the imaginary |
---|
| 1394 | parts when getrealimag = True, or the amplitude(absolute value) |
---|
| 1395 | and the phase(argument) when getrealimag = False. The key for |
---|
| 1396 | these values are 'real' and 'imag', or 'ampl' and 'phase', |
---|
[2177] | 1397 | respectively. |
---|
| 1398 | """ |
---|
[2349] | 1399 | if rowno is None: |
---|
| 1400 | rowno = [] |
---|
[2177] | 1401 | if isinstance(rowno, int): |
---|
| 1402 | rowno = [rowno] |
---|
| 1403 | elif not (isinstance(rowno, list) or isinstance(rowno, tuple)): |
---|
[2186] | 1404 | raise TypeError("The row number(s) must be int, list or tuple.") |
---|
| 1405 | if len(rowno) == 0: rowno = [i for i in xrange(self.nrow())] |
---|
| 1406 | |
---|
[2411] | 1407 | usecommonmask = True |
---|
| 1408 | |
---|
| 1409 | if mask is None: |
---|
| 1410 | mask = [] |
---|
| 1411 | if isinstance(mask, list) or isinstance(mask, tuple): |
---|
| 1412 | if len(mask) == 0: |
---|
| 1413 | mask = [[]] |
---|
| 1414 | else: |
---|
| 1415 | if isinstance(mask[0], bool): |
---|
| 1416 | if len(mask) != self.nchan(self.getif(rowno[0])): |
---|
| 1417 | raise ValueError("The spectra and the mask have " |
---|
| 1418 | "different length.") |
---|
| 1419 | mask = [mask] |
---|
| 1420 | elif isinstance(mask[0], list) or isinstance(mask[0], tuple): |
---|
| 1421 | usecommonmask = False |
---|
| 1422 | if len(mask) != len(rowno): |
---|
| 1423 | raise ValueError("When specifying masks for each " |
---|
| 1424 | "spectrum, the numbers of them " |
---|
| 1425 | "must be identical.") |
---|
| 1426 | for i in xrange(mask): |
---|
| 1427 | if len(mask[i]) != self.nchan(self.getif(rowno[i])): |
---|
| 1428 | raise ValueError("The spectra and the mask have " |
---|
| 1429 | "different length.") |
---|
| 1430 | else: |
---|
| 1431 | raise TypeError("The mask must be a boolean list or " |
---|
| 1432 | "a list of boolean list.") |
---|
| 1433 | else: |
---|
[2349] | 1434 | raise TypeError("The mask must be a boolean list or a list of " |
---|
| 1435 | "boolean list.") |
---|
[2186] | 1436 | |
---|
| 1437 | res = [] |
---|
| 1438 | |
---|
| 1439 | imask = 0 |
---|
| 1440 | for whichrow in rowno: |
---|
| 1441 | fspec = self._fft(whichrow, mask[imask], getrealimag) |
---|
| 1442 | nspec = len(fspec) |
---|
[2177] | 1443 | |
---|
[2349] | 1444 | i = 0 |
---|
| 1445 | v1 = [] |
---|
| 1446 | v2 = [] |
---|
| 1447 | reselem = {"real":[],"imag":[]} if getrealimag \ |
---|
| 1448 | else {"ampl":[],"phase":[]} |
---|
[2177] | 1449 | |
---|
[2186] | 1450 | while (i < nspec): |
---|
| 1451 | v1.append(fspec[i]) |
---|
| 1452 | v2.append(fspec[i+1]) |
---|
[2349] | 1453 | i += 2 |
---|
[2186] | 1454 | |
---|
[2177] | 1455 | if getrealimag: |
---|
[2186] | 1456 | reselem["real"] += v1 |
---|
| 1457 | reselem["imag"] += v2 |
---|
[2177] | 1458 | else: |
---|
[2186] | 1459 | reselem["ampl"] += v1 |
---|
| 1460 | reselem["phase"] += v2 |
---|
[2177] | 1461 | |
---|
[2186] | 1462 | res.append(reselem) |
---|
| 1463 | |
---|
[2349] | 1464 | if not usecommonmask: |
---|
| 1465 | imask += 1 |
---|
[2186] | 1466 | |
---|
[2177] | 1467 | return res |
---|
| 1468 | |
---|
| 1469 | @asaplog_post_dec |
---|
[113] | 1470 | def create_mask(self, *args, **kwargs): |
---|
[1846] | 1471 | """\ |
---|
[1118] | 1472 | Compute and return a mask based on [min, max] windows. |
---|
[189] | 1473 | The specified windows are to be INCLUDED, when the mask is |
---|
[113] | 1474 | applied. |
---|
[1846] | 1475 | |
---|
[102] | 1476 | Parameters: |
---|
[1846] | 1477 | |
---|
[1118] | 1478 | [min, max], [min2, max2], ... |
---|
[1024] | 1479 | Pairs of start/end points (inclusive)specifying the regions |
---|
[102] | 1480 | to be masked |
---|
[1855] | 1481 | |
---|
[189] | 1482 | invert: optional argument. If specified as True, |
---|
| 1483 | return an inverted mask, i.e. the regions |
---|
| 1484 | specified are EXCLUDED |
---|
[1855] | 1485 | |
---|
[513] | 1486 | row: create the mask using the specified row for |
---|
| 1487 | unit conversions, default is row=0 |
---|
| 1488 | only necessary if frequency varies over rows. |
---|
[1846] | 1489 | |
---|
| 1490 | Examples:: |
---|
| 1491 | |
---|
[113] | 1492 | scan.set_unit('channel') |
---|
[1846] | 1493 | # a) |
---|
[1118] | 1494 | msk = scan.create_mask([400, 500], [800, 900]) |
---|
[189] | 1495 | # masks everything outside 400 and 500 |
---|
[113] | 1496 | # and 800 and 900 in the unit 'channel' |
---|
| 1497 | |
---|
[1846] | 1498 | # b) |
---|
[1118] | 1499 | msk = scan.create_mask([400, 500], [800, 900], invert=True) |
---|
[189] | 1500 | # masks the regions between 400 and 500 |
---|
[113] | 1501 | # and 800 and 900 in the unit 'channel' |
---|
[1846] | 1502 | |
---|
| 1503 | # c) |
---|
| 1504 | #mask only channel 400 |
---|
[1554] | 1505 | msk = scan.create_mask([400]) |
---|
[1846] | 1506 | |
---|
[102] | 1507 | """ |
---|
[1554] | 1508 | row = kwargs.get("row", 0) |
---|
[513] | 1509 | data = self._getabcissa(row) |
---|
[113] | 1510 | u = self._getcoordinfo()[0] |
---|
[1859] | 1511 | if u == "": |
---|
| 1512 | u = "channel" |
---|
| 1513 | msg = "The current mask window unit is %s" % u |
---|
| 1514 | i = self._check_ifs() |
---|
| 1515 | if not i: |
---|
| 1516 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i)) |
---|
| 1517 | asaplog.push(msg) |
---|
[2348] | 1518 | n = len(data) |
---|
[1295] | 1519 | msk = _n_bools(n, False) |
---|
[710] | 1520 | # test if args is a 'list' or a 'normal *args - UGLY!!! |
---|
| 1521 | |
---|
[2349] | 1522 | ws = (isinstance(args[-1][-1], int) |
---|
| 1523 | or isinstance(args[-1][-1], float)) and args or args[0] |
---|
[710] | 1524 | for window in ws: |
---|
[1554] | 1525 | if len(window) == 1: |
---|
| 1526 | window = [window[0], window[0]] |
---|
| 1527 | if len(window) == 0 or len(window) > 2: |
---|
[2349] | 1528 | raise ValueError("A window needs to be defined as " |
---|
| 1529 | "[start(, end)]") |
---|
[1545] | 1530 | if window[0] > window[1]: |
---|
| 1531 | tmp = window[0] |
---|
| 1532 | window[0] = window[1] |
---|
| 1533 | window[1] = tmp |
---|
[102] | 1534 | for i in range(n): |
---|
[1024] | 1535 | if data[i] >= window[0] and data[i] <= window[1]: |
---|
[1295] | 1536 | msk[i] = True |
---|
[113] | 1537 | if kwargs.has_key('invert'): |
---|
| 1538 | if kwargs.get('invert'): |
---|
[1295] | 1539 | msk = mask_not(msk) |
---|
[102] | 1540 | return msk |
---|
[710] | 1541 | |
---|
[1931] | 1542 | def get_masklist(self, mask=None, row=0, silent=False): |
---|
[1846] | 1543 | """\ |
---|
[1819] | 1544 | Compute and return a list of mask windows, [min, max]. |
---|
[1846] | 1545 | |
---|
[1819] | 1546 | Parameters: |
---|
[1846] | 1547 | |
---|
[1819] | 1548 | mask: channel mask, created with create_mask. |
---|
[1855] | 1549 | |
---|
[1819] | 1550 | row: calcutate the masklist using the specified row |
---|
| 1551 | for unit conversions, default is row=0 |
---|
| 1552 | only necessary if frequency varies over rows. |
---|
[1846] | 1553 | |
---|
[1819] | 1554 | Returns: |
---|
[1846] | 1555 | |
---|
[1819] | 1556 | [min, max], [min2, max2], ... |
---|
| 1557 | Pairs of start/end points (inclusive)specifying |
---|
| 1558 | the masked regions |
---|
[1846] | 1559 | |
---|
[1819] | 1560 | """ |
---|
| 1561 | if not (isinstance(mask,list) or isinstance(mask, tuple)): |
---|
| 1562 | raise TypeError("The mask should be list or tuple.") |
---|
[2427] | 1563 | if len(mask) <= 0: |
---|
| 1564 | raise TypeError("The mask elements should be > 0") |
---|
[2348] | 1565 | data = self._getabcissa(row) |
---|
| 1566 | if len(data) != len(mask): |
---|
[1819] | 1567 | msg = "Number of channels in scantable != number of mask elements" |
---|
| 1568 | raise TypeError(msg) |
---|
| 1569 | u = self._getcoordinfo()[0] |
---|
[1859] | 1570 | if u == "": |
---|
| 1571 | u = "channel" |
---|
| 1572 | msg = "The current mask window unit is %s" % u |
---|
| 1573 | i = self._check_ifs() |
---|
| 1574 | if not i: |
---|
| 1575 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i)) |
---|
[1931] | 1576 | if not silent: |
---|
| 1577 | asaplog.push(msg) |
---|
[2349] | 1578 | masklist = [] |
---|
[1819] | 1579 | ist, ien = None, None |
---|
| 1580 | ist, ien=self.get_mask_indices(mask) |
---|
| 1581 | if ist is not None and ien is not None: |
---|
| 1582 | for i in xrange(len(ist)): |
---|
| 1583 | range=[data[ist[i]],data[ien[i]]] |
---|
| 1584 | range.sort() |
---|
| 1585 | masklist.append([range[0],range[1]]) |
---|
| 1586 | return masklist |
---|
| 1587 | |
---|
| 1588 | def get_mask_indices(self, mask=None): |
---|
[1846] | 1589 | """\ |
---|
[1819] | 1590 | Compute and Return lists of mask start indices and mask end indices. |
---|
[1855] | 1591 | |
---|
| 1592 | Parameters: |
---|
| 1593 | |
---|
[1819] | 1594 | mask: channel mask, created with create_mask. |
---|
[1846] | 1595 | |
---|
[1819] | 1596 | Returns: |
---|
[1846] | 1597 | |
---|
[1819] | 1598 | List of mask start indices and that of mask end indices, |
---|
| 1599 | i.e., [istart1,istart2,....], [iend1,iend2,....]. |
---|
[1846] | 1600 | |
---|
[1819] | 1601 | """ |
---|
| 1602 | if not (isinstance(mask,list) or isinstance(mask, tuple)): |
---|
| 1603 | raise TypeError("The mask should be list or tuple.") |
---|
[2427] | 1604 | if len(mask) <= 0: |
---|
| 1605 | raise TypeError("The mask elements should be > 0") |
---|
[2349] | 1606 | istart = [] |
---|
| 1607 | iend = [] |
---|
| 1608 | if mask[0]: |
---|
| 1609 | istart.append(0) |
---|
[1819] | 1610 | for i in range(len(mask)-1): |
---|
| 1611 | if not mask[i] and mask[i+1]: |
---|
| 1612 | istart.append(i+1) |
---|
| 1613 | elif mask[i] and not mask[i+1]: |
---|
| 1614 | iend.append(i) |
---|
[2349] | 1615 | if mask[len(mask)-1]: |
---|
| 1616 | iend.append(len(mask)-1) |
---|
[1819] | 1617 | if len(istart) != len(iend): |
---|
| 1618 | raise RuntimeError("Numbers of mask start != mask end.") |
---|
| 1619 | for i in range(len(istart)): |
---|
| 1620 | if istart[i] > iend[i]: |
---|
| 1621 | raise RuntimeError("Mask start index > mask end index") |
---|
| 1622 | break |
---|
| 1623 | return istart,iend |
---|
| 1624 | |
---|
[2013] | 1625 | @asaplog_post_dec |
---|
[2349] | 1626 | def parse_maskexpr(self, maskstring): |
---|
[2013] | 1627 | """ |
---|
| 1628 | Parse CASA type mask selection syntax (IF dependent). |
---|
| 1629 | |
---|
| 1630 | Parameters: |
---|
| 1631 | maskstring : A string mask selection expression. |
---|
| 1632 | A comma separated selections mean different IF - |
---|
| 1633 | channel combinations. IFs and channel selections |
---|
| 1634 | are partitioned by a colon, ':'. |
---|
| 1635 | examples: |
---|
[2015] | 1636 | '' = all IFs (all channels) |
---|
[2013] | 1637 | '<2,4~6,9' = IFs 0,1,4,5,6,9 (all channels) |
---|
| 1638 | '3:3~45;60' = channels 3 to 45 and 60 in IF 3 |
---|
| 1639 | '0~1:2~6,8' = channels 2 to 6 in IFs 0,1, and |
---|
| 1640 | all channels in IF8 |
---|
| 1641 | Returns: |
---|
| 1642 | A dictionary of selected (valid) IF and masklist pairs, |
---|
| 1643 | e.g. {'0': [[50,250],[350,462]], '2': [[100,400],[550,974]]} |
---|
| 1644 | """ |
---|
| 1645 | if not isinstance(maskstring,str): |
---|
| 1646 | asaplog.post() |
---|
[2611] | 1647 | asaplog.push("Mask expression should be a string.") |
---|
[2013] | 1648 | asaplog.post("ERROR") |
---|
| 1649 | |
---|
| 1650 | valid_ifs = self.getifnos() |
---|
| 1651 | frequnit = self.get_unit() |
---|
| 1652 | seldict = {} |
---|
[2015] | 1653 | if maskstring == "": |
---|
| 1654 | maskstring = str(valid_ifs)[1:-1] |
---|
[2611] | 1655 | ## split each selection "IF range[:CHAN range]" |
---|
[2013] | 1656 | sellist = maskstring.split(',') |
---|
| 1657 | for currselstr in sellist: |
---|
| 1658 | selset = currselstr.split(':') |
---|
| 1659 | # spw and mask string (may include ~, < or >) |
---|
[2349] | 1660 | spwmasklist = self._parse_selection(selset[0], typestr='integer', |
---|
[2611] | 1661 | minval=min(valid_ifs), |
---|
[2349] | 1662 | maxval=max(valid_ifs)) |
---|
[2013] | 1663 | for spwlist in spwmasklist: |
---|
| 1664 | selspws = [] |
---|
| 1665 | for ispw in range(spwlist[0],spwlist[1]+1): |
---|
| 1666 | # Put into the list only if ispw exists |
---|
| 1667 | if valid_ifs.count(ispw): |
---|
| 1668 | selspws.append(ispw) |
---|
| 1669 | del spwmasklist, spwlist |
---|
| 1670 | |
---|
| 1671 | # parse frequency mask list |
---|
| 1672 | if len(selset) > 1: |
---|
[2349] | 1673 | freqmasklist = self._parse_selection(selset[1], typestr='float', |
---|
| 1674 | offset=0.) |
---|
[2013] | 1675 | else: |
---|
| 1676 | # want to select the whole spectrum |
---|
| 1677 | freqmasklist = [None] |
---|
| 1678 | |
---|
| 1679 | ## define a dictionary of spw - masklist combination |
---|
| 1680 | for ispw in selspws: |
---|
| 1681 | #print "working on", ispw |
---|
| 1682 | spwstr = str(ispw) |
---|
| 1683 | if len(selspws) == 0: |
---|
| 1684 | # empty spw |
---|
| 1685 | continue |
---|
| 1686 | else: |
---|
| 1687 | ## want to get min and max of the spw and |
---|
| 1688 | ## offset to set for '<' and '>' |
---|
| 1689 | if frequnit == 'channel': |
---|
| 1690 | minfreq = 0 |
---|
| 1691 | maxfreq = self.nchan(ifno=ispw) |
---|
| 1692 | offset = 0.5 |
---|
| 1693 | else: |
---|
| 1694 | ## This is ugly part. need improvement |
---|
| 1695 | for ifrow in xrange(self.nrow()): |
---|
| 1696 | if self.getif(ifrow) == ispw: |
---|
| 1697 | #print "IF",ispw,"found in row =",ifrow |
---|
| 1698 | break |
---|
| 1699 | freqcoord = self.get_coordinate(ifrow) |
---|
| 1700 | freqs = self._getabcissa(ifrow) |
---|
| 1701 | minfreq = min(freqs) |
---|
| 1702 | maxfreq = max(freqs) |
---|
| 1703 | if len(freqs) == 1: |
---|
| 1704 | offset = 0.5 |
---|
| 1705 | elif frequnit.find('Hz') > 0: |
---|
[2349] | 1706 | offset = abs(freqcoord.to_frequency(1, |
---|
| 1707 | unit=frequnit) |
---|
| 1708 | -freqcoord.to_frequency(0, |
---|
| 1709 | unit=frequnit) |
---|
| 1710 | )*0.5 |
---|
[2013] | 1711 | elif frequnit.find('m/s') > 0: |
---|
[2349] | 1712 | offset = abs(freqcoord.to_velocity(1, |
---|
| 1713 | unit=frequnit) |
---|
| 1714 | -freqcoord.to_velocity(0, |
---|
| 1715 | unit=frequnit) |
---|
| 1716 | )*0.5 |
---|
[2013] | 1717 | else: |
---|
| 1718 | asaplog.post() |
---|
| 1719 | asaplog.push("Invalid frequency unit") |
---|
| 1720 | asaplog.post("ERROR") |
---|
| 1721 | del freqs, freqcoord, ifrow |
---|
| 1722 | for freq in freqmasklist: |
---|
| 1723 | selmask = freq or [minfreq, maxfreq] |
---|
| 1724 | if selmask[0] == None: |
---|
| 1725 | ## selection was "<freq[1]". |
---|
| 1726 | if selmask[1] < minfreq: |
---|
| 1727 | ## avoid adding region selection |
---|
| 1728 | selmask = None |
---|
| 1729 | else: |
---|
| 1730 | selmask = [minfreq,selmask[1]-offset] |
---|
| 1731 | elif selmask[1] == None: |
---|
| 1732 | ## selection was ">freq[0]" |
---|
| 1733 | if selmask[0] > maxfreq: |
---|
| 1734 | ## avoid adding region selection |
---|
| 1735 | selmask = None |
---|
| 1736 | else: |
---|
| 1737 | selmask = [selmask[0]+offset,maxfreq] |
---|
| 1738 | if selmask: |
---|
| 1739 | if not seldict.has_key(spwstr): |
---|
| 1740 | # new spw selection |
---|
| 1741 | seldict[spwstr] = [] |
---|
| 1742 | seldict[spwstr] += [selmask] |
---|
| 1743 | del minfreq,maxfreq,offset,freq,selmask |
---|
| 1744 | del spwstr |
---|
| 1745 | del freqmasklist |
---|
| 1746 | del valid_ifs |
---|
| 1747 | if len(seldict) == 0: |
---|
| 1748 | asaplog.post() |
---|
[2349] | 1749 | asaplog.push("No valid selection in the mask expression: " |
---|
| 1750 | +maskstring) |
---|
[2013] | 1751 | asaplog.post("WARN") |
---|
| 1752 | return None |
---|
| 1753 | msg = "Selected masklist:\n" |
---|
| 1754 | for sif, lmask in seldict.iteritems(): |
---|
| 1755 | msg += " IF"+sif+" - "+str(lmask)+"\n" |
---|
| 1756 | asaplog.push(msg) |
---|
| 1757 | return seldict |
---|
| 1758 | |
---|
[2611] | 1759 | @asaplog_post_dec |
---|
| 1760 | def parse_idx_selection(self, mode, selexpr): |
---|
| 1761 | """ |
---|
| 1762 | Parse CASA type mask selection syntax of SCANNO, IFNO, POLNO, |
---|
| 1763 | BEAMNO, and row number |
---|
| 1764 | |
---|
| 1765 | Parameters: |
---|
| 1766 | mode : which column to select. |
---|
| 1767 | ['scan',|'if'|'pol'|'beam'|'row'] |
---|
| 1768 | selexpr : A comma separated selection expression. |
---|
| 1769 | examples: |
---|
| 1770 | '' = all (returns []) |
---|
| 1771 | '<2,4~6,9' = indices less than 2, 4 to 6 and 9 |
---|
| 1772 | (returns [0,1,4,5,6,9]) |
---|
| 1773 | Returns: |
---|
| 1774 | A List of selected indices |
---|
| 1775 | """ |
---|
| 1776 | if selexpr == "": |
---|
| 1777 | return [] |
---|
| 1778 | valid_modes = {'s': 'scan', 'i': 'if', 'p': 'pol', |
---|
| 1779 | 'b': 'beam', 'r': 'row'} |
---|
| 1780 | smode = mode.lower()[0] |
---|
| 1781 | if not (smode in valid_modes.keys()): |
---|
| 1782 | msg = "Invalid mode '%s'. Valid modes are %s" %\ |
---|
| 1783 | (mode, str(valid_modes.values())) |
---|
| 1784 | asaplog.post() |
---|
| 1785 | asaplog.push(msg) |
---|
| 1786 | asaplog.post("ERROR") |
---|
| 1787 | mode = valid_modes[smode] |
---|
| 1788 | minidx = None |
---|
| 1789 | maxidx = None |
---|
| 1790 | if smode == 'r': |
---|
| 1791 | minidx = 0 |
---|
| 1792 | maxidx = self.nrow() |
---|
| 1793 | else: |
---|
| 1794 | idx = getattr(self,"get"+mode+"nos")() |
---|
| 1795 | minidx = min(idx) |
---|
| 1796 | maxidx = max(idx) |
---|
| 1797 | del idx |
---|
| 1798 | sellist = selexpr.split(',') |
---|
| 1799 | idxlist = [] |
---|
| 1800 | for currselstr in sellist: |
---|
| 1801 | # single range (may include ~, < or >) |
---|
| 1802 | currlist = self._parse_selection(currselstr, typestr='integer', |
---|
| 1803 | minval=minidx,maxval=maxidx) |
---|
| 1804 | for thelist in currlist: |
---|
| 1805 | idxlist += range(thelist[0],thelist[1]+1) |
---|
| 1806 | msg = "Selected %s: %s" % (mode.upper()+"NO", str(idxlist)) |
---|
| 1807 | asaplog.push(msg) |
---|
| 1808 | return idxlist |
---|
| 1809 | |
---|
[2349] | 1810 | def _parse_selection(self, selstr, typestr='float', offset=0., |
---|
[2351] | 1811 | minval=None, maxval=None): |
---|
[2013] | 1812 | """ |
---|
| 1813 | Parameters: |
---|
| 1814 | selstr : The Selection string, e.g., '<3;5~7;100~103;9' |
---|
| 1815 | typestr : The type of the values in returned list |
---|
| 1816 | ('integer' or 'float') |
---|
| 1817 | offset : The offset value to subtract from or add to |
---|
| 1818 | the boundary value if the selection string |
---|
[2611] | 1819 | includes '<' or '>' [Valid only for typestr='float'] |
---|
[2013] | 1820 | minval, maxval : The minimum/maximum values to set if the |
---|
| 1821 | selection string includes '<' or '>'. |
---|
| 1822 | The list element is filled with None by default. |
---|
| 1823 | Returns: |
---|
| 1824 | A list of min/max pair of selections. |
---|
| 1825 | Example: |
---|
[2611] | 1826 | _parse_selection('<3;5~7;9',typestr='int',minval=0) |
---|
| 1827 | --> returns [[0,2],[5,7],[9,9]] |
---|
| 1828 | _parse_selection('<3;5~7;9',typestr='float',offset=0.5,minval=0) |
---|
| 1829 | --> returns [[0.,2.5],[5.0,7.0],[9.,9.]] |
---|
[2013] | 1830 | """ |
---|
| 1831 | selgroups = selstr.split(';') |
---|
| 1832 | sellists = [] |
---|
| 1833 | if typestr.lower().startswith('int'): |
---|
| 1834 | formatfunc = int |
---|
[2611] | 1835 | offset = 1 |
---|
[2013] | 1836 | else: |
---|
| 1837 | formatfunc = float |
---|
| 1838 | |
---|
| 1839 | for currsel in selgroups: |
---|
| 1840 | if currsel.find('~') > 0: |
---|
[2611] | 1841 | # val0 <= x <= val1 |
---|
[2013] | 1842 | minsel = formatfunc(currsel.split('~')[0].strip()) |
---|
| 1843 | maxsel = formatfunc(currsel.split('~')[1].strip()) |
---|
[2611] | 1844 | elif currsel.strip().find('<=') > -1: |
---|
| 1845 | bound = currsel.split('<=') |
---|
| 1846 | try: # try "x <= val" |
---|
| 1847 | minsel = minval |
---|
| 1848 | maxsel = formatfunc(bound[1].strip()) |
---|
| 1849 | except ValueError: # now "val <= x" |
---|
| 1850 | minsel = formatfunc(bound[0].strip()) |
---|
| 1851 | maxsel = maxval |
---|
| 1852 | elif currsel.strip().find('>=') > -1: |
---|
| 1853 | bound = currsel.split('>=') |
---|
| 1854 | try: # try "x >= val" |
---|
| 1855 | minsel = formatfunc(bound[1].strip()) |
---|
| 1856 | maxsel = maxval |
---|
| 1857 | except ValueError: # now "val >= x" |
---|
| 1858 | minsel = minval |
---|
| 1859 | maxsel = formatfunc(bound[0].strip()) |
---|
| 1860 | elif currsel.strip().find('<') > -1: |
---|
| 1861 | bound = currsel.split('<') |
---|
| 1862 | try: # try "x < val" |
---|
| 1863 | minsel = minval |
---|
| 1864 | maxsel = formatfunc(bound[1].strip()) \ |
---|
| 1865 | - formatfunc(offset) |
---|
| 1866 | except ValueError: # now "val < x" |
---|
| 1867 | minsel = formatfunc(bound[0].strip()) \ |
---|
[2013] | 1868 | + formatfunc(offset) |
---|
[2611] | 1869 | maxsel = maxval |
---|
| 1870 | elif currsel.strip().find('>') > -1: |
---|
| 1871 | bound = currsel.split('>') |
---|
| 1872 | try: # try "x > val" |
---|
| 1873 | minsel = formatfunc(bound[1].strip()) \ |
---|
| 1874 | + formatfunc(offset) |
---|
| 1875 | maxsel = maxval |
---|
| 1876 | except ValueError: # now "val > x" |
---|
| 1877 | minsel = minval |
---|
| 1878 | maxsel = formatfunc(bound[0].strip()) \ |
---|
| 1879 | - formatfunc(offset) |
---|
[2013] | 1880 | else: |
---|
| 1881 | minsel = formatfunc(currsel) |
---|
| 1882 | maxsel = formatfunc(currsel) |
---|
| 1883 | sellists.append([minsel,maxsel]) |
---|
| 1884 | return sellists |
---|
| 1885 | |
---|
[1819] | 1886 | # def get_restfreqs(self): |
---|
| 1887 | # """ |
---|
| 1888 | # Get the restfrequency(s) stored in this scantable. |
---|
| 1889 | # The return value(s) are always of unit 'Hz' |
---|
| 1890 | # Parameters: |
---|
| 1891 | # none |
---|
| 1892 | # Returns: |
---|
| 1893 | # a list of doubles |
---|
| 1894 | # """ |
---|
| 1895 | # return list(self._getrestfreqs()) |
---|
| 1896 | |
---|
| 1897 | def get_restfreqs(self, ids=None): |
---|
[1846] | 1898 | """\ |
---|
[256] | 1899 | Get the restfrequency(s) stored in this scantable. |
---|
| 1900 | The return value(s) are always of unit 'Hz' |
---|
[1846] | 1901 | |
---|
[256] | 1902 | Parameters: |
---|
[1846] | 1903 | |
---|
[1819] | 1904 | ids: (optional) a list of MOLECULE_ID for that restfrequency(s) to |
---|
| 1905 | be retrieved |
---|
[1846] | 1906 | |
---|
[256] | 1907 | Returns: |
---|
[1846] | 1908 | |
---|
[1819] | 1909 | dictionary containing ids and a list of doubles for each id |
---|
[1846] | 1910 | |
---|
[256] | 1911 | """ |
---|
[1819] | 1912 | if ids is None: |
---|
[2349] | 1913 | rfreqs = {} |
---|
[1819] | 1914 | idlist = self.getmolnos() |
---|
| 1915 | for i in idlist: |
---|
[2349] | 1916 | rfreqs[i] = list(self._getrestfreqs(i)) |
---|
[1819] | 1917 | return rfreqs |
---|
| 1918 | else: |
---|
[2349] | 1919 | if type(ids) == list or type(ids) == tuple: |
---|
| 1920 | rfreqs = {} |
---|
[1819] | 1921 | for i in ids: |
---|
[2349] | 1922 | rfreqs[i] = list(self._getrestfreqs(i)) |
---|
[1819] | 1923 | return rfreqs |
---|
| 1924 | else: |
---|
| 1925 | return list(self._getrestfreqs(ids)) |
---|
[102] | 1926 | |
---|
[2349] | 1927 | @asaplog_post_dec |
---|
[931] | 1928 | def set_restfreqs(self, freqs=None, unit='Hz'): |
---|
[1846] | 1929 | """\ |
---|
[931] | 1930 | Set or replace the restfrequency specified and |
---|
[1938] | 1931 | if the 'freqs' argument holds a scalar, |
---|
[931] | 1932 | then that rest frequency will be applied to all the selected |
---|
| 1933 | data. If the 'freqs' argument holds |
---|
| 1934 | a vector, then it MUST be of equal or smaller length than |
---|
| 1935 | the number of IFs (and the available restfrequencies will be |
---|
| 1936 | replaced by this vector). In this case, *all* data have |
---|
| 1937 | the restfrequency set per IF according |
---|
| 1938 | to the corresponding value you give in the 'freqs' vector. |
---|
[1118] | 1939 | E.g. 'freqs=[1e9, 2e9]' would mean IF 0 gets restfreq 1e9 and |
---|
[931] | 1940 | IF 1 gets restfreq 2e9. |
---|
[1846] | 1941 | |
---|
[1395] | 1942 | You can also specify the frequencies via a linecatalog. |
---|
[1153] | 1943 | |
---|
[931] | 1944 | Parameters: |
---|
[1846] | 1945 | |
---|
[931] | 1946 | freqs: list of rest frequency values or string idenitfiers |
---|
[1855] | 1947 | |
---|
[931] | 1948 | unit: unit for rest frequency (default 'Hz') |
---|
[402] | 1949 | |
---|
[1846] | 1950 | |
---|
| 1951 | Example:: |
---|
| 1952 | |
---|
[1819] | 1953 | # set the given restfrequency for the all currently selected IFs |
---|
[931] | 1954 | scan.set_restfreqs(freqs=1.4e9) |
---|
[1845] | 1955 | # set restfrequencies for the n IFs (n > 1) in the order of the |
---|
| 1956 | # list, i.e |
---|
| 1957 | # IF0 -> 1.4e9, IF1 -> 1.41e9, IF3 -> 1.42e9 |
---|
| 1958 | # len(list_of_restfreqs) == nIF |
---|
| 1959 | # for nIF == 1 the following will set multiple restfrequency for |
---|
| 1960 | # that IF |
---|
[1819] | 1961 | scan.set_restfreqs(freqs=[1.4e9, 1.41e9, 1.42e9]) |
---|
[1845] | 1962 | # set multiple restfrequencies per IF. as a list of lists where |
---|
| 1963 | # the outer list has nIF elements, the inner s arbitrary |
---|
| 1964 | scan.set_restfreqs(freqs=[[1.4e9, 1.41e9], [1.67e9]]) |
---|
[391] | 1965 | |
---|
[1846] | 1966 | *Note*: |
---|
[1845] | 1967 | |
---|
[931] | 1968 | To do more sophisticate Restfrequency setting, e.g. on a |
---|
| 1969 | source and IF basis, use scantable.set_selection() before using |
---|
[1846] | 1970 | this function:: |
---|
[931] | 1971 | |
---|
[1846] | 1972 | # provided your scantable is called scan |
---|
| 1973 | selection = selector() |
---|
[2431] | 1974 | selection.set_name('ORION*') |
---|
[1846] | 1975 | selection.set_ifs([1]) |
---|
| 1976 | scan.set_selection(selection) |
---|
| 1977 | scan.set_restfreqs(freqs=86.6e9) |
---|
| 1978 | |
---|
[931] | 1979 | """ |
---|
| 1980 | varlist = vars() |
---|
[1157] | 1981 | from asap import linecatalog |
---|
| 1982 | # simple value |
---|
[1118] | 1983 | if isinstance(freqs, int) or isinstance(freqs, float): |
---|
[1845] | 1984 | self._setrestfreqs([freqs], [""], unit) |
---|
[1157] | 1985 | # list of values |
---|
[1118] | 1986 | elif isinstance(freqs, list) or isinstance(freqs, tuple): |
---|
[1157] | 1987 | # list values are scalars |
---|
[1118] | 1988 | if isinstance(freqs[-1], int) or isinstance(freqs[-1], float): |
---|
[1845] | 1989 | if len(freqs) == 1: |
---|
| 1990 | self._setrestfreqs(freqs, [""], unit) |
---|
| 1991 | else: |
---|
| 1992 | # allow the 'old' mode of setting mulitple IFs |
---|
| 1993 | savesel = self._getselection() |
---|
[2599] | 1994 | sel = self.get_selection() |
---|
[1845] | 1995 | iflist = self.getifnos() |
---|
| 1996 | if len(freqs)>len(iflist): |
---|
| 1997 | raise ValueError("number of elements in list of list " |
---|
| 1998 | "exeeds the current IF selections") |
---|
| 1999 | iflist = self.getifnos() |
---|
| 2000 | for i, fval in enumerate(freqs): |
---|
| 2001 | sel.set_ifs(iflist[i]) |
---|
| 2002 | self._setselection(sel) |
---|
| 2003 | self._setrestfreqs([fval], [""], unit) |
---|
| 2004 | self._setselection(savesel) |
---|
| 2005 | |
---|
| 2006 | # list values are dict, {'value'=, 'name'=) |
---|
[1157] | 2007 | elif isinstance(freqs[-1], dict): |
---|
[1845] | 2008 | values = [] |
---|
| 2009 | names = [] |
---|
| 2010 | for d in freqs: |
---|
| 2011 | values.append(d["value"]) |
---|
| 2012 | names.append(d["name"]) |
---|
| 2013 | self._setrestfreqs(values, names, unit) |
---|
[1819] | 2014 | elif isinstance(freqs[-1], list) or isinstance(freqs[-1], tuple): |
---|
[1157] | 2015 | savesel = self._getselection() |
---|
[2599] | 2016 | sel = self.get_selection() |
---|
[1322] | 2017 | iflist = self.getifnos() |
---|
[1819] | 2018 | if len(freqs)>len(iflist): |
---|
[1845] | 2019 | raise ValueError("number of elements in list of list exeeds" |
---|
| 2020 | " the current IF selections") |
---|
| 2021 | for i, fval in enumerate(freqs): |
---|
[1322] | 2022 | sel.set_ifs(iflist[i]) |
---|
[1259] | 2023 | self._setselection(sel) |
---|
[1845] | 2024 | self._setrestfreqs(fval, [""], unit) |
---|
[1157] | 2025 | self._setselection(savesel) |
---|
| 2026 | # freqs are to be taken from a linecatalog |
---|
[1153] | 2027 | elif isinstance(freqs, linecatalog): |
---|
| 2028 | savesel = self._getselection() |
---|
[2599] | 2029 | sel = self.get_selection() |
---|
[1153] | 2030 | for i in xrange(freqs.nrow()): |
---|
[1322] | 2031 | sel.set_ifs(iflist[i]) |
---|
[1153] | 2032 | self._setselection(sel) |
---|
[1845] | 2033 | self._setrestfreqs([freqs.get_frequency(i)], |
---|
| 2034 | [freqs.get_name(i)], "MHz") |
---|
[1153] | 2035 | # ensure that we are not iterating past nIF |
---|
| 2036 | if i == self.nif()-1: break |
---|
| 2037 | self._setselection(savesel) |
---|
[931] | 2038 | else: |
---|
| 2039 | return |
---|
| 2040 | self._add_history("set_restfreqs", varlist) |
---|
| 2041 | |
---|
[2349] | 2042 | @asaplog_post_dec |
---|
[1360] | 2043 | def shift_refpix(self, delta): |
---|
[1846] | 2044 | """\ |
---|
[1589] | 2045 | Shift the reference pixel of the Spectra Coordinate by an |
---|
| 2046 | integer amount. |
---|
[1846] | 2047 | |
---|
[1589] | 2048 | Parameters: |
---|
[1846] | 2049 | |
---|
[1589] | 2050 | delta: the amount to shift by |
---|
[1846] | 2051 | |
---|
| 2052 | *Note*: |
---|
| 2053 | |
---|
[1589] | 2054 | Be careful using this with broadband data. |
---|
[1846] | 2055 | |
---|
[1360] | 2056 | """ |
---|
[2349] | 2057 | varlist = vars() |
---|
[1731] | 2058 | Scantable.shift_refpix(self, delta) |
---|
[2349] | 2059 | s._add_history("shift_refpix", varlist) |
---|
[931] | 2060 | |
---|
[1862] | 2061 | @asaplog_post_dec |
---|
[2820] | 2062 | def history(self, filename=None, nrows=-1, start=0): |
---|
[1846] | 2063 | """\ |
---|
[1259] | 2064 | Print the history. Optionally to a file. |
---|
[1846] | 2065 | |
---|
[1348] | 2066 | Parameters: |
---|
[1846] | 2067 | |
---|
[1928] | 2068 | filename: The name of the file to save the history to. |
---|
[1846] | 2069 | |
---|
[1259] | 2070 | """ |
---|
[2820] | 2071 | n = self._historylength() |
---|
| 2072 | if nrows == -1: |
---|
| 2073 | nrows = n |
---|
| 2074 | if start+nrows > n: |
---|
| 2075 | nrows = nrows-start |
---|
| 2076 | if n > 1000 and nrows == n: |
---|
| 2077 | nrows = 1000 |
---|
| 2078 | start = n-1000 |
---|
| 2079 | asaplog.push("Warning: History has {0} entries. Displaying last " |
---|
| 2080 | "1000".format(n)) |
---|
| 2081 | hist = list(self._gethistory(nrows, start)) |
---|
[794] | 2082 | out = "-"*80 |
---|
[484] | 2083 | for h in hist: |
---|
[2820] | 2084 | if not h.strip(): |
---|
| 2085 | continue |
---|
| 2086 | if h.find("---") >-1: |
---|
| 2087 | continue |
---|
[489] | 2088 | else: |
---|
| 2089 | items = h.split("##") |
---|
| 2090 | date = items[0] |
---|
| 2091 | func = items[1] |
---|
| 2092 | items = items[2:] |
---|
[794] | 2093 | out += "\n"+date+"\n" |
---|
| 2094 | out += "Function: %s\n Parameters:" % (func) |
---|
[489] | 2095 | for i in items: |
---|
[1938] | 2096 | if i == '': |
---|
| 2097 | continue |
---|
[489] | 2098 | s = i.split("=") |
---|
[1118] | 2099 | out += "\n %s = %s" % (s[0], s[1]) |
---|
[2820] | 2100 | out = "\n".join([out, "*"*80]) |
---|
[1259] | 2101 | if filename is not None: |
---|
| 2102 | if filename is "": |
---|
| 2103 | filename = 'scantable_history.txt' |
---|
| 2104 | filename = os.path.expandvars(os.path.expanduser(filename)) |
---|
| 2105 | if not os.path.isdir(filename): |
---|
| 2106 | data = open(filename, 'w') |
---|
| 2107 | data.write(out) |
---|
| 2108 | data.close() |
---|
| 2109 | else: |
---|
| 2110 | msg = "Illegal file name '%s'." % (filename) |
---|
[1859] | 2111 | raise IOError(msg) |
---|
| 2112 | return page(out) |
---|
[2349] | 2113 | |
---|
[513] | 2114 | # |
---|
| 2115 | # Maths business |
---|
| 2116 | # |
---|
[1862] | 2117 | @asaplog_post_dec |
---|
[2818] | 2118 | def average_time(self, mask=None, scanav=False, weight='tint', align=False, |
---|
| 2119 | avmode="NONE"): |
---|
[1846] | 2120 | """\ |
---|
[2349] | 2121 | Return the (time) weighted average of a scan. Scans will be averaged |
---|
| 2122 | only if the source direction (RA/DEC) is within 1' otherwise |
---|
[1846] | 2123 | |
---|
| 2124 | *Note*: |
---|
| 2125 | |
---|
[1070] | 2126 | in channels only - align if necessary |
---|
[1846] | 2127 | |
---|
[513] | 2128 | Parameters: |
---|
[1846] | 2129 | |
---|
[513] | 2130 | mask: an optional mask (only used for 'var' and 'tsys' |
---|
| 2131 | weighting) |
---|
[1855] | 2132 | |
---|
[558] | 2133 | scanav: True averages each scan separately |
---|
| 2134 | False (default) averages all scans together, |
---|
[1855] | 2135 | |
---|
[1099] | 2136 | weight: Weighting scheme. |
---|
| 2137 | 'none' (mean no weight) |
---|
| 2138 | 'var' (1/var(spec) weighted) |
---|
| 2139 | 'tsys' (1/Tsys**2 weighted) |
---|
| 2140 | 'tint' (integration time weighted) |
---|
| 2141 | 'tintsys' (Tint/Tsys**2) |
---|
| 2142 | 'median' ( median averaging) |
---|
[535] | 2143 | The default is 'tint' |
---|
[1855] | 2144 | |
---|
[931] | 2145 | align: align the spectra in velocity before averaging. It takes |
---|
| 2146 | the time of the first spectrum as reference time. |
---|
[2818] | 2147 | avmode: 'SOURCE' - also select by source name - or |
---|
| 2148 | 'NONE' (default). Not applicable for scanav=True or |
---|
| 2149 | weight=median |
---|
[1846] | 2150 | |
---|
| 2151 | Example:: |
---|
| 2152 | |
---|
[513] | 2153 | # time average the scantable without using a mask |
---|
[710] | 2154 | newscan = scan.average_time() |
---|
[1846] | 2155 | |
---|
[513] | 2156 | """ |
---|
| 2157 | varlist = vars() |
---|
[1593] | 2158 | weight = weight or 'TINT' |
---|
| 2159 | mask = mask or () |
---|
[2818] | 2160 | scanav = (scanav and 'SCAN') or avmode.upper() |
---|
[1118] | 2161 | scan = (self, ) |
---|
[1859] | 2162 | |
---|
| 2163 | if align: |
---|
| 2164 | scan = (self.freq_align(insitu=False), ) |
---|
[2818] | 2165 | asaplog.push("Note: Alignment is don on a source-by-source basis") |
---|
| 2166 | asaplog.push("Note: Averaging (by default) is not") |
---|
| 2167 | # we need to set it to SOURCE averaging here |
---|
[1859] | 2168 | s = None |
---|
| 2169 | if weight.upper() == 'MEDIAN': |
---|
| 2170 | s = scantable(self._math._averagechannel(scan[0], 'MEDIAN', |
---|
| 2171 | scanav)) |
---|
| 2172 | else: |
---|
| 2173 | s = scantable(self._math._average(scan, mask, weight.upper(), |
---|
| 2174 | scanav)) |
---|
[1099] | 2175 | s._add_history("average_time", varlist) |
---|
[513] | 2176 | return s |
---|
[710] | 2177 | |
---|
[1862] | 2178 | @asaplog_post_dec |
---|
[876] | 2179 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None): |
---|
[1846] | 2180 | """\ |
---|
[513] | 2181 | Return a scan where all spectra are converted to either |
---|
| 2182 | Jansky or Kelvin depending upon the flux units of the scan table. |
---|
| 2183 | By default the function tries to look the values up internally. |
---|
| 2184 | If it can't find them (or if you want to over-ride), you must |
---|
| 2185 | specify EITHER jyperk OR eta (and D which it will try to look up |
---|
| 2186 | also if you don't set it). jyperk takes precedence if you set both. |
---|
[1846] | 2187 | |
---|
[513] | 2188 | Parameters: |
---|
[1846] | 2189 | |
---|
[513] | 2190 | jyperk: the Jy / K conversion factor |
---|
[1855] | 2191 | |
---|
[513] | 2192 | eta: the aperture efficiency |
---|
[1855] | 2193 | |
---|
[1928] | 2194 | d: the geometric diameter (metres) |
---|
[1855] | 2195 | |
---|
[513] | 2196 | insitu: if False a new scantable is returned. |
---|
| 2197 | Otherwise, the scaling is done in-situ |
---|
| 2198 | The default is taken from .asaprc (False) |
---|
[1846] | 2199 | |
---|
[513] | 2200 | """ |
---|
| 2201 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 2202 | self._math._setinsitu(insitu) |
---|
[513] | 2203 | varlist = vars() |
---|
[1593] | 2204 | jyperk = jyperk or -1.0 |
---|
| 2205 | d = d or -1.0 |
---|
| 2206 | eta = eta or -1.0 |
---|
[876] | 2207 | s = scantable(self._math._convertflux(self, d, eta, jyperk)) |
---|
| 2208 | s._add_history("convert_flux", varlist) |
---|
| 2209 | if insitu: self._assign(s) |
---|
| 2210 | else: return s |
---|
[513] | 2211 | |
---|
[1862] | 2212 | @asaplog_post_dec |
---|
[876] | 2213 | def gain_el(self, poly=None, filename="", method="linear", insitu=None): |
---|
[1846] | 2214 | """\ |
---|
[513] | 2215 | Return a scan after applying a gain-elevation correction. |
---|
| 2216 | The correction can be made via either a polynomial or a |
---|
| 2217 | table-based interpolation (and extrapolation if necessary). |
---|
| 2218 | You specify polynomial coefficients, an ascii table or neither. |
---|
| 2219 | If you specify neither, then a polynomial correction will be made |
---|
| 2220 | with built in coefficients known for certain telescopes (an error |
---|
| 2221 | will occur if the instrument is not known). |
---|
| 2222 | The data and Tsys are *divided* by the scaling factors. |
---|
[1846] | 2223 | |
---|
[513] | 2224 | Parameters: |
---|
[1846] | 2225 | |
---|
[513] | 2226 | poly: Polynomial coefficients (default None) to compute a |
---|
| 2227 | gain-elevation correction as a function of |
---|
| 2228 | elevation (in degrees). |
---|
[1855] | 2229 | |
---|
[513] | 2230 | filename: The name of an ascii file holding correction factors. |
---|
| 2231 | The first row of the ascii file must give the column |
---|
| 2232 | names and these MUST include columns |
---|
[2431] | 2233 | 'ELEVATION' (degrees) and 'FACTOR' (multiply data |
---|
[513] | 2234 | by this) somewhere. |
---|
| 2235 | The second row must give the data type of the |
---|
| 2236 | column. Use 'R' for Real and 'I' for Integer. |
---|
| 2237 | An example file would be |
---|
| 2238 | (actual factors are arbitrary) : |
---|
| 2239 | |
---|
| 2240 | TIME ELEVATION FACTOR |
---|
| 2241 | R R R |
---|
| 2242 | 0.1 0 0.8 |
---|
| 2243 | 0.2 20 0.85 |
---|
| 2244 | 0.3 40 0.9 |
---|
| 2245 | 0.4 60 0.85 |
---|
| 2246 | 0.5 80 0.8 |
---|
| 2247 | 0.6 90 0.75 |
---|
[1855] | 2248 | |
---|
[513] | 2249 | method: Interpolation method when correcting from a table. |
---|
[2431] | 2250 | Values are 'nearest', 'linear' (default), 'cubic' |
---|
| 2251 | and 'spline' |
---|
[1855] | 2252 | |
---|
[513] | 2253 | insitu: if False a new scantable is returned. |
---|
| 2254 | Otherwise, the scaling is done in-situ |
---|
| 2255 | The default is taken from .asaprc (False) |
---|
[1846] | 2256 | |
---|
[513] | 2257 | """ |
---|
| 2258 | |
---|
| 2259 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 2260 | self._math._setinsitu(insitu) |
---|
[513] | 2261 | varlist = vars() |
---|
[1593] | 2262 | poly = poly or () |
---|
[513] | 2263 | from os.path import expandvars |
---|
| 2264 | filename = expandvars(filename) |
---|
[876] | 2265 | s = scantable(self._math._gainel(self, poly, filename, method)) |
---|
| 2266 | s._add_history("gain_el", varlist) |
---|
[1593] | 2267 | if insitu: |
---|
| 2268 | self._assign(s) |
---|
| 2269 | else: |
---|
| 2270 | return s |
---|
[710] | 2271 | |
---|
[1862] | 2272 | @asaplog_post_dec |
---|
[931] | 2273 | def freq_align(self, reftime=None, method='cubic', insitu=None): |
---|
[1846] | 2274 | """\ |
---|
[513] | 2275 | Return a scan where all rows have been aligned in frequency/velocity. |
---|
| 2276 | The alignment frequency frame (e.g. LSRK) is that set by function |
---|
| 2277 | set_freqframe. |
---|
[1846] | 2278 | |
---|
[513] | 2279 | Parameters: |
---|
[1855] | 2280 | |
---|
[513] | 2281 | reftime: reference time to align at. By default, the time of |
---|
| 2282 | the first row of data is used. |
---|
[1855] | 2283 | |
---|
[513] | 2284 | method: Interpolation method for regridding the spectra. |
---|
[2431] | 2285 | Choose from 'nearest', 'linear', 'cubic' (default) |
---|
| 2286 | and 'spline' |
---|
[1855] | 2287 | |
---|
[513] | 2288 | insitu: if False a new scantable is returned. |
---|
| 2289 | Otherwise, the scaling is done in-situ |
---|
| 2290 | The default is taken from .asaprc (False) |
---|
[1846] | 2291 | |
---|
[513] | 2292 | """ |
---|
[931] | 2293 | if insitu is None: insitu = rcParams["insitu"] |
---|
[2429] | 2294 | oldInsitu = self._math._insitu() |
---|
[876] | 2295 | self._math._setinsitu(insitu) |
---|
[513] | 2296 | varlist = vars() |
---|
[1593] | 2297 | reftime = reftime or "" |
---|
[931] | 2298 | s = scantable(self._math._freq_align(self, reftime, method)) |
---|
[876] | 2299 | s._add_history("freq_align", varlist) |
---|
[2429] | 2300 | self._math._setinsitu(oldInsitu) |
---|
[2349] | 2301 | if insitu: |
---|
| 2302 | self._assign(s) |
---|
| 2303 | else: |
---|
| 2304 | return s |
---|
[513] | 2305 | |
---|
[1862] | 2306 | @asaplog_post_dec |
---|
[1725] | 2307 | def opacity(self, tau=None, insitu=None): |
---|
[1846] | 2308 | """\ |
---|
[513] | 2309 | Apply an opacity correction. The data |
---|
| 2310 | and Tsys are multiplied by the correction factor. |
---|
[1846] | 2311 | |
---|
[513] | 2312 | Parameters: |
---|
[1855] | 2313 | |
---|
[1689] | 2314 | tau: (list of) opacity from which the correction factor is |
---|
[513] | 2315 | exp(tau*ZD) |
---|
[1689] | 2316 | where ZD is the zenith-distance. |
---|
| 2317 | If a list is provided, it has to be of length nIF, |
---|
| 2318 | nIF*nPol or 1 and in order of IF/POL, e.g. |
---|
| 2319 | [opif0pol0, opif0pol1, opif1pol0 ...] |
---|
[1725] | 2320 | if tau is `None` the opacities are determined from a |
---|
| 2321 | model. |
---|
[1855] | 2322 | |
---|
[513] | 2323 | insitu: if False a new scantable is returned. |
---|
| 2324 | Otherwise, the scaling is done in-situ |
---|
| 2325 | The default is taken from .asaprc (False) |
---|
[1846] | 2326 | |
---|
[513] | 2327 | """ |
---|
[2349] | 2328 | if insitu is None: |
---|
| 2329 | insitu = rcParams['insitu'] |
---|
[876] | 2330 | self._math._setinsitu(insitu) |
---|
[513] | 2331 | varlist = vars() |
---|
[1689] | 2332 | if not hasattr(tau, "__len__"): |
---|
| 2333 | tau = [tau] |
---|
[876] | 2334 | s = scantable(self._math._opacity(self, tau)) |
---|
| 2335 | s._add_history("opacity", varlist) |
---|
[2349] | 2336 | if insitu: |
---|
| 2337 | self._assign(s) |
---|
| 2338 | else: |
---|
| 2339 | return s |
---|
[513] | 2340 | |
---|
[1862] | 2341 | @asaplog_post_dec |
---|
[513] | 2342 | def bin(self, width=5, insitu=None): |
---|
[1846] | 2343 | """\ |
---|
[513] | 2344 | Return a scan where all spectra have been binned up. |
---|
[1846] | 2345 | |
---|
[1348] | 2346 | Parameters: |
---|
[1846] | 2347 | |
---|
[513] | 2348 | width: The bin width (default=5) in pixels |
---|
[1855] | 2349 | |
---|
[513] | 2350 | insitu: if False a new scantable is returned. |
---|
| 2351 | Otherwise, the scaling is done in-situ |
---|
| 2352 | The default is taken from .asaprc (False) |
---|
[1846] | 2353 | |
---|
[513] | 2354 | """ |
---|
[2349] | 2355 | if insitu is None: |
---|
| 2356 | insitu = rcParams['insitu'] |
---|
[876] | 2357 | self._math._setinsitu(insitu) |
---|
[513] | 2358 | varlist = vars() |
---|
[876] | 2359 | s = scantable(self._math._bin(self, width)) |
---|
[1118] | 2360 | s._add_history("bin", varlist) |
---|
[1589] | 2361 | if insitu: |
---|
| 2362 | self._assign(s) |
---|
| 2363 | else: |
---|
| 2364 | return s |
---|
[513] | 2365 | |
---|
[1862] | 2366 | @asaplog_post_dec |
---|
[2672] | 2367 | def reshape(self, first, last, insitu=None): |
---|
| 2368 | """Resize the band by providing first and last channel. |
---|
| 2369 | This will cut off all channels outside [first, last]. |
---|
| 2370 | """ |
---|
| 2371 | if insitu is None: |
---|
| 2372 | insitu = rcParams['insitu'] |
---|
| 2373 | varlist = vars() |
---|
| 2374 | if last < 0: |
---|
| 2375 | last = self.nchan()-1 + last |
---|
| 2376 | s = None |
---|
| 2377 | if insitu: |
---|
| 2378 | s = self |
---|
| 2379 | else: |
---|
| 2380 | s = self.copy() |
---|
| 2381 | s._reshape(first,last) |
---|
| 2382 | s._add_history("reshape", varlist) |
---|
| 2383 | if not insitu: |
---|
| 2384 | return s |
---|
| 2385 | |
---|
| 2386 | @asaplog_post_dec |
---|
[513] | 2387 | def resample(self, width=5, method='cubic', insitu=None): |
---|
[1846] | 2388 | """\ |
---|
[1348] | 2389 | Return a scan where all spectra have been binned up. |
---|
[1573] | 2390 | |
---|
[1348] | 2391 | Parameters: |
---|
[1846] | 2392 | |
---|
[513] | 2393 | width: The bin width (default=5) in pixels |
---|
[1855] | 2394 | |
---|
[513] | 2395 | method: Interpolation method when correcting from a table. |
---|
[2431] | 2396 | Values are 'nearest', 'linear', 'cubic' (default) |
---|
| 2397 | and 'spline' |
---|
[1855] | 2398 | |
---|
[513] | 2399 | insitu: if False a new scantable is returned. |
---|
| 2400 | Otherwise, the scaling is done in-situ |
---|
| 2401 | The default is taken from .asaprc (False) |
---|
[1846] | 2402 | |
---|
[513] | 2403 | """ |
---|
[2349] | 2404 | if insitu is None: |
---|
| 2405 | insitu = rcParams['insitu'] |
---|
[876] | 2406 | self._math._setinsitu(insitu) |
---|
[513] | 2407 | varlist = vars() |
---|
[876] | 2408 | s = scantable(self._math._resample(self, method, width)) |
---|
[1118] | 2409 | s._add_history("resample", varlist) |
---|
[2349] | 2410 | if insitu: |
---|
| 2411 | self._assign(s) |
---|
| 2412 | else: |
---|
| 2413 | return s |
---|
[513] | 2414 | |
---|
[1862] | 2415 | @asaplog_post_dec |
---|
[946] | 2416 | def average_pol(self, mask=None, weight='none'): |
---|
[1846] | 2417 | """\ |
---|
[946] | 2418 | Average the Polarisations together. |
---|
[1846] | 2419 | |
---|
[946] | 2420 | Parameters: |
---|
[1846] | 2421 | |
---|
[946] | 2422 | mask: An optional mask defining the region, where the |
---|
| 2423 | averaging will be applied. The output will have all |
---|
| 2424 | specified points masked. |
---|
[1855] | 2425 | |
---|
[946] | 2426 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 2427 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
[1846] | 2428 | |
---|
[946] | 2429 | """ |
---|
| 2430 | varlist = vars() |
---|
[1593] | 2431 | mask = mask or () |
---|
[1010] | 2432 | s = scantable(self._math._averagepol(self, mask, weight.upper())) |
---|
[1118] | 2433 | s._add_history("average_pol", varlist) |
---|
[992] | 2434 | return s |
---|
[513] | 2435 | |
---|
[1862] | 2436 | @asaplog_post_dec |
---|
[1145] | 2437 | def average_beam(self, mask=None, weight='none'): |
---|
[1846] | 2438 | """\ |
---|
[1145] | 2439 | Average the Beams together. |
---|
[1846] | 2440 | |
---|
[1145] | 2441 | Parameters: |
---|
| 2442 | mask: An optional mask defining the region, where the |
---|
| 2443 | averaging will be applied. The output will have all |
---|
| 2444 | specified points masked. |
---|
[1855] | 2445 | |
---|
[1145] | 2446 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 2447 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
[1846] | 2448 | |
---|
[1145] | 2449 | """ |
---|
| 2450 | varlist = vars() |
---|
[1593] | 2451 | mask = mask or () |
---|
[1145] | 2452 | s = scantable(self._math._averagebeams(self, mask, weight.upper())) |
---|
| 2453 | s._add_history("average_beam", varlist) |
---|
| 2454 | return s |
---|
| 2455 | |
---|
[1586] | 2456 | def parallactify(self, pflag): |
---|
[1846] | 2457 | """\ |
---|
[1843] | 2458 | Set a flag to indicate whether this data should be treated as having |
---|
[1617] | 2459 | been 'parallactified' (total phase == 0.0) |
---|
[1846] | 2460 | |
---|
[1617] | 2461 | Parameters: |
---|
[1855] | 2462 | |
---|
[1843] | 2463 | pflag: Bool indicating whether to turn this on (True) or |
---|
[1617] | 2464 | off (False) |
---|
[1846] | 2465 | |
---|
[1617] | 2466 | """ |
---|
[1586] | 2467 | varlist = vars() |
---|
| 2468 | self._parallactify(pflag) |
---|
| 2469 | self._add_history("parallactify", varlist) |
---|
| 2470 | |
---|
[1862] | 2471 | @asaplog_post_dec |
---|
[992] | 2472 | def convert_pol(self, poltype=None): |
---|
[1846] | 2473 | """\ |
---|
[992] | 2474 | Convert the data to a different polarisation type. |
---|
[1565] | 2475 | Note that you will need cross-polarisation terms for most conversions. |
---|
[1846] | 2476 | |
---|
[992] | 2477 | Parameters: |
---|
[1855] | 2478 | |
---|
[992] | 2479 | poltype: The new polarisation type. Valid types are: |
---|
[2431] | 2480 | 'linear', 'circular', 'stokes' and 'linpol' |
---|
[1846] | 2481 | |
---|
[992] | 2482 | """ |
---|
| 2483 | varlist = vars() |
---|
[1859] | 2484 | s = scantable(self._math._convertpol(self, poltype)) |
---|
[1118] | 2485 | s._add_history("convert_pol", varlist) |
---|
[992] | 2486 | return s |
---|
| 2487 | |
---|
[1862] | 2488 | @asaplog_post_dec |
---|
[2269] | 2489 | def smooth(self, kernel="hanning", width=5.0, order=2, plot=False, |
---|
| 2490 | insitu=None): |
---|
[1846] | 2491 | """\ |
---|
[513] | 2492 | Smooth the spectrum by the specified kernel (conserving flux). |
---|
[1846] | 2493 | |
---|
[513] | 2494 | Parameters: |
---|
[1846] | 2495 | |
---|
[513] | 2496 | kernel: The type of smoothing kernel. Select from |
---|
[1574] | 2497 | 'hanning' (default), 'gaussian', 'boxcar', 'rmedian' |
---|
| 2498 | or 'poly' |
---|
[1855] | 2499 | |
---|
[513] | 2500 | width: The width of the kernel in pixels. For hanning this is |
---|
| 2501 | ignored otherwise it defauls to 5 pixels. |
---|
| 2502 | For 'gaussian' it is the Full Width Half |
---|
| 2503 | Maximum. For 'boxcar' it is the full width. |
---|
[1574] | 2504 | For 'rmedian' and 'poly' it is the half width. |
---|
[1855] | 2505 | |
---|
[1574] | 2506 | order: Optional parameter for 'poly' kernel (default is 2), to |
---|
| 2507 | specify the order of the polnomial. Ignored by all other |
---|
| 2508 | kernels. |
---|
[1855] | 2509 | |
---|
[1819] | 2510 | plot: plot the original and the smoothed spectra. |
---|
| 2511 | In this each indivual fit has to be approved, by |
---|
| 2512 | typing 'y' or 'n' |
---|
[1855] | 2513 | |
---|
[513] | 2514 | insitu: if False a new scantable is returned. |
---|
| 2515 | Otherwise, the scaling is done in-situ |
---|
| 2516 | The default is taken from .asaprc (False) |
---|
[1846] | 2517 | |
---|
[513] | 2518 | """ |
---|
| 2519 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 2520 | self._math._setinsitu(insitu) |
---|
[513] | 2521 | varlist = vars() |
---|
[1819] | 2522 | |
---|
| 2523 | if plot: orgscan = self.copy() |
---|
| 2524 | |
---|
[1574] | 2525 | s = scantable(self._math._smooth(self, kernel.lower(), width, order)) |
---|
[876] | 2526 | s._add_history("smooth", varlist) |
---|
[1819] | 2527 | |
---|
[2610] | 2528 | action = 'H' |
---|
[1819] | 2529 | if plot: |
---|
[2150] | 2530 | from asap.asapplotter import new_asaplot |
---|
| 2531 | theplot = new_asaplot(rcParams['plotter.gui']) |
---|
[2535] | 2532 | from matplotlib import rc as rcp |
---|
| 2533 | rcp('lines', linewidth=1) |
---|
[2150] | 2534 | theplot.set_panels() |
---|
[1819] | 2535 | ylab=s._get_ordinate_label() |
---|
[2150] | 2536 | #theplot.palette(0,["#777777","red"]) |
---|
[1819] | 2537 | for r in xrange(s.nrow()): |
---|
| 2538 | xsm=s._getabcissa(r) |
---|
| 2539 | ysm=s._getspectrum(r) |
---|
| 2540 | xorg=orgscan._getabcissa(r) |
---|
| 2541 | yorg=orgscan._getspectrum(r) |
---|
[2610] | 2542 | if action != "N": #skip plotting if rejecting all |
---|
| 2543 | theplot.clear() |
---|
| 2544 | theplot.hold() |
---|
| 2545 | theplot.set_axes('ylabel',ylab) |
---|
| 2546 | theplot.set_axes('xlabel',s._getabcissalabel(r)) |
---|
| 2547 | theplot.set_axes('title',s._getsourcename(r)) |
---|
| 2548 | theplot.set_line(label='Original',color="#777777") |
---|
| 2549 | theplot.plot(xorg,yorg) |
---|
| 2550 | theplot.set_line(label='Smoothed',color="red") |
---|
| 2551 | theplot.plot(xsm,ysm) |
---|
| 2552 | ### Ugly part for legend |
---|
| 2553 | for i in [0,1]: |
---|
| 2554 | theplot.subplots[0]['lines'].append( |
---|
| 2555 | [theplot.subplots[0]['axes'].lines[i]] |
---|
| 2556 | ) |
---|
| 2557 | theplot.release() |
---|
| 2558 | ### Ugly part for legend |
---|
| 2559 | theplot.subplots[0]['lines']=[] |
---|
| 2560 | res = self._get_verify_action("Accept smoothing?",action) |
---|
| 2561 | #print "IF%d, POL%d: got result = %s" %(s.getif(r),s.getpol(r),res) |
---|
| 2562 | if r == 0: action = None |
---|
| 2563 | #res = raw_input("Accept smoothing ([y]/n): ") |
---|
[1819] | 2564 | if res.upper() == 'N': |
---|
[2610] | 2565 | # reject for the current rows |
---|
[1819] | 2566 | s._setspectrum(yorg, r) |
---|
[2610] | 2567 | elif res.upper() == 'R': |
---|
| 2568 | # reject all the following rows |
---|
| 2569 | action = "N" |
---|
| 2570 | s._setspectrum(yorg, r) |
---|
| 2571 | elif res.upper() == 'A': |
---|
| 2572 | # accept all the following rows |
---|
| 2573 | break |
---|
[2150] | 2574 | theplot.quit() |
---|
| 2575 | del theplot |
---|
[1819] | 2576 | del orgscan |
---|
| 2577 | |
---|
[876] | 2578 | if insitu: self._assign(s) |
---|
| 2579 | else: return s |
---|
[513] | 2580 | |
---|
[2186] | 2581 | @asaplog_post_dec |
---|
[2435] | 2582 | def regrid_channel(self, width=5, plot=False, insitu=None): |
---|
| 2583 | """\ |
---|
| 2584 | Regrid the spectra by the specified channel width |
---|
| 2585 | |
---|
| 2586 | Parameters: |
---|
| 2587 | |
---|
| 2588 | width: The channel width (float) of regridded spectra |
---|
| 2589 | in the current spectral unit. |
---|
| 2590 | |
---|
| 2591 | plot: [NOT IMPLEMENTED YET] |
---|
| 2592 | plot the original and the regridded spectra. |
---|
| 2593 | In this each indivual fit has to be approved, by |
---|
| 2594 | typing 'y' or 'n' |
---|
| 2595 | |
---|
| 2596 | insitu: if False a new scantable is returned. |
---|
| 2597 | Otherwise, the scaling is done in-situ |
---|
| 2598 | The default is taken from .asaprc (False) |
---|
| 2599 | |
---|
| 2600 | """ |
---|
| 2601 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 2602 | varlist = vars() |
---|
| 2603 | |
---|
| 2604 | if plot: |
---|
| 2605 | asaplog.post() |
---|
| 2606 | asaplog.push("Verification plot is not implemtnetd yet.") |
---|
| 2607 | asaplog.post("WARN") |
---|
| 2608 | |
---|
| 2609 | s = self.copy() |
---|
| 2610 | s._regrid_specchan(width) |
---|
| 2611 | |
---|
| 2612 | s._add_history("regrid_channel", varlist) |
---|
| 2613 | |
---|
| 2614 | # if plot: |
---|
| 2615 | # from asap.asapplotter import new_asaplot |
---|
| 2616 | # theplot = new_asaplot(rcParams['plotter.gui']) |
---|
[2535] | 2617 | # from matplotlib import rc as rcp |
---|
| 2618 | # rcp('lines', linewidth=1) |
---|
[2435] | 2619 | # theplot.set_panels() |
---|
| 2620 | # ylab=s._get_ordinate_label() |
---|
| 2621 | # #theplot.palette(0,["#777777","red"]) |
---|
| 2622 | # for r in xrange(s.nrow()): |
---|
| 2623 | # xsm=s._getabcissa(r) |
---|
| 2624 | # ysm=s._getspectrum(r) |
---|
| 2625 | # xorg=orgscan._getabcissa(r) |
---|
| 2626 | # yorg=orgscan._getspectrum(r) |
---|
| 2627 | # theplot.clear() |
---|
| 2628 | # theplot.hold() |
---|
| 2629 | # theplot.set_axes('ylabel',ylab) |
---|
| 2630 | # theplot.set_axes('xlabel',s._getabcissalabel(r)) |
---|
| 2631 | # theplot.set_axes('title',s._getsourcename(r)) |
---|
| 2632 | # theplot.set_line(label='Original',color="#777777") |
---|
| 2633 | # theplot.plot(xorg,yorg) |
---|
| 2634 | # theplot.set_line(label='Smoothed',color="red") |
---|
| 2635 | # theplot.plot(xsm,ysm) |
---|
| 2636 | # ### Ugly part for legend |
---|
| 2637 | # for i in [0,1]: |
---|
| 2638 | # theplot.subplots[0]['lines'].append( |
---|
| 2639 | # [theplot.subplots[0]['axes'].lines[i]] |
---|
| 2640 | # ) |
---|
| 2641 | # theplot.release() |
---|
| 2642 | # ### Ugly part for legend |
---|
| 2643 | # theplot.subplots[0]['lines']=[] |
---|
| 2644 | # res = raw_input("Accept smoothing ([y]/n): ") |
---|
| 2645 | # if res.upper() == 'N': |
---|
| 2646 | # s._setspectrum(yorg, r) |
---|
| 2647 | # theplot.quit() |
---|
| 2648 | # del theplot |
---|
| 2649 | # del orgscan |
---|
| 2650 | |
---|
| 2651 | if insitu: self._assign(s) |
---|
| 2652 | else: return s |
---|
| 2653 | |
---|
| 2654 | @asaplog_post_dec |
---|
[2186] | 2655 | def _parse_wn(self, wn): |
---|
| 2656 | if isinstance(wn, list) or isinstance(wn, tuple): |
---|
| 2657 | return wn |
---|
| 2658 | elif isinstance(wn, int): |
---|
| 2659 | return [ wn ] |
---|
| 2660 | elif isinstance(wn, str): |
---|
[2277] | 2661 | if '-' in wn: # case 'a-b' : return [a,a+1,...,b-1,b] |
---|
[2186] | 2662 | val = wn.split('-') |
---|
| 2663 | val = [int(val[0]), int(val[1])] |
---|
| 2664 | val.sort() |
---|
| 2665 | res = [i for i in xrange(val[0], val[1]+1)] |
---|
[2277] | 2666 | elif wn[:2] == '<=' or wn[:2] == '=<': # cases '<=a','=<a' : return [0,1,...,a-1,a] |
---|
[2186] | 2667 | val = int(wn[2:])+1 |
---|
| 2668 | res = [i for i in xrange(val)] |
---|
[2277] | 2669 | elif wn[-2:] == '>=' or wn[-2:] == '=>': # cases 'a>=','a=>' : return [0,1,...,a-1,a] |
---|
[2186] | 2670 | val = int(wn[:-2])+1 |
---|
| 2671 | res = [i for i in xrange(val)] |
---|
[2277] | 2672 | elif wn[0] == '<': # case '<a' : return [0,1,...,a-2,a-1] |
---|
[2186] | 2673 | val = int(wn[1:]) |
---|
| 2674 | res = [i for i in xrange(val)] |
---|
[2277] | 2675 | elif wn[-1] == '>': # case 'a>' : return [0,1,...,a-2,a-1] |
---|
[2186] | 2676 | val = int(wn[:-1]) |
---|
| 2677 | res = [i for i in xrange(val)] |
---|
[2411] | 2678 | elif wn[:2] == '>=' or wn[:2] == '=>': # cases '>=a','=>a' : return [a,-999], which is |
---|
| 2679 | # then interpreted in C++ |
---|
| 2680 | # side as [a,a+1,...,a_nyq] |
---|
| 2681 | # (CAS-3759) |
---|
[2186] | 2682 | val = int(wn[2:]) |
---|
[2411] | 2683 | res = [val, -999] |
---|
| 2684 | #res = [i for i in xrange(val, self.nchan()/2+1)] |
---|
| 2685 | elif wn[-2:] == '<=' or wn[-2:] == '=<': # cases 'a<=','a=<' : return [a,-999], which is |
---|
| 2686 | # then interpreted in C++ |
---|
| 2687 | # side as [a,a+1,...,a_nyq] |
---|
| 2688 | # (CAS-3759) |
---|
[2186] | 2689 | val = int(wn[:-2]) |
---|
[2411] | 2690 | res = [val, -999] |
---|
| 2691 | #res = [i for i in xrange(val, self.nchan()/2+1)] |
---|
| 2692 | elif wn[0] == '>': # case '>a' : return [a+1,-999], which is |
---|
| 2693 | # then interpreted in C++ |
---|
| 2694 | # side as [a+1,a+2,...,a_nyq] |
---|
| 2695 | # (CAS-3759) |
---|
[2186] | 2696 | val = int(wn[1:])+1 |
---|
[2411] | 2697 | res = [val, -999] |
---|
| 2698 | #res = [i for i in xrange(val, self.nchan()/2+1)] |
---|
| 2699 | elif wn[-1] == '<': # case 'a<' : return [a+1,-999], which is |
---|
| 2700 | # then interpreted in C++ |
---|
| 2701 | # side as [a+1,a+2,...,a_nyq] |
---|
| 2702 | # (CAS-3759) |
---|
[2186] | 2703 | val = int(wn[:-1])+1 |
---|
[2411] | 2704 | res = [val, -999] |
---|
| 2705 | #res = [i for i in xrange(val, self.nchan()/2+1)] |
---|
[2012] | 2706 | |
---|
[2186] | 2707 | return res |
---|
| 2708 | else: |
---|
| 2709 | msg = 'wrong value given for addwn/rejwn' |
---|
| 2710 | raise RuntimeError(msg) |
---|
| 2711 | |
---|
[2713] | 2712 | @asaplog_post_dec |
---|
[2810] | 2713 | def apply_bltable(self, insitu=None, retfitres=None, inbltable=None, outbltable=None, overwrite=None): |
---|
[2767] | 2714 | """\ |
---|
| 2715 | Subtract baseline based on parameters written in Baseline Table. |
---|
| 2716 | |
---|
| 2717 | Parameters: |
---|
[2809] | 2718 | insitu: if True, baseline fitting/subtraction is done |
---|
[2810] | 2719 | in-situ. If False, a new scantable with |
---|
| 2720 | baseline subtracted is returned. Actually, |
---|
| 2721 | format of the returned value depends on both |
---|
| 2722 | insitu and retfitres (see below). |
---|
[2767] | 2723 | The default is taken from .asaprc (False) |
---|
[2810] | 2724 | retfitres: if True, the results of baseline fitting (i.e., |
---|
| 2725 | coefficients and rms) are returned. |
---|
| 2726 | default is False. |
---|
| 2727 | The format of the returned value of this |
---|
| 2728 | function varies as follows: |
---|
| 2729 | (1) in case insitu=True and retfitres=True: |
---|
| 2730 | fitting result. |
---|
| 2731 | (2) in case insitu=True and retfitres=False: |
---|
| 2732 | None. |
---|
| 2733 | (3) in case insitu=False and retfitres=True: |
---|
| 2734 | a dictionary containing a new scantable |
---|
| 2735 | (with baseline subtracted) and the fitting |
---|
| 2736 | results. |
---|
| 2737 | (4) in case insitu=False and retfitres=False: |
---|
| 2738 | a new scantable (with baseline subtracted). |
---|
[2767] | 2739 | inbltable: name of input baseline table. The row number of |
---|
| 2740 | scantable and that of inbltable must be |
---|
| 2741 | identical. |
---|
| 2742 | outbltable: name of output baseline table where baseline |
---|
| 2743 | parameters and fitting results recorded. |
---|
| 2744 | default is ''(no output). |
---|
[2809] | 2745 | overwrite: if True when an existing baseline table is |
---|
| 2746 | specified for outbltable, overwrites it. |
---|
| 2747 | Otherwise there is no harm. |
---|
[2767] | 2748 | default is False. |
---|
| 2749 | """ |
---|
| 2750 | |
---|
| 2751 | try: |
---|
| 2752 | varlist = vars() |
---|
[2810] | 2753 | if retfitres is None: retfitres = False |
---|
[2767] | 2754 | if inbltable is None: raise ValueError("bltable missing.") |
---|
| 2755 | if outbltable is None: outbltable = '' |
---|
| 2756 | if overwrite is None: overwrite = False |
---|
| 2757 | |
---|
| 2758 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 2759 | if insitu: |
---|
| 2760 | workscan = self |
---|
| 2761 | else: |
---|
| 2762 | workscan = self.copy() |
---|
| 2763 | |
---|
| 2764 | sres = workscan._apply_bltable(inbltable, |
---|
[2810] | 2765 | retfitres, |
---|
[2767] | 2766 | outbltable, |
---|
| 2767 | os.path.exists(outbltable), |
---|
| 2768 | overwrite) |
---|
[2810] | 2769 | if retfitres: res = parse_fitresult(sres) |
---|
[2767] | 2770 | |
---|
| 2771 | workscan._add_history('apply_bltable', varlist) |
---|
| 2772 | |
---|
| 2773 | if insitu: |
---|
| 2774 | self._assign(workscan) |
---|
[2810] | 2775 | if retfitres: |
---|
| 2776 | return res |
---|
| 2777 | else: |
---|
| 2778 | return None |
---|
[2767] | 2779 | else: |
---|
[2810] | 2780 | if retfitres: |
---|
| 2781 | return {'scantable': workscan, 'fitresults': res} |
---|
| 2782 | else: |
---|
| 2783 | return workscan |
---|
[2767] | 2784 | |
---|
| 2785 | except RuntimeError, e: |
---|
| 2786 | raise_fitting_failure_exception(e) |
---|
| 2787 | |
---|
| 2788 | @asaplog_post_dec |
---|
[2810] | 2789 | def sub_baseline(self, insitu=None, retfitres=None, blinfo=None, bltable=None, overwrite=None): |
---|
[2767] | 2790 | """\ |
---|
| 2791 | Subtract baseline based on parameters written in the input list. |
---|
| 2792 | |
---|
| 2793 | Parameters: |
---|
[2809] | 2794 | insitu: if True, baseline fitting/subtraction is done |
---|
[2810] | 2795 | in-situ. If False, a new scantable with |
---|
| 2796 | baseline subtracted is returned. Actually, |
---|
| 2797 | format of the returned value depends on both |
---|
| 2798 | insitu and retfitres (see below). |
---|
[2767] | 2799 | The default is taken from .asaprc (False) |
---|
[2810] | 2800 | retfitres: if True, the results of baseline fitting (i.e., |
---|
| 2801 | coefficients and rms) are returned. |
---|
| 2802 | default is False. |
---|
| 2803 | The format of the returned value of this |
---|
| 2804 | function varies as follows: |
---|
| 2805 | (1) in case insitu=True and retfitres=True: |
---|
| 2806 | fitting result. |
---|
| 2807 | (2) in case insitu=True and retfitres=False: |
---|
| 2808 | None. |
---|
| 2809 | (3) in case insitu=False and retfitres=True: |
---|
| 2810 | a dictionary containing a new scantable |
---|
| 2811 | (with baseline subtracted) and the fitting |
---|
| 2812 | results. |
---|
| 2813 | (4) in case insitu=False and retfitres=False: |
---|
| 2814 | a new scantable (with baseline subtracted). |
---|
[2767] | 2815 | blinfo: baseline parameter set stored in a dictionary |
---|
| 2816 | or a list of dictionary. Each dictionary |
---|
| 2817 | corresponds to each spectrum and must contain |
---|
| 2818 | the following keys and values: |
---|
| 2819 | 'row': row number, |
---|
| 2820 | 'blfunc': function name. available ones include |
---|
| 2821 | 'poly', 'chebyshev', 'cspline' and |
---|
| 2822 | 'sinusoid', |
---|
| 2823 | 'order': maximum order of polynomial. needed |
---|
| 2824 | if blfunc='poly' or 'chebyshev', |
---|
| 2825 | 'npiece': number or piecewise polynomial. |
---|
| 2826 | needed if blfunc='cspline', |
---|
| 2827 | 'nwave': a list of sinusoidal wave numbers. |
---|
| 2828 | needed if blfunc='sinusoid', and |
---|
| 2829 | 'masklist': min-max windows for channel mask. |
---|
| 2830 | the specified ranges will be used |
---|
| 2831 | for fitting. |
---|
| 2832 | bltable: name of output baseline table where baseline |
---|
| 2833 | parameters and fitting results recorded. |
---|
| 2834 | default is ''(no output). |
---|
[2809] | 2835 | overwrite: if True when an existing baseline table is |
---|
| 2836 | specified for bltable, overwrites it. |
---|
| 2837 | Otherwise there is no harm. |
---|
[2767] | 2838 | default is False. |
---|
| 2839 | |
---|
| 2840 | Example: |
---|
| 2841 | sub_baseline(blinfo=[{'row':0, 'blfunc':'poly', 'order':5, |
---|
| 2842 | 'masklist':[[10,350],[352,510]]}, |
---|
| 2843 | {'row':1, 'blfunc':'cspline', 'npiece':3, |
---|
| 2844 | 'masklist':[[3,16],[19,404],[407,511]]} |
---|
| 2845 | ]) |
---|
| 2846 | |
---|
| 2847 | the first spectrum (row=0) will be fitted with polynomial |
---|
| 2848 | of order=5 and the next one (row=1) will be fitted with cubic |
---|
| 2849 | spline consisting of 3 pieces. |
---|
| 2850 | """ |
---|
| 2851 | |
---|
| 2852 | try: |
---|
| 2853 | varlist = vars() |
---|
[2810] | 2854 | if retfitres is None: retfitres = False |
---|
[2767] | 2855 | if blinfo is None: blinfo = [] |
---|
| 2856 | if bltable is None: bltable = '' |
---|
| 2857 | if overwrite is None: overwrite = False |
---|
| 2858 | |
---|
| 2859 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 2860 | if insitu: |
---|
| 2861 | workscan = self |
---|
| 2862 | else: |
---|
| 2863 | workscan = self.copy() |
---|
| 2864 | |
---|
| 2865 | nrow = workscan.nrow() |
---|
| 2866 | |
---|
| 2867 | in_blinfo = pack_blinfo(blinfo=blinfo, maxirow=nrow) |
---|
| 2868 | |
---|
| 2869 | print "in_blinfo=< "+ str(in_blinfo)+" >" |
---|
| 2870 | |
---|
| 2871 | sres = workscan._sub_baseline(in_blinfo, |
---|
[2810] | 2872 | retfitres, |
---|
[2767] | 2873 | bltable, |
---|
| 2874 | os.path.exists(bltable), |
---|
| 2875 | overwrite) |
---|
[2810] | 2876 | if retfitres: res = parse_fitresult(sres) |
---|
[2767] | 2877 | |
---|
| 2878 | workscan._add_history('sub_baseline', varlist) |
---|
| 2879 | |
---|
| 2880 | if insitu: |
---|
| 2881 | self._assign(workscan) |
---|
[2810] | 2882 | if retfitres: |
---|
| 2883 | return res |
---|
| 2884 | else: |
---|
| 2885 | return None |
---|
[2767] | 2886 | else: |
---|
[2810] | 2887 | if retfitres: |
---|
| 2888 | return {'scantable': workscan, 'fitresults': res} |
---|
| 2889 | else: |
---|
| 2890 | return workscan |
---|
[2767] | 2891 | |
---|
| 2892 | except RuntimeError, e: |
---|
| 2893 | raise_fitting_failure_exception(e) |
---|
| 2894 | |
---|
| 2895 | @asaplog_post_dec |
---|
[2713] | 2896 | def calc_aic(self, value=None, blfunc=None, order=None, mask=None, |
---|
| 2897 | whichrow=None, uselinefinder=None, edge=None, |
---|
| 2898 | threshold=None, chan_avg_limit=None): |
---|
| 2899 | """\ |
---|
| 2900 | Calculates and returns model selection criteria for a specified |
---|
| 2901 | baseline model and a given spectrum data. |
---|
| 2902 | Available values include Akaike Information Criterion (AIC), the |
---|
| 2903 | corrected Akaike Information Criterion (AICc) by Sugiura(1978), |
---|
| 2904 | Bayesian Information Criterion (BIC) and the Generalised Cross |
---|
| 2905 | Validation (GCV). |
---|
[2186] | 2906 | |
---|
[2713] | 2907 | Parameters: |
---|
| 2908 | value: name of model selection criteria to calculate. |
---|
| 2909 | available ones include 'aic', 'aicc', 'bic' and |
---|
| 2910 | 'gcv'. default is 'aicc'. |
---|
| 2911 | blfunc: baseline function name. available ones include |
---|
| 2912 | 'chebyshev', 'cspline' and 'sinusoid'. |
---|
| 2913 | default is 'chebyshev'. |
---|
| 2914 | order: parameter for basline function. actually stands for |
---|
| 2915 | order of polynomial (order) for 'chebyshev', |
---|
| 2916 | number of spline pieces (npiece) for 'cspline' and |
---|
| 2917 | maximum wave number for 'sinusoid', respectively. |
---|
| 2918 | default is 5 (which is also the default order value |
---|
| 2919 | for [auto_]chebyshev_baseline()). |
---|
| 2920 | mask: an optional mask. default is []. |
---|
| 2921 | whichrow: row number. default is 0 (the first row) |
---|
| 2922 | uselinefinder: use sd.linefinder() to flag out line regions |
---|
| 2923 | default is True. |
---|
| 2924 | edge: an optional number of channel to drop at |
---|
| 2925 | the edge of spectrum. If only one value is |
---|
| 2926 | specified, the same number will be dropped |
---|
| 2927 | from both sides of the spectrum. Default |
---|
| 2928 | is to keep all channels. Nested tuples |
---|
| 2929 | represent individual edge selection for |
---|
| 2930 | different IFs (a number of spectral channels |
---|
| 2931 | can be different) |
---|
| 2932 | default is (0, 0). |
---|
| 2933 | threshold: the threshold used by line finder. It is |
---|
| 2934 | better to keep it large as only strong lines |
---|
| 2935 | affect the baseline solution. |
---|
| 2936 | default is 3. |
---|
| 2937 | chan_avg_limit: a maximum number of consequtive spectral |
---|
| 2938 | channels to average during the search of |
---|
| 2939 | weak and broad lines. The default is no |
---|
| 2940 | averaging (and no search for weak lines). |
---|
| 2941 | If such lines can affect the fitted baseline |
---|
| 2942 | (e.g. a high order polynomial is fitted), |
---|
| 2943 | increase this parameter (usually values up |
---|
| 2944 | to 8 are reasonable). Most users of this |
---|
| 2945 | method should find the default value sufficient. |
---|
| 2946 | default is 1. |
---|
| 2947 | |
---|
| 2948 | Example: |
---|
| 2949 | aic = scan.calc_aic(blfunc='chebyshev', order=5, whichrow=0) |
---|
| 2950 | """ |
---|
| 2951 | |
---|
| 2952 | try: |
---|
| 2953 | varlist = vars() |
---|
| 2954 | |
---|
| 2955 | if value is None: value = 'aicc' |
---|
| 2956 | if blfunc is None: blfunc = 'chebyshev' |
---|
| 2957 | if order is None: order = 5 |
---|
| 2958 | if mask is None: mask = [] |
---|
| 2959 | if whichrow is None: whichrow = 0 |
---|
| 2960 | if uselinefinder is None: uselinefinder = True |
---|
| 2961 | if edge is None: edge = (0, 0) |
---|
| 2962 | if threshold is None: threshold = 3 |
---|
| 2963 | if chan_avg_limit is None: chan_avg_limit = 1 |
---|
| 2964 | |
---|
| 2965 | return self._calc_aic(value, blfunc, order, mask, |
---|
| 2966 | whichrow, uselinefinder, edge, |
---|
| 2967 | threshold, chan_avg_limit) |
---|
| 2968 | |
---|
| 2969 | except RuntimeError, e: |
---|
| 2970 | raise_fitting_failure_exception(e) |
---|
| 2971 | |
---|
[1862] | 2972 | @asaplog_post_dec |
---|
[2771] | 2973 | def sinusoid_baseline(self, mask=None, applyfft=None, |
---|
[2269] | 2974 | fftmethod=None, fftthresh=None, |
---|
[2771] | 2975 | addwn=None, rejwn=None, |
---|
| 2976 | insitu=None, |
---|
| 2977 | clipthresh=None, clipniter=None, |
---|
| 2978 | plot=None, |
---|
| 2979 | getresidual=None, |
---|
| 2980 | showprogress=None, minnrow=None, |
---|
| 2981 | outlog=None, |
---|
[2767] | 2982 | blfile=None, csvformat=None, |
---|
| 2983 | bltable=None): |
---|
[2047] | 2984 | """\ |
---|
[2349] | 2985 | Return a scan which has been baselined (all rows) with sinusoidal |
---|
| 2986 | functions. |
---|
| 2987 | |
---|
[2047] | 2988 | Parameters: |
---|
[2186] | 2989 | mask: an optional mask |
---|
| 2990 | applyfft: if True use some method, such as FFT, to find |
---|
| 2991 | strongest sinusoidal components in the wavenumber |
---|
| 2992 | domain to be used for baseline fitting. |
---|
| 2993 | default is True. |
---|
| 2994 | fftmethod: method to find the strong sinusoidal components. |
---|
| 2995 | now only 'fft' is available and it is the default. |
---|
| 2996 | fftthresh: the threshold to select wave numbers to be used for |
---|
| 2997 | fitting from the distribution of amplitudes in the |
---|
| 2998 | wavenumber domain. |
---|
| 2999 | both float and string values accepted. |
---|
| 3000 | given a float value, the unit is set to sigma. |
---|
| 3001 | for string values, allowed formats include: |
---|
[2349] | 3002 | 'xsigma' or 'x' (= x-sigma level. e.g., |
---|
| 3003 | '3sigma'), or |
---|
[2186] | 3004 | 'topx' (= the x strongest ones, e.g. 'top5'). |
---|
| 3005 | default is 3.0 (unit: sigma). |
---|
| 3006 | addwn: the additional wave numbers to be used for fitting. |
---|
| 3007 | list or integer value is accepted to specify every |
---|
| 3008 | wave numbers. also string value can be used in case |
---|
| 3009 | you need to specify wave numbers in a certain range, |
---|
| 3010 | e.g., 'a-b' (= a, a+1, a+2, ..., b-1, b), |
---|
| 3011 | '<a' (= 0,1,...,a-2,a-1), |
---|
| 3012 | '>=a' (= a, a+1, ... up to the maximum wave |
---|
| 3013 | number corresponding to the Nyquist |
---|
| 3014 | frequency for the case of FFT). |
---|
[2411] | 3015 | default is [0]. |
---|
[2186] | 3016 | rejwn: the wave numbers NOT to be used for fitting. |
---|
| 3017 | can be set just as addwn but has higher priority: |
---|
| 3018 | wave numbers which are specified both in addwn |
---|
| 3019 | and rejwn will NOT be used. default is []. |
---|
[2771] | 3020 | insitu: if False a new scantable is returned. |
---|
| 3021 | Otherwise, the scaling is done in-situ |
---|
| 3022 | The default is taken from .asaprc (False) |
---|
[2081] | 3023 | clipthresh: Clipping threshold. (default is 3.0, unit: sigma) |
---|
[2349] | 3024 | clipniter: maximum number of iteration of 'clipthresh'-sigma |
---|
| 3025 | clipping (default is 0) |
---|
[2081] | 3026 | plot: *** CURRENTLY UNAVAILABLE, ALWAYS FALSE *** |
---|
| 3027 | plot the fit and the residual. In this each |
---|
| 3028 | indivual fit has to be approved, by typing 'y' |
---|
| 3029 | or 'n' |
---|
| 3030 | getresidual: if False, returns best-fit values instead of |
---|
| 3031 | residual. (default is True) |
---|
[2189] | 3032 | showprogress: show progress status for large data. |
---|
| 3033 | default is True. |
---|
| 3034 | minnrow: minimum number of input spectra to show. |
---|
| 3035 | default is 1000. |
---|
[2081] | 3036 | outlog: Output the coefficients of the best-fit |
---|
| 3037 | function to logger (default is False) |
---|
| 3038 | blfile: Name of a text file in which the best-fit |
---|
| 3039 | parameter values to be written |
---|
[2186] | 3040 | (default is '': no file/logger output) |
---|
[2641] | 3041 | csvformat: if True blfile is csv-formatted, default is False. |
---|
[2767] | 3042 | bltable: name of a baseline table where fitting results |
---|
| 3043 | (coefficients, rms, etc.) are to be written. |
---|
| 3044 | if given, fitting results will NOT be output to |
---|
| 3045 | scantable (insitu=True) or None will be |
---|
| 3046 | returned (insitu=False). |
---|
| 3047 | (default is "": no table output) |
---|
[2047] | 3048 | |
---|
| 3049 | Example: |
---|
[2349] | 3050 | # return a scan baselined by a combination of sinusoidal curves |
---|
| 3051 | # having wave numbers in spectral window up to 10, |
---|
[2047] | 3052 | # also with 3-sigma clipping, iteration up to 4 times |
---|
[2186] | 3053 | bscan = scan.sinusoid_baseline(addwn='<=10',clipthresh=3.0,clipniter=4) |
---|
[2081] | 3054 | |
---|
| 3055 | Note: |
---|
| 3056 | The best-fit parameter values output in logger and/or blfile are now |
---|
| 3057 | based on specunit of 'channel'. |
---|
[2047] | 3058 | """ |
---|
| 3059 | |
---|
[2186] | 3060 | try: |
---|
| 3061 | varlist = vars() |
---|
[2047] | 3062 | |
---|
[2186] | 3063 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 3064 | if insitu: |
---|
| 3065 | workscan = self |
---|
| 3066 | else: |
---|
| 3067 | workscan = self.copy() |
---|
| 3068 | |
---|
[2410] | 3069 | if mask is None: mask = [] |
---|
[2186] | 3070 | if applyfft is None: applyfft = True |
---|
| 3071 | if fftmethod is None: fftmethod = 'fft' |
---|
| 3072 | if fftthresh is None: fftthresh = 3.0 |
---|
[2411] | 3073 | if addwn is None: addwn = [0] |
---|
[2186] | 3074 | if rejwn is None: rejwn = [] |
---|
| 3075 | if clipthresh is None: clipthresh = 3.0 |
---|
| 3076 | if clipniter is None: clipniter = 0 |
---|
| 3077 | if plot is None: plot = False |
---|
| 3078 | if getresidual is None: getresidual = True |
---|
[2189] | 3079 | if showprogress is None: showprogress = True |
---|
| 3080 | if minnrow is None: minnrow = 1000 |
---|
[2186] | 3081 | if outlog is None: outlog = False |
---|
| 3082 | if blfile is None: blfile = '' |
---|
[2641] | 3083 | if csvformat is None: csvformat = False |
---|
[2767] | 3084 | if bltable is None: bltable = '' |
---|
[2047] | 3085 | |
---|
[2767] | 3086 | sapplyfft = 'true' if applyfft else 'false' |
---|
| 3087 | fftinfo = ','.join([sapplyfft, fftmethod.lower(), str(fftthresh).lower()]) |
---|
[2641] | 3088 | |
---|
[2767] | 3089 | scsvformat = 'T' if csvformat else 'F' |
---|
| 3090 | |
---|
[2081] | 3091 | #CURRENTLY, PLOT=true is UNAVAILABLE UNTIL sinusoidal fitting is implemented as a fitter method. |
---|
[2767] | 3092 | workscan._sinusoid_baseline(mask, |
---|
| 3093 | fftinfo, |
---|
| 3094 | #applyfft, fftmethod.lower(), |
---|
| 3095 | #str(fftthresh).lower(), |
---|
[2349] | 3096 | workscan._parse_wn(addwn), |
---|
[2643] | 3097 | workscan._parse_wn(rejwn), |
---|
| 3098 | clipthresh, clipniter, |
---|
| 3099 | getresidual, |
---|
[2349] | 3100 | pack_progress_params(showprogress, |
---|
[2641] | 3101 | minnrow), |
---|
[2767] | 3102 | outlog, scsvformat+blfile, |
---|
| 3103 | bltable) |
---|
[2186] | 3104 | workscan._add_history('sinusoid_baseline', varlist) |
---|
[2767] | 3105 | |
---|
| 3106 | if bltable == '': |
---|
| 3107 | if insitu: |
---|
| 3108 | self._assign(workscan) |
---|
| 3109 | else: |
---|
| 3110 | return workscan |
---|
[2047] | 3111 | else: |
---|
[2767] | 3112 | if not insitu: |
---|
| 3113 | return None |
---|
[2047] | 3114 | |
---|
| 3115 | except RuntimeError, e: |
---|
[2186] | 3116 | raise_fitting_failure_exception(e) |
---|
[2047] | 3117 | |
---|
| 3118 | |
---|
[2186] | 3119 | @asaplog_post_dec |
---|
[2771] | 3120 | def auto_sinusoid_baseline(self, mask=None, applyfft=None, |
---|
[2349] | 3121 | fftmethod=None, fftthresh=None, |
---|
[2771] | 3122 | addwn=None, rejwn=None, |
---|
| 3123 | insitu=None, |
---|
| 3124 | clipthresh=None, clipniter=None, |
---|
| 3125 | edge=None, threshold=None, chan_avg_limit=None, |
---|
| 3126 | plot=None, |
---|
| 3127 | getresidual=None, |
---|
| 3128 | showprogress=None, minnrow=None, |
---|
| 3129 | outlog=None, |
---|
[2767] | 3130 | blfile=None, csvformat=None, |
---|
| 3131 | bltable=None): |
---|
[2047] | 3132 | """\ |
---|
[2349] | 3133 | Return a scan which has been baselined (all rows) with sinusoidal |
---|
| 3134 | functions. |
---|
[2047] | 3135 | Spectral lines are detected first using linefinder and masked out |
---|
| 3136 | to avoid them affecting the baseline solution. |
---|
| 3137 | |
---|
| 3138 | Parameters: |
---|
[2189] | 3139 | mask: an optional mask retreived from scantable |
---|
| 3140 | applyfft: if True use some method, such as FFT, to find |
---|
| 3141 | strongest sinusoidal components in the wavenumber |
---|
| 3142 | domain to be used for baseline fitting. |
---|
| 3143 | default is True. |
---|
| 3144 | fftmethod: method to find the strong sinusoidal components. |
---|
| 3145 | now only 'fft' is available and it is the default. |
---|
| 3146 | fftthresh: the threshold to select wave numbers to be used for |
---|
| 3147 | fitting from the distribution of amplitudes in the |
---|
| 3148 | wavenumber domain. |
---|
| 3149 | both float and string values accepted. |
---|
| 3150 | given a float value, the unit is set to sigma. |
---|
| 3151 | for string values, allowed formats include: |
---|
[2349] | 3152 | 'xsigma' or 'x' (= x-sigma level. e.g., |
---|
| 3153 | '3sigma'), or |
---|
[2189] | 3154 | 'topx' (= the x strongest ones, e.g. 'top5'). |
---|
| 3155 | default is 3.0 (unit: sigma). |
---|
| 3156 | addwn: the additional wave numbers to be used for fitting. |
---|
| 3157 | list or integer value is accepted to specify every |
---|
| 3158 | wave numbers. also string value can be used in case |
---|
| 3159 | you need to specify wave numbers in a certain range, |
---|
| 3160 | e.g., 'a-b' (= a, a+1, a+2, ..., b-1, b), |
---|
| 3161 | '<a' (= 0,1,...,a-2,a-1), |
---|
| 3162 | '>=a' (= a, a+1, ... up to the maximum wave |
---|
| 3163 | number corresponding to the Nyquist |
---|
| 3164 | frequency for the case of FFT). |
---|
[2411] | 3165 | default is [0]. |
---|
[2189] | 3166 | rejwn: the wave numbers NOT to be used for fitting. |
---|
| 3167 | can be set just as addwn but has higher priority: |
---|
| 3168 | wave numbers which are specified both in addwn |
---|
| 3169 | and rejwn will NOT be used. default is []. |
---|
[2771] | 3170 | insitu: if False a new scantable is returned. |
---|
| 3171 | Otherwise, the scaling is done in-situ |
---|
| 3172 | The default is taken from .asaprc (False) |
---|
[2189] | 3173 | clipthresh: Clipping threshold. (default is 3.0, unit: sigma) |
---|
[2349] | 3174 | clipniter: maximum number of iteration of 'clipthresh'-sigma |
---|
| 3175 | clipping (default is 0) |
---|
[2189] | 3176 | edge: an optional number of channel to drop at |
---|
| 3177 | the edge of spectrum. If only one value is |
---|
| 3178 | specified, the same number will be dropped |
---|
| 3179 | from both sides of the spectrum. Default |
---|
| 3180 | is to keep all channels. Nested tuples |
---|
| 3181 | represent individual edge selection for |
---|
| 3182 | different IFs (a number of spectral channels |
---|
| 3183 | can be different) |
---|
| 3184 | threshold: the threshold used by line finder. It is |
---|
| 3185 | better to keep it large as only strong lines |
---|
| 3186 | affect the baseline solution. |
---|
| 3187 | chan_avg_limit: a maximum number of consequtive spectral |
---|
| 3188 | channels to average during the search of |
---|
| 3189 | weak and broad lines. The default is no |
---|
| 3190 | averaging (and no search for weak lines). |
---|
| 3191 | If such lines can affect the fitted baseline |
---|
| 3192 | (e.g. a high order polynomial is fitted), |
---|
| 3193 | increase this parameter (usually values up |
---|
| 3194 | to 8 are reasonable). Most users of this |
---|
| 3195 | method should find the default value sufficient. |
---|
| 3196 | plot: *** CURRENTLY UNAVAILABLE, ALWAYS FALSE *** |
---|
| 3197 | plot the fit and the residual. In this each |
---|
| 3198 | indivual fit has to be approved, by typing 'y' |
---|
| 3199 | or 'n' |
---|
| 3200 | getresidual: if False, returns best-fit values instead of |
---|
| 3201 | residual. (default is True) |
---|
| 3202 | showprogress: show progress status for large data. |
---|
| 3203 | default is True. |
---|
| 3204 | minnrow: minimum number of input spectra to show. |
---|
| 3205 | default is 1000. |
---|
| 3206 | outlog: Output the coefficients of the best-fit |
---|
| 3207 | function to logger (default is False) |
---|
| 3208 | blfile: Name of a text file in which the best-fit |
---|
| 3209 | parameter values to be written |
---|
| 3210 | (default is "": no file/logger output) |
---|
[2641] | 3211 | csvformat: if True blfile is csv-formatted, default is False. |
---|
[2767] | 3212 | bltable: name of a baseline table where fitting results |
---|
| 3213 | (coefficients, rms, etc.) are to be written. |
---|
| 3214 | if given, fitting results will NOT be output to |
---|
| 3215 | scantable (insitu=True) or None will be |
---|
| 3216 | returned (insitu=False). |
---|
| 3217 | (default is "": no table output) |
---|
[2047] | 3218 | |
---|
| 3219 | Example: |
---|
[2186] | 3220 | bscan = scan.auto_sinusoid_baseline(addwn='<=10', insitu=False) |
---|
[2081] | 3221 | |
---|
| 3222 | Note: |
---|
| 3223 | The best-fit parameter values output in logger and/or blfile are now |
---|
| 3224 | based on specunit of 'channel'. |
---|
[2047] | 3225 | """ |
---|
| 3226 | |
---|
[2186] | 3227 | try: |
---|
| 3228 | varlist = vars() |
---|
[2047] | 3229 | |
---|
[2186] | 3230 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 3231 | if insitu: |
---|
| 3232 | workscan = self |
---|
[2047] | 3233 | else: |
---|
[2186] | 3234 | workscan = self.copy() |
---|
| 3235 | |
---|
[2410] | 3236 | if mask is None: mask = [] |
---|
[2186] | 3237 | if applyfft is None: applyfft = True |
---|
| 3238 | if fftmethod is None: fftmethod = 'fft' |
---|
| 3239 | if fftthresh is None: fftthresh = 3.0 |
---|
[2411] | 3240 | if addwn is None: addwn = [0] |
---|
[2186] | 3241 | if rejwn is None: rejwn = [] |
---|
| 3242 | if clipthresh is None: clipthresh = 3.0 |
---|
| 3243 | if clipniter is None: clipniter = 0 |
---|
| 3244 | if edge is None: edge = (0,0) |
---|
| 3245 | if threshold is None: threshold = 3 |
---|
| 3246 | if chan_avg_limit is None: chan_avg_limit = 1 |
---|
| 3247 | if plot is None: plot = False |
---|
| 3248 | if getresidual is None: getresidual = True |
---|
[2189] | 3249 | if showprogress is None: showprogress = True |
---|
| 3250 | if minnrow is None: minnrow = 1000 |
---|
[2186] | 3251 | if outlog is None: outlog = False |
---|
| 3252 | if blfile is None: blfile = '' |
---|
[2641] | 3253 | if csvformat is None: csvformat = False |
---|
[2767] | 3254 | if bltable is None: bltable = '' |
---|
[2047] | 3255 | |
---|
[2767] | 3256 | sapplyfft = 'true' if applyfft else 'false' |
---|
| 3257 | fftinfo = ','.join([sapplyfft, fftmethod.lower(), str(fftthresh).lower()]) |
---|
[2641] | 3258 | |
---|
[2767] | 3259 | scsvformat = 'T' if csvformat else 'F' |
---|
| 3260 | |
---|
[2277] | 3261 | #CURRENTLY, PLOT=true is UNAVAILABLE UNTIL sinusoidal fitting is implemented as a fitter method. |
---|
[2767] | 3262 | workscan._auto_sinusoid_baseline(mask, |
---|
| 3263 | fftinfo, |
---|
[2349] | 3264 | workscan._parse_wn(addwn), |
---|
| 3265 | workscan._parse_wn(rejwn), |
---|
| 3266 | clipthresh, clipniter, |
---|
| 3267 | normalise_edge_param(edge), |
---|
| 3268 | threshold, chan_avg_limit, |
---|
| 3269 | getresidual, |
---|
| 3270 | pack_progress_params(showprogress, |
---|
| 3271 | minnrow), |
---|
[2767] | 3272 | outlog, scsvformat+blfile, bltable) |
---|
[2047] | 3273 | workscan._add_history("auto_sinusoid_baseline", varlist) |
---|
[2767] | 3274 | |
---|
| 3275 | if bltable == '': |
---|
| 3276 | if insitu: |
---|
| 3277 | self._assign(workscan) |
---|
| 3278 | else: |
---|
| 3279 | return workscan |
---|
[2047] | 3280 | else: |
---|
[2767] | 3281 | if not insitu: |
---|
| 3282 | return None |
---|
[2047] | 3283 | |
---|
| 3284 | except RuntimeError, e: |
---|
[2186] | 3285 | raise_fitting_failure_exception(e) |
---|
[2047] | 3286 | |
---|
| 3287 | @asaplog_post_dec |
---|
[2771] | 3288 | def cspline_baseline(self, mask=None, npiece=None, insitu=None, |
---|
[2349] | 3289 | clipthresh=None, clipniter=None, plot=None, |
---|
| 3290 | getresidual=None, showprogress=None, minnrow=None, |
---|
[2767] | 3291 | outlog=None, blfile=None, csvformat=None, |
---|
| 3292 | bltable=None): |
---|
[1846] | 3293 | """\ |
---|
[2349] | 3294 | Return a scan which has been baselined (all rows) by cubic spline |
---|
| 3295 | function (piecewise cubic polynomial). |
---|
| 3296 | |
---|
[513] | 3297 | Parameters: |
---|
[2771] | 3298 | mask: An optional mask |
---|
| 3299 | npiece: Number of pieces. (default is 2) |
---|
[2189] | 3300 | insitu: If False a new scantable is returned. |
---|
| 3301 | Otherwise, the scaling is done in-situ |
---|
| 3302 | The default is taken from .asaprc (False) |
---|
| 3303 | clipthresh: Clipping threshold. (default is 3.0, unit: sigma) |
---|
[2349] | 3304 | clipniter: maximum number of iteration of 'clipthresh'-sigma |
---|
| 3305 | clipping (default is 0) |
---|
[2189] | 3306 | plot: *** CURRENTLY UNAVAILABLE, ALWAYS FALSE *** |
---|
| 3307 | plot the fit and the residual. In this each |
---|
| 3308 | indivual fit has to be approved, by typing 'y' |
---|
| 3309 | or 'n' |
---|
| 3310 | getresidual: if False, returns best-fit values instead of |
---|
| 3311 | residual. (default is True) |
---|
| 3312 | showprogress: show progress status for large data. |
---|
| 3313 | default is True. |
---|
| 3314 | minnrow: minimum number of input spectra to show. |
---|
| 3315 | default is 1000. |
---|
| 3316 | outlog: Output the coefficients of the best-fit |
---|
| 3317 | function to logger (default is False) |
---|
| 3318 | blfile: Name of a text file in which the best-fit |
---|
| 3319 | parameter values to be written |
---|
| 3320 | (default is "": no file/logger output) |
---|
[2641] | 3321 | csvformat: if True blfile is csv-formatted, default is False. |
---|
[2767] | 3322 | bltable: name of a baseline table where fitting results |
---|
| 3323 | (coefficients, rms, etc.) are to be written. |
---|
| 3324 | if given, fitting results will NOT be output to |
---|
| 3325 | scantable (insitu=True) or None will be |
---|
| 3326 | returned (insitu=False). |
---|
| 3327 | (default is "": no table output) |
---|
[1846] | 3328 | |
---|
[2012] | 3329 | Example: |
---|
[2349] | 3330 | # return a scan baselined by a cubic spline consisting of 2 pieces |
---|
| 3331 | # (i.e., 1 internal knot), |
---|
[2012] | 3332 | # also with 3-sigma clipping, iteration up to 4 times |
---|
| 3333 | bscan = scan.cspline_baseline(npiece=2,clipthresh=3.0,clipniter=4) |
---|
[2081] | 3334 | |
---|
| 3335 | Note: |
---|
| 3336 | The best-fit parameter values output in logger and/or blfile are now |
---|
| 3337 | based on specunit of 'channel'. |
---|
[2012] | 3338 | """ |
---|
| 3339 | |
---|
[2186] | 3340 | try: |
---|
| 3341 | varlist = vars() |
---|
| 3342 | |
---|
| 3343 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 3344 | if insitu: |
---|
| 3345 | workscan = self |
---|
| 3346 | else: |
---|
| 3347 | workscan = self.copy() |
---|
[1855] | 3348 | |
---|
[2410] | 3349 | if mask is None: mask = [] |
---|
[2189] | 3350 | if npiece is None: npiece = 2 |
---|
| 3351 | if clipthresh is None: clipthresh = 3.0 |
---|
| 3352 | if clipniter is None: clipniter = 0 |
---|
| 3353 | if plot is None: plot = False |
---|
| 3354 | if getresidual is None: getresidual = True |
---|
| 3355 | if showprogress is None: showprogress = True |
---|
| 3356 | if minnrow is None: minnrow = 1000 |
---|
| 3357 | if outlog is None: outlog = False |
---|
| 3358 | if blfile is None: blfile = '' |
---|
[2767] | 3359 | if csvformat is None: csvformat = False |
---|
| 3360 | if bltable is None: bltable = '' |
---|
[1855] | 3361 | |
---|
[2767] | 3362 | scsvformat = 'T' if csvformat else 'F' |
---|
[2641] | 3363 | |
---|
[2012] | 3364 | #CURRENTLY, PLOT=true UNAVAILABLE UNTIL cubic spline fitting is implemented as a fitter method. |
---|
[2767] | 3365 | workscan._cspline_baseline(mask, npiece, |
---|
| 3366 | clipthresh, clipniter, |
---|
[2349] | 3367 | getresidual, |
---|
| 3368 | pack_progress_params(showprogress, |
---|
[2641] | 3369 | minnrow), |
---|
[2767] | 3370 | outlog, scsvformat+blfile, |
---|
| 3371 | bltable) |
---|
[2012] | 3372 | workscan._add_history("cspline_baseline", varlist) |
---|
[2767] | 3373 | |
---|
| 3374 | if bltable == '': |
---|
| 3375 | if insitu: |
---|
| 3376 | self._assign(workscan) |
---|
| 3377 | else: |
---|
| 3378 | return workscan |
---|
[2012] | 3379 | else: |
---|
[2767] | 3380 | if not insitu: |
---|
| 3381 | return None |
---|
[2012] | 3382 | |
---|
| 3383 | except RuntimeError, e: |
---|
[2186] | 3384 | raise_fitting_failure_exception(e) |
---|
[1855] | 3385 | |
---|
[2186] | 3386 | @asaplog_post_dec |
---|
[2771] | 3387 | def auto_cspline_baseline(self, mask=None, npiece=None, insitu=None, |
---|
[2349] | 3388 | clipthresh=None, clipniter=None, |
---|
| 3389 | edge=None, threshold=None, chan_avg_limit=None, |
---|
| 3390 | getresidual=None, plot=None, |
---|
| 3391 | showprogress=None, minnrow=None, outlog=None, |
---|
[2767] | 3392 | blfile=None, csvformat=None, bltable=None): |
---|
[2012] | 3393 | """\ |
---|
| 3394 | Return a scan which has been baselined (all rows) by cubic spline |
---|
| 3395 | function (piecewise cubic polynomial). |
---|
| 3396 | Spectral lines are detected first using linefinder and masked out |
---|
| 3397 | to avoid them affecting the baseline solution. |
---|
| 3398 | |
---|
| 3399 | Parameters: |
---|
[2771] | 3400 | mask: an optional mask retreived from scantable |
---|
| 3401 | npiece: Number of pieces. (default is 2) |
---|
[2189] | 3402 | insitu: if False a new scantable is returned. |
---|
| 3403 | Otherwise, the scaling is done in-situ |
---|
| 3404 | The default is taken from .asaprc (False) |
---|
| 3405 | clipthresh: Clipping threshold. (default is 3.0, unit: sigma) |
---|
[2349] | 3406 | clipniter: maximum number of iteration of 'clipthresh'-sigma |
---|
| 3407 | clipping (default is 0) |
---|
[2189] | 3408 | edge: an optional number of channel to drop at |
---|
| 3409 | the edge of spectrum. If only one value is |
---|
| 3410 | specified, the same number will be dropped |
---|
| 3411 | from both sides of the spectrum. Default |
---|
| 3412 | is to keep all channels. Nested tuples |
---|
| 3413 | represent individual edge selection for |
---|
| 3414 | different IFs (a number of spectral channels |
---|
| 3415 | can be different) |
---|
| 3416 | threshold: the threshold used by line finder. It is |
---|
| 3417 | better to keep it large as only strong lines |
---|
| 3418 | affect the baseline solution. |
---|
| 3419 | chan_avg_limit: a maximum number of consequtive spectral |
---|
| 3420 | channels to average during the search of |
---|
| 3421 | weak and broad lines. The default is no |
---|
| 3422 | averaging (and no search for weak lines). |
---|
| 3423 | If such lines can affect the fitted baseline |
---|
| 3424 | (e.g. a high order polynomial is fitted), |
---|
| 3425 | increase this parameter (usually values up |
---|
| 3426 | to 8 are reasonable). Most users of this |
---|
| 3427 | method should find the default value sufficient. |
---|
| 3428 | plot: *** CURRENTLY UNAVAILABLE, ALWAYS FALSE *** |
---|
| 3429 | plot the fit and the residual. In this each |
---|
| 3430 | indivual fit has to be approved, by typing 'y' |
---|
| 3431 | or 'n' |
---|
| 3432 | getresidual: if False, returns best-fit values instead of |
---|
| 3433 | residual. (default is True) |
---|
| 3434 | showprogress: show progress status for large data. |
---|
| 3435 | default is True. |
---|
| 3436 | minnrow: minimum number of input spectra to show. |
---|
| 3437 | default is 1000. |
---|
| 3438 | outlog: Output the coefficients of the best-fit |
---|
| 3439 | function to logger (default is False) |
---|
| 3440 | blfile: Name of a text file in which the best-fit |
---|
| 3441 | parameter values to be written |
---|
| 3442 | (default is "": no file/logger output) |
---|
[2641] | 3443 | csvformat: if True blfile is csv-formatted, default is False. |
---|
[2767] | 3444 | bltable: name of a baseline table where fitting results |
---|
| 3445 | (coefficients, rms, etc.) are to be written. |
---|
| 3446 | if given, fitting results will NOT be output to |
---|
| 3447 | scantable (insitu=True) or None will be |
---|
| 3448 | returned (insitu=False). |
---|
| 3449 | (default is "": no table output) |
---|
[1846] | 3450 | |
---|
[1907] | 3451 | Example: |
---|
[2012] | 3452 | bscan = scan.auto_cspline_baseline(npiece=3, insitu=False) |
---|
[2081] | 3453 | |
---|
| 3454 | Note: |
---|
| 3455 | The best-fit parameter values output in logger and/or blfile are now |
---|
| 3456 | based on specunit of 'channel'. |
---|
[2012] | 3457 | """ |
---|
[1846] | 3458 | |
---|
[2186] | 3459 | try: |
---|
| 3460 | varlist = vars() |
---|
[2012] | 3461 | |
---|
[2186] | 3462 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 3463 | if insitu: |
---|
| 3464 | workscan = self |
---|
[1391] | 3465 | else: |
---|
[2186] | 3466 | workscan = self.copy() |
---|
| 3467 | |
---|
[2410] | 3468 | #if mask is None: mask = [True for i in xrange(workscan.nchan())] |
---|
| 3469 | if mask is None: mask = [] |
---|
[2186] | 3470 | if npiece is None: npiece = 2 |
---|
| 3471 | if clipthresh is None: clipthresh = 3.0 |
---|
| 3472 | if clipniter is None: clipniter = 0 |
---|
| 3473 | if edge is None: edge = (0, 0) |
---|
| 3474 | if threshold is None: threshold = 3 |
---|
| 3475 | if chan_avg_limit is None: chan_avg_limit = 1 |
---|
| 3476 | if plot is None: plot = False |
---|
| 3477 | if getresidual is None: getresidual = True |
---|
[2189] | 3478 | if showprogress is None: showprogress = True |
---|
| 3479 | if minnrow is None: minnrow = 1000 |
---|
[2186] | 3480 | if outlog is None: outlog = False |
---|
| 3481 | if blfile is None: blfile = '' |
---|
[2641] | 3482 | if csvformat is None: csvformat = False |
---|
[2767] | 3483 | if bltable is None: bltable = '' |
---|
[1819] | 3484 | |
---|
[2767] | 3485 | scsvformat = 'T' if csvformat else 'F' |
---|
[2641] | 3486 | |
---|
[2277] | 3487 | #CURRENTLY, PLOT=true UNAVAILABLE UNTIL cubic spline fitting is implemented as a fitter method. |
---|
[2767] | 3488 | workscan._auto_cspline_baseline(mask, npiece, |
---|
| 3489 | clipthresh, clipniter, |
---|
[2269] | 3490 | normalise_edge_param(edge), |
---|
| 3491 | threshold, |
---|
| 3492 | chan_avg_limit, getresidual, |
---|
| 3493 | pack_progress_params(showprogress, |
---|
| 3494 | minnrow), |
---|
[2767] | 3495 | outlog, |
---|
| 3496 | scsvformat+blfile, |
---|
| 3497 | bltable) |
---|
[2012] | 3498 | workscan._add_history("auto_cspline_baseline", varlist) |
---|
[2767] | 3499 | |
---|
| 3500 | if bltable == '': |
---|
| 3501 | if insitu: |
---|
| 3502 | self._assign(workscan) |
---|
| 3503 | else: |
---|
| 3504 | return workscan |
---|
[1856] | 3505 | else: |
---|
[2767] | 3506 | if not insitu: |
---|
| 3507 | return None |
---|
[2012] | 3508 | |
---|
| 3509 | except RuntimeError, e: |
---|
[2186] | 3510 | raise_fitting_failure_exception(e) |
---|
[513] | 3511 | |
---|
[1931] | 3512 | @asaplog_post_dec |
---|
[2771] | 3513 | def chebyshev_baseline(self, mask=None, order=None, insitu=None, |
---|
[2645] | 3514 | clipthresh=None, clipniter=None, plot=None, |
---|
| 3515 | getresidual=None, showprogress=None, minnrow=None, |
---|
[2767] | 3516 | outlog=None, blfile=None, csvformat=None, |
---|
| 3517 | bltable=None): |
---|
[2645] | 3518 | """\ |
---|
| 3519 | Return a scan which has been baselined (all rows) by Chebyshev polynomials. |
---|
| 3520 | |
---|
| 3521 | Parameters: |
---|
[2771] | 3522 | mask: An optional mask |
---|
| 3523 | order: the maximum order of Chebyshev polynomial (default is 5) |
---|
[2645] | 3524 | insitu: If False a new scantable is returned. |
---|
| 3525 | Otherwise, the scaling is done in-situ |
---|
| 3526 | The default is taken from .asaprc (False) |
---|
| 3527 | clipthresh: Clipping threshold. (default is 3.0, unit: sigma) |
---|
| 3528 | clipniter: maximum number of iteration of 'clipthresh'-sigma |
---|
| 3529 | clipping (default is 0) |
---|
| 3530 | plot: *** CURRENTLY UNAVAILABLE, ALWAYS FALSE *** |
---|
| 3531 | plot the fit and the residual. In this each |
---|
| 3532 | indivual fit has to be approved, by typing 'y' |
---|
| 3533 | or 'n' |
---|
| 3534 | getresidual: if False, returns best-fit values instead of |
---|
| 3535 | residual. (default is True) |
---|
| 3536 | showprogress: show progress status for large data. |
---|
| 3537 | default is True. |
---|
| 3538 | minnrow: minimum number of input spectra to show. |
---|
| 3539 | default is 1000. |
---|
| 3540 | outlog: Output the coefficients of the best-fit |
---|
| 3541 | function to logger (default is False) |
---|
| 3542 | blfile: Name of a text file in which the best-fit |
---|
| 3543 | parameter values to be written |
---|
| 3544 | (default is "": no file/logger output) |
---|
| 3545 | csvformat: if True blfile is csv-formatted, default is False. |
---|
[2767] | 3546 | bltable: name of a baseline table where fitting results |
---|
| 3547 | (coefficients, rms, etc.) are to be written. |
---|
| 3548 | if given, fitting results will NOT be output to |
---|
| 3549 | scantable (insitu=True) or None will be |
---|
| 3550 | returned (insitu=False). |
---|
| 3551 | (default is "": no table output) |
---|
[2645] | 3552 | |
---|
| 3553 | Example: |
---|
| 3554 | # return a scan baselined by a cubic spline consisting of 2 pieces |
---|
| 3555 | # (i.e., 1 internal knot), |
---|
| 3556 | # also with 3-sigma clipping, iteration up to 4 times |
---|
| 3557 | bscan = scan.cspline_baseline(npiece=2,clipthresh=3.0,clipniter=4) |
---|
| 3558 | |
---|
| 3559 | Note: |
---|
| 3560 | The best-fit parameter values output in logger and/or blfile are now |
---|
| 3561 | based on specunit of 'channel'. |
---|
| 3562 | """ |
---|
| 3563 | |
---|
| 3564 | try: |
---|
| 3565 | varlist = vars() |
---|
| 3566 | |
---|
| 3567 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 3568 | if insitu: |
---|
| 3569 | workscan = self |
---|
| 3570 | else: |
---|
| 3571 | workscan = self.copy() |
---|
| 3572 | |
---|
| 3573 | if mask is None: mask = [] |
---|
| 3574 | if order is None: order = 5 |
---|
| 3575 | if clipthresh is None: clipthresh = 3.0 |
---|
| 3576 | if clipniter is None: clipniter = 0 |
---|
| 3577 | if plot is None: plot = False |
---|
| 3578 | if getresidual is None: getresidual = True |
---|
| 3579 | if showprogress is None: showprogress = True |
---|
| 3580 | if minnrow is None: minnrow = 1000 |
---|
| 3581 | if outlog is None: outlog = False |
---|
| 3582 | if blfile is None: blfile = '' |
---|
[2767] | 3583 | if csvformat is None: csvformat = False |
---|
| 3584 | if bltable is None: bltable = '' |
---|
[2645] | 3585 | |
---|
[2767] | 3586 | scsvformat = 'T' if csvformat else 'F' |
---|
[2645] | 3587 | |
---|
| 3588 | #CURRENTLY, PLOT=true UNAVAILABLE UNTIL cubic spline fitting is implemented as a fitter method. |
---|
[2767] | 3589 | workscan._chebyshev_baseline(mask, order, |
---|
| 3590 | clipthresh, clipniter, |
---|
[2645] | 3591 | getresidual, |
---|
| 3592 | pack_progress_params(showprogress, |
---|
| 3593 | minnrow), |
---|
[2767] | 3594 | outlog, scsvformat+blfile, |
---|
| 3595 | bltable) |
---|
[2645] | 3596 | workscan._add_history("chebyshev_baseline", varlist) |
---|
[2767] | 3597 | |
---|
| 3598 | if bltable == '': |
---|
| 3599 | if insitu: |
---|
| 3600 | self._assign(workscan) |
---|
| 3601 | else: |
---|
| 3602 | return workscan |
---|
[2645] | 3603 | else: |
---|
[2767] | 3604 | if not insitu: |
---|
| 3605 | return None |
---|
[2645] | 3606 | |
---|
| 3607 | except RuntimeError, e: |
---|
| 3608 | raise_fitting_failure_exception(e) |
---|
| 3609 | |
---|
| 3610 | @asaplog_post_dec |
---|
[2771] | 3611 | def auto_chebyshev_baseline(self, mask=None, order=None, insitu=None, |
---|
[2645] | 3612 | clipthresh=None, clipniter=None, |
---|
| 3613 | edge=None, threshold=None, chan_avg_limit=None, |
---|
| 3614 | getresidual=None, plot=None, |
---|
| 3615 | showprogress=None, minnrow=None, outlog=None, |
---|
[2767] | 3616 | blfile=None, csvformat=None, bltable=None): |
---|
[2645] | 3617 | """\ |
---|
| 3618 | Return a scan which has been baselined (all rows) by Chebyshev polynomials. |
---|
| 3619 | Spectral lines are detected first using linefinder and masked out |
---|
| 3620 | to avoid them affecting the baseline solution. |
---|
| 3621 | |
---|
| 3622 | Parameters: |
---|
[2771] | 3623 | mask: an optional mask retreived from scantable |
---|
| 3624 | order: the maximum order of Chebyshev polynomial (default is 5) |
---|
[2645] | 3625 | insitu: if False a new scantable is returned. |
---|
| 3626 | Otherwise, the scaling is done in-situ |
---|
| 3627 | The default is taken from .asaprc (False) |
---|
| 3628 | clipthresh: Clipping threshold. (default is 3.0, unit: sigma) |
---|
| 3629 | clipniter: maximum number of iteration of 'clipthresh'-sigma |
---|
| 3630 | clipping (default is 0) |
---|
| 3631 | edge: an optional number of channel to drop at |
---|
| 3632 | the edge of spectrum. If only one value is |
---|
| 3633 | specified, the same number will be dropped |
---|
| 3634 | from both sides of the spectrum. Default |
---|
| 3635 | is to keep all channels. Nested tuples |
---|
| 3636 | represent individual edge selection for |
---|
| 3637 | different IFs (a number of spectral channels |
---|
| 3638 | can be different) |
---|
| 3639 | threshold: the threshold used by line finder. It is |
---|
| 3640 | better to keep it large as only strong lines |
---|
| 3641 | affect the baseline solution. |
---|
| 3642 | chan_avg_limit: a maximum number of consequtive spectral |
---|
| 3643 | channels to average during the search of |
---|
| 3644 | weak and broad lines. The default is no |
---|
| 3645 | averaging (and no search for weak lines). |
---|
| 3646 | If such lines can affect the fitted baseline |
---|
| 3647 | (e.g. a high order polynomial is fitted), |
---|
| 3648 | increase this parameter (usually values up |
---|
| 3649 | to 8 are reasonable). Most users of this |
---|
| 3650 | method should find the default value sufficient. |
---|
| 3651 | plot: *** CURRENTLY UNAVAILABLE, ALWAYS FALSE *** |
---|
| 3652 | plot the fit and the residual. In this each |
---|
| 3653 | indivual fit has to be approved, by typing 'y' |
---|
| 3654 | or 'n' |
---|
| 3655 | getresidual: if False, returns best-fit values instead of |
---|
| 3656 | residual. (default is True) |
---|
| 3657 | showprogress: show progress status for large data. |
---|
| 3658 | default is True. |
---|
| 3659 | minnrow: minimum number of input spectra to show. |
---|
| 3660 | default is 1000. |
---|
| 3661 | outlog: Output the coefficients of the best-fit |
---|
| 3662 | function to logger (default is False) |
---|
| 3663 | blfile: Name of a text file in which the best-fit |
---|
| 3664 | parameter values to be written |
---|
| 3665 | (default is "": no file/logger output) |
---|
| 3666 | csvformat: if True blfile is csv-formatted, default is False. |
---|
[2767] | 3667 | bltable: name of a baseline table where fitting results |
---|
| 3668 | (coefficients, rms, etc.) are to be written. |
---|
| 3669 | if given, fitting results will NOT be output to |
---|
| 3670 | scantable (insitu=True) or None will be |
---|
| 3671 | returned (insitu=False). |
---|
| 3672 | (default is "": no table output) |
---|
[2645] | 3673 | |
---|
| 3674 | Example: |
---|
| 3675 | bscan = scan.auto_cspline_baseline(npiece=3, insitu=False) |
---|
| 3676 | |
---|
| 3677 | Note: |
---|
| 3678 | The best-fit parameter values output in logger and/or blfile are now |
---|
| 3679 | based on specunit of 'channel'. |
---|
| 3680 | """ |
---|
| 3681 | |
---|
| 3682 | try: |
---|
| 3683 | varlist = vars() |
---|
| 3684 | |
---|
| 3685 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 3686 | if insitu: |
---|
| 3687 | workscan = self |
---|
| 3688 | else: |
---|
| 3689 | workscan = self.copy() |
---|
| 3690 | |
---|
| 3691 | if mask is None: mask = [] |
---|
| 3692 | if order is None: order = 5 |
---|
| 3693 | if clipthresh is None: clipthresh = 3.0 |
---|
| 3694 | if clipniter is None: clipniter = 0 |
---|
| 3695 | if edge is None: edge = (0, 0) |
---|
| 3696 | if threshold is None: threshold = 3 |
---|
| 3697 | if chan_avg_limit is None: chan_avg_limit = 1 |
---|
| 3698 | if plot is None: plot = False |
---|
| 3699 | if getresidual is None: getresidual = True |
---|
| 3700 | if showprogress is None: showprogress = True |
---|
| 3701 | if minnrow is None: minnrow = 1000 |
---|
| 3702 | if outlog is None: outlog = False |
---|
| 3703 | if blfile is None: blfile = '' |
---|
| 3704 | if csvformat is None: csvformat = False |
---|
[2767] | 3705 | if bltable is None: bltable = '' |
---|
[2645] | 3706 | |
---|
[2767] | 3707 | scsvformat = 'T' if csvformat else 'F' |
---|
[2645] | 3708 | |
---|
| 3709 | #CURRENTLY, PLOT=true UNAVAILABLE UNTIL cubic spline fitting is implemented as a fitter method. |
---|
[2767] | 3710 | workscan._auto_chebyshev_baseline(mask, order, |
---|
| 3711 | clipthresh, clipniter, |
---|
[2645] | 3712 | normalise_edge_param(edge), |
---|
| 3713 | threshold, |
---|
| 3714 | chan_avg_limit, getresidual, |
---|
| 3715 | pack_progress_params(showprogress, |
---|
| 3716 | minnrow), |
---|
[2767] | 3717 | outlog, scsvformat+blfile, |
---|
| 3718 | bltable) |
---|
[2645] | 3719 | workscan._add_history("auto_chebyshev_baseline", varlist) |
---|
[2767] | 3720 | |
---|
| 3721 | if bltable == '': |
---|
| 3722 | if insitu: |
---|
| 3723 | self._assign(workscan) |
---|
| 3724 | else: |
---|
| 3725 | return workscan |
---|
[2645] | 3726 | else: |
---|
[2767] | 3727 | if not insitu: |
---|
| 3728 | return None |
---|
[2645] | 3729 | |
---|
| 3730 | except RuntimeError, e: |
---|
| 3731 | raise_fitting_failure_exception(e) |
---|
| 3732 | |
---|
| 3733 | @asaplog_post_dec |
---|
[2771] | 3734 | def poly_baseline(self, mask=None, order=None, insitu=None, |
---|
[2767] | 3735 | clipthresh=None, clipniter=None, plot=None, |
---|
[2269] | 3736 | getresidual=None, showprogress=None, minnrow=None, |
---|
[2767] | 3737 | outlog=None, blfile=None, csvformat=None, |
---|
| 3738 | bltable=None): |
---|
[1907] | 3739 | """\ |
---|
| 3740 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 3741 | Parameters: |
---|
[2771] | 3742 | mask: an optional mask |
---|
| 3743 | order: the order of the polynomial (default is 0) |
---|
[2189] | 3744 | insitu: if False a new scantable is returned. |
---|
| 3745 | Otherwise, the scaling is done in-situ |
---|
| 3746 | The default is taken from .asaprc (False) |
---|
[2767] | 3747 | clipthresh: Clipping threshold. (default is 3.0, unit: sigma) |
---|
| 3748 | clipniter: maximum number of iteration of 'clipthresh'-sigma |
---|
| 3749 | clipping (default is 0) |
---|
[2189] | 3750 | plot: plot the fit and the residual. In this each |
---|
| 3751 | indivual fit has to be approved, by typing 'y' |
---|
| 3752 | or 'n' |
---|
| 3753 | getresidual: if False, returns best-fit values instead of |
---|
| 3754 | residual. (default is True) |
---|
| 3755 | showprogress: show progress status for large data. |
---|
| 3756 | default is True. |
---|
| 3757 | minnrow: minimum number of input spectra to show. |
---|
| 3758 | default is 1000. |
---|
| 3759 | outlog: Output the coefficients of the best-fit |
---|
| 3760 | function to logger (default is False) |
---|
| 3761 | blfile: Name of a text file in which the best-fit |
---|
| 3762 | parameter values to be written |
---|
| 3763 | (default is "": no file/logger output) |
---|
[2641] | 3764 | csvformat: if True blfile is csv-formatted, default is False. |
---|
[2767] | 3765 | bltable: name of a baseline table where fitting results |
---|
| 3766 | (coefficients, rms, etc.) are to be written. |
---|
| 3767 | if given, fitting results will NOT be output to |
---|
| 3768 | scantable (insitu=True) or None will be |
---|
| 3769 | returned (insitu=False). |
---|
| 3770 | (default is "": no table output) |
---|
[2012] | 3771 | |
---|
[1907] | 3772 | Example: |
---|
| 3773 | # return a scan baselined by a third order polynomial, |
---|
| 3774 | # not using a mask |
---|
| 3775 | bscan = scan.poly_baseline(order=3) |
---|
| 3776 | """ |
---|
[1931] | 3777 | |
---|
[2186] | 3778 | try: |
---|
| 3779 | varlist = vars() |
---|
[1931] | 3780 | |
---|
[2269] | 3781 | if insitu is None: |
---|
| 3782 | insitu = rcParams["insitu"] |
---|
[2186] | 3783 | if insitu: |
---|
| 3784 | workscan = self |
---|
| 3785 | else: |
---|
| 3786 | workscan = self.copy() |
---|
[1907] | 3787 | |
---|
[2410] | 3788 | if mask is None: mask = [] |
---|
[2189] | 3789 | if order is None: order = 0 |
---|
[2767] | 3790 | if clipthresh is None: clipthresh = 3.0 |
---|
| 3791 | if clipniter is None: clipniter = 0 |
---|
[2189] | 3792 | if plot is None: plot = False |
---|
| 3793 | if getresidual is None: getresidual = True |
---|
| 3794 | if showprogress is None: showprogress = True |
---|
| 3795 | if minnrow is None: minnrow = 1000 |
---|
| 3796 | if outlog is None: outlog = False |
---|
[2767] | 3797 | if blfile is None: blfile = '' |
---|
[2641] | 3798 | if csvformat is None: csvformat = False |
---|
[2767] | 3799 | if bltable is None: bltable = '' |
---|
[1907] | 3800 | |
---|
[2767] | 3801 | scsvformat = 'T' if csvformat else 'F' |
---|
[2641] | 3802 | |
---|
[2012] | 3803 | if plot: |
---|
[2269] | 3804 | outblfile = (blfile != "") and \ |
---|
[2349] | 3805 | os.path.exists(os.path.expanduser( |
---|
| 3806 | os.path.expandvars(blfile)) |
---|
| 3807 | ) |
---|
[2269] | 3808 | if outblfile: |
---|
| 3809 | blf = open(blfile, "a") |
---|
[2012] | 3810 | |
---|
[1907] | 3811 | f = fitter() |
---|
| 3812 | f.set_function(lpoly=order) |
---|
[2186] | 3813 | |
---|
| 3814 | rows = xrange(workscan.nrow()) |
---|
| 3815 | #if len(rows) > 0: workscan._init_blinfo() |
---|
[2610] | 3816 | |
---|
| 3817 | action = "H" |
---|
[1907] | 3818 | for r in rows: |
---|
| 3819 | f.x = workscan._getabcissa(r) |
---|
| 3820 | f.y = workscan._getspectrum(r) |
---|
[2541] | 3821 | if mask: |
---|
| 3822 | f.mask = mask_and(mask, workscan._getmask(r)) # (CAS-1434) |
---|
| 3823 | else: # mask=None |
---|
| 3824 | f.mask = workscan._getmask(r) |
---|
| 3825 | |
---|
[1907] | 3826 | f.data = None |
---|
| 3827 | f.fit() |
---|
[2541] | 3828 | |
---|
[2610] | 3829 | if action != "Y": # skip plotting when accepting all |
---|
| 3830 | f.plot(residual=True) |
---|
| 3831 | #accept_fit = raw_input("Accept fit ( [y]/n ): ") |
---|
| 3832 | #if accept_fit.upper() == "N": |
---|
| 3833 | # #workscan._append_blinfo(None, None, None) |
---|
| 3834 | # continue |
---|
| 3835 | accept_fit = self._get_verify_action("Accept fit?",action) |
---|
| 3836 | if r == 0: action = None |
---|
[1907] | 3837 | if accept_fit.upper() == "N": |
---|
| 3838 | continue |
---|
[2610] | 3839 | elif accept_fit.upper() == "R": |
---|
| 3840 | break |
---|
| 3841 | elif accept_fit.upper() == "A": |
---|
| 3842 | action = "Y" |
---|
[2012] | 3843 | |
---|
| 3844 | blpars = f.get_parameters() |
---|
| 3845 | masklist = workscan.get_masklist(f.mask, row=r, silent=True) |
---|
| 3846 | #workscan._append_blinfo(blpars, masklist, f.mask) |
---|
[2269] | 3847 | workscan._setspectrum((f.fitter.getresidual() |
---|
| 3848 | if getresidual else f.fitter.getfit()), r) |
---|
[1907] | 3849 | |
---|
[2012] | 3850 | if outblfile: |
---|
| 3851 | rms = workscan.get_rms(f.mask, r) |
---|
[2269] | 3852 | dataout = \ |
---|
| 3853 | workscan.format_blparams_row(blpars["params"], |
---|
| 3854 | blpars["fixed"], |
---|
| 3855 | rms, str(masklist), |
---|
[2641] | 3856 | r, True, csvformat) |
---|
[2012] | 3857 | blf.write(dataout) |
---|
| 3858 | |
---|
[1907] | 3859 | f._p.unmap() |
---|
| 3860 | f._p = None |
---|
[2012] | 3861 | |
---|
[2349] | 3862 | if outblfile: |
---|
| 3863 | blf.close() |
---|
[1907] | 3864 | else: |
---|
[2767] | 3865 | workscan._poly_baseline(mask, order, |
---|
| 3866 | clipthresh, clipniter, # |
---|
| 3867 | getresidual, |
---|
[2269] | 3868 | pack_progress_params(showprogress, |
---|
| 3869 | minnrow), |
---|
[2767] | 3870 | outlog, scsvformat+blfile, |
---|
| 3871 | bltable) # |
---|
[1907] | 3872 | |
---|
| 3873 | workscan._add_history("poly_baseline", varlist) |
---|
| 3874 | |
---|
| 3875 | if insitu: |
---|
| 3876 | self._assign(workscan) |
---|
| 3877 | else: |
---|
| 3878 | return workscan |
---|
| 3879 | |
---|
[1919] | 3880 | except RuntimeError, e: |
---|
[2186] | 3881 | raise_fitting_failure_exception(e) |
---|
[1907] | 3882 | |
---|
[2186] | 3883 | @asaplog_post_dec |
---|
[2771] | 3884 | def auto_poly_baseline(self, mask=None, order=None, insitu=None, |
---|
[2767] | 3885 | clipthresh=None, clipniter=None, |
---|
| 3886 | edge=None, threshold=None, chan_avg_limit=None, |
---|
| 3887 | getresidual=None, plot=None, |
---|
| 3888 | showprogress=None, minnrow=None, outlog=None, |
---|
| 3889 | blfile=None, csvformat=None, bltable=None): |
---|
[1846] | 3890 | """\ |
---|
[1931] | 3891 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
[880] | 3892 | Spectral lines are detected first using linefinder and masked out |
---|
| 3893 | to avoid them affecting the baseline solution. |
---|
| 3894 | |
---|
| 3895 | Parameters: |
---|
[2771] | 3896 | mask: an optional mask retreived from scantable |
---|
| 3897 | order: the order of the polynomial (default is 0) |
---|
[2189] | 3898 | insitu: if False a new scantable is returned. |
---|
| 3899 | Otherwise, the scaling is done in-situ |
---|
| 3900 | The default is taken from .asaprc (False) |
---|
[2767] | 3901 | clipthresh: Clipping threshold. (default is 3.0, unit: sigma) |
---|
| 3902 | clipniter: maximum number of iteration of 'clipthresh'-sigma |
---|
| 3903 | clipping (default is 0) |
---|
[2189] | 3904 | edge: an optional number of channel to drop at |
---|
| 3905 | the edge of spectrum. If only one value is |
---|
| 3906 | specified, the same number will be dropped |
---|
| 3907 | from both sides of the spectrum. Default |
---|
| 3908 | is to keep all channels. Nested tuples |
---|
| 3909 | represent individual edge selection for |
---|
| 3910 | different IFs (a number of spectral channels |
---|
| 3911 | can be different) |
---|
| 3912 | threshold: the threshold used by line finder. It is |
---|
| 3913 | better to keep it large as only strong lines |
---|
| 3914 | affect the baseline solution. |
---|
| 3915 | chan_avg_limit: a maximum number of consequtive spectral |
---|
| 3916 | channels to average during the search of |
---|
| 3917 | weak and broad lines. The default is no |
---|
| 3918 | averaging (and no search for weak lines). |
---|
| 3919 | If such lines can affect the fitted baseline |
---|
| 3920 | (e.g. a high order polynomial is fitted), |
---|
| 3921 | increase this parameter (usually values up |
---|
| 3922 | to 8 are reasonable). Most users of this |
---|
| 3923 | method should find the default value sufficient. |
---|
| 3924 | plot: plot the fit and the residual. In this each |
---|
| 3925 | indivual fit has to be approved, by typing 'y' |
---|
| 3926 | or 'n' |
---|
| 3927 | getresidual: if False, returns best-fit values instead of |
---|
| 3928 | residual. (default is True) |
---|
| 3929 | showprogress: show progress status for large data. |
---|
| 3930 | default is True. |
---|
| 3931 | minnrow: minimum number of input spectra to show. |
---|
| 3932 | default is 1000. |
---|
| 3933 | outlog: Output the coefficients of the best-fit |
---|
| 3934 | function to logger (default is False) |
---|
| 3935 | blfile: Name of a text file in which the best-fit |
---|
| 3936 | parameter values to be written |
---|
| 3937 | (default is "": no file/logger output) |
---|
[2641] | 3938 | csvformat: if True blfile is csv-formatted, default is False. |
---|
[2767] | 3939 | bltable: name of a baseline table where fitting results |
---|
| 3940 | (coefficients, rms, etc.) are to be written. |
---|
| 3941 | if given, fitting results will NOT be output to |
---|
| 3942 | scantable (insitu=True) or None will be |
---|
| 3943 | returned (insitu=False). |
---|
| 3944 | (default is "": no table output) |
---|
[1846] | 3945 | |
---|
[2012] | 3946 | Example: |
---|
| 3947 | bscan = scan.auto_poly_baseline(order=7, insitu=False) |
---|
| 3948 | """ |
---|
[880] | 3949 | |
---|
[2186] | 3950 | try: |
---|
| 3951 | varlist = vars() |
---|
[1846] | 3952 | |
---|
[2269] | 3953 | if insitu is None: |
---|
| 3954 | insitu = rcParams['insitu'] |
---|
[2186] | 3955 | if insitu: |
---|
| 3956 | workscan = self |
---|
| 3957 | else: |
---|
| 3958 | workscan = self.copy() |
---|
[1846] | 3959 | |
---|
[2410] | 3960 | if mask is None: mask = [] |
---|
[2186] | 3961 | if order is None: order = 0 |
---|
[2767] | 3962 | if clipthresh is None: clipthresh = 3.0 |
---|
| 3963 | if clipniter is None: clipniter = 0 |
---|
[2186] | 3964 | if edge is None: edge = (0, 0) |
---|
| 3965 | if threshold is None: threshold = 3 |
---|
| 3966 | if chan_avg_limit is None: chan_avg_limit = 1 |
---|
| 3967 | if plot is None: plot = False |
---|
| 3968 | if getresidual is None: getresidual = True |
---|
[2189] | 3969 | if showprogress is None: showprogress = True |
---|
| 3970 | if minnrow is None: minnrow = 1000 |
---|
[2186] | 3971 | if outlog is None: outlog = False |
---|
| 3972 | if blfile is None: blfile = '' |
---|
[2641] | 3973 | if csvformat is None: csvformat = False |
---|
[2767] | 3974 | if bltable is None: bltable = '' |
---|
[1846] | 3975 | |
---|
[2767] | 3976 | scsvformat = 'T' if csvformat else 'F' |
---|
[2641] | 3977 | |
---|
[2186] | 3978 | edge = normalise_edge_param(edge) |
---|
[880] | 3979 | |
---|
[2012] | 3980 | if plot: |
---|
[2269] | 3981 | outblfile = (blfile != "") and \ |
---|
| 3982 | os.path.exists(os.path.expanduser(os.path.expandvars(blfile))) |
---|
[2012] | 3983 | if outblfile: blf = open(blfile, "a") |
---|
| 3984 | |
---|
[2186] | 3985 | from asap.asaplinefind import linefinder |
---|
[2012] | 3986 | fl = linefinder() |
---|
[2269] | 3987 | fl.set_options(threshold=threshold, avg_limit=chan_avg_limit) |
---|
[2012] | 3988 | fl.set_scan(workscan) |
---|
[2186] | 3989 | |
---|
[2012] | 3990 | f = fitter() |
---|
| 3991 | f.set_function(lpoly=order) |
---|
[880] | 3992 | |
---|
[2186] | 3993 | rows = xrange(workscan.nrow()) |
---|
| 3994 | #if len(rows) > 0: workscan._init_blinfo() |
---|
[2610] | 3995 | |
---|
| 3996 | action = "H" |
---|
[2012] | 3997 | for r in rows: |
---|
[2186] | 3998 | idx = 2*workscan.getif(r) |
---|
[2541] | 3999 | if mask: |
---|
| 4000 | msk = mask_and(mask, workscan._getmask(r)) # (CAS-1434) |
---|
| 4001 | else: # mask=None |
---|
| 4002 | msk = workscan._getmask(r) |
---|
| 4003 | fl.find_lines(r, msk, edge[idx:idx+2]) |
---|
[907] | 4004 | |
---|
[2012] | 4005 | f.x = workscan._getabcissa(r) |
---|
| 4006 | f.y = workscan._getspectrum(r) |
---|
| 4007 | f.mask = fl.get_mask() |
---|
| 4008 | f.data = None |
---|
| 4009 | f.fit() |
---|
| 4010 | |
---|
[2610] | 4011 | if action != "Y": # skip plotting when accepting all |
---|
| 4012 | f.plot(residual=True) |
---|
| 4013 | #accept_fit = raw_input("Accept fit ( [y]/n ): ") |
---|
| 4014 | accept_fit = self._get_verify_action("Accept fit?",action) |
---|
| 4015 | if r == 0: action = None |
---|
[2012] | 4016 | if accept_fit.upper() == "N": |
---|
| 4017 | #workscan._append_blinfo(None, None, None) |
---|
| 4018 | continue |
---|
[2610] | 4019 | elif accept_fit.upper() == "R": |
---|
| 4020 | break |
---|
| 4021 | elif accept_fit.upper() == "A": |
---|
| 4022 | action = "Y" |
---|
[2012] | 4023 | |
---|
| 4024 | blpars = f.get_parameters() |
---|
| 4025 | masklist = workscan.get_masklist(f.mask, row=r, silent=True) |
---|
| 4026 | #workscan._append_blinfo(blpars, masklist, f.mask) |
---|
[2349] | 4027 | workscan._setspectrum( |
---|
| 4028 | (f.fitter.getresidual() if getresidual |
---|
| 4029 | else f.fitter.getfit()), r |
---|
| 4030 | ) |
---|
[2012] | 4031 | |
---|
| 4032 | if outblfile: |
---|
| 4033 | rms = workscan.get_rms(f.mask, r) |
---|
[2269] | 4034 | dataout = \ |
---|
| 4035 | workscan.format_blparams_row(blpars["params"], |
---|
| 4036 | blpars["fixed"], |
---|
| 4037 | rms, str(masklist), |
---|
[2641] | 4038 | r, True, csvformat) |
---|
[2012] | 4039 | blf.write(dataout) |
---|
| 4040 | |
---|
| 4041 | f._p.unmap() |
---|
| 4042 | f._p = None |
---|
| 4043 | |
---|
| 4044 | if outblfile: blf.close() |
---|
| 4045 | else: |
---|
[2767] | 4046 | workscan._auto_poly_baseline(mask, order, |
---|
| 4047 | clipthresh, clipniter, |
---|
| 4048 | edge, threshold, |
---|
[2269] | 4049 | chan_avg_limit, getresidual, |
---|
| 4050 | pack_progress_params(showprogress, |
---|
| 4051 | minnrow), |
---|
[2767] | 4052 | outlog, scsvformat+blfile, |
---|
| 4053 | bltable) |
---|
| 4054 | workscan._add_history("auto_poly_baseline", varlist) |
---|
[2012] | 4055 | |
---|
[2767] | 4056 | if bltable == '': |
---|
| 4057 | if insitu: |
---|
| 4058 | self._assign(workscan) |
---|
| 4059 | else: |
---|
| 4060 | return workscan |
---|
[2012] | 4061 | else: |
---|
[2767] | 4062 | if not insitu: |
---|
| 4063 | return None |
---|
[2012] | 4064 | |
---|
| 4065 | except RuntimeError, e: |
---|
[2186] | 4066 | raise_fitting_failure_exception(e) |
---|
[2012] | 4067 | |
---|
| 4068 | def _init_blinfo(self): |
---|
| 4069 | """\ |
---|
| 4070 | Initialise the following three auxiliary members: |
---|
| 4071 | blpars : parameters of the best-fit baseline, |
---|
| 4072 | masklists : mask data (edge positions of masked channels) and |
---|
| 4073 | actualmask : mask data (in boolean list), |
---|
| 4074 | to keep for use later (including output to logger/text files). |
---|
| 4075 | Used by poly_baseline() and auto_poly_baseline() in case of |
---|
| 4076 | 'plot=True'. |
---|
| 4077 | """ |
---|
| 4078 | self.blpars = [] |
---|
| 4079 | self.masklists = [] |
---|
| 4080 | self.actualmask = [] |
---|
| 4081 | return |
---|
[880] | 4082 | |
---|
[2012] | 4083 | def _append_blinfo(self, data_blpars, data_masklists, data_actualmask): |
---|
| 4084 | """\ |
---|
| 4085 | Append baseline-fitting related info to blpars, masklist and |
---|
| 4086 | actualmask. |
---|
| 4087 | """ |
---|
| 4088 | self.blpars.append(data_blpars) |
---|
| 4089 | self.masklists.append(data_masklists) |
---|
| 4090 | self.actualmask.append(data_actualmask) |
---|
| 4091 | return |
---|
| 4092 | |
---|
[1862] | 4093 | @asaplog_post_dec |
---|
[914] | 4094 | def rotate_linpolphase(self, angle): |
---|
[1846] | 4095 | """\ |
---|
[914] | 4096 | Rotate the phase of the complex polarization O=Q+iU correlation. |
---|
| 4097 | This is always done in situ in the raw data. So if you call this |
---|
| 4098 | function more than once then each call rotates the phase further. |
---|
[1846] | 4099 | |
---|
[914] | 4100 | Parameters: |
---|
[1846] | 4101 | |
---|
[914] | 4102 | angle: The angle (degrees) to rotate (add) by. |
---|
[1846] | 4103 | |
---|
| 4104 | Example:: |
---|
| 4105 | |
---|
[914] | 4106 | scan.rotate_linpolphase(2.3) |
---|
[1846] | 4107 | |
---|
[914] | 4108 | """ |
---|
| 4109 | varlist = vars() |
---|
[936] | 4110 | self._math._rotate_linpolphase(self, angle) |
---|
[914] | 4111 | self._add_history("rotate_linpolphase", varlist) |
---|
| 4112 | return |
---|
[710] | 4113 | |
---|
[1862] | 4114 | @asaplog_post_dec |
---|
[914] | 4115 | def rotate_xyphase(self, angle): |
---|
[1846] | 4116 | """\ |
---|
[914] | 4117 | Rotate the phase of the XY correlation. This is always done in situ |
---|
| 4118 | in the data. So if you call this function more than once |
---|
| 4119 | then each call rotates the phase further. |
---|
[1846] | 4120 | |
---|
[914] | 4121 | Parameters: |
---|
[1846] | 4122 | |
---|
[914] | 4123 | angle: The angle (degrees) to rotate (add) by. |
---|
[1846] | 4124 | |
---|
| 4125 | Example:: |
---|
| 4126 | |
---|
[914] | 4127 | scan.rotate_xyphase(2.3) |
---|
[1846] | 4128 | |
---|
[914] | 4129 | """ |
---|
| 4130 | varlist = vars() |
---|
[936] | 4131 | self._math._rotate_xyphase(self, angle) |
---|
[914] | 4132 | self._add_history("rotate_xyphase", varlist) |
---|
| 4133 | return |
---|
| 4134 | |
---|
[1862] | 4135 | @asaplog_post_dec |
---|
[914] | 4136 | def swap_linears(self): |
---|
[1846] | 4137 | """\ |
---|
[1573] | 4138 | Swap the linear polarisations XX and YY, or better the first two |
---|
[1348] | 4139 | polarisations as this also works for ciculars. |
---|
[914] | 4140 | """ |
---|
| 4141 | varlist = vars() |
---|
[936] | 4142 | self._math._swap_linears(self) |
---|
[914] | 4143 | self._add_history("swap_linears", varlist) |
---|
| 4144 | return |
---|
| 4145 | |
---|
[1862] | 4146 | @asaplog_post_dec |
---|
[914] | 4147 | def invert_phase(self): |
---|
[1846] | 4148 | """\ |
---|
[914] | 4149 | Invert the phase of the complex polarisation |
---|
| 4150 | """ |
---|
| 4151 | varlist = vars() |
---|
[936] | 4152 | self._math._invert_phase(self) |
---|
[914] | 4153 | self._add_history("invert_phase", varlist) |
---|
| 4154 | return |
---|
| 4155 | |
---|
[1862] | 4156 | @asaplog_post_dec |
---|
[876] | 4157 | def add(self, offset, insitu=None): |
---|
[1846] | 4158 | """\ |
---|
[513] | 4159 | Return a scan where all spectra have the offset added |
---|
[1846] | 4160 | |
---|
[513] | 4161 | Parameters: |
---|
[1846] | 4162 | |
---|
[513] | 4163 | offset: the offset |
---|
[1855] | 4164 | |
---|
[513] | 4165 | insitu: if False a new scantable is returned. |
---|
| 4166 | Otherwise, the scaling is done in-situ |
---|
| 4167 | The default is taken from .asaprc (False) |
---|
[1846] | 4168 | |
---|
[513] | 4169 | """ |
---|
| 4170 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 4171 | self._math._setinsitu(insitu) |
---|
[513] | 4172 | varlist = vars() |
---|
[876] | 4173 | s = scantable(self._math._unaryop(self, offset, "ADD", False)) |
---|
[1118] | 4174 | s._add_history("add", varlist) |
---|
[876] | 4175 | if insitu: |
---|
| 4176 | self._assign(s) |
---|
| 4177 | else: |
---|
[513] | 4178 | return s |
---|
| 4179 | |
---|
[1862] | 4180 | @asaplog_post_dec |
---|
[1308] | 4181 | def scale(self, factor, tsys=True, insitu=None): |
---|
[1846] | 4182 | """\ |
---|
| 4183 | |
---|
[1938] | 4184 | Return a scan where all spectra are scaled by the given 'factor' |
---|
[1846] | 4185 | |
---|
[513] | 4186 | Parameters: |
---|
[1846] | 4187 | |
---|
[1819] | 4188 | factor: the scaling factor (float or 1D float list) |
---|
[1855] | 4189 | |
---|
[513] | 4190 | insitu: if False a new scantable is returned. |
---|
| 4191 | Otherwise, the scaling is done in-situ |
---|
| 4192 | The default is taken from .asaprc (False) |
---|
[1855] | 4193 | |
---|
[513] | 4194 | tsys: if True (default) then apply the operation to Tsys |
---|
| 4195 | as well as the data |
---|
[1846] | 4196 | |
---|
[513] | 4197 | """ |
---|
| 4198 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 4199 | self._math._setinsitu(insitu) |
---|
[513] | 4200 | varlist = vars() |
---|
[1819] | 4201 | s = None |
---|
| 4202 | import numpy |
---|
| 4203 | if isinstance(factor, list) or isinstance(factor, numpy.ndarray): |
---|
[2320] | 4204 | if isinstance(factor[0], list) or isinstance(factor[0], |
---|
| 4205 | numpy.ndarray): |
---|
[1819] | 4206 | from asapmath import _array2dOp |
---|
[2320] | 4207 | s = _array2dOp( self, factor, "MUL", tsys, insitu ) |
---|
[1819] | 4208 | else: |
---|
[2320] | 4209 | s = scantable( self._math._arrayop( self, factor, |
---|
| 4210 | "MUL", tsys ) ) |
---|
[1819] | 4211 | else: |
---|
[2320] | 4212 | s = scantable(self._math._unaryop(self, factor, "MUL", tsys)) |
---|
[1118] | 4213 | s._add_history("scale", varlist) |
---|
[876] | 4214 | if insitu: |
---|
| 4215 | self._assign(s) |
---|
| 4216 | else: |
---|
[513] | 4217 | return s |
---|
| 4218 | |
---|
[2349] | 4219 | @preserve_selection |
---|
| 4220 | def set_sourcetype(self, match, matchtype="pattern", |
---|
[1504] | 4221 | sourcetype="reference"): |
---|
[1846] | 4222 | """\ |
---|
[1502] | 4223 | Set the type of the source to be an source or reference scan |
---|
[1846] | 4224 | using the provided pattern. |
---|
| 4225 | |
---|
[1502] | 4226 | Parameters: |
---|
[1846] | 4227 | |
---|
[1504] | 4228 | match: a Unix style pattern, regular expression or selector |
---|
[1855] | 4229 | |
---|
[1504] | 4230 | matchtype: 'pattern' (default) UNIX style pattern or |
---|
| 4231 | 'regex' regular expression |
---|
[1855] | 4232 | |
---|
[1502] | 4233 | sourcetype: the type of the source to use (source/reference) |
---|
[1846] | 4234 | |
---|
[1502] | 4235 | """ |
---|
| 4236 | varlist = vars() |
---|
| 4237 | stype = -1 |
---|
[2480] | 4238 | if sourcetype.lower().startswith("r") or sourcetype.lower() == "off": |
---|
[1502] | 4239 | stype = 1 |
---|
[2480] | 4240 | elif sourcetype.lower().startswith("s") or sourcetype.lower() == "on": |
---|
[1502] | 4241 | stype = 0 |
---|
[1504] | 4242 | else: |
---|
[2480] | 4243 | raise ValueError("Illegal sourcetype use s(ource)/on or r(eference)/off") |
---|
[1504] | 4244 | if matchtype.lower().startswith("p"): |
---|
| 4245 | matchtype = "pattern" |
---|
| 4246 | elif matchtype.lower().startswith("r"): |
---|
| 4247 | matchtype = "regex" |
---|
| 4248 | else: |
---|
| 4249 | raise ValueError("Illegal matchtype, use p(attern) or r(egex)") |
---|
[1502] | 4250 | sel = selector() |
---|
| 4251 | if isinstance(match, selector): |
---|
| 4252 | sel = match |
---|
| 4253 | else: |
---|
[2480] | 4254 | sel.set_query("SRCNAME=%s('%s')" % (matchtype, match)) |
---|
| 4255 | self.set_selection(sel) |
---|
[1502] | 4256 | self._setsourcetype(stype) |
---|
[1573] | 4257 | self._add_history("set_sourcetype", varlist) |
---|
[1502] | 4258 | |
---|
[2818] | 4259 | |
---|
| 4260 | def set_sourcename(self, name): |
---|
| 4261 | varlist = vars() |
---|
| 4262 | self._setsourcename(name) |
---|
| 4263 | self._add_history("set_sourcename", varlist) |
---|
| 4264 | |
---|
[1862] | 4265 | @asaplog_post_dec |
---|
[1857] | 4266 | @preserve_selection |
---|
[1819] | 4267 | def auto_quotient(self, preserve=True, mode='paired', verify=False): |
---|
[1846] | 4268 | """\ |
---|
[670] | 4269 | This function allows to build quotients automatically. |
---|
[1819] | 4270 | It assumes the observation to have the same number of |
---|
[670] | 4271 | "ons" and "offs" |
---|
[1846] | 4272 | |
---|
[670] | 4273 | Parameters: |
---|
[1846] | 4274 | |
---|
[710] | 4275 | preserve: you can preserve (default) the continuum or |
---|
| 4276 | remove it. The equations used are |
---|
[1857] | 4277 | |
---|
[670] | 4278 | preserve: Output = Toff * (on/off) - Toff |
---|
[1857] | 4279 | |
---|
[1070] | 4280 | remove: Output = Toff * (on/off) - Ton |
---|
[1855] | 4281 | |
---|
[1573] | 4282 | mode: the on/off detection mode |
---|
[1348] | 4283 | 'paired' (default) |
---|
| 4284 | identifies 'off' scans by the |
---|
| 4285 | trailing '_R' (Mopra/Parkes) or |
---|
| 4286 | '_e'/'_w' (Tid) and matches |
---|
| 4287 | on/off pairs from the observing pattern |
---|
[1502] | 4288 | 'time' |
---|
| 4289 | finds the closest off in time |
---|
[1348] | 4290 | |
---|
[1857] | 4291 | .. todo:: verify argument is not implemented |
---|
| 4292 | |
---|
[670] | 4293 | """ |
---|
[1857] | 4294 | varlist = vars() |
---|
[1348] | 4295 | modes = ["time", "paired"] |
---|
[670] | 4296 | if not mode in modes: |
---|
[876] | 4297 | msg = "please provide valid mode. Valid modes are %s" % (modes) |
---|
| 4298 | raise ValueError(msg) |
---|
[1348] | 4299 | s = None |
---|
| 4300 | if mode.lower() == "paired": |
---|
[2840] | 4301 | from asap._asap import srctype |
---|
[1857] | 4302 | sel = self.get_selection() |
---|
[2840] | 4303 | #sel.set_query("SRCTYPE==psoff") |
---|
| 4304 | sel.set_types(srctype.psoff) |
---|
[1356] | 4305 | self.set_selection(sel) |
---|
[1348] | 4306 | offs = self.copy() |
---|
[2840] | 4307 | #sel.set_query("SRCTYPE==pson") |
---|
| 4308 | sel.set_types(srctype.pson) |
---|
[1356] | 4309 | self.set_selection(sel) |
---|
[1348] | 4310 | ons = self.copy() |
---|
| 4311 | s = scantable(self._math._quotient(ons, offs, preserve)) |
---|
| 4312 | elif mode.lower() == "time": |
---|
| 4313 | s = scantable(self._math._auto_quotient(self, mode, preserve)) |
---|
[1118] | 4314 | s._add_history("auto_quotient", varlist) |
---|
[876] | 4315 | return s |
---|
[710] | 4316 | |
---|
[1862] | 4317 | @asaplog_post_dec |
---|
[1145] | 4318 | def mx_quotient(self, mask = None, weight='median', preserve=True): |
---|
[1846] | 4319 | """\ |
---|
[1143] | 4320 | Form a quotient using "off" beams when observing in "MX" mode. |
---|
[1846] | 4321 | |
---|
[1143] | 4322 | Parameters: |
---|
[1846] | 4323 | |
---|
[1145] | 4324 | mask: an optional mask to be used when weight == 'stddev' |
---|
[1855] | 4325 | |
---|
[1143] | 4326 | weight: How to average the off beams. Default is 'median'. |
---|
[1855] | 4327 | |
---|
[1145] | 4328 | preserve: you can preserve (default) the continuum or |
---|
[1855] | 4329 | remove it. The equations used are: |
---|
[1846] | 4330 | |
---|
[1855] | 4331 | preserve: Output = Toff * (on/off) - Toff |
---|
| 4332 | |
---|
| 4333 | remove: Output = Toff * (on/off) - Ton |
---|
| 4334 | |
---|
[1217] | 4335 | """ |
---|
[1593] | 4336 | mask = mask or () |
---|
[1141] | 4337 | varlist = vars() |
---|
| 4338 | on = scantable(self._math._mx_extract(self, 'on')) |
---|
[1143] | 4339 | preoff = scantable(self._math._mx_extract(self, 'off')) |
---|
| 4340 | off = preoff.average_time(mask=mask, weight=weight, scanav=False) |
---|
[1217] | 4341 | from asapmath import quotient |
---|
[1145] | 4342 | q = quotient(on, off, preserve) |
---|
[1143] | 4343 | q._add_history("mx_quotient", varlist) |
---|
[1217] | 4344 | return q |
---|
[513] | 4345 | |
---|
[1862] | 4346 | @asaplog_post_dec |
---|
[718] | 4347 | def freq_switch(self, insitu=None): |
---|
[1846] | 4348 | """\ |
---|
[718] | 4349 | Apply frequency switching to the data. |
---|
[1846] | 4350 | |
---|
[718] | 4351 | Parameters: |
---|
[1846] | 4352 | |
---|
[718] | 4353 | insitu: if False a new scantable is returned. |
---|
| 4354 | Otherwise, the swictching is done in-situ |
---|
| 4355 | The default is taken from .asaprc (False) |
---|
[1846] | 4356 | |
---|
[718] | 4357 | """ |
---|
| 4358 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 4359 | self._math._setinsitu(insitu) |
---|
[718] | 4360 | varlist = vars() |
---|
[876] | 4361 | s = scantable(self._math._freqswitch(self)) |
---|
[1118] | 4362 | s._add_history("freq_switch", varlist) |
---|
[1856] | 4363 | if insitu: |
---|
| 4364 | self._assign(s) |
---|
| 4365 | else: |
---|
| 4366 | return s |
---|
[718] | 4367 | |
---|
[1862] | 4368 | @asaplog_post_dec |
---|
[780] | 4369 | def recalc_azel(self): |
---|
[1846] | 4370 | """Recalculate the azimuth and elevation for each position.""" |
---|
[780] | 4371 | varlist = vars() |
---|
[876] | 4372 | self._recalcazel() |
---|
[780] | 4373 | self._add_history("recalc_azel", varlist) |
---|
| 4374 | return |
---|
| 4375 | |
---|
[1862] | 4376 | @asaplog_post_dec |
---|
[513] | 4377 | def __add__(self, other): |
---|
[2574] | 4378 | """ |
---|
| 4379 | implicit on all axes and on Tsys |
---|
| 4380 | """ |
---|
[513] | 4381 | varlist = vars() |
---|
[2574] | 4382 | s = self.__op( other, "ADD" ) |
---|
[513] | 4383 | s._add_history("operator +", varlist) |
---|
| 4384 | return s |
---|
| 4385 | |
---|
[1862] | 4386 | @asaplog_post_dec |
---|
[513] | 4387 | def __sub__(self, other): |
---|
| 4388 | """ |
---|
| 4389 | implicit on all axes and on Tsys |
---|
| 4390 | """ |
---|
| 4391 | varlist = vars() |
---|
[2574] | 4392 | s = self.__op( other, "SUB" ) |
---|
[513] | 4393 | s._add_history("operator -", varlist) |
---|
| 4394 | return s |
---|
[710] | 4395 | |
---|
[1862] | 4396 | @asaplog_post_dec |
---|
[513] | 4397 | def __mul__(self, other): |
---|
| 4398 | """ |
---|
| 4399 | implicit on all axes and on Tsys |
---|
| 4400 | """ |
---|
| 4401 | varlist = vars() |
---|
[2574] | 4402 | s = self.__op( other, "MUL" ) ; |
---|
[513] | 4403 | s._add_history("operator *", varlist) |
---|
| 4404 | return s |
---|
| 4405 | |
---|
[710] | 4406 | |
---|
[1862] | 4407 | @asaplog_post_dec |
---|
[513] | 4408 | def __div__(self, other): |
---|
| 4409 | """ |
---|
| 4410 | implicit on all axes and on Tsys |
---|
| 4411 | """ |
---|
| 4412 | varlist = vars() |
---|
[2574] | 4413 | s = self.__op( other, "DIV" ) |
---|
| 4414 | s._add_history("operator /", varlist) |
---|
| 4415 | return s |
---|
| 4416 | |
---|
| 4417 | @asaplog_post_dec |
---|
| 4418 | def __op( self, other, mode ): |
---|
[513] | 4419 | s = None |
---|
| 4420 | if isinstance(other, scantable): |
---|
[2574] | 4421 | s = scantable(self._math._binaryop(self, other, mode)) |
---|
[513] | 4422 | elif isinstance(other, float): |
---|
| 4423 | if other == 0.0: |
---|
[718] | 4424 | raise ZeroDivisionError("Dividing by zero is not recommended") |
---|
[2574] | 4425 | s = scantable(self._math._unaryop(self, other, mode, False)) |
---|
[2144] | 4426 | elif isinstance(other, list) or isinstance(other, numpy.ndarray): |
---|
[2349] | 4427 | if isinstance(other[0], list) \ |
---|
| 4428 | or isinstance(other[0], numpy.ndarray): |
---|
[2144] | 4429 | from asapmath import _array2dOp |
---|
[2574] | 4430 | s = _array2dOp( self, other, mode, False ) |
---|
[2144] | 4431 | else: |
---|
[2574] | 4432 | s = scantable( self._math._arrayop( self, other, |
---|
| 4433 | mode, False ) ) |
---|
[513] | 4434 | else: |
---|
[718] | 4435 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 4436 | return s |
---|
| 4437 | |
---|
[1862] | 4438 | @asaplog_post_dec |
---|
[530] | 4439 | def get_fit(self, row=0): |
---|
[1846] | 4440 | """\ |
---|
[530] | 4441 | Print or return the stored fits for a row in the scantable |
---|
[1846] | 4442 | |
---|
[530] | 4443 | Parameters: |
---|
[1846] | 4444 | |
---|
[530] | 4445 | row: the row which the fit has been applied to. |
---|
[1846] | 4446 | |
---|
[530] | 4447 | """ |
---|
| 4448 | if row > self.nrow(): |
---|
| 4449 | return |
---|
[976] | 4450 | from asap.asapfit import asapfit |
---|
[530] | 4451 | fit = asapfit(self._getfit(row)) |
---|
[1859] | 4452 | asaplog.push( '%s' %(fit) ) |
---|
| 4453 | return fit.as_dict() |
---|
[530] | 4454 | |
---|
[2349] | 4455 | @preserve_selection |
---|
[1483] | 4456 | def flag_nans(self): |
---|
[1846] | 4457 | """\ |
---|
[1483] | 4458 | Utility function to flag NaN values in the scantable. |
---|
| 4459 | """ |
---|
| 4460 | import numpy |
---|
| 4461 | basesel = self.get_selection() |
---|
| 4462 | for i in range(self.nrow()): |
---|
[1589] | 4463 | sel = self.get_row_selector(i) |
---|
| 4464 | self.set_selection(basesel+sel) |
---|
[1483] | 4465 | nans = numpy.isnan(self._getspectrum(0)) |
---|
| 4466 | if numpy.any(nans): |
---|
| 4467 | bnans = [ bool(v) for v in nans] |
---|
| 4468 | self.flag(bnans) |
---|
| 4469 | |
---|
[1588] | 4470 | def get_row_selector(self, rowno): |
---|
[1992] | 4471 | return selector(rows=[rowno]) |
---|
[1573] | 4472 | |
---|
[484] | 4473 | def _add_history(self, funcname, parameters): |
---|
[1435] | 4474 | if not rcParams['scantable.history']: |
---|
| 4475 | return |
---|
[484] | 4476 | # create date |
---|
| 4477 | sep = "##" |
---|
| 4478 | from datetime import datetime |
---|
| 4479 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S') |
---|
| 4480 | hist = dstr+sep |
---|
| 4481 | hist += funcname+sep#cdate+sep |
---|
[2349] | 4482 | if parameters.has_key('self'): |
---|
| 4483 | del parameters['self'] |
---|
[1118] | 4484 | for k, v in parameters.iteritems(): |
---|
[484] | 4485 | if type(v) is dict: |
---|
[1118] | 4486 | for k2, v2 in v.iteritems(): |
---|
[484] | 4487 | hist += k2 |
---|
| 4488 | hist += "=" |
---|
[1118] | 4489 | if isinstance(v2, scantable): |
---|
[484] | 4490 | hist += 'scantable' |
---|
| 4491 | elif k2 == 'mask': |
---|
[1118] | 4492 | if isinstance(v2, list) or isinstance(v2, tuple): |
---|
[513] | 4493 | hist += str(self._zip_mask(v2)) |
---|
| 4494 | else: |
---|
| 4495 | hist += str(v2) |
---|
[484] | 4496 | else: |
---|
[513] | 4497 | hist += str(v2) |
---|
[484] | 4498 | else: |
---|
| 4499 | hist += k |
---|
| 4500 | hist += "=" |
---|
[1118] | 4501 | if isinstance(v, scantable): |
---|
[484] | 4502 | hist += 'scantable' |
---|
| 4503 | elif k == 'mask': |
---|
[1118] | 4504 | if isinstance(v, list) or isinstance(v, tuple): |
---|
[513] | 4505 | hist += str(self._zip_mask(v)) |
---|
| 4506 | else: |
---|
| 4507 | hist += str(v) |
---|
[484] | 4508 | else: |
---|
| 4509 | hist += str(v) |
---|
| 4510 | hist += sep |
---|
| 4511 | hist = hist[:-2] # remove trailing '##' |
---|
| 4512 | self._addhistory(hist) |
---|
| 4513 | |
---|
[710] | 4514 | |
---|
[484] | 4515 | def _zip_mask(self, mask): |
---|
| 4516 | mask = list(mask) |
---|
| 4517 | i = 0 |
---|
| 4518 | segments = [] |
---|
| 4519 | while mask[i:].count(1): |
---|
| 4520 | i += mask[i:].index(1) |
---|
| 4521 | if mask[i:].count(0): |
---|
| 4522 | j = i + mask[i:].index(0) |
---|
| 4523 | else: |
---|
[710] | 4524 | j = len(mask) |
---|
[1118] | 4525 | segments.append([i, j]) |
---|
[710] | 4526 | i = j |
---|
[484] | 4527 | return segments |
---|
[714] | 4528 | |
---|
[626] | 4529 | def _get_ordinate_label(self): |
---|
| 4530 | fu = "("+self.get_fluxunit()+")" |
---|
| 4531 | import re |
---|
| 4532 | lbl = "Intensity" |
---|
[1118] | 4533 | if re.match(".K.", fu): |
---|
[626] | 4534 | lbl = "Brightness Temperature "+ fu |
---|
[1118] | 4535 | elif re.match(".Jy.", fu): |
---|
[626] | 4536 | lbl = "Flux density "+ fu |
---|
| 4537 | return lbl |
---|
[710] | 4538 | |
---|
[876] | 4539 | def _check_ifs(self): |
---|
[2349] | 4540 | # return len(set([self.nchan(i) for i in self.getifnos()])) == 1 |
---|
[1986] | 4541 | nchans = [self.nchan(i) for i in self.getifnos()] |
---|
[2004] | 4542 | nchans = filter(lambda t: t > 0, nchans) |
---|
[876] | 4543 | return (sum(nchans)/len(nchans) == nchans[0]) |
---|
[976] | 4544 | |
---|
[1862] | 4545 | @asaplog_post_dec |
---|
[1916] | 4546 | def _fill(self, names, unit, average, opts={}): |
---|
[976] | 4547 | first = True |
---|
| 4548 | fullnames = [] |
---|
| 4549 | for name in names: |
---|
| 4550 | name = os.path.expandvars(name) |
---|
| 4551 | name = os.path.expanduser(name) |
---|
| 4552 | if not os.path.exists(name): |
---|
| 4553 | msg = "File '%s' does not exists" % (name) |
---|
| 4554 | raise IOError(msg) |
---|
| 4555 | fullnames.append(name) |
---|
| 4556 | if average: |
---|
| 4557 | asaplog.push('Auto averaging integrations') |
---|
[1079] | 4558 | stype = int(rcParams['scantable.storage'].lower() == 'disk') |
---|
[976] | 4559 | for name in fullnames: |
---|
[1073] | 4560 | tbl = Scantable(stype) |
---|
[2004] | 4561 | if is_ms( name ): |
---|
| 4562 | r = msfiller( tbl ) |
---|
| 4563 | else: |
---|
| 4564 | r = filler( tbl ) |
---|
[976] | 4565 | msg = "Importing %s..." % (name) |
---|
[1118] | 4566 | asaplog.push(msg, False) |
---|
[2349] | 4567 | r.open(name, opts) |
---|
[2480] | 4568 | rx = rcParams['scantable.reference'] |
---|
| 4569 | r.setreferenceexpr(rx) |
---|
[1843] | 4570 | r.fill() |
---|
[976] | 4571 | if average: |
---|
[1118] | 4572 | tbl = self._math._average((tbl, ), (), 'NONE', 'SCAN') |
---|
[976] | 4573 | if not first: |
---|
| 4574 | tbl = self._math._merge([self, tbl]) |
---|
| 4575 | Scantable.__init__(self, tbl) |
---|
[1843] | 4576 | r.close() |
---|
[1118] | 4577 | del r, tbl |
---|
[976] | 4578 | first = False |
---|
[1861] | 4579 | #flush log |
---|
| 4580 | asaplog.post() |
---|
[976] | 4581 | if unit is not None: |
---|
| 4582 | self.set_fluxunit(unit) |
---|
[1824] | 4583 | if not is_casapy(): |
---|
| 4584 | self.set_freqframe(rcParams['scantable.freqframe']) |
---|
[976] | 4585 | |
---|
[2610] | 4586 | def _get_verify_action( self, msg, action=None ): |
---|
| 4587 | valid_act = ['Y', 'N', 'A', 'R'] |
---|
| 4588 | if not action or not isinstance(action, str): |
---|
| 4589 | action = raw_input("%s [Y/n/a/r] (h for help): " % msg) |
---|
| 4590 | if action == '': |
---|
| 4591 | return "Y" |
---|
| 4592 | elif (action.upper()[0] in valid_act): |
---|
| 4593 | return action.upper()[0] |
---|
| 4594 | elif (action.upper()[0] in ['H','?']): |
---|
| 4595 | print "Available actions of verification [Y|n|a|r]" |
---|
| 4596 | print " Y : Yes for current data (default)" |
---|
| 4597 | print " N : No for current data" |
---|
| 4598 | print " A : Accept all in the following and exit from verification" |
---|
| 4599 | print " R : Reject all in the following and exit from verification" |
---|
| 4600 | print " H or ?: help (show this message)" |
---|
| 4601 | return self._get_verify_action(msg) |
---|
| 4602 | else: |
---|
| 4603 | return 'Y' |
---|
[2012] | 4604 | |
---|
[1402] | 4605 | def __getitem__(self, key): |
---|
| 4606 | if key < 0: |
---|
| 4607 | key += self.nrow() |
---|
| 4608 | if key >= self.nrow(): |
---|
| 4609 | raise IndexError("Row index out of range.") |
---|
| 4610 | return self._getspectrum(key) |
---|
| 4611 | |
---|
| 4612 | def __setitem__(self, key, value): |
---|
| 4613 | if key < 0: |
---|
| 4614 | key += self.nrow() |
---|
| 4615 | if key >= self.nrow(): |
---|
| 4616 | raise IndexError("Row index out of range.") |
---|
| 4617 | if not hasattr(value, "__len__") or \ |
---|
| 4618 | len(value) > self.nchan(self.getif(key)): |
---|
| 4619 | raise ValueError("Spectrum length doesn't match.") |
---|
| 4620 | return self._setspectrum(value, key) |
---|
| 4621 | |
---|
| 4622 | def __len__(self): |
---|
| 4623 | return self.nrow() |
---|
| 4624 | |
---|
| 4625 | def __iter__(self): |
---|
| 4626 | for i in range(len(self)): |
---|
| 4627 | yield self[i] |
---|