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« prev ^ index » next coverage.py v7.6.4, created at 2024-10-31 19:53 +0000
1##################### generated by xml-casa (v2) from immath.xml ####################
2##################### cd5491adbb52564df09390ab9c67dee0 ##############################
3from __future__ import absolute_import
4import numpy
5from casatools.typecheck import CasaValidator as _val_ctor
6_pc = _val_ctor( )
7from casatools.coercetype import coerce as _coerce
8from casatools.errors import create_error_string
9from .private.task_immath import immath as _immath_t
10from casatasks.private.task_logging import start_log as _start_log
11from casatasks.private.task_logging import end_log as _end_log
12from casatasks.private.task_logging import except_log as _except_log
14class _immath:
15 """
16 immath ---- Perform math operations on images
18 math on images
20 --------- parameter descriptions ---------------------------------------------
22 imagename a list of input images
23 mode mode for math operation (evalexpr, spix, pola, poli, lpoli, tpoli)
24 outfile File where the output is saved
25 expr Mathematical expression using images
26 varnames a list of variable names to use with the image files
27 sigma standard deviation of noise for debiasing
28 polithresh Threshold in linear polarization intensity image below which to mask pixels.
29 mask Mask to use. Default is none.
30 region Region selection. Default is to use the full image.
31 box Rectangular region to select in direction plane. Default is to use the entire direction plane.
32 chans Channels to use. Default is to use all channels.
33 stokes Stokes planes to use. Default is to use all Stokes planes.
34 stretch Stretch the mask if necessary and possible? See help stretch.par
35 imagemd An image name from which metadata should be copied. The input can be either an image listed under imagename or any other image on disk. Leaving this parameter unset may copy header metadata from any of the input images, which one is not guaranteed.
36 prec Precision for the output image pixels if mode="evalexpr" or "spix". "float" or "double" (minimum match supported)
37 [1;42mRETURNS[1;m bool
39 --------- examples -----------------------------------------------------------
43 This task evaluates mathematical expressions involving existing
44 image files. The results of the calculations are stored in the
45 designated output file. Options are available to specify mathematical
46 expression directly or pre-defined expression for calculation of
47 spectral index image, and polarization intensity and position angle
48 images are available. The image file names imbedded in the expression or
49 specified in the imagename parameter for the pre-defined calculations may
50 be CASA images or FITS images.
53 NOTE: Index values start at 0 Use the imhead task to see the range of
54 index values for each axes.
57 Keyword arguments:
58 imagename input image name(s)
59 Default: none;
60 Examples: mode='evalexpr'; imagename=['image1.im', 'image2.im' ]
61 The text 'IM0' is replaced by 'image1.im' in the
62 expression and 'IM1' is repalced with 'image2.im'
63 mode='spix'; imagename=['image1.im','image2.im'] will calculate
64 an image of log(S1/S2)/log(f1/f2), where S1 and S2 are fluxes and
65 f1 and f2 are frequencies
66 mode='pola'; imagename='multistokes.im' (where that image contains both Q and U
67 stokes planes) or imagename=['imageQ.im','imageU.im'] will calculate
68 an image of polarization angle distribution, where imageQ.im and
69 imageU.im are Stokes Q and U images, respectively. Calculate 0.5*arctan(U/Q).
70 mode='poli'; imagename=['imageQ.im','imageU.im','imageV.im'] will calculate
71 total polarization intensity image, where imageQ.im, imageU.im, imageV.im
72 are Stokes Q, U, and V images, respectively. Alternatively, with
73 imagename = ['imageQ.im','imageU.im'] the linear polarization intensity
74 image will be calculated. In the case where imagename is a single multi-stokes
75 image, the total polarization image will be calculated if all of the Q, U, and
76 V stokes planes are present, and the linear polarization intensity image will
77 be calculated if the Q and U (but not V) planes are present.
79 mode mode for mathematical operation
80 Default: evalexpr
81 Options: 'evalexpr' : evalulate a mathematical expression defined in 'expr'
82 'spix' : spectalindex image
83 'pola' : polarization position angle image
84 'poli' : polarization intesity image
85 >>> mode expandable parameters
86 sigma (for mode='poli') standard deviation of noise of Stokes images with unit such as
87 Jy/beam to correct for bias
88 Default: '0.0Jy/beam' (= no debiasing)
89 polithresh (for mode='pola') Quantity (eg '30uJy/beam') describing the linear (not total;
90 the stokes V contribution is not included) polarization threshold. A mask ('mask0')
91 is written to the output image and is False for all corresponding linear polarization
92 values below this threshold. This parameter overrides the mask input parameter
93 (below). Default ('') means use the value given in mask, or no masking if that
94 value is empty as well.
95 expr (for mode='evalexpr') A LEL expression with images.
96 Image file names are specified in the imagenames paramter, and
97 the variables IM0, IM1, ... (or optionally via the varnames parameter, see below)
98 are used to represent these files
99 in the expression. Explicit notations of file names in the
100 expression are also supported, in which cases the file names must
101 be enclosed in double quotes (") and imagename is ignored.
102 Examples:
103 Make an image that is image1.im - image2.im
104 expr=' (IM0 - IM1 )'
105 or with an explicit notation,
106 expr='("image1.im" - "image2.im")'
107 Clip an image below a value (0.5 in this case)
108 expr = ' iif( IM0 >=0.5, IM0, 0.0) '
109 Note: iif (a, b, c) a is the boolean expression
110 b is the value if true
111 c is the value if false
112 Take the rms value of two images
113 expr = ' sqrt(IM0 * IM0 + IM1 * IM1) '
114 Build an image pixel by pixel from the minimum of (image2.im, 2*image1.im)
115 expr='min(IM1,2*max(IM0))'
116 varnames For mode="evalexpr". Instead of the default variable names IM0, IM1, ..., use
117 the names in this array to represent the input images.
118 outfile The output image. Overwriting an existing outfile is not permitted.
119 Default: immath_results.im; Example: outfile='results.im'
120 mask Mask to use. Default is none. Also see polithresh.
121 stretch Stretch the input mask if necessary and possible. See below.
122 region Region selection. Default is to use the full image.
123 box Rectangular region to select in direction plane. Default
124 is to use the entire direction plane.
125 Example: box='10,10,50,50'
126 chans Channels to use. Default is to use all channels.
127 stokes Stokes planes to use. Default is to use all Stokes planes.
128 Not used in for cases of mode='poli' or mode='pola'
129 imagemd The image from which metadata should be copied to the output. Default means no guarantee from
130 which image is used. The image must exist and should conform to the output image spec.
132 Available functions in the expr and mask parameters:
133 pi(), e(), sin(), sinh(), asinh(), cos(), cosh(), tan(), tanh(),
134 atan(), exp(), log(), log10(), pow(), sqrt(), complex(), conj()
135 real(), imag(), abs(), arg(), phase(), amplitude(), min(), max()
136 round(), isgn(), floor(), ceil(), rebin(), spectralindex(), pa(),
137 iif(), indexin(), replace(), ...
139 If the mask has fewer dimensions than the image and if the shape
140 of the dimensions the mask and image have in common are the same,
141 the mask will automatically have the missing dimensions added so
142 it conforms to the image.
144 For a full description of the allowed syntax see the
145 Lattice Expression Language (LEL) documentation on the at:
146 http://aips2.nrao.edu/docs/notes/223/223.html
148 NOTE: where indexing and axis numbering are used in the above
149 functions they are 1-based, ie. numbering starts at 1.
151 If stretch is true and if the number of mask dimensions is less than
152 or equal to the number of image dimensions and some axes in the
153 mask are degenerate while the corresponding axes in the image are not,
154 the mask will be stetched in the degenerate axis dimensions. For example,
155 if the input image has shape [100, 200, 10] and the input
156 mask has shape [100, 200, 1] and stretch is true, the mask will be
157 stretched along the third dimension to shape [100, 200, 10]. However if
158 the mask is shape [100, 200, 2], stretching is not possible and an
159 error will result.
161 CAUTIONS REGARDING OUTPUT IMAGE METADATA, INCLUDING BRIGHTNESS UNIT
163 EXCEPT IN THE CASES NOTED BELOW, THIS APPLICATION MAKES NO ATTEMPT TO
164 DETERMINE WHAT THE CORRECT BRIGHTNESS UNIT OF THE OUTPUT IMAGE SHOULD BE. THIS
165 RESPONSIBILITY LIES SOLELY WITH THE USER. The brightness unit of the output image
166 can be modified using tool method ia.setbrightnessunit() or task imhead with
167 mode='put' and hdkey='bunit'.
169 Note that when multiple image are used in the expression, there is
170 no garauntee about which of those images will be used to create the metadata
171 of the output image, unless imagemd is specified. If imagemd is specified, the following
172 rules of metadata copying will be followed:
174 1. The pixel data type of the image specified by imagemd and the output image must
175 be the same.
176 2. The metadata copied include the coordinate system (and so of course the dimensionality of
177 the output image must correspond to the coordinate system to be copied), the image_info record
178 (which contains things like the beam(s)), the misc_info record (should one exist in the image
179 specified by imagemd), and the units.
180 3. If the output image is a spectral image, the brightness units are set to the empty string.
181 4. If the ouptut image is a polarization angle image, the brightness unit is set to "deg" and
182 the stokes coordinate is set to have a single plane of type of Pangle.
184 Examples:
185 # Double all values in an image.
186 immath( imagesname='myimage.im', expr='IM0*2', outfile='double.im' )
187 # or with an explicit notation,
188 immath( expr='"myimage.im"*2', outfile='double.im' )
190 # Taking the sin of an image and adding it to another
191 # Note that the images need to be the same size
192 immath(images=['image1.im', 'image2.im'], expr='sin(IM1)+IM0;',outfile='newImage.im')
194 # Adding only the plane associated with the 'V' stokes value and
195 # the 1st channel together in two images
196 immath(imagename=[image1', 'image2'], expr='IM0+IM1',chans='1',stokes='V')
199 # Selecting a single plane (5th channel), of the 3-D cube and
200 # adding it to the original image. In this example the 2-D plane
201 # gets expanded out and the values are applied to each plane in the
202 # 3-D cube.
203 default('immath')
204 imagename='ngc7538.image'
205 outfile='chanFive.im'
206 expr='IM0'
207 chans='5'
208 go
209 default('immath')
210 imagename=['ngc7538.image', chanFive.im']
211 outfile='ngc7538_chanFive.im'
212 expr='IM0+IM1'
213 go
215 # Selecting and saving the inner 3/4 of an image for channels 40,42,44
216 # as well as channels less than 10
217 default('immath')
218 imagename='my_image.im'
219 expr='IM0'
220 box='25,25,123,123'
221 chans='<10;40,42,44'
222 outfile='my_image_inner.im' )
223 go
225 # Dividing an image by another, making sure we aren't dividing by zero
226 default('immath')
227 imagename=['orion.image', 'my.image']
228 expr='IM0/iif(IM1==0,1.0,IM1)'
229 outfile='my_orion.image'
230 go
232 # Applying a mask to all of the images in the expression
233 default('immath')
234 imagename=['ngc7538.image','ngc7538_clean.image']
235 expr='(IM0*10)+IM1'
236 mask='"ngc7538.mask"'
237 outfile='really_noisy_ngc7538.image'
238 go
241 # Applying a pixel mask contained in the image information
242 default('immath')
243 imagename='ngc5921.image'
244 expr='IM0*10'
245 mask='mask("ngc5921.mask")'
246 outfile='ngc5921.masked.image'
247 go
249 # Creating a total polarization intensity image from an multi-stokes image
250 # containing IQUV.
251 default('immath')
252 outfile='pol_intensity'
253 stokes=''
254 # in imagename, you can also specify a list containing single stokes images
255 # of Q and U (for linear polarization intensity) and V (for total
256 # polarization intensity)
257 imagename='3C138_pcal'
258 mode='poli'
259 go
261 # Creating a polarization position angle image
262 default('immath')
263 outfile='pol_angle.im'
264 mode='pola'
265 # you can also do imagename=['Q.im','U.im'] for single stokes images, order of
266 # the two Stokes images does not matter
267 imagename='3C138_pcal' # multi-stokes image containing at least Q and U stokes
268 go
270 # same as before but write a mask with values of False for pixels for which the
271 # corresponding linear polarization ( sqrt(Q*Q+U*U)) is less than 30 microJy/beam
272 polithresh='30uJy/beam'
273 go
275 # Creating a spectral index image from the images at two different observing frequencies
276 default('immath')
277 outfile='mySource_sp.im'
278 mode='spix'
279 imagename=['mySource_5GHz.im','mySource_8GHz.im']
280 go
282 TEMPORARY IMAGES
284 At this time, it is usually necessary for this task to create intermediate, temporary disk images.
285 The names of these images start with '_immath' and are created in the directory in which the task
286 is run. The task makes reasonable attempts to remove these images before it exits, but there are
287 conceivably instances where the temporary images may not be automatically deleted. It is generally
288 safe to delete them by hand, assuming no immath instance is currently in progress.
290 The hope and plan is that the necessity of these images will decrease in the future (i.e. the computations
291 will require only RAM and not temporary persistent storage of intermediate results).
296 """
298 _info_group_ = """analysis"""
299 _info_desc_ = """Perform math operations on images"""
301 def __call__( self, imagename='', mode='evalexpr', outfile='immath_results.im', expr='IM0', varnames='', sigma='0.0mJy/beam', polithresh='', mask='', region='', box='', chans='', stokes='', stretch=False, imagemd='', prec='float' ):
302 schema = {'imagename': {'type': 'cVariant', 'coerce': [_coerce.to_variant]}, 'mode': {'type': 'cStr', 'coerce': _coerce.to_str, 'allowed': [ 'lpoli', 'poli', 'evalexpr', 'spix', 'tpoli', 'pola' ]}, 'outfile': {'type': 'cStr', 'coerce': _coerce.to_str}, 'expr': {'type': 'cStr', 'coerce': _coerce.to_str}, 'varnames': {'type': 'cVariant', 'coerce': [_coerce.to_variant]}, 'sigma': {'type': 'cStr', 'coerce': _coerce.to_str}, 'polithresh': {'type': 'cStr', 'coerce': _coerce.to_str}, 'mask': {'type': 'cStr', 'coerce': _coerce.to_str}, 'region': {'type': 'cStr', 'coerce': _coerce.to_str}, 'box': {'type': 'cStr', 'coerce': _coerce.to_str}, 'chans': {'type': 'cStr', 'coerce': _coerce.to_str}, 'stokes': {'type': 'cStr', 'coerce': _coerce.to_str}, 'stretch': {'type': 'cBool'}, 'imagemd': {'type': 'cStr', 'coerce': _coerce.to_str}, 'prec': {'type': 'cStr', 'coerce': _coerce.to_str}}
303 doc = {'imagename': imagename, 'mode': mode, 'outfile': outfile, 'expr': expr, 'varnames': varnames, 'sigma': sigma, 'polithresh': polithresh, 'mask': mask, 'region': region, 'box': box, 'chans': chans, 'stokes': stokes, 'stretch': stretch, 'imagemd': imagemd, 'prec': prec}
304 assert _pc.validate(doc,schema), create_error_string(_pc.errors)
305 _logging_state_ = _start_log( 'immath', [ 'imagename=' + repr(_pc.document['imagename']), 'mode=' + repr(_pc.document['mode']), 'outfile=' + repr(_pc.document['outfile']), 'expr=' + repr(_pc.document['expr']), 'varnames=' + repr(_pc.document['varnames']), 'sigma=' + repr(_pc.document['sigma']), 'polithresh=' + repr(_pc.document['polithresh']), 'mask=' + repr(_pc.document['mask']), 'region=' + repr(_pc.document['region']), 'box=' + repr(_pc.document['box']), 'chans=' + repr(_pc.document['chans']), 'stokes=' + repr(_pc.document['stokes']), 'stretch=' + repr(_pc.document['stretch']), 'imagemd=' + repr(_pc.document['imagemd']), 'prec=' + repr(_pc.document['prec']) ] )
306 task_result = None
307 try:
308 task_result = _immath_t( _pc.document['imagename'], _pc.document['mode'], _pc.document['outfile'], _pc.document['expr'], _pc.document['varnames'], _pc.document['sigma'], _pc.document['polithresh'], _pc.document['mask'], _pc.document['region'], _pc.document['box'], _pc.document['chans'], _pc.document['stokes'], _pc.document['stretch'], _pc.document['imagemd'], _pc.document['prec'] )
309 except Exception as exc:
310 _except_log('immath', exc)
311 raise
312 finally:
313 task_result = _end_log( _logging_state_, 'immath', task_result )
314 return task_result
316immath = _immath( )