#
# stub function definition file for docstring parsing
#
[docs]def imbaseline(imagename, linefile='', output_cont=False, bloutput='', maskmode='list', chans='', thresh=5.0, avg_limit=4, minwidth=4, edge=[0, 0], blfunc='poly', order=5, npiece=3, applyfft=True, fftthresh=3.0, addwn=[0], rejwn='', blparam='', clipniter=0, clipthresh=3.0, dirkernel='none', major='', minor='', pa='', kimage='', scale=-1.0, spkernel='none', kwidth=5):
r"""
Image-based baseline subtraction for single-dish data
[`Description`_] [`Examples`_] [`Development`_] [`Details`_]
Parameters
- imagename_ (path) - Name of the input spectral line image
- linefile_ (path='') - output continuum subtracted image file name. If it is not specified, it will be imagename + "_bs".
- output_cont_ (bool=False) - output continuum image. Name will be imagename + ".cont"
- bloutput_ (path='') - name of file in which best-fit parameters are written. No output if "" (default).
- maskmode_ (string='list') - mode of setting additional channel masks. "list" and "auto" are available now.
.. raw:: html
<details><summary><i> maskmode = auto </i></summary>
- thresh_ (double=5.0) - S/N threshold for linefinder
- avg_limit_ (int=4) - channel averaging for broad lines
- minwidth_ (int=4) - the minimum channel width to detect as a line
- edge_ (intVec=[0, 0]) - channels to drop at beginning and end of spectrum
.. raw:: html
</details>
- blfunc_ (string='poly') - baseline model function ["poly", "chebyshev", "cspline", "sinusoid", or "variable"(expert mode)]
.. raw:: html
<details><summary><i> blfunc = poly </i></summary>
- order_ (int=5) - order of baseline model function
- clipthresh_ (double=3.0) - clipping threshold for iterative fitting
- clipniter_ (int=0) - maximum iteration number for iterative fitting
.. raw:: html
</details>
.. raw:: html
<details><summary><i> blfunc = chebyshev </i></summary>
- order_ (int=5) - order of baseline model function
- clipthresh_ (double=3.0) - clipping threshold for iterative fitting
- clipniter_ (int=0) - maximum iteration number for iterative fitting
.. raw:: html
</details>
.. raw:: html
<details><summary><i> blfunc = cspline </i></summary>
- npiece_ (int=3) - number of element polynomials for cubic spline curve
- clipthresh_ (double=3.0) - clipping threshold for iterative fitting
- clipniter_ (int=0) - maximum iteration number for iterative fitting
.. raw:: html
</details>
.. raw:: html
<details><summary><i> blfunc = sinusoid </i></summary>
- applyfft_ (bool=True) - automatically set wave numbers of sinusoids
- fftthresh_ (double=3.0) - threshold to select wave numbers of sinusoids
- addwn_ (intVec=[0]) - additional wave numbers to use
- rejwn_ (intVec='') - wave numbers NOT to use
- clipthresh_ (double=3.0) - clipping threshold for iterative fitting
- clipniter_ (int=0) - maximum iteration number for iterative fitting
.. raw:: html
</details>
.. raw:: html
<details><summary><i> blfunc = variable </i></summary>
- blparam_ (string='') - text file that stores per spectrum fit parameters
.. raw:: html
</details>
- dirkernel_ (string='none') - Type of kernel to use to direction plane smoothing. Acceptable values are "none" to omit smoothing(default), "boxcar" for a boxcar kernel, "gaussian" for a gaussian kernel, "image" to use an image as the kernel.
.. raw:: html
<details><summary><i> dirkernel = gaussian </i></summary>
- major_ (string='') - Major axis for the kernels. Standard quantity representation. Must be specified for dirkernel="boxcar" or "gaussian".
- minor_ (string='') - Minor axis. Standard quantity representation. Must be specified for dirkernel="boxcar" or "gaussian".
- pa_ (string='') - Position angle used only for gaussian kernel. Standard quantity representation.
.. raw:: html
</details>
.. raw:: html
<details><summary><i> dirkernel = boxcar </i></summary>
- major_ (string='') - Major axis for the kernels. Standard quantity representation. Must be specified for dirkernel="boxcar" or "gaussian".
- minor_ (string='') - Minor axis. Standard quantity representation. Must be specified for dirkernel="boxcar" or "gaussian".
.. raw:: html
</details>
.. raw:: html
<details><summary><i> dirkernel = image </i></summary>
- kimage_ (path='') - Kernel image name. Only used if dirkernel="image".
- scale_ (double=-1.0) - Scale factor. -1.0 means auto-scale. Only used if dirkernel="image".
.. raw:: html
</details>
- spkernel_ (string='none') - Type of spectral smoothing kernel. Acceptable values are "none" to omit smoothing(default), "gaussian" for a gaussian kernel, "boxcar" for a boxcar kernel.
.. raw:: html
<details><summary><i> spkernel = gaussian </i></summary>
- kwidth_ (int=5) - smoothing kernel width in channel. Only used if spkernel="gaussian" or "boxcar".
.. raw:: html
</details>
.. raw:: html
<details><summary><i> spkernel = boxcar </i></summary>
- kwidth_ (int=5) - smoothing kernel width in channel. Only used if spkernel="gaussian" or "boxcar".
.. raw:: html
</details>
.. _Description:
Description
`imbaseline <./casatasks.analysis.imbaseline.html>`__ is a task to do image-based baseline subtraction for single-dish data. This task is based on `sdbaseline <casatasks.single.sdbaseline.html>`__. Input file format of `sdbaseline <casatasks.single.sdbaseline.html>`__ is Measurement Set, while CASA Image format is used for the input of `imbaseline <./casatasks.analysis.imbaseline.html>`__. The computing processes of fitting and subtracting are common in both tasks, and the options of `imbaseline <./casatasks.analysis.imbaseline.html>`__ consist of subset of `sdbaseline <casatasks.single.sdbaseline.html>`__.
If users need to reduce the noise in input data before baseline subtraction, `imbaseline <./casatasks.analysis.imbaseline.html>`__ can make smoothing in the spatial plane and/or spectral axis setting parameters of *dirkernel* and *spkernel*, respectively. These features are based on `imsmooth <./casatasks.analysis.imsmooth.html>`__ and `sdsmooth <./casatasks.single.sdsmooth.html>`__, respectively.
**Spatial plane smoothing** performs a Fourier-based convolution to smooth the spatial plane of input data using a user-specified smoothing kernel. The parameter *dirkernel* can be specified as *gaussian*, *boxcar*, or *image*. They are same parameters *kernel* of the task `imsmooth <./casatasks.analysis.imsmooth.html>`__. Usage of parameters related *dirkernel* is same as those used in `imsmooth <./casatasks.analysis.imsmooth.html>`__.
**Spectral axis smoothing** can be performed using a user-specified smoothing kernel. The parameter *spkernel* can be specified as *gaussian* or *boxcar*. They are same parameters *kernel* of the task `sdsmooth <./casatasks.single.sdsmooth.html>`__. Usage of parameters related *spkernel* is same as those used in `sdsmooth <./casatasks.single.sdsmooth.html>`__.
**Baseline fitting and subtraction** can be performed with specifying a parameter *blfunc* either *poly*, *chebyshev*, *cspline*, *sinusoid*, or *variable*. The parameter *maskmode* can be specified as *list* or *auto*. Usage of parameters related *blfunc* and *maskmode* are same as those used in `sdbaseline <casatasks.single.sdbaseline.html>`__.
Note
* The format of the file specified by *bloutput* should be CSV format when using `imbaseline <./casatasks.analysis.imbaseline.html>`__.
* If the parameter *output_cont* sets *True*, the output continuum image is saved by subtracting an output image from an input image. The file will be named as *imagename* + "*.cont*".
.. _Examples:
Example
**Example 1**
This is one of the simplest examples fitting baselines using the sinusoidal function and subtracting. No smoothing processes are applied.
::
imbaseline(imagename='my_image.im',
linefile='output.im',
blfunc='sinusoid')
**Example 2**
Following example shows baseline fitting and subtracting smoothing with the spatial plane. Parameters such as *major*, *minor*, and *pa*, should be specified when *dirkernel='gaussian'*.
::
imbaseline(imagename='my_image.im',
linefile='output.im',
blfunc='sinusoid',
dirkernel='gaussian',
major='20arcsec',
minor='10arcsec',
pa='0deg')
**Example 3**
Following examples shows baseline fitting and subtracting smoothing with the spectral axis.
::
imbaseline(imagename='my_image.im',
linefile='output.im',
spkernel='boxcar',
kwidth=5)
.. _Development:
Development
No additional development details
.. _Details:
Parameter Details
Detailed descriptions of each function parameter
.. _imagename:
| ``imagename (path)`` - Name of the input spectral line image
.. _linefile:
| ``linefile (path='')`` - output continuum subtracted image file name. If it is not specified, it will be imagename + "_bs".
.. _output_cont:
| ``output_cont (bool=False)`` - output continuum image. Name will be imagename + ".cont"
.. _bloutput:
| ``bloutput (path='')`` - name of file in which best-fit parameters are written. No output if "" (default).
.. _maskmode:
| ``maskmode (string='list')`` - mode of setting additional channel masks. "list" and "auto" are available now.
.. _chans:
| ``chans (string='')`` - Channels to be included in the fitting
.. _thresh:
| ``thresh (double=5.0)`` - S/N threshold for linefinder
.. _avg_limit:
| ``avg_limit (int=4)`` - channel averaging for broad lines
.. _minwidth:
| ``minwidth (int=4)`` - the minimum channel width to detect as a line
.. _edge:
| ``edge (intVec=[0, 0])`` - channels to drop at beginning and end of spectrum
.. _blfunc:
| ``blfunc (string='poly')`` - baseline model function ["poly", "chebyshev", "cspline", "sinusoid", or "variable"(expert mode)]
.. _order:
| ``order (int=5)`` - order of baseline model function
.. _npiece:
| ``npiece (int=3)`` - number of element polynomials for cubic spline curve
.. _applyfft:
| ``applyfft (bool=True)`` - automatically set wave numbers of sinusoids
.. _fftthresh:
| ``fftthresh (double=3.0)`` - threshold to select wave numbers of sinusoids
.. _addwn:
| ``addwn (intVec=[0])`` - additional wave numbers to use
.. _rejwn:
| ``rejwn (intVec='')`` - wave numbers NOT to use
.. _blparam:
| ``blparam (string='')`` - text file that stores per spectrum fit parameters
.. _clipniter:
| ``clipniter (int=0)`` - maximum iteration number for iterative fitting
.. _clipthresh:
| ``clipthresh (double=3.0)`` - clipping threshold for iterative fitting
.. _dirkernel:
| ``dirkernel (string='none')`` - Type of kernel to use to direction plane smoothing. Acceptable values are "none" to omit image smoothing(default), "boxcar" for a boxcar kernel, "gaussian" for a gaussian kernel, "image" to use an image as the kernel.
.. _major:
| ``major (string='')`` - Major axis for the kernels. Standard quantity representation. Must be specified for dirkernel="boxcar" or "gaussian".
.. _minor:
| ``minor (string='')`` - Minor axis. Standard quantity representation. Must be specified for dirkernel="boxcar" or "gaussian".
.. _pa:
| ``pa (string='')`` - Position angle used only for gaussian kernel. Standard quantity representation.
.. _kimage:
| ``kimage (path='')`` - Kernel image name. Only used if dirkernel="image".
.. _scale:
| ``scale (double=-1.0)`` - Scale factor. -1.0 means auto-scale. Only used if dirkernel="image".
.. _spkernel:
| ``spkernel (string='none')`` - Type of spectral smoothing kernel. Acceptable values are "none" to omit smoothing(default), "gaussian" for a gaussian kernel, "boxcar" for a boxcar kernel.
.. _kwidth:
| ``kwidth (int=5)`` - smoothing kernel width in channel. Only used if spkernel="gaussian" or "boxcar".
"""
pass