Exemplo n.º 1
0
def drawmaskinimage(image='', maskname='maskoo', makedefault=True):
    """
    Till casa think graphical interaction is important.
    Ugly Function that uses interactive clean image mask  to 
    allow users to draw a mask and store it as a bit mask in the image 
    so it can be used by imageanalysis methods or to mask an image

    Parameters

    image: is the image to put a bit mask in
    maskname: name of bit mask 
    makedefault: if True will make new bit mask drawn be the default mask

    """
    if (not os.path.exists(image)):
        return
    tmpmaskimage = '__muluktani'
    if (os.path.exists(tmpmaskimage)):
        shutil.rmtree(tmpmaskimage, True)
    im.drawmask(image=image, mask=tmpmaskimage)
    ia.open(image)
    ia.calcmask(mask='__muluktani < 0.5', name=maskname, asdefault=makedefault)
    ia.done()
    print 'regions/mask in ', image, rg.namesintable(image)
    shutil.rmtree(tmpmaskimage, True)
Exemplo n.º 2
0
def drawmaskinimage(image='', maskname='maskoo', makedefault=True):
    """
    Till casa think graphical interaction is important.
    Ugly Function that uses interactive clean image mask  to 
    allow users to draw a mask and store it as a bit mask in the image 
    so it can be used by imageanalysis methods or to mask an image

    Parameters

    image: is the image to put a bit mask in
    maskname: name of bit mask 
    makedefault: if True will make new bit mask drawn be the default mask

    """
    if(not os.path.exists(image)):
        return
    tmpmaskimage='__muluktani'
    if(os.path.exists(tmpmaskimage)):
        shutil.rmtree(tmpmaskimage, True)
    im.drawmask(image=image, mask=tmpmaskimage)
    ia.open(image)
    ia.calcmask(mask='__muluktani < 0.5', name=maskname, asdefault=makedefault)
    ia.done()
    print 'regions/mask in ', image, rg.namesintable(image)
    shutil.rmtree(tmpmaskimage, True)
Exemplo n.º 3
0
def blankcube(image,
              dummyMS,
              smooth=True,
              verbose=True,
              region='centerbox[[10h21m45s,18.05.14.9],[15arcmin,15arcmin]]',
              ruthless=False,
              extension='.image',
              beamround='int',
              blankThreshold=2.5,
              moments=[0]):
    '''
    Parameters
    ----------
    image : string
        Base name of image. If target image has extension other than '.image',
        change the extension keyword.

    dummyMS : string
        MS file required for blanking process in CASA

    smooth : bool, optional
        Smooth the image to a circular beam before blanking?
        Default True

    verbose : bool, optional

    region : string, optional
        region parameter featured in CASA

    ruthless : bool, optional
        Delete previous outputs from blankcube

    extension : string, optional
        Extension of the target image. Must include the '.', e.g., '.restored'
        Default '.image'

    beamround : string,float
        P

    blankThreshold : float, optional
        Initial blanking threshold of all pixels scaled by the standard
        deviation times the blankingthreshold
        Default = 2.5 (Walter et al. 2008)

    moments : list, optional
        Moments to calculate from cube. Options are 0,1,2.
        Example: [0,1,2]
        Default: [0]

    Returns
    -------
    out : null

    Examples
    --------

    '''

    from casa import immath, imsmooth, immoments
    from casa import image as ia
    from casa import imager as im
    from casa import quanta as qa
    import os
    import numpy as np

    # Delete files associated with previous runs
    if ruthless:
        os.system('rm -rf ' + image + '.smooth.blk.image')
        os.system('rm -rf ' + image + '.smooth.image')
        os.system('rm -rf ' + image + '.blk.image')
        os.system('rm -rf ' + image + '.mask')

    imageDir = './'

    # Create moment maps
    mom0, mom1, mom2 = False, False, False
    if len(moments) > 0:
        for i, moment in enumerate(moments):
            if moment == 0:
                mom0 = True
            if moment == 1:
                mom1 = True
            if moment == 2:
                mom2 = True
    if mom1 == True or mom2 == True:
        beamScale = 1.01
    elif mom0 == True:
        beamScale = 2.

    # determine beamsize of cube
    ia.open(imageDir + image + extension)
    beamsizes = np.zeros(ia.shape()[2])
    for i in range(ia.shape()[2]):
        beamsizes[i] = ia.restoringbeam(channel=i)['major']['value']
    beamsizeUnit = ia.restoringbeam(channel=i)['major']['unit']
    beamsize = qa.convert(str(beamsizes.max()) + beamsizeUnit,
                          'arcsec')['value']
    if type(beamround) == float:
        beamsize_smooth = beamround * beamsize
    else:
        beamsize_smooth = np.ceil(beamsize)  #beamsize_smooth = 1.01 * beamsize
    ia.close()

    if verbose:
        print 'Max beamsize is ' + str(beamsize) + '"'

    if not os.path.exists(image + '.blk.image'):
        # create cube for blanking
        if smooth:  # smooth to a larger beam if the user desires
            if verbose:
                print 'Convolving to ' + str(beamsize_smooth) + '"'

            imsmooth(imagename=image + extension,
                     outfile=image + '.blk.image',
                     major=str(beamsize_smooth) + 'arcsec',
                     minor=str(beamsize_smooth) + 'arcsec',
                     region=region,
                     pa='0deg',
                     targetres=True)
        else:  # do no smooth
            immath(imagename=image + extension,
                   outfile=image + '.blk.image',
                   mode='evalexpr',
                   region=region,
                   expr='IM0')

    if not os.path.exists(image + '.smooth.image'):
        # convolve cube to 2X beam for blanking
        imsmooth(imagename=image + extension,
                 outfile=image + '.smooth.image',
                 major=str(beamsize * beamScale) + 'arcsec',
                 minor=str(beamsize * beamScale) + 'arcsec',
                 pa='0deg',
                 region=region,
                 targetres=True)

    # determine threshold of cube
    ia.open(image + '.smooth.image')
    threshold = ia.statistics()['sigma'][0] * blankThreshold
    ia.close()

    # blank the cube at threshold*sigma
    ia.open(image + '.smooth.image')
    ia.calcmask(mask=image + '.smooth.image > ' + str(threshold), name='mask1')
    wait = 'waits for calcmask to close'
    ia.close()

    # hand blank the cube
    im.open(dummyMS)
    pause = None
    while pause is None:
        im.drawmask(image=image + '.smooth.image', mask=image + '.mask')
        pause = 0
    im.close

    # mask contains values of 0 and 1, change to a mask with only values of 1
    ia.open(image + '.mask')
    ia.calcmask(image + '.mask' + '>0.5')
    ia.close()

    # apply mask on smoothed image
    immath(imagename=image + '.smooth.image',
           outfile=image + '.smooth.blk.image',
           mode='evalexpr',
           mask='mask(' + image + '.mask)',
           expr='IM0')

    # apply mask on image
    ia.open(imageDir + image + '.blk.image')
    ia.maskhandler('copy', [image + '.smooth.blk.image:mask0', 'newmask'])
    ia.maskhandler('set', 'newmask')
    ia.done()

    cube = '.blk.image'  # specify name of cube for moment calculation

    # create moment 0 map
    if mom0:
        if ruthless:
            os.system('rm -rf ' + image + '.mom0.image')
        immoments(imagename=image + cube,
                  moments=[0],
                  axis='spectra',
                  chans='',
                  mask='mask(' + image + cube + ')',
                  outfile=image + '.mom0.image')

    # create moment 1 map
    if mom1:
        if ruthless:
            os.system('rm -rf ' + image + '.mom1.image')
        immoments(imagename=image + cube,
                  moments=[1],
                  axis='spectra',
                  chans='',
                  mask='mask(' + image + cube + ')',
                  outfile=image + '.mom1.image')

    # create moment 2 map
    if mom2:
        if ruthless:
            os.system('rm -rf ' + image + '.mom2.image')
        immoments(imagename=image + cube,
                  moments=[2],
                  axis='spectra',
                  chans='',
                  mask='mask(' + image + cube + ')',
                  outfile=image + '.mom2.image')

    if verbose and mom0:
        from casa import imstat
        flux = imstat(image + '.mom0.image')['flux'][0]
        ia.open(image + '.mom0.image')
        beammaj = ia.restoringbeam(channel=0)['major']['value']
        beammin = ia.restoringbeam(channel=0)['minor']['value']
        beamsizeUnit = ia.restoringbeam(channel=0)['major']['unit']
        ia.close()
        print 'Moment Image: ' + str(image) + '.mom0.image'
        print 'Beamsize: ' + str(beammaj) + '" X ' + str(beammin) + '"'
        print 'Flux: ' + str(flux) + ' Jy km/s'
Exemplo n.º 4
0
def blankcube(image,
              dummyMS,
              smooth=True,
              verbose=True,
              region='centerbox[[10h21m45s,18.05.14.9],[15arcmin,15arcmin]]',
              ruthless=False,
              extension='.image',
              beamround='int',
              blankThreshold=2.5,
              moments=[0]):

    '''
    Parameters
    ----------
    image : string
        Base name of image. If target image has extension other than '.image',
        change the extension keyword.

    dummyMS : string
        MS file required for blanking process in CASA

    smooth : bool, optional
        Smooth the image to a circular beam before blanking?
        Default True

    verbose : bool, optional

    region : string, optional
        region parameter featured in CASA

    ruthless : bool, optional
        Delete previous outputs from blankcube

    extension : string, optional
        Extension of the target image. Must include the '.', e.g., '.restored'
        Default '.image'

    beamround : string,float
        P

    blankThreshold : float, optional
        Initial blanking threshold of all pixels scaled by the standard
        deviation times the blankingthreshold
        Default = 2.5 (Walter et al. 2008)

    moments : list, optional
        Moments to calculate from cube. Options are 0,1,2.
        Example: [0,1,2]
        Default: [0]

    Returns
    -------
    out : null

    Examples
    --------

    '''

    from casa import immath,imsmooth,immoments
    from casa import image as ia
    from casa import imager as im
    from casa import quanta as qa
    import os
    import numpy as np

    # Delete files associated with previous runs
    if ruthless:
        os.system('rm -rf ' + image + '.smooth.blk.image')
        os.system('rm -rf ' + image + '.smooth.image')
        os.system('rm -rf ' + image + '.blk.image')
        os.system('rm -rf ' + image + '.mask')

    imageDir = './'

    # Create moment maps
    mom0,mom1,mom2 = False,False,False
    if len(moments) > 0:
        for i, moment in enumerate(moments):
            if moment == 0:
                mom0 = True
            if moment == 1:
                mom1 = True
            if moment == 2:
                mom2 = True
    if mom1 == True or mom2 == True:
        beamScale = 1.01
    elif mom0 == True:
        beamScale = 2.

    # determine beamsize of cube
    ia.open(imageDir + image + extension)
    beamsizes = np.zeros(ia.shape()[2])
    for i in range(ia.shape()[2]):
        beamsizes[i] = ia.restoringbeam(channel=i)['major']['value']
    beamsizeUnit = ia.restoringbeam(channel=i)['major']['unit']
    beamsize = qa.convert(str(beamsizes.max()) + beamsizeUnit,'arcsec')['value']
    if type(beamround) == float:
        beamsize_smooth = beamround*beamsize
    else:
        beamsize_smooth = np.ceil(beamsize)   #beamsize_smooth = 1.01 * beamsize
    ia.close()

    if verbose:
        print 'Max beamsize is ' + str(beamsize) + '"'

    if not os.path.exists(image + '.blk.image'):
        # create cube for blanking
        if smooth: # smooth to a larger beam if the user desires
            if verbose:
                print 'Convolving to ' + str(beamsize_smooth) + '"'

            imsmooth(imagename=image + extension,
                     outfile=image + '.blk.image',
                     major=str(beamsize_smooth) + 'arcsec',
                     minor=str(beamsize_smooth) + 'arcsec',
                     region=region,
                     pa='0deg',
                     targetres=True)
        else: # do no smooth
            immath(imagename=image + extension,
               outfile=image + '.blk.image',
                mode='evalexpr',
                region=region,
                expr='IM0')

    if not os.path.exists(image + '.smooth.image'):
        # convolve cube to 2X beam for blanking
        imsmooth(imagename=image + extension,
             outfile=image + '.smooth.image',
             major=str(beamsize*beamScale) + 'arcsec',
             minor=str(beamsize*beamScale) + 'arcsec',
             pa='0deg',
             region=region,
             targetres=True)

    # determine threshold of cube
    ia.open(image + '.smooth.image')
    threshold = ia.statistics()['sigma'][0] * blankThreshold
    ia.close()

    # blank the cube at threshold*sigma
    ia.open(image + '.smooth.image')
    ia.calcmask(mask=image + '.smooth.image > ' + str(threshold),
             name='mask1')
    wait = 'waits for calcmask to close'
    ia.close()

    # hand blank the cube
    im.open(dummyMS)
    pause = None
    while pause is None:
        im.drawmask(image=image + '.smooth.image',
                           mask=image + '.mask')
        pause = 0
    im.close

    # mask contains values of 0 and 1, change to a mask with only values of 1
    ia.open(image + '.mask')
    ia.calcmask(image + '.mask' + '>0.5')
    ia.close()

    # apply mask on smoothed image
    immath(imagename=image + '.smooth.image',
       outfile=image + '.smooth.blk.image',
       mode='evalexpr',
       mask='mask(' + image + '.mask)',
       expr='IM0')

    # apply mask on image
    ia.open(imageDir + image + '.blk.image')
    ia.maskhandler('copy',[image + '.smooth.blk.image:mask0', 'newmask'])
    ia.maskhandler('set','newmask')
    ia.done()

    cube = '.blk.image' # specify name of cube for moment calculation


    # create moment 0 map
    if mom0:
        if ruthless:
            os.system('rm -rf ' + image + '.mom0.image')
        immoments(imagename=image + cube,
                  moments=[0],
                  axis='spectra',
                  chans='',
                  mask='mask(' + image + cube + ')',
                  outfile=image + '.mom0.image')

    # create moment 1 map
    if mom1:
        if ruthless:
            os.system('rm -rf ' + image + '.mom1.image')
        immoments(imagename=image + cube,
                  moments=[1],
                  axis='spectra',
                  chans='',
                  mask='mask(' + image + cube + ')',
                  outfile=image + '.mom1.image')

    # create moment 2 map
    if mom2:
        if ruthless:
            os.system('rm -rf ' + image + '.mom2.image')
        immoments(imagename=image + cube,
                  moments=[2],
                  axis='spectra',
                  chans='',
                  mask='mask(' + image + cube + ')',
                  outfile=image + '.mom2.image')

    if verbose and mom0:
	from casa import imstat
        flux = imstat(image + '.mom0.image')['flux'][0]
        ia.open(image + '.mom0.image')
        beammaj = ia.restoringbeam(channel=0)['major']['value']
        beammin = ia.restoringbeam(channel=0)['minor']['value']
        beamsizeUnit = ia.restoringbeam(channel=0)['major']['unit']
        ia.close()
        print 'Moment Image: ' + str(image) + '.mom0.image'
        print 'Beamsize: ' + str(beammaj) + '" X ' + str(beammin) + '"'
        print 'Flux: ' + str(flux) + ' Jy km/s'