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- imexam() User Methods

# imexam() User Methods

These are methods particular to the imexam package which are meant to aid users in their image analysis. They are called from the main object you created with imexam.connect().

close ():

  close the image viewing window and end the connection.

      viewer.close()

view (img, header=None, frame=None, asFits=False):

  Load an image array into the image viewing frame, if no frame is specified, the current frame is used. If no frame exists, then a new one is created. A basic header is created and sent to DS9. You can look at this header with disp_header() but get_header() will return an error because it looks for a filename, and no file was loaded, just the array. No header is sent to the Ginga widget.

      image_array=fits.getdata('image.fits')
      viewer.view(image_array)

      or

      image_array=numpy.ones([100,100])*numpy.random.rand(100)
      viewer.view(image_array)

readcursor ():

  Returns image coordinate postion and key pressed as a tuple of the for float(x), float(y), str(key).

      In [1]: viewer.readcursor()
      Out[2]: (56.0, 28.333333, 'a')

      or with a click of the first mouse button

      In [1]: viewer.readcursor()
      Out[2]: (67.333333, 80.0, '<1>')

make_region (infile,doLabels=False):

  Make an input reg file which contains rows with “x,y,comment” into a region file that the DS9 viewer recognizes.

  infile: str
    input filename
  labels: bool
    add labels to the regions
  header: int
    number of header lines in text file to skip
  textoff: int
    offset in pixels for labels
  rtype: str
    region type, one of the acceptable DS9 regions
  size: int
    size of the region type

      Here's what the input file 'test' looks like:

      100,100, 1
      200,200, 2
      300,300, comment 3

      viewer.make_region('test',labels=True)

      And the output region file:

      image; circle(100,100,5)
      image;text(110.0,110.0{ 1 })# font="time 12 bold"
      image; circle(200,200,5)
      image;text(210.0,210.0{ 2 })# font="time 12 bold"
      image; circle(300,300,5)
      image;text(310.0,310.0{ comment 3 })# font="time 12 bold"

Now let’s load the region file into our image:

mark_region_from_array (input_points,rtype=”circle”,ptype=”image”,textoff=10,size=5):

  mark regions on the display given a list of tuples, a single tuple, or a string, where each object has x,y,comment specified

  input_points: a tuple, or list of tuples, or a string which contain: (x,y,comment),

  ptype: string
    the reference system for the point locations, image|physical|fk5
  rtype: string
    the matplotlib style marker type to display
  size: int
    the size of the region marker
  textoff: string
    the offset for the comment text, if comment is empty it will not show

      locations=list()
      locations.append( (100,100,1) )
      locations.append( (200,200,2) )
      locations.append( (300,300,'comment 3') )

      viewer.mark_region_from_array(locations)

setlog (self, filename=None, on=True, level=logging.DEBUG):

  Turn on and off imexam logging to the a file. You can set the filename to something specific or let the package record to the default logfile. Once you give the object a logfile name, it will continue to use that file until you change it.

      In [5]: viewer.setlog()
      Saving imexam commands to imexam_log.txt

This is what’s displayed in the terminal when you use imexam():

and this is what shows up in the logfile:

You can see there are some leftovers from a previous logging session to the same file. You can toggle logging during a session too:

>     viewer.setlog(on=False)

set_region (region_string):
  Use this to send the DS9 viewer a formatted region string it’s expecting

For example, in DS9:

    viewer.set_region("text 110.0 110.0 '1' #font=times")

    See the DS9 XPA documentation for more examples.

unlearn ():
  Reset all the imexam default parameters
get_data_filename ():

  Return the filename for the data in the current window

      In [1]: viewer.get_data_filename()
      Out[2]: '/Users/sosey/ssb/imexam/iabf01bzq_flt.fits'

get_frame_info ():

  Return more explicit information about the data displayed in the current frame. A dictionary of the information is returned.

      In [1]: viewer.get_frame_info()

          {'extname': 'SCI',
          'extver': 1,
          'filename': '/Users/sosey/ssb/imexam/iabf01bzq_flt.fits',
          'iscube': False,
          'mef': True,
          'naxis': 0,
          'numaxis': 2,
          'user_array': None}

get_viewer_info ():

  Return a dictionary which contains information about all frames which have data loaded. This could be useful to users who are scripting an analysis for polling what items are available, how many frames or displayed, what type of data is hanging around, etc ...

      In [1]: viewer.get_viewer_info()

      {'1': {'extname': 'SCI',
        'extver': 1,
        'filename': '/Users/sosey/ssb/imexam/iabf01bzq_flt.fits',
        'iscube': False,
        'mef': True,
        'naxis': 0,
        'numaxis': 2,
        'user_array': None}}

plotname:

  change or show the default save plotname for imexamine

      In [1]: viewer.plotname()
      imexam_plot.pdf

      In [2]: viewer.plotname('myplot.jpg')
      In [3]: viewer.plotname()
      myplot.jpg

The extension of the filename controls the plot type.

**display_help**():

  Display the help documentation into a webpage from the locally installed version. This is done from the main package:

      In [1]: import imexam

      In [2]: imexam.display_help()