A User's Manual For the CCD Data Acquisition User Interface
The following generic tools are found in every observing session
- Expose: form used to initiate
- Raster: form used to set up CCD raster
- Focus: form used to initiate manual focus
- Fraster: form used to set up CCD raster for
- Chip: form to set up preflash parameters
- Modes: form used to set up automatic display
and TCS enabling
- Image: form used to display and image with the
- Graph: form used to display image cuts.
- IQE: form used to compute image quality.
- Files: form used to manage image files on disc
and copy to tape.
- Suggestions: form used to send suggestions for
improvements or fixes to the system manager.
- News: delivers the latest news on the Data
Acquisition User Interface and the instrument.
- Aloha: form used to exit the observing
A CCD exposure is initiated by clicking the
Expose button in the menubar, filling out
the form and pressing Accept.
The user can enter the following:
- Exposure type:
object, bias, flat, dark or comparison.
- Exposure time in seconds.
- Number of iterations (not applicable for ``object'' type).
- Median processing: on / off
- Object name: will be written to the FITS header.
- Observer: will be written to the FITS header.
- Comment: will be written to the FITS header.
Note that the observer and
object name fields are ``sticky''. The exposure type
defaults to ``object'' each time when opening the form.
The Median option provides an online
capability for a fast and accurate combine algorithm for image sequences
(Iterations > 1). When you select
``normal'' median data option, a background
process will start (the process is currently handled by
``wiki'' the summit Sun SPARCstation). After each image is acquired, a
copy will be automatically sent to wiki, which will then convert the
FITS file to IRAF file format. After
completion of the acquisition of the sequence of images, a
``combine'' task will be invoked. It is based on the well
tested and widely used CCDRED/COMBINE task in the NOAO/IRAF data
processing environment. After extensive testing, we have decided to use
the ``average sigma clip'' option offered
by this task; it provides for the final image a mean identical to a
``median'' option, but with a standard
deviation better by 10%-15%. The average sigma
clip algorithm works as followings: a mean and a standard
deviation value are computed for each image pixel from the set of
images, after rejecting the minimum and maximum values, then pixels which values
are more than X (X~3) times
the standard deviation are rejected, and a final mean value is computed.
The current implementation of this option is extremely reliable and has
been extensively tested. We strongly recommend that you use it for
bias/flat/dark sequences. Many observers are not storing the individual
images of a sequence anymore, which saves both storage space and time.
Currently, we are saving all the images of a sequence to the optical
disc, but we are planning to save only the final combined image in the
second semester 1991. The current processing time for a sequence of ten
1024x1024 images is 10 minutes; this will be reduced to 90
seconds for ten 2048x2048 images by the end of 1991, with the
installation of more powerful computers.
Once the fields have been editted/selected, take the appropriate
action with one of the four
Start a CCD exposure by pressing Accept.
A CCD status icon will then appear.
It contains the following information:
- The file name that has been automatically linked to the CCD data
being acquired. It has the form of a number, representing the exposure
number in the CFHT archive system, followed by a letter:
o for object, f for flat, d
for dark, b for bias, c for comparison.
The extension .fits is added to indicate that the data on disc
is stored in FITS format. The file name is a crucial parameter to allow
you to locate your data, either on the summit discs while observing, or on
the CFHT archive
- The sequence number of the exposure (if you are running a
- The status of the CCD controller: expose when the
CCD is integrating, readout when the data is being read
- A count down timer: it indicates the remaining exposure time while
the CCD is integrating.
Moreover, a set of 5 buttons appear on the bottom of the icon. They offer the
- Stop will stop the exposure. This will
read-out the CCD and create a file of the appropriate name. You can do
this at any time during an integration. This will of course shorten the
- Abort will abort the exposure. No CCD
read out is provided and consequently the data is lost.
- Hold will stop the exposure, but will not read
out the CCD. You can later use Restart to resume the
exposure. Although the total integration time is not modified, the CCD
dark current will keep accumulating while the exposure is on hold. The
total dark time is therefore the exposure time plus the hold time
(the field DARKTIME in the FITS
header will indicate the exact dark current time).
- Break will break a sequence. The exposure
currently being taken will be lost, and no further image will be
At the end of a CCD exposure, the data is transferred from the CCD
controller to the Data Acquisition Computer disc, and stored under the
FITS file name that was automatically assigned. Also, a copy of the file
is sent through the CFHT network down to Waimea, where it will be
automatically saved to an archive system. In case you
``lose'' or delete a file by mistake on the summit
disc, don't panic, make a note of the file number, and have someone
retrieve the file from the optical disc for you.
controls the area of interest and the binning factor to use when
reading out the CCD.
For CCD exposures controlled with Expose,
Raster applies, for focus exposures
controlled with Focus,
The Raster and Fraster forms
allow the user to modify the following parameters:
- Xc: the center of the raster along the CCD rows.
- Yc: the center of the raster along the CCD columns.
- Xs: the size of the raster along the CCD rows.
- Ys: the size of the raster along the CCD columns.
- Xbin: the binning factor along the CCD rows.
- Ybin: the binning factor along the CCD columns.
The Focus form allows the user
to define and start a (manual) focussing sequence.
The user can select:
- Video focus mode.
This mode reads the CCD out as fast as possible, and displays
the image only on the video system. No files are generated.
The following fields affect video focus:
- The exposure time in seconds.
- Analytical focus mode.
This mode takes an exposure, writes it to disc, and then runs IQE
on it to provide a quantitative evaluation of the focus.
The following fields affect analytical focus:
- The exposure time in seconds.
- The border of the frame to ignore in the background computation
for the image quality computation (edges often have saturated pixels
from the CCD control electronics in this mode).
- The location of the background computation.
When activated with Accept,
Focus uses the raster parameters defined in Fraster.
This form allows the user
to control the preflashing of the CCD.
Preflash defines the duration of the preflash. This must be set
depending on the individual CCD requirements. A preflash time of 0.0
must be entered for CCDs with no preflash.
The Modes form allows the user to select
automatic or manual image display after an exposure and automatic or manual
graphic display after an exposure.
The Image form allows the user to display
the image of his choice. After selecting/editing the fields, clicking
accept will start a new process call SAOimage or
CFHTimage (the local version of SAOimage.
- File name: image to be displayed. current.fits
refers to the most recent image acquired. Also previous.fits
refers to the image acquired previous to the most recent one.
- Contrast: ``Linear'' or ``Equalized
Histogram''. ``Linear'' will display the image scaled
linearly between a minimum and a maximum value computed automatically or
entered manually (see ``Level setting''). ``Equalized
Histogram'' will compute the image histogram, and select its
scaling based on the histogram mode: it is usually quite well adapted to
seeing the faintest object in an image.
- Level setting: ``Automatic'' will compute the min and
max values in the image and scale the greyscale to map the full range
of intensities. ``Manual'' will take the min and max values
entered by the user to map the greyscale.
The SAOimage display package was originally created by Mike
VanHilst at the Smithsonian Astrophysical Observatory.
It is a stand-alone image display with associated
built in functions. The CFHT version, CFHTimage, has been modified to
incorporate a few custom features.
Upon initial examination of
the SAOimage window (after activating
Image on the image of your choice)
you will notice several different areas:
- A large image display area. This is where the image is displayed
with the best resolution.
- Two small display areas on the upper right corner:
- The left one represents the full image in the memory buffer. The
box (green if you can see green) indicates which part of the image is
being seen on the large display area (under pan/zoom).
- The right one is a zoomed portion of the image around the cursor,
when it is moved in the large image display.
- A menubar: the top row corresponds to sets of possible actions,
while the bottom row corresponds to direct actions. Clicking with the
left mouse button on a button in the top row will bring a new set of
buttons, single actions, on the bottom row.
- A greyscale at the bottom of the window. The greyscale coding will
change according to any modification of the look up table.
- A coordinate display in the upper left window area. When SAOimage
is opened from ``Image'', the coordinate
display (i.e. X,Y position and intensity value) will update as you move
Modifying the image scaling and look up table
We describe here two examples of image scaling and look up table
Faint intensity levels:
for this you need to select scale in the top menubar,
then histeq in the bottom menubar. This will apply an
histogram equalization to the image, with emphasis on the mode of the
histogram. Most of the time, the mode of the histogram is close to the
median sky level, so that the scaling will be perfectly adequate to
reveal faint objects. The selection of color in the
top menubar allows the user to modify the image contrast and thresholds
by pressing the left mouse button, and dragging the cursor in the image
while still pressing on the left button. As you do this, you will see the
image contrast and thresholds change. Note that in the
color menu, you can select invert
to flip the look up table with white becoming black and vice et
High intensity levels: To
be able to see the highest intensity pixels in an image, from SAOimage
commands (see the ``Image'' form for an alternative way),
select scale, then sqrt, this will
compress the intensities and the look up table will allow a good look at
the highest values.
Pan and Zoom
Pan and Zoom is very easy within SAOimage. For this you have first
to select Pan in the top menubar.
Zoom: in the bottom
menubar, you can now see a set of zoom options including 2, 4, 1/2
and 1/4. Clicking on any of these buttons will zoom the image by the
corresponding factor. The alternative is to click with the middle mouse
button in the image display: you can zoom by as much as you want (!) by
a series of clicks. To unzoom click on ``zoom 1''.
Pan: position the cursor
on the image location that you would like to see in the middle of the
display, then click with the left mouse button and the selected image
area will move to the center of the display. One can also use the full
image display in the small top left area: a similar cursor action will
move the (green) box center to the desired image location, and the large
image display will be updated.
Other useful options
- new: display a new image.
- track: small zoom window is updated as the cursor is moved in the
large display window. This is set automatically when SAOimage is opened
- coord: coordinate display is updated as the cursor is moved in the
large display window. This is set automatically when SAOimage is opened
- print: send image display to PostScript printer. This can take some
time: 10 minutes for a 1024x1024 image on a QMS printer, 1 minute on a Sparc
- raise: raise the full SAOimage window (including all sub-areas)
above all other windows.
- QUIT: quit and kill the SAOimage process.
The Graph form
allows you to view cuts in an
image. The options are as follows:
- Cutting along: X axis to cut along a CCD row,
Y axis to cut along a CCD column.
- Cut # (1-2-3): up to three different cuts can be
displayed simultaneously on the grapher display. Clicking on the box
below ``cut #'' enables or disables the corresponding
- For each cut you have the following options:
- File name: the name of the file to be
- Position of cut: the row or column number to
which the cut has to be applied.
- Width to average: the number of rows or columns
to be averaged before display.
- Subtraction position: by clicking in the box,
the grapher will subtract the columns/rows identified by the
Subtraction position/width to average fields from the
main cut defined above. This is for instance quite useful for a quick
sky subtraction from a raw spectrum.
Grapher is an integrated interactive plotting program.
The Grapher window opens after your
selection of Accept in the Graph
form. It provides the following possibilities:
- Plots: pop-up menu (press on the left mouse
button, and keep pressing while you browse through the menu) allows to
reconfigure each plot (file name, cut location, subtraction).
- Options: pop-up menu allows to modify the
line type, compute statistics on the graph, or add labels.
- Print: pop-up menu allows to print the
displayed graph to the summit or waimea printers.
- Zoom: pop-up menu allows to select a zoom
factor from 1/4 to 4.
- Show plot: by clicking on the appropriate
boxes, you can enable or disable one of the 4 plots allowed
- Scaling adjustment: you can tell the program to
automatically adjust the X and Y scales by clicking in the ``X
scale'' and ``Y scale'' boxes.
- Pan: by either clicking or dragging the black
horizontal bar at the bottom of the window, you can pan across the
plotted line or column.
The IQE form
allows for the computation of various statistics from
a FITS file. These include simple minimum and maximum values, as well
as more complex values such as mean, standard deviation,
full-width-at-half-maximum, and centroids.
At the top of the IQE form, you will notice a large field for the
FITS file name. This will be the file on which statistics are
performed, and all locations, both entered and reported, will be
relative to this file and in image pixel units.
The following options can be modified:
- Subraster options: The subraster options are
necessary to narrow down the area to perform the statistic on. The use
of the entire FITS file as the area from which to perform statistics is
not recommended, due to the nature of the calculations. For example, the
centroid values reported from a FITS file (or subraster!) containing
more than one star will be between the stars! The user is responsible
for the proper selection of the subraster so as to include only those
object(s) upon which the statistics are wanted. To accomplish this,
first select the radio button labeled ``As Follows:'', and then fill the
desired values into the ``Xc'', ``Yc'', ``Xs'', and ``Ys'' edit fields. Use the
raster image in the lower right of the form as a guide to the meanings
of these variables. It is expected that you will use an image display
tool (SAOimage) to determine your values. If the FITS file only contains
the items you are interested in, perhaps because of the use of raster
options when obtaining the data, you can select the ``Entire data area,
ignoring edges'' radio button. The edge of the data is always ignored,
due to various edge effects found in CFHT CCD's.
- Values computed: This area of the form allows
the selecting of the desired values, using a standard list of
- Background from: The background for the FWHM
values can be generated as the mean of the entire edge of the selected
area, which is normal for use on images. For spectroscopic data, the use
of the first and last X (or Y) values may give a better approximation of
the actual background. Selection is via radio button.
- Other option: The FWHM values are usually
computed on the maximum pixel's X and Y coordinate vectors. If the
entire area selected is useful for the calculations, the ``Collapse for
Fwhm/Pwhm'' may be selected. This may be useful for spectroscopic
After the Accept button is pressed, the output
of these statistics is presented in a popup window, as text. After you
are finished viewing this data, press the ``Quit'' button that appears
across the bottom of the result popup.
The Files form
allows four types of action to be applied to FITS files:
- List FITS files: list the file names (default
- List FITS Headers: display the selected files' FITS
- Write FITS files to tape: write the selected
FITS files to magnetic tape.
- Remove FITS files: remove the selected FITS
files from disc.
These FITS files can be selected in several ways (by clicking in
the appropriate box):
- One file: perform the selected action on only
one file, you can enter to file name on the field reserved for it.
- All files (default): performs the selected
action on all the files in the directory.
- Already on tape: performs the selected action
only on files which have been saved to tape.
- Not on tape: performs the selected actions only
on files which have not yet been saved to tape.
If you have selected All files,
Already on tape, or Not on
tape, you can narrow your file selection further by
selecting one or both of the following:
- File Type Override: performs the selected
action only on the files with the selected file type: o
for object, f for flat, b for bias,
d for dark, and c for comparison.
- Range Override: performs the selected action
only for the files with exposure numbers (``odometer'')
falling into a given range which may be entered in the two dedicated
After selecting the action desired, and the set of FITS files to
apply this action to, pressing the Accept button
will result in the desired action being performed. As each file is
processed, it will be listed in a popup window. When the last file has
been handled, a message will be displayed in this window to that effect,
the popup window should then be ``closed'' with the ``Quit'' button. As
files are listed in this popup window, those that have been saved to
tape will be surrounded by parentheses, while those that have not been
saved to tape will appear simply as the file name. It follows that
selecting only files that have been saved to tape will result in all the
file names being enclosed in parentheses.
It is suggested that you use the list-files action to verify that
the files you have selected are indeed the appropriate
files, and then bring the Files form up again to perform your
To end the session, click on Aloha.
This will bring up another form
which asks you if you want to really quit (then press Accept) or not
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