ARC 3.5m | Agile

Table of Contents

1. Instrument Description 2. Instrument Design and Operation 2.1 Choosing and Exposure Time 2.2 Choosing the CCD Gain 2.3 Choices of Available Filters 2.4 Software Control 2.5 Configuring Agile 2.6 Acquiring Agile Exposures 3. Instrument Performance 3.1 Instrument Timing 3.1.1 Absolute Timing 3.1.2 Relative Timing 3.2 Read Times and Read Noise 3.3 Linearity and Gain 3.4 Linearity and Saturation 3.5 Wavelength Response 3.6 Dark Current Characterization 3.7 Throughput Measurements

4. Calibration Frames 4.1 Bias Frames 4.2 Dark Frames 4.3 Dome Flats 4.4 Sky Flats 5. Instrument Issues 5.1 Vignetting 5.2 Data Corruption 5.3 New Port Issues 6. End of Your Run 6.1 Data Storage and Retrieval 7. Data Reduction Appendicies A. Instrument Design B. Instrument History C. Sample Agile data D. Basic low-level commands (for scripting) E. Other information

1. Instrument Description

Agile is a high-speed time-series CCD photometer based on the original design of Argos, a timeseries photometer at the 2.1m telescope at McDonald Observatory (Nather & Mukadam 2004). Agile comprises of a Princeton Instruments Micromax camera with a frame transfer CCD, which has 1Kx1K active pixels, each of size 13âx3 Using a focal reducer at the Nasmyth focus of the 3.5m telescope at Apache Point Observatory (APO), we yield a field of view of approximately 2.5 arcminâ2.5 arcmin with an unbinned platescale of 0.130 arcsec/pixel¹. The CCD is back-illuminated and thinned for improved blue sensitivity and provides a quantum efficiency ≥ 80% in the wavelength range 450–750 nm. The unbinned full frame readout time can be as fast as 1.1 s; this is achieved using a low noise amplifier operating at 1MHz with an average read noise of order 6.6 ē RMS². At the slow read rate of 100 KHz to be used for exposure times longer than a few seconds, we determine an average read noise of order 3.7 ē RMS³.

Device	E2V Technologies CCD 47-20
Active Pixels	1024 â 1024
Pixel Size	13 µ â 13 µ
Field of View1	2.2 arcminâ2.2 arcmin
Platescale1	0.258 arcsec/pixel, binned 2x2
Fast Readout	Read Rate 1 MHz; Read Noise 6.62 ē RMS2
Slow Readout	Read Rate 100 KHz; Read Noise 3.66 ē RMS3
Dark Current	13.3 electrons/pixel/s

Table 1: Agile: Summary of Features

¹ Agile can also be requested without the focal reducer for very special science objectives. Without the focal reducer, the field of view is merely 1.3 arcmin×1.3 arcmin with an unbinned platescale of 0.077 arcsec/pixel.
² The read noise is measured to be 7.54 ē RMS at the read rate of 1MHz with the low gain setting.
³ The read noise is measured to be 4.52 ē RMS at the read rate of 100 KHz with the low gain setting.

2. Instrument Design and Operation

Understanding the instrument design of Agile should help the observer choose a suitable exposure time and a configuration for observing, and learn the implications of these choices.

2.1. Choosing an exposure time

• Agile is a frame transfer CCD camera. The CCD has 1K×2K pixels, half of which are active and exposed to light and the other half are masked from light. At the end of an exposure, the image from the active region of the CCD is transferred to the masked portion in hundreds of microseconds. This process is known as a frame transfer. The transferred image can be read out slowly from the masked portion, while a new exposure can commencein the active region of the CCD. As a result, the dead time between consecutive exposures is a fraction of a millisecond. Observers can choose an exposure time and windowing knowing that readout time does not contribute to any dead time between exposures.


• Agile does not have a mechanical shutter. The frame transfer operation of the CCD is utilized to end an exposure and initiate the subsequent new exposure, and it is triggered by the negative edge of a pulse. Housed in the data acquisition computer Nimble is a Brandywine GPS card that is synchronized to the Observatory’s GPS clock. When the observer requests an exposure time of n seconds, the GPS-based timer card generates a train of pulses with an even spacing of n seconds. These GPS-synchronized pulses are transmitted to the camera controller, and their negative edges effectively dictate both the start and end of each exposure. Therefore we expect that both the exposure start and the exposure duration should have an uncertainty smaller than a millisecond.


• Operating the instrument in the manner described above requires that the desired exposure time should always be greater than the sum of the CCD readout time (with the chosen binning and windowing) and the time required to write the image to disk. The data acquisition program typically needs a hundredth of a second to write the image in the buffer to a local disk. Hence we conservatively require that the exposure time must be greater than the CCD readout time by at least 0.03 s to account for the jitter in readout time and the time to write the image to disk.

Read Rate	Binning	Readout Time (s)	Minimum Exposure Time for Full Frame Images (s)
1 MHz	1x1	1.10	1.13
1 MHz	2x2	0.462	0.5
1 MHz	3x3	0.268	0.3
100 KHz	1x1	10.7	10.73
100 KHz	2x2	3.1	3.13
100 KHz	3x3	1.6	1.63

Table 2: Exposure time must be greater than the readout time by at least 0.03 s.

• The Agile CCD camera has two readout amplifiers, one of which is capable of reading at the fast readrate of 1MHz while introducing a read noise of order 7 ē RMS, and the other capable of reading at 100 KHz with a low read noise of order 4 ē RMS. Once the observer chooses the binning and windowing configuration and specifies an exposure time, the software will select the slowest read rate that satisfies the above condition. The read rate and exact read noise values will be included in the FITS headers.


• The chosen exposure time must additionally satisfy the constraint 0.3 ≤ Exptime ≤ 655.34 s; this excludes bias frames. Please note that we are presently unable to test the accuracy of absolute or relative timing for exposure times shorter than 0.3 s. The constraint on the maximum exposure time is due to the GPS timer card. The constraint on the minimum exposure time is presently due to the software. Should observers require to push this limit for scientific reasons, we can work hard to modify the software and conduct extensive timing tests to allow exposure times smaller than 0.3 s. The exposure time should also be an integral multiple of 0.02 s (present software restriction).


• It is also possible to operate the CCD camera without controlling the exposure time using GPS-synchronized pulses. This mode is presently enabled to allow the observer to acquire bias frames, and gets activated whenever the exposure time is set to zero. However if in the future several observers indicate that their science would benefit from exposure times longer than 655.34 s inspite of the high dark current, we can enable the use of internal timing for substantially long exposures acquired at the cost of reduced timing accuracy. We expect the uncertainty in timing may then be of the order of a hundredth of a second or more. Operated in this fashion, Agile will just be an imaging system and should not then be called a timeseries photometer.

2.2. Choosing the CCD gain

The photons incident on a CCD are converted into electrons due to the photoelectric effect. The CCD gain effectively decides how many counts or ADU (Analog to Digital Units) we get for the accrued electrons. The Agile CCD camera offers three choices of gain: high, medium, and low; these choices have slightly different values under the two different read rates, as shown in the table below.

Read Rate	Gain
1 MHz	High = 0.95
1 MHz	Medium = 1.93
1 MHz	Low = 3.88
100 KHz	High = 0.97
100 KHz	Medium = 1.96
100 KHz	Low = 4.10

Table 3: The three different choices of gain have slightly different values depending on the read rate. The correct value is automatically entered in the acquired FITS images.

The values of gain may appear to be counter-intuitive, but make sense when we think in terms of the net ADU counts. For example at the read rate of 1 MHz, the high gain setting will yield 31580 ADU or counts for 30000 electrons, while the medium gain setting will yield 15540 counts, and the low gain setting will yield 7730 counts for the same number of electrons. The observer must select the gain setting so that at the desired exposure time, the stars of interest have counts in the linear regime of the CCD, while utilizing the dynamic range well. Please note that when using the low gain setting and binning 1x1, the CCD will saturate at about 43000 counts. However when binning 2x2, the saturation point is always given by the digitization limit of 65535 counts.

The examples below are meant to be an illustration on how to decide between the different choices of gain:

• Suppose a bright star observer was getting 50000 counts/pixel (non-linear regime) at the peak of the stellar profile in a one second exposure at the default setting of medium gain ~2. Should this observer switch the CCD gain to low ~1, he/she will now derive about 25000 counts at the peak pixel during the one second exposure. This lower value is well within the linear regime of the CCD, and allows the observer to continue acquiring data at the same exposure time. This observer could also choose to expose the CCD for 0.5 s instead to reduce the counts, but would end up increasing the effect of read noise in his/her data as he/she would be reading out twice in a second instead of once a second with the low gain setting.

• Similarly, suppose another observer was acquiring 15000 counts/pixel at the peak pixel of his/her star. This observer could either increase the exposure time by two or simply increase the gain from medium ~2 to high ~4. The observer could thus use the CCD gain to his/her advantage to get twice the count rate, utilizing the dynamic range well, and without decreasing the effective time resolution.

• On the other hand, consider an observer with a faint target and relatively bright comparison stars. This observer could switch the CCD gain to high, but perhaps such an action would bring the bright comparison stars in the nonlinear regime of the CCD or close to saturation even. The observer could switch to low CCD gain as in the first example, but that could bring his/her target star of interest to very low counts. It would be better for such an observer to stay with the default choice of medium gain, so as to get reasonable counts for both the faint target star and the brighter comparison stars.

2.3 Choices of Available Filters

All square filters listed in the online filter inventory (with the exception of the Sloan set dedicated to Agile FW 2) are
available for use in Agile’s filter slide; However, currently on one filter can be loaded at a time.

2.4 Software Control

Agile is operated within the Telescope User Interface (TUI) software written and maintained by Russell Owen at the University of Washington. A detailed manual is available at under the top menu Telescope->TUI->Manual. The main TUI status window is shown below.

2.5 Configuring Agile

The instrument is configured using the Agile window accessible under the Instrument menu from the main TUI window. This brings up the following Agile control Graphic User Interface (GUI).

2.6 Acquiring Agile Exposures

The Agile instrument exposure control is in standard TUI format (for detailed description see here ), and, as for other instruments, shows status of the current exposure at the top, and allows you to set the object Type (for the FITS image header), exposure Time, number of Exposures, and root File Name. If you wish to add comments to the file header, place them in the Comments field.

All data will automatically be stored on arc-gateway under /export/images/<program ID>/<filename>. However, most users set TUI up to automatically transfer images to their local computer using the Preferences options in the main TUI window menu (see AutoGet and Save To options under Exposures). You can also define a subdirectory (TUI will even create it for you) by entering a name such as <subdir1>/<subdir2>/<filename> ; note, however, that a separate image number sequence will be started in each subdirectory.

The FITS header for each image stores the exposure time values (duration, start, stop) plus telescope parameters for future reference.

The Start button begins the exposure or exposure sequence.

• Start - This button starts the exposure or exposure sequence.
• Pause - This button pauses the exposure, you can start it again later.
• Abort - This button aborts an exposure and the sequence.
  • NOTE: Currently clicking Abort puts the agile Expose GUI into a strange unresponsive state. The Obs-Spec can clear this for you. However, it is important that once the Abort button is clicked no other commands are sent from this window UNTIL the Obs-Spec has cleared it for you. When possible please warn the Obs-Spec when you intend to use the Abort button.

We have moved Agile to its own permanent port at TR2. This creates some changes for users who are familiar with Agile at NA2. Please see Sec 5.3.New Port Issues.

2.7 Focusing the Telescope

The telescope is focused by inspection of Agile images. As with all instruments, monitoring focus is advisable, as it will change over the course of the night, especially at the beginning of the night before the telescope has reached equilibrium.

3. Instrument Performance

3.1 Instrument Timing

There is more to time-series photometry than meets the eye; it is not just relative photometry with a precise measurement of the observation epoch. A good time series photometer not only requires a precise measurement of the start time of an exposure, but also as precise a measurement of the duration of the exposure. Besides accuracy in timing, a good time-series photometer must be able to provide sufficient time resolution to sample the variable phenomena well. This requires that the photometer allow short exposure times and also include insignificant dead times between consecutive exposures. Frame transfer CCDs are ideal for time-series photometry as they can provide contiguous exposures with no dead time.

3.1.1 Absolute Timing

The PC clock of the data acquisition computer Nimble is disciplined via the Network Time Protocol (NTP) using the time server galileo.apo.nmsu.edu, which is in turn disciplined by the Observatory’s GPS clock. Time in the CCD images at the accuracy of an integral second comes via the NTPdisciplined Nimble clock. Nimble houses a Brandywine GPS card that is also synchronized to the Observatory’s GPS clock. Sub-second absolute timing up to the accuracy of a millisecond in the CCD images comes from this internal GPS card.

3.1.2 Relative Timing

The GPS timer card internal to Nimble is programmable and capable of producing a heartbeat (train of pulses) at the desired exposure time. The negative edges of these pulses trigger the frame transfer operation, ending the ongoing exposure and starting a new one. The relative timing is thus controlled entirely in hardware without any software intervention. The genius of this design belongs to Dr. Nather of the University of Texas at Austin, which affords us a precision in relative timing better than a millisecond.

The new Agile software written by Russell Owen includes the following tests that constantly check the relative timing as follows:

• If noise pickup in the sync pulse cable poses as false pulses, then the software will detect extra images that arrive prematurely. A premature image is one that fails to arrive within 0.2 s of the expected arrival time. The software will stop the data acquisition and report the situation to the observer. We have addressed this problem in hardware by using fiber-optic cable to transmit the GPS sync pulses from the timing card right up to the instrument. We only use a foot of co-axial cable to send the pulse to the camera controller. This cable is wrapped in aluminium tape for 100% shielding.

• Should images fail to arrive altogether, then the software will stop the data acquisition. Such an event can occur for non-zero exposure times if the sync pulses are not reaching the camera controller. Such an event may also possibly be caused by a system corruption or crash, and power cycling the instrument may be the next step. The observing specialist should be notified in either case.

3.2 Read Times & Read Noise

We measure the read noise to be 6.62 ē RMS for the high and medium gain settings at the read rate of 1 MHz. We find that the read noise at the low gain setting is somewhat higher at 7.54 ē RMS for the read rate of 1 MHz. At the slow read rate of 100 KHz, the high and medium gain settings yield a read noise of 3.66 ē RMS and the low gain setting yields a read noise of 4.52 ē RMS.

The readout time for an unbinned full frame is 1.1 s operating at 1 MHz. With 2x2 and 3x3 binning, the readout times of a full frame reduce to about 0.462 s and 0.268 s respectively. At the slow read rate of 100 KHz, the readout time for an unbinned full frame is about 10.7 s, and with 2x2 and 3x3 binning, the readout times drop down to 3.1 s and 1.6 s respectively. The jitter in these readout times is no more than a few milliseconds, and does not affect the instrument timing at all.

3.3 Linearity and Gain

Agile has two possible read rates of 1MHz and 100 KHz, and three possible gain settings of high, medium, and low. For each of the six possible combinations as above, we carried out the following process to determine values for the read rate and gain at each setting. We acquired two consecutive domeflats using the dim quartz lamp with increasing exposure times until saturation. We show the mean counts of both the images along the x axis and the variance in the difference of these images along the y axis. These CCD transfer curves obtained with 1x1 binning show the region of linearity (see Figure 1). The inverse of the slope of the linear regime gives us a value of the gain at that setting. At the read rate of 1 MHz, we determine the high, medium, and low gain settings to correspond to values of 0.95, 1.93, and 3.88 electrons/ADU respectively. At the read rate of 100 KHz, we find that the high, medium, and low gain settings correspond to 0.97, 1.96, and 4.10 electrons/ADU respectively.

3.4 Linearity & Saturation as a function of Binning and Gain

The saturation limit and shape of the linearity curve are affected by the choice of binning and gain. For example, the linearity curves shown above indicate a saturation limit of 65535 counts for 1x1 binning and high or medium gain. The saturation limit changes to ~43000 counts for 1x1 binning and low gain because it is caused by overflow of the single pixel full well. In every other case, the saturation comes from the 16-bit digitization limit, i.e. 2¹⁶ − 1 = 65535.

With 2x2 binning and higher bin factors, the linear range of the CCD is extended. For example, the saturation limit for both 1x1 and 2x2 binning is given by the digitization limit of 65535 for medium gain. Binning 2x2 implies that we are packing in 4 times the number of electrons per pixel as with 1x1 binning. But since the saturation cutoff stays the same at 65535, we are effectively looking at the first quarter of the linearity curve shown for medium gain with 1x1 binning.