Changes

*'''Camera''': [[Media:Andor iKon-M 934 Specifications.pdf|Andor DU934P]] deep depletion camera, 1024 × 1024 CCD, 13 μm pixels([[Media:Mookodi iKon test.pdf|CCD performance test sheet]])

*'''Plate scaleSpectral resolution:''' 0*:'''Dispersion:''' 3.6 arcsec88&thinsp;&Aring;/px *:'''Resolution:'''*::80µm slit*:::R = 301.0 @4671.23&plusmnthinsp; &Aring;*:::R = 374.4 @5823.89&thinsp;&Aring;*:::R= 492.5 @7642.02&thinsp;&Aring;*::160µm slit*:::R = 172 @4671.23&thinsp;&Aring;*'''Plate scale:''' 0.06 588 arcsec/px <ref name="spec" />*'''Field of view:''' 10.07'&thinsp;&times;&thinsp;10.07'*'''Slit:''' Long slit with narrow (80µm, 2") and wide (160µm, 4") sections.

*Low-cadence imaging: the camera is not a frame transfer camera, and in the current implementation normal operation exposures are controlled via readout after the closure of an iris shutter. The shutter is life-cycle limited and not suitable for high-cadence observations.*High-cadence imaging: it is possible to deactivate the shutter and take continues short exposure but users should be aware that the camera is not a frame transfer camera and this mode will result in some readout smearing. There is currently also no GPS triggering of the exposures and that the time recorded in the header (Keyword = DATE-OBS, note: is the start of the exposure) is obtained from the CPU time that is NTP synched. However, the header time has been measured to be accurate within at least 100ms of exact time (see [[Mookodi time-stamp tests|here]]). '''NB. High cadence observing (e.g. multiple continues exposures with exposure times < 60sec) SHOULD NOT be done with the shutter on AUTO mode. It is very important to set the shutter to "ALWAYS OPEN" which will deactivate the shutter in the open state but flush the CCD before the start of each new exposure. Failure to do so will likely cause serious damage to the camera's shutter'''

== Operating Mookodi Data Reduction Pipelines ===== Spectroscopy ===

Prepare the Lesedi telescope by following the The python-based data reduction pipeline ASPIRED ([https://topswikiarxiv.saaoorg/pdf/2012.ac03505.za/indexpdf M.php?title=Lesedi&action=submit#Start-up_recipes Lesedi start-up recipes]C. As Lam et. al.]) developed for Mookodi 's sister-instrument SPRAT is on the old SHOC port, references to the SHOC port should be taken to mean the compatible and recommended for Mookodi portspectroscopic data. General installation and usage instruction can be found [https://aspired.readthedocs.io/en/latest/index.html# here].

The simplest way to operate More specific Mookodi is via the web GUIinstallation and usage instructions (see included README), but navigation via a command line interface is also possiblewith example code and data, can be downloaded [[Media:Mookodi ASPIRED example. Scripted observations are in developmentzip|here]].

''Note: Dark and bias frames cannot === Photometry ===Differential photometry can be taken via the web GUI at this stageextracted from Mookodi data using a new "SAAO version", TEA-Phot-SAAO, which is a modified TEA-Phot pipeline developed by Dominic Bowman and Daniel Holdsworth ([https://arxiv.org/pdf/1907.04421.pdf D. M. Bowman et. al]) ==== Installation Instructions ===='' They can only be taken via 'NB. If you use the [[#Operation via TEA-Phot-SAAO code to produce results for a scientific publication, we ask that you please adhere to the command line interface citation requests of the developers that are on the main repository page (CLIlink below)|command line interface (CLI)]].'''

Open the web GUI at *These instructions should be identical for a Linux or Mac environment and Python 3.7 or a later version is recommended.*TEA-Phot-SAAO can be directly downloaded from [httphttps://mookodi.suthbitbucket.org/saao.ac.za/tea-phot-saao here] or the repository can quickly be cloned through the following command in the terminal:5000 mookodi.suth git clone https://bitbucket.org/saao/tea-phot-saao.ac.za:5000]. The GUI is divided into git* TEA-Phot-SAAO requires only four sections: Instrument configuration, target acquisition, camera configuration, and exposure controladditional Python modules. At this stage the target acquisition features are To install (if not implemented.already) run the following command in the terminal: pip install numpy matplotlib sep astropy

# '''Instrument Configuration:'''#* Select the desired configuration for each componentNB. The pneumatics and lamps will respond on the push of the button, and indicate when they are busy or in the desired configuration. '''To conserve lamp lifetime, don't leave them on for extended periods of time.'''#* Select the required filter via the dropdown menu under the Filter A or Filter B headings and press the SET button you may need to activate the filter slides. The box above the dropdown indicates the name of the filter in position for each slide, or BUSY use "pip3" if the slide is still finding its requested position.# you haven'''Target Acquisition:''' NOT IMPLEMENTED# '''Camera Configuration:'''<br /> Select the desired configuration for each setting using the dropdown menu below the relevant heading, then press the SET button t linked your pip to issue the command to the camera. #*'''Binning:''' Options are 1x1, 2x2, 3x3, and 4x4.#*'''Gain:''' High (faint objects), medium, and low (bright objects)#*'''Rate (readout rate):''' Fast (5 MHz), and slow (0.05 MHz)#*'''Mode:''' NOT IMPLEMENTED#*'''Number of exposures:''' NOT IMPLEMENTED#*'''Exposure time (in ms):''' Note the exposure time display does not update when the SET button is pushed, it only updates after the exposure is started. This is a [[#Known Issues|known issue]].#'''Exposure Control:'''<br /> This contains an image display of the last completed exposure, using [https://js9.si.edu/ JS9].#*'''Take exposure/Start:''' Starts an exposure with the SET camera configuration#*'''Abort:''' Aborts the current exposure. #*'''CCD Temperature:''' Displays the current CCD temperature, and buttons for cooling down and warming up. The camera takes 10 - 15 minutes to cool, and will stabilise at approximately -70 &ordm;C. Cool the camera at the start of observations and warm it up once you are donepython 3.6+

=== Operation via the command line interface (CLI) = Usage Instructions ====

* To reduce and extract photometry from Mookodi data using TEA-phot-SAAO, in the terminal navigate to the folder that contains the ''Note'TEA-Phot.py''' file.* To display basic usage and optional arguments run: Dark python TEA-Phot.py -hNB. you may need to use "python3" if you haven't linked your python to python 3.6+* A typical example to reduce and bias frames can only extract photomery from Mookodi data would be performed with the command line interface at something like this stage: python TEA-Phot.py SAAO Mookodi MKD --bias MKD --flat MKD --image_dir /full/path/to/science/fits/files/ --bias_dir /full/path/to/bias/fits/files/ --flat_dir /full/path/to/flat/fits/files/ --out_dir /full/path/to/chosen/output/directory/ --do_plot True --source_sigma 1.5NB.you may need to use "python3" if you haven''t linked your python to python 3.6+* Wait for window to appear and select target and comparison star with mouse-clicks.* Follow further prompts from the pipeline for inputs (aperture size etc.) in the terminal.

Type <code>help<Prepare the Lesedi telescope by following the [https:/code> in to display options/topswiki. Either the desired keyword or its number can be enteredsaao. Entering <code>1<ac.za/code> displays index.php/Lesedi#Start-up_recipes Lesedi start-up recipes]. As Mookodi is on the old SHOC port, any relic references to the SHOC port should be taken to mean the current camera configurationMookodi port.

Type <code>help<Open the web GUI at [http:/code> in to display options/mookodi. Either the desired keyword or its number can be enteredsuth. Entering <code>1</code> displays the current instrument saao.ac.za:5000 mookodi.suth.saao.ac.za:5000]. The GUI is roughly divided into five sections. From top to bottom: opto-mechanic configuration(lamps, slit, filters etc.<!), target acquisition (auto acquisition of a user defined sky-coordinate on a user specified x and y pixel position), exposure configuration (exposure time, binning etc.), higher level instrument control (start exposures, auto- === Scripted observations === -->focus instrument etc.), and an image display.

=# '''Opto-Mechanic Configuration:'''#* Select the desired configuration for each component. The components moved in/out of the beam via pneumatics (eg. mirrors, slit, grism) and lamps will respond on the push of the button, and indicate when they are busy or in the desired configuration. '''To conserve lamp lifetime, do not leave them on unneccessary for extended periods of time.'''#* Select the required filter via the dropdown menu under the Filter A or Filter B headings and press the SET button to activate the filter slides. The box above the dropdown indicates the name of the filter in position for each slide, or BUSY if the slide is still finding its requested position.# '''Target Acquisition:''' TO DO# '''Exposure Configuration:'''<br /> Select the desired configuration for each setting using the dropdown menu below the relevant heading, then press the SET button to issue the command to the camera. #*'''Binning:''' Options are 1×1, 2×2, 3×3, and 4×4.#*'''Gain:''' High (faint objects), medium, and low (bright objects)#*'''Rate (readout rate):''' Fast (5 MHz) - read-noise of 13.6 electrons, and slow (0.05 MHz) - read-noise of 3.3 electrons#*'''Image Type:''' This has no physical effect on the instrument configuration and only populates a header keyword with the selection (possibly useful for automated data reduction)#*'''Instrument Mode:''' This has no physical effect on the instrument configuration and only populates a header keyword with the selection (possibly useful for automated data reduction)#*'''Number of exposures:''' The number of exposures to take at the set camera/instrument configuration. '''NB. see note on [[#Suitable_Uses|high cadence imaging]] in the Suitable uses section at the top of this page.'''#*'''Exposure time (in ms):''' Note the exposure time display does not update when the SET button is pushed, it only updates after the exposure is started. This is a [[#Known Issues|known issue]].# '''Higher Level Instrument Control:'''#*'''Exposure Control:'''#**'''Take exposure/Start:''' Starts an exposure with the SET exposure configuration#**'''Abort:''' Aborts the current exposure. #*'''Guider Control:''' TODO#*'''Shutter Control:''' TODO#*'''Save images:''' TODO#*'''Exposure Information:''' TODO#*'''Nudge telescope pointing:''' TODO#*'''Focus control:''' TODO#*'''CCD Temperature Control:''' Displays the current CCD temperature, and buttons for cooling down and warming up. The camera takes 10 - 15 minutes to cool, and will stabilise at approximately -70 &ordm;C. Cool the camera at the start of observations and warm it up once you are done.# '''Image Display:'''#*Contains an image display of the last completed exposure, using [https://js9.si.edu/ JS9].#*A red and blue circle will appear where the preset values are for the pixel positions for the narrow and wide slit locations. Known bug: only appears after the second image is taken and only displays correctly for 1×1 binning. #*TIPS: TODO. ''Note: It is advisable that DARK frames should be taken with the shutter in the "ALWAYS CLOSED" mode. BIAS frames (especially if multiple frames are taken) SHOULD ALWAYS be taken with the shutter in the "ALWAYS CLOSED" mode since this will deactivate the iris-shutter in the closed state and prolong the lifetime, see also [[#Suitable_Uses|high cadence imaging]] in the Suitable uses section at the top of this page. == Data storage and retrieval =Access ==

scp mookodiobserver@mookodi.suth.saao.ac.za:/data/lesedi/mkd/yyyy/mmdd/* .<local path to copy to> Password: Same as username shown above with "Saao" prefixed. Where <code>yyyy</code> is the year, <code>mm</code> is the month, and <code>dd</code> is the day. The convention is that the data rolls over to the current date at 1200 UTC, hence all the files from a given night are stored in the folder corresponding to the date at the start of the night. e.g. All observations started on the night of 2021/12/11 will be stored in <code>/data/lesedi/mkd/2021/1211/</code>.

*There are three services that need to be run before Mookodi can be operated via the web GUI: opto-mechanics, camera, and web server. Each should be run in a separate screen session, otherwise they will shutdown when you close your ssh session.*The opto-mechanics and camera servers need to be started before the web server. ssh mookodi@mookodi.suth.saao.ac.za ./run_camera_server.sh ./run_optomechanics_server.sh ./run_web_server.sh*The web GUI can now be accessed at [http://mookodi.suth.saao.ac.za:5000 mookodi.suth.saao.ac.za:5000]

If there is an issue starting TODO - instructions on how to restart all services in the web server, Mookodi can be operated via correct order with a single "restart_services" terminal command line interface. With the camera and optomechanics servers running, follow the [[#Operation via the command line interface (CLI)|instructions for CLI operation]].