Default AutoProf Pipeline

In the Getting Started section, we learned how to run AutoProf, now we will dive into what is actually happening. Here you will learn what is going on by default, and some of the ways that you can change the setting to suit your project.

If your just looking for a config file to get you started, here it is:

ap_process_mode = "image"

ap_image_file = "<path to your image file>.fits"
ap_name = "yourimagename"
ap_pixscale = 0.262
ap_zeropoint = 22.5
ap_doplot = True
ap_isoclip = True

Below are some details on what will actually happen when you run the code!

Standard Photometry

The default photometry pipeline includes a minimalist set of pipeline steps to go from an image to an SB profile. In general, AutoProf attempts to make no assumptions about the size of the object in the image, although certain requirements are included for practical purposes. The main ones to keep in mind is that the galaxy should be roughly centered, there should be a border of sky around the galaxy (ie, it doesn’t go to the edge), and it should not be overlapping with a similarly size or larger object.

Put plainly, the default AutoProf pipeline is as follows:

  1. Background: Background_Mode()

  2. PSF: PSF_StarFind()

  3. Center: Center_HillClimb()

  4. Initial Isophote: Isophote_Initialize()

  5. Fit Isophotes: Isophote_Fit_FFT_Robust()

  6. Extract SB Profile: Isophote_Extract()

  7. Check Fit: Check_Fit()

  8. Write the SB Profile: WriteProf()

each function above links to a detailed description of the method, and the parameters that it accepts.

The reason a boarder is needed around the galaxy is because the Background_Mode() method uses a 1/5th border around the image to estimate the average background level. The galaxy needs to be roughly centered on the image because Center_HillClimb() starts at the image center by default, you can change this and give it alternate starting coordinates if you like. The galaxy should be non-overlapping with large sources because that would violate the assumptions in the Isophote_Fit_FFT_Robust() step and the Isophote_Extract() step.

The final output should be two files: a profile and an aux file. The profile (.prof) contains the SB profile and a number of other important parameters. These include the profile of ellipticity and position angle, but also some other useful calculations. The profile is extended by certain options, for example you can choose to add Fourier coefficients to the profile (typically used to examing b4/a4), or you can run steps like the Radial_Profiles() which will add more columns. The aux file contains global information such as the time when the fit completed, the settings used, the global PA/ellipticity, and any other diagnostic messages added by the various pipeline steps.

Forced Photometry

Forced photometry allows a user to apply the solution from one image onto another image. The default forced photometry pipeline works as follows:

  1. Background: Background_Mode()

  2. PSF: PSF_StarFind()

  3. Center: Center_Forced()

  4. Initial Isophote: Isophote_Init_Forced()

  5. Fit Isophotes: Isophote_Fit_Forced()

  6. Extract SB Profile: Isophote_Extract_Forced()

  7. Write the SB Profile: WriteProf()

each function above links to a detailed description of the method, and the parameters that it accepts.

Note that some steps remain unchanged. THe background is still calculated as normal, this is because it is typical for the background to change from image-to-image and between bands, so there is little reason to expect that to remain constant. A similar argument applies for the PSF, between observing nights and bands, the PSF can be very different so it is re-calculated. By default the previously fit center is used, however if you would like a new center to be fit, you can swap out this step with the standard centering method; this is explained in AutoProf Pipeline Control. The global isophote fit, and the full isophote fit are of course taken from the original fit, the pixel scale can vary between images and AutoProf will adjust accordingly. The isophote extraction has a forcing specific method which is near identical to the standard extraction method, except that it is set up to evaluate at exactly the same ellipse parameters as the original fit. There is no need for fit checks as no fitting has occured. Then the profile is written as usual.

Main Config Parameters

Below is a list of parameters which affect the pipeline at a global level. Method specific parameters are included in their documentation.

Required Parameters

ap_pixscale

pixel scale in arcsec/pixel (float)

ap_image_file

path to fits file with image data (string)

ap_process_mode

analysis mode for AutoProf to run in (string)

ap_forcing_profile

(required for forced photometry) file path to .prof file providing forced photometry PA and ellip values to apply to ap_image_file (string)

High Level Parameters

ap_saveto

path to directory where final profile should be saved. Default is the current directory. (string)

ap_name

name to use for the galaxy, this will be the name used in output files and in the log file. Default is taken from the filename of the fits image. (string)

ap_n_procs

number of processes to create when running in batch mode. Default is 1. (int)

ap_doplot

Generate diagnostic plots during processing. Default is False. (bool).

ap_plotpath

Path to file where diagnostic plots should be written, see also ap_doplot. Default is current directory. (string)

ap_plotdpi

sets dpi for plots (default 300). Can be used to reduce file size, or to increase detail in images (int)

ap_hdulelement

index for hdul of fits file where image exists. Default is 0. (int)

ap_new_pipeline_methods

Allows user to set methods for the AutoProf pipeline analysis. See AutoProf Pipeline Control for more information (dict)

ap_new_pipeline_steps

Allows user to change the AutoProf analysis pipeline by adding, removing, or re-ordering steps. See AutoProf Pipeline Control for more information (list)

ap_zeropoint

Photometric zero point, default is 22.5 (float)

ap_nologo

tells AutoProf not to put it’s logo on plots. Please only use this for figures that will be used in publications that don’t allow logos (bool)

There is one argument that AutoProf can take in the command line, which is the name of the log file. The log file stores information about everything that AutoProf is doing, this is useful for diagnostic purposes. By default, AutoProf will name the log file AutoProf.log, if you wish to make it a different filename then add the filename when running AutoProf:

autoprof config.py newlogfilename.log