Deprecated, see https://github.com/jkeger/arctic

ArCTIC python

AlgoRithm for Charge Transfer Inefficiency (CTI) Correction

Add or remove image trails due to charge transfer inefficiency in CCD detectors by modelling the trapping, releasing, and moving of charge along pixels.

https://github.com/jkeger/arcticpy

Jacob Kegerreis: jacob.kegerreis@durham.ac.uk
Richard Massey: r.j.massey@durham.ac.uk
James Nightingale

This file contains general documentation and some examples. See also the docstrings and comments throughout the code for further details, and the unit tests for more examples and tests.

Contents

• Minimal example
• Installation
• Documentation
  • Files
  • Add/remove CTI
  • CCD
  • ROE
  • Trap species
  • Trap managers
  • Image files
  • Preset models
• Examples

Minimal example

See the documentation below and the code docstrings for more detail.

import arcticpy as ac

image_no_cti = ... # Initial image

# CCD, ROE, and trap species parameters
ccd = ac.CCD(well_fill_power=0.8, full_well_depth=1e5)
roe = ac.ROE()
trap = ac.Trap(density=3.141, release_timescale=1.234)

image_cti_added = ac.add_cti(
    image=image_no_cti,
    parallel_traps=[trap],
    parallel_ccd=ccd,
    parallel_roe=roe,
)

image_cti_removed = ac.remove_cti(
    image=image_cti_added,
    iterations=5,
    parallel_traps=[trap],
    parallel_ccd=ccd,
    parallel_roe=roe,
)

Installation

• Install the package with pip install arcticpy, see https://pypi.org/project/arcticpy/
• Or download the code with git clone https://github.com/jkeger/arcticpy.git
  • Cython set up: python setup.py build_ext --inplace
  • Run the unit tests with pytest test_arcticpy/
• Requires:
  • Python 3 (tested with 3.6.9)
  • See requirements.txt

Documentation

The code docstrings contain the full documentation for each class and function. This section provides an overview of the main usage and the different options available for reference.

It is aimed at general users with a few extra details for anyone wanting to navigate or work on the code itself.

Files

A quick summary of the code files and their content:

• arcticpy/ Main code directory

  • main.py
    Contains the primary user-facing functions add_cti() and remove_cti().

    These are wrappers for cy_clock_charge_in_one_direction(), in main_utils.pyx, which contains the primary nested for loops over an image to add CTI to (in order) each column, express pass (see below), and row.

    Also contains preset CTI models for e.g. the HST ACS.

  • ccd.py
    Defines the user-facing CCD classes that describes how electrons fill the volume inside each (phase of a) pixel in a CCD detector.

  • roe.py
    Defines the user-facing ROE classes that describes the properties of readout electronics (ROE) used to operate a CCD detector.

  • traps.py
    Defines the user-facing Trap classes that describes the properties of a single species of traps.

  • trap_managers.py and trap_managers_utils.pyx
    Defines the internal TrapManager classes that organise one or many species of traps.

    Contains the core function n_electrons_released_and_captured() called from cy_clock_charge_in_one_direction() to model the capture and release of electrons and to track the trapped electrons using the "watermarks".

  • util.py
    Miscellaneous internal utilities.

• test_arcticpy/ Unit test directory
  • test_main.py General add/remove CTI tests
  • test_ccd.py CCD tests
  • test_roe.py ROE tests
  • test_traps.py Traps and trap manager tests
• examples/ General examples to complement the documentation in this file.
  • correct_HST_ACS_image.py Remove CTI trails from a Hubble image slice
  • More coming soon...

Add/remove CTI

Add CTI

To add (and remove) CTI trails, the primary inputs are the initial image followed by the properties of the CCD, readout electronics (ROE), and trap species, for either or both parallel and serial clocking:

import arcticpy as ac

image_with_cti = ac.add_cti(
    image,
    
    parallel_ccd=None,
    parallel_roe=None,
    parallel_traps=None,
    parallel_express=0,
    parallel_offset=0,
    parallel_window=None,
    
    serial_ccd=None,
    serial_roe=None,
    serial_traps=None,
    serial_express=0,
    serial_offset=0,
    serial_window=None,
    
    time_window=None,
)

These parameters are set using the CCD, ROE, and Trap classes, as described below.

See this function's docstring in main.py for the full details.

Image

The input image should be a 2D array of (float) charge values, where the first dimension runs over the rows of pixels and the second inner dimension runs over the separate columns, as in this example of an image before and after calling add_cti() (with arbitrary trap parameters):

# Initial image with one bright pixel in the first three columns:
[[0.0,     0.0,     0.0,     0.0  ], 
 [200.0,   0.0,     0.0,     0.0  ], 
 [0.0,     200.0,   0.0,     0.0  ], 
 [0.0,     0.0,     200.0,   0.0  ], 
 [0.0,     0.0,     0.0,     0.0  ], 
 [0.0,     0.0,     0.0,     0.0  ]]
# Image with parallel CTI trails:
[[0.0,     0.0,     0.0,     0.0  ], 
 [196.0,   0.0,     0.0,     0.0  ], 
 [3.0,     194.1,   0.0,     0.0  ], 
 [2.0,     3.9,     192.1,   0.0  ], 
 [1.3,     2.5,     4.8,     0.0  ], 
 [0.8,     1.5,     2.9,     0.0  ]]
# Final image with parallel and serial CTI trails:
[[0.0,     0.0,     0.0,     0.0  ], 
 [194.1,   1.9,     1.5,     0.9  ], 
 [2.9,     190.3,   2.9,     1.9  ], 
 [1.9,     3.8,     186.5,   3.7  ], 
 [1.2,     2.4,     4.7,     0.9  ], 
 [0.7,     1.4,     2.8,     0.6  ]]

As this illustrates, by default, charge is transferred "up" from row N to row 0 along each independent column, such that the charge in the first element/pixel 0 undergoes 1 transfer, and the final row N is furthest from the readout register so undergoes N+1 transfers. The CTI trails appear behind bright pixels as the traps capture electrons from their original pixels and release them at a later time.

Parallel clocking is the transfer along each independent column, while serial clocking is across the columns and is performed after parallel clocking, if the parameters for both are not None.

Note that instead of actually moving the charges past the traps in each pixel, as happens in the real hardware, the code tracks the occupancies of the traps (see watermarks below) and updates them by scanning over each pixel. This simplifies the code structure and keeps the image array conveniently static.

See the 'Image files' section below for useful functions for loading images.

Express

As described in more detail in Massey et al. (2014) section 2.1.5, the effects of each individual pixel-to-pixel transfer can be very similar, so multiple transfers can be computed at once for efficiency.

This allows faster computation with a mild decrease in accuracy.

For example, the electrons in the pixel closest to the readout have only one transfer, those in the 2nd pixel undergo 2, those in the 3rd have 3, and so on. The express input sets the number of times the transfers are calculated. express = 1 is the fastest and least accurate, express = 2 means the transfers are re-computed half-way through the readout, up to express = N where N is the total number of pixels for the full computation of every step without assumptions.

The default express = 0 is a convenient alternative input for express = N.

Offsets and windows

To account for additional transfers before the first image pixel reaches the readout (e.g. a prescan region), offset sets the number of separating pixels.

Somewhat similarly, instead of adding CTI to the entire supplied image, only a subset of pixels can be selected using the window_range = range(min, max) input. Note that, because of edge effects, you should start the range several pixels before the actual region of interest.

Finally, a window in time can be chosen with time_window_range to only model a subset of transfers. This could be used to e.g. add cosmic rays during readout of simulated images.

Remove CTI

Removing CTI trails is done by iteratively modelling the addition of CTI, as described in Massey et al. (2010) section 3.2 and Table 1.

The remove_cti() function takes all the same parameters as add_cti() plus the number of iterations for the forward modelling:

image_remove_cti = ac.remove_cti(
    image=image_with_cti,
    iterations=3,
    # Same as add_cti()...
)

More iterations provide higher accuracy at the cost of longer runtime. In practice, just 1 to 3 iterations are usually sufficient.

CCD

How electrons fill the volume inside each (phase of a) pixel.

See the CCD class docstring in ccd.py for the full documentation.

By default, charge is assumed to move instantly from one pixel to another, but multiple phases per pixel can be used in the CCD and ROE classes for more complicated multi-phase clocking or modelling of trap pumping etc.

Default CCD

ccd = ac.CCD(
    # The maximum number of electrons that can be contained within a pixel
    full_well_depth=1e4, 
    
    # The number of electrons that fit inside a 'notch' at the bottom of a 
    # potential well, avoiding any traps
    well_notch_depth=0.0,
    
    # The exponent in the power-law model for the volume occupied by the electrons
    well_fill_power=0.58,
    
    # For multiphase clocking: the proportion of traps within each phase or, in 
    # other words, the relative physical width (in any units) of each phase
    fraction_of_traps_per_phase=[1], 
    
    # Equivalent to the notch but for surface traps
    well_bloom_level=None,
)

Multi-phase clocking

# Four phases of different widths, each with different well depths but the same 
# other values of the fill power and the (default) notch depth
ccd = ac.CCD(
    fraction_of_traps_per_phase=[0.5, 0.2, 0.2, 0.1],
    full_well_depth=[8.47e4, 1e5, 2e5, 3e5],
    well_fill_power=0.8,
)

ROE

The properties of readout electronics (ROE) used to operate a CCD.

See the ROE and child class docstrings in roe.py for the full documentation.

Default ROE

roe = ac.ROE(
    # The time between steps in the clocking sequence, in the same units as 
    # the trap capture and release timescales
    dwell_times=[1],
    
    # True: explicitly models the first pixel-to-pixel transfer differently to 
    # the rest by starting with empty traps for every pixel
    empty_traps_at_start=True,
    
    # True: columns have independent traps. False: columns move through the same
    # traps, may be appropriate for serial clocking
    empty_traps_between_columns=True,
    
    # True: force electrons to be released in a pixel further from the readout,
    # may be relevant for multi-phase clocking
    force_release_away_from_readout=True,
    
    # The type for the express multipliers, can be int for backwards compatibility
    express_matrix_dtype=float,
)

For multi-phase clocking, dwell_times should be the same length as the CCD's fraction_of_traps_per_phase.

In addition to the time spent in each phase, for multi-phase clocking in detail, see the ROEAbstract._generate_clock_sequence() function, which sets up e.g. the high and low phases in each step of a multi-phase sequence. Any sequence could be used or added with a user-defined version of this function in a child class, but the current assumption if of a particular type of sequence that gives sensible Hubble or Euclid-like behaviour set by the user with only the length of the dwell_times array that sets the number of phases.

Charge injection

roe = ac.ROEChargeInjection(
    # The number of pixels between the charge injection structure and the 
    # readout register, through which the electrons are transferred
    n_pixel_transfers=None,
)

In this mode, electrons are directly created by a charge injection structure at the end of a CCD, then clocked the same number of times through all of the n_pixel_transfers pixels to the readout register, compared with the standard case where electrons start in image pixels at different distances from readout.

The other options still apply in the same way.

Trap pumping

AKA pocket pumping.

roe = ac.ROETrapPumping(
    # The dwell times here include both the forward and reverse transfers, so 
    # there should be an even number, usually double the number of phases
    dwell_times=[1] * 6, 
    
    # The number of times the charge is pumped back and forth
    n_pumps=2
)

In this mode, charge is clocked back and forth across traps in a pixel to create dipoles as electrons are repeatedly transferred from one pixel to its neighbour.

The pixel index containing the traps should be set using the window_range argument of add_cti(), so that only those charges are pumped.

See the docstring of ROEAbstract._generate_clock_sequence() in arcticpy/roe.py for a full explanation and diagram, alongside TestTrapPumping.test__traps_in_different_phases_make_dipoles() in test_arcticpy/test_main.py for simple examples.

Express matrix

The ROE class also contains the express_matrix_and_monitor_traps_matrix_from_pixels_and_express() function used to generate both the express matrix and a related array used to control when traps are monitored.

Trap species

The parameters for a trap species.

See the Trap and child class docstrings in traps.py for the full documentation.

Default trap species

trap = ac.Trap(
    # The density of the trap species in a pixel
    density=0.13, 
    
    # The release timescale of the trap 
    release_timescale=0.25, 
    
    # The capture timescale of the trap, default 0 for instant capture
    capture_timescale=0, 
)

Combined release and capture, allowing for instant or non-zero capture times, following Lindegren (1998) section 3.2.

Instant capture

For the old algorithm of release first then instant-capture, used in previous versions of ArCTIC.

trap = ac.TrapInstantCapture(density=0.13, release_timescale=0.25)

Continuum distributions of lifetimes

For a trap species with a log-normal distribution of release lifetimes.

trap = ac.TrapLogNormalLifetimeContinuum(
    # The total density of the trap species in a pixel
    density=10,
    
    # The median timescale of the distribution
    release_timescale_mu=1,
    
    # The sigma timescale for the width of the distribution
    release_timescale_sigma=0.5,
)

This is a special case of the TrapLifetimeContinuum class which allows any arbitrary distribution to be used instead of log-normal.

Uses the same release then capture algorithm as the instant-capture traps.

Trap managers

This is not relevant for typical users, but is key to the internal structure of the code and the "watermark" approach to tracking the trap occupancies.

The different trap managers also implement the different algorithms required for the corresponding types of trap species described above, primarily with their n_electrons_released_and_captured() method.

See the TrapManager and child class docstrings in trap_managers.py for the full documentation, and the AllTrapManager class for how multiple trap managers are stored if required for different types of traps and/or different phases.

Watermarks

A 2D array of fractional volumes -- the watermark levels -- and the corresponding fill fractions of each trap species:
[[volume, fill, fill, ...], [volume, fill, fill, ...], ... ]
This way, the proportion of filled traps can be tracked efficiently through the release and capture processes, including for multiple trap species.

In the simplest sense, capture of electrons creates a new watermark level at the "height" of the charge cloud and can overwrite lower ones as the traps are filled up, while release lowers the fraction of filled traps in each watermark level. Note that the stored volumes give the size of that level, not the cumulative total.

The details can vary for different trap managers, e.g. TrapManagerTrackTime, which stores the time elapsed since the traps were filled instead of the fill fraction, in order to manage trap species with a continuum distribution of lifetimes.

All the trap species managed by one trap manager must use watermarks in the same way. If different trap types are used, then multiple trap managers are created (see the AllTrapManager class).

Image files

Convenient loading and saving of images to fits files is available in arcticpy via the autoarray package (https://github.com/Jammy2211/PyAutoArray).

Cleaner functionality and full documentation for these utilities coming soon.

image = ac.acs.FrameACS.from_fits(file_path="HST_ACS_example.fits", quadrant_letter="A")

Preset models

Instead of creating the CCD, ROE, and Trap species yourself, some preset options are available for common applications.

These functions in main.py return objects ready to be passed to add_cti() or remove_cti():

traps, ccd, roe = ac.model_for_HST_ACS(date=2455123)

which sets up model objects suitable for the Hubble Space Telescope (HST) Advanced Camera for Surveys (ACS), with parameters adjusted for the Julian date.

Examples

See examples/correct_HST_ACS_image.py for an example of correcting CTI in an image from the Hubble Space Telescope (HST) Advanced Camera for Surveys (ACS) instrument.

More coming soon...