ocrreject_exam¶

Checks STIS CCD 1D spectroscopic data for cosmic ray overflagging.

Examples¶

In Python:

>>> import stistools
>>> stistools.ocrreject_exam.ocrreject_exam("odvkl1040", plot=True)

[{'rootname': 'odvkl1040',
'extr_fracs': array([0.31530762, 0.32006836]),
'outside_fracs': array([0.00884673, 0.00810278]),
'ratios': array([35.64113429, 39.50106762]),
'avg_extr_frac': 0.31768798828125,
'avg_outside_frac': 0.008474755474901575,
'avg_ratio': 37.486389928547126}]

Stacked example ocrreject_exam plot output

Split example ocrreject_exam plot output

From command line:

ocrreject_exam -h
usage: ocrreject_exam [-h] [-d DATA_DIR] [-p] [-o PLOT_DIR] [-i] obs_id [obs_id ...]

Calculate fractions of cosmic ray rejected pixels inside and outside of an extraction box to test for CR algorithm failures.

positional arguments:
obs_id       observation id(s) in ipppssoot format

options:
-h, --help   show this help message and exit
-d DATA_DIR  directory containing observation flt and sx1/x1d files. Defaults to current working directory.
-p           option to create diagnostic plots
-o PLOT_DIR  output directory to store diagnostic plots if plot=True. Defaults to data_dir.
-i           option to create zoomable html plots instead of static pngs. Defaults to False and requires Plotly if True

v1.0; Written by Matt Dallas, Joleen Carlberg, Sean Lockwood, STScI, December 2024.

exception stistools.ocrreject_exam.BoxExtended(message='Extraction box extends beyond frame')¶

stistools.ocrreject_exam.call_ocrreject_exam()¶: Command line usage of ocrreject_exam

stistools.ocrreject_exam.ocrreject_exam(obs_ids, data_dir='.', plot=False, plot_dir=None, interactive=False, verbose=False)¶

Compares the rate of cosmic rays in the extraction box and everywhere else in a CCD spectroscopic image. Based on crrej_exam from STIS ISR 2019-02.

Higher ratios of cosmic ray rates in the extraction box to the rest of the image may indicate the need to rerun stistools.ocrreject() with different parameters.

Parameters:

obs_ids: iter of str or str: One of more STIS observation ID rootnames in ipppssoot format (e.g. odvkl1040).
data_dir: str: Directory containing both the flat fielded (_flt.fits) and extracted spectrum (_sx1.fits or _x1d.fits) files of the observation if using obs_ids argument. Defaults to current working directory.
plot: bool: Option to generate diagnostic plots, default=False
plot_dir: str or None: Directory to save diagnostic plots in if plot=True. Defaults to data_dir parameter
interactive: bool: Option to generate zoomable html plots using plotly, default=False
verbose: bool: Option to print some results

Returns:

results: list of dict

rootname: obs_id
extr_fracs: cosmic ray rejection rates in the extraction boxes for each CR-SPLIT
outside_fracs: cosmic ray rejection rates outside the extraction boxes for each CR-SPLIT
ratios: extr_fracs/outside_fracs
avg_extr_frac: The average of extr_fracs
avg_outside_frac: The average of outside_fracs
avg_ratio: avg_extr_frac/avg_outside_frac

If called from the command line, prints the avg extraction, outside, and ratio values for quick verification.

stistools.ocrreject_exam.split_plot(splits, box_lower, box_upper, split_num, individual_exposure_times, texpt, obs_id, propid, plot_dir, interactive)¶

Creates a visualization of where CR pixels are in each subexposure

Parameters:

splits: list: list of CR flagged pixels in each subexposure
box_lower: array: 1d array of ints of the bottom of the extraction box (0 indexed)
box_upper: array: 1d array of ints of the top of the extraction box (0 indexed)
split_num: int: Number of splits in the stack
individual_exposure_times: list: List of exposure times for each subexposure
texpt: float: Value of total exposure time
obs_id: str: ipppssoot of observation
propid: int: proposal id of observation
plot_dir: str: Directory to save plot in
interactive: bool: If True, uses Plotly to create an interactive zoomable html plot

stistools.ocrreject_exam.stack_plot(stack_image, box_lower, box_upper, split_num, texpt, obs_id, propid, plot_dir, interactive)¶

Creates a visualization of where CR pixels are in a stacked image

Parameters:

stack_image: array: 2d array to plot
box_lower: array: 1d array of ints of the bottom of the extraction box (0 indexed)
box_upper: array: 1d array of ints of the top of the extraction box (0 indexed)
split_num: int: Number of splits in the stack
texpt: float: Value of total exposure time
obs_id: str: ipppssoot of observation
propid: int: proposal id of observation
plot_dir: str: Directory to save plot in
interactive: bool: If True, uses Plotly to create an interactive zoomable html plot