# Combining images and generating masks from clipping¶

Note

No attempt has been made yet to optimize memory usage in Combiner. A copy is made, and a mask array constructed, for each input image.

The first step in combining a set of images is creating a Combiner instance:

>>> from astropy import units as u
>>> from ccdproc import CCDData, Combiner
>>> import numpy as np
>>> ccd1 = CCDData(np.random.normal(size=(10,10)),
>>> ccd2 = ccd1.copy()
>>> ccd3 = ccd1.copy()
>>> combiner = Combiner([ccd1, ccd2, ccd3])


The combiner task really combines two things: generation of masks for individual images via several clipping techniques and combination of images.

There are currently three methods of clipping. None affect the data directly; instead each constructs a mask that is applied when images are combined.

Masking done by clipping operations is combined with the image mask provided when the Combiner is created.

### Min/max clipping¶

minmax_clipping masks all pixels above or below user-specified levels. For example, to mask all values above the value 0.1 and below the value -0.3:

>>> combiner.minmax_clipping(min_clip=-0.3, max_clip=0.1)


Either min_clip or max_clip can be omitted.

### Sigma clipping¶

For each pixel of an image in the combiner, sigma_clipping masks the pixel if is more than a user-specified number of deviations from the central value of that pixel in the list of images.

The sigma_clipping method is very flexible: you can specify both the function for calculating the central value and the function for calculating the deviation. The default is to use the mean (ignoring any masked pixels) for the central value and the standard deviation (again ignoring any masked values) for the deviation.

You can mask pixels more than 5 standard deviations above or 2 standard deviations below the median with

>>> combiner.sigma_clipping(low_thresh=2, high_thresh=5, func=np.ma.median)


Note

Numpy masked median can be very slow in exactly the situation typically encountered in reducing ccd data: a cube of data in which one dimension (in the case the number of frames in the combiner) is much smaller than the number of pixels.

### Extrema clipping¶

For each pixel position in the input arrays, the algorithm will mask the highest nhigh and lowest nlow pixel values. The resulting image will be a combination of Nimages-nlow-nhigh pixel values instead of the combination of Nimages worth of pixel values.

You can mask the lowest pixel value and the highest two pixel values with:

>>> combiner.clip_extrema(nlow=1, nhigh=2)


### Iterative clipping¶

To clip iteratively, continuing the clipping process until no more pixels are rejected, loop in the code calling the clipping method:

>>> old_n_masked = 0  # dummy value to make loop execute at least once
...     combiner.sigma_clipping(func=np.ma.median)


Note that the default values for the high and low thresholds for rejection are 3 standard deviations.

## Image combination¶

Image combination is straightforward; to combine by taking the average, excluding any pixels mapped by clipping:

>>> combined_average = combiner.average_combine()


Performing a median combination is also straightforward,

>>> combined_median = combiner.median_combine()  # can be slow, see below


## With image scaling¶

In some circumstances it may be convenient to scale all images to some value before combining them. Do so by setting scaling:

>>> scaling_func = lambda arr: 1/np.ma.average(arr)
>>> combiner.scaling = scaling_func
>>> combined_average_scaled = combiner.average_combine()


This will normalize each image by its mean before combining (note that the underlying images are not scaled; scaling is only done as part of combining using average_combine or median_combine).

## With image transformation¶

Note

Flux conservation Whether flux is conserved in performing the reprojection depends on the method you use for reprojecting and the extent to which pixel area varies across the image. wcs_project rescales counts by the ratio of pixel area of the pixel indicated by the keywords CRPIX of the input and output images.

The reprojection methods available are described in detail in the documentation for the reproject project; consult those documents for details.

You should carefully check whether flux conservation provided in CCDPROC is adequate for your needs. Suggestions for improvement are welcome!

Align and then combine images based on World Coordinate System (WCS) information in the image headers in two steps.

First, reproject each image onto the same footprint using wcs_project. The example below assumes you have an image with WCS information and another image (or WCS) onto which you want to project your images:

>>> from ccdproc import wcs_project
>>> reprojected_image = wcs_project(input_image, target_wcs)


Repeat this for each of the images you want to combine, building up a list of reprojected images:

>>> reprojected = []
>>> for img in my_list_of_images:
...     new_image = wcs_project(img, target_wcs)
...     reprojected.append(new_image)


Then, combine the images as described above for any set of images:

>>> combiner = Combiner(reprojected)
>>> stacked_image = combiner.average_combine()