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Please rename your default branch from master to main as part of astropy/astropy-project#151 , preferably by 2021-03-22. Also a friendly reminder to check documentation, workflows, etc., and update them accordingly. Please don't forget to communicate this change to your users and stakeholders. To summarize:

• Rename branch from master to main, preferably by 2021-03-22.
• Update documentation, workflows, etc., accordingly. -- See #299
• Communicate this change to your users and stakeholders.

Once this is taken care of, you may close this issue.

This is an automated issue. If this is opened in error, please let @pllim know!

The guide is at https://github.com/orgs/astropy/projects/4 and the broken link is here: https://github.com/mwcraig/ccd-reduction-and-photometry-guide/pull/198#pullrequestreview-370061482

Rebuilding takes a while and the artifact is being built/uploaded for the PR so it ought to be possible to grab that instead of rebuilding.

See https://github.com/mwcraig/ccd-reduction-and-photometry-guide/pull/209#pullrequestreview-370062661

When first loading the Palomar data, if we want to be consistent with previous notebooks, we should use

calibrated_images = Path('./python_imred_data')

not

calibrated_images = Path('./')

as it currently is. However, even with that, the reduced dark file doesn't appear to be exist there.

Assuming this file is downloadable, include a link, if not, if it was supposed to be produced in a previous notebook, link to that notebook.

From running notebook 01.04:

WARNING: AstropyDeprecationWarning: The MexicanHat2D class is deprecated and may be removed in a future version.
        Use RickerWavelet2D instead. [

This notebook refers to "An astronomical image like the one shown below" without actually showing an image! One should probably be added or the first sentence restructured.

It depends on a 'reduced' directory of Palomar reduced biases that doesn't exist.

What works:

trimmed_bias.data = trimmed_bias.data.astype('float32')

Great idea, though! Would be nice to have some sort of option to set property in CCDData to do this automatically when writing files.

jpm

Not sure what is generating this one; comes up in running 01.04

/Users/mattcraig/development/ccd-reduction-and-photometry-guide/notebooks/image_sim.py:121: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
  dark_im[[hot_y, hot_x]] = hot_current * exposure_time / gain

When calibrating the dark frames from Palomar you have the code state:

for ccd, file_name in ex1_darks_raw.ccds(imagetyp='DARK',            # Just get the bias frames
                                         ccd_kwargs={'unit': 'adu'}, # CCDData requires a unit for the image if 
                                                                     # it is not in the header
                                         return_fname=True           # Provide the file name too.
                                        ):

The comments in the code should say you are getting just the DARK frames.

Also, what does showing the reduced frames after triming the overscan in the 'calibrating dark frames' loop supposed to show? I think you need to reload the directory via:

ex1_images_reduced = ImageFileCollection(ex1_path_reduced)

otherwise you show the File Collection before the newly reduced data was added.

Couldn't do anything with the example-thermo-electric data because it isn't available.

At some point, we'll want to add an author list.

These notebooks are ready for copy editing:

• Notebook whose name starts "00"
• All notebooks whose name starts with "01"

There is a missing comma on line 74 of the notebook that prevents the notebook from loading.

There are quite a few grammatical errors in this notebook but most importantly it ends with "Example 2: No overscan subtraction, but trim the images" but there is no link to the data provided.

• What does changing the gain affect?
• What does changing the exposure time affect?

Attempts to install ccdproc under Python 3.7 using conda seem to trigger a reversion to python 3.6? A dependency issue?

The suggestion was made here: https://github.com/mwcraig/ccd-reduction-and-photometry-guide/pull/105#discussion_r311702332

This suggestion was made by @tstibor at https://github.com/mwcraig/ccd-reduction-and-photometry-guide/pull/110#discussion_r330014215

I've always used the mode to scale (sky/twilight) flats since I worry about the median being biased high by stars. This is obviously more processing intensive, though, so there's a trade-off. Can be implemented with statistics.mode or scipy.stats.mode.

Ideally across notebooks too...

https://zenodo.org/record/2634177/files/master_dark_exposure_1000.0.fit.bz2?download=1

It should be BSD 3-clause

It has been observed that due to a ":" in 01.02-IRAF-like:-photutils.ipynb and 01.03-SExtractor-like:-sep-and-photutils.ipynb files, one cannot successfully clone the repository.

$ git clone https://github.com/astropy/ccd-reduction-and-photometry-guide.git
Cloning into 'ccd-reduction-and-photometry-guide'...
remote: Enumerating objects: 1162, done.
remote: Total 1162 (delta 0), reused 0 (delta 0), pack-reused 1162
Receiving objects: 100% (1162/1162), 12.74 MiB | 4.54 MiB/s, done.
Resolving deltas: 100% (810/810), done.
error: invalid path 'notebooks/photometry/01.02-IRAF-like:-photutils.ipynb'
fatal: unable to checkout working tree
warning: Clone succeeded, but checkout failed.
You can inspect what was checked out with 'git status'
and retry with 'git restore --source=HEAD :/'

Removing the ":" in those file names fixed the problem and enabled successful cloning of this repository.

Thank you.

Adding caching should avoid rebuilding the whole set of notebooks. For now, either all notebooks need to be rebuilt or none because some of them rely on the output of earlier notebooks to work.

When running the construction of a realistic (synthetic) image in notebook 01.04, I get

image_sim.py:121: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
  dark_im[[hot_y, hot_x]] = hot_current * exposure_time / gain

Looks like the indexing for dark_im needs to be fixed.

Good examples of this are in the overscan notebook:

• Rendered: https://mwcraig.github.io/ccd-as-book/01-08-Overscan.html
• Raw: https://github.com/mwcraig/ccd-reduction-and-photometry-guide/blob/master/notebooks/01.08-Overscan.ipynb

Should be a CC-by license in the book.

Probably due to some reorganization in the past, there users are asked to process python_imred_data files that don't exist. I found a link in the 02.01 notebook that said

The data for this example can be downloaded from [http://www.stsci.edu/~etollerud/python_imred_data.tar](http://www.stsci.edu/~etollerud/python_imred_data.tar)

I suggest adding this link right above that cell in the notebook.

The call to

ccd = CCDData.read('/Users/mattcraig/Desktop/2018-07-23-reduced/kelt-16-S001-R001-C110-r.fit')

is likely to work only on Matt Craig's laptop... I have a copy of the file if we need to make it publicly available.

Some specific questions:

1. Keep section that adds stars?
2. Keep section that adds cosmic rays?
3. Keep interactive? (Only thing I don't like is that the sliders have to be set up

Suggestion made at https://github.com/mwcraig/ccd-reduction-and-photometry-guide/pull/109#pullrequestreview-270184071

See https://github.com/mwcraig/ccd-reduction-and-photometry-guide/pull/14#discussion_r289652308 for more

This may mean changing the default dpi and plot size. Images are way too big now.

• This sentence in 05-03 needs to be fixed: "The raw images are at XXX, and this notebook assumes that"
• This sentence in 08-01 needs a link: "We will see in the notebook [XXX]()"

Not sure how to fix this...

The issue in the first draft was that stars were totally visible in the output image.

From #5:

notebook 01.05 calibration overview still contains a note to self and seems to be missing a summary line at the end, perhaps it's not finished?

The current version adds target="_blank" to the link by putting it in braces at the end of a markdown link. That worked (I think?) when the links went through a markdown stage in the rendering in jupyter-book, but they do not anymore.

Since HTML is valid markdown we might as well just add the link as HTML with the attributes we need.

Being anal, but the first sentence of the "Impact of combining images on noise" section likely needs to be reworked for clarity.

The default for this changed in astropy 4.0 from True to False. We need True for these images to render well.