Sofia-image-pipeline

This version of the SoFiA Image Pipeline contains several new features and improvements. It also **fixes a major issue for velocities in the source rest frame** from the last release (fixed in development version 1.3.4) in which the velocity convention for the source rest frame had inadvertently been flipped.

New Features
* Ability to **generate images of the full catalog/field** (mom0, mom1, mom2). These images will appear in the same directory as the catalog file. 70
* Ability to **work in offline mode** (-s none). 20
* Ability to **plot on SDSS false color images** when available (-s sdss).
* Ability to **specify a range of source ids**.

What's Changed
* Improve dependencies, new python version by lboschman in https://github.com/kmhess/SoFiA-image-pipeline/pull/98
* Catches errors when retrieving archive images. Instead of crashing, will carry on with making HI images. Related to 20.
* No longer crash if the SNR plot is not available. 100

**Full Changelog**: https://github.com/kmhess/SoFiA-image-pipeline/compare/v1.3.0...v1.3.5

This version of SIP includes some major improvements and new capabilities. When possible (if the cubes are in frequency and not already converted to velocity), we now plot moment maps in the **source rest frame** rather than in the observed frame. This is critical for making 1-to-1 comparisons of galaxy properties across cosmic time. However, spectra are plotted in the observed frame. We also make figures for mom2 maps, and position-velocity diagrams along the minor axis when available. Finally, we have added the capability of plotting a limited number of spectral lines other than HI.

New Features
* Plots will contain warnings if the beam info is not contained in the expected header keyword (BMAJ, BMIN, BPA), but will still be made.
* Will plot the **position velocity diagram along the minor axis (with mask) if the fits file is available**, and indicate pv_min angle on mom1 map. 61
* **Added capability of plotting multiple spectral lines (for now just CO(1-0), OH 1667 MHz, and HI)**. This is a work in progress. 1
* **HI column density calculation includes correction for redshift**. 73
* Can now retrieve full images from decals/decals-dr9 when images are greater than default pixel scale *3000 pixels, by changing requested scale.
* **Makes moment 2 figures when fits file is available**. 83 90
* Ability to plot on [DECaPS false color images](https://decaps.legacysurvey.org/viewer) when available (`-s decaps`). #95

What's Changed
* Removed dependency on reproject.
* 800kB combo png limit + decals-dev by paoloserra in https://github.com/kmhess/SoFiA-image-pipeline/pull/72
* fix 79 by paoloserra in https://github.com/kmhess/SoFiA-image-pipeline/pull/80
* Improved contour and SNR plotting for absorption line sources.
* Default DECaLS image is now from DR-10. Can ask for DR-9 with `-s decals-dr9`. 76
* Can deal with cubes in which the BUNIT has been written as `'beam-1 Jy*Hz'` as is done by SpectralCube. 48
* Improved treatment of different spectral axes (especially VRAD). 77
* Some security fixes and requirement upgrades.
* np.int() is now int(). 86
* Improved plot axes--generally larger for color bars, secondary axes, and spectra.
* Can now make plots of full cube spectrum even if the name is different from SoFiA output. 45
* Plot secondary frequency axis on spectra when cube is in Hz.
* **Moment 1, moment 2, w20, w50, are plotted in the source rest frame** rather than in the observed frame **when possible**.

Known Issues
* Currently does not work with matplotlib 3.8 due to a compatibility issue between matplotlib and astropy. 94

**Full Changelog**: https://github.com/kmhess/SoFiA-image-pipeline/compare/v1.2.0...v1.3.0

New Features
* Can retrieve and plot contours on **WISE images** (only in equatorial coordinates, not yet Galactic).
* Can process a **user-supplied subset** of sources, by paoloserra in https://github.com/kmhess/SoFiA-image-pipeline/pull/52
* Detect and appropriately plot **single-channel sources**, by paoloserra in https://github.com/kmhess/SoFiA-image-pipeline/pull/56

What's changed
* **FASTER CODE**: now plots HI figures without regridding to ancillary data https://github.com/kmhess/SoFiA-image-pipeline/pull/57, by healytwin1 https://github.com/kmhess/SoFiA-image-pipeline/pull/58
* This means that the HI data is no longer artificially smoothed to the resolution of the ancillary data.
* Better contour plotting for both emission and absorption line sources.
* Will plot a combined image using imagemagick even when ancillary data+HI contour plot is not present.
* `overview_fig.py` has now become a **command line tool called `download_usr_fig`**.
* Bump pillow from 9.1.0 to 9.1.1, by dependabot in https://github.com/kmhess/SoFiA-image-pipeline/pull/62
* Bump numpy from 1.21.0 to 1.22.0, by dependabot in https://github.com/kmhess/SoFiA-image-pipeline/pull/68

New Contributors
* healytwin1 made their first contribution in https://github.com/kmhess/SoFiA-image-pipeline/pull/58

**Full Changelog**: https://github.com/kmhess/SoFiA-image-pipeline/compare/v1.1.0...v1.2.0

New Features
* DevOps by axshen in https://github.com/kmhess/SoFiA-image-pipeline/pull/47
* Dockerimage available
* pip installable version available
* works with command line interface
* Improved spectral plotting for very bright sources
* Will **make plots when only a moment 0 map and catalog are provided**
* Can now do plots for data in **Galactic coordinates**
* Will plot **dashed contours** in mom0 and pv maps for **absorption line sources**

New Contributors
* axshen made their first contribution in https://github.com/kmhess/SoFiA-image-pipeline/pull/47

**Full Changelog**: https://github.com/kmhess/SoFiA-image-pipeline/compare/v1.0.0...v1.1.0

SIP 1.0.0 is the first stable release of the SoFiA Image Pipeline. The program generates figures of spectral line sources, for publication or quick inspection, based on SoFiA-2 output catalog and fits files.

Features
* Overlays HI total intensity contours on a user selection of multi-wavelength surveys and/or user provided image.
* Labels figures and color bars in the native spatial and spectral coordinate system of the provided HI FITS images.
* Plots HI contours based on the noise of the data. Prints equivalent column density [cm^-2] based on the brightness and spectral units of the HI FITS images.
* Plots moment 1 velocity contours based on the width of the source; annotates figure with contour width.
* Annotates figures with SIP derived HI column density, SoFiA derived kinematic position angle, w_50, w_20, as appropriate.
* Annotates figures with synthesized beam when available in the header, as provided by the user, or as estimated from the pixel size.
* Plots integrated HI spectra "without noise" from SoFiA, and "with noise" by integrating each channel by the projected 2D mask.
* Plots extent of the SoFiA mask in the position-velocity diagram.

Known Issues
* Saving figures with .ps or .eps format has issues with transparency and background colors appearing black.
* `overview_fig.py` can download full color images from PanSTARRS and DECaLS, but these can not yet be read as user supplied input to `image_pipeline.py`
* The mask (red line) on pv-diagram plots may not be perfectly aligned from left-to-right. Please use this line only as a rough indication of the mask position. Refer to actual data for the truth. Any suggestions for how to improve this are welcome.
* For data with channels that are not uniform in width (e.g. `SPECSYS = FELO-OPT`), SIP's conversion to km/s is off compared to SoFiA-2's: the programs use formula from [here](https://www.astro.rug.nl/software/kapteyn/spectralbackground.html#aips-axis-type-felo) or wcslib to do the conversion, respectively. We haven't tracked down the discrepancy. To the best of our knowledge, only old radio data observing nearby galaxies, might be in this `FELO` format.
* No exceptions are caught for `socket.timeout` during downloads (seen for `-s panstarrs` when image requested was 20.5 arcmin.)

Contributors
* paoloserra made their first contribution in https://github.com/kmhess/SoFiA-image-pipeline/pull/5
* lboschman made their first contribution in https://github.com/kmhess/SoFiA-image-pipeline/pull/17
* dependabot made their first contribution in https://github.com/kmhess/SoFiA-image-pipeline/pull/42

**Full Changelog**: https://github.com/kmhess/SoFiA-image-pipeline/commits/v1.0.0