Install

The preferred method of installation is using pip: pip install goodman-pipeline

We do not have the resources to provide installation support. However, the installation process is simple, and is described below (we hope that in enough detail) so that users can follow the steps and end up with a running version of the pipeline.

Note

In this tutorial we use Miniconda3 but you can also do it with Anaconda by visiting https://www.anaconda.com/download/ for downloading the Anaconda installer for either operating system.

Warning

For most cases doing ``pip install goodman-pipeline`` is enough. You might need to compile DCR separately (see instructions below).

Using pip (Recommended)

The Goodman Spectroscopic Pipeline can be installed using pip, which is the preferred and simplest installation method:

For the latest stable version:

pip install goodman-pipeline

For the latest release candidate (if available):

pip install --pre goodman-pipeline

Note: This method does not install dcr, so if you need cosmic ray rejection, you’ll need to install it separately (see the DCR installation section below).

If you are updating your goodman pipeline installation, you can use:

pip install --upgrade goodman-pipeline

Installing DCR

If you need cosmic ray rejection functionality, you’ll need to install DCR separately:

1. Download the DCR installation script from the repository

2. Run the installation script in your active environment:

sh install_dcr.sh

To test if DCR installed correctly:

dcr

You should see output similar to:

This is a modified version of DCR! for the Goodman Spectroscopic Pipeline
Please visit the author's site to get the original version:
Modification Version: 0.0.1

http://users.camk.edu.pl/pych/DCR/

USAGE:  dcr  input_file  cleaned_file  cosmicrays_file

File ‘dcr.par’ must be present in the working directory.

Installing Astrometry.net Binary

Note

This is critical if you want to do astrometry or photometry. If not you can ignore it.

Full instructions are on Astrometry’s page. For mac, the recommended way is using brew.

brew install astrometry-net

Installing Astrometry.net Index Files

If you plan to use the redastrometry command for astrometric solutions, you’ll need to download astrometry.net index files locally. The choice of index files depends on your image’s pixel scale, which varies with CCD binning.

Goodman Pixel Scale by Binning

• 1x1 binning (unbinned): 0.15 arcsec/pixel

• 2x2 binning: 0.30 arcsec/pixel

• 3x3 binning: 0.45 arcsec/pixel

Selecting Index Files

Choose index files based on your typical binning mode:

Binning	Pixel Scale	Recommended Index Series	Field of View Coverage
1x1	0.15”/pixel	4200-4204	~0.1° to 2°
2x2	0.30”/pixel	4200-4206	~0.2° to 4°
3x3	0.45”/pixel	4200-4207	~0.3° to 6°

Download Script

Use this script to download the necessary index files:

#!/bin/bash
# Target directory for index files
INDEX_DIR="$HOME/astrometry/index"
mkdir -p "$INDEX_DIR"

# Range of index series (4200 to 4207)
START_INDEX=4200
END_INDEX=4204  # Adjust based on your binning needs

# Range of tile numbers (00 to 47)
TILE_MIN=0
TILE_MAX=47

# Base URL
BASE_URL="http://data.astrometry.net/4200"

echo "Downloading index files for series ${START_INDEX}–${END_INDEX}..."

for SERIES in $(seq $START_INDEX $END_INDEX); do
  for TILE in $(seq -w $TILE_MIN $TILE_MAX); do
    FILENAME="index-${SERIES}-${TILE}.fits"
    DEST="${INDEX_DIR}/${FILENAME}"
    URL="${BASE_URL}/${FILENAME}"

    if [ -f "$DEST" ]; then
      echo "✓ $FILENAME already exists, skipping."
    else
      echo "↓ Downloading $FILENAME..."
      curl -L -o "$DEST" "$URL"
      if [ $? -eq 0 ]; then
        echo "✓ Downloaded $FILENAME"
      else
        echo "✗ Failed to download $FILENAME"
        rm -f "$DEST"  # Clean up incomplete file
      fi
    fi
  done
done

echo "Download complete! Index files saved to: $INDEX_DIR"

Usage Notes

• For 1x1 binning: Use END_INDEX=4204 in the script

• For 2x2 binning: Use END_INDEX=4206 in the script

• For 3x3 binning: Use END_INDEX=4207 in the script

• Mixed binning: Use END_INDEX=4207 to cover all cases

Using Custom Index Directory

If you download index files to a custom location, specify the path when running redastrometry:

redastrometry image.fits --index-directory $HOME/astrometry/index

Alternative Installation Methods

Ubuntu

This installation process has been tested in a live version (previously known as Live CD) of Ubuntu 18.04.

1. Install make and gcc

sudo apt install gcc make

2. Download Miniconda

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh

Mac OS

This installation was tested on MacOS High Sierra and newer versions.

1. Install Xcode command Line Tools. You can do it from the App Store or from command line.

xcode-select --install

2. Download Anaconda or Miniconda

curl https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-arm64.sh --output miniconda.sh

If you have a different processor like intel, you can search miniconda installer url for your system.

Manual Installation from Source

Warning

This installation method is for advanced users only. The pip installation method is recommended for most users.

Note

This installation instructions work with BASH only.

1. Install Miniconda (if not already installed)

bash miniconda.sh

Answer the questions and reopen the terminal at the end.

2. Configure conda to use the Astroconda Channel

conda config --add channels http://ssb.stsci.edu/astroconda

3. Get the latest release of the Goodman Spectroscopic Pipeline from github. There is a .zip and .tar.gz files, the following steps will continue with the latter.

   Make sure there is a green tag that says Latest release. For instance, for the version v1.3.11 the file is called:

   goodman_pipeline-1.3.11.tar.gz

4. Extract the file (you can’t copy and paste this line)

tar -xvf goodman_pipeline-<latest tag>.tar.gz

where <latest tag> is the version number of the latest release.

5. Move into the directory containing the package.

cd goodman_pipeline-<latest tag>

If you do ls you should find files such as pyproject.toml and install_dcr.sh.

6. Create the virtual environment. The environment.yml file contains a preset definition of a virtual environment that Anaconda will understand, and ensures that the Goodman Spectroscopic Pipeline will work. Even the name of the virtual environment is set there.

conda env create -f environment.yml

This will create a virtual environment called goodman_pipeline. To activate it:

source activate goodman_pipeline

7. Install DCR (if needed). This script requires a virtual environment activated.

sh install_dcr.sh

To test if it worked you can do:

dcr

You should get the DCR usage information as shown above.

8. Install the pipeline using pip

pip install .

Or for an editable installation (if you plan to modify the code):

pip install -e .

Verification

To verify that the installation was successful, you can run:

redccd --help

and

redspec --help

Both commands should display their respective help messages without errors.

Repository Information

The Goodman Pipeline repository is located at: soar-telescope/goodman_pipeline

For issues, bug reports, or feature requests, please visit the GitHub Issues page.