# SAUSERO
__SAUSERO__ is a reduction software for the Broad Band Imaging mode of OSIRIS+ at GTC.
Developed by __Fabricio M. Pérez-Toledo__
## General Description
**S**oftware to **AU**omatize in a **S**imple **E**nvironment the **R**eduction of **O**siris+ data (**SAUSERO**) processes OSIRIS+ raw science frames to address noise, cosmetic defects, and pixel heterogeneity, preparing them for photometric analysis. Correcting these artifacts is a critical prerequisite for reliable scientific analysis. The software applies observation-specific reduction steps, ensuring optimized treatment for different data types. Developed with a focus on simplicity and efficiency, **SAUSERO** streamlines the reduction pipeline, enabling researchers to obtain calibrated data ready for photometric studies.
### Key Reduction Steps:
1. Application of a __Bad Pixel Mask (BPM)__ to all frames.
2. Creation of the __Master Bias__.
3. Creation of the __Master Flat__.
4. Application of master calibration frames to both __standard star__ and __science frames__.
5. Removal of __cosmic rays__.
6. __Sky subtraction__.
7. Alignment of __science frames__.
8. __Astrometric calibration__.
9. __Flux calibration__.
### Input Requirements:
The software requires the following frames as input:
- __Bias frames__
- __Sky flat frames__
- __Photometric standard star frames__
- __Science frames__
## Outputs
The generated results consist of one image per observed band. For each image, the following corrections and calibrations will have been applied:
- __Bias subtraction__
- __Flat-field correction__ (including fringing correction for the Sloan z band, if applicable)
- __Image alignment and stacking__
- __Astrometric calibration__
- __Photometric calibration__ (estimation of the zero-point, ZP ± error)
To address cosmetic defects, a __Bad Pixel Mask (BPM)__ is applied, and the __LACosmic algorithm__ is used to handle cosmic ray removal.
## Requirements
### Operative System
- __Any__: The software is designed to run within a __Conda environment__, ensuring compatibility across platforms.
### Dependencies
The following Python packages are required (minimum versions specified), however, they will be installed
automatically together the :
astroalign>=2.4.1
astrometry_net_client>=0.3.0
astropy>=5.3.4
astroquery>=0.4.6
ccdproc>=2.4.1
lacosmic>=1.1.0
loguru>=0.7.2
matplotlib>=3.8.0
numpy>=1.25.2
PyYAML>=6.0.2
sep>=1.2.1`
### Hardware Requirements
- __RAM__: Minimum 4GB (higher is recommended for large datasets).
## Installation
Installing SAUSERO is straightforward. Follow these steps:
1. __Activate your Conda environment__ (or create a new one if needed (see below)):
```
conda activate <your_env>
2. __Install SAUSERO__ using `pip`:
```
pip install sausero
That's it! SAUSERO is now almost ready to use ;)
### Optional: Creating a New Conda Environment
If you don’t have an existing Conda environment, you can create one specifically for SAUSERO with the following commands:
conda create -n sausero_env python=3.9 -y
conda activate sausero_env
pip install sausero
## First-Time Setup
Once Conda is set up, you should run __SAUSERO__ for the first time to create the file `configuration.json` that has to be configured.
sausero -pr <your_program> -bl <your_ob>
- `-pr`: Your GTC program indicator.
- `-bl`: The observed block number.
**ATTENTION**: The first time, the code will 'fail' because the configuration file does not know the root
directory where the images are stored and your astrometry-api-key. To fix this, follow the instructions below.
You must edit the configuration file, which is located in your home directory inside
a folder named `sausero/`.
You need to set the following parameters in the configuration file:
1. `PATH_DATA`: Set this to the root directory containing your frames. Example:
```
"PATH_DATA": "/path/to/your/frames/"
The directory structure must follow the format `<Your_Program>_<Your_OB>/`. Inside this directory, you should have
a `raw/` folder where the original frames are stored. During execution, __SAUSERO__ will create a new folder named
`reduced/`, where the reduced frames will be saved.
2. `No_Session`: This is your Astrometry.net API key. Example:
```
"No_Session":"astrometry-api-key"
To obtain this key, create an account on [Astrometry.net](https://nova.astrometry.net/). Copy your API key and paste it into the configuration file.
## Running SAUSERO
After updating and saving the configuration file, you can run the command again. This time, the software will execute successfully.
sausero -pr <your_program> -bl <your_ob>
### Outputs and Results
Once the process is complete, you will find a collection of reduced frames in the `reduced/` folder inside your frame
directory. The output includes:
A. __Reduced science frames__:
- One version with the sky included.
- One version with the sky subtracted.
B. __Aligned frames__:
- Both sky-included and sky-subtracted versions.
C. __Astrometrized frames__:
- Frames with astrometric calibration applied.
D. __Visualization PNG files__:
- A PNG showing the detected sources in the Field of View (FoV).
- A PNG showing the photometric standard star.
E. __Final reduced science frames__:
- Both sky-included and sky-subtracted versions.
### Important Notes
- By default, __SAUSERO__ ensures your data remains private when using Astrometry.net. The software's internal configuration avoids sharing any data with the Astrometry.net community, ensuring your data's security.
## Project Structure
SAUSERO/
BPM/
BPM_OSIRIS_PLUS.fits -> BAD PIXEL MASK
config/
configuration.json -> Configuration file.
check_files.py -> It determines which steps can be performed by the pipeline based on the available FITS files.
aligning_osirisplus.py -> Aligns the science frames.
astrometry_osirisplus.py -> Astrometrization of the science frames.
Color_Codes.py -> Gives color to the comments
OsirisDRP.py -> Handles all the sofware and manages the frames.
photometry_osirisplus.py -> Carries out the photometric calibration.
reduction_osirisplus.py -> Carries out the clean process.
## Note about the frames
The code is designed to work with __OSIRIS+__ frames. They must be in __FITS__ format.
## LICENSE
This software is under __GPL v3.0__ license. More information is available in the
repository.
## CONTACT
- __Email__: [fabricio.perez@gtc.iac.es](fabricio.perez@gtc.iac.es)
- __Repository__: [https://github.com/Kennicutt/SAUSERO](https://github.com/Kennicutt/SAUSERO)
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"description": "# SAUSERO\n\n__SAUSERO__ is a reduction software for the Broad Band Imaging mode of OSIRIS+ at GTC.\n\nDeveloped by __Fabricio M. P\u00e9rez-Toledo__\n\n## General Description\n\n**S**oftware to **AU**omatize in a **S**imple **E**nvironment the **R**eduction of **O**siris+ data (**SAUSERO**) processes OSIRIS+ raw science frames to address noise, cosmetic defects, and pixel heterogeneity, preparing them for photometric analysis. Correcting these artifacts is a critical prerequisite for reliable scientific analysis. The software applies observation-specific reduction steps, ensuring optimized treatment for different data types. Developed with a focus on simplicity and efficiency, **SAUSERO** streamlines the reduction pipeline, enabling researchers to obtain calibrated data ready for photometric studies.\n\n### Key Reduction Steps:\n\n1. Application of a __Bad Pixel Mask (BPM)__ to all frames.\n2. Creation of the __Master Bias__.\n3. Creation of the __Master Flat__.\n4. Application of master calibration frames to both __standard star__ and __science frames__.\n5. Removal of __cosmic rays__.\n6. __Sky subtraction__.\n7. Alignment of __science frames__.\n8. __Astrometric calibration__.\n9. __Flux calibration__.\n\n### Input Requirements:\n\nThe software requires the following frames as input:\n\n- __Bias frames__\n- __Sky flat frames__\n- __Photometric standard star frames__\n- __Science frames__\n\n## Outputs\n\nThe generated results consist of one image per observed band. For each image, the following corrections and calibrations will have been applied:\n\n- __Bias subtraction__\n- __Flat-field correction__ (including fringing correction for the Sloan z band, if applicable)\n- __Image alignment and stacking__\n- __Astrometric calibration__\n- __Photometric calibration__ (estimation of the zero-point, ZP \u00b1 error)\n\nTo address cosmetic defects, a __Bad Pixel Mask (BPM)__ is applied, and the __LACosmic algorithm__ is used to handle cosmic ray removal.\n\n## Requirements\n\n### Operative System\n- __Any__: The software is designed to run within a __Conda environment__, ensuring compatibility across platforms.\n\n### Dependencies\nThe following Python packages are required (minimum versions specified), however, they will be installed\nautomatically together the :\n\n astroalign>=2.4.1\n astrometry_net_client>=0.3.0\n astropy>=5.3.4\n astroquery>=0.4.6\n ccdproc>=2.4.1\n lacosmic>=1.1.0\n loguru>=0.7.2\n matplotlib>=3.8.0\n numpy>=1.25.2\n PyYAML>=6.0.2\n sep>=1.2.1`\n\n### Hardware Requirements\n- __RAM__: Minimum 4GB (higher is recommended for large datasets).\n\n## Installation\n\nInstalling SAUSERO is straightforward. Follow these steps:\n\n1. __Activate your Conda environment__ (or create a new one if needed (see below)):\n ```\n conda activate <your_env>\n\n2. __Install SAUSERO__ using `pip`:\n ```\n pip install sausero\n\nThat's it! SAUSERO is now almost ready to use ;)\n\n### Optional: Creating a New Conda Environment\n\nIf you don\u2019t have an existing Conda environment, you can create one specifically for SAUSERO with the following commands:\n\n conda create -n sausero_env python=3.9 -y\n conda activate sausero_env\n pip install sausero\n\n## First-Time Setup\n\nOnce Conda is set up, you should run __SAUSERO__ for the first time to create the file `configuration.json` that has to be configured.\n\n sausero -pr <your_program> -bl <your_ob>\n\n- `-pr`: Your GTC program indicator.\n- `-bl`: The observed block number.\n\n**ATTENTION**: The first time, the code will 'fail' because the configuration file does not know the root \ndirectory where the images are stored and your astrometry-api-key. To fix this, follow the instructions below.\n\nYou must edit the configuration file, which is located in your home directory inside \na folder named `sausero/`.\n\nYou need to set the following parameters in the configuration file:\n\n1. `PATH_DATA`: Set this to the root directory containing your frames. Example:\n\n ```\n \"PATH_DATA\": \"/path/to/your/frames/\"\n\nThe directory structure must follow the format `<Your_Program>_<Your_OB>/`. Inside this directory, you should have \na `raw/` folder where the original frames are stored. During execution, __SAUSERO__ will create a new folder named \n`reduced/`, where the reduced frames will be saved.\n\n2. `No_Session`: This is your Astrometry.net API key. Example:\n\n ```\n \"No_Session\":\"astrometry-api-key\"\n\nTo obtain this key, create an account on [Astrometry.net](https://nova.astrometry.net/). Copy your API key and paste it into the configuration file.\n\n## Running SAUSERO\n\nAfter updating and saving the configuration file, you can run the command again. This time, the software will execute successfully.\n\n sausero -pr <your_program> -bl <your_ob>\n\n### Outputs and Results\n\nOnce the process is complete, you will find a collection of reduced frames in the `reduced/` folder inside your frame \ndirectory. The output includes:\n\nA. __Reduced science frames__:\n- One version with the sky included.\n- One version with the sky subtracted.\n\nB. __Aligned frames__:\n- Both sky-included and sky-subtracted versions.\n\nC. __Astrometrized frames__:\n- Frames with astrometric calibration applied.\n\nD. __Visualization PNG files__:\n- A PNG showing the detected sources in the Field of View (FoV).\n- A PNG showing the photometric standard star.\n\nE. __Final reduced science frames__:\n- Both sky-included and sky-subtracted versions.\n\n\n### Important Notes\n\n- By default, __SAUSERO__ ensures your data remains private when using Astrometry.net. The software's internal configuration avoids sharing any data with the Astrometry.net community, ensuring your data's security.\n\n## Project Structure\n\n SAUSERO/\n BPM/\n BPM_OSIRIS_PLUS.fits -> BAD PIXEL MASK\n config/\n configuration.json -> Configuration file.\n check_files.py -> It determines which steps can be performed by the pipeline based on the available FITS files.\n aligning_osirisplus.py -> Aligns the science frames. \n astrometry_osirisplus.py -> Astrometrization of the science frames.\n Color_Codes.py -> Gives color to the comments\n OsirisDRP.py -> Handles all the sofware and manages the frames. \n photometry_osirisplus.py -> Carries out the photometric calibration.\n reduction_osirisplus.py -> Carries out the clean process.\n\n## Note about the frames\n\nThe code is designed to work with __OSIRIS+__ frames. They must be in __FITS__ format.\n\n## LICENSE\n\nThis software is under __GPL v3.0__ license. More information is available in the\nrepository.\n\n## CONTACT\n\n- __Email__: [fabricio.perez@gtc.iac.es](fabricio.perez@gtc.iac.es)\n\n- __Repository__: [https://github.com/Kennicutt/SAUSERO](https://github.com/Kennicutt/SAUSERO)\n",
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