README.md

## csst_proto 
[![Documentation Status](https://readthedocs.org/projects/csst-proto/badge/?version=latest)](https://csst-proto.readthedocs.io/en/latest/?badge=latest)
 
CSST L1 pipeline prototype.

## homepage

This code is available at *CSST GitLab*:
- [https://csst-tb.bao.ac.cn/code/csst-l1/csst_proto](https://csst-tb.bao.ac.cn/code/csst-l1/csst_proto).

## documentation

A sphinx-based documentation is available at
- [https://csst-proto.readthedocs.io/en/latest/](https://csst-proto.readthedocs.io/en/latest/)

## installation

`csst_proto` can be installed with the following shell command

```bash
git clone https://csst-tb.bao.ac.cn/code/csst-l1/csst_proto.git
cd csst_proto
pip install -r requirements.txt
python setup.py install
```

or a single-line command

```bash
sh -c "$(curl -fsSL https://csst-tb.bao.ac.cn/code/csst-l1/csst_proto/-/raw/main/install.sh)"
```

## instruction

A simple example on how to use this package:

```python
from csst_proto.top_level_interface import flip_image
from astropy.io import fits

# read an L0 image
img = fits.getdata("CSST_MS_SCI_06_L0_img.fits")
# flip the image
img_flipped = flip_image(img=img)
```

## algorithm description

The `csst_proto` uses an awesome algorithm based on `numpy.ndarray` indices to flip images.


## timeline

| file / directory   | description                     | urgent | C6  | C7  |
|--------------------|---------------------------------|--------|-----|-----|
| `csst_proto/`      | source code & data              | √√     | √   |     |
| `doc/`             | sphinx-based documentation      |        |     | √   |
| `example/`         | code examples                   | -      | -   | -   |
| `tests/`           | unit tests                      |        |     | √   |
| `.gitignore`       | git file                        |        | √   |     |
| `.gitlab-ci.yml`   | gitlab CI/CD pipeline           |        |     | √   |
| `LICENSE`          | code license                    |        | √   |     |
| `README.md`        | readme file                     | √√     | √   |     |
| `install.sh`       | single-line installation script |        | √   |     |
| `install_local.sh` | local installation script       |        | √   |     |
| `readthedocs.yml`  | readthedocs.io configuration    |        |     | √   |
| `requirements.txt` | code requirements               | √      | √   |     |
| `setup.py`         | sphinx-based documentation      | √√     | √   |     |

## important stages
1. **code**, **code style** & `top_level_interface`
2. **installation**: `source code` & `setup.py` -> `pip install <package_name>`
3. **a simple instruction**: `README.md`
4. **unittest**: `pytest`
5. *gitlab CI/CD pipeline: `.gitlab-ci.yml`
6. *sphinx-based documentation: `doc/` & `readthedocs.yml`

## useful links
- python packaging user guide: https://packaging.python.org/en/latest/
- packaging binary extensions (C/C++): https://packaging.python.org/en/latest/guides/packaging-binary-extensions
- `setuptools`: https://packaging.python.org/en/latest/tutorials/installing-packages/
- recommended IDEs
  - PyCharm: https://www.jetbrains.com/pycharm/
  - VS Code: https://code.visualstudio.com/
- `git`: https://git-scm.com/
  - Pro Git: https://git-scm.com/book/en/v2
- Numpydoc: https://numpydoc.readthedocs.io/en/latest/format.html
  - for C: https://peps.python.org/pep-0007/
  - for Python: https://peps.python.org/pep-0008/
- `unittest`: https://docs.python.org/3.8/library/unittest.html
- gitlab CI/CD pipeline: https://docs.gitlab.com/ee/ci/pipelines/
- gitlab runners: https://docs.gitlab.com/runner/
- `sphinx`: https://www.sphinx-doc.org/en/master/index.html
- markdown: https://www.markdownguide.org/
- restructured text: https://docutils.sourceforge.io/rst.html
- readthedocs: https://readthedocs.io/ or https://rtfd.io/

## `data manager`

```python
import os
from csst.ms.data_manager import CsstMscDataManager
from csst.ms.backbone import CCD_ID_LIST

# initialize data manager
dm = CsstMscDataManager(
    ver_sim="C5.1", dir_l0="/data/sim_data/MSC_0000100", dir_l1="/home/user/L1Pipeline/msc/work")
# process all CCDs
dm.set_ccd_ids(CCD_ID_LIST)

print("----- available ccd_ids -----")
print(dm.available_ccd_ids)
for ccd_id in dm.target_ccd_ids:
    print("----- L0 images -----")
    print(dm.l0_ccd(ccd_id=ccd_id))
    print(os.path.exists(dm.l0_ccd(ccd_id=ccd_id)))
    print("----- L0 crs -----")
    print(dm.l0_crs(ccd_id=ccd_id))
    print(os.path.exists(dm.l0_ccd(ccd_id=ccd_id)))
    print("----- L0 input cat -----")
    print(dm.l0_cat(ccd_id=ccd_id))
    print(os.path.exists(dm.l0_cat(ccd_id=ccd_id)))
    print("----- L0 input log -----")
    print(dm.l0_log(ccd_id=ccd_id))
    print(os.path.exists(dm.l0_log(ccd_id=ccd_id)))
    print("----- L1 images -----")
    print(dm.l1_ccd(ccd_id, post="img.fits"))
```