enchase 2.1.0__tar.gz

enchase-2.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025-2026 Waleed Ajmal
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

enchase-2.1.0/NOTICE

@@ -0,0 +1,49 @@
+chase-pipeline
+Copyright (c) 2025-2026 Waleed Ajmal
+Licensed under the MIT License (see LICENSE).
+
+================================================================================
+Third-party components
+================================================================================
+
+This product includes software adapted from `satprocess`
+(https://github.com/FinlayDavis/satprocess), used under the BSD 3-Clause License.
+
+    BSD 3-Clause License
+
+    Copyright (c) 2025, Finlay Davis
+    All rights reserved.
+
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions are met:
+
+    1. Redistributions of source code must retain the above copyright notice,
+       this list of conditions and the following disclaimer.
+    2. Redistributions in binary form must reproduce the above copyright notice,
+       this list of conditions and the following disclaimer in the documentation
+       and/or other materials provided with the distribution.
+    3. Neither the name of the copyright holder nor the names of its
+       contributors may be used to endorse or promote products derived from this
+       software without specific prior written permission.
+
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+    AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+    IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+    ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+    LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+    CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+    SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+    INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+    CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+    ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+    POSSIBILITY OF SUCH DAMAGE.
+
+Specifically, the following functions were ported/adapted from satprocess and
+carry the BSD-3 notice in their source:
+  - chase.calib.spatial.hough_disk_center        (preprocess_image + detect_circles)
+  - chase.calib.wavelength.cross_correlation_shift, align_spectrum   (calculate_shift)
+  - chase.calib.intensity.integral_scaling       (calculate_scaling)
+  - chase.shifts_cache.*                          (CSV shift-cache)
+
+The absolute intensity calibration uses ISPy (https://github.com/ISP-SST/ISPy)
+when the optional `atlas` extra is installed.

enchase-2.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: enchase
+Version: 2.1.0
+Summary: enCHASE: calibration and analysis pipeline for CHASE/HIS solar spectroscopy (TUI + SDK + CLI)
+Author: Waleed Ajmal
+License: MIT
+Project-URL: Homepage, https://github.com/Majboor/enchase
+Project-URL: Repository, https://github.com/Majboor/enchase
+Project-URL: Changelog, https://github.com/Majboor/enchase/blob/main/CHANGELOG.md
+Keywords: solar,CHASE,HIS,spectroscopy,flare,calibration,astronomy
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Topic :: Scientific/Engineering :: Astronomy
+Classifier: Intended Audience :: Science/Research
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: NOTICE
+Requires-Dist: numpy>=1.21
+Requires-Dist: scipy>=1.7
+Requires-Dist: astropy>=5.0
+Requires-Dist: scikit-image>=0.19
+Requires-Dist: opencv-python>=4.5
+Requires-Dist: matplotlib>=3.4
+Requires-Dist: Pillow>=9.0
+Requires-Dist: tqdm>=4.60
+Requires-Dist: requests>=2.25
+Requires-Dist: tomli>=1.2; python_version < "3.11"
+Provides-Extra: tui
+Requires-Dist: textual>=0.40; extra == "tui"
+Provides-Extra: portal
+Requires-Dist: playwright>=1.40; extra == "portal"
+Provides-Extra: atlas
+Requires-Dist: ISPy; extra == "atlas"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Provides-Extra: all
+Requires-Dist: textual>=0.40; extra == "all"
+Requires-Dist: ISPy; extra == "all"
+Requires-Dist: pytest>=7.0; extra == "all"
+Dynamic: license-file
+
+# enchase
+
+Calibration and flare analysis for CHASE/HIS solar spectroscopy. Install one package, point it at data, get aligned cubes, animations, contrast profiles, and temperature maps.
+
+[![tests](https://github.com/Majboor/enchase/actions/workflows/test.yml/badge.svg)](https://github.com/Majboor/enchase/actions/workflows/test.yml)
+[![PyPI](https://img.shields.io/pypi/v/enchase)](https://pypi.org/project/enchase/)
+![python](https://img.shields.io/badge/python-3.9%2B-blue)
+![license](https://img.shields.io/badge/license-MIT-green)
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/Majboor/enchase/main/assets/flare.gif" width="760" alt="Stabilised 2-panel animation of the 2023-03-29 X2.1 flare"><br>
+  <em>The 2023-03-29 X2.1 flare, stabilised by this pipeline. Photosphere left, chromosphere right.</em>
+</p>
+
+## Install
+
+```bash
+pip install enchase
+```
+
+That gives you the `chase` module, the `chase` command, and the `chase-tui` interactive app. Extras: `pip install 'enchase[tui]'` (TUI), `'enchase[atlas]'` (absolute Fe I calibration), `'enchase[all]'` (everything).
+
+## Get data
+
+Two ways.
+
+**Option 1: our hosted dataset.** We host ready-to-use CHASE observations on an S3 server, including the 2026-07-04 M3.2 flare (48 files, 8.65 GiB). No portal account, no expiring links:
+
+```python
+import boto3
+s3 = boto3.client("s3", endpoint_url="https://s3.preservemy.world",
+                  aws_access_key_id=ACCESS_KEY, aws_secret_access_key=SECRET_KEY,
+                  region_name="garage")
+s3.download_file("chase-data",
+                 "events/2026/07/04/M3.2/raw/HA/RSM20260704T132940_0000_HA.fits",
+                 "data/RSM20260704T132940_0000_HA.fits")
+```
+
+Read credentials are free for research use: see [docs/S3_DATA.md](docs/S3_DATA.md) for the full guide (bucket layout, Colab setup, s3fs) and how to get keys.
+
+**Option 2: the CHASE portal.** The portal ([ssdc.nju.edu.cn](https://ssdc.nju.edu.cn)) has a captcha, so you log in once in a real browser; after that everything is command line:
+
+```bash
+pip install enchase[portal] && playwright install chromium
+
+chase-portal login          # opens the portal once; log in, close the window
+chase-portal search --start "2023-03-29 02:00" --end "2023-03-29 03:00"
+chase-portal urls   --start "2023-03-29 02:00" --end "2023-03-29 03:00" -o links.txt
+chase links.txt             # downloads the files and runs the pipeline
+```
+
+`urls` writes one signed link per line (they expire in ~24h, so mint right before downloading). `chase` also accepts a single URL or a folder of already-downloaded `*.fits`. Walkthrough: [docs/DATA_ACQUISITION.md](docs/DATA_ACQUISITION.md).
+
+## Run it
+
+**Run this:**
+
+```bash
+chase ./data --patch 940 1080 1870 2040 --contrast --temperature halpha
+```
+
+**What happens:** loads every scan, tracks the patch across frames, resamples wavelengths onto one grid, stabilises with optical flow, then writes results to `./chase_out/`:
+
+| You get | What it is |
+|---|---|
+| `quicklook.gif` | photosphere / chromosphere animation |
+| `contrast_profile.gif` + `.npy` | wavelength-vs-time flare contrast |
+| `ha_temp_maps.npy` + `temperature.gif` | chromospheric temperature maps |
+| `aligned_data.npz` | the aligned cubes (also the resume checkpoint) |
+| `diag_*.png` | patch overlay, quiet-Sun spectrum |
+
+No patch coordinates yet? Run with `--full-fov --no-optical-flow --no-track` first, look at `diag_qs_spectrum.png` and the GIF, then pick a `[y0 y1 x0 x1]` box.
+
+## Rerun just one thing
+
+The first run saved a checkpoint, so reruns skip the slow loading and alignment:
+
+```bash
+chase ./data --out ./chase_out --only gif           # re-render the animation. Takes seconds
+chase ./data --out ./chase_out --only contrast      # recompute contrast only
+chase ./data --out ./chase_out --only temperature --temperature fe_voigt
+```
+
+## Turn things off
+
+Every stage has a switch. Mix freely:
+
+| Flag | What it disables |
+|---|---|
+| `--no-track` | cross-correlation patch tracking |
+| `--no-resample` | per-frame wavelength resampling |
+| `--no-drift` | spectral drift correction in the contrast stage |
+| `--no-optical-flow` | optical-flow stabilisation |
+| `--no-gif`, `--no-npz`, `--no-diagnostics` | those outputs |
+
+`--no-resample --no-drift` together = completely untouched wavelength axis.
+
+## The same thing in Python
+
+```python
+from chase import Config, run_pipeline
+
+results = run_pipeline(Config(fits_dir="./data", patch=[940, 1080, 1870, 2040],
+                              contrast=True, temperature="halpha"))
+
+results["aligned"]["ha"].shape    # (nframes, 118, H, W) stabilised float32
+results["contrast"].shape         # (nframes, 118)
+results["gif"]                    # './chase_out/quicklook.gif'
+```
+
+Rerun one step from the checkpoint: add `resume=True` and only the toggles you want.
+
+Or skip the pipeline and call single functions:
+
+```python
+import chase
+
+cube, hdr, wav = chase.load_cube("RSM..._HA.fits")          # one cube: (118, H, W) + wavelengths
+seq = chase.load_flare_sequence("./data", patch=[...])      # tracked + resampled sequence
+ha_al = chase.optical_flow_align(seq["ha_cubes"], reference=seq["align_ref"])
+contrast, _ = chase.contrast_profile(ha_al, background=seq["ha_bg"])
+T, width = chase.halpha_width_temperature(ha_al[12], seq["wavelength_ha"])
+```
+
+Each line works on its own. Full list with snippets: [docs/SDK.md](docs/SDK.md).
+
+## Prefer clicking to typing?
+
+```bash
+chase-tui
+```
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/Majboor/enchase/main/assets/tui_e2e_walkthrough.gif" width="800" alt="End-to-end chase-tui walkthrough">
+</p>
+
+Every checkbox is one of the switches above. There is also a one-file config workflow: `chase --config my.toml`, keys mirror the flags ([examples/config.toml](examples/config.toml)).
+
+## Why this exists (statement of need)
+
+CHASE (the Chinese Hα Solar Explorer) scans the full solar disk in Hα (118 wavelengths, 6559.4 to 6565.1 Å) and Fe I (46 wavelengths near 6569 Å). The portal ships full-disk cubes with no co-alignment and a wavelength zero-point that drifts by ~0.8 channels per frame. Getting a science-ready region out of that takes real calibration work, which is why the data is under-used. Earlier scripts (the original `chase-pipeline`, Finlay Davis's `satprocess`) each solved part of the problem. This package merges them into one installable tool that preserves the physics: shift-then-crop tracking, per-frame wavelength resampling, alignment on a flare-free channel, absolute atlas calibration, and the correct temperature inversion per line. The reasoning behind each rule is in [docs/CALIBRATION.md](docs/CALIBRATION.md).
+
+## What lives where
+
+| Subpackage | Does | |
+|---|---|---|
+| `chase.io` | resumable download, FITS discovery, cube + sequence loading | <img src="assets/diag_patch.png" width="220"> |
+| `chase.calib.spatial` / `.align` | shift-then-crop tracking, optical-flow stabilisation | <img src="assets/diag_optical_flow.png" width="220"> |
+| `chase.calib.wavelength` | per-frame resampling onto a common grid, spectral-drift xcorr | <img src="assets/diag_qs_spectrum.png" width="220"> |
+| `chase.calib.intensity` | quiet-Sun norm, integral scaling, FTS-atlas absolute calibration | <img src="assets/atlas_calibration.png" width="220"> |
+| `chase.analysis.contrast` | wavelength-vs-time flare contrast | <img src="assets/contrast_profile.png" width="220"> |
+| `chase.analysis.temperature` | Hα width to T (Molnar), Fe I to T (Planck / EB / Voigt) | <img src="assets/double_temp_map_peak.png" width="220"> |
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/Majboor/enchase/main/assets/temperature.gif" width="720" alt="Double temperature map animation"><br>
+  <em>Double temperature map: chromosphere from Hα width (~10⁴ K), photosphere from Fe I Planck inversion (~5100 K).</em>
+</p>
+
+## Documentation
+
+- [docs/S3_DATA.md](docs/S3_DATA.md): use our hosted CHASE datasets from anywhere (incl. Google Colab)
+- [docs/DATA_ACQUISITION.md](docs/DATA_ACQUISITION.md): CHASE portal to processed cube, end to end
+- [docs/SDK.md](docs/SDK.md): every function, with snippets
+- [docs/TUI.md](docs/TUI.md): TUI walkthrough
+- [docs/CALIBRATION.md](docs/CALIBRATION.md): the science behind each calibration step
+- [docs/CONTRIBUTING.md](docs/CONTRIBUTING.md): dev setup, tests, style
+
+## Development
+
+```bash
+git clone https://github.com/Majboor/enchase.git
+cd enchase
+pip install -e '.[all]'
+pytest -q            # 27 tests, synthetic FITS fixtures, no big data needed
+```
+
+## Acknowledgements
+
+Built with the guidance and corrections of **Dr. Alexander Pietrow** (AIP) and **Dr. Malcolm Druett**. The Hough-circle limb centring, spectral cross-correlation, integral intensity scaling, and CSV shift-cache are adapted from **Finlay Davis**'s [`satprocess`](https://github.com/FinlayDavis/satprocess) (BSD-3-Clause; see [`NOTICE`](NOTICE)). Affiliation support from **Prof. Dr. Sayed Amer Mahmood** (University of the Punjab). Data courtesy of the **CHASE/HIS** mission and the [Solar Science Data Center, Nanjing University](https://ssdc.nju.edu.cn/NdchaseSatellite).
+
+## Citing
+
+Author: Waleed Ajmal, ORCID [0009-0006-8222-1983](https://orcid.org/0009-0006-8222-1983). Software citation metadata is in [`CITATION.cff`](CITATION.cff).
+
+If you use this pipeline, cite the methods it builds on:
+
+- Molnar et al. 2019, *ApJ* **881**, 99. Hα width to temperature ([10.3847/1538-4357/ab2ba3](https://doi.org/10.3847/1538-4357/ab2ba3))
+- The Eddington-Barbier photospheric inversion (A&A 2013, aa21259-13)
+- The **ISPy** FTS solar-atlas calibration ([ISP-SST/ISPy](https://github.com/ISP-SST/ISPy))
+
+## License
+
+MIT. Ported `satprocess` code stays BSD-3-Clause, listed in [`NOTICE`](NOTICE).

enchase-2.1.0/README.md

@@ -0,0 +1,193 @@
+# enchase
+
+Calibration and flare analysis for CHASE/HIS solar spectroscopy. Install one package, point it at data, get aligned cubes, animations, contrast profiles, and temperature maps.
+
+[![tests](https://github.com/Majboor/enchase/actions/workflows/test.yml/badge.svg)](https://github.com/Majboor/enchase/actions/workflows/test.yml)
+[![PyPI](https://img.shields.io/pypi/v/enchase)](https://pypi.org/project/enchase/)
+![python](https://img.shields.io/badge/python-3.9%2B-blue)
+![license](https://img.shields.io/badge/license-MIT-green)
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/Majboor/enchase/main/assets/flare.gif" width="760" alt="Stabilised 2-panel animation of the 2023-03-29 X2.1 flare"><br>
+  <em>The 2023-03-29 X2.1 flare, stabilised by this pipeline. Photosphere left, chromosphere right.</em>
+</p>
+
+## Install
+
+```bash
+pip install enchase
+```
+
+That gives you the `chase` module, the `chase` command, and the `chase-tui` interactive app. Extras: `pip install 'enchase[tui]'` (TUI), `'enchase[atlas]'` (absolute Fe I calibration), `'enchase[all]'` (everything).
+
+## Get data
+
+Two ways.
+
+**Option 1: our hosted dataset.** We host ready-to-use CHASE observations on an S3 server, including the 2026-07-04 M3.2 flare (48 files, 8.65 GiB). No portal account, no expiring links:
+
+```python
+import boto3
+s3 = boto3.client("s3", endpoint_url="https://s3.preservemy.world",
+                  aws_access_key_id=ACCESS_KEY, aws_secret_access_key=SECRET_KEY,
+                  region_name="garage")
+s3.download_file("chase-data",
+                 "events/2026/07/04/M3.2/raw/HA/RSM20260704T132940_0000_HA.fits",
+                 "data/RSM20260704T132940_0000_HA.fits")
+```
+
+Read credentials are free for research use: see [docs/S3_DATA.md](docs/S3_DATA.md) for the full guide (bucket layout, Colab setup, s3fs) and how to get keys.
+
+**Option 2: the CHASE portal.** The portal ([ssdc.nju.edu.cn](https://ssdc.nju.edu.cn)) has a captcha, so you log in once in a real browser; after that everything is command line:
+
+```bash
+pip install enchase[portal] && playwright install chromium
+
+chase-portal login          # opens the portal once; log in, close the window
+chase-portal search --start "2023-03-29 02:00" --end "2023-03-29 03:00"
+chase-portal urls   --start "2023-03-29 02:00" --end "2023-03-29 03:00" -o links.txt
+chase links.txt             # downloads the files and runs the pipeline
+```
+
+`urls` writes one signed link per line (they expire in ~24h, so mint right before downloading). `chase` also accepts a single URL or a folder of already-downloaded `*.fits`. Walkthrough: [docs/DATA_ACQUISITION.md](docs/DATA_ACQUISITION.md).
+
+## Run it
+
+**Run this:**
+
+```bash
+chase ./data --patch 940 1080 1870 2040 --contrast --temperature halpha
+```
+
+**What happens:** loads every scan, tracks the patch across frames, resamples wavelengths onto one grid, stabilises with optical flow, then writes results to `./chase_out/`:
+
+| You get | What it is |
+|---|---|
+| `quicklook.gif` | photosphere / chromosphere animation |
+| `contrast_profile.gif` + `.npy` | wavelength-vs-time flare contrast |
+| `ha_temp_maps.npy` + `temperature.gif` | chromospheric temperature maps |
+| `aligned_data.npz` | the aligned cubes (also the resume checkpoint) |
+| `diag_*.png` | patch overlay, quiet-Sun spectrum |
+
+No patch coordinates yet? Run with `--full-fov --no-optical-flow --no-track` first, look at `diag_qs_spectrum.png` and the GIF, then pick a `[y0 y1 x0 x1]` box.
+
+## Rerun just one thing
+
+The first run saved a checkpoint, so reruns skip the slow loading and alignment:
+
+```bash
+chase ./data --out ./chase_out --only gif           # re-render the animation. Takes seconds
+chase ./data --out ./chase_out --only contrast      # recompute contrast only
+chase ./data --out ./chase_out --only temperature --temperature fe_voigt
+```
+
+## Turn things off
+
+Every stage has a switch. Mix freely:
+
+| Flag | What it disables |
+|---|---|
+| `--no-track` | cross-correlation patch tracking |
+| `--no-resample` | per-frame wavelength resampling |
+| `--no-drift` | spectral drift correction in the contrast stage |
+| `--no-optical-flow` | optical-flow stabilisation |
+| `--no-gif`, `--no-npz`, `--no-diagnostics` | those outputs |
+
+`--no-resample --no-drift` together = completely untouched wavelength axis.
+
+## The same thing in Python
+
+```python
+from chase import Config, run_pipeline
+
+results = run_pipeline(Config(fits_dir="./data", patch=[940, 1080, 1870, 2040],
+                              contrast=True, temperature="halpha"))
+
+results["aligned"]["ha"].shape    # (nframes, 118, H, W) stabilised float32
+results["contrast"].shape         # (nframes, 118)
+results["gif"]                    # './chase_out/quicklook.gif'
+```
+
+Rerun one step from the checkpoint: add `resume=True` and only the toggles you want.
+
+Or skip the pipeline and call single functions:
+
+```python
+import chase
+
+cube, hdr, wav = chase.load_cube("RSM..._HA.fits")          # one cube: (118, H, W) + wavelengths
+seq = chase.load_flare_sequence("./data", patch=[...])      # tracked + resampled sequence
+ha_al = chase.optical_flow_align(seq["ha_cubes"], reference=seq["align_ref"])
+contrast, _ = chase.contrast_profile(ha_al, background=seq["ha_bg"])
+T, width = chase.halpha_width_temperature(ha_al[12], seq["wavelength_ha"])
+```
+
+Each line works on its own. Full list with snippets: [docs/SDK.md](docs/SDK.md).
+
+## Prefer clicking to typing?
+
+```bash
+chase-tui
+```
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/Majboor/enchase/main/assets/tui_e2e_walkthrough.gif" width="800" alt="End-to-end chase-tui walkthrough">
+</p>
+
+Every checkbox is one of the switches above. There is also a one-file config workflow: `chase --config my.toml`, keys mirror the flags ([examples/config.toml](examples/config.toml)).
+
+## Why this exists (statement of need)
+
+CHASE (the Chinese Hα Solar Explorer) scans the full solar disk in Hα (118 wavelengths, 6559.4 to 6565.1 Å) and Fe I (46 wavelengths near 6569 Å). The portal ships full-disk cubes with no co-alignment and a wavelength zero-point that drifts by ~0.8 channels per frame. Getting a science-ready region out of that takes real calibration work, which is why the data is under-used. Earlier scripts (the original `chase-pipeline`, Finlay Davis's `satprocess`) each solved part of the problem. This package merges them into one installable tool that preserves the physics: shift-then-crop tracking, per-frame wavelength resampling, alignment on a flare-free channel, absolute atlas calibration, and the correct temperature inversion per line. The reasoning behind each rule is in [docs/CALIBRATION.md](docs/CALIBRATION.md).
+
+## What lives where
+
+| Subpackage | Does | |
+|---|---|---|
+| `chase.io` | resumable download, FITS discovery, cube + sequence loading | <img src="assets/diag_patch.png" width="220"> |
+| `chase.calib.spatial` / `.align` | shift-then-crop tracking, optical-flow stabilisation | <img src="assets/diag_optical_flow.png" width="220"> |
+| `chase.calib.wavelength` | per-frame resampling onto a common grid, spectral-drift xcorr | <img src="assets/diag_qs_spectrum.png" width="220"> |
+| `chase.calib.intensity` | quiet-Sun norm, integral scaling, FTS-atlas absolute calibration | <img src="assets/atlas_calibration.png" width="220"> |
+| `chase.analysis.contrast` | wavelength-vs-time flare contrast | <img src="assets/contrast_profile.png" width="220"> |
+| `chase.analysis.temperature` | Hα width to T (Molnar), Fe I to T (Planck / EB / Voigt) | <img src="assets/double_temp_map_peak.png" width="220"> |
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/Majboor/enchase/main/assets/temperature.gif" width="720" alt="Double temperature map animation"><br>
+  <em>Double temperature map: chromosphere from Hα width (~10⁴ K), photosphere from Fe I Planck inversion (~5100 K).</em>
+</p>
+
+## Documentation
+
+- [docs/S3_DATA.md](docs/S3_DATA.md): use our hosted CHASE datasets from anywhere (incl. Google Colab)
+- [docs/DATA_ACQUISITION.md](docs/DATA_ACQUISITION.md): CHASE portal to processed cube, end to end
+- [docs/SDK.md](docs/SDK.md): every function, with snippets
+- [docs/TUI.md](docs/TUI.md): TUI walkthrough
+- [docs/CALIBRATION.md](docs/CALIBRATION.md): the science behind each calibration step
+- [docs/CONTRIBUTING.md](docs/CONTRIBUTING.md): dev setup, tests, style
+
+## Development
+
+```bash
+git clone https://github.com/Majboor/enchase.git
+cd enchase
+pip install -e '.[all]'
+pytest -q            # 27 tests, synthetic FITS fixtures, no big data needed
+```
+
+## Acknowledgements
+
+Built with the guidance and corrections of **Dr. Alexander Pietrow** (AIP) and **Dr. Malcolm Druett**. The Hough-circle limb centring, spectral cross-correlation, integral intensity scaling, and CSV shift-cache are adapted from **Finlay Davis**'s [`satprocess`](https://github.com/FinlayDavis/satprocess) (BSD-3-Clause; see [`NOTICE`](NOTICE)). Affiliation support from **Prof. Dr. Sayed Amer Mahmood** (University of the Punjab). Data courtesy of the **CHASE/HIS** mission and the [Solar Science Data Center, Nanjing University](https://ssdc.nju.edu.cn/NdchaseSatellite).
+
+## Citing
+
+Author: Waleed Ajmal, ORCID [0009-0006-8222-1983](https://orcid.org/0009-0006-8222-1983). Software citation metadata is in [`CITATION.cff`](CITATION.cff).
+
+If you use this pipeline, cite the methods it builds on:
+
+- Molnar et al. 2019, *ApJ* **881**, 99. Hα width to temperature ([10.3847/1538-4357/ab2ba3](https://doi.org/10.3847/1538-4357/ab2ba3))
+- The Eddington-Barbier photospheric inversion (A&A 2013, aa21259-13)
+- The **ISPy** FTS solar-atlas calibration ([ISP-SST/ISPy](https://github.com/ISP-SST/ISPy))
+
+## License
+
+MIT. Ported `satprocess` code stays BSD-3-Clause, listed in [`NOTICE`](NOTICE).

enchase-2.1.0/chase/__init__.py

@@ -0,0 +1,119 @@
+"""chase — a modular CHASE/HIS calibration + flare-analysis pipeline.
+
+Nothing here is a forced pipeline: every stage is an importable function you can
+call on its own, *and* there is a one-call orchestrator (:func:`run_pipeline`), a
+config-file workflow (:class:`Config`), a CLI (``chase``), and a TUI
+(``chase-tui``) layered on top of the exact same functions.
+
+Quick start (SDK)
+-----------------
+>>> import chase
+>>> cube, hdr, wav = chase.load_cube("RSM..._HA.fits")
+>>> seq = chase.load_flare_sequence("/path/to/fits", patch=[940, 1080, 1870, 2040])
+>>> aligned = chase.optical_flow_align(seq["ha_cubes"], reference=seq["align_ref"])
+>>> contrast, _ = chase.contrast_profile(aligned, background=seq["ha_bg"])
+
+Quick start (lazy)
+------------------
+>>> from chase import Config, run_pipeline
+>>> run_pipeline(Config(fits_dir="/path/to/fits", patch=[940, 1080, 1870, 2040],
+...                     contrast=True, temperature="double"))
+"""
+
+from __future__ import annotations
+
+from . import _compat  # noqa: F401  (lzma stub + headless matplotlib)
+
+__version__ = "2.1.0"
+
+# --- I/O -------------------------------------------------------------------
+from .io import (
+    discover_fits,
+    download_file,
+    extract_disk_center,
+    load_cube,
+    load_fits_data,
+    load_flare_sequence,
+    resolve_inputs,
+    save_cube_fits,
+    save_npz,
+)
+download = download_file  # SDK alias
+
+# --- Calibration -----------------------------------------------------------
+from .calib import (
+    align_spectrum,
+    derotate,
+    derotate_crop,
+    atlas_calibrate,
+    atlas_fit_quality,
+    correct_spectral_drift,
+    find_quiet_patch,
+    quiet_sun_mask,
+    create_optical_flow_solver,
+    find_disk_center,
+    hough_disk_center,
+    integral_scaling,
+    normalize_intensity,
+    optical_flow_align,
+    phase_shift,
+    planck_inversion,
+    recenter,
+    resample_wavelength,
+    track_and_crop,
+    warp_cube,
+)
+
+# --- Analysis --------------------------------------------------------------
+from .analysis import (
+    contrast_profile,
+    fe_eb_temperature,
+    fe_planck_temperature,
+    fe_voigt_temperature,
+    frame_rms,
+    halpha_width_map,
+    line_centroid,
+    residual_pointing,
+    residual_wavelength,
+    stray_light_estimate,
+    halpha_width_temperature,
+    width_to_temperature,
+)
+
+# --- Visualisation ---------------------------------------------------------
+from .viz import (
+    make_animation,
+    make_contrast_animation,
+    make_temperature_animation,
+)
+
+# --- Orchestration ---------------------------------------------------------
+from .config import Config, load_config
+from .pipeline import run_pipeline
+
+__all__ = [
+    "__version__",
+    # io
+    "download", "download_file", "resolve_inputs", "discover_fits",
+    "load_cube", "load_fits_data", "load_flare_sequence", "extract_disk_center",
+    "save_cube_fits", "save_npz",
+    # calib
+    "derotate", "derotate_crop",
+    "find_disk_center", "hough_disk_center", "recenter", "phase_shift",
+    "track_and_crop", "optical_flow_align", "warp_cube",
+    "create_optical_flow_solver", "resample_wavelength", "correct_spectral_drift",
+    "align_spectrum", "normalize_intensity", "integral_scaling",
+    "atlas_calibrate", "atlas_fit_quality", "quiet_sun_mask", "find_quiet_patch",
+    "planck_inversion",
+    # analysis
+    "contrast_profile", "halpha_width_map", "halpha_width_temperature",
+    "width_to_temperature", "fe_planck_temperature", "fe_eb_temperature",
+    "fe_voigt_temperature",
+    # validation
+    "residual_pointing", "line_centroid", "residual_wavelength", "frame_rms",
+    "stray_light_estimate",
+    # viz
+    "make_animation", "make_contrast_animation", "make_temperature_animation",
+    # orchestration
+    "Config", "load_config", "run_pipeline",
+]