chasepy 2.0.0__tar.gz

chasepy-2.0.0/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.

chasepy-2.0.0/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.

chasepy-2.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: chasepy
+Version: 2.0.0
+Summary: Modular CHASE/HIS solar calibration and flare-analysis pipeline (TUI + SDK + CLI)
+Author: Waleed Ajmal
+License: MIT
+Project-URL: Homepage, https://github.com/Majboor/chase-pipeline
+Project-URL: Repository, https://github.com/Majboor/chase-pipeline
+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: 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
+
+# chase-pipeline
+
+**A modular calibration and flare-analysis pipeline for CHASE / HIS solar spectroscopy — with a TUI, a Python SDK, and a one-file config workflow.**
+
+[![tests](https://github.com/Majboor/chase-pipeline/actions/workflows/test.yml/badge.svg)](https://github.com/Majboor/chase-pipeline/actions/workflows/test.yml)
+![python](https://img.shields.io/badge/python-3.9%2B-blue)
+![license](https://img.shields.io/badge/license-MIT-green)
+
+CHASE (the **Chinese Hα Solar Explorer**) scans the full solar disk in Hα (118
+wavelengths, 6559.4–6565.1 Å) and Fe I (46 wavelengths, ~6569 Å). The raw data is
+scientifically rich but awkward to use — every frame drifts spatially *and*
+spectrally, and turning a stack of `RSM…_HA.fits` cubes into a clean, aligned,
+calibrated data product takes a lot of careful work. `chase-pipeline` does that
+work for you, and lets you do as much or as little of it as you want.
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/Majboor/chase-pipeline/feat/unified-pipeline-tui-sdk/assets/flare.gif" width="760" alt="Stabilised 2-panel animation of the 2023-03-29 X2.1 flare"><br>
+  <em>The 2023-03-29 <strong>X2.1</strong> flare, stabilised by this pipeline:
+  photosphere (Hα continuum) | chromosphere (Hα core). 25 frames, per-frame colour scaling.<br>
+  Rendered with <code>--flow-method farneback</code>: TV-L1 optical flow blocks at the flare peak
+  (its total-variation regularizer turns the brightening into a rigid motion block); Farneback stays
+  clean. See <a href="docs/FLARE_STABILIZATION.md">docs/FLARE_STABILIZATION.md</a>.</em>
+</p>
+
+---
+
+## Why this exists (statement of need)
+
+CHASE data is under-used because it is hard to use: the portal ships full-disk
+cubes with no co-alignment, a per-frame wavelength zero-point that drifts by ~0.8
+channels, and no turnkey way to extract a science-ready region. Existing scripts
+(including the original `chase-pipeline` and Finlay Davis's `satprocess`) each
+solved part of the problem. **This package unifies them into one installable
+tool** that:
+
+- **just works for the lazy user** — point at a folder, set a field of view and a
+  few true/false flags in a text file (or use the TUI), run once, get an aligned
+  **FITS/npz cube + images/GIF** out;
+- **stays hackable for the power user** — every stage is an importable function
+  (`import chase`), nothing is a forced monolithic pipeline;
+- **preserves the physics** — shift-then-crop tracking, per-frame wavelength
+  resampling, flare-free alignment, absolute atlas calibration, and the correct
+  temperature inversions per line (it does not "simplify away" the hard-won fixes).
+
+## Install
+
+From PyPI (the package is named `chasepy`; it installs the `chase` module and
+the `chase` / `chase-tui` commands):
+
+```bash
+pip install chasepy              # core
+pip install 'chasepy[tui]'       # + Textual TUI  (chase-tui)
+pip install 'chasepy[atlas]'     # + ISPy for absolute Fe I temperature calibration
+pip install 'chasepy[all]'       # everything, incl. test deps
+```
+
+Or for development, clone and install editable:
+
+```bash
+git clone https://github.com/Majboor/chase-pipeline.git
+cd chase-pipeline
+pip install -e '.[all]'
+```
+
+## Three ways to use it
+
+### 1. TUI — interactive, no flags to memorise
+
+```bash
+chase-tui
+```
+
+**End-to-end walkthrough** — the real TUI configured on the 2023-03-29 X2.1
+flare (data source → field of view → calibration → temperature → a before/after
+of the stabilisation → the actual `flare.gif` / `temperature.gif` /
+`contrast_profile.gif` output):
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/Majboor/chase-pipeline/feat/unified-pipeline-tui-sdk/assets/tui_e2e_walkthrough.gif" width="800" alt="End-to-end chase-tui walkthrough">
+</p>
+
+> Prefer the full-resolution, scrubbable version?
+> [assets/tui_e2e_walkthrough.mp4](https://github.com/Majboor/chase-pipeline/raw/feat/unified-pipeline-tui-sdk/assets/tui_e2e_walkthrough.mp4).
+
+Pick a data source, enter a full FOV or an arbitrary patch (and a separate, smaller
+*alignment* patch if you want), tick the calibrations you want, and hit **Run** —
+live progress streams into the log pane. The TUI is a thin front-end over the SDK;
+it duplicates no logic.
+
+**Before / after** — what the spatial calibration buys you. Left: a raw fixed
+crop of the portal data, drifting frame to frame. Right: the same patch after
+shift-then-crop tracking + optical-flow stabilisation (Hα core):
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/Majboor/chase-pipeline/feat/unified-pipeline-tui-sdk/assets/before_after.gif" width="760" alt="Raw fixed crop vs tracked + optical-flow stabilised, Hα core">
+</p>
+
+### 2. Config file — the "lazy" one-shot workflow
+
+```bash
+chase --config examples/config.toml
+```
+
+```toml
+# examples/config.toml
+fits_dir = "/data/20230329_X12/fits"
+out_dir  = "./chase_out"
+patch    = [940, 1080, 1870, 2040]   # [y0, y1, x0, x1]; omit + full_fov=true for whole disk
+contrast = true
+temperature = "double"               # halpha + fe_planck
+gif = true
+freeze_clim = true
+```
+
+### 3. CLI — explicit flags (backward compatible)
+
+```bash
+chase /data/20230329_X12/fits \
+      --patch 940 1080 1870 2040 \
+      --align-patch 980 1040 1920 1990 \
+      --contrast --temperature double --freeze-clim
+```
+
+Every run checkpoints the aligned cubes to `out_dir/aligned_data.npz`, so you
+never have to redo the slow load + align stages just to tweak an output —
+rerun a single step against the checkpoint with `--only` (implies `--resume`):
+
+```bash
+chase /data/20230329_X12/fits --out ./chase_out --only gif            # just re-render the animation
+chase /data/20230329_X12/fits --out ./chase_out --only contrast,gif --no-drift
+chase /data/20230329_X12/fits --out ./chase_out --only temperature --temperature fe_voigt
+```
+
+Steps: `gif`, `contrast`, `temperature`, `npz`, `fits`, `diagnostics`. Plain
+`--resume` keeps your normal toggles and only skips load + align. (Changing the
+patch or alignment options needs a fresh run *without* `--resume` — the
+checkpoint stores the cubes as they were cropped and aligned.)
+
+### …and the SDK — call any single stage
+
+```python
+import chase
+
+# Load + crop-track a sequence (shift-then-crop, per-frame wavelength resample)
+seq = chase.load_flare_sequence("/data/20230329_X12/fits",
+                                patch=[940, 1080, 1870, 2040])
+
+# Fine-stabilise with optical flow on the flare-free channel; HA stays float32
+aligned = chase.optical_flow_align(seq["ha_cubes"], reference=seq["align_ref"])
+
+# Science products
+contrast, _ = chase.contrast_profile(aligned, background=seq["ha_bg"])
+ha_T, _ = chase.halpha_width_temperature(aligned[24], seq["wavelength_ha"])  # Molnar 2019
+```
+
+Or run the whole thing in one call:
+
+```python
+from chase import Config, run_pipeline
+run_pipeline(Config(fits_dir="/data/.../fits", patch=[940,1080,1870,2040],
+                    contrast=True, temperature="double"))
+
+# Later: rerun only the outputs you care about, from the saved checkpoint
+run_pipeline(Config(fits_dir="/data/.../fits", out_dir="./chase_out",
+                    resume=True, gif=True, temperature="fe_voigt"))
+```
+
+## What each subpackage does (one figure each)
+
+| Subpackage | What it does | |
+|---|---|---|
+| `chase.io` | Resumable download, folder / list-file / URL 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` | QS norm, integral scaling, FTS-atlas absolute calibration (ISPy) | <img src="assets/atlas_calibration.png" width="220"> |
+| `chase.analysis.contrast` | `(flare−bg)/bg − frame0` wavelength-vs-time profile | <img src="assets/contrast_profile.png" width="220"> |
+| `chase.analysis.temperature` | Hα width→T (Molnar) + Fe I →T (Planck/EB/Voigt) | <img src="assets/double_temp_map_peak.png" width="220"> |
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/Majboor/chase-pipeline/feat/unified-pipeline-tui-sdk/assets/temperature.gif" width="720" alt="Double temperature map animation"><br>
+  <em>Double temperature map: chromosphere from Hα width (~10⁴ K) and photosphere
+  from Fe I Planck inversion (~5,100 K, absolute-calibrated against the FTS atlas).</em>
+</p>
+
+## Documentation
+
+- **[docs/DATA_ACQUISITION.md](docs/DATA_ACQUISITION.md)** — get from the CHASE portal to a processed cube, end to end.
+- **[docs/SDK.md](docs/SDK.md)** — the Python API, every function + parameters.
+- **[docs/TUI.md](docs/TUI.md)** — TUI walkthrough.
+- **[docs/CALIBRATION.md](docs/CALIBRATION.md)** — the science: what each calibration does and why.
+- **[docs/CONTRIBUTING.md](docs/CONTRIBUTING.md)** — dev setup, tests, style.
+
+## Tests
+
+```bash
+pip install -e '.[dev]' && pytest -q     # 22 fast tests on synthetic FITS fixtures
+```
+
+## 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
+
+If you use this pipeline, please cite the methods it builds on:
+
+- Molnar et al. 2019, *ApJ* **881**, 99 — Hα width → 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)).
+- CHASE/HIS: Li et al. 2022, *Science China* — the CHASE mission.
+
+## License
+
+MIT © 2025-2026 Waleed Ajmal. Ported `satprocess` components are BSD-3-Clause © 2025
+Finlay Davis — see [`NOTICE`](NOTICE).

chasepy-2.0.0/README.md

@@ -0,0 +1,221 @@
+# chase-pipeline
+
+**A modular calibration and flare-analysis pipeline for CHASE / HIS solar spectroscopy — with a TUI, a Python SDK, and a one-file config workflow.**
+
+[![tests](https://github.com/Majboor/chase-pipeline/actions/workflows/test.yml/badge.svg)](https://github.com/Majboor/chase-pipeline/actions/workflows/test.yml)
+![python](https://img.shields.io/badge/python-3.9%2B-blue)
+![license](https://img.shields.io/badge/license-MIT-green)
+
+CHASE (the **Chinese Hα Solar Explorer**) scans the full solar disk in Hα (118
+wavelengths, 6559.4–6565.1 Å) and Fe I (46 wavelengths, ~6569 Å). The raw data is
+scientifically rich but awkward to use — every frame drifts spatially *and*
+spectrally, and turning a stack of `RSM…_HA.fits` cubes into a clean, aligned,
+calibrated data product takes a lot of careful work. `chase-pipeline` does that
+work for you, and lets you do as much or as little of it as you want.
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/Majboor/chase-pipeline/feat/unified-pipeline-tui-sdk/assets/flare.gif" width="760" alt="Stabilised 2-panel animation of the 2023-03-29 X2.1 flare"><br>
+  <em>The 2023-03-29 <strong>X2.1</strong> flare, stabilised by this pipeline:
+  photosphere (Hα continuum) | chromosphere (Hα core). 25 frames, per-frame colour scaling.<br>
+  Rendered with <code>--flow-method farneback</code>: TV-L1 optical flow blocks at the flare peak
+  (its total-variation regularizer turns the brightening into a rigid motion block); Farneback stays
+  clean. See <a href="docs/FLARE_STABILIZATION.md">docs/FLARE_STABILIZATION.md</a>.</em>
+</p>
+
+---
+
+## Why this exists (statement of need)
+
+CHASE data is under-used because it is hard to use: the portal ships full-disk
+cubes with no co-alignment, a per-frame wavelength zero-point that drifts by ~0.8
+channels, and no turnkey way to extract a science-ready region. Existing scripts
+(including the original `chase-pipeline` and Finlay Davis's `satprocess`) each
+solved part of the problem. **This package unifies them into one installable
+tool** that:
+
+- **just works for the lazy user** — point at a folder, set a field of view and a
+  few true/false flags in a text file (or use the TUI), run once, get an aligned
+  **FITS/npz cube + images/GIF** out;
+- **stays hackable for the power user** — every stage is an importable function
+  (`import chase`), nothing is a forced monolithic pipeline;
+- **preserves the physics** — shift-then-crop tracking, per-frame wavelength
+  resampling, flare-free alignment, absolute atlas calibration, and the correct
+  temperature inversions per line (it does not "simplify away" the hard-won fixes).
+
+## Install
+
+From PyPI (the package is named `chasepy`; it installs the `chase` module and
+the `chase` / `chase-tui` commands):
+
+```bash
+pip install chasepy              # core
+pip install 'chasepy[tui]'       # + Textual TUI  (chase-tui)
+pip install 'chasepy[atlas]'     # + ISPy for absolute Fe I temperature calibration
+pip install 'chasepy[all]'       # everything, incl. test deps
+```
+
+Or for development, clone and install editable:
+
+```bash
+git clone https://github.com/Majboor/chase-pipeline.git
+cd chase-pipeline
+pip install -e '.[all]'
+```
+
+## Three ways to use it
+
+### 1. TUI — interactive, no flags to memorise
+
+```bash
+chase-tui
+```
+
+**End-to-end walkthrough** — the real TUI configured on the 2023-03-29 X2.1
+flare (data source → field of view → calibration → temperature → a before/after
+of the stabilisation → the actual `flare.gif` / `temperature.gif` /
+`contrast_profile.gif` output):
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/Majboor/chase-pipeline/feat/unified-pipeline-tui-sdk/assets/tui_e2e_walkthrough.gif" width="800" alt="End-to-end chase-tui walkthrough">
+</p>
+
+> Prefer the full-resolution, scrubbable version?
+> [assets/tui_e2e_walkthrough.mp4](https://github.com/Majboor/chase-pipeline/raw/feat/unified-pipeline-tui-sdk/assets/tui_e2e_walkthrough.mp4).
+
+Pick a data source, enter a full FOV or an arbitrary patch (and a separate, smaller
+*alignment* patch if you want), tick the calibrations you want, and hit **Run** —
+live progress streams into the log pane. The TUI is a thin front-end over the SDK;
+it duplicates no logic.
+
+**Before / after** — what the spatial calibration buys you. Left: a raw fixed
+crop of the portal data, drifting frame to frame. Right: the same patch after
+shift-then-crop tracking + optical-flow stabilisation (Hα core):
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/Majboor/chase-pipeline/feat/unified-pipeline-tui-sdk/assets/before_after.gif" width="760" alt="Raw fixed crop vs tracked + optical-flow stabilised, Hα core">
+</p>
+
+### 2. Config file — the "lazy" one-shot workflow
+
+```bash
+chase --config examples/config.toml
+```
+
+```toml
+# examples/config.toml
+fits_dir = "/data/20230329_X12/fits"
+out_dir  = "./chase_out"
+patch    = [940, 1080, 1870, 2040]   # [y0, y1, x0, x1]; omit + full_fov=true for whole disk
+contrast = true
+temperature = "double"               # halpha + fe_planck
+gif = true
+freeze_clim = true
+```
+
+### 3. CLI — explicit flags (backward compatible)
+
+```bash
+chase /data/20230329_X12/fits \
+      --patch 940 1080 1870 2040 \
+      --align-patch 980 1040 1920 1990 \
+      --contrast --temperature double --freeze-clim
+```
+
+Every run checkpoints the aligned cubes to `out_dir/aligned_data.npz`, so you
+never have to redo the slow load + align stages just to tweak an output —
+rerun a single step against the checkpoint with `--only` (implies `--resume`):
+
+```bash
+chase /data/20230329_X12/fits --out ./chase_out --only gif            # just re-render the animation
+chase /data/20230329_X12/fits --out ./chase_out --only contrast,gif --no-drift
+chase /data/20230329_X12/fits --out ./chase_out --only temperature --temperature fe_voigt
+```
+
+Steps: `gif`, `contrast`, `temperature`, `npz`, `fits`, `diagnostics`. Plain
+`--resume` keeps your normal toggles and only skips load + align. (Changing the
+patch or alignment options needs a fresh run *without* `--resume` — the
+checkpoint stores the cubes as they were cropped and aligned.)
+
+### …and the SDK — call any single stage
+
+```python
+import chase
+
+# Load + crop-track a sequence (shift-then-crop, per-frame wavelength resample)
+seq = chase.load_flare_sequence("/data/20230329_X12/fits",
+                                patch=[940, 1080, 1870, 2040])
+
+# Fine-stabilise with optical flow on the flare-free channel; HA stays float32
+aligned = chase.optical_flow_align(seq["ha_cubes"], reference=seq["align_ref"])
+
+# Science products
+contrast, _ = chase.contrast_profile(aligned, background=seq["ha_bg"])
+ha_T, _ = chase.halpha_width_temperature(aligned[24], seq["wavelength_ha"])  # Molnar 2019
+```
+
+Or run the whole thing in one call:
+
+```python
+from chase import Config, run_pipeline
+run_pipeline(Config(fits_dir="/data/.../fits", patch=[940,1080,1870,2040],
+                    contrast=True, temperature="double"))
+
+# Later: rerun only the outputs you care about, from the saved checkpoint
+run_pipeline(Config(fits_dir="/data/.../fits", out_dir="./chase_out",
+                    resume=True, gif=True, temperature="fe_voigt"))
+```
+
+## What each subpackage does (one figure each)
+
+| Subpackage | What it does | |
+|---|---|---|
+| `chase.io` | Resumable download, folder / list-file / URL 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` | QS norm, integral scaling, FTS-atlas absolute calibration (ISPy) | <img src="assets/atlas_calibration.png" width="220"> |
+| `chase.analysis.contrast` | `(flare−bg)/bg − frame0` wavelength-vs-time profile | <img src="assets/contrast_profile.png" width="220"> |
+| `chase.analysis.temperature` | Hα width→T (Molnar) + Fe I →T (Planck/EB/Voigt) | <img src="assets/double_temp_map_peak.png" width="220"> |
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/Majboor/chase-pipeline/feat/unified-pipeline-tui-sdk/assets/temperature.gif" width="720" alt="Double temperature map animation"><br>
+  <em>Double temperature map: chromosphere from Hα width (~10⁴ K) and photosphere
+  from Fe I Planck inversion (~5,100 K, absolute-calibrated against the FTS atlas).</em>
+</p>
+
+## Documentation
+
+- **[docs/DATA_ACQUISITION.md](docs/DATA_ACQUISITION.md)** — get from the CHASE portal to a processed cube, end to end.
+- **[docs/SDK.md](docs/SDK.md)** — the Python API, every function + parameters.
+- **[docs/TUI.md](docs/TUI.md)** — TUI walkthrough.
+- **[docs/CALIBRATION.md](docs/CALIBRATION.md)** — the science: what each calibration does and why.
+- **[docs/CONTRIBUTING.md](docs/CONTRIBUTING.md)** — dev setup, tests, style.
+
+## Tests
+
+```bash
+pip install -e '.[dev]' && pytest -q     # 22 fast tests on synthetic FITS fixtures
+```
+
+## 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
+
+If you use this pipeline, please cite the methods it builds on:
+
+- Molnar et al. 2019, *ApJ* **881**, 99 — Hα width → 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)).
+- CHASE/HIS: Li et al. 2022, *Science China* — the CHASE mission.
+
+## License
+
+MIT © 2025-2026 Waleed Ajmal. Ported `satprocess` components are BSD-3-Clause © 2025
+Finlay Davis — see [`NOTICE`](NOTICE).

chasepy-2.0.0/chase/__init__.py

@@ -0,0 +1,104 @@
+"""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__ = "2.0.0"
+
+# --- 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,
+    atlas_calibrate,
+    correct_spectral_drift,
+    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,
+    halpha_width_map,
+    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
+    "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", "planck_inversion",
+    # analysis
+    "contrast_profile", "halpha_width_map", "halpha_width_temperature",
+    "width_to_temperature", "fe_planck_temperature", "fe_eb_temperature",
+    "fe_voigt_temperature",
+    # viz
+    "make_animation", "make_contrast_animation", "make_temperature_animation",
+    # orchestration
+    "Config", "load_config", "run_pipeline",
+]