solarc-eclipse 0.6.2__tar.gz → 0.7.0__tar.gz

{solarc_eclipse-0.6.2/solarc_eclipse.egg-info → solarc_eclipse-0.7.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: solarc-eclipse
-Version: 0.6.2
+Version: 0.7.0
 Summary: ECLIPSE: Emission Calculation and Line Prediction for SOLAR-C EUVST
 Home-page: https://github.com/jamesmckevitt/eclipse
 Author: James McKevitt
@@ -12,11 +12,9 @@ Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
 Classifier: Topic :: Scientific/Engineering :: Astronomy
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Requires-Python: >=3.8
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy
@@ -31,6 +29,13 @@ Requires-Dist: dill
 Requires-Dist: pyyaml
 Requires-Dist: reproject
 Requires-Dist: sunpy[all]
+Requires-Dist: dask
+Requires-Dist: psutil
+Requires-Dist: mendeleev
+Requires-Dist: h5py
+Requires-Dist: fiasco
+Provides-Extra: mpi
+Requires-Dist: mpi4py; extra == "mpi"
 Provides-Extra: dev
 Requires-Dist: pytest; extra == "dev"
 Requires-Dist: black; extra == "dev"
@@ -73,7 +78,7 @@ After installation, you can run ECLIPSE from the command line:
 
 ```bash
 # Run synthesis script (convert 3D MHD data to synthetic spectra)
-synthesise-spectra --data-dir ./data/atmosphere --goft-file ./data/gofnt.sav --output-dir ./run/input
+synthesise-spectra --data-dir ./data/atmosphere --lines Fe12_195.1190 --output-dir ./run/input
 
 # Run instrument response simulation
 eclipse --config ./run/input/config.yaml
@@ -98,7 +103,7 @@ detector = Detector_SWC()
 print(f"Telescope collecting area: {telescope.collecting_area:.4f}")
 print(f"Detector QE (EUV): {detector.qe_euv:.2f}")
 
-# Calculate effective area at Fe XII 195.119 Å
+# Calculate effective area at Fe XII 195.119 Angstrom
 fe12_wl = 195.119 * u.AA
 effective_area = telescope.collecting_area * telescope.throughput(fe12_wl) * detector.qe_euv
 
@@ -141,18 +146,9 @@ combo = get_results_for_combination(results, **{"simulation.expos": 40*u.s, "sim
 
 ## Detailed instructions
 
-### 1. Generate contribution functions for the desired emission lines
+### 1. Run the line synthesis
 
-Edit `make_gofnt.pro` to specify the desired emission lines and the location of the CHIANTI files. You can use CHIANTI to identify the required lines.
-
-Run the following command:
-```bash
-idl -e "make_goft"
-```
-
-### 2. Run the line synthesis
-
-The synthesis script converts 3D MHD simulation data into synthetic solar spectra. It can be run directly from the command line with extensive configuration options.
+The synthesis script converts 3D MHD simulation data into synthetic solar spectra. Contribution functions G(T, n_e) are computed on-the-fly using [fiasco](https://fiasco.readthedocs.io/) (a Python interface to the CHIANTI atomic database).
 
 #### Basic Usage
 
@@ -160,7 +156,9 @@ The synthesis script converts 3D MHD simulation data into synthetic solar spectr
 # Example using all available command line options
 synthesise-spectra \
   --data-dir ./data/atmosphere \
-  --goft-file ./data/gofnt.sav \
+  --lines Fe12_195.1190 Fe12_195.1790 \
+  --abundance sun_coronal_2021_chianti \
+  --n-workers 4 \
   --output-dir ./run/input \
   --output-name synthesised_spectra.pkl \
   --temp-file temp/eosT.0270000 \
@@ -180,8 +178,7 @@ synthesise-spectra \
   --crop-z "0 Mm" "20 Mm" \
   --downsample 1 \
   --precision float64 \
-  --mean-mol-wt 1.29 \
-  --limit-lines Fe12_195.1190
+  --mean-mol-wt 1.29
 
 # Show all available options
 synthesise-spectra --help
@@ -191,10 +188,14 @@ synthesise-spectra --help
 
 **Input/Output Paths:**
 - `--data-dir`: Directory containing simulation data (default: `data/atmosphere`)
-- `--goft-file`: Path to CHIANTI G(T,N) save file (default: `./data/gofnt.sav`)
 - `--output-dir`: Output directory for results (default: `./run/input`)
 - `--output-name`: Output filename (default: `synthesised_spectra.pkl`)
 
+**Line and Abundance Selection:**
+- `--lines`: Emission lines to synthesise, e.g., `--lines Fe12_195.1190 Fe12_195.1790` (required)
+- `--abundance`: CHIANTI abundance dataset name (default: `sun_coronal_2021_chianti`)
+- `--n-workers`: Number of parallel workers for the fiasco G(T, n_e) computation. Each distinct ion is computed in a separate process. `0` uses all available CPUs (default: `0`). Set to `1` for serial execution.
+
 **Simulation Files:**
 - `--temp-file`: Temperature file relative to data-dir (default: `temp/eosT.0270000`)
 - `--rho-file`: Density file relative to data-dir (default: `rho/result_prim_0.0270000`)
@@ -227,9 +228,6 @@ synthesise-spectra --help
 - `--precision`: Numerical precision `float32` or `float64` (default: `float64`)
 - `--mean-mol-wt`: Mean molecular weight (default: `1.29`)
 
-**Line Selection:**
-- `--limit-lines`: Limit to specific lines, e.g., `--limit-lines Fe12_195.1190 Fe12_195.1790`
-
 #### Dynamic Mode (Time-varying Atmospheres)
 
 For simulating raster scans over evolving atmospheres, use dynamic mode which combines MHD timesteps based on instrument scanning:
@@ -237,7 +235,8 @@ For simulating raster scans over evolving atmospheres, use dynamic mode which co
 ```bash
 synthesise-spectra \
   --data-dir ./data/atmosphere \
-  --goft-file ./data/gofnt.sav \
+  --lines Fe12_195.1190 \
+  --abundance sun_coronal_2021_chianti \
   --output-dir ./run/input \
   --slit-rest-time "40 s" \
   --slit-width "0.2 arcsec" \
@@ -275,7 +274,6 @@ The synthesis produces a pickle file containing:
 
 - Use `--downsample 2` or `--downsample 4` for initial testing
 - Use `--precision float32` to reduce memory usage (may affect accuracy)
-- Use `--limit-lines` to synthesise only specific lines for development
 - Use spatial cropping to focus on regions of interest and reduce computation time
 - Monitor memory usage - full resolution synthesis can require 50+ GB RAM
 - Side views (`--integration-axis x` or `y`) may require different velocity files
@@ -288,7 +286,7 @@ The synthesis results can be loaded and analyzed using the package API:
 import euvst_response
 
 # Load synthesis results - this sums all line cubes into a single cube
-# By default uses Fe XII 195.119 Å as reference for wavelength grid
+# By default uses Fe XII 195.119 Angstrom as reference for wavelength grid
 cube = euvst_response.load_atmosphere("./run/input/synthesised_spectra.pkl")
 print(f"Combined cube shape: {cube.data.shape}")
 
@@ -306,13 +304,7 @@ print(f"Rest wavelength: {fe12_195.meta['rest_wav']}")
 print(f"Available spectral lines: {list(data['line_cubes'].keys())}")
 ```
 
-#### Pre-computed Atmospheres
-
-This step can require a lot of memory at full resolution. A fully synthesised atmosphere using the Cheung et al. (2018) atmosphere (doi:10.1038/s41550-018-0629-3) for the Fe XII 195.119 and 195.179 lines, including 5 background lines from each side, can be downloaded here: https://liveuclac-my.sharepoint.com/:f:/g/personal/ucasjem_ucl_ac_uk/Es-ts6rwXIlInAweGI7hmdMB5BoGqv9uSpIXOvMkzhS3cw?e=54si7R
-
-**Important:** You can place the synthesised atmosphere file anywhere and specify its location using the `synthesis_file` parameter in your YAML configuration file. The default location is `./run/input/synthesised_spectra.pkl`.
-
-### 3. Simulate the instrument response
+### 2. Simulate the instrument response
 
 #### Configuration File
 
@@ -328,6 +320,7 @@ simulation runs every combination (cartesian product).
 - `reference_line`: spectral line used as the wavelength-grid reference (default `Fe12_195.1190`)
 - `n_iter`: number of Monte Carlo iterations
 - `ncpu`: CPU cores to use (`-1` = all available)
+- `offchip_bin_slit`: off-chip slit binning factor (default `1`)
 - `pinhole_sizes`, `pinhole_positions`: fixed paired lists for pinhole diffraction tests (SWC only)
 - `uniform_intensity`, `rest_wavelength`, `thermal_width`: uniform-intensity mode (alternative to synthesis file)
 
@@ -342,6 +335,7 @@ reference_line: Fe12_195.1190
 # Global settings (apply to all combinations)
 n_iter: 500
 ncpu: -1
+offchip_bin_slit: [1, 2]  # sweep no-binning and 2-pixel off-chip binning
 
 # Simulation parameters
 # Any field listed as a list is swept over; all combinations are run.
@@ -380,6 +374,37 @@ detector:
 
 For guidance on recommended values, see McKevitt et al. (2025) (in prep.).
 
+By default, both the DN and photon signals are fitted at every Monte Carlo iteration. To speed up the simulation when only one is needed, use the `fit_signals` option:
+
+```yaml
+fit_signals: dn       # Fit only the DN signal
+fit_signals: photon   # Fit only the photon signal
+fit_signals: both     # Fit both (default)
+```
+
+To fit blended spectral lines with multiple Gaussian components, add a `fitting` block:
+
+```yaml
+fitting:
+  primary_component: 0           # index of the component whose velocity is reported
+  constrain_positive_intensity: true  # reject fits with negative amplitudes
+  backend: scipy                 # optimiser: "scipy" (default) or "mpfit"
+  components:
+    - wavelength: 195.119 angstrom     # component 0: free centre, width, amplitude
+    - wavelength: 195.179 angstrom     # component 1: centre & width tied to component 0
+      tie_center: 0
+      tie_width: 0
+```
+
+Each component requires a `wavelength` field giving its rest wavelength.
+
+Each entry in `components` corresponds to one Gaussian. Optional per-component keys:
+- `tie_center: <i>`: constrain this component's centre to match component *i*
+- `tie_width: <i>`: constrain this component's line width to match component *i*
+- `amplitude_greater_than: <i>`: constrain amplitude to exceed that of component *i*
+
+Omitting the `fitting` block fits a single Gaussian (default behaviour).
+
 If you synthesised data in dynamic mode, your configuration must specify:
 - Exactly one slit width matching the synthesis slit width
 - Exactly one exposure time matching the synthesis exposure time
@@ -395,6 +420,12 @@ eclipse --config ./run/input/config.yaml
 - `--config`: Path to YAML configuration file (required)
 - `--debug`: Enable debug mode with IPython breakpoints on errors (optional)
 
+#### Multi-node MPI parallelisation
+
+When launched with multiple MPI ranks on a SLURM cluster (via `srun` or `mpirun`, and setting `--ntasks-per-node`), ECLIPSE automatically distributes Monte Carlo iterations across ranks and gathers results on rank 0. No code or configuration changes are needed - MPI is auto-detected at runtime. If `mpi4py` is not installed or only one rank is present, the code falls back to single-process mode.
+
+Requirements: `mpi4py` and `intel-mpi` (load with `module load intel-mpi` before launching).
+
 #### Output
 
 Results are saved as pickle files in the `run/result/` directory with the same base name as the configuration file. The output includes:

{solarc_eclipse-0.6.2 → solarc_eclipse-0.7.0}/README.md

@@ -30,7 +30,7 @@ After installation, you can run ECLIPSE from the command line:
 
 ```bash
 # Run synthesis script (convert 3D MHD data to synthetic spectra)
-synthesise-spectra --data-dir ./data/atmosphere --goft-file ./data/gofnt.sav --output-dir ./run/input
+synthesise-spectra --data-dir ./data/atmosphere --lines Fe12_195.1190 --output-dir ./run/input
 
 # Run instrument response simulation
 eclipse --config ./run/input/config.yaml
@@ -55,7 +55,7 @@ detector = Detector_SWC()
 print(f"Telescope collecting area: {telescope.collecting_area:.4f}")
 print(f"Detector QE (EUV): {detector.qe_euv:.2f}")
 
-# Calculate effective area at Fe XII 195.119 Å
+# Calculate effective area at Fe XII 195.119 Angstrom
 fe12_wl = 195.119 * u.AA
 effective_area = telescope.collecting_area * telescope.throughput(fe12_wl) * detector.qe_euv
 
@@ -98,18 +98,9 @@ combo = get_results_for_combination(results, **{"simulation.expos": 40*u.s, "sim
 
 ## Detailed instructions
 
-### 1. Generate contribution functions for the desired emission lines
+### 1. Run the line synthesis
 
-Edit `make_gofnt.pro` to specify the desired emission lines and the location of the CHIANTI files. You can use CHIANTI to identify the required lines.
-
-Run the following command:
-```bash
-idl -e "make_goft"
-```
-
-### 2. Run the line synthesis
-
-The synthesis script converts 3D MHD simulation data into synthetic solar spectra. It can be run directly from the command line with extensive configuration options.
+The synthesis script converts 3D MHD simulation data into synthetic solar spectra. Contribution functions G(T, n_e) are computed on-the-fly using [fiasco](https://fiasco.readthedocs.io/) (a Python interface to the CHIANTI atomic database).
 
 #### Basic Usage
 
@@ -117,7 +108,9 @@ The synthesis script converts 3D MHD simulation data into synthetic solar spectr
 # Example using all available command line options
 synthesise-spectra \
   --data-dir ./data/atmosphere \
-  --goft-file ./data/gofnt.sav \
+  --lines Fe12_195.1190 Fe12_195.1790 \
+  --abundance sun_coronal_2021_chianti \
+  --n-workers 4 \
   --output-dir ./run/input \
   --output-name synthesised_spectra.pkl \
   --temp-file temp/eosT.0270000 \
@@ -137,8 +130,7 @@ synthesise-spectra \
   --crop-z "0 Mm" "20 Mm" \
   --downsample 1 \
   --precision float64 \
-  --mean-mol-wt 1.29 \
-  --limit-lines Fe12_195.1190
+  --mean-mol-wt 1.29
 
 # Show all available options
 synthesise-spectra --help
@@ -148,10 +140,14 @@ synthesise-spectra --help
 
 **Input/Output Paths:**
 - `--data-dir`: Directory containing simulation data (default: `data/atmosphere`)
-- `--goft-file`: Path to CHIANTI G(T,N) save file (default: `./data/gofnt.sav`)
 - `--output-dir`: Output directory for results (default: `./run/input`)
 - `--output-name`: Output filename (default: `synthesised_spectra.pkl`)
 
+**Line and Abundance Selection:**
+- `--lines`: Emission lines to synthesise, e.g., `--lines Fe12_195.1190 Fe12_195.1790` (required)
+- `--abundance`: CHIANTI abundance dataset name (default: `sun_coronal_2021_chianti`)
+- `--n-workers`: Number of parallel workers for the fiasco G(T, n_e) computation. Each distinct ion is computed in a separate process. `0` uses all available CPUs (default: `0`). Set to `1` for serial execution.
+
 **Simulation Files:**
 - `--temp-file`: Temperature file relative to data-dir (default: `temp/eosT.0270000`)
 - `--rho-file`: Density file relative to data-dir (default: `rho/result_prim_0.0270000`)
@@ -184,9 +180,6 @@ synthesise-spectra --help
 - `--precision`: Numerical precision `float32` or `float64` (default: `float64`)
 - `--mean-mol-wt`: Mean molecular weight (default: `1.29`)
 
-**Line Selection:**
-- `--limit-lines`: Limit to specific lines, e.g., `--limit-lines Fe12_195.1190 Fe12_195.1790`
-
 #### Dynamic Mode (Time-varying Atmospheres)
 
 For simulating raster scans over evolving atmospheres, use dynamic mode which combines MHD timesteps based on instrument scanning:
@@ -194,7 +187,8 @@ For simulating raster scans over evolving atmospheres, use dynamic mode which co
 ```bash
 synthesise-spectra \
   --data-dir ./data/atmosphere \
-  --goft-file ./data/gofnt.sav \
+  --lines Fe12_195.1190 \
+  --abundance sun_coronal_2021_chianti \
   --output-dir ./run/input \
   --slit-rest-time "40 s" \
   --slit-width "0.2 arcsec" \
@@ -232,7 +226,6 @@ The synthesis produces a pickle file containing:
 
 - Use `--downsample 2` or `--downsample 4` for initial testing
 - Use `--precision float32` to reduce memory usage (may affect accuracy)
-- Use `--limit-lines` to synthesise only specific lines for development
 - Use spatial cropping to focus on regions of interest and reduce computation time
 - Monitor memory usage - full resolution synthesis can require 50+ GB RAM
 - Side views (`--integration-axis x` or `y`) may require different velocity files
@@ -245,7 +238,7 @@ The synthesis results can be loaded and analyzed using the package API:
 import euvst_response
 
 # Load synthesis results - this sums all line cubes into a single cube
-# By default uses Fe XII 195.119 Å as reference for wavelength grid
+# By default uses Fe XII 195.119 Angstrom as reference for wavelength grid
 cube = euvst_response.load_atmosphere("./run/input/synthesised_spectra.pkl")
 print(f"Combined cube shape: {cube.data.shape}")
 
@@ -263,13 +256,7 @@ print(f"Rest wavelength: {fe12_195.meta['rest_wav']}")
 print(f"Available spectral lines: {list(data['line_cubes'].keys())}")
 ```
 
-#### Pre-computed Atmospheres
-
-This step can require a lot of memory at full resolution. A fully synthesised atmosphere using the Cheung et al. (2018) atmosphere (doi:10.1038/s41550-018-0629-3) for the Fe XII 195.119 and 195.179 lines, including 5 background lines from each side, can be downloaded here: https://liveuclac-my.sharepoint.com/:f:/g/personal/ucasjem_ucl_ac_uk/Es-ts6rwXIlInAweGI7hmdMB5BoGqv9uSpIXOvMkzhS3cw?e=54si7R
-
-**Important:** You can place the synthesised atmosphere file anywhere and specify its location using the `synthesis_file` parameter in your YAML configuration file. The default location is `./run/input/synthesised_spectra.pkl`.
-
-### 3. Simulate the instrument response
+### 2. Simulate the instrument response
 
 #### Configuration File
 
@@ -285,6 +272,7 @@ simulation runs every combination (cartesian product).
 - `reference_line`: spectral line used as the wavelength-grid reference (default `Fe12_195.1190`)
 - `n_iter`: number of Monte Carlo iterations
 - `ncpu`: CPU cores to use (`-1` = all available)
+- `offchip_bin_slit`: off-chip slit binning factor (default `1`)
 - `pinhole_sizes`, `pinhole_positions`: fixed paired lists for pinhole diffraction tests (SWC only)
 - `uniform_intensity`, `rest_wavelength`, `thermal_width`: uniform-intensity mode (alternative to synthesis file)
 
@@ -299,6 +287,7 @@ reference_line: Fe12_195.1190
 # Global settings (apply to all combinations)
 n_iter: 500
 ncpu: -1
+offchip_bin_slit: [1, 2]  # sweep no-binning and 2-pixel off-chip binning
 
 # Simulation parameters
 # Any field listed as a list is swept over; all combinations are run.
@@ -337,6 +326,37 @@ detector:
 
 For guidance on recommended values, see McKevitt et al. (2025) (in prep.).
 
+By default, both the DN and photon signals are fitted at every Monte Carlo iteration. To speed up the simulation when only one is needed, use the `fit_signals` option:
+
+```yaml
+fit_signals: dn       # Fit only the DN signal
+fit_signals: photon   # Fit only the photon signal
+fit_signals: both     # Fit both (default)
+```
+
+To fit blended spectral lines with multiple Gaussian components, add a `fitting` block:
+
+```yaml
+fitting:
+  primary_component: 0           # index of the component whose velocity is reported
+  constrain_positive_intensity: true  # reject fits with negative amplitudes
+  backend: scipy                 # optimiser: "scipy" (default) or "mpfit"
+  components:
+    - wavelength: 195.119 angstrom     # component 0: free centre, width, amplitude
+    - wavelength: 195.179 angstrom     # component 1: centre & width tied to component 0
+      tie_center: 0
+      tie_width: 0
+```
+
+Each component requires a `wavelength` field giving its rest wavelength.
+
+Each entry in `components` corresponds to one Gaussian. Optional per-component keys:
+- `tie_center: <i>`: constrain this component's centre to match component *i*
+- `tie_width: <i>`: constrain this component's line width to match component *i*
+- `amplitude_greater_than: <i>`: constrain amplitude to exceed that of component *i*
+
+Omitting the `fitting` block fits a single Gaussian (default behaviour).
+
 If you synthesised data in dynamic mode, your configuration must specify:
 - Exactly one slit width matching the synthesis slit width
 - Exactly one exposure time matching the synthesis exposure time
@@ -352,6 +372,12 @@ eclipse --config ./run/input/config.yaml
 - `--config`: Path to YAML configuration file (required)
 - `--debug`: Enable debug mode with IPython breakpoints on errors (optional)
 
+#### Multi-node MPI parallelisation
+
+When launched with multiple MPI ranks on a SLURM cluster (via `srun` or `mpirun`, and setting `--ntasks-per-node`), ECLIPSE automatically distributes Monte Carlo iterations across ranks and gathers results on rank 0. No code or configuration changes are needed - MPI is auto-detected at runtime. If `mpi4py` is not installed or only one rank is present, the code falls back to single-process mode.
+
+Requirements: `mpi4py` and `intel-mpi` (load with `module load intel-mpi` before launching).
+
 #### Output
 
 Results are saved as pickle files in the `run/result/` directory with the same base name as the configuration file. The output includes:

{solarc_eclipse-0.6.2 → solarc_eclipse-0.7.0}/euvst_response/__init__.py

@@ -4,7 +4,7 @@ ECLIPSE: Emission Calculation and Line Prediction for SOLAR-C EUVST
 This package provides tools for modeling the performance of the EUV spectrograph EUVST, on SOLAR-C.
 """
 
-__version__ = "0.6.2"
+__version__ = "0.7.0"
 __author__ = "James McKevitt"
 __email__ = "jm2@mssl.ucl.ac.uk"
 
@@ -13,11 +13,11 @@ from .config import Detector_SWC, Detector_EIS, Telescope_EUVST, Telescope_EIS,
 from .utils import wl_to_vel, vel_to_wl, angle_to_distance, distance_to_angle
 from .radiometric import (
     intensity_to_photons, add_telescope_throughput, photons_to_pixel_counts,
-    apply_exposure_and_poisson, add_poisson, apply_focusing_optics_psf, to_electrons, 
+    apply_exposure, sample_photon_arrivals, add_poisson, apply_focusing_optics_psf, to_electrons, 
     to_dn, add_visible_stray_light, add_pinhole_visible_light
 )
 from .pinhole_diffraction import apply_euv_pinhole_diffraction, airy_disk_pattern
-from .fitting import fit_cube_gauss, velocity_from_fit, width_from_fit, analyse
+from .fitting import fit_cube_gauss, velocity_from_fit, width_from_fit, analyse, FitConfig, FitComponent
 from .monte_carlo import simulate_once, monte_carlo
 from .main import main
 from .data_processing import load_atmosphere, create_uniform_intensity_cube
@@ -36,9 +36,10 @@ __all__ = [
     "Simulation", "AluminiumFilter",
     "wl_to_vel", "vel_to_wl", "angle_to_distance", "distance_to_angle",
     "intensity_to_photons", "add_telescope_throughput", "photons_to_pixel_counts",
-    "apply_exposure_and_poisson", "add_poisson", "apply_focusing_optics_psf", "to_electrons", 
+    "apply_exposure", "sample_photon_arrivals", "add_poisson", "apply_focusing_optics_psf", "to_electrons", 
     "to_dn", "add_visible_stray_light", "add_pinhole_visible_light",
     "fit_cube_gauss", "velocity_from_fit", "width_from_fit", "analyse",
+    "FitConfig", "FitComponent",
     "simulate_once", "monte_carlo",
     "main",
     "load_atmosphere",

{solarc_eclipse-0.6.2 → solarc_eclipse-0.7.0}/euvst_response/analysis.py

@@ -119,7 +119,8 @@ def get_parameter_combinations(results: Dict[str, Any]) -> List[Dict]:
 def analyse_fit_statistics(
     combination_results: Dict[str, Any],
     rest_wavelength: u.Quantity,
-    data_type: str = "dn"
+    data_type: str = "dn",
+    fit_config=None,
 ) -> Dict[str, Any]:
     """
     Analyze fit statistics to compute velocity and line width statistics.
@@ -132,35 +133,52 @@ def analyse_fit_statistics(
         Rest wavelength for velocity conversion.
     data_type : str, optional
         Either "dn" or "photon" to specify which fit statistics to analyze.
+    fit_config : FitConfig, optional
+        Multi-component fitting configuration. When provided the primary-
+        component indices are used; otherwise indices 1 (centre) and
+        2 (sigma) are assumed (single-component default).
         
     Returns
     -------
     dict
         Dictionary containing velocity and width statistics.
     """
+    # Determine parameter indices for the primary component
+    if fit_config is not None and not fit_config.is_single:
+        idx_center = fit_config.idx_center
+        idx_sigma = fit_config.idx_sigma
+    else:
+        idx_center = 1
+        idx_sigma = 2
+
     # Get fit statistics
     fit_stats_key = f"{data_type}_fit_stats"
     if fit_stats_key not in combination_results:
         raise ValueError(f"No {fit_stats_key} found in combination results")
     
     fit_stats = combination_results[fit_stats_key]
+    if fit_stats is None:
+        raise ValueError(
+            f"'{data_type}' signal was not fitted for this combination. "
+            f"Check the 'fit_signals' setting in your YAML config."
+        )
     fit_truth_data = combination_results["ground_truth"]["fit_truth_data"]
     fit_truth_units = combination_results["ground_truth"]["fit_truth_units"]
     
     # Extract data and units
-    mean_data = fit_stats["mean_data"]      # Shape: (nx, ny, 4)
-    std_data = fit_stats["std_data"]        # Shape: (nx, ny, 4)
-    units = fit_stats["units"]              # List of 4 astropy units
+    mean_data = fit_stats["mean_data"]      # Shape: (nx, ny, n_params)
+    std_data = fit_stats["std_data"]        # Shape: (nx, ny, n_params)
+    units = fit_stats["units"]              # List of n_params astropy units
     
-    # Get center statistics (parameter index 1)
-    center_mean_data = mean_data[..., 1]    # (nx, ny) - values only
-    center_std_data = std_data[..., 1]      # (nx, ny) - values only
-    center_unit = units[1]                  # wavelength unit
+    # Get center statistics for the primary component
+    center_mean_data = mean_data[..., idx_center]
+    center_std_data = std_data[..., idx_center]
+    center_unit = units[idx_center]
     
-    # Get width statistics (parameter index 2)
-    width_mean_data = mean_data[..., 2]     # (nx, ny) - values only
-    width_std_data = std_data[..., 2]       # (nx, ny) - values only
-    width_unit = units[2]                   # wavelength unit
+    # Get width statistics for the primary component
+    width_mean_data = mean_data[..., idx_sigma]
+    width_std_data = std_data[..., idx_sigma]
+    width_unit = units[idx_sigma]
     
     # Create quantities
     center_mean_q = center_mean_data * center_unit
@@ -177,7 +195,7 @@ def analyse_fit_statistics(
     
     # Convert to velocities
     v_mean = centers_to_velocity(center_mean_q, rest_wavelength)
-    v_true = centers_to_velocity(fit_truth_data[..., 1] * fit_truth_units[1], rest_wavelength)
+    v_true = centers_to_velocity(fit_truth_data[..., idx_center] * fit_truth_units[idx_center], rest_wavelength)
     v_err = v_true - v_mean
     
     # Convert center std to velocity std using differential: dv/dlambda = c/lambda
@@ -377,11 +395,12 @@ def summary_table(results: Dict[str, Any]) -> None:
 
 def create_sunpy_maps_from_combo(
     combination_results: Dict[str, Any],
-    cube_reb,
+    cube_reb=None,
     rest_wavelength: u.Quantity = 195.119 * u.AA,
     data_type: str = "dn",
     precision_requirement: u.Quantity = 2.0 * u.km / u.s,
-    exposure_time_results: List[Dict[str, Any]] | None = None
+    exposure_time_results: List[Dict[str, Any]] | None = None,
+    fit_config=None,
 ) -> Dict[str, Any]:
     """
     Create SunPy maps from combination results using the new fit statistics structure.
@@ -390,8 +409,9 @@ def create_sunpy_maps_from_combo(
     ----------
     combination_results : dict
         Results for a specific parameter combination from get_results_for_combination().
-    cube_reb : NDCube
+    cube_reb : NDCube, optional
         NDCube with helioprojective WCS to use for all maps.
+        If not provided, the WCS stored in the combination results is used.
     rest_wavelength : u.Quantity, optional
         Rest wavelength for velocity conversion (default: 195.119 A for Fe XII).
     data_type : str, optional
@@ -401,6 +421,9 @@ def create_sunpy_maps_from_combo(
     exposure_time_results : list of dict, optional
         List of results from get_results_for_combination() for different exposure times.
         If provided, will create an exposure time map showing minimum exposure needed.
+    fit_config : FitConfig, optional
+        Multi-component fitting configuration. When provided, the primary-
+        component indices are used to extract centre and width parameters.
         
     Returns
     -------
@@ -426,19 +449,27 @@ def create_sunpy_maps_from_combo(
             # Extract exposure time from parameters
             exposure_time = result["parameters"]["simulation.expos"].to_value(u.s)
             # Create analysis for this exposure
-            analysis = analyse_fit_statistics(result, rest_wavelength, data_type)
+            analysis = analyse_fit_statistics(result, rest_wavelength, data_type, fit_config=fit_config)
             analysis_per_exp[exposure_time] = analysis
     else:
         analysis_per_exp = None
     
-    # Extract 2D helioprojective WCS from the cube
-    wcs_2d = cube_reb.wcs.celestial.swapaxes(0, 1)
+    # Extract 2D helioprojective WCS from the cube or stored signal WCS
+    if cube_reb is not None:
+        wcs_2d = cube_reb.wcs.celestial.swapaxes(0, 1)
+    else:
+        wcs_2d = combination_results["first_signal_wcs"].celestial.swapaxes(0, 1)
     
     # Get the data arrays - now only first iteration is saved
     first_photon_signal = combination_results["first_photon_signal"]  # Shape: (nx, ny, nwave)
     first_dn_signal = combination_results["first_dn_signal"]         # Shape: (nx, ny, nwave)
     fit_stats_key = f"{data_type}_fit_stats"
     fit_stats = combination_results[fit_stats_key]          # Contains first_fit_data, mean_data, std_data, units
+    if fit_stats is None:
+        raise ValueError(
+            f"'{data_type}' signal was not fitted for this combination. "
+            f"Check the 'fit_signals' setting in your YAML config."
+        )
     
     maps = {}
 
@@ -457,14 +488,22 @@ def create_sunpy_maps_from_combo(
     maps['total_dn'] = sunpy.map.Map(total_dn_data.T, wcs_2d)
     maps['total_dn'].meta['bunit'] = str(total_dn_unit)
     
+    # Determine parameter indices for the primary component
+    if fit_config is not None and not fit_config.is_single:
+        idx_center = fit_config.idx_center
+        idx_sigma = fit_config.idx_sigma
+    else:
+        idx_center = 1
+        idx_sigma = 2
+
     # --- Get velocity and width analysis for this combination ---
-    analysis = analyse_fit_statistics(combination_results, rest_wavelength, data_type)
+    analysis = analyse_fit_statistics(combination_results, rest_wavelength, data_type, fit_config=fit_config)
 
     # --- Velocity maps ---
-    # Velocity from first fit (parameter 1 = center)
-    first_fit_data = fit_stats["first_fit_data"]  # Shape: (nx, ny, 4)
-    center_first_data = first_fit_data[..., 1]    # Extract center parameter
-    center_first_unit = fit_stats["units"][1]     # Get units for center parameter
+    # Velocity from first fit (primary component center)
+    first_fit_data = fit_stats["first_fit_data"]  # Shape: (nx, ny, n_params)
+    center_first_data = first_fit_data[..., idx_center]
+    center_first_unit = fit_stats["units"][idx_center]
 
     def centers_to_velocity(centers_data, centers_unit, lambda0):
         """Convert wavelength centers to velocities"""
@@ -492,9 +531,9 @@ def create_sunpy_maps_from_combo(
     maps['velocity_err'].meta['bunit'] = str(analysis["v_err"].unit)
 
     # --- Line width maps ---
-    # Line width from first fit (parameter 2 = width)
-    width_first_data = first_fit_data[..., 2]     # Extract width parameter data
-    width_first_unit = fit_stats["units"][2]      # Get units for width parameter
+    # Line width from first fit (primary component sigma)
+    width_first_data = first_fit_data[..., idx_sigma]
+    width_first_unit = fit_stats["units"][idx_sigma]
 
     # Create quantity with proper units
     width_quantity = width_first_data * width_first_unit