solarc-eclipse 0.6.1__tar.gz → 0.6.1.2__tar.gz

{solarc_eclipse-0.6.1/solarc_eclipse.egg-info → solarc_eclipse-0.6.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: solarc-eclipse
-Version: 0.6.1
+Version: 0.6.1.2
 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
@@ -361,6 +359,15 @@ ccd_temperature: -60 Celsius  # Default (expected operating temperature)
 
 # Visible stray light level
 vis_sl: 0 photon / (s * pixel)  # Default, (ideal case, no stray light)
+
+# Multi-component Gaussian fitting (optional, omit for single-Gaussian)
+fitting:
+  primary_component: 0
+  components:
+    - wavelength: 195.119 angstrom
+    - wavelength: 195.179 angstrom
+      tie_center: 0  # Centroid offset tied to component 0
+      tie_width: 0  # Same width as component 0
 ```
 
 For guidance on recommended values, see McKevitt et al. (2025) (in prep.).

{solarc_eclipse-0.6.1 → solarc_eclipse-0.6.1.2}/README.md

@@ -318,6 +318,15 @@ ccd_temperature: -60 Celsius  # Default (expected operating temperature)
 
 # Visible stray light level
 vis_sl: 0 photon / (s * pixel)  # Default, (ideal case, no stray light)
+
+# Multi-component Gaussian fitting (optional, omit for single-Gaussian)
+fitting:
+  primary_component: 0
+  components:
+    - wavelength: 195.119 angstrom
+    - wavelength: 195.179 angstrom
+      tie_center: 0  # Centroid offset tied to component 0
+      tie_width: 0  # Same width as component 0
 ```
 
 For guidance on recommended values, see McKevitt et al. (2025) (in prep.).

{solarc_eclipse-0.6.1 → solarc_eclipse-0.6.1.2}/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__ = "0.6.1"
+__version__ = "0.6.1.2"
 __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
@@ -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-0.6.1 → solarc_eclipse-0.6.1.2}/euvst_response/analysis.py

@@ -112,7 +112,8 @@ def get_parameter_combinations(results: Dict[str, Any]) -> List[Tuple]:
 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.
@@ -125,12 +126,24 @@ 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:
@@ -141,19 +154,19 @@ def analyse_fit_statistics(
     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
@@ -170,7 +183,7 @@ 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
@@ -459,7 +472,8 @@ def create_sunpy_maps_from_combo(
     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.
@@ -479,6 +493,9 @@ 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
     -------
@@ -504,7 +521,7 @@ def create_sunpy_maps_from_combo(
             # Extract exposure time from parameters
             exposure_time = result["parameters"]["exposure"].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
@@ -535,14 +552,22 @@ 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"""
@@ -570,9 +595,9 @@ 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

{solarc_eclipse-0.6.1 → solarc_eclipse-0.6.1.2}/euvst_response/config.py

@@ -243,7 +243,8 @@ class Telescope_EUVST:
     microroughness_sigma: u.Quantity = 0.3 * u.nm  # RMS microroughness for primary mirror
     filter: AluminiumFilter = field(default_factory=AluminiumFilter)
     psf_type: str = "gaussian"
-    psf_params: list = field(default_factory=lambda: [0.343 * u.pixel])  # FWHM of 0.805 pix from 0.128 arcsec from optical design RSC-2022021B in sigma
+    # psf_params: list = field(default_factory=lambda: [1.26 * u.pixel, 1.95 * u.pixel])  # [spatial_fwhm, spectral_fwhm] in pixels. From 0.200 arcsec (w/ slit-scan; FOV2) and 33.00 mA in RSC-2022021 (Oct 2023) and RSC-2022021B (Feb 2024).
+    psf_params: list = field(default_factory=lambda: [2.66 * u.pixel, 2.54 * u.pixel])  # [spatial_fwhm, spectral_fwhm] in pixels. From 0.423 arcsec (w/ slit-scan; FOV2) and 43.00 mA in RSC-2022021C (Mar 2025).
     
     # Wavelength-dependent efficiency tables
     pm_table: Path = field(default_factory=lambda: files('euvst_response') / 'data' / 'throughput' / 'primary_mirror_coating_reflectance.dat')
@@ -251,7 +252,7 @@ class Telescope_EUVST:
 
     @property
     def collecting_area(self) -> u.Quantity:
-        return 0.5 * np.pi * (self.D_ap / 2) ** 2
+        return 0.5 * np.pi * (self.D_ap / 2) ** 2  # Accounting for 50% loss due to beam division between SW and LW channels.
 
     def primary_mirror_efficiency(self, wl0: u.Quantity) -> float:
         """
@@ -293,7 +294,10 @@ class Telescope_EUVST:
         """
         Calculate the efficiency reduction due to primary mirror microroughness.
         
-        Formula: 1 - (4*pi*sigma/lambda)^2
+        Uses the Debye-Waller factor for specular reflectance:
+        
+            efficiency = exp(-(4*pi*sigma/lambda)^2)
+        
         where sigma is the RMS microroughness and lambda is the wavelength.
         
         Parameters
@@ -313,8 +317,8 @@ class Telescope_EUVST:
         # Calculate (4*pi*sigma/lambda)^2
         roughness_term = (4 * np.pi * sigma_nm / wl_nm) ** 2
         
-        # Return 1 - (4*pi*sigma/lambda)^2
-        return 1.0 - roughness_term.value
+        # Return exp(-(4*pi*sigma/lambda)^2)  [Debye-Waller specular efficiency]
+        return np.exp(-roughness_term.value)
 
     def throughput(self, wl0: u.Quantity) -> float:
         """
@@ -348,7 +352,7 @@ class Telescope_EUVST:
 class Telescope_EIS:
     """Hinode/EIS telescope configuration for comparison."""
     psf_type: str = "gaussian"
-    psf_params: list = field(default_factory=lambda: [1.28 * u.pixel])  # FWHM of 3 in sigma
+    psf_params: list = field(default_factory=lambda: [3.0 * u.pixel, 3.0 * u.pixel])  # [spatial_fwhm, spectral_fwhm] in pixels
     
     def ea_and_throughput(self, wl0: u.Quantity) -> u.Quantity:
         # Effective area including detector QE is 0.23 cm2

{solarc_eclipse-0.6.1 → solarc_eclipse-0.6.1.2}/euvst_response/data_processing.py

@@ -152,18 +152,37 @@ def resample_ndcube_spectral_axis(ndcube, spectral_axis, output_resolution, ncpu
     data = np.moveaxis(ndcube.data, spectral_axis, -1)
     shape = data.shape
     flat_data = data.reshape(-1, shape[-1])
-
-    resampler = FluxConservingResampler(extrapolation_treatment="zero_fill")
-    resampled = np.zeros((flat_data.shape[0], n_spec))
-
-    def _resample_pixel(i):
-        spec = Spectrum(flux=flat_data[i] * ndcube.unit, spectral_axis=spectral_world)
-        res = resampler(spec, new_spec_grid)
-        return res.flux.value
-
-    with tqdm_joblib(tqdm(total=flat_data.shape[0], desc="Resampling spectral axis", unit="pixel", leave=False)):
+    n_pixels = flat_data.shape[0]
+
+    # Determine number of workers
+    import os
+    if ncpu == -1:
+        n_workers = os.cpu_count() or 1
+    else:
+        n_workers = ncpu
+    
+    # Calculate batch size: aim for ~4 batches per worker to balance load
+    # but ensure each batch has enough work to justify overhead
+    min_pixels_per_batch = 100
+    n_batches = max(1, min(n_pixels // min_pixels_per_batch, n_workers * 4))
+    batch_size = (n_pixels + n_batches - 1) // n_batches  # ceiling division
+    
+    # Create batch indices
+    batch_indices = [(i, min(i + batch_size, n_pixels)) for i in range(0, n_pixels, batch_size)]
+
+    def _resample_batch(start_idx, end_idx):
+        """Resample a batch of pixels."""
+        resampler = FluxConservingResampler(extrapolation_treatment="zero_fill")
+        batch_results = np.empty((end_idx - start_idx, n_spec))
+        for i, pixel_idx in enumerate(range(start_idx, end_idx)):
+            spec = Spectrum(flux=flat_data[pixel_idx] * ndcube.unit, spectral_axis=spectral_world)
+            res = resampler(spec, new_spec_grid)
+            batch_results[i] = res.flux.value
+        return batch_results
+
+    with tqdm_joblib(tqdm(total=len(batch_indices), desc="Resampling spectral axis", unit="batch", leave=False)):
         results = Parallel(n_jobs=ncpu)(
-            delayed(_resample_pixel)(i) for i in range(flat_data.shape[0])
+            delayed(_resample_batch)(start, end) for start, end in batch_indices
         )
     resampled = np.vstack(results)
 
@@ -186,8 +205,21 @@ def resample_ndcube_spectral_axis(ndcube, spectral_axis, output_resolution, ncpu
     return NDCube(resampled, wcs=new_wcs, unit=ndcube.unit, meta=ndcube.meta)
 
 
-def reproject_ndcube_heliocentric_to_helioprojective(new_cube_spec, sim, det):
-    """ Reproject an NDCube from heliocentric to helioprojective coordinates. """
+def reproject_ndcube_heliocentric_to_helioprojective(new_cube_spec, sim, det, ncpu=-1):
+    """ Reproject an NDCube from heliocentric to helioprojective coordinates.
+    
+    Parameters
+    ----------
+    new_cube_spec : NDCube
+        Input NDCube in heliocentric coordinates
+    sim : Simulation
+        Simulation configuration object
+    det : Detector
+        Detector configuration object
+    ncpu : int, optional
+        Number of CPU cores for parallel reprojection. -1 uses all cores,
+        positive integers specify exact count. Default is -1.
+    """
 
     nx, ny, _ = new_cube_spec.shape
     wcs_hc = new_cube_spec.wcs
@@ -234,11 +266,16 @@ def reproject_ndcube_heliocentric_to_helioprojective(new_cube_spec, sim, det):
                         (det.plate_scale_angle * u.pix).to_value(u.arcsec),
                         (sim.slit_width).to_value(u.arcsec)]
 
+    # Determine parallelization setting:
+    # - If ncpu=-1, use True (all available cores)
+    # - If ncpu is a positive integer, pass it directly to control thread count
+    parallel_setting = True if ncpu == -1 else ncpu
+    
     new_cube_spec_hp_spat = new_cube_spec_hp.reproject_to(
         wcs_tgt,
         shape_out=shape_out,
         algorithm='interpolation',
-        parallel=True,
+        parallel=parallel_setting,
         order='bilinear',
     ) * new_cube_spec_hp.unit
 
@@ -273,7 +310,8 @@ def rebin_atmosphere(cube_sim, det, sim, use_dask=False):
     cube_det = reproject_ndcube_heliocentric_to_helioprojective(
         cube_spec,
         sim,
-        det
+        det,
+        ncpu=sim.ncpu
     )
 
     return cube_det