solarc-eclipse 0.6.1.4__tar.gz → 0.7.0__tar.gz

{solarc_eclipse-0.6.1.4/solarc_eclipse.egg-info → solarc_eclipse-0.7.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: solarc-eclipse
-Version: 0.6.1.4
+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
@@ -93,6 +93,7 @@ eclipse --help
 You can also use ECLIPSE as a Python library:
 
 ```python
+import astropy.units as u
 import euvst_response
 from euvst_response import AluminiumFilter, Detector_SWC, Telescope_EUVST
 
@@ -122,7 +123,7 @@ For analyzing simulation results, see the included Jupyter notebook `analysis_tu
 - Analyze fit statistics and compute velocity/line width errors
 - Create SunPy maps for visualization
 
-The analysis functions are now available directly from the package:
+The analysis functions are available directly from the package:
 
 ```python
 from euvst_response import (
@@ -134,15 +135,13 @@ from euvst_response import (
 )
 
 # Load results
-results = load_instrument_response_results("run/result/my_results.pkl")
+results = load_instrument_response_results("run/result/my_run.pkl")
 
-# Get results for a specific parameter combination:
-combo = get_results_for_combination(
-    results, exposure=40*u.s, slit_width=0.4*u.arcsec, offchip_bin_slit=2
-)
+# Print a summary table (auto-discovers all parameters and shows git commit)
+summary_table(results)
 
-# Create SunPy maps
-maps = create_sunpy_maps_from_combo(combo, rest_wavelength=195.119*u.AA, data_type='dn')
+# Retrieve a specific combination using full section.attribute names
+combo = get_results_for_combination(results, **{"simulation.expos": 40*u.s, "simulation.psf": True})
 ```
 
 ## Detailed instructions
@@ -305,105 +304,72 @@ 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`.
-
 ### 2. Simulate the instrument response
 
 #### Configuration File
 
-ECLIPSE uses YAML configuration files to specify simulation parameters. You can specify single values or lists of values for parameter sweeps.
-
-**Key configuration options:**
-- `instrument`: Choose between SWC (EUVST-SW) or EIS (Hinode)
-- `synthesis_file`: Path to the synthesised spectra pickle file (default: `./run/input/synthesised_spectra.pkl`)
-- `reference_line`: Spectral line to use as reference for wavelength grid when combining all lines (default: `Fe12_195.1190`)
-- `expos`: Exposure time(s) for simulations
-- `n_iter`: Number of Monte Carlo iterations
-- Parameter sweeps for filters, detector settings, etc.
+ECLIPSE uses YAML configuration files to specify simulation parameters.
+Parameters are organised into four sections - `simulation`, `detector`, `telescope`, and `filter` - each corresponding directly to a configuration class in `config.py`.
+Any field of those classes can be set here.
+**Any parameter that is given as a list is automatically swept over** and the
+simulation runs every combination (cartesian product).
+
+**Top-level keys** (not sections):
+- `instrument`: `SWC` (EUVST Short Wavelength) or `EIS` (Hinode/EIS)
+- `synthesis_file`: path to the synthesised spectra pickle file
+- `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)
 
 Here's a complete example configuration file:
 
 ```yaml
-# Instrument selection
-instrument: SWC  # Options: SWC (EUVST Short Wavelength) or EIS (Hinode/EIS)
-
-# Synthesis file path - location of the synthesised spectra pickle file
-synthesis_file: ./run/input/synthesised_spectra.pkl  # Default location
-
-# Reference line for wavelength grid and metadata when combining all spectral lines
-reference_line: Fe12_195.1190  # Default reference line (Fe XII 195.119 Angstrom)
-
-# Point Spread Function
-psf: False  # Enable PSF convolution
-# Or test with and without PSF:
-# psf: [True, False]  # Run simulations both with and without PSF
-
-# Exposure times - can be single value or list
-expos: [0.5 s, 1 s, 2 s, 5 s, 10 s, 20 s, 40 s, 80 s]
-
-# Monte Carlo simulation parameters
-n_iter: 1000      # Number of Monte Carlo iterations
-ncpu: -1        # Number of CPU cores (-1 = use all available)
-
-# Parameter sweeps - you can specify single values or lists for any parameter
-# The simulation will run all combinations of parameters
-
-# Slit width
-slit_width: 0.2 arcsec  # Narrowest slit on EUVST
-
-# Filter parameters (SWC only)
-# Thickness of aluminum oxide layer on entrance filter
-oxide_thickness: 95 angstrom  # Default (expected value)
-
-# Carbon contamination thickness on filter
-c_thickness: 0 angstrom  # Default (ideal case, no contamination)
-
-# Aluminum filter thickness
-aluminium_thickness: 1485 angstrom  # Default (expected value)
-
-# CCD temperature for dark current calculation
-ccd_temperature: -60 Celsius  # Default (expected operating temperature)
-
-# Visible stray light level
-vis_sl: 0 photon / (s * cm**2)  # Default, (ideal case, no stray light)
-
-# Multi-component Gaussian fitting (optional, omit for single-Gaussian)
-fitting:
-  primary_component: 0
-  constrain_positive_intensity: true
-  components:
-    - wavelength: 195.119 angstrom
-      amplitude_greater_than: 1  # must be brighter than component 1
-    - wavelength: 195.179 angstrom
-      tie_center: 0  # Centroid offset tied to component 0
-      tie_width: 0  # Same width as component 0
-```
-
-Off-chip binning in the slit direction can also be performed:
-
-```yaml
-offchip_bin_slit: 2          # Bin every 2 slit pixels
-offchip_bin_slit: [1, 2, 4]  # Sweep over multiple binning factors
+# Input
+instrument: SWC
+synthesis_file: ./run/input/synthesised_spectra.pkl
+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.
+simulation:
+  slit_width: [0.2 arcsec, 0.4 arcsec]  # sweep over two slit widths
+  expos: [5 s, 10 s, 20 s, 40 s, 80 s]  # sweep over five exposure times
+  psf: True
+  vis_sl: 0 photon / (s * cm^2)
+  enable_pinholes: False
+
+# Detector parameters
+detector:
+  ccd_temperature: -60 Celsius  # used to compute dark current via the CCD model
+
+# Telescope parameters
+telescope:
+  microroughness_sigma: 0.3 nm  # RMS surface roughness
+
+# Aluminium filter parameters (SWC only)
+filter:
+  al_thickness: 1485 angstrom
+  oxide_thickness: 95 angstrom
+  c_thickness: 40 angstrom
+  mesh_throughput: 0.8
 ```
 
-Alternatively, you can specify paired slit width and off-chip binning values to only simulate specific combinations:
+Any parameter from the `Detector_SWC`, `Telescope_EUVST`, or `AluminiumFilter`
+dataclasses in `config.py` can be added to the corresponding section. For
+example, to sweep over detector quantum efficiency:
 
 ```yaml
-# Paired slit width / off-chip binning
-# Only the listed (slit_width, offchip_bin_slit) pairs are simulated
-slit_bin_pairs:
-  - slit_width: 0.2 arcsec
-    offchip_bin_slit: 1
-  - slit_width: 0.4 arcsec
-    offchip_bin_slit: 2
-  - slit_width: 0.8 arcsec
-    offchip_bin_slit: 5
-  - slit_width: 1.6 arcsec
-    offchip_bin_slit: 10
+detector:
+  ccd_temperature: -60 Celsius
+  qe_euv: [0.5, 0.65, 0.76]   # sweep over three QE values
 ```
 
 For guidance on recommended values, see McKevitt et al. (2025) (in prep.).
@@ -416,6 +382,29 @@ 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
@@ -444,6 +433,10 @@ Results are saved as pickle files in the `run/result/` directory with the same b
 - Fitted spectral line parameters (intensity, velocity, width)
 - Statistical analysis of velocity precision vs. exposure time
 - Ground truth comparisons
+- Full config objects (`Detector`, `Telescope`, `Simulation`) for each parameter combination
+- The git commit ID and software version used to produce the results
+
+Use `summary_table(results)` after loading to see all parameter combinations and the run metadata.
 
 ## Acknowledgements
 

{solarc_eclipse-0.6.1.4 → solarc_eclipse-0.7.0}/README.md

@@ -45,6 +45,7 @@ eclipse --help
 You can also use ECLIPSE as a Python library:
 
 ```python
+import astropy.units as u
 import euvst_response
 from euvst_response import AluminiumFilter, Detector_SWC, Telescope_EUVST
 
@@ -74,7 +75,7 @@ For analyzing simulation results, see the included Jupyter notebook `analysis_tu
 - Analyze fit statistics and compute velocity/line width errors
 - Create SunPy maps for visualization
 
-The analysis functions are now available directly from the package:
+The analysis functions are available directly from the package:
 
 ```python
 from euvst_response import (
@@ -86,15 +87,13 @@ from euvst_response import (
 )
 
 # Load results
-results = load_instrument_response_results("run/result/my_results.pkl")
+results = load_instrument_response_results("run/result/my_run.pkl")
 
-# Get results for a specific parameter combination:
-combo = get_results_for_combination(
-    results, exposure=40*u.s, slit_width=0.4*u.arcsec, offchip_bin_slit=2
-)
+# Print a summary table (auto-discovers all parameters and shows git commit)
+summary_table(results)
 
-# Create SunPy maps
-maps = create_sunpy_maps_from_combo(combo, rest_wavelength=195.119*u.AA, data_type='dn')
+# Retrieve a specific combination using full section.attribute names
+combo = get_results_for_combination(results, **{"simulation.expos": 40*u.s, "simulation.psf": True})
 ```
 
 ## Detailed instructions
@@ -257,105 +256,72 @@ 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`.
-
 ### 2. Simulate the instrument response
 
 #### Configuration File
 
-ECLIPSE uses YAML configuration files to specify simulation parameters. You can specify single values or lists of values for parameter sweeps.
-
-**Key configuration options:**
-- `instrument`: Choose between SWC (EUVST-SW) or EIS (Hinode)
-- `synthesis_file`: Path to the synthesised spectra pickle file (default: `./run/input/synthesised_spectra.pkl`)
-- `reference_line`: Spectral line to use as reference for wavelength grid when combining all lines (default: `Fe12_195.1190`)
-- `expos`: Exposure time(s) for simulations
-- `n_iter`: Number of Monte Carlo iterations
-- Parameter sweeps for filters, detector settings, etc.
+ECLIPSE uses YAML configuration files to specify simulation parameters.
+Parameters are organised into four sections - `simulation`, `detector`, `telescope`, and `filter` - each corresponding directly to a configuration class in `config.py`.
+Any field of those classes can be set here.
+**Any parameter that is given as a list is automatically swept over** and the
+simulation runs every combination (cartesian product).
+
+**Top-level keys** (not sections):
+- `instrument`: `SWC` (EUVST Short Wavelength) or `EIS` (Hinode/EIS)
+- `synthesis_file`: path to the synthesised spectra pickle file
+- `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)
 
 Here's a complete example configuration file:
 
 ```yaml
-# Instrument selection
-instrument: SWC  # Options: SWC (EUVST Short Wavelength) or EIS (Hinode/EIS)
-
-# Synthesis file path - location of the synthesised spectra pickle file
-synthesis_file: ./run/input/synthesised_spectra.pkl  # Default location
-
-# Reference line for wavelength grid and metadata when combining all spectral lines
-reference_line: Fe12_195.1190  # Default reference line (Fe XII 195.119 Angstrom)
-
-# Point Spread Function
-psf: False  # Enable PSF convolution
-# Or test with and without PSF:
-# psf: [True, False]  # Run simulations both with and without PSF
-
-# Exposure times - can be single value or list
-expos: [0.5 s, 1 s, 2 s, 5 s, 10 s, 20 s, 40 s, 80 s]
-
-# Monte Carlo simulation parameters
-n_iter: 1000      # Number of Monte Carlo iterations
-ncpu: -1        # Number of CPU cores (-1 = use all available)
-
-# Parameter sweeps - you can specify single values or lists for any parameter
-# The simulation will run all combinations of parameters
-
-# Slit width
-slit_width: 0.2 arcsec  # Narrowest slit on EUVST
-
-# Filter parameters (SWC only)
-# Thickness of aluminum oxide layer on entrance filter
-oxide_thickness: 95 angstrom  # Default (expected value)
-
-# Carbon contamination thickness on filter
-c_thickness: 0 angstrom  # Default (ideal case, no contamination)
-
-# Aluminum filter thickness
-aluminium_thickness: 1485 angstrom  # Default (expected value)
-
-# CCD temperature for dark current calculation
-ccd_temperature: -60 Celsius  # Default (expected operating temperature)
-
-# Visible stray light level
-vis_sl: 0 photon / (s * cm**2)  # Default, (ideal case, no stray light)
-
-# Multi-component Gaussian fitting (optional, omit for single-Gaussian)
-fitting:
-  primary_component: 0
-  constrain_positive_intensity: true
-  components:
-    - wavelength: 195.119 angstrom
-      amplitude_greater_than: 1  # must be brighter than component 1
-    - wavelength: 195.179 angstrom
-      tie_center: 0  # Centroid offset tied to component 0
-      tie_width: 0  # Same width as component 0
-```
-
-Off-chip binning in the slit direction can also be performed:
-
-```yaml
-offchip_bin_slit: 2          # Bin every 2 slit pixels
-offchip_bin_slit: [1, 2, 4]  # Sweep over multiple binning factors
+# Input
+instrument: SWC
+synthesis_file: ./run/input/synthesised_spectra.pkl
+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.
+simulation:
+  slit_width: [0.2 arcsec, 0.4 arcsec]  # sweep over two slit widths
+  expos: [5 s, 10 s, 20 s, 40 s, 80 s]  # sweep over five exposure times
+  psf: True
+  vis_sl: 0 photon / (s * cm^2)
+  enable_pinholes: False
+
+# Detector parameters
+detector:
+  ccd_temperature: -60 Celsius  # used to compute dark current via the CCD model
+
+# Telescope parameters
+telescope:
+  microroughness_sigma: 0.3 nm  # RMS surface roughness
+
+# Aluminium filter parameters (SWC only)
+filter:
+  al_thickness: 1485 angstrom
+  oxide_thickness: 95 angstrom
+  c_thickness: 40 angstrom
+  mesh_throughput: 0.8
 ```
 
-Alternatively, you can specify paired slit width and off-chip binning values to only simulate specific combinations:
+Any parameter from the `Detector_SWC`, `Telescope_EUVST`, or `AluminiumFilter`
+dataclasses in `config.py` can be added to the corresponding section. For
+example, to sweep over detector quantum efficiency:
 
 ```yaml
-# Paired slit width / off-chip binning
-# Only the listed (slit_width, offchip_bin_slit) pairs are simulated
-slit_bin_pairs:
-  - slit_width: 0.2 arcsec
-    offchip_bin_slit: 1
-  - slit_width: 0.4 arcsec
-    offchip_bin_slit: 2
-  - slit_width: 0.8 arcsec
-    offchip_bin_slit: 5
-  - slit_width: 1.6 arcsec
-    offchip_bin_slit: 10
+detector:
+  ccd_temperature: -60 Celsius
+  qe_euv: [0.5, 0.65, 0.76]   # sweep over three QE values
 ```
 
 For guidance on recommended values, see McKevitt et al. (2025) (in prep.).
@@ -368,6 +334,29 @@ 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
@@ -396,6 +385,10 @@ Results are saved as pickle files in the `run/result/` directory with the same b
 - Fitted spectral line parameters (intensity, velocity, width)
 - Statistical analysis of velocity precision vs. exposure time
 - Ground truth comparisons
+- Full config objects (`Detector`, `Telescope`, `Simulation`) for each parameter combination
+- The git commit ID and software version used to produce the results
+
+Use `summary_table(results)` after loading to see all parameter combinations and the run metadata.
 
 ## Acknowledgements
 

{solarc_eclipse-0.6.1.4 → 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__ = "0.6.1.4"
+__version__ = "0.7.0"
 __author__ = "James McKevitt"
 __email__ = "jm2@mssl.ucl.ac.uk"
 
@@ -20,7 +20,7 @@ from .pinhole_diffraction import apply_euv_pinhole_diffraction, airy_disk_patter
 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
+from .data_processing import load_atmosphere, create_uniform_intensity_cube
 from .analysis import (
     load_instrument_response_results,
     get_parameter_combinations,
@@ -43,6 +43,7 @@ __all__ = [
     "simulate_once", "monte_carlo",
     "main",
     "load_atmosphere",
+    "create_uniform_intensity_cube",
     "load_instrument_response_results",
     "get_parameter_combinations",
     "analyse_fit_statistics",