solarc-eclipse 0.5.0__tar.gz → 0.6.0__tar.gz

{solarc_eclipse-0.5.0/solarc_eclipse.egg-info → solarc_eclipse-0.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: solarc-eclipse
-Version: 0.5.0
+Version: 0.6.0
 Summary: ECLIPSE: Emission Calculation and Line Intensity Prediction for SOLAR-C EUVST
 Home-page: https://github.com/jamesmckevitt/eclipse
 Author: James McKevitt
@@ -49,6 +49,8 @@ Contact: James McKevitt (jm2@mssl.ucl.ac.uk). License: Contact for permission to
 
 The instrument response generated by this code will be updated during instrument development, testing, and commissioning.
 
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17543844.svg)](https://doi.org/10.5281/zenodo.17543844)
+
 ## Installation
 
 ### From PyPI (recommended)
@@ -158,15 +160,15 @@ synthesise-spectra \
   --vy-file vy/result_prim_3.0270000 \
   --vz-file vz/result_prim_2.0270000 \
   --cube-shape 512 768 256 \
-  --voxel-dx 0.192 \
-  --voxel-dy 0.192 \
-  --voxel-dz 0.064 \
-  --vel-res 5.0 \
-  --vel-lim 300.0 \
+  --voxel-dx "0.192 Mm" \
+  --voxel-dy "0.192 Mm" \
+  --voxel-dz "0.064 Mm" \
+  --vel-res "5.0 km/s" \
+  --vel-lim "300.0 km/s" \
   --integration-axis z \
-  --crop-x -50 50 \
-  --crop-y -50 50 \
-  --crop-z 0 20 \
+  --crop-x "-50 Mm" "50 Mm" \
+  --crop-y "-50 Mm" "50 Mm" \
+  --crop-z "0 Mm" "20 Mm" \
   --downsample 1 \
   --precision float64 \
   --mean-mol-wt 1.29 \
@@ -193,11 +195,11 @@ synthesise-spectra --help
 
 **Grid Parameters:**
 - `--cube-shape`: Cube dimensions as three integers (default: `512 768 256`)
-- `--voxel-dx`, `--voxel-dy`, `--voxel-dz`: Voxel sizes in Mm (default: `0.192 0.192 0.064`)
+- `--voxel-dx`, `--voxel-dy`, `--voxel-dz`: Voxel sizes with units (default: `"0.192 Mm"`, `"0.192 Mm"`, `"0.064 Mm"`)
 
 **Velocity Grid:**
-- `--vel-res`: Velocity resolution in km/s (default: `5.0`)
-- `--vel-lim`: Velocity limit ±km/s (default: `300.0`)
+- `--vel-res`: Velocity resolution with units (default: `"5.0 km/s"`)
+- `--vel-lim`: Velocity limit +-km/s with units (default: `"300.0 km/s"`)
 
 **Integration and Viewing:**
 - `--integration-axis`: Integration axis: `x`, `y`, or `z` (default: `z`)
@@ -205,10 +207,10 @@ synthesise-spectra --help
   - `x`: Side view from the left (integrates left-to-right)
   - `y`: Side view from the front (integrates front-to-back)
 
-**Spatial Cropping (Heliocentric coordinates in Mm):**
-- `--crop-x`: X-range to crop, e.g., `--crop-x -50 50` (optional)
-- `--crop-y`: Y-range to crop, e.g., `--crop-y -50 50` (optional)  
-- `--crop-z`: Z-range to crop, e.g., `--crop-z 0 20` (optional)
+**Spatial Cropping (Heliocentric coordinates with units):**
+- `--crop-x`: X-range to crop with units, e.g., `--crop-x "-50 Mm" "50 Mm"` (optional)
+- `--crop-y`: Y-range to crop with units, e.g., `--crop-y "-50 Mm" "50 Mm"` (optional)
+- `--crop-z`: Z-range to crop with units, e.g., `--crop-z "0 Mm" "20 Mm"` (optional)
 - Omit any crop option to use the full range in that dimension
 
 **Processing Options:**
@@ -219,6 +221,40 @@ synthesise-spectra --help
 **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:
+
+```bash
+synthesise-spectra \
+  --data-dir ./data/atmosphere \
+  --goft-file ./data/gofnt.sav \
+  --output-dir ./run/input \
+  --slit-rest-time "40 s" \
+  --slit-width "0.2 arcsec" \
+  --temp-dir temp \
+  --temp-filename eosT \
+  --rho-dir rho \
+  --rho-filename result_prim_0 \
+  --vz-dir vz \
+  --vz-filename result_prim_2 \
+  --time-dir time \
+  --time-filename tau_slice_0.100 \
+  --cube-shape 512 768 256 \
+  --voxel-dx "0.192 Mm" \
+  --voxel-dy "0.192 Mm" \
+  --voxel-dz "0.064 Mm" \
+  --vel-res "5.0 km/s" \
+  --vel-lim "300.0 km/s" \
+  --integration-axis z
+```
+
+**Dynamic Mode Options:**
+- `--slit-rest-time`: Slit rest time per position - enables dynamic mode
+- `--slit-width`: Slit width
+- `--temp-dir`, `--rho-dir`, `--vx-dir`, `--vy-dir`, `--vz-dir`, `--time-dir`: Directories containing timestep files
+- `--temp-filename`, `--rho-filename`, `--vx-filename`, `--vy-filename`, `--vz-filename`, `--time-filename`: Filename prefix before timestep suffix
+
 #### Output
 
 The synthesis produces a pickle file containing:
@@ -230,7 +266,7 @@ 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 synthesize only specific lines for development
+- 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
@@ -328,7 +364,11 @@ ccd_temperature: -60 Celsius  # Default (expected operating temperature)
 vis_sl: 0 photon / (s * pixel)  # Default, (ideal case, no stray light)
 ```
 
-For guidence on recommended values, see McKevitt et al. (2025) (in prep.).
+For guidance on recommended values, see McKevitt et al. (2025) (in prep.).
+
+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
 
 #### Running Simulations
 

{solarc_eclipse-0.5.0 → solarc_eclipse-0.6.0}/README.md

@@ -6,6 +6,8 @@ Contact: James McKevitt (jm2@mssl.ucl.ac.uk). License: Contact for permission to
 
 The instrument response generated by this code will be updated during instrument development, testing, and commissioning.
 
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17543844.svg)](https://doi.org/10.5281/zenodo.17543844)
+
 ## Installation
 
 ### From PyPI (recommended)
@@ -115,15 +117,15 @@ synthesise-spectra \
   --vy-file vy/result_prim_3.0270000 \
   --vz-file vz/result_prim_2.0270000 \
   --cube-shape 512 768 256 \
-  --voxel-dx 0.192 \
-  --voxel-dy 0.192 \
-  --voxel-dz 0.064 \
-  --vel-res 5.0 \
-  --vel-lim 300.0 \
+  --voxel-dx "0.192 Mm" \
+  --voxel-dy "0.192 Mm" \
+  --voxel-dz "0.064 Mm" \
+  --vel-res "5.0 km/s" \
+  --vel-lim "300.0 km/s" \
   --integration-axis z \
-  --crop-x -50 50 \
-  --crop-y -50 50 \
-  --crop-z 0 20 \
+  --crop-x "-50 Mm" "50 Mm" \
+  --crop-y "-50 Mm" "50 Mm" \
+  --crop-z "0 Mm" "20 Mm" \
   --downsample 1 \
   --precision float64 \
   --mean-mol-wt 1.29 \
@@ -150,11 +152,11 @@ synthesise-spectra --help
 
 **Grid Parameters:**
 - `--cube-shape`: Cube dimensions as three integers (default: `512 768 256`)
-- `--voxel-dx`, `--voxel-dy`, `--voxel-dz`: Voxel sizes in Mm (default: `0.192 0.192 0.064`)
+- `--voxel-dx`, `--voxel-dy`, `--voxel-dz`: Voxel sizes with units (default: `"0.192 Mm"`, `"0.192 Mm"`, `"0.064 Mm"`)
 
 **Velocity Grid:**
-- `--vel-res`: Velocity resolution in km/s (default: `5.0`)
-- `--vel-lim`: Velocity limit ±km/s (default: `300.0`)
+- `--vel-res`: Velocity resolution with units (default: `"5.0 km/s"`)
+- `--vel-lim`: Velocity limit +-km/s with units (default: `"300.0 km/s"`)
 
 **Integration and Viewing:**
 - `--integration-axis`: Integration axis: `x`, `y`, or `z` (default: `z`)
@@ -162,10 +164,10 @@ synthesise-spectra --help
   - `x`: Side view from the left (integrates left-to-right)
   - `y`: Side view from the front (integrates front-to-back)
 
-**Spatial Cropping (Heliocentric coordinates in Mm):**
-- `--crop-x`: X-range to crop, e.g., `--crop-x -50 50` (optional)
-- `--crop-y`: Y-range to crop, e.g., `--crop-y -50 50` (optional)  
-- `--crop-z`: Z-range to crop, e.g., `--crop-z 0 20` (optional)
+**Spatial Cropping (Heliocentric coordinates with units):**
+- `--crop-x`: X-range to crop with units, e.g., `--crop-x "-50 Mm" "50 Mm"` (optional)
+- `--crop-y`: Y-range to crop with units, e.g., `--crop-y "-50 Mm" "50 Mm"` (optional)
+- `--crop-z`: Z-range to crop with units, e.g., `--crop-z "0 Mm" "20 Mm"` (optional)
 - Omit any crop option to use the full range in that dimension
 
 **Processing Options:**
@@ -176,6 +178,40 @@ synthesise-spectra --help
 **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:
+
+```bash
+synthesise-spectra \
+  --data-dir ./data/atmosphere \
+  --goft-file ./data/gofnt.sav \
+  --output-dir ./run/input \
+  --slit-rest-time "40 s" \
+  --slit-width "0.2 arcsec" \
+  --temp-dir temp \
+  --temp-filename eosT \
+  --rho-dir rho \
+  --rho-filename result_prim_0 \
+  --vz-dir vz \
+  --vz-filename result_prim_2 \
+  --time-dir time \
+  --time-filename tau_slice_0.100 \
+  --cube-shape 512 768 256 \
+  --voxel-dx "0.192 Mm" \
+  --voxel-dy "0.192 Mm" \
+  --voxel-dz "0.064 Mm" \
+  --vel-res "5.0 km/s" \
+  --vel-lim "300.0 km/s" \
+  --integration-axis z
+```
+
+**Dynamic Mode Options:**
+- `--slit-rest-time`: Slit rest time per position - enables dynamic mode
+- `--slit-width`: Slit width
+- `--temp-dir`, `--rho-dir`, `--vx-dir`, `--vy-dir`, `--vz-dir`, `--time-dir`: Directories containing timestep files
+- `--temp-filename`, `--rho-filename`, `--vx-filename`, `--vy-filename`, `--vz-filename`, `--time-filename`: Filename prefix before timestep suffix
+
 #### Output
 
 The synthesis produces a pickle file containing:
@@ -187,7 +223,7 @@ 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 synthesize only specific lines for development
+- 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
@@ -285,7 +321,11 @@ ccd_temperature: -60 Celsius  # Default (expected operating temperature)
 vis_sl: 0 photon / (s * pixel)  # Default, (ideal case, no stray light)
 ```
 
-For guidence on recommended values, see McKevitt et al. (2025) (in prep.).
+For guidance on recommended values, see McKevitt et al. (2025) (in prep.).
+
+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
 
 #### Running Simulations
 

{solarc_eclipse-0.5.0 → solarc_eclipse-0.6.0}/euvst_response/__init__.py

@@ -4,7 +4,7 @@ ECLIPSE: Emission Calculation and Line Intensity Prediction for SOLAR-C EUVST
 This package provides tools for modeling the performance of the EUV spectrograph EUVST, on SOLAR-C.
 """
 
-__version__ = "0.5.0"
+__version__ = "0.6.0"
 __author__ = "James McKevitt"
 __email__ = "jm2@mssl.ucl.ac.uk"
 

{solarc_eclipse-0.5.0 → solarc_eclipse-0.6.0}/euvst_response/analysis.py

@@ -561,6 +561,9 @@ def create_sunpy_maps_from_combo(
 
     maps['velocity_std'] = sunpy.map.Map(analysis["v_std"].value.T, wcs_2d)
     maps['velocity_std'].meta['bunit'] = str(analysis["v_std"].unit)
+
+    maps['velocity_true'] = sunpy.map.Map(analysis["v_true"].value.T, wcs_2d)
+    maps['velocity_true'].meta['bunit'] = str(analysis["v_true"].unit)
     
     # Velocity error (truth - mean)
     maps['velocity_err'] = sunpy.map.Map(analysis["v_err"].value.T, wcs_2d)

{solarc_eclipse-0.5.0 → solarc_eclipse-0.6.0}/euvst_response/data_processing.py

@@ -16,7 +16,7 @@ from tqdm import tqdm
 from .utils import tqdm_joblib, distance_to_angle
 
 
-def load_atmosphere(pkl_file: str, metadata_line: str = None) -> NDCube:
+def load_atmosphere(pkl_file: str, metadata_line: str = None) -> tuple:
     """
     Load synthetic atmosphere cube from pickle file.
     
@@ -34,9 +34,10 @@ def load_atmosphere(pkl_file: str, metadata_line: str = None) -> NDCube:
         
     Returns
     -------
-    NDCube
-        Summed cube of all line intensities with proper WCS and metadata.
-        Uses the wavelength grid from the metadata_line.
+    tuple
+        (summed_cube, dynamic_mode_info) where:
+        - summed_cube: NDCube with summed line intensities
+        - dynamic_mode_info: dict with dynamic mode metadata (or None if static)
     """
     with open(pkl_file, "rb") as f:
         tmp = dill.load(f)
@@ -49,6 +50,9 @@ def load_atmosphere(pkl_file: str, metadata_line: str = None) -> NDCube:
     if not line_cubes:
         raise ValueError("No line cubes found in synthesis results")
     
+    # Get dynamic mode info if present
+    dynamic_mode_info = tmp.get("dynamic_mode", {"enabled": False})
+    
     # Get the line names
     line_names = list(line_cubes.keys())
     
@@ -96,7 +100,8 @@ def load_atmosphere(pkl_file: str, metadata_line: str = None) -> NDCube:
         "combined_lines": line_names,
         "n_lines": len(line_names),
         "metadata_source": metadata_line,
-        "summed_intensity": True
+        "summed_intensity": True,
+        "dynamic_mode": dynamic_mode_info,
     })
     
     # Create the summed cube using the reference cube's WCS
@@ -107,7 +112,7 @@ def load_atmosphere(pkl_file: str, metadata_line: str = None) -> NDCube:
         meta=combined_meta
     )
     
-    return summed_cube
+    return summed_cube, dynamic_mode_info
 
 
 def resample_ndcube_spectral_axis(ndcube, spectral_axis, output_resolution, ncpu=-1):
@@ -248,7 +253,7 @@ def rebin_atmosphere(cube_sim, det, sim, use_dask=False):
     sim : Simulation
         Simulation configuration
     use_dask : bool, optional
-        Whether to use Dask for automatic parallelization (default: True)
+        Whether to use Dask for automatic parallelization (default: False)
         
     Returns
     -------

{solarc_eclipse-0.5.0 → solarc_eclipse-0.6.0}/euvst_response/main.py

@@ -226,7 +226,51 @@ def main() -> None:
     # Load synthetic atmosphere cube
     print("Loading atmosphere...")
     print(f"Using '{reference_line}' as reference line for wavelength grid and metadata...")
-    cube_sim = load_atmosphere(synthesis_file, reference_line)
+    cube_sim, dynamic_mode_info = load_atmosphere(synthesis_file, reference_line)
+    
+    # Check for dynamic mode and validate parameters
+    is_dynamic_mode = dynamic_mode_info.get("enabled", False)
+    if is_dynamic_mode:
+        print("Synthesis was done in DYNAMIC MODE (time-varying atmosphere)")
+        print(f"  Slit width: {dynamic_mode_info['slit_width']}")
+        print(f"  Slit rest time: {dynamic_mode_info['slit_rest_time']}")
+        print(f"  Timesteps used: {len(dynamic_mode_info['available_timesteps'])}")
+        
+        # Check that exactly one slit width is provided for dynamic mode
+        synth_slit_width = dynamic_mode_info["slit_width"]
+        if len(slit_widths) != 1:
+            raise ValueError(
+                f"Dynamic mode synthesis requires exactly one slit width. "
+                f"Config specifies {len(slit_widths)} slit widths: {slit_widths}. "
+                f"Please provide only the synthesis slit width: {synth_slit_width}"
+            )
+        
+        # Validate that the single slit width matches synthesis
+        if not np.isclose(slit_widths[0].to_value(u.arcsec), synth_slit_width.to_value(u.arcsec), rtol=1e-6):
+            raise ValueError(
+                f"Slit width mismatch: synthesis was done with {synth_slit_width}, "
+                f"but config specifies {slit_widths[0]}. "
+                f"For dynamic mode synthesis, the slit width must match exactly: {synth_slit_width}"
+            )
+        
+        # Check that exactly one exposure time is provided for dynamic mode
+        synth_rest_time = dynamic_mode_info["slit_rest_time"]
+        if len(exposures) != 1:
+            raise ValueError(
+                f"Dynamic mode synthesis requires exactly one exposure time. "
+                f"Config specifies {len(exposures)} exposure times: {exposures}. "
+                f"Please provide only the synthesis slit rest time: {synth_rest_time}"
+            )
+        
+        # Validate that the single exposure time matches synthesis
+        if not np.isclose(exposures[0].to_value(u.s), synth_rest_time.to_value(u.s), rtol=1e-6):
+            raise ValueError(
+                f"Exposure time mismatch: synthesis was done with {synth_rest_time}, "
+                f"but config specifies {exposures[0]}. "
+                f"For dynamic mode synthesis, the exposure time must match exactly: {synth_rest_time}"
+            )
+        
+        print("  Dynamic mode parameters validated successfully!")
     
     # Set up base detector configuration (doesn't change with parameters)
     if instrument == "SWC":

{solarc_eclipse-0.5.0 → solarc_eclipse-0.6.0}/euvst_response/radiometric.py

@@ -243,8 +243,12 @@ def to_electrons(photon_counts: NDCube, t_exp: u.Quantity, det) -> NDCube:
 
     e = electron_counts * (u.electron / u.pixel)
 
-    # Add dark current and read noise (these still depend on exposure time)
-    e += det.dark_current * t_exp                                     # dark current
+    # Add dark current with Poisson noise
+    dark_current_mean = (det.dark_current * t_exp).to(u.electron / u.pixel).value
+    dark_current_poisson = np.random.poisson(dark_current_mean) * (u.electron / u.pixel)
+    e += dark_current_poisson
+    
+    # Add read noise
     e += np.random.normal(0, det.read_noise_rms.value,
                           photon_counts.data.shape) * (u.electron / u.pixel)  # read noise
 
@@ -279,7 +283,7 @@ def to_dn(electrons: NDCube, det) -> NDCube:
     dn_q = (electrons.data * electrons.unit) / det.gain_e_per_dn          # Quantity
     dn_q = dn_q.to(det.max_dn.unit)
 
-    dn_val = dn_q.value
+    dn_val = np.round(dn_q.value)                                         # round to nearest whole number
     dn_val[dn_val > det.max_dn.value] = det.max_dn.value                  # clip
 
     return NDCube(