Parameters
PRESTUS parameters
Parameters are organised in nested structs that map directly to YAML keys. PRESTUS uses a two-layer configuration system: config_default.yaml defines all parameters and their default values and should not be edited. A study-specific config (e.g. config_study.yaml) is loaded on top and only needs to specify values that differ from the defaults. Parameters can also be set or overridden programmatically in MATLAB before calling prestus_pipeline_start(parameters). Mandatory parameters have no meaningful default and must always be provided.
General
| Parameter |
Description |
Default |
Comments |
subject_id |
Subject identifier used for file naming and folder management. |
— |
Mandatory. Set before calling prestus_pipeline_start(parameters). |
platform |
Execution platform. |
'auto' |
auto / slurm / qsub / matlab |
Simulation type (simulation)
| Parameter |
Description |
Default |
Comments |
medium |
Simulation medium type. |
'layered' |
water / layered / phantom. Mandatory. |
code_type |
k-Wave backend. |
'matlab_gpu' |
matlab_cpu / matlab_gpu / cpp_cpu / cpp_gpu. See doc_backend.md. |
precision |
Computational precision for acoustic and thermal simulations. |
'single' |
single / double |
interactive |
Interactive mode with prompts and evolving plots. |
0 |
1 = yes, 0 = no. If 0, see overwrite_files. |
debug |
Verbose debug mode with additional intermediate outputs. |
1 |
1 = yes, 0 = no |
Data paths (path)
| Parameter |
Description |
Default |
Comments |
anat |
Absolute path to structural input data. |
— |
Mandatory |
sim |
Absolute path to simulation outputs. |
— |
Mandatory |
seg |
Absolute path to SimNIBS segmentations (m2m folders). |
— |
Mandatory |
localite |
Path to Localite neuronavigation output folder. |
— |
Optional |
t1_pattern |
T1 image path template relative to path.anat. |
'sub-%1$03d_T1w.nii*' |
Supports %03d-style subject ID substitution |
t2_pattern |
T2 image path template relative to path.anat. |
'sub-%1$03d_T2w.nii*' |
Optional |
| Parameter |
Description |
Comments |
simnibs_bin_path |
Absolute path to SimNIBS binaries. |
Mandatory for segmentation and MNI conversion |
matlab_bin_path |
Absolute path to MATLAB binary. |
Required for pseudoCT generation on HPC (e.g. /opt/matlab/R2024a/bin/matlab). Local execution falls back to matlabroot. |
fsl_bin_path |
Absolute path to FSL bin directory. |
Required for pseudoCT generation (e.g. /opt/fsl/bin). Prepended to PATH at runtime. |
ants_bin_path |
Absolute path to ANTs bin directory. |
Required for pseudoCT generation (e.g. /opt/ants/bin). Prepended to PATH at runtime. |
paths_to_add |
Paths to add with addpath(). |
[cell] e.g. {"path/to/x"} |
subpaths_to_add |
Paths to add recursively with addpath(genpath()). |
[cell]; relative to config file location |
I/O management (io)
| Parameter |
Description |
Default |
Comments |
output_affix |
Optional affix for output file names. |
'' |
Differentiates outputs for the same subject/transducer (e.g. different intensities or targets) |
overwrite_files |
File overwrite behaviour. |
'always' |
never / always / ask. Does NOT apply to SimNIBS segmentations. |
overwrite_simnibs |
Overwrite SimNIBS segmentation results? |
0 |
1 = yes, 0 = no |
save_matrices |
Save acoustic/thermal simulation outputs as .mat? |
0 |
1 = yes, 0 = no. Set to 0 for large batch runs to save disk space. |
save_source_matrices |
|
|
|
save_acoustic_matrices |
|
|
|
save_thermal_matrices |
|
|
|
save_source_matrices |
|
|
|
save_property_maps |
Save per-property NIfTIs to nii/properties/ (layered medium only)? |
0 |
|
save_MNI |
Save NIfTI outputs in MNI space in addition to native T1w space (requires SimNIBS m2m folder)? |
|
|
save_heatingvideo |
Save a video of incremental heating? |
0 |
1 = yes, 0 = no |
adopted_heatmap |
Path to an existing temperature heatmap NIfTI (heating_end.nii.gz) to use as the thermal starting point for a follow-up simulation. Set automatically by the sequential dispatcher; can be overridden manually. |
— |
Optional. Used for sequential multi-target runs. |
adopted_cem43 |
Path to an existing CEM43 heatmap NIfTI to accumulate heating across runs. Set automatically by the sequential dispatcher. |
— |
Optional. Used for sequential multi-target runs. |
adopted_cem43_iso |
Path to an existing ISO-variant CEM43 heatmap NIfTI (CEM43_iso_end.nii.gz) to accumulate across runs. Set automatically alongside adopted_cem43 by the sequential dispatcher. |
— |
Optional. Used for sequential multi-target runs. |
Runtime-derived (set by path_log_setup):
| Field |
Description |
dir_output |
Resolved per-subject output directory. Set from path.sim (+ subject subfolder). |
dir_nii |
NIfTI output subfolder (nii/). Created automatically. |
dir_nii_T1w |
Alias for dir_nii; space encoded in filename. |
dir_nii_MNI |
Alias for dir_nii; space encoded in filename. |
dir_img |
Image/figure output subfolder (img/). Used for all acoustic, thermal, and preprocessing figures. Created automatically. |
dir_tabular |
Directory for per-subject CSV results tables (same as dir_output). |
dir_reports |
Directory for simulation reports (same as dir_output). |
dir_logs |
Log subfolder (log/). Created automatically. |
dir_cache |
Cache subfolder (cache/). Created automatically. |
dir_debug |
Debug subfolder (debug/). Created when simulation.debug = 1. |
dir_debug_preproc |
Debug subfolder for preprocessing (debug/preproc/). |
dir_debug_medium |
Debug subfolder for medium setup (debug/medium/). |
dir_debug_source |
Debug subfolder for source setup (debug/source/). |
dir_pct |
Resolved subject pCT directory. Set from path.seg or path.pct. |
filename_table |
Path to the per-subject CSV results table. |
filename_kwave_source |
Path to cached k-Wave source .mat file. Set by source_sensor_setup. |
Pipeline modules (modules)
| Parameter |
Description |
Default |
Comments |
run_grid_setup |
Setup grid and run head processing. |
1 |
Mandatory for simulations. |
run_medium_setup |
Map medium acoustic properties. |
1 |
Mandatory for simulations. |
run_source_setup |
Set up acoustic source. |
1 |
Mandatory for simulations. |
run_acoustic_sims |
Run acoustic simulations. |
1 |
|
run_acoustic_analysis |
Run acoustic analysis. |
1 |
|
run_heating_sims |
Run thermal simulations. |
0 |
Enable after acoustic results are validated. |
run_thermal_analysis |
Run thermal analysis. |
1 |
|
run_nifti_creation |
Export results as NIfTI files. |
1 |
|
run_posthoc_water_sims |
Run free-water reference simulations after head simulations. |
1 |
|
generate_report |
Generate self-contained HTML simulation report. |
1 |
|
segmentation_only |
Stop after segmentation; skip grid setup and all simulations. |
0 |
Only has effect when simulation.medium = 'layered'. |
All flags: 1 = yes, 0 = no.
Transducer specification (transducer)
See doc_transducer.md.
All fields are mandatory and have no defaults — they must be set in the study config.
| Parameter |
Description |
Comments |
type |
Type of transducer array. |
annular / matrix. Mandatory. |
freq_hz |
Fundamental frequency [Hz]. |
Shared across all elements. |
trans_pos |
Transducer position (XYZ, T1 grid). |
|
focus_pos |
Focus (target) position (XYZ, T1 grid). |
|
focal_distance_ep |
Expected focal distance from transducer exit plane [mm]. |
Alternative to trans_pos/focus_pos. Either focal_distance_ep, focal_distance_bowl, or both must be set. |
focal_distance_bowl |
Expected focal distance from transducer bowl [mm]. |
|
focal_distance_offset |
Offset between transducer bowl and exit plane [mm]. |
Derived from curv_radius_mm − dist_geom_ep_mm. Not set by user. |
Annular Array Definition (annular)
| Parameter |
Description |
Comments |
elem_amp |
Pressure amplitude [Pa]. |
Must be calibrated. |
elem_phase_deg |
Source phase per element [degrees]. |
Must be calibrated. |
elem_n |
Number of transducer elements. |
|
elem_id_mm |
Inner diameter of each element [mm]. |
|
elem_od_mm |
Outer diameter of each element [mm]. |
|
curv_radius_mm |
Radius of curvature of the transducer bowl [mm]. |
|
dist_geom_ep_mm |
Distance from geometric focus to transducer plane [mm]. |
Calculated automatically from curv_radius_mm if not provided. |
depth_mm |
Transducer depth [mm]. |
Visualization only. |
Matrix Array Definition (matrix)
| Parameter |
Description |
Comments |
elem_amp |
Pressure amplitude [Pa]. |
Must be calibrated. |
depth_mm |
Transducer depth [mm]. |
Visualization only. |
steering |
Steering mode of the transducer. |
1D = axial only, 3D = volumetric steering. |
elem_shape |
Shape of individual elements. |
Options: rect, disc, bowl. Element area is defined using the rectangular dimensions and projected onto the selected shape. |
elem_height_mm |
Element height [mm]. |
Used to define equivalent area. |
elem_width_mm |
Element width [mm]. |
Used to define equivalent area. |
outer_diameter_mm |
Outer diameter of the transducer [mm]. |
Defines active aperture boundary. |
is_curved |
Whether the array has a curved surface. |
|
curv_radius_mm |
Radius of curvature (ROC) of the transducer bowl [mm]. |
Defines natural focus. Depends on is_curved. |
dist_geom_ep_mm |
Distance from geometric focus to transducer plane [mm]. |
Calculated automatically from curv_radius_mm and outer_diameter_mm if not provided. Depends on is_curved. |
is_clover_setup |
Enables Clover (multi-array) configuration. |
Replicates array into multiple leaves. |
matrix_shape.type |
Method used to define element positions. |
Options: define_here, extract_from_file. |
Matrix: Clover (clover)
| Parameter |
Description |
Comments |
n_leaves |
Number of Clover leaves. |
Maximum: 3. |
ROC_parent |
Radius of curvature of the combined Clover setup [mm]. |
Can differ from individual array ROC. |
Matrix: Grid distribution (define_here)
Warning: The define_here options are experimental and may contain bugs due to limited testing time.
| Parameter |
Description |
Comments |
grid_shape.type |
Grid distribution type. |
Options: rect, fibonacci, fermat. |
Rectangular Grid
| Parameter |
Description |
Comments |
elem_n_row |
Number of element rows. |
|
elem_n_col |
Number of element columns. |
|
elem_spacing_height_mm |
Spacing between elements in height direction [mm]. |
Edge-to-edge spacing. |
elem_spacing_width_mm |
Spacing between elements in width direction [mm]. |
Edge-to-edge spacing. |
sparsity_factor |
Fraction of active elements. |
Range: 0.1–1.0. |
Fibonacci Grid
| Parameter |
Description |
Comments |
elem_n |
Total number of elements. |
|
kerf_mm |
Minimum spacing between elements [mm]. |
|
Fermat Grid
| Parameter |
Description |
Comments |
elem_n |
Total number of elements. |
Uses spiral distribution. |
| Parameter |
Description |
Comments |
file_path |
Path to coordinate file. |
Must contain (x, y, z). |
start_row |
Row index where data starts. |
MATLAB may skip header row. |
start_col |
Column index where data starts. |
|
elem_n |
Number of elements to extract. |
Can exceed final active count. |
select_random_subset |
Enable random subset selection. |
Useful for sparse arrays. |
subset.random_seed |
Controls reproducibility of subset. |
true = new subset each run. |
subset.subset_n_elements |
Number of elements in subset. |
Must be ≤ total elements. |
project_on_new_ROC |
Project elements onto new curvature. |
May introduce unrealistic layouts. |
ROC_projection.new_ROC_mm |
New radius of curvature [mm]. |
Used when projection enabled. |
Transducer placement (placement)
See doc_placement.md.
placement.localite
See doc_placement_neuronav.md.
| Parameter |
Description |
Default |
Comments |
enabled |
Load transducer position from Localite neuronavigation files? |
0 |
1 = yes, 0 = no |
reference_distance_mm |
Distance from tracker to transducer exit plane [mm]. |
15 |
Corrects for varying tracker-to-exit-plane distances. Only applies when enabled=1. |
placement.heuristic
See doc_placement_heuristic.md.
| Parameter |
Description |
Default |
Comments |
save_localite_t1 |
Save Localite-aligned T1 output for header correction? |
false |
See doc_placement_heuristic.md. |
dist_close |
Distance from target considered sufficiently close [mm]. |
[] |
|
ear_radius |
Radius of the ear exclusion zone [mm]. |
35 |
|
left_ear_center |
Approximate coordinates for left ear [image voxels]. |
[] |
Optional |
right_ear_center |
Approximate coordinates for right ear [image voxels]. |
[] |
Optional |
criterion_intersection |
Max fraction of exit plane intersecting skin. |
0.05 |
5% |
criterion_skin_mean |
Mean distance of EP voxels from skin [quantile]. |
[] |
|
criterion_skull_mean |
Mean distance of EP voxels from skull [quantile]. |
[] |
|
criterion_skin_var |
Variance of EP voxel distance from skin [quantile]. |
[] |
|
criterion_skull_var |
Variance of EP voxel distance from skull [quantile]. |
[] |
|
expand_step |
Expansion step for skin intersection criterion. |
0.01 |
1% |
Simulation grid (grid)
| Parameter |
Description |
Default |
Comments |
resolution_mm |
Grid resolution (must be isotropic) [mm]. |
0.5 |
|
default_dims |
Requested grid dimensions [voxels per dimension]. |
[144, 144, 400] |
Directly sets the simulation grid for water and phantom media. For layered, the grid is determined by head preprocessing and this value is not used. |
axisymmetric |
Run axisymmetric 2D simulation (kspaceFirstOrderAS). |
0 |
1 = yes, 0 = no. See doc_simulations-acoustic.md. |
pml_size |
Perfectly Matched Layer (PML) size [voxels]. |
10 |
Absorbs waves at boundaries. Recommended for 3D. See k-Wave docs. |
source_ppw |
Points per wavelength (PPW) override. |
[] |
Calculated internally from resolution_mm and the medium's maximum sound speed if not set. Setting this overrides the internal calculation and fixes the number of spatial samples per wavelength used to derive the time step. |
min_ppw |
Minimum acceptable PPW at the fundamental frequency. |
6 |
Checked against the slowest medium sound speed (worst-case spatial sampling). A warning is raised if the actual PPW falls below this value, along with the maximum resolution_mm that would satisfy it. |
source_cfl |
Courant-Friedrichs-Lewy (CFL) fraction. |
0.15 |
Controls temporal resolution independently of spatial resolution. Given a fixed spatial step dx, the time step is dt = CFL × dx / c_max, where c_max is the fastest medium sound speed (typically skull at ~2800 m/s). Smaller CFL = finer temporal sampling and must remain below the stability limit. Set to 0.15 (half k-Wave's default of 0.3) for additional stability margin in heterogeneous skull simulations. Can be relaxed toward 0.3 to reduce runtime, but should be validated against checkStability output. |
source_limit_fraction |
Fraction of the stability limit to use for time step. |
0.9 |
After source setup, checkStability is called; if the CFL-derived dt exceeds the estimated limit, source setup reruns with dt = source_limit_fraction × dt_stability_limit. The final effective dt may therefore be smaller than CFL × dx / c_max. Set to 0 to disable. |
max_expand |
Maximum grid expansion for prime-number FFT optimisation [voxels]. |
40 |
|
use_kWaveArray |
Use the kWaveArray class for transducer modelling? |
1 |
1 = yes, 0 = no |
Segmentation (segmentation)
| Parameter |
Description |
Default |
Comments |
use_qform |
Force qform reorientation before charm segmentation? |
0 |
Set to 1 if charm reports a qform/sform mismatch error. |
debug |
Pass --debug to charm for verbose segmentation output? |
0 |
1 = yes, 0 = no |
Head model & segmentation preprocessing (headmodel)
See doc_preproc.md.
| Parameter |
Description |
Default |
Comments |
head_pad_mm |
Symmetric padding applied to the cropped head grid prior to transducer + PML setup [mm]. |
0 |
|
csf_expansion |
Dilation of the CSF brain mask into surrounding head regions [grid voxels]. |
40 |
|
smooth_method |
Mask smoothing filter type. |
'gaussian' |
gaussian / box / off |
smooth_threshold_skull |
Binarisation threshold for skull mask; higher = thinner mask. |
0.5 |
|
smooth_threshold_other |
Binarisation threshold for other masks; higher = thinner mask. |
0.5 |
|
smooth_fwhm_mm |
FWHM of smoothing kernel [mm]. |
1 |
|
smooth_properties |
Apply smoothing to acoustic property maps as well? |
false |
|
skull_fill_method |
Method for filling holes in the skull. |
'rubberwrap' |
rubberwrap / imclose |
skull_wrap_radius |
Rubber-wrap radius [grid voxels]. |
10 |
Larger = tighter wrap ignoring bigger dents. Recommended: 2–10. |
skull_wrap_visualize |
Visualize rubber-wrap result? |
0 |
1 = yes, 0 = no. Avoid on HPC. |
Pseudo-CT skull property mapping (pct)
See doc_pseudoCT.md.
| Parameter |
Description |
Default |
Comments |
enabled |
Use (pseudo-)CT to inform skull medium properties? |
0 |
1 = yes, 0 = no. When enabled, pseudoCT is generated automatically from the UTE image (specified via path.t2_pattern) if not already present in the SimNIBS folder. |
skull_mapping |
UTE→HU linear mapping algorithm used during pseudoCT generation. |
'kosciessa' |
kosciessa / miscouridou / carpino / wiesinger / treeby. See doc. |
debug |
Keep intermediate NIfTI files in the pseudoCT/ subfolder. |
1 |
1 = keep, 0 = delete after generation. |
mapping_density |
HU-to-density mapping algorithm. |
'k-plan' |
k-plan / k-wave / marsac / aubry / none. See doc. |
mapping_soundspeed |
HU-to-sound-speed mapping algorithm. |
'k-plan' |
k-plan / marsac / aubry / none. See doc. |
mapping_attenuation |
HU-to-attenuation mapping algorithm. |
'k-plan' |
k-plan / mueller / aubry / none. See doc. |
Tissue layers (layers)
See doc_preproc.md.
Maps tissue compartment names to their SimNIBS charm label indices. Compartments are modelled in listed order; any voxel label not assigned to a named compartment is treated as water. Charm label values are hardcoded in charm_seg_labels(). Layers can be removed or added.
| Layer |
Default charm labels |
Comments |
water |
[0, 3, 6, 9, 10] |
Baseline layer; all unassigned voxels are treated as water |
brain |
[1, 2] |
White matter + grey matter |
skin |
[5] |
|
skull |
[4] |
Single skull layer; used when cortical/trabecular split is not needed |
skull_cortical |
[7] |
Cortical bone; used in multi-layer skull model |
skull_trabecular |
[8] |
Trabecular bone; used in multi-layer skull model |
Tissue acoustic & thermal properties (medium_properties)
See doc_medium.md.
Each tissue compartment (water, brain, skin, skull, skull_trabecular, skull_cortical) carries the following fields:
| Field |
Description |
Units / Reference |
sound_speed |
Speed of sound. |
m/s — ITRUSST benchmarks |
density |
Density. |
kg/m³ — ITRUSST benchmarks |
alpha_coeff |
Attenuation coefficient. |
dB/cm/MHz |
alpha_power |
Attenuation power law exponent. |
— |
thermal_conductivity |
Thermal conductivity. |
W/m/°C — Tissue Properties DB |
specific_heat_capacity |
Specific heat capacity. |
J/kg/°C — Tissue Properties DB |
perfusion |
Perfusion / heat transfer rate. |
mL/min/kg — Tissue Properties DB |
absorption_fraction |
Fraction of attenuation converted to heat. |
[0–1] — Pinton et al., 2012 |
Sonication timing (timing)
See doc_simulations-thermal.md.
Protocol duration fields must be set for thermal simulations.
| Parameter |
Description |
Default |
Comments |
pd |
Pulse Duration (PD) [s]. |
NaN |
Duty cycle = pd/pri. |
pri |
Pulse Repetition Interval (PRI) [s]. |
NaN |
PRF = 1/pri. |
ptd |
Pulse Train Duration (PTD) [s]. |
NaN |
|
pt_timestep |
Modelling time step within a pulse train [s]. |
0.02 |
|
ptri |
Pulse Train Repetition Interval (PTRI) [s]. |
NaN |
OFF duration = ptri − ptd. |
ptrd |
Pulse Train Repetition Duration (PTRD) [s]. |
NaN |
|
post_ptri_dur |
Post-PTRI steady-state duration [s]. |
NaN |
|
post_pt_timestep |
Modelling time step following PT & PTRI [s]. |
1 |
|
equal_step_duration |
Equal step durations for on and off cycles? |
0 |
1 = yes, 0 = no |
Thermal settings (thermal)
See doc_simulations-thermal.md.
| Parameter |
Description |
Default |
Comments |
cem43_iso |
Calculate CEM43 per ISO norm (1) or kWaveDiffusion (0)? |
0 |
|
temp_0.{tissue} |
Initial temperature per tissue compartment [°C]. |
37 |
Tissues: water, skull, brain, skin, skull_trabecular, skull_cortical |
sensor_xy_halfsize |
Sensor window half-size for temperature recording [grid units]. |
100 |
|
record_t_at_every_step |
Record temperature at every time step for the full sensor window? |
0 |
Memory-intensive; disable if out-of-memory errors occur. |
Output analysis (analysis)
| Parameter |
Description |
Default |
Comments |
focus_area_radius |
Radius around the focus in which IPA is averaged for outputs [mm]. |
5 |
|
See doc_backend.md and doc_hpc.md.
| Parameter |
Description |
Default |
Comments |
gpu |
Request a specific GPU. |
'' |
e.g. "nvidia_a100-sxm4-40gb:1" |
partition |
Request a dedicated queue partition. |
'' |
|
reservation |
Request a reserved queue. |
'' |
|
wait_for_job |
Block MATLAB until the submitted HPC job completes? |
false |
|
timelimit |
Job time limit. |
'04:00:00' |
|
memorylimit |
Memory limit [GB]. |
20 |
|
ld_library_path |
LD_LIBRARY path for SimNIBS installation. |
'' |
Set if you see undefined symbol errors. e.g. /opt/gcc/7.2.0/lib64 |
job_prefix |
Prefix string for HPC job names. |
'PRESTUS' |
Overridden to 'TP' for transducer positioning jobs. |
max_wait_checks |
Maximum number of job status checks when wait_for_job = true. |
540 |
At 1 check/20 s, 540 ≈ 3 hours. |
Transducer calibration (calibration)
See doc_calibration.md.
A separate config_calibration.yaml applies for calibration workflows and is loaded as parameters.calibration.
| Parameter |
Description |
Comments |
path_input_axial |
Directory containing axial intensity profiles. |
|
path_input_phase |
Directory containing phase data. |
|
path_output |
Directory for saving free-water simulation results. |
|
path_output_profiles |
Directory for saving optimised profile data. |
|
filename_calibrated_CSV |
Filename of calibrated CSV data. |
Mandatory only when not generated within standalone script. |
save_in_calibration_folder |
Save in path_output (TRUE) or sim_path (FALSE). |
If TRUE, results are appended to existing calibration data. |
combinations |
Equipment combinations (must refer to entries in config_equipment.yaml). |
Multiple combinations can be specified. |
focal_depths_wrt_exit_plane |
List of focal depths to characterise [mm]. |
|
desired_intensities |
Desired free-water intensities [W/cm²]. |
|
add_FDO |
Append Focal Distance Offset (bowl-to-exit-plane distance)? |
Set to 1 if zero point in profiles reflects exit plane rather than bowl. |
axisymmetric2D |
Use axisymmetric 2D instead of default 3D free-water simulations? |
1 = yes, 0 = no |
force_kwavearray |
Force use of kWaveArray for free-water simulations? |
If 0, uses the setting in the default/study config. |
opt_method |
Optimisation method. |
FEXminimize (open source) / GlobalSearch (MATLAB Global Optimization Toolbox) |
opt_limits |
Distance limits for optimisation [mm]. |
|
opt_weights |
Weighting of original profile during fitting. |
1 = equal; >1 = Gaussian (narrower with larger values) |
opt_seed |
Random seed for optimisation. |
|
opt_use_initial_phases |
Use phases from transducer.annular.elem_phase_rad as the initial guess instead of random initialization. |
false (default); set to true when manufacturer-provided or previously calibrated phases are available. |
opt_upper_velocity |
Upper velocity in global search |
|
opt_phase_precession |
Constrain element phases during optimisation. |
false (default) = independent; 'linear' = strict ramp (phase_start + i * phase_step, 2 free params); 'monotonic' = ordered phases via cumulative non-negative increments (N params, monotonically constrained). |
opt_amp_validation |
Run free-water simulation to validate phases and amplitudes? |
'always' (default) / 'never' / 'initial' (only for the first target intensity) / 'final' (only for the final target intensity) |
skip_front_peak_mm |
Distance from profile start to ignore [mm]. |
Avoids near-field artefacts in peak/FWHM calculations. |