Feature/whole body

README.md

@@ -68,6 +68,31 @@ python scripts/experiment.py --config-name config_prod params=params_test params
 python scripts/experiment.py --config-name config_prod params=params_test params/scanner=discovery params.do_simulation=0 params.scanner.scanner_radius=35
 ```
 
+# Whole Body Simulation
+
+You can perform whole body simulations following the same logic described in the last section. You may want to add `z_min` and `z_max` parameters to the `params` configuration group. Here you can find the configuration templates:
+
+- Example of [`global`](configs/config_test_wholebody.yaml) configuration.
+- Example of [`params`](configs/params/test_wholebody.yaml) configuration group.
+
+Then you can launch an experiment with:
+
+```
+python3.9 scripts/experiment_wholebody.py --config-name <your_config_name>
+```
+
+Even add `z_min` and `z_max` on the fly:
+
+```
+python3.9 scripts/experiment_wholebody.py --config-name <your_config_name> +params.z_min=29 +params.z_max=89
+```
+
+Or override them:
+
+```
+python3.9 scripts/experiment_wholebody.py --config-name <your_config_name> params.z_min=29 params.z_max=89
+```
+
 **NOTES ON USAGE**: 
 
 - Monte Carlo simulations usually take a lot of space. If you want to change the default Data and Results directories you can do so in the in the `global` configuration group or using [facebook-hydra](https://hydra.cc) CLI overriding syntax.
@@ -80,7 +105,7 @@ python scripts/experiment.py --config-name config_prod params=params_test params
 - Jesús Silva-Rodríguez
 - Pablo Aguiar
 - Aida Ninyerola-Baizan
-- Jeremiah Póveda
+- Jeremiah Poveda
 - Francisco Javier López-González
 - Nikos Efthimiou
 - Arnau Farre

configs/config_test_wholebody.yaml

@@ -0,0 +1,21 @@
+defaults:
+  - params: test_wholebody
+interactive_mode: 0
+dir_stir: ${root_path:root}/include/STIR/install
+dir_simset: ${root_path:root}/include/SimSET/2.9.2
+matlab_mcr_path: ""
+spm_path: ""
+dir_data_path: ${root_path:root}/Data
+dir_results_path: ${root_path:root}/Results
+stratification: "true"
+forced_detection: "true"
+forced_non_absortion: "true"
+acceptance_angle: 90.0
+positron_range: "true"
+isotope: "f18"
+non_colinearity: "true"
+minimum_energy: 350.0
+weight_window_ratio: 1.0
+point_source_voxels: "false"
+coherent_scatter_object: "false"
+coherent_scatter_detector: "false"

configs/params/test_wholebody.yaml

@@ -0,0 +1,26 @@
+defaults:
+ - scanner: discovery_st
+
+simulation_environment: 0
+sim_type: "SimSET"
+do_simulation: 1
+do_reconstruction: 1
+divisions: 2
+model_type: "cylindrical"
+patient_dirname: "test_image"
+act_map: "act.hdr"
+att_map: "att.hdr"
+output_dir: "test_image"
+center_slice: 7
+total_dose: 0.1
+simulation_time: 30
+sampling_photons: 0
+photons: 0
+add_randoms: 1
+phglistmode: 0
+detlistmode: 1
+maximumIteration: 1
+
+# Variables needed for whole body simulation
+z_min: 75
+z_max: 316

scripts/experiment_wholebody.py

@@ -0,0 +1,29 @@
+import sys
+import hydra
+import yaml
+from typing import Union, Mapping, Any
+from pathlib import Path
+from pyprojroot import here
+from omegaconf import DictConfig, OmegaConf
+
+sys.path.append(str(here()))
+import wholebody
+
+
+try:
+    OmegaConf.register_new_resolver("root_path", lambda s: str(here()))
+    OmegaConf.register_new_resolver("home_path", lambda s: str(Path.home()))
+except ValueError:
+    pass
+
+
+@hydra.main(version_base=None, config_path=str(here().joinpath("configs")), config_name="config_test_wholebody")
+def simulate(cfg: DictConfig) -> None:
+    OmegaConf.resolve(cfg)
+    wb = wholebody.WholebodySimulation(cfg)
+    wb.run()
+    cfg = OmegaConf.to_container(cfg)
+
+
+if __name__ == "__main__":
+    simulate()