Merge pull request #15 from SFB-ELAINE/add_license_header

Last touches before pre-release

leaddbsinterface/__init__.py

@@ -1 +1,4 @@
+# Copyright 2023, 2024 Julius Zimmermann
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 """Lead-DBS interface: generate input files for OSS-DBS."""

leaddbsinterface/convert_input_dictionary.py

@@ -1,3 +1,6 @@
+# Copyright 2023, 2024 Konstantin Butenko, Julius Zimmermann
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 import argparse
 import json
 

leaddbsinterface/default_settings.py

@@ -1,3 +1,7 @@
+# Copyright 2023, 2024 Konstantin Butenko, Jan Philipp Payonk, Julius Zimmermann
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+
 def load_default_for_lead(settings):
     """Add parameters that are not defined in Lead-DBS GUI.
 

leaddbsinterface/lead_settings.py

@@ -1,3 +1,6 @@
+# Copyright 2023, 2024 Konstantin Butenko, Jan Philipp Payonk, Julius Zimmermann
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 import os
 from dataclasses import asdict
 
@@ -186,8 +189,9 @@ def make_oss_settings(self, hemis_idx: int = 0, output_path: str = "") -> dict:
             "FailFlag": side,
             "TemplateSpace": self.get_est_in_temp(),
             "Solver": {},
-            "FEMOrder": 2 + int(self.get_calc_axon_act()),  # 2nd order is enough for stim volumes
-            "OutOfCore": bool(self.get_out_of_core())
+            # 2nd order enough for stim volumes
+            "FEMOrder": 2 + int(self.get_calc_axon_act()),
+            "OutOfCore": bool(self.get_out_of_core()),
         }
 
         # use actual signal parameters for PAM
@@ -332,10 +336,9 @@ def get_rot_z(self, index_side: int):
          Always recalculated from the other settings
         *IMPORTANT*: it is actually not native but scrf!
         """
-
         if self.get_est_in_temp():
             head_MNI = self.get_head_mni()[index_side, :]
-            y = self.get_y_mark_mni()[index_side, :] - head_MNI        
+            y = self.get_y_mark_mni()[index_side, :] - head_MNI
         else:
             head_nat = self.get_head_nat()[index_side, :]
             y = self.get_y_mark_nat()[index_side, :] - head_nat
@@ -394,7 +397,7 @@ def get_case_grnd(self):
     def get_calc_axon_act(self):
         """Calculate axon activation."""
         return self._get_num("calcAxonActivation")
-        
+
     def get_out_of_core(self):
         """Check if intermediate solution is unloaded."""
         return self._get_num("outOfCore")
@@ -611,7 +614,7 @@ def import_implantation_settings(self, hemis_idx, elec_dict=None):
             "DIXI D08-10AM": "DixiSEEG10",
             "DIXI D08-12AM": "DixiSEEG12",
             "DIXI D08-15AM": "DixiSEEG15",
-            "DIXI D08-18AM": "DixiSEEG18"
+            "DIXI D08-18AM": "DixiSEEG18",
         }
 
         for lead in electrode_names.keys():

ossdbs/__init__.py

@@ -1,3 +1,6 @@
+# Copyright 2023, 2024 Konstantin Butenko, Jan Philipp Payonk, Julius Zimmermann
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 """Open-source software for deep brain stimulation."""
 import logging
 

ossdbs/api.py

@@ -1,3 +1,7 @@
+# Copyright 2023, 2024 Konstantin Butenko, Shruthi Chakravarthy
+# Copyright 2023, 2024 Jan Philipp Payonk, Julius Zimmermann
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 import logging
 
 import numpy as np
@@ -362,7 +366,7 @@ def prepare_stimulation_signal(settings) -> FrequencyDomainSignal:
         fourier_coefficients = np.ones(len(frequencies))
         base_frequency = frequencies[0]
         cutoff_frequency = frequencies[0]
-        signal_length = 1
+        signal_length = len(frequencies)
     else:
         spectrum_mode = signal_settings["SpectrumMode"]
         if spectrum_mode == "OctaveBand":
@@ -424,6 +428,10 @@ def run_volume_conductor_model(settings, volume_conductor):
             _logger.info("Will export solution to VTK")
     else:
         export_vtk = False
+    if "ExportFrequency" in settings:
+        export_frequency = settings["ExportFrequency"]
+        if export_frequency is not None:
+            _logger.info(f"Set custom export frequency to {export_frequency}.")
 
     point_models = generate_point_models(settings)
 
@@ -433,6 +441,7 @@ def run_volume_conductor_model(settings, volume_conductor):
         point_models=point_models,
         activation_threshold=settings["ActivationThresholdVTA"],
         out_of_core=out_of_core,
+        export_frequency=export_frequency
     )
     return vcm_timings
 

ossdbs/dielectric_model/__init__.py

@@ -1,3 +1,6 @@
+# Copyright 2023, 2024 Johannes Reding, Julius Zimmermann
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 """Dielectric properties of required tissues."""
 from .colecole3 import ColeCole3Model, default_cole_cole3_parameters
 from .colecole4 import ColeCole4Model, ColeColeParameters, default_cole_cole4_parameters

ossdbs/dielectric_model/colecole3.py

@@ -1,3 +1,6 @@
+# Copyright 2023, 2024 Konstantin Butenko, Julius Zimmermann
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 import numpy as np
 
 from .colecole4 import ColeCole4Model, ColeColeParameters

ossdbs/dielectric_model/colecole4.py

@@ -1,3 +1,6 @@
+# Copyright 2023, 2024 Johannes Reding, Julius Zimmermann
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 from dataclasses import dataclass
 
 import numpy as np

ossdbs/dielectric_model/constant.py

@@ -1,3 +1,6 @@
+# Copyright 2023, 2024 Johannes Reding, Julius Zimmermann
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 from dataclasses import dataclass
 
 from scipy.constants import epsilon_0 as e0

ossdbs/dielectric_model/dielectric_model.py

@@ -1,3 +1,6 @@
+# Copyright 2023, 2024 Jan Philipp Payonk, Johannes Reding, Julius Zimmermann
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 from abc import ABC, abstractmethod
 
 import numpy as np

ossdbs/electrodes/__init__.py

@@ -1,3 +1,7 @@
+# Copyright 2023, 2024 Konstantin Butenko, Shruthi Chakravarthy
+# Copyright 2023, 2024 Jan Philipp Payonk, Johannes Reding, Julius Zimmermann
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 """Electrode models for DBS."""
 from .abbott_stjude import (
     AbbottStJudeActiveTipModel,

ossdbs/electrodes/abbott_stjude.py

@@ -1,3 +1,7 @@
+# Copyright 2023, 2024 Konstantin Butenko, Shruthi Chakravarthy
+# Copyright 2023, 2024 Jan Philipp Payonk, Julius Zimmermann
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 # Abbott/St Jude Active Tip 6142-6145
 from dataclasses import dataclass
 

ossdbs/electrodes/boston_scientific_vercise.py

@@ -1,3 +1,8 @@
+# Copyright 2023, 2024 Konstantin Butenko, Shruthi Chakravarthy
+# Copyright 2023, 2024 Jan Philipp Payonk, Johannes Reding
+# Copyright 2023, 2024 Tom Reincke, Julius Zimmermann
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 # Boston Scientific (Marlborough, Massachusetts, USA) vercise
 from dataclasses import dataclass
 

ossdbs/electrodes/defaults.py

@@ -1,3 +1,7 @@
+# Copyright 2023, 2024 Konstantin Butenko, Shruthi Chakravarthy
+# Copyright 2023, 2024 Jan Philipp Payonk, Julius Zimmermann
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 from .abbott_stjude import (
     AbbottStJudeActiveTipModel,
     AbbottStJudeActiveTipParameters,
@@ -383,13 +387,15 @@ def PINSMedicalL303(
 def DixiSEEG5(
     rotation: float = 0, direction: tuple = (0, 0, 1), position: tuple = (0, 0, 0)
 ):
+    """DixiSEEG5 electrode."""
     parameters = default_electrode_parameters["DixiSEEG5"]
     return DixiSEEGModel(parameters, rotation, direction, position)
 
 
 def DixiSEEG8(
     rotation: float = 0, direction: tuple = (0, 0, 1), position: tuple = (0, 0, 0)
 ):
+    """DixiSEEG8 electrode."""
     parameters = default_electrode_parameters["DixiSEEG8"]
     return DixiSEEGModel(parameters, rotation, direction, position)
 
@@ -405,6 +411,7 @@ def DixiSEEG10(
 def DixiSEEG12(
     rotation: float = 0, direction: tuple = (0, 0, 1), position: tuple = (0, 0, 0)
 ):
+    """DixiSEEG12 electrode."""
     parameters = default_electrode_parameters["DixiSEEG12"]
     return DixiSEEGModel(parameters, rotation, direction, position)
 
@@ -420,5 +427,6 @@ def DixiSEEG15(
 def DixiSEEG18(
     rotation: float = 0, direction: tuple = (0, 0, 1), position: tuple = (0, 0, 0)
 ):
+    """DixiSEEG18 electrode."""
     parameters = default_electrode_parameters["DixiSEEG18"]
     return DixiSEEGModel(parameters, rotation, direction, position)

ossdbs/electrodes/dixi_microtechniques.py

@@ -1,3 +1,6 @@
+# Copyright 2023, 2024 Jan Philipp Payonk, Julius Zimmermann
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 # Dixi Microtechniques SEEG
 from dataclasses import asdict, dataclass
 

ossdbs/electrodes/electrode_model_template.py

@@ -1,3 +1,7 @@
+# Copyright 2023, 2024 Konstantin Butenko, Shruthi Chakravarthy
+# Copyright 2023, 2024 Jan Philipp Payonk, Julius Zimmermann
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 import logging
 from abc import ABC, abstractmethod
 from dataclasses import asdict, dataclass
@@ -195,10 +199,15 @@ def export_electrode(self, output_path, brain_dict, n_electrode) -> None:
             )
             / 2
         )
+        try:
+            radius = self._parameters.lead_diameter / 2
+        except AttributeError:
+            radius = 1  # Set larger radius in case lead_diameter is not defined
+
         cylinder = netgen.occ.Cylinder(
             p=self._position,
             d=self._direction,
-            r=self._parameters.lead_diameter,
+            r=radius,
             h=height,
         )
 

ossdbs/electrodes/medtronic.py

@@ -1,3 +1,7 @@
+# Copyright 2023, 2024 Konstantin Butenko, Shruthi Chakravarthy
+# Copyright 2023, 2024 Jan Philipp Payonk, Julius Zimmermann
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 # Medtronic 3387
 from dataclasses import dataclass
 

ossdbs/electrodes/micro_probes.py

@@ -1,3 +1,7 @@
+# Copyright 2023, 2024 Konstantin Butenko, Shruthi Chakravarthy
+# Copyright 2023, 2024 Jan Philipp Payonk, Julius Zimmermann
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 from dataclasses import asdict, dataclass
 
 import netgen

ossdbs/electrodes/microelectrode.py

@@ -1,3 +1,6 @@
+# Copyright 2023, 2024 Jan Philipp Payonk, Julius Zimmermann
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 from dataclasses import dataclass
 
 import netgen

ossdbs/electrodes/neuro_pace.py

@@ -1,3 +1,6 @@
+# Copyright 2023, 2024 Jan Philipp Payonk, Julius Zimmermann
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 # Boston Scientific (Marlborough, Massachusetts, USA) vercise
 from dataclasses import dataclass
 
@@ -22,7 +25,7 @@ class NeuroPaceParameters:
 
     def get_center_first_contact(self) -> float:
         """Returns distance between electrode tip and center of first contact."""
-        return 0.5 * self.tip_length
+        return self.tip_length + 0.5 * self.contact_length
 
     def get_distance_l1_l4(self) -> float:
         """Returns distance between first level contact and fourth level contacts."""

ossdbs/electrodes/pins_medical.py

@@ -1,3 +1,7 @@
+# Copyright 2023, 2024 Konstantin Butenko, Shruthi Chakravarthy
+# Copyright 2023, 2024 Jan Philipp Payonk, Julius Zimmermann
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 # PINS Medical L301
 from dataclasses import dataclass
 

ossdbs/electrodes/utilities.py

@@ -1,3 +1,6 @@
+# Copyright 2023, 2024 Julius Zimmermann
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 import netgen.occ as occ
 
 

ossdbs/fem/__init__.py

@@ -1,3 +1,6 @@
+# Copyright 2023, 2024 Johannes Reding, Julius Zimmermann
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 """FEM part of OSS-DBS."""
 
 from .mesh import Mesh

ossdbs/fem/mesh.py

@@ -1,3 +1,6 @@
+# Copyright 2023, 2024 Johannes Reding, Julius Zimmermann
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 import os
 from typing import List
 

ossdbs/fem/preconditioner.py

@@ -1,3 +1,6 @@
+# Copyright 2023, 2024 Johannes Reding, Julius Zimmermann
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 import logging
 from abc import ABC, abstractmethod
 

ossdbs/fem/solver.py

@@ -1,3 +1,6 @@
+# Copyright 2023, 2024 Jan Philipp Payonk, Johannes Reding, Julius Zimmermann
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 from abc import ABC, abstractmethod
 
 import ngsolve

ossdbs/fem/volume_conductor/__init__.py

@@ -1,3 +1,6 @@
+# Copyright 2023, 2024 Johannes Reding, Julius Zimmermann
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 """Core module for volume-conductor model."""
 from .conductivity import ConductivityCF
 from .floating import VolumeConductorFloating

ossdbs/fem/volume_conductor/conductivity.py

@@ -1,3 +1,6 @@
+# Copyright 2023, 2024 Julius Zimmermann
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 import logging
 
 import ngsolve

ossdbs/fem/volume_conductor/floating.py

@@ -1,3 +1,6 @@
+# Copyright 2023, 2024 Jan Philipp Payonk, Johannes Reding, Julius Zimmermann
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 import logging
 
 import ngsolve

ossdbs/fem/volume_conductor/floating_impedance.py

@@ -1,3 +1,6 @@
+# Copyright 2023, 2024 Jan Philipp Payonk, Johannes Reding, Julius Zimmermann
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 import ngsolve
 
 from ossdbs.fem.solver import Solver
@@ -60,18 +63,14 @@ def compute_solution(self, frequency: float) -> ngsolve.comp.GridFunction:
         components = solution.components[1:]
         self._floating_values = {
             contact.name: component.vec[0]
-            for (contact, component) in zip(
-                self.contacts.floating, components
-            )
+            for (contact, component) in zip(self.contacts.floating, components)
         }
 
     def __create_space(self):
         boundaries = [contact.name for contact in self.contacts.active]
 
         h1_space = self.h1_space(boundaries=boundaries)
-        number_spaces = [
-            self.number_space() for _ in self.contacts.floating
-        ]
+        number_spaces = [self.number_space() for _ in self.contacts.floating]
         spaces = [h1_space, *number_spaces]
         finite_elements_space = ngsolve.FESpace(spaces=spaces)
         return ngsolve.CompressCompound(fespace=finite_elements_space)

ossdbs/fem/volume_conductor/nonfloating.py

@@ -1,3 +1,6 @@
+# Copyright 2023, 2024 Johannes Reding, Julius Zimmermann
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 import logging
 
 import ngsolve