diff --git a/docs/electrode_files/Abbott_Active_Tip.rst b/docs/electrode_files/Abbott_Active_Tip.rst index edc3bd3..643ec62 100644 --- a/docs/electrode_files/Abbott_Active_Tip.rst +++ b/docs/electrode_files/Abbott_Active_Tip.rst @@ -2,53 +2,51 @@ Abbott St. Jude Active Tip ========================== -* Manufacturer: Abbott / St. Jude -* Products: Abbott / St. Jude 6142- 6145, Abbott / St. Jude 6146-6149 -* Models: 6142, 6143, 6144, 6145, 6146, 6147, 6148, 6149 +* **Manufacturer:** `Abbott `_ +* **Products:** Abbott / St. Jude 6142-6145, Abbott / St. Jude 6146-6149 +* **Models:** 6142, 6143, 6144, 6145, 6146, 6147, 6148, 6149 -Source documentation: `Source `_. -The source documentation also contains information -about :doc:`Abbot St. Jude Directed <./Abbott_StJude_Directed>`. +Source documentation: `Source `_. +The source documentation also contains information about :doc:`Abbott St. Jude Directed <./Abbott_StJude_Directed>`. ----------------------------------- St. Jude Traditional Lead 6142-6145 ----------------------------------- .. image:: electrode_pictures/St-Jude-6142-6145.svg - + :alt: Illustration of St. Jude Traditional Lead 6142-6145 ~~~~~~~~~~~~~~~~~~~~~~~ Default Parameters (mm) ~~~~~~~~~~~~~~~~~~~~~~~ - * tip_length = 3.0 - * contact_length = 1.5 - * contact_spacing = 1.5 - * lead_diameter = 1.4 - * total_length = 400.0 - - + +* tip_length = 3.0 +* contact_length = 1.5 +* contact_spacing = 1.5 +* lead_diameter = 1.4 +* total_length = 400.0 + ----------------------------------- St. Jude Traditional Lead 6146-6149 ----------------------------------- - -.. image:: electrode_pictures/St-Jude-6146-6149.svg +.. image:: electrode_pictures/St-Jude-6146-6149.svg + :alt: Illustration of St. Jude Traditional Lead 6146-6149 ~~~~~~~~~~~~~~~~~~~~~~~ Default Parameters (mm) ~~~~~~~~~~~~~~~~~~~~~~~ - * tip_length = 3.0 - * contact_length = 1.5 - * contact_spacing = 0.5 - * lead_diameter = 1.4 - * total_length = 400.0 -.. note:: The total length does not influence the computational domain that's why all the above electrodes are modeled at 400mm +* tip_length = 3.0 +* contact_length = 1.5 +* contact_spacing = 0.5 +* lead_diameter = 1.4 +* total_length = 400.0 ---- Code ---- .. autoclass:: ossdbs.electrodes.abbott_stjude.AbbottStJudeActiveTipModel - :members: - :show-inheritance: + :members: + :show-inheritance: diff --git a/docs/electrode_files/Abbott_StJude_Directed.rst b/docs/electrode_files/Abbott_StJude_Directed.rst index f5c44d9..6afa63b 100644 --- a/docs/electrode_files/Abbott_StJude_Directed.rst +++ b/docs/electrode_files/Abbott_StJude_Directed.rst @@ -1,53 +1,52 @@ ======================== -Abbott St. Jude Directed +Abbott St. Jude Directed ======================== -* Manufacturer: Abbott / St. Jude -* Products: Abbott / St. Jude 6172, Abbott / St. Jude 6173 -* Models: 6172, 6173 +* **Manufacturer:** `Abbott `_ +* **Products:** Abbott / St. Jude 6172, Abbott / St. Jude 6173 +* **Models:** 6172, 6173 -Source documentation: `Source `_. -The source documentation also contains information -about :doc:`Abbot St. Jude Active Tip <./Abbott_Active_Tip>` +Source documentation: `Source `_. +The source documentation also contains information about :doc:`Abbott St. Jude Active Tip <./Abbott_Active_Tip>`. ------------------------------------------------- St. Jude Medical Infinity ™ Directional Lead 6172 ------------------------------------------------- .. image:: electrode_pictures/Abott_St_Jude_6172.svg - + :alt: Illustration of Abbott St. Jude Infinity Directional Lead 6172 ~~~~~~~~~~~~~~~~~~~~~~~ Default Parameters (mm) ~~~~~~~~~~~~~~~~~~~~~~~ - * tip_length = 1.5 - * contact_length = 1.5 - * contact_spacing = 0.5 - * lead_diameter = 1.29 - * total_length = 400.0 - +* tip_length = 1.0 +* contact_length = 1.5 +* contact_spacing = 0.5 +* lead_diameter = 1.29 +* total_length = 400.0 ------------------------------------------------- St. Jude Medical Infinity ™ Directional Lead 6173 ------------------------------------------------- - -.. image:: electrode_pictures/Abott_St_Jude_6173.svg +.. image:: electrode_pictures/Abott_St_Jude_6173.svg + :alt: Illustration of Abbott St. Jude Infinity Directional Lead 6173 ~~~~~~~~~~~~~~~~~~~~~~~ Default Parameters (mm) ~~~~~~~~~~~~~~~~~~~~~~~ - * tip_length = 1.5 - * contact_length = 1.5 - * contact_spacing = 1.5 - * lead_diameter = 1.29 - * total_length = 400.0 + +* tip_length = 1.0 +* contact_length = 1.5 +* contact_spacing = 1.5 +* lead_diameter = 1.29 +* total_length = 400.0 ---- Code ---- .. autoclass:: ossdbs.electrodes.abbott_stjude.AbbottStJudeDirectedModel - :members: - :show-inheritance: + :members: + :show-inheritance: diff --git a/docs/electrode_files/Boston_Scientific_Cartesia.rst b/docs/electrode_files/Boston_Scientific_Cartesia.rst index 12a7a89..28feeba 100644 --- a/docs/electrode_files/Boston_Scientific_Cartesia.rst +++ b/docs/electrode_files/Boston_Scientific_Cartesia.rst @@ -2,62 +2,58 @@ Boston Scientific Cartesia ========================== -* Manufacturer: Boston Scientific -* Product: Boston Scientific Cartesia -* Serial name: CartesiaX, CartesiaHX +* **Manufacturer:** `Boston Scientific `_ +* **Product:** Boston Scientific Cartesia +* **Serial name:** CartesiaX, CartesiaHX -Source documentation: -`Source PDF `_. -`Source Webpage `_. +Source documentation: +`Source PDF `_ +`Source Webpage `_ - -The source documentation also contains information about -:doc:`Boston Scientific Directed Lead (DB-2202) <./Boston_Scientific_Vercise_Directed>`. +The source documentation also contains information about :doc:`Boston Scientific Directed Lead (DB-2202) <./Boston_Scientific_Vercise_Directed>`. --------------------------- Boston Scientific CartesiaX --------------------------- - ~~~~~~~~~~~~~~~~~~~~~~~ Default Parameters (mm) ~~~~~~~~~~~~~~~~~~~~~~~ - * tip_length = 1.1 - * contact_length = 1.5 - * contact_spacing = 0.5 - * lead_diameter = 1.3 - * total_length = 450.0 - * contacts_skipped = 5.0 +* tip_length = 1.1 +* contact_length = 1.5 +* contact_spacing = 0.5 +* lead_diameter = 1.3 +* total_length = 450.0 +* contacts_skipped = 5.0 ---- Code ---- .. autoclass:: ossdbs.electrodes.boston_scientific_cartesia.BostonScientificCartesiaXModel - :members: - :show-inheritance: + :members: + :show-inheritance: ---------------------------- Boston Scientific CartesiaHX ---------------------------- - ~~~~~~~~~~~~~~~~~~~~~~~ Default Parameters (mm) ~~~~~~~~~~~~~~~~~~~~~~~ - * tip_length = 1.1 - * contact_length = 1.5 - * contact_spacing = 0.5 - * lead_diameter = 1.3 - * total_length = 450.0 - * contacts_skipped = 7.0 +* tip_length = 1.1 +* contact_length = 1.5 +* contact_spacing = 0.5 +* lead_diameter = 1.3 +* total_length = 450.0 +* contacts_skipped = 7.0 ---- Code ---- .. autoclass:: ossdbs.electrodes.boston_scientific_cartesia.BostonScientificCartesiaHXModel - :members: - :show-inheritance: \ No newline at end of file + :members: + :show-inheritance: diff --git a/docs/electrode_files/Boston_Scientific_Vercise.rst b/docs/electrode_files/Boston_Scientific_Vercise.rst index 876fbad..4047fdd 100644 --- a/docs/electrode_files/Boston_Scientific_Vercise.rst +++ b/docs/electrode_files/Boston_Scientific_Vercise.rst @@ -2,23 +2,22 @@ Boston Scientific Vercise ========================= -* Manufacturer: Boston Scientific -* Product: Boston Scientific Standard Lead -* Serial name: DB-2201 +* **Manufacturer:** `Boston Scientific `_ +* **Product:** Boston Scientific Standard Lead +* **Serial name:** DB-2201 -Source documentation: -`Source PDF `_. -`Source Webpage `_. +Source documentation: +`Source PDF `_ +`Source Webpage `_ -The source documentation also contains information about -:doc:`Boston Scientific Directed Lead (DB-2202) <./Boston_Scientific_Vercise_Directed>`. +The source documentation also contains information about :doc:`Boston Scientific Directed Lead (DB-2202) <./Boston_Scientific_Vercise_Directed>`. --------------------------------------- Boston Scientific Standard Lead DB-2201 --------------------------------------- .. image:: electrode_pictures/Boston-Scientific-Vercise.svg - + :alt: Illustration of Boston Scientific Standard Lead DB-2201 ~~~~~~~~~~~~~~~~~~~~~~~ Default Parameters (mm) @@ -35,5 +34,5 @@ Code ---- .. autoclass:: ossdbs.electrodes.boston_scientific_vercise.BostonScientificVerciseModel - :members: - :show-inheritance: + :members: + :show-inheritance: diff --git a/docs/electrode_files/Boston_Scientific_Vercise_Directed.rst b/docs/electrode_files/Boston_Scientific_Vercise_Directed.rst index daf8e8b..966da3d 100644 --- a/docs/electrode_files/Boston_Scientific_Vercise_Directed.rst +++ b/docs/electrode_files/Boston_Scientific_Vercise_Directed.rst @@ -1,23 +1,23 @@ ================================== Boston Scientific Vercise Directed ================================== -* Manufacturer: Boston Scientific -* Product: Boston Scientific Directional Lead -* Serial name: DB-2202 -Source documentation: -`Source PDF `_. -`Source Webpage `_. +* **Manufacturer:** `Boston Scientific `_ +* **Product:** Boston Scientific Directional Lead +* **Serial name:** DB-2202 -The source documentation also contains information about -:doc:`Boston Scientific Standard Lead (DB-2201) <./Boston_Scientific_Vercise>`. +Source documentation: +`Source PDF `_ +`Source Webpage `_ + +The source documentation also contains information about :doc:`Boston Scientific Standard Lead (DB-2201) <./Boston_Scientific_Vercise>`. ------------------------------------------ Boston Scientific Directional Lead DB-2202 ------------------------------------------ .. image:: electrode_pictures/Boston-Scientific-Vercise-directed.svg - + :alt: Illustration of Boston Scientific Directional Lead DB-2202 ~~~~~~~~~~~~~~~~~~~~~~~ Default Parameters (mm) @@ -34,5 +34,5 @@ Code ---- .. autoclass:: ossdbs.electrodes.boston_scientific_vercise.BostonScientificVerciseDirectedModel - :members: - :show-inheritance: + :members: + :show-inheritance: diff --git a/docs/electrode_files/Dixi_Microtechniques.rst b/docs/electrode_files/Dixi_Microtechniques.rst index 7d06061..e511b64 100644 --- a/docs/electrode_files/Dixi_Microtechniques.rst +++ b/docs/electrode_files/Dixi_Microtechniques.rst @@ -2,63 +2,76 @@ Dixi Microtechniques ==================== -* Manufacturer: Dixi Microtechniques -* Products: SEEG multiple channel electrodes -* Models: 5 channels, 8 channels, 10 channels, 12 channels, 15 channels +* **Manufacturer:** `Dixi Microtechniques `_ +* **Products:** SEEG multiple channel electrodes +* **Models:** 5 channels, 8 channels, 10 channels, 12 channels, 15 channels, 18 channels -Source documentation: `Source `_. +Source documentation: `Source `_ ------------------------------------- Dixi Microtechniques SEEG 5 channels ------------------------------------- + .. image:: electrode_pictures/D08_05AM.svg + :alt: Illustration of Dixi Microtechniques SEEG 5-channel electrode ~~~~~~~~~~~~~~~~~~~~~~~ Default Parameters (mm) ~~~~~~~~~~~~~~~~~~~~~~~ - * tip_length=0.8, - * contact_length=2.0, - * contact_spacing=1.5, - * lead_diameter=0.8, - * total_length=400.0, + +* tip_length = 2.0 +* contact_length = 2.0 +* contact_spacing = 1.5 +* lead_diameter = 0.8 +* total_length = 400.0 ------------------------------------- Dixi Microtechniques SEEG 8 channels ------------------------------------- + .. image:: electrode_pictures/D08_08AM.svg + :alt: Illustration of Dixi Microtechniques SEEG 8-channel electrode ~~~~~~~~~~~~~~~~~~~~~~~ Default Parameters (mm) ~~~~~~~~~~~~~~~~~~~~~~~ - * tip_length=0.8, - * contact_length=2.0, - * contact_spacing=1.5, - * lead_diameter=0.8, - * total_length=400.0, -.. note:: The following electrodes with 10, 12 and 15 channels follow the same conventions. +* tip_length = 2.0 +* contact_length = 2.0 +* contact_spacing = 1.5 +* lead_diameter = 0.8 +* total_length = 400.0 + +.. note:: The following electrodes with 10, 12, 15 and 18 channels follow the same conventions. ------------------------------------- Dixi Microtechniques SEEG 10 channels ------------------------------------- +(No unique image or parameters provided) ------------------------------------- Dixi Microtechniques SEEG 12 channels ------------------------------------- +(No unique image or parameters provided) ------------------------------------- Dixi Microtechniques SEEG 15 channels ------------------------------------- +(No unique image or parameters provided) + +------------------------------------- +Dixi Microtechniques SEEG 18 channels +------------------------------------- -.. note:: The total length does not influence the computational domain that's why all the above electrodes are modeled at 400mm. +(No unique image or parameters provided) ---- Code ---- .. autoclass:: ossdbs.electrodes.dixi_microtechniques.DixiSEEGModel - :members: - :show-inheritance: + :members: + :show-inheritance: diff --git a/docs/electrode_files/Electrode_Examples.ipynb b/docs/electrode_files/Electrode_Examples.ipynb index 00eff31..48448c3 100644 --- a/docs/electrode_files/Electrode_Examples.ipynb +++ b/docs/electrode_files/Electrode_Examples.ipynb @@ -39,19 +39,22 @@ "metadata": {}, "outputs": [], "source": [ - "import ossdbs\n", - "from ngsolve import Draw, Mesh, TaskManager\n", - "from ngsolve.webgui import Draw\n", "import netgen.occ as occ\n", + "from ngsolve import Draw, Mesh, TaskManager\n", "\n", - "settings = {\"Electrodes\":\n", - " [{\"Name\": \"MedtronicSenSightB33015\",\n", - " \"Rotation[Degrees]\": 0,\n", - " \"Direction\": {\"x[mm]\": 0, \"y[mm]\": 0, \"z[mm]\": 1},\n", - " \"TipPosition\": {\"x[mm]\": 0, \"y[mm]\": 0, \"z[mm]\": 0},\n", - " \"EncapsulationLayer\": {\"Thickness[mm]\": 0.1}\n", - " }]\n", - " }" + "import ossdbs\n", + "\n", + "settings = {\n", + " \"Electrodes\": [\n", + " {\n", + " \"Name\": \"MedtronicSenSightB33015\",\n", + " \"Rotation[Degrees]\": 0,\n", + " \"Direction\": {\"x[mm]\": 0, \"y[mm]\": 0, \"z[mm]\": 1},\n", + " \"TipPosition\": {\"x[mm]\": 0, \"y[mm]\": 0, \"z[mm]\": 0},\n", + " \"EncapsulationLayer\": {\"Thickness[mm]\": 0.1},\n", + " }\n", + " ]\n", + "}" ] }, { @@ -72,7 +75,9 @@ "electrodes = ossdbs.generate_electrodes(settings)\n", "SenSight_settings = settings[\"Electrodes\"][0]\n", "SenSight = electrodes[0]\n", - "encapsulation_layer = SenSight.encapsulation_geometry(SenSight_settings[\"EncapsulationLayer\"][\"Thickness[mm]\"])\n", + "encapsulation_layer = SenSight.encapsulation_geometry(\n", + " SenSight_settings[\"EncapsulationLayer\"][\"Thickness[mm]\"]\n", + ")\n", "occgeo = occ.OCCGeometry(occ.Glue([SenSight.geometry, encapsulation_layer]))" ] }, @@ -122,27 +127,27 @@ "metadata": {}, "outputs": [], "source": [ - "import ossdbs\n", - "from ngsolve import Draw, Mesh, TaskManager\n", - "from ngsolve.webgui import Draw\n", - "import netgen.occ as occ\n", - "\n", - "parameters ={'exposed_wire': 0.12,\n", - " 'contact_radius': 0.1125,\n", - " 'lead_radius': 0.1175,\n", - " 'total_length': 13.3, \n", - " 'wire_radius' :0.09 }\n", + "parameters = {\n", + " \"exposed_wire\": 0.12,\n", + " \"contact_radius\": 0.1125,\n", + " \"lead_radius\": 0.1175,\n", + " \"total_length\": 13.3,\n", + " \"wire_radius\": 0.09,\n", + "}\n", "\n", "\n", - "settings = {\"Electrodes\":\n", - " [{\"Name\": \"MicroProbesRodentElectrodeCustom\",\n", - " 'CustomParameters': parameters,\n", - " \"Rotation[Degrees]\": 0,\n", - " \"Direction\": {\"x[mm]\": 0, \"y[mm]\": 0, \"z[mm]\": 1},\n", - " \"TipPosition\": {\"x[mm]\": 0, \"y[mm]\": 0, \"z[mm]\": 0},\n", - " \"EncapsulationLayer\": {\"Thickness[mm]\": 0.1}\n", - " }]\n", - " }" + "settings = {\n", + " \"Electrodes\": [\n", + " {\n", + " \"Name\": \"MicroProbesRodentElectrodeCustom\",\n", + " \"CustomParameters\": parameters,\n", + " \"Rotation[Degrees]\": 0,\n", + " \"Direction\": {\"x[mm]\": 0, \"y[mm]\": 0, \"z[mm]\": 1},\n", + " \"TipPosition\": {\"x[mm]\": 0, \"y[mm]\": 0, \"z[mm]\": 0},\n", + " \"EncapsulationLayer\": {\"Thickness[mm]\": 0.1},\n", + " }\n", + " ]\n", + "}" ] }, { @@ -163,7 +168,9 @@ "electrodes = ossdbs.generate_electrodes(settings)\n", "electrode_settings = settings[\"Electrodes\"][0]\n", "electrode = electrodes[0]\n", - "encap = electrode.encapsulation_geometry(electrode_settings[\"EncapsulationLayer\"][\"Thickness[mm]\"])\n", + "encap = electrode.encapsulation_geometry(\n", + " electrode_settings[\"EncapsulationLayer\"][\"Thickness[mm]\"]\n", + ")\n", "occgeo = occ.OCCGeometry(occ.Glue([electrode.geometry, encap]))\n", "with TaskManager():\n", " mesh = Mesh(occgeo.GenerateMesh())\n", @@ -186,31 +193,32 @@ "metadata": {}, "outputs": [], "source": [ - "import ossdbs\n", - "from ngsolve import Draw, Mesh, TaskManager\n", - "from ngsolve.webgui import Draw\n", - "import netgen.occ as occ\n", - "\n", - "settings = {\"Electrodes\":\n", - " [{\"Name\": \"BostonScientificVercise\",\n", - " \"Rotation[Degrees]\": 0,\n", - " \"Direction\": {\"x[mm]\": 0, \"y[mm]\": 0, \"z[mm]\": 1},\n", - " \"TipPosition\": {\"x[mm]\": 0, \"y[mm]\": 0, \"z[mm]\": 0},\n", - " \"EncapsulationLayer\": {\"Thickness[mm]\": 0.1}\n", - " },\n", - " {\"Name\": \"BostonScientificVercise\",\n", - " \"Rotation[Degrees]\": 0,\n", - " \"Direction\": {\"x[mm]\": 0, \"y[mm]\": 0, \"z[mm]\": 1},\n", - " \"TipPosition\": {\"x[mm]\": 30, \"y[mm]\": 0, \"z[mm]\": 0},\n", - " \"EncapsulationLayer\": {\"Thickness[mm]\": 0.5}\n", - " }]\n", - " }\n", + "settings = {\n", + " \"Electrodes\": [\n", + " {\n", + " \"Name\": \"BostonScientificVercise\",\n", + " \"Rotation[Degrees]\": 0,\n", + " \"Direction\": {\"x[mm]\": 0, \"y[mm]\": 0, \"z[mm]\": 1},\n", + " \"TipPosition\": {\"x[mm]\": 0, \"y[mm]\": 0, \"z[mm]\": 0},\n", + " \"EncapsulationLayer\": {\"Thickness[mm]\": 0.1},\n", + " },\n", + " {\n", + " \"Name\": \"BostonScientificVercise\",\n", + " \"Rotation[Degrees]\": 0,\n", + " \"Direction\": {\"x[mm]\": 0, \"y[mm]\": 0, \"z[mm]\": 1},\n", + " \"TipPosition\": {\"x[mm]\": 30, \"y[mm]\": 0, \"z[mm]\": 0},\n", + " \"EncapsulationLayer\": {\"Thickness[mm]\": 0.5},\n", + " },\n", + " ]\n", + "}\n", "\n", "electrodes = ossdbs.generate_electrodes(settings)\n", "geo = None\n", "for idx, vercise_settings in enumerate(settings[\"Electrodes\"]):\n", " vercise = electrodes[idx]\n", - " encap = vercise.encapsulation_geometry(vercise_settings[\"EncapsulationLayer\"][\"Thickness[mm]\"])\n", + " encap = vercise.encapsulation_geometry(\n", + " vercise_settings[\"EncapsulationLayer\"][\"Thickness[mm]\"]\n", + " )\n", " if geo is None:\n", " geo = occ.Glue([vercise.geometry, encap])\n", " else:\n", @@ -226,7 +234,7 @@ "metadata": { "celltoolbar": "Slideshow", "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Python 3", "language": "python", "name": "python3" }, @@ -240,7 +248,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.6" + "version": "3.9.10" } }, "nbformat": 4, diff --git a/docs/electrode_files/Medtronic_DBS.rst b/docs/electrode_files/Medtronic_DBS.rst index 5f0f8fe..cfec710 100644 --- a/docs/electrode_files/Medtronic_DBS.rst +++ b/docs/electrode_files/Medtronic_DBS.rst @@ -2,68 +2,68 @@ Medtronic DBS ============= +* **Manufacturer:** `Medtronic `_ +* **Products:** Medtronic DBS 3387, Medtronic DBS 3389, Medtronic DBS 3391 +* **Models:** 3387, 3389, 3391 -* Manufacturer: Medtronic -* Products: Medtronic DBS 3387, Medtronic DBS 3389, Medtronic DBS 3391 -* Models: 3387, 3389, 3391 - -Source documentation for models 3387 and 3389: `Source 3387/3389 `_. -Source documentation for model 3391: `Source 3391 `_. +Source documentation for models 3387 and 3389: `Source 3387/3389 `_ +Source documentation for model 3391: `Source 3391 `_ ------------------ Medtronic DBS 3387 ------------------ .. image:: electrode_pictures/Medtronic-3387.svg + :alt: Illustration of Medtronic DBS 3387 electrode ~~~~~~~~~~~~~~~~~~~~~~~ Default Parameters (mm) ~~~~~~~~~~~~~~~~~~~~~~~ - * tip_length = 1.5 - * contact_length = 1.5 - * contact_spacing = 1.5 - * lead_diameter = 1.27 - * total_length = 400.0 - +* tip_length = 1.5 +* contact_length = 1.5 +* contact_spacing = 1.5 +* lead_diameter = 1.27 +* total_length = 400.0 + ------------------ Medtronic DBS 3389 ------------------ .. image:: electrode_pictures/Medtronic-3389.svg + :alt: Illustration of Medtronic DBS 3389 electrode ~~~~~~~~~~~~~~~~~~~~~~~ Default Parameters (mm) ~~~~~~~~~~~~~~~~~~~~~~~ - * tip_length = 1.5 - * contact_length = 1.5 - * contact_spacing = 0.5 - * lead_diameter = 1.27 - * total_length = 400.0 +* tip_length = 1.5 +* contact_length = 1.5 +* contact_spacing = 0.5 +* lead_diameter = 1.27 +* total_length = 400.0 ------------------------- +------------------ Medtronic DBS 3391 ------------------------- +------------------ .. image:: electrode_pictures/Medtronic-3391.svg + :alt: Illustration of Medtronic DBS 3391 electrode ~~~~~~~~~~~~~~~~~~~~~~~ Default Parameters (mm) ~~~~~~~~~~~~~~~~~~~~~~~ - * tip_length = 1.5 - * contact_length = 3.0 - * contact_spacing = 4.0 - * lead_diameter = 1.27 - * total_length = 400.0 - -.. note:: The total length does not influence the computational domain that's why all the above electrodes are modeled at 400mm +* tip_length = 1.5 +* contact_length = 3.0 +* contact_spacing = 4.0 +* lead_diameter = 1.27 +* total_length = 400.0 ---- Code ---- .. autoclass:: ossdbs.electrodes.medtronic.MedtronicModel - :members: - :show-inheritance: + :members: + :show-inheritance: diff --git a/docs/electrode_files/Medtronic_SenSight.rst b/docs/electrode_files/Medtronic_SenSight.rst index 20d9088..2823d84 100644 --- a/docs/electrode_files/Medtronic_SenSight.rst +++ b/docs/electrode_files/Medtronic_SenSight.rst @@ -2,51 +2,50 @@ Medtronic SenSight ================== +* **Manufacturer:** `Medtronic `_ +* **Products:** Medtronic B33005, Medtronic B33015 +* **Models:** B33005, B33015 -* Manufacturer: Medtronic -* Products: Medtronic B33005, Medtronic B33015 -* Models: B33005, B33015 - -Source documentation: `Source `_. +Source documentation: `Medtronic SenSight Lead Documentation `_ -------------------------------------------- -Medtronic B33005 SenSight ™ directional lead +Medtronic B33005 SenSight ™ Directional Lead -------------------------------------------- .. image:: electrode_pictures/SensightB33005.svg - + :alt: Illustration of Medtronic B33005 SenSight Directional Lead ~~~~~~~~~~~~~~~~~~~~~~~ Default Parameters (mm) ~~~~~~~~~~~~~~~~~~~~~~~ - * tip_length = 1.0 - * contact_length = 1.5 - * contact_spacing = 0.5 - * lead_diameter = 1.36 - * total_length = 330 +* tip_length = 0.9 +* contact_length = 1.5 +* contact_spacing = 0.5 +* lead_diameter = 1.36 +* total_length = 330 -------------------------------------------- -Medtronic B33015 SenSight ™ directional lead +Medtronic B33015 SenSight ™ Directional Lead -------------------------------------------- .. image:: electrode_pictures/SensightB33015.svg - + :alt: Illustration of Medtronic B33015 SenSight Directional Lead ~~~~~~~~~~~~~~~~~~~~~~~ Default Parameters (mm) ~~~~~~~~~~~~~~~~~~~~~~~ - * tip_length = 1.0 - * contact_length = 1.5 - * contact_spacing = 1.5 - * lead_diameter = 1.36 - * total_length = 330 - +* tip_length = 0.9 +* contact_length = 1.5 +* contact_spacing = 1.5 +* lead_diameter = 1.36 +* total_length = 330 + ---- Code ---- .. autoclass:: ossdbs.electrodes.medtronic.MedtronicSenSightModel - :members: - :show-inheritance: + :members: + :show-inheritance: diff --git a/docs/electrode_files/MicroElectrode.rst b/docs/electrode_files/MicroElectrode.rst index e0b92cd..97057d0 100644 --- a/docs/electrode_files/MicroElectrode.rst +++ b/docs/electrode_files/MicroElectrode.rst @@ -1,32 +1,30 @@ -========================== +========================= Alpha Omega MicroElectrode -========================== +========================= +* **Manufacturer:** `Alpha Omega `_ +* **Products:** MicroElectrode +* **Models:** MicroElectrode -* Manufacturer: Alpha Omega -* Products: MicroElectrode -* Models: MicroElectrode - -Source documentation: `Source `_. +Source documentation: `Source `_ .. image:: electrode_pictures/AlphaOmega_MicroElectrode.svg - + :alt: Illustration of Alpha Omega MicroElectrode ~~~~~~~~~~~~~~~~~~~~~~~ Default Parameters (mm) ~~~~~~~~~~~~~~~~~~~~~~~ - * tip_length=1.0, - * tip_diameter=0.7, - * contact_length=1.0, - * lead_diameter=1.0, - * total_length=200.0, -.. note:: The total length does not affect the computational domain, so the above electrode is modelled with a length of 200mm. +* tip_length = 1.0 +* tip_diameter = 0.7 +* contact_length = 1.0 +* lead_diameter = 1.0 +* total_length = 200.0 ---- Code ---- .. autoclass:: ossdbs.electrodes.microelectrode.MicroElectrodeModel - :members: - :show-inheritance: + :members: + :show-inheritance: diff --git a/docs/electrode_files/Micro_Probes_Custom_Rodent.rst b/docs/electrode_files/Micro_Probes_Custom_Rodent.rst index 1f1ea55..5fd06f2 100644 --- a/docs/electrode_files/Micro_Probes_Custom_Rodent.rst +++ b/docs/electrode_files/Micro_Probes_Custom_Rodent.rst @@ -2,32 +2,31 @@ MicroProbes Custom Rodent ========================= +* **Manufacturer:** `MicroProbes for Life Science `_ +* **Products:** MicroProbes Custom Electrode +* **Models:** Custom -* Manufacturer: TODO -* Products: MicroProbes Custom Electrode -* Models: TODO +Source documentation: `MicroProbes for Life Science `_ -Source documentation: `TODO `_. - .. image:: electrode_pictures/MicroProbesCustomRodent.svg - + :alt: Illustration of MicroProbes Custom Rodent electrode ~~~~~~~~~~~~~~~~~~~~~~~ Default Parameters (mm) ~~~~~~~~~~~~~~~~~~~~~~~ - * exposed_wire = 0 - * contact_radius = 0.1125 - * lead_radius = 0.1175 - * total_length = 13.3 - * wire_radius = 0 +* exposed_wire = 0 +* contact_radius = 0.1125 +* lead_radius = 0.1175 +* total_length = 13.3 +* wire_radius = 0 -.. note:: The exposed_wire parameter is used to represent any exposed wire between the tip and the lead. The default parameters assume there is no exposed wire and is therefore set to zero. +.. note:: The `exposed_wire` parameter is used to represent any exposed wire between the tip and the lead. The default parameters assume there is no exposed wire and is therefore set to zero. ---- Code ---- .. autoclass:: ossdbs.electrodes.micro_probes.MicroProbesRodentElectrodeModel - :members: - :show-inheritance: + :members: + :show-inheritance: diff --git a/docs/electrode_files/Micro_Probes_Snex100.rst b/docs/electrode_files/Micro_Probes_Snex100.rst index 096ca83..e1758f7 100644 --- a/docs/electrode_files/Micro_Probes_Snex100.rst +++ b/docs/electrode_files/Micro_Probes_Snex100.rst @@ -1,38 +1,38 @@ ===================== -Microprobes SNEX 100 +MicroProbes SNEX 100 ===================== -* Manufacturer: MicroProbes for Life Science -* Products: Microprobes SNEX 100 -* Model: SNEX 100 -* Serial Number: CEAX-200-SS +* **Manufacturer:** `MicroProbes for Life Science `_ +* **Products:** MicroProbes SNEX 100 +* **Model:** SNEX 100 +* **Serial Number:** CEAX-200-SS -Source documentation: - * `Source `_. - * `Source 2 `_. +Source documentation: +* `Source `_ +* `Source 2 `_ - -This model were designed to replicated the peter-rhodes-produced SNEX-100 concentric. +This model was designed to replicate the Peter-Rhodes-produced SNEX-100 concentric electrode. .. image:: electrode_pictures/SNEX-100.svg + :alt: Illustration of MicroProbes SNEX 100 electrode ~~~~~~~~~~~~~~~~~~~~~~~ Default Parameters (mm) ~~~~~~~~~~~~~~~~~~~~~~~ - * core_electrode_length = 0.25 - * core_electrode_diameter = 0.1 - * core_tubing_length = 0.5 - * core_tubing_diameter = 0.140 - * outer_electrode_length = 0.25 - * outer_electrode_diameter = 0.330 - * outer_tubing_diameter = 0.411 - * total_length = 100.0 +* core_electrode_length = 0.25 +* core_electrode_diameter = 0.1 +* core_tubing_length = 0.5 +* core_tubing_diameter = 0.140 +* outer_electrode_length = 0.25 +* outer_electrode_diameter = 0.330 +* outer_tubing_diameter = 0.411 +* total_length = 100.0 ---- Code ---- .. autoclass:: ossdbs.electrodes.micro_probes.MicroProbesSNEX100Model - :members: - :show-inheritance: + :members: + :show-inheritance: diff --git a/docs/electrode_files/Neuro_Pace.rst b/docs/electrode_files/Neuro_Pace.rst index 40b3837..f6013c8 100644 --- a/docs/electrode_files/Neuro_Pace.rst +++ b/docs/electrode_files/Neuro_Pace.rst @@ -2,53 +2,51 @@ Neuro Pace ========== +* **Manufacturer:** `NeuroPace, Inc. `_ +* **Products:** NeuroPace DL-344 +* **Models:** 3.5, 10 -* Manufacturer: NeuroPace, Inc. -* Products: NeuroPace DL-344, NeuroPace DL-344 -* Models: 3.5, 10 - -Source documentation for model 3.5: `Source DL-344-3.5 `_. -Source documentation for model 10: `Source DL-344-10 `_. +Source documentation for model 3.5: `Source DL-344-3.5 `_ +Source documentation for model 10: `Source DL-344-10 `_ --------------------- Neuro Pace DL-344-3.5 --------------------- .. image:: electrode_pictures/NeuroPace_DL-344-3_5.svg + :alt: Illustration of Neuro Pace DL-344-3.5 electrode ~~~~~~~~~~~~~~~~~~~~~~~ Default Parameters (mm) ~~~~~~~~~~~~~~~~~~~~~~~ - * tip_length = 1.1 - * contact_length = 2.0 - * contact_spacing = 1.5 - * lead_diameter = 1.27 - * total_length = 400.0 - +* tip_length = 1.1 +* contact_length = 2.0 +* contact_spacing = 1.5 +* lead_diameter = 1.27 +* total_length = 400.0 + -------------------- Neuro Pace DL-344-10 -------------------- .. image:: electrode_pictures/NeuroPace_DL-344-10.svg + :alt: Illustration of Neuro Pace DL-344-10 electrode ~~~~~~~~~~~~~~~~~~~~~~~ Default Parameters (mm) ~~~~~~~~~~~~~~~~~~~~~~~ - * tip_length = 1.1 - * contact_length = 2.0 - * contact_spacing = 8.0 - * lead_diameter = 1.27 - * total_length = 400.0 - - -.. note:: The total length does not influence the computational domain that's why all the above electrodes are modeled at 400mm +* tip_length = 1.1 +* contact_length = 2.0 +* contact_spacing = 8.0 +* lead_diameter = 1.27 +* total_length = 400.0 ---- Code ---- .. autoclass:: ossdbs.electrodes.neuro_pace.NeuroPaceModel - :members: - :show-inheritance: + :members: + :show-inheritance: diff --git a/docs/electrode_files/PMTsEEG.rst b/docs/electrode_files/PMTsEEG.rst new file mode 100644 index 0000000..f6115b0 --- /dev/null +++ b/docs/electrode_files/PMTsEEG.rst @@ -0,0 +1,87 @@ +=============== +PMT Corporation +=============== + +* **Manufacturer:** `PMT Corporation `_ +* **Products:** PMT sEEG multiple channel electrodes +* **Models:** 2102_08, 2102_10, 2102_12, 2102_14, 2102_16 + +Source documentation: `Source `_ + +--------------------- +PMT SEEG 2102_08 +--------------------- + +~~~~~~~~~~~~~~~~~~~~~~~ +Default Parameters (mm) +~~~~~~~~~~~~~~~~~~~~~~~ + +* tip_length = 0.8 +* contact_length = 2.0 +* contact_spacing = 1.5 +* lead_diameter = 0.8 +* total_length = 400.0 +* n_contacts = 8 + +--------------------- +PMT SEEG 2102_10 +--------------------- + +~~~~~~~~~~~~~~~~~~~~~~~ +Default Parameters (mm) +~~~~~~~~~~~~~~~~~~~~~~~ + +* tip_length = 0.8 +* contact_length = 2.0 +* contact_spacing = 1.5 +* lead_diameter = 0.8 +* total_length = 400.0 +* n_contacts = 10 + +--------------------- +PMT SEEG 2102_12 +--------------------- + +~~~~~~~~~~~~~~~~~~~~~~~ +Default Parameters (mm) +~~~~~~~~~~~~~~~~~~~~~~~ + +* tip_length = 0.8 +* contact_length = 2.0 +* contact_spacing = 1.5 +* lead_diameter = 0.8 +* total_length = 400.0 +* n_contacts = 12 + +--------------------- +PMT SEEG 2102_14 +--------------------- + +~~~~~~~~~~~~~~~~~~~~~~~ +Default Parameters (mm) +~~~~~~~~~~~~~~~~~~~~~~~ + +* tip_length = 0.8 +* contact_length = 2.0 +* contact_spacing = 1.5 +* lead_diameter = 0.8 +* total_length = 400.0 +* n_contacts = 14 + +--------------------- +PMT SEEG 2102_16 +--------------------- + +~~~~~~~~~~~~~~~~~~~~~~~ +Default Parameters (mm) +~~~~~~~~~~~~~~~~~~~~~~~ + +* tip_length = 0.8 +* contact_length = 2.0 +* contact_spacing = 1.5 +* lead_diameter = 0.8 +* total_length = 400.0 +* n_contacts = 16 + + +.. note:: These models share the same structure as Dixi Microtechniques SEEG electrodes. Refer to the Dixi Microtechniques page for the shared implementation details. \ No newline at end of file diff --git a/docs/electrode_files/Pins_Medical.rst b/docs/electrode_files/Pins_Medical.rst index bb52dc1..bf9d4ab 100644 --- a/docs/electrode_files/Pins_Medical.rst +++ b/docs/electrode_files/Pins_Medical.rst @@ -2,70 +2,69 @@ PINS Medical ============ -* Manufacturer: PINS -* Products: PINS Medical L301, PINS Medical L302, PINS Medical L303 -* Models: L301, L302, L303 +* **Manufacturer:** `PINS `_ +* **Products:** PINS Medical L301, PINS Medical L302, PINS Medical L303 +* **Models:** L301, L302, L303 -This electrode model for L301 and L302 is created after the information -given on the following website. +This electrode model for L301 and L302 is created based on the information provided on the following website: -Source: `Website `_. +Source: `Website `_ ----------------- PINS Medical L301 ----------------- .. image:: electrode_pictures/L301.svg - + :alt: Illustration of PINS Medical L301 electrode ~~~~~~~~~~~~~~~~~~~~~~~ Default Parameters (mm) ~~~~~~~~~~~~~~~~~~~~~~~ - * tip_length = 1.5 - * contact_length = 1.5 - * contact_spacing = 1.5 - * lead_diameter = 1.3 - * total_length = 400.0 +* tip_length = 1.5 +* contact_length = 1.5 +* contact_spacing = 1.5 +* lead_diameter = 1.3 +* total_length = 400.0 ----------------- PINS Medical L302 ----------------- .. image:: electrode_pictures/L302.svg - + :alt: Illustration of PINS Medical L302 electrode ~~~~~~~~~~~~~~~~~~~~~~~ Default Parameters (mm) ~~~~~~~~~~~~~~~~~~~~~~~ - * tip_length = 1.5 - * contact_length = 1.5 - * contact_spacing = 1.5 - * lead_diameter = 1.3 - * total_length = 400.0 +* tip_length = 1.5 +* contact_length = 1.5 +* contact_spacing = 1.5 +* lead_diameter = 1.3 +* total_length = 400.0 ----------------- PINS Medical L303 ----------------- -.. image:: electrode_pictures/L303.svg - +.. image:: electrode_pictures/L303.svg + :alt: Illustration of PINS Medical L303 electrode ~~~~~~~~~~~~~~~~~~~~~~~ Default Parameters (mm) ~~~~~~~~~~~~~~~~~~~~~~~ - * tip_length = 1.5 - * contact_length = 3.0 - * contact_spacing = 3.0 - * lead_diameter = 1.3 - * total_length = 400.0 - +* tip_length = 1.5 +* contact_length = 3.0 +* contact_spacing = 3.0 +* lead_diameter = 1.3 +* total_length = 400.0 + ---- Code ---- .. autoclass:: ossdbs.electrodes.pins_medical.PINSMedicalModel - :members: - :show-inheritance: + :members: + :show-inheritance: diff --git a/docs/electrode_files/add_electrode.rst b/docs/electrode_files/add_electrode.rst index 0f3f094..da31f8e 100644 --- a/docs/electrode_files/add_electrode.rst +++ b/docs/electrode_files/add_electrode.rst @@ -1,4 +1,4 @@ -Adding an electrode +Adding an Electrode =================== Introduction @@ -7,17 +7,57 @@ Introduction This guide walks you through the process of adding a new electrode to OSS-DBS. Follow these steps to ensure seamless integration of your custom electrode. -Prepare the geometry +Prepare the Geometry -------------------- -**Before you begin, remember to replace electrodename with a descriptive name for your electrode in the following steps.** +**Before you begin, replace `electrodename` with a descriptive name for your electrode in the following steps.** -.. note:: When following the steps below, you can copy an existing electrode and modify it according to your new design. +.. note:: When following the steps below, you can use an existing electrode as a template and modify it to suit your new design. -1. Create a file named `electrodename_model.py` within the `ossdbs/electrodes` directory. -2. Implement a `dataclass` named `ElectrodenameParameters`, which encompass all parameters necessary for constructing the electrode. -3. Implement the electrode model within a class named `ElectrodenameModel`. You can utilize the template provided in :class:`ossdbs.electrodes.ElectrodeModel`. Ensure that the following methods are implemented at a minimum: `parameter_check`, `_construct_encapsulation_geometry`, `_construct_geometry`, `_body`, `_contacts`, `get_center_first_contact`, and `get_distance_l1_l4`. -4. Import the model into the `ossdbs/electrodes/defaults.py` file at the beginning of the file. Additionally, add the default parameters of the electrode and a function named `Electrodename` to this file. -5. Import the module into the `ossdbs/electrodes/__init__.py` file, along with importing from the `.defaults` at the top of the file. Furthermore, add the model name/class name to the `ELECTRODE_MODELS`, `ELECTRODES`, `ELECTRODE_PARAMETERS`, and `__all__` dictionaries. +1. **Create a New File:** + Create a file named `electrodename_model.py` within the `ossdbs/electrodes` directory. -Following these steps ensures proper integration of the new electrode into the software environment. +2. **Define Electrode Parameters:** + Implement a `dataclass` named `ElectrodenameParameters`. This class should include all parameters required for constructing the electrode geometry and defining its properties. + +3. **Implement the Electrode Model:** + Create a class named `ElectrodenameModel` to define the electrode model. Use the base class :class:`ossdbs.electrodes.ElectrodeModel` as a template. At a minimum, ensure the following methods are implemented: + - `parameter_check` + - `_construct_encapsulation_geometry` + - `_construct_geometry` + - `_body` + - `_contacts` + - `get_center_first_contact` + - `get_distance_l1_l4` + +4. **Add Default Parameters:** + Import the model into the `ossdbs/electrodes/defaults.py` file. At the beginning of this file: + - Define the default parameters for your electrode in a `dataclass` or dictionary. + - Add a function named `Electrodename()` to return the electrode's default parameter instance. + +5. **Update Initialization File:** + Import the new module into the `ossdbs/electrodes/__init__.py` file. At the top of the file: + - Add the module to the imports list. + - Include your model in the following dictionaries: + + - `ELECTRODE_MODELS` + - `ELECTRODES` + - `ELECTRODE_PARAMETERS` + - `__all__` + +Following these steps ensures that the new electrode is fully integrated into the OSS-DBS framework and is available for use. + +Tips for Testing +----------------- + +- Use the provided templates and methods to verify the geometry and parameters of your electrode. +- Ensure that the parameter names, data types, and default values are consistent with the conventions used for existing electrodes. +- Implement unit tests to validate the new electrode's behavior and ensure compatibility with the rest of the software. + +Final Verification +------------------- + +Once the new electrode is integrated: +1. Generate the Sphinx documentation for your electrode and verify its appearance. +2. Check that the electrode appears correctly in the list of available electrodes in OSS-DBS. +3. Validate its geometry and functionality through simulation or testing with existing workflows. diff --git a/docs/electrodes.rst b/docs/electrodes.rst index 7c5d822..2017dbc 100644 --- a/docs/electrodes.rst +++ b/docs/electrodes.rst @@ -19,4 +19,7 @@ This is an overview about the electrode models used for simulation. electrode_files/Micro_Probes_Snex100 electrode_files/Neuro_Pace electrode_files/Pins_Medical + electrode_files/PMTsEEG electrode_files/add_electrode + +.. note:: The total length does not influence the computational domain; therefore, the above electrodes are modeled at 400 mm. \ No newline at end of file diff --git a/ossdbs/electrodes/defaults.py b/ossdbs/electrodes/defaults.py index 54ceaf2..a52b2b0 100644 --- a/ossdbs/electrodes/defaults.py +++ b/ossdbs/electrodes/defaults.py @@ -63,14 +63,14 @@ total_length=400.0, ), "AbbottStJudeDirected6172": AbbottStJudeParameters( - tip_length=1.5, + tip_length=1.0, contact_length=1.5, contact_spacing=0.5, lead_diameter=1.29, total_length=400.0, ), "AbbottStJudeDirected6173": AbbottStJudeParameters( - tip_length=1.5, + tip_length=1.0, contact_length=1.5, contact_spacing=1.5, lead_diameter=1.29, @@ -128,14 +128,14 @@ total_length=400.0, ), "MedtronicSenSightB33015": MedtronicParameters( - tip_length=1.0, + tip_length=0.9, contact_length=1.5, contact_spacing=1.5, lead_diameter=1.36, total_length=330, ), "MedtronicSenSightB33005": MedtronicParameters( - tip_length=1.0, + tip_length=0.9, contact_length=1.5, contact_spacing=0.5, lead_diameter=1.36, @@ -201,7 +201,7 @@ total_length=400.0, ), "DixiSEEG5": DixiSEEGParameters( - tip_length=0.8, + tip_length=2.0, contact_length=2.0, contact_spacing=1.5, lead_diameter=0.8, @@ -209,7 +209,7 @@ n_contacts=5, ), "DixiSEEG8": DixiSEEGParameters( - tip_length=0.8, + tip_length=2.0, contact_length=2.0, contact_spacing=1.5, lead_diameter=0.8, @@ -217,7 +217,7 @@ n_contacts=8, ), "DixiSEEG10": DixiSEEGParameters( - tip_length=0.8, + tip_length=2.0, contact_length=2.0, contact_spacing=1.5, lead_diameter=0.8, @@ -225,7 +225,7 @@ n_contacts=10, ), "DixiSEEG12": DixiSEEGParameters( - tip_length=0.8, + tip_length=2.0, contact_length=2.0, contact_spacing=1.5, lead_diameter=0.8, @@ -233,7 +233,7 @@ n_contacts=12, ), "DixiSEEG15": DixiSEEGParameters( - tip_length=0.8, + tip_length=2.0, contact_length=2.0, contact_spacing=1.5, lead_diameter=0.8, @@ -241,7 +241,7 @@ n_contacts=15, ), "DixiSEEG18": DixiSEEGParameters( - tip_length=0.8, + tip_length=2.0, contact_length=2.0, contact_spacing=1.5, lead_diameter=0.8, @@ -249,41 +249,41 @@ n_contacts=18, ), "PMTsEEG2102_08": DixiSEEGParameters( - tip_length=0.8, + tip_length=2.0, contact_length=2.0, - contact_spacing=2.0, + contact_spacing=1.5, lead_diameter=0.8, total_length=400.0, n_contacts=8, ), "PMTsEEG2102_10": DixiSEEGParameters( - tip_length=0.8, + tip_length=2.0, contact_length=2.0, - contact_spacing=2.0, + contact_spacing=1.5, lead_diameter=0.8, total_length=400.0, n_contacts=10, ), "PMTsEEG2102_12": 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