Version 1.1.1:

Dose calculation for custom patient. Update eclipse_photon_dose_calculation.ipynb
Add docstring in clinical criteria.
Add more methods to data explorer for accessing data from hugging face.
Add unit test
Remove redundant max constraints from optimization.py

Author: gourav3017

examples/eclipse_photon_dose_calculation.ipynb

@@ -15,8 +15,7 @@
     "---\n",
     "\n",
     "### **1. Download the Photon Dose Calculation Module**\n",
-    "Download the required module from Varian's GitHub repository: [Photon Dose Calculation Module](https://github.com/Varian-MedicalAffairsAppliedSolutions/MAAS-DoseInfluenceMatrix/tree/main) **Note:** This repository is currently not public. Please allow it sometime to become public\n",
-    "\n",
+    "Download the required module from Varian's GitHub repository under release tab: [CalculateInfluenceMatrix](https://github.com/Varian-MedicalAffairsAppliedSolutions/MAAS-DoseInfluenceMatrix/tree/main) \n",
     "\n",
     "### **2. Prepare Your Plan in Eclipse**\n",
     "Before running dose calculation, you must set up your plan correctly in Eclipse.\n",
@@ -46,15 +45,15 @@
     "For users unfamiliar with command-line scripting, the plugin provides a **graphical interface** for dose calculation.\n",
     "\n",
     "##### **Steps:**\n",
-    "1. Navigate to the [Plugin Directory](https://github.com/Varian-MedicalAffairsAppliedSolutions/MAAS-DoseInfluenceMatrix/tree/main/PhotonDoseCalc/Plugin/bin/Release) in photon dose calculation module  \n",
+    "1. Navigate to the release [tab](https://github.com/Varian-MedicalAffairsAppliedSolutions/MAAS-DoseInfluenceMatrix/releases) tab for dose calculation module and download the latest version of CalculateInfluenceMatrix  \n",
     "2. Modify the config file:  \n",
-    "   - Edit [PhotonInfluenceMatrixCalcPlugin.esapi.config](https://github.com/Varian-MedicalAffairsAppliedSolutions/MAAS-DoseInfluenceMatrix/blob/main/PhotonDoseCalc/Source_C%23/bin/release/PhotonInfluenceMatrixCalcPlugin.esapi.config).  \n",
-    "   - Set `OutputRootFolder` to your preferred output directory.  You can also modify `BeamletSizeX` and `BeamletSizeY` for choosing the beamlet size in X and Y direction. Please modify the `EclipseVolumeDoseCalcModel` based on your dose calculation version available at your institution.\n",
+    "   - Edit CalculateInfluenceMatrix.esapi.dll.config.  \n",
+    "   - Set `Photon_OutputRootFolder` to your preferred output directory.  You can also modify `BeamletSizeX` and `BeamletSizeY` for choosing the beamlet size in X and Y direction. Please modify the `Photon_EclipseVolumeDoseCalcModel` based on your dose calculation version available at your institution.\n",
     "3. In Eclipse:\n",
     "   - Open your patient plan (e.g., **PortPy_Plan**).  \n",
     "   - Navigate to **Tools → Scripts → Change Folder**.  \n",
-    "   - Change the path to downloaded [Plugin Directory](https://github.com/Varian-MedicalAffairsAppliedSolutions/MAAS-DoseInfluenceMatrix/tree/main/PhotonDoseCalc/Plugin/bin/Release) and click **Open**.  \n",
-    "   - Select **PhotonInfluenceMatrixCalcPlugin.esapi.dll** and click **Run**\n",
+    "   - Change the path to downloaded folder from release and click **Open**.  \n",
+    "   - Select **CalculateInfluenceMatrix.esapi.dll** and click **Run**\n",
     "   - (Optional) Add the plugin to **Favorites** for quicker access.  \n",
     "\n",
     "**Output:** PortPy-compatible data will be saved in the `OutputRootFolder` specified in the config file.\n",
@@ -64,14 +63,14 @@
     "For users comfortable with command-line execution.\n",
     "\n",
     "##### **Steps:**\n",
-    "1. Navigate to the [Executable Directory](https://github.com/Varian-MedicalAffairsAppliedSolutions/MAAS-DoseInfluenceMatrix/tree/main/PhotonDoseCalc/Source_C%23/bin/release).  \n",
+    "1. Navigate to the release [tab](https://github.com/Varian-MedicalAffairsAppliedSolutions/MAAS-DoseInfluenceMatrix/releases) tab for dose calculation module and download the latest version of CalculateInfluenceMatrix.  \n",
     "2. Modify the config file:\n",
-    "   - Edit [PhotonInfluenceMatrixCalc.exe.config](https://github.com/Varian-MedicalAffairsAppliedSolutions/MAAS-DoseInfluenceMatrix/blob/main/PhotonDoseCalc/Source_C%23/bin/release/PhotonInfluenceMatrixCalc.exe.config).  \n",
-    "   - Set `OutputRootFolder` to your preferred output directory. You can also modify `BeamletSizeX` and `BeamletSizeY` for choosing the beamlet size in X and Y direction. Please modify the `EclipseVolumeDoseCalcModel` based on your dose calculation version available at your institution.\n",
+    "   - Edit CalculateInfluenceMatrix.exe.config.  \n",
+    "   - Set `Photon_OutputRootFolder` to your preferred output directory. You can also modify `Photon_BeamletSizeX` and `Photon_BeamletSizeY` for choosing the beamlet size in X and Y direction. Please modify the `Photon_EclipseVolumeDoseCalcModel` based on your dose calculation version available at your institution.\n",
     "     \n",
     "3. Run the following command in a terminal or command prompt:  \n",
     "   ```bash\n",
-    "   PhotonInfluenceMatrixCalc.exe <patient_mrn> <course_name> <plan_name>"
+    "   CalculateInfluenceMatrix.exe <patient_mrn> <course_name> <plan_name>"
    ]
   },
   {

examples/python_files/1_basic_tutorial.py

@@ -59,15 +59,15 @@ def basic_tutorial():
     data_dir = r'../../data'
     data = pp.DataExplorer(data_dir=data_dir)
     # OR
-    # data = pp.DataExplorer(hf_repo_id="PortPy-Project/PortPy_Dataset")
+    # data = pp.DataExplorer(hf_repo_id="PortPy-Project/PortPy_Dataset", local_download_dir='your_local_directory')
 
     # display the existing patients in console or browser.
     data.display_list_of_patients()
 
     # pick a patient from the existing patient list to get detailed info (e.g., beam angles, structures).
     data.patient_id = 'Lung_Phantom_Patient_1'
 
-    # download patient data with planner beams from hugging face
+    # download patient data with planner beams from hugging face. Run it only once for the initial run to download the data. Skip it for next run
     # data.filter_and_download_hf_dataset()
 
     # display the data of the patient in console or browser.

portpy/__init__.py

@@ -1,3 +1,3 @@
-__version__ = "1.1.0"
+__version__ = "1.1.1"
 
 from portpy import photon

portpy/photon/clinical_criteria.py

@@ -6,6 +6,7 @@
 from typing import TYPE_CHECKING, Union
 if TYPE_CHECKING:
     from portpy.photon.plan import Plan
+    from portpy.photon.influence_matrix import InfluenceMatrix
 from copy import deepcopy
 import numpy as np
 
@@ -288,7 +289,34 @@ def get_dvh_table(self, my_plan: Plan, constraint_list: list = None, opt_params:
         return self.dvh_table
 
 
-    def get_low_dose_vox_ind(self, my_plan: Plan, dose: np.ndarray):
+    def get_low_dose_vox_ind(self, my_plan: Plan, dose: np.ndarray, inf_matrix: InfluenceMatrix):
+        """
+        Identifies and stores the indices of low-dose voxels for each DVH constraint or goal.
+
+        For each row in the DVH table, the method:
+        - Retrieves the relevant structure name, dose threshold, and volume percentage.
+        - Adjusts the volume percentage based on the fraction of the volume in the dose calculation box.
+        - Sorts the structure's voxels based on dose values (ascending).
+        - Accumulates voxel volumes until the specified volume percentage is reached.
+        - Marks these as low-dose voxels and stores them in the `low_dose_voxels` column.
+
+        Parameters
+        ----------
+        my_plan : Plan
+            The treatment plan object that includes the influence matrix.
+        dose : np.ndarray
+            A 1D array representing the dose values for all optimization voxels.
+        inf_matrix : InfluenceMatrix, optional
+            The influence matrix that provides voxel-related metadata. If not provided,
+            it defaults to `my_plan.inf_matrix`.
+
+        Returns
+        -------
+        pd.DataFrame
+            Updated DVH table with a new column `low_dose_voxels` indicating voxel indices
+            in each structure that received the lowest doses contributing up to the specified
+            volume percentage.
+        """
         dvh_table = self.dvh_table
         inf_matrix = my_plan.inf_matrix
         for ind in dvh_table.index: