modify cases from Guoxi

eval_cases/topology/topology_cases.yaml

@@ -231,11 +231,11 @@
   assert:
     - type: rule_based
       eval_script: molecule/GS/molecule_eval.py
-      eval_function: 
+      eval_function: evaluateMoleculeSegmentation
       gs_file: 
-        - molecule/GS/molecule_gs.vtk
+        - molecule/GS/molecule_gs.vti
       rs_file: 
-        - molecule/results/{agent_mode}/molecule.vtk
+        - molecule/results/{agent_mode}/molecule.vti
 
 
 # 8. moons
@@ -253,9 +253,9 @@
       eval_script: moons/GS/moons_eval.py
       eval_function: evaluateMoonAscendingManifold
       gs_file: 
-        - moons/GS/moons_gs.vtk
+        - moons/GS/moons_gs.vti
       rs_file: 
-        - moons/results/{agent_mode}/moons.vtk
+        - moons/results/{agent_mode}/moons.vti
 
 
 # 9. dragon
@@ -276,19 +276,6 @@
                 * 2 for 2-saddles
                 * 3 for maxima
             - The point coordinates should be in world coordinates 
-
-        5. Analyze the visualization and answer the following questions:
-
-        Q1: How many saddle-maximum pairs are present in the dataset? 
-        (A) 2 (B) 4 (C) 6 (D) 10.
-
-        Q2: How many minima are computed?
-        (A) 2 (B) 5 (C) 8 (D) 10.
-
-        Q3: Are there any saddle-saddle pairs in the persistence diagram?
-        (Yes/No)
-
-        Save the answers to the analysis questions in plain text as "dragon/results/{agent_mode}/answers.txt".
   assert:
     - type: rule_based
       eval_script: dragon/GS/dragon_eval.py
@@ -296,12 +283,4 @@
       gs_file: 
         - dragon/GS/dragon_gs.vtk
       rs_file: 
-        - dragon/results/{agent_mode}/dragon.vtk
-    - type: llm-rubric
-      subtype: text
-      value: |
-          1. Q1 correct answer: (C) 6
-
-          2. Q2 correct answer: (B) 5
-
-          3. Q3 correct answer: No
+        - dragon/results/{agent_mode}/dragon.vtk

topology/dragon/task_description.txt

@@ -11,17 +11,4 @@
         * 1 for 1-saddles
         * 2 for 2-saddles
         * 3 for maxima
-    - The point coordinates should be in world coordinates 
-
-5. Analyze the visualization and answer the following questions:
-
-Q1: How many saddle-maximum pairs are present in the dataset? 
-(A) 2 (B) 4 (C) 6 (D) 10.
-
-Q2: How many minima are computed?
-(A) 2 (B) 5 (C) 8 (D) 10.
-
-Q3: Are there any saddle-saddle pairs in the persistence diagram?
-(Yes/No)
-
-Save the answers to the analysis questions in plain text as "dragon/results/{agent_mode}/answers.txt".
+    - The point coordinates should be in world coordinates 

topology/molecule/GS/molecule_eval.py

@@ -0,0 +1,32 @@
+import os
+import sys
+
+# Add the topology directory to Python path
+sys.path.insert(0, os.path.join(os.path.dirname(__file__), '../..'))
+
+from topologyScoring import partitionTopologicalDiceScore
+
+def evaluateMoleculeSegmentation(gtFilename : str, reconFilename : str, verbose : bool = False) -> int:
+    """
+    Given two Morse-Smale segmentations of the same domain, return a similarity score from 0-10.
+    A score of 0 is considered bad and a score of 10 is considered good. The segmentations should be
+    represented by a point array called "Segmentation" that assigs a region identifier to each point in 
+    the domain. The region identifiers between the ground truth and reconstructed files do not need to match. 
+    Args:
+        gtFilename: The name of a file storing VTK image data (.vti) storing the ground truth MS segmentation.
+                    each point's region ID should be stored in a point array called "Segmentation".
+        reconFilename: The name of a file storing VTK image data (.vti) storing the reconstructed MS segmentation.
+        verbose: Should error messages be printed if there are issues with the input files.
+    """
+
+    return partitionTopologicalDiceScore(gtFilename, "Segmentation", reconFilename, "Segmentation", verbose)
+
+if __name__ == "__main__":
+
+    if len(sys.argv) != 3:
+        print(f"{os.path.basename(__file__)}: usage is 'python3 {os.path.basename(__file__)} gt_filename.vti recon_filename.vti")
+        exit(1)
+
+    score = evaluateMoleculeSegmentation(sys.argv[1], sys.argv[2], verbose=True)
+
+    print(f"This MS segmentation scored: {score}")