update yaml files

eval_cases/molecular_vis/actions/basic_actions.yaml

@@ -12,7 +12,7 @@
 # Loading a CIF file
 - vars:
     question: |
-        Remove all molecules from and load the data "/Users/kuangshiai/Documents/ND-VIS/Code/SciVisAgentBench/SciVisAgentBench-tasks/molecular_vis/data/1CRN.cif".
+        Remove all molecules from and load the data from "data/1CRN.cif".
         Take a screenshot to confirm if the dataset has been loaded.
         Respond with <1> if the cif file has been loaded and the molecule is visible in the viewport, or <0> if it failed. Only respond with <1> or <0>.
   assert:

eval_cases/napari/0_actions/eval_basic_napari_functions.yaml

@@ -14,7 +14,7 @@
 # Test: open_file - Load a multi-dimensional image file (T, Z, Y, X, C)
 - vars:
     question: |
-      Load the file "dataset_001/dataset_001.tiff" into the viewer.
+      Load the file "data/dataset_001/dataset_001.tiff" into the viewer.
       Respond with <1> if the file was successfully loaded, or <0> if it failed. Only respond with <1> or <0>.
   assert:
     - type: contains-all
@@ -42,7 +42,7 @@
 # Test: open_file - Load a single image file
 - vars:
     question: |
-      Load the file "dataset_002/dataset_002.tif" into the viewer.
+      Load the file "data/dataset_002/dataset_002.tif" into the viewer.
       Respond with <1> if the file was successfully loaded, or <0> if it failed. Only respond with <1> or <0>.
   assert:
     - type: contains-all

eval_cases/napari/1_workflows/eval_visualization_workflows.yaml

@@ -4,7 +4,7 @@
 # Test: Multi-channel Overlay with Colormaps with channels
 - vars:
     question: |
-      1. Load the "data/dataset_001/dataset_002.tif" dataset into napari. 
+      1. Load the "data/dataset_002/dataset_002.tif" dataset into napari. 
       2. Depending on the number of channels, set the colormap for the first channel 0 to red and channel 1 to green.
       3. Switch to the 3D view. 
       4. Use additive blending for all channels to create an overlay visualization.

eval_cases/selected_15_cases.yaml

@@ -0,0 +1,87 @@
+# Selected 15 Cases for Human Evaluation
+# These cases represent diverse visualization capabilities across the benchmark
+#
+# Each case specifies:
+#   - name: The case directory name
+#   - path: Path to the case directory (relative to workspace root)
+#   - yaml: Path to the YAML file containing evaluation criteria
+#   - description: Brief description of what the case tests
+
+cases:
+  # From main benchmark (7 cases)
+  - name: argon-bubble
+    path: SciVisAgentBench-tasks/main/argon-bubble
+    yaml: benchmark/eval_cases/paraview/main_cases.yaml
+    description: Color & Opacity Mapping, Volume Rendering
+
+  - name: bonsai
+    path: SciVisAgentBench-tasks/main/bonsai
+    yaml: benchmark/eval_cases/paraview/main_cases.yaml
+    description: Volume Rendering
+
+  - name: trl-velocity_streamline
+    path: SciVisAgentBench-tasks/main/trl-velocity_streamline
+    yaml: benchmark/eval_cases/paraview/main_cases.yaml
+    description: Temporal Processing (Streamline)
+
+  - name: tornado
+    path: SciVisAgentBench-tasks/main/tornado
+    yaml: benchmark/eval_cases/paraview/main_cases.yaml
+    description: Glyph & Marker Placement
+
+  - name: tgc-velocity_contour
+    path: SciVisAgentBench-tasks/main/tgc-velocity_contour
+    yaml: benchmark/eval_cases/paraview/main_cases.yaml
+    description: Surface & Contour Extraction
+
+  - name: rti-velocity_slices
+    path: SciVisAgentBench-tasks/main/rti-velocity_slices
+    yaml: benchmark/eval_cases/paraview/main_cases.yaml
+    description: View & Camera Control, Data Subsetting & Extraction
+
+  - name: supernova-velocity_isosurface
+    path: SciVisAgentBench-tasks/main/supernova-velocity_isosurface
+    yaml: benchmark/eval_cases/paraview/main_cases.yaml
+    description: Surface & Contour Extraction (isosurface)
+
+  # From chatvis_bench (6 cases)
+  - name: time-varying
+    path: SciVisAgentBench-tasks/chatvis_bench/time-varying
+    yaml: benchmark/eval_cases/paraview/chatvis_bench_cases.yaml
+    description: Temporal Processing
+
+  - name: chart-opacity
+    path: SciVisAgentBench-tasks/chatvis_bench/chart-opacity
+    yaml: benchmark/eval_cases/paraview/chatvis_bench_cases.yaml
+    description: Plot & Chart Generation
+
+  - name: climate
+    path: SciVisAgentBench-tasks/chatvis_bench/climate
+    yaml: benchmark/eval_cases/paraview/chatvis_bench_cases.yaml
+    description: Field Computation
+
+  - name: materials
+    path: SciVisAgentBench-tasks/chatvis_bench/materials
+    yaml: benchmark/eval_cases/paraview/chatvis_bench_cases.yaml
+    description: Scientific Insight Derivation
+
+  - name: subseries-of-time-series
+    path: SciVisAgentBench-tasks/chatvis_bench/subseries-of-time-series
+    yaml: benchmark/eval_cases/paraview/chatvis_bench_cases.yaml
+    description: Dataset Restructuring
+
+  - name: shrink-sphere
+    path: SciVisAgentBench-tasks/chatvis_bench/shrink-sphere
+    yaml: benchmark/eval_cases/paraview/chatvis_bench_cases.yaml
+    description: Geometric & Topological Transformation
+
+  # From molecular_vis/workflows (2 cases)
+  - name: curved-membrane
+    path: SciVisAgentBench-tasks/molecular_vis/workflows/curved-membrane
+    yaml: benchmark/eval_cases/molecular_vis/workflows/eval_analysis_workflows.yaml
+    description: Data Subsetting & Extraction
+
+  - name: ras-raf-membrane
+    path: SciVisAgentBench-tasks/molecular_vis/workflows/ras-raf-membrane
+    yaml: benchmark/eval_cases/molecular_vis/workflows/eval_analysis_workflows.yaml
+    description: View & Camera Control

eval_cases/topology/topology_cases.yaml

@@ -26,6 +26,7 @@
           Q2: What is the type of critical point closest to coordinates (4,58,12): 
           (A) minimum (B) 1-saddle (C) 2-saddle (D) maximum
         Save the answers to the analysis questions in plain text as "QMCPACK/results/{agent_mode}/answers.txt".
+        Do not save any files other than the specified result files.
   assert:
     - type: rule_based
       eval_script: QMCPACK/GS/QMCPACK_eval.py
@@ -56,6 +57,7 @@
           Q2: Out of all degenerate points, the sum of one point's coordinates is the highest. What is this highest sum, rounded to the nearest integer?
           (A) 124 (B) 136 (C) 148 (D) 160
         Save the answers to the analysis questions in plain text as "brain/results/{agent_mode}/answers.txt".
+        Do not save any files other than the specified result files.
   assert:
     - type: rule_based
       eval_script: brain/GS/brain_eval.py
@@ -87,6 +89,7 @@
           Q2: How many points are in the largest partition region?
           (A) 6879 (B) 7968 (C) 8796 (D) 9687
         Save the answers to the analysis questions in plain text as "cylinder/results/{agent_mode}/answers.txt".
+        Do not save any files other than the specified result files.
   assert:
     - type: rule_based
       eval_script: cylinder/GS/cylinder_eval.py
@@ -127,6 +130,7 @@
           Q3: What is the highest scalar field value of a minimum, rounded to the nearest whole number?
           (A) 12 (B) 26 (C) 31 (D) 58
           Save the answers to the analysis questions in plain text as "isabel/results/{agent_mode}/answers.txt".
+          Do not save any files other than the specified result files.
   assert:
     - type: rule_based
       eval_script: isabel/GS/isabel_eval.py
@@ -176,6 +180,7 @@
           Q3: Which is the least common classification in the eigenvalue partition?
           (A) Positive scaling (B) counterclockwise rotation (C) negative scaling (D) clockwise rotation
           Save the answers to the analysis questions in plain text as "ocean/results/{agent_mode}/answers.txt".
+          Do not save any files other than the specified result files.
   assert:
     - type: rule_based
       eval_script: ocean/GS/ocean_eval.py
@@ -209,6 +214,7 @@
               * "Birth" array: store the birth value of each pair.
               * "Persistence" array: store the persistence value of each pair.
               * "IsFinite" array: use 1 to mark finite persistence and 0 to mark infinite persistence.
+          Do not save any files other than the specified result files.
   assert:
     - type: rule_based
       eval_script: noisyTerrain/GS/noisyTerrain_eval.py
@@ -228,6 +234,7 @@
           3. Save the Morse-Smale segmentation as "molecule/results/{agent_mode}/molecule.vti". 
           It should have a point array called "Segmentation". 
           For each point x, the array "Segmentation" should store the id number of the region in the segmentation that x belongs to.
+          Do not save any files other than the specified result files.
   assert:
     - type: rule_based
       eval_script: molecule/GS/molecule_eval.py
@@ -248,6 +255,7 @@
           4. Save only the Ascending Manifold as "moons/results/{agent_mode}/moons.vti".
           It should have a point array called "AscendingManifold". 
           For each point x, the array "AscendingManifold" should store the id number of the region that x belongs to.
+          Do not save any files other than the specified result files.
   assert:
     - type: rule_based
       eval_script: moons/GS/moons_eval.py
@@ -276,6 +284,7 @@
                 * 2 for 2-saddles
                 * 3 for maxima
             - The point coordinates should be in world coordinates 
+        Do not save any files other than the specified result files.
   assert:
     - type: rule_based
       eval_script: dragon/GS/dragon_eval.py