compose basic action operations into tasks

eval_cases/molecular_vis/actions/basic_actions.yaml

@@ -1,6 +1,13 @@
 # Basic Actions for Molecular Visualization Benchmark
 # These actions test core functionality of molecular visualization tools
-#https://www.rcsb.org/structure/1CRN
+# https://www.rcsb.org/structure/1CRN
+#
+# Taxonomy Level: Task (small-scale visualization task involving a few operations)
+# Each task is marked with a comment indicating the end of the task and the task name
+
+# ============================================================
+# TASK 1: 1CRN - Load & Basic Representations
+# ============================================================
 
 # Loading a CIF file
 - vars:
@@ -47,6 +54,13 @@
     cache: false
     runSerially: true
 
+# END OF TASK 1: 1CRN - Load & Basic Representations
+# Operations: Load CIF file, Van der Waals representation, Licorice representation
+
+# ============================================================
+# TASK 2: 1CRN - Color by Properties
+# ============================================================
+
 # Coloring by element
 - vars:
     question: |
@@ -92,6 +106,13 @@
     cache: false
     runSerially: true
 
+# END OF TASK 2: 1CRN - Color by Properties
+# Operations: Color by element, color by chain, color by residue type
+
+# ============================================================
+# TASK 3: 1CRN - Region Selection
+# ============================================================
+
 # Selecting and coloring specific residues
 - vars:
     question: |
@@ -122,6 +143,13 @@
     cache: false
     runSerially: true
 
+# END OF TASK 3: 1CRN - Region Selection
+# Operations: Select and color specific residues, select and color specific atoms
+
+# ============================================================
+# TASK 4: 1CRN - Multi-Representation
+# ============================================================
+
 # Multiple representations
 - vars:
     question: |
@@ -167,6 +195,13 @@
     cache: false
     runSerially: true
 
+# END OF TASK 4: 1CRN - Multi-Representation
+# Operations: Create multiple representations (cartoon + licorice), adjust material properties (opaque), adjust representation parameters (radius)
+
+# ============================================================
+# TASK 5: 1CRN - Advanced Coloring
+# ============================================================
+
 # Coloring by B-factor (temperature factor)
 - vars:
     question: |
@@ -227,6 +262,13 @@
     cache: false
     runSerially: true
 
+# END OF TASK 5: 1CRN - Advanced Coloring
+# Operations: Color by B-factor, select and color water molecules, color by charge, color by hydrophobicity
+
+# ============================================================
+# TASK 6: 1CRN - Active Site Selection
+# ============================================================
+
 # Selecting and highlighting active site
 - vars:
     question: |
@@ -272,6 +314,13 @@
     cache: false
     runSerially: true
 
+# END OF TASK 6: 1CRN - Active Site Selection
+# Operations: Distance-based selection (5Å around residue), distinguish protein vs non-protein components, adjust view settings (background color)
+
+# ============================================================
+# TASK 7: 1CRN - Spatial Queries
+# ============================================================
+
 # Selecting specific atom types in a range
 - vars:
     question: |
@@ -302,6 +351,13 @@
     cache: false
     runSerially: true
 
+# END OF TASK 7: 1CRN - Spatial Queries
+# Operations: Select specific atom types in residue ranges, distance-based atom selection
+
+# ============================================================
+# TASK 8: 1CRN - Visibility Control
+# ============================================================
+
 # Selecting and hiding specific residues
 - vars:
     question: |
@@ -362,6 +418,13 @@
     cache: false
     runSerially: true
 
+# END OF TASK 8: 1CRN - Visibility Control
+# Operations: Hide specific residues, show only specific element types, show only backbone, show only side chains
+
+# ============================================================
+# TASK 9: 1CRN - Residue Selection
+# ============================================================
+
 # Selecting aromatic residues
 - vars:
     question: |
@@ -392,6 +455,13 @@
     cache: false
     runSerially: true
 
+# END OF TASK 9: 1CRN - Residue Selection
+# Operations: Select aromatic residues, select charged residues with differential coloring
+
+# ============================================================
+# TASK 10: 1CRN - Combined Representations
+# ============================================================
+
 # Multiple selections with different representations
 - vars:
     question: |
@@ -422,6 +492,13 @@
     cache: false
     runSerially: true
 
+# END OF TASK 10: 1CRN - Combined Representations
+# Operations: Multiple representations with different color schemes (cartoon by chain + VdW by element), multiple representations with structural segmentation (backbone vs side chains)
+
+# ============================================================
+# TASK 11: 1CRN - Distance-based Selection
+# ============================================================
+
 # Selecting and coloring by distance from specific atom
 - vars:
     question: |
@@ -467,6 +544,13 @@
     cache: false
     runSerially: true
 
+# END OF TASK 11: 1CRN - Distance-based Selection
+# Operations: Distance from specific atom (CA of residue), combined criteria (element type AND residue range), element-specific coloring (sulfur atoms)
+
+# ============================================================
+# TASK 12: 1CRN - Gradient Coloring
+# ============================================================
+
 # Coloring by residue number
 - vars:
     question: |
@@ -527,6 +611,13 @@
     cache: false
     runSerially: true
 
+# END OF TASK 12: 1CRN - Gradient Coloring
+# Operations: Color by residue number (gradient), element selection in residue ranges, element + residue type combination (oxygen in polar residues), distance-based with element filter
+
+# ============================================================
+# TASK 13: 1CRN - Multi-Criteria Selection
+# ============================================================
+
 # Selecting and coloring by atom selection - backbone with sidechain by element
 - vars:
     question: |
@@ -631,3 +722,6 @@
   options:
     cache: false
     runSerially: true
+
+# END OF TASK 13: 1CRN - Multi-Criteria Selection
+# Operations: Multi-representation with element-specific coloring (backbone cartoon + side chain licorice by element), complex distance and element queries (carbon near nitrogen atoms), Boolean logic selection (OR criteria), complex multi-criteria with distance, CA-only visualization, heteroatom isolation, multiple element type filtering

eval_cases/napari/0_actions/eval_basic_napari_functions.yaml

@@ -3,6 +3,13 @@
 # Each test focuses on testing one specific function with appropriate parameters
 # We suggest using https://www.ebi.ac.uk/bioimage-archive/galleries/S-BIAD7.html IM1 as dataset_001
 # We suggest using https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/pages/S-BIAD573.html IM1 as dataset_002
+#
+# Taxonomy Level: Task (small-scale visualization task involving a few operations)
+# Each task is marked with a comment indicating the end of the task and the task name
+
+# ============================================================
+# TASK 1: Napari - Load & Layer Management
+# ============================================================
 
 # Test: open_file - Load a multi-dimensional image file (T, Z, Y, X, C)
 - vars:
@@ -60,6 +67,13 @@
     cache: false
     runSerially: true
 
+# END OF TASK 1: Napari - Load & Layer Management
+# Operations: Load multi-dimensional file, delete layers, load single image file, retrieve layer information
+
+# ============================================================
+# TASK 2: Napari - 3D/4D Navigation
+# ============================================================
+
 # Test: Z-stack Navigation - Scroll through different depths
 - vars:
     question: |
@@ -91,7 +105,14 @@
   options:
     cache: false
     runSerially: true
-    
+
+# END OF TASK 2: Napari - 3D/4D Navigation
+# Operations: Z-stack navigation, time series navigation
+
+# ============================================================
+# TASK 3: Napari - Color & Opacity
+# ============================================================
+
 # Test: set_colormap - Change layer colormap
 - vars:
     question: |
@@ -134,6 +155,13 @@
     cache: false
     runSerially: true
 
+# END OF TASK 3: Napari - Color & Opacity
+# Operations: Set colormap, adjust opacity, change blending mode
+
+# ============================================================
+# TASK 4: Napari - Contrast Adjustment
+# ============================================================
+
 # Test: auto_contrast - Auto-adjust contrast
 - vars:
     question: |
@@ -190,6 +218,13 @@
     cache: false
     runSerially: true
 
+# END OF TASK 4: Napari - Contrast Adjustment
+# Operations: Auto-adjust contrast, set specific contrast limits, adjust gamma correction, change interpolation mode
+
+# ============================================================
+# TASK 5: Napari - Camera Control
+# ============================================================
+
 # Test: toggle_view - Switch between 2D and 3D view
 - vars:
     question: |
@@ -260,6 +295,13 @@
     cache: false
     runSerially: true
 
+# END OF TASK 5: Napari - Camera Control
+# Operations: Switch 2D/3D view, get dimension info, get camera settings, reset camera, adjust camera zoom
+
+# ============================================================
+# TASK 6: Napari - Visibility & Screenshot
+# ============================================================
+
 # Test: set_layer_visibility - Toggle layer visibility
 - vars:
     question: |
@@ -302,6 +344,13 @@
     cache: false
     runSerially: true
 
+# END OF TASK 6: Napari - Visibility & Screenshot
+# Operations: Hide layer, show layer, take screenshot
+
+# ============================================================
+# TASK 7: Napari - Annotations
+# ============================================================
+
 # # Test: get_layer_statistics - Get layer statistics
 # - vars:
 #     question: |
@@ -344,6 +393,13 @@
     cache: false
     runSerially: true
 
+# END OF TASK 7: Napari - Annotations
+# Operations: Add shape annotations
+
+# ============================================================
+# TASK 8: Napari - Scale Bar & Export
+# ============================================================
+
 # # Test: measure_distance - Measure distance between points - doesn't work 
 # - vars:
 #     question: |
@@ -400,6 +456,13 @@
     cache: false
     runSerially: true
 
+# END OF TASK 8: Napari - Scale Bar & Export
+# Operations: Show scale bar with units, save screenshot to file
+
+# ============================================================
+# TASK 9: Napari - Export & Cleanup
+# ============================================================
+
 # Test: save_layers - Save layer to file
 - vars:
     question: |
@@ -428,6 +491,13 @@
     cache: false
     runSerially: true
 
+# END OF TASK 9: Napari - Export & Cleanup
+# Operations: Save layer to file, remove layer
+
+# ============================================================
+# TASK 10: Napari - Error Handling
+# ============================================================
+
 # Test: Error handling - Try to load non-existent file
 - vars:
     question: |
@@ -456,6 +526,13 @@
     cache: false
     runSerially: true
 
+# END OF TASK 10: Napari - Error Handling
+# Operations: Handle non-existent file, handle non-existent layer removal
+
+# ============================================================
+# TASK 11: Napari - 3D Rendering
+# ============================================================
+
 # Test: 3D View and Iso-surface Rendering
 - vars:
     question: |
@@ -483,4 +560,7 @@
       value: "<0>"
   options:
     cache: false
-    runSerially: true
+    runSerially: true
+
+# END OF TASK 11: Napari - 3D Rendering
+# Operations: Enable iso-surface rendering in 3D, remove test layers for cleanup