eval_cases/napari/0_actions/eval_basic_napari_functions.yaml

# Basic Napari Function Tests - Action Level
# These tests evaluate individual server functions with simple, single-function calls
# 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:
    question: |
      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
      value: "<1>"
    - type: not-contains
      value: "<0>"
  options:
    cache: false
    runSerially: true

# Test: delete layers - Delete all loaded layers from the viewer
- vars:
    question: |
      Delete the all currently loaded layers.
      Respond with <1> if all layers were successfully deleted, or <0> if the operation failed. Only respond with <1> or <0>.
  assert:
    - type: contains-all
      value: "<1>"
    - type: not-contains
      value: "<0>"
  options:
    cache: false
    runSerially: true
    
# Test: open_file - Load a single image file
- vars:
    question: |
      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
      value: "<1>"
    - type: not-contains
      value: "<0>"
  options:
    cache: false
    runSerially: true

# Test: list_layers - Get information about loaded layers
- vars:
    question: |
      Retrieve information about all currently loaded layers in the viewer.
      Respond with <1> if you successfully retrieved layer information, or <0> if it failed. Only respond with <1> or <0>.
  assert:
    - type: contains-all
      value: "<1>"
    - type: not-contains
      value: "<0>"
  options:
    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: |
      Navigate through the z-stack of the loaded image. Use set_z_slice to jump to at least z-slice 0 to examine structures at different depths. 
      Take a screenshot at each z-slice to verify navigation. 
      Respond with <1> if you successfully navigated through different z-slices and could see structural changes, or <0> if it failed. Only respond with <1> or <0>.
  assert:
    - type: contains-all
      value: "<1>"
    - type: not-contains
      value: "<0>"
  options:
    cache: false
    runSerially: true


# Test: Time Series Navigation - Navigate through time points
- vars:
    question: |
      If the data has time dimensions, use set_timestep to navigate through different time points.
      Take screenshots at different time points to show temporal changes.
      If no time dimension exists, simulate time navigation by adjusting the current view and taking multiple screenshots.
      Respond with <1> if you successfully navigated through time points or simulated time navigation, or <0> if it failed. Only respond with <1> or <0>.
  assert:
    - type: contains-all
      value: "<1>"
    - type: not-contains
      value: "<0>"
  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: |
      Change the colormap of the active image layer (dataset_002_ch1) to 'viridis'.
      Respond with <1> if the colormap was successfully changed, or <0> if it failed. Only respond with <1> or <0>.
  assert:
    - type: contains-all
      value: "<1>"
    - type: not-contains
      value: "<0>"
  options:
    cache: false
    runSerially: true

# Test: set_opacity - Adjust layer transparency
- vars:
    question: |
      Set the opacity of the active layer (dataset_002_ch1) to 0.5 (50% transparent).
      Respond with <1> if the opacity was successfully changed, or <0> if it failed. Only respond with <1> or <0>.
  assert:
    - type: contains-all
      value: "<1>"
    - type: not-contains
      value: "<0>"
  options:
    cache: false
    runSerially: true

# Test: set_blending - Change layer blending mode
- vars:
    question: |
      Change the blending mode of the active layer to 'additive'.
      Respond with <1> if the blending mode was successfully changed, or <0> if it failed. Only respond with <1> or <0>.
  assert:
    - type: contains-all
      value: "<1>"
    - type: not-contains
      value: "<0>"
  options:
    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: |
      Automatically adjust the contrast of the active image layer.
      Respond with <1> if the contrast was successfully auto-adjusted, or <0> if it failed. Only respond with <1> or <0>.
  assert:
    - type: contains-all
      value: "<1>"
    - type: not-contains
      value: "<0>"
  options:
    cache: false
    runSerially: true

# Test: set_contrast_limits - Set specific contrast limits
- vars:
    question: |
      Set the contrast limits of the active layer to min=0.1 and max=0.9.
      Respond with <1> if the contrast limits were successfully set, or <0> if it failed. Only respond with <1> or <0>.
  assert:
    - type: contains-all
      value: "<1>"
    - type: not-contains
      value: "<0>"
  options:
    cache: false
    runSerially: true

# Test: set_gamma - Adjust gamma correction
- vars:
    question: |
      Set the gamma correction of the active layer to 1.5.
      Respond with <1> if the gamma was successfully adjusted, or <0> if it failed. Only respond with <1> or <0>.
  assert:
    - type: contains-all
      value: "<1>"
    - type: not-contains
      value: "<0>"
  options:
    cache: false
    runSerially: true

# Test: set_interpolation - Change interpolation mode - doesn't work
- vars:
    question: |
      Change the interpolation mode of the active layer to 'linear'.
      Respond with <1> if the interpolation mode was successfully changed, or <0> if it failed. Only respond with <1> or <0>.
  assert:
    - type: contains-all
      value: "<1>"
    - type: not-contains
      value: "<0>"
  options:
    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: |
      Switch the viewer to 3D mode.
      Respond with <1> if the view was successfully switched to 3D, or <0> if it failed. Only respond with <1> or <0>.
  assert:
    - type: contains-all
      value: "<1>"
    - type: not-contains
      value: "<0>"
  options:
    cache: false
    runSerially: true

# Test: get_dims_info - Get dimension information
- vars:
    question: |
      Get information about the viewer's current dimension settings.
      Respond with <1> if you successfully retrieved dimension information, or <0> if it failed. Only respond with <1> or <0>.
  assert:
    - type: contains-all
      value: "<1>"
    - type: not-contains
      value: "<0>"
  options:
    cache: false
    runSerially: true

# Test: get_camera - Get current camera settings
- vars:
    question: |
      Retrieve the current camera settings of the viewer.
      Respond with <1> if you successfully retrieved camera settings, or <0> if it failed. Only respond with <1> or <0>.
  assert:
    - type: contains-all
      value: "<1>"
    - type: not-contains
      value: "<0>"
  options:
    cache: false
    runSerially: true

# Test: reset_camera - Reset camera to default view
- vars:
    question: |
      Reset the camera to the default view.
      Respond with <1> if the camera was successfully reset, or <0> if it failed. Only respond with <1> or <0>.
  assert:
    - type: contains-all
      value: "<1>"
    - type: not-contains
      value: "<0>"
  options:
    cache: false
    runSerially: true

# Test: set_camera - Adjust camera settings
- vars:
    question: |
      Set the camera zoom to 2.0.
      Respond with <1> if the camera zoom was successfully set, or <0> if it failed. Only respond with <1> or <0>.
  assert:
    - type: contains-all
      value: "<1>"
    - type: not-contains
      value: "<0>"
  options:
    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: |
      Hide the active layer (set visible to false).
      Respond with <1> if the layer visibility was successfully changed, or <0> if it failed. Only respond with <1> or <0>.
  assert:
    - type: contains-all
      value: "<1>"
    - type: not-contains
      value: "<0>"
  options:
    cache: false
    runSerially: true

# Test: set_layer_visibility - Show layer again
- vars:
    question: |
      Show the active layer again (set visible to true).
      Respond with <1> if the layer visibility was successfully changed, or <0> if it failed. Only respond with <1> or <0>.
  assert:
    - type: contains-all
      value: "<1>"
    - type: not-contains
      value: "<0>"
  options:
    cache: false
    runSerially: true

# Test: screenshot - Take a screenshot
- vars:
    question: |
      Take a screenshot of the current view.
      Respond with <1> if the screenshot was successfully taken, or <0> if it failed. Only respond with <1> or <0>.
  assert:
    - type: contains-all
      value: "<1>"
    - type: not-contains
      value: "<0>"
  options:
    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: |
#       Retrieve basic statistics (min, max, mean, std) for the active layer.
#       Respond with <1> if you successfully retrieved layer statistics, or <0> if it failed. Only respond with <1> or <0>.
#   assert:
#     - type: contains-all
#       value: "<1>"
#     - type: not-contains
#       value: "<0>"
#   options:
#     cache: false
#     runSerially: true

# # Test: add_points - Add point annotations - doesn't work
# - vars:
#     question: |
#       Add two point markers at coordinates [[100, 100], [200, 200]] with the name "test_points".
#       Respond with <1> if the points were successfully added, or <0> if it failed. Only respond with <1> or <0>.
#   assert:
#     - type: contains-all
#       value: "<1>"
#     - type: not-contains
#       value: "<0>"
#   options:
#     cache: false
#     runSerially: true

# Test: add_shapes - Add shape annotations
- vars:
    question: |
      Add a rectangle shape with coordinates [[[50, 50], [150, 50], [150, 150], [50, 150]]] and name "test_rectangle".
      Respond with <1> if the shape was successfully added, or <0> if it failed. Only respond with <1> or <0>.
  assert:
    - type: contains-all
      value: "<1>"
    - type: not-contains
      value: "<0>"
  options:
    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: |
#       Measure the distance between point [100, 100] and point [200, 200].
#       Respond with <1> if the distance was successfully measured, or <0> if it failed. Only respond with <1> or <0>.
#   assert:
#     - type: contains-all
#       value: "<1>"
#     - type: not-contains
#       value: "<0>"
#   options:
#     cache: false
#    runSerially: true

# Test: set_scale_bar - Show scale bar
- vars:
    question: |
      Show the scale bar with unit 'um'.
      Respond with <1> if the scale bar was successfully shown, or <0> if it failed. Only respond with <1> or <0>.
  assert:
    - type: contains-all
      value: "<1>"
    - type: not-contains
      value: "<0>"
  options:
    cache: false
    runSerially: true

# # Test: set_axis_labels - Set axis labels - doesn't work
# - vars:
#     question: |
#       Set axis labels to ['y', 'x'] for the 2D data.
#       Respond with <1> if the axis labels were successfully set, or <0> if it failed. Only respond with <1> or <0>.
#   assert:
#     - type: contains-all
#       value: "<1>"
#     - type: not-contains
#       value: "<0>"
#   options:
#     cache: false
#     runSerially: true

# Test: screenshot - Save screenshot to file
- vars:
    question: |
      Save a screenshot.
      Respond with <1> if the screenshot was successfully exported, or <0> if it failed. Only respond with <1> or <0>.
  assert:
    - type: contains-all
      value: "<1>"
    - type: not-contains
      value: "<0>"
  options:
    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: |
      Save the active layer to the file "test_layer.tif".
      Respond with <1> if the layer was successfully saved, or <0> if it failed. Only respond with <1> or <0>.
  assert:
    - type: contains-all
      value: "<1>"
    - type: not-contains
      value: "<0>"
  options:
    cache: false
    runSerially: true

# Test: remove_layer - Remove a layer
- vars:
    question: |
      Remove the layer named "test_rectangle".
      Respond with <1> if the layer was successfully removed, or <0> if it failed. Only respond with <1> or <0>.
  assert:
    - type: contains-all
      value: "<1>"
    - type: not-contains
      value: "<0>"
  options:
    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: |
      Try to load the non-existent file "nonexistent.tif" and handle the error gracefully.
      Respond with <1> if the error was handled gracefully (no crash), or <0> if it crashed. Only respond with <1> or <0>.
  assert:
    - type: contains-all
      value: "<1>"
    - type: not-contains
      value: "<0>"
  options:
    cache: false
    runSerially: true

# Test: Error handling - Try to remove non-existent layer
- vars:
    question: |
      Try to remove a layer that doesn't exist named "nonexistent_layer" and handle the error gracefully.
      Respond with <1> if the error was handled gracefully (no crash), or <0> if it crashed. Only respond with <1> or <0>.
  assert:
    - type: contains-all
      value: "<1>"
    - type: not-contains
      value: "<0>"
  options:
    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: |
      Enable iso-surface rendering for the loaded layer.
      Take a screenshot to verify the 3D iso-surface rendering.
      Respond with <1> if the 3D iso-surface rendering was successfully set up, or <0> if it failed. Only respond with <1> or <0>.
  assert:
    - type: contains-all
      value: "<1>"
    - type: not-contains
      value: "<0>"
  options:
    cache: false
    runSerially: true

# Test: Cleanup - Remove remaining test layers
- vars:
    question: |
      Remove the layer named "test_rectangle" to clean up test annotations.
      Respond with <1> if the layer was successfully removed, or <0> if it failed. Only respond with <1> or <0>.
  assert:
    - type: contains-all
      value: "<1>"
    - type: not-contains
      value: "<0>"
  options:
    cache: false
    runSerially: true

# END OF TASK 11: Napari - 3D Rendering
# Operations: Enable iso-surface rendering in 3D, remove test layers for cleanup