new results

outputs/main_paper/blueberry_20260526_160106/.hydra/config.yaml

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+focus_stack:
+  dataset_dir: ${dataset_dir}
+  scan_prefix: scan
+  scan_dirs: null
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  find_sharpest_image: true
+  sharpness_score: tenengrad
+  sharpness_selection_mode: window
+  sharpness_window_weights: uniform
+  sharpness_gaussian_sigma: null
+  output_paths:
+    output_dir: ${..output_dir}/${..experiment_name}/focus_stack
+    images_subdir: focus_stacked_images
+    masks_subdir: focus_stacked_masks
+    depthmaps_subdir: depthmaps
+    sharpness_scores_subdir: sharpness_scores
+    poses_filename: poses.json
+    intrinsics_filename: intrinsics.json
+  focus_stack_params:
+    focal_stack_size: 7
+    full_resolution_align: true
+    global_align: true
+    align_keep_size: true
+    no_contrast: true
+  low_pass_output: true
+  low_pass_kernel_size: 5
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: ${output_dir}/${experiment_name}
+    output_subdir: .hydra
+  random_seed: ${random_seed}
+masking:
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  random_seed: ${random_seed}
+  input_paths:
+    images_dir: ${...output_dir}/${...experiment_name}/focus_stack/focus_stacked_images
+    valid_regions_dir: ${...output_dir}/${...experiment_name}/focus_stack/focus_stacked_masks
+  output_paths:
+    output_dir: ${..output_dir}/${..experiment_name}/masking
+    masks_subdir: masks
+  bootstrap:
+    bootstrap_stem: scan00
+    focus_mask_border_padding: 8
+    edge_blur_kernel_size: 5
+    canny_threshold1: 25.0
+    canny_threshold2: 150.0
+    point_sampling_scale: 0.9
+    point_prompt_count: 80
+    firstpass_shrink_scale: 0.9
+    points_refine_kernel_size: 9
+    points_refine_dilate_iterations: 1
+  sam2:
+    model_id: facebook/sam2.1-hiera-large
+    device: cuda
+    offload_video_to_cpu: true
+  visualization:
+    overlay_alpha: 0.4
+    overlay_color:
+    - 255
+    - 0
+    - 0
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: ${output_dir}/${experiment_name}
+    output_subdir: .hydra
+colmap:
+  random_seed: ${random_seed}
+  run:
+    colmap_feat_extract_match: true
+    colmap_reconstruct: true
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  feat_extract_match:
+    input_paths:
+      images_dir: ${...output_dir}/${...experiment_name}/focus_stack/focus_stacked_images
+      masks_dir: ${...output_dir}/${...experiment_name}/masking/masks
+    output_paths:
+      output_dir: ${...output_dir}/${...experiment_name}
+      database_filename: database.db
+    extraction:
+      device: cpu
+      camera_model: OPENCV
+      num_threads: 1
+      max_num_features: 8192
+      estimate_affine_shape: true
+    matching:
+      use_gpu: false
+      num_threads: 1
+      guided_matching: true
+  reconstruction:
+    mode: automatic
+    load_prior_poses: true
+    load_prior_intrinsics: true
+    refine_intrinsics: true
+    input_paths:
+      poses_json: ${...output_dir}/${...experiment_name}/poses.json
+      prior_intrinsics_filepath: ${...output_dir}/${...experiment_name}/intrinsics.json
+      images_dir: ${...feat_extract_match.input_paths.images_dir}
+      database_filepath: ${...feat_extract_match.output_paths.output_dir}/${...feat_extract_match.output_paths.database_filename}
+    output_paths:
+      output_dir: ${...output_dir}/${...experiment_name}
+      model_dirname: sparse_model
+    mapping_params:
+      min_focal_length_ratio: 0.1
+      max_focal_length_ratio: 10.0
+      max_extra_param: .inf
+      ba_local_max_num_iterations: 30
+      ba_local_max_refinements: 3
+      ba_global_max_num_iterations: 75
+      ba_use_gpu: true
+      num_threads: 1
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: ${output_dir}/${experiment_name}
+    output_subdir: .hydra
+gs_3d:
+  random_seed: ${random_seed}
+  strategy:
+    _target_: gsplat.strategy.DefaultStrategy
+    verbose: true
+    prune_opa: 0.1
+    grow_grad2d: 0.0004
+    grow_scale3d: 0.01
+    prune_scale3d: 0.1
+    refine_start_iter: 500
+    refine_stop_iter: 15000
+    reset_every: 3000
+    refine_every: 100
+    absgrad: false
+    revised_opacity: false
+    key_for_gradient: means2d
+  disable_viewer: true
+  ckpt: null
+  compression: null
+  render_traj_path: interp
+  render_traj_trim: 5
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  input_paths:
+    model_dir: ${..output_dir}/${..experiment_name}/sparse_model
+    images_dir: ${..output_dir}/${..experiment_name}/masking/masked_images
+    masks_dir: ${..output_dir}/${..experiment_name}/masking/masks
+    valid_region_masks_dir: ${..output_dir}/${..experiment_name}/focus_stack/focus_stacked_masks
+  output_paths:
+    splat_dir: ${..output_dir}/${..experiment_name}/gs_3d
+  data_factor: 1
+  test_every: 8
+  patch_size: null
+  global_scale: 1.0
+  normalize_world_space: true
+  camera_model: pinhole
+  port: 8080
+  batch_size: 1
+  steps_scaler: 1.0
+  max_steps: 30000
+  eval_steps:
+  - 7000
+  - 30000
+  save_steps:
+  - 7000
+  - 30000
+  save_ply: true
+  ply_steps:
+  - 7000
+  - 30000
+  disable_video: true
+  init_type: sfm
+  init_num_pts: 100000
+  init_extent: 3.0
+  sh_degree: 3
+  sh_degree_interval: 1000
+  init_opa: 0.1
+  init_scale: 1.0
+  ssim_lambda: 0.2
+  near_plane: 0.01
+  far_plane: 10000000000.0
+  packed: false
+  sparse_grad: false
+  visible_adam: false
+  antialiased: false
+  random_bkgd: false
+  means_lr: 0.00016
+  scales_lr: 0.005
+  opacities_lr: 0.05
+  quats_lr: 0.001
+  sh0_lr: 0.0025
+  shN_lr: 0.000125
+  opacity_reg: 0.0
+  scale_reg: 0.0
+  pose_opt: false
+  pose_opt_lr: 1.0e-05
+  pose_opt_reg: 1.0e-06
+  pose_noise: 0.0
+  app_opt: false
+  app_embed_dim: 16
+  app_opt_lr: 0.001
+  app_opt_reg: 1.0e-06
+  use_bilateral_grid: false
+  bilateral_grid_shape:
+  - 16
+  - 16
+  - 8
+  depth_loss: false
+  depth_lambda: 0.01
+  bg_alpha_loss: true
+  bg_alpha_lambda: 0.5
+  tb_every: 100
+  tb_save_image: false
+  lpips_net: alex
+  with_ut: false
+  with_eval3d: false
+  use_fused_bilagrid: false
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: outputs/hydra/${now:%Y-%m-%d_%H-%M-%S}
+    output_subdir: .hydra
+output_dir: outputs/main_paper
+experiment_name: blueberry_20260526_160106
+random_seed: 0
+dataset_dir: data/blueberry_20260526_160106
+run:
+  focus_stack: true
+  masking: true
+  colmap: true
+  gs_3d: true

outputs/main_paper/blueberry_20260526_160106/.hydra/hydra.yaml

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+hydra:
+  run:
+    dir: ${output_dir}/${experiment_name}
+  sweep:
+    dir: multirun/${now:%Y-%m-%d}/${now:%H-%M-%S}
+    subdir: ${hydra.job.num}
+  launcher:
+    _target_: hydra._internal.core_plugins.basic_launcher.BasicLauncher
+  sweeper:
+    _target_: hydra._internal.core_plugins.basic_sweeper.BasicSweeper
+    max_batch_size: null
+    params: null
+  help:
+    app_name: ${hydra.job.name}
+    header: '${hydra.help.app_name} is powered by Hydra.
+
+      '
+    footer: 'Powered by Hydra (https://hydra.cc)
+
+      Use --hydra-help to view Hydra specific help
+
+      '
+    template: '${hydra.help.header}
+
+      == Configuration groups ==
+
+      Compose your configuration from those groups (group=option)
+
+
+      $APP_CONFIG_GROUPS
+
+
+      == Config ==
+
+      Override anything in the config (foo.bar=value)
+
+
+      $CONFIG
+
+
+      ${hydra.help.footer}
+
+      '
+  hydra_help:
+    template: 'Hydra (${hydra.runtime.version})
+
+      See https://hydra.cc for more info.
+
+
+      == Flags ==
+
+      $FLAGS_HELP
+
+
+      == Configuration groups ==
+
+      Compose your configuration from those groups (For example, append hydra/job_logging=disabled
+      to command line)
+
+
+      $HYDRA_CONFIG_GROUPS
+
+
+      Use ''--cfg hydra'' to Show the Hydra config.
+
+      '
+    hydra_help: ???
+  hydra_logging:
+    version: 1
+    formatters:
+      simple:
+        format: '[%(asctime)s][HYDRA] %(message)s'
+    handlers:
+      console:
+        class: logging.StreamHandler
+        formatter: simple
+        stream: ext://sys.stdout
+    root:
+      level: INFO
+      handlers:
+      - console
+    loggers:
+      logging_example:
+        level: DEBUG
+    disable_existing_loggers: false
+  job_logging:
+    version: 1
+    formatters:
+      simple:
+        format: '[%(asctime)s][%(name)s][%(levelname)s] - %(message)s'
+    handlers:
+      console:
+        class: logging.StreamHandler
+        formatter: simple
+        stream: ext://sys.stdout
+      file:
+        class: logging.FileHandler
+        formatter: simple
+        filename: ${hydra.runtime.output_dir}/${hydra.job.name}.log
+    root:
+      level: INFO
+      handlers:
+      - console
+      - file
+    disable_existing_loggers: false
+  env: {}
+  mode: RUN
+  searchpath: []
+  callbacks: {}
+  output_subdir: .hydra
+  overrides:
+    hydra:
+    - hydra.mode=RUN
+    task:
+    - +experiment=main_paper
+    - experiment_name=blueberry_20260526_160106
+    - dataset_dir=data/blueberry_20260526_160106
+  job:
+    name: run_pipeline
+    chdir: false
+    override_dirname: +experiment=main_paper,dataset_dir=data/blueberry_20260526_160106,experiment_name=blueberry_20260526_160106
+    id: ???
+    num: ???
+    config_name: pipeline
+    env_set: {}
+    env_copy: []
+    config:
+      override_dirname:
+        kv_sep: '='
+        item_sep: ','
+        exclude_keys: []
+  runtime:
+    version: 1.3.2
+    version_base: '1.3'
+    cwd: /storage/scratch1/8/razarcon3/Microscopic-3D-Reconstruction/reconstruction
+    config_sources:
+    - path: hydra.conf
+      schema: pkg
+      provider: hydra
+    - path: /storage/scratch1/8/razarcon3/Microscopic-3D-Reconstruction/reconstruction/configs
+      schema: file
+      provider: main
+    - path: ''
+      schema: structured
+      provider: schema
+    output_dir: /storage/scratch1/8/razarcon3/Microscopic-3D-Reconstruction/reconstruction/outputs/main_paper/blueberry_20260526_160106
+    choices:
+      experiment: main_paper
+      gs_3d: default
+      colmap: default
+      masking: default
+      focus_stack: default
+      hydra/env: default
+      hydra/callbacks: null
+      hydra/job_logging: default
+      hydra/hydra_logging: default
+      hydra/hydra_help: default
+      hydra/help: default
+      hydra/sweeper: basic
+      hydra/launcher: basic
+      hydra/output: default
+  verbose: false

outputs/main_paper/blueberry_20260526_160106/.hydra/overrides.yaml

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+- +experiment=main_paper
+- experiment_name=blueberry_20260526_160106
+- dataset_dir=data/blueberry_20260526_160106

outputs/main_paper/blueberry_20260526_160106/database.db

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:445ead555738a7a83cd2aaa7b59ad5819438cecb91ac6e449ea384d14ebce286
+size 128966656