add almond + blueberry

outputs/automatic/almond/.hydra/config.yaml

@@ -1,344 +0,0 @@
-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: laplacian
-  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
-  output_paths:
-    output_dir: ${..output_dir}/${..experiment_name}/masking
-    masks_subdir: masks
-  bootstrap:
-    min_contour_area: 100.0
-    morph_kernel_size: 5
-    bootstrap_stem: scan00
-    bbox_padding: 20
-  sam3:
-    checkpoint_path: null
-    bpe_path: null
-    compile: false
-    prompt: null
-    output_prob_thresh: 0.5
-    device: null
-  visualization:
-    overlay_alpha: 0.4
-    overlay_color:
-    - 255
-    - 0
-    - 0
-  appearance:
-    enabled: true
-    top_k: 5
-    tau: 3.0
-    min_mutual_neighbors: 1
-  mask_sanity:
-    min_mask_area_frac: 1.0e-05
-    max_bbox_area_frac: 0.8
-    min_mask_fill_ratio: 0.02
-    max_mask_components: 3
-  rerun:
-    enabled: true
-    anchor_top_k: 3
-    anchor_strategy: hybrid
-    anchor_index_weight: 0.15
-  dinov3:
-    model: vit_small_patch16_dinov3
-    pretrained: true
-    image_size: 512
-    device: null
-    patch_similarity_threshold: 0.45
-    max_bad_patch_fraction: 0.2
-    min_patch_mean_score: -1.0
-    max_patch_bank: 20000
-  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: triangulate
-    load_prior_poses: false
-    load_prior_intrinsics: false
-    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: false
-      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
-gs_2d:
-  random_seed: ${random_seed}
-  disable_viewer: false
-  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}/focus_stack/focus_stacked_images
-    masks_dir: ${..output_dir}/${..experiment_name}/masking/masks
-  output_paths:
-    splat_dir: ${..output_dir}/${..experiment_name}/gs_2d
-  data_factor: 4
-  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: false
-  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
-  model_type: 2dgs
-  near_plane: 0.2
-  far_plane: 200
-  packed: false
-  sparse_grad: false
-  absgrad: false
-  antialiased: false
-  revised_opacity: false
-  random_bkgd: false
-  prune_opa: 0.05
-  grow_grad2d: 0.0002
-  grow_scale3d: 0.01
-  prune_scale3d: 0.1
-  refine_start_iter: 500
-  refine_stop_iter: 15000
-  reset_every: 3000
-  refine_every: 100
-  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
-  depth_loss: false
-  depth_lambda: 0.01
-  bg_alpha_loss: true
-  bg_alpha_lambda: 0.5
-  normal_loss: false
-  normal_lambda: 0.05
-  normal_start_iter: 7000
-  dist_loss: false
-  dist_lambda: 0.01
-  dist_start_iter: 3000
-  tb_every: 100
-  tb_save_image: false
-  hydra:
-    job:
-      chdir: false
-    run:
-      dir: outputs/hydra/${now:%Y-%m-%d_%H-%M-%S}
-    output_subdir: .hydra
-output_dir: ../microscope-data/outputs/automatic
-experiment_name: almond
-random_seed: 0
-dataset_dir: /home/rmineyev3/Microscopic-3D-Reconstruction/microscope-data/scans/almond
-run:
-  focus_stack: true
-  masking: true
-  colmap: true
-  splatting_method: gs_3d
-reconstruction:
-  mode: automatic

outputs/automatic/almond/.hydra/hydra.yaml

@@ -1,163 +0,0 @@
-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=automatic
-    - dataset_dir=/home/rmineyev3/Microscopic-3D-Reconstruction/microscope-data/scans/almond
-    - experiment_name=almond
-  job:
-    name: run_pipeline
-    chdir: false
-    override_dirname: +experiment=automatic,dataset_dir=/home/rmineyev3/Microscopic-3D-Reconstruction/microscope-data/scans/almond,experiment_name=almond
-    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: /home/rmineyev3/Microscopic-3D-Reconstruction/reconstruction
-    config_sources:
-    - path: hydra.conf
-      schema: pkg
-      provider: hydra
-    - path: /home/rmineyev3/Microscopic-3D-Reconstruction/reconstruction/configs
-      schema: file
-      provider: main
-    - path: ''
-      schema: structured
-      provider: schema
-    output_dir: /home/rmineyev3/Microscopic-3D-Reconstruction/microscope-data/outputs/automatic/almond
-    choices:
-      experiment: automatic
-      gs_2d: default
-      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/automatic/almond/.hydra/overrides.yaml

@@ -1,3 +0,0 @@
-- +experiment=automatic
-- dataset_dir=/home/rmineyev3/Microscopic-3D-Reconstruction/microscope-data/scans/almond
-- experiment_name=almond

outputs/automatic/almond/database.db

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:47defee062f377bd9a6153f887001a35f07c99621fa938b1590cafc41c0b1729
-size 118804480