Package the tubes

pyproject.toml

@@ -112,6 +112,9 @@ dev = [
 [project.scripts]
 cala = "cala.main:cli"
 
+[project.entry-points."noob.add_sources"]
+tubes = "cala.hooks:add_noob_sources"
+
 [build-system]
 requires = ["pdm-backend"]
 build-backend = "pdm.backend"

src/cala/data/long_recording.yaml

@@ -0,0 +1,212 @@
+noob_id: long-recording
+noob_model: noob.tube.TubeSpecification
+noob_version: 0.1.1.dev118+g64d81b7
+
+assets:
+  buffer:
+    type: cala.arrays.Buffer
+    params:
+      size: 100
+    scope: runner
+  footprints:
+    type: cala.arrays.Footprints
+    params:
+      sparsify: True
+    scope: runner
+  traces:
+    type: cala.arrays.Traces
+    scope: runner
+    params:
+      zarr_path: traces/
+      peek_size: 100
+      flush_interval: 1000
+  pix_stats:
+    type: cala.arrays.PixStats
+    scope: runner
+  comp_stats:
+    type: cala.arrays.CompStats
+    scope: runner
+  overlaps:
+    type: cala.arrays.Overlaps
+    scope: runner
+  residuals:
+    type: cala.arrays.Buffer
+    params:
+      size: 100
+    scope: runner
+
+
+nodes:
+  source:
+    type: cala.nodes.io.stream
+    params:
+      subdir: long_recording
+      extension: .avi
+  counter:
+    type: cala.nodes.prep.counter
+  frame:
+    type: cala.nodes.prep.package_frame
+    depends:
+      - frame: source.value
+      - index: counter.idx
+
+  #PREPROCESS BEGINS
+  hotpix:
+    type: cala.nodes.prep.blur
+    params:
+      method: median
+      kwargs:
+        ksize: 3
+    depends:
+      - frame: frame.value
+  flatten:
+    type: cala.nodes.prep.butter
+    params:
+      kwargs:
+        cutoff_frequency_ratio: 0.010
+    depends:
+      - frame: hotpix.frame
+  lines:
+    type: cala.nodes.prep.remove_mean
+    params:
+      orient: both
+    depends:
+      - frame: flatten.frame
+  motion:
+    type: cala.nodes.prep.Anchor
+    depends:
+      - frame: lines.frame
+  glow:
+    type: cala.nodes.prep.GlowRemover
+    depends:
+      - frame: motion.frame
+  gather:
+    type: gather
+    params:
+      n: 4
+    depends:
+      - glow.frame
+  downsample: # 20fps -> 5fps
+    type: cala.nodes.prep.downsample
+    params:
+      x_range: [ 250, 350 ]
+      y_range: [ 250, 350 ]
+      t_downsample: 4
+    depends:
+      - frames: gather.value
+  size_est:
+    type: cala.nodes.prep.SizeEst
+    params:
+      hardset_radius: 8
+    depends:
+      - frame: downsample.frame
+  cache:
+    type: cala.nodes.omf.pixel_stats.fill_buffer
+    depends:
+      - buffer: assets.buffer
+      - frame: downsample.frame
+  #PREPROCESS ENDS
+
+  # FRAME UPDATE BEGINS
+  trace_frame:
+    type: cala.nodes.omf.traces.Tracer
+    params:
+      tol: 0.001
+      max_iter: 100
+    depends:
+      - traces: assets.traces
+      - footprints: assets.footprints
+      - frame: downsample.frame
+      - overlaps: assets.overlaps
+  pix_frame:
+    type: cala.nodes.omf.pixel_stats.ingest_frame
+    depends:
+      - pixel_stats: assets.pix_stats
+      - frame: downsample.frame
+      - new_traces: trace_frame.latest_trace
+      - footprints: assets.footprints
+  comp_frame:
+    type: cala.nodes.omf.component_stats.ingest_frame
+    depends:
+      - component_stats: assets.comp_stats
+      - frame: downsample.frame
+      - new_traces: trace_frame.latest_trace
+  footprints_frame:
+    type: cala.nodes.omf.footprints.Footprinter
+    params:
+      bep: 0
+      tol: 0.0001
+      max_iter: 5
+      ratio_lb: 0.10
+    depends:
+      - footprints: assets.footprints
+      - pixel_stats: pix_frame.value
+      - component_stats: comp_frame.value
+
+  residual:
+    type: cala.nodes.omf.residual.Residuer
+    depends:
+      - frame: downsample.frame
+      - footprints: footprints_frame.footprints
+      - traces: assets.traces
+      - residuals: assets.residuals
+  # FRAME UPDATE ENDS
+
+  # DETECT BEGINS
+  nmf:
+    type: cala.nodes.segment.SliceNMF
+    params:
+      min_frames: 100
+      detect_thresh: 8.0
+      reprod_tol: 0.005
+    depends:
+      - residuals: residual.movie
+      - energy: residual.std
+      - detect_radius: size_est.radius
+  catalog:
+    type: cala.nodes.segment.Cataloger
+    params:
+      age_limit: 100
+      shape_smooth_kwargs:
+        ksize: [ 5, 5 ]
+        sigmaX: 0
+      trace_smooth_kwargs:
+        sigma: 2
+      merge_threshold: 0.9
+      val_threshold: 0.5
+      cnt_threshold: 5
+    depends:
+      - new_fps: nmf.new_fps
+      - new_trs: nmf.new_trs
+      - existing_fp: assets.footprints
+      - existing_tr: assets.traces
+  detect_update:
+    type: cala.nodes.segment.update_assets
+    depends:
+      - new_footprints: catalog.new_footprints
+      - new_traces: catalog.new_traces
+      - footprints: assets.footprints
+      - traces: assets.traces
+      - pixel_stats: assets.pix_stats
+      - component_stats: assets.comp_stats
+      - overlaps: assets.overlaps
+      - buffer: assets.buffer
+  #  DETECT ENDS
+
+  save_trace:
+    type: cala.nodes.io.save_asset
+    params:
+      target_epoch: 855999 #  formula: 1000 * n_chunks - 1
+      path: traces_fin/
+    depends:
+      - asset: assets.traces
+      - curr_epoch: counter.idx
+
+  save_shape:
+    type: cala.nodes.io.save_asset
+    params:
+      target_epoch: 855999 #  formula: 1000 * n_chunks - 1
+      path: footprints_fin/
+    depends:
+      - asset: assets.footprints
+      - curr_epoch: counter.idx

src/cala/hooks.py

@@ -0,0 +1,8 @@
+from pathlib import Path
+
+
+def add_noob_sources() -> list[Path]:
+    """
+    Expose packages tubes to noob via its ``noob.add_sources`` entrypoint.
+    """
+    return [Path(__file__).parent / "data"]