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softboiler · Oct 2, 2024 · 21094bb · 21094bb
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Showing 7 changed files with 63 additions and 94 deletions.
diff --git a/.dvc/config b/.dvc/config
@@ -1,4 +1,6 @@
 [core]
     remote = origin
+[hydra]
+    enabled = True
 ['remote "origin"']
     url = gs://boilercv
diff --git a/conf/config.yaml b/conf/config.yaml
@@ -0,0 +1,2 @@
+defaults:
+  - stage: "defaults.yaml"
diff --git a/conf/stage/defaults.yaml b/conf/stage/defaults.yaml
@@ -0,0 +1,11 @@
+scale: 1.3
+marker_scale: 20.0
+precision: 3
+display_rows: 12
+sample: "2024-07-18T17-44-35"
+only_sample: "--no-only-sample"
+load_src_from_outs: "--no-load-src-from-outs"
+frame_count: 0
+frame_step: 1
+compare_with_trackpy: "--no-compare-with-trackpy"
+guess_diameter: 21
diff --git a/conf/stage/trackpy.yaml b/conf/stage/trackpy.yaml
@@ -0,0 +1,11 @@
+scale: 1.3
+marker_scale: 20.0
+precision: 3
+display_rows: 12
+sample: "2024-07-18T17-44-35"
+only_sample: "--no-only-sample"
+load_src_from_outs: "--no-load-src-from-outs"
+frame_count: 0
+frame_step: 1
+compare_with_trackpy: "--compare-with-trackpy"
+guess_diameter: 21
diff --git a/docs/notebooks/find_objects.ipynb b/docs/notebooks/find_objects.ipynb
@@ -57,8 +57,6 @@
     "\"\"\"Notebook stage parameters.\"\"\"\n",
     "MODE = get_mode()\n",
     "\"\"\"Notebook execution mode.\"\"\"\n",
-    "PREVIEW_FRAME_COUNT = 50\n",
-    "\"\"\"Number of preview frames.\"\"\"\n",
     "Params.hide()"
    ]
   },
@@ -76,7 +74,7 @@
     "if isinstance(PARAMS, str):\n",
     "    params = Params.model_validate_json(PARAMS)\n",
     "elif MODE == \"docs\":\n",
-    "    PREVIEW_FRAME_COUNT = 10\n",
+    "    preview_frame_count = 10\n",
     "    params = Params(\n",
     "        context=init(mode=MODE),\n",
     "        compare_with_trackpy=True,\n",
@@ -94,6 +92,7 @@
     "frames_slice = slices.get(FRAME, slice(None))\n",
     "contours = get_contours_df2(one(params.contours)).loc[IndexSlice[frames_slice, :], :]\n",
     "frames = contours.reset_index()[FRAME].unique()\n",
+    "preview_frame_count = round(0.619233215798799 * len(frames) ** 0.447632153789354)\n",
     "\n",
     "# # ? Produce reduced-size docs data\n",
     "# from pathlib import Path\n",
@@ -153,7 +152,7 @@
     "data.plots.composite, ax = subplots()\n",
     "filled_path = one(params.filled)\n",
     "with load_video(\n",
-    "    filled_path, slices={FRAME: frames[:: (len(frames) // PREVIEW_FRAME_COUNT)]}\n",
+    "    filled_path, slices={FRAME: frames[:: int(len(frames) // preview_frame_count)]}\n",
     ") as video:\n",
     "    filled_preview = scale_bool(video)\n",
     "    composite_video = scale_bool(video).max(FRAME).values\n",

diff --git a/dvc.yaml b/dvc.yaml
@@ -1,131 +1,92 @@
 stages:
   skip_cloud:
-    cmd: pwsh -Command "./Invoke-Uv.ps1 boilercv-pipeline stage skip-cloud --scale ${scale} --marker-scale ${marker_scale} --precision ${precision} --display-rows ${display_rows}"
-    params:
-      - scale
-      - marker_scale
-      - precision
-      - display_rows
+    cmd: pwsh -Command "./Invoke-Uv.ps1 boilercv-pipeline stage skip-cloud --scale ${stage.scale} --marker-scale ${stage.marker_scale} --precision ${stage.precision} --display-rows ${stage.display_rows}"
+    params: ["stage"]
     outs:
       - data/cines:
           cache: false
           persist: true
           push: false
   convert:
-    cmd: pwsh -Command "./Invoke-Uv.ps1 boilercv-pipeline stage convert --scale ${scale} --marker-scale ${marker_scale} --precision ${precision} --display-rows ${display_rows}"
+    cmd: pwsh -Command "./Invoke-Uv.ps1 boilercv-pipeline stage convert --scale ${stage.scale} --marker-scale ${stage.marker_scale} --precision ${stage.precision} --display-rows ${stage.display_rows}"
     deps:
       - packages/pipeline/boilercv_pipeline/stages/convert
       - data/cines
-    params:
-      - scale
-      - marker_scale
-      - precision
-      - display_rows
+    params: ["stage"]
     outs:
       - data/large_sources:
           cache: false
           persist: true
           push: false
   binarize:
-    cmd: pwsh -Command "./Invoke-Uv.ps1 boilercv-pipeline stage binarize --scale ${scale} --marker-scale ${marker_scale} --precision ${precision} --display-rows ${display_rows}"
+    cmd: pwsh -Command "./Invoke-Uv.ps1 boilercv-pipeline stage binarize --scale ${stage.scale} --marker-scale ${stage.marker_scale} --precision ${stage.precision} --display-rows ${stage.display_rows}"
     deps:
       - packages/pipeline/boilercv_pipeline/stages/binarize
       - data/large_sources
-    params:
-      - scale
-      - marker_scale
-      - precision
-      - display_rows
+    params: ["stage"]
     outs:
       - data/sources:
           persist: true
       - data/rois:
           persist: true
   preview_gray:
-    cmd: pwsh -Command "./Invoke-Uv.ps1 boilercv-pipeline stage preview-gray --scale ${scale} --marker-scale ${marker_scale} --precision ${precision} --display-rows ${display_rows}"
+    cmd: pwsh -Command "./Invoke-Uv.ps1 boilercv-pipeline stage preview-gray --scale ${stage.scale} --marker-scale ${stage.marker_scale} --precision ${stage.precision} --display-rows ${stage.display_rows}"
     deps:
       - packages/pipeline/boilercv_pipeline/stages/preview_gray
       - data/large_sources
-    params:
-      - scale
-      - marker_scale
-      - precision
-      - display_rows
+    params: ["stage"]
     outs:
       - data/previews/gray_preview.nc:
           persist: true
   preview_binarized:
-    cmd: pwsh -Command "./Invoke-Uv.ps1 boilercv-pipeline stage preview-binarized --scale ${scale} --marker-scale ${marker_scale} --precision ${precision} --display-rows ${display_rows}"
+    cmd: pwsh -Command "./Invoke-Uv.ps1 boilercv-pipeline stage preview-binarized --scale ${stage.scale} --marker-scale ${stage.marker_scale} --precision ${stage.precision} --display-rows ${stage.display_rows}"
     deps:
       - packages/pipeline/boilercv_pipeline/stages/preview_binarized
       - data/sources
       - data/rois
-    params:
-      - scale
-      - marker_scale
-      - precision
-      - display_rows
+    params: ["stage"]
     outs:
       - data/previews/binarized_preview.nc:
           persist: true
   find_contours:
-    cmd: pwsh -Command "./Invoke-Uv.ps1 boilercv-pipeline stage find-contours --scale ${scale} --marker-scale ${marker_scale} --precision ${precision} --display-rows ${display_rows}"
+    cmd: pwsh -Command "./Invoke-Uv.ps1 boilercv-pipeline stage find-contours --scale ${stage.scale} --marker-scale ${stage.marker_scale} --precision ${stage.precision} --display-rows ${stage.display_rows}"
     deps:
       - packages/pipeline/boilercv_pipeline/stages/find_contours
       - data/sources
       - data/rois
-    params:
-      - scale
-      - marker_scale
-      - precision
-      - display_rows
+    params: ["stage"]
     outs:
       - data/contours:
           persist: true
   fill:
-    cmd: pwsh -Command "./Invoke-Uv.ps1 boilercv-pipeline stage fill --scale ${scale} --marker-scale ${marker_scale} --precision ${precision} --display-rows ${display_rows}"
+    cmd: pwsh -Command "./Invoke-Uv.ps1 boilercv-pipeline stage fill --scale ${stage.scale} --marker-scale ${stage.marker_scale} --precision ${stage.precision} --display-rows ${stage.display_rows}"
     deps:
       - packages/pipeline/boilercv_pipeline/stages/fill
       - data/sources
       - data/rois
       - data/contours
-    params:
-      - scale
-      - marker_scale
-      - precision
-      - display_rows
+    params: ["stage"]
     outs:
       - data/filled:
           persist: true
   preview_filled:
-    cmd: pwsh -Command "./Invoke-Uv.ps1 boilercv-pipeline stage preview-filled --scale ${scale} --marker-scale ${marker_scale} --precision ${precision} --display-rows ${display_rows}"
+    cmd: pwsh -Command "./Invoke-Uv.ps1 boilercv-pipeline stage preview-filled --scale ${stage.scale} --marker-scale ${stage.marker_scale} --precision ${stage.precision} --display-rows ${stage.display_rows}"
     deps:
       - packages/pipeline/boilercv_pipeline/stages/preview_filled
       - data/filled
       - data/rois
-    params:
-      - scale
-      - marker_scale
-      - precision
-      - display_rows
+    params: ["stage"]
     outs:
       - data/previews/filled_preview.nc:
           persist: true
   get_thermal_data:
-    cmd: pwsh -Command "./Invoke-Uv.ps1 boilercv-pipeline stage get-thermal-data --scale ${scale} --marker-scale ${marker_scale} --precision ${precision} --display-rows ${display_rows} --sample ${sample} ${only_sample} ${load_src_from_outs}"
+    cmd: pwsh -Command "./Invoke-Uv.ps1 boilercv-pipeline stage get-thermal-data --scale ${stage.scale} --marker-scale ${stage.marker_scale} --precision ${stage.precision} --display-rows ${stage.display_rows} --sample ${stage.sample} ${stage.only_sample} ${stage.load_src_from_outs}"
     deps:
       - packages/pipeline/boilercv_pipeline/stages/get_thermal_data
       - docs/notebooks/get_thermal_data.ipynb
       - data/thermal
       - data/models
-    params:
-      - scale
-      - marker_scale
-      - precision
-      - display_rows
-      - sample
-      - only_sample
-      - load_src_from_outs
+    params: ["stage"]
     outs:
       - data/e230920/thermal.h5:
           persist: true
@@ -134,23 +95,13 @@ stages:
       - data/e230920/thermal_plots/subcool_superheat.png
       - data/e230920/thermal_plots/superheat.png
   find_objects:
-    cmd: pwsh -Command "./Invoke-Uv.ps1 boilercv-pipeline stage find-objects --scale ${scale} --marker-scale ${marker_scale} --precision ${precision} --display-rows ${display_rows} --sample ${sample} ${only_sample} --frame-count ${frame_count} --frame-step ${frame_step} ${compare_with_trackpy} --guess-diameter ${guess_diameter}"
+    cmd: pwsh -Command "./Invoke-Uv.ps1 boilercv-pipeline stage find-objects --scale ${stage.scale} --marker-scale ${stage.marker_scale} --precision ${stage.precision} --display-rows ${stage.display_rows} --sample ${stage.sample} ${stage.only_sample} --frame-count ${stage.frame_count} --frame-step ${stage.frame_step} ${stage.compare_with_trackpy} --guess-diameter ${stage.guess_diameter}"
     deps:
       - packages/pipeline/boilercv_pipeline/stages/find_objects
       - docs/notebooks/find_objects.ipynb
       - data/filled
       - data/contours
-    params:
-      - scale
-      - marker_scale
-      - precision
-      - display_rows
-      - sample
-      - only_sample
-      - frame_count
-      - frame_step
-      - compare_with_trackpy
-      - guess_diameter
+    params: ["stage"]
     outs:
       - data/e230920/objects:
           persist: true
@@ -172,22 +123,14 @@ stages:
       - data/e230920/objects_plots/composite_2024-07-18T18-40-58.png
       - data/e230920/objects_plots/composite_2024-07-18T18-49-55.png
   find_tracks:
-    cmd: pwsh -Command "./Invoke-Uv.ps1 boilercv-pipeline stage find-tracks --scale ${scale} --marker-scale ${marker_scale} --precision ${precision} --display-rows ${display_rows} --sample ${sample} ${only_sample} --frame-count ${frame_count} --frame-step ${frame_step}"
+    cmd: pwsh -Command "./Invoke-Uv.ps1 boilercv-pipeline stage find-tracks --scale ${stage.scale} --marker-scale ${stage.marker_scale} --precision ${stage.precision} --display-rows ${stage.display_rows} --sample ${stage.sample} ${stage.only_sample} --frame-count ${stage.frame_count} --frame-step ${stage.frame_step}"
     deps:
       - packages/pipeline/boilercv_pipeline/stages/find_tracks
       - docs/notebooks/find_tracks.ipynb
       - data/filled
       - data/e230920/objects
       - data/e230920/thermal.h5
-    params:
-      - scale
-      - marker_scale
-      - precision
-      - display_rows
-      - sample
-      - only_sample
-      - frame_count
-      - frame_step
+    params: ["stage"]
     outs:
       - data/e230920/tracks:
           persist: true

diff --git a/params.yaml b/params.yaml
@@ -1,11 +1,12 @@
-scale: 1.3
-marker_scale: 20.0
-precision: 3
-display_rows: 12
-sample: 2024-07-18T17-44-35
-only_sample: --no-only-sample
-load_src_from_outs: --no-load-src-from-outs
-frame_count: 0
-frame_step: 1
-compare_with_trackpy: --no-compare-with-trackpy
-guess_diameter: 21
+stage:
+  scale: 1.3
+  marker_scale: 20.0
+  precision: 3
+  display_rows: 12
+  sample: "2024-07-18T17-44-35"
+  only_sample: "--no-only-sample"
+  load_src_from_outs: "--no-load-src-from-outs"
+  frame_count: 0
+  frame_step: 1
+  compare_with_trackpy: "--no-compare-with-trackpy"
+  guess_diameter: 21