Revert "Updated the paths in configs (merged from main)"

This reverts commit 4d42ed9.
AllenCell · Nov 25, 2024 · 35e7977 · 35e7977
1 parent 4d42ed9
commit 35e7977
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Showing 12 changed files with 47 additions and 311 deletions.
diff --git a/configs/experiment/npm1_variance/image_sdf_classical.yaml b/configs/experiment/npm1_variance/image_sdf_classical.yaml
diff --git a/configs/experiment/npm1_variance/image_sdf_so3.yaml b/configs/experiment/npm1_variance/image_sdf_so3.yaml
diff --git a/configs/experiment/npm1_variance/image_seg_classical.yaml b/configs/experiment/npm1_variance/image_seg_classical.yaml
diff --git a/configs/experiment/npm1_variance/image_seg_so3.yaml b/configs/experiment/npm1_variance/image_seg_so3.yaml
diff --git a/configs/experiment/npm1_variance/pc_implicit.yaml b/configs/experiment/npm1_variance/pc_implicit.yaml
diff --git a/configs/logger/csv.yaml b/configs/logger/csv.yaml
@@ -4,4 +4,4 @@ csv:
   _target_: lightning.pytorch.loggers.csv_logs.CSVLogger
   save_dir: "${paths.output_dir}"
   name: "csv/"
-  prefix: ""
+  prefix: ""
diff --git a/configs/results/cellpack.yaml b/configs/results/cellpack.yaml
@@ -17,11 +17,13 @@ names:
     "Rotation_invariant_pointcloud",
     "Rotation_invariant_pointcloud_jitter",
   ]
-data_paths: [
-    "./configs/data/cellpack/image.yaml",
-    "./configs/data/cellpack/image.yaml",
-    "./configs/data/cellpack/pc.yaml",
-    "./configs/data/cellpack/pc.yaml",
-    # "./src/br/configs/data/cellpack/pc_jitter.yaml",
-    "./configs/data/cellpack/pc.yaml",
+data_paths:
+  [
+    "/data/cellpack/image.yaml",
+    "/data/cellpack/image.yaml",
+    "/data/cellpack/pc.yaml",
+    "/data/cellpack/pc.yaml",
+    "/data/cellpack/pc.yaml",
   ]
+classification_label: ["rule"]
+regression_label:
diff --git a/configs/results/npm1.yaml b/configs/results/npm1.yaml
@@ -19,9 +19,12 @@ names:
   ]
 data_paths:
   [
-    "./configs/data/npm1/pc.yaml",
-    "./configs/data/npm1/so3_image_sdf.yaml",
-    "./configs/data/npm1/so3_image_seg.yaml",
-    "./configs/data/npm1/classical_image_sdf.yaml",
-    "./configs/data/npm1/classical_image_seg.yaml",
+    "/data/npm1/pc.yaml",
+    "/data/npm1/so3_image_sdf.yaml",
+    "/data/npm1/so3_image_seg.yaml",
+    "/data/npm1/classical_image_sdf.yaml",
+    "/data/npm1/classical_image_seg.yaml",
   ]
+classification_label: ["STR_connectivity_cc_thresh"]
+regression_label:
+  ["mean_centroid_distances", "mean_nucleolus_volume", "mean_nucleolus_area"]
diff --git a/configs/results/npm1_perturb.yaml b/configs/results/npm1_perturb.yaml
@@ -19,9 +19,9 @@ names:
   ]
 data_paths:
   [
-    "./configs/data/npm1_perturb/pc.yaml",
-    "./configs/data/npm1_perturb/classical_image_sdf.yaml",
-    "./configs/data/npm1_perturb/classical_image_seg.yaml",
-    "./configs/data/npm1_perturb/so3_image_sdf.yaml",
-    "./configs/data/npm1_perturb/so3_image_seg.yaml",
+    "/data/npm1_perturb/pc.yaml",
+    "/data/npm1_perturb/classical_image_sdf.yaml",
+    "/data/npm1_perturb/classical_image_seg.yaml",
+    "/data/npm1_perturb/so3_image_sdf.yaml",
+    "/data/npm1_perturb/so3_image_seg.yaml",
   ]
diff --git a/configs/results/other_polymorphic.yaml b/configs/results/other_polymorphic.yaml
@@ -19,9 +19,11 @@ names:
   ]
 data_paths:
   [
-    "./configs/data/other_polymorphic/pc.yaml",
-    "./configs/data/other_polymorphic/so3_image_sdf.yaml",
-    "./configs/data/other_polymorphic/so3_image_seg.yaml",
-    "./configs/data/other_polymorphic/classical_image_sdf.yaml",
-    "./configs/data/other_polymorphic/classical_image_seg.yaml",
+    "/data/other_polymorphic/pc.yaml",
+    "/data/other_polymorphic/so3_image_sdf.yaml",
+    "/data/other_polymorphic/so3_image_seg.yaml",
+    "/data/other_polymorphic/classical_image_sdf.yaml",
+    "/data/other_polymorphic/classical_image_seg.yaml",
   ]
+classification_label: ["structure_name"]
+regression_label: ["avg_dists", "mean_volume", "mean_surface_area"]
diff --git a/configs/results/other_punctate.yaml b/configs/results/other_punctate.yaml
@@ -6,22 +6,21 @@ model_checkpoints:
     "./morphology_appropriate_representation_learning/model_checkpoints/other_punctate/Classical_image.ckpt",
     "./morphology_appropriate_representation_learning/model_checkpoints/other_punctate/Rotation_invariant_image.ckpt",
     "./morphology_appropriate_representation_learning/model_checkpoints/other_punctate/Classical_pointcloud.ckpt",
-    "./morphology_appropriate_representation_learning/model_checkpoints/other_punctate/Rotation_invariant_pointcloud.ckpt",
     "./morphology_appropriate_representation_learning/model_checkpoints/other_punctate/Rotation_invariant_pointcloud_structurenorm.ckpt",
   ]
 names:
   [
     "Classical_image",
     "Rotation_invariant_image",
     "Classical_pointcloud",
-    "Rotation_invariant_pointcloud",
     "Rotation_invariant_pointcloud_structurenorm",
   ]
 data_paths:
   [
-    "./configs/data/other_punctate/image.yaml",
-    "./configs/data/other_punctate/image.yaml",
-    "./configs/data/other_punctate/pc.yaml",
-    "./configs/data/other_punctate/pc_intensity.yaml",
-    "./configs/data/other_punctate/pc_intensity_structurenorm.yaml",
+    "/data/other_punctate/image.yaml",
+    "/data/other_punctate/image.yaml",
+    "/data/other_punctate/pc.yaml",
+    "/data/other_punctate/pc_intensity_structurenorm.yaml",
   ]
+classification_label: ["structure_name", "cell_stage"]
+regression_label: