Updated the paths in configs (merged from main)

configs/experiment/npm1_variance/image_sdf_classical.yaml

@@ -0,0 +1,54 @@
+# @package _global_
+
+# to execute this experiment run:
+# python train.py experiment=example
+
+defaults:
+  - override /data: other_polymorphic/classical_image_sdf.yaml
+  - override /model: image/classical_sdf_35.yaml
+  - override /callbacks: default.yaml
+  - override /trainer: default.yaml
+  - override /logger: csv.yaml
+
+# all parameters below will be merged with parameters from default configurations set above
+# this allows you to overwrite only specified parameters
+
+experiment_name: npm1_variance
+tags: ["equivariance"]
+
+seed: 42
+
+data:
+  batch_size: 4
+
+model:
+  x_label: image
+
+trainer:
+  check_val_every_n_epoch: 1
+  min_epochs: 400
+  max_epochs: 2000
+  accelerator: gpu
+  devices: [0]
+
+callbacks:
+  early_stopping:
+    monitor: val/loss
+
+  model_checkpoint:
+    dirpath: ./npm1_variance/ckpts
+    monitor: val/loss
+    save_top_k: 2
+    every_n_epochs: 1
+
+logger:
+  csv:
+    save_dir: ./npm1_variance
+    name: "classical_sdf"
+    prefix:
+
+##### ONLY USE WITH A100s
+extras:
+  precision:
+    _target_: torch.set_float32_matmul_precision
+    precision: medium

configs/experiment/npm1_variance/image_sdf_so3.yaml

@@ -0,0 +1,55 @@
+# @package _global_
+
+# to execute this experiment run:
+# python train.py experiment=example
+
+defaults:
+  - override /data: npm1/classical_image_sdf.yaml
+  - override /model: image/classical_sdf_35.yaml
+  - override /callbacks: default.yaml
+  - override /trainer: default.yaml
+  - override /logger: csv.yaml
+
+# all parameters below will be merged with parameters from default configurations set above
+# this allows you to overwrite only specified parameters
+
+experiment_name: npm1_variance
+tags: ["equivariance"]
+
+seed: 42
+
+data:
+  batch_size: 4
+
+model:
+  x_label: image
+  group: so3
+
+trainer:
+  check_val_every_n_epoch: 1
+  min_epochs: 400
+  max_epochs: 2000
+  accelerator: gpu
+  devices: [0]
+
+callbacks:
+  early_stopping:
+    monitor: val/loss
+
+  model_checkpoint:
+    dirpath: ./npm1_variance/ckpts
+    monitor: val/loss
+    save_top_k: 2
+    every_n_epochs: 1
+
+logger:
+  csv:
+    save_dir: ./npm1_variance
+    name: "so3_sdf"
+    prefix:
+
+##### ONLY USE WITH A100s
+extras:
+  precision:
+    _target_: torch.set_float32_matmul_precision
+    precision: medium

configs/experiment/npm1_variance/image_seg_classical.yaml

@@ -0,0 +1,54 @@
+# @package _global_
+
+# to execute this experiment run:
+# python train.py experiment=example
+
+defaults:
+  - override /data: npm1/classical_image_seg.yaml
+  - override /model: image/classical_seg_35.yaml
+  - override /callbacks: default.yaml
+  - override /trainer: default.yaml
+  - override /logger: csv.yaml
+
+# all parameters below will be merged with parameters from default configurations set above
+# this allows you to overwrite only specified parameters
+
+experiment_name: npm1_variance
+tags: ["equivariance"]
+
+seed: 42
+
+data:
+  batch_size: 4
+
+model:
+  x_label: image
+
+trainer:
+  check_val_every_n_epoch: 1
+  min_epochs: 400
+  max_epochs: 2000
+  accelerator: gpu
+  devices: [0]
+
+callbacks:
+  early_stopping:
+    monitor: val/loss
+
+  model_checkpoint:
+    dirpath: ./npm1_variance/ckpts
+    monitor: val/loss
+    save_top_k: 2
+    every_n_epochs: 1
+
+logger:
+  csv:
+    save_dir: ./npm1_variance
+    name: "classical_seg"
+    prefix:
+
+##### ONLY USE WITH A100s
+extras:
+  precision:
+    _target_: torch.set_float32_matmul_precision
+    precision: medium

configs/experiment/npm1_variance/image_seg_so3.yaml

@@ -0,0 +1,55 @@
+# @package _global_
+
+# to execute this experiment run:
+# python train.py experiment=example
+
+defaults:
+  - override /data: npm1/classical_image_seg.yaml
+  - override /model: image/classical_seg_35.yaml
+  - override /callbacks: default.yaml
+  - override /trainer: default.yaml
+  - override /logger: csv.yaml
+
+# all parameters below will be merged with parameters from default configurations set above
+# this allows you to overwrite only specified parameters
+
+experiment_name: npm1_variance
+tags: ["equivariance"]
+
+seed: 42
+
+data:
+  batch_size: 4
+
+model:
+  x_label: image
+  group: so3
+
+trainer:
+  check_val_every_n_epoch: 1
+  min_epochs: 400
+  max_epochs: 2000
+  accelerator: gpu
+  devices: [0]
+
+callbacks:
+  early_stopping:
+    monitor: val/loss
+
+  model_checkpoint:
+    dirpath: ./npm1_variance/ckpts
+    monitor: val/loss
+    save_top_k: 2
+    every_n_epochs: 1
+
+logger:
+  csv:
+    save_dir: ./npm1_variance
+    name: "so3_seg"
+    prefix:
+
+##### ONLY USE WITH A100s
+extras:
+  precision:
+    _target_: torch.set_float32_matmul_precision
+    precision: medium

configs/experiment/npm1_variance/pc_implicit.yaml

@@ -0,0 +1,54 @@
+# @package _global_
+
+# to execute this experiment run:
+# python train.py experiment=example
+
+defaults:
+  - override /data: npm1/pc.yaml
+  - override /model: pc/implicit.yaml
+  - override /callbacks: default.yaml
+  - override /trainer: default.yaml
+  - override /logger: csv.yaml
+
+# all parameters below will be merged with parameters from default configurations set above
+# this allows you to overwrite only specified parameters
+
+experiment_name: npm1_variance
+tags: ["equivariance"]
+
+seed: 42
+
+data:
+  batch_size: 4
+
+model:
+  x_label: pcloud
+
+trainer:
+  check_val_every_n_epoch: 1
+  min_epochs: 400
+  max_epochs: 2000
+  accelerator: gpu
+  devices: [0]
+
+callbacks:
+  early_stopping:
+    monitor: val/loss
+
+  model_checkpoint:
+    dirpath: ./npm1_variance/ckpts
+    monitor: val/loss
+    save_top_k: 2
+    every_n_epochs: 1
+
+logger:
+  csv:
+    save_dir: ./npm1_variance
+    name: "pc_implicit"
+    prefix:
+
+##### ONLY USE WITH A100s
+extras:
+  precision:
+    _target_: torch.set_float32_matmul_precision
+    precision: medium

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: ""

configs/results/cellpack.yaml

@@ -17,13 +17,11 @@ names:
     "Rotation_invariant_pointcloud",
     "Rotation_invariant_pointcloud_jitter",
   ]
-data_paths:
-  [
-    "/data/cellpack/image.yaml",
-    "/data/cellpack/image.yaml",
-    "/data/cellpack/pc.yaml",
-    "/data/cellpack/pc.yaml",
-    "/data/cellpack/pc.yaml",
+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",
   ]
-classification_label: ["rule"]
-regression_label:

configs/results/npm1.yaml

@@ -19,12 +19,9 @@ names:
   ]
 data_paths:
   [
-    "/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",
+    "./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",
   ]
-classification_label: ["STR_connectivity_cc_thresh"]
-regression_label:
-  ["mean_centroid_distances", "mean_nucleolus_volume", "mean_nucleolus_area"]

configs/results/npm1_perturb.yaml

@@ -19,9 +19,9 @@ names:
   ]
 data_paths:
   [
-    "/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",
+    "./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",
   ]

configs/results/other_polymorphic.yaml

@@ -19,11 +19,9 @@ names:
   ]
 data_paths:
   [
-    "/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",
+    "./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",
   ]
-classification_label: ["structure_name"]
-regression_label: ["avg_dists", "mean_volume", "mean_surface_area"]

configs/results/other_punctate.yaml

@@ -6,21 +6,22 @@ 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:
   [
-    "/data/other_punctate/image.yaml",
-    "/data/other_punctate/image.yaml",
-    "/data/other_punctate/pc.yaml",
-    "/data/other_punctate/pc_intensity_structurenorm.yaml",
+    "./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",
   ]
-classification_label: ["structure_name", "cell_stage"]
-regression_label: