diff --git a/configs/experiment/npm1_variance/image_sdf_classical.yaml b/configs/experiment/npm1_variance/image_sdf_classical.yaml deleted file mode 100644 index 360d017..0000000 --- a/configs/experiment/npm1_variance/image_sdf_classical.yaml +++ /dev/null @@ -1,54 +0,0 @@ -# @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 diff --git a/configs/experiment/npm1_variance/image_sdf_so3.yaml b/configs/experiment/npm1_variance/image_sdf_so3.yaml deleted file mode 100644 index 41d3805..0000000 --- a/configs/experiment/npm1_variance/image_sdf_so3.yaml +++ /dev/null @@ -1,55 +0,0 @@ -# @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 diff --git a/configs/experiment/npm1_variance/image_seg_classical.yaml b/configs/experiment/npm1_variance/image_seg_classical.yaml deleted file mode 100644 index 825db57..0000000 --- a/configs/experiment/npm1_variance/image_seg_classical.yaml +++ /dev/null @@ -1,54 +0,0 @@ -# @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 diff --git a/configs/experiment/npm1_variance/image_seg_so3.yaml b/configs/experiment/npm1_variance/image_seg_so3.yaml deleted file mode 100644 index aef8ada..0000000 --- a/configs/experiment/npm1_variance/image_seg_so3.yaml +++ /dev/null @@ -1,55 +0,0 @@ -# @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 diff --git a/configs/experiment/npm1_variance/pc_implicit.yaml b/configs/experiment/npm1_variance/pc_implicit.yaml deleted file mode 100644 index fb4df04..0000000 --- a/configs/experiment/npm1_variance/pc_implicit.yaml +++ /dev/null @@ -1,54 +0,0 @@ -# @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 diff --git a/configs/logger/csv.yaml b/configs/logger/csv.yaml index c524e13..fa028e9 100644 --- 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: "" \ No newline at end of file + prefix: "" diff --git a/configs/results/cellpack.yaml b/configs/results/cellpack.yaml index ed588ed..67cd66e 100644 --- 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 index 97c2f9c..d2c2dd0 100644 --- 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 index 5a5a5ea..492e61b 100644 --- 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 index 2b4319f..cccc773 100644 --- 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 index da1f528..3ea855b 100644 --- a/configs/results/other_punctate.yaml +++ b/configs/results/other_punctate.yaml @@ -6,7 +6,6 @@ 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: @@ -14,14 +13,14 @@ 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: diff --git a/configs/results/pcna.yaml b/configs/results/pcna.yaml index 9c4f184..e481b22 100644 --- a/configs/results/pcna.yaml +++ b/configs/results/pcna.yaml @@ -3,25 +3,27 @@ image_path: ./morphology_appropriate_representation_learning/preprocessed_data/p pc_path: ./morphology_appropriate_representation_learning/preprocessed_data/pcna/manifest.csv model_checkpoints: [ - "./morphology_appropriate_representation_learning/model_checkpoints/pcna/Classical_pointcloud.ckpt", - "./morphology_appropriate_representation_learning/model_checkpoints/pcna/Rotation_invariant_pointcloud.ckpt", "./morphology_appropriate_representation_learning/model_checkpoints/pcna/Classical_image.ckpt", "./morphology_appropriate_representation_learning/model_checkpoints/pcna/Rotation_invariant_image.ckpt", + "./morphology_appropriate_representation_learning/model_checkpoints/pcna/Classical_pointcloud.ckpt", + "./morphology_appropriate_representation_learning/model_checkpoints/pcna/Rotation_invariant_pointcloud.ckpt", "./morphology_appropriate_representation_learning/model_checkpoints/pcna/Rotation_invariant_pointcloud_jitter.ckpt", ] names: [ - "Classical_pointcloud", - "Rotation_invariant_pointcloud", "Classical_image", "Rotation_invariant_image", + "Classical_pointcloud", + "Rotation_invariant_pointcloud", "Rotation_invariant_pointcloud_jitter", ] data_paths: [ - "./configs/data/pcna/pc.yaml", - "./configs/data/pcna/pc_intensity.yaml", - "./configs/data/pcna/image.yaml", - "./configs/data/pcna/image.yaml", + "/data/pcna/image.yaml", + "/data/pcna/image.yaml", + "/data/pcna/pc.yaml", + "/data/pcna/pc_intensity.yaml", # "./src/br/configs/data/pcna/pc_intensity_jitter.yaml", - "./configs/data/pcna/pc_intensity.yaml", + "/data/pcna/pc_intensity.yaml", ] +classification_label: ["cell_stage_fine", "flag_comment"] +regression_label: