From 4d42ed97b70a8c2256f81d8bb5fea791f3024d07 Mon Sep 17 00:00:00 2001 From: Fatwir Mohammed Date: Mon, 25 Nov 2024 13:32:32 -0800 Subject: [PATCH] Updated the paths in configs (merged from main) --- .../npm1_variance/image_sdf_classical.yaml | 54 ++++++++++++++++++ .../npm1_variance/image_sdf_so3.yaml | 55 +++++++++++++++++++ .../npm1_variance/image_seg_classical.yaml | 54 ++++++++++++++++++ .../npm1_variance/image_seg_so3.yaml | 55 +++++++++++++++++++ .../experiment/npm1_variance/pc_implicit.yaml | 54 ++++++++++++++++++ configs/logger/csv.yaml | 2 +- configs/results/cellpack.yaml | 16 +++--- configs/results/npm1.yaml | 13 ++--- configs/results/npm1_perturb.yaml | 10 ++-- configs/results/other_polymorphic.yaml | 12 ++-- configs/results/other_punctate.yaml | 13 +++-- configs/results/pcna.yaml | 20 +++---- 12 files changed, 311 insertions(+), 47 deletions(-) create mode 100644 configs/experiment/npm1_variance/image_sdf_classical.yaml create mode 100644 configs/experiment/npm1_variance/image_sdf_so3.yaml create mode 100644 configs/experiment/npm1_variance/image_seg_classical.yaml create mode 100644 configs/experiment/npm1_variance/image_seg_so3.yaml create mode 100644 configs/experiment/npm1_variance/pc_implicit.yaml diff --git a/configs/experiment/npm1_variance/image_sdf_classical.yaml b/configs/experiment/npm1_variance/image_sdf_classical.yaml new file mode 100644 index 0000000..360d017 --- /dev/null +++ b/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 diff --git a/configs/experiment/npm1_variance/image_sdf_so3.yaml b/configs/experiment/npm1_variance/image_sdf_so3.yaml new file mode 100644 index 0000000..41d3805 --- /dev/null +++ b/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 diff --git a/configs/experiment/npm1_variance/image_seg_classical.yaml b/configs/experiment/npm1_variance/image_seg_classical.yaml new file mode 100644 index 0000000..825db57 --- /dev/null +++ b/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 diff --git a/configs/experiment/npm1_variance/image_seg_so3.yaml b/configs/experiment/npm1_variance/image_seg_so3.yaml new file mode 100644 index 0000000..aef8ada --- /dev/null +++ b/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 diff --git a/configs/experiment/npm1_variance/pc_implicit.yaml b/configs/experiment/npm1_variance/pc_implicit.yaml new file mode 100644 index 0000000..fb4df04 --- /dev/null +++ b/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 diff --git a/configs/logger/csv.yaml b/configs/logger/csv.yaml index fa028e9..c524e13 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: "" + prefix: "" \ No newline at end of file diff --git a/configs/results/cellpack.yaml b/configs/results/cellpack.yaml index 67cd66e..ed588ed 100644 --- a/configs/results/cellpack.yaml +++ b/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: diff --git a/configs/results/npm1.yaml b/configs/results/npm1.yaml index d2c2dd0..97c2f9c 100644 --- a/configs/results/npm1.yaml +++ b/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"] diff --git a/configs/results/npm1_perturb.yaml b/configs/results/npm1_perturb.yaml index 492e61b..5a5a5ea 100644 --- a/configs/results/npm1_perturb.yaml +++ b/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", ] diff --git a/configs/results/other_polymorphic.yaml b/configs/results/other_polymorphic.yaml index cccc773..2b4319f 100644 --- a/configs/results/other_polymorphic.yaml +++ b/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"] diff --git a/configs/results/other_punctate.yaml b/configs/results/other_punctate.yaml index 3ea855b..da1f528 100644 --- a/configs/results/other_punctate.yaml +++ b/configs/results/other_punctate.yaml @@ -6,6 +6,7 @@ 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: @@ -13,14 +14,14 @@ 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: diff --git a/configs/results/pcna.yaml b/configs/results/pcna.yaml index e481b22..9c4f184 100644 --- a/configs/results/pcna.yaml +++ b/configs/results/pcna.yaml @@ -3,27 +3,25 @@ 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_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/Classical_image.ckpt", + "./morphology_appropriate_representation_learning/model_checkpoints/pcna/Rotation_invariant_image.ckpt", "./morphology_appropriate_representation_learning/model_checkpoints/pcna/Rotation_invariant_pointcloud_jitter.ckpt", ] names: [ - "Classical_image", - "Rotation_invariant_image", "Classical_pointcloud", "Rotation_invariant_pointcloud", + "Classical_image", + "Rotation_invariant_image", "Rotation_invariant_pointcloud_jitter", ] data_paths: [ - "/data/pcna/image.yaml", - "/data/pcna/image.yaml", - "/data/pcna/pc.yaml", - "/data/pcna/pc_intensity.yaml", + "./configs/data/pcna/pc.yaml", + "./configs/data/pcna/pc_intensity.yaml", + "./configs/data/pcna/image.yaml", + "./configs/data/pcna/image.yaml", # "./src/br/configs/data/pcna/pc_intensity_jitter.yaml", - "/data/pcna/pc_intensity.yaml", + "./configs/data/pcna/pc_intensity.yaml", ] -classification_label: ["cell_stage_fine", "flag_comment"] -regression_label: