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ericspodericspod
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Merge branch 'main' into fix-tcia
2 parents 0fd967c + 9f6d19f commit 0f3c940

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-1110
lines changed

‎generation/maisi/README.md

+69-29
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‎generation/maisi/configs/config_infer.json

+6-5
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@@ -1,9 +1,9 @@
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{
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"num_output_samples": 1,
3-
"body_region": ["abdomen"],
4-
"anatomy_list": ["liver","hepatic tumor"],
3+
"body_region": ["chest"],
4+
"anatomy_list": ["lung tumor"],
55
"controllable_anatomy_size": [],
6-
"num_inference_steps": 1000,
6+
"num_inference_steps": 30,
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"mask_generation_num_inference_steps": 1000,
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"output_size": [
99
256,
@@ -18,10 +18,11 @@
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2.0
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],
2020
"autoencoder_sliding_window_infer_size": [48,48,48],
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"autoencoder_sliding_window_infer_overlap": 0.25,
21+
"autoencoder_sliding_window_infer_overlap": 0.6666,
2222
"controlnet": "$@controlnet_def",
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"diffusion_unet": "$@diffusion_unet_def",
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"autoencoder": "$@autoencoder_def",
2525
"mask_generation_autoencoder": "$@mask_generation_autoencoder_def",
26-
"mask_generation_diffusion": "$@mask_generation_diffusion_def"
26+
"mask_generation_diffusion": "$@mask_generation_diffusion_def",
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"modality": 1
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}

‎generation/maisi/configs/config_infer_16g_256x256x128.json

+10-4
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@@ -1,9 +1,9 @@
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{
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"num_output_samples": 1,
3-
"body_region": ["abdomen"],
4-
"anatomy_list": ["liver","hepatic tumor"],
3+
"body_region": ["chest"],
4+
"anatomy_list": ["lung tumor"],
55
"controllable_anatomy_size": [],
6-
"num_inference_steps": 1000,
6+
"num_inference_steps": 30,
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"mask_generation_num_inference_steps": 1000,
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"output_size": [
99
256,
@@ -19,5 +19,11 @@
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],
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"autoencoder_sliding_window_infer_size": [96,96,96],
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"autoencoder_sliding_window_infer_overlap": 0.25,
22-
"autoencoder_tp_num_splits": 2
22+
"autoencoder_tp_num_splits": 2,
23+
"controlnet": "$@controlnet_def",
24+
"diffusion_unet": "$@diffusion_unet_def",
25+
"autoencoder": "$@autoencoder_def",
26+
"mask_generation_autoencoder": "$@mask_generation_autoencoder_def",
27+
"mask_generation_diffusion": "$@mask_generation_diffusion_def",
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"modality": 1
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}

‎generation/maisi/configs/config_infer_16g_256x256x256.json

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@@ -1,9 +1,9 @@
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{
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"num_output_samples": 1,
3-
"body_region": ["abdomen"],
4-
"anatomy_list": ["liver","hepatic tumor"],
3+
"body_region": ["chest"],
4+
"anatomy_list": ["lung tumor"],
55
"controllable_anatomy_size": [],
6-
"num_inference_steps": 1000,
6+
"num_inference_steps": 30,
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"mask_generation_num_inference_steps": 1000,
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"output_size": [
99
256,
@@ -18,6 +18,12 @@
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2.0
1919
],
2020
"autoencoder_sliding_window_infer_size": [48,48,64],
21-
"autoencoder_sliding_window_infer_overlap": 0.25,
22-
"autoencoder_tp_num_splits": 2
21+
"autoencoder_sliding_window_infer_overlap": 0.6666,
22+
"autoencoder_tp_num_splits": 4,
23+
"controlnet": "$@controlnet_def",
24+
"diffusion_unet": "$@diffusion_unet_def",
25+
"autoencoder": "$@autoencoder_def",
26+
"mask_generation_autoencoder": "$@mask_generation_autoencoder_def",
27+
"mask_generation_diffusion": "$@mask_generation_diffusion_def",
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"modality": 1
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}

‎generation/maisi/configs/config_infer_16g_512x512x128.json

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@@ -1,9 +1,9 @@
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{
22
"num_output_samples": 1,
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"body_region": ["abdomen"],
4-
"anatomy_list": ["liver","hepatic tumor"],
3+
"body_region": ["chest"],
4+
"anatomy_list": ["lung tumor"],
55
"controllable_anatomy_size": [],
6-
"num_inference_steps": 1000,
6+
"num_inference_steps": 30,
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"mask_generation_num_inference_steps": 1000,
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"output_size": [
99
512,
@@ -18,6 +18,12 @@
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4.0
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],
2020
"autoencoder_sliding_window_infer_size": [64,64,32],
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"autoencoder_sliding_window_infer_overlap": 0.25,
22-
"autoencoder_tp_num_splits": 1
21+
"autoencoder_sliding_window_infer_overlap": 0.5,
22+
"autoencoder_tp_num_splits": 2,
23+
"controlnet": "$@controlnet_def",
24+
"diffusion_unet": "$@diffusion_unet_def",
25+
"autoencoder": "$@autoencoder_def",
26+
"mask_generation_autoencoder": "$@mask_generation_autoencoder_def",
27+
"mask_generation_diffusion": "$@mask_generation_diffusion_def",
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"modality": 1
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}

‎generation/maisi/configs/config_infer_24g_256x256x256.json

+10-4
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@@ -1,9 +1,9 @@
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{
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"num_output_samples": 1,
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"body_region": ["abdomen"],
4-
"anatomy_list": ["liver","hepatic tumor"],
3+
"body_region": ["chest"],
4+
"anatomy_list": ["lung tumor"],
55
"controllable_anatomy_size": [],
6-
"num_inference_steps": 1000,
6+
"num_inference_steps": 30,
77
"mask_generation_num_inference_steps": 1000,
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"output_size": [
99
256,
@@ -19,5 +19,11 @@
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],
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"autoencoder_sliding_window_infer_size": [64,64,64],
2121
"autoencoder_sliding_window_infer_overlap": 0.25,
22-
"autoencoder_tp_num_splits": 4
22+
"autoencoder_tp_num_splits": 4,
23+
"controlnet": "$@controlnet_def",
24+
"diffusion_unet": "$@diffusion_unet_def",
25+
"autoencoder": "$@autoencoder_def",
26+
"mask_generation_autoencoder": "$@mask_generation_autoencoder_def",
27+
"mask_generation_diffusion": "$@mask_generation_diffusion_def",
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"modality": 1
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}

‎generation/maisi/configs/config_infer_24g_512x512x128.json

+11-5
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@@ -1,9 +1,9 @@
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{
22
"num_output_samples": 1,
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"body_region": ["abdomen"],
4-
"anatomy_list": ["liver","hepatic tumor"],
3+
"body_region": ["chest"],
4+
"anatomy_list": ["lung tumor"],
55
"controllable_anatomy_size": [],
6-
"num_inference_steps": 1000,
6+
"num_inference_steps": 30,
77
"mask_generation_num_inference_steps": 1000,
88
"output_size": [
99
512,
@@ -18,6 +18,12 @@
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4.0
1919
],
2020
"autoencoder_sliding_window_infer_size": [80,80,32],
21-
"autoencoder_sliding_window_infer_overlap": 0.25,
22-
"autoencoder_tp_num_splits": 1
21+
"autoencoder_sliding_window_infer_overlap": 0.4,
22+
"autoencoder_tp_num_splits": 2,
23+
"controlnet": "$@controlnet_def",
24+
"diffusion_unet": "$@diffusion_unet_def",
25+
"autoencoder": "$@autoencoder_def",
26+
"mask_generation_autoencoder": "$@mask_generation_autoencoder_def",
27+
"mask_generation_diffusion": "$@mask_generation_diffusion_def",
28+
"modality": 1
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}

‎generation/maisi/configs/config_infer_24g_512x512x512.json

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{
22
"num_output_samples": 1,
3-
"body_region": ["abdomen"],
4-
"anatomy_list": ["liver","hepatic tumor"],
3+
"body_region": ["chest"],
4+
"anatomy_list": ["lung tumor"],
55
"controllable_anatomy_size": [],
6-
"num_inference_steps": 1000,
6+
"num_inference_steps": 30,
77
"mask_generation_num_inference_steps": 1000,
88
"output_size": [
99
512,
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1818
1.0
1919
],
2020
"autoencoder_sliding_window_infer_size": [64,64,48],
21-
"autoencoder_sliding_window_infer_overlap": 0.25,
22-
"autoencoder_tp_num_splits": 2
21+
"autoencoder_sliding_window_infer_overlap": 0.4,
22+
"autoencoder_tp_num_splits": 2,
23+
"controlnet": "$@controlnet_def",
24+
"diffusion_unet": "$@diffusion_unet_def",
25+
"autoencoder": "$@autoencoder_def",
26+
"mask_generation_autoencoder": "$@mask_generation_autoencoder_def",
27+
"mask_generation_diffusion": "$@mask_generation_diffusion_def",
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"modality": 1
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}

‎generation/maisi/configs/config_infer_32g_512x512x512.json

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@@ -1,9 +1,9 @@
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{
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"num_output_samples": 1,
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"body_region": ["abdomen"],
4-
"anatomy_list": ["liver","hepatic tumor"],
3+
"body_region": ["chest"],
4+
"anatomy_list": ["lung tumor"],
55
"controllable_anatomy_size": [],
6-
"num_inference_steps": 1000,
6+
"num_inference_steps": 30,
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"mask_generation_num_inference_steps": 1000,
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"output_size": [
99
512,
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0.75,
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1.0
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],
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"autoencoder_sliding_window_infer_size": [64,64,64],
21-
"autoencoder_sliding_window_infer_overlap": 0.25,
22-
"autoencoder_tp_num_splits": 2
20+
"autoencoder_sliding_window_infer_size": [80,80,48],
21+
"autoencoder_sliding_window_infer_overlap": 0.4,
22+
"autoencoder_tp_num_splits": 4,
23+
"controlnet": "$@controlnet_def",
24+
"diffusion_unet": "$@diffusion_unet_def",
25+
"autoencoder": "$@autoencoder_def",
26+
"mask_generation_autoencoder": "$@mask_generation_autoencoder_def",
27+
"mask_generation_diffusion": "$@mask_generation_diffusion_def",
28+
"modality": 1
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}

‎generation/maisi/configs/config_infer_80g_512x512x128.json

-23
This file was deleted.

‎generation/maisi/configs/config_infer_80g_512x512x512.json

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{
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"num_output_samples": 1,
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"body_region": ["abdomen"],
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"anatomy_list": ["liver","hepatic tumor"],
3+
"body_region": ["chest"],
4+
"anatomy_list": ["lung tumor"],
55
"controllable_anatomy_size": [],
6-
"num_inference_steps": 1000,
6+
"num_inference_steps": 30,
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"mask_generation_num_inference_steps": 1000,
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"output_size": [
99
512,
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1.0
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],
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"autoencoder_sliding_window_infer_size": [80,80,80],
21-
"autoencoder_sliding_window_infer_overlap": 0.25,
22-
"autoencoder_tp_num_splits": 2
21+
"autoencoder_sliding_window_infer_overlap": 0.4,
22+
"autoencoder_tp_num_splits": 2,
23+
"controlnet": "$@controlnet_def",
24+
"diffusion_unet": "$@diffusion_unet_def",
25+
"autoencoder": "$@autoencoder_def",
26+
"mask_generation_autoencoder": "$@mask_generation_autoencoder_def",
27+
"mask_generation_diffusion": "$@mask_generation_diffusion_def",
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"modality": 1
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}

‎generation/maisi/configs/config_infer_80g_512x512x768.json

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{
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"num_output_samples": 1,
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"body_region": ["abdomen"],
4-
"anatomy_list": ["liver","hepatic tumor"],
4+
"anatomy_list": ["liver"],
55
"controllable_anatomy_size": [],
6-
"num_inference_steps": 1000,
6+
"num_inference_steps": 30,
77
"mask_generation_num_inference_steps": 1000,
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"output_size": [
99
512,
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0.75,
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0.66667
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],
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"autoencoder_sliding_window_infer_size": [80,80,112],
21-
"autoencoder_sliding_window_infer_overlap": 0.25,
22-
"autoencoder_tp_num_splits": 4
20+
"autoencoder_sliding_window_infer_size": [80,80,96],
21+
"autoencoder_sliding_window_infer_overlap": 0.4,
22+
"autoencoder_tp_num_splits": 4,
23+
"controlnet": "$@controlnet_def",
24+
"diffusion_unet": "$@diffusion_unet_def",
25+
"autoencoder": "$@autoencoder_def",
26+
"mask_generation_autoencoder": "$@mask_generation_autoencoder_def",
27+
"mask_generation_diffusion": "$@mask_generation_diffusion_def",
28+
"modality": 1
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}

‎generation/maisi/configs/config_maisi.json ‎generation/maisi/configs/config_maisi3d-ddpm.json

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"spatial_dims": 3,
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"image_channels": 1,
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"latent_channels": 4,
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"include_body_region": true,
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"mask_generation_latent_shape": [
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4,
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],
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"num_res_blocks": 2,
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"use_flash_attention": true,
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"include_top_region_index_input": true,
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"include_bottom_region_index_input": true,
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"include_top_region_index_input": "@include_body_region",
65+
"include_bottom_region_index_input": "@include_body_region",
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"include_spacing_input": true
6667
},
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"controlnet_def": {

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