Duplicate from zeahub/picmus

Co-authored-by: Tristan Stevens <tristan-deep@users.noreply.huggingface.co>

.gitattributes

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+*.7z filter=lfs diff=lfs merge=lfs -text
+*.arrow filter=lfs diff=lfs merge=lfs -text
+*.bin filter=lfs diff=lfs merge=lfs -text
+*.bz2 filter=lfs diff=lfs merge=lfs -text
+*.ckpt filter=lfs diff=lfs merge=lfs -text
+*.ftz filter=lfs diff=lfs merge=lfs -text
+*.gz filter=lfs diff=lfs merge=lfs -text
+*.h5 filter=lfs diff=lfs merge=lfs -text
+*.joblib filter=lfs diff=lfs merge=lfs -text
+*.lfs.* filter=lfs diff=lfs merge=lfs -text
+*.lz4 filter=lfs diff=lfs merge=lfs -text
+*.mds filter=lfs diff=lfs merge=lfs -text
+*.mlmodel filter=lfs diff=lfs merge=lfs -text
+*.model filter=lfs diff=lfs merge=lfs -text
+*.msgpack filter=lfs diff=lfs merge=lfs -text
+*.npy filter=lfs diff=lfs merge=lfs -text
+*.npz filter=lfs diff=lfs merge=lfs -text
+*.onnx filter=lfs diff=lfs merge=lfs -text
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+*.parquet filter=lfs diff=lfs merge=lfs -text
+*.pb filter=lfs diff=lfs merge=lfs -text
+*.pickle filter=lfs diff=lfs merge=lfs -text
+*.pkl filter=lfs diff=lfs merge=lfs -text
+*.pt filter=lfs diff=lfs merge=lfs -text
+*.pth filter=lfs diff=lfs merge=lfs -text
+*.rar filter=lfs diff=lfs merge=lfs -text
+*.safetensors filter=lfs diff=lfs merge=lfs -text
+saved_model/**/* filter=lfs diff=lfs merge=lfs -text
+*.tar.* filter=lfs diff=lfs merge=lfs -text
+*.tar filter=lfs diff=lfs merge=lfs -text
+*.tflite filter=lfs diff=lfs merge=lfs -text
+*.tgz filter=lfs diff=lfs merge=lfs -text
+*.wasm filter=lfs diff=lfs merge=lfs -text
+*.xz filter=lfs diff=lfs merge=lfs -text
+*.zip filter=lfs diff=lfs merge=lfs -text
+*.zst filter=lfs diff=lfs merge=lfs -text
+*tfevents* filter=lfs diff=lfs merge=lfs -text
+# Audio files - uncompressed
+*.pcm filter=lfs diff=lfs merge=lfs -text
+*.sam filter=lfs diff=lfs merge=lfs -text
+*.raw filter=lfs diff=lfs merge=lfs -text
+# Audio files - compressed
+*.aac filter=lfs diff=lfs merge=lfs -text
+*.flac filter=lfs diff=lfs merge=lfs -text
+*.mp3 filter=lfs diff=lfs merge=lfs -text
+*.ogg filter=lfs diff=lfs merge=lfs -text
+*.wav filter=lfs diff=lfs merge=lfs -text
+# Image files - uncompressed
+*.bmp filter=lfs diff=lfs merge=lfs -text
+*.gif filter=lfs diff=lfs merge=lfs -text
+*.png filter=lfs diff=lfs merge=lfs -text
+*.tiff filter=lfs diff=lfs merge=lfs -text
+# Image files - compressed
+*.jpg filter=lfs diff=lfs merge=lfs -text
+*.jpeg filter=lfs diff=lfs merge=lfs -text
+*.webp filter=lfs diff=lfs merge=lfs -text
+# Video files - compressed
+*.mp4 filter=lfs diff=lfs merge=lfs -text
+*.webm filter=lfs diff=lfs merge=lfs -text
+database/experiments/contrast_speckle/contrast_speckle_expe_dataset_iq/contrast_speckle_expe_dataset_iq.hdf5 filter=lfs diff=lfs merge=lfs -text
+database/experiments/contrast_speckle/contrast_speckle_expe_dataset_rf/contrast_speckle_expe_dataset_rf.hdf5 filter=lfs diff=lfs merge=lfs -text
+database/experiments/resolution_distorsion/resolution_distorsion_expe_dataset_iq/resolution_distorsion_expe_dataset_iq.hdf5 filter=lfs diff=lfs merge=lfs -text
+database/experiments/resolution_distorsion/resolution_distorsion_expe_dataset_rf/resolution_distorsion_expe_dataset_rf.hdf5 filter=lfs diff=lfs merge=lfs -text
+database/simulation/contrast_speckle/contrast_speckle_simu_dataset_iq/contrast_speckle_simu_dataset_iq.hdf5 filter=lfs diff=lfs merge=lfs -text
+database/simulation/contrast_speckle/contrast_speckle_simu_dataset_rf/contrast_speckle_simu_dataset_rf.hdf5 filter=lfs diff=lfs merge=lfs -text
+database/simulation/resolution_distorsion/resolution_distorsion_simu_dataset_iq/resolution_distorsion_simu_dataset_iq.hdf5 filter=lfs diff=lfs merge=lfs -text
+database/simulation/resolution_distorsion/resolution_distorsion_simu_dataset_rf/resolution_distorsion_simu_dataset_rf.hdf5 filter=lfs diff=lfs merge=lfs -text

README.md

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+---
+pretty_name: Plane-wave Imaging Challenge in Medical UltraSound
+source_datasets:
+  - https://www.creatis.insa-lyon.fr/Challenge/IEEE_IUS_2016/home
+tags:
+  - medical-imaging
+  - ultrasound
+  - plane-wave
+  - benchmark
+  - zea
+converted_by: "@tristan-deep"
+---
+
+## Dataset Description
+
+[PICMUS](https://www.creatis.insa-lyon.fr/Challenge/IEEE_IUS_2016/home) (Plane-wave Imaging Challenge in Medical UltraSound). Converted to the [zea format](https://usbmd-toolbox.web.app/data-acquisition.html) for use with the [zea toolbox](https://github.com/tue-bmd/zea).
+
+
+### Folder Structure
+
+```
+database/
+├── experiments/
+│   ├── contrast_speckle/
+│   │   ├── contrast_speckle_expe_dataset_iq/
+│   │   │   └── contrast_speckle_expe_dataset_iq.hdf5
+│   │   └── contrast_speckle_expe_dataset_rf/
+│   │       └── contrast_speckle_expe_dataset_rf.hdf5
+│   └── resolution_distorsion/
+│       ├── resolution_distorsion_expe_dataset_iq/
+│       │   └── resolution_distorsion_expe_dataset_iq.hdf5
+│       └── resolution_distorsion_expe_dataset_rf/
+│           └── resolution_distorsion_expe_dataset_rf.hdf5
+└── simulation/
+    ├── contrast_speckle/
+    │   ├── contrast_speckle_simu_dataset_iq/
+    │   │   └── contrast_speckle_simu_dataset_iq.hdf5
+    │   └── contrast_speckle_simu_dataset_rf/
+    │       └── contrast_speckle_simu_dataset_rf.hdf5
+    └── resolution_distorsion/
+        ├── resolution_distorsion_simu_dataset_iq/
+        │   └── resolution_distorsion_simu_dataset_iq.hdf5
+        └── resolution_distorsion_simu_dataset_rf/
+            └── resolution_distorsion_simu_dataset_rf.hdf5
+```
+
+## Description
+
+- **experiments/**: Contains experimental datasets for two tasks:
+  - `contrast_speckle`: Datasets for contrast and speckle experiments, with both IQ and RF data.
+  - `resolution_distorsion`: Datasets for resolution and distortion experiments, with both IQ and RF data.
+
+- **simulation/**: Contains simulated datasets for the same tasks, with both IQ and RF data.

config_iq.yaml

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+scan:
+  selected_transmits: all
+  grid_size_x: 400
+  grid_size_z: 600
+  apply_lens_correction: false
+  lens_sound_speed: 1000
+  lens_thickness: 0.001
+  zlims: [0.006, 0.055]
+  xlims: [-0.02, 0.02]
+
+pipeline:
+  operations:
+    - name: "beamform"
+      params:
+        beamformer: delay_and_sum
+        enable_pfield: false
+        num_patches: 200
+    - name: envelope_detect
+    - name: normalize
+    - name: log_compress

config_rf.yaml

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+scan:
+  selected_transmits: all
+  grid_size_x: 400
+  grid_size_z: 600
+  apply_lens_correction: false
+  lens_sound_speed: 1000
+  lens_thickness: 0.001
+  zlims: [0.006, 0.055]
+  xlims: [-0.02, 0.02]
+
+pipeline:
+  operations:
+    - name: demodulate
+    - name: downsample
+      params:
+        factor: 4
+    - name: "beamform"
+      params:
+        beamformer: delay_and_sum
+        enable_pfield: false
+        num_patches: 200
+    - name: envelope_detect
+    - name: normalize
+    - name: log_compress

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