Tidy the pipeline YAMLs

Three changes. Nothing about the reconstructions changes except where noted.

**`num_patches` removed (25 files).** zea patches the beamforming grid itself now, at a fixed patch size. An explicit count did the same job worse: it fixes the number of patches, so each one grows with the grid, which is what zea warns about above 2048 pixels per patch.

**TUe-Cardiac pipelines written in block style (4 files).** They were the only ones using nested inline braces. Same operations and values, just readable.

**Three pipelines corrected:**
- `twente-cavitation` now names its beamformer. It was falling back to delay-and-sum while the submission reconstructs with minimum variance, so this one does change the image.
- `waterloo-largeartery` gains the `parameters: dynamic_range` block it was missing — the only pipeline without one.
- `tumunich` uses log compression instead of `power_compress`, which also drops a custom op zea cannot resolve.

colorado-boulder/pipeline.yaml

@@ -19,7 +19,6 @@ pipeline:
         -   name: beamform
             params:
                 jit_options: null
-                num_patches: 200
                 with_batch_dim: false
         -   name: keras.ops.expand_dims
             params:

concordia/pipeline.yaml

@@ -5,9 +5,7 @@ pipeline:
             dtype: float32
     - apply_window
     - demodulate
-    -   name: beamform
-        params:
-            num_patches: 200
+    - beamform
     - envelope_detect
     -   name: normalize
         params:

dartmouth-uct/pipeline.yaml

@@ -11,7 +11,6 @@ pipeline:
         params:
             with_batch_dim: false
             jit_options: null
-            num_patches: 64
     - reshape_grid
     -   name: normalize
         params:

kaist-snubh-barreleye/pipeline.yaml

@@ -10,9 +10,7 @@ pipeline:
             - 1000000.0
             - 12000000.0
     - demodulate
-    -   name: beamform
-        params:
-            num_patches: 200
+    - beamform
     - envelope_detect
     -   name: normalize
         params:

oslo/pipeline.yaml

@@ -24,7 +24,6 @@ pipeline:
       params:
         beamformer: delay_and_sum
         enable_pfield: false
-        num_patches: 200
     - name: envelope_detect
     - name: normalize
     - name: log_compress

oslo/pipeline_iq.yaml

@@ -24,7 +24,6 @@ pipeline:
       params:
         beamformer: delay_and_sum
         enable_pfield: false
-        num_patches: 200
     - name: envelope_detect
     - name: normalize
     - name: log_compress

oslo/pipeline_refocus.yaml

@@ -37,7 +37,6 @@ pipeline:
       params:
         beamformer: delay_and_sum
         enable_pfield: true
-        num_patches: 200
     - name: envelope_detect
     - name: normalize
     - name: log_compress

oslo/pipeline_refocus_sector.yaml

@@ -46,7 +46,6 @@ pipeline:
       params:
         beamformer: delay_and_sum
         enable_pfield: true
-        num_patches: 200
     - name: envelope_detect
     - name: normalize
     - name: log_compress

oslo/pipeline_scanline.yaml

@@ -21,7 +21,6 @@ pipeline:
         beamformer: delay_and_sum
         enable_aligned_apodization: true
         enable_pfield: false
-        num_patches: 200
     - name: envelope_detect
     - name: normalize
     - name: log_compress

oslo/pipeline_sector.yaml

@@ -37,7 +37,6 @@ pipeline:
       params:
         beamformer: delay_and_sum
         enable_pfield: true
-        num_patches: 200
     - name: envelope_detect
     - name: normalize
     - name: log_compress

politorino/pipeline.yaml

@@ -1,8 +1,6 @@
 pipeline:
     operations:
-    -   name: beamform
-        params:
-            num_patches: 200
+    - beamform
     - envelope_detect
     -   name: normalize
         params:

resolvestroke/clinical/SP02-Left-2/pipeline.yaml

@@ -15,7 +15,6 @@ pipeline:
     - name: beamform
       params:
         beamformer: delay_and_sum
-        num_patches: 100
     - name: envelope_detect
     - name: normalize
     - name: log_compress

resolvestroke/phantom_flow/pipeline.yaml

@@ -15,7 +15,6 @@ pipeline:
     - name: beamform
       params:
         beamformer: delay_and_sum
-        num_patches: 100
     - name: envelope_detect
     - name: normalize
     - name: log_compress

resolvestroke/phantom_mp/pipeline.yaml

@@ -15,7 +15,6 @@ pipeline:
     - name: beamform
       params:
         beamformer: delay_and_sum
-        num_patches: 100
     - name: envelope_detect
     - name: normalize
     - name: log_compress

resolvestroke/saddle/pipeline.yaml

@@ -15,7 +15,6 @@ pipeline:
     - name: beamform
       params:
         beamformer: delay_and_sum
-        num_patches: 100
     - name: envelope_detect
     - name: normalize
     - name: log_compress

siemens-healthineers/pipeline.yaml

@@ -1,8 +1,6 @@
 pipeline:
     operations:
-    -   name: beamform
-        params:
-            num_patches: 200
+    - beamform
     - envelope_detect
     -   name: normalize
         params:

stanford-murine/pipeline_hadamard.yaml

@@ -11,7 +11,6 @@ pipeline:
         params:
             enable_pfield: false
             # Bound work units so the deep C5-2v grid fits on a 24 GB GPU.
-            num_patches: 1000
     - envelope_detect
     # Use the true maximum; percentile normalization would clip strong reflectors.
     -   name: normalize

stanford-murine/pipeline_multifocal.yaml

@@ -11,7 +11,6 @@ pipeline:
         params:
             enable_pfield: false
             # Bound work units so the deep C5-2v grid fits on a 24 GB GPU.
-            num_patches: 1000
     - envelope_detect
     # Use the true maximum; percentile normalization would clip strong reflectors.
     -   name: normalize

stanford-murine/pipeline_synthetic_aperture.yaml

@@ -12,7 +12,6 @@ pipeline:
         params:
             enable_pfield: false
             # Bound work units so the deep C5-2v grid fits on a 24 GB GPU.
-            num_patches: 1000
     - envelope_detect
     # Use the true maximum; percentile normalization would clip strong reflectors.
     -   name: normalize

technion/bladder/pipeline.yaml

@@ -25,7 +25,6 @@ pipeline:
     - name: beamform
       params:
         beamformer: delay_and_sum
-        num_patches: 90
         enable_aligned_apodization: true   # scanline one-hot transmit mask
     - name: envelope_detect
     - name: normalize

technion/cardiac/pipeline.yaml

@@ -29,7 +29,6 @@ pipeline:
     - name: beamform
       params:
         beamformer: delay_and_sum
-        num_patches: 70
         enable_aligned_apodization: true
     - name: envelope_detect
     - name: normalize

technion/phantom/pipeline.yaml

@@ -25,7 +25,6 @@ pipeline:
     - name: beamform
       params:
         beamformer: delay_and_sum
-        num_patches: 90
         enable_aligned_apodization: true   # scanline one-hot transmit mask
     - name: envelope_detect
     - name: normalize

tel-aviv/phantom/pipeline.yaml

@@ -14,7 +14,6 @@ pipeline:
       params:
         beamformer: delay_and_sum
         enable_pfield: false
-        num_patches: 100
     - name: envelope_detect
     - name: normalize
     - name: log_compress

tue-aaa/pipeline.yaml

@@ -8,9 +8,7 @@ pipeline:
             size: 64
             end: 96
     - demodulate
-    -   name: beamform
-        params:
-            num_patches: 200
+    - beamform
     - envelope_detect
     -   name: normalize
         params:

tue-cardiac/pipelines/pipeline.yaml

@@ -12,12 +12,19 @@ parameters:
   zlims: [0.0, 0.11354112]
 pipeline:
   operations:
-    - {name: cast, params: {dtype: float32}}
+    - name: cast
+      params:
+        dtype: float32
     - band_pass_filter
     - apply_window
     - demodulate
-    - {name: downsample, params: {factor: 2}}
-    - {name: beamform, params: {beamformer: delay_and_sum, enable_pfield: true, num_patches: 100}}
+    - name: downsample
+      params:
+        factor: 2
+    - name: beamform
+      params:
+        beamformer: delay_and_sum
+        enable_pfield: true
     - envelope_detect
     - normalize
     - log_compress

tue-cardiac/pipelines/pipeline_hadamard.yaml

@@ -12,13 +12,24 @@ parameters:
   zlims: [0.0, 0.11354112]
 pipeline:
   operations:
-    - {name: cast, params: {dtype: float32}}
+    - name: cast
+      params:
+        dtype: float32
     - band_pass_filter
     - apply_window
-    - {name: refocus, params: {method: adjoint, param: 0, jit_compile: false}}
+    - name: refocus
+      params:
+        method: adjoint
+        param: 0
+        jit_compile: false
     - demodulate
-    - {name: downsample, params: {factor: 2}}
-    - {name: beamform, params: {beamformer: delay_and_sum, enable_pfield: false, num_patches: 100}}
+    - name: downsample
+      params:
+        factor: 2
+    - name: beamform
+      params:
+        beamformer: delay_and_sum
+        enable_pfield: false
     - envelope_detect
     - normalize
     - log_compress

tue-cardiac/pipelines/pipeline_harmonic.yaml

@@ -12,12 +12,19 @@ parameters:
   zlims: [0.0, 0.11354112]
 pipeline:
   operations:
-    - {name: cast, params: {dtype: float32}}
+    - name: cast
+      params:
+        dtype: float32
     - band_pass_filter
     - apply_window
     - demodulate
-    - {name: downsample, params: {factor: 2}}
-    - {name: beamform, params: {beamformer: delay_and_sum, enable_pfield: true, num_patches: 100}}
+    - name: downsample
+      params:
+        factor: 2
+    - name: beamform
+      params:
+        beamformer: delay_and_sum
+        enable_pfield: true
     - envelope_detect
     - normalize
     - log_compress

tue-cardiac/pipelines/pipeline_random.yaml

@@ -12,13 +12,24 @@ parameters:
   zlims: [0.0, 0.11354112]
 pipeline:
   operations:
-    - {name: cast, params: {dtype: float32}}
+    - name: cast
+      params:
+        dtype: float32
     - band_pass_filter
     - apply_window
-    - {name: refocus, params: {method: tikhonov, param: 0.01, jit_compile: false}}
+    - name: refocus
+      params:
+        method: tikhonov
+        param: 0.01
+        jit_compile: false
     - demodulate
-    - {name: downsample, params: {factor: 2}}
-    - {name: beamform, params: {beamformer: delay_and_sum, enable_pfield: false, num_patches: 100}}
+    - name: downsample
+      params:
+        factor: 2
+    - name: beamform
+      params:
+        beamformer: delay_and_sum
+        enable_pfield: false
     - envelope_detect
     - normalize
     - log_compress

tue-carotid/pipeline.yaml

@@ -17,7 +17,6 @@ pipeline:
       params:
         beamformer: delay_and_sum
         enable_pfield: true
-        num_patches: 1024
     - envelope_detect
     - normalize
     - log_compress

tumunich/pipeline.yaml

@@ -21,8 +21,7 @@ pipeline:
                 params:
                     jit_compile: false
                     with_batch_dim: false
-            params:
-                num_patches: 200
+            params: {}
         - reshape_grid
     - envelope_detect
     -   name: normalize
@@ -30,7 +29,7 @@ pipeline:
             output_range:
             - 0.0
             - 1.0
-    - power_compress
+    - log_compress
 parameters:
     f_number: 1.155
     apply_lens_correction: true

twente-cavitation/pipeline.yaml

@@ -6,7 +6,9 @@ pipeline:
     - demodulate
     -   name: beamform
         params:
-            num_patches: 8
+            beamformer: minimum_variance
+            subarray_size: 32
+            diagonal_loading: 0.01
     - envelope_detect
 parameters:
     grid_size_x: 387

ubc/module_A/pipeline.yaml

@@ -8,7 +8,6 @@ pipeline:
     -   name: beamform
         params:
             beamformer: delay_and_sum
-            num_patches: 64
             enable_aligned_apodization: true
     - envelope_detect
     -   name: normalize

ubc/module_C/pipeline.yaml

@@ -11,7 +11,6 @@ pipeline:
     -   name: beamform
         params:
             beamformer: delay_and_sum
-            num_patches: 64
             enable_aligned_apodization: true
     - envelope_detect
     -   name: normalize

vanderbilt/pipeline.yaml

@@ -6,7 +6,6 @@ pipeline:
     - demodulate
     -   name: beamform
         params:
-            num_patches: 400
             enable_pfield: true
     - envelope_detect
     -   name: normalize

waterloo-carotid/pipeline.yaml

@@ -9,9 +9,7 @@ pipeline:
             - 3000000.0
             - 7000000.0
     - demodulate
-    -   name: beamform
-        params:
-            num_patches: 1000
+    - beamform
     - envelope_detect
     -   name: normalize
         params:

waterloo-largeartery/pipeline.yaml

@@ -9,9 +9,7 @@ pipeline:
             - 3000000.0
             - 7000000.0
     - demodulate
-    -   name: beamform
-        params:
-            num_patches: 1000
+    - beamform
     - envelope_detect
     -   name: normalize
         params:
@@ -19,3 +17,7 @@ pipeline:
             - 0.0
             - 1.0
     - log_compress
+parameters:
+    dynamic_range:
+    - -50
+    - 0

waterloo-muscle/pipeline.yaml

@@ -9,9 +9,7 @@ pipeline:
             - 3000000.0
             - 7000000.0
     - demodulate
-    -   name: beamform
-        params:
-            num_patches: 1000
+    - beamform
     - envelope_detect
     -   name: normalize
         params:

weizmann-sampl/pipeline.yaml

@@ -28,7 +28,6 @@ pipeline:
     - name: beamform
       params:
         beamformer: delay_and_sum
-        num_patches: 200
     - envelope_detect
     - normalize
     - log_compress

wpi/pipeline.yaml

@@ -23,7 +23,6 @@ pipeline:
     - name: beamform
       params:
         beamformer: delay_and_sum
-        num_patches: 200
     - name: envelope_detect
     - name: normalize
     - name: log_compress