zea 0.0.8__py3-none-any.whl → 0.0.9__py3-none-any.whl

zea/probes.py

@@ -22,7 +22,7 @@ We can initialize a generic probe with the following code:
 
     >>> probe = Probe.from_name("generic")
     >>> print(probe.get_parameters())
-    {'probe_geometry': None, 'center_frequency': None, 'sampling_frequency': None, 'xlims': None, 'zlims': None}
+    {'probe_geometry': None, 'center_frequency': None, 'sampling_frequency': None, 'xlims': None, 'zlims': None, 'n_el': None}
 """  # noqa: E501
 
 import numpy as np
@@ -114,6 +114,7 @@ class Probe(Object):
             "sampling_frequency": self.sampling_frequency,
             "xlims": self.xlims,
             "zlims": self.zlims,
+            "n_el": self.n_el,
         }
 
     @classmethod
@@ -231,12 +232,3 @@ class Esaote_sll1543(Probe):
             bandwidth_MHz=bandwidth_MHz,
             probe_type="linear",
         )
-
-    def get_parameters(self):
-        return {
-            "probe_geometry": self.probe_geometry,
-            "center_frequency": self.center_frequency,
-            "sampling_frequency": self.sampling_frequency,
-            "xlims": self.xlims,
-            "zlims": self.zlims,
-        }

zea/scan.py

@@ -158,7 +158,6 @@ class Scan(Parameters):
         phi_range (tuple, optional): Range of phi angles for 3D imaging.
         rho_range (tuple, optional): Range of rho (radial) distances for 3D imaging.
         fill_value (float, optional): Value to use for out-of-bounds pixels.
-            Defaults to 0.0.
         attenuation_coef (float, optional): Attenuation coefficient in dB/(MHz*cm).
             Defaults to 0.0.
         selected_transmits (None, str, int, list, slice, or np.ndarray, optional):
@@ -222,7 +221,7 @@ class Scan(Parameters):
         "theta_range": {"type": (tuple, list)},
         "phi_range": {"type": (tuple, list)},
         "rho_range": {"type": (tuple, list)},
-        "fill_value": {"type": float, "default": 0.0},
+        "fill_value": {"type": float},
         "resolution": {"type": float, "default": None},
     }
 
@@ -241,16 +240,7 @@ class Scan(Parameters):
         if selected_transmits_input is not None:
             self.set_transmits(selected_transmits_input)
 
-    @cache_with_dependencies(
-        "xlims",
-        "zlims",
-        "grid_size_x",
-        "grid_size_z",
-        "sound_speed",
-        "center_frequency",
-        "pixels_per_wavelength",
-        "grid_type",
-    )
+    @cache_with_dependencies("xlims", "zlims", "grid_size_x", "grid_size_z", "grid_type")
     def grid(self):
         """The beamforming grid of shape (grid_size_z, grid_size_x, 3)."""
         if self.grid_type == "polar":
@@ -270,12 +260,7 @@ class Scan(Parameters):
                 "'cartesian' and 'polar'."
             )
 
-    @cache_with_dependencies(
-        "xlims",
-        "wavelength",
-        "pixels_per_wavelength",
-        "grid_type",
-    )
+    @cache_with_dependencies("xlims", "wavelength", "pixels_per_wavelength")
     def grid_size_x(self):
         """Grid width in pixels. For a cartesian grid, this is the lateral (x) pixels in the grid,
         set to prevent aliasing if not provided. For a polar grid, this can be thought of as
@@ -310,7 +295,7 @@ class Scan(Parameters):
         """Calculate the wavelength based on sound speed and center frequency."""
         return self.sound_speed / self.center_frequency
 
-    @cache_with_dependencies("zlims", "grid_type", "polar_limits", "probe_geometry")
+    @cache_with_dependencies("zlims", "polar_limits", "probe_geometry")
     def xlims(self):
         """The x-limits of the beamforming grid [m]. If not explicitly set, it is computed based
         on the polar limits and probe geometry.
@@ -552,12 +537,24 @@ class Scan(Parameters):
 
         return value[self.selected_transmits]
 
+    @property
+    def n_waveforms(self):
+        """The number of unique transmit waveforms."""
+
+        if self.waveforms_one_way is not None:
+            return self.waveforms_one_way.shape[0]
+
+        if self.waveforms_two_way is not None:
+            return self.waveforms_two_way.shape[0]
+
+        return 1
+
     @property
     def t_peak(self):
         """The time of the peak of the pulse in seconds of shape (n_waveforms,)."""
         t_peak = self._params.get("t_peak")
         if t_peak is None:
-            t_peak = np.array([1 / self.center_frequency])
+            t_peak = np.array([1 / self.center_frequency] * self.n_waveforms)
 
         return t_peak
 

zea/tools/fit_scan_cone.py

@@ -17,7 +17,7 @@ import matplotlib.pyplot as plt
 import numpy as np
 
 from zea import log
-from zea.tensor_ops import translate
+from zea.func.tensor import translate
 
 
 def filter_edge_points_by_boundary(edge_points, is_left=True, min_cone_half_angle_deg=20):

zea/tools/selection_tool.py

@@ -48,6 +48,7 @@ from skimage.measure import approximate_polygon, find_contours
 from sklearn.metrics import pairwise_distances
 
 from zea import log
+from zea.func.tensor import translate
 from zea.internal.viewer import (
     filename_from_window_dialog,
     get_matplotlib_figure_props,
@@ -55,7 +56,6 @@ from zea.internal.viewer import (
 )
 from zea.io_lib import _SUPPORTED_VID_TYPES, load_image, load_video
 from zea.metrics import get_metric
-from zea.tensor_ops import translate
 from zea.visualize import plot_rectangle_from_mask, plot_shape_from_mask
 
 

zea/tracking/lucas_kanade.py

@@ -10,7 +10,7 @@ from typing import Tuple
 
 from keras import ops
 
-from zea.tensor_ops import gaussian_filter, translate
+from zea.func.tensor import gaussian_filter, translate
 
 from .base import BaseTracker
 

zea/tracking/segmentation.py

@@ -8,7 +8,7 @@
 
 from keras import ops
 
-from zea.tensor_ops import find_contour
+from zea.func.tensor import find_contour
 
 from .base import BaseTracker
 

{zea-0.0.8.dist-info → zea-0.0.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: zea
-Version: 0.0.8
+Version: 0.0.9
 Summary: A Toolbox for Cognitive Ultrasound Imaging. Provides a set of tools for processing of ultrasound data, all built in your favorite machine learning framework.
 License-File: LICENSE
 Keywords: ultrasound,machine learning,beamforming
@@ -72,6 +72,8 @@ Requires-Dist: schema (>=0.7)
 Requires-Dist: scikit-image (>=0.23)
 Requires-Dist: scikit-learn (>=1.4)
 Requires-Dist: scipy (>=1.13)
+Requires-Dist: simpleitk (>=2.2.1) ; extra == "dev"
+Requires-Dist: simpleitk (>=2.2.1) ; extra == "tests"
 Requires-Dist: sphinx ; extra == "dev"
 Requires-Dist: sphinx ; extra == "docs"
 Requires-Dist: sphinx-argparse ; extra == "dev"

{zea-0.0.8.dist-info → zea-0.0.9.dist-info}/RECORD

@@ -1,14 +1,14 @@
-zea/__init__.py,sha256=Q_ky8oIIbUeOQPmtJTXEIEsnt2kW-aHNct4lu2c3Sz8,4119
+zea/__init__.py,sha256=iFIT8ZmOVQ_UtIUSLd4hCwdACTZdrDC82MCV_1dCeMw,4107
 zea/__main__.py,sha256=4OCFujuZ5ooIDMF7xxE4Esin9dfFlgX9PdOi9uB64y8,1569
 zea/agent/__init__.py,sha256=0wnGArcPvSo_lDHN9-jE8d7IBP-bk3fuceoRu2VEVEw,976
 zea/agent/gumbel.py,sha256=WbvSrM8meXtZmDLkyXDGUyRzjB4dWZmNO_qzloRxB_s,3770
-zea/agent/masks.py,sha256=_vUhlzzw_g8_RN-k0mMqa_h4hfGHViJdkA24o6AYqYk,6666
-zea/agent/selection.py,sha256=ut8I_TcfcoDRQnBBsxiVjNqjFp_PLNNHxgoE1FTP4rw,27072
-zea/backend/__init__.py,sha256=XiBtxpXMYgcSBXjJ-uEWh7a92XqWs-4uDUh6NeKeUE4,6922
+zea/agent/masks.py,sha256=mQC4o3_zTQtFomvWdDTUE7xuHyp2Pt-RhmxXzpGPHIE,6664
+zea/agent/selection.py,sha256=jHd3HG8tYOTS_KvuVX-VlOoetHkVNBfmvHTVCHQ5jt0,27065
+zea/backend/__init__.py,sha256=XV8_V8A0tfoZLoXH-QzTlMjWl0-YmZLbjoU-uyk7qys,6916
 zea/backend/autograd.py,sha256=buWy19ctDFsAoktZaLm5qyLN9nQRicI91-V3ND-t3f4,6868
 zea/backend/jax/__init__.py,sha256=AvO6tUDTMiyrRuY_M2KKwUpzzzqWIRlSh3NhI_lcw9w,1056
 zea/backend/tensorflow/__init__.py,sha256=FQAMCrUgvHm4LCVfnP9sXGACQSMFx3nIarPve_MgxYM,422
-zea/backend/tensorflow/dataloader.py,sha256=WXIF0ivyZARj_K7dqzuAAQR_YiAQ_ydSWDMQ-mFD_FQ,14208
+zea/backend/tensorflow/dataloader.py,sha256=PoEAAj1ddvnyR_9c2U9rRIPrMLRgzgfuhkZgBpG5AAU,14209
 zea/backend/tensorflow/layers/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 zea/backend/tensorflow/layers/apodization.py,sha256=Pi5GpkoMSwPq8_FL1fqkuGINmOD-sIHkHXEtF62VNSc,826
 zea/backend/tensorflow/layers/utils.py,sha256=kiEH-6_Rq5dq0D7dkziUkhhqdOyf5O9POYZ-uXLHkNA,3446
@@ -24,41 +24,44 @@ zea/backend/tf2jax.py,sha256=qld6VecFEVOpUI4wUqA8wj9xvpsIjH2o72TcQqOyxbY,384
 zea/backend/torch/__init__.py,sha256=YMNTzqRqhPu7pjGPczupT3jo4SwjYpI8Ch97GI0OPDg,1119
 zea/backend/torch/losses.py,sha256=7ITD_p630eyJzjgAT79XUNiff7XmW-naMGOUgKFnAAQ,2114
 zea/beamform/__init__.py,sha256=rlRy-Og_KsbnU4Qm0NR8SP5ymePCwSr2aMW9jjOaeHI,1018
-zea/beamform/beamformer.py,sha256=XKG8HDj0Arje3rVRBwd20cdD8s87BJNn3KGNJ4u0cP8,20653
+zea/beamform/beamformer.py,sha256=zEhTxgHcH96FcPR-Ax1W50dFe07eh1oJ9VxxTaOlRUg,20772
 zea/beamform/delays.py,sha256=ItD6_WavcWmXns4QJqo_oq674F5Q0s0mVVacfo_775U,5590
 zea/beamform/lens_correction.py,sha256=eqsVaooyi_EFWd8F3LxdQX2bLxxF_L8eGVkROKl3rOA,7828
-zea/beamform/pfield.py,sha256=2rJMV8EuGoDZk1ZVSjdkn7I_p3gQJWxlCGtM50qc1sA,14910
+zea/beamform/pfield.py,sha256=H7NH6ZE3G6AGzDN26YX7ias40LoOtxgZU1mEeL-ZG2w,14920
 zea/beamform/phantoms.py,sha256=zow6j4mPXOJjSl31dLQbuDW8rH_qEV2dsfcy-TqkhkI,1108
 zea/beamform/pixelgrid.py,sha256=MVGyYQvsZJeDgGixADEP1wgWPn5dtwjH66qAyG8B2YA,5441
 zea/config.py,sha256=q0ADj83bpFt7kXq32tJFQT3Kpcvrf-O_RCzTxxk1yHw,19811
 zea/data/__init__.py,sha256=Rw22Ny5OflnAdw4JgjSvOQSX3PDPkNwkgo2G_BLOUlo,1645
 zea/data/__main__.py,sha256=xEXj3m3gJ6MoV1f9WbDl3QVPMbDXedTj1J9WeT83NrI,909
-zea/data/augmentations.py,sha256=dv43xN8yw20rIz2fDD0G8lYRskE2P_--WGfWbHx7S40,21651
+zea/data/augmentations.py,sha256=GWlSpo3kl5GsfOzeYVvsR7UollVG1IfcoDm78G2ch-U,21652
 zea/data/convert/__init__.py,sha256=Aaw-AE7ZXDh0Rtz1NIrmQJeZo02qvUwEXcCdMPcrqJ4,62
-zea/data/convert/__main__.py,sha256=ryZX4h_miAnhHYsOTE-TrhV_blRFQq4GS1L7lYKXOZM,4455
-zea/data/convert/camus.py,sha256=jQaWpHxPzUydNfObuoKxvS0wi-DZqACbXXXHAt9oJuU,12358
-zea/data/convert/echonet.py,sha256=PPdARPj7MdQeSQ9_Z15UKw1fGZ1Bi2fNs9D1-X_NLZE,19120
+zea/data/convert/__main__.py,sha256=DPdgIAoGTzNvjbNVdsBFrtXtjUyv7vUoUUDuOW59JHY,5998
+zea/data/convert/camus.py,sha256=TjrMsXJ6YZcevK4ZuRfAQuVoM3JmduDjz_KP0Emap74,12579
+zea/data/convert/echonet.py,sha256=Uryox91C74wx2vq0yl_WddL36eE1s3qPsn1b4_0L88E,19121
 zea/data/convert/echonetlvh/README.md,sha256=NFCwez0KngQIrTwAa0pO-8VxRnfLWmGXRhafMfgzw80,602
-zea/data/convert/echonetlvh/__init__.py,sha256=GdCO9t6IEmmowWIqxUEF17bemYrzci3m4TQ6MKyZUj4,21195
+zea/data/convert/echonetlvh/__init__.py,sha256=St-CaakcusN2V-A82zd6k7JxZq_0Sot7X7nE_EurHFI,21196
 zea/data/convert/echonetlvh/manual_rejections.txt,sha256=xXxUQ68YLF6uybUWgjicGwzbqhAvON1QLxDcnquxf0s,1382
 zea/data/convert/echonetlvh/precompute_crop.py,sha256=uqyBUu5CUr8GlCmm-X9yAavQ916t1gd2Xn-wVwZHEZI,8120
 zea/data/convert/images.py,sha256=8a2oHqAA_fLhFuNnqBsNCjKTdX5pADX-ntZ6BHUoZdQ,5229
 zea/data/convert/picmus.py,sha256=iZik4rHqyyfk-tsUYhnM8kzL3qgFmeuW6MG-u8ZWt68,6527
 zea/data/convert/utils.py,sha256=B6yDAqqVrkmFV32uQ2PGpIonEJAXUf3jZSS6hMrRinQ,2932
-zea/data/convert/verasonics.py,sha256=jcvvxmK3Qvu1420uM81mize9JjQ4mKoFVDxRJ_kSlss,41723
-zea/data/data_format.py,sha256=wkqbx_GaudSd9SY41vx651f-jRtPjKNllrI_y34-U1I,29452
+zea/data/convert/verasonics.py,sha256=Jx1Ja-j90D5wec4QbZEo5Q9IRSA0bUPcZLbQuMclTh0,48175
+zea/data/data_format.py,sha256=vMbMm85n_fC9sueD8GwBkAvDvq1cUzUpQLy4E6WU-VA,29351
 zea/data/dataloader.py,sha256=64p8FunD-5bWKYvMQQIW2vDdCrosDN8slWkUEwrIJSo,14993
 zea/data/datasets.py,sha256=NcbNbG9Mb3HtP40yHuBfnqXMTDwt5Lct4_sufAERjJw,25887
-zea/data/file.py,sha256=2_FFjhtGqBxeLfwmg8tZMLaYEWOZxbHCMBxU-ZWbTPw,31171
+zea/data/file.py,sha256=PtTTJPeZMdVHSQ4UjUI52ZTPo6BDDHWrnLKWFZ1B9Ew,32704
 zea/data/file_operations.py,sha256=jIYneXVmRPGYJ1hS0CCQP-Z-LhO6QXCkKqPno-kXlGs,17093
 zea/data/layers.py,sha256=W9GMkNTpb8BOzXJoa7w6xr4xD0bFb9rsJEcO8_vK3pk,6705
-zea/data/preset_utils.py,sha256=auan71rc67eczu9Ddp9t7Ib9ckuC894eVdMkA7CBRAA,4411
+zea/data/preset_utils.py,sha256=uCEqSDW6bX73VaR42ISHLk0wiQRLPk6Nvpm09EeJnDk,4419
 zea/data/utils.py,sha256=Y8eO7DznJFiq89SUQmDdiYetQ3aHjf72sC8ih9ooht4,2687
 zea/datapaths.py,sha256=TqqALvtQRbbQEaIH7QEUaH0BEF_0GUKubuLCn8t90lA,20529
-zea/display.py,sha256=xqzpluv-thKdiSU4JiornnkOuB4DH_liaEhq3CZ7ilA,24530
-zea/doppler.py,sha256=PG8-GhgTxo2eUjFQ2D6Ag74HD2SkJa6b5LUQjXCS8a8,2994
+zea/display.py,sha256=0EMiVSRgliKZn36mxNDJwd1R_jY2wMFQDldMRneswcM,24531
+zea/doppler.py,sha256=LCwDN-4WM_suW79Ew5mWPdEzvz267CVICjkeODPO2-s,2979
+zea/func/__init__.py,sha256=EuAePMgzeg1UY5Zen7NyuMUxZZuvtsU4YGdu73ePAik,2474
+zea/func/tensor.py,sha256=YjsK2JE_hdJ6jP-xvC3ZrmG9j31wM70YpEz5zcN56vs,63014
+zea/func/ultrasound.py,sha256=uydxNYVnVgk31nO3hyI5P11GQNXnWdzIW3Qfu4z-Co0,17814
 zea/interface.py,sha256=hd2mU7-WttfCCeGsri91WWrFjDoN1uVMCblbyG0bEuU,18097
-zea/internal/_generate_keras_ops.py,sha256=7RwmavpsqOALr_Zsby9xtIbUcMacwU3mw7MLtrz4q9Y,3848
+zea/internal/_generate_keras_ops.py,sha256=8cEJugo2Mf-16DmDdm12lwnfT0IIrVRttI6Jcc8Hr4g,3869
 zea/internal/cache.py,sha256=EMKuy2WT7J84Bo-hi5DNKWLBXMAlfmTdgJQGadTqutc,8468
 zea/internal/checks.py,sha256=4XcObKo-rOizlte75riP82hgNisE9ugLzMPFECF7Kco,10731
 zea/internal/config/create.py,sha256=f8dy6YcAUZbROxwCvORI26ACMRO4Q7EL188KyTL8Bpk,5447
@@ -76,19 +79,18 @@ zea/internal/setup_zea.py,sha256=kQGyQ8lapi4P-soNZY2j3oRqNbfj8eFoyJEGLYndvbk,780
 zea/internal/utils.py,sha256=Sf9b7_qjNwvyKmdJi7IQ8LPdaF6sW3YhwWFHZwY9uS4,9445
 zea/internal/viewer.py,sha256=nXTJwaWM9x8_R3X8YB9B5bNkZwwfVGKUu8pIr2HMweQ,15840
 zea/io_lib.py,sha256=FpWf_XEwpaLXBRK5nQuRRiwKBTPVQYWQuO6Bqt9Lj14,18185
-zea/keras_ops.py,sha256=wqrYKcX-KuekJUBMfQcuyL_RwJL4To4CJq3DamEKRZY,67874
 zea/log.py,sha256=cpbkRQhHE0vDvHOvXS91RHjG22F9insgV48qVPNz66g,10593
-zea/metrics.py,sha256=fp_Ducef_bc22SFSFWq-EPdBBj5txrD94WMuXgOH3HU,15579
+zea/metrics.py,sha256=9WdIBVTACMJlodUeL6RFpehCXJdQK2ddPl1ZZgFCCsg,15584
 zea/models/__init__.py,sha256=7OJVGSJ2rGOnRC8gNnH_oIsimpZj3gnmYUEXrshqOZY,4852
 zea/models/base.py,sha256=OwV1VfcK0xLLOsfpOIxCEEwIoxJ1sUogZjljd1KolQY,8065
 zea/models/carotid_segmenter.py,sha256=TfklE8UB_-Wl5VwjqmXc6fKle4PscGVB4IrgfOIvQfo,5799
 zea/models/deeplabv3.py,sha256=Ew-JIaQgekumVZN--pIQ5XQR5xTj1qMbfLm_xQH9qYo,4967
 zea/models/dense.py,sha256=EwrSawfSTi9oWE55Grr7jtwLXC9MNqEOO3su4oYHqfg,4067
-zea/models/diffusion.py,sha256=OAEKZ7CBoc2yQI2zjrPB668jSBzi6Xp2kaBAvKSFeX8,39375
+zea/models/diffusion.py,sha256=-0r8SoRvHSm2UzksY7PyNMeBGjjlR36I-5FsJRSofx8,39376
 zea/models/echonet.py,sha256=7ZK0nKVz3dZh0aBn9LoGmaqkrFJ05SzLeNYYdOoO0_E,6690
-zea/models/echonetlvh.py,sha256=WSR0MaZc2a2h0wzfyVdOwKGiA6C1CIHGo1Ok_lroHUE,11083
+zea/models/echonetlvh.py,sha256=vbVWzlmcGoWOr9DtDG1smwn9gklc5p4eR48ePna1CNs,11084
 zea/models/generative.py,sha256=iujicyFDuCD7NEk_cZ8thlZ2Rl3Qa8LfkwPsZdWYpR0,2625
-zea/models/gmm.py,sha256=6YYoiizsD7BtISOToEXkki6Cc8iXMkgmPH_rMFQKs3E,8324
+zea/models/gmm.py,sha256=RHhoyb1wnPnzvbbo_i89pI_xOTdVRKQjVPsf5-ZUcqA,8325
 zea/models/layers.py,sha256=hhtBLQgt6ZMKj60FXBNIpThI7gZZeEqkzBMsub_TNFM,1920
 zea/models/lpips.py,sha256=TmzI0qU8BV22gpHD_ovCw6G33EF05JHemdReYq9FGCs,6590
 zea/models/lv_segmentation.py,sha256=BaX9c5G3nlKqatVlgL9guIPA_n_Ea0lHMw6jos4lVs0,3447
@@ -98,25 +100,29 @@ zea/models/regional_quality.py,sha256=ohlgGXCHwlluJgx2wBKMUDert71neXwJ1mzxdt0KyX
 zea/models/taesd.py,sha256=lOej2B4pE8CHn8SMHVFO4gBkNdsYbB0QKmC18RxPiUg,8611
 zea/models/unet.py,sha256=BiFgC2qfe75ZqzE-6IV7c2PXhXuj1IQXTRL0PiavEdo,6682
 zea/models/utils.py,sha256=My6VY27S4udOn7xatIM22Qgn8jED1FmnA2yZw1mcuVw,2015
-zea/ops.py,sha256=uPLTCETRtfP4Zb8jNBN7v7f3HE26TjHgDAfOyFBuR4o,125273
-zea/probes.py,sha256=udA-YXwYhTAk7-PofS6chYQJ3Y4lmW-7f0O-Km5Bu5o,7767
-zea/scan.py,sha256=Dng_2mRr_S8FuW4eFUcddBkwUPjYUAFWp665DYMJie8,29883
+zea/ops/__init__.py,sha256=EEZ4h442JOm1wQ7ffp5J5ShrVABUamavrBnU_5BGAJA,4135
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