AOT-biomaps 2.1.3__py3-none-any.whl → 2.9.233__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (50) hide show
  1. AOT_biomaps/AOT_Acoustic/AcousticEnums.py +64 -0
  2. AOT_biomaps/AOT_Acoustic/AcousticTools.py +221 -0
  3. AOT_biomaps/AOT_Acoustic/FocusedWave.py +244 -0
  4. AOT_biomaps/AOT_Acoustic/IrregularWave.py +66 -0
  5. AOT_biomaps/AOT_Acoustic/PlaneWave.py +43 -0
  6. AOT_biomaps/AOT_Acoustic/StructuredWave.py +392 -0
  7. AOT_biomaps/AOT_Acoustic/__init__.py +15 -0
  8. AOT_biomaps/AOT_Acoustic/_mainAcoustic.py +978 -0
  9. AOT_biomaps/AOT_Experiment/Focus.py +55 -0
  10. AOT_biomaps/AOT_Experiment/Tomography.py +505 -0
  11. AOT_biomaps/AOT_Experiment/__init__.py +9 -0
  12. AOT_biomaps/AOT_Experiment/_mainExperiment.py +532 -0
  13. AOT_biomaps/AOT_Optic/Absorber.py +24 -0
  14. AOT_biomaps/AOT_Optic/Laser.py +70 -0
  15. AOT_biomaps/AOT_Optic/OpticEnums.py +17 -0
  16. AOT_biomaps/AOT_Optic/__init__.py +10 -0
  17. AOT_biomaps/AOT_Optic/_mainOptic.py +204 -0
  18. AOT_biomaps/AOT_Recon/AOT_Optimizers/DEPIERRO.py +191 -0
  19. AOT_biomaps/AOT_Recon/AOT_Optimizers/LS.py +106 -0
  20. AOT_biomaps/AOT_Recon/AOT_Optimizers/MAPEM.py +456 -0
  21. AOT_biomaps/AOT_Recon/AOT_Optimizers/MLEM.py +333 -0
  22. AOT_biomaps/AOT_Recon/AOT_Optimizers/PDHG.py +221 -0
  23. AOT_biomaps/AOT_Recon/AOT_Optimizers/__init__.py +5 -0
  24. AOT_biomaps/AOT_Recon/AOT_PotentialFunctions/Huber.py +90 -0
  25. AOT_biomaps/AOT_Recon/AOT_PotentialFunctions/Quadratic.py +86 -0
  26. AOT_biomaps/AOT_Recon/AOT_PotentialFunctions/RelativeDifferences.py +59 -0
  27. AOT_biomaps/AOT_Recon/AOT_PotentialFunctions/__init__.py +3 -0
  28. AOT_biomaps/AOT_Recon/AlgebraicRecon.py +1023 -0
  29. AOT_biomaps/AOT_Recon/AnalyticRecon.py +154 -0
  30. AOT_biomaps/AOT_Recon/BayesianRecon.py +230 -0
  31. AOT_biomaps/AOT_Recon/DeepLearningRecon.py +35 -0
  32. AOT_biomaps/AOT_Recon/PrimalDualRecon.py +210 -0
  33. AOT_biomaps/AOT_Recon/ReconEnums.py +375 -0
  34. AOT_biomaps/AOT_Recon/ReconTools.py +273 -0
  35. AOT_biomaps/AOT_Recon/__init__.py +11 -0
  36. AOT_biomaps/AOT_Recon/_mainRecon.py +288 -0
  37. AOT_biomaps/Config.py +95 -0
  38. AOT_biomaps/Settings.py +45 -13
  39. AOT_biomaps/__init__.py +271 -18
  40. aot_biomaps-2.9.233.dist-info/METADATA +22 -0
  41. aot_biomaps-2.9.233.dist-info/RECORD +43 -0
  42. {AOT_biomaps-2.1.3.dist-info → aot_biomaps-2.9.233.dist-info}/WHEEL +1 -1
  43. AOT_biomaps/AOT_Acoustic.py +0 -1881
  44. AOT_biomaps/AOT_Experiment.py +0 -541
  45. AOT_biomaps/AOT_Optic.py +0 -219
  46. AOT_biomaps/AOT_Reconstruction.py +0 -1416
  47. AOT_biomaps/config.py +0 -54
  48. AOT_biomaps-2.1.3.dist-info/METADATA +0 -20
  49. AOT_biomaps-2.1.3.dist-info/RECORD +0 -11
  50. {AOT_biomaps-2.1.3.dist-info → aot_biomaps-2.9.233.dist-info}/top_level.txt +0 -0
@@ -1,1881 +0,0 @@
1
- import scipy.io
2
- import numpy as np
3
- import h5py
4
- from scipy.signal import hilbert
5
- from math import ceil, floor
6
- import os
7
- from kwave.kgrid import kWaveGrid
8
- from kwave.kmedium import kWaveMedium
9
- from kwave.ksource import kSource
10
- from kwave.ksensor import kSensor
11
- from kwave.kspaceFirstOrder3D import kspaceFirstOrder3D
12
- from kwave.kspaceFirstOrder2D import kspaceFirstOrder2D
13
- from kwave.utils.signals import tone_burst
14
- from kwave.options.simulation_options import SimulationOptions
15
- from kwave.options.simulation_execution_options import SimulationExecutionOptions
16
- import matplotlib.pyplot as plt
17
- import matplotlib.animation as animation
18
- import matplotlib as mpl
19
- from tempfile import gettempdir
20
- from .config import config
21
- import AOT_biomaps.Settings
22
- from concurrent.futures import ThreadPoolExecutor
23
- import time
24
-
25
- if config.get_process() == 'gpu':
26
- import cupy as cp
27
- from cupyx.scipy.signal import hilbert as cp_hilbert
28
- import pynvml
29
- from scipy.signal import hilbert as np_hilbert
30
-
31
-
32
- from abc import ABC, abstractmethod
33
- from enum import Enum
34
-
35
-
36
- class TypeSim(Enum):
37
- """
38
- Enum for the type of simulation to be performed.
39
-
40
- Selection of simulation types:
41
- - KWAVE: k-Wave simulation.
42
- - FIELD2: Field II simulation.
43
- - HYDRO: Hydrophone acquisition.
44
- """
45
- KWAVE = 'k-wave'
46
- """k-Wave simulation."""
47
-
48
- FIELD2 = 'Field2'
49
- """Field II simulation."""
50
-
51
- HYDRO = 'Hydrophone'
52
- """Hydrophone acquisition."""
53
-
54
- class Dim(Enum):
55
- """
56
- Enum for the dimension of the acoustic field.
57
-
58
- Selection of dimensions:
59
- - D2: 2D field.
60
- - D3: 3D field.
61
- """
62
- D2 = '2D'
63
- """2D field."""
64
- D3 = '3D'
65
- """3D field."""
66
-
67
- class FormatSave(Enum):
68
- """
69
- Enum for different file formats to save the acoustic field.
70
-
71
- Selection of file formats:
72
- - HDR_IMG: Interfile format (.hdr and .img).
73
- - H5: HDF5 format (.h5).
74
- - NPY: NumPy format (.npy).
75
- """
76
- HDR_IMG = '.hdr'
77
- """Interfile format (.hdr and .img)."""
78
- H5 = '.h5'
79
- """HDF5 format (.h5)."""
80
- NPY = '.npy'
81
- """NumPy format (.npy)."""
82
-
83
- class WaveType(Enum):
84
- """
85
- Enum for different types of acoustic waves.
86
-
87
- Selection of wave types:
88
- - FocusedWave: A wave type where the energy is focused at a specific point.
89
- - StructuredWave: A wave type characterized by a specific pattern or structure.
90
- - PlaneWave: A wave type where the wavefronts are parallel and travel in a single direction.
91
- """
92
- FocusedWave = 'focus'
93
- """A wave type where the energy is focused at a specific point."""
94
- StructuredWave = 'structured'
95
- """A wave type characterized by a specific pattern or structure."""
96
- PlaneWave = 'plane'
97
- """A wave type where the wavefronts are parallel and travel in a single direction."""
98
-
99
- ####### ABSTRACT CLASS #######
100
-
101
- class AcousticField(ABC):
102
- """
103
- Abstract class to generate and manipulate acoustic fields for ultrasound imaging.
104
- Provides methods to initialize parameters, generate fields, save and load data, and calculate envelopes.
105
-
106
- Principal parameters:
107
- - field: Acoustic field data.
108
- - enveloppe: Analytic envelope squared of the acoustic field.
109
- - burst: Burst signal used for generating the field for each piezo elements.
110
- - delayedSignal: Delayed burst signal for each piezo element.
111
- - medium: Medium properties for k-Wave simulation. Because field2 and Hydrophone simulation are not implemented yet, this attribute is set to None for these types of simulation.
112
- """
113
-
114
- def __init__(self, params):
115
- """
116
- Initialize global properties of the AcousticField object.
117
-
118
- Parameters:
119
- - typeSim (TypeSim): Type of simulation to be performed. Options include KWAVE, FIELD2, and HYDRO. Default is TypeSim.KWAVE.
120
- - dim (Dim): Dimension of the acoustic field. Can be 2D or 3D. Default is Dim.D2.
121
- - c0 (float): Speed of sound in the medium, specified in meters per second (m/s). Default is 1540 m/s.
122
- - f_US (float): Frequency of the ultrasound signal, specified in Hertz (Hz). Default is 6 MHz.
123
- - f_AQ (float): Frequency of data acquisition, specified in Hertz (Hz). Default is 180 MHz.
124
- - f_saving (float): Frequency at which the acoustic field data is saved, specified in Hertz (Hz). Default is 10 MHz.
125
- - num_cycles (int): Number of cycles in the burst signal. Default is 4 cycles.
126
- - num_elements (int): Number of elements in the transducer array. Default is 192 elements.
127
- - element_width (float): Width of each transducer element, specified in meters (m). Default is 0.2 mm.
128
- - element_height (float): Height of each transducer element, specified in meters (m). Default is 6 mm.
129
- - Xrange (list of float): Range of X coordinates for the acoustic field, specified in meters (m). Default is from -20 mm to 20 mm.
130
- - Yrange (list of float, optional): Range of Y coordinates for the acoustic field, specified in meters (m). Default is None, indicating no specific Y range.
131
- - Zrange (list of float): Range of Z coordinates for the acoustic field, specified in meters (m). Default is from 0 m to 37 mm.
132
- """
133
- required_keys = [
134
- 'c0', 'f_US', 'f_AQ', 'f_saving', 'num_cycles', 'num_elements',
135
- 'element_width', 'element_height', 'Xrange', 'Zrange', 'dim',
136
- 'typeSim', 'dx', 'dz'
137
- ]
138
-
139
- # Verify required keys
140
- try:
141
- if params != None:
142
- for key in required_keys:
143
- if key not in params.acoustic and key not in params.general:
144
- raise ValueError(f"{key} must be provided in the parameters.")
145
- except ValueError as e:
146
- print(f"Initialization error: {e}")
147
- raise
148
- if params != None:
149
- if type(params) != AOT_biomaps.Settings.Params:
150
- raise TypeError("params must be an instance of the Params class")
151
-
152
- self.params = {
153
- 'c0': params.acoustic['c0'],
154
- 'f_US': int(float(params.acoustic['f_US'])),
155
- 'f_AQ': params.acoustic['f_AQ'],
156
- 'f_saving': int(float(params.acoustic['f_saving'])),
157
- 'num_cycles': params.acoustic['num_cycles'],
158
- 'num_elements': params.acoustic['num_elements'],
159
- 'element_width': params.acoustic['element_width'],
160
- 'element_height': params.acoustic['element_height'],
161
- 'Xrange': params.general['Xrange'],
162
- 'Yrange': params.general['Yrange'],
163
- 'Zrange': params.general['Zrange'],
164
- 'dim': params.acoustic['dim'],
165
- 'typeSim': params.acoustic['typeSim'],
166
- 'dx': params.general['dx'],
167
- 'dy': params.general['dy'] if params.general['Yrange'] is not None else None,
168
- 'dz': params.general['dz'],
169
- 'Nx': int(np.round((params.general['Xrange'][1] - params.general['Xrange'][0])/params.general['dx'])),
170
- 'Ny': int(np.round((params.general['Yrange'][1] - params.general['Yrange'][0])/params.general['dy'])) if params.general['Yrange'] is not None else 1,
171
- 'Nz': int(np.round((params.general['Zrange'][1] - params.general['Zrange'][0])/params.general['dz'])),
172
- 'probeWidth': params.acoustic['num_elements'] * params.acoustic['element_width'],
173
- 'IsAbsorbingMedium': params.acoustic['isAbsorbingMedium'],
174
- }
175
- self.kgrid = kWaveGrid([self.params["Nx"], self.params["Nz"]], [self.params["dx"], self.params["dz"]])
176
- if params.acoustic['f_AQ'] == "AUTO":
177
-
178
- self.kgrid.makeTime(self.params['c0'])
179
-
180
- self.params['f_AQ'] = int(1/self.kgrid.dt)
181
- else:
182
- Nt = ceil((self.params['Zrange'][1] - self.params['Zrange'][0])*float(params.acoustic['f_AQ']) / self.params['c0'])
183
-
184
- self.kgrid.setTime(Nt,1/float(params.acoustic['f_AQ']))
185
- self.params['f_AQ'] = int(float(params.acoustic['f_AQ']))
186
-
187
- self._generate_burst_signal()
188
- if self.params["dim"] == Dim.D3 and self.params["Yrange"] is None:
189
- raise ValueError("Yrange must be provided for 3D fields.")
190
- if self.params['typeSim'] == TypeSim.KWAVE.value:
191
- if self.params ['IsAbsorbingMedium'] == True:
192
- self.medium = kWaveMedium(
193
- sound_speed=self.params['c0'],
194
- density=params.acoustic['Absorption']['density'],
195
- alpha_coeff=params.acoustic['Absorption']['alpha_coeff'], # dB/(MHz·cm)
196
- alpha_power=params.acoustic['Absorption']['alpha_power'], # 0.5
197
- absorbing=True
198
- )
199
- else:
200
- self.medium = kWaveMedium(sound_speed=self.params['c0'])
201
- elif self.params['typeSim'] == TypeSim.FIELD2.value:
202
- self.medium = None
203
- else:
204
- self.medium = None
205
-
206
- self.waveType = None
207
- self.field = None
208
- self.enveloppe = None
209
-
210
- def __str__(self):
211
- """
212
- Returns a string representation of the AcousticField object, including its parameters and attributes.
213
- The string is formatted in a table-like structure for better readability.
214
- """
215
- try:
216
- # Get all attributes of the instance
217
- attrs = {**self.params, **{k: v for k, v in vars(self).items() if k not in self.params}}
218
-
219
- # Base attributes of AcousticField
220
- base_attrs_keys = ['c0', 'f_US', 'f_AQ', 'f_saving', 'num_cycles', 'num_elements',
221
- 'element_width', 'element_height',
222
- 'Xrange', 'Yrange', 'Zrange', 'dim', 'typeSim', 'Nx', 'Ny', 'Nz',
223
- 'dx', 'dy', 'dz', 'probeWidth']
224
- base_attrs = {key: value for key, value in attrs.items() if key in base_attrs_keys}
225
-
226
- # Attributes specific to the derived class, excluding 'params'
227
- derived_attrs = {key: value for key, value in attrs.items() if key not in base_attrs_keys and key != 'params'}
228
-
229
- # Create lines for base and derived attributes
230
- base_attr_lines = [f" {key}: {value}" for key, value in base_attrs.items()]
231
-
232
- derived_attr_lines = []
233
- for key, value in derived_attrs.items():
234
- if key in {'burst', 'delayedSignal'}:
235
- continue
236
- elif key == 'pattern':
237
- # Inspect the pattern object
238
- try:
239
- pattern_attrs = vars(value)
240
- pattern_str = ", ".join([f"{k}={v}" for k, v in pattern_attrs.items()])
241
- derived_attr_lines.append(f" pattern: {{{pattern_str}}}")
242
- except Exception as e:
243
- derived_attr_lines.append(f" pattern: <unreadable: {e}>")
244
- else:
245
- try:
246
- derived_attr_lines.append(f" {key}: {value}")
247
- except Exception as e:
248
- derived_attr_lines.append(f" {key}: <unprintable: {e}>")
249
-
250
- # Add shapes for burst and delayedSignal
251
- if 'burst' in derived_attrs:
252
- derived_attr_lines.append(f" burst: shape={self.burst.shape}")
253
- if 'delayedSignal' in derived_attrs:
254
- derived_attr_lines.append(f" delayedSignal: shape={self.delayedSignal.shape}")
255
-
256
- # Define borders and titles
257
- border = "+" + "-" * 40 + "+"
258
- title = f"|Type : {self.__class__.__name__} wave |"
259
- base_title = "| AcousticField Attributes |"
260
- derived_title = f"| {self.__class__.__name__} Specific Attributes |" if derived_attrs else ""
261
-
262
- # Convert attributes to strings
263
- base_attr_str = "\n".join(base_attr_lines)
264
- derived_attr_str = "\n".join(derived_attr_lines)
265
-
266
- # Assemble the final result
267
- result = f"{border}\n{title}\n{border}\n{base_title}\n{border}\n{base_attr_str}\n"
268
- if derived_attrs:
269
- result += f"\n{border}\n{derived_title}\n{border}\n{derived_attr_str}\n"
270
- result += border
271
-
272
- return result
273
- except Exception as e:
274
- print(f"Error in __str__ method: {e}")
275
- raise
276
-
277
- def __del__(self):
278
- """
279
- Destructor for the AcousticField class. Cleans up the field and envelope attributes.
280
- """
281
- try:
282
- self.field = None
283
- self.enveloppe = None
284
- self.burst = None
285
- self.delayedSignal = None
286
- if config.get_process() == 'gpu':
287
- cp.cuda.Device(config.bestGPU).synchronize()
288
- except Exception as e:
289
- print(f"Error in __del__ method: {e}")
290
- raise
291
-
292
- ## TOOLS METHODS ##
293
-
294
- def generate_field(self, isGpu=config.get_process() == 'gpu'):
295
- """
296
- Generate the acoustic field based on the specified simulation type and parameters.
297
- """
298
- try:
299
- if self.params['typeSim'] == TypeSim.FIELD2.value:
300
- raise NotImplementedError("FIELD2 simulation is not implemented yet.")
301
- elif self.params['typeSim'] == TypeSim.KWAVE.value:
302
- if self.params["dim"] == Dim.D2.value:
303
- self.field = self._generate_2Dacoustic_field_KWAVE(isGpu)
304
- elif self.params["dim"] == Dim.D3.value:
305
- self.field = self._generate_3Dacoustic_field_KWAVE(isGpu)
306
- elif self.params['typeSim'] == TypeSim.HYDRO.value:
307
- raise ValueError("Cannot generate field for Hydrophone simulation, load exciting acquisitions.")
308
- else:
309
- raise ValueError("Invalid simulation type. Supported types are: FIELD2, KWAVE, HYDRO.")
310
- except Exception as e:
311
- print(f"Error in generate_field method: {e}")
312
- raise
313
-
314
- def calculate_envelope_squared(self, isGPU=True if config.get_process() == 'gpu' else False):
315
- """
316
- Calculate the analytic envelope of the acoustic field using either CPU or GPU.
317
-
318
- Parameters:
319
- - use_gpu (bool): If True, use GPU for computation. Otherwise, use CPU.
320
-
321
- Returns:
322
- - envelope (numpy.ndarray or cupy.ndarray): The squared analytic envelope of the acoustic field.
323
- """
324
- try:
325
- if self.field is None:
326
- raise ValueError("Acoustic field is not generated. Please generate the field first.")
327
-
328
- if isGPU:
329
-
330
- pynvml.nvmlInit()
331
- handle = pynvml.nvmlDeviceGetHandleByIndex(0) # Assuming you want to check the first GPU
332
- info = pynvml.nvmlDeviceGetMemoryInfo(handle)
333
- total_memory = info.total / (1024 ** 2) # Convert to MB
334
- used_memory = info.used / (1024 ** 2) # Convert to MB
335
- free_memory = int(total_memory - used_memory)
336
-
337
- if free_memory < self.field.nbytes / (1024 ** 2):
338
- print(f"GPU memory insufficient {int(self.field.nbytes / (1024 ** 2))} MB, Free GPU memory: {free_memory} MB, falling back to CPU.")
339
- isGPU = False
340
- acoustic_field = np.asarray(self.field)
341
- else:
342
- acoustic_field = cp.asarray(self.field)
343
- else:
344
- acoustic_field = np.asarray(self.field)
345
-
346
- if len(acoustic_field.shape) not in [3, 4]:
347
- raise ValueError("Input acoustic field must be a 3D or 4D array.")
348
-
349
- def process_slice(slice_index,isGPU):
350
- """Calculate the envelope for a given slice of the acoustic field."""
351
- if isGPU:
352
- hilbert = cp_hilbert
353
- else:
354
- hilbert = np_hilbert
355
-
356
- if len(acoustic_field.shape) == 3:
357
- return np.abs(hilbert(acoustic_field[slice_index], axis=0))**2
358
- elif len(acoustic_field.shape) == 4:
359
- envelope_slice = np.zeros_like(acoustic_field[slice_index])
360
- for y in range(acoustic_field.shape[2]):
361
- for z in range(acoustic_field.shape[1]):
362
- envelope_slice[:, z, y, :] = np.abs(hilbert(acoustic_field[slice_index][:, z, y, :], axis=0))**2
363
- return envelope_slice
364
-
365
- # Determine the number of slices to process in parallel
366
- num_slices = acoustic_field.shape[0]
367
- slice_indices = [(i,) for i in range(num_slices)]
368
-
369
- if isGPU:
370
- # Use GPU directly without multithreading
371
- envelopes = [process_slice(slice_index,isGPU) for slice_index in slice_indices]
372
- else:
373
- # Use ThreadPoolExecutor to parallelize the computation on CPU
374
- with ThreadPoolExecutor() as executor:
375
- envelopes = list(executor.map(lambda index: process_slice(index,isGPU), slice_indices))
376
-
377
- # Combine the results into a single array
378
- if isGPU:
379
- self.enveloppe = cp.stack(envelopes, axis=0).get()
380
- else:
381
- self.enveloppe = np.stack(envelopes, axis=0)
382
-
383
- except Exception as e:
384
- print(f"Error in calculate_envelope_squared method: {e}")
385
- raise
386
-
387
- def save_field(self, filePath, formatSave=FormatSave.HDR_IMG):
388
- """
389
- Save the acoustic field to a file in the specified format.
390
-
391
- Parameters:
392
- - filePath (str): The path where the file will be saved.
393
- """
394
- try:
395
- if formatSave.value == FormatSave.HDR_IMG.value:
396
- self._save2D_HDR_IMG(filePath)
397
- elif formatSave.value == FormatSave.H5.value:
398
- self._save2D_H5(filePath)
399
- elif formatSave.value == FormatSave.NPY.value:
400
- self._save2D_NPY(filePath)
401
- else:
402
- raise ValueError("Unsupported format. Supported formats are: HDR_IMG, H5, NPY.")
403
- except Exception as e:
404
- print(f"Error in save_field method: {e}")
405
- raise
406
-
407
- def load_field(self, folderPath, formatSave=FormatSave.HDR_IMG):
408
- """
409
- Load the acoustic field from a file in the specified format.
410
-
411
- Parameters:
412
- - filePath (str): The folder path from which to load the file.
413
- """
414
- try:
415
- if str(type(formatSave)) != str(AOT_biomaps.AOT_Acoustic.FormatSave):
416
- raise ValueError(f"Unsupported file format: {formatSave}. Supported formats are: HDR_IMG, H5, NPY.")
417
-
418
- if self.params['typeSim'] == TypeSim.FIELD2.value:
419
- raise NotImplementedError("FIELD2 simulation is not implemented yet.")
420
- elif self.params['typeSim'] == TypeSim.KWAVE.value:
421
- if formatSave.value == FormatSave.HDR_IMG.value:
422
- if self.params["dim"] == Dim.D2.value:
423
- self._load_fieldKWAVE_XZ(os.path.join(folderPath,self.getName_field()+formatSave.value))
424
- self.calculate_envelope_squared()
425
- elif self.params["dim"] == Dim.D3.value:
426
- raise NotImplementedError("3D KWAVE field loading is not implemented yet.")
427
- elif formatSave.value == FormatSave.H5.value:
428
- if self.params["dim"] == Dim.D2.value:
429
- self._load_field_h5(folderPath)
430
- elif self.params["dim"] == Dim.D3.value:
431
- raise NotImplementedError("H5 KWAVE field loading is not implemented yet.")
432
- elif formatSave.value == FormatSave.NPY.value:
433
- if self.params["dim"] == Dim.D2.value:
434
- self.field = np.load(os.path.join(folderPath,self.getName_field()+formatSave.value))
435
- elif self.params["dim"] == Dim.D3.value:
436
- raise NotImplementedError("3D NPY KWAVE field loading is not implemented yet.")
437
- elif self.params['typeSim'] == TypeSim.HYDRO.value:
438
- print("Loading Hydrophone field...")
439
- if formatSave.value == FormatSave.HDR_IMG.value:
440
- raise ValueError("HDR_IMG format is not supported for Hydrophone acquisition.")
441
- if formatSave.value == FormatSave.H5.value:
442
- if self.params["dim"] == Dim.D2.value:
443
- self.field, self.params['Xrange'], self.params['Zrange'] = self._load_fieldHYDRO_XZ(os.path.join(folderPath, self.getName_field() + '.h5'), os.path.join(folderPath, "PARAMS_" +self.getName_field() + '.mat'))
444
- elif self.params["dim"] == Dim.D3.value:
445
- self._load_fieldHYDRO_XYZ(os.path.join(folderPath, self.getName_field() + '.h5'), os.path.join(folderPath, "PARAMS_" +self.getName_field() + '.mat'))
446
- elif formatSave.value == FormatSave.NPY.value:
447
- if self.params["dim"] == Dim.D2.value:
448
- self.field = np.load(folderPath)
449
- elif self.params["dim"] == Dim.D3.value:
450
- raise NotImplementedError("3D NPY Hydrophone field loading is not implemented yet.")
451
- else:
452
- raise ValueError("Invalid simulation type. Supported types are: FIELD2, KWAVE, HYDRO.")
453
-
454
- except Exception as e:
455
- print(f"Error in load_field method: {e}")
456
- raise
457
-
458
- def iSFieldInFolder(self, folderPath,formatSave=FormatSave.HDR_IMG):
459
- """
460
- Check if the field is already in the specified folder.
461
-
462
- Parameters:
463
- - filePath (str): The path to check.
464
-
465
- Returns:
466
- - bool: True if the field is in the folder, False otherwise.
467
- """
468
- try:
469
- if type(folderPath) != str:
470
- raise TypeError("folderPath must be a string")
471
- if not os.path.exists(folderPath):
472
- raise FileNotFoundError(f"The specified folder does not exist: {folderPath}")
473
- if type(formatSave) != FormatSave:
474
- raise TypeError("formatSave must be an instance of FormatSave Enum")
475
- if os.path.exists(os.path.join(folderPath, self.getName_field())+formatSave.value):
476
- return True
477
- else:
478
- return False
479
- except Exception as e:
480
- print(f"Error in iSFieldInFolder method: {e}")
481
- raise
482
-
483
- @abstractmethod
484
- def getName_field(self):
485
- pass
486
-
487
- ## DISPLAY METHODS ##
488
-
489
- def plot_burst_signal(self):
490
- """
491
- Plot the burst signal used for generating the acoustic field.
492
- """
493
- try:
494
- time2plot = np.arange(0, len(self.burst)) / self.params['f_AQ'] * 1000000 # Convert to microseconds
495
- plt.figure(figsize=(8, 8))
496
- plt.plot(time2plot, self.burst)
497
- plt.title('Excitation burst signal')
498
- plt.xlabel('Time (µs)')
499
- plt.ylabel('Amplitude')
500
- plt.grid()
501
- plt.show()
502
- except Exception as e:
503
- print(f"Error in plot_burst_signal method: {e}")
504
- raise
505
-
506
- def animated_plot_AcousticField(self, desired_duration_ms = 5000, save_dir=None):
507
- """
508
- Plot synchronized animations of A_matrix slices for selected angles.
509
-
510
- Args:
511
- step (int): Time step between frames (default is every 10 frames).
512
- save_dir (str): Directory to save the animation gif; if None, animation will not be saved.
513
-
514
- Returns:
515
- ani: Matplotlib FuncAnimation object.
516
- """
517
- try:
518
-
519
- maxF = np.max(self.enveloppe[:,20:,:])
520
- minF = np.min(self.enveloppe[:,20:,:])
521
- # Set the maximum embedded animation size to 100 MB
522
- plt.rcParams['animation.embed_limit'] = 100
523
-
524
- if save_dir is not None:
525
- os.makedirs(save_dir, exist_ok=True)
526
-
527
- # Create a figure and axis
528
- fig, ax = plt.subplots()
529
-
530
- # Set main title
531
- if self.waveType.value == WaveType.FocusedWave.value:
532
- fig.suptitle("[System Matrix Animation] Focused Wave", fontsize=12, y=0.98)
533
- elif self.waveType.value == WaveType.PlaneWave.value:
534
- fig.suptitle(f"[System Matrix Animation] Plane Wave | Angles {self.angle}°", fontsize=12, y=0.98)
535
- elif self.waveType.value == WaveType.StructuredWave.value:
536
- fig.suptitle(f"[System Matrix Animation] Structured Wave | Pattern structure: {self.pattern.activeList} | Angles {self.angle}°", fontsize=12, y=0.98)
537
- else:
538
-
539
- raise ValueError("Invalid wave type. Supported types are: FocusedWave, PlaneWave, StructuredWave.")
540
-
541
- # Initial plot
542
- im = ax.imshow(
543
- self.enveloppe[0, :, :],
544
- extent=(self.params['Xrange'][0] * 1000, self.params['Xrange'][-1] * 1000, self.params['Zrange'][-1] * 1000, self.params['Zrange'][0] * 1000),
545
- vmin = 1.2*minF,
546
- vmax=0.8*maxF,
547
- aspect='equal',
548
- cmap='jet',
549
- animated=True
550
- )
551
- ax.set_title(f"t = 0 ms", fontsize=10)
552
- ax.set_xlabel("x (mm)", fontsize=8)
553
- ax.set_ylabel("z (mm)", fontsize=8)
554
-
555
-
556
- # Unified update function for all subplots
557
- def update(frame):
558
- im.set_data(self.enveloppe[frame, :, :])
559
- ax.set_title(f"t = {frame / self.params['f_AQ'] * 1000:.2f} ms", fontsize=10)
560
- return [im] # Return a list of artists that were modified
561
-
562
- interval = desired_duration_ms / self.AcousticFields.shape[0]
563
-
564
- # Create animation
565
- ani = animation.FuncAnimation(
566
- fig, update,
567
- frames=range(0, self.enveloppe.shape[0]),
568
- interval=interval, blit=True
569
- )
570
-
571
- # Save animation if needed
572
- if save_dir is not None:
573
- if self.waveType == WaveType.FocusedWave:
574
- save_filename = f"Focused_Wave_.gif"
575
- elif self.waveType == WaveType.PlaneWave:
576
- save_filename = f"Plane_Wave_{self._format_angle()}.gif"
577
- else:
578
- save_filename = f"Structured_Wave_PatternStructure_{self.pattern.activeList}_{self._format_angle()}.gif"
579
- save_path = os.path.join(save_dir, save_filename)
580
- ani.save(save_path, writer='pillow', fps=20)
581
- print(f"Saved: {save_path}")
582
-
583
- plt.close(fig)
584
-
585
- return ani
586
- except Exception as e:
587
- print(f"Error creating animation: {e}")
588
- return None
589
-
590
-
591
- ## PRIVATE METHODS ##
592
-
593
- def _generate_burst_signal(self):
594
- if self.params['typeSim'] == TypeSim.FIELD2.value:
595
- raise NotImplementedError("FIELD2 simulation is not implemented yet.")
596
- elif self.params['typeSim'] == TypeSim.KWAVE.value:
597
- self._generate_burst_signalKWAVE()
598
- elif self.params['typeSim'] == TypeSim.HYDRO.value:
599
- raise ValueError("Cannot generate burst signal for Hydrophone simulation.")
600
-
601
- def _generate_burst_signalKWAVE(self):
602
- """
603
- Private method to generate a burst signal based on the specified parameters.
604
- """
605
- try:
606
- self.burst = tone_burst(1/self.kgrid.dt, self.params['f_US'], self.params['num_cycles']).squeeze()
607
- except Exception as e:
608
- print(f"Error in __generate_burst_signal method: {e}")
609
- raise
610
-
611
- @abstractmethod
612
- def _generate_2Dacoustic_field_KWAVE(self, isGpu):
613
- """
614
- Generate a 2D acoustic field using k-Wave simulation.
615
- Must be implemented in subclasses.
616
- """
617
- pass
618
-
619
- @abstractmethod
620
- def _generate_3Dacoustic_field_KWAVE(self, isGpu):
621
- """
622
- Generate a 3D acoustic field using k-Wave simulation.
623
- Must be implemented in subclasses.
624
- """
625
- pass
626
-
627
- @abstractmethod
628
- def _save2D_HDR_IMG(self, filePath):
629
- """
630
- Save the 2D acoustic field as an HDR_IMG file.
631
- Must be implemented in subclasses.
632
- """
633
- pass
634
-
635
- def _load_field_h5(self, filePath):
636
- """
637
- Load the 2D acoustic field from an H5 file.
638
-
639
- Parameters:
640
- - filePath (str): The path to the H5 file.
641
-
642
- Returns:
643
- - field (numpy.ndarray): The loaded acoustic field.
644
- """
645
- try:
646
- with h5py.File(filePath+self.getName_field()+".h5", 'r') as f:
647
- self.enveloppe = f['data'][:]
648
- except Exception as e:
649
- print(f"Error in _load_field_h5 method: {e}")
650
- raise
651
-
652
- def _save2D_H5(self, filePath):
653
- """
654
- Save the 2D acoustic field as an H5 file.
655
-
656
- Parameters:
657
- - filePath (str): The path where the file will be saved.
658
- """
659
- try:
660
- with h5py.File(filePath+self.getName_field()+"h5", 'w') as f:
661
- for key, value in self.__dict__.items():
662
- if key != 'enveloppe':
663
- f.create_dataset(key, data=value)
664
- f.create_dataset('data', data=self.enveloppe, compression='gzip')
665
- except Exception as e:
666
- print(f"Error in _save2D_H5 method: {e}")
667
- raise
668
-
669
- def _save2D_NPY(self, filePath):
670
- """
671
- Save the 2D acoustic field as a NPY file.
672
-
673
- Parameters:
674
- - filePath (str): The path where the file will be saved.
675
- """
676
- try:
677
- np.save(filePath+self.getName_field()+"npy", self.enveloppe)
678
- except Exception as e:
679
- print(f"Error in _save2D_NPY method: {e}")
680
- raise
681
-
682
- def _load_fieldKWAVE_XZ(self, hdr_path):
683
- """
684
- Read an Interfile (.hdr) and its binary file (.img) to reconstruct an acoustic field.
685
-
686
- Parameters:
687
- - hdr_path (str): The path to the .hdr file.
688
-
689
- Returns:
690
- - field (numpy.ndarray): The reconstructed acoustic field with dimensions reordered to (X, Z, time).
691
- - header (dict): A dictionary containing the metadata from the .hdr file.
692
- """
693
- try:
694
- header = {}
695
- # Read the .hdr file
696
- with open(hdr_path, 'r') as f:
697
- for line in f:
698
- if ':=' in line:
699
- key, value = line.split(':=', 1)
700
- key = key.strip().lower().replace('!', '')
701
- value = value.strip()
702
- header[key] = value
703
-
704
- # Get the associated .img file name
705
- data_file = header.get('name of data file') or header.get('name of date file')
706
- if data_file is None:
707
- raise ValueError(f"Cannot find the data file associated with the header file {hdr_path}")
708
- img_path = os.path.join(os.path.dirname(hdr_path), os.path.basename(data_file))
709
-
710
- # Determine the field size from metadata
711
- shape = [int(header[f'matrix size [{i}]']) for i in range(1, 3) if f'matrix size [{i}]' in header]
712
- if not shape:
713
- raise ValueError("Cannot determine the shape of the acoustic field from metadata.")
714
-
715
- # Data type
716
- data_type = header.get('number format', 'short float').lower()
717
- dtype_map = {
718
- 'short float': np.float32,
719
- 'float': np.float32,
720
- 'int16': np.int16,
721
- 'int32': np.int32,
722
- 'uint16': np.uint16,
723
- 'uint8': np.uint8
724
- }
725
- dtype = dtype_map.get(data_type)
726
- if dtype is None:
727
- raise ValueError(f"Unsupported data type: {data_type}")
728
-
729
- # Byte order (endianness)
730
- byte_order = header.get('imagedata byte order', 'LITTLEENDIAN').lower()
731
- endianess = '<' if 'little' in byte_order else '>'
732
-
733
- # Verify the actual size of the .img file
734
- fileSize = os.path.getsize(img_path)
735
- timeDim = int(fileSize / (np.dtype(dtype).itemsize * np.prod(shape)))
736
- shape = shape + [timeDim]
737
-
738
- # Read binary data
739
- with open(img_path, 'rb') as f:
740
- data = np.fromfile(f, dtype=endianess + np.dtype(dtype).char)
741
-
742
- # Reshape data to (time, Z, X)
743
- field = data.reshape(shape[::-1]) # NumPy interprets in C order (opposite of MATLAB)
744
-
745
- # Apply scaling factors if available
746
- rescale_slope = float(header.get('data rescale slope', 1))
747
- rescale_offset = float(header.get('data rescale offset', 0))
748
- field = field * rescale_slope + rescale_offset
749
-
750
- self.field = field
751
- except Exception as e:
752
- print(f"Error in _load_fieldKWAVE_XZ method: {e}")
753
- raise
754
-
755
- def _load_fieldHYDRO_XZ(self, file_path_h5, param_path_mat):
756
- """
757
- Load the 2D acoustic field for Hydrophone simulation from H5 and MAT files.
758
-
759
- Parameters:
760
- - file_path_h5 (str): The path to the H5 file.
761
- - param_path_mat (str): The path to the MAT file.
762
-
763
- Returns:
764
- - envelope_transposed (numpy.ndarray): The transposed envelope of the acoustic field.
765
- """
766
- try:
767
- # Load parameters from the .mat file
768
- param = scipy.io.loadmat(param_path_mat)
769
-
770
- # Load the ranges for x and z
771
- x_test = param['x'].flatten()
772
- z_test = param['z'].flatten()
773
-
774
- x_range = np.arange(-23, 21.2, 0.2)
775
- z_range = np.arange(0, 37.2, 0.2)
776
- X, Z = np.meshgrid(x_range, z_range)
777
-
778
- # Load the data from the .h5 file
779
- with h5py.File(file_path_h5, 'r') as file:
780
- data = file['data'][:]
781
-
782
- # Initialize a matrix to store the acoustic data
783
- acoustic_field = np.zeros((len(z_range), len(x_range), data.shape[1]))
784
-
785
- # Fill the grid with acoustic data
786
- index = 0
787
- for i in range(len(z_range)):
788
- if i % 2 == 0:
789
- # Traverse left to right
790
- for j in range(len(x_range)):
791
- acoustic_field[i, j, :] = data[index]
792
- index += 1
793
- else:
794
- # Traverse right to left
795
- for j in range(len(x_range) - 1, -1, -1):
796
- acoustic_field[i, j, :] = data[index]
797
- index += 1
798
-
799
- self.field =np.transpose(acoustic_field, (2, 0, 1)).T
800
- # Calculate the analytic envelope
801
- envelope = np.abs(hilbert(acoustic_field, axis=2))
802
- # Reorganize the array to have the shape (Times, Z, X)
803
- envelope_transposed = np.transpose(envelope, (2, 0, 1)).T
804
-
805
- self.enveloppe = envelope_transposed
806
- self.params['Xrange'] = x_range
807
- self.params['Zrange'] = z_range
808
-
809
- except Exception as e:
810
- print(f"Error in _load_fieldHYDRO_XZ method: {e}")
811
- raise
812
-
813
- def _load_fieldHYDRO_YZ(self, file_path_h5, param_path_mat):
814
- """
815
- Load the 2D acoustic field for Hydrophone simulation from H5 and MAT files.
816
-
817
- Parameters:
818
- - file_path_h5 (str): The path to the H5 file.
819
- - param_path_mat (str): The path to the MAT file.
820
-
821
- Returns:
822
- - envelope_transposed (numpy.ndarray): The transposed envelope of the acoustic field.
823
- - y_range (numpy.ndarray): The range of y values.
824
- - z_range (numpy.ndarray): The range of z values.
825
- """
826
- try:
827
- # Load parameters from the .mat file
828
- param = scipy.io.loadmat(param_path_mat)
829
-
830
- # Extract the ranges for y and z
831
- y_range = param['y'].flatten()
832
- z_range = param['z'].flatten()
833
-
834
- # Load the data from the .h5 file
835
- with h5py.File(file_path_h5, 'r') as file:
836
- data = file['data'][:]
837
-
838
- # Calculate the number of scans
839
- Ny = len(y_range)
840
- Nz = len(z_range)
841
-
842
- # Create the scan positions
843
- positions_y = []
844
- positions_z = []
845
-
846
- for i in range(Nz):
847
- if i % 2 == 0:
848
- # Traverse top to bottom for even rows
849
- positions_y.extend(y_range)
850
- else:
851
- # Traverse bottom to top for odd rows
852
- positions_y.extend(y_range[::-1])
853
- positions_z.extend([z_range[i]] * Ny)
854
-
855
- Positions = np.column_stack((positions_y, positions_z))
856
-
857
- # Initialize a matrix to store the reorganized data
858
- reorganized_data = np.zeros((Ny, Nz, data.shape[1]))
859
-
860
- # Reorganize the data according to the scan positions
861
- for index, (j, k) in enumerate(Positions):
862
- y_idx = np.where(y_range == j)[0][0]
863
- z_idx = np.where(z_range == k)[0][0]
864
- reorganized_data[y_idx, z_idx, :] = data[index, :]
865
-
866
- # Calculate the analytic envelope
867
- envelope = np.abs(hilbert(reorganized_data, axis=2))
868
- # Reorganize the array to have the shape (Times, Z, Y)
869
- envelope_transposed = np.transpose(envelope, (2, 0, 1))
870
- return envelope_transposed, y_range, z_range
871
- except Exception as e:
872
- print(f"Error in _load_fieldHYDRO_YZ method: {e}")
873
- raise
874
-
875
- def _load_fieldHYDRO_XYZ(self, file_path_h5, param_path_mat):
876
- """
877
- Load the 3D acoustic field for Hydrophone simulation from H5 and MAT files.
878
-
879
- Parameters:
880
- - file_path_h5 (str): The path to the H5 file.
881
- - param_path_mat (str): The path to the MAT file.
882
-
883
- Returns:
884
- - EnveloppeField (numpy.ndarray): The envelope of the acoustic field.
885
- - x_range (numpy.ndarray): The range of x values.
886
- - y_range (numpy.ndarray): The range of y values.
887
- - z_range (numpy.ndarray): The range of z values.
888
- """
889
- try:
890
- # Load parameters from the .mat file
891
- param = scipy.io.loadmat(param_path_mat)
892
-
893
- # Extract the ranges for x, y, and z
894
- x_range = param['x'].flatten()
895
- y_range = param['y'].flatten()
896
- z_range = param['z'].flatten()
897
-
898
- # Create a meshgrid for x, y, and z
899
- X, Y, Z = np.meshgrid(x_range, y_range, z_range, indexing='ij')
900
-
901
- # Load the data from the .h5 file
902
- with h5py.File(file_path_h5, 'r') as file:
903
- data = file['data'][:]
904
-
905
- # Calculate the number of scans
906
- Nx = len(x_range)
907
- Ny = len(y_range)
908
- Nz = len(z_range)
909
- Nscans = Nx * Ny * Nz
910
-
911
- # Create the scan positions
912
- if Ny % 2 == 0:
913
- X = np.tile(np.concatenate([x_range[:, np.newaxis], x_range[::-1, np.newaxis]]), (Ny // 2, 1))
914
- Y = np.repeat(y_range, Nx)
915
- else:
916
- X = np.concatenate([x_range[:, np.newaxis], np.tile(np.concatenate([x_range[::-1, np.newaxis], x_range[:, np.newaxis]]), ((Ny - 1) // 2, 1))])
917
- Y = np.repeat(y_range, Nx)
918
-
919
- XY = np.column_stack((X.flatten(), Y))
920
-
921
- if Nz % 2 == 0:
922
- XYZ = np.tile(np.concatenate([XY, np.flipud(XY)]), (Nz // 2, 1))
923
- Z = np.repeat(z_range, Nx * Ny)
924
- else:
925
- XYZ = np.concatenate([XY, np.tile(np.concatenate([np.flipud(XY), XY]), ((Nz - 1) // 2, 1))])
926
- Z = np.repeat(z_range, Nx * Ny)
927
-
928
- Positions = np.column_stack((XYZ, Z))
929
-
930
- # Initialize a matrix to store the reorganized data
931
- reorganized_data = np.zeros((Nx, Ny, Nz, data.shape[1]))
932
-
933
- # Reorganize the data according to the scan positions
934
- for index, (i, j, k) in enumerate(Positions):
935
- x_idx = np.where(x_range == i)[0][0]
936
- y_idx = np.where(y_range == j)[0][0]
937
- z_idx = np.where(z_range == k)[0][0]
938
- reorganized_data[x_idx, y_idx, z_idx, :] = data[index, :]
939
-
940
- self.field = np.transpose(reorganized_data, (3, 2, 1, 0))
941
- EnveloppeField = np.zeros_like(reorganized_data)
942
-
943
- for y in range(reorganized_data.shape[1]):
944
- for z in range(reorganized_data.shape[2]):
945
- EnveloppeField[:, y, z, :] = np.abs(hilbert(reorganized_data[:, y, z, :], axis=1))
946
- self.enveloppe = np.transpose(EnveloppeField, (3, 2, 1, 0))
947
- self.params['Xrange'] = [x_range[0], x_range[-1]]
948
- self.params['Yrange'] = [y_range[0], y_range[-1]]
949
- self.params['Zrange'] = [z_range[0], z_range[-1]]
950
- self.params['Nx'] = Nx
951
- self.params['Ny'] = Ny
952
- self.params['Nz'] = Nz
953
- except Exception as e:
954
- print(f"Error in _load_fieldHYDRO_XYZ method: {e}")
955
- raise
956
-
957
- ####### SUBCLASS #######
958
-
959
- class StructuredWave(AcousticField):
960
-
961
- class PatternParams:
962
- def __init__(self, space_0, space_1, move_head_0_2tail, move_tail_1_2head):
963
- """
964
- Initialize the PatternParams object with given parameters.
965
-
966
- Args:
967
- space_0 (int): Number of zeros in the pattern.
968
- space_1 (int): Number of ones in the pattern.
969
- move_head_0_2tail (int): Number of zeros to move from head to tail.
970
- move_tail_1_2head (int): Number of ones to move from tail to head.
971
- """
972
- self.space_0 = space_0
973
- self.space_1 = space_1
974
- self.move_head_0_2tail = move_head_0_2tail
975
- self.move_tail_1_2head = move_tail_1_2head
976
- self.activeList = None
977
- self.len_hex = None
978
-
979
- def __str__(self):
980
- """Return a string representation of the PatternParams object."""
981
- pass
982
-
983
- def generate_pattern(self):
984
- """
985
- Generate a binary pattern and return it as a hex string.
986
-
987
- Returns:
988
- str: Hexadecimal representation of the binary pattern.
989
- """
990
- try:
991
- total_bits = self.len_hex * 4
992
- unit = "0" * self.space_0 + "1" * self.space_1
993
- repeat_time = (total_bits + len(unit) - 1) // len(unit)
994
- pattern = (unit * repeat_time)[:total_bits]
995
-
996
- # Move 0s from head to tail
997
- if self.move_head_0_2tail > 0:
998
- head_zeros = '0' * self.move_head_0_2tail
999
- pattern = pattern[self.move_head_0_2tail:] + head_zeros
1000
-
1001
- # Move 1s from tail to head
1002
- if self.move_tail_1_2head > 0:
1003
- tail_ones = '1' * self.move_tail_1_2head
1004
- pattern = tail_ones + pattern[:-self.move_tail_1_2head]
1005
-
1006
- # Convert to hex
1007
- hex_output = hex(int(pattern, 2))[2:]
1008
- hex_output = hex_output.zfill(self.len_hex)
1009
-
1010
- return hex_output
1011
- except Exception as e:
1012
- print(f"Error generating pattern: {e}")
1013
- return None
1014
-
1015
- def generate_paths(self, base_path):
1016
- """Generate the list of system matrix .hdr file paths for this wave."""
1017
- #pattern_str = self.pattern_params.to_string()
1018
- pattern_str = self.generate_pattern()
1019
- paths = []
1020
- for angle in self.angles:
1021
- angle_str = self.format_angle(angle)
1022
- paths.append(f"{base_path}/field_{pattern_str}_{angle_str}.hdr")
1023
- return paths
1024
-
1025
- def to_string(self):
1026
- """
1027
- Format the pattern parameters into a string like '0_48_0_0'.
1028
-
1029
- Returns:
1030
- str: Formatted string of pattern parameters.
1031
- """
1032
- return f"{self.space_0}_{self.space_1}_{self.move_head_0_2tail}_{self.move_tail_1_2head}"
1033
-
1034
- def describe(self):
1035
- """
1036
- Return a readable description of the pattern parameters.
1037
-
1038
- Returns:
1039
- str: Description of the pattern parameters.
1040
- """
1041
- return f"Pattern structure: {self.to_string()}"
1042
-
1043
- def __init__(self, angle_deg, space_0, space_1, move_head_0_2tail, move_tail_1_2head, **kwargs):
1044
- """
1045
- Initialize the StructuredWave object.
1046
-
1047
- Args:
1048
- angle_deg (float): Angle in degrees.
1049
- space_0 (int): Number of zeros in the pattern.
1050
- space_1 (int): Number of ones in the pattern.
1051
- move_head_0_2tail (int): Number of zeros to move from head to tail.
1052
- move_tail_1_2head (int): Number of ones to move from tail to head.
1053
- **kwargs: Additional keyword arguments.
1054
- """
1055
- try:
1056
- super().__init__(**kwargs)
1057
- self.waveType = WaveType.StructuredWave
1058
- self.kgrid.setTime(int(self.kgrid.Nt*1.5),self.kgrid.dt) # Extend the time grid to allow for delays
1059
- self.pattern = self.PatternParams(space_0, space_1, move_head_0_2tail, move_tail_1_2head)
1060
- self.pattern.len_hex = self.params['num_elements'] // 4
1061
- self.pattern.activeList = self.pattern.generate_pattern()
1062
- self.angle = angle_deg
1063
- self.f_s = self._getDecimationFrequency()
1064
-
1065
- if self.angle < -20 or self.angle > 20:
1066
- raise ValueError("Angle must be between -20 and 20 degrees.")
1067
-
1068
- if len(self.pattern.activeList) != self.params["num_elements"] // 4:
1069
- raise ValueError(f"Active list string must be {self.params['num_elements'] // 4} characters long.")
1070
- self.delayedSignal = self._apply_delay()
1071
- except Exception as e:
1072
- print(f"Error initializing StructuredWave: {e}")
1073
-
1074
- def getName_field(self):
1075
- """
1076
- Generate the list of system matrix .hdr file paths for this wave.
1077
-
1078
- Returns:
1079
- str: File path for the system matrix .hdr file.
1080
- """
1081
- try:
1082
- pattern_str = self.pattern.activeList
1083
- angle_str = self._format_angle()
1084
- return f"field_{pattern_str}_{angle_str}"
1085
- except Exception as e:
1086
- print(f"Error generating file path: {e}")
1087
- return None
1088
-
1089
- def _getDecimationFrequency(self):
1090
- """
1091
- Calculate the decimation frequency based on the pattern parameters.
1092
-
1093
- Returns:
1094
- int: Decimation frequency.
1095
- """
1096
- try:
1097
- return 1/(self.pattern.space_0 + self.pattern.space_1)/self.params['element_width']
1098
- except Exception as e:
1099
- print(f"Error calculating decimation frequency: {e}")
1100
- return None
1101
-
1102
- @staticmethod
1103
- def getPattern(pathFile):
1104
- """
1105
- Get the pattern from a file path.
1106
-
1107
- Args:
1108
- pathFile (str): Path to the file containing the pattern.
1109
-
1110
- Returns:
1111
- str: The pattern string.
1112
- """
1113
- try:
1114
- # Pattern between first _ and last _
1115
- pattern = os.path.basename(pathFile).split('_')[1:-1]
1116
- pattern_str = ''.join(pattern)
1117
- return pattern_str
1118
- except Exception as e:
1119
- print(f"Error reading pattern from file: {e}")
1120
- return None
1121
-
1122
- @staticmethod
1123
- def getAngle(pathFile):
1124
- """
1125
- Get the angle from a file path.
1126
-
1127
- Args:
1128
- pathFile (str): Path to the file containing the angle.
1129
-
1130
- Returns:
1131
- int: The angle in degrees.
1132
- """
1133
- try:
1134
- # Angle between last _ and .
1135
- angle_str = os.path.basename(pathFile).split('_')[-1].replace('.', '')
1136
- if angle_str.startswith('0'):
1137
- angle_str = angle_str[1:]
1138
- elif angle_str.startswith('1'):
1139
- angle_str = '-' + angle_str[1:]
1140
- else:
1141
- raise ValueError("Invalid angle format in file name.")
1142
- return int(angle_str)
1143
- except Exception as e:
1144
- print(f"Error reading angle from file: {e}")
1145
- return None
1146
-
1147
- ## PRIVATE METHODS ##
1148
-
1149
- def _format_angle(self):
1150
- """
1151
- Format an angle into a 3-digit code like '120' for -20°, '020' for +20°.
1152
-
1153
- Args:
1154
- angle (float): Angle in degrees.
1155
-
1156
- Returns:
1157
- str: Formatted angle string.
1158
- """
1159
- return f"{'1' if self.angle < 0 else '0'}{abs(self.angle):02d}"
1160
-
1161
- def _apply_delay(self):
1162
- """
1163
- Apply a temporal delay to the signal for each transducer element.
1164
-
1165
- Returns:
1166
- ndarray: Array of delayed signals.
1167
- """
1168
- try:
1169
- is_positive = self.angle >= 0
1170
-
1171
- # Calculate the total number of grid points for all elements
1172
- total_grid_points = self.params['num_elements'] * int(round(self.params['element_width'] / self.params['dx']))
1173
-
1174
- # Initialize delays array with size total_grid_points
1175
- delays = np.zeros(total_grid_points)
1176
-
1177
- # Calculate the physical positions of the elements starting from Xrange[0]
1178
- element_positions = np.linspace(0, total_grid_points * self.params['dx'], total_grid_points)
1179
-
1180
- # Calculate delays based on physical positions
1181
- for i in range(total_grid_points):
1182
- delays[i] = (element_positions[i] * np.tan(np.deg2rad(abs(self.angle)))) / self.params['c0'] # Delay in seconds
1183
-
1184
-
1185
- delay_samples = np.round(delays / self.kgrid.dt).astype(int)
1186
- max_delay = np.max(np.abs(delay_samples))
1187
-
1188
- delayed_signals = np.zeros((total_grid_points, len(self.burst) + max_delay))
1189
- for i in range(total_grid_points):
1190
- shift = delay_samples[i]
1191
-
1192
- if is_positive:
1193
- delayed_signals[i, shift:shift + len(self.burst)] = self.burst # Right shift
1194
- else:
1195
- delayed_signals[i, max_delay - shift:max_delay - shift + len(self.burst)] = self.burst # Left shift
1196
-
1197
- return delayed_signals
1198
- except Exception as e:
1199
- print(f"Error applying delay: {e}")
1200
- return None
1201
-
1202
- def plot_delay(self):
1203
- """
1204
- Plot the time of the maximum of each delayed signal to visualize the wavefront.
1205
- """
1206
- try:
1207
- # Find the index of the maximum for each delayed signal
1208
- max_indices = np.argmax(self.delayedSignal, axis=1)
1209
- element_indices = np.linspace(0, self.params['num_elements'] - 1, self.delayedSignal.shape[0])
1210
- # Convert indices to time
1211
- max_times = max_indices / self.params['f_AQ']
1212
-
1213
- # Plot the times of the maxima
1214
- plt.figure(figsize=(10, 6))
1215
- plt.plot(element_indices, max_times, 'o-')
1216
- plt.title('Time of Maximum for Each Delayed Signal')
1217
- plt.xlabel('Transducer Element Index')
1218
- plt.ylabel('Time of Maximum (s)')
1219
- plt.grid(True)
1220
- plt.show()
1221
- except Exception as e:
1222
- print(f"Error plotting max times: {e}")
1223
-
1224
- def _save2D_HDR_IMG(self, pathFolder):
1225
- """
1226
- Save the acoustic field to .img and .hdr files.
1227
-
1228
- Args:
1229
- pathFolder (str): Path to the folder where files will be saved.
1230
- """
1231
- try:
1232
- t_ex = 1 / self.params['f_US']
1233
- angle_sign = '1' if self.angle < 0 else '0'
1234
- formatted_angle = f"{angle_sign}{abs(self.angle):02d}"
1235
-
1236
- # Define file names (img and hdr)
1237
- file_name = f"field_{self.pattern.activeList}_{formatted_angle}"
1238
-
1239
- img_path = os.path.join(pathFolder, file_name + ".img")
1240
- hdr_path = os.path.join(pathFolder, file_name + ".hdr")
1241
-
1242
- # Save the acoustic field to the .img file
1243
- with open(img_path, "wb") as f_img:
1244
- self.field.astype('float32').tofile(f_img) # Save in float32 format (equivalent to "single" in MATLAB)
1245
-
1246
- # Generate headerFieldGlob
1247
- headerFieldGlob = (
1248
- f"!INTERFILE :=\n"
1249
- f"modality : AOT\n"
1250
- f"voxels number transaxial: {self.field.shape[2]}\n"
1251
- f"voxels number transaxial 2: {self.field.shape[1]}\n"
1252
- f"voxels number axial: {1}\n"
1253
- f"field of view transaxial: {(self.params['Xrange'][1] - self.params['Xrange'][0]) * 1000}\n"
1254
- f"field of view transaxial 2: {(self.params['Zrange'][1] - self.params['Zrange'][0]) * 1000}\n"
1255
- f"field of view axial: {1}\n"
1256
- )
1257
-
1258
- # Generate header
1259
- header = (
1260
- f"!INTERFILE :=\n"
1261
- f"!imaging modality := AOT\n\n"
1262
- f"!GENERAL DATA :=\n"
1263
- f"!data offset in bytes := 0\n"
1264
- f"!name of data file := system_matrix/{file_name}.img\n\n"
1265
- f"!GENERAL IMAGE DATA\n"
1266
- f"!total number of images := {self.field.shape[0]}\n"
1267
- f"imagedata byte order := LITTLEENDIAN\n"
1268
- f"!number of frame groups := 1\n\n"
1269
- f"!STATIC STUDY (General) :=\n"
1270
- f"number of dimensions := 3\n"
1271
- f"!matrix size [1] := {self.field.shape[2]}\n"
1272
- f"!matrix size [2] := {self.field.shape[1]}\n"
1273
- f"!matrix size [3] := {self.field.shape[0]}\n"
1274
- f"!number format := short float\n"
1275
- f"!number of bytes per pixel := 4\n"
1276
- f"scaling factor (mm/pixel) [1] := {self.params['dx'] * 1000}\n"
1277
- f"scaling factor (mm/pixel) [2] := {self.params['dx'] * 1000}\n"
1278
- f"scaling factor (s/pixel) [3] := {1 / self.params['f_AQ']}\n"
1279
- f"first pixel offset (mm) [1] := {self.params['Xrange'][0] * 1e3}\n"
1280
- f"first pixel offset (mm) [2] := {self.params['Zrange'][0] * 1e3}\n"
1281
- f"first pixel offset (s) [3] := 0\n"
1282
- f"data rescale offset := 0\n"
1283
- f"data rescale slope := 1\n"
1284
- f"quantification units := 1\n\n"
1285
- f"!SPECIFIC PARAMETERS :=\n"
1286
- f"angle (degree) := {self.angle}\n"
1287
- f"activation list := {''.join(f'{int(self.pattern.activeList[i:i+2], 16):08b}' for i in range(0, len(self.pattern.activeList), 2))}\n"
1288
- f"number of US transducers := {self.params['num_elements']}\n"
1289
- f"delay (s) := 0\n"
1290
- f"us frequency (Hz) := {self.params['f_US']}\n"
1291
- f"excitation duration (s) := {t_ex}\n"
1292
- f"!END OF INTERFILE :=\n"
1293
- )
1294
- # Save the .hdr file
1295
- with open(hdr_path, "w") as f_hdr:
1296
- f_hdr.write(header)
1297
-
1298
- with open(os.path.join(pathFolder, "field.hdr"), "w") as f_hdr2:
1299
- f_hdr2.write(headerFieldGlob)
1300
- except Exception as e:
1301
- print(f"Error saving HDR/IMG files: {e}")
1302
-
1303
- def _generate_2Dacoustic_field_KWAVE(self, isGPU=True if config.get_process() == 'gpu' else False):
1304
- """
1305
- Generate a 2D acoustic field using k-Wave.
1306
-
1307
- Args:
1308
- isGpu (bool): Flag indicating whether to use GPU for simulation.
1309
-
1310
- Returns:
1311
- ndarray: Simulated acoustic field data.
1312
- """
1313
- try:
1314
- active_list = np.array([int(char) for char in ''.join(f"{int(self.pattern.activeList[i:i+2], 16):08b}" for i in range(0, len(self.pattern.activeList), 2))])
1315
-
1316
- # Probe mask: aligned in the XZ plane
1317
- source = kSource()
1318
- source.p_mask = np.zeros((self.params['Nx'], self.params['Nz'])) # Create an empty grid for the source mask
1319
-
1320
- # Calculate the number of grid points per element
1321
- element_width_meters = self.params['element_width'] # Element width in meters
1322
- dx = self.params['dx'] # Spatial resolution in meters
1323
- element_width_grid_points = int(round(element_width_meters / dx)) # Element width in grid points
1324
-
1325
- # Calculate the spacing between elements
1326
- total_elements_width = self.params['num_elements'] * element_width_grid_points
1327
- remaining_space = self.params['Nx'] - total_elements_width
1328
- spacing = remaining_space // (self.params['num_elements'] + 1) # Spacing between elements
1329
-
1330
-
1331
- center_index = np.argmin(np.abs(np.linspace(self.params['Xrange'][0], self.params['Xrange'][1], self.params['Nx'])))
1332
-
1333
- activeListGrid = np.zeros(total_elements_width, dtype=int)
1334
-
1335
- # Place active transducers in the mask and count active elements
1336
- active_indices = []
1337
- current_position = center_index - (total_elements_width + (self.params['num_elements'] - 1) * spacing) // 2
1338
- for i in range(self.params['num_elements']):
1339
- if active_list[i] == 1: # Check if the element is active
1340
- x_pos = current_position
1341
- source.p_mask[x_pos:x_pos + element_width_grid_points, 0] = 1 # Position in the XZ plane
1342
- active_indices.append(i) # Record the index of the active element
1343
- start_idx = i * element_width_grid_points
1344
- end_idx = start_idx + element_width_grid_points
1345
- activeListGrid[start_idx:end_idx] = 1
1346
- current_position += element_width_grid_points + spacing # Move to the next element position
1347
- source.p_mask = source.p_mask.astype(int)
1348
-
1349
- # Ensure source.p matches the number of active elements
1350
- source.p = self.delayedSignal[activeListGrid == 1, :]
1351
-
1352
- # Define sensors to observe acoustic fields
1353
- sensor = kSensor()
1354
- sensor.mask = np.ones((self.params['Nx'], self.params['Nz'])) # Sensor covering the entire domain
1355
-
1356
- # Simulation options
1357
- simulation_options = SimulationOptions(
1358
- pml_inside=False, # Prevent PML from being added inside the grid
1359
- pml_x_size=20, # PML size on the X-axis
1360
- pml_z_size=20, # PML size on the Z-axis
1361
- use_sg=False,
1362
- save_to_disk=True,
1363
- input_filename=os.path.join(gettempdir(), "KwaveIN.h5"),
1364
- output_filename=os.path.join(gettempdir(), "KwaveOUT.h5")
1365
- )
1366
-
1367
- execution_options = SimulationExecutionOptions(
1368
- is_gpu_simulation=config.get_process() == 'gpu' and isGPU,
1369
- device_num=config.bestGPU
1370
- )
1371
- # Run the simulation
1372
- print("Starting simulation...")
1373
- sensor_data = kspaceFirstOrder2D(
1374
- # kgrid=self.kgrid,
1375
- kgrid=self.kgrid,
1376
- medium=self.medium,
1377
- source=source,
1378
- sensor=sensor,
1379
- simulation_options=simulation_options,
1380
- execution_options=execution_options,
1381
- )
1382
- print("Simulation completed successfully.")
1383
-
1384
- return sensor_data['p'].reshape(self.kgrid.Nt, self.params['Nz'], self.params['Nx'])
1385
- except Exception as e:
1386
- print(f"Error generating 2D acoustic field: {e}")
1387
- return None
1388
-
1389
- def _generate_3Dacoustic_field_KWAVE(self):
1390
- """
1391
- Generate a 3D acoustic field using k-Wave.
1392
-
1393
- Returns:
1394
- ndarray: Simulated acoustic field data.
1395
- """
1396
- try:
1397
- active_list = np.array([int(char) for char in ''.join(f"{int(self.pattern.activeList[i:i+2], 16):08b}" for i in range(0, len(self.pattern.activeList), 2))])
1398
-
1399
- # Initialize grid and medium
1400
- kgrid = kWaveGrid([self.params['Nx'], self.params['Ny'], self.params['Nz']], [self.params['dx'], self.params['dy'], self.params['dz']])
1401
- kgrid.setTime(Nt=self.params['Nt'], dt=1 / self.params['f_AQ'])
1402
-
1403
- # Probe mask: aligned in the XZ plane
1404
- source = kSource()
1405
- source.p_mask = np.zeros((self.params['Nx'], self.params['Ny'], self.params['Nz'])) # Create an empty grid for the source mask
1406
-
1407
- # Place active transducers in the mask
1408
- for i in range(self.params['num_elements']):
1409
- if active_list[i] == 1: # Check if the element is active
1410
- x_pos = i + self.params['Nx'] // 2 - self.params['num_elements'] // 2 # Position of elements on the X-axis
1411
- source.p_mask[x_pos, self.params['Ny'] // 2, 0] = 1 # Position in the XZ plane
1412
-
1413
- source.p_mask = source.p_mask.astype(int)
1414
- source.p = self.delayedSignal[active_list == 1, :]
1415
-
1416
- # Define sensors to observe acoustic fields
1417
- sensor = kSensor()
1418
- sensor.mask = np.ones((self.params['Nx'], self.params['Ny'], self.params['Nz'])) # Sensor covering the entire domain
1419
-
1420
- # Simulation options
1421
- simulation_options = SimulationOptions(
1422
- pml_inside=False, # Prevent PML from being added inside the grid
1423
- pml_auto=True,
1424
- use_sg=False,
1425
- save_to_disk=True,
1426
- input_filename=os.path.join(gettempdir(), "KwaveIN.h5"),
1427
- output_filename=os.path.join(gettempdir(), "KwaveOUT.h5")
1428
- )
1429
-
1430
- execution_options = SimulationExecutionOptions(
1431
- is_gpu_simulation=config.get_process() == 'gpu',
1432
- device_num=config.bestGPU() if config.get_process() == 'gpu' else None
1433
- )
1434
-
1435
- # Run the simulation
1436
- print("Starting simulation...")
1437
- sensor_data = kspaceFirstOrder3D(
1438
- kgrid=kgrid,
1439
- medium=self.medium,
1440
- source=source,
1441
- sensor=sensor,
1442
- simulation_options=simulation_options,
1443
- execution_options=execution_options,
1444
- )
1445
- print("Simulation completed successfully.")
1446
-
1447
- return sensor_data['p'].reshape(kgrid.Nt, (self.params['Nz'], self.params['Ny'], self.params['Nx']))
1448
- except Exception as e:
1449
- print(f"Error generating 3D acoustic field: {e}")
1450
- return None
1451
-
1452
- class PlaneWave(StructuredWave):
1453
- def __init__(self, angle, space_0 = 0, space_1 = 192, move_head_0_2tail = 0, move_tail_1_2head = 0, **kwargs):
1454
- """
1455
- Initialize the PlaneWave object.
1456
-
1457
- Args:
1458
- angle_deg (float): Angle in degrees.
1459
- **kwargs: Additional keyword arguments.
1460
- """
1461
- try:
1462
- super().__init__(angle, space_0, space_1, move_head_0_2tail, move_tail_1_2head, **kwargs)
1463
- self.waveType = WaveType.PlaneWave
1464
- except Exception as e:
1465
- print(f"Error initializing PlaneWave: {e}")
1466
- raise
1467
-
1468
- def _check_angle(self):
1469
- """
1470
- Check if the angle is within the valid range.
1471
-
1472
- Raises:
1473
- ValueError: If the angle is not between -20 and 20 degrees.
1474
- """
1475
- if self.angle < -20 or self.angle > 20:
1476
- raise ValueError("Angle must be between -20 and 20 degrees.")
1477
-
1478
- def getName_field(self):
1479
- """
1480
- Generate the list of system matrix .hdr file paths for this wave.
1481
-
1482
- Returns:
1483
- str: File path for the system matrix .hdr file.
1484
- """
1485
- try:
1486
- angle_str = self._format_angle()
1487
- return f"field_{self.pattern.activeList}_{angle_str}"
1488
- except Exception as e:
1489
- print(f"Error generating file path: {e}")
1490
- return None
1491
-
1492
- class FocusedWave(AcousticField):
1493
-
1494
- def __init__(self, focal_point, **kwargs):
1495
- """
1496
- Initialize the FocusedWave object.
1497
-
1498
- Parameters:
1499
- - focal_point (tuple): The focal point coordinates (x, z) in meters.
1500
- - **kwargs: Additional keyword arguments for AcousticField initialization.
1501
- """
1502
- super().__init__(**kwargs)
1503
- self.waveType = WaveType.FocusedWave
1504
- self.kgrid.setTime(int(self.kgrid.Nt*2),self.kgrid.dt) # Extend the time grid to allow for delays
1505
- self.focal_point = (focal_point[0] / 1000, focal_point[1] / 1000)
1506
- self.delayedSignal = self._apply_delay()
1507
-
1508
- def getName_field(self):
1509
- """
1510
- Generate the name for the field file based on the focal point.
1511
-
1512
- Returns:
1513
- str: File name for the system matrix file.
1514
- """
1515
- try:
1516
- x_focal, z_focal = self.focal_point
1517
- return f"field_focused_X{x_focal*1000:.2f}_Z{z_focal*1000:.2f}"
1518
- except Exception as e:
1519
- print(f"Error generating file name: {e}")
1520
- return None
1521
-
1522
- def _apply_delay(self):
1523
- """
1524
- Apply a temporal delay to the signal for each transducer element to focus the wave at the desired focal point.
1525
-
1526
- Returns:
1527
- ndarray: Array of delayed signals.
1528
- """
1529
- try:
1530
- x_focal, z_focal = self.focal_point
1531
-
1532
- # Calculate the total number of grid points for all elements
1533
- total_grid_points = self.params['num_elements'] * int(round(self.params['element_width'] / self.params['dx']))
1534
-
1535
- # Initialize delays array with size total_grid_points
1536
- delays = np.zeros(total_grid_points)
1537
-
1538
- # Calculate the physical positions of the elements starting from Xrange[0]
1539
- element_positions = np.linspace(self.params['Xrange'][0], self.params['Xrange'][1], total_grid_points)
1540
-
1541
- # Calculate delays based on physical positions
1542
- for i in range(total_grid_points):
1543
- distance = np.sqrt((x_focal - element_positions[i])**2 + (z_focal)**2)
1544
- delays[i] = distance / self.params['c0'] # Delay in seconds
1545
-
1546
- delay_samples = np.round(delays / self.kgrid.dt).astype(int)
1547
- max_delay = np.max(np.abs(delay_samples))
1548
- delayed_signals = np.zeros((total_grid_points, len(self.burst) + max_delay))
1549
- for i in range(total_grid_points):
1550
- shift = delay_samples[i]
1551
- delayed_signals[i, shift:shift + len(self.burst)] = self.burst # Apply delay
1552
-
1553
- return delayed_signals
1554
- except Exception as e:
1555
- print(f"Error applying delay: {e}")
1556
- return None
1557
-
1558
- def plot_delay(self):
1559
- """
1560
- Plot the time of the maximum of each delayed signal to visualize the wavefront.
1561
- """
1562
- try:
1563
- # Find the index of the maximum for each delayed signal
1564
- max_indices = np.argmax(self.delayedSignal, axis=1)
1565
- element_indices = np.linspace(0, self.params['num_elements'] - 1, self.delayedSignal.shape[0])
1566
- # Convert indices to time
1567
- max_times = max_indices / self.params['f_AQ']
1568
-
1569
- # Plot the times of the maxima
1570
- plt.figure(figsize=(10, 6))
1571
- plt.plot(element_indices, max_times, 'o-')
1572
- plt.title('Time of Maximum for Each Delayed Signal')
1573
- plt.xlabel('Transducer Element Index')
1574
- plt.ylabel('Time of Maximum (s)')
1575
- plt.grid(True)
1576
- plt.show()
1577
- except Exception as e:
1578
- print(f"Error plotting max times: {e}")
1579
-
1580
- def _generate_2Dacoustic_field_KWAVE(self, isGpu=True if config.get_process() == 'gpu' else False):
1581
- """
1582
- Generate a 2D acoustic field using k-Wave simulation for a focused wave.
1583
-
1584
- Parameters:
1585
- - isGpu (bool): Flag indicating whether to use GPU for simulation.
1586
-
1587
- Returns:
1588
- ndarray: Simulated acoustic field data.
1589
- """
1590
- try:
1591
- # Create a source mask for the transducer
1592
- source = kSource()
1593
- source.p_mask = np.zeros((self.params['Nx'], self.params['Nz']))
1594
- source.p = np.zeros((self.params['num_elements'], self.delayedSignal.shape[1])) # Initialize source pressure
1595
- # Calculate the center of the transducer
1596
- center_index = self.params['Nx'] // 2
1597
-
1598
- coeff = self.delayedSignal.shape[0] // self.params['num_elements']
1599
-
1600
- if not coeff.is_integer():
1601
- raise ValueError("The number of elements must be a divisor of the delayed signal length.")
1602
-
1603
- # Set the active elements in the source mask
1604
- element_width_grid_points = int(round(self.params['element_width'] / self.params['dx']))
1605
- for i in range(self.params['num_elements']):
1606
- source.p[i] = self.delayedSignal[i*coeff]
1607
- x_pos = center_index - (self.params['num_elements'] // 2) * element_width_grid_points + i * element_width_grid_points
1608
- source.p_mask[x_pos, 0] = 1
1609
-
1610
-
1611
- # Define sensors to observe acoustic fields
1612
- sensor = kSensor()
1613
- sensor.mask = np.ones((self.params['Nx'], self.params['Nz']))
1614
-
1615
- # Simulation options
1616
- simulation_options = SimulationOptions(
1617
- pml_inside=False,
1618
- pml_x_size=20,
1619
- pml_z_size=20,
1620
- use_sg=False,
1621
- save_to_disk=True,
1622
- input_filename=os.path.join(gettempdir(), "KwaveIN.h5"),
1623
- output_filename=os.path.join(gettempdir(), "KwaveOUT.h5")
1624
- )
1625
-
1626
- execution_options = SimulationExecutionOptions(
1627
- is_gpu_simulation=config.get_process() == 'gpu' and isGpu,
1628
- device_num=config.bestGPU
1629
- )
1630
-
1631
- # Run the simulation
1632
- print("Starting simulation...")
1633
- sensor_data = kspaceFirstOrder2D(
1634
- kgrid=self.kgrid,
1635
- medium=self.medium,
1636
- source=source,
1637
- sensor=sensor,
1638
- simulation_options=simulation_options,
1639
- execution_options=execution_options,
1640
- )
1641
- print("Simulation completed successfully.")
1642
-
1643
- return sensor_data['p'].reshape(self.kgrid.Nt, self.params['Nz'], self.params['Nx'])
1644
- except Exception as e:
1645
- print(f"Error generating 2D acoustic field: {e}")
1646
- return None
1647
-
1648
- def _generate_3Dacoustic_field_KWAVE(self, isGpu=True if config.get_process() == 'gpu' else False):
1649
- """
1650
- Generate a 3D acoustic field using k-Wave simulation for a focused wave.
1651
-
1652
- Parameters:
1653
- - isGpu (bool): Flag indicating whether to use GPU for simulation.
1654
-
1655
- Returns:
1656
- ndarray: Simulated acoustic field data.
1657
- """
1658
- try:
1659
- # Create a source mask for the transducer
1660
- source = kSource()
1661
- source.p_mask = np.zeros((self.params['Nx'], self.params['Ny'], self.params['Nz']))
1662
-
1663
- # Calculate the center of the transducer
1664
- center_index_x = self.params['Nx'] // 2
1665
- center_index_y = self.params['Ny'] // 2
1666
-
1667
- # Set the active elements in the source mask
1668
- element_width_grid_points = int(round(self.params['element_width'] / self.params['dx']))
1669
- for i in range(self.params['num_elements']):
1670
- x_pos = center_index_x - (self.params['num_elements'] // 2) * element_width_grid_points + i * element_width_grid_points
1671
- source.p_mask[x_pos, center_index_y, 0] = 1
1672
-
1673
- # Apply delays to the burst signal using the _apply_delay method
1674
- delayed_signals = self._apply_delay()
1675
-
1676
- source.p = delayed_signals.T
1677
-
1678
- # Define sensors to observe acoustic fields
1679
- sensor = kSensor()
1680
- sensor.mask = np.ones((self.params['Nx'], self.params['Ny'], self.params['Nz']))
1681
-
1682
- # Simulation options
1683
- simulation_options = SimulationOptions(
1684
- pml_inside=False,
1685
- pml_auto=True,
1686
- use_sg=False,
1687
- save_to_disk=True,
1688
- input_filename=os.path.join(gettempdir(), "KwaveIN.h5"),
1689
- output_filename=os.path.join(gettempdir(), "KwaveOUT.h5")
1690
- )
1691
-
1692
- execution_options = SimulationExecutionOptions(
1693
- is_gpu_simulation=config.get_process() == 'gpu' and isGpu,
1694
- device_num=config.bestGPU
1695
- )
1696
-
1697
- # Run the simulation
1698
- print("Starting simulation...")
1699
- sensor_data = kspaceFirstOrder3D(
1700
- kgrid=self.kgrid,
1701
- medium=self.medium,
1702
- source=source,
1703
- sensor=sensor,
1704
- simulation_options=simulation_options,
1705
- execution_options=execution_options,
1706
- )
1707
- print("Simulation completed successfully.")
1708
-
1709
- return sensor_data['p'].reshape(self.kgrid.Nt, self.params['Nz'], self.params['Ny'], self.params['Nx'])
1710
- except Exception as e:
1711
- print(f"Error generating 3D acoustic field: {e}")
1712
- return None
1713
-
1714
- def _save2D_HDR_IMG(self, filePath):
1715
- """
1716
- Save the acoustic field to .img and .hdr files.
1717
-
1718
- Parameters:
1719
- - filePath (str): Path to the folder where files will be saved.
1720
- """
1721
- try:
1722
- t_ex = 1 / self.params['f_US']
1723
- x_focal, z_focal = self.focal_point
1724
-
1725
- # Define file names (img and hdr)
1726
- file_name = f"field_focused_{x_focal:.2f}_{z_focal:.2f}"
1727
-
1728
- img_path = os.path.join(filePath, file_name + ".img")
1729
- hdr_path = os.path.join(filePath, file_name + ".hdr")
1730
-
1731
- # Save the acoustic field to the .img file
1732
- with open(img_path, "wb") as f_img:
1733
- self.field.astype('float32').tofile(f_img)
1734
-
1735
- # Generate headerFieldGlob
1736
- headerFieldGlob = (
1737
- f"!INTERFILE :=\n"
1738
- f"modality : AOT\n"
1739
- f"voxels number transaxial: {self.field.shape[2]}\n"
1740
- f"voxels number transaxial 2: {self.field.shape[1]}\n"
1741
- f"voxels number axial: {1}\n"
1742
- f"field of view transaxial: {(self.params['Xrange'][1] - self.params['Xrange'][0]) * 1000}\n"
1743
- f"field of view transaxial 2: {(self.params['Zrange'][1] - self.params['Zrange'][0]) * 1000}\n"
1744
- f"field of view axial: {1}\n"
1745
- )
1746
-
1747
- # Generate header
1748
- header = (
1749
- f"!INTERFILE :=\n"
1750
- f"!imaging modality := AOT\n\n"
1751
- f"!GENERAL DATA :=\n"
1752
- f"!data offset in bytes := 0\n"
1753
- f"!name of data file := system_matrix/{file_name}.img\n\n"
1754
- f"!GENERAL IMAGE DATA\n"
1755
- f"!total number of images := {self.field.shape[0]}\n"
1756
- f"imagedata byte order := LITTLEENDIAN\n"
1757
- f"!number of frame groups := 1\n\n"
1758
- f"!STATIC STUDY (General) :=\n"
1759
- f"number of dimensions := 3\n"
1760
- f"!matrix size [1] := {self.field.shape[2]}\n"
1761
- f"!matrix size [2] := {self.field.shape[1]}\n"
1762
- f"!matrix size [3] := {self.field.shape[0]}\n"
1763
- f"!number format := short float\n"
1764
- f"!number of bytes per pixel := 4\n"
1765
- f"scaling factor (mm/pixel) [1] := {self.params['dx'] * 1000}\n"
1766
- f"scaling factor (mm/pixel) [2] := {self.params['dx'] * 1000}\n"
1767
- f"scaling factor (s/pixel) [3] := {1 / self.params['f_AQ']}\n"
1768
- f"first pixel offset (mm) [1] := {self.params['Xrange'][0] * 1e3}\n"
1769
- f"first pixel offset (mm) [2] := {self.params['Zrange'][0] * 1e3}\n"
1770
- f"first pixel offset (s) [3] := 0\n"
1771
- f"data rescale offset := 0\n"
1772
- f"data rescale slope := 1\n"
1773
- f"quantification units := 1\n\n"
1774
- f"!SPECIFIC PARAMETERS :=\n"
1775
- f"focal point (x, z) := {x_focal}, {z_focal}\n"
1776
- f"number of US transducers := {self.params['num_elements']}\n"
1777
- f"delay (s) := 0\n"
1778
- f"us frequency (Hz) := {self.params['f_US']}\n"
1779
- f"excitation duration (s) := {t_ex}\n"
1780
- f"!END OF INTERFILE :=\n"
1781
- )
1782
-
1783
- # Save the .hdr file
1784
- with open(hdr_path, "w") as f_hdr:
1785
- f_hdr.write(header)
1786
-
1787
- with open(os.path.join(filePath, "field.hdr"), "w") as f_hdr2:
1788
- f_hdr2.write(headerFieldGlob)
1789
- except Exception as e:
1790
- print(f"Error saving HDR/IMG files: {e}")
1791
-
1792
- class HydroWave(AcousticField):
1793
-
1794
- def __init__(self, waveType, dim=Dim.D3,**kwargs):
1795
- super().__init__(**kwargs)
1796
- if type(dim) != Dim:
1797
- raise TypeError("dim must be an instance of the Dim Enum")
1798
- if type(waveType) != WaveType:
1799
- raise TypeError("waveType must be an instance of the WaveType Enum")
1800
- self.waveType = waveType
1801
- self.params = {
1802
- 'typeSim': TypeSim.HYDRO.value,
1803
- 'dim': dim.value,
1804
- }
1805
-
1806
-
1807
- def getName_field(self):
1808
- raise NotImplementedError("getName_field method not implemented for HydroWave.")
1809
- pass
1810
-
1811
- def _generate_2Dacoustic_field_KWAVE(self):
1812
- raise NotImplementedError("2D acoustic field generation not implemented for HydroWave.")
1813
-
1814
- def _generate_3Dacoustic_field_KWAVE(self):
1815
- raise NotImplementedError("3D acoustic field generation not implemented for HydroWave.")
1816
-
1817
- def _save2D_HDR_IMG(sel):
1818
- raise NotImplementedError("HDR/IMG saving not implemented for HydroWave.")
1819
-
1820
- class IrregularWave(AcousticField):
1821
- """
1822
- Class for irregular wave types, inheriting from AcousticField.
1823
- This class is a placeholder for future implementation of irregular wave types.
1824
- """
1825
-
1826
- def __init__(self, **kwargs):
1827
- super().__init__(**kwargs)
1828
- self.waveType = WaveType.IrregularWave
1829
- self.params = {
1830
- 'typeSim': TypeSim.IRREGULAR.value,
1831
- }
1832
-
1833
- def getName_field(self):
1834
- raise NotImplementedError("getName_field method not implemented for IrregularWave.")
1835
-
1836
- def _generate_diverse_structurations(self,num_elements, num_sequences, num_frequencies):
1837
- """
1838
- Génère num_sequences structurations irrégulières ON/OFF pour une sonde de num_elements éléments.
1839
- Chaque structuration contient exactement num_frequencies fréquences spatiales distinctes.
1840
-
1841
- :param num_elements: Nombre total d'éléments piézoélectriques de la sonde.
1842
- :param num_sequences: Nombre total de structurations générées.
1843
- :param num_frequencies: Nombre de fréquences spatiales distinctes par structuration.
1844
- :return: Matrice de structuration de taille (num_sequences, num_elements)
1845
- """
1846
-
1847
- # Définition des fréquences spatiales disponibles
1848
- max_freq = num_elements // 2 # Nyquist limit
1849
- available_frequencies = np.arange(1, max_freq + 1) # Fréquences possibles
1850
-
1851
- # Matrice des structurations
1852
- structurations = np.zeros((num_sequences, num_elements), dtype=int)
1853
-
1854
- # Sélectionner des fréquences uniques pour chaque structuration
1855
- chosen_frequencies = []
1856
- for _ in range(num_sequences):
1857
- freqs = np.random.choice(available_frequencies, size=num_frequencies, replace=False)
1858
- chosen_frequencies.append(freqs)
1859
-
1860
- # Construire la structuration correspondante
1861
- structuration = np.zeros(num_elements)
1862
- for f in freqs:
1863
- structuration += np.cos(2 * np.pi * f * np.arange(num_elements) / num_elements) # Ajouter la fréquence
1864
-
1865
- structuration = np.where(structuration >= 0, 1, 0) # Binarisation ON/OFF
1866
- structurations[_] = structuration
1867
-
1868
- return structurations, chosen_frequencies
1869
-
1870
- def getName_field(self):
1871
- raise NotImplementedError("getName_field method not implemented for IrregularWave.")
1872
-
1873
- def _generate_2Dacoustic_field_KWAVE(self, isGpu):
1874
- raise NotImplementedError("2D acoustic field generation not implemented for IrregularWave.")
1875
-
1876
- def _generate_3Dacoustic_field_KWAVE(self, isGpu):
1877
- raise NotImplementedError("3D acoustic field generation not implemented for IrregularWave.")
1878
-
1879
- def _save2D_HDR_IMG(self, filePath):
1880
- raise NotImplementedError("HDR/IMG saving not implemented for IrregularWave.")
1881
-