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KWave adapter rotation bug fix #270

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merged 4 commits into from
Jun 7, 2024
Merged

KWave adapter rotation bug fix #270

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7c67b46
Fixes #264
TomTomRixRix Mar 15, 2024
10eed83
Fixes #271, added field of view definition and spacing
TomTomRixRix Mar 26, 2024
c5505ca
Changed all rot90(,-1) occurrences to .T
TomTomRixRix Mar 26, 2024
12c49d5
Merge branch 'develop' into T264_KWaveRotationBug
jgroehl Jun 7, 2024
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16 changes: 4 additions & 12 deletions ...core/simulation_modules/acoustic_forward_module/acoustic_forward_module_k_wave_adapter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -110,14 +110,10 @@ def forward_model(self, detection_geometry: DetectionGeometryBase) -> np.ndarray
axes = (0, 2)
image_slice = np.s_[:]

data_dict[Tags.DATA_FIELD_SPEED_OF_SOUND] = np.rot90(data_dict[Tags.DATA_FIELD_SPEED_OF_SOUND][image_slice],
3, axes=axes)
data_dict[Tags.DATA_FIELD_DENSITY] = np.rot90(data_dict[Tags.DATA_FIELD_DENSITY][image_slice],
3, axes=axes)
data_dict[Tags.DATA_FIELD_ALPHA_COEFF] = np.rot90(data_dict[Tags.DATA_FIELD_ALPHA_COEFF][image_slice],
3, axes=axes)
data_dict[Tags.DATA_FIELD_INITIAL_PRESSURE] = np.rot90(data_dict[Tags.DATA_FIELD_INITIAL_PRESSURE]
[image_slice], 3, axes=axes)
data_dict[Tags.DATA_FIELD_SPEED_OF_SOUND] = data_dict[Tags.DATA_FIELD_SPEED_OF_SOUND][image_slice].T
data_dict[Tags.DATA_FIELD_DENSITY] = data_dict[Tags.DATA_FIELD_DENSITY][image_slice].T
data_dict[Tags.DATA_FIELD_ALPHA_COEFF] = data_dict[Tags.DATA_FIELD_ALPHA_COEFF][image_slice].T
data_dict[Tags.DATA_FIELD_INITIAL_PRESSURE] = data_dict[Tags.DATA_FIELD_INITIAL_PRESSURE][image_slice].T

time_series_data, global_settings = self.k_wave_acoustic_forward_model(
detection_geometry,
Expand Down Expand Up @@ -249,10 +245,6 @@ def k_wave_acoustic_forward_model(self, detection_geometry: DetectionGeometryBas
subprocess.run(cmd)

raw_time_series_data = sio.loadmat(optical_path)[Tags.DATA_FIELD_TIME_SERIES_DATA]

# reverse the order of detector elements from matlab to python order
raw_time_series_data = raw_time_series_data[::-1, :]

time_grid = sio.loadmat(optical_path + "dt.mat")
num_time_steps = int(np.round(time_grid["number_time_steps"]))

Expand Down
2 changes: 1 addition & 1 deletion ...e/simulation_modules/reconstruction_module/reconstruction_module_time_reversal_adapter.py
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Expand Up @@ -178,7 +178,7 @@ def reconstruction_algorithm(self, time_series_sensor_data, detection_geometry):

reconstructed_data = sio.loadmat(acoustic_path + "tr.mat")[Tags.DATA_FIELD_RECONSTRUCTED_DATA]

reconstructed_data = np.flipud(np.rot90(reconstructed_data, 1, axes))
reconstructed_data = reconstructed_data.T

field_of_view_mm = detection_geometry.get_field_of_view_mm()
field_of_view_voxels = (field_of_view_mm / spacing_in_mm).astype(np.int32)
Expand Down
8 changes: 4 additions & 4 deletions simpa/visualisation/matplotlib_data_visualisation.py
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Expand Up @@ -221,10 +221,10 @@ def visualise_data(wavelength: int = None,
plt.title(data_item_names[i])
if len(np.shape(data_to_show[i])) > 2:
pos = int(np.shape(data_to_show[i])[1] / 2) - 1
data = np.rot90(data_to_show[i][:, pos, :], -1)
data = data_to_show[i][:, pos, :].T
plt.imshow(np.log10(data) if logscales[i] else data, cmap=cmaps[i])
else:
data = np.rot90(data_to_show[i][:, :], -1)
data = data_to_show[i][:, :].T
plt.imshow(np.log10(data) if logscales[i] else data, cmap=cmaps[i])
plt.colorbar()

Expand All @@ -233,10 +233,10 @@ def visualise_data(wavelength: int = None,
plt.title(data_item_names[i])
if len(np.shape(data_to_show[i])) > 2:
pos = int(np.shape(data_to_show[i])[0] / 2)
data = np.rot90(data_to_show[i][pos, :, :], -1)
data = data_to_show[i][pos, :, :].T
plt.imshow(np.log10(data) if logscales[i] else data, cmap=cmaps[i])
else:
data = np.rot90(data_to_show[i][:, :], -1)
data = data_to_show[i][:, :].T
plt.imshow(np.log10(data) if logscales[i] else data, cmap=cmaps[i])
plt.colorbar()

Expand Down
4 changes: 2 additions & 2 deletions simpa_examples/perform_iterative_qPAI_reconstruction.py
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Original file line number Diff line number Diff line change
Expand Up @@ -208,7 +208,7 @@ def __init__(self):
if i == 0:
plt.ylabel("x-z", fontsize=10)
plt.title(label[i], fontsize=10)
plt.imshow(np.rot90(quantity, -1))
plt.imshow(quantity.T)
plt.xticks(fontsize=6)
plt.yticks(fontsize=6)
plt.colorbar()
Expand All @@ -222,7 +222,7 @@ def __init__(self):
if i == 0:
plt.ylabel("y-z", fontsize=10)
plt.title(label[i], fontsize=10)
plt.imshow(np.rot90(quantity, -1))
plt.imshow(quantity.T)
plt.xticks(fontsize=6)
plt.yticks(fontsize=6)
plt.colorbar()
Expand Down
6 changes: 3 additions & 3 deletions simpa_tests/manual_tests/__init__.py
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Expand Up @@ -228,15 +228,15 @@ def visualise_result(self, show_figure_on_screen=True, save_path=None):
plt.figure(figsize=(9, 3))
plt.subplot(1, 3, 1)
plt.title("Initial pressure")
plt.imshow(np.rot90(initial_pressure[:, 20, :], 3))
plt.imshow(initial_pressure[:, 20, :].T)
plt.subplot(1, 3, 2)
plt.title("Pipeline\nReconstruction")
if self.reconstructed_image_pipeline is not None:
plt.imshow(np.rot90(self.reconstructed_image_pipeline, 3))
plt.imshow(self.reconstructed_image_pipeline.T)
plt.subplot(1, 3, 3)
plt.title("Convenience Method\nReconstruction")
if self.reconstructed_image_convenience is not None:
plt.imshow(np.rot90(self.reconstructed_image_convenience, 3))
plt.imshow(self.reconstructed_image_convenience.T)

plt.tight_layout()
if show_figure_on_screen:
Expand Down
27 changes: 6 additions & 21 deletions simpa_tests/manual_tests/acoustic_forward_models/KWaveAcousticForwardConvenienceFunction.py
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Original file line number Diff line number Diff line change
Expand Up @@ -83,7 +83,7 @@ def setup(self):
self.VOLUME_PLANAR_DIM_IN_MM/2,
0]))
self.device.set_detection_geometry(LinearArrayDetectionGeometry(device_position_mm=self.device.device_position_mm, pitch_mm=0.25,
number_detector_elements=200))
number_detector_elements=200, field_of_view_extent_mm=[-37.5, 37.5, 0, 0, 0, 25]))
self.device.add_illumination_geometry(SlitIlluminationGeometry(slit_vector_mm=[100, 0, 0]))

# run pipeline including volume creation and optical mcx simulation
Expand All @@ -107,29 +107,14 @@ def test_convenience_function(self):
self.VOLUME_NAME + ".hdf5",
Tags.DATA_FIELD_INITIAL_PRESSURE, wavelength=700)
image_slice = np.s_[:, 40, :]
self.initial_pressure = np.rot90(initial_pressure[image_slice], -1)

# define acoustic settings and run simulation with convenience function
acoustic_settings = {
Tags.ACOUSTIC_SIMULATION_3D: True,
Tags.ACOUSTIC_MODEL_BINARY_PATH: self.path_manager.get_matlab_binary_path(),
Tags.KWAVE_PROPERTY_ALPHA_POWER: 0.00,
Tags.KWAVE_PROPERTY_SENSOR_RECORD: "p",
Tags.KWAVE_PROPERTY_PMLInside: False,
Tags.KWAVE_PROPERTY_PMLSize: [31, 32],
Tags.KWAVE_PROPERTY_PMLAlpha: 1.5,
Tags.KWAVE_PROPERTY_PlotPML: False,
Tags.RECORDMOVIE: False,
Tags.MOVIENAME: "visualization_log",
Tags.ACOUSTIC_LOG_SCALE: True,
Tags.MODEL_SENSOR_FREQUENCY_RESPONSE: False
}
self.initial_pressure = initial_pressure[image_slice].T

time_series_data = perform_k_wave_acoustic_forward_simulation(initial_pressure=self.initial_pressure,
detection_geometry=self.device.
get_detection_geometry(),
speed_of_sound=1540, density=1000,
alpha_coeff=0.0)

alpha_coeff=0.0, spacing_mm=0.25)
# reconstruct the time series data to compare it with initial pressure
self.settings.set_reconstruction_settings({
Tags.RECONSTRUCTION_MODE: Tags.RECONSTRUCTION_MODE_PRESSURE,
Expand All @@ -155,7 +140,7 @@ def visualise_result(self, show_figure_on_screen=True, save_path=None):
plt.imshow(self.initial_pressure)
plt.subplot(2, 2, 2)
plt.title("Reconstructed Image Pipeline")
plt.imshow(np.rot90(self.reconstructed, -1))
plt.imshow(self.reconstructed.T)
plt.tight_layout()
if show_figure_on_screen:
plt.show()
Expand Down
6 changes: 3 additions & 3 deletions simpa_tests/manual_tests/acoustic_forward_models/MinimalKWaveTest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -121,13 +121,13 @@ def visualise_result(self, show_figure_on_screen=True, save_path=None):
plt.figure(figsize=(9, 3))
plt.subplot(1, 3, 1)
plt.title(f"{self.SPEED_OF_SOUND * 0.975} m/s")
plt.imshow(np.rot90(self.reconstructed_image_950, 3))
plt.imshow(self.reconstructed_image_950.T)
plt.subplot(1, 3, 2)
plt.title(f"{self.SPEED_OF_SOUND} m/s")
plt.imshow(np.rot90(self.reconstructed_image_1000, 3))
plt.imshow(self.reconstructed_image_1000.T)
plt.subplot(1, 3, 3)
plt.title(f"{self.SPEED_OF_SOUND * 1.025} m/s")
plt.imshow(np.rot90(self.reconstructed_image_1050, 3))
plt.imshow(self.reconstructed_image_1050.T)
plt.tight_layout()
if show_figure_on_screen:
plt.show()
Expand Down
6 changes: 3 additions & 3 deletions simpa_tests/manual_tests/processing_components/QPAIReconstruction.py
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Expand Up @@ -178,7 +178,7 @@ def visualise_result(self, show_figure_on_screen=True, save_path=None):
plt.subplot(4, int(np.ceil(len(self.list_2d_reconstructed_absorptions) / 2)), i + 1)
if i == 0:
plt.ylabel("y-z", fontsize=10)
plt.imshow(np.rot90(quantity, -1))
plt.imshow(quantity.T)
plt.title(label[i], fontsize=10)
plt.xticks(fontsize=6)
plt.yticks(fontsize=6)
Expand All @@ -193,7 +193,7 @@ def visualise_result(self, show_figure_on_screen=True, save_path=None):
i + int(np.ceil(len(self.list_2d_reconstructed_absorptions) / 2)) + 1)
if i == 0:
plt.ylabel("x-z", fontsize=10)
plt.imshow(np.rot90(quantity, -1))
plt.imshow(quantity.T)
plt.title(label[i], fontsize=10)
plt.xticks(fontsize=6)
plt.yticks(fontsize=6)
Expand All @@ -207,7 +207,7 @@ def visualise_result(self, show_figure_on_screen=True, save_path=None):
plt.subplot(4, int(np.ceil(len(self.list_2d_reconstructed_absorptions) / 2)),
i + 2 * int(np.ceil(len(self.list_2d_reconstructed_absorptions) / 2)) + 1)
plt.title("Iteration step: " + str(i + 1), fontsize=8)
plt.imshow(np.rot90(quantity, -1)) # absorption maps in list are already 2-d
plt.imshow(quantity.T) # absorption maps in list are already 2-d
plt.colorbar()
plt.clim(cmin, cmax)
plt.axis('off')
Expand Down
6 changes: 3 additions & 3 deletions simpa_tests/manual_tests/processing_components/TestLinearUnmixingVisual.py
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Expand Up @@ -104,15 +104,15 @@ def visualise_result(self, show_figure_on_screen=True, save_path=None):
plt.suptitle("Linear Unmixing - Visual Test")
plt.subplot(131)
plt.title("Ground Truth sO2 [%]")
plt.imshow(np.rot90(ground_truth_sO2[:, y_dim, :] * 100, -1), vmin=0, vmax=100)
plt.imshow(ground_truth_sO2[:, y_dim, :].T * 100, vmin=0, vmax=100)
plt.colorbar(fraction=0.05)
plt.subplot(132)
plt.title("Estimated sO2 [%]")
plt.imshow(np.rot90(self.sO2[:, y_dim, :] * 100, -1), vmin=0, vmax=100)
plt.imshow(self.sO2[:, y_dim, :].T * 100, vmin=0, vmax=100)
plt.colorbar(fraction=0.05)
plt.subplot(133)
plt.title("Absolute Difference")
plt.imshow(np.rot90(np.abs(self.sO2 * 100 - ground_truth_sO2 * 100)[:, y_dim, :], -1), cmap="Reds", vmin=0)
plt.imshow(np.abs(self.sO2 * 100 - ground_truth_sO2 * 100)[:, y_dim, :].T, cmap="Reds", vmin=0)
plt.colorbar()
plt.tight_layout()
if show_figure_on_screen:
Expand Down
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