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T239 wavelength independent volume creation #240

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merged 7 commits into from
Sep 19, 2023
Merged

T239 wavelength independent volume creation #240

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1d9f70b
Split Tissue properties in wavelength-dependent and wavelength-indepe…
kdreher Sep 19, 2023
ba7dc7f
Create wavelength-independent properties only in the first wavelength…
kdreher Sep 19, 2023
393e025
Crop wavelength-independent properties only in the last wavelength run
kdreher Sep 19, 2023
170b96b
Get wavelength only once from settings in k-wave adapter
kdreher Sep 19, 2023
635ce5e
Added comments to clarify if clauses
kdreher Sep 19, 2023
87ff8c9
Fixed bug of wavelength keys being integers instead of strings
kdreher Sep 19, 2023
d15bfdd
Update volume creation such that empty volumes for wavelength-indepen…
kdreher Sep 19, 2023
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9 changes: 6 additions & 3 deletions simpa/core/processing_components/monospectral/field_of_view_cropping.py
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Original file line number Diff line number Diff line change
Expand Up @@ -57,11 +57,14 @@ def run(self, device: DigitalDeviceTwinBase):

self.logger.debug(f"field of view to crop: {field_of_view_voxels}")

wavelength = self.global_settings[Tags.WAVELENGTH]

for data_field in data_fields:
# Crop wavelength-independent properties only in the last wavelength run
if (data_field in TissueProperties.wavelength_independent_properties
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Having a comment of what happens in these lines would be super helpful for reading. E.g. for wavelength-independent data field skip all wavelengths except of the last one and only crop it then

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Yes indeed :)

and wavelength != self.global_settings[Tags.WAVELENGTHS][-1]):
continue
self.logger.debug(f"Cropping data field {data_field}...")

# load
wavelength = self.global_settings[Tags.WAVELENGTH]
data_array = load_data_field(self.global_settings[Tags.SIMPA_OUTPUT_PATH], data_field, wavelength)
self.logger.debug(f"data array shape before cropping: {np.shape(data_array)}")
self.logger.debug(f"data array shape len: {len(np.shape(data_array))}")
Expand Down
9 changes: 5 additions & 4 deletions ...core/simulation_modules/acoustic_forward_module/acoustic_forward_module_k_wave_adapter.py
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Expand Up @@ -76,14 +76,16 @@ def forward_model(self, detection_geometry: DetectionGeometryBase) -> np.ndarray

"""

wavelength = self.global_settings[Tags.WAVELENGTH]
optical_path = generate_dict_path(Tags.OPTICAL_MODEL_OUTPUT_NAME,
wavelength=self.global_settings[Tags.WAVELENGTH])
wavelength=wavelength)

self.logger.debug(f"OPTICAL_PATH: {str(optical_path)}")

data_dict = {}
file_path = self.global_settings[Tags.SIMPA_OUTPUT_PATH]
data_dict[Tags.DATA_FIELD_INITIAL_PRESSURE] = load_data_field(file_path, Tags.DATA_FIELD_INITIAL_PRESSURE)
data_dict[Tags.DATA_FIELD_INITIAL_PRESSURE] = load_data_field(file_path, Tags.DATA_FIELD_INITIAL_PRESSURE,
wavelength=wavelength)
data_dict[Tags.DATA_FIELD_SPEED_OF_SOUND] = load_data_field(file_path, Tags.DATA_FIELD_SPEED_OF_SOUND)
data_dict[Tags.DATA_FIELD_DENSITY] = load_data_field(file_path, Tags.DATA_FIELD_DENSITY)
data_dict[Tags.DATA_FIELD_ALPHA_COEFF] = load_data_field(file_path, Tags.DATA_FIELD_ALPHA_COEFF)
Expand All @@ -108,15 +110,14 @@ def forward_model(self, detection_geometry: DetectionGeometryBase) -> np.ndarray
axes = (0, 2)
image_slice = np.s_[:]

wavelength = str(self.global_settings[Tags.WAVELENGTH])
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]
[wavelength][image_slice], 3, axes=axes)
[image_slice], 3, axes=axes)

time_series_data, global_settings = self.k_wave_acoustic_forward_model(
detection_geometry,
Expand Down
19 changes: 9 additions & 10 deletions simpa/core/simulation_modules/volume_creation_module/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
import numpy as np
from simpa.core import SimulationModule
from simpa.utils.dict_path_manager import generate_dict_path
from simpa.io_handling import save_hdf5
from simpa.io_handling import save_data_field
from simpa.utils.quality_assurance.data_sanity_testing import assert_equal_shapes, assert_array_well_defined


Expand All @@ -31,7 +31,13 @@ def create_empty_volumes(self):
volume_z_dim = int(round(self.global_settings[Tags.DIM_VOLUME_Z_MM] / voxel_spacing))
sizes = (volume_x_dim, volume_y_dim, volume_z_dim)

wavelength = self.global_settings[Tags.WAVELENGTH]
first_wavelength = self.global_settings[Tags.WAVELENGTHS][0]

for key in TissueProperties.property_tags:
# Create wavelength-independent properties only in the first wavelength run
if key in TissueProperties.wavelength_independent_properties and wavelength != first_wavelength:
continue
volumes[key] = np.zeros(sizes)

return volumes, volume_x_dim, volume_y_dim, volume_z_dim
Expand Down Expand Up @@ -60,13 +66,6 @@ def run(self, device):
continue
assert_array_well_defined(volumes[_volume_name], array_name=_volume_name)

save_volumes = dict()
for key, value in volumes.items():
if key in [Tags.DATA_FIELD_ABSORPTION_PER_CM, Tags.DATA_FIELD_SCATTERING_PER_CM,
Tags.DATA_FIELD_ANISOTROPY]:
save_volumes[key] = {self.global_settings[Tags.WAVELENGTH]: value}
else:
save_volumes[key] = value

volume_path = generate_dict_path(Tags.SIMULATION_PROPERTIES, self.global_settings[Tags.WAVELENGTH])
save_hdf5(save_volumes, self.global_settings[Tags.SIMPA_OUTPUT_PATH], file_dictionary_path=volume_path)
save_data_field(value, self.global_settings[Tags.SIMPA_OUTPUT_PATH],
data_field=key, wavelength=self.global_settings[Tags.WAVELENGTH])
25 changes: 16 additions & 9 deletions simpa/utils/tissue_properties.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,15 +7,22 @@

class TissueProperties(dict):

property_tags = [Tags.DATA_FIELD_ABSORPTION_PER_CM,
Tags.DATA_FIELD_SCATTERING_PER_CM,
Tags.DATA_FIELD_ANISOTROPY,
Tags.DATA_FIELD_GRUNEISEN_PARAMETER,
Tags.DATA_FIELD_SEGMENTATION,
Tags.DATA_FIELD_OXYGENATION,
Tags.DATA_FIELD_DENSITY,
Tags.DATA_FIELD_SPEED_OF_SOUND,
Tags.DATA_FIELD_ALPHA_COEFF]
wavelength_dependent_properties = [
Tags.DATA_FIELD_ABSORPTION_PER_CM,
Tags.DATA_FIELD_SCATTERING_PER_CM,
Tags.DATA_FIELD_ANISOTROPY
]

wavelength_independent_properties = [
Tags.DATA_FIELD_GRUNEISEN_PARAMETER,
Tags.DATA_FIELD_SEGMENTATION,
Tags.DATA_FIELD_OXYGENATION,
Tags.DATA_FIELD_DENSITY,
Tags.DATA_FIELD_SPEED_OF_SOUND,
Tags.DATA_FIELD_ALPHA_COEFF
]

property_tags = wavelength_dependent_properties + wavelength_independent_properties

def __init__(self):
super().__init__()
Expand Down
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