# Copyright (c) Thomas Else 2023.
# License: MIT
import numpy as np
from ...core.image_structures.reconstruction_image import Reconstruction
from ..attribute_tags import ReconAttributeTags
from ..hdf.fileimporter import ReaderInterface
class SimpaImporter(ReaderInterface):
"""An importer for HDF5 files created by the SIMPA toolkit.
"""
# Currently, aiming to just support 2D
def _get_rois(self):
return None
def get_speed_of_sound(self):
import simpa as sp
f = sp.get_data_field_from_simpa_output(self.file, sp.Tags.DATA_FIELD_SPEED_OF_SOUND)
return np.mean(f)
def _original_shape(self):
return self._get_segmentation().shape
def _get_segmentation(self):
import simpa as sp
seg = sp.get_data_field_from_simpa_output(self.file, sp.Tags.DATA_FIELD_SEGMENTATION)
if seg.ndim == 2:
seg = seg[:, :, None]
return seg
def get_scan_comment(self):
return ""
def _get_sampling_frequency(self):
if "dt_acoustic_sim" not in self.file["settings"]:
return 1
return 1 / self.file["settings"]["dt_acoustic_sim"]
def _simpa_get_initial_pressure(self, wavelength):
import simpa as sp
recon = sp.get_data_field_from_simpa_output(self.file, sp.Tags.DATA_FIELD_INITIAL_PRESSURE,
wavelength)
if recon.ndim == 2:
recon = recon[:, :, None]
return recon
def _get_datasets(self):
wavelengths = self.wavelengths
recon_size = self._simpa_get_initial_pressure(wavelengths[0]).shape
recon_data = np.zeros((1, len(self.wavelengths),) + recon_size)
for i, w in enumerate(wavelengths):
recon_data[0, i] = self._simpa_get_initial_pressure(w)
attributes = {ReconAttributeTags.X_NUMBER_OF_PIXELS: recon_data.shape[-1],
ReconAttributeTags.Y_NUMBER_OF_PIXELS: recon_data.shape[-2],
ReconAttributeTags.Z_NUMBER_OF_PIXELS: recon_data.shape[-3],
ReconAttributeTags.X_FIELD_OF_VIEW: self._simpa_fov[0],
ReconAttributeTags.Y_FIELD_OF_VIEW: self._simpa_fov[1],
ReconAttributeTags.Z_FIELD_OF_VIEW: self._simpa_fov[2]}
# recon_data = recon_data.swapaxes(0, 3).copy()
recon_class = Reconstruction(recon_data, self._get_wavelengths(),
attributes=dict(attributes),
field_of_view=self._simpa_fov, hdf5_sub_name="initial_pressure")
return {"recons": {("initial_pressure", "0"): recon_class}}
[docs]
def __init__(self, filename):
super().__init__()
import simpa as sp
self.file = sp.load_hdf5(filename)
self.filename = filename
z0, _, x0, _, y0, _ = self.file["digital_device"].get_detection_geometry().get_field_of_view_mm()/1000
nz, ny, nx = self._original_shape()
dx = self.file["settings"]["voxel_spacing_mm"]/1000
self._simpa_fov = [(x0, x0+dx*nx), (y0, y0+dx*ny), (z0, z0+dx*nz)]
self.wavelengths = self.file["settings"]["wavelengths"]
self.nz = 1 # for backwards compatibility
def get_scan_datetime(self):
return 0
def _get_pa_data(self):
import simpa as sp
try:
attrs = {"fs": self.get_sampling_frequency()}
pa = np.array([sp.get_data_field_from_simpa_output(self.file, sp.Tags.DATA_FIELD_TIME_SERIES_DATA, w) for w in
self.wavelengths])
return (pa[None],
attrs)
except KeyError:
return (np.full((1, len(self.wavelengths), 256, 2), np.nan), {})
def get_scan_name(self):
return self.filename
def _get_temperature(self):
return np.zeros((self.nz, len(self.wavelengths)))
def _get_correction_factor(self):
return np.ones((self.nz, len(self.wavelengths)))
def _get_scanner_z_position(self):
return np.arange(self.nz)[:, None] * np.ones((len(self.wavelengths),))[None, :] * self.file["settings"][
"voxel_spacing_mm"]
def _get_run_numbers(self):
return np.zeros((self.nz, len(self.wavelengths)))
def _get_repetition_numbers(self):
return np.zeros((self.nz, len(self.wavelengths)))
def _get_scan_times(self):
return np.arange(self.nz * len(self.wavelengths)).reshape((self.nz, len(self.wavelengths)))
def _get_sensor_geometry(self):
g = self.file["digital_device"].get_detection_geometry().get_detector_element_positions_accounting_for_field_of_view()
return g / 1000
def get_us_data(self):
return None
def get_impulse_response(self):
irf = np.zeros((self.get_pa_data()[0].shape[-1],))
irf[irf.shape[0] // 2] = 1
return irf
def _get_wavelengths(self):
return self.wavelengths
def _get_water_absorption(self):
return np.zeros((len(self.wavelengths),)), 0
