def rois_additional(idx, outdir=os.path.join("scoring","rois","additional")):
images = [
("JHU", 24),
("JHU", 25),
("JHU", 26),
("JHU", 27),
("JHU", 28),
("JHU", 29),
("JHU", 30),
("JHU", 31),
("JHU", 32),
("JHU", 33),
("JHU", 34),
]
data_source, acq = images[idx]
P, xl, zl = load_data(data_source, acq)
# Define pixel grid limits (assume y == 0)
wvln = P.c / P.fc
dx = wvln / 3
dz = dx # Use square pixels
desired_grid = [400, 300]
xlims = np.array([-0.5, 0.5]) * (desired_grid[1] - 1) * dx + (xl[0] + xl[1]) / 2
zlims = np.array([-0.5, 0.5]) * (desired_grid[0] - 1) * dz + (zl[0] + zl[1]) / 2
xlims = [np.maximum(xlims[0], xl[0]), np.minimum(xlims[1], xl[1])]
zlims = [np.maximum(zlims[0], zl[0]), np.minimum(zlims[1], zl[1])]
grid = make_pixel_grid(xlims, zlims, dx, dz)
fnum = 1
# Normalize input to [-1, 1] range
maxval = np.maximum(np.abs(P.idata).max(), np.abs(P.qdata).max())
P.idata /= maxval
P.qdata /= maxval
# Make data torch tensors
x = (P.idata, P.qdata)
# Make 75-angle image
dasN = DAS_PW(P, grid, rxfnum=fnum)
idasN, qdasN = dasN(x)
idasN, qdasN = idasN.detach().cpu().numpy(), qdasN.detach().cpu().numpy()
iqN = idasN + 1j * qdasN
ground_truth = np.abs(iqN)
ground_truth /= np.amax(ground_truth)
# Normalize to have RMS = 1
# ground_truth /= np.sqrt(np.mean(ground_truth ** 2))
# Display images via matplotlib
xext = (np.array([-0.5, grid.shape[1] - 0.5]) * dx + xlims[0]) * 1e3
zext = (np.array([-0.5, grid.shape[0] - 0.5]) * dz + zlims[0]) * 1e3
extent = [xext[0], xext[1], zext[1], zext[0]]
plt.clf()
bimgN = 20 * np.log10(ground_truth) # Log-compress
bimgN -= np.amax(bimgN) # Normalize by max value
plt.imshow(bimgN, vmin=-60, cmap="gray", extent=extent, origin="upper")
plt.suptitle("%s%03d (c = %d m/s)" % (data_source, acq, np.round(P.c)))
# Check to make sure save directory exists, if not, create it
if not os.path.exists(outdir):
os.makedirs(outdir)
plt.savefig(os.path.join(outdir,"roi%02d.png" % (idx)))
# Save
mdict = {
"grid": grid,
"data_source": data_source,
"acq": acq,
"extent": extent,
"ground_truth": ground_truth,
}
hdf5storage.savemat(os.path.join(outdir,"roi%02d" % (idx)), mdict)
def rois_lesion(idx, outdir=os.path.join("scoring", "rois", "lesion")):
if idx == 0:
data_source, acq = "UFL", 1
xctr, zctr, r0, r1 = -0.8e-3, 30.3e-3, 2.8e-3, 4.5e-3
P, _, _ = load_data(data_source, acq)
elif idx == 1:
data_source, acq = "UFL", 5
xctr, zctr, r0, r1 = 0.2e-3, 16.4e-3, 2.2e-3, 3.5e-3
P, _, _ = load_data(data_source, acq)
elif idx == 2:
data_source, acq = "UFL", 5
xctr, zctr, r0, r1 = -0.5e-3, 45e-3, 2.2e-3, 3.5e-3
P, _, _ = load_data(data_source, acq)
elif idx == 3:
data_source, acq = "OSL", 7
xctr, zctr, r0, r1 = -8.2e-3, 39.1e-3, 2.5e-3, 4.5e-3
P, _, _ = load_data(data_source, acq)
elif idx == 4:
data_source, acq = "MYO", 1
xctr, zctr, r0, r1 = 15.5e-3, 16.5e-3, 1.3e-3, 3e-3
P, _, _ = load_data(data_source, acq)
elif idx == 5:
data_source, acq = "MYO", 4
xctr, zctr, r0, r1 = 12.2e-3, 25.8e-3, 1.3e-3, 3e-3
P, _, _ = load_data(data_source, acq)
elif idx == 6:
data_source, acq = "INS", 8
xctr, zctr, r0, r1 = 11.4e-3, 42.3e-3, 2.8e-3, 4.5e-3
P, _, _ = load_data(data_source, acq)
elif idx == 7:
data_source, acq = "INS", 21
xctr, zctr, r0, r1 = -7e-3, 41.2e-3, 2.8e-3, 4.5e-3
P, _, _ = load_data(data_source, acq)
else:
raise NotImplementedError
xlims = [-6e-3 + xctr, 6e-3 + xctr]
zlims = [-6e-3 + zctr, 6e-3 + zctr]
r2 = np.sqrt(r0**2 + r1**2)
# Define pixel grid limits (assume y == 0)
wvln = P.c / P.fc
dx = wvln / 3
dz = dx # Use square pixels
grid = make_pixel_grid(xlims, zlims, dx, dz)
fnum = 1
# Normalize input to [-1, 1] range
maxval = np.maximum(np.abs(P.idata).max(), np.abs(P.qdata).max())
P.idata /= maxval
P.qdata /= maxval
# Make ROI
dist = np.sqrt((grid[:, :, 0] - xctr)**2 + (grid[:, :, 2] - zctr)**2)
roi_i = dist <= r0
roi_o = (r1 <= dist) * (dist <= r2)
# Make data torch tensors
x = (P.idata, P.qdata)
# Make 75-angle image
dasN = DAS_PW(P, grid, rxfnum=fnum)
idasN, qdasN = dasN(x)
idasN, qdasN = idasN.detach().cpu().numpy(), qdasN.detach().cpu().numpy()
iqN = idasN + 1j * qdasN
bimgN = 20 * np.log10(np.abs(iqN)) # Log-compress
bimgN -= np.amax(bimgN) # Normalize by max value
# Display images via matplotlib
xext = (np.array([-0.5, grid.shape[1] - 0.5]) * dx + xlims[0]) * 1e3
zext = (np.array([-0.5, grid.shape[0] - 0.5]) * dz + zlims[0]) * 1e3
extent = [xext[0], xext[1], zext[1], zext[0]]
plt.clf()
opts = {"extent": extent, "origin": "upper"}
plt.imshow(bimgN, vmin=-40, cmap="gray", **opts)
plt.contour(roi_i, [0.5], colors="c", **opts)
plt.contour(roi_o, [0.5], colors="m", **opts)
plt.suptitle("%s%03d (c = %d m/s)" % (data_source, acq, np.round(P.c)))
# Check to make sure save directory exists, if not, create it
if not os.path.exists(outdir):
os.makedirs(outdir)
plt.savefig(os.path.join(outdir, "roi%02d.png" % (idx)))
# Save ROI locations
xgrid = grid[:, :, 0]
ygrid = grid[:, :, 1]
zgrid = grid[:, :, 2]
grid_i = np.stack([xgrid[roi_i], ygrid[roi_i], zgrid[roi_i]], axis=1)
grid_o = np.stack([xgrid[roi_o], ygrid[roi_o], zgrid[roi_o]], axis=1)
grid_i = np.expand_dims(grid_i, 1)
grid_o = np.expand_dims(grid_o, 1)
mdict = {
"grid": grid,
"grid_i": grid_i,
"grid_o": grid_o,
"data_source": data_source,
"acq": acq,
"xctr": xctr,
"zctr": zctr,
"r0": r0,
"r1": r1,
"r2": r2,
"extent": extent,
"roi_i": roi_i,
"roi_o": roi_o,
}
hdf5storage.savemat(os.path.join(outdir, "roi%02d" % (idx)), mdict)
def measure_speckle(beamformer, moniker, center_angle=False, verbose=True):
snrs = []
bimgs = []
for idx in range(nrois):
torch.cuda.empty_cache()
# Load ROI information
mdict = hdf5storage.loadmat(
os.path.join("scoring", "rois", "speckle", "roi%02d.mat" % idx))
data_source = mdict["data_source"]
acq = mdict["acq"]
img_grid = mdict["grid"]
extent = mdict["extent"]
# Load plane wave channel data
P, _, _ = load_data(data_source, acq)
if center_angle:
# Grab only the center angle's worth of data
aidx = len(P.angles) // 2
P.idata = P.idata[[aidx]]
P.qdata = P.qdata[[aidx]]
P.angles = P.angles[[aidx]]
P.time_zero = P.time_zero[[aidx]]
# Normalize input to [-1, 1] range
maxval = np.maximum(np.abs(P.idata).max(), np.abs(P.qdata).max())
P.idata /= maxval
P.qdata /= maxval
# Beamform the ROI
bimg = beamformer(P, img_grid)
bimgs.append(bimg)
# Compute statistics
snrs.append(snr(bimg))
if verbose:
print("roi%02d SNR: %f" % (idx, snrs[idx]))
hdf5storage.savemat(os.path.join("results", moniker, "speckle"), {
"snrs": snrs,
"bimgs": bimgs
})
plt.figure(figsize=[10, 6])
for idx in range(nrois):
# Display images via matplotlib
plt.subplot(2, 3, idx + 1)
plt.imshow(
20 * np.log10(bimgs[idx]),
vmin=-40,
cmap="gray",
extent=extent,
origin="upper",
)
plt.suptitle("%s: Speckle Targets" % moniker)
plt.pause(0.01)
outdir = os.path.join("results", moniker)
if not os.path.exists(outdir):
os.makedirs(outdir)
plt.savefig(os.path.join(outdir, "speckle.jpg"))
import torch
import matplotlib.pyplot as plt
import numpy as np
from cubdl.das_torch import DAS_PW
from datasets.PWDataLoaders import load_data, get_filelist
from cubdl.PixelGrid import make_pixel_grid
device = torch.device("cuda:0")
# Find all the CUBDL Task 1 Data
# Optional other data subsets:
# "all", "phantom", "invivo", "postcubdl", "simulation", "task1"
filelist = get_filelist(data_type="task1")
for data_source in filelist:
for acq in filelist[data_source]:
P, xlims, zlims = load_data(data_source, acq)
# Define pixel grid limits (assume y == 0)
wvln = P.c / P.fc
dx = wvln / 2.5
dz = dx # Use square pixels
grid = make_pixel_grid(xlims, zlims, dx, dz)
fnum = 1
# Make data torch tensors
x = (P.idata, P.qdata)
# Make 75-angle image
dasN = DAS_PW(P, grid, rxfnum=fnum)
idasN, qdasN = dasN(x)
idasN, qdasN = idasN.detach().cpu().numpy(), qdasN.detach().cpu(
def measure_image(beamformer, moniker, center_angle=False, verbose=True):
nrois = 12
l1_lins, l2_lins, l1_logs, l2_logs, = [], [], [], []
psnrs, nccs, bimgs, exts = [], [], [], []
for idx in range(nrois):
torch.cuda.empty_cache()
# Load ROI information
mdict = hdf5storage.loadmat(os.path.join("scoring","rois","image","roi%02d.mat" % idx))
data_source = mdict["data_source"]
acq = mdict["acq"]
img_grid = mdict["grid"]
extent = mdict["extent"]
yimg = mdict["ground_truth"]
exts.append(extent)
# Load plane wave channel data
P, _, _ = load_data(data_source, acq)
if center_angle:
# Grab only the center angle's worth of data
aidx = len(P.angles) // 2
P.idata = P.idata[[aidx]]
P.qdata = P.qdata[[aidx]]
P.angles = P.angles[[aidx]]
P.time_zero = P.time_zero[[aidx]]
# Normalize input to [-1, 1] range
maxval = np.maximum(np.abs(P.idata).max(), np.abs(P.qdata).max())
P.idata /= maxval
P.qdata /= maxval
# Beamform the ROI
bimg = beamformer(P, img_grid)
# Statistics will only be computed using image values within -40dB of max value
mask = (20 * np.log10(yimg / np.amax(yimg))) >= -40
mask2 = (20 * np.log10(bimg / np.amax(bimg))) < -40
bimg[mask & mask2] = 10 ** (-40 / 20) * np.amax(bimg)
# Find L1, L2 optimal image scaling factors
bimg_l1 = bimg * wopt_mae(yimg[mask], bimg[mask])
bimg_l2 = bimg * wopt_mse(yimg[mask], bimg[mask])
bimgs.append(bimg_l2)
# Compute statistics
l1_lins.append(l1loss(yimg[mask], bimg_l1[mask]))
l2_lins.append(l2loss(yimg[mask], bimg_l2[mask]))
l1_logs.append(l1loss(np.log(yimg[mask]), np.log(bimg_l1[mask])))
l2_logs.append(l2loss(np.log(yimg[mask]), np.log(bimg_l2[mask])))
psnrs.append(psnr(yimg[mask], bimg_l2[mask]))
nccs.append(ncc(yimg[mask], bimg[mask]))
if verbose:
print("roi%02d L1 lin: %f" % (idx, l1_lins[idx]))
print("roi%02d L1 log: %f" % (idx, l1_logs[idx]))
print("roi%02d L2 lin: %f" % (idx, l2_lins[idx]))
print("roi%02d L2 log: %f" % (idx, l2_logs[idx]))
print("roi%02d PSNR: %f" % (idx, psnrs[idx]))
print("roi%02d NCC: %f" % (idx, nccs[idx]))
hdf5storage.savemat(
os.path.join("results", moniker, "image"),
{
"l1_lins": l1_lins,
"l1_logs": l1_logs,
"l2_lins": l2_lins,
"l2_logs": l2_logs,
"psnrs": psnrs,
"nccs": nccs,
"bimgs": bimgs,
"mask": mask,
},
)
plt.figure(figsize=[10, 6])
for idx in range(nrois):
# Display images via matplotlib
plt.subplot(3, 4, idx + 1)
plt.imshow(
20 * np.log10(bimgs[idx]),
vmin=-60,
cmap="gray",
extent=exts[idx],
origin="upper",
)
plt.suptitle("%s: Image Targets" % moniker)
plt.pause(0.01)
outdir = os.path.join("results",moniker)
if not os.path.exists(outdir):
os.makedirs(outdir)
plt.savefig(os.path.join(outdir, "image.jpg"))
savedir = os.path.join("datasets", "soundspeed",
"%s%03d" % (data_source, acq))
pathlib.Path(savedir).mkdir(parents=True, exist_ok=True)
# If the output file already exists, skip
fname = "%s/data.mat" % savedir
if os.path.exists(fname):
print("%s exists. Skipping..." % fname)
continue
else:
print("Processing %s..." % fname)
xlims = [-10e-3, 10e-3]
zlims = [20e-3, 40e-3]
P, _, _ = load_data(data_source, acq)
P.c = 1540
if data_source == "MYO":
zlims = [15e-3, 35e-3]
elif data_source == "EUT":
zlims = [15e-3, 35e-3]
elif data_source == "INS":
if acq == 24:
# Acqs 10, 11, 23, 24 are challenging to find a good speckle ROI
xlims = [-12e-3, 12e-3]
zlims = [14e-3, 24e-3]
# Define pixel grid limits (assume y == 0)
wvln = P.c / P.fc
dx = wvln / 3
def rois_point(idx, outdir=os.path.join("scoring", "rois", "point")):
if idx == 0:
data_source, acq = "MYO", 3
P, _, _ = load_data(data_source, acq)
xlims = [0e-3, 20e-3]
zlims = [22e-3, 32e-3]
pts = [[13.4e-3, 0, 27.75e-3], [14.55e-3, 0, 26.8e-3],
[15.15e-3, 0, 25.85e-3]]
elif idx == 1:
data_source, acq = "UFL", 4
P, _, _ = load_data(data_source, acq)
xlims = [-6e-3, 10e-3]
zlims = [22e-3, 32e-3]
pts = [[-2.8e-3, 0, 27.65e-3], [-3.95e-3, 0, 26.7e-3],
[-4.56e-3, 0, 25.7e-3]]
elif idx == 2:
data_source, acq = "UFL", 2
P, _, _ = load_data(data_source, acq)
xlims = [-3e-3, 3e-3]
zlims = [12e-3, 38e-3]
pts = [
[-0.29e-3, 0, 15.5e-3],
[-0.31e-3, 0, 20.6e-3],
[-0.43e-3, 0, 25.4e-3],
[-0.20e-3, 0, 30.8e-3],
[-0.12e-3, 0, 35.7e-3],
]
elif idx == 3:
data_source, acq = "MYO", 2
P, _, _ = load_data(data_source, acq)
xlims = [-15e-3, 11e-3]
zlims = [38e-3, 42e-3]
pts = [[-11.95e-3, 0, 39.4e-3], [-2e-3, 0, 39.55e-3],
[8e-3, 0, 39.6e-3]]
else:
raise NotImplementedError
# Define pixel grid limits (assume y == 0)
wvln = P.c / P.fc
dx = wvln / 3
dz = dx # Use square pixels
grid = make_pixel_grid(xlims, zlims, dx, dz)
fnum = 1
# Normalize input to [-1, 1] range
maxval = np.maximum(np.abs(P.idata).max(), np.abs(P.qdata).max())
P.idata /= maxval
P.qdata /= maxval
# Make data torch tensors
x = (P.idata, P.qdata)
# Make 75-angle image
dasN = DAS_PW(P, grid, rxfnum=fnum)
idasN, qdasN = dasN(x)
idasN, qdasN = idasN.detach().cpu().numpy(), qdasN.detach().cpu().numpy()
iqN = idasN + 1j * qdasN
bimgN = 20 * np.log10(np.abs(iqN)) # Log-compress
bimgN -= np.amax(bimgN) # Normalize by max value
# Display images via matplotlib
xext = (np.array([-0.5, grid.shape[1] - 0.5]) * dx + xlims[0]) * 1e3
zext = (np.array([-0.5, grid.shape[0] - 0.5]) * dz + zlims[0]) * 1e3
extent = [xext[0], xext[1], zext[1], zext[0]]
plt.clf()
plt.imshow(bimgN, vmin=-40, cmap="gray", extent=extent, origin="upper")
plt.suptitle("%s%03d (c = %d m/s)" % (data_source, acq, np.round(P.c)))
bar = np.array([-1e-3, 1e-3])
tmp = np.array([0, 0])
for pt in pts:
plt.plot((pt[0] + bar) * 1e3, (pt[2] + tmp) * 1e3, "c-")
plt.plot((pt[0] + tmp) * 1e3, (pt[2] + bar) * 1e3, "c-")
# Check to make sure save directory exists, if not, create it
if not os.path.exists(outdir):
os.makedirs(outdir)
plt.savefig(os.path.join(outdir, "roi%02d.png" % (idx)))
# Save
mdict = {
"grid": grid,
"data_source": data_source,
"acq": acq,
"extent": extent,
"pts": pts,
}
hdf5storage.savemat(os.path.join(outdir, "roi%02d" % (idx)), mdict)
def measure_point(beamformer, moniker, center_angle=False, verbose=True):
x_fwhms = []
z_fwhms = []
bimgs = []
exts = []
for idx in range(4):
torch.cuda.empty_cache()
# Load ROI information
mdict = hdf5storage.loadmat(os.path.join("scoring","rois","point","roi%02d.mat" % idx))
data_source = mdict["data_source"]
acq = mdict["acq"]
img_grid = mdict["grid"]
extent = mdict["extent"]
pts = mdict["pts"]
exts.append(extent)
# Load plane wave channel data
P, _, _ = load_data(data_source, acq)
if center_angle:
# Grab only the center angle's worth of data
aidx = len(P.angles) // 2
P.idata = P.idata[[aidx]]
P.qdata = P.qdata[[aidx]]
P.angles = P.angles[[aidx]]
P.time_zero = P.time_zero[[aidx]]
# Normalize input to [-1, 1] range
maxval = np.maximum(np.abs(P.idata).max(), np.abs(P.qdata).max())
P.idata /= maxval
P.qdata /= maxval
# Make grid based on ROIs
bimg = beamformer(P, img_grid)
bimgs.append(bimg)
x_fwhm = []
z_fwhm = []
for i, pt in enumerate(pts):
# One option is to directly beamform a line of pixels over the point targets
# at high pixel density. However, this may be unfair to methods that rely on
# a consistent pixel spacing, or to those that require 2D images to operate
# upon.
# Instead, we choose to interpolate the original beamformed image.
ax = img_grid[:, 0, 2] # Axial pixel positions [m]
az = img_grid[0, :, 0] # Azimuthal pixel positions [m]
f = interp2d(ax, az, bimg)
# Define pixel grid limits (assume y == 0)
dp = P.c / P.fc / 3 / 100 # Interpolate 100-fold
roi = np.arange(-1e-3, 1e-3, dp)
roi -= np.mean(roi)
zeros = np.zeros_like(roi)
# Horizontal grid
xroi = f(pt[2] + zeros, pt[0] + roi)[0]
zroi = f(pt[2] + roi, pt[0] + zeros)[:, 0]
x_fwhm.append(res_FWHM(xroi) * dp)
z_fwhm.append(res_FWHM(zroi) * dp)
x_fwhms.append(np.mean(x_fwhm))
z_fwhms.append(np.mean(z_fwhm))
if verbose:
print("ROI %d, x-FWHM: %dum" % (idx, np.round(x_fwhms[idx] * 1e6)))
print("ROI %d, z-FWHM: %dum" % (idx, np.round(z_fwhms[idx] * 1e6)))
hdf5storage.savemat(
os.path.join("results",moniker,"point"),
{"x_fwhms": x_fwhms, "z_fwhms": z_fwhms, "bimgs": bimgs, "exts": exts},
)
# Display images via matplotlib
plt.figure(figsize=[10, 6])
plt.subplot(2, 3, 1)
plt.imshow(_dB(bimgs[0]), vmin=-40, cmap="gray", extent=exts[0], origin="upper")
plt.subplot(2, 3, 2)
plt.imshow(_dB(bimgs[1]), vmin=-40, cmap="gray", extent=exts[1], origin="upper")
plt.subplot(1, 3, 3)
plt.imshow(_dB(bimgs[2]), vmin=-40, cmap="gray", extent=exts[2], origin="upper")
plt.subplot(2, 2, 3)
plt.imshow(_dB(bimgs[3]), vmin=-40, cmap="gray", extent=exts[3], origin="upper")
plt.suptitle("Point Targets")
plt.pause(0.01)
outdir = os.path.join("results",moniker)
if not os.path.exists(outdir):
os.makedirs(outdir)
plt.savefig(os.path.join(outdir,"point.jpg"))
def rois_speckle(idx, outdir=os.path.join("scoring", "rois", "speckle")):
if idx == 0:
data_source, acq = "UFL", 4
P, _, _ = load_data(data_source, acq)
xlims = [0e-3, 12e-3]
zlims = [14e-3, 26e-3]
elif idx == 1:
data_source, acq = "OSL", 7
P, _, _ = load_data(data_source, acq)
xlims = [-6e-3, 6e-3]
zlims = [14e-3, 26e-3]
elif idx == 2:
data_source, acq = "MYO", 2
P, _, _ = load_data(data_source, acq)
xlims = [-6e-3, 6e-3]
zlims = [14e-3, 26e-3]
elif idx == 3:
data_source, acq = "EUT", 3
P, _, _ = load_data(data_source, acq)
xlims = [-6e-3, 6e-3]
zlims = [25e-3, 37e-3]
elif idx == 4:
data_source, acq = "INS", 4
P, _, _ = load_data(data_source, acq)
xlims = [-6e-3, 6e-3]
zlims = [25e-3, 37e-3]
elif idx == 5:
data_source, acq = "INS", 16
P, _, _ = load_data(data_source, acq)
xlims = [-6e-3, 6e-3]
zlims = [25e-3, 37e-3]
else:
raise NotImplementedError
# Define pixel grid limits (assume y == 0)
wvln = P.c / P.fc
dx = wvln / 3
dz = dx # Use square pixels
grid = make_pixel_grid(xlims, zlims, dx, dz)
fnum = 1
# Normalize input to [-1, 1] range
maxval = np.maximum(np.abs(P.idata).max(), np.abs(P.qdata).max())
P.idata /= maxval
P.qdata /= maxval
# Make data torch tensors
x = (P.idata, P.qdata)
# Make 75-angle image
dasN = DAS_PW(P, grid, rxfnum=fnum)
idasN, qdasN = dasN(x)
idasN, qdasN = idasN.detach().cpu().numpy(), qdasN.detach().cpu().numpy()
iqN = idasN + 1j * qdasN
bimgN = 20 * np.log10(np.abs(iqN)) # Log-compress
bimgN -= np.amax(bimgN) # Normalize by max value
# Display images via matplotlib
xext = (np.array([-0.5, grid.shape[1] - 0.5]) * dx + xlims[0]) * 1e3
zext = (np.array([-0.5, grid.shape[0] - 0.5]) * dz + zlims[0]) * 1e3
extent = [xext[0], xext[1], zext[1], zext[0]]
plt.clf()
plt.imshow(bimgN, vmin=-40, cmap="gray", extent=extent, origin="upper")
plt.suptitle("%s%03d (c = %d m/s)" % (data_source, acq, np.round(P.c)))
# Check to make sure save directory exists, if not, create it
if not os.path.exists(outdir):
os.makedirs(outdir)
plt.savefig(os.path.join(outdir, "roi%02d.png" % (idx)))
# Save
mdict = {
"grid": grid,
"data_source": data_source,
"acq": acq,
"extent": extent
}
hdf5storage.savemat(os.path.join(outdir, "roi%02d" % (idx)), mdict)
def measure_lesion(beamformer, moniker, center_angle=False, verbose=True):
contrasts = []
cnrs = []
gcnrs = []
brois = []
bimgs = []
for idx in range(8):
torch.cuda.empty_cache()
# Load ROI information
mdict = hdf5storage.loadmat(os.path.join("scoring","rois","lesion","roi%02d.mat" % idx))
data_source = mdict["data_source"]
acq = mdict["acq"]
# roi_grid = np.concatenate((mdict["grid_i"], mdict["grid_o"]), axis=0)
roi_i = mdict["roi_i"]
roi_o = mdict["roi_o"]
img_grid = mdict["grid"]
extent = mdict["extent"]
# ni = mdict["grid_i"].shape[0]
# Load plane wave channel data
P, _, _ = load_data(data_source, acq)
# Normalize input to [-1, 1] range
maxval = np.maximum(np.abs(P.idata).max(), np.abs(P.qdata).max())
P.idata /= maxval
P.qdata /= maxval
if center_angle:
# Grab only the center angle's worth of data
aidx = len(P.angles) // 2
P.idata = P.idata[[aidx]]
P.qdata = P.qdata[[aidx]]
P.angles = P.angles[[aidx]]
P.time_zero = P.time_zero[[aidx]]
# Beamform the ROI and image
# broi = beamformer(P, roi_grid)
bimg = beamformer(P, img_grid)
# brois.append(broi)
bimgs.append(bimg)
# Compute statistics
# b_inner, b_outer = broi[:ni], broi[ni:]
b_inner = bimgs[idx][roi_i]
b_outer = bimgs[idx][roi_o]
contrasts.append(contrast(b_inner, b_outer))
cnrs.append(cnr(b_inner, b_outer))
gcnrs.append(gcnr(b_inner, b_outer))
if verbose:
print("roi%02d Contrast: %f" % (idx, contrasts[idx]))
print("roi%02d CNR: %f" % (idx, cnrs[idx]))
print("roi%02d gCNR: %f" % (idx, gcnrs[idx]))
hdf5storage.savemat(
os.path.join("results",moniker,"lesion"),
{
"contrasts": contrasts,
"cnrs": cnrs,
"gcnrs": gcnrs,
"brois": brois,
"bimgs": bimgs,
},
)
plt.figure(figsize=[10, 6])
for idx in range(8):
# Display images via matplotlib
plt.subplot(2, 4, idx + 1)
plt.imshow(
20 * np.log10(bimgs[idx]),
vmin=-40,
cmap="gray",
extent=extent,
origin="upper",
)
plt.suptitle("%s: Anechoic Lesions" % moniker)
plt.pause(0.01)
outdir = os.path.join("results",moniker)
if not os.path.exists(outdir):
os.makedirs(outdir)
plt.savefig(os.path.join(outdir,"lesion.jpg"))