From 7e65e47d6f42c0cd1c8d1734c60c4bd138291dd8 Mon Sep 17 00:00:00 2001
From: Tamino Huxohl <thuxohl@techfak.uni-bielefeld.de>
Date: Wed, 26 Oct 2022 12:16:43 +0200
Subject: [PATCH] fix reconstruction impl
---
mu_map/util.py | 40 ++++++++++++++++++----------------------
1 file changed, 18 insertions(+), 22 deletions(-)
diff --git a/mu_map/util.py b/mu_map/util.py
index 4a4fabb..871a688 100644
--- a/mu_map/util.py
+++ b/mu_map/util.py
@@ -47,52 +47,47 @@ def grayscale_to_rgb(img: np.ndarray):
return img.repeat(3).reshape((*img.shape, 3))
-def reconstruct(recon, mu_map=None, use_gpu=True, seed=42):
+def reconstruct(recon, mu_map=None, iterations=10, use_gpu=True, seed=42, test_flag=True):
random.seed(seed)
- print("Init scan")
spect = SPECT_Static_Scan()
spect.set_use_gpu(use_gpu)
recon_t = np.transpose(recon, (2, 1, 0)).astype(np.float32)
n_pixels = recon_t.shape[0]
- print(f"Set to NPixels {n_pixels}, {recon_t.shape}")
- # spect.set_n_pixels(n_pixels, n_pixels)
- spect.set_n_pixels(128, 128)
+
+ padding = (n_pixels - recon_t.shape[2]) / 2
+ padding_lower = math.ceil(padding)
+ padding_upper = math.floor(padding)
+ recon_t = np.pad(recon_t, [(0, 0), (0, 0), (padding_lower, padding_upper)])
+
+ spect.set_n_pixels(n_pixels, n_pixels)
spect.set_gantry_angular_positions(0.0, 360.0, 59)
+ # print("Forward projection .....", end="\r")
+ measurement = spect.project(recon_t)
+ # print(f"Measurement: {measurement.data.shape}")
+ spect.set_measurement(measurement.data)
+ # print("Forward projection DONE!")
+
if mu_map is not None:
mu_map_t = np.transpose(mu_map, (2, 1, 0)).astype(np.float32)
-
- padding_lower = math.ceil(n_pixels - mu_map_t.shape[2])
- padding_upper = math.floor(n_pixels - mu_map_t.shape[2])
mu_map_t = np.pad(mu_map_t, [(0, 0), (0, 0), (padding_lower, padding_upper)])
-
- print("Set attenuation map...")
spect.set_attenuation(mu_map_t)
- print("Forward projection .....", end="\r")
- measurement = spect.project(recon_t)
- print(f"Measurement: {measurement.data.shape}")
- spect.set_measurement(measurement.data)
- print("Forward projection DONE!")
-
- print("init more parameters...")
spect.set_pixel_size(4.8, 4.8)
spect.set_radius(200.0)
spect.set_psf(fwhm0_mm=5.0, depth_dependence=0.0001)
- print("Reconstruction .....", end="\r")
+ # print("Reconstruction .....", end="\r")
activity = spect.estimate_activity(
- iterations=10, subset_size=16, subset_mode="random", method="EM"
+ iterations=iterations, subset_size=16, subset_mode="random", method="EM"
)
- print("Reconstruction DONE!")
+ # print("Reconstruction DONE!")
activity = activity.data
activity = np.transpose(activity, (2, 1, 0))
- _shape = activity.shape
activity, _ = align_images(activity, recon)
- print(f"Realign activity from {_shape} to {activity.shape}")
return activity
if __name__ == "__main__":
@@ -125,6 +120,7 @@ if __name__ == "__main__":
s = np.full((1024, 10), 239, np.uint8)
return np.hstack((img1, s, img2))
+ exit(0)
i = 0
wname = "Test"
--
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