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angle = float(sys.argv[2]) if len(sys.argv) > 2 else 32.5
dz = float(sys.argv[3]) if len(sys.argv) > 3 else 0.4
dx = 0.1
xzRatio = dx / (np.deg2rad(angle) * dz)
rotated = rotateGPU(im, angle, xzRatio)
tf.imshow(rotated, vmin=0, vmax=rotated.max() * 0.5)
plt.show()
elif (sys.argv[1] == "decon") or (sys.argv[1] == "deconv"):
im = tf.imread(
"/Users/talley/Dropbox (HMS)/CBMF/lattice_sample_data/lls_bidirectional/bidir_ch0_stack0000_488nm_0000000msec_0007232334msecAbs.tif"
)
otfpath = "/Users/talley/Dropbox (HMS)/CBMF/lattice_sample_data/lls_PSFs/488_otf.tif"
RL_init(im.shape, otfpath, dzdata=0.4)
decon = RL_decon(im, nIters=15)
tf.imshow(decon, vmin=0, vmax=decon.max() * 0.5)
plt.show()
RL_cleanup()
elif sys.argv[1] == "camcor":
from llspy import llsdir
from llspy import samples
import time
E = llsdir.LLSdir(samples.stickypix)
# from llspy.util import util
# from llspy.camera.camera import CameraParameters, CameraROI
# camparams = CameraParameters()
# camparams = camparams.get_subroi(CameraROI(E.settings.camera.roi))
# for i in sys.argv[2:]:
# p = p = os.path.abspath(i).replace('\\', '')
# if os.path.isfile(p):
# tf.imshow(deskewGPU(tf.imread(p), float(zstep)))
# plt.show()
elif sys.argv[1] == "rotate":
im = tf.imread(
"/Users/talley/Dropbox (HMS)/CBMF/lattice_sample_data/lls_registration_samp/reg_ex1/tspeck/GPUdecon/tspeck_ch0_stack0000_488nm_0000000msec_0001881189msecAbs_decon.tif"
)
angle = float(sys.argv[2]) if len(sys.argv) > 2 else 32.5
dz = float(sys.argv[3]) if len(sys.argv) > 3 else 0.4
dx = 0.1
xzRatio = dx / (np.deg2rad(angle) * dz)
rotated = rotateGPU(im, angle, xzRatio)
tf.imshow(rotated, vmin=0, vmax=rotated.max() * 0.5)
plt.show()
elif (sys.argv[1] == "decon") or (sys.argv[1] == "deconv"):
im = tf.imread(
"/Users/talley/Dropbox (HMS)/CBMF/lattice_sample_data/lls_bidirectional/bidir_ch0_stack0000_488nm_0000000msec_0007232334msecAbs.tif"
)
otfpath = "/Users/talley/Dropbox (HMS)/CBMF/lattice_sample_data/lls_PSFs/488_otf.tif"
RL_init(im.shape, otfpath, dzdata=0.4)
decon = RL_decon(im, nIters=15)
tf.imshow(decon, vmin=0, vmax=decon.max() * 0.5)
plt.show()
RL_cleanup()
elif sys.argv[1] == "camcor":
from llspy import llsdir
from llspy import samples
if len(sys.argv) >= 2:
if sys.argv[1] == "affine":
# affine test
im = tf.imread(
"/Users/talley/Dropbox (HMS)/CBMF/lattice_sample_data/lls_basic_samp/Deskewed/cell5_ch0_stack0001_488nm_0000000msec_0020931273msecAbs_deskewed.tif"
)
T = np.array([[1, 0, 0, -50], [0, 1, 0, -100], [0, 0, 1, 0], [0, 0, 0, 1]])
q = affineGPU(im, T)
tf.imshow(q, vmin=-10, vmax=150)
plt.show()
elif sys.argv[1] == "deskew":
# deskew test
im = tf.imread(
"/Users/talley/Dropbox (HMS)/CBMF/lattice_sample_data/lls_basic_samp/cell5_ch0_stack0000_488nm_0000000msec_0020931273msecAbs.tif"
)
tf.imshow(deskewGPU(im, 0.3))
plt.show()
# zstep = sys.argv[1]
# for i in sys.argv[2:]:
# p = p = os.path.abspath(i).replace('\\', '')
# if os.path.isfile(p):
# tf.imshow(deskewGPU(tf.imread(p), float(zstep)))
# plt.show()
elif sys.argv[1] == "rotate":
im = tf.imread(
"/Users/talley/Dropbox (HMS)/CBMF/lattice_sample_data/lls_registration_samp/reg_ex1/tspeck/GPUdecon/tspeck_ch0_stack0000_488nm_0000000msec_0001881189msecAbs_decon.tif"
)
angle = float(sys.argv[2]) if len(sys.argv) > 2 else 32.5
dz = float(sys.argv[3]) if len(sys.argv) > 3 else 0.4
dx = 0.1
def imshow(*args, **kwargs):
return tifffile.imshow(*args, **kwargs)
return decon_result
if __name__ == "__main__":
import tifffile as tf
import matplotlib.pyplot as plt
if len(sys.argv) >= 2:
if sys.argv[1] == "affine":
# affine test
im = tf.imread(
"/Users/talley/Dropbox (HMS)/CBMF/lattice_sample_data/lls_basic_samp/Deskewed/cell5_ch0_stack0001_488nm_0000000msec_0020931273msecAbs_deskewed.tif"
)
T = np.array([[1, 0, 0, -50], [0, 1, 0, -100], [0, 0, 1, 0], [0, 0, 0, 1]])
q = affineGPU(im, T)
tf.imshow(q, vmin=-10, vmax=150)
plt.show()
elif sys.argv[1] == "deskew":
# deskew test
im = tf.imread(
"/Users/talley/Dropbox (HMS)/CBMF/lattice_sample_data/lls_basic_samp/cell5_ch0_stack0000_488nm_0000000msec_0020931273msecAbs.tif"
)
tf.imshow(deskewGPU(im, 0.3))
plt.show()
# zstep = sys.argv[1]
# for i in sys.argv[2:]:
# p = p = os.path.abspath(i).replace('\\', '')
# if os.path.isfile(p):
# tf.imshow(deskewGPU(tf.imread(p), float(zstep)))
# plt.show()
def plot_img(img, channels=(1, 2, 3), **kwargs):
"""plot the ndarray images
Args:
img (ndarray): the ndarray image.
channels (tuple, optional): target channel to show. Defaults to (1,2,3).
kwargs (dict, optional): the plt.imshow kwargs.
"""
plt.figure(figsize=(10, 8))
channels = channels if isinstance(channels, int) else [x - 1 for x in channels]
if img.ndim == 2:
tifffile.imshow(img, cmap="gray", **kwargs)
else:
tifffile.imshow(img[..., channels], **kwargs)
def plot_img(img, channels=(1, 2, 3), **kwargs):
"""plot the ndarray images
Args:
img (ndarray): the ndarray image.
channels (tuple, optional): target channel to show. Defaults to (1,2,3).
kwargs (dict, optional): the plt.imshow kwargs.
"""
plt.figure(figsize=(10, 8))
channels = channels if isinstance(channels, int) else [x - 1 for x in channels]
if img.ndim == 2:
tifffile.imshow(img, cmap="gray", **kwargs)
else:
tifffile.imshow(img[..., channels], **kwargs)