def test_diffread_on_dm3_vs_dm4_image():
""" Test that diffread() works on DM3 images """
im3 = diffread(TEST_DM3)
im4 = diffread(TEST_DM4)
assert im3.shape == (256, 256)
assert im3.dtype == np.dtype("int8")
assert im4.shape == (256, 256)
assert im4.dtype == np.dtype("int8")
assert np.allclose(im3, im4)
def test_on_dm3_vs_dm4_image(self):
""" Test that diffread() works on DM3 images """
im3 = diffread(TEST_DM3)
im4 = diffread(TEST_DM4)
with self.subTest("DM3"):
self.assertEqual(im3.shape, (2048, 2048))
self.assertEqual(im3.dtype, np.dtype("int8"))
with self.subTest("DM4"):
self.assertEqual(im4.shape, (2048, 2048))
self.assertEqual(im4.dtype, np.dtype("int8"))
with self.subTest("DM3 vs. DM4"):
self.assertTrue(np.allclose(im3, im4))
def test_diffread_on_npy():
""" Test diffread() on *.npy files """
arr = np.random.random(size=(128, 128))
with tempfile.TemporaryDirectory() as tmpdir:
np.save(Path(tmpdir) / "skued_test.npy", arr)
arr2 = diffread(Path(tmpdir) / "skued_test.npy")
assert np.allclose(arr, arr2)
def raw_data(self, timedelay, scan=1, bgr=True, **kwargs):
"""
Returns an array of the image at a timedelay and scan.
Parameters
----------
timdelay : float
Acquisition time-delay.
scan : int, optional
Scan number. Default is 1.
bgr : bool, optional
If True (default), laser background is removed before being returned.
Returns
-------
arr : `~numpy.ndarray`, ndim 2
Raises
------
IOError : Filename is not associated with an image/does not exist.
"""
fname = Path(
self.source
) / f"data.nscan.{str(int(timedelay)).zfill(2)}.pumpoff.tif"
if not fname.exists():
raise IOError(
f"Expected the file {fname} to exist, but could not find it.")
im = np.asfarray(diffread(fname))
if bgr:
im -= self.background
im[im < 0] = 0
return im
def raw_data(self, timedelay, scan=1, bgr=True, **kwargs):
"""
Returns an array of the image at a timedelay and scan.
Parameters
----------
timdelay : float
Acquisition time-delay.
scan : int, optional
Scan number. Default is 1.
bgr : bool, optional
If True (default), laser background is removed before being returned.
Returns
-------
arr : `~numpy.ndarray`, ndim 2
Raises
------
ValueError : if ``timedelay`` or ``scan`` are invalid / out of bounds.
IOError : Filename is not associated with an image/does not exist.
"""
# Template filename looks like:
# 'data.timedelay.+1.00.nscan.04.pumpon.tif'
sign = "" if timedelay < 0 else "+"
str_time = sign + f"{timedelay:.2f}"
filename = ("data.timedelay." + str_time + ".nscan." +
str(scan).zfill(2) + ".pumpon.tif")
im = diffread(join(self.source, filename)).astype(np.float)
if bgr:
im -= self.background
im[im < 0] = 0
return im
def nearest_laserbg(self, timestamp):
""" Laser background taken nearest to ``timestamp`` """
fnames = {
abs(v) - timestamp: k
for (k, v) in self.timestamps.items()
if k.parent == Path("laser_background")
}
nearest_timestamp = min(fnames.keys())
return diffread(self.source / fnames[nearest_timestamp])
def nearest_dark(self, timestamp):
""" Dark image taken nearest to ``timestamp`` """
fnames = {
abs(v) - timestamp: k
for (k, v) in self.timestamps.items()
if k.parent == Path("dark_image")
}
nearest_timestamp = min(fnames.keys())
return diffread(self.source / fnames[nearest_timestamp])
def test_on_tiff(self):
""" Test diffread() on tiff files """
im = np.random.randint(0, 127, size=(512, 512))
path = Path(".\\test_tif.tif")
# Annoying low contrast warning
with suppress_warnings():
imsave(str(path), im)
from_skued = diffread(path)
self.assertTrue(np.allclose(im, from_skued))
os.remove(path)
def peakpos_evolution(file_list, mask_total, laser_bkg, FF, peakpos_all, numrefine, window_size):
peakpos_evolution = []
no_files = len(file_list)
no_peaks = np.shape(peakpos_all)[0]
for idx, f in tqdm.tqdm(enumerate(file_list)):
image = np.array(skued.diffread(f), dtype = np.int64)
#checks for saturation
#if nanmax(nanmax(Image))==65000
# msgbox(['Warning: Image ',num2str(k),' is saturated!'])
# end
#Apply mask
image = image*mask_total
#Substract background and flatfield
image = remove_bgk(image, laser_bkg, FF)
new_peakpos_all = refine_peakpos_arb_dim(peakpos_all, image, numrefine, window_size)
peakpos_evolution.append(new_peakpos_all)
peakpos_all = new_peakpos_all
peakpos_evolution = np.array(peakpos_evolution).reshape(no_files, 2*no_peaks)
return peakpos_evolution
def raw_data(self, timedelay, scan=1, bgr=True, **kwargs):
"""
Returns an array of the image at a timedelay and scan. Laser background is
removed by default.
Parameters
----------
timdelay : float
Acquisition time-delay.
scan : int, optional
Scan number. Default is 1.
bgr : bool, optional
If True (default), the laser background is removed as well.
kwargs
Extra keyword arguments are ignored.
Returns
-------
arr : `~numpy.ndarray`, ndim 2
Raises
------
ValueError : if ``timedelay`` or ``scan`` are invalid / out of bounds.
IOError : Filename is not associated with an image/does not exist.
"""
# In this case, the time-delay is the pump-off timestamp
fname = self.source / "pump_off" / f"pump_off_epoch_{timedelay:010.0f}s.tif"
if not fname.exists():
raise IOError(
f"Expected the file for {timedelay}ps and scan {scan} to exist, but could not find it."
)
im = diffread(fname)
if bgr:
dark_bg = self.nearest_dark(
timestamp=self.timestamps[fname.relative_to(self.source)])
im -= dark_bg
return im
def load_single_picture(self):
path = self.file_dialog.getOpenFileName(
parent=self,
caption="Load diffraction picture",
filter="Images (*.tif *.tiff *.mib *.dm3 *.dm4)",
)[0]
if not path:
return
self.image_viewer = pg.ImageView(parent=self)
self.image_viewer.setImage(diffread(path))
layout = QtWidgets.QVBoxLayout()
fname_label = QtWidgets.QLabel("Filename: " + path, parent=self)
fname_label.setAlignment(QtCore.Qt.AlignCenter)
layout.addWidget(fname_label)
layout.addWidget(self.image_viewer)
dialog = QtWidgets.QDialog()
dialog.setLayout(layout)
dialog.resize(0.75 * self.size())
return dialog.exec_()
def raw_data(self, timedelay, scan=1, **kwargs):
"""
Returns an array of the image at a timedelay and scan. Dark background is
always removed.
Parameters
----------
timdelay : float
Acquisition time-delay.
scan : int, optional
Scan number. Default is 1.
kwargs
Extra keyword arguments are ignored.
Returns
-------
arr : `~numpy.ndarray`, ndim 2
Raises
------
ValueError : if ``timedelay`` or ``scan`` are invalid / out of bounds.
IOError : Filename is not associated with an image/does not exist.
"""
# scan directory looks like 'scan 0132'
# Note that a glob pattern is required because every diffraction pattern
# has a timestamp in the filename.
directory = join(self.source, "scan {:04d}".format(scan))
try:
fname = next(
iglob(
join(directory,
"pumpon_{:+010.3f}ps_*.tif".format(timedelay))))
except StopIteration:
raise IOError(
"Expected the file for {t}ps and scan {s} to exist, but could not find it."
.format(t=timedelay, s=scan))
return diffread(fname)
# This code used to be part of the documentation
# and rendered with sphinx
#
# However, the phase_cross_correlation function requires
# too much memory, and so readthedocs would kill the documentation
# build. Therefore, we render the image locally instead.
import matplotlib.pyplot as plt
import numpy as np
from skimage.registration import phase_cross_correlation
from skued import diffread, shift_image
ref = diffread("Cr_1.tif")
im = diffread("Cr_2.tif")
mask = np.ones_like(ref, dtype=np.bool)
mask[0:1250, 950:1250] = False
shift = phase_cross_correlation(im, ref, reference_mask=mask)
shifted = shift_image(im, -1 * shift)
fig, ((ax1, ax2, ax3), (ax4, ax5, ax6)) = plt.subplots(nrows=2, ncols=3, figsize=(9, 6))
ax1.imshow(ref, vmin=0, vmax=200)
ax2.imshow(im, vmin=0, vmax=200)
ax3.imshow(ref - im, cmap="RdBu_r", vmin=-100, vmax=100)
ax4.imshow(mask, vmin=0, vmax=1, cmap="binary")
ax5.imshow(shifted, vmin=0, vmax=200)
ax6.imshow(ref - shifted, cmap="RdBu_r", vmin=-100, vmax=100)
for ax in (ax1, ax2, ax3, ax4, ax5, ax6):
def test_on_skimage_png(self):
""" Test the last resort of using skimage.io for pngs """
from_skimage = diffread(TEST_PNG)
self.assertTupleEqual(from_skimage.shape, (256, 256))
self.assertTrue(np.allclose(from_skimage, np.ones_like(from_skimage)))
def test_diffread_on_merlin_image_binary():
""" Test diffread() on Merlin Image Binary (.mib) """
im = diffread(TEST_MIB)
assert im.shape == (256, 256)
assert im.dtype == np.dtype(">u2")
def test_diffread_on_skimage_png():
""" Test the last resort of using skimage.io for pngs """
from_skimage = diffread(TEST_PNG)
assert from_skimage.shape == (256, 256)
assert np.allclose(from_skimage, np.ones_like(from_skimage))
def test_on_merlin_image_binary(self):
""" Test diffread() on Merlin Image Binary (.mib) """
im = diffread(TEST_MIB)
self.assertEqual(im.shape, (256, 256))
self.assertEqual(im.dtype, np.dtype(">u2"))