def _read_images(self):
"""Read diffraction patterns and save them within the object."""
#should I normalize images??
list_of_all_files = os.listdir(".")
list_of_images = [
f for f in list_of_all_files if re.search("^image_[0-9]{4}.h5$", f)
]
prefix = "."
if len(list_of_images) == 0:
# maybe this is an old run with images output in debug
list_of_all_files = os.listdir("debug")
list_of_images = [
f for f in list_of_all_files
if re.search("^image_[0-9]{4}.h5$", f)
]
prefix = "debug"
if len(list_of_images) == 0:
self.read_error.emit()
self._number_of_images = len(list_of_images)
for i in range(self._number_of_images):
try:
image, mask = sphelper.import_spimage(
"%s/image_%.4d.h5" % (prefix, i), ['image', 'mask'])
except IOError:
print "{0} is bad".format(i)
image = numpy.zeros(self._images[0].shape, dtype="float32")
mask = numpy.zeros(self._images[0].shape, dtype="int32")
self._images.append(image)
self._masks.append(mask)
def create_main_frame(self, filename):
self.main_frame = QtWidgets.QWidget()
self.image = None
self.image, self.image_center = sphelper.import_spimage(
filename, ["image", "image_center"])
x_array = numpy.arange(self.image.shape[0]) - self.image_center[0]
y_array = numpy.arange(self.image.shape[1]) - self.image_center[1]
X_array, Y_array = numpy.meshgrid(x_array, y_array)
X_array = numpy.transpose(X_array)
Y_array = numpy.transpose(Y_array)
self.r = numpy.sqrt(X_array**2 + Y_array**2)
ft = numpy.fft.fft2(self.image)
self.auto_unfiltered = numpy.fft.fftshift(abs(ft))
self.dpi = 100
self.fig = Figure((10.0, 10.0), dpi=self.dpi)
self.canvas = FigureCanvasQTAgg(self.fig)
self.canvas.setParent(self.main_frame)
self.axes = self.fig.add_subplot(111)
self.mpl_toolbar = NavigationToolbar2QT(self.canvas, self.main_frame)
self.a_slider = QtWidgets.QSlider(QtCore.Qt.Vertical)
self.a_slider.setMinimum(1)
self.a_slider.setMaximum(300)
self.a_slider.setValue(self.a)
self.a_slider.setTracking(False)
self.a_label = QtWidgets.QLabel("a = %g" % self.a)
self.a_slider.sliderMoved.connect(self.a_changed)
self.a_slider.valueChanged.connect(self.update_image)
self.filter_box = QtWidgets.QCheckBox("Use filter")
self.filter_box.stateChanged.connect(self.box_state_changed)
vbox1 = QtWidgets.QVBoxLayout()
vbox1.addWidget(self.canvas)
vbox1.addWidget(self.mpl_toolbar)
vbox2 = QtWidgets.QVBoxLayout()
vbox2.addWidget(self.a_label)
vbox2.addWidget(self.a_slider)
vbox2.addWidget(self.filter_box)
hbox = QtWidgets.QHBoxLayout()
hbox.addLayout(vbox1)
hbox.addLayout(vbox2)
self.main_frame.setLayout(hbox)
self.setCentralWidget(self.main_frame)
self.update_image()
def get_mask(self, iteration):
"""Return the mask of the 3D model as an array for the requested iteration."""
try:
if iteration >= 0:
mask = sphelper.import_spimage(
'%s_%.4d.h5' % (self._file_prefix, iteration), ['mask'])
elif iteration == -1:
mask = sphelper.import_spimage(
'%s_init.h5' % (self._file_prefix), ['mask'])
elif iteration == -2:
mask = sphelper.import_spimage(
'%s_final.h5' % (self._file_prefix), ['mask'])
except IOError:
self.read_error.emit()
return
if self._side != mask.shape[0]:
self._side = mask.shape[0]
self.properties_changed.emit()
return mask
def read_image(image_file, mask):
if mask:
field = 'mask'
else:
field = 'image'
try:
img = sphelper.import_spimage(image_file, [field])
except IOError:
raise IOError(f"{image_file} is not a readable h5 image.")
return img
def get_image(self, index, reload_data=False):
"""Get image of certain index."""
if index >= self._number_of_images:
raise ValueError("Image index out of range. %d is above %d" %
(index, self._number_of_images))
if index in self._images.keys() and not reload_data:
return abs(self._images[index])
self._images[index] = sphelper.import_spimage("image_%.4d.h5" % index,
["image"])
return abs(self._images[index])
def read_image(image_file, mask):
if mask:
field = 'mask'
else:
field = 'image'
try:
img = sphelper.import_spimage(image_file, [field])
except:
raise IOError("%s is not a readable h5 image." % image_file)
return img
def get_map(self, iteration):
"""Return the 3D model as an array for the requested iteration."""
try:
if iteration >= 0:
modelmap = sphelper.import_spimage(
'%s_%.4d.h5' % (self._file_prefix, iteration), ['image'])
elif iteration == -1:
modelmap = sphelper.import_spimage(
'%s_init.h5' % (self._file_prefix), ['image'])
elif iteration == -2:
modelmap = sphelper.import_spimage(
'%s_final.h5' % (self._file_prefix), ['image'])
except (IOError, KeyError):
self.read_error.emit()
if self._side:
return numpy.zeros((self._side, ) * 3)
else:
return numpy.zeros((10, ) * 3)
if self._side != modelmap.shape[0]:
self._side = modelmap.shape[0]
self.properties_changed.emit()
return modelmap
def _create_main_frame(self, filename):
self._main_frame = QtGui.QWidget()
self._image = None
try:
self._image = sphelper.import_spimage(filename)
except IOError:
print("Must provide a file")
exit(1)
self._dpi = 100
self._fig = Figure((10.0, 10.0), dpi=self._dpi)
self._fig.subplots_adjust(left=0., right=1., bottom=0., top=1.)
self._canvas = FigureCanvasQTAgg(self._fig)
self._canvas.setParent(self._main_frame)
self._axes = self._fig.add_subplot(111)
self._axes.set_xticks([])
self._axes.set_yticks([])
self._mpl_toolbar = NavigationToolbar2QT(self._canvas,
self._main_frame)
self._slider_length = 100
self._angle_slider = QtGui.QSlider(QtCore.Qt.Vertical)
self._angle_slider.setMinimum(0)
self._angle_slider.setMaximum(self._slider_length)
self._angle_slider.setValue(self._angle)
self._angle_slider.setTracking(True)
self._angle_label = QtGui.QLabel(
f"angle = {self._angle/numpy.pi*180.}")
self._angle_label.setFixedWidth(100)
self._angle_slider.sliderMoved.connect(self._angle_changed)
vbox1 = QtGui.QVBoxLayout()
vbox1.addWidget(self._canvas)
vbox1.addWidget(self._mpl_toolbar)
vbox2 = QtGui.QVBoxLayout()
vbox2.addWidget(self._angle_label)
vbox2.addWidget(self._angle_slider)
hbox = QtGui.QHBoxLayout()
hbox.addLayout(vbox1)
hbox.addLayout(vbox2)
self._main_frame.setLayout(hbox)
self.setCentralWidget(self._main_frame)
self._update_image()
def _read_image_and_mask(self, index):
"""Load the image and mask if they have not been viewed before."""
if index in self._images and index in self._masks:
return
prefix = "."
try:
image, mask = sphelper.import_spimage(
os.path.join(prefix, "image_{0:04}.h5".format(index)),
["image", "mask"])
except IOError:
print "Image {0} is bad".format(index)
self._images[index] = numpy.zeros(self._images[0].shape,
dtype="float64")
self._masks[index] = numpy.zeros(self._images[0].shape,
dtype="int32")
return
self._images[index] = image
self._masks[index] = mask
def plot_image(in_file, function, plot_mask, plot_log, plot_shifted):
# try:
# #img = spimage.sp_image_read(in_file,0)
image, mask = sphelper.import_spimage(in_file, ['image', 'mask'])
# except:
# raise TypeError("Error: %s is not a readable .h5 file\n" % in_file)
plot_flags = ['abs','mask','phase','real','imag']
shift_flags = ['shift']
log_flags = ['log']
plot_flag = 0
shift_flag = 0
log_flag = 0
colormap = "jet"
if function == "phase":
colormap = "hsv"
if plot_shifted:
#img = spimage.sp_image_shift(img)
image = pylab.fftshift(image)
mask = pylab.fftshift(mask)
def no_log(x):
return x
if plot_log:
log_function = pylab.log
else:
log_function = no_log
if plot_mask:
plot_input = mask
else:
plot_input = image
function_dict = {"abs" : abs, "phase" : pylab.angle, "real" : pylab.real, "imag" : pylab.imag}
pylab.imshow(log_function(function_dict[function](plot_input)), cmap=colormap, origin="lower", interpolation="nearest")
pylab.show()
def plot_image(in_file, function, plot_mask, plot_log, plot_shifted):
image, mask = sphelper.import_spimage(in_file, ['image', 'mask'])
colormap = "jet"
if function == "phase":
colormap = "hsv"
if plot_shifted:
image = numpy.fft.fftshift(image)
mask = numpy.fft.fftshift(mask)
def no_log(x):
return x
if plot_log:
log_function = numpy.log
else:
log_function = no_log
if plot_mask:
plot_input = mask
else:
plot_input = image
function_dict = {
"abs": abs,
"phase": numpy.angle,
"real": numpy.real,
"imag": numpy.imag
}
matplotlib.pyplot.imshow(log_function(function_dict[function](plot_input)),
cmap=colormap,
origin="lower",
interpolation="nearest")
matplotlib.pyplot.show()
def on_checkbox(self, state):
print(f"checkbox: {state}")
iterator = zip(self._synchronized_interactor_style,
self._single_interactor_style, self._vtk_widget)
if state:
for synchronized_style, single_style, interactor in iterator:
synchronized_style.SetInteractor(None)
single_style.SetInteractor(interactor)
else:
for synchronized_style, single_style, interactor in iterator:
single_style.SetInteractor(None)
synchronized_style.SetInteractor(interactor)
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument("volume", nargs="+")
args = parser.parse_args()
volumes = [
sphelper.import_spimage(volume_file, ["image"])
for volume_file in args.volume
]
app = QtWidgets.QApplication(["eke_plot_multiple_3d.py"])
program = MainWindow(volumes)
program.show()
program.initialize()
sys.exit(app.exec_())
layout.addLayout(plot_layout)
layout.addWidget(self._surface_slider)
vtk_tools.synchronize_renderers(self._renderer)
self._central_widget.setLayout(layout)
self.setCentralWidget(self._central_widget)
@staticmethod
def _value_calculator(ratio):
return ratio
def initialize(self):
for vtk_widget in self._vtk_widget:
vtk_widget.Initialize()
for renderer in self._renderer:
renderer.Render()
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument("volume", nargs="+")
args = parser.parse_args()
volumes = [sphelper.import_spimage(volume_file, ["image"]) for volume_file in args.volume]
app = QtGui.QApplication(["eke_plot_multiple_3d.py"])
program = MainWindow(volumes)
program.show()
program.initialize()
sys.exit(app.exec_())
def _create_main_frame(self, filename):
self._main_frame = QtGui.QWidget()
self._image = None
self._image = numpy.complex128(sphelper.import_spimage(filename))
self._image = crop_to_square(self._image)
if self._crop is None:
self._crop = min(self._image.shape)
if self._crop > min(self._image.shape):
self._image = embedd_image(self._image, pad=self._crop)
else:
self._image = embedd_image(self._image)
self._image = embedd_image(self._image)
self._x = numpy.fft.fftshift(
(numpy.arange(self._image.shape[0]) - self._image.shape[0] / 2 +
0.5) / self._image.shape[0])[numpy.newaxis, :]
self._y = numpy.fft.fftshift(
(numpy.arange(self._image.shape[1]) - self._image.shape[1] / 2 +
0.5) / self._image.shape[1])[:, numpy.newaxis]
self._dpi = 100
self._fig = Figure((10.0, 10.0), dpi=self._dpi)
self._fig.subplots_adjust(left=0., right=1., bottom=0., top=1.)
self._canvas = FigureCanvasQTAgg(self._fig)
self._canvas.setParent(self._main_frame)
self._axes = self._fig.add_subplot(111)
self._axes.set_xticks([])
self._axes.set_yticks([])
self._mpl_toolbar = NavigationToolbar2QT(self._canvas,
self._main_frame)
self._slider_length = 1000
self._angle_slider = QtGui.QSlider(QtCore.Qt.Vertical)
self._angle_slider.setMinimum(0)
self._angle_slider.setMaximum(self._slider_length)
self._angle_slider.setValue(self._angle / 360. * self._slider_length)
self._angle_slider.setTracking(True)
self._angle_slider.valueChanged.connect(self._angle_changed)
self._angle_label = QtGui.QLabel(
f"angle = {self._angle/numpy.pi*180.}")
self._angle_label.setFixedWidth(100)
self._split_slider = QtGui.QSlider(QtCore.Qt.Vertical)
self._split_slider.setMinimum(0)
self._split_slider.setMaximum(self._slider_length)
self._split_slider.setValue(self._split / self._max_split *
self._slider_length)
self._split_slider.setTracking(True)
self._split_slider.valueChanged.connect(self._split_changed)
self._split_label = QtGui.QLabel("split = %g" % (self._split))
self._split_label.setFixedWidth(100)
self._phase_slider = QtGui.QSlider(QtCore.Qt.Vertical)
self._phase_slider.setMinimum(0)
self._phase_slider.setMaximum(self._slider_length)
self._phase_slider.setValue(self._phase / 360. * self._slider_length)
self._phase_slider.setTracking(True)
self._phase_slider.valueChanged.connect(self._phase_changed)
self._phase_label = QtGui.QLabel(
f"phase = {self._phase/numpy.pi*180.}")
self._phase_label.setFixedWidth(100)
vbox1 = QtGui.QVBoxLayout()
vbox1.addWidget(self._canvas)
vbox1.addWidget(self._mpl_toolbar)
vbox2 = QtGui.QVBoxLayout()
vbox2.addWidget(self._angle_label)
vbox2.addWidget(self._angle_slider)
vbox3 = QtGui.QVBoxLayout()
vbox3.addWidget(self._split_label)
vbox3.addWidget(self._split_slider)
vbox4 = QtGui.QVBoxLayout()
vbox4.addWidget(self._phase_label)
vbox4.addWidget(self._phase_slider)
hbox = QtGui.QHBoxLayout()
hbox.addLayout(vbox1)
hbox.addLayout(vbox2)
hbox.addLayout(vbox3)
hbox.addLayout(vbox4)
self._main_frame.setLayout(hbox)
self.setCentralWidget(self._main_frame)
self._update_image()
