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import numpy as np
import h5py
import cv2 as cv
import algotom.rec.reconstruction as rec
import algotom.prep.filtering as filt
import h5py
import pvaccess as pva
channel_name = 'test'
import os
from superqt import QLabeledRangeSlider, QLabeledDoubleSlider, QLabeledSlider
#filepath2x = r"/raid-ssd/CT/2024/2024_03/Markoetter/W-sphere/00009_W-sphere_8___Z155_Y3500_35000eV_2x_100ms/240326_111109_00001.h5"
#filepath10x = r"/raid-ssd/CT/2024/2024_03/Markoetter/W-sphere/00011_W-sphere_8___Z155_Y3500_35000eV_10x_100ms/240326_112852_00001.h5"
#file = h5py.File(filepath2x,'r')
import sys
from PyQt5.QtCore import QSize, Qt
from PyQt5.QtWidgets import QApplication, QMainWindow, QPushButton, QSlider, QGridLayout, QWidget, QLabel, QFileDialog, QCheckBox, QDoubleSpinBox, QSpinBox
from PyQt5 import QtCore, QtGui
# Subclass QMainWindow to customize your application's main window
class MainWindow(QMainWindow):
def __init__(self):
super(MainWindow, self).__init__()
self.setWindowTitle("My App")
layout = QGridLayout()
self.load_button = QPushButton("Load hdf5")
self.usedprojslider = QLabeledRangeSlider(QtCore.Qt.Orientation.Horizontal)
self.usedprojslider.setMinimum(0)
self.labelproj = QLabel('Proj')
self.usedFFslider = QLabeledRangeSlider(QtCore.Qt.Orientation.Horizontal)
self.usedFFslider.setMinimum(0)
self.usedFFslider.setValue((0,20))
self.labelFF = QLabel('FF')
self.CORslider = QLabeledDoubleSlider(QtCore.Qt.Orientation.Horizontal)
self.CORslider.setMaximum(2000)
self.CORslider.setValue(1247)
self.labelCOR = QLabel('COR')
self.sliceslider = QLabeledSlider(QtCore.Qt.Orientation.Vertical)
self.filtering_checkbox = QCheckBox("Fresnel filter")
self.filtering_ratio = QDoubleSpinBox()
self.filtering_ratio.setMaximum(1)
self.filtering_ratio.setMinimum(0)
self.downsample_checkbox = QCheckBox("Down-sampling")
self.downsample_slider = QLabeledRangeSlider(QtCore.Qt.Orientation.Horizontal)
self.downsample_spinbox_high = QSpinBox()
self.labeldown_high = QLabel('High sampling')
self.downsample_spinbox_low = QSpinBox()
self.labeldown_low = QLabel('Low sampling')
# Set the central widget of the Window.
self.button = QPushButton("Send Reco")
layout.addWidget(self.usedprojslider,0,0)
layout.addWidget(self.labelproj,0,1)
layout.addWidget(self.usedFFslider,1,0)
layout.addWidget(self.labelFF, 1, 1)
layout.addWidget(self.CORslider,2,0)
layout.addWidget(self.labelCOR, 2, 1)
layout.addWidget(self.button,3,0)
layout.addWidget(self.load_button,3,1)
layout.addWidget(self.sliceslider,4,0,1,2)
layout.addWidget(self.filtering_checkbox,5,0)
layout.addWidget(self.filtering_ratio,5,1)
layout.addWidget(self.downsample_checkbox,6,0)
layout.addWidget(self.downsample_slider,7,0,1,2)
layout.addWidget(self.labeldown_high, 8, 0)
layout.addWidget(self.downsample_spinbox_high, 8, 1)
layout.addWidget(self.labeldown_low, 8, 2)
layout.addWidget(self.downsample_spinbox_low, 8,3)
self.filtering_ratio.hide()
self.downsample_slider.hide()
self.labeldown_low.hide()
self.labeldown_high.hide()
self.downsample_spinbox_high.hide()
self.downsample_spinbox_low.hide()
widget = QWidget()
widget.setLayout(layout)
self.setCentralWidget(widget)
pva_image_dict = {'value': ({'booleanValue': [pva.pvaccess.ScalarType.BOOLEAN], 'byteValue':
[pva.pvaccess.ScalarType.BYTE], 'shortValue': [pva.pvaccess.ScalarType.SHORT], 'intValue':
[pva.pvaccess.ScalarType.INT], 'longValue': [pva.pvaccess.ScalarType.LONG],
'ubyteValue':
[pva.pvaccess.ScalarType.UBYTE],
'ushortValue': [pva.pvaccess.ScalarType.USHORT], 'uintValue':
[pva.pvaccess.ScalarType.UINT], 'ulongValue': [pva.pvaccess.ScalarType.ULONG],
'floatValue':
[pva.pvaccess.ScalarType.FLOAT],
'doubleValue': [pva.pvaccess.ScalarType.DOUBLE]},), 'codec':
{'name': pva.pvaccess.ScalarType.STRING, 'parameters': ()}, 'compressedSize':
pva.pvaccess.ScalarType.LONG, 'uncompressedSize': pva.pvaccess.ScalarType.LONG,
'dimension':
[{'size': pva.pvaccess.ScalarType.INT, 'offset': pva.pvaccess.ScalarType.INT, 'fullSize':
pva.pvaccess.ScalarType.INT, 'binning': pva.pvaccess.ScalarType.INT, 'reverse':
pva.pvaccess.ScalarType.BOOLEAN}], 'uniqueId': pva.pvaccess.ScalarType.INT,
'dataTimeStamp':
{'secondsPastEpoch': pva.pvaccess.ScalarType.LONG,
'nanoseconds': pva.pvaccess.ScalarType.INT,
'userTag': pva.pvaccess.ScalarType.INT}, 'attribute':
[{'name': pva.pvaccess.ScalarType.STRING, 'value': (),
'descriptor': pva.pvaccess.ScalarType.STRING,
'sourceType': pva.pvaccess.ScalarType.INT, 'source': pva.pvaccess.ScalarType.STRING}],
'descriptor':
pva.pvaccess.ScalarType.STRING,
'alarm': {'severity': pva.pvaccess.ScalarType.INT, 'status':
pva.pvaccess.ScalarType.INT, 'message': pva.pvaccess.ScalarType.STRING}, 'timeStamp':
{'secondsPastEpoch': pva.pvaccess.ScalarType.LONG,
'nanoseconds': pva.pvaccess.ScalarType.INT, 'userTag':
pva.pvaccess.ScalarType.INT},
'display': {'limitLow': pva.pvaccess.ScalarType.DOUBLE, 'limitHigh':
pva.pvaccess.ScalarType.DOUBLE, 'description': pva.pvaccess.ScalarType.STRING, 'format':
pva.pvaccess.ScalarType.STRING, 'units': pva.pvaccess.ScalarType.STRING}}
self.pv_rec = pva.PvObject(pva_image_dict)
self.pvaServer = pva.PvaServer(channel_name, self.pv_rec)
self.pvaServer.start()
self.new = True
self.usedprojslider.valueChanged.connect(self.slice_changed)
self.usedFFslider.valueChanged.connect(self.slice_changed)
self.button.clicked.connect(self.send_reco)
self.sliceslider.valueChanged.connect(self.slice_changed)
self.load_button.clicked.connect(self.load_file)
self.filtering_checkbox.toggled.connect(self.filter_show)
self.downsample_checkbox.toggled.connect(self.downsample_show)
self.downsample_slider.valueChanged.connect(self.slice_changed)
def load_file(self):
path_klick = QFileDialog.getOpenFileName(self, 'Select hdf5-file, please.', r"/raid-ssd/CT/2024/2024_03/Markoetter/ISM_F/")
if path_klick[0]:
print(path_klick[0])
self.file = h5py.File(path_klick[0],'r')
self.usedprojslider.setMaximum(self.file['entry/data/data'].shape[0])
self.usedprojslider.setValue((80, self.file['entry/data/data'].shape[0]))
self.usedFFslider.setMaximum(self.file['entry/data/data'].shape[0])
self.sliceslider.setMaximum(self.file['entry/data/data'].shape[1])
print('file loaded')
else:
print("User cancelled the dialog.")
def filter_show(self):
if self.filtering_checkbox.isChecked():
self.filtering_ratio.show()
else:
self.filtering_ratio.hide()
def downsample_show(self):
if self.downsample_checkbox.isChecked():
self.downsample_slider.show()
self.labeldown_low.show()
self.labeldown_high.show()
self.downsample_spinbox_high.show()
self.downsample_spinbox_low.show()
else:
self.downsample_slider.hide()
self.labeldown_low.hide()
self.labeldown_high.hide()
self.downsample_spinbox_high.hide()
self.downsample_spinbox_low.hide()
def slice_changed(self):
self.new = True
self.downsample_slider.setMinimum(self.usedprojslider.value()[0])
self.downsample_slider.setMaximum(self.usedprojslider.value()[1])
def create_indices_list(self):
self.selected_indices = []
for i in range(self.usedprojslider.value()[0], self.usedprojslider.value()[1] + 1):
if self.downsample_slider.value()[0] <= i <= self.downsample_slider.value()[1]:
# Inside slider values, select every xth index
if (i - self.downsample_slider.value()[0]) % self.downsample_spinbox_high.value() == 0:
self.selected_indices.append(i)
else:
# Outside slider values, select every yth index
if i < self.downsample_slider.value()[0]:
if (self.downsample_slider.value()[0] - i) % self.downsample_spinbox_low.value() == 0:
self.selected_indices.append(i)
else:
if (i - self.downsample_slider.value()[1]) % self.downsample_spinbox_low.value() == 0:
self.selected_indices.append(i)
def send_reco(self):
if self.new:
print('loading new data')
if self.downsample_checkbox.isChecked():
print('using downsampling')
self.create_indices_list()
self.proj = self.file['entry/data/data'][self.selected_indices,
self.sliceslider.value(), :]
self.angles = np.radians(self.file['entry/instrument/NDAttributes/SAMPLE_MICOS_W2'][self.selected_indices])
print('using ', self.angles.shape, ' angles')
else:
print('loading everything')
self.proj = self.file['entry/data/data'][self.usedprojslider.value()[0]:self.usedprojslider.value()[1],
self.sliceslider.value(), :]
self.angles = np.radians(self.file['entry/instrument/NDAttributes/SAMPLE_MICOS_W2']
[self.usedprojslider.value()[0]:self.usedprojslider.value()[1]])
print('using ', self.angles.shape, ' angles')
self.ff = np.mean(self.file['entry/data/data'][self.usedFFslider.value()[0]:self.usedFFslider.value()[1],self.sliceslider.value(),:],axis=0)
self.norm = np.divide(self.proj,self.ff)
self.new = False
if self.filtering_checkbox.isChecked():
print('filtering')
self.norm_final = filt.fresnel_filter(self.norm, self.filtering_ratio.value(), dim=1)
else:
self.norm_final = self.norm
print('reconstructing')
self.original_reconstruction = rec.fbp_reconstruction(self.norm_final, self.CORslider.value(),angles=self.angles,
gpu=True,
apply_log=True)
self.pv_rec['dimension'] = [
{'size': self.original_reconstruction.shape[1], 'fullSize': self.original_reconstruction.shape[1], 'binning': 1},
{'size': self.original_reconstruction.shape[0], 'fullSize': self.original_reconstruction.shape[0], 'binning': 1}]
self.pv_rec['value'] = ({'floatValue': self.original_reconstruction.flatten()},)
print('reco done')
app = QApplication(sys.argv)
window = MainWindow()
window.show()
app.exec()Editor is loading...
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