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toolbox.py
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toolbox.py
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from PySide6 import QtCore, QtGui, QtWidgets
from PySide6.QtCore import QObject, Signal, Slot, QAbstractTableModel, Qt
import pandas as pd
import sys
import imagej
import os
class LogTextEdit(QtWidgets.QPlainTextEdit):
def write(self, message):
if not hasattr(self, "flag"):
self.flag = False
message = message.replace('\r', '').rstrip()
if message:
method = "replace_last_line" if self.flag else "appendPlainText"
QtCore.QMetaObject.invokeMethod(self,
method,
QtCore.Qt.QueuedConnection,
QtCore.Q_ARG(str, message))
self.flag = True
else:
self.flag = False
@QtCore.Slot(str)
def replace_last_line(self, text):
cursor = self.textCursor()
cursor.movePosition(QtGui.QTextCursor.End)
cursor.select(QtGui.QTextCursor.BlockUnderCursor)
cursor.removeSelectedText()
cursor.insertBlock()
self.setTextCursor(cursor)
self.insertPlainText(text)
class PandasModel(QAbstractTableModel):
"""
Class to populate a table view with a pandas dataframe
"""
def __init__(self, data, parent=None):
QAbstractTableModel.__init__(self, parent)
self._data = data
def rowCount(self, parent=None):
return len(self._data.values)
def columnCount(self, parent=None):
return self._data.columns.size
def data(self, index, role=Qt.DisplayRole):
if index.isValid():
if role == Qt.DisplayRole:
return str(self._data.iloc[index.row()][index.column()])
return None
def headerData(self, col, orientation, role):
if orientation == Qt.Horizontal and role == Qt.DisplayRole:
return self._data.columns[col]
return None
class DFLParticleFinder(QObject):
finished = Signal()
progress = Signal(int)
def __init__(self, algorithm, project, size, threshold, IJ):
super().__init__()
self.algorithm = algorithm
self.project = project
self.size = size
self.threshold = threshold
self.IJ = IJ
@QtCore.Slot()
def run(self):
if self.algorithm == 'ComDet':
try:
self.project.call_ComDet(size = self.size, threshold = self.threshold, progress_signal=self.progress, IJ=self.IJ)
except:
print(sys.exc_info())
elif self.algorithm == 'PyStar':
try:
self.project.call_Trevor(erode_size = self.size, bg_thres = self.threshold, progress_signal=self.progress)
except:
print(sys.exc_info())
else:
pass
self.finished.emit()
return 1
class ReportWriter(QObject):
finished = Signal()
progress = Signal(int)
def __init__(self, project):
super().__init__()
self.project = project
@QtCore.Slot()
def run(self):
try:
self.project.generate_reports(progress_signal=self.progress)
except:
print(sys.exc_info())
self.finished.emit()
return 1
class LipoAssayWorker(QObject):
finished = Signal()
progress = Signal(int)
log = Signal(str)
def __init__(self, project, threshold):
super().__init__()
self.project = project
self.threshold = threshold
@QtCore.Slot()
def run(self):
try:
self.project.run_analysis(threshold=self.threshold, progress_signal=self.progress, log_signal=self.log)
except:
print(sys.exc_info())
self.finished.emit()
return 1
class SRWorker(QObject):
finished = Signal()
progress = Signal(int)
def __init__(self, job, project, IJ):
super().__init__()
self.job = job
self.project = project
self.IJ = IJ
@QtCore.Slot()
def run(self):
if self.job == 'Reconstruction':
try:
self.project.superRes_reconstruction(progress_signal=self.progress, IJ=self.IJ)
except:
print(sys.exc_info())
elif self.job == 'FiducialCorrection':
try:
self.project.superRes_fiducialCorrection(progress_signal=self.progress, IJ=self.IJ)
except:
print(sys.exc_info())
elif self.job == 'Clustering':
try:
self.project.superRes_clustering(progress_signal=self.progress)
except:
print(sys.exc_info())
else:
pass
self.finished.emit()
return 1