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start.py
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start.py
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# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'seriesLoadWidget.ui'
#
# Created by: PyQt5 UI code generator 5.7.1
#
# WARNING! All changes made in this file will be lost!
from datetime import datetime
import json
import numpy
import os
import sys
from PyQt5 import QtCore, QtGui, QtWidgets
from skimage import io
from skimage.transform import warp
from sqlalchemy import create_engine
from sqlalchemy.exc import OperationalError
from sqlalchemy.orm import sessionmaker
from pyrecon.classes.transform import get_skimage_transform
from pyrecon.tools.reconstruct_reader import process_series_directory
from pyrecon.tools.reconstruct_writer import write_series
from pyrecon.tools.mergetool import backend
MERGETOOL_DIR = "mergetool"
DB_FILENAME = "{project_name}.db"
JSON_FILENAME = "{project_name}.json"
def get_db_session():
database_uri = os.environ["SQLALCHEMY_DATABASE_URI"]
engine = create_engine(database_uri, echo=False)
session = sessionmaker(bind=engine)()
return session
def init_mergetool_project(series_path_list):
""" Initializes the mergetool project environment.
* Creates relevant files/directories if needed
* Sets SQLALCHEMY_DATABASE_URI to the db file
"""
main_series_path = series_path_list[0] if os.path.isdir(series_path_list[0]) \
else os.path.dirname(series_path_list[0])
mergetool_dir = os.path.join(main_series_path, MERGETOOL_DIR)
if not os.path.exists(mergetool_dir):
os.makedirs(mergetool_dir)
project_name = os.path.basename(main_series_path)
# Make DB file
db_fn = DB_FILENAME.format(project_name=project_name)
db_fp = os.path.join(mergetool_dir, db_fn)
with open(db_fp, 'a'):
os.utime(db_fp, None)
os.environ["SQLALCHEMY_DATABASE_URI"] = "sqlite:///{}".format(db_fp)
session = get_db_session()
engine = session.get_bind()
try:
engine.execute("SELECT * FROM contours LIMIT 1")
except OperationalError:
backend.create_database(engine)
# Make JSON file
json_fn = JSON_FILENAME.format(project_name=project_name)
json_fp = os.path.join(mergetool_dir, json_fn)
with open(json_fp, 'a'):
os.utime(json_fp, None)
os.environ["MERGETOOL_JSON_FILEPATH"] = json_fp
def start_database(series_path_list, app):
db_session = get_db_session()
splash_pix = QtGui.QPixmap('loading2.gif')
splash = QtWidgets.QSplashScreen(splash_pix, QtCore.Qt.WindowStaysOnTopHint)
progressBar = QtWidgets.QProgressBar(splash)
progressBar.setMinimum(0)
splash.setMask(splash_pix.mask())
splash.show()
i = 0
progressBar.setValue(i)
# Load series from series_path_list
print (series_path_list)
series_list = []
for series_path in series_path_list:
series_path = series_path if os.path.isdir(series_path) \
else os.path.dirname(series_path)
series_list.append(process_series_directory(series_path, data_check=True))
# Assign "Main" Series (one with ideal alignment)
main_series_path = series_path_list[0] if os.path.isdir(series_path_list[0]) \
else os.path.dirname(series_path_list[0])
progressBar.setMaximum(len((series_list[0]).sections) + 6)
i = 1
progressBar.setValue(i)
app.processEvents()
# Load each Series' contours into the database
section_indices = set()
for series in series_list:
section_indices.update(series.sections.keys())
for series_number, series in enumerate(series_list):
for section_index in section_indices:
section = series.sections.get(section_index)
if section:
# Load Section contours into database and determine matches
backend.load_db_contours_from_pyrecon_section(db_session, section, series_number)
i = 2
progressBar.setValue(i)
app.processEvents()
# Find matches
for section_index in section_indices:
i = 2 + (section_index)
progressBar.setValue(i)
app.processEvents()
db_contours = backend.query_all_contours_in_section(db_session, section_index).all()
backend.load_db_contourmatches_from_db_contours_and_pyrecon_series_list(
db_session,
db_contours,
series_list
)
i += 1
progressBar.setValue(i)
app.processEvents()
backend.cleanup_redundant_matches(db_session)
i += 1
progressBar.setValue(i)
app.processEvents()
# Generate payload for frontend
series_matches = backend.prepare_frontend_payload(db_session, series_list)
i += 1
progressBar.setValue(i)
app.processEvents()
with open(os.environ["MERGETOOL_JSON_FILEPATH"], "w") as f:
json.dump(series_matches, f)
i += 1
progressBar.setValue(i)
app.processEvents()
splash.close()
return series_matches
def write_merged_series(series_dict, series_name=None):
db_session = get_db_session()
to_keep = backend.get_output_contours_from_series_dict(
db_session, series_dict["sections"])
series_path_list = []
for path in series_dict["series"]:
path = path if os.path.isdir(path) else os.path.dirname(path)
series_path_list.append(path)
new_series = backend.create_output_series(db_session, to_keep, series_path_list,
series_name=series_name)
merged_fp = series_path_list[0] + "/{}/".format(MERGETOOL_DIR)
write_series(new_series, merged_fp, sections=True, overwrite=False)
return True
def write_realigned_log(series_dict):
potential_realigned = []
for _, section in series_dict["sections"].items():
for group in section["potential_realigned"]:
for contour in group:
if contour["keepBool"]:
realigned_kept = "{}.{}".format(
contour["section"],
contour["name"]
)
potential_realigned.append(realigned_kept)
if potential_realigned:
path = series_dict["series"][0]
path = path if os.path.isdir(path) else os.path.dirname(path)
realigned_log = path + "/{}/realigned.log".format(MERGETOOL_DIR)
with open(realigned_log, "w") as f:
f.write("\n".join(realigned_log))
class Ui_RestoreDialog(object):
def setupUi(self, RestoreDialog):
RestoreDialog.setObjectName("RestoreDialog")
RestoreDialog.resize(406, 330)
self.verticalLayoutWidget = QtWidgets.QWidget(RestoreDialog)
self.verticalLayoutWidget.setGeometry(QtCore.QRect(9, 9, 381, 311))
self.verticalLayoutWidget.setObjectName("verticalLayoutWidget")
self.verticalLayout = QtWidgets.QVBoxLayout(self.verticalLayoutWidget)
self.verticalLayout.setContentsMargins(0, 0, 0, 0)
self.verticalLayout.setObjectName("verticalLayout")
self.welcomeLabel = QtWidgets.QLabel(self.verticalLayoutWidget)
self.welcomeLabel.setScaledContents(False)
self.welcomeLabel.setWordWrap(True)
self.welcomeLabel.setObjectName("welcomeLabel")
self.verticalLayout.addWidget(self.welcomeLabel)
self.buttonBox = QtWidgets.QDialogButtonBox(self.verticalLayoutWidget)
self.buttonBox.setOrientation(QtCore.Qt.Horizontal)
self.buttonBox.setStandardButtons(QtWidgets.QDialogButtonBox.No|QtWidgets.QDialogButtonBox.Yes)
self.buttonBox.setObjectName("buttonBox")
self.verticalLayout.addWidget(self.buttonBox)
self.retranslateUi(RestoreDialog)
#restoring from json
self.buttonBox.accepted.connect(RestoreDialog.yesClicked)
#not restoring from json
self.buttonBox.rejected.connect(RestoreDialog.noClicked)
QtCore.QMetaObject.connectSlotsByName(RestoreDialog)
def retranslateUi(self, RestoreDialog):
_translate = QtCore.QCoreApplication.translate
RestoreDialog.setWindowTitle(_translate("RestoreDialog", "pyRECONSTRUCT"))
self.welcomeLabel.setText(_translate("RestoreDialog", "Welcome to pyRECONSTRUCT! Are you restoring your session from a mergetool JSON file?"))
class RestoreDialog(QtWidgets.QDialog):
def __init__(self):
super(RestoreDialog, self).__init__()
self.ui = Ui_RestoreDialog()
self.ui.setupUi(self)
self.reload = False
self.restoreBool = True
self.fileList = []
self.jsonFile = None
self.exec_()
def yesClicked(self):
""" Restoring from a previous session.
"""
self.ui.selectSessionLabel = QtWidgets.QLabel(self.ui.verticalLayoutWidget)
self.ui.selectSessionLabel.setObjectName("selectSessionLabel")
self.ui.verticalLayout.addWidget(self.ui.selectSessionLabel)
self.ui.horizontalLayout = QtWidgets.QHBoxLayout()
self.ui.horizontalLayout.setObjectName("horizontalLayout")
self.ui.lineEdit = QtWidgets.QLineEdit(self.ui.verticalLayoutWidget)
self.ui.lineEdit.setObjectName("lineEdit")
self.ui.lineEdit.setReadOnly(True)
self.ui.horizontalLayout.addWidget(self.ui.lineEdit)
self.ui.browseButton = QtWidgets.QPushButton(self.ui.verticalLayoutWidget)
self.ui.browseButton.setObjectName("browseButton")
self.ui.browseButton.clicked.connect(self.loadJson)
self.ui.horizontalLayout.addWidget(self.ui.browseButton)
self.ui.verticalLayout.addLayout(self.ui.horizontalLayout)
#load or cancel the .json file
self.ui.buttonBox_2 = QtWidgets.QDialogButtonBox(self.ui.verticalLayoutWidget)
self.ui.buttonBox_2.setStandardButtons(QtWidgets.QDialogButtonBox.Cancel|QtWidgets.QDialogButtonBox.Ok)
self.ui.buttonBox_2.setObjectName("buttonBox_2")
self.ui.verticalLayout.addWidget(self.ui.buttonBox_2)
#load the json file
self.ui.buttonBox_2.accepted.connect(self.close)
#cancel the .json load: just reload restore dialog
self.ui.buttonBox_2.rejected.connect(self.cancelClicked)
self.ui.buttonBox_2.rejected.connect(self.close)
self.ui.selectSessionLabel.setText(
"Please select the mergetool JSON file.")
self.ui.browseButton.setText("Browse...")
#clicking yes starts the Main Window with the given dictionary
self.ui.welcomeLabel.close()
self.ui.buttonBox.close()
def noClicked(self):
""" Not restoring from a previous session.
"""
self.restoreBool = False
self.close()
def loadJson(self):
fileName = QtWidgets.QFileDialog.getOpenFileName(
self, "Open Series", "/home/", "Json File (*.json)")
self.ui.lineEdit.setText(str(fileName[0]))
self.jsonFile = fileName[0]
self.fileList = [fileName[0]]
def returnFileList(self):
return self.fileList
def cancelClicked(self):
self.close()
class Ui_loadDialog(object):
def setupUi(self, loadDialog):
loadDialog.setObjectName("loadDialog")
loadDialog.resize(400, 300)
self.verticalLayoutWidget = QtWidgets.QWidget(loadDialog)
self.verticalLayoutWidget.setGeometry(QtCore.QRect(10, 10, 381, 281))
self.verticalLayoutWidget.setObjectName("verticalLayoutWidget")
self.verticalLayout = QtWidgets.QVBoxLayout(self.verticalLayoutWidget)
self.verticalLayout.setContentsMargins(0, 0, 0, 0)
self.verticalLayout.setObjectName("verticalLayout")
self.verticalLayout_2 = QtWidgets.QVBoxLayout()
self.verticalLayout_2.setObjectName("verticalLayout_2")
self.gridLayout = QtWidgets.QGridLayout()
self.gridLayout.setObjectName("gridLayout")
self.verticalLayout_3 = QtWidgets.QVBoxLayout()
self.verticalLayout_3.setObjectName("verticalLayout_3")
self.welcomeLabel = QtWidgets.QLabel(self.verticalLayoutWidget)
self.welcomeLabel.setMaximumSize(QtCore.QSize(16777215, 20))
self.welcomeLabel.setObjectName("welcomeLabel")
self.verticalLayout_3.addWidget(self.welcomeLabel)
self.horizontalLayout_3 = QtWidgets.QHBoxLayout()
self.horizontalLayout_3.setObjectName("horizontalLayout_3")
self.loadLineEdit = QtWidgets.QLineEdit(self.verticalLayoutWidget)
self.loadLineEdit.setObjectName("loadLineEdit")
self.loadLineEdit.setReadOnly(True)
self.horizontalLayout_3.addWidget(self.loadLineEdit)
self.loadSeriesButton = QtWidgets.QPushButton(self.verticalLayoutWidget)
self.loadSeriesButton.setObjectName("loadSeriesButton")
self.horizontalLayout_3.addWidget(self.loadSeriesButton)
self.verticalLayout_3.addLayout(self.horizontalLayout_3)
self.gridLayout.addLayout(self.verticalLayout_3, 0, 0, 1, 1)
self.addSeriesButton = QtWidgets.QPushButton(self.verticalLayoutWidget)
self.addSeriesButton.setObjectName("addSeriesButton")
self.gridLayout.addWidget(self.addSeriesButton, 1, 0, 1, 1)
self.verticalLayout_2.addLayout(self.gridLayout)
self.verticalLayout.addLayout(self.verticalLayout_2)
self.horizontalLayout_4 = QtWidgets.QHBoxLayout()
self.horizontalLayout_4.setObjectName("horizontalLayout_4")
self.cancelButton = QtWidgets.QPushButton(self.verticalLayoutWidget)
self.cancelButton.setObjectName("cancelButton")
self.horizontalLayout_4.addWidget(self.cancelButton)
self.selectButton = QtWidgets.QPushButton(self.verticalLayoutWidget)
self.selectButton.setObjectName("selectButton")
self.horizontalLayout_4.addWidget(self.selectButton)
self.verticalLayout.addLayout(self.horizontalLayout_4)
self.retranslateUi(loadDialog)
self.loadSeriesButton.clicked.connect(loadDialog.loadSeries)
self.cancelButton.clicked.connect(loadDialog.close)
self.selectButton.clicked.connect(loadDialog.startMainWindow)
self.addSeriesButton.clicked.connect(loadDialog.addSeries)
QtCore.QMetaObject.connectSlotsByName(loadDialog)
def retranslateUi(self, loadDialog):
_translate = QtCore.QCoreApplication.translate
loadDialog.setWindowTitle(_translate("loadDialog", "Dialog"))
self.welcomeLabel.setText(_translate(
"loadDialog", "Welcome to pyRECONSTRUCT! Please select a series."))
self.addSeriesButton.setText(_translate("loadDialog", "Add Series..."))
self.loadSeriesButton.setText(_translate("loadDialog", "Load Series..."))
self.cancelButton.setText(_translate("loadDialog", "Cancel"))
self.selectButton.setText(_translate("loadDialog", "Import Series"))
class loadJsonSeriesDialog(QtWidgets.QDialog):
def __init__(self, jsonFile):
super(loadJsonSeriesDialog, self).__init__()
self.jsonFile = jsonFile
self.ui = Ui_loadJsonSeriesDialog()
self.ui.setupUi(self)
self.counter = 5
self.fileList = []
json_data = json.load(open(self.jsonFile))
for i, path in enumerate(json_data["series"]):
if i == 0:
path_input = getattr(self.ui, 'loadLineEdit')
else:
self.addSeries()
path_input = getattr(self.ui, 'loadLineEdit_{}'.format(self.counter))
path_input.setText(path)
self.exec_()
def loadSeries(self):
# NOTE: for some reason this is never being called
fileName = QtWidgets.QFileDialog.getOpenFileName(
self, "Open Series", "/home/", "Series File (*.ser)")
if fileName != None:
if (self.sender().objectName() == 'loadSeriesButton'):
self.ui.loadLineEdit.setText(str(fileName[0]))
else:
number = (self.sender().objectName())[-1]
getattr(self.ui, 'loadLineEdit_'+str(self.counter)).setText(str(fileName[0]))
self.fileList.append(str(fileName[0]))
def addSeries(self):
self.counter += 1
setattr(self.ui, 'horizontalLayout_'+str(self.counter), QtWidgets.QHBoxLayout())
setattr(self.ui, 'loadLineEdit_'+str(self.counter), QtWidgets.QLineEdit(self.ui.verticalLayoutWidget))
getattr(self.ui, 'loadLineEdit_'+str(self.counter)).setReadOnly(True)
getattr(self.ui, 'horizontalLayout_'+str(self.counter)).addWidget(getattr(self.ui, 'loadLineEdit_'+str(self.counter)))
setattr(self.ui, 'loadSeriesButton'+str(self.counter),QtWidgets.QPushButton(self.ui.verticalLayoutWidget))
getattr(self.ui, 'horizontalLayout_'+str(self.counter)).addWidget(getattr(self.ui, 'loadSeriesButton'+str(self.counter)))
getattr(self.ui, 'loadSeriesButton'+str(self.counter)).setText("Load Series...")
getattr(self.ui, 'loadSeriesButton'+str(self.counter)).setObjectName('loadSeriesButton'+str(self.counter))
getattr(self.ui, 'loadSeriesButton'+str(self.counter)).clicked.connect(self.loadSeries)
self.ui.verticalLayoutWidget.setGeometry(QtCore.QRect(10, 10, 381, 281+(30*(self.counter - 5))))
self.resize(400, 300 + (30*(self.counter - 5)))
self.ui.verticalLayout_3.addLayout(getattr(self.ui, 'horizontalLayout_'+str(self.counter)))
def startMainWindow(self):
if (len(self.fileList) > 1):
alignSelection = MultipleSeriesDialog(self.fileList)
if (alignSelection.result() == 0):
pass
elif (alignSelection.result() == 1):
newFileList = alignSelection.returnFileList()
self.fileList = newFileList
self.close()
class Ui_loadJsonSeriesDialog(object):
def setupUi(self, loadJsonSeriesDialog):
loadJsonSeriesDialog.setObjectName("loadJsonSeriesDialog")
loadJsonSeriesDialog.resize(400, 300)
self.verticalLayoutWidget = QtWidgets.QWidget(loadJsonSeriesDialog)
self.verticalLayoutWidget.setGeometry(QtCore.QRect(10, 10, 381, 281))
self.verticalLayoutWidget.setObjectName("verticalLayoutWidget")
self.verticalLayout = QtWidgets.QVBoxLayout(self.verticalLayoutWidget)
self.verticalLayout.setContentsMargins(0, 0, 0, 0)
self.verticalLayout.setObjectName("verticalLayout")
self.verticalLayout_2 = QtWidgets.QVBoxLayout()
self.verticalLayout_2.setObjectName("verticalLayout_2")
self.gridLayout = QtWidgets.QGridLayout()
self.gridLayout.setObjectName("gridLayout")
self.verticalLayout_3 = QtWidgets.QVBoxLayout()
self.verticalLayout_3.setObjectName("verticalLayout_3")
self.welcomeLabel = QtWidgets.QLabel(self.verticalLayoutWidget)
self.welcomeLabel.setMaximumSize(QtCore.QSize(16777215, 20))
self.welcomeLabel.setObjectName("welcomeLabel")
self.verticalLayout_3.addWidget(self.welcomeLabel)
self.horizontalLayout_3 = QtWidgets.QHBoxLayout()
self.horizontalLayout_3.setObjectName("horizontalLayout_3")
self.loadLineEdit = QtWidgets.QLineEdit(self.verticalLayoutWidget)
self.loadLineEdit.setObjectName("loadLineEdit")
self.loadLineEdit.setReadOnly(True)
self.horizontalLayout_3.addWidget(self.loadLineEdit)
self.loadSeriesButton = QtWidgets.QPushButton(self.verticalLayoutWidget)
self.loadSeriesButton.setObjectName("loadSeriesButton")
self.horizontalLayout_3.addWidget(self.loadSeriesButton)
self.verticalLayout_3.addLayout(self.horizontalLayout_3)
self.gridLayout.addLayout(self.verticalLayout_3, 0, 0, 1, 1)
self.addSeriesButton = QtWidgets.QPushButton(self.verticalLayoutWidget)
self.addSeriesButton.setObjectName("addSeriesButton")
self.gridLayout.addWidget(self.addSeriesButton, 1, 0, 1, 1)
self.verticalLayout_2.addLayout(self.gridLayout)
self.verticalLayout.addLayout(self.verticalLayout_2)
self.horizontalLayout_4 = QtWidgets.QHBoxLayout()
self.horizontalLayout_4.setObjectName("horizontalLayout_4")
self.cancelButton = QtWidgets.QPushButton(self.verticalLayoutWidget)
self.cancelButton.setObjectName("cancelButton")
self.horizontalLayout_4.addWidget(self.cancelButton)
self.selectButton = QtWidgets.QPushButton(self.verticalLayoutWidget)
self.selectButton.setObjectName("selectButton")
self.horizontalLayout_4.addWidget(self.selectButton)
self.verticalLayout.addLayout(self.horizontalLayout_4)
self.retranslateUi(loadJsonSeriesDialog)
self.loadSeriesButton.clicked.connect(loadJsonSeriesDialog.loadSeries)
self.cancelButton.clicked.connect(loadJsonSeriesDialog.close)
self.selectButton.clicked.connect(loadJsonSeriesDialog.startMainWindow)
self.addSeriesButton.clicked.connect(loadJsonSeriesDialog.addSeries)
QtCore.QMetaObject.connectSlotsByName(loadJsonSeriesDialog)
def retranslateUi(self, loadJsonSeriesDialog):
_translate = QtCore.QCoreApplication.translate
loadJsonSeriesDialog.setWindowTitle(_translate("loadJsonSeriesDialog", "Dialog"))
self.welcomeLabel.setText(_translate(
"loadJsonSeriesDialog",
("Please locate the series used in this .json file. "
"Import the series in the same order used originally.")
))
self.addSeriesButton.setText(_translate("loadJsonSeriesDialog", "Add Series..."))
self.loadSeriesButton.setText(_translate("loadJsonSeriesDialog", "Load Series..."))
self.cancelButton.setText(_translate("loadJsonSeriesDialog", "Cancel"))
self.selectButton.setText(_translate("loadJsonSeriesDialog", "Import Series"))
class loadDialog(QtWidgets.QDialog):
def __init__(self):
super(loadDialog, self).__init__()
self.ui = Ui_loadDialog()
self.ui.setupUi(self)
self.counter = 5
self.fileList = []
self.exec_()
def loadSeries(self):
fileName = QtWidgets.QFileDialog.getOpenFileName(self, "Open Series", "/home/",
"Series File (*.ser)")
if fileName != None:
if (self.sender().objectName() == 'loadSeriesButton'):
self.ui.loadLineEdit.setText(str(fileName[0]))
else:
number = (self.sender().objectName())[-1]
getattr(self.ui, 'loadLineEdit_'+str(self.counter)).setText(str(fileName[0]))
self.fileList.append(str(fileName[0]))
def addSeries(self):
self.counter += 1
setattr(self.ui, 'horizontalLayout_'+str(self.counter), QtWidgets.QHBoxLayout())
setattr(self.ui, 'loadLineEdit_'+str(self.counter), QtWidgets.QLineEdit(self.ui.verticalLayoutWidget))
getattr(self.ui, 'loadLineEdit_'+str(self.counter)).setReadOnly(True)
getattr(self.ui, 'horizontalLayout_'+str(self.counter)).addWidget(getattr(self.ui, 'loadLineEdit_'+str(self.counter)))
setattr(self.ui, 'loadSeriesButton'+str(self.counter),QtWidgets.QPushButton(self.ui.verticalLayoutWidget))
getattr(self.ui, 'horizontalLayout_'+str(self.counter)).addWidget(getattr(self.ui, 'loadSeriesButton'+str(self.counter)))
getattr(self.ui, 'loadSeriesButton'+str(self.counter)).setText("Load Series...")
getattr(self.ui, 'loadSeriesButton'+str(self.counter)).setObjectName('loadSeriesButton'+str(self.counter))
getattr(self.ui, 'loadSeriesButton'+str(self.counter)).clicked.connect(self.loadSeries)
self.ui.verticalLayoutWidget.setGeometry(QtCore.QRect(10, 10, 381, 281+(30*(self.counter - 5))))
self.resize(400, 300 + (30*(self.counter - 5)))
self.ui.verticalLayout_3.addLayout(getattr(self.ui, 'horizontalLayout_'+str(self.counter)))
def startMainWindow(self):
if (len(self.fileList) > 1):
alignSelection = MultipleSeriesDialog(self.fileList)
if (alignSelection.result() == 0):
pass
elif (alignSelection.result() == 1):
self.fileList = alignSelection.returnFileList()
self.close()
class Ui_MultipleSeriesDialog(object):
def setupUi(self, MultipleSeriesDialog, fileList):
MultipleSeriesDialog = MultipleSeriesDialog
MultipleSeriesDialog.setObjectName("MultipleSeriesDialog")
MultipleSeriesDialog.resize(400, 300)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Preferred)
MultipleSeriesDialog.setSizePolicy(sizePolicy)
self.verticalLayoutWidget = QtWidgets.QWidget(MultipleSeriesDialog)
self.verticalLayoutWidget.setGeometry(QtCore.QRect(9, 0, 381, 291))
self.verticalLayoutWidget.setObjectName("verticalLayoutWidget")
self.verticalLayout = QtWidgets.QVBoxLayout(self.verticalLayoutWidget)
self.verticalLayout.setSizeConstraint(QtWidgets.QLayout.SetNoConstraint)
self.verticalLayout.setContentsMargins(0, 0, 0, 0)
self.verticalLayout.setObjectName("verticalLayout")
self.questionLabel = QtWidgets.QLabel(self.verticalLayoutWidget)
font = QtGui.QFont()
font.setPointSize(16)
self.questionLabel.setFont(font)
self.questionLabel.setWordWrap(True)
self.questionLabel.setObjectName("questionLabel")
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Preferred)
self.questionLabel.setSizePolicy(sizePolicy)
self.verticalLayout.addWidget(self.questionLabel)
self.horizontalLayout = QtWidgets.QHBoxLayout()
self.horizontalLayout.setObjectName("horizontalLayout")
self.horizontalLayout.setSizeConstraint(QtWidgets.QLayout.SetNoConstraint)
self.noButton = QtWidgets.QPushButton(self.verticalLayoutWidget)
self.noButton.setObjectName("noButton")
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Fixed)
self.noButton.setSizePolicy(sizePolicy)
self.horizontalLayout.addWidget(self.noButton)
self.yesButton = QtWidgets.QPushButton(self.verticalLayoutWidget)
self.yesButton.setObjectName("yesButton")
self.yesButton.setSizePolicy(sizePolicy)
self.horizontalLayout.addWidget(self.yesButton)
self.verticalLayout.addLayout(self.horizontalLayout)
self.noButton.clicked.connect(MultipleSeriesDialog.close)
self.yesButton.clicked.connect(MultipleSeriesDialog.yesClicked)
self.retranslateUi(MultipleSeriesDialog)
QtCore.QMetaObject.connectSlotsByName(MultipleSeriesDialog)
def retranslateUi(self, MultipleSeriesDialog):
_translate = QtCore.QCoreApplication.translate
MultipleSeriesDialog.setWindowTitle(_translate("MultipleSeriesDialog", "Dialog"))
self.questionLabel.setText(_translate("MultipleSeriesDialog", "You have selected multiple series. Do these series have differing alignments or attributes?"))
self.noButton.setText(_translate("MultipleSeriesDialog", "No"))
self.yesButton.setText(_translate("MultipleSeriesDialog", "Yes"))
class MultipleSeriesDialog(QtWidgets.QDialog):
def __init__(self, fileList):
super(MultipleSeriesDialog, self).__init__()
#self.setResult(0)
self.ui = Ui_MultipleSeriesDialog()
self.ui.setupUi(self, fileList)
self.fileList = fileList
self.exec_()
def yesClicked(self):
self.setResult(1)
self.ui.question2Label = QtWidgets.QLabel(self.ui.verticalLayoutWidget)
self.ui.question2Label.setText("Which series/alignment would you like to output to?")
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Fixed)
self.ui.question2Label.setSizePolicy(sizePolicy)
self.ui.question2Label.setObjectName("question2Label")
self.ui.verticalLayout.addWidget(self.ui.question2Label)
self.ui.verticalLayout_5 = QtWidgets.QVBoxLayout()
self.ui.verticalLayout_5.setSizeConstraint(QtWidgets.QLayout.SetNoConstraint)
self.ui.verticalLayout_5.setObjectName("verticalLayout_5")
for i in range (len(self.fileList)):
setattr(self.ui, 'horizontalLayout_'+str(i), QtWidgets.QHBoxLayout())
setattr(self.ui, 'series'+str(i)+'button', QtWidgets.QRadioButton(self.ui.verticalLayoutWidget))
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Preferred)
getattr(self.ui, 'series'+str(i)+'button').setSizePolicy(sizePolicy)
getattr(self.ui, 'series'+str(i)+'button').setMinimumSize(QtCore.QSize(0, 20))
getattr(self.ui, 'series'+str(i)+'button').setText("")
getattr(self.ui, 'horizontalLayout_'+str(i)).addWidget(getattr(self.ui, 'series'+str(i)+'button'))
setattr(self.ui,'lineEdit'+str(i), QtWidgets.QLineEdit(self.ui.verticalLayoutWidget))
getattr(self.ui,'lineEdit'+str(i)).setReadOnly(True)
getattr(self.ui, 'horizontalLayout_'+str(i)).addWidget(getattr(self.ui,'lineEdit'+str(i)))
getattr(self.ui, 'horizontalLayout_'+str(i)).setStretch(1,20)
self.ui.verticalLayout_5.addWidget(getattr(self.ui, 'series'+str(i)+'button'))
getattr(self.ui,'lineEdit'+str(i)).setText(str(self.fileList[i]))
self.ui.verticalLayout_5.addLayout(getattr(self.ui, 'horizontalLayout_'+str(i)))
self.ui.verticalLayoutWidget.setGeometry(QtCore.QRect(10, 10, 381, 281+(50*(i-1))))
self.resize(400, 300 + (50*(i - 1)))
self.ui.verticalLayout.addLayout(self.ui.verticalLayout_5)
#whatever
self.ui.buttonBox_2 = QtWidgets.QDialogButtonBox(self.ui.verticalLayoutWidget)
self.ui.buttonBox_2.setOrientation(QtCore.Qt.Horizontal)
self.ui.buttonBox_2.setStandardButtons(QtWidgets.QDialogButtonBox.Cancel|QtWidgets.QDialogButtonBox.Ok)
self.ui.buttonBox_2.accepted.connect(self.seriesSelected)
self.ui.buttonBox_2.rejected.connect(self.close)
self.ui.buttonBox_2.setObjectName("buttonBox_2")
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Fixed)
self.ui.buttonBox_2.setSizePolicy(sizePolicy)
self.ui.verticalLayout.addWidget(self.ui.buttonBox_2)
def seriesSelected(self):
for i in range (len(self.fileList)):
if getattr(self.ui, 'series'+str(i)+'button').isChecked():
self.fileList.insert(0, self.fileList.pop(i))
self.accept()
break
else:
continue
def returnFileList(self):
return self.fileList
class Ui_MainWindow(object):
def setupUi(self, MainWindow):
MainWindow.setObjectName("MainWindow")
MainWindow.resize(761, 551)
self.centralwidget = QtWidgets.QWidget(MainWindow)
self.centralwidget.setObjectName("centralwidget")
self.gridLayoutWidget = QtWidgets.QWidget(self.centralwidget)
self.gridLayoutWidget.setGeometry(QtCore.QRect(10, 0, 371, 501))
self.gridLayoutWidget.setObjectName("gridLayoutWidget")
self.gridLayout = QtWidgets.QGridLayout(self.gridLayoutWidget)
self.gridLayout.setContentsMargins(0, 0, 0, 0)
self.gridLayout.setObjectName("gridLayout")
self.verticalLayout_2 = QtWidgets.QVBoxLayout()
self.verticalLayout_2.setObjectName("verticalLayout_2")
self.unresolvedLabel = QtWidgets.QLabel(self.gridLayoutWidget)
font = QtGui.QFont()
font.setFamily("Helvetica")
self.unresolvedLabel.setFont(font)
self.unresolvedLabel.setObjectName("unresolvedLabel")
self.verticalLayout_2.addWidget(self.unresolvedLabel)
self.legendLabel1 = QtWidgets.QLabel(self.gridLayoutWidget)
self.legendLabel1.setFont(font)
self.legendLabel1.setObjectName("legendLabel1")
self.verticalLayout_2.addWidget(self.legendLabel1)
self.unresolvedView = QtWidgets.QListView(self.gridLayoutWidget)
self.unresolvedModel = QtGui.QStandardItemModel(self.unresolvedView)
self.unresolvedView.setModel(self.unresolvedModel)
self.unresolvedView.setEditTriggers(QtWidgets.QAbstractItemView.NoEditTriggers)
self.unresolvedView.setSelectionMode(QtWidgets.QAbstractItemView.ExtendedSelection)
self.unresolvedView.setContextMenuPolicy(QtCore.Qt.CustomContextMenu)
self.unresolvedView.customContextMenuRequested.connect(MainWindow.unresolvedMenu)
self.unresolvedView.setObjectName("unresolvedView")
self.verticalLayout_2.addWidget(self.unresolvedView)
self.resolveButton = QtWidgets.QPushButton(self.gridLayoutWidget)
self.resolveButton.setObjectName("resolveButton")
self.verticalLayout_2.addWidget(self.resolveButton)
self.transferLeftButton = QtWidgets.QPushButton(self.gridLayoutWidget)
self.transferLeftButton.setObjectName("transferLeftButton")
self.verticalLayout_2.addWidget(self.transferLeftButton)
self.viewAllButton = QtWidgets.QPushButton(self.gridLayoutWidget)
self.viewAllButton.setObjectName("viewAllButton")
self.verticalLayout_2.addWidget(self.viewAllButton)
self.transferAllButton = QtWidgets.QPushButton(self.gridLayoutWidget)
self.transferAllButton.setObjectName("transferAllButton")
self.verticalLayout_2.addWidget(self.transferAllButton)
self.gridLayout.addLayout(self.verticalLayout_2, 0, 0, 1, 1)
self.gridLayoutWidget_2 = QtWidgets.QWidget(self.centralwidget)
self.gridLayoutWidget_2.setGeometry(QtCore.QRect(390, 0, 371, 501))
self.gridLayoutWidget_2.setObjectName("gridLayoutWidget_2")
self.gridLayout_2 = QtWidgets.QGridLayout(self.gridLayoutWidget_2)
self.gridLayout_2.setContentsMargins(0, 0, 0, 0)
self.gridLayout_2.setObjectName("gridLayout_2")
self.verticalLayout = QtWidgets.QVBoxLayout()
self.verticalLayout.setObjectName("verticalLayout")
self.resolvedLabel = QtWidgets.QLabel(self.gridLayoutWidget_2)
font = QtGui.QFont()
font.setFamily("Helvetica")
self.resolvedLabel.setFont(font)
self.resolvedLabel.setObjectName("resolvedLabel")
self.verticalLayout.addWidget(self.resolvedLabel)
self.legendLabel2 = QtWidgets.QLabel(self.gridLayoutWidget_2)
self.legendLabel2.setFont(font)
self.legendLabel2.setObjectName("legendLabel2")
self.verticalLayout.addWidget(self.legendLabel2)
self.resolvedView = QtWidgets.QListView(self.gridLayoutWidget_2)
self.resolvedModel = QtGui.QStandardItemModel(self.resolvedView)
self.resolvedView.setModel(self.resolvedModel)
self.resolvedView.setEditTriggers(QtWidgets.QAbstractItemView.NoEditTriggers)
self.resolvedView.setSelectionMode(QtWidgets.QAbstractItemView.ExtendedSelection)
self.resolvedView.setObjectName("resolvedView")
self.verticalLayout.addWidget(self.resolvedView)
self.transferRightButton = QtWidgets.QPushButton(self.gridLayoutWidget_2)
self.transferRightButton.setObjectName("transferRightButton")
self.verticalLayout.addWidget(self.transferRightButton)
self.horizontalLayout = QtWidgets.QHBoxLayout()
self.horizontalLayout.setObjectName("horizontalLayout")
self.saveStatusButton = QtWidgets.QPushButton(self.gridLayoutWidget_2)
self.saveStatusButton.setObjectName("saveStatusButton")
self.horizontalLayout.addWidget(self.saveStatusButton)
self.completeButton = QtWidgets.QPushButton(self.gridLayoutWidget_2)
self.completeButton.setObjectName("completeButton")
self.horizontalLayout.addWidget(self.completeButton)
self.verticalLayout.addLayout(self.horizontalLayout)
self.gridLayout_2.addLayout(self.verticalLayout, 0, 0, 1, 1)
MainWindow.setCentralWidget(self.centralwidget)
self.statusbar = QtWidgets.QStatusBar(MainWindow)
self.statusbar.setObjectName("statusbar")
MainWindow.setStatusBar(self.statusbar)
self.actionSave_Resolutions = QtWidgets.QAction(MainWindow)
self.actionSave_Resolutions.setObjectName("actionSave_Resolutions")
self.actionResolve_all_Left = QtWidgets.QAction(MainWindow)
self.actionResolve_all_Left.setObjectName("actionResolve_all_Left")
self.actionResolve_all_Right = QtWidgets.QAction(MainWindow)
self.actionResolve_all_Right.setObjectName("actionResolve_all_Right")
self.actionTransfer_all = QtWidgets.QAction(MainWindow)
self.actionTransfer_all.setObjectName("actionTransfer_all")
self.actionView_All = QtWidgets.QAction(MainWindow)
self.actionView_All.setObjectName("actionView_All")
self.actionExit = QtWidgets.QAction(MainWindow)
self.actionExit.setObjectName("actionExit")
self.retranslateUi(MainWindow)
self.resolveButton.clicked.connect(MainWindow.loadResolveLeft)
self.transferAllButton.clicked.connect(MainWindow.transferAllRight)
self.transferLeftButton.clicked.connect(MainWindow.transferFromLeft)
self.transferRightButton.clicked.connect(MainWindow.transferFromRight)
self.viewAllButton.clicked.connect(MainWindow.viewAll)
self.completeButton.clicked.connect(MainWindow.saveSeries)
self.actionSave_Resolutions.triggered.connect(MainWindow.saveSeries)
self.saveStatusButton.clicked.connect(MainWindow.saveSeries)
self.actionExit.triggered.connect(MainWindow.close)
self.actionTransfer_all.triggered.connect(MainWindow.transferAllRight)
self.actionView_All.triggered.connect(MainWindow.viewAll)
QtCore.QMetaObject.connectSlotsByName(MainWindow)
def retranslateUi(self, MainWindow):
_translate = QtCore.QCoreApplication.translate
MainWindow.setWindowTitle(_translate("MainWindow", "MainWindow"))
self.unresolvedLabel.setText(_translate("MainWindow", "Unresolved Traces"))
self.legendLabel1.setText(_translate("MainWindow", "red - potential duplicate, orange - potential realignment"))
self.legendLabel2.setText(_translate("MainWindow", "yellow - auto resolved, green - unique"))
self.resolveButton.setText(_translate("MainWindow", "Resolve Selected (one-by-one)"))
self.transferLeftButton.setText(_translate("MainWindow", "Transfer Selected (without resolving) >>"))
self.viewAllButton.setText(_translate("MainWindow", "Resolve All (one-by-one)"))
self.transferAllButton.setText(_translate("MainWindow", "Transfer All (without resolving) >>"))
self.resolvedLabel.setText(_translate("MainWindow", "User/Auto-resolved & Unique Traces"))
self.transferRightButton.setText(_translate("MainWindow", "<< Transfer Selected (keep resolution)"))
self.actionSave_Resolutions.setText(_translate("MainWindow", "Save Resolutions"))
self.actionResolve_all_Left.setText(_translate("MainWindow", "Resolve All (Left)"))
self.actionResolve_all_Right.setText(_translate("MainWindow", "Resolve All (Right)"))
self.actionTransfer_all.setText(_translate("MainWindow", "Transfer All"))
self.actionView_All.setText(_translate("MainWindow", "View All"))
self.saveStatusButton.setText(_translate("MainWindow", "Save Merge Session"))
self.completeButton.setText(_translate("MainWindow", "Output Merge Series"))
self.actionExit.setText(_translate("MainWindow", "Exit"))
class MainWindow(QtWidgets.QMainWindow):
def __init__(self, data, fileList):
super(MainWindow, self).__init__()
self.fileList = fileList
self.ui = Ui_MainWindow()
self.ui.setupUi(self)
self.initializeDataset(data)
def initializeDataset(self, data):
# Convert string keys to ints
data = {int(k): v for k,v in data["sections"].items()}
for section_index, matches in data.items():
# Potential duplicates
potential_matches = matches["potential"]
if len(potential_matches) > 0:
for j in range (0, len(potential_matches)):
potential_data = potential_matches[j]
unresolvedItem = QtGui.QStandardItem(potential_matches[j][0]["name"])
unresolvedItem.setData(potential_data)
unresolvedItem.setText(
str(section_index)+"."+str(potential_data[0]["name"]))
if potential_data[0].get("side"):
if potential_data[0]["side"] == ("L"):
self.ui.unresolvedModel.appendRow(unresolvedItem)
elif potential_data[0]["side"] == ("R"):
self.ui.resolvedModel.appendRow(unresolvedItem)
else:
self.ui.unresolvedModel.appendRow(unresolvedItem)
unresolvedItem.setBackground(QtGui.QColor('red'))
# Potential realigned duplicates
pot_realigned_matches = matches["potential_realigned"]
if len(pot_realigned_matches) > 0:
for j in range (0, len(pot_realigned_matches)):
unresolvedItem = QtGui.QStandardItem(pot_realigned_matches[j][0]["name"])
pot_realigned_data = pot_realigned_matches[j]
unresolvedItem.setData(pot_realigned_data)
unresolvedItem.setText(
str(section_index)+"."+str(pot_realigned_data[0]["name"]))
if pot_realigned_data[0].get("side"):
if pot_realigned_data[0]["side"] == ("L"):
self.ui.unresolvedModel.appendRow(unresolvedItem)
elif pot_realigned_data[0]["side"] == ("R"):
self.ui.resolvedModel.appendRow(unresolvedItem)
else:
self.ui.unresolvedModel.appendRow(unresolvedItem)
unresolvedItem.setBackground(QtGui.QColor('orange'))
# Exact duplicates
exact_matches = matches["exact"]
if len(exact_matches) > 0:
for j in range(0, len(exact_matches)):
resolvedItem = QtGui.QStandardItem(exact_matches[j][0]["name"])
exact_data = exact_matches[j]
resolvedItem.setData(exact_data)
resolvedItem.setText(str(section_index)+"."+str(exact_data[0]["name"]))
if exact_data[0].get("side"):
if exact_data[0]["side"] == ("L"):
self.ui.unresolvedModel.appendRow(resolvedItem)
elif exact_data[0]["side"] == ("R"):
self.ui.resolvedModel.appendRow(resolvedItem)
else:
self.ui.resolvedModel.appendRow(resolvedItem)
resolvedItem.setBackground(QtGui.QColor('yellow'))
# Unique contours
unique_matches = matches["unique"]
if len(unique_matches) > 0:
for j in range (0, len(unique_matches)):
resolvedItem = QtGui.QStandardItem(unique_matches[j][0]["name"])
unique_data = unique_matches[j]
resolvedItem.setData(unique_data)
resolvedItem.setText(
str(section_index)+"."+str(unique_data[0]["name"]))
if unique_data[0].get("side"):
if unique_data[0]["side"] == ("L"):
self.ui.unresolvedModel.appendRow(resolvedItem)
elif unique_data[0]["side"] == ("R"):
self.ui.resolvedModel.appendRow(resolvedItem)
else:
self.ui.resolvedModel.appendRow(resolvedItem)
resolvedItem.setBackground(QtGui.QColor('green'))
self.ui.unresolvedView.doubleClicked.connect(self.loadResolveLeft)
self.ui.resolvedView.doubleClicked.connect(self.loadResolveRight)
def loadSeries(self):
pass
def transferAllRight(self):
rowCount = self.ui.unresolvedModel.rowCount()
for idx in range (0, rowCount):
indexObj = self.ui.unresolvedModel.index(0, 0)
selectedItem = self.ui.unresolvedModel.itemFromIndex(indexObj)
self.ui.unresolvedModel.takeRow(0)
self.ui.resolvedModel.appendRow(selectedItem)
self.ui.resolvedView.update()
self.ui.unresolvedView.update()
def transferFromLeft(self):
selected = self.ui.unresolvedView.selectedIndexes()
rowNumbers = []
for idx in selected:
rowNumbers.append(idx.row())
oldIndex = 0
rowNumbers = sorted(rowNumbers)
for i in range (len(rowNumbers)):
indexObj = self.ui.unresolvedModel.index(rowNumbers[i] - oldIndex, 0)
selectedItem = self.ui.unresolvedModel.itemFromIndex(indexObj)
self.ui.unresolvedModel.takeRow(rowNumbers[i] - oldIndex)
self.ui.resolvedModel.appendRow(selectedItem)
oldIndex +=1
self.ui.resolvedView.update()
self.ui.unresolvedView.update()
def transferFromRight(self):
selected = self.ui.resolvedView.selectedIndexes()
rowNumbers = []
for idx in selected:
rowNumbers.append(idx.row())
oldIndex = 0
rowNumbers = sorted(rowNumbers)
for i in range (len(rowNumbers)):
indexObj = self.ui.resolvedModel.index(rowNumbers[i] - oldIndex, 0)
selectedItem = self.ui.resolvedModel.itemFromIndex(indexObj)
self.ui.resolvedModel.takeRow(rowNumbers[i] - oldIndex)
self.ui.unresolvedModel.appendRow(selectedItem)
oldIndex +=1
self.ui.resolvedView.update()
self.ui.unresolvedView.update()
def viewAll(self):
for idx in range (0, self.ui.unresolvedModel.rowCount()):
nextItemIndex = self.ui.unresolvedModel.index(0, 0)
nextItem = self.ui.unresolvedModel.itemFromIndex(nextItemIndex)
resolution = resolveDialog(nextItem)
resoMarker = resolution.DialogCode()
if resoMarker:
self.ui.unresolvedModel.takeRow(0)
self.ui.resolvedModel.appendRow(nextItem)
self.ui.resolvedView.update()
self.ui.unresolvedView.update()
def saveSeries(self):
outputDict = {
"series": self.fileList,
"sections": {}
}
outputDict["sections"]["0"] = {
"potential_realigned": [],
"unique": [],
"potential": [],
"exact": [],
"section": 0
}
for idx in range (0, self.ui.unresolvedModel.rowCount()):
nextItemIndex = self.ui.unresolvedModel.index(idx, 0)
nextItem = self.ui.unresolvedModel.itemFromIndex(nextItemIndex)
nextItemSection = nextItem.data()[0]["section"]
nextItemData = nextItem.data()
nextItemData[0]["side"] = "L"
nextItem.setData(nextItemData)
next_section = str(nextItemSection)
if outputDict["sections"].get(next_section):
if (nextItem.background().color().name()) == "#ff0000":
outputDict["sections"][next_section]["potential"].append(
nextItem.data())
elif (nextItem.background().color().name()) == "#ffa500":
outputDict["sections"][next_section]["potential_realigned"].append(
nextItem.data())