def execute(self, settings: Settings) -> bool:
self.loadSetiings(settings)
if self.exec() != QDialog.Accepted:
return False
self.saveSetiings(settings)
settings.write()
return True
def pack(args: Namespace) -> None:
settings = Settings.from_env()
projects: list[str]
if args.all:
librarian = Librarian(settings)
projects = librarian.get_expanded_epubs().get(args.type, [])
else:
projects = args.projects
if len(projects) > 0:
print("Packing projects...")
packer = Packer(settings)
packer.pack_projects(projects, args.type, args.compression)
def build(args: Namespace) -> None:
settings = Settings.from_env()
projects: list[str]
if args.all:
librarian = Librarian(settings)
projects = librarian.get_projects()
else:
projects = args.projects
if len(projects) > 0:
print("Building projects...")
builder = Builder(settings)
builder.build_projects(projects, args.type, args.bundles)
def main() -> None:
default_settings = Settings()
installer = Installer(default_settings)
installer.install_epubcheck()
project_types = sorted(
path.name
for path in default_settings.expanded_epubs_directory.iterdir()
if path.is_dir())
for project_type in project_types:
pack_all(default_settings, project_type)
check_all(default_settings, project_type)
release(default_settings, project_type)
summary_file = summarize(default_settings)
release_summary(summary_file)
def check(args: Namespace) -> None:
settings = Settings.from_env()
if args.install:
print("Installing EPUBCheck...")
installer = Installer(settings)
installer.install_epubcheck()
projects: list[str]
if args.all:
librarian = Librarian(settings)
projects = librarian.get_packaged_epubs().get(args.type, [])
else:
projects = args.projects
if len(projects) > 0:
print("Checking projects...")
checker = Checker(settings)
checker.check_projects(projects, args.type)
def sync(args: Namespace) -> None:
settings = Settings.from_env()
new_books: list[str] = []
projects: list[str]
if args.all:
librarian = Librarian(settings)
projects = librarian.get_packaged_epubs().get(args.type, [])
else:
projects = args.projects
for project in projects:
epub_project = EPUBProject(Path(settings.projects_directory, project))
metadata = epub_project.epub_metadata
search_terms: list[str] = []
search_terms.append(f"title:\"={metadata.title}\"")
for creator_name, creator_roles in metadata.creators.items():
if not creator_roles or "aut" in creator_roles:
search_terms.append(f"author:\"={creator_name}\"")
search_expression = " ".join(search_terms)
book_ids = calibredb.search(search_expression,
with_library=args.with_library,
username=args.username,
password=args.password,
timeout=args.timeout)
ebook_file = Path(settings.packaged_epubs_directory, args.type,
f"{project}.{args.type}.epub").as_posix()
if not book_ids:
new_books.append(ebook_file)
elif len(book_ids) == 1:
a = calibredb.add_format(book_ids[0],
ebook_file,
with_library=args.with_library,
username=args.username,
password=args.password,
timeout=args.timeout)
print(a)
else:
print(f"Skipping {project} due to ambiguous metadata")
if new_books:
calibredb.add(new_books,
with_library=args.with_library,
username=args.username,
password=args.password,
timeout=args.timeout)
def __init__(self):
self.title = u'Tracks detection'
# Настройки
self.settings = Settings()
class Application:
def __init__(self):
self.title = u'Tracks detection'
# Настройки
self.settings = Settings()
def application_init(self):
'''Инициализация Qt приложения'''
# Создание приложение
self.qapp = QApplication(sys.argv)
self.__app_working_status = True
# Установка локлизатора
translator = QTranslator(self.qapp)
translator.load('lang/tr_ru', os.path.dirname(__file__))
self.qapp.installTranslator(translator)
self.mainDialog = MainDialog(self, self.title)
self.mainDialog.closeApp.connect(self.__finalize_before_quit)
self.controls = {
'step': ['X', 'Y', 'Z', 'A'],
'servo': ['B', 'C'],
'pins': {
'P1': [],
'P2': ['UV', 'VIS']
}
}
self.mainDialog.show()
self.project_init()
self.gui_init()
self.communication_init()
sys.exit(self.qapp.exec_())
def __finalize_before_quit(self):
self.__app_working_status = False
if self.grbl.connection: self.grbl.connection.close()
if self.communication_thread: self.communication_thread.join()
self.qapp.exit()
def retuenicon(self, name):
return QIcon(
QPixmap(
os.path.normpath(
os.path.join(os.path.dirname(os.path.realpath(__file__)),
'', name + '.png'))))
def project_init(self):
self.project = Project('New')
def async_sleep(self, sleep):
for i in range(sleep):
time.sleep(1)
if not self.__app_working_status: break
def __connection_worker(self):
while self.__app_working_status:
status = self.__current_conacion_procedure()
if status: break
if status:
self.__current_conacion_procedure = self.grbl.getStatus
else:
self.__current_conacion_procedure = self.__auto_seach__
self.async_sleep(5)
self.cnc_indicator.setStatus(status)
def communication_init(self):
self.grbl = GRBL(HOST=self.settings.grblip)
self.__current_conacion_procedure = self.__auto_seach__
self.communication_thread = threading.Thread(
target=self.__connection_worker)
self.communication_thread.setDaemon(True)
self.communication_thread.start()
def gui_init(self):
pref_menu = menu_item(u'Preferences')
ref_menu = menu_item(u'Reference')
gen_menu = menu_item(u'Device')
gen_menu.addChildren(menu_item(u'GRBL', self.showGrblDialog))
file_menu = menu_item(self.qapp.tr(u'File'))
file_menu.addChildren(menu_item(u'New', self.newProject),
menu_item(u'Open', self.openProject),
menu_item(u'Import...', self.openFile),
menu_item(u'Save', self.saveProject),
menu_item(u'Exit', self.qapp.exit))
pref_menu.addChildren(gen_menu, menu_item(u'Settings'))
ref_menu.addChildren(menu_item(u'Help'),
menu_item(u'About', self.showAbout))
self.mainDialog.addMenuItems(file_menu, pref_menu, ref_menu)
self.cnc_indicator = work_indicator(u'CNC')
self.mainDialog.addStatusObj(self.cnc_indicator)
self.progressBar = QProgressBar()
self.progressBar.setTextVisible(True)
self.progressBar.setAlignment(Qt.AlignCenter)
self.progressBar.minimum = 1
self.progressBar.maximum = 100
self.mainDialog.addPermanentStatusObj(self.progressBar)
'''Инициализациия таблицы содержания'''
treeDock = QDockWidget(self.qapp.tr(u'Project tree'), self.mainDialog)
treeDock.setAllowedAreas(Qt.LeftDockWidgetArea
| Qt.RightDockWidgetArea)
self.mainDialog.addDockWidget(Qt.LeftDockWidgetArea, treeDock)
self.mainnodes = [Node("Samples"), Node("Other")]
self.project_tree = ProjectTree(self, self.mainnodes)
self.project_tree.doubleClicked.connect(self.on_tree_clicked)
treeDock.setWidget(self.project_tree)
'''Инициализациия центра'''
jog = JogWidget(app=self.qapp,
axies=self.controls,
pinAcions=self.pinAcions,
motorActions=self.send_to_grbl)
self.mainDialog.addToCenter(jog)
jog.raise_()
def send_to_grbl(self, text, send_type):
if len(text):
self.grbl.send_task(text, send_type)
def pinAcions(self, status, pin):
task = 'M62 {pin}'.format(pin=pin) if status else 'M63 {pin}'.format(
pin=pin)
self.grbl.send_task(task, SENDTYPE.IDLE)
def setProgress(self, step, steps):
value = step / float(len(steps)) * 100.
indx = int(ceil(step - 1))
text = self.qapp.tr(steps[indx])
self.progressBar.setFormat("{0} - {1}%".format(text, round(value, 0)))
self.progressBar.setValue(value)
self.qapp.processEvents()
def on_tree_clicked(self, index):
item = self.project_tree.selectedIndexes()[0]
if self.project.current_sample != item.model().itemFromIndex(
index).obj:
self.project.current_sample = item.model().itemFromIndex(index).obj
self.refresh()
def newProject(self):
self.mainDialog.PreparedArea.clear()
self.mainDialog.ThroughArea.clear()
self.mainDialog.BacklightArea.clear()
self.mainnodes = [Node("Samples"), Node("Other")]
self.project_tree.setMainNodes(self.mainnodes)
self.project = Project('TEMP')
self.refresh()
def openProject(self):
fileName, _ = QFileDialog.getOpenFileName(
self.mainDialog, self.qapp.tr("Load project"), ".\\",
self.qapp.tr("Project file (*.tpr)"))
infile = open(fileName, 'rb')
self.project = pickle.load(infile)
infile.close()
self.mainDialog.PreparedArea.clear()
self.mainDialog.ThroughArea.clear()
self.mainDialog.BacklightArea.clear()
self.mainnodes = [Node("Samples"), Node("Other")]
self.project_tree.setMainNodes(self.mainnodes)
self.refresh()
def saveProject(self):
fileName, _ = QFileDialog.getSaveFileName(
self.mainDialog, self.qapp.tr("Save project"), ".\\",
self.qapp.tr("Project file (*.tpr)"))
outfile = open(fileName, "wb")
pickle.dump(self.project, outfile)
outfile.close()
def draw_tree(self):
target = self.mainnodes[0]
children = target.children()
samples_in_tree = []
for sample in self.project.samples.get_sorted_by_id():
if len(children) > 0:
samples_in_tree = [node.obj for node in children]
if sample not in samples_in_tree:
target.addChild(Node(sample))
self.project_tree.refresh()
def openFile(self):
path_to_file, _ = QFileDialog.getOpenFileName(
self.mainDialog, self.qapp.tr("Load Image"),
self.qapp.tr(u".\example_imgs"), self.qapp.tr("Images (*.jpg)"))
# path_to_file, _ = QFileDialog.getOpenFileName(self.mainDialog, self.app.tr("Load Image"), self.app.tr("~/Desktop/"), self.app.tr("Images (*.jpg)"))
# Определяем тип файла на просвет или на подсветку
tools.processing(path_to_file, self.project, self.separator,
self.segmentation, self.counter, self.setProgress)
self.refresh()
def refresh(self):
self.draw_tree()
self.fill_table()
self.updete_viewers()
def fill_table(self):
data = []
sample = self.project.current_sample
if not sample:
data = [['', '', '']]
self.mainDialog.tablemodel.setData(data)
return
for track in sample.tracks.get_sorted():
data.append([str(track.id), str(track.count), str(track.area)])
self.mainDialog.tablemodel.setData(data)
self.mainDialog.table.resizeRowsToContents()
self.mainDialog.table.resizeColumnsToContents()
count = round(
np.sum([track.count
for track in sample.tracks.get_sorted_by_id()]), 2)
general_area = round(
np.sum([track.area for track in sample.tracks.get_sorted_by_id()]),
2)
self.mainDialog.infolabel.setText('''
<p align="center">General tracks count<br>{tracks_count}</p>
<p align="center">General tracks area (%)<br>{general_area}</p>
'''.format(tracks_count=count,
general_area=general_area))
def draw_objects(self, viewer, sample):
for track in sample.tracks.get_sorted():
viewer.add_rect(track.left, track.rigth, track.top, track.bottom)
viewer.add_Polygon(track.contour, track.left, track.top)
text = 'Count: {tracks_count}\nArea (%): {general_area}'.format(
tracks_count=track.count, general_area=track.area)
viewer.add_Text(text, track.left, track.top)
def updete_viewers(self):
sample = self.project.current_sample
if not sample:
return
self.mainDialog.ThroughArea.load_image(sample.through)
self.mainDialog.BacklightArea.load_image(sample.backlight)
self.mainDialog.PreparedArea.load_image(sample.prepared)
self.draw_objects(self.mainDialog.ThroughArea, sample)
self.draw_objects(self.mainDialog.BacklightArea, sample)
self.draw_objects(self.mainDialog.PreparedArea, sample)
def __connect_to_grbl__(self):
'''Функция подключения к CNC сканера, которая передается в настройки станка'''
status = self.grbl.connect()
if not status: return
self.cnc_indicator.setStatus(-1)
self.grbl.reset_alarm()
self.cnc_indicator.setStatus(status)
return status
def __check_ip__(self, ip):
status = False
test_grbl = GRBL(HOST=self.settings.grblip)
test_grbl.setHost(ip)
try:
status = test_grbl.connect(check=False)
test_grbl.connection.close()
except OSError:
pass
return ip if status else None
def __auto_seach__(self, property=None):
'''Функция авто поиска IP станка
property нужен, чтобы вернуть результат в inputField окна настроек
'''
if self.grbl.connection: self.grbl.connection.close()
devices = [device for device in os.popen('arp -a')]
ip_candidates = [
re.findall(r"\b\d{1,3}\.\d{1,3}\.\d{1,3}\.\d{1,3}\b", device)[0]
for device in devices if
len(re.findall(r"\b\d{1,3}\.\d{1,3}\.\d{1,3}\.\d{1,3}\b",
device)) != 0
]
if self.settings.grblip in ip_candidates:
ip_candidates.remove(self.settings.grblip)
ip_candidates.insert(0, self.settings.grblip)
pool = ThreadPool(4)
results = pool.map(self.__check_ip__, ip_candidates)
index = np.where(results != None)[0][0]
if not results[index]:
# print(self.qapp.tr('There is not devices in current net'))
return
pool.close()
pool.join()
self.grbl.setHost(results[index])
self.__connect_to_grbl__()
if property:
property.setText(
results[index]
) # property нужен, чтобы вернуть результат в inputField
self.settings.grblip = results[index]
self.settings.write()
print(self.qapp.tr('Connected to') + ' {ip}'.format(ip=results[index]))
return True
def showAbout(self):
about = about_dialog(self)
about.open()
def showGrblDialog(self):
dialog = grblDialog(self,
connection_func=self.__connect_to_grbl__,
auto_seach_func=self.__auto_seach__)
dialog.execute(self.settings)
from app import db, Settings db.create_all() default_settings = Settings(owner_id=None, feedback=1, constant_time_version=0, t_value=2500, trial_count=15) db.session.add(default_settings) db.session.commit()
def openSettingsWindow(self):
if not hasattr(self, 'settingsWidget'):
self.settingsWidget = Settings()
if self.settingsWidget.isclosed:
self.settingsWidget.show()
self.settingsWidget.isclosed = False
class Synapse_MainWindow(QtGui.QMainWindow):
def __init__(self,
parent=None,
startpath=None,
hideScopeToolbox=True,
layout=None):
super(Synapse_MainWindow, self).__init__(parent)
# Set up the GUI window
self.setupUi(self)
# Set the treeview model for directory
self.setDataBrowserTreeView(startpath=startpath)
self.hideScopeToolbox = hideScopeToolbox
self.scopeLayout = layout
def setupUi(self, MainWindow):
"""This function is converted from the .ui file from the designer"""
# Set up basic layout of the main window
MainWindow.setObjectName(_fromUtf8("Synpase TreeView"))
MainWindow.resize(1000, 500)
self.centralwidget = QtGui.QWidget(MainWindow)
self.centralwidget.setObjectName(_fromUtf8("centralwidget"))
self.horizontalLayout = QtGui.QHBoxLayout(self.centralwidget)
self.horizontalLayout.setObjectName(_fromUtf8("horizontalLayout"))
# Set splitter for two panels
self.splitter = QtGui.QSplitter(self.centralwidget)
sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding,
QtGui.QSizePolicy.Preferred)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(
self.splitter.sizePolicy().hasHeightForWidth())
self.splitter.setSizePolicy(sizePolicy)
self.splitter.setOrientation(QtCore.Qt.Horizontal)
self.splitter.setObjectName(_fromUtf8("splitter"))
# Set treeview
self.treeview = QtGui.QTreeView(self.splitter)
sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Preferred,
QtGui.QSizePolicy.Expanding)
sizePolicy.setHorizontalStretch(1)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(
self.treeview.sizePolicy().hasHeightForWidth())
self.treeview.setSizePolicy(sizePolicy)
# self.treeview.setTextElideMode(QtCore.Qt.ElideNone)
self.treeview.header().setResizeMode(
QtGui.QHeaderView.ResizeToContents)
self.treeview.header().setStretchLastSection(False)
self.treeview.setObjectName(_fromUtf8("treeview"))
# Set up Episode list table view
self.tableview = QtGui.QTableView(self.splitter)
sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding,
QtGui.QSizePolicy.Expanding)
sizePolicy.setHorizontalStretch(3)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(
self.tableview.sizePolicy().hasHeightForWidth())
self.tableview.setSizePolicy(sizePolicy)
self.tableview.setObjectName(_fromUtf8("tableview"))
# additional tableview customizations
self.tableview.setSelectionMode(
QtGui.QAbstractItemView.ExtendedSelection)
self.tableview.setSelectionBehavior(QtGui.QAbstractItemView.SelectRows)
self.tableview.setItemDelegate(TableviewDelegate(self.tableview))
self.tableview.headers = [
'Epi', 'Time', 'Duration', 'Drug Level', 'Drug Name', 'Drug Time',
'Comment', 'Dirs'
]
self.tableview.hiddenColumnList = [4, 5,
7] # Drug Name, Drug Time, Dirs
self.tableview.horizontalHeader().setStretchLastSection(True)
# self.tableview.setShowGrid(False)
self.tableview.setStyleSheet(
"""QTableView{border : 20px solid white}""")
self.horizontalLayout.addWidget(self.splitter)
MainWindow.setCentralWidget(self.centralwidget)
# Set up menu bar
self.menubar = QtGui.QMenuBar(MainWindow)
self.menubar.setGeometry(QtCore.QRect(0, 0, 638, 100))
self.menubar.setObjectName(_fromUtf8("menubar"))
self.setMenuBarItems() # call function to set menubar
MainWindow.setMenuBar(self.menubar)
# Set up status bar
self.statusbar = QtGui.QStatusBar(MainWindow)
self.statusbar.setObjectName(_fromUtf8("statusbar"))
MainWindow.setStatusBar(self.statusbar)
# Execution
self.retranslateUi(MainWindow)
QtCore.QMetaObject.connectSlotsByName(MainWindow)
# ---------------- Additional main window behaviors -----------------------
def setMenuBarItems(self):
# File Menu
fileMenu = self.menubar.addMenu('&File')
# File: Refresh. Refresh currently selected item/directory
refreshAction = QtGui.QAction('Refresh', self)
refreshAction.setShortcut('F5')
refreshAction.setStatusTip(
'Refresh currently selected item / directory')
refreshAction.triggered.connect(self.refreshCurrentBranch)
fileMenu.addAction(refreshAction)
# File: Settings
settingsAction = QtGui.QAction("Settings", self)
settingsAction.setStatusTip('Configure settings of PySynapse')
settingsAction.triggered.connect(self.openSettingsWindow)
fileMenu.addAction(settingsAction)
# File: Exit
exitAction = QtGui.QAction(QtGui.QIcon('exit.png'), 'Exit', self)
exitAction.setShortcut('Ctrl+Q')
exitAction.setStatusTip('Exit Synapse')
exitAction.triggered.connect(self.close)
fileMenu.addAction(exitAction)
# View Menu
viewMenu = self.menubar.addMenu('&View')
# View: Column
columnMenu = viewMenu.addMenu('&Additional Columns')
drugNameAction = QtGui.QAction('Drug Name',
self,
checkable=True,
checked=False)
drugNameAction.triggered.connect(
lambda: self.toggleTableViewColumnAction(4, drugNameAction))
columnMenu.addAction(drugNameAction)
drugTimeAction = QtGui.QAction('Drug Time',
self,
checkable=True,
checked=False)
drugTimeAction.triggered.connect(
lambda: self.toggleTableViewColumnAction(5, drugTimeAction))
columnMenu.addAction(drugTimeAction)
dirsAction = QtGui.QAction('Directory',
self,
checkable=True,
checked=False)
dirsAction.triggered.connect(
lambda: self.toggleTableViewColumnAction(7, dirsAction))
columnMenu.addAction(dirsAction)
def toggleTableViewColumnAction(self, column, action):
if self.tableview.isColumnHidden(column):
self.tableview.showColumn(column)
action.setChecked(True)
self.tableview.hiddenColumnList.remove(column)
else:
self.tableview.hideColumn(column)
action.setChecked(False)
self.tableview.hiddenColumnList.append(column)
def refreshCurrentBranch(self):
# Get parent index
index = self.treeview.selectionModel().currentIndex()
node = self.treeview.model.getNode(index)
if node.type == "directory":
self.treeview.model.refreshNode(index)
def openSettingsWindow(self):
if not hasattr(self, 'settingsWidget'):
self.settingsWidget = Settings()
if self.settingsWidget.isclosed:
self.settingsWidget.show()
self.settingsWidget.isclosed = False
def closeEvent(self, event):
"""Override default behavior when closing the main window"""
return
#quit_msg = "Are you sure you want to exit the program?"
#reply = QtGui.QMessageBox.question(self, 'Message', quit_msg,
# QtGui.QMessageBox.Yes,
# QtGui.QMessageBox.No)
#if reply == QtGui.QMessageBox.Yes:
# event.accept()
#else:
# event.ignore()
# Consider if close children windows when closing Synapse main window
# children = ['settingsWidget', 'sw']
# for c in children:
# if hasattr(self, c):
# getattr(self, c).close()
def retranslateUi(self, MainWindow):
"""Set window title and other miscellaneous"""
MainWindow.setWindowTitle(_translate(__version__, __version__, None))
MainWindow.setWindowIcon(QtGui.QIcon('resources/icons/Synapse.png'))
# ---------------- Data browser behaviors ---------------------------------
def setDataBrowserTreeView(self, startpath=None):
# Set file system as model of the tree view
# self.treeview.model = QtGui.QFileSystemModel()
self.treeview.model = FileSystemTreeModel(path=startpath)
self.treeview.setModel(self.treeview.model)
# Set behavior upon clicked
self.treeview.clicked.connect(self.onSequenceClicked)
@QtCore.pyqtSlot(QtCore.QModelIndex)
def onSequenceClicked(self, index):
""" Display a list of episodes upon sequence clicked"""
#indexItem = self.treeview.model.index(index.row(), 0, index.parent())
self.raise_()
node = self.treeview.model.getNode(index)
# Check if the item clicked is sequence instead of a folder / file
if node.type == "sequence":
# populuate the table view on the other panel
self.setEpisodeListTableView(node.info)
# --------------- Episode list behaviors ----------------------------------
def setEpisodeListTableView(self, sequence=None):
if not sequence:
return # do nothing if there is no sequence information
# Render the data frame from sequence
df = pd.DataFrame.from_dict(sequence)
# sort the data frame by 'Epi' column
epi_sort = df['Epi'].tolist()
ind = pd.DataFrame([[int(k) for k in re.findall('\d+', m)] \
for m in epi_sort])
ind = ind.sort_values([0, 1], ascending=[1, 1]).index.tolist()
df = df.reindex_axis(ind, axis=0)
self.tableview.sequence = df.reset_index(drop=True).to_dict(
'list') # data information
self.tableview.sequence['Name'] = self.tableview.sequence['Name'][
0] # remove any duplication
# get the subset of columns based on column settings
df = df.reindex_axis(self.tableview.headers, axis=1)
self.tableview.model = EpisodeTableModel(df)
self.tableview.setModel(self.tableview.model)
self.tableview.verticalHeader().hide()
# Hide some columns from display
for c in self.tableview.hiddenColumnList: # Drug Name, Drug Time, Dirs
self.tableview.setColumnHidden(c, True)
# Set behavior upon selection
self.tableview.selectionModel().selectionChanged.connect(
self.onItemSelected)
# self.tableview.clicked.connect(self.onItemSelected)
@QtCore.pyqtSlot(QtCore.QModelIndex)
def onItemSelected(self, selected, deselected):
"""Executed when an episode in the tableview is clicked"""
# Get the information of last selected item
if not selected and not deselected:
return
try:
ind = selected.indexes()[-1].row()
except:
ind = deselected.indexes()[-1].row()
sequence = self.tableview.sequence
drugName = sequence['Drug Name'][ind]
if not drugName: # in case of empty string
drugName = str(sequence['Drug Level'][ind])
ep_info_str = "ts: {:0.1f} ms; Drug: {} ({})".format(
sequence['Sampling Rate'][ind], drugName,
sequence['Drug Time'][ind])
self.statusBar().showMessage(ep_info_str)
self.setWindowTitle("{} {}".format(__version__,
sequence['Dirs'][ind]))
# Get selected row
indexes = self.tableview.selectionModel().selectedRows()
rows = [index.row() for index in sorted(indexes)]
# if not rows: # When nothing is selected, keep the last selected item on the Scope
# return
# Call scope window
if not hasattr(self, 'sw'): # Start up a new window
# self.sw = ScopeWindow(parent=self)
self.sw = ScopeWindow(partner=self,
hideDock=self.hideScopeToolbox,
layout=self.scopeLayout) # new window
if self.sw.isclosed:
self.sw.show()
self.sw.isclosed = False
# update existing window
self.sw.updateEpisodes(episodes=sequence, index=rows)
def openSettingsWindow(self):
if not hasattr(self, 'settingsWidget'):
self.settingsWidget = Settings()
if self.settingsWidget.isclosed:
self.settingsWidget.show()
self.settingsWidget.isclosed = False
class Synapse_MainWindow(QtWidgets.QMainWindow):
def __init__(self, parent=None, startpath=None, hideScopeToolbox=True, layout=None):
super(Synapse_MainWindow, self).__init__(parent)
# Set up the GUI window
self.setupUi(self)
# Set the treeview model for directory
self.setDataBrowserTreeView(startpath=startpath)
self.hideScopeToolbox = hideScopeToolbox
self.scopeLayout = layout
self.startpath=startpath
def setupUi(self, MainWindow):
"""This function is converted from the .ui file from the designer"""
# Set up basic layout of the main window
MainWindow.setObjectName(_fromUtf8("Synpase TreeView"))
MainWindow.resize(1000, 500)
self.centralwidget = QtWidgets.QWidget(MainWindow)
self.centralwidget.setObjectName(_fromUtf8("centralwidget"))
self.horizontalLayout = QtWidgets.QHBoxLayout(self.centralwidget)
self.horizontalLayout.setObjectName(_fromUtf8("horizontalLayout"))
# Set splitter for two panels
self.splitter = QtWidgets.QSplitter(self.centralwidget)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Preferred)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.splitter.sizePolicy().hasHeightForWidth())
self.splitter.setSizePolicy(sizePolicy)
self.splitter.setOrientation(QtCore.Qt.Horizontal)
self.splitter.setObjectName(_fromUtf8("splitter"))
# Set treeview
self.treeview = QtWidgets.QTreeView(self.splitter)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Expanding)
sizePolicy.setHorizontalStretch(1)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.treeview.sizePolicy().hasHeightForWidth())
self.treeview.setSizePolicy(sizePolicy)
# self.treeview.setTextElideMode(QtCore.Qt.ElideNone)
self.treeview.header().setResizeMode(QtWidgets.QHeaderView.ResizeToContents)
self.treeview.header().setStretchLastSection(False)
self.treeview.setObjectName(_fromUtf8("treeview"))
# Set up Episode list table view
self.tableview = QtWidgets.QTableView(self.splitter)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Expanding)
sizePolicy.setHorizontalStretch(3)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.tableview.sizePolicy().hasHeightForWidth())
self.tableview.setSizePolicy(sizePolicy)
self.tableview.setObjectName(_fromUtf8("tableview"))
# additional tableview customizations
self.tableview.setSelectionMode(QtWidgets.QAbstractItemView.ExtendedSelection)
self.tableview.setSelectionBehavior(QtWidgets.QAbstractItemView.SelectRows)
self.tableview.setItemDelegate(TableviewDelegate(self.tableview))
self.tableview.horizontalHeader().setStretchLastSection(True)
# self.tableview.setShowGrid(False)
self.tableview.setStyleSheet("""QTableView{border : 20px solid white}""")
self.horizontalLayout.addWidget(self.splitter)
MainWindow.setCentralWidget(self.centralwidget)
# Set up menu bar
self.menubar = QtWidgets.QMenuBar(MainWindow)
self.menubar.setGeometry(QtCore.QRect(0, 0, 638, 100))
self.menubar.setObjectName(_fromUtf8("menubar"))
self.setMenuBarItems() # call function to set menubar
MainWindow.setMenuBar(self.menubar)
# Set up status bar
self.statusbar = QtWidgets.QStatusBar(MainWindow)
self.statusbar.setObjectName(_fromUtf8("statusbar"))
MainWindow.setStatusBar(self.statusbar)
# Execution
self.retranslateUi(MainWindow)
QtCore.QMetaObject.connectSlotsByName(MainWindow)
# ---------------- Additional main window behaviors -----------------------
def setMenuBarItems(self):
# File Menu
fileMenu = self.menubar.addMenu('&File')
# File: Load csv
loadDBAction = QtWidgets.QAction('Load Database', self)
loadDBAction.setStatusTip('Load a database table from a .csv, .xlsx, or .xls file')
loadDBAction.triggered.connect(self.loadDatabase)
fileMenu.addAction(loadDBAction)
# File: Refresh. Refresh currently selected item/directory
refreshAction = QtWidgets.QAction('Refresh', self)
refreshAction.setShortcut('F5')
refreshAction.setStatusTip('Refresh currently selected item / directory')
refreshAction.triggered.connect(self.refreshCurrentBranch)
fileMenu.addAction(refreshAction)
# File: Settings
settingsAction = QtWidgets.QAction("Settings", self)
settingsAction.setStatusTip('Configure settings of PySynapse')
settingsAction.triggered.connect(self.openSettingsWindow)
fileMenu.addAction(settingsAction)
# File: Exit
exitAction = QtWidgets.QAction(QtGui.QIcon('exit.png'),'Exit', self)
exitAction.setShortcut('Ctrl+Q')
exitAction.setStatusTip('Exit Synapse')
exitAction.triggered.connect(self.close)
fileMenu.addAction(exitAction)
# View Menu
viewMenu = self.menubar.addMenu('&View')
# View: Column
columnMenu = viewMenu.addMenu('&Additional Columns')
drugNameAction = QtWidgets.QAction('Drug Name', self, checkable=True, checked=False)
drugNameAction.triggered.connect(lambda: self.toggleTableViewColumnAction(4, drugNameAction))
columnMenu.addAction(drugNameAction)
drugTimeAction = QtWidgets.QAction('Drug Time', self, checkable=True, checked=False)
drugTimeAction.triggered.connect(lambda: self.toggleTableViewColumnAction(5, drugTimeAction))
columnMenu.addAction(drugTimeAction)
dirsAction = QtWidgets.QAction('Directory', self, checkable=True, checked=False)
dirsAction.triggered.connect(lambda: self.toggleTableViewColumnAction(7, dirsAction))
columnMenu.addAction(dirsAction)
def toggleTableViewColumnAction(self, column, action):
if self.tableview.isColumnHidden(column):
self.tableview.showColumn(column)
action.setChecked(True)
self.tableview.hiddenColumnList.remove(column)
else:
self.tableview.hideColumn(column)
action.setChecked(False)
self.tableview.hiddenColumnList.append(column)
def loadDatabase(self):
# TODO: Need to design this more carefully
#raise(NotImplementedError())
# Opens up the file explorer
filename, _ = QtWidgets.QFileDialog.getOpenFileName(self, 'Open File', '/', 'Spreadsheet (*.csv *.xlsx *.xls);;All Files (*)')#
rename_dict = {"Cell":"Name", "Episode":"Epi", "SweepWindow":"Duration","Drug":"Drug Name","DrugTime":"Drug Time","WCTime":"Time", "StimDescription":"Comment"}
if ".csv" in filename:
df = pd.read_csv(filename)
elif ".xlsx" in filename or "xls" in filename:
df = pd.read_excel(filename)
else:
return
col_lower = [c.lower() for c in df.columns.tolist()]
if "show" in col_lower:
df = df.loc[df.iloc[:, col_lower.index("show")],:]
drop_columns = np.setdiff1d(df.columns.tolist(), list(rename_dict.keys()))
df = df.drop(drop_columns, axis=1).rename(columns=rename_dict)
df["Sampling Rate"] = 0.1
df["Drug Level"] = 0
df.loc[df["Drug Name"].isnull(), "Drug Name"] = ""
df["Time"] = [NeuroData.epiTime(ttt) for ttt in df["Time"]]
df["Drug Time"] = [NeuroData.epiTime(ttt) for ttt in df["Drug Time"]]
# TODO: Tentitative path
df["Dirs"] = [os.path.join(self.startpath, get_cellpath(cb, ep)).replace("\\", "/") for cb, ep in zip(df["Name"], df["Epi"])]
self.tableview.sequence = df.reset_index(drop=True).to_dict('list')
df = df.reindex(["Name", "Epi", "Time", "Duration", "Drug Name", "Drug Time", "Comment"], axis=1) # drop columns not to be displayed
# print('loaded')
# Populate the loaded data unto the table widget
self.tableview.headers = df.columns.tolist()
self.tableview.model = EpisodeTableModel(df)
self.tableview.setModel(self.tableview.model)
self.tableview.verticalHeader().hide()
# Show all columns
for cc in range(len(self.tableview.headers)):
self.tableview.showColumn(cc)
self.tableview.selectionModel().selectionChanged.connect(self.onItemSelected)
def refreshCurrentBranch(self):
# Get parent index
index = self.treeview.selectionModel().currentIndex()
node = self.treeview.model.getNode(index)
if node.type == "directory":
self.treeview.model.refreshNode(index)
def openSettingsWindow(self):
if not hasattr(self, 'settingsWidget'):
self.settingsWidget = Settings()
if self.settingsWidget.isclosed:
self.settingsWidget.show()
self.settingsWidget.isclosed = False
def closeEvent(self, event):
"""Override default behavior when closing the main window"""
return
#quit_msg = "Are you sure you want to exit the program?"
#reply = QtWidgets.QMessageBox.question(self, 'Message', quit_msg,
# QtWidgets.QMessageBox.Yes,
# QtWidgets.QMessageBox.No)
#if reply == QtWidgets.QMessageBox.Yes:
# event.accept()
#else:
# event.ignore()
# Consider if close children windows when closing Synapse main window
# children = ['settingsWidget', 'sw']
# for c in children:
# if hasattr(self, c):
# getattr(self, c).close()
def retranslateUi(self, MainWindow):
"""Set window title and other miscellaneous"""
MainWindow.setWindowTitle(_translate(__version__, __version__, None))
MainWindow.setWindowIcon(QtGui.QIcon('resources/icons/Synapse.png'))
# ---------------- Data browser behaviors ---------------------------------
def setDataBrowserTreeView(self, startpath=None):
# Set file system as model of the tree view
# self.treeview.model = QtWidgets.QFileSystemModel()
self.treeview.model = FileSystemTreeModel(path=startpath)
self.treeview.setModel(self.treeview.model)
# Set behavior upon clicked
self.treeview.clicked.connect(self.onSequenceClicked)
@QtCore.pyqtSlot(QtCore.QModelIndex)
def onSequenceClicked(self, index):
""" Display a list of episodes upon sequence clicked"""
#indexItem = self.treeview.model.index(index.row(), 0, index.parent())
self.raise_()
node = self.treeview.model.getNode(index)
# Check if the item clicked is sequence instead of a folder / file
if node.type == "sequence":
# populate the table view on the other panel
self.setEpisodeListTableView(node.info)
# --------------- Episode list behaviors ----------------------------------
def setEpisodeListTableView(self, sequence=None):
if not sequence:
return # do nothing if there is no sequence information
self.tableview.headers = ['Epi', 'Time', 'Duration', 'Drug Level', 'Drug Name', 'Drug Time', 'Comment','Dirs', 'Stimulus', 'StimDuration']
self.tableview.hiddenColumnList = [4, 5, 7, 8, 9] # Drug Name, Drug Time, Dirs
# Render the data frame from sequence
df = pd.DataFrame.from_dict(sequence)
# sort the data frame by 'Epi' column
epi_sort = df['Epi'].tolist()
ind = pd.DataFrame([[int(k) for k in re.findall('\d+', m)] \
for m in epi_sort])
ind = ind.sort_values([0,1], ascending=[1,1]).index.tolist()
df = df.reindex(ind, axis=0)
self.tableview.sequence = df.reset_index(drop=True).to_dict('list') # data information
# self.tableview.sequence['Name'] = self.tableview.sequence['Name'][0] # remove any duplication
# get the subset of columns based on column settings
df = df.reindex(self.tableview.headers, axis=1)
self.tableview.model = EpisodeTableModel(df)
self.tableview.setModel(self.tableview.model)
self.tableview.verticalHeader().hide()
# Hide some columns from display
for c in self.tableview.hiddenColumnList: # Drug Name, Drug Time, Dirs
self.tableview.setColumnHidden(c, True)
# Set behavior upon selection
self.tableview.selectionModel().selectionChanged.connect(self.onItemSelected)
# self.tableview.clicked.connect(self.onItemSelected)
@QtCore.pyqtSlot(QtCore.QItemSelection, QtCore.QItemSelection)
def onItemSelected(self, selected, deselected):
"""Executed when an episode in the tableview is clicked"""
# Get the information of last selected item
if not selected and not deselected:
return
try:
ind = selected.indexes()[-1].row()
except:
ind = deselected.indexes()[-1].row()
sequence = self.tableview.sequence
drugName = sequence['Drug Name'][ind]
if not drugName: # in case of empty string
drugName = str(sequence['Drug Level'][ind])
ep_info_str = "ts: {:0.1f} ms; Drug: {} ({})".format(sequence['Sampling Rate'][ind], drugName, sequence['Drug Time'][ind])
self.statusBar().showMessage(ep_info_str)
self.setWindowTitle("{} {}".format(__version__, sequence['Dirs'][ind]))
# Get selected row
indexes = self.tableview.selectionModel().selectedRows()
rows = [index.row() for index in sorted(indexes)]
# if not rows: # When nothing is selected, keep the last selected item on the Scope
# return
# Call scope window
if not hasattr(self, 'sw'): # Start up a new window
# self.sw = ScopeWindow(parent=self)
self.sw = ScopeWindow(partner=self, hideDock=self.hideScopeToolbox, layout=self.scopeLayout) # new window
if self.sw.isclosed:
self.sw.show()
self.sw.isclosed = False
# update existing window
self.sw.updateEpisodes(episodes=sequence, index=rows)
def saveSetiings(self, settings: Settings):
settings.grblip = self._ip_label.text
def setUp(self):
app.config['TESTING'] = True
app.config['BASE_URI'] = 'http://*****:*****@somewhere-org'
settings.test_business_id = 'test.someone@somewhere-org'
settings.submission_url = 'http://not-a-real-url'
settings.test_submission_url = 'http://test-not-a-real-url'
settings.verification_url = 'http://not-a-real-verification-url'
settings.test_verification_url = 'http://test-not-a-real-verification-url'
settings.smtp_host = 'somewhere-org'
settings.smtp_port = 465
settings.smtp_login = '******'
settings.smtp_pass = '******'
settings.notification_email = 'someone.who.cares@somewhere-org'
settings.test_notification_email = 'test.someone.who.cares@somewhere-org'
settings.contact_email = 'someone.who.cares@somewhere-org'
settings.test_contact_email = 'test.someone.who.cares@somewhere-org'
settings.organization_name = 'Somewhere'
settings.organization_url = 'http://somewhere-org'
settings.paypal_rate = 0.022
settings.paypal_surcharge = 0.30
db.session.add(settings)
db.session.commit()
