def openDialog(self):
od = QFileDialog(self, 'Open MaLPi drive data directory')
od.setAcceptMode(QFileDialog.AcceptOpen)
od.setFileMode(QFileDialog.Directory)
od.setOption(QFileDialog.DontUseNativeDialog, True)
# Try to select multiple files and directories at the same time in QFileDialog
if False:
l = od.findChild(QListView, "listView")
if l is not None:
l.setSelectionMode(QAbstractItemView.MultiSelection)
t = od.findChild(QTreeView)
if t is not None:
t.setSelectionMode(QAbstractItemView.MultiSelection)
nMode = od.exec()
if nMode == QDialog.Accepted:
_fnames = od.selectedFiles() # QStringList
try:
if 1 == len(_fnames) and os.path.isdir(_fnames[0]):
self.loadData(_fnames[0])
elif 0 != len(_fnames):
self.statusBar().showMessage(
"Formats other than MaLPi and Tub are not yet supported"
)
except Exception as ex:
msg = "Error loading data: {}".format(str(ex))
self.statusBar().showMessage(msg)
print(msg)
def open_file_dialog(self):
options = QFileDialog.Options()
options |= QFileDialog.DontUseNativeDialog
options |= QFileDialog.ShowDirsOnly
dialog = QFileDialog(self)
dialog.setFileMode(QFileDialog.DirectoryOnly)
dialog.setOptions(options)
file_view = dialog.findChild(QListView, 'listView')
# to make it possible to select multiple directories:
if file_view:
file_view.setSelectionMode(QAbstractItemView.ExtendedSelection)
f_tree_view = dialog.findChild(QTreeView)
if f_tree_view:
f_tree_view.setSelectionMode(QAbstractItemView.ExtendedSelection)
if dialog.exec():
paths = dialog.selectedFiles()
for patient_data_directory in paths:
patient_identifier = os.path.basename(patient_data_directory)
if patient_identifier not in self.patient_data_sets:
dp_file_path = os.path.join(patient_data_directory,
'result_images',
'exported_data',
'diffusion_parameters.mat')
if os.path.exists(dp_file_path):
data = loadmat(dp_file_path)
self.load_data(patient_identifier, data)
else:
error_dialog = QtWidgets.QErrorMessage()
error_dialog.showMessage(
f'File path error: {patient_data_directory} does not contain diffusion '
f'parameters')
error_dialog.exec_()
def from_folder(self): file_dialog = QFileDialog() file_dialog.setFileMode(QFileDialog.DirectoryOnly) file_dialog.setOption(QFileDialog.DontUseNativeDialog, True) file_view = file_dialog.findChild(QListView, 'listView') if file_view: file_view.setSelectionMode(QAbstractItemView.MultiSelection) f_tree_view = file_dialog.findChild(QTreeView) if f_tree_view: f_tree_view.setSelectionMode(QAbstractItemView.MultiSelection) if file_dialog.exec(): for path in file_dialog.selectedFiles(): self.add_gallery(path, os.path.split(path)[1])
def select_folders():
file_dialog = QFileDialog()
file_dialog.setFileMode(QFileDialog.DirectoryOnly)
file_dialog.setOption(QFileDialog.DontUseNativeDialog, True)
file_view = file_dialog.findChild(QListView, 'listView')
if file_view:
file_view.setSelectionMode(QAbstractItemView.MultiSelection)
f_tree_view = file_dialog.findChild(QTreeView)
if f_tree_view:
f_tree_view.setSelectionMode(QAbstractItemView.MultiSelection)
paths = []
if file_dialog.exec() == QDialog.Accepted:
paths = file_dialog.selectedFiles()
return paths
def show_ui(self):
file_dialog = QFileDialog(self, self.caption, self.default_dir)
file_dialog.setFileMode(QFileDialog.DirectoryOnly)
file_dialog.setDirectory(self.default_dir)
file_dialog.setOption(QFileDialog.DontUseNativeDialog, True)
file_view = file_dialog.findChild(QListView, 'listView')
# to make it possible to select multiple directories:
file_view.setSelectionMode(QAbstractItemView.MultiSelection)
f_tree_view = file_dialog.findChild(QTreeView)
f_tree_view.setSelectionMode(QAbstractItemView.MultiSelection)
# execute the modified file dialog and return result
self.close_later.emit()
if file_dialog.exec():
self.file_names = file_dialog.selectedFiles()
def on_click(self):
file_dialog = QFileDialog()
file_dialog.setFileMode(QFileDialog.DirectoryOnly)
file_dialog.setOption(QFileDialog.DontUseNativeDialog, True)
file_view = file_dialog.findChild(QListView, 'listView')
# to make it possible to select multiple directories:
if file_view:
file_view.setSelectionMode(QAbstractItemView.MultiSelection)
f_tree_view = file_dialog.findChild(QTreeView)
if f_tree_view:
f_tree_view.setSelectionMode(QAbstractItemView.MultiSelection)
file_dialog = QFileDialog()
file_dialog.setFileMode(QFileDialog.DirectoryOnly)
file_dialog.setOption(QFileDialog.DontUseNativeDialog, True)
file_view = file_dialog.findChild(QListView, 'listView')
if file_dialog.exec():
sourceFolder = file_dialog.selectedFiles()
return sourceFolder
class Open_files(QWidget):
def __init__(self):
super(QWidget, self).__init__()
self.layout = QHBoxLayout(self)
self.file_dialog = QFileDialog()
self.file_dialog.setWindowFlags(Qt.Widget)
self.file_dialog.setModal(False)
self.file_dialog.setOption(QFileDialog.DontUseNativeDialog)
# Remove open and cancel button from widget
self.buttonBox = self.file_dialog.findChild(QDialogButtonBox,
"buttonBox")
self.buttonBox.clear()
# Only open following file types
# self.file_dialog.setNameFilter("Images (*.czi *.nd2 *.tiff *.tif *.jpg *.png)")
self.file_dialog.setNameFilter(
"Images (*.czi *.ome.tiff *ome.tif *.tiff *.tif)")
self.layout.addWidget(self.file_dialog)
self.file_dialog.currentChanged.connect(self.open_path)
def open_path(self, path):
if os.path.isfile(path):
# remove exiting layers from napari
viewer.layers.select_all()
viewer.layers.remove_selected()
# get the metadata
md, addmd = imf.get_metadata(path)
# temporary workaround for slider / floating point issue
# https://forum.image.sc/t/problem-with-dimension-slider-when-adding-array-as-new-layer-for-ome-tiff/39092/2?u=sebi06
md['XScale'] = np.round(md['XScale'], 3)
md['YScale'] = np.round(md['YScale'], 3)
md['ZScale'] = np.round(md['ZScale'], 3)
# get AICSImageIO object using the python wrapper for libCZI (if file is CZI)
img = AICSImage(path)
stack = img.get_image_data()
if md['ImageType'] == 'czi':
use_pylibczi = True
if md['ImageType'] == 'ometiff':
use_pylibczi = False
add_napari(stack,
md,
blending='additive',
gamma=0.85,
verbose=True,
use_pylibczi=use_pylibczi,
rename_sliders=True)
def requestOpenFileOrDir ( parent=None, caption='', directory='',
filter='All Files ( * )', initialFilter='', options=None ):
def updateText ():
# update the contents of the line edit widget with the selected files
selected = []
for index in view.selectionModel ().selectedRows ():
selected.append ( '"{}"'.format ( index.data () ) )
lineEdit.setText ( ' '.join ( selected ) )
dialog = QFileDialog ( parent, caption = caption )
dialog.setFileMode ( QFileDialog.ExistingFiles )
if options:
dialog.setOptions ( options )
dialog.setOption ( QFileDialog.DontUseNativeDialog, True )
if directory:
dialog.setDirectory ( directory )
if filter:
dialog.setNameFilter ( filter )
if initialFilter:
dialog.selectNameFilter ( initialFilter )
# by default, if a directory is opened in file listing mode,
# QFileDialog.accept() shows the contents of that directory, but we
# need to be able to "open" directories as we can do with files, so we
# just override accept() with the default QDialog implementation which
# will just return exec_()
dialog.accept = lambda: QtWidgets.QDialog.accept ( dialog )
# there are many item views in a non-native dialog, but the ones displaying
# the actual contents are created inside a QStackedWidget; they are a
# QTreeView and a QListView, and the tree is only used when the
# viewMode is set to QFileDialog.Details, which is not this case
stackedWidget = dialog.findChild ( QtWidgets.QStackedWidget )
view = stackedWidget.findChild ( QtWidgets.QListView )
view.selectionModel ().selectionChanged.connect ( updateText )
lineEdit = dialog.findChild ( QtWidgets.QLineEdit )
# clear the line edit contents whenever the current directory changes
dialog.directoryEntered.connect ( lambda: lineEdit.setText ( '' ) )
dialog.exec_ ()
return dialog.selectedFiles ()
def addFolderTriggered(self):
no_native = not self.app.prefs.use_native_dialogs
title = tr("Select a folder to add to the scanning list")
file_dialog = QFileDialog(self, title, self.lastAddedFolder)
file_dialog.setFileMode(QFileDialog.DirectoryOnly)
file_dialog.setOption(QFileDialog.DontUseNativeDialog, no_native)
if no_native:
file_view = file_dialog.findChild(QListView, "listView")
if file_view:
file_view.setSelectionMode(QAbstractItemView.MultiSelection)
f_tree_view = file_dialog.findChild(QTreeView)
if f_tree_view:
f_tree_view.setSelectionMode(QAbstractItemView.MultiSelection)
if not file_dialog.exec():
return
paths = file_dialog.selectedFiles()
self.lastAddedFolder = paths[-1]
[self.app.model.add_directory(path) for path in paths]
[self.recentFolders.insertItem(path) for path in paths]
def on_browseFolders_clicked(self, widget):
index = self.usbDevicesChooser.currentIndex()
file_dialog = QFileDialog()
file_dialog.setFileMode(QFileDialog.DirectoryOnly)
file_dialog.setOption(QFileDialog.DontUseNativeDialog, True)
file_view = file_dialog.findChild(QListView, 'listView')
if file_view:
file_view.setSelectionMode(QAbstractItemView.MultiSelection)
ftree_view = file_dialog.findChild(QTreeView)
if ftree_view:
ftree_view.setSelectionMode(QAbstractItemView.MultiSelection)
file_dialog.setDirectory(self.usbDevices[index].getPath())
if file_dialog.exec():
paths = file_dialog.selectedFiles()
self.pathToFolders.setText(";".join(paths))
class Open_files(QWidget):
def __init__(self):
super(QWidget, self).__init__()
self.layout = QHBoxLayout(self)
self.file_dialog = QFileDialog()
self.file_dialog.setWindowFlags(Qt.Widget)
self.file_dialog.setModal(False)
self.file_dialog.setOption(QFileDialog.DontUseNativeDialog)
# Remove open and cancel button from widget
self.buttonBox = self.file_dialog.findChild(QDialogButtonBox,
"buttonBox")
self.buttonBox.clear()
# Only open following file types
self.file_dialog.setNameFilter(
"Images (*.czi *.ome.tiff *ome.tif *.tiff *.tif)")
self.layout.addWidget(self.file_dialog)
self.file_dialog.currentChanged.connect(self.open_path)
def open_path(self, path):
if os.path.isfile(path):
# remove exitings layers from napari
viewer.layers.select_all()
viewer.layers.remove_selected()
# get the metadata
md, addmd = imf.get_metadata(path)
# add the metadata and adapt the table display
mdbrowser.update_metadata(md)
mdbrowser.update_style()
use_dask = checkbox.cbox.isChecked()
print('Use Dask : ', use_dask)
# get AICSImageIO object
img = AICSImage(path)
if use_dask:
stack = img.dask_data
if not use_dask:
stack = img.get_image_data()
# add the image stack to the napari viewer
show_image_napari(stack,
md,
blending='additive',
gamma=0.85,
rename_sliders=True)
def ab_clicked(self):
file_dialog = QFileDialog()
file_dialog.setFileMode(QFileDialog.DirectoryOnly)
file_dialog.setDirectory(self.mainwindow.options.get_default_last_folder_opened())
file_dialog.setOption(QFileDialog.DontUseNativeDialog, True)
file_view = file_dialog.findChild(QListView, 'listView')
# to make it possible to select multiple directories:
if file_view:
file_view.setSelectionMode(QAbstractItemView.MultiSelection)
f_tree_view = file_dialog.findChild(QTreeView)
if f_tree_view:
f_tree_view.setSelectionMode(QAbstractItemView.MultiSelection)
if file_dialog.exec():
folders = file_dialog.selectedFiles()
if len(folders) != 0:
for folder in folders:
parent_folder = os.path.dirname(r"{}".format(folder))
self.mainwindow.options.save_user_defaults(music_folder=folder, last_folder_opened=parent_folder)
self.folder_list.addItem(folder)
self.folder_list.sortItems()
def btnChooseDirs_clicked(self):
# https://stackoverflow.com/questions/38252419/how-to-get-qfiledialog-to-select-and-return-multiple-folders
# just copied :)
file_dialog = QFileDialog()
file_dialog.setFileMode(QFileDialog.DirectoryOnly)
file_dialog.setOption(QFileDialog.DontUseNativeDialog, True)
file_dialog.setDirectory(self.sett['/Private settings/Load kinetics last path'])
file_view = file_dialog.findChild(QListView, 'listView')
# to make it possible to select multiple directories:
if file_view:
file_view.setSelectionMode(QAbstractItemView.MultiSelection)
f_tree_view = file_dialog.findChild(QTreeView)
if f_tree_view:
f_tree_view.setSelectionMode(QAbstractItemView.MultiSelection)
if file_dialog.exec():
for path in file_dialog.selectedFiles():
head, tail = os.path.split(path)
head2, tail2 = os.path.split(head)
name = os.path.join(tail2, tail)
self.sett['/Private settings/Load kinetics last path'] = head
if name not in self.lwFolders.item_names:
self.lwFolders.addItem(name, path)
class FileBrowser(QWidget):
def __init__(self, defaultfolder=r'c:\Zen_Output'):
super(QWidget, self).__init__()
self.layout = QHBoxLayout(self)
self.file_dialog = QFileDialog()
self.file_dialog.setWindowFlags(Qt.Widget)
self.file_dialog.setModal(False)
self.file_dialog.setOption(QFileDialog.DontUseNativeDialog)
self.file_dialog.setDirectory(defaultfolder)
# remove open and cancel button from widget
self.buttonBox = self.file_dialog.findChild(QDialogButtonBox, "buttonBox")
self.buttonBox.clear()
# only show the following file types
self.file_dialog.setNameFilter("Images (*.czi *.ome.tiff *ome.tif *.tiff *.tif)")
self.layout.addWidget(self.file_dialog)
self.file_dialog.currentChanged.connect(open_image_stack)
class Open_files(QWidget):
def __init__(self):
super(QWidget, self).__init__()
self.layout = QHBoxLayout(self)
self.file_dialog = QFileDialog()
self.file_dialog.setWindowFlags(Qt.Widget)
self.file_dialog.setModal(False)
self.file_dialog.setOption(QFileDialog.DontUseNativeDialog)
# Remove open and cancel button from widget
self.buttonBox = self.file_dialog.findChild(QDialogButtonBox,
"buttonBox")
self.buttonBox.clear()
# Only open following file types
# self.file_dialog.setNameFilter("Images (*.czi *.nd2 *.tiff *.tif *.jpg *.png)")
self.file_dialog.setNameFilter(
"Images (*.czi *.ome.tiff *ome.tif *.tiff *.tif)")
self.layout.addWidget(self.file_dialog)
self.file_dialog.currentChanged.connect(self.open_path)
def open_path(self, path):
if os.path.isfile(path):
# remove exiting layers from napari
viewer.layers.select_all()
viewer.layers.remove_selected()
# get the metadata
md, addmd = imf.get_metadata(path)
# get AICSImageIO object
img = AICSImage(path)
stack = img.get_image_data()
add_napari(stack,
md,
blending='additive',
gamma=0.85,
rename_sliders=True)
class Open_files(QWidget):
def __init__(self):
super(QWidget, self).__init__()
self.layout = QHBoxLayout(self)
self.file_dialog = QFileDialog()
self.file_dialog.setWindowFlags(Qt.Widget)
self.file_dialog.setModal(False)
self.file_dialog.setOption(QFileDialog.DontUseNativeDialog)
# Remove open and cancel button from widget
self.buttonBox = self.file_dialog.findChild(QDialogButtonBox,
"buttonBox")
self.buttonBox.clear()
# Only open following file types
#self.file_dialog.setNameFilter("Images (*.czi *.nd2 *.tiff *.tif *.jpg *.png)")
self.file_dialog.setNameFilter(
"Images (*.czi *.ome.tiff *ome.tif *.tiff *.tif *.jpg *.png)")
self.layout.addWidget(self.file_dialog)
self.file_dialog.currentChanged.connect(self.open_path)
def open_path(self, path):
if os.path.isfile(path):
viewer.layers.select_all()
viewer.layers.remove_selected()
if path.endswith((".tiff", ".tif", ".czi")):
# Uses aicsimageio to open these files
# (image.io but the channel in last dimension which doesn't)
# work with napari
image = imread(path)
if path.endswith((".jpg", ".png")):
image = io.imread(path)
if path.endswith((".ome.tiff", "ome.tif")):
# a little slow but dask_image imread doesn't work well
javabridge.start_vm(class_path=bioformats.JARS)
#image = load_bioformats(path)
image = imread(path)
viewer.add_image(image, name="image_1")
