def _chooseDirectory(self):
# Find the directory of the most recently opened image file
mostRecentStackDirectory = preferences.get("DataSelection",
"recent stack directory")
if mostRecentStackDirectory is not None:
defaultDirectory = os.path.split(mostRecentStackDirectory)[0]
else:
defaultDirectory = os.path.expanduser("~")
options = QFileDialog.Options(QFileDialog.ShowDirsOnly)
if ilastik.config.cfg.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
# Launch the "Open File" dialog
directory = QFileDialog.getExistingDirectory(self,
"Image Stack Directory",
defaultDirectory,
options=options)
if not directory:
# User cancelled
return
preferences.set("DataSelection", "recent stack directory", directory)
self.directoryEdit.setText(directory)
try:
globstring = self._getGlobString(directory)
self.patternEdit.setText(globstring)
self._applyPattern()
except StackFileSelectionWidget.DetermineStackError as e:
QMessageBox.warning(self, "Invalid selection", str(e))
def addModelClicked(self):
"""
When AddModel button is clicked.
"""
# open dialog in recent model folder if possible
folder = preferences.get("DataSelection", "recent model")
if folder is None:
folder = os.path.expanduser("~")
# get folder from user
filename = self.getModelToOpen(self, folder)
if filename:
projectManager = self.parentApplet._StandardApplet__workflow._shell.projectManager
# save whole project (specifically important here: the labels)
if not projectManager.currentProjectIsReadOnly:
projectManager.saveProject()
with open(filename, "rb") as modelFile:
modelBytes = modelFile.read()
self._uploadModel(modelBytes)
preferences.set("DataSelection", "recent model", filename)
self.parentApplet.appletStateUpdateRequested()
def _exportAllObjectMeshes(self):
"""
Export all objects in the project as separate .obj files, stored to a user-specified directory.
"""
mst = self.topLevelOperatorView.MST.value
if not list(mst.object_lut.keys()):
QMessageBox.critical(
self, "Can't Export",
"You have no saved objets, so there are no meshes to export.")
return
recent_dir = preferences.get("carving", "recent export mesh directory")
if recent_dir is None:
defaultPath = os.path.join(os.path.expanduser("~"))
else:
defaultPath = os.path.join(recent_dir)
export_dir = QFileDialog.getExistingDirectory(
self, "Select export directory for mesh files", defaultPath)
if not export_dir:
return
export_dir = str(export_dir)
preferences.set("carving", "recent export mesh directory", export_dir)
# Get the list of all object names
object_names = []
obj_filepaths = []
for object_name in list(mst.object_lut.keys()):
object_names.append(object_name)
obj_filepaths.append(
os.path.join(export_dir, "{}.obj".format(object_name)))
if object_names:
self._exportMeshes(object_names, obj_filepaths)
def store_to_preferences(self):
"""
Immediately serialize the current set of shortcuts to the preferences file.
"""
# Auto-save after we're done setting prefs
# Just save the entire shortcut dict as a single pickle value
reversemap = self.get_keyseq_reversemap(self._keyseq_target_actions)
preferences.set(self.PreferencesGroup, "all_shortcuts", reversemap)
def store_to_preferences(self) -> None:
shortcuts = [{
"group": group,
"name": name,
"keyseq": keyseq
} for keyseq, targets in self._keyseq_target_actions.items()
for group, name in targets]
preferences.set(self.PreferencesGroup, self.PreferencesSetting,
shortcuts)
def addDvidVolume(self, roleIndex, laneIndex):
group = "DataSelection"
recent_hosts_key = "Recent DVID Hosts"
recent_hosts = preferences.get(group, recent_hosts_key)
if not recent_hosts:
recent_hosts = ["localhost:8000"]
recent_hosts = [
h for h in recent_hosts if h
] # There used to be a bug where empty strings could be saved. Filter those out.
recent_nodes_key = "Recent DVID Nodes"
recent_nodes = preferences.get(group, recent_nodes_key) or {}
from .dvidDataSelectionBrowser import DvidDataSelectionBrowser
browser = DvidDataSelectionBrowser(recent_hosts,
recent_nodes,
parent=self)
if browser.exec_() == DvidDataSelectionBrowser.Rejected:
return
if None in browser.get_selection():
QMessageBox.critical("Couldn't use your selection.")
return
rois = None
hostname, repo_uuid, volume_name, node_uuid, typename = browser.get_selection(
)
dvid_url = f"http://{hostname}/api/node/{node_uuid}/{volume_name}"
subvolume_roi = browser.get_subvolume_roi()
# Relocate host to top of 'recent' list, and limit list to 10 items.
try:
i = recent_hosts.index(hostname)
del recent_hosts[i]
except ValueError:
pass
finally:
recent_hosts.insert(0, hostname)
recent_hosts = recent_hosts[:10]
# Save pref
preferences.set(group, recent_hosts_key, recent_hosts)
recent_nodes[hostname] = node_uuid
preferences.set(group, recent_nodes_key, recent_nodes)
self.addLanes(
[UrlDatasetInfo(url=dvid_url, subvolume_roi=subvolume_roi)],
roleIndex)
def getSelectedPaths(self) -> List[Path]:
if not super().exec_():
return []
preferences.set(self.preferences_group, self.preferences_setting,
Path(self.selectedFiles()[0]).as_posix())
filePaths = []
for selected_file in self.selectedFiles():
path = Path(selected_file)
if path.name.lower() == "attributes.json" and any(
p.suffix.lower() == ".n5" for p in path.parents):
# For the n5 extension the attributes.json file has to be selected in the file dialog.
# However we need just the *.n5 directory-file.
filePaths.append(path.parent)
else:
filePaths.append(path)
return filePaths
def _loadModelButtonClicked(self):
"""
When Load Model button is clicked.
"""
mostRecentModelFile = preferences.get("DataSelection",
"recent neural net")
if mostRecentModelFile is not None:
defaultDirectory = os.path.split(mostRecentModelFile)[0]
else:
defaultDirectory = os.path.expanduser("~")
fileName = self.getModelFileNameToOpen(self, defaultDirectory)
if fileName is not None:
self._setClassifierModel(fileName)
preferences.set("DataSelection", "recent neural net", fileName)
self._setModelGuiVisible(True)
def _onContextMenuExportMesh(self, _name):
"""
Export a single object mesh to a user-specified filename.
"""
recent_dir = preferences.get("carving", "recent export mesh directory")
if recent_dir is None:
defaultPath = os.path.join(os.path.expanduser("~"),
"{}obj".format(_name))
else:
defaultPath = os.path.join(recent_dir, "{}.obj".format(_name))
filepath, _filter = QFileDialog.getSaveFileName(
self, "Save meshes for object '{}'".format(_name), defaultPath,
"OBJ Files (*.obj)")
if not filepath:
return
obj_filepath = str(filepath)
preferences.set("carving", "recent export mesh directory",
os.path.split(obj_filepath)[0])
self._exportMeshes([_name], [obj_filepath])
def prompt_export_settings_and_export_layer(layer: Layer, parent_widget=None) -> None:
"""
Prompt the user for layer export settings, and perform the layer export.
"""
opExport = get_export_operator(layer)
export_dir = preferences.get("layer", "export-dir", default=os.path.expanduser("~"))
opExport.OutputFilenameFormat.setValue(os.path.join(export_dir, layer.name))
# Use this dialog to populate the operator's slot settings
settingsDlg = DataExportOptionsDlg(parent_widget, opExport)
# If user didn't cancel, run the export now.
if settingsDlg.exec_() == DataExportOptionsDlg.Accepted:
export_dir = PathComponents(opExport.ExportPath.value).externalDirectory
preferences.set("layer", "export-dir", export_dir)
helper = ExportHelper(parent_widget)
helper.run(opExport)
# Clean up our temporary operators
opExport.cleanUp()
def _setTileWidth(self, value):
key, _ = self._getTileWidthConfigKeyDefault()
preferences.set("ImageScene2D", key, value)
self._updateTileWidth()
def accept(self):
preferences.set("WYSIWYG", "export directory",
str(self.directoryEdit.text()))
super(WysiwygExportOptionsDlg, self).accept()
def saveSize():
size = self.featureDlg.size()
s = (size.width(), size.height())
preferences.set("featureSelection", "dialog size", s)
def _selectFiles(self):
# Find the directory of the most recently opened image file
mostRecentStackDirectory = preferences.get("DataSelection",
"recent stack directory")
if mostRecentStackDirectory is not None:
defaultDirectory = os.path.split(mostRecentStackDirectory)[0]
else:
defaultDirectory = os.path.expanduser("~")
options = QFileDialog.Options(QFileDialog.ShowDirsOnly)
if ilastik.config.cfg.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
h5exts = [x.lstrip(".") for x in OpStreamingH5N5SequenceReaderM.H5EXTS]
# Launch the "Open File" dialog
extensions = vigra.impex.listExtensions().split()
extensions.extend(h5exts)
extensions.extend(OpInputDataReader.n5Selection)
filt = "Image files (" + " ".join("*." + x for x in extensions) + ")"
options = QFileDialog.Options()
if ilastik.config.cfg.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
fileNames, _filter = QFileDialog.getOpenFileNames(
self,
"Select Images for Stack",
defaultDirectory,
filt,
options=options)
# For the n5 extension, the attributes.json file has to be selected in the file dialog.
# However we need just the n5 directory-file.
for i in range(len(fileNames)):
if os.path.join("n5", "attributes.json") in fileNames[i]:
fileNames[i] = fileNames[i].replace(
os.path.sep + "attributes.json", "")
msg = ""
if len(fileNames) == 0:
return
pathComponents = PathComponents(fileNames[0])
if ((len(fileNames) == 1) and pathComponents.extension
not in OpStreamingH5N5SequenceReaderM.H5EXTS +
OpStreamingH5N5SequenceReaderM.N5EXTS):
msg += "Cannot create stack: You only chose a single file. "
msg += "If your stack is contained in a single file (e.g. a multi-page tiff) "
msg += 'please use the "Add File" button.'
QMessageBox.warning(self, "Invalid selection", msg)
return None
directory = pathComponents.externalPath
preferences.set("DataSelection", "recent stack directory", directory)
if (pathComponents.extension in OpStreamingH5N5SequenceReaderM.H5EXTS
or pathComponents.extension
in OpStreamingH5N5SequenceReaderM.N5EXTS):
if len(fileNames) == 1:
# open the dialog for globbing:
file_name = fileNames[0]
dlg = H5N5StackingDlg(
parent=self,
list_of_paths=self._findInternalStacks(file_name))
if dlg.exec_() == QDialog.Accepted:
globstring = "{}/{}".format(file_name,
dlg.get_globstring())
self.patternEdit.setText(globstring)
self._applyPattern()
return None
else:
return None
else:
# check for internal paths
internal_paths = self._h5N5FindCommonInternal(fileNames)
if len(internal_paths) == 0:
msg += "Could not find a unique common internal path in"
msg += directory + "\n"
QMessageBox.warning(self, "Invalid selection", msg)
return None
elif len(internal_paths) == 1:
fileNames = [
"{}/{}".format(fn, internal_paths[0])
for fn in fileNames
]
else:
# Ask the user which dataset to choose
dlg = SubvolumeSelectionDlg(internal_paths, self)
if dlg.exec_() == QDialog.Accepted:
selected_index = dlg.combo.currentIndex()
selected_dataset = str(internal_paths[selected_index])
fileNames = [
"{}/{}".format(fn, selected_dataset)
for fn in fileNames
]
else:
msg = "No valid internal path selected."
QMessageBox.warning(self, "Invalid selection", msg)
return None
self._updateFileList(fileNames)
def setTileWidth(self, tileWidth):
self._tileWidth = tileWidth
preferences.set("ImageScene2D", "tileWidth", tileWidth)
