def export(self):
from tifffile import imsave
from pyqtgraph import FileDialog
start_doc = getattr(self.catalog, self.stream).metadata['start']
if 'FileName' in start_doc:
current_dir = str(Path(start_doc['FileName']).parent)
current_name = Path(start_doc['FileName']).stem
elif 'sample_name' in start_doc:
current_dir = str(
Path.home()) # sample name is usually just te file stem
current_name = Path(start_doc['sample_name']).stem
else:
current_dir = Path.home()
current_name = 'xicamNCEM_output'
# Get a file path to save to in current directory
fd = FileDialog()
fd.setNameFilter("TIF (*.tif)")
fd.setDirectory(current_dir)
fd.selectFile(current_name)
fd.setFileMode(FileDialog.AnyFile)
fd.setAcceptMode(FileDialog.AcceptSave)
if fd.exec_():
file_names = fd.selectedFiles()[0]
outPath = Path(file_names)
else:
return
if outPath.suffix != '.tif':
outPath = outPath.with_suffix('.tif')
scale0, units0 = self._get_physical_size()
# Avoid overflow in field of view later
if units0[0] == 'm':
units0 = ['um', 'um']
scale0 = [ii * 1e6 for ii in scale0]
# Change scale from pixel to 1/pixel
FOV = [1 / ii for ii in scale0]
# Add units to metadata for Imagej type output
metadata = {'unit': units0[0]}
# Get the data and change to float
image = self.xarray[self.currentIndex, :, :].astype('f')
imsave(outPath, image, imagej=True, resolution=FOV, metadata=metadata)
class LibraryEditor(QtWidgets.QWidget):
sigApplyClicked = QtCore.Signal()
sigReloadClicked = QtCore.Signal(object)
def __init__(self, ctrlWidget, library):
super().__init__()
self.setWindowTitle("Manage Library")
self.modules = {} # {mod : [nodes]}
self.paths = set()
self.ctrl = ctrlWidget
self.library = library
self.layout = QtWidgets.QGridLayout(self)
self.loadBtn = QtWidgets.QPushButton("Load Modules", parent=self)
self.loadBtn.clicked.connect(self.loadFile)
# self.reloadBtn = QtWidgets.QPushButton("Reload Selected Modules", parent=self)
# self.reloadBtn.clicked.connect(self.reloadFile)
self.tree = QtWidgets.QTreeWidget(parent=self)
self.tree.setHeaderHidden(True)
self.applyBtn = QtWidgets.QPushButton("Apply", parent=self)
self.applyBtn.clicked.connect(self.applyClicked)
self.layout.addWidget(self.loadBtn, 1, 1, 1, -1)
# self.layout.addWidget(self.reloadBtn, 1, 2, 1, 1)
self.layout.addWidget(self.tree, 2, 1, 1, -1)
self.layout.addWidget(self.applyBtn, 3, 1, 1, -1)
def loadFile(self):
file_filters = "*.py"
self.fileDialog = FileDialog(None, "Load Nodes", None, file_filters)
self.fileDialog.setFileMode(FileDialog.ExistingFiles)
self.fileDialog.filesSelected.connect(self.fileDialogFilesSelected)
self.fileDialog.show()
def fileDialogFilesSelected(self, pths):
dirs = set(map(os.path.dirname, pths))
for pth in dirs:
if pth not in sys.path:
sys.path.append(pth)
self.paths.update(pths)
for mod in pths:
mod = os.path.basename(mod)
mod = os.path.splitext(mod)[0]
mod = importlib.import_module(mod)
if mod in self.modules:
continue
nodes = [getattr(mod, name) for name in dir(mod) if isNodeClass(getattr(mod, name))]
if not nodes:
continue
self.modules[mod] = nodes
parent = QtWidgets.QTreeWidgetItem(self.tree, [mod.__name__])
parent.mod = mod
for node in nodes:
child = QtWidgets.QTreeWidgetItem(parent, [node.__name__])
child.mod = mod
self.tree.expandAll()
def reloadFile(self):
mods = set()
for item in self.tree.selectedItems():
mods.add(item.mod)
for mod in mods:
pg.reload.reload(mod)
self.sigReloadClicked.emit(mods)
def applyClicked(self):
loaded = False
for mod, nodes in self.modules.items():
for node in nodes:
try:
self.library.addNodeType(node, [(mod.__name__, )])
loaded = True
except Exception as e:
printExc(e)
if not loaded:
return
self.ctrl.ui.clear_model(self.ctrl.ui.node_tree)
self.ctrl.ui.create_model(self.ctrl.ui.node_tree, self.library.getLabelTree(rebuild=True))
self.sigApplyClicked.emit()
def saveState(self):
return {'paths': list(self.paths)}
def restoreState(self, state):
self.fileDialogFilesSelected(state['paths'])
class SourceConfiguration(QtGui.QWidget):
sigApply = QtCore.Signal(object) # src_cfg dict
def __init__(self, parent=None):
super().__init__(parent)
self.setWindowTitle("Configure")
self.formLayout = QtWidgets.QFormLayout(self)
self.interval = QtGui.QDoubleSpinBox(self)
self.interval.setValue(0.01)
self.formLayout.addRow("Interval", self.interval)
self.init_time = QtGui.QDoubleSpinBox(self)
self.init_time.setValue(0.5)
self.formLayout.addRow("Init Time", self.init_time)
self.hb_period = QtGui.QSpinBox(self)
self.hb_period.setValue(10)
self.formLayout.addRow("Heartbeat Period", self.hb_period)
self.source_type = QtGui.QComboBox(self)
self.source_type.addItem("hdf5")
self.source_type.addItem("psana")
self.formLayout.addRow("Source Type", self.source_type)
self.repeat = QtWidgets.QCheckBox(self)
self.repeat.setChecked(True)
self.formLayout.addRow("Repeat", self.repeat)
self.files = []
self.fileListView = QtWidgets.QListView(self)
self.fileListView.setSelectionMode(
QtWidgets.QAbstractItemView.ExtendedSelection)
self.fileListModel = QtCore.QStringListModel(self.files)
self.fileListView.setModel(self.fileListModel)
self.formLayout.addRow(self.fileListView)
self.horizontalLayout = QtWidgets.QHBoxLayout()
self.addBtn = QtWidgets.QPushButton("Add", parent=self)
self.addBtn.clicked.connect(self.addFile)
self.horizontalLayout.addWidget(self.addBtn)
self.removeBtn = QtWidgets.QPushButton("Remove", parent=self)
self.removeBtn.clicked.connect(self.removeFiles)
self.horizontalLayout.addWidget(self.removeBtn)
self.applyBtn = QtWidgets.QPushButton("Apply", parent=self)
self.applyBtn.clicked.connect(self.applyClicked)
self.horizontalLayout.addWidget(self.applyBtn)
self.formLayout.addRow(self.horizontalLayout)
def addFile(self):
file_filters = self.source_type.currentText()
if file_filters == "hdf5":
file_filters = "*.h5 *.hdf5"
elif file_filters == "psana":
file_filters = "*.xtc2"
self.fileDialog = FileDialog(None, "Load Data", None, file_filters)
self.fileDialog.setFileMode(FileDialog.ExistingFiles)
self.fileDialog.filesSelected.connect(self.fileDialogFilesSelected)
self.fileDialog.show()
def removeFiles(self):
selectionModel = self.fileListView.selectionModel()
for pth in selectionModel.selection().indexes():
pth = pth.data()
self.files.remove(pth)
self.fileListModel.setStringList(self.files)
def fileDialogFilesSelected(self, pths):
self.files.extend(pths)
self.fileListModel.setStringList(self.files)
def saveState(self):
cfg = {}
cfg['type'] = self.source_type.currentText()
cfg['interval'] = self.interval.value()
cfg['init_time'] = self.init_time.value()
cfg['hb_period'] = self.hb_period.value()
cfg['files'] = self.files
cfg['repeat'] = self.repeat.isChecked()
return cfg
def restoreState(self, state):
self.source_type.setCurrentText(state['type'])
self.interval.setValue(state['interval'])
self.init_time.setValue(state['init_time'])
self.hb_period.setValue(state['hb_period'])
self.files = state['files']
self.fileListModel.setStringList(self.files)
self.repeat.setChecked(state['repeat'])
def applyClicked(self):
cfg = self.saveState()
self.sigApply.emit(cfg)